Methods, compositions, kits, and systems for assessing immune status

Abstract

The disclosure relates to methods, compositions, kits, and systems for assessing immune status by analyzing genomic DNA from a subject. In some embodiments, the DNA is cell-free DNA from a subject with a hyperproliferative disorder. In some embodiments, the DNA is cell-free DNA from a subject with cancer.

Description

DOCKET NO. STFD-015-PCT PATENT APPLICATION METHODS, COMPOSITIONS, KITS, AND SYSTEMS FOR ASSESSING IMMUNE STATUSCROSS REFERENCE TO RELATED APPLICATION

[0001] This application claims the benefit of U.S. Provisional Application No. 63 / 748,975, which was filed January 24, 2025, is titled “System For Detecting Immune Status and Methods of Using the Same,” and is incorporated herein by reference in its entirety.FIELD

[0002] The disclosure relates to methods, compositions, kits, and systems for assessing immune status, determining the number of T cells and / or B cells in a cell-free DNA sample taken from a subject, and methods of monitoring T cell and / or B cells in a subject being treated for a hyperproliferative disorder.SEQUENCE LISTING

[0003] The sequence listing filed herewith, titled “STFD-015-PCT_SL.xml,” prepared on January 26, 2026, and having a file size of 13,050,048 bytes is incorporated herein by reference in its entirety.BACKGROUND

[0004] As immunotherapy has become increasingly popular in recent years, accurate methods of assessing immune status have become important for disease monitoring and biomarker discovery. Among these, the total amount of T and B / Plasma cells is the most basic and important information. However, since most T and B cells do not circulate, the analysis using peripheral blood mononuclear cells cannot predict how much turnover of T cells (αβT-cells, γδT-cells) and B / Plasma cells (IgK+, IgL+, IgM+, IgG1-4+, IgA+) occurs throughout the body. It is impossible to directly evaluate tum-over of T-cell s / B-cells in the whole body including noncirculating T-cells / B-cells.

[0005] Prior to the present disclosure, it was impossible to directly evaluate tum-over of T / B-cells in the whole body including non-circulating T cells and / or B cells. Further, there was no frequent and non-invasive way of monitoring immune responses as necessary to identifyDOCKET NO. STFD-015-PCT PATENT APPLICATIONbiomarkers and predict the efficacy of immune therapies. Still further, sequence data of cfDNA has a high amount of noise in sequence depth, which prevented its use for predicting the efficacy of immune therapies.SUMMARY

[0006] In some embodiments, the disclosure relates to a composition. In some embodiments, the composition comprises a first set of capture probes comprising at least a first nucleic acid molecule comprising a first nucleic acid sequence comprising a maximal rearrangement domain of TRA, TRB, TRG, IGH, IGK, or IGL In some embodiments, the composition comprises a second set of capture probes comprising at least a second nucleic acid molecule comprising a second nucleic acid sequence comprising a low recombination domain at or proximal to TRA, TRB, TRG, IGH, IGK, or IGL. In some embodiments, the first nucleic acid sequence comprises one or a combination of at least two of: SEQ ID NO: 1 or a functional variant thereof, SEQ ID NO: 2 or a functional variant thereof, SEQ ID NO: 3 or a functional variant thereof, SEQ ID NO: 4 or a functional variant thereof, SEQ ID NO: 5 or a functional variant thereof, SEQ ID NO: 6 or a functional variant thereof, SEQ ID NO: 7 or a functional variant thereof, SEQ ID NO: 8 or a functional variant thereof, SEQ ID NO: 9 or a functional variant thereof, SEQ ID NO: 10 or a functional variant thereof, SEQ ID NO: 11 or a functional variant thereof, SEQ ID NO: 12 or a functional variant thereof, SEQ ID NO: 13 or a functional variant thereof, SEQ ID NO: 14 or a functional variant thereof, SEQ ID NO: 15 or a functional variant thereof, SEQ ID NO: 16 or a functional variant thereof, and SEQ ID NO: 17 or a functional variant thereof. In some embodiments, the second nucleic acid sequence comprises one or a combination of at least two of: SEQ ID NO: 18 or a functional variant thereof, SEQ ID NO: 19 or a functional variant thereof, SEQ ID NO: 20 or a functional variant thereof, SEQ ID NO: 21 or a functional variant thereof, SEQ ID NO: 22 or a functional variant thereof, SEQ ID NO: 23 or a functional variant thereof, SEQ ID NO: 24 or a functional variant thereof, SEQ ID NO: 25 or a functional variant thereof, SEQ ID NO: 26 or a functional variant thereof, SEQ ID NO: 27 or a functional variant thereof, SEQ ID NO: 28 or a functional variant thereof, SEQ ID NO: 29 or a functional variant thereof, SEQ ID NO: 30 or a functional variant thereof, SEQ ID NO: 31 or a functional variant thereof, SEQ ID NO: 32 or a functional variant thereof, SEQ ID NO: 33 or a functional variant thereof, SEQ ID NO: 34 or a functional variant thereof, SEQDOCKET NO. STFD-015-PCT PATENT APPLICATION ID NO: 35 or a functional variant thereof, and SEQ ID NO: 36 or a functional variant thereof. In some embodiments, each first nucleic acid sequence independently comprises a sequence comprising at least a portion of SEQ ID NOS: 1-17. 131-602, 702-108, 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746. 5749-5751, 5763, 5764. 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034, or a functional vanant thereof having at least about 75% sequence identity to SEQ ID NOS: 1–17, 131–602, 702–108, 1147–1381, 1515–3882, 5054–5530, 5586–5715, 5740, 5743, 5746, 5749–5751, 5763, 5764, 5767, 5769–6048, 6573–6630, 6746–6783, 6860–6923, 6938, 6939, 7010–7079, 7080–7479,7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034. In some embodiments, each first nucleic acid sequence independently comprises a sequence of SEQ ID NOS: 1-17, 131-602, 702-108, 1147-1381, 1515-3882, 5054–5530, 5586–5715, 5740, 5743, 5746, 5749–5751, 5763, 5764, 5767, 5769–6048, 6573–6630, 6746–6783, 6860–6923, 6938, 6939, 7010–7079, 7080–7479, 7480–7619, 7620–7681, 8206–8263, 8379–8416, 8493–8556, 8571–8572, or 8643–9034, or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 1–17, 131–602, 702–108, 1147–1381, 1515–3882, 5054–5530, 5586–5715, 5740, 5743, 5746, 5749–5751, 5763, 5764, 5767, 5769–6048, 6573–6630, 6746–6783, 6860–6923, 6938, 6939, 7010–7079, 7080–7479, 7480–7619, 7620–7681, 8206–8263, 8379–8416, 8493–8556, 8571–8572, or 8643–9034. In some embodiments, each second nucleic acid sequence independently comprises a sequence comprising at least a portion of SEQ ID NOS: 18–36, 37–130, 603–701, 1009–1146, 1382–1514, 3883–5053, 5531–5585, 5716–5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752–5762, 5965, 5966, 5768, 6049–6572, 6631–6745, 6784–6859, 6924–6937, 6940–7009, 7682–8205, 8264–8378, 8417–8492, 8557–8570, or 8573–8642, or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 18–36, 37–130, 603–701, 1009–1146, 1382–1514, 3883–5053, 5531–5585, 5716–5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752–5762, 5965, 5966, 5768, 6049–6572, 6631–6745, 6784–6859, 6924–6937, 6940–7009, 7682–8205, 8264–8378, 8417–8492, 8557–8570, or 8573–8642. In some embodiments, each second nucleic acid sequence independently comprises a sequence of SEQ ID NOS: 18-36, 37-130, 603–701, 1009–1146, 1382–1514, 3883–5053, 5531–5585, 5716–5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752–5762, 5965, 5966, 5768, 6049–6572, 6631–6745, 6784–DOCKET NO. STFD-015-PCT PATENT APPLICATION6859, 6924–6937, 6940–7009, 7682–8205, 8264–8378, 8417–8492, 8557–8570, or 8573–8642, or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 18–36, 37–130, 603–701, 1009–1146, 1382–1514, 3883–5053, 5531–5585, 5716–5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752–5762, 5965, 5966, 5768, 6049–6572, 6631–6745, 6784–6859, 6924–6937, 6940–7009, 7682–8205, 8264–8378, 8417–8492, 8557–8570, or 8573–8642.

[0007] In some embodiments, the first set of capture probes comprises two nucleic acid molecules. In some embodiments, the second set of capture probes comprises two nucleic acid molecules. In some embodiments, each of the two nucleic acid molecules of the first set of capture probes comprises a nucleic acid sequence targeting a different maximal rearrangement domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL. In some embodiments, each of the two nucleic acid molecules of the second set of capture probes comprises a nucleic acid sequence targeting a different low recombination domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL.

[0008] In some embodiments, the first set of capture probes comprises three nucleic acid molecules. In some embodiments, the second set of capture probes comprises three nucleic acid molecules. In some embodiments, each of the three nucleic acid molecules of the first set of capture probes comprises a nucleic acid sequence targeting a different maximal rearrangement domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL. In some embodiments, each of the three nucleic acid molecules of the second set of capture probes comprises a nucleic acid sequence targeting a different low recombination domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL.

[0009] In some embodiments, the first set of capture probes comprises four nucleic acid molecules. In some embodiments, the second set of capture probes comprises four nucleic acid molecules. In some embodiments, each of the four nucleic acid molecules of the first set of capture probes comprises a nucleic acid sequence targeting a different maximal rearrangement domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL. In some embodiments, each of the four nucleic acid molecules of the second set of capture probes comprises a nucleic acid sequence targeting a different low recombination domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL.DOCKET NO. STFD-015-PCT PATENT APPLICATION

[0010] In some embodiments, the first set of capture probes comprises five nucleic acid molecules. In some embodiments, the second set of capture probes comprises five nucleic acid molecules. In some embodiments, each of the five nucleic acid molecules of the first set of capture probes comprises a nucleic acid sequence targeting a different maximal rearrangement domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL. In some embodiments, each of the five nucleic acid molecules of the second set of capture probes comprises a nucleic acid sequence targeting a different low recombination domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL; or

[0011] In some embodiments, the first set of capture probes comprises six nucleic acid molecules. In some embodiments, the second set of capture probes comprises six nucleic acid molecules. In some embodiments, each of the six nucleic acid molecules of the first set of capture probes comprises a nucleic acid sequence targeting a different maximal rearrangement domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL. In some embodiments, each of the six nucleic acid molecules of the second set of capture probes comprises a nucleic acid sequence targeting a different low recombination domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL.

[0012] In some embodiments, the composition further comprises a third set of capture probes comprising at least a third nucleic acid molecule comprising a third nucleic acid sequence targeting V, D, or J domain from at least one of: TRA, TRB, TRG, IGH, IGK, or IGL. In some embodiments, each third nucleic acid sequence independently comprises a sequence comprising at least a portion of SEQ ID NOS: 9035-9553, or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 9035-9553. In some embodiments, each third nucleic acid sequence independently comprises a sequence of SEQ ID NOS: 9035-9553, or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 9035-9553.

[0013] In some embodiments, the composition further comprises a fourth set of capture probes comprising at least a fourth nucleic acid sequence targeting one or both of (i) recurrently mutated genes in tumor DNA and (ii) TCR and BCR V and J regions. In some embodiments, each fourth nucleic acid sequence targeting (i) recurrently mutated genes in tumor DNA independently comprises a sequence comprising at least a portion of SEQ ID NOS: 11,815— 13,436. or a functional variant thereof having at least about 75% sequence identity to SEQ IDDOCKET NO. STFD-015-PCT PATENT APPLICATION NOS: 11,815-13,436. In some embodiments, each fourth nucleic acid sequence targeting (i) recurrently mutated genes in tumor DNA independently comprises one of SEQ ID NOS: 11,815-13,436, or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 11,815-13,436. In some embodiments, each fourth nucleic acid sequence targeting (ii) TCR and BCR V and J regions independently comprises a sequence comprising at least a portion of SEQ ID NOS: 9,554-11,814, or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 9,554–11,814. In some embodiments, each fourth nucleic acid sequence targeting (ii) TCR and BCR V and J regions independently comprises one of SEQ ID NOS: 9,554–11,814, or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 9,554–11,814.

[0014] In some embodiments, the disclosure relates to a kit comprising at least one of: a first set of capture probes, a second set of capture probes, a third set of capture probes, and a fourth set of capture probes. In some embodiments, the first set of capture probes comprises a nucleic acid sequence comprising SEQ ID NO:1 or a functional variant thereof, SEQ ID NO:2 or a functional variant thereof, SEQ ID NO: 3 or a functional variant thereof, SEQ ID NO:4 or a functional variant thereof, SEQ ID NO:5 or a functional variant thereof, and SEQ ID NO:6 or a functional variant thereof. In some embodiments, the second set of capture probes comprises a nucleic acid sequence comprising SEQ ID NO: 7 or a functional variant thereof, SEQ ID NO: 8 or a functional variant thereof, SEQ ID NO:9 or a functional variant thereof, SEQ ID NO: 10 or a functional variant thereof, SEQ ID NO: 11 or a functional variant thereof, and SEQ ID NO: 12 or a functional variant thereof. In some embodiments, the third set of capture probes comprises a nucleic acid sequence comprising SEQ ID NO: 13 or a functional variant thereof. SEQ ID NO: 14 or a functional variant thereof, SEQ ID NO: 15 or a functional variant thereof, SEQ ID NO: 16 or a functional variant thereof, SEQ ID NO: 17 or a functional variant thereof, and SEQ ID NO: 18 or a functional variant thereof. In some embodiments, the fourth set of capture probes comprises a nucleic acid sequence comprising SEQ ID NO: 19 or a functional variant thereof, SEQ ID NO: 20 or a functional variant thereof, SEQ ID NO:21 or a functional variant thereof, SEQ ID NO:22 or a functional variant thereof, SEQ ID NO:23 or a functional variant thereof, and SEQ ID NO:24 or a functional variant thereof. In some embodiments, at least one nucleic acid sequence from the capture probes is immobilized to one or a plurality of solid supports. In some embodiments, the kit comprises a single solid support comprising aDOCKET NO. STFD-015-PCT PATENT APPLICATIONseries of vessels, each vessel comprising a bottom surface and side walls, wherein the at least one nucleic acid sequence from the capture probes is immobilized to the solid support at the bottom surface. In some embodiments, the kit comprises a plurality of solid supports, each solid support comprising a vessel. In some embodiments, at least one nucleic acid sequence of a set of capture probes is positioned within at least one vessel. In some embodiments, the at least one nucleic acid sequence is in solid phase, and, optionally, lyophilized in the at least one vessel. In some embodiments, the kit comprises the at least one nucleic acid sequence in solution and, optionally, immobilized to a surface of the vessel.

[0015] In some embodiments, the disclosure relates to a kit. In some embodiments, the kit comprises at least one of: a first set of capture probes, and / or a second set of capture probes, and / or a third set of capture probes, and / or a fourth set of capture probes. In some embodiments, the first set of capture probes comprises a plurality of first nucleic acid sequences, each of the plurality of first nucleic acid sequence independently selected from SEQ ID NOS: 1-17. 131— 602, 702-108, 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749–5751, 5763, 5764, 5767, 5769–6048, 6573–6630, 6746–6783, 6860–6923, 6938, 6939, 7010–7079, 7080–7479, 7480–7619, 7620–7681, 8206–8263, 8379–8416, 8493–8556, 8571–8572, or 8643–9034 or a functional variant thereof having at least about 75% sequence identity to 1–17, 131–602, 702–108, 1147–1381, 1515–3882, 5054–5530, 5586–5715, 5740, 5743, 5746, 5749–5751, 5763, 5764, 5767, 5769–6048, 6573–6630, 6746–6783, 6860–6923, 6938, 6939, 7010–7079, 7080–7479, 7480–7619, 7620–7681, 8206–8263, 8379–8416, 8493–8556, 8571–8572, or 8643–9034. In some embodiments, the second set of capture probes comprises one or a plurality of second nucleic acids sequences, each of the second nucleic acid nucleic acid sequences independently selected from SEQ ID NOS: 18-36, 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752-5762, 5965, 5966. 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642 or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 18-36, 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752-5762, 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570. or 8573-8642. In some embodiments, the third set of capture probes comprises one or a plurality of third nucleic acidDOCKET NO. STFD-015-PCT PATENT APPLICATIONsequences, each third nucleic acid sequence independently selected from SEQ ID NOS: 9035-9553 or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 9035-9553. In some embodiments, fourth set of capture probes comprises one or a plurality of fourth nucleic acid sequences, each fourth nucleic acid sequence independently selected from SEQ ID NOS: 9554–13,436 or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 9554–13,436. In some embodiments, at least one nucleic acid sequence from the capture probes is immobilized to one or a plurality of solid supports. In some embodiments, the kit comprises a single solid support comprising a series of vessels, each vessel comprising a bottom surface and side walls, wherein the at least one nucleic acid sequence from the capture probes is immobilized to the solid support at the bottom surface. In some embodiments, the kit comprises a plurality of solid supports, each solid support comprising a vessel. In some embodiments, at least one nucleic acid sequence of a set of capture probes is positioned within at least one vessel. In some embodiments, the at least one nucleic acid sequence is in solid phase, and, optionally, lyophilized in the at least one vessel. In some embodiments, the kit comprises the at least one nucleic acid sequence in solution and, optionally, immobilized to a surface of the vessel.

[0016] In some embodiments, the disclosure relates to a system comprising a solid support, and a first set of probes, a second set of probes and a third set of probes. In some embodiments, the first set of probes are complementary to a maximal rearrangement domain of one or a combination of two or more of TRA, TRB, TRG, IGH, IGK, or IGL. In some embodiments, the second set of probes are complementary to a low recombination domain of one or a combination of two or more of TRA, TRB. TRG, IGH, IGK, or IGL. In some embodiments, the third set of probes are complementary to a V, D, or J domain from at least one of: TRA, TRB, TRG, IGH, IGK, or IGL.

[0017] In some embodiments, the disclosure relates to a system comprising a solid support comprising a plurality of vessels. In some embodiments, each vessel comprises: (i) at least a first set of capture probes and / or a second set of capture probes; and (ii) a set of sequencing primers. In some embodiments, each sequencing primer in the set of sequencing primers comprises a nucleic acid sequence complementary to a maximal rearrangement domain ( MRD " or, interchangeably, a location of maximal rearrangement) the respective genes for TRA, TRB, TRG, IGH, IGK, or IGL. In some embodiments, the first set of probes areDOCKET NO. STFD-015-PCT PATENT APPLICATIONcomplementary to a maximal rearrangement domain of one or a combination of two or more of TRA, TRB, TRG, IGH, IGK, or IGL. In some embodiments, the second set of probes are complementary to a low recombination domain of one or a combination of two or more of TRA, TRB, TRG, IGH, IGK, or IGL. In some embodiments, the third set of probes are complementary to a V, D, or J domains from at least one of: TRA, TRB, TRG, IGH, IGK, or IGL.

[0018] In some embodiments, the disclosure relates to a method of preparing a sample. In some embodiments, the method comprises exposing the sample to: (i) a composition herein or (ii) a system herein. In some embodiments, the sample comprises genomic DNA from a subject. In some embodiments, the genomic DNA is cell-free DNA. In some embodiments, the sample of DNA is isolated or within a whole blood sample from a healthy subj ect, or the sample is isolated from a patient diagnosed with or suspected of having a hyperproliferative disorder. In some embodiments, the sample is from a test subject. In some embodiments, the subject is receiving CAR-T therapy. In some embodiments, the test subject has a hyperproliferative disorder or has been diagnosed with a hyperproliferative disorder oris suspected of having a hyperproliferative disorder. In some embodiments, the test subj ect is selected from a peripheral T-cell lymphoma patient, a myeloma patient, a patient receiving CAR-T therapy, or a bladder cancer patient. In some embodiments, the method further comprises subjecting the sample to hybridization conditions in the presence of at least one of the first set of capture probes, the second set of capture probes, the third set of capture probes, and / or the fourth set of capture probes. In some embodiments, the method further comprises a step of obtaining the sample prior to the step of exposing. In some embodiments, the method further comprises extracting the cfDNA from the sample prior to the step of exposing. In some embodiments, the method further comprises sequencing the cfDNA to produce sequence data. In some embodiments, the step of sequencing comprises polymerization from a set of sequencing primers. In some embodiments, each sequencing primer in the set of sequencing primers comprises sequencing nucleic acid sequence complementary to one of the location of maximal rearrangement (LMR) for a different one of the genes for TRA, TRB, TRG, IGH, IGK, or IGL. In some embodiments, each sequencing primer in the set of sequencing primers comprises sequencing nucleic acid sequence complementary’ to one of the location of low recombination close to the respective genes for TRA, TRB, TRG, IGH, IGK, or IGL.DOCKET NO. STFD-015-PCT PATENT APPLICATION

[0019] In some embodiments, the disclosure relates to a method of determining the total amount of T-cells and / or B-cells in a subject or a fraction of the T cells and / or B cells of a total fraction of cells in a sample. In some embodiments, the method comprises exposing a sample comprising DNA to: (i) a composition herein; or (ii) a system herein. In some embodiments, the sample comprises cell-free DNA (cfDNA), genomic DNA, or high-molecular weight DNA from a subject. In some embodiments, the sample is cell-free DNA, whole blood, plasma, urine, tissue from a tumor or biopsy, cerebral spinal fluid, saliva or other bodily fluid from a subject. In some embodiments, the method further comprises sequencing at least a portion of the DNA, and, in some embodiments, the DNA is genomic DNA from urine, saliva, cerebral spinal fluid, plasma. In some embodiments, the DNA is genomic DNA from a cell-free DNA sample in urine, saliva, cerebral spinal fluid, plasma or other bodily fluid.

[0020] The disclosure relates to a method of determining the total amount of T-cells and / or B-cells in a subject or a fraction of the T cells and / or B cells of a total number of cells in a sample comprising exposing a sample comprising DNA to: (i) a composition herein; or (ii) a system herein and sequencing a LMR for a gene for one of TRA, TRB, TRG, IGH, IGK, or IGL is a valley region and the location of low recombination close to the gene for TRA, TRB, TRG, IGH, IGK, or IGL is a shoulder region; In some embodiments, the method further comprises determining a median sequence depth for each valley region and a median sequence depth for each shoulder region, subtracting the median sequence depth for each valley region from the median sequence depth for each respective shoulder region to obtain a respective depth of valley for each valley region, and dividing each respective depth of valley by the median depth for the respective shoulder region to obtain a fraction of the T-cells and / or B-cells. In some embodiments, the method further comprises extracting genomic DNA from the cfDNA prior to the step of exposing.

[0021] In some embodiments, the disclosure relates to a method of determining the total amount of T-cells and / or B-cells in a subject or determining a fraction of the T cells and / or B cells in a sample. In some embodiments, the method comprises: (a) extracting genomic DNA from a cell-free DNA sample from the subject; (b) sequencing at least a portion of the genomic DNA; (c) exposing the genomic DNA to a composition herein or a system herein. In some embodiments, the method further comprises a step of obtaining baseline read depth of at least the portion of the genomic data. In some embodiments, the method further comprisesDOCKET NO. STFD-015-PCT PATENT APPLICATIONdetermining the total amount of T-cells and / or B-cells in the subject or determining a fraction of the T cells and / or B cells in the sample by one or more of: (a) determining the number and / or sequence of location of maximal rearrangement (LMR) in the genomic DNA; (b) calculating the ratio of αβTcells to γδTcells from the genomic DNA; (c) calculating the number and / or sequence of LMR in an IgH portion of the genomic DNA; (d) calculating the ratio of Igκ to Igλ in the genomic DNA; and (e) quantifying the number of Ig class switches in the genomic DNA. In some embodiments, the method further comprises correlating the number and / or sequence of MRD in an IgH portion of the genomic DNA and / or to the number Ig class switches in the genomic DNA to the number of B cells in sample. In some embodiments, the method further comprises correlating one or more of: (i) the number and / or sequence of LMR in the genomic DNA; (ii) the ratio of αβT cells to γδT cells; and (iii) the ratio of Igκ to Igλ, in the genomic DNA, to the number of T cells in the sample.

[0022] In some embodiments, the disclosure relates to a computer-implemented method of determining the total amount of T-cells and / or B-cells in a subject or in a sample. In some embodiments, the method comprises sequencing the genomic cfDNA to produce sequence data, and executing processor executable instructions for determining a median sequence depth across at least a portion of the cfDNA. In some embodiments, the method further comprises (i) extracting genomic DNA from a sample comprising cfDNA from the subject and (ii) contacting the genomic DNA with a composition herein or a system herein. In some embodiments, the location of maximal rearrangement for a gene for one of TRA, TRB, TRG, IGH, IGK, or IGL is a valley region and the location of low recombination proximate to TRA, TRB, TRG, IGH, IGK. or IGL is a shoulder region; and wherein the step of determining a median sequence depth comprises subtracting the median sequence depth for each valley region from the median sequence depth for each respective shoulder region to obtain a respective depth of valley for each valley region, and dividing each respective depth of valley by the median depth for the respective shoulder region to obtain a fraction of the T-cells and / or B-cells.

[0023] In some embodiments, the disclosure relates to a computer program product encoded on a computer-readable storage medium. In some embodiments, the computer program product comprises instructions for: (a) determining, from sequence data comprising valley region sequence, reads for a location of maximal rearrangement for one or more gene selected from V, D, and J genes in the cfDNA; (b) determining, from the sequence data, shoulder regionDOCKET NO. STFD-015-PCT PATENT APPLICATIONsequence reads for a location of low recombination proximate to the one or more gene; and (c) determining a median sequence depth for each valley region and a median sequence depth for each shoulder region, the median sequence depth calculated by subtracting the median sequence depth for each valley region from the median sequence depth for each respective shoulder region to obtain a respective depth of valley for each valley region; and dividing each respective depth of valley by the median depth for the respective shoulder region. In some embodiments, the method further comprises instructions for: (d) determining a fraction of the T-cells and / or B-cells by correlating the values of any of steps (a), (b), (c), or combination thereof.

[0024] In some embodiments, the disclosure relates to a method of monitoring disease progression of a subject comprising determining the total amount of T-cells and / or B-cells in the subject. In some embodiments, the method comprises (a) obtaining sequence data from cfDNA from the subject; and (b) determining a median sequence depth of a set of genomic DNA within the cfDNA sample by subtracting the median sequence depth for each valley region from the median sequence depth for each respective shoulder region to obtain a respective depth of valley for each valley region, and subsequently dividing each respective depth of valley by the median depth for the respective shoulder region. In some embodiments, the method further comprises a step of (c) exposing at least a portion of the cfDNA to a set of primers complementary to the cfDNA and specific, such that sequence data are generated for one or more of: (i) determining the number and / or sequence of LMR in the genomic DNA; (ii) calculating the ratio of αβ T cells to γδ T cells from the genomic DNA; (iii) calculating the number and / or sequence of MRD in an IgH portion of the genomic DNA; (iv) calculating the ratio of Igκ to Igλ in the genomic DNA; and (v) quantifying the number Ig class switches in the genomic DNA. In some embodiments, the method further comprises a step of (d) of correlating the sequence data across a portion of genomic DNA in the cfDNA to a fraction of the T-cells and / or B-cells in the subject. In some embodiments, if monitoring the number of B cells in the subject, the method further comprises correlating the number and / or sequence of MRD in an IgH portion of the genomic DNA and / or to the number Ig class switches in the genomic DNA to the number of B cells in the subject. In some embodiments, if the monitoring the number of T cells, the method further comprises correlating one or more of: (i) the number and / or sequence of LMR in the genomic DNA; (ii) the ratio of αβT cells to γδT cells; and (iii)DOCKET NO. STFD-015-PCT PATENT APPLICATIONthe ratio of Igκ to Igλ in the genomic DNA to the number of T cells in the subject. In some embodiments, the subject has been diagnosed with or is suspected of having a hyperproliferative disorder. In some embodiments, the subject has a hyperproliferative disorder. In some embodiments, the subj ect is a peripheral T-cell lymphoma patient, a myeloma patient, a patient receiving CAR-T therapy, or a bladder cancer patient. In some embodiments, the sequence data comprises valley region sequence reads for a location of maximal rearrangement for one or more gene selected from V, D, and J genes and shoulder region sequence reads for a location of low recombination proximate to the one or more genes. In some embodiments, the method further comprises a step of correlating the sequence data to the number of T cells and / or B cells in the subject; and subsequently correlating the number of T cells and / or B cells in the subject with disease progression. In some embodiments, if the number of T cells and / or B cells are elevated in the subject, the disease progression is negligible or limited; and if the number of T cells and / or B cells are not elevated in the subject, the disease has likely progressed.

[0025] In some embodiments the disclosure relates to a method of determining whether a subject is a responder or non-responder to a therapeutic agent. In some embodiments, the method comprises (a) obtaining sequence data from cfDNA from the subject exposed to a therapeutic agent; and (b) determining a median sequence depth of a set of genomic DNA within the cfDNA sample by subtracting the median sequence depth for each valley region from the median sequence depth for each respective shoulder region to obtain a respective depth of valley for each valley region, and subsequently dividing each respective depth of valley by the median depth for the respective shoulder region; and (c) determining the number of T cells and / or B cells in the subject by comparing the sequence data and the median sequence depth of the cfDNA to the number of T cells and or B cells in a control subject. In some embodiments, if the number of T cells and / or B cells in the subject is higher than a control subject and the control subject is a non-responder to the therapeutic agent, then determining that the subject is a responder to the therapeutic agent.. In some embodiments, if the number of T cells and / or B cells in the subject is about equivalent to a control subject and the control subject is a responder to the therapeutic agent, then determining the subject is a responder to the therapeutic agent. In some embodiments, if the number of T cells and / or B cells in the subject is lower than a control subject and the control subject is a responder to the therapeuticDOCKET NO. STFD-015-PCT PATENT APPLICATIONagent, then determining that the subject is a non-responder to the therapeutic agent. In some embodiments, if the number of T cells and / or B cells in the subject is about equivalent to a control subject and the control subject is a non-responder to the therapeutic agent, then determining that the subject is a non-responder to the therapeutic agent. In some embodiments the step of obtaining sequence data comprises exposing at least a portion of the cfDNA to a set of primers complementary to the cfDNA and specific, such that sequence data are generated for one or more of: (i) determining the number and / or sequence of LMR in the genomic DNA; (ii) calculating the ratio of αβTcells to γδTcells from the genomic DNA; (iii) calculating the number and / or sequence of MRD in an IgH portion of the genomic DNA; (iv) calculating the ratio of Igκ to Igλ in the genomic DNA; and (v) quantifying the number Ig class switches in the genomic DNA. In some embodiments the method further comprises a step (c) of correlating the sequence data across a portion of genomic DNA in the cfDNA to a fraction of the T-cells and / or B-cells in the subject. In some embodiments, if monitoring the number of B cells in the subject, the method comprises correlating the number and / or sequence of MRD in an IgH portion of the genomic DNA and / or to the number Ig class switches in the genomic DNA to the number of B cells in the subject. In some embodiments, if the monitoring the number of T cells, the method further comprises correlating one or more of: (i) the number and / or sequence of maximal rearranged regions (MRD) in the genomic DNA; (ii) the ratio of αβT cells to γδT cells; and (iii) the ratio of Igκ to Igλ in the genomic DNA; to the number of T cells in the subject. In some embodiments, the subject has been diagnosed with or is suspected of having a hyperproliferative disorder. In some embodiments, the subject has a hyperproliferative disorder. In some embodiments, the subject is subject with peripheral T-cell lymphoma, myeloma, or bladder cancer patient. In some embodiments, the sequence data comprises valley region sequence reads for a location of maximal rearrangement for one or more gene selected from V, D, and J genes and shoulder region sequence reads for a location of low recombination proximate to the one or more genes. In some embodiments, the therapeutic agent is CAR-T therapy. In some embodiments, the method further comprises a step of correlating the sequence data to the number of T cells and / or B cells in the subj ect. In some embodiments, if the number of T cells and / or B cells are elevated in the subject and the subject has been diagnosed with a hyperproliferative disorder, then the therapeutic agent is likely working.DOCKET NO. STFD-015-PCT PATENT APPLICATION BRIEF DESCRIPTION OF THE DRAWINGS

[0013] The following detailed description of embodiments of the present invention will be better understood when read in conjunction with the appended drawings. For the purpose of illustrating the invention, there are shown in the drawings certain embodiments. It is understood, however, that the invention is not limited to the precise arrangements and instrumentalities shown. In the drawings:

[0026] FIG. 1 illustrates a workflow for methods herein.

[0027] FIGS. 2A and 2B illustrates a workflow for a method herein (A) and applications of methods herein (B).

[0028] FIG. 3 illustrates advantages of QUAntification of Rearranged Targeted Zones (QUARTZ).

[0029] FIG. 4 illustrates the fraction of T-cell derived cfDNA estimated by QUARTZ.

[0030] FIGS. 5A-5C illustrate biological benchmark by using T-cell / B-cell mixture.

[0031] FIGS. 5A and 5B show data from a cell mixture of T-cells and B-cells made by FACS sorting, while FIG. 5C shows data from healthy donor PBMC.

[0032] FIGS. 5D-DF illustrate examples of B-cell subset analysis. Myeloma samples (tumor cells being plasma cells with class switch rearrangement) were analyzed.

[0033] FIGS. 6A and 6B illustrate a combination of QUARTZ and Repertoire analysis.

[0034] FIGS. 6C-6F compare QUARTZ to other strategies.

[0035] FIG. 7 illustrates the large amount of noise in sequence depth. A prior method targeted large genomic region, while QUARTZ targets less noisy regions, uses a novel mathematical approach with cfDNA specific GC% normalization.

[0036] FIGS. 8A-8C illustrates identification of the appropriate bin size for GC% correction

[0037] FIGS. 9A-9B illustrate an effect of GC% correction.

[0038] FIG. 10 illustrates a flow of a method herein.

[0039] FIG. 11A and 11B illustrate the effect of GPR correction, which leads to a flatter curve.

[0040] FIG. 12 illustrates an effect of GPR correction. Here LOD95 is improved.

[0041] FIGS. 13A and 13B illustrate that the intergenomic region between TRGV and TRGJ is the maximal rearranged region for TCR.DOCKET NO. STFD-015-PCT PATENT APPLICATION

[0042] FIGS. 14A-14C also illustrate that the intergenomic region between TRGV and TRGJ is the maximal rearranged region for TCR

[0043] FIG. 15 illustrates gd / ab T-cell ratio.

[0044] FIGS. 16A and 16B illustrate that the intergenomic region between IGHD and IGHJ is the maximal rearranged region for BCR.

[0045] FIGS. 17Aand 17B illustrate Kappa / Lambda ratio.

[0046] FIGS. 18A and 18B illustrate differential quantification of B / plasma cells with class switch.

[0047] FIG. 19 illustrates an exemplary analysis of disease monitoring for PTCL.

[0048] FIG. 20 illustrate disease monitoring for myeloma.

[0049] FIG. 21 illustrates T-Cell amount after CAR-T.

[0050] FIG. 22 illustrates T-cell in urine after BCG for bladder cancer.

[0051] FIGS. 23A-23C illustrates a biological spike-in experiment.

[0052] FIGS. 24A-24C illustrate validation of QUARTZ using plasma cfDNA from T-cell lymphoma.

[0053] FIGS. 25A–25F illustrate GC bias correction.

[0054] FIG. 26 illustrates a denoising process by GPR model.

[0055] FIG. 27 illustrates B-cell subset analysis.

[0056] FIG. 28A illustrates a comparison of QUARTZ to a prior method.

[0057] FIG. 28B illustrates WGS of peripheral blood mononuclear cells.

[0058] FIG. 28C illustrates sorted nonT. a[3T, y5T-cells.

[0059] FIG. 28D illustrates a biological spike-in experiment.

[0060] FIG. 28E illustrates validation by using Plasma cfDNA from T-cell lymphoma.

[0061] FIG. 28F illustrates the impact of allelic exclusion in TCRB for estimation of abT / gdT ratio.

[0062] FIG. 29 shows an overview of the QUARTZ workflow for absolute quantification of T and B-cell derived cfDNA.

[0063] FIG. 30 shows applications of QUARTZ.

[0064] FIGS. 31A-31D illustrate exemplary methods for normalization and denoising of sequencing depth. A) illustrates GC-content dependent bias in sequencing depth and GC normalization using a LOESS model with optimized window size. (B) illustrates the presenceDOCKET NO. STFD-015-PCT PATENT APPLICATIONof sample-type-specific noise after GC normalization. (C) illustrates a workflow for Gaussian Process Regression(GPR)-based denoising using correlated control samples. (D) illustrates removal of sample-type-specific noise following GPR-based denoising.

[0065] FIGS. 32A-32H illustrate Quantitative validation of QUARTZ for T- and B-cell fraction estimation. FIG. 32A. Flow cytometry-based sorting strategy for generating T-cell and B-cell mixtures with defined proportions. FIG. 32B. Mixtures containing defined proportions of T cells and B cells were generated using flow cytometric sorting. FIG. 32C. Using the same cell mixtures and analytical workflow, the x-axis indicates the fraction of B cells in the input cell mixture, and they-axis indicates the B-cell fraction estimated by QUARTZ. FIGS. 32D–4G. In-silico Spike-in data.

[0066] FIGS. 33A-33C illustrate performance of ImmuneLENS for cell spike-in samples.

[0067] FIGS. 34Aand 34B illustrate performance comparison of ImmuneLENS and QUARTZ for cfDNA analysis. FIG. 34A: T-cell detection in cfDNA. FIG. 34B: B-cell detection in cfDNA.

[0068] FIG. 35 A illustrates transition of T-cell fraction in cfDNA (left) and transition of T-cell derived cfDNA (right).

[0069] FIG. 35B illustrates transition of B-cell turnover (left) and transition of B-cell derived cfDNA (right).

[0070] FIGS. 36A-36D illustrate that QUARTZ enables non-invasive prediction of CAR-T therapy response from the pre-treatment immune state. FIG. 36A: Tcell fraction in cfDNA at Baseline by disease subtypes. FIG. 36B: Subtype-dependent relationships between T-cell fraction and therapeutic outcomes. FIG. 36C: Tumor-Tcell cfDNA balance at Baseline. FIG.36D: Tumor-Tcell cfDNA balance and EFS.

[0071] FIGS. 37A-37D illustrate that QUARTZ enables non-invasive detection of prognostically significant systemic T-cell expansion. FIG. 37A: T-Cell-Derived cfDNA Mirrors CAR-T Genome Burden. FIG. 37B: Effect of prior usage of Bendamustine. FIG. 37C: Tumor-Tcell cfDNA balance at Day7 after CART infusion. FIG. 37D: Tumor-T cell cfDNA balance and EFS.

[0072] FIGS. 38A-38C illustrate CMV and HIV responses.

[0073] FIGS. 39A-39C illustrate QUARTZ Analysis of Sequential Urine cfDNA Reveals Elevated T-Cell Fraction in Responders to BCG Therapy. FIG. 39A: Urine cfDNA atDOCKET NO. STFD-015-PCT PATENT APPLICATIONPre? TURBT. FIG. 39B: Urine cfDNA during BCG therapy. FIG. 39C: Urine cfDNAafter BCG therapy.

[0074] FIGS. 40A-40D illustrate quantification of immunoglobulin class-switch recombination (CSR) and its application to B-cell malignancies using QUARTZ. FIG. 40A: Schematic Overview of B? Cell Fraction Estimation by CSR Status and Isotype. FIG. 40B: Differential Correlation of CSR Status With Mutation AF Across B? Cell COO Subtypes. FIG.40C: CSR(+) B?cell fractions are correlated with Mutation AF in Multiple Myeloma patients. FIG. 40D: Profiling of Tumor IGH Constant-Region Isotypes in Multiple Myeloma.

[0075] FIGS. 41 A and 41 B illustrate QUARTZ analysis by Whole genome sequence data

[0076] FIGS. 42A and 42B illustrate Quantitative longitudinal tracking of TCR clonotypes using QUARTZ

[0077] FIG. 43 illustrates estimation of γδ T-cell and γδ T-cell fractions using QUARTZ and TCR repertoire analysis.DETAILED DESCRIPTION

[0051] Certain terminology is used in the following description for convenience only and is not limiting. The words ‘Tight ’ “left,” “top,” and “bottom” designate directions in the drawings to which reference is made.Definitions

[0078] The words “a” and “one,” as used in the claims and in the corresponding portions of the specification, are defined as including one or more of the referenced item unless specifically stated otherw ise. As used in the present disclosure and claims, the singular forms “a,” “an” and “the” include plural forms unless the context clearly dictates otherwise. The phrase “at least one” followed by a list of two or more items, such as “A, B, or C” or “A, B, and C,” means any individual one of A, B or C as well as any combination thereof. Likewise, the phrase “one or more of’ followed by a list of two or more items, such as “A, B, or C” or “A, B, and C,” means any individual one of A, B or C as well as any combination thereof. The term “and / or” as used in a phrase such as “A and / or B” herein includes both A and B, A or B, A (alone), and B (alone). Likewise, the term “and / or” as used in a phrase such as “A, B, and / or C” encompasses each ofDOCKET NO. STFD-015-PCT PATENT APPLICATIONthe following embodiments: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone).

[0079] Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. For example, Singleton et al., Dictionary of Microbiology and Molecular Biology 2nd ed., J. Wiley & Sons (New York, NY 1994), provide one skilled in the art with a general guide to many of the terms used in the present application. Additionally, the practice of the present disclosure will employ, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, and biochemistry, which are within the skill of the art. Such techniques are explained fully in the literature, such as, “Molecular Cloning: A Laboratory Manual,” 2nd edition (Sambrook et al., 1989); “Oligonucleotide Synthesis” (M. J. Gait, ed., 1984); “Animal Cell Culture” (R. I. Freshney, ed., 1987); “Methods in Enzymology” (Academic Press, Inc.); “Handbook of Experimental Immunology,” 4th edition (D M. Weir & C. C. Blackwell, eds., Blackwell Science Inc., 1987); “Gene Transfer Vectors for Mammalian Cells” (J. M. Miller & M. P. Calos, eds., 1987); “Current Protocols in Molecular Biology” (F. M. Ausubel et al., eds., 1987); and “PCR: The Polymerase Chain Reaction,” (Mullis et al., eds.. 1994).

[0080] It is understood that wherever embodiments are described herein with the language “comprising” otherwise analogous embodiments described in terms of “consisting of’ and / or “consisting essentially of’ are also provided. It is also understood that wherever embodiments are described herein with the language “consisting essentially of’ otherwise analogous embodiments described in terms of “consisting of’ are also provided.

[0081] The term “about” as used herein when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of ±20% from the specified value, as such variations are appropriate to perform the disclosed methods. Further embodiments herein comprise modification of any numerical value herein with ±10%, ±5%, ± 1 %, or ±0.1 %. For recitation of numeric ranges herein, each intervening number therebetween with the same degree of precision is explicitly contemplated. For example, for the range of 6-9, the numbers 7 and 8 are contemplated in addition to 6 and 9, and for the range 6.0-7.0, the numbers 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, and 7.0 are explicitly contemplated.DOCKET NO. STFD-015-PCT PATENT APPLICATION

[0082] The phrase “and / or,” as used herein in the specification and in the claims, should be understood to mean “either or both” of the elements so conjoined, i.e., elements that are conjunctively present in some cases and disjunctively present in other cases. Other elements may optionally be present other than the elements specifically identified by the "and / or” clause, whether related or unrelated to those elements specifically identified unless clearly indicated to the contrary. Thus, as a non-limiting example, a reference to “A and / or B,” when used in conjunction with open-ended language such as “comprising” can refer, in some embodiments, to A without B (optionally including elements other than B); in another embodiments, to B without A (optionally including elements other than A); in yet another embodiments, to both A and B (optionally including other elements); etc.

[0083] As used herein in the specification and in the claims, “or” should be understood to have the same meaning as “and / or” as defined above. For example, when separating items in a list, “or” or “and / or” shall be interpreted as being inclusive, i.e., the inclusion of at least one, but also including more than one, of a number or list of elements, and, optionally, additional unlisted items. Only terms clearly indicated to the contrary, such as “only one of’ or “exactly one of,” or, when used in the claims, “consisting of,” will refer to the inclusion of exactly one element of a number or list of elements. In general, the term “or” as used herein shall only be interpreted as indicating exclusive alternatives (i.e. “one or the other but not both”) when preceded by terms of exclusivity, “either,” “one of,” “only one of,” or “exactly one of.” “Consisting essentially of,” when used in the claims, shall have its ordinary meaning as used in the field of patent law.

[0084] The term “at least” prior to a number or series of numbers (e.g., “at least two”) is understood to include the number adjacent to the term “at least,” and all subsequent numbers or integers that could logically be included, as clear from context. When “at least” is present before a series of numbers or a range, it is understood that “at least” modifies each of the numbers in the series or range. Ranges provided herein are understood to include all individual integer values and all subranges within the ranges.

[0085] The term “about” prior to a number or series of numbers (e.g, “about two”) is understood to include the number adjacent to the term “about,” and all subsequent numbers or integers that could logically be included, as clear from context. When “about” is present beforeDOCKET NO. STFD-015-PCT PATENT APPLICATIONa series of numbers or a range, it is understood that “about” modifies each of the numbers in the series or range.

[0086] As used herein, the term “animal” includes, but is not limited to. humans and nonhuman vertebrates such as wild animals, rodents, such as rats, ferrets, and domesticated animals, and farm animals, such as dogs, cats, horses, pigs, cows, sheep, and goats. In some embodiments, the animal is a mammal. In some embodiments, the animal is a human. In some embodiments, the animal is a non-human mammal.

[0087] As used herein, the terms “comprising” (and any form of comprising, such as “comprise,” “comprises,” and “comprised”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”), or “containing” (and any form of containing, such as “contains” and “contain”), are inclusive or open-ended and do not exclude additional, unrecited elements or method steps.

[0088] The terms “functional fragment” means any portion of a polypeptide or nucleic acid sequence from which the respective full-length polypeptide or nucleic acid relates that is of a sufficient length and has a sufficient structure to confer a biological affect that is at least similar or substantially similar to the full-length polypeptide or nucleic acid upon which the fragment is based. In some embodiments, a functional fragment is a portion of a full-length or wild-type nucleic acid sequence that encodes any one of the nucleic acid sequences disclosed herein, and said portion encodes a polypeptide of a certain length and / or structure that is less than full-length but encodes a domain that still biologically functional as compared to the full-length or wild-type protein. In some embodiments, the functional fragment may have a reduced biological activity, about equivalent biological activity, or an enhanced biological activity as compared to the wild-type or full-length polypeptide sequence upon which the fragment is based (such wild-type or full-length sequences “reference sequences” or each individually a “reference sequence”). In some embodiments, the functional fragment is derived from the sequence of an organism, such as a human. In such embodiments, the functional fragment may retain about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% sequence identity to the wild-type human sequence upon which the sequence is derived. In some embodiments, the functional fragment may retain about 85%, 80%, 75%, 70%, 65%, or 60% sequence identity to the wild-type sequence upon which the sequence is derived.DOCKET NO. STFD-015-PCT PATENT APPLICATION

[0089] By “fragment” is meant a portion of a polypeptide or nucleic acid molecule. This portion contains, in some embodiments, at least about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or about 95% of the entire length of the reference nucleic acid molecule or polypeptide.

[0090] The term “functional variant thereof’ refers to a nucleic acid or peptide varying from a reference sequence but retaining biological activity compared to a nucleic acid or peptide having the reference sequence. Functional variants may have one or a plurality of additions, deletions, truncations, single nucleotide polymorphisms, or other mutation as compared to the reference sequence upon which it is based. In some embodiments, the biological activity is measured by a functional assay disclosed herein. In some embodiments, a “functional variant thereof’ has at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to a reference sequence. In some embodiments, a “functional variant thereof’ has a sequence identity to a reference sequence between any two of about 70%, about 75%, about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity. In some embodiments, a “functional variant thereof’ has a sequence identity of about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% to a stated reference sequence.

[0091] “Variant” as the term is used herein, is a nucleic acid sequence or a peptide sequence that differs in sequence from a reference nucleic acid sequence or peptide sequence, respectively. In some embodiments, a variant is a functional variant in that it retains essential biological properties of the reference nucleic acid molecule or amino acid sequence. Changes in the sequence of a nucleic acid variant, in some embodiments, do not alter the amino acid sequence of a peptide encoded by the reference nucleic acid, or may result in amino acid substitutions, additions, deletions, fusions and truncations. Changes in the sequence of peptide variants are typically limited or conservative, so that the sequences of the reference peptide and the variant are closely similar overall and, in many regions, identical. A variant and reference peptide can differ in amino acid sequence by one or more substitutions, additions, deletions in any combination. A variant of a nucleic acid or peptide can be a naturally occurring, such as an allelic variant, or can be a variant that is not known to occur naturally. Non-naturally occurring variants of nucleic acids and peptides may be made by mutagenesis techniques or by directDOCKET NO. STFD-015-PCT PATENT APPLICATIONsynthesis. In some embodiments, a nucleic acid sequence variant has at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% sequence identity to a reference nucleic acid molecule herein. In some embodiments, an amino acid sequence variant has at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% sequence identity to a reference amino acid sequence herein.

[0092] “Optional” or “optionally” means that the subsequently described event, circumstance, or material may or may not occur or be present, and that the description includes instances where the event, circumstance, or material occurs or is present and instances where it does not occur or is not present.

[0093] The term “diagnosis” or “prognosis” as used herein refers to the use of information (e g., genetic information or data from other molecular tests on biological samples, signs and symptoms, physical exam findings, cognitive performance results, etc.) to anticipate the most likely outcomes, timeframes, and / or response to a particular treatment for a given disease, disorder, or condition, based on comparisons with a plurality of individuals sharing common nucleotide sequences, symptoms, signs, family histories, or other data relevant to consideration of a patient’s health status.

[0094] As used herein, the phrase “in need thereof’ means that the animal or mammal has been identified or suspected as having a need for the particular method or treatment. In some embodiments, the identification can be by any means of diagnosis or observation. In any of the methods and treatments described herein, the animal or mammal can be in need thereof. In some embodiments, the subject in need thereof is a human seeking prevention of a disease or disorder (e.g., viral and bacterial diseases, cancers, neurodegenerative diseases, and neuropsychiatric disorders.

[0095] The term “long-read sequencing” means the process of nucleic acid sequencing that produces genomic data by generating individual reads that are each derived from a single molecule which is thousands of nucleotides or more in length. In some embodiments, the long-read sequencing comprising producing genomic data in the form of a computer program product file comprising over about 2 kilobases in length, about 3 kilobases in length, about 4DOCKET NO. STFD-015-PCT PATENT APPLICATIONkilobases in length, about 5 kilobases in length, about 6 kilobases in length, about 7 kilobases in length, about 8 kilobases in length, about 9 kilobases in length, about 10 kilobases in length, about 11 kilobases in length, about 12 kilobases in length, about 13 kilobases in length, about 14 kilobases in length, about 15 kilobases in length, about 16 kilobases in length, about 17 kilobases in length, about 18 kilobases in length, about 19 kilobases in length, or about 20 or more kilobases in length.

[0096] As used herein, the term “mammal” means any animal in the class Mammalia such as rodent (i.e., mouse, rat, or guinea pig), monkey, cat, dog, cow, horse, pig, or human. In some embodiments, the mammal is a human. In some embodiments, the mammal refers to any nonhuman mammal. In some embodiments, the present disclosure relates to any of the methods or compositions of matter wherein the sample is taken from a mammal or non-human mammal. In some embodiments, the present disclosure relates to any of the methods or compositions of matter wherein the sample is taken from a human or non-human primate.

[0097] The terms “polynucleotide,” “oligonucleotide” and “nucleic acid” are used interchangeably throughout and include DNA molecules (e.g., cDNA or genomic DNA), RNA molecules (e.g., mRNA), analogs of the DNA or RNA generated using nucleotide analogs (e.g., peptide nucleic acids and non-naturally occurring nucleotide analogs), and hybrids thereof. Thus, the term “expressible nucleic acid” or “expressible nucleic acid sequence” as used herein refers to expressible DNA or RNA molecules or expressible DNA or RNA sequences.

[0098] A nucleic acid molecule and / or sequences of embodiments herein can be single-stranded or double-stranded. In some embodiments, the nucleic acid molecules of the disclosure comprise a contiguous open reading frame encoding an antibody, or a fragment thereof, as described herein. “Nucleic acid” or “oligonucleotide” or “polynucleotide” as used herein may mean at least two nucleotides covalently linked together. The depiction of a single strand also defines the sequence of the complementary strand. Thus, a nucleic acid also encompasses the complementary strand of a depicted single strand. Many variants of a nucleic acid may he used for the same purpose as a given nucleic acid. Thus, a nucleic acid also encompasses substantially identical nucleic acids and complements thereof. In some embodiments, a single strand provides a probe that may hybridize to a target sequence under stringent hybridization conditions. Thus, a nucleic acid also encompasses a probe that hybridizes under stringent hybridization conditions. Nucleic acids may be single stranded orDOCKET NO. STFD-015-PCT PATENT APPLICATIONdouble stranded, or may contain portions of both double stranded and single stranded sequence. The nucleic acid may be DNA, both genomic and cDNA, RNA, or a hybrid, where the nucleic acid may contain combinations of deoxyribo- and ribo-nucleotides, and combinations of bases including uracil, adenine, thymine, cytosine, guanine, inosine, xanthine, hypoxanthine, isocytosine and isoguanine. Nucleic acids may be obtained by chemical synthesis methods or by recombinant methods. A nucleic acid will generally contain phosphodiester bonds, although nucleic acid analogs maybe included that may have at least one different linkage, e.g., phosphoramidate, phosphorothioate, phosphorodithioate, or o-methylphosphoroamidite linkages and peptide nucleic acid backbones and linkages. Other analog nucleic acids include those with positive backbones; non-ionic backbones, and non-ribose backbones, including those described in U. S. Pat. Nos. 5,235,033 and 5,034,506, which are incorporated by reference in their entireties. Nucleic acids containing one or more non-naturally occurring or modified nucleotides are also included within one definition of nucleic acids. The modified nucleotide analog may be located for example at the 5’-end and / or the 3’-end of the nucleic acid molecule. Representative examples of nucleotide analogs may be selected from sugar- or backbone-modified ribonucleotides. It should be noted, however, that also nucleobase-modified ribonucleotides, i.e. ribonucleotides, containing a non-naturally occurring nucleobase instead of a naturally occurring nucleobase such as uridines or cytidines modified at the 5-position, e.g. 5-(2-amino)propyl uridine, 5-bromo uridine; adenosines and guanosines modified at the 8-position, e.g. 8-bromo guanosine; deaza nucleotides, e.g. 7-deaza-adenosine; 0- and N-alkylated nucleotides, e.g. N6-methyl adenosine are suitable. The 2’-OH-group may be replaced by a group selected from H, OR. R, halo, SH, SR, NH2. NHR, N2 or CN. wherein R is Cl -C6 alkyl, alkenyl or alkynyl and halo is F, Cl, Br or I. Modified nucleotides also include nucleotides conjugated with cholesterol through, e.g., a hydroxyprolinol linkage as described in Krutzfeldt et al., Nature (Oct. 30, 2005), Soutschek et al., Nature 432:173-178 (2004), and U. S. Patent Publication No. 20050107325, which are incorporated herein by reference in their entireties. Modified nucleotides and nucleic acids may also include locked nucleic acids (LNA), as described in U. S. Patent No. 20020115080, which is incorporated herein by reference. Additional modified nucleotides and nucleic acids are described in U. S. Patent Publication No. 20050182005, which is incorporated herein by reference in its entirety. Modifications of the ribose-phosphate backbone may be done for a variety of reasons, e.g., toDOCKET NO. STFD-015-PCT PATENT APPLICATIONincrease the stability and half-life of such molecules in physiological environments, to enhance diffusion across cell membranes, or as probes on a biochip. Mixtures of naturally occurring nucleic acids and analogs may be made; alternatively, mixtures of different nucleic acid analogs, and mixtures of naturally occurring nucleic acids and analogs may be made. In some embodiments, the expressible nucleic acid sequence is in the form of DNA. In some embodiments, the expressible nucleic acid is in the form of RNA with a sequence that encodes the polypeptide sequences disclosed herein and, in some embodiments, the expressible nucleic acid sequence is an RNA / DNA hybrid molecule that encodes any one or plurality of polypeptide sequences disclosed herein.

[0099] As used herein, the term “nucleic acid molecule” is a molecule that comprises one or more nucleotide sequences.

[0100] As used herein, the term “kit” refers to a set of components provided in the context of a system for practicing the methods disclosed herein. A kit may include reagents (e.g., oligonucleotides, enzymes, extracellular matrix components etc. in appropriate containers) and / or supporting materials (e.g., buffers, media, cells, written instructions for performing the assay etc.) from one location to another. For example, in some embodiments, kits include one or more enclosures (e.g.. boxes) containing relevant reaction reagents and / or supporting materials. As used herein, the term “fragmented kit” refers to an assay comprising two or more separate containers that each contain a subportion of total kit components. Containers may be delivered to an intended recipient together or separately. For example, a first container may contain a petri dish or polysterene plate for use in a cell culture assay, while a second container may contain cells, such as control cells. The term “fragmented kit” is intended to encompass kits containing Analyte Specific Reagents (ASR’s) regulated under section 520(e) of the Federal Food, Drug, and Cosmetic Act, but are not limited thereto. Indeed, any delivery system comprising two or more separate containers that each contain a sub-portion of total kit components are included in the term “fragmented kit.” In contrast, a “combined kit” refers to a delivery system containing all components in a single container (e.g., in a single box housing each of the desired components). The term “kit” includes both fragmented and combined kits. In some embodiments, the kit comprises a computer program product disclosed herein and one or plurality of containers, each container, such as a test tube.DOCKET NO. STFD-015-PCT PATENT APPLICATION

[0101] Any probes may be used in concert with any of the devices, systems, kits, or methods disclosed herein. As used herein, the term “probe’’ refers to any molecule that may bind or associate, indirectly or directly, covalently or non-covalently, to any of the substrates and / or reaction products and / or nucleic acid sequences disclosed herein and whose association or binding is detectable using the methods disclosed herein. In some embodiments, the probe is a fluorogenic, fluorescent, or chemiluminescent probe, an antibody, or an absorbance-based probe. In some embodiments, an absorbance-based probe, for example the chromophore pNA (para-nitroanaline), may be used as a probe for detection and / or quantification of a number of nucleic acid sequences encoding 1g amino acid sequences disclosed herein on genomic DNA from a cell free DNA sample. In some embodiments, the probe comprises a nucleic acid disclosed herein and / or an analog or salt thereof, including those analogs that comprise at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 87%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the sequence identifiers disclosed herein. A probe may be immobilized, adsorbed, or otherwise non-covalently bound to a solid surface, such that, upon exposure to complementary target genomic DNA for a time period sufficient to perform an hybridization, hybridization and. optionally, quantitative or semi-quantitative PCR can be performed. In some embodiments, the probe is a probe for detection and / or quantification of a number of nucleic acid sequences encoding Ig or T cell receptor amino acid sequences disclosed herein on genomic DNA from a cell-free DNA sample conjugated to a fluorescent or chemiluminescent protein enabling detection after stimulation with a certain wavelength and frequency of light. For instance, if the step of detecting comprises use of FRET, excitation of the protein conjugated to a nucleic acid probe specific for nucleic acid target sequences disclosed herein causes one of the chromophore to emit a fluorescent light under exposure to a wavelength sufficient to activate such a fluorescent molecule. The intensity, length, or amplitude of a wavelength emitted from fluorescent marker can be measured and is, in some embodiments, proportional to the presence, absence or quantity of enzyme present in the reaction vessel, thereby the quantity of enzyme can be determined from detection of the intensity of or fluorescence at a known wavelength of light.

[0102] As used herein, “PCR” refers to the “polymerase chain reaction.” PCR can be used to generate an amplified DNA in some embodiments herein. Methods for performing PCR areDOCKET NO. STFD-015-PCT PATENT APPLICATIONwell known in the art. Primers for use in PCR are designed to have regions that are substantially complementarity to regions of the DNA to be used as a template for the PCR. “Substantially complementarity,” as used herein, refers to sequences of nucleotides where a majority or all of the bases in the primer sequence are complementarity, or one or more bases are noncomplementarity, or mismatched. Substantially complementarity sequences are able to anneal or hybridize with the intended DNA target under annealing conditions used for PCR. The primers can be designed to be substantially complementarity' to any portion of the DNA template. Primers useful for PCR can be generated by synthetic methods that are well known in the art. “Forward primers” are primers that contain a region of nucleotides that are substantially complementarity to nucleotides on the DNA template that are upstream of the DNA sequence that is to be amplified. “Upstream” is used herein to refer to a location 5, to the DNA sequence to be amplified relative to the coding strand. “Reverse primers” are primers that contain a region of nucleotides that are substantially complementarity to a double-stranded DNA template that are downstream of the DNA sequence that is to be amplified. “Downstream” is used herein to refer to a location 3’ to the DNA sequence to be amplified relative to the coding strand. Any DNA polymerase useful for PCR can be used in the methods disclosed herein. The reagents and polymerase are commercially available from a number of sources.

[0103] “Hybridization” as used herein typically refers to the technique of allowing two single-stranded polynucleotide sequences with some degree of complementarity to bind to one another to form a stable double-stranded polynucleotide. “Complementary” and its equivalents as used herein generally refers to the hybridization or base pairing between nucleotides or nucleic acids, such as, for instance, between the two strands of a double stranded DNA molecule or between an oligonucleotide primer and a primer binding site on a single stranded nucleic acid to be sequenced or amplified. Complementary nucleotides are, generally, A and T (or A and U), or C and G. Two single stranded RNA or DNA molecules are said to be complementary when the nucleotides of one strand, optimally aligned and compared and with appropriate nucleotide insertions or deletions, pair with at least about 70% of the nucleotides of the other strand, usually at least about 80%, 85%, 90% to 95%, and more preferably from about 98 to 100%. See, M. Kanehisa Nucleic Acids Res. 12:203 (1984), incorporated herein by reference.

[0104] Hybridization usually involves the steps of 1) allowing binding between probe and target; and 2) washing away unbound or weakly bound probes under stringent conditions.DOCKET NO. STFD-015-PCT PATENT APPLICATIONwherein stringent hybridization conditions are those washing conditions that provide dissociation for imperfect complexes while preserving the intended complexes between targetspecific probes and corresponding targets. Improvements in hybridization characteristics can be improvements in the selectivity of hybridization (sequence specificity and mismatch discrimination), the sensitivity of hybridization (ratio of absolute signal to background signal, signal -to-noise ratio), the affinity between probe and target (ratio of binding rate to dissociation rate between hybridization probes and targets); the stability of the duplex or complex (thermal stability, Tm; also kinetic inertness of dissociation or kinetic trap), or the efficiency or efficacy of hybridization (hybridization rate and / or yield of complex between probe and target for a fixed time of incubation under hybridization conditions). Methods for conducting polynucleotide hybridization assays have been well developed in the art. Hybridization assay procedures and conditions will vary depending on the application and are selected in accordance with the general binding methods known including those referred to in: Maniatis et al. Molecular Cloning: A Laboratory Manual (2nd Ed. Cold Spring Harbor, N. Y, 1989); Berger and Kimmel Methods in Enzymology, Vol. 152, Guide to Molecular Cloning Techniques (Academic Press, Inc., San Diego, Calif., 1987); Young and Davism, P. N. A. S, 80: 1194 (1983). Methods and apparatus for carrying out repeated and controlled hybridization reactions have been described in U. S. Pat. Nos. 5,871,928, 5,874,219, 6,045,996 and 6,386,749, 6,391,623 all of which are incorporated herein by reference.

[0105] Massive parallel sequencing or whole genome sequencing has become routine. Exemplary methods are described in U. S. Patent No. 10,370,652 (‘“Methods of nucleic acid amplification and sequencing” to Illumina Inc), which is incorporated herein by reference as if fully set forth.

[0106] The “percent identity” or “percent homology” of two polynucleotide or two polypeptide sequences is determined by comparing the sequences using the GAP computer program (a part of the GCG Wisconsin Package, version 10.3 (Accelrys, San Diego. Calif.)) using its default parameters. “Identical” or '‘identity” as used herein in the context of two or more nucleic acids or amino acid sequences, may mean that the sequences have a specified percentage of residues that are the same over a specified region. The percentage may be calculated by optimally aligning the two sequences, comparing the two sequences over the specified region, determining the number of positions at which the identical residue occurs in both sequences toDOCKET NO. STFD-015-PCT PATENT APPLICATIONyield the number of matched positions, dividing the number of matched positions by the total number of positions in the specified region, and multiplying the result by 100 to yield the percentage of sequence identity. In cases where the two sequences are of different lengths or the alignment produces one or more staggered ends and the specified region of comparison includes only a single sequence, the residues of single sequence are included in the denominator but not the numerator of the calculation. When comparing DNA and RNA, thymine (T) and uracil (U) may be considered equivalent. Identity may be performed manually or by using a computer sequence algorithm such as BLAST or BLAST 2.0. Briefly, the BLAST algorithm, which stands for Basic Local Alignment Search Tool is suitable for determining sequence similarity. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http: / / www.ncbi.nlm.nih.gov). This algorithm involves first identifying high scoring sequence pair (HSPs) by identifying short words of length Win the query sequence that either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Extension for the word hits in each direction are halted when: 1) the cumulative alignment score falls off by the quantity X from its maximum achieved value; 2) the cumulative score goes to zero or below, due to the accumulation of one or more negativescoring residue alignments; or 3) the end of either sequence is reached. The Blast algorithm parameters W, T and X determine the sensitivity and speed of the alignment. The Blast program uses as defaults a word length (W) of 11, the BLOSUM62 scoring matrix (see Henikoff et al., Proc. Natl. Acad. Sci. USA, 1992, 89, 10915-10919, which is incorporated herein by reference in its entirety) alignments (B) of 50, expectation (E) of 10, M=5, N=4, and a comparison of both strands. The BLAST algorithm (Karlin et al., Proc. Natl. Acad. Sci. USA, 1993, 90, 5873-5787, which is incorporated herein by reference in its entirety) and Gapped BLAST perform a statistical analysis of the similarity between two sequences. One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide sequences would occur by chance. For example, a nucleic acid is considered similar to another if the smallest sum probability inDOCKET NO. STFD-015-PCT PATENT APPLICATIONcomparison of the test nucleic acid to the other nucleic acid is less than about 1, less than about 0.1, less than about 0.01, or less than about 0.001.

[0107] The terms “subject,” “individual,” and “patient” are used interchangeably herein to refer to a vertebrate, a mammal in some embodiments, a human in some embodiments. Mammals include, but are not limited to, murine, simians, humans, farm animals, cows, pigs, goats, sheep, horses, dogs, sport animals, and pets. Tissues, cells and their progeny obtained in vivo or cultured in vitro are also encompassed by the definition of the term “subject.” The term “subject” is also used throughout the specification in some embodiments to describe an animal from which a cell sample is taken or an animal to which a disclosed cell or nucleic acid sequences have been administered. In some embodiments, the subject is a human. For treatment of those conditions which are specific for a specific subject, such as a human being, the term “patient” may be interchangeably used. In some embodiments, in the description of the present disclosure, the term “patient” will refer to human patients suffering from a particular disease or disorder. In some embodiments, the subject may be a non-human animal. The term “mammal” encompasses both humans and non-humans and includes but is not limited to humans, non-human primates, canines, felines, murine, bovines, equines, caprine, and porcines. In some embodiments, the mammal is a donkey, camel, rabbit, guinea pig, horse, pig, cow, cat, dog, rat, mouse, monkey, non-human, ape, or human. In some embodiments, the term “subject” is a human diagnosed with or suspected of having a hyperproliferative disorder, such as cancer.

[0108] As used herein, “expression” refers to the process by which a polynucleotide is transcribed from a DNA template (such as into and mRNA or other RNA transcript) and / or the process by which a transcribed mRNA (or administered mRNA) is translated into peptides, polypeptides, or proteins. Transcripts and encoded polypeptides may be collectively referred to as “gene product.” If the polynucleotide is derived from genomic DNA. expression may include splicing of the mRNA in a eukaryotic cell. In some embodiments, the at least one expressible nucleic acid sequence comprises only DNA nucleotides, RNA nucleotides or comprises both RNA and DNA nucleotides. In some embodiments, the at least one expressible nucleic acid consists of DNA. In some embodiments, the at least one expressible nucleic acid consists of RNA. In some embodiments, the expressible nucleic acid sequence, also known asDOCKET NO. STFD-015-PCT PATENT APPLICATIONa coding sequence, encodes one or a plurality of polypeptides associated with T-cells or B-cells and is positioned within a sequence of genomic DNA in the cell-free DNA sample.

[0109] The term “fragment’' means a portion of a polypeptide or nucleic acid molecule. This portion contains, in some embodiments, at least about 5%. at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or at least about 90% of the entire length of the reference nucleic acid molecule or polypeptide. A fragment may contain about 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200. 300, 400, 500, 600, 700, 800, 900. 1000 or more nucleotides or amino acids.

[0110] The term “pharmaceutically acceptable excipient.” “pharmaceutically acceptable carrier,” or “pharmaceutically acceptable diluent” as used herein is meant to refer to an excipient, carrier or diluent that can be administered to a subject, together with an agent or the pharmaceutical compositions disclosed herein, and which is inert or fails to eliminate the pharmacological activity of the active agent of the pharmaceutical composition. In some embodiments, the pharmaceutically acceptable carrier fails to destroy or is incapable of eliminating the pharmacological activity of an active agent / vaccine and is nontoxic when administered in doses sufficient to deliver a therapeutic amount of the active agent. The term “pharmaceutically acceptable salt” of nucleic acids as used herein may be an acid or base salt that is generally considered in the art to be suitable for use in contact with the tissues of human beings or animals without excessive toxicity, irritation, allergic response, or other problem or complication. Such salts include mineral and organic acid salts of basic residues such as amines, as well as alkali or organic salts of acidic residues such as carboxylic acids. Specific pharmaceutical salts include, but are not limited to, salts of acids such as hydrochloric, phosphoric, hydrobromic, malic, glycolic, fumaric, sulfuric, sulfamic, suifanilic, formic, toluenesulfonic, methanesulfonic, benzene sulfonic, ethane disulfonic, 2-hydroxyethyl sulfonic, nitric, benzoic, 2-acetoxybenzoic, citric, tartaric, lactic, stearic, salicylic, glutamic, ascorbic, pamoic. succinic, fumaric, maleic, propionic, hydroxymaleic, hydroiodic, phenylacetic, alkanoic such as acetic, HOOC-(CH2)n-COOH where n is 0-4, and the like. Similarly, pharmaceutically acceptable cations include, but are not limited to sodium, potassium, calcium, aluminum, lithium, and ammonium. Those of ordinary skill in the art will recognize from this disclosure and the knowledge in the art that further pharmaceutically acceptable salts, including those listed by Remington’s Pharmaceutical Sciences, 17th ed..DOCKET NO. STFD-015-PCT PATENT APPLICATIONMack Publishing Company, Easton, PA, p. 1418 (1985). In general, a pharmaceutically acceptable acid or base salt can be synthesized from a parent compound that contains a basic or acidic moiety by any conventional chemical method. Briefly, such salts can be prepared by reacting the free acid or base forms of these compounds with a stoichiometric amount of the appropriate base or acid in an appropriate solvent.

[0111] The terms “polypeptide,’’ “peptide” and “protein” are used interchangeably herein to refer to polymers of amino acids of any length. The polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non-natural amino acids or chemical groups that are not amino acids. The terms also encompass an amino acid polymer that has been modified; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation, such as conjugation with a labeling component. As used herein the term “amino acid” includes natural and / or unnatural or synthetic amino acids, including glycine and both the D or L optical isomers, and amino acid analogs and peptidomimetics.

[0112] The terms “treat,” “treated,” “treating,” “treatment,” and the like as used herein are meant to refer to reducing or ameliorating a disorder and / or symptoms associated therewith (e.g., a viral infection). “Treating” can refer to administration of a chemotherapeutic agent, a DNA and / or RNA therapeutic or vaccine, a vaccine, a CAR-T therapy, or a cell therapy to a subject after the onset, or suspected onset, of a disease, disorder, or hyperproliferative disorder. “Treating” includes the concepts of “alleviating,” which refers to lessening the frequency of occurrence or recurrence, or the severity, of any symptoms or other ill effects related to a disease, disorder, or hyperproliferative disorder and / or the side effects associated with therapy thereof. The term “treating” also encompasses the concept of “managing” which refers to reducing the severity of a particular disease or disorder in a patient or delaying its recurrence, e.g., lengthening the period of remission in a patient who had suffered from the disease. It is appreciated that, although not precluded, treating a disorder or condition does not require that the disorder, condition, or symptoms associated therewith be eliminated completely.

[0113] For any therapeutic agent described herein the therapeutically effective amount may be initially determined from preliminary in vitro studies and / or animal models. A therapeutically effective dose may also be determined from human data. The applied dose can be adjusted based on the relative bioavailability and potency of the administered agent. Adjusting the doseDOCKET NO. STFD-015-PCT PATENT APPLICATIONto achieve maximal efficacy based on the methods described above and other well-known methods is within the capabilities of the ordinarily skilled artisan. General principles for determining therapeutic effectiveness, which may be found in Chapter 1 of Goodman and Gilman's The Pharmacological Basis of Therapeutics. 10th Edition. McGraw-Hill (New York) (2001), incorporated herein by reference, are summarized below. Pharmacokinetic principles provide a basis for modifying a dosage regimen to obtain a desired degree of therapeutic efficacy with a minimum of unacceptable adverse effects. In situations where a drug’s plasma concentration can be measured and related to the therapeutic window; additional guidance for dosage modification can be obtained. Drug products are considered to be pharmaceutical equivalents if they contain the same active ingredients and are identical in strength or concentration, dosage form, and route of administration. Two pharmaceutically equivalent drug products are considered to be bioequivalent when the rates and extents of bioavailability of the active ingredient in the two products are not significantly different under suitable test conditions.

[0114] As used herein, the phrase means that the animal or mammal has been identified or suspected as having a need for the particular method or treatment. In some embodiments, the identification can be by any means of diagnosis or observation. In any of the methods and treatments described herein, the animal or mammal can be in need of treatment for viral infection or cancer or in need of treatment for prevention of viral infection or malignant hyperproliferative disease. In some embodiments, the animal or mammal is in an environment or will be traveling to an environment in which a particular disorder or condition is prevalent or more likely to occur.

[0115] As used herein, the terms “comprising” (and any form of comprising, such as “comprise”, “comprises”, and “comprised”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”), or “containing” (and any form of containing, such as “contains” and “contain”), are inclusive or open-ended and do not exclude additional, unrecited elements or method steps.

[0116] The term “hyperproliferative disorder” refers to a disease or disorder characterized by abnormal proliferation, abnormal growth, abnormal senescence, abnormal quiescence, or abnormal removal of cells in an organism, and includes all forms of hyperplasias, neoplasias, and cancer. In some embodiments, a hyperproliferative disease is a cancer derived from theDOCKET NO. STFD-015-PCT PATENT APPLICATIONgastrointestinal tract or urinary system. In some embodiments, a hyperproliferative disease is a cancer of the adrenal gland, bladder, bone, bone marrow, brain, spine, breast, cervix, gall bladder, ganglia, gastrointestinal tract, stomach, colon, heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid, or uterus. In some embodiments, a hyperproliferative disease is a cancer chosen from: lung cancer, bone cancer, CMML, pancreatic cancer, skin cancer, cancer of the head and neck, cutaneous or intraocular melanoma, uterine cancer, ovarian cancer, rectal cancer, cancer of the anal region, stomach cancer, colon cancer, breast cancer, testicular cancer, gynecologic tumors (e.g., uterine sarcomas, carcinoma of the fallopian tubes, carcinoma of the endometrium, carcinoma of the cervix, carcinoma of the vagina or carcinoma of the vulva), Hodgkin’s disease, cancer of the esophagus, cancer of the small intestine, cancer of the endocrine system (e.g., cancer of the thyroid, parathyroid or adrenal glands), sarcomas of soft tissues, cancer of the urethra, cancer of the penis, prostate cancer, chronic or acute leukemia, solid tumors of childhood, lymphocytic lymphomas, cancer of the bladder, cancer of the kidney or ureter (e.g., renal cell carcinoma, carcinoma of the renal pelvis), or neoplasms of the central nervous system (e.g., primary CNS lymphoma, spinal axis tumors, brain stem gliomas or pituitary adenomas).

[0117] As used herein, “Location of Maximal Recombination” (or Rearrangement), LMR, refers to intergenic regions between V-D or D-J for TRD, TRB, IGH; V-J for TRG, IGK, IGL). The term “maximal rearrangement domain,” as used herein, is synonymous with LMR.

[0118] As used herein, “Valley” refers to a region of maximal rearrangement.

[0119] As used herein. “Plateau” refers to genomic regions close to V genes but with minimal or without rearrangement. For all IGHC isotypes (IgG, IgA, IgE, IgM) were covered. Regions of minimal rearrangement are also referred to as plateau or plateau regions. As used herein, “low recombination domain” is synonymous with region of minimal rearrangement.Computer Program Product

[0120] In some embodiments, the disclosure relates to a method of reducing interference in collecting data from a sample of a nucleic acid from a subject and identifying genomic DNA the sample. In some embodiments, the method includes reducing the interference from non-genomic DNA in the sample, collecting data associated with genomic DNA in the sample; and calculating the total number of T cells or B cells in the sample. In the above disclosed methods,DOCKET NO. STFD-015-PCT PATENT APPLICATIONany or all of the steps may be performed by a computer-implemented method after sequencing DNA in the sample. In some embodiments, reducing interference or ‘"noise” created from nongenomic DNA in the sample is performed by calculating the GC% of reads in sequence data derived from the sample and correcting the sequence data by removing the sequences that do not have a percentage of GC content; and performing sequencing analysis on the corrected sequence data by performing at least one of: (i) determining the number and / or sequence of LMR in the genomic DNA; (ii) calculating the ratio of αβTcells to γδTcells from the genomic DNA; (iii) calculating the number and / or sequence of LMR in an IgH portion of the genomic DNA; (iv) calculating the ratio of Igκ to Igλ in the genomic DNA; and (v) quantifying the number Ig class switches in the genomic DNA.

[0121] In some embodiments, the sample of a nucleic acid in a subject is a cell-free DNA sample (cfDNA). In some embodiments, the disclosure relates to a method of reducing interference in collecting data from a cell-free sample of a nucleic acid from a subject and identifying genomic DNA in a cell-free sample. In some embodiments, the method includes reducing the interference from non-genomic DNA in a cell-free DNA sample, collecting data associated with genomic DNA in the sample; and calculating the total number of T cells or B cells in the sample. In the above disclosed methods, any or all of the steps may be performed by a computer-implemented method after sequencing DNA in a cell-free DNA sample. In some embodiments, reducing interference or “noise” created from nongenomic DNA in a cell-free DNA sample is performed by calculating the GC% of reads in sequence data derived from the sample and correcting the sequence data by removing the sequences that do not have a percentage of GC content; and performing sequencing analysis on the corrected sequence data by performing at least one of: (i) determining the number and / or sequence of LMR in the genomic DNA; (ii) calculating the ratio of αβT cells to γδ T cells from the genomic DNA; (iii) calculating the number and / or sequence of LMR in an IgH portion of the genomic DNA; (iv) calculating the ratio of IgK to Igλ in the genomic DNA; and (v) quantifying the number Ig class switches in the genomic DNA.

[0122] The disclosure further relates to a computer program product encoded on a computer-readable storage medium that comprises instructions for performing any of the methods described herein. In some embodiments, the disclosure relates to a method of quantifying a number of B cells and / or T cells in a subject by analyzing genomic DNA in a sample of nucleicDOCKET NO. STFD-015-PCT PATENT APPLICATIONacid from the subject, the method comprising: (a) obtaining sequencing data from the sample; (b) reducing interference from non-genomic DNA in the sample by performing a GC% scan of the sequence data; and, optionally performing a GPR correction. In some embodiments, the instructions are for, using the sequence data over a web-based server and performing one or a combination or two or more of: (i) determining the number and / or sequence of LMR in the genomic DNA; (ii) calculating the ratio of αβTcells to γδTcells from the genomic DNA; (iii) calculating the number and / or sequence of LMR in an IgH portion of the genomic DNA; (iv) calculating the ratio of IgK to Igλ in the genomic DNA; and (v) quantifying the number Ig class switches in the genomic DNA. In some embodiments, the sample is a cell-free DNA sample.

[0123] In some embodiments, the instructions further comprise correlating the data generated in any or a combination of (i) through (v) to prepare an estimated number of T cells in the subject from whom the sample is derived and / or to prepare an estimated number of B cells in the subject from whom the sample is derived. In some embodiments, the instructions cause the display of an advertisement unit on the webpage if exit behavior is detected. In some embodiments, the advertisement unit contains one or more advertisements at least partially based upon the data associated with the user. In some embodiments, the advertisement unit contains one or more advertisements at least partially based upon the data collected by the one or more methods disclosed herein.

[0124] In some embodiments, the computer program product comprises instructions for a step of identify ing and reducing DNA sequence reads that are not genomic DNA by detecting the GC% rich sequence reads in a sample. In some embodiments, the computer program product with instructions for a step of performing GPR optionally comprising reducing DNA sequence reads that are not genomic DNA by detecting the GC% rich sequence reads in a sample.

[0125] In some embodiments, the disclosure relates to a computer program product with instructions for: (i) determining the number and / or sequence of LMR in the genomic DNA; (ii) calculating the ratio of αβTcells to γδTcells from the genomic DNA; (iii) calculating the number and / or sequence of LMR in an IgH portion of the genomic DNA; (iv) calculating the ratio of IgK to Igλ in the genomic DNA; and (v) quantifying the number Ig class switches in the genomic DNA. In some embodiments, the computer program product comprises instructions for a step of correlating the sequence data across a portion of genomic DNA in theDOCKET NO. STFD-015-PCT PATENT APPLICATIONsample to a fraction of the T-cells and / or B-cells in the subject. In some embodiment, the sample is a cfDNA sample.

[0126] In some embodiments, disclosed is a system comprising a disclosed computer program product, and one or more of: (a) a processor operable to execute programs; and (b) a memory associated with the processor.

[0127] In some embodiment, the disclosure relates to a computer program product encoded on a computer-readable storage medium. In some embodiment, the computer program product comprises executable instructions for: (a) determining, from sequence data comprising valley region sequence, reads for a location of maximal rearrangement for one or more gene selected from V, D, and J genes in the sample of nucleic acid; (b) determining, from the sequence data, shoulder region sequence reads for a location of low recombination proximate to the one or more gene; and (c) determining a median sequence depth for each valley region and a median sequence depth for each shoulder region, the median sequence depth calculated by subtracting the median sequence depth for each valley region from the median sequence depth for each respective shoulder region to obtain a respective depth of valley for each valley region; and dividing each respective depth of valley by the median depth for the respective shoulder region. In some embodiment, the computer program product encoded on a computer-readable storage medium further comprises instructions for: (d) determining a fraction of the T-cells and / or B-cells by correlating the values of any of steps (a), (b), (c), or combination thereof. In some embodiments, the sample of nucleic acid is a cfDNA sample.

[0128] Further, it should be appreciated that a computer may be embodied in any of a number of forms, such as a rack-mounted computer, a desktop computer, a laptop computer, or a tablet computer. Additionally, a computer may be embedded in a device not generally regarded as a computer but with suitable processing capabilities, including a Personal Digital Assistant (PDA), a smart phone, or any other suitable portable or fixed electronic device.

[0129] Also, a computer may have one or more input and output devices. These devices can be used, among other things, to present a user interface. Examples of output devices that can be used to provide a user interface include printers or display screens for visual presentation of output and speakers or other sound generating devices for audible presentation of output. Examples of input devices that can be used for a user interface include keyboards, and pointingDOCKET NO. STFD-015-PCT PATENT APPLICATIONdevices, such as mice, touch pads, and digitizing tablets. As another example, a computer may receive input information through speech recognition or in other audible format.

[0130] Such computers may be interconnected by one or more networks in any suitable form, including a local area network or a wide area network, such as an enterprise network, and intelligent network (IN) or the Internet. Such networks may be based on any suitable technology and may operate according to any suitable protocol and may include wireless networks, wired networks, or fiber optic networks.

[0131] A computer employed to implement at least a portion of the functionality described herein may include a memory, coupled to one or more processing units (also referred to herein simply as “processors”), one or more communication interfaces, one or more display units, and one or more user input devices. The memory may include any computer-readable media, and may store computer instructions (also referred to herein as “processor-executable instructions”) for implementing the various functionalities described herein. The processing unit(s) may be used to execute the instructions. The communication interface(s) may be coupled to a wired or wireless network, bus, or other communication means and may therefore allow the computer to transmit communications to and / or receive communications from other devices. The display unit(s) may be provided, for example, to allow a user to view various information in connection with execution of the instructions. The user input device(s) may be provided, for example, to allow the user to make manual adjustments, make selections, enter data or various other information, and / or interact in any of a variety of manners with the processor during execution of the instructions.

[0132] The various methods or processes outlined herein may be coded as software that is executable on one or more processors that employ any one of a variety of operating systems or platforms. The disclosure also relates to a computer readable storage medium comprising executable instructions. Additionally, such software may be written using any of a number of suitable programming languages and / or programming or scripting tools, and also may be compiled as executable machine language code or intermediate code that is executed on a framework or virtual machine.

[0133] In this respect, various inventive concepts may be embodied as a computer readable storage medium (or multiple computer readable storage media) (e.g., a computer memory one or more floppy discs, compact discs, optical discs, magnetic tapes, flash memories, circuitDOCKET NO. STFD-015-PCT PATENT APPLICATIONconfigurations in Field Programmable Gate Arrays or other semiconductor devices, or other non-transitory medium or tangible computer storage medium) encoded with one or more programs that, when executed on one or more computers or other processors, perform methods that implement the various embodiments disclosed herein. The computer readable medium or media can be transportable, such that the program or programs stored thereon can be loaded onto one or more different computers or other processors to implement various aspects of embodiments discussed herein. In some embodiments, the system comprises cloud-based software that executes one or all of the steps of each disclosed method instruction.

[0134] The terms “program’' or “software” are used herein in a generic sense to refer to any type of computer code or set of computer-executable instructions that can be employed to program a computer or other processor to implement various aspects of embodiments as discussed above. Additionally, it should be appreciated that according to one aspect, one or more computer programs that when executed perform methods of the present disclosure need not reside on a single computer or processor, but may be distributed in a modular fashion amongst a number of different computers or processors to implement various aspects of the present invention.

[0135] Computer-executable instructions may be in many forms, such as program modules, executed by one or more computers or other devices. Generally, program modules include routines, programs, objects, components, data structures, etc. thatyperform particular tasks or implement particular abstract data types. Typically, the functionality of the program modules may be combined or distributed as desired in various embodiments.

[0136] Also, data structures may be stored in computer-readable media in any suitable form. For simplicity of illustration, data structures may be shown to have fields that are related through location in the data structure. Such relationships may likewise be achieved by assigning storage for the fields with locations in a computer-readable medium that convey relationship between the fields. However, any suitable mechanism may be used to establish a relationship between information in fields of a data structure, including through the use of pointers, tags or other mechanisms that establish relationship between data elements.

[0137] The acts performed as part of a method herein may be ordered in any suitable way. Accordingly, embodiments may be constructed in which acts are performed in an orderDOCKET NO. STFD-015-PCT PATENT APPLICATIONdifferent than illustrated, which may include performing some acts simultaneously, even though shown as sequential acts in illustrative embodiments.

[0138] Computer-implemented embodiments of the disclosure relate to methods of quantifying the number of T cells and / or B cells in a sample comprising DNA and methods of reducing interference in a sample comprising cell-free DNA by identifying a fraction of the cell-free DNA that is genomic DNA as opposed to non-gnomic DNA. In some embodiments one or a plurality f steps herein are In some embodiments, the method of reducing interference in a sample comprises detecting the median read depth of DNA in a sample. And, in some embodiments, the step of detecting median read depth of DNA in a sample comprises detecting GC% of DNAin the sample and performing GPR correction. In some embodiments, computer-implemented methods of the disclosure relate to methods of quantify ing the number of T cells and / or B cells in a sample comprising DNA and methods of reducing interference in a sample comprising cell-free DNA, each method comprising: (a) sequencing the DNA in the sample; (b) detecting GC% of DNA in the sample and performing GPR correction to reduce the data from non-genomic DNA. In some embodiments, the methods further comprise performing one or a combination of tw o or more of the following with a computer implemented method: (i) determining the number and / or LMR in the genomic DNA sequence; (ii) calculating the ratio of αβTcells to γδTcells from the genomic DNA; (iii) calculating the number and / or sequence of LMR in an IgH portion of the genomic DNA; (iv) calculating the ratio of Igκ to Igλ in the genomic DNA; and (v) quantifying the number Ig class switches in the genomic DNA. In some embodiments, the methods further comprise a step of correlating the sequence data across a portion of genomic DNAin the cfDNAto a fraction of the T-cells and / or B-cells in the subject.

[0139] In some embodiments, the disclosure relates to a system that comprises at least one processor, a program storage, such as memory, for storing program code executable on the processor, and one or more input / output devices and / or interfaces, such as data communication and / or peripheral devices and / or interfaces. In some embodiments, the user device and computer system or systems are communicably connected by a data communication network, such as a Local Area Netw ork (LAN), the Internet, or the like, which may also be connected to a number of other client and / or server computer systems. The user device and client and / or server computer systems may further include appropriate operating system software. In some embodiments, the system comprises a processor comprising a computer program product forDOCKET NO. STFD-015-PCT PATENT APPLICATIONquantifying the number of T cells or B cells in a sample from a subject. In some embodiments, the system comprises a processor comprising a computer program product for determining whether a subject is a responder or non-responder to a therapeutic agent by: obtaining a sample of cell-free DNA after a treatment is administered; analyzing the sequence data from genomic DNA in the sample using any one or more steps identified herein, and correlating the number of T cells and / or B cells quantified by the sequence analysis to correlate the number of cells with the activity of the therapeutic agent.

[0140] In some embodiments, components and / or units of the devices described herein may be able to interact through one or more communication channels or mediums or links, for example, a shared access medium, a global communication network, the Internet, the World Wide Web, a wired network, a wireless network, a combination of one or more wired networks and / or one or more wireless networks, one or more communication networks, an a-synchronic or asynchronous wireless network, a synchronic wireless network, a managed wireless network, a non-managed wireless network, a burstable wireless network, a non-burstable wireless network, a scheduled wireless network, a non-scheduled wireless network, or the like.

[0141] Discussions herein utilizing terms such as, for example, “processing,"’ “computing,” “calculating,"’ “determining.” or the like, may refer to operation(s) and / or process(es) of a computer, a computing platform, a computing system, or other electronic computing device, that manipulate and / or transform data represented as physical (e.g., electronic) quantities within the computer’s registers and / or memories into other data similarly represented as physical quantities within the computer's registers and / or memories or other information storage medium that may store instructions to perform operations and / or processes.

[0142] Some embodiments may take the form of an entirely hardware embodiment, an entirely software embodiment, or an embodiment including both hardware and software elements. Some embodiments may be implemented in software, which includes but is not limited to firmware, resident software, microcode, or the like.

[0143] Furthermore, some embodiments may take the form of a computer program product accessible from a computer-usable or computer-readable medium providing program code for use by or in connection with a computer or any instruction execution system. For example, a computer-usable or computer-readable medium may be or may include any apparatus that canDOCKET NO. STFD-015-PCT PATENT APPLICATIONcontain, store, communicate, propagate, or transport the program for use by or in connection with the instruction execution system, apparatus, or device.

[0144] In some embodiments, the medium may be or may include an electronic, magnetic, optical, electromagnetic. InfraRed (IR), or semiconductor system (or apparatus or device) or a propagation medium. Some demonstrative examples of a computer-readable medium may include a semiconductor or solid state memory', magnetic tape, a removable computer diskette, a Random Access Memory' (RAM), a Read-Only Memory (ROM), a rigid magnetic disk, an optical disk, or the like. Some demonstrative examples of optical disks include Compact Disk-Read-Only Memory (CD-ROM), Compact Disk-Read / Write (CD-R / W), DVD, or the like.

[0145] In some embodiments, a data processing system suitable for storing and / or executing program code may include at least one processor coupled directly or indirectly to memory elements, for example, through a system bus. The memory' elements may include, for example, local memory employed during actual execution of the program code, bulk storage, and cache memories which may provide temporary storage of at least some program code in order to reduce the number of times code must be retrieved from bulk storage during execution.

[0146] In some embodiments, input / output or I / O devices (including but not limited to keyboards, displays, pointing devices, etc.) may be coupled to the system either directly or through intervening I / O controllers. In some embodiments, network adapters may be coupled to the system to enable the data processing system to become coupled to other data processing systems or remote printers or storage devices, for example, through intervening private or public networks. In some embodiments, modems, cable modems and Ethernet cards are demonstrative examples of types of network adapters. Other suitable components may be used.

[0147] Some embodiments may be implemented by software, by hardware, or by any combination of software and / or hardware as may be suitable for specific applications or in accordance with specific design requirements. Some embodiments may include units and / or sub-units, which may be separate of each other or combined together, in whole or in part, and may be implemented using specific, multi-purpose or general processors or controllers. Some embodiments may include buffers, registers, stacks, storage units and / or memory units, for temporary or long-term storage of data or in order to facilitate the operation of particular implementations.DOCKET NO. STFD-015-PCT PATENT APPLICATION

[0148] Some embodiments may be implemented, for example, using a machine-readable medium or article which may store an instruction or a set of instructions that, if executed by a machine, cause the machine to perform a method steps and / or operations described herein. Such machine may include, for example, any suitable processing platform, computing platform, computing device, processing device, electronic device, electronic system, computing system, processing system, computer, processor, or the like, and may be implemented using any suitable combination of hardware and / or software. The machine-readable medium or article may include, for example, any suitable type of memory unit, memory device, memory article, memory medium, storage device, storage article, storage medium and / or storage unit; for example, memory, removable or non-removable media, erasable or non-erasable media, writeable or re-writeable media, digital or analog media, hard disk drive, floppy disk, Compact Disk Read Only Memory' (CD-ROM), Compact Disk Recordable (CD-R). Compact Disk Re-Writeable (CD-RW), optical disk, magnetic media, various types of Digital Versatile Disks (DVDs), a tape, a cassette, or the like. The instructions may include any suitable type of code, for example, source code, compiled code, interpreted code, executable code, static code, dynamic code, or the like, and may be implemented using any suitable high-level, low-level, object-oriented, visual, compiled and / or interpreted programming language, e.g., C, C++, Java™, BASIC, Pascal, Fortran, Cobol, assembly language, machine code, or the like.

[0149] Many of the functional units described in this specification have been labeled as circuits, in order to more particularly emphasize their implementation independence. For example, a circuit may be implemented as a hardware circuit comprising custom very-large-scale integration (VLSI) circuits or gate arrays, off-the-shelf semiconductors such as logic chips, transistors, or other discrete components. A circuit may also be implemented in programmable hardware devices such as field programmable gate arrays, programmable array logic, programmable logic devices or the like.

[0150] In some embodiments, the circuits may also be implemented in machine-readable medium for execution by various types of processors. An identified circuit of executable code may, for instance, comprise one or more physical or logical blocks of computer instructions, which may, for instance, be organized as an object, procedure, or function. Nevertheless, the executables of an identified circuit need not be physically located together but may compriseDOCKET NO. STFD-015-PCT PATENT APPLICATIONdisparate instructions stored in different locations which, when joined logically together, comprise the circuit and achieve the stated purpose for the circuit. Indeed, a circuit of computer readable program code may be a single instruction, or many instructions, and may even be distributed over several different code segments, among different programs, and across several memory devices. Similarly, operational data may be identified and illustrated herein within circuits and may be embodied in any suitable form and organized within any suitable type of data structure. The operational data may be collected as a single data set, or may be distributed over different locations including over different storage devices, and may exist, at least partially, merely as electronic signals on a system or network.

[0151] The computer readable medium (also referred to herein as machine-readable media or machine-readable content) may be a tangible computer readable storage medium storing the computer readable program code. The computer readable storage medium may be, for example, but not limited to. an electronic, magnetic, optical, electromagnetic, infrared, holographic, micromechanical, or semiconductor system, apparatus, or device, or any suitable combination of the foregoing. As alluded to above, examples of the computer readable storage medium may include but are not limited to a portable computer diskette, a hard disk, a random access memory (RAM), a read-only memory (ROM), an erasable programmable read-only memory (EPROM or Flash memory). a portable compact disc read-only memory (CD-ROM), a digital versatile disc (DVD), an optical storage device, a magnetic storage device, a holographic storage medium, a micromechanical storage device, or any suitable combination of the foregoing. In the context of this document, a computer readable storage medium may be any tangible medium that can contain, and / or store computer readable program code for use by and / or in connection with an instruction execution system, apparatus, or device.

[0152] The computer readable medium may also be a computer readable signal medium. A computer readable signal medium may include a propagated data signal with computer readable program code embodied therein, for example, in baseband or as part of a carrier wave. Such a propagated signal may take any of a variety of forms, including, but not limited to, electrical, electro-magnetic, magnetic, optical, or any suitable combination thereof. A computer readable signal medium may be any computer readable medium that is not a computer readable storage medium and that can communicate, propagate, or transport computer readable program code for use by or in connection with an instruction execution system, apparatus, or device. AsDOCKET NO. STFD-015-PCT PATENT APPLICATIONalso alluded to above, computer readable program code embodied on a computer readable signal medium may be transmitted using any appropriate medium, including but not limited to wireless, wireline, optical fiber cable, Radio Frequency (RF), or the like, or any suitable combination of the foregoing. In some embodiments, the computer readable medium may comprise a combination of one or more computer readable storage mediums and one or more computer readable signal mediums. For example, computer readable program code may be both propagated as an electro-magnetic signal through a fiber optic cable for execution by a processor and stored on RAM storage device for execution by the processor.

[0153] Computer readable program code for carrying out operations for aspects of the present disclosure may be written in any combination of one or more programming languages, including an obj ect oriented programming language such as Java, Smalltalk, C++ or the like and conventional procedural programming languages, such as the “C” programming language or similar programming languages. The computer readable program code may execute entirely on a user’s computer, partly on the user’s computer, as a stand-alone computer-readable package, partly on the user’s computer and partly on a remote computer or entirely on the remote computer or server. In the latter scenario, the remote computer may be connected to the user’s computer through any type of network, including a local area network (LAN) or a wide area network (WAN), or the connection may be made to an external computer (for example, through the Internet using an Internet Service Provider).

[0154] The program code may also be stored in a computer readable medium that can direct a computer, other programmable data processing apparatus, or other devices to function in a particular manner, such that the instructions stored in the computer readable medium produce an article of manufacture including instructions which implement the function / act specified in the schematic flowchart diagrams and / or schematic block diagrams block or blocks.Nucleic Acid Compositions

[0155] In some embodiments, the disclosure relates to a composition comprising one or more nucleic acid molecules selected from a first set of capture probes. In some embodiments, the first set of capture probes comprises at least one first nucleic acid molecule, each comprising a first nucleic acid sequence capable of hybridizing to a maximal rearrangement domain (LMR) of TRA, TRB, TRG. IGH. IGK, or 1GL.DOCKET NO. STFD-015-PCT PATENT APPLICATION

[0156] In some embodiments, the disclosure relates to a composition comprising one or more nucleic acid molecules selected from a second set of capture probes. In some embodiments, the second set of capture probes comprises at least one second nucleic acid molecule, each comprising a second nucleic acid sequence capable of hybridizing to a low recombination domain (plateau) at or proximal to TRA, TRB, TRG, IGH, IGK, or IGL.

[0157] Table A, categorizes sequences herein by SEQ ID NO as to whether the sequences an LMR sequences or plateau sequence, and which of TRA, TRB, TRG, IGH, IGK, or IGL the sequences if associated with. Embodiments herein comprising first and second capture probes or first and second probes may also comprise segregation of (i) first capture probes or first probes into subsets specific for TRA, TRB, TRG, IGH, IGK, or IGL and / or (ii) second capture probes or second probes into subsets specific for TRA, TRB, TRG, IGH, IGK, or IGL. Whether first or second, further subsets of IGH specific sequences may be further divided into subsets for IGHM, IGHA2, IGHE, IGHG4, IGHG2, IGHA1. IGHG1, IGHG3, and IGHD. The selection of sequences, functions variants thereof, portions thereof, or functional variants of portions thereof may be as set forth in Table A.Table AGene-LMR or Plateau SEQ ID NOSTRA-LMR SEQ ID NOS: 1, 2, 3, 1515-3882, 5749-5751,5847-5986, 7480-7619TRB-LMR SEQ ID NOS: 4, 5, 6, 1147-1381, 5746, 7166-7401,8799-9034TRG-LMR SEQ ID NOS: 7, 8, 9, 10, 702-1008, 5743, 7010- 7079, 8643-8712IGH-LMR SEQ ID NOS: 11, 12, 5054-5546, 5763-5764,6573-6630, 8206-8263IGK-LMR SEQ ID NOS: 13, 14, 131-602, 5740, 6746-6783,8379-8416IGL-LMR SEQ ID NOS: 15, 16, 17, 5586-5715, 5767, 6860- 6923, 8493-8556TRA-Plateau SEQ ID NOS: 18, 19, 1382-1514, 3883-3964,5747-5748, 5752, 5769-5846, 5987-6048, 7402- 7479, 7620-7681TRB-Plateau SEQ ID NOS: 20-21, 1042-1146, 5745, 6938-6939,7080-7165, 8571-8572, 8713-8798TRG-Plateau SEQ ID NOS: 21-22, 603-701, 1009-1041, 5741,5742, 5744, 6940-7009, 8573-8642IGH-Plateau SEQ ID NOS: 23, 28-36, 3965-5053, 5753-5762,6049-6572, 7682-8205IGHM SEQ ID NOS: 23, 4952-5053, 5762 IGHA2 SEQ ID NOS: 28, 29, 3896–4087, 5754IGHE SEQ ID NOS: 30, 4088-4185, 5755 IGHG4 SEQ ID NOS: 31, 4186-4285, 5756IGHG2 SEQ ID NOS: 32, 4286-4379, 5757DOCKET NO. STFD-015-PCT PATENT APPLICATION IGHA1 SEQ ID NOS 33, 4380-4481, 5758 IGHG1 SEQ ID NOS 34, 4482-4604, 5759 IGHG3 SEQ ID NOS 35, 4606-4731, 5760 IGHD SEQ ID NOS 36, 4732-4951, 5761 IGK-Plateau SEQ ID NOS: 24, 25, 37-130, 5738-5739, 6631- 6745, 8264-8378IGL-Plateau SEQ ID NOS: 26, 27, 5547-5585, 5716-5737, 5765,5766, 5768, 6784-6859, 6924-6935, 6936-6937,8417-8492, 8557-8568, 8569-8570

[0158] In some embodiments, the disclosure relates to a composition comprising one or more nucleic acid molecules selected from the first set of capture probes and one or more nucleic acid molecules selected from the second set of capture probes.

[0159] In some embodiments, at least one of the first nucleic acid sequences comprises the sequence of one of SEQ ID NOS: 1-17 or a functional variant thereof, where SEQ ID NOS: 1-17 are sequences within a maximal rearrangement domain ofTRA, TRB, TRG, IGH, IGK, and IGL, respectively. See Table 1, below. In some embodiments, each of the first nucleic acid sequences comprises the sequence of one of SEQ ID NOS: 1-17 or a functional variant thereof. In some embodiments, one of the first nucleic acid sequences comprises SEQ ID NO:1 or a functional variant thereof, one of the first nucleic acid sequences comprises SEQ ID NO: 2 or a functional variant thereof, one of the first nucleic acid sequences comprises SEQ ID NO: 3 or a functional variant thereof, one of the first nucleic acid sequences comprises SEQ ID NO: 4 or a functional variant thereof, one of the first nucleic acid sequences comprises SEQ ID NO: 5 or a functional variant thereof, one of the first nucleic acid sequences comprises SEQ ID NO: 6 or a functional variant thereof, one of the first nucleic acid sequences comprises SEQ ID NO: 7 or a functional variant thereof, one of the first nucleic acid sequences comprises SEQ ID NO: 8 or a functional variant thereof, one of the first nucleic acid sequences comprises SEQ ID NO: 9 or a functional variant thereof, one of the first nucleic acid sequences comprises SEQ ID NO: 10 or a functional variant thereof, one of the first nucleic acid sequences comprises SEQ ID NO: 11 or a functional variant thereof, one of the first nucleic acid sequences comprises SEQ ID NO: 12 or a functional variant thereof, one of the first nucleic acid sequences comprises SEQ ID NO: 13 or a functional variant thereof, one of the first nucleic acid sequences comprises SEQ ID NO: 14 or a functional variant thereof, one of the first nucleic acid sequences comprises SEQ ID NO: 15 or a functional variant thereof, one of the first nucleicDOCKET NO. STFD-015-PCT PATENT APPLICATIONacid sequences comprises SEQ ID NO: 16 or a functional variant thereof, and one of the first nucleic acid sequences comprises SEQ ID NO: 17 or a functional variant thereof.

[0160] In some embodiments, at least one, a plurality of, or each of the first nucleic acid sequences independently comprises, consists essentially of, or consists of a sequence having at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 1-17, 131-602. 702-108, 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740, 5743. 5746, 5749-5751, 5763, 5764, 5767. 5769-6048, 6573-6630. 6746-6783, 6860-6923, 6938. 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034. In some embodiments, at least one, a plurality7of, or each of the first nucleic acid sequences independently comprises, consists essentially of, or consists of a sequence having from about 75% to about 80%, about 85%, about 86%. about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 1-17, 131-602, 702-108, 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938. 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034. In some embodiments, at least one, a plurality of, or each of the first nucleic acid sequences independently comprises, consists essentially of, or consists of a sequence having from about 80% to about 85%, about 86%, about 87%, about 88%, about 89%, about 90%. about 91%. about 92%. about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 1-17, 131-602, 702-108, 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681. 8206-8263, 8379-8416, 8493-8556, 8571-8572. or 8643-9034. In some embodiments, at least one, a plurality of, or each of the first nucleic acid sequences independently comprises, consists essentially of, or consists of a sequence having from about 85% to about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%. about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 1-17, 131-602, 702-108, 1147-1381.DOCKET NO. STFD-015-PCT PATENT APPLICATION1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034. In some embodiments, at least one, a plurality of, or each of the first nucleic acid sequences independently comprises, consists essentially of, or consists of a sequence having from about 90% to about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 1-17, 131— 602, 702-108, 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740. 5743, 5746. 5749-5751, 5763, 5764, 5767. 5769-6048, 6573-6630. 6746-6783, 6860-6923, 6938. 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034. In some embodiments, at least one, a plurality of, or each of the first nucleic acid sequences independently comprises, consists essentially of, or consists of a sequence having from about 91% to about 92%, about 93%, about 94%. about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 1-17, 131-602, 702-108, 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034. In some embodiments, at least one, a plurality of, or each of the first nucleic acid sequences independently comprises, consists essentially of, or consists of a sequence having from about 92% to about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 1-17, 131-602, 702-108. 1147-1381, 1515-3882, 5054-5530. 5586-5715, 5740, 5743, 5746. 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034. In some embodiments, at least one, a plurality of, or each of the first nucleic acid sequences independently comprises, consists essentially of, or consists of a sequence having from about 93% to about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 1-17, 131-602, 702-108, 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034. In someDOCKET NO. STFD-015-PCT PATENT APPLICATIONembodiments, at least one, a plurality of, or each of the first nucleic acid sequences independently comprises, consists essentially of, or consists of a sequence having from about 94% to about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one ofSEQ ID NOS: 1-17, 131-602, 702-108, 1147-1381. 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034. In some embodiments, at least one, a plurality of, or each of the first nucleic acid sequences independently comprises, consists essentially of, or consists of a sequence having from about 95% to about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 1-17, 131— 602, 702-108, 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749- 5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034. In some embodiments, at least one, a plurality of, or each of the first nucleic acid sequences independently comprises, consists essentially of, or consists of a sequence having from about 96% to about 97%, about 98%, about 99%, or about 100% sequence identity to one ofSEQ ID NOS: 1-17, 131-602, 702-108. 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034. In some embodiments, at least one, a plurality of, or each of the first nucleic acid sequences independently comprises, consists essentially of, or consists of a sequence having from about 97% to about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 1-17, 131-602, 702-108, 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556. 8571-8572, or 8643-9034. In some embodiments, at least one, a plurality of, or each of the first nucleic acid sequences independently comprises, consists essentially of, or consists of a sequence having from about 98% to about 99%, or about 100% sequence identity to one of SEQ ID NOS: 1-17, 131-602, 702-108, 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740. 5743, 5746, 5749-5751. 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479. 7480-7619, 7620-7681.DOCKET NO. STFD-015-PCT PATENT APPLICATION8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034. In some embodiments, at least one, a plurality of, or each of the first nucleic acid sequences independently comprises, consists essentially of, or consists of a sequence having from about 99% to about 100% sequence identity to one ofSEQ ID NOS: 1-17, 131-602, 702-108, 1147-1381. 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034. In some embodiments, each first nucleic acid molecule in the first set of capture probes comprises, consists essentially of, or consists of a first nucleic acid sequence of this paragraph. In some embodiments, at least one first nucleic acid molecule in the first set of capture probes comprises, consists essentially of, or consists of a first nucleic acid sequence comprising at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%. about 96%. about 97%, about 98%, about 99%. or about 100% sequence identity to one of SEQ ID NOS: 1–17, 131–602, 702–108, 1147–1381, 1515–3882, 5054–5530, 5586–5715, 5740, 5743, 5746, 5749–5751, 5763, 5764, 5767, 5769–6048, 6573–6630, 6746–6783, 6860–6923, 6938, 6939, 7010–7079, 7080–7479, 7480–7619, 7620–7681, 8206–8263, 8379–8416, 8493–8556, 8571–8572, or 8643–9034. In some embodiments, each first nucleic acid molecule in the first set of capture probes comprises, consists essentially of, or consists of a first nucleic acid sequence comprising at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 1–17, 131–602, 702–108, 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034. In some embodiments, each of a first, a second, a third, a fourth, a fifth, and a sixth first nucleic acid molecule in the first set of capture probes comprises, consists essentially of, or consists of a first nucleic acid sequence of one of SEQ ID NOS: 1-17, 131-602, 702-108, 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263. 8379-8416, 8493-8556. 8571-8572, or 8643-9034, respectively, atDOCKET NO. STFD-015-PCT PATENT APPLICATIONpercent identity as set forth in this paragraph. In some embodiments, at least one of a first, a second, a third, a fourth, a fifth, and a sixth first nucleic acid molecule in the first set of capture probes comprises, consists essentially of, or consists of a first nucleic acid sequence comprising at least a portion of an LMR sequence from Tables 1, 2.1, 2.1.1, 2.1.2, or 2.2, at the percent identity as set forth in this paragraph. In some embodiments, each of a first, a second, a third, a fourth, a fifth, and a sixth first nucleic acid molecule in the first set of capture probes comprises, consists essentially of, or consists of a first nucleic acid sequence comprising at least a portion of an LMR sequence from Tables 1, 2.1, 2.1.1, 2.1.2. or 2.2. at the percent identity as set forth in this paragraph. In some embodiments, one, a plurality of. or each first nucleic acid molecule in the first set of capture probes comprises, consists essentially of, or consists of a first nucleic acid sequence comprising at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%. or about 100% sequence identity to at least a portion of one of SEQ ID NOS: 1-17, 131-602, 702-108, 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416. 8493-8556, 8571-8572, or 8643-9034. In some embodiments, the at least a portion comprises about 10 to about 15, about 20, about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, or about 100 nucleotides. In some embodiments, the at least a portion comprises about 15 to about 20, about 25, about 30, about 35, about 40, about 45, about 50. about 55. about 60, about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 20 to about 25, about 30, about 35, about 40, about 45, about 50, about 55. about 60, about 65, about 70, about 75, about 80. about 90. about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 25 to about 30, about 35, about 40, about 45, about 50, about 55, about 60. about 65, about 70, about 75, about 80. about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides.DOCKET NO. STFD-015-PCT PATENT APPLICATIONabout 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 30 to about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 35 to about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 40 to about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 45 to about 50. about 55, about 60, about 65. about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 50 to about 55, about 60, about 65, about 70. about 75. about 80. about 90. about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 55 to about 60, about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 60 to about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 65 to about 70, about 75, about 80, about 90. about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 70 to about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portionDOCKET NO. STFD-015-PCT PATENT APPLICATIONcomprises about 75 to about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 80 to about 90. about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 90 to about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 95 to about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 100 nucleotides to about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 105 nucleotides to about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 110 nucleotides to about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 115 nucleotides to about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 120 nucleotides to about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 125 nucleotides to about 130 nucleotides.

[0161] In some embodiments, at least one of the second nucleic acid sequences of the second set of capture probes comprises the sequence of one of SEQ ID NOS: 18-36 or a functional variant thereof, where SEQ ID NOS: 18-36 are sequences within a low recombination domain at or proximal to TRA, TRB, TRG, IGH. IGK, or IGL, respectively. See Table 2, below. In some embodiments, each of the second nucleic acid sequences comprises the sequence of one of SEQ ID NOS: 18-36 or a functional variant thereof. In some embodiments, one of the second nucleic acid sequences comprises SEQ ID NO: 18 or a functional variant thereof, one of the second nucleic acid sequences comprises SEQ ID NO: 19 or a functional variant thereof, one of the second nucleic acid sequences comprises SEQ ID NO: 20 or a functional variant thereof, one of the second nucleic acid sequences comprises SEQ ID NO: 21 or a functional variantDOCKET NO. STFD-015-PCT PATENT APPLICATIONthereof, one of the second nucleic acid sequences comprises SEQ ID NO: 22 or a functional variant thereof, one of the second nucleic acid sequences comprises SEQ ID NO: 23 or a functional variant thereof, one of the second nucleic acid sequences comprises SEQ ID NO: 24 or a functional variant thereof, one of the second nucleic acid sequences comprises SEQ ID NO: 25 or a functional variant thereof, one of the second nucleic acid sequences comprises SEQ ID NO: 26 or a functional variant thereof, one of the second nucleic acid sequences comprises SEQ ID NO: 27 or a functional variant thereof, one of the second nucleic acid sequences comprises SEQ ID NO: 28 or a functional variant thereof, one of the second nucleic acid sequences comprises SEQ ID NO: 29 or a functional variant thereof, one of the second nucleic acid sequences comprises SEQ ID NO: 30 or a functional variant thereof, one of the second nucleic acid sequences comprises SEQ ID NO: 31 or a functional variant thereof, one of the second nucleic acid sequences comprises SEQ ID NO: 32 or a functional variant thereof, one of the second nucleic acid sequences comprises SEQ ID NO: 33 or a functional variant thereof, one of the second nucleic acid sequences comprises SEQ ID NO: 34 or a functional variant thereof, one of the second nucleic acid sequences comprises SEQ ID NO: 35 or a functional variant thereof, and one of the second nucleic acid sequences comprises SEQ ID NO: 36 or a functional variant thereof.

[0162] In some embodiments, at least one of, a plurality of, or each of the second nucleic acid sequences comprise, consists essentially of, or consists of a sequence having at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%. about 93%, about 94%, about 95%, about 96%, about 97%, about 98%. about 99%, or about 100% sequence identitv to one of SEQ ID NOS: 18-36, 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752-5762, 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642. In some embodiments, at least one of, a plurality of, or each of the second nucleic acid sequence comprises, consists essentially of, or consists of a sequence having from about 75% to about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 18-3618-36, 37-130, 603-701, 1009-1146, 1382-1514. 3883-5053, 5531-5585. 5716-5737, 5738, 5739. 5741, 5742, 5744.DOCKET NO. STFD-015-PCT PATENT APPLICATION5745, 5747, 5748, 5752-5762, 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642. In some embodiments, at least one of, a plurality of, or each of the second nucleic acid sequence comprises, consists essentially of. or consists of a sequence having from about 80% to about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 18-3618-36, 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752-5762, 5965, 5966. 5768, 6049-6572, 6631-6745, 6784-6859. 6924-6937, 6940-7009.7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642. In some embodiments, at least one of, a plurality7of, or each of the second nucleic acid sequence comprises, consists essentially of, or consists of a sequence having from about 85% to about 86%, about 87%, about 88%. about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 18-3618-36, 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752-5762, 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642. In some embodiments, at least one of, a plurality of, or each of the second nucleic acid sequence comprises, consists essentially of, or consists of a sequence having from about 90% to about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 18–3618–36, 37–130, 603–701, 1009–1146, 1382–1514, 3883–5053, 5531–5585, 5716–5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752-5762, 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642. In some embodiments, at least one of. a plurality of, or each of the second nucleic acid sequence comprises, consists essentially of, or consists of a sequence having from about 91% to about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 18-3618-36, 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748. 5752-5762, 5965, 5966. 5768, 6049-6572, 6631-6745, 6784-6859. 6924-6937, 6940-7009. 7682-8205, 8264-8378, 8417-8492, 8557-DOCKET NO. STFD-015-PCT PATENT APPLICATION8570, or 8573-8642. In some embodiments, at least one of, a plurality of, or each of the second nucleic acid sequence comprises, consists essentially of, or consists of a sequence having from about 92% to about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%. or about 100% sequence identity to one of SEQ ID NOS: 18-3618-36, 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752-5762, 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642. In some embodiments, at least one of, a plurality of, or each of the second nucleic acid sequence comprises, consists essentially of, or consists of a sequence having from about 93% to about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 18-3618-36, 37-130, 603-701, 1009-1146, 1382-1514, 3883- 5053, 5531-5585, 5716-5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752-5762, 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642. In some embodiments, at least one of, a plurality of, or each of the second nucleic acid sequence comprises, consists essentially of, or consists of a sequence having from about 94% to about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 18-3618-36, 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752-5762, 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642. In some embodiments, at least one of, a plurality of, or each of the second nucleic acid sequence comprises, consists essentially of, or consists of a sequence having from about 95% to about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS:18-3618-36, 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752-5762, 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642. In some embodiments, at least one of, a plurality of, or each of the second nucleic acid sequence comprises, consists essentially of, or consists of a sequence having from about 96% to about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 18-3618-36, 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738. 5739, 5741, 5742, 5744. 5745, 5747, 5748.DOCKET NO. STFD-015-PCT PATENT APPLICATION5752-5762, 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642. In some embodiments, at least one of, a plurality' of, or each of the second nucleic acid sequence comprises, consists essentially of, or consists of a sequence having from about 97% to about 98%. about 99%, or about 100% sequence identity to one of SEQ ID NOS: 18-3618-36, 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752-5762, 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642. In some embodiments, at least one of, a plurality of, or each of the second nucleic acid sequence comprises, consists essentially of, or consists of a sequence having from about 98% to about 99%, or about 100% sequence identity to one of SEQ ID NOS: 18–3618–36, 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752-5762. 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642. In some embodiments, at least one of, a plurality of, or each of the second nucleic acid sequence comprises, consists essentially of, or consists of a sequence having from about 99% to about 100% sequence identity to one of SEQ ID NOS: 18–3618–36, 37-130. 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752-5762, 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642. In some embodiments, each second nucleic acid molecule in the second set of capture probes comprises, consists essentially of, or consists of a second nucleic acid sequence of this paragraph. In some embodiments, each of a first, a second, a third, a fourth, a fifth, and a sixth second nucleic acid molecule in the second set of capture probes comprises, consists essentially of, or consists of a second nucleic acid sequence of one of SEQ ID NOS: 18-3618-36, 37-130, 603-701, 1009-1146. 1382-1514, 3883-5053. 5531-5585, 5716-5737. 5738, 5739, 5741. 5742, 5744, 5745, 5747, 5748, 5752-5762, 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642, respectively, atypercent identity as set forth in this paragraph. In some embodiments, at least one second nucleic acid molecule in the second set of capture probes comprises, consists essentially of, or consists of a second nucleic acid sequence comprising at least about 70%, about 75%, about 80%, aboutDOCKET NO. STFD-015-PCT PATENT APPLICATION85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 18-3618-36. 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738. 5739, 5741, 5742, 5744. 5745, 5747, 5748, 5752-5762, 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642. In some embodiments, each second nucleic acid molecule in the second set of capture probes comprises, consists essentially of, or consists of a second nucleic acid sequence comprising at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to one of SEQ ID NOS: 18–3618–36, 37–130, 603–701, 1009–1146, 1382–1514, 3883–5053, 5531–5585, 5716–5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752–5762, 5965, 5966, 5768, 6049–6572, 6631–6745, 6784–6859, 6924–6937, 6940–7009, 7682–8205, 8264–8378, 8417–8492, 8557–8570, or 8573–8642. In some embodiments, each of a first, a second, a third, a fourth, a fifth, and a sixth first nucleic acid molecule in the second set of capture probes comprises, consists essentially of, or consists of a second nucleic acid sequence comprising at least a portion of a Plateau sequence from Tables 2, 2.1, 2.1.1, 2.1.2, or 2.2, at the percent identity as set forth in this paragraph. In some embodiments, one, a plurality of, or each second nucleic acid molecule in the second set of capture probes comprises, consists essentially of, or consists of a second nucleic acid sequence comprising at least about 70%, about 75%. about 80%, about 85%, about 86%, about 87%, about 88%. about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to at least a portion of one of SEQ ID NOS: 18–3618–36, 37–130, 603–701, 1009–1146, 1382–1514, 3883–5053, 5531–5585, 5716–5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752–5762, 5965, 5966, 5768, 6049–6572, 6631–6745, 6784–6859, 6924–6937, 6940–7009, 7682–8205, 8264–8378, 8417–8492, 8557–8570, or 8573–8642. In some embodiments, the at least a portion comprises about 10 to about 15, about 20, about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, or about 100 nucleotides. In some embodiments, the at least a portion comprises about 15 to about 20, about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60,DOCKET NO. STFD-015-PCT PATENT APPLICATIONabout 65, about 70, about 75, about 80, about 90, about 95, or about 100 nucleotides. In some embodiments, the at least a portion comprises about 20 to about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, or about 100 nucleotides. In some embodiments, the at least a portion comprises about 25 to about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, or about 100 nucleotides. In some embodiments, the at least a portion comprises about 30 to about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95. or about 100 nucleotides. In some embodiments, the at least a portion comprises about 35 to about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, or about 100 nucleotides. In some embodiments, the at least a portion comprises about 40 to about 45, about 50, about 55. about 60, about 65, about 70, about 75, about 80, about 90, about 95, or about 100 nucleotides. In some embodiments, the at least a portion comprises about 45 to about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, or about 100 nucleotides. In some embodiments, the at least a portion comprises about 50 to about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, or about 100 nucleotides. In some embodiments, the at least a portion comprises about 55 to about 60, about 65, about 70, about 75, about 80, about 90, about 95, or about 100 nucleotides. In some embodiments, the at least a portion comprises about 60 to about 65, about 70, about 75, about 80, about 90, about 95, or about 100 nucleotides. In some embodiments, the at least a portion comprises about 65 to about 70, about 75, about 80, about 90, about 95, or about 100 nucleotides. In some embodiments, the at least a portion comprises about 70 to about 75, about 80, about 90, about 95, or about 100 nucleotides. In some embodiments, the at least a portion comprises about 75 to about 80, about 90, about 95, or about 100 nucleotides. In some embodiments, the at least a portion comprises about 80 to about 90, about 95, or about 100 nucleotides. In some embodiments, the at least a portion comprises about 90 to about 95, or about 100 nucleotides. In some embodiments, the at least a portion comprises about 95 to about 100 nucleotides.

[0163] In some embodiments, the first set of capture probes comprises two first nucleic acid molecules as set described herein, and the second set of capture probes comprises two second nucleic acid molecules as set described herein. In some embodiments, each of the two nucleicDOCKET NO. STFD-015-PCT PATENT APPLICATIONacid molecules of the first set of capture probes comprises a nucleic acid sequence targeting a different maximal rearrangement domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL, and each of the two nucleic acid molecules of the second set of capture probes comprises a nucleic acid sequence targeting a different low recombination domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL.

[0164] In some embodiments, the first set of capture probes comprises three first nucleic acid molecules as described herein, and the second set of capture probes comprises three second nucleic acid molecules as described herein. In some embodiments, each of the three first nucleic acid molecules of the first set of capture probes comprises a nucleic acid sequence targeting a different maximal rearrangement domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL, and each of the three second nucleic acid molecules of the second set of capture probes comprises a nucleic acid sequence targeting a different low recombination domain selected from: TRA, TRB. TRG. IGH. IGK. or IGL.

[0165] In some embodiments, the first set of capture probes comprises four first nucleic acid molecules as described herein, and the second set of capture probes comprises four second nucleic acid molecules as described herein. In some embodiments, each of the four first nucleic acid molecules of the first set of capture probes comprises a nucleic acid sequence targeting a different maximal rearrangement domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL, and each of the four second nucleic acid molecules of the second set of capture probes comprises a nucleic acid sequence targeting a different low recombination domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL.

[0166] In some embodiments, the first set of capture probes comprises five first nucleic acid molecules as described herein, and the second set of capture probes comprises five second nucleic acid molecules as described herein. In some embodiments, each of the five first nucleic acid molecules of the first set of capture probes comprises a nucleic acid sequence targeting a different maximal rearrangement domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL, and each of the five second nucleic acid molecules of the second set of capture probes comprises a nucleic acid sequence targeting a different low recombination domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL.

[0167] In some embodiments, the first set of capture probes comprises six first nucleic acid molecules as described herein, and the second set of capture probes comprises six secondDOCKET NO. STFD-015-PCT PATENT APPLICATIONnucleic acid molecules as described herein. In some embodiments, each of the six first nucleic acid molecules of the first set of capture probes comprises a nucleic acid sequence targeting a different maximal rearrangement domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL, and each of the six second nucleic acid molecules of the second set of capture probes comprises a nucleic acid sequence targeting a different low recombination domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL.

[0168] In some embodiments, the composition further comprises a third set of capture probes comprising at least one third nucleic acid molecule comprising a third nucleic acid sequence targeting a V, D, or J domain from at least one of: TRA, TRB, TRG, IGH, IGK, or IGL. In some embodiments, the composition further comprises a third set of capture probes comprising at least one third nucleic acid molecule comprising a third nucleic acid sequence targeting a V, D, or J domain from Table 3, below, which provides exemplary nucleic acid sequences of a capture probe in the third set of capture probes. In some embodiments, at least one, a plurality of, or each capture probe in the third set of capture probes independently comprises, consists essentially of, or consists of the sequence of one of SEQ ID NOS: 9035-9553. See Table 3. In some embodiments, at least one, a plurality' of, or each capture probe in the third set of capture probes independently comprises, consists essentially of, or consists of a sequence having at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to the sequence of one of SEQ ID NOS: 9035-9553. In some embodiments, at least one, a plurality of, or each capture probe in the third set of capture probes independently comprises, consists essentially of. or consists of a sequence having from about 75% to 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%. about 98%, about 99%, or about 100% sequence identity to the sequence of one of SEQ ID NOS: 9035-9553. In some embodiments, at least one. a plurality of, or each capture probe in the third set of capture probes independently comprises, consists essentially of, or consists of a sequence having from about 80% to about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to the sequence of one of SEQ ID NOS: 9035-9553. In some embodiments, at least one, a plurality of, or eachDOCKET NO. STFD-015-PCT PATENT APPLICATIONcapture probe in the third set of capture probes independently comprises, consists essentially of, or consists of a sequence having from about 85% to about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%. about 98%, about 99%, or about 100% sequence identity to the sequence of one of SEQ ID NOS: 9035-9553. In some embodiments, at least one, a plurality of, or each capture probe in the third set of capture probes independently comprises, consists essentially of, or consists of a sequence having from about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%. about 99%, or about 100% sequence identity to the sequence of one of SEQ ID NOS: 9035-9553. In some embodiments, at least one, a plurality of, or each capture probe in the third set of capture probes independently comprises, consists essentially of, or consists of a sequence having from about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%. about 98%, about 99%, or about 100% sequence identity to the sequence of one of SEQ ID NOS: 9035-9553. In some embodiments, at least one, a plurality of, or each capture probe in the third set of capture probes independently comprises, consists essentially of, or consists of a sequence having from about 92% to about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity’ to the sequence of one of SEQ ID NOS: 9035-9553. In some embodiments, at least one, a plurality of, or each capture probe in the third set of capture probes independently comprises, consists essentially of, or consists of a sequence having from about 93% to about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to the sequence of one of SEQ ID NOS: 9035-9553. In some embodiments, at least one, a plurality of, or each capture probe in the third set of capture probes independently comprises, consists essentially of, or consists of a sequence having from about 94% to about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity’ to the sequence of one of SEQ ID NOS: 9035-9553. In some embodiments, at least one. a plurality of, or each capture probe in the third set of capture probes independently comprises, consists essentially of, or consists of a sequence having from about 95% to about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to the sequence of one of SEQ ID NOS: 9035-9553. In some embodiments, at least one, a plurality of, or each capture probe in the third set of capture probes independently comprises, consists essentially of, or consists of a sequence having from about 96% to about 97%, about 98%, about 99%, or about 100%DOCKET NO. STFD-015-PCT PATENT APPLICATIONsequence identity to the sequence of one of SEQ ID NOS: 9035-9553. In some embodiments, at least one, a plurality of, or each capture probe in the third set of capture probes independently comprises, consists essentially of, or consists of a sequence having from about 97% to about 98%. about 99%, or about 100% sequence identity to the sequence of one of SEQ ID NOS: 9035-9553. In some embodiments, at least one, a plurality of, or each capture probe in the third set of capture probes independently comprises, consists essentially of, or consists of a sequence having from about 98% to about 99%, or about 100% sequence identity to the sequence of one of SEQ ID NOS: 9035-9553. In some embodiments, at least one, a plurality of, or each capture probe in the third set of capture probes independently comprises, consists essentially of, or consists of a sequence having from about 99% to about 100% sequence identity to the sequence of one of SEQ ID NOS: 9035-9553. In some embodiments, at least one, a plurality of, or each capture probe in the third set of capture probes independently comprises, consists essentially of, or consists of a sequence having at least about 70%, about 75%. about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to at least a portion of the sequence of one of SEQ ID NOS: 9035-9553. In some embodiments, at least one. a plurality of, or each capture probe in the third set of capture probes independently comprises, consists essentially of, or consists of a sequence having at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to the sequence of one of SEQ ID NOS: 9035–11,814. In some embodiments, at least one, a plurality of, or each capture probe in the third set of capture probes independently comprises, consists essentially of, or consists of a sequence having at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%. about 90%, about 91%, about 92%, about 93%, about 94%, about 95%. about 96%, about 97%, about 98%. about 99%, or about 100% sequence identity to at least a portion of the sequence of one of SEQ ID NOS: 9035–11,814. In some embodiments, the at least a portion comprises about 15 to about 20, about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments.DOCKET NO. STFD-015-PCT PATENT APPLICATIONthe at least a portion comprises about 20 to about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 25 to about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 30 to about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 35 to about 40. about 45. about 50, about 55, about 60, about 65. about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 40 to about 45, about 50, about 55, about 60, about 65. about 70, about 75, about 80, about 90. about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 45 to about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95. about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 50 to about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 55 to about 60, about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 60 to about 65. about 70, about 75, about 80, about 90. about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120DOCKET NO. STFD-015-PCT PATENT APPLICATIONnucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 65 to about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 70 to about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 75 to about 80, about 90. about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 80 to about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 90 to about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 95 to about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 100 nucleotides to about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 105 nucleotides to about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 110 nucleotides to about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 115 nucleotides to about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 120 nucleotides to about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 125 nucleotides to about 130 nucleotides.

[0169] In some embodiments, the composition further comprises a fourth set of capture probes comprising at least a fourth nucleic acid sequence targeting a gene of a disease, disorder, or hyperproliferative disorder. In some embodiments, the gene of a disease, disorder, orDOCKET NO. STFD-015-PCT PATENT APPLICATIONhyperproliferative disorder is a recurrent mutated gene of a lymphoma. In some embodiments, the fourth set of capture probes targets (i) recurrently mutated genes in tumor DNA and (ii) TCR and BCR V and J regions. In some embodiments, at least one, a plurality' of, or each of the capture probes targeting recurrently mutated genes in tumor DNA independently comprise, consist essentially of, or consist of a fourth nucleic acid comprising the sequence of SEQ ID NOS: 11,815-13,436 or functional variant thereof having at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to the respective one of SEQ ID NOS: 11,815-13,436. See Table 6. In some embodiments, at least one, a plurality of, or each of the capture probes targeting recurrently mutated genes in tumor DNA independently comprise, consist essentially of, or consist of a fourth nucleic acid sequence comprising at least a portion of SEQ ID NOS: 11,815— 13.436 or functional variant thereof having at least about 70%. about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to the respective one of SEQ ID NOS: 11,815-13,436. In some embodiments, the recurrently mutated genes are a recurrent mutated gene(s) of a lymphoma. In some embodiments, the lymphoma is T-cell and / or B-cell lymphoma. In some embodiments, at least one, a plurality of, or each of the capture probes targeting BCR V and J regions independently comprise, consist essentially of, or consist of a fourth nucleic acid sequence comprising the sequence of SEQ ID NOS: 9,554–11,814 or functional variant thereof having at least about 70%. about 75%. about 80%. about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91 %, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to the respective one of SEQ ID NOS: 9,554–11,814. See Table 5. In some embodiments, at least one, a plurality of, or each of the capture probes targeting BCR V and J regions independently comprise, consist essentially of, or consist of a fourth nucleic acid sequence comprising at least a portion of the sequence of SEQ ID NOS: 9,554–11,814 or functional variant thereof having at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%. about 93%. about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to the respective one of SEQ ID NOS: 9,554-11,814.DOCKET NO. STFD-015-PCT PATENT APPLICATIONIn some embodiments, at least one, a plurality of, or each of the fourth nucleic acid sequences is independently selected from SEQ ID NOS: 9554-13,436 or functional variant thereof having at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%. about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to the respective one of SEQ ID NOS: 9554-13,436. In some embodiments, at least one, a plurality of, or each of the fourth capture probes independently comprises, consists essentially of, or consists of a fourth nucleic acid sequence comprising at least a portion of SEQ ID NOS: 9554-13.436 or functional variant thereof having at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to the respective one of SEQ ID NOS: 9554-13,436. In some embodiments, the at least a portion comprises about 15 to about 20. about 25, about 30, about 35. about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 20 to about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 25 to about 30, about 35, about 40, about 45, about 50, about 55, about 60. about 65, about 70, about 75. about 80. about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 30 to about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70. about 75. about 80. about 90. about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 35 to about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In someDOCKET NO. STFD-015-PCT PATENT APPLICATIONembodiments, the at least a portion comprises about 40 to about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 45 to about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 50 to about 55, about 60, about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 55 to about 60, about 65. about 70, about 75, about 80, about 90. about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 60 to about 65, about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 65 to about 70, about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 70 to about 75, about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 75 to about 80, about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 80 to about 90, about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 90 to about 95, about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, theDOCKET NO. STFD-015-PCT PATENT APPLICATIONat least a portion comprises about 95 to about 100 nucleotides, about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 100 nucleotides to about 105 nucleotides, about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 105 nucleotides to about 110 nucleotides, about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 110 nucleotides to about 115 nucleotides, about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 115 nucleotides to about 120 nucleotides, about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 120 nucleotides to about 125 nucleotides, or about 130 nucleotides. In some embodiments, the at least a portion comprises about 125 nucleotides to about 130 nucleotides.

[0170] In some embodiments, the first set of capture probes comprises at least a first nucleic acid molecule comprising a first nucleic acid sequence targeting a maximal rearrangement domain of TRA, TRB, TRG, IGH, IGK, or IGL within a sequence described in Table 4, below. In some embodiments, the first set of capture probes comprises at least a first nucleic acid molecule comprising a first nucleic acid sequence targeting a maximal rearrangement domain of TRA, TRB, TRG, IGH, IGK, or IGL and having at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%. or about 100% sequence identity to a selected from a sequence described in Table 4. below.

[0171] In some embodiments, the second set of capture probes comprises at least a second nucleic acid molecule comprising a second nucleic acid sequence targeting a low recombination domain at or proximal to TRA, TRB, TRG, IGH, IGK, or IGL having a sequence described in Table 4, below. In some embodiments, the second set of capture probes comprises at least a second nucleic acid molecule comprising a second nucleic acid sequence targeting a low recombination domain at or proximal to TRA, TRB, TRG, IGH, IGK, or IGL and having at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%. about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%,DOCKET NO. STFD-015-PCT PATENT APPLICATIONabout 97%, about 98%, about 99%, or about 100% sequence identity to a selected from a sequence described in Table 4, below.

[0172] In some embodiments, the third set of capture probes comprises at least a third nucleic acid molecule comprising a third nucleic acid sequence targeting a V, D. or J domain from at least one of TRA, TRB, TRG, IGH, IGK, or IGL and having a sequence described in Table 4, below. In some embodiments, the third set of capture probes comprises at least a third nucleic acid molecule comprising a third nucleic acid sequence targeting a V, D, or J domain from at least one TRA, TRB, TRG, IGH. IGK, or IGL and having at least about 70%, about 75%, about 80%, about 85%, about 86%. about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% sequence identity to a selected from a sequence described in Table 4, below.14 22432490 22433463 TCRα_LMR1(TRD AAGCCGTGGGACATAGGAGAACAAATTTGAAAGA 1V-DD) TTCCTGAGATACAGGAGTATGGATTCCTGCAGCTG ATTCCTTTATGTGACCCAGTAAGGATAAAATCGAA AAAAGGAACTAAACGAAATACACTCTTGATTAAT CA. AAGGGGATTGAAAGTCGTGGCTAACCTCACAC CTACCTTGCATCACCTCCAGCTCACCTCCCTTGAG ACACTCCTCCTCTTCTTTAATGCCTCATCATGATTC TCAAAAACTGTGATCACTCAAGGTTGAAGCTTTTA ATCTCCCATGTATAAAAGGATATGCAAATAGAGTT CAGTTTCCTGTTGAGTCTCTGCCAAGGTCTTAGCC TGGCAGTTCTGGGAAAAGAGCCAAAGACCTCATA TTTCTTGGCTGTTAACATTCTCCCATCTGTGCTCAA GTCAGCAGCCTAGGCTTCAGGCTGTGGTTTGTCTT TAGTCTTACACTTTCCCAAGTTTTCTGAAGGAACC CTTTAGAATGTTCCTGCAAGAAAGTAAGATACAA GTGGCTCCCAAGAAACCAGACAGAGGATTATCTG GTTATATTTGGAGGCAGTAAGAAAAAGACCAGGA AGTCTATATTCCTATAGTATATAGCCACAGAATCC AATCTTGCAAGCTACTTGAAATGCTGATATTAATT AAGTCTTAGGCAGGGCTTTCAATAAGTCATCTGTG TCTCCAATATGGGATGTCCCACATCATGCATATGC ACAGTGAAAAAAAGCGAGGTCCTTGGGTACAGTA CAGCATTCAAAAATTAAAGATCTGAAAAACACAA GACATCTCAGTGTGCTTCCGGGCTGGAGGCTCTGC TAAACAACAGAAGCAGAGACCGGACTAATTGTCC CCCATGTCTCTTTGACTGAACTCACACAAAATAGA ATCTACCATTTTTACTCAGTGCGGGGTACCCAGAC TCAAGTTTACTGCAATGTTGTTACCAATATTCTAA TG14 22434013 22435992 TCRα_LMR1(TRD ATTCTCTTCAAATTTCCCACCTCTTAGTTCTCCTCC 2V-DD) CACTCTCTCCCACCCTGAGCCTTACACCTCCAACA ATGATCATTCTAAGACCATTTATATCTCAATAGGA AAGTGATGTAAAACGGGTCTCCTTACTCTGTTTTG GAGGGTTTTTTTGTTGTTGCTGTTGCTTGCTTCTCT GTCCCACCCCAAACTCATGTGTGTCTGAAATTTAG CACCACCTTGCGACGTTTGTGAGCATTTTTCTCAG AGCAGCATTTTGAGACTGAGCCTGAACTCCACTGA TGTTATGACCCTTAAAAGTGTCTGGCTCCAAAAGACTAAGGAGTTCCTGCGTAAATCCAGGTCCAGCTACDOCKET NO. STFD-015-PCT PATENT APPLICATION TTCATCACTGTGACTTGTTATTGGAAAAGGTTGAG CTATCAACATATTGCTCCTGTAAAGGCTCAGAACT GAATCTTAGATTCTTCAGGATATTTGAGTCCTCTG AGGCTCCTGGGTAAAGACTCCAATGTAGCAGTTCT GTGGACTATAAATGGGAGATATCCAGATCATACA CCTTCAATGGAAGAAAAAGCACTGTCACCTTAGA CGACTCCAACTCTGTAGTCTACTTTTGTCTTCCTAA TATCATACCTCATTCTCCAGTGGGTTTATGGCAAG CCTCATCTACTCAGAAGTAACCAAGTACAAGCCA ACACACTCTTGTGTTAGTGTGGAGGCCCAAAGTGG CATAAGTGAATGTGACTCCAGATGAAAACCTTCCC C TCTCC AAC ACAAAGA TGCC AAAGAC T A TGI AT A AAGCAAGTCTTAAATCACTCTATAITTCCATTTGA ATATATTTCCCCAGTTCCTGTGCATTGCTTCTGCAT ACACAGAATTCAATGATAAAAATTGAGACTGTCTC CTAGATACAGTAATTAACTCAGCTATCAATGCCAA TTGACTGTGTAGAGGGGAGACAATTTTGTACCAAG ATTTACTAACCTCTATTTTAATGGAAAAACAATGG AAAAGCTTTCTTCCTACTATGACTCTCTCTGGATA AATTGCTTGCCAGGAAGCGTTAGGATAATTCTGCC ATGACTCTTTGTCTTCCACACCCAAAGACATTTGG TCTCCATCACATATGGAGGAAGGATCTCCTTGTTC AGCAGTATTTACACCATCACCCTGACACCCGCAGT CAGATCTAACTATACAGCTTGGCTAATAAACCTGG AGAAGCTCATATTCTAAGAAAAAAGTGGAGAGTG GTGGGACAGATGGGGCCTGAGTGCTGGGAAACTG CCCGTGCCCACTGCTGACTTGGTCTTCTCACCAGC TGCTTGATCTAACAGATGCATCTTCCTTATGAGGC ACCAGAGAACCAGAATGTCCACATCCTGTGGTCCC CTGTACCCTTAACACCCCACATTTGAGTTCCTTTCC AATTCAGAAAACAAAACCTGCAGGCTTTGAGCCA ATTTACAACAGATGTGGGTCACAACAACCAACTA CCCAGGAAGCCTCCACCAGAACGCAGCGTGAGAA TCAGCTTCTTAGATATTCCCATACGTGTGATCCCA TCAATCATTTAACAACTGTCAAAGAGAAAGACTA GGAGACTTTCTCCCGAGCATCTCCAGGGATTTAAT TCACTATGTTGGAAATTAAGAGATTACTACTAAGC CATAAGAAGGCTAAGACAGAGTTAAAAGAATTAT TGGAAGGTTGGCATTACAACTTTACGTGTACACTA GGAAAATCTGCAGCTCTACCTGTAGCTTTGACATA ATGCCTTCCTATACCCTGTCCTTGCCCAACTGTGA CTCCCACATCATGGTCATACCCTGGATAGGCCCCT CTCTGCATGTAGAGCAATGTGAATGGGGATTCTGC TTATCAGGATATCATCACTAGTCTGTGCCAGGCCT TGCAAGAATGTCCTTGTACTGCAACTATTTGTACC AGATGGTACCCTGGCCACCCCTAAGTGTGCAGACT TTTTAACTTTTTCCCCCAAGAAAGTG14 22436419 22436720 TCRα_LMR1(TRD CCATTCCTCATATGTTCTCATTCTATTTCCATCAAA 3V-DD) CCTCAATCTCAAGAAATGACCTGAAATCAATTCGT ACTAATGTTTGAGTCATGAAAACAGAGGAAGGCT TTAGCTTCTCTGAGATTGGCAGGGAGGGTCGCTAG TGAGCATTGTATTTTCATAAAGATAATAGCCATAA GCTAAACACTGCAGCAACCACAGCAGAATTTTCC AAGCCTGAGGAACACTGCCCAAYATGAAAGACAG AGGTTTGTTCTCTCTTTGTTTGGAGGTTCAGTGTGG ATCATACACAGAGAGTCTGGAGC7 142774537 142775500 TCRβ_LMR CCAATAAAGTGACCCTGCTCTCACTGTCTGTGTCT 4GTGCCTCCTCCTTCACACTCCTTCACATTGGAAAG CATCCTCCAYCCTCAGGTCAGACAGGGCTCTCCCC CTTAYACATAAGAAGAGCCTCCAGCTCCCAAATGT GTTCCATGGT AC ACT AGATTAACACAT ACAAAGA GGTGGAATCCAAAAATAAGAAGCTTGGGAGAAAG GGGGGCACTGTTTTCTAGAGAAACGTGTGTTTCAG AAAGGTGGTCTTCGGCAGGGGCTATTGTTTTATTT GGGCTTCTCAGAGTGGTTAGAGCTACTCTGCCTTC AGAACAATCACAGTACAGAAAATGTGTCAGCATC TTCGAGGTGGCCCA. AAATATTTGACCAGCTGAAAC TTCTTGCTAAAATACAACAATAATTACAAATGCTG CTGGTGATGACGTGACTCTCCCAGGAATGTGTCGGCACCAAACCCTCGACCAAGCCCTCCCTTCTCATTCDOCKET NO. STFD-015-PCT PATENT APPLICATION GCCTGGAAAATCAGACTCAAATAAATCTTCCTGGC CCTCCGACTCTTCCCTTAATTCCCTAGTTCCATCTC TGTGAGCAGGCTAGAGAGATGTTCCACCTACCAC AGCGGGAGCCAGACTGCGACTTGGGAATCAAGCC CAGCTCTTCATGCTGCATTTTTATCTTCTTTGCCTT TGGGGTAGGATGCCACAGTGAATCCCACAGCTAA CACCAGCTCCTCACTCTGACCAGGGAAAGAAACT ACAGAGGGTCAGGATTCACCCATTTGATCAATTAA CTGAGAAAGGATTCATTTTCATA. AAACTTGCTTGA CTTTGAGACACTTCAAGTGAGTTATTTGGGATTCT TTAAAAAAGGTGGAAGGAAAGATCTGAGGACTGT GACACAACCAGCCACTCTGACCACACATTGACTG GCTTGCACCCACTGGACACAGCAGAGGGAGGCAG GCTTCATGGCACTTGCGGCACCTGCCA7 142778000 142778500 TCRβ_LMR TTTTTCAAAGAAAAACCAAAGGTAAAGTGATAAT 5GATCTTCCACACCTGAACCAGTTTGTAGCCACCAG AGCCTGCTGGGAAGGGGCCCCTCACGCATGCATT GATC TTG1 GACC TGGAAT T TGAGAGA TCAA TAAGC CCCGTAGCAACCTACCATACAACTGCCCATCAGCG C TGATCC1 Tl CATGGGAT TAGCTCAAT TCTGGC TCI GCAGACACTGGCAGCCACAGTTGACAAACCCTGG GCCTCTGTGGGCTTCCTTTGTCACCCAGGGCCACA GTGGGCTGCCTGTCCTAGGCAGAGACGCAGCAAC ATTCTCTTAAACTGAAATTAAGCATAAATCCACTT CACCGATAATCATCTGAGGGCTCAGTCCCTGCCTC CTTCCTCGGGGATTTTAAAACACACATTTCTCTGA CCAAACAGGTAGGTGAGATCTGACTTTAAAAGGA GGGAAAATCGGGTTGAATTGGGGTATCAGGAATG AATCCCAAGCATTTTT7 142779643 142781250 TCRβ_LMR CTCCTGCTCCTGCTCCTCCATCACAGCACTGCCCTC 6CTTCTGCTTCCTCTCCTCCTCTGCCCTCCAGAACAG TGGTCTTAAAGAGGTTTCTTGGCCTTGGCACTTCT GTGGGCTCCCAATGTGCTGATGTGTGACACGCTGG CATGCTTGGCAAGACCTCACTGCTGCCTTTGACTA CACAGGGTCCTCTCTGTACCCAGAGCAAACATATG CAAGGAAACCCCAGCACTGACCGAATCAGCTTCC TCGGAGGCCCCTCTCCACATGTGCTCCTGCTAACC CAGTCTGTACTCCCCACAAGCTGATGTCCTGCTTG GAGATGATCGTGCTGGCCCTCTTGCCCAACAACTG GCTCCTGTGTCTGGAGGGGAGAAGACAAATCCTT GGTCTCCATCCCTCATGTTCTTGAGAAGTCTGCCTT TTATTCCTCCACAGAATAATACCAACATGTTTACA CTATTCCTATGTATAGACATTTTCCCATTTAGTTTT CTCTCCCCTCCGGAGTGGTTATTAATCCAGCGGTA CAGATAAGAAAACAGGTTC. XAAGAGGCTTATTAG TTTACCCACGTCCCAAGCCCAGCAGATGGTAGGTC TGGGGTTGACTCCTCATTTGCCTGGCTTC. XAAGCC CACGCTCTCTGTGCCCCGCCTCACATCCCGCTATG ACTGTGGTCTGAGGTGATGACAAGTCCGTCAGCGC TGACCTCTGATGTTTCTCCAGCCCCCTGTCACTATC ACCCATTCCCTTCCTCCCTGCATCTCCTGAGGGGC ACCTCCCAATTGTCCCATTCCATGCGGCAAGACGA CTGCTCTCAGAGAGCTCCTGGTTATGGCATTGCTC CCTACCCTCCCACAGTGATCAAACTAGAATTCAAG CTCCCTGGGGAAATGTAGGGTTCTCCTGGCACCAC CCTTGCCCCCACTCCCAGTCTCATGCCTCTTCACTG CTCTCCTCCCCTGTCCCCTCCCCTGCTCAGAAGCCC TGGTGGCCCATCCAACAAGCCATGCGCCTCCTGCC TCTGTCTCTGGACACTATGGCACTCTCAGACTGGA AGCCGTTCCTAACCTCCCCTTCACCCTTTTCAGAA AAGTCTTCCTGATTCTTCCTTGTCCCCACCTCCCTT GGGTCTGGCTCTGCTGGCCCTCCCTCGGGTCTGAG GCAGCCATCCTCCTCCTGTCTCCGCTTGCCTCTGTC CTAGTCCTGCTCAGGTGCTCAGGTGCAATAGATGC GTCCATCCTGGCAATCAACTGTGTGCTCCTCAAGC GGGTACATCTTGTCTTACATATCCTGATATCTCCA GTGATTAAGCAAAGCCTGGGATGTAATAAGCACC CAGTGAGTGGAGGAATAAACATGGAGTGGAGGGA AATGTGCTGAGAAAAGAAAGACCCTTCCAGAAGAATGATTCTCAAAGAGTGGTCCCTAAGCCAGCAACDOCKET NO. STFD-015-PCT PATENT APPLICATION ACCAAAATCTCCTGGGAATTTAGGAGAAACACAA AAGCTAGGCCCTACCCCACACCCACCGAGTCAGA TCTCCTGGGACAGGGCCCAACAAACAGCATATTTT TTTATTTGAGATAGGGTCTTGCTCTGTTGCCCAGG CTGAAGTGCAATGGCATGATCACTGCTCACTGC7 38277932 38278467 TCRγ_LMR AATTCTCCAGAAAATGTGTCAAATATGTGTGCATA 7TTTAAAACACGCTGCAGCATTTTTAAATTGAAAGG AAATGATGGATTGTTTGGAAACGGGCATTAGGAA AATAATTACCTTAGAAAATAAAAATACCACTCTAC CTCATCCCAGATAACACAGGGTCCAAATAGATTA AAATTAAAATTACAAAGCAACACGTGGCCAGAAG GAACATATTGGAGATTTATTGTATCCATTGAGTAA AGGGGCATGGGATGGAAATGGGGTAGGAGAAACT TAACACATTAATTTTTAGGAAGTAAGCATGTGGAA AATTTTCTATTTTTATAGTATTTTCAAATAAATGTT TITGAAAGAATAGACAATGAGGACTTGCTAAAAA ATITAGAGAGGAAAGTGACATGATCACATITGCA CTGGAGAAAGATAGATGTGCAAGCAGAAAGGAAG GGGCGCTCCCCAGGACAGCAATTTGGCTGAAGCA GATGG'nTTATAGGTGGTCGCCATAATCCAATAAG AGGCAACCAGGACCTGAA7 38278856 38279290 TCRγ_LMR CTTATTTCTGTGTCTTTTTATCTGAAAATAATAAGT 8T A TTGT T ACl TOG T AC TG TC AA T1 ACCC T T TGC ACC TG TCATAGA TGGGATGAl GCCCA IT CAATCCCTCT TTGTCC TC TGC TTTTCCTTAlTCCAGAACCA TGTGG GGAAGTATCAGAAGTCTTAGAAGCTGTCTACATTT CAACAGCCATGAAAGATTTAAGTAATACAATGTA AAAAGTAAGTAATGAATTATAACATATTTTATTAA GTTTAC.\AAAAAAAAGAACTATGTGA\GACCATG ATGTTCAGTTTTACTAAAGGCGTAAAATGAAACCC AAATGAATGTGTATAAAGATAAGCAGTTTCGCCTC TAACCCTGTGTTTTGGAACACATACATCCTCCCCG CCACATTTGTCATGTCTTGAGTTAACAAACTGAGG CAACTT.\AATCCTG7 38279713 38281551 TCRγ_LMR ATAAATTAGCATAATTTGATTTCACATATGTCATC 9ACTTAGATAATATCAGATATGTTACAATATAGTCC AGTGGATCTTCACTTGTTTCTAAAAACACCAGGGC AGTGTTTGGGAGAGGCCGGGTCACTGCACTTTCAA TCAGATTCTCCCTTTTAGCAATTGTGCCACCTGTCT TCATTCTTAACCTGAAGATTTAGTCTTTTAGGGTTT CTTTTGCACTTGGGGTACTTAACATGCCACTATGC ATATTGTAGATTTATAGATACTTTTCAACTGATAC TGCTCCCACAGGCAAACATGCCTGGTGAAACACTT GTTTCTTTTTGGCAAACAAGAAATGTTTGCATAAA AGACTCGTGTCTGGAAAAATGTCTTGAGAAATTGA TATGCTACTCTAAGCCCCAAATCTCCTTTTCACTTA CCTTCCCCCTGCTGCAGGATGACAATCCATGGGCC TGTGCTTTCTGATAGTGAAAGAGAAGAA. XACTCAT AAATATAGTGTCTACCATGAGTCAGGCACTAACTA TGCATTTATCTCTTTCTGCTTTACCCTATAAATGGT TATTACCATTAAAAGTCATGTGAGGAAACAGAATT AGGGAGTTCAAACTGAGCCAGGATTTCAGTTCAA GTTTTCCAGATCCCAAACCCTGTTCATCAATTACTT CACAGTTGGAGAGATATGTGTGG. XAGGAACGCAG TTCCCAAGTATAGTCTAGGTCTGTATAMATAGAG AATCTGTATCTCAXATGGCCATATAGAGGATGCTG GGTATTGCTTTCTAGGAATCACAGAACATATTAAA CGAAATAAAAAGCAGATGAAATGGTTGATTTGCA TATTCTAAAAAGCATTGAGTAGTCAGTGACAACAC CTAGCAAAATAATCTGTGAGGAGCGGGGCTAGTT GAATCTGAATATCAAATTATATCTCACAATTTACT TTCTTTTTATTTGTCTTTCAGTGACACCAGGAGATT ATACATCCATGGGGCCATTTGGGCCATGCACTTCA GAYTGACAATCATTGCCGTCATGGCTGGCCTATTG CCCTGCACATGTCAGGGGGAACACAAAGAGTTTC TAAACCTGCAGTAAGTTAGAGAGAAGACTGGGTC TTCCCTGCATTGGGTCTGTAGTGTTTCGGTCAGGG GCTCTGTTGAGACAGCCTACTCCAGTCTCAGATTG GACCACACAGGGTTGGGCCTGGTTTGTGGGTGTCTTTCTCGCAGGTGAAACCATAGCTTCAAGAGCTCCTDOCKET NO. STFD-015-PCT PATENT APPLICATION GTAAACTCCCTTCAGATCTCATATCACAGGAAACT CAGTAATAGTTGGGTCTCTGCACTCTTCTCTCATTA CTAGGAGAAACAAAAAACACAGAAGTCAACAAA ACACTATCTGCTTGAGAAAACACCCTTGCCATTCC ATCAGATGATACAATATACTGTTGCCATTTACTGC AATAGGAAAGTCTGGGGAGGAAAATAATACATGC TTGGAGATTGGGGGAAGGGAGTGGAATTGGAATC AATAATTTTTTTGGCTACTTGTCAGACATCCAAAA AGAGAGGTACTGAGCTAAATGTAATGGTATAGAT ATGGTTGCTACTATTGTTCTTGCTATTTTCTAGGTG TGGCTGGTAAGGCCTTGGACATGAACAAGTCCTA GGTCACTCTAAGAAGGCAGAAAGCAGGCCAGGAC TACCCAATTTGAACCAAGTGTGTGGCCAGCCCCTT GGGATTGGTTCCAGCTTTCAGAGTGAAGAGTAGG AAATTCCAGCCTTGGTTCAGCAGGTCCTTCTATTA TAAGAATTTACTAATCTAGTCAG. AAAAAAAGCTA ATCTCTATGTCCCACATGCCCATATG7 38281877 38282092 TCRγ_LMR CTTATCACGTTCTGACACTTAGCAAGATTCCCTGG 10TTCACTACCACACTAACCATCAGATCACATAGGGG TCTGCAGATTTTA1T1ATTTTACATGGCCAGTCCCA CGAATTAAAGGAACAGAAAAACAAGAAATTATGA TTTAATTGATCTGTTAGGTTTTGAACTTCTATGAGG TTCCTGTTGCTCATTTAGTATCTAATTAATGAAAGT AATT14 105866036 105866377 IgH_LMR(D-J) CCGGCGGGGGTTGCCTGGTTGGTTCCACCTGTTCA 11CCGTCGTCCCACTGAACGGGAGGCCTCAGTGGGT GGCACTGGGCCTCACTCACCACGGCGCCCTGGCGT GGGCTCCCTGCGTGTCCACCAGTGCTGGGTCCCTT CTCTGAGCCTCAGCTGGTCCTCAGTGAGTCTCAGC TCTTCCCATGGTGGGTGCCAGGGAAGGTGCAAGG TGGTCTAAGGAGAGCCCCTCCCCAGGCCTGCACTG GCTGCCTTCCGCCGAGTCTGGGTGAGGGGCTTTGC ACGCACCACTGGCCAGACGCGGGCTGGGTGGGGC CCTCAGGGAGGCTGAGGCCTGCGGCCAGGT14 105866701 105867118 IgH_LMR(D-J) GCCTGGATGTGGGGAGAGGGTTGGGGCTCCTGTA 12GGGGTGTGGACAGAATGGCGGCGGTTTGTGGAGT TTCCTACAGGGTTCCAGGCAGGACGGGGGACCCT GAGGTGCTGTCTGGGACAGTGGATCTCTCTAGACA TGGTTGAACAGCTGCCAGCATGGGGATGGAGCCT TAGGCTGGGAATGGTGAGAGAACCCACCTCCAGC CACGAGGGGCCGAGAACCCATTTGTTTAGGGGTG GTTGGGCCCTGATGGCCTGGGAGGCACCTGTGAG GGGGTGAGGTGGGGGAGTGAGGAAGAGGGTGGTC TGGCGCTGGGGGAGTGGCTCTCTGGCCTGAGGAC CCTCTGCCCCCACCTGCCACAAGCACACACCAGGG AAAGCACACGAGTGTCACAGGCGTGGCGGCTGGA TCCTACAA2 88864376 88865220 Igκ_LMR TAAATTGTGCTTGGTAGTTATCTCCTGGGATTGCA 13GAGGAGGAACAATGACACTTTATGCCATCTCCTCC TACTCTTCTGTATGGTGATGTGAATATATTCATTTT ATAGTTTTTAGAAATAATAAAACTGTACTAATTTT GAAAAACAGTAAACTCTGACATTGCCTATTAGCAT TCTCGATATTCCTGTGCAATGCATAAACATAACTT TTTAAAAGATATGTACACACATGTGTGAGTTTTCT TTGTCAAATACTTTTCTATAATCTTTAAATCAAGC ATGCCAAAAAGGTAAAAGCTTTCCTGTTTCAGTGT AGGAGATAGTCGTCTGCAAAGGAAAGAGATGTAG GGGATAGAAACAGGAATGAAAAAGATGACTGAGC TGTTCGAGGGACTTATGTTCCTAAGTGAGCTAATT GGAAATCTAATATGAACAGTGCAACCGAATAACT ATTGTAAAGCAGTATTTGTAAACAATAAAAGATG ATTATCAT. XAGTACCATTGTTGCAA. XAACTATTTT ATTGATCACATGCAGTGGTGATCTGTAGGAATGAT TGTTGTGATGTTTGCTGTAACATAAAATGAAACAT GGGAAGTGGCTGAGATCTTTAGGATGTGTGTGGTT CATTTTTTGAAAGCAAATGTTGTCTCAGAAGCATC TGTGAGACTCTGCCAGGATCCACCGTTCTACA. AXA TATCTGTGATGGACATTGATAAGATTGATCTGTTG AGGAAAGGCAAGGTGTCAGTAAGATAGTCTGAGAGCTTCTTGGATTTCATGTAAAAGAGTGCTGGAAATDOCKET NO. STFD-015-PCT PATENT APPLICATION AGAATTTCTTGGGGAACATTCCAACTAACTCATCA CTGAAGGTG2 88884061 88885396 Igκ_LMR ATTTCTTTGGCCATAGCATTTGTAAGGAGACTGGG 14ACATATAGGTGAGCAAATGGAACATATACAAAGT AATAATGTCTCTAAGATAAATATTTACAATTCACA AATGTACAAAGAATTTTATAGATGCATCCATAATT CACATTTTGTGTCATTATCACCATTTTCTCCTAAAT TACATAAAACTTATTTTATTTATTGACATGTGCTTC ATATTTATCATTTATCACTGCCTGCTAATTTTCATC AGGAGCATCAATGGCTATTCAATATCCTATTTATG TACCATAGTTTATAAATGTATTGACATTTAAGTGA TAATTTATTATGGTTTTTTGCTATTATAACTTATTG AATTGATGAAATGACATACTTTTATTAACTGATTT TTCTAATATTAATTTCTAGTTCCATGAGGCTTTCCA CTTTGGATGGTAAAAAGGGAGATAGCATTTCTACT rAlArGCWTAAAlT AA1 TCTAGGTAGTGAATTTTA T 1 1 Arc TGGGAA TAAT IT TTAGA TA TGGCAAC TC 1 CATTCATTTTGACAAGAAAAATCTAAAGCTCATAA ACCCTGAATCCTATATGCTTACTCTCACAAAAATC TCTAATGTCCTGCTGGGATTTATCCACAGTTTAGA TTAGACCTGGAATACATATGGTCATGCAACAATGA TCTTAGAACAGGACTTTAACTTGGCTTTAGGAACT GAGGCTGAGAGTAATAGAATTGATTTTTTTGTGTG TGTGTGAAGCTCCTATTATAATAATGAGAATACTT TGATTCACTCAGTTAAAGTTTTCCCCTGATTTATTG TGTACATACAATGAAGGATCAAGAAAGAGAAATT TTTAAATGGAAGCATTAGCCAGACAAGTTTGACCT CACAGTTTTACTAGGGGATATATCACCTAGTTTTG GATCTATTTCTAACATCTTAACATTGTGAAAAGAG TCTTGGGAAACTGGTTAAATCCCAAAGAATGCTGC AATAGGAGGTTGGCCCTTATGAGTTATTTAATATC TTGAGCTGCCTTCGGAAAATGTTGCTGAGCAGGCA TTGAAGAGTATCGATAAAATTTATTGAGAATTTGT TTATTATGATTAACAGAGGTAAAAGCCAGTATATT ACTGATTAATATAGGTAAAAGGCAGTTAAGAAAT TGGGAATGCTTTCTCTTCTGCTTTCTTCTACGATGC ACAAGGCGTTTCACATTTATGCCCCTATGAAAATT ACTAGGCTGTCCTAGTCATTAGATCTTTCAGCAGT TTGTAGTTTTAGAGCTTCTAAGTTGACTTCTGTCTT TTCTATTCATACAATTACACATTCTGTGATGATATT22 22882024 22882234 Igλ_LMR TATTGTTTTCACCCTCATCCACCTGGGAAAGAGTA 15TCCTGGAACCAGCAGTTAACATTGACACAGCTGGT CTCGGTCCTCAGCACAAACATTCATTGCAGGCTGA AAAGTGACAACGGAAGAGAAAGGAGTTTATTAAA TCCCTAGACAC. AAACAAATCCATAAGCAGAGATG AGAGATGCGGGCTCAGCTGGCCCAGTCCCACAGG GGTC22 22884397 22884748 Igλ_LMR CAGGTTGGCAAGTCCACTCTGTGACATCTACAAAG 16GGAGCAGGGATCTCTTCCATTTCCTGGAGGAGAGC TGGGGTGGAGGCTGCAACCCAGGATCACCAGAGG AGCTGGGGTCTTTGGGGTTCCTGAGGACTCCTCAG AGGGGGATCAGGAGCTGCAGAGCCAGCTTCT. AAC TCTGGGGACTCAGAGATCCAGAACCTTTGTCATAT CCCCAGCCAATACTTTGTCATCCTGTGCCTCAGAC TCCCCCAGATCCCAAGAGTGAGAAGCTC. AAGATG AGAC. AAGAAAGACCAGCCAGCTTGAATTTAGGGA TGGTGGGGAGTGGGGAGCTGGGGACCCCTGGACC TGGGGGA22 22885333 22885565 Igλ_LMR GGGCTGGAAGGGAGCAGCTTCAGCCTAGACTCCC 17AGGGCAGACCCTGCCCCAGCCCCGAATATCCAAG GAGCCC. AAGATCAGAGGCAGGAATAGGCC. AAGCT CCCCAGTGGAGAAGCTGTGCTGGACCAGGGGTTT CCCAGGGCCCTCCCTTGTGCCCTGAATGATGTCTG TTAGGGCACCTACACCCTGTTACTGCTCAGTGCCTTGCCTATTTTGAAGGACAGGGATGTGTTable 2DOCKET NO. STFD-015-PCT PATENT APPLICATIONSequence (each cell includes one contiguous sequence SEQ Chr Start End Category regardless of spacing within the cell) ID NO TAAAGATTAAGCTTTGAGGGATGTGGGCTATAGGT 18 CATCCTCTTGCCCAATGATGGTGAGAAGGAAGGC CATCTGACTAAAGGGTAAAATTAGAAATACAAGA AAACATACACACTTTTTCCTTAGAAAGATTTCACT TCTTCACCTAGTGCCCCTCAGCATTTACGAGAAAG AGTTTATTTCAACAACACCCAAGTTAGGGTAAAAC TCCCTACCTGGTGTCTCCGTATTAGCATGGCAACT CATCACAGGGGCAAAATCCTGCTATTCCTAAGCAT ACTAATTTAAGAAACTTTTGTTGAATATTAATAGG ATTAATAATCAATAGGGTTCAATAAGGAAAACAA CCAGGAAAAATGATTCTTCCTAAATGGATCTTTGT AAGCTCTGTTTTCTCATTTTTAAAATTAGCTAACCA AATGAGTTTAGTAACCTATTAGTAAAATTAGTTAC AGCAAGGATTCCAGCCTCCTTCCCCACTTCCCAAT GCCCAAATGCTGAGCTTACATCTTTGATTTGAACT GTAAACTCCTTTTCATCCATGCCTCGGCGAAGTTT GGTGAACTGGGCTGCCGCTGTGCTGACTGCAGATG14 21392000 21392625 TCRα_Plateau3 CTTCCTCCTCTGCCATGGAAGCTGCACTACTAC CTGTTTGTTACCTTGGGCCACTCAGAGGCTCTTTGT 19 CTTTCCTGCAGTAGCAGAAGCTCAGGGGTCATTTG TTCTCCATCTTCATTTGGGAATCCATCTTGGGACAT AGTGAGGGACAGGAGACTCTCTTCATCATAGAGCT’l ”1 GAGCGGGACl GGTCAGCTGG TAAGAGAGCCC ATAGAATGTGTGAGAAAAGATGGAAGAATAATGT CATATGGTAATGGTATTATATGGGCTTTGAATAAA GGCCCAAAGAATGGCACTCTTTTGACATTTTATCA AATCAAAATCCAAATCTCTCTCAAGAGGATGCATT TAGAAAAGGGAAAGAGAAGAGAGGGGGAAATAG GGAAGGGGGCCAACAGCCTGTCACATGCACTCAC TTAGCTTCTCTTCCTTCTCATCCTCACTCTCATCAG TGCTGGAGCTGGAGCTGGATGAGGATGAGGAAGA AGAAGAAGATGGTGACAGCTTGCTCAAGTCCAGC TCAGAGTCCGAATCATCCTCATCCTCCAGTTTGAC TGGTGGAACACTCCGGGAAACCAGAGGGGTAGTA TCAGAGGGGGATACTCGCATCTCATAGTCTTGTGG GGTTGGTCGGCTCCTGGCCACCACCTCGTGCTCTA GCTTTAAAGTCAGACTCTCCAGACTGGGGACCTGG GTAGCTGTCTCCTCGGGTGACTTTTCAACAGGAGC ATCTGGGCGCAGGGGCAGTGGTGAGGCAGTGCGT GAGGTATACTGCTGGTGCAGCAGTGGAGTAGAGC AGCGTGACAAGGATGGAGCTGGTGCTCCTGCTTG ATGGTTCTGCATATAATTCATACGGGCAGCCAGAA AAGAGAAGTCTGGGTCCTGCATGATGTTGCAGTCT GTTTGGCTCACCCCATGGCGGGCTGCCCCTCTTAG14 21393095 21394000 TCRα_Plateau3 AAGCT ATTCTTTATAGAACATCCTGCAAATCCAGACCATA 20 CACAATAAGTATTTGAGTGACTCGAATCCACTAAA AGTTGGGTATATTAGAATCTGGGGTGTGAATACCT ATGTGACACAAGTCAGTTTCACCTATGACAACCGG CAATTTATGGAGACAAATTTCAAGAGTGAACCTTA TAATCAGGTAGGTCTGAAAGGAATATTAGCATATC ACAAGTAAATTTTATCATTCTGCAAAATTATCACC AATAATTTTGCTAACAATTAAAATTATCATTGTTA AATTTTCATGTATTAGATGGTTATAAATACGTGCA ATAGATATGTTCCTGAAAAGTTGCAAATGTTGAAT CATATTGTAAAATATGCAACATTAATGGTCTTTCC AGTATGGCCTAGGGGTCAGTGATCACTGGCCTGAT GAGATCCTCTCCATGTATTTACCAAAGAGACTGTG CTATGTTTTGATAGGTTAGTCTTCCACATTAGCAA AATAAAACTTATTTCTGCTGCAGAGGCTAAAACAA AGGAAAGGGTGATTCCCTAAAGCTGTTGAAGGTT GCCCCCATGCTTCCTGCAGTTATTCATGTCCCTGGT CAAATTGATGGATCTTATAGGTAGACGAAAATTG GCAGTAAACTGTGGTAATCTTCGAATGAATACATC CCACCTGTGGTATAGGATAAAAGGTTGATAAAAC AGGGGGACATAAATAGCAGGCCCTACTAGAGGAT TCTAGAATCAACTAAACCAGAATTTTGGAAGATG7 142218350 142219949 TCRβ Plateau AAATACCAATAGTTACCAAAGGCAACCACAAAGADOCKET NO. STFD-015-PCT PATENT APPLICATION AAAAAGTATCTCACTTTTAGAACATAAGACAACAT AAATACGGAACCAGCAACCCAAAAGGGATGGTTT AGAAAAGTGAAAATGGATAACCATAGTTCTTGTTT TCTAAAACGTGAAATGAGTGCCCTGATGGTATTTG GACTTTGGAAAATGGCCCCTCTGAGCACTCAAATA GATCTTCTCCCTCTAGGCTCTTCTGGGTATTTACCT TAAAGCATTTTACCTGGACTATTGAGTTCAAAACC ACTCTTTGCAAGTAATTGCTTCTAGTTAAGATTGT GCAGAAAATCCTTGAATACCTTCTTTTTAAAAACT CTATGGCATATCTGATGCCTATTATGTGCCAGACA CCATACTGTTTGAAATGAGGAAAACATGAAACTA ACCTGCTGTCAAGAGGACTAAAACCCAATGGCAA AGC’AAAGAGA 11 TTAATAAATGTTGG111 TAATCA CAGCTACAAATATTTGTAAACAATAAGGTTCTGAC TAAATGAAGTGAAAAGAAAAGATTTCCAGCATAG GGATTATGCACACAGAGCATCTCTCTGTATTTATC TGACCAAAATCAACATGACCTAACCCAAAAAGGA ATGTTTATATCCTATTACTGGAAAGGAATGAATCC ATCATTTTTTGTTAAATTGTAATTTAAGAGGTGAG CTACATGTGAGGTTTAAGAAGTTCTAAAATACCCA TTTATATCTCTTCTTTTCTGGCAGATACTAACTATT CAATTGACTGACAAGACTATCAACCTGGAAAAGT TAACTGAGGTTACTTGGATTGATGGTGGTCCTGT TATTAATAATATAAGTACTCCTGTTCAAACAAATA 21 CTACTAATGCTAGCACTAGTACTAATGTTGCTAAT ATAACTGCTACCTCTCATACAAGTACTGATGATAC TGTTCCTAATAATACTGTTCCAGTTACAGCTATTCC TTCTCTTGCAAATACTGGTGTTGACACTACTAGCA ACAGTTTTTCCATTATGACCACTTCTTTCTCTGAAA GTACTAATGCTATGAACACTACTGTTATTATGGCA ACTACTTCTCCTACAAGTACTGATGTTGCTAGCAC AAATAATGATGCTTCTATGACAAATTTTCTTTTAG CTACAATGTCTGCTGGTAATATAACTAGTAATAGT ATTTCCATAACAACTACTTCTTTTGGTAATAGTGTT CCTTTTGTGACTACTCCTTCTCCAAGTACTGATGCT ACTACTACAAGTAATAATACTAATCCTGGCATGAC TACTTATTACCAGACTTCTCCTACCATTCCTACCCA TACTCTTACTTCTATTCCTAGCTCTATTACTTCTAT TTTGAGCATGTTTCCAACAAGTAATACATTCACTA CTGATAAAATTACTAATTTTACTACCCCTACAAAT GCAAACACCATTATTTTCAACACTCTTGATACAAA AAGTACCATGGTAATAGATGCTACGGTCACTACTA CCAGCACCAAAGATAATACCATGAGTCCAGATAC AACAGTTACTTCCATAGACAAATTCACCACACACA TCACACAGTTCGCTACTCCCCATTCTGCTACTACT ACAACACTGGCCTTAAGCCACACCTCATTAGCTCC TACAAATCTTTCTAATCTAGGCACCATGGATATTA CTGATGCAGATAACTCCAGCAGTGTTACAGGTAAC ACGACACACATTTCTGTTTCAAATCTCACAACAGC CTCAGTCACAATAACAGCCACTGGTCTAGATTCAC AAACTCCCCATATGGTAATAAATTCTGTGGCTACT TATTTACCTATTACTGCAACTAGTGCTACCACAGA TACTACAAATATTACAAAATATGCTTTAAATACTA CCACTCCTGATAGTACAGTACATACCTCTGCTACT GCACCTACTTATATTGCAAATGCCATAAATGCTAC TCAAGTTCCATGATTACTACTCAAGGCAGGATAGT TACCTCAGATAACGCCTACAAACAACTATTACAGA TATAGAAAATCAGTTACGAGACACTCTATCTATCT TATGCTACTTAAGTTTTCACGGATATTAGTACTCT AGCCATAAAAGACACAGCTACTCCAAACACTCTC GTCATTGCAGACATGTTTAGGAAGGTTTACAAACC TTATAGGTTTCACCAAAGAAGCTGTGGGTACTTAT TTTGCAACCATAGTATGTGCTCTTATTCTTTTAAAT TATAGTTATTACTCCTATAACCTCATCAGTTAAAC TACAGATGTTTTATATATCCTATATATCCTTGCTAC AGATTTCACAGGTAATTTTGGTATCTCAGATAACA CCACATTAGGCTCTGTAAATACTATTGCCTTAGAT TTAGTTACTGAAATAGCCCAACTTGTTTCTTGGGT CACATGACGTACCATAACTGAGAGTACTGGTGAT7 142220922 142223356 TCRγ_Plateau ACCCCCAGCACTCA. AATGGTTTCTATACCAACAGTDOCKET NO. STFD-015-PCT PATENT APPLICATION TATTGATATTACAGGAGAGTATGTAATTAGTAATG CTAAAAAAATGCACTTTATTATCCTATGGACTTTT CCAAATGCCATAGCTACCAATAGAGTCATTTGCAT TACACATACTAATAGTATTATTTCTTCTGAGGAGA TCCTAGCTGTAGCTACAGATATAGAAAATTCTACC ATTGAAGATCTTGTATAACCTTACTTCAGCCACTG AAATAATTTAAATTATAAATATTACATGTGGGTTT GACTATCACAGAAAATAAAATGATTATAGATCCT AAAAACATAAATTCCTGAACTTTGCAACCATTAAT TCATAGGTACTACTAATACTCTTACTACAGATTTT ATAAGTACTTCCACTTATAGACAGAAGAGCATTCT CAGAAAATTAGAATTAATCTAAATTATGAGATAGT CTTAAAGCCTCACTGTTACCACCAATGACTGGCTC TGACTCTAGTATAAATCAGAAATTATCCAGACAGA GGTGAGAATGTAAATATACAGCATGAGGAAGACA GCCTCCACATTGGAATCAGAGTTCATAATCTTATT TGCATTTTCTTCTATTAATACAAGCTTTTCCCTTAT AATTTCACTGTTCAGACTCCCCTTCATTGTGTTAGG GTTTTCAGTCTATTCCTGGTTTTTCATATCCAAATT CATCATCCATCCTTGATCCATTGTTTTCTTAGATCA CTCAAACCCCCATGAGTAGACCCATGGTCATTACC AAATCTGGTCATTTGGGTACTATTGTAGGTTTAAC CCTAGGGCAATAT ATGAGAATAAAGTGCATTGTATGCCCTCATGATAG 22 TATATTATGTATTGTGTACATAACCAGTAATCTAC CAGTTTAAAACTTATTATGTAACTGTTTTTATTTAG ATGATGTTTTGCGTATTATTAAAGATGAAGACTTC AAAATACTGGAGCAAAGACAAGTAGTATTATCGG AAAAAGAAGCACAAGCACTGTGCAAGGAATATGA AAATGAAGACTATTTTAATAAACTTATAGAAAAC ATGACCAGGTAGAATCCAGGTTGAGAAAATTCAG TCTGATTTATTTTTGAATCATGTAAACTTTCTCTTA AGTCTGGTTTCTATTTAAGCTGCCAAACTCCTCAA GTCTGTAAACATGTTCTGAGTTTACTTCTCTACCA GTCCTGCTCCCATCCCAATCCTCTGCTCACCTGCCT GTCTTCTCTAGTCTTCCTGGAATGTTACTGGAATA GTAGGAAGGTCTCAGAGGAAGTTACTGGAGTCCC ATTGAGTTGAACACCAGAAGTCCAGGGTGTACAA TACTATGAAGTTTAAGCAGAGAACTGACTGACTCT CAAGAGCTTTTGTAATCTTATAGTTAACTAGTTCT AGGAAAGAATGAGTTGCTAGAAATGTGCTGGGTT TCTTTCTAGAAGAATGACTGAAATAGCAATTGAGG CTGAAATCCTGCAAGGGCATATAAACCAGCAGGA CC ATGGG AAC A ATG AAAG A AAC ATCT AC AAG AAT CATGGCACTCCCCTTCCCTTCCTTTCCCTGCTTCTA TTCTTTTATAGATATGCTCTTGAAAACATATCAAC GGAAAAAAATCACAGACCTCTGTTAAAAGATTAT TTTACATGTTACATGTTTTTGATCTATTTAACAATA TGCATTTGTATTGCCTATACATAATTAGCTACTGA GCTACACTTCTTATTACCTCTTCTTTGTTTTCTTTTC TAATAGTGGTCCATCTCTAGCCCTTGTTTTATTGAG AGACAATGGCTTGCAATACTGGAAACAATTACTG GGACCAAGAACTGTTGAAGAAGCCATTGAATATT TTCCAGAGAGGTAGGATTCATACCATGGGTCACTA TCTGTTTTCGTGGGCTCCATTTTAAACACCTTTTTA GATGTAGAGTATTGGAACCACAGCTCTAGTCCAA GGGAGCTTCTCAGGAAAGCTACCTTTCCTGGGGAC GGAGTGGACTGCTTATGACTGGAGGTCCAACCCA GTGACAGCCTGAGGATGGCCAAAGATTTTCAAGA AACCACTGTGAGGTGCTAGGCTTGGGGCTGGGAG CTAAGAGGTGTATATTTCAGTCAACAGGTCATCTC TTGGGAG. AAATATCCACCCTACCCGCTATTTAGGA GAAATTCCTTTGAGAAGGTTATGGTGGCAGCTGTA GCTTCTTTAACTGATCATGAGTTTTAAGACAATGA TGACTAATTGAATATGTACTCTACAATTCAGGGGG AACATTTATTGACTTAGCTTACTGATTAATCTTAG AAGTCAGCTAAACTTTGTAATCAACTTGACCCCTG GCATATTACCTGGCACATAGGGGGAACTCTTTCAA TATTTTCTGAGCTTACCTGCTAGGCTTAGTATCATC7 37884197 37886300 TCRγ_Plateau2 TGCAGGATAGAAATAGTATCTCACGCATCTCCATADOCKET NO. STFD-015-PCT PATENT APPLICATION TTTGGCATGAAGCTGATGGAAACAAATTGAATTTC AATTCCCTTGAATTCTTCTTGCTGATTTTAGGGTAG GATTCAATTCAAAGGAAGAAAGGACACCCCTCAT ACTCCCTTCAGGTGTGCAAGAATATAGATGCTCTT TAAGGTACTGCAAACATGACATACATGTTGACAC AATAAATAACAATAGTTATGAAGCCTCACTTACAT GAAAGCTGAAGTGCTTTCTTTTGGGTGGGATACAC TTAAATCTGACTTGTGTTGCATTAACATGTATTGC CCCTTAGTTAGCCCTACTCAATTATGTCTTTGCTTA TGTGCCAATGACTGTGAAGGATAATAAGCATAGA ACCTCTGCAAGTGGTGTGAGCAGAGTGCCATGGA ATCATTTAATAAAATGTGGCATAGAGTGCAATGCA TGCTACCAGAGAGAGGGATTGCTATCAACACAAG GCCTGTGCCAGTA CAGGTCACTCACCGGGGACACACATGGAGGACGC 23 ATTCTGCTGGAAGGTCAGGCCCCTGTGATCCACGC GGCAGGTGAACATGCTCTGGCCGAGCCAGTCGCT CTCTTTGATGGTCAGTGTGCTGGTCACCTTGTAGG TCGTGGGCCCAGACTCTTTGGCCTCAGCCTGCACC TGGTCCGTGGTGACGCCAGACCCCACCTGCTTCCC CTCGCGCAGCCAGGACACCTGAATCTGCCGGGGA CTGAAACCCGTGGCCTGGCAGATGAGCTTGGACTT GCGGGGGTTGCCGAAGAAGCCGTCGCGGGGTGGG ACGAAGACGCTCACTTTGGGAGGCAGCTCAGCAA TCACTGCAGTGAGGGACACGTGTCAGCCCGGTGC CCGCCACTCCCGCCCCCTTCGGCTCCCTCTCTGTCC CGGTGGCTGGGCCCGGCCCTCACCTGGAAGAGGC ACGTTCTTTTCTTTGTTGCCGTTGGGGTGCTGGACT TTGCACACCACGTGTTCGTCTGTGCCCTGCATGAC GTCCTTGGAAGGCAGCAGCACCTGTGAGGTGGCT GCGTACTTGCCCCCTCTCAGGACTGATGGGAAGCC CCGGGTGCTGCTGATGTCAGAGTTGTTCTTGTATT TCCAGGAGAAAGTGATGGAGTCGGGAAGGAAGTC CTGTGCGAGGCAGCCAACGGCCACGCTGCTCGTAT CCGACGGGGAATTCTCACAGGAGACGAGGGGGAA AAGGGTTGGGGCGGATGCACTCCCTGAGGACCCG CAGGACAAAAGAGAAAGGGAGGGTGAGGAGCTG CCTCCTCGTGCCCTGCCTGTCGGGGCTGAGTGGCG TTCTGAGTGCCCTCACTACTTGCGTCCCGCTGTGG CTGCCCCACCAAGGCCGAGCCCACCTGCAGGCCTC CAAAGCCCAGACTGTCATGGCTATCAGGGGTGGC GGGGCCGTGGTGAGGCCTCAGGTCTTTGTCCAAGG CTGCTGGGGCTGCAGGCCTCAGCCCATCCTGCTGC AGGGCCCAGCACTGAACACCTGGACAGACCTGGG GTCTCCTGGAGCAGGCTGAGCCATCCCTGCCACCAIgll PlateaulO TTCAGCTGGCTGCCCTGCTGCACTCTGAGGCCTGA 14 105855468 105856600 (IGHM) CTGCCCCTGGCTCCCTGCTCAGAATG ATGTGAGAACCAGCGCACCGATGGTCGGAGGGCA 24 GCTTGACAGAGAGAAATCAAAAGAATACAGTACC AAGAGGGCAAAACAAGGATAGCCAAAGCCCACCT GGTCGGTCAGCAGCCAGAATGTCTGGAGGAAGGG ACAAAAGAAAGGGACGGTGTAAAGGAAGCACAT GTTCCATCATCTTGTTTATTTTGTGCACTGTCCTGT CATATGACCTTATTTAAACTTCACATCAATGCTGT GAAGAAACTGAGTTCTAAGAGGTTGAGTTACCAC CCATTAATCTTACTACAGTGTTGGCAAAAACCTAC TGTCAACATAAAGTGATCTAAATTCTAAACTATCA TTATAAATTCCCAAGTTTCCTCCCTTCATGGGCCCC ATGGGCCAATCAATCAAAAACCCTTAGCTATTTAG CATTCGAGACTCTTTGCAGGGAGTCCAAGGAACTT CGCACTTGGCACCATCCCCACCTACCAGAAGCTGG CAAATTCACCGGGAGAAGATTCCTCCCAAGTTCAT CTTTCCACCTGCAATCAACCGTGGATGAACTGGTG CTTTGTTTGAATAGCTAAGTAGAGTGTTTTCGGCA TGGAAAACTGTAGACATAAAGCACTGAAAAGAAA ACAAACATAACAAACAAACAAATAAATGGAAAT AACTTTTCATTCCCTCATTAGTATTAACTTAAAAC ATCTATTAATAGTAATAAAACAAGCTTACTTAAAA TCTACCCCTCATTATGAAATAAGAAACAACATATG2 88259503 88260515 IgK Plateaul CTGTTCAAAAGCTTTTGTGCAGAGGAGTAAAATGCDOCKET NO. STFD-015-PCT PATENT APPLICATION CTTTGAGTAAAAGTGATACAATCCTCTAACTGCTC ACTTAATTAAACCTAATTTTATTTATGGATTCCTCC TGGCCTTTCCCTTGCTTTGGTTCTCTTCCCATTTAA GCTCTTCTAGTTCTTTCAGATCCAACTGCTGGTCAC TTTTTCTCCTTTCTAGTAGCGTCTTTGGGTCTTGCA GAGAAAACTTTCTCTTATTTCTCTCAAGCCCAGCC AGAGGAAGGGATGGGAGCAGGCCAGAAGGGAAG 25 GGGCTGTCTGCAGGGGGTCATAAGCAAAGTGTGA CGGAAGCCAGCAGAAGACTGGACTAGCTGGAGAA AGATATGGAGAGGAAGCAGACAGGTCTTAGCCAT CAGCCTGAGGGCTGGGCCCTGGCTCACCTCCCCTG GGGTCCATCCTTAGTCCTCCTTCACTTTCTGAATTT TTACCAGTTTATGTCTTCAATTAGGCTGAAAGCTC TGAGAAAAGGGACTGTCTGTCTTCCTTTGTATCTT CCATACCCAGTAGCACAGAGCTTTATGCAGAGTGT CCAACAAATATTGACCCTATTGACACCAACCCCTA CTGAATGCTAGTATCTGGGCCTTTGCAGACCAATG GCACAACCAAAGGGGTAAGAGGGAGTGGTGGGG ATTCCAGTCACTGGACAGGCTACTGGATGAGCTGT CTGATTCCTGCTTCACATTCCCCTATGGCTAATTT TGGAGAAATGATAGGCAAGGAATTCAGCCCCCAT GTTGTTTTCGGAGAGTGCAGGATTGTGTGTTTCCA GATCTCTTATCTGTTGCATCTCCCAAGTTTTACCAG GAGGGCAGACCTTAGCACTCCCAGCCAGCCCAGC CCTCCCTAACCCACCTCCGTTCCCACGAGGCAGCC CAGATGTGACAGTAGCTCATCAGAGAGCTGTTTGT GTCTTTCTTATTTACAGTATAAACAGCATTTAGAC TGCAGCTTTGGAAGGCCTCCGTCTATTTGTTCAGG TAAATCCACAGCCCTGGATGTGGTTTCCCTGTGAG ATCTCAGGCCAGCAGCTTCTGGATTGCTCCTCTTT GCTGGCCATCACAGAAAGAAGAAATCCTCTGGTC TTCATTGCCTTTGCATGTATTCTGTTGACTAATATT GTTCCTAGCAGAAATTCTCCCAGGAGAAAAGATG GGGTTTGCTTTTCTGTACCTCCATCTGTTCCTTCTC ACACACAGCACTACTTTAAATAACAAATCCCTTGG GAACATAGCTCTATAACAAAGTTCATTGGATTAAA AGCAAAGTCAATAATAAAAGAAATTTTCATAATC AAAGACTATAGAGCAGACTGCTTCTGCAGCTATGT AACCAAAAACTCTCTGTTTCTGATAAATAGATGTG TTGTTGGAATTTCCTGGCTTTTTTACAAATCCAGGT ACATTTATAACCGGCATCTTTTACTTTACAGAAGA GTTGAATTCTAGCAAAGCTAACTCGTAGTAGATTC TGTTTCCAAGGGAAGCCTATTGTTTTTCTCTTAATT TTCTTTGTAAAATTGAAAACGCTTTCTCTGCTTCTC ACAGTCTTTTTAAAGTCTGGGTTTCGAAAGTAACA ATC. XAGAGGCATTTCCATTCCTCCTAGGCATTTTG TCTTCAATTAGAATAATTACCACCATTTGGATAGT AATGCTTCATGATTCCACCACCCAAGCTTCTCATA GGGTCCTTGCCCCAAAGAAAAAGGAACACAATTC TTTAGATGTACCTTTGAAAGGTAAAAGCCTTAACA TTGGTTATGACCACAAAGCAAGAGTCCCAAAGAA GAAAATTATAAGAAAAATAAATCTAGATAAAAAT TTGGAACTTTTCCACAAACTCTTTTTTATTATTAAT CAATGCTTAAGATAGTTCTGACTTTGGTTTTCCTCC AGGGTGAAAGAAGGGTCTCTTTTAACTCACCCTTG ATGTGAACACTTCCTCAAGTCAAAAGCCTTTCCTG GGGCTGCTACTGGTGACTTCAATCTTCATCTGAGC2 88261281 88263063 IgK Plateaul TGG CCACCCCTTCTTACTTGCATTCCAGGCACATTTAA 26 ATCATTCACAAAGAAAGTGCCATATTCCAACC GATGGTGCCTGAAGACTAAGCCTTGGCCAGCAGG GATAGGACACTGATGGGGAAGGCATAGCCATCCT CCTTCCTACCTTTAGGGCAGGGCCCTTCTCGCTTG CCCTCTCGCTGGCTCGCTTCCCCTCCAGCCCCAGC TGCACAAACAACTCCAACAGGTTCATGAGCAGCT CATCCACCAGGTGCTCGTCTTGGATGTTGGCCGCG ATGTTGGCCAGGGCATTAATCACTGCCAGGGAGC AATGCCTGAAGAAGAAGGAGTGAAATAACAGCCA CTGCCAGGCCCTCAACCGTCCCCAAGGGACGGCA22 20796000 20796804 IgX Plateau2 CTGCAGGGGTGAGGCGAGCTGAGCGGGCCAGGCCDOCKET NO. STFD-015-PCT PATENT APPLICATION CAGCCTGCCTTACCACACTCCTCCCAGTGTCTGTA AACCAAAGAACTCTCAAGTGGAGAAGAACATGTC ATCTTCGTGAAAAACAACCTGTAGAATAAAGCCA ACTGATGCAGAAATGACTGCAATCCTCTCTCCTGA AATGTAGTAAGGACCTCCAGGAGACTAAGTTCTA GGCATCTGCAACACTGGGTACCTGTGAGGGTCTCA GGACACTTCCCTCAGGGCTGAAAATGAAAGGGCC CATGCCCAGGCATTCCAGGTTGGATCTTGCTTCCC CCCTACAAATCACAAAGAGCCTTAAAGCATCATTT ACCACCCACAGAACTTTCACCTCATGACCAGCTTC TCCCTAACGCTGCCTCCACCTTGGAGCTGATGTCA GTATTTTTCAC GTTTTCTTGCAAGAAGAGTTTATTTAAGAGACAAA 27 TTCACAAACCTCACATTTTTAAAGTAAGTTAAATA CTGTCATGATAAAAAAGTGACAATGAGGTCCAGT TACCTAAGCCGTGGTCCTTGTAATCTTTGGTGGC TGAGTATACAACGGAGCTGGCCTTCACACTGATCT GCTGGAAGAGGTTCCACACTTCCTGATAGATGTAT TGCTGGGAGAGAGCAAGATGCACTGTCACCATGC AGGATGCCCTGATGAGGCCCCTCCTGTCATCACCT AGAGAGAAAGCTCTGGAATCCTGGGGCACAACAG CCCAAAGACTATCAGCCCAAAGATCATCCATTTCT AAAGCTTTAATCAAACCTCAAATTAAAAGCTAAA AGGGACATGGCTTAGATTCAAATCTTCTGTTATAA TACACTGACAAGAAATTAAACCTCTTTTTCCCCAG CACTCACAGCATCTTACACTATTCTTACTACTCCG CATTAAAACCGTTGTCAGCATTTAGCTCATCTGCA AGGTATATTTAATCTGTATTTGTACATCCCTTATAG TCAAGAGTTTAACGTAGCTTGCACAGGGTTAGTGG TGTTCTGGCTCTGGCCTCCCTTACATTTCCGGTGAT AACCAGGCAGCCCAGCTGGTCAATAATCAGCACA TCGAGGGGGGAGGGTGGCTGGCAGAATTTCTGCT GTAGGATCTGCAGAATGGGCTCCATGACCTTCGGG GTGTCCCTCAAGGCCACCGCAATGTGTCCCAAGGC TCGGATTGTGTGGTCGGGAATCAAGTGAGCGTCCC TACAGAAGGAAGAACAGAAGCGCCCTAGCAACAG TCCCTCCAGCATGCAGTAGTGAAACAGTACCCAG AGACTACGATCTAGACCTTAATTTCATAACAGTCT TGATGCAGTGTTCATCTGAAACTGACAGCCCAGGA TTTTAACCACGGGCAGAAACATAAGCCCCAGGCA CTAGTCTGGATGACAAAGATCTTTCTCGACTTCCA CACAGTGGTCCAGGAAGTACAATCCAAGGTGGGC TTCACCTTAAATCTTGTGACAACCCTGATACATGC CTATGCTCTGAGACAAGGAGATAAGGACAGAGGC ATGCATACGCACAATGCCAGGTGCCCCACACGAG CCTGCTGAGAACAATGGGCTGCCTCTGAGAGACA GGAATAGGGGCGTACTTGTCGCTCTCCTGAGAGAT GTAGAGCCGGTTGGACAGGCTGGCCAAGAACGCC TCCACAATCACTGGGTCCACCGTCAATCCAGCCTT CAGGCACCTGAGGAGCAAGAA. AACCCATGTGGCA CTGAGGCATCAAACCAAGATAGGTTTTTTGTTTTT TAATTTTTCCTTCCTTAGGCCTACAAAGTTTAAAG AACTGCTCTGAATTTTCTTCCCCCCAAATTGGAGG TCATAACACAGAATGAATTCAAAGAATTACTCCA GATTTTGCCCACTTGATAAATGTCTCAGTCGGAAA CAATAATTTCATTATTTTGCCCAGAACAGTTTCCTT TGGAATATCATGCTCACCCTAATTCCAATTTCAAT CCCTTGTACTGTTTCTTAAGGTCACAGTGACTGAT TCCAAAGACAAACGGTCCCAAGATAGCATAGTAA ACATCACAATTATATACCAAGGTTTTCATGGTAAG GAGAAACATTTACGTTACAGAGAAAAGGGGAAAA ATTTAAAGCCCCTAAAAACATAAAATCTTGTAAGA TGTCCTAGCTCTCCACATCTGTTTGGCTCCTGGGCC AGAGTTTGGAAAACAGTTTGAGTCTGACAGACAA GCTGCCATCTTGATTTAGCTTCTAAGGGCAAGGAA CCAGAATCCAGGGAAAGAAGTATTTGCATGGAAA TCAGACTGTATGTAGCTCTCAAGTTGGAAGAACAA GAGTCCACAGTGCAGGAGTCTGGGCAGCAAGGGG TACCTAATCATATTTTAAAACCTCACATTTATATTA22 20798477 20800460 IgX Plateau2 AACATDOCKET NO. STFD-015-PCT PATENT APPLICATION GTCACGTTCTGTCCGCTTTCGCTCCAGGTCACACT 28 IgH_Plateau2 GAGTGGCTCCTGGGGGAAG. AAGCCCTGGACCAGG 14 105588250 105588350 (IGHA2) CATGCGACGACCACGTTCCCATCTTGGGGGGT CACAGTTTCTGAACATGCTCCTTAGATAGGGCCTC 29 IgH_Plateau2 TGACCCAGGCCATCCCAGACACAAGTTATATTAAA 14 105588577 105588650 (IGHA2) CAGG CCCTGGAGCAGACTGGGGGAGAGCTGGTGGTCAT 30 GAGGGTTGTTGGCCTCTCTGAGCTCTGTGTGCCCT CCTCTTGCCCCCGCGTCCTGGCCCGGGTCCCCAGG CATGCTGGGTGTTCCCACGTTTGAGCCCACCCACC CCCTCAACCCCTGCCCACTCTGCCAGCCCTCAGCC TGGCACTCCTGGGAACTGTGGTCTCTGAGCTTGGC CCTCTCTTACCGCTGAAGGTTTTGTTGTCGACCCA GTCTGTGGACGATGGAGTGTGTGCCACACGGCAG GTGAACATCTGCTTGGCCCACGCACCCGAGACGGT CAGCAAGCTGATGGTGGCATAGTGACCAGAGAGC GTGAGGGTGGTGGCTGGTAAGGTCATAGTTGTCCC GTTGAGGGAGCCTGTGTCCCAGGTCACCATCACCG GCTCCGGGAAGTAGCCCGTGGCCAGGCAGCCCAG AGTCACGGAGGTGGCATTGGAGGGAATGTTTTTGC AGC AGCGGG TC AAGGGGAAGACGGA TGGGC TC TG TGTGGAGGCTGTGAGGACAGAACCTAGTCAGTGC CAGCCTCAGGCCAGCGCCCATCAGGCCTGGGGGG CC TGGATGGGGGAGC TGGGGACCCCG TGGCAGGG ATCCAGATGGCCAGGCTCATTCTGGGCCTTTTTCC CCACAATCCCCAGGCCCAGGGCGGCTCCCAGGGCIgH Plateau3 CCCCATTCCCCCACCAGAAGCTGTTGCTCAGCCAC 14 105601200 105601950 (IGHE) TATCATCAGGCTGGGCTCAGGAAGG CTGGAGGGCGAGGCCTGGGTTGGCTTACCTGGGC 31 ATGATGGGCATGGGGGACCATATTTGGACTCTGCA GAGAGAAGATTGGGAGTTACTCAGATCTGGGAGG AGAGAAGGTGTCTGAGCTGAGGGAGTGGAGAGTT TGGCCTTTGGGGTGGGCTTAGGTCAGGGGCAGGG TCCTCCCGGATATGGCTCTTGGCAGGTCTGAGCGC AGCACCTGCCCCTGTATGCGCAGGGCCTGGGGTA GGGGCATCCAGCCTGTGGCTGCCCGGAGCCTGGT GGAAAAATCCAGAAGACCCTCTCCCTGAGCATGA GTGGGGTGGTCAGAGGCCTCCGGGTGAGGAGACA GATGGGGCCTGCCTTGCTGCCCTGGGCTGGGGCTG CACAGCCGGGGTGCGTCCAGGCAGGAGGGCTGAG CCTGGCTTCCAGCAGACACCCTCCCTCCCTGTGCT GGCCTCTCACCAACTCTCTTGTCCACCTTGGTGTTG CTGGGCTTGTGATCTACGTTGCAGGTGTAGGTCTT CGTGCCCAAGCTGCTGGAGGGCACGGTCACCACG CTGCTGAGGGAGTAGAGTCCTGAGGACTGTAGGA CAGCCGGGAAGGTGTGCACGCCGCTGGTCAGGGC GCCTGAGTTCCACGACACCGTCACCGGTTCGGGGA AGTAGTCCTTGACCAGGCAGCCCAGGGCGGCTGTIgH Plateau4 GCTCTCGGAGGTGCTCCTGGAGCAGGGCGCCAGG 14 105625316 105626066 (IGHG4) GGGAAGACCGATGGGCCCTTGGTGGAAGC CTGGAGGGCGAGGCCTGGGCTGGCTTACCTGGGC 32 ACGGTGGGCACTCGACACAACATTTGCGCTCTGCA GAGAGAAGATTGGGAGTTACTCGGATCTGGGAGG AGAGAAGGTGTCCGAGCTGAGGGAGTGGACAGTT TGGCCTTTGGGGTCGGCTTAGGTCAGGGGCAGGGT CCTCCCGGATATGGCTTTTGGCAGGTCTGAGCCAA GCACCTGCCCCTGTGTGTGAAGGGCCTGGGGTAG GGGCACCCAGCCTGTGCCTGCCTGGAGCCTGGTGG AAAAAGCCAGAAGACCCTCTCCCTGAGCATGAGT GGGGCGGGCAGAGGCCTCCGGGTGAGGAGACAGA TGGGGCCTGCCTTGCTGCCCTGGGCTGGGGCTGCA CAGCCGGGGTGCGTCCAGGCAGGAGGGCTGAGCC TGGCTTCCAGCAGACACCCTCCCTCCCTGAGCTGGIgH_Plateau5 CCTCTCACCAACTGTCTTGTCCACCTTGGTGTTGCT 14 105644040 105644540 (IGHG2) GGGCTTGTGATCTACGT GAGGTCACGCTCAGGTGGTCCTTGAACAGCGCTCT 33 TCCCACTTGAGGGCGTCCAGGTGAAGGTGACACCT GAGGCATCTCTCAGGCCGGTCAGTGTGCACGTGAIgH Plateau6 GGTTCGCTTCTGAACCTAAGAGCAGGTCCTCGAGG14 105707915 105708415 (IGHA1) GCCGGTCGGTGCAGTGACAGTCGGGGGTGGCAGCDOCKET NO. STFD-015-PCT PATENT APPLICATION ATGAGGGAGATGGGGTAGGTGGAGTTGAGGGAGA TGGGGTAGGTGGAGTTGAGGGAACTGGAGTGGAG AGATGGCCTGAGCTGGTCAGCACATACTTCCCCAT GCCCCCGCCTCGCCCCTCCTGGCCTGTCCACCACC ACCTCCTGGGGCTCGGCCCGCGGTCCACTCTGGTG TGAGTGAAGGGGCGGCTCCCTGTGGGGAACACGG GTGCAGGCGCAGTGTCAGGGCACGACGGGGTGGC CCCGCCCCACTCCCCAGCCTGCCCTCTGACCTGGG CAGGGCACAGTCACATCCTGGCTGGGATTCGTGTA GTGCTTCACGTGGCATG CGAGGCCTGGGCTGGCTTACCTGGGCACGGTGGG 34 CATGTGTGAGTTTTGTCACAAGATTTGGGCTCTGC AGAGAGAAGATTGGGAGTTACTGGAATCTGGGAG GAGAGAAGGTGTCCGAGCTGAGGGAGTGGAGAGT TTGGCCTTTGGGGTGGGCTTAGGTCAGGGGCAGG GTCCTCCCGGATATGGCTCTTGGCAGGTCTGAGCC CAGCACCTGCCCCTTTGTGTGCAGGGCCTGGGTTA GGGGCACCTAGCCTGTGCCTGCCCAGAGCCTGGG GAAAAAGCCAGAAGACCCTCTCCCTGAGCATGAG TGGGGCGGGCAGAGGCCTCCGGGTGAAGAGGCAG ACGGGGCCTGCCTTGCTGCCCTGGACTGGGGCTGC ATAGCCGGGATGCGTCCAGGCAGGAGCGCTGAGC CTGGCTTCCAGCAGACACCCTCCCTCCCTGTGCTG GCCTCTCACCAACTTTCTTGTCCACCTTGGTGTTGC TGGGCTTGTGATTCACGTTGCAGATGTAGGTCTGG GTGCCCAAGCTGCTGGAGGGCACGGTCACCACGC TGCTGAGGGAGTAGAGTCCTGAGGACTGTAGGAC AGCCGGGAAGGTGTGCACGCCGCTGGTCAGGGCG CCTGAGTTCCACGACACCGTCACCGGTTCGGGGAA GTAGTCCTTGACCAGGCAGCCCAGGGCTGCTGTGCIgH_Plateau7 CCCCAGAGGTGCTCTTGGAGGAGGGTGCCAGGGG 14 105742321 105743071 (IGHG1) GAAGACCGATGGGCCCTTGGTGGAGGC ACCAAGTGGGGTTTTGAGCTCTGCAGAGAGAAGA 35 TTGGGAGTTACTCAGATCTGGGAAGAGAGAAGGT ATCTGAGCTGAGTGAGTAGAGAGTTTGGCCTTTGG GGTGGGCTTAGGTCAGGGGCAGGGTCCTCCTGGA TATGGCTCTTGGCAGCTCTGAGCGCAGCACCTGCC CCTGTGTGTGAAGGGCCTGGGGTAGGGGCATCCA GCCTGTGCCTGCCCGGAGCCTGGTGGAAAAAGCC AGAAGACCCTCTCCCTGAGCATGAGTGGGGCGGG CAGAGGCCTCCGGGTGAGGAGTCAGACGGGGCCT GCCTTGGTGCCCTGGGCTGGGACTGCACAGCCGG GATGCGTCCAGGCAGGAGGGCTGAGCCTGGCTTC CAGCAGACACCCTCCCTCCCTGCGCTGGCCTCTCA CCAACTCTCTTGTCCACCTTGGTGTTGCTGGGCTTGIgH Plateau8 TGATTCACGTTGCAGGTGTAGGTCTGGGTGCCCAA 14 105770700 105771200 (IGHG3) GCTGCTGGAGGGCACGGTC ACTCTTGCTGGCGGTGTGCTGGACCACGCATTTGT 36 ACTCGCCTTGGCGCCACTGCTGGAGGGGGGTGGA GAGCTGGCTGCTTGTCATGTAGTAGCTGTCCCGTC TTTGTATCTCAGGGAAGGTTCTCTGGGGCTGGCTC TGTGTCCCCATGTACCAGGTGACAGTCACGGACGT TGGGTGGTACCCAGTTATCAAGCATGCCAGGACC ACAGGGCTGTTATCCTTTGGGTGTCTGCACCCTGA TATGATGGGGAACACATCCGGAGCCTTGGTGGGT GCTGGAAGACAGACACAGTGGGAGTCTGAGGCTG GAGGCTCTGAGGACAAGGGGCAGGGCAGGGCAG AGGACCCTGGCAGCAGGGTGACAGGGAAGGCAGG GAAAAGGGGCCCAGGAGGAGTGCCCAGGGTGAGC GGGGCTGACCAAGTGGCCCGTGAACACGAATGCC CCTGCTGCCGCTCCTGTGTTGTGAGTCAGAATAAC CGAGTGGGACCTGTGGCTTTGTGGACCCTGGGCTC TTGTTGCCGAGAGCTCCTGGAAGGGAGGGGTCTTC CCTCCAGAGGCTTTGGTGCCCCTCTGGGCATTCCT GGGACCTCCACCTTCCCTGCTGCCCCCAACCTCTC TGGAACCCACTTCCCTTGGGCCCCTGAGGGGAGG AGGGGCACTCAAGCCTGGGAGCAACGGGCCTAGGIgH Plateau9 GCTGTATGACCCTCCTGCCCAGGCTCCCAGCCACG14 105845400 105846150 (IGHD) GGTCCTCAGCTGCCCTGCAGGGGCCATDOCKET NO. STFD-015-PCT PATENT APPLICATIONTable 2.1SEQ ID NO (each cell includes one contiguous sequence regardless of spacing within the cell) 37 IgK Plateau 1 AAAGGTACCAAACACACAAATGTGAGAACCAGCGCACCGATGGTCGGAGG 38 GCAGCTTGACAGAGAGAAATCAAAAGAATACAGTACCAAGAGGGCAAAAC 39 AAGGATAGCCAAAGCCCACCTGGTCGGTCAGCAGCCAGAATGTCTGGAGG 40 AAGGGACAAAAGAAAGGGACGGTGTAAAGGAAGCACATGTTCCATCATCT 41 TGTTTATTTTGTGCACTGTCCTGTCATATGACCTTATTTAAACTTCACAT 42 CAATGCTGTGAAGAAACTGAGTTCTAAGAGGTTGAGTTACCACCCATTAA 43 TCTTACTACAGTGTTGGCAAAAACCTACTGTCAACATAAAGTGATCTAAA 44 TTCTAAACTATCATTATAAATTCCCAAGTTTCCTCCCTTCATGGGCCCCA 45 TGGGCCAATCAATCAAAAACCCTTAGCTATTTAGCATTCGAGACTCTTTG 46 CAGGGAGTCCAAGGAACTTCGCACTTGGCACCATCCCCACCTACCAGAAG 47 CTGGCAAATTCACCGGGAGAAGATTCCTCCCAAGTTCATCTTTCCACCTG 48 CAATCAACCGTGGATGAACTGGTGCTTTGTTTGAATAGCTAAGTAGAGTG 49 TTTTCGGCATGGAAAACTGTAGACATAAAGCACTGaaaacaaaacaaaac 50 ataacaaacaaacaaataaaTGGAAATAACTTTTCATTCCCTCATTAGTA51 TTAACCTTAAAACATCTATTAATAGTAATAAAACAAGCTTACTTAAAATC 52 TACCCCTCATTATGAAATAAGAAACAACATATGCTGTTCAAAAGCTTTTG 53 TGCAGAGGAGTAAAATGCCTTGAGTAAAAGTGATACAATCCTCTAACTG 54 CTCACTTAATTAAACCTAATTTTATTTATGGATTCCTCCTGGCCTTTCCC 55 TTGCTTTGGTTCTCTTCCCATTTAAGCTCTTCTAGTTCTTTCAGATCCAA 56 CTGCTGGTCACTTTTTCTCCTTTCTAGTAGCGTCTTTGGGTCTTGCAGAG 57 AAAACTTTCTCTTATTTCTCTCAAGCCCAGCCCAAGGGTAAACCAAACAA 58 ACAAGCAGAAAAACCTAGCTTGCTTTGCAAGTACACACACGAGAAGATAA 59 AACAAGAATTCACGTCTTAAATGCTATGTGTGTCTAGTGAATCTTCTAGA 60 C ca gaa gtttccaa actttctcca gtcat gga aactta gtgtctctgtaa61 ttttctcatggtgccccaggccaaaagaaataccaacacttctgtttatt62 aagtaattaagtaattaggtccaaacgacttaataagtgtttgtggctta63 aaaatttagtagccatttgaaaaattaatacgcaaaaagtagaaagaaaa64 aaggtttgtattccattattaaataattacaatgacttatttatgggcac65 gacacaacttctcagatcttggaatcaggctgtacagagccaccctcatt66 ttctgttccacattgattttcacatggaatttatttgttttaatcacagc67 aactggaaaaaaaattccatcaaaaggaatgtggtacaatctaatgttga68 aactgggcactaccttgagttaggagtttgtgtgatgtttgacagatgtt69 ttcttggagaaaatggacaatattccatagctcaatgcagtgccctaagc70 acatcggcacacagtttgagaaccacagTTCTACACGATAAATGCAGTGA71 GCACTCAAAGGAGGAACAAAAACTTTCCACTAAGATGGTTCACAGATTTC72 GTGGAGGAGGAGAAATTGAAGCCGGGCTTGCTGGCTTGGCTGGGTAAAGADOCKET NO. STFD-015-PCT PATENT APPLICATION73 GGAAGGGATGGGAGCAGGCCAGAAGGGAAGGGGCTGTCTGCAGGGGGTCA 74 TAAGCAAAGTGTGACGGAAGCCAGCAGAAGACTGGACTAGCTGGAGAAAG 75 ATATGGAGAGGAAGCAGACAGGTCTTAGCCATCAGCCTGAGggctgggcc 76 ctggctcacctcccctggggtccatccttagtcctccttcactttctgaa77 ttttaccagtttatgtcttcaattaggctgaaagctctgagaaaaggga78 ctgtctgtcttcctttgtatcttccatacccagtagcacagagctttatg79 cagagtgtccaacaaatattGACCCTATTGACACCAACCCCTACTGAATG80 CTAGTATCTGGGCCTTTGCAGACCAATGGCACAACCAAAGGGGTAAGAGG 81 GAGTGGTGGGGATTCCAGTCACTGGACAGGCTACTGGATGAGCTGTCTGA 82 TTCCTGCTTCACATTCCCCTATGGCTAATTTTTGGAGAAATGATAGGCAA 83 GGAATTCAGCCCCCATGTTGTTTTCGGAGAGTGCAGGATTGTGTGTTTCC 84 AGATCTCTTATCTGTTGCATCTCCCAAGTTTTACCAGGAGGGCAGACCTT 85 AGCACTCCCAGCCAGCCCAGCCCTCCCTAACCCACCTCCGTTCCCACGAG 86 GCAGCCCAGATGTGACAGTAGCTCATCAGAGAGCTGTTTGTGTCTTTCTT 87 ATTTACAGTATAAACAGCATTTAGACTGCAGCTTTGGAAGGCCTCCGTCT 88 ATTTGTTCAGGTAAATCCACAGCCCTGGATGTGGTTTCCCTGTGAGATCT 89 CAGGCCAGCAGCTTCTGGATTGCTCCTCTTTGCTGGCCATCACAGAAAGA 90 AGAAATCCTCTGGTCTTCATTGCCTTTGCATGTATTCTGTTGACTAATAT 91 TGTTCCTAGCAGAAATTCTCCCAGGAGAAAAGATGGGGTTTGCTTTTCTG 92 TACCTCCATCTGTTCCTTCTCACACACAGCACTACTTTAAATAACAAATC 93 CCTTGGGAACATAGCTCTATAACAAAGTTCATTGGATTAAAAGCAAAGTC 94 AATAATAAAAGAAATTTTCATAATCAAAGACTATAGAGCAGACTGCTTCT 95 GCAGCTATGTAACCAAAAACTCTCTGTTTCTGATAAATAGATGTGTTGTT 96 GGAATTTCCTGGCTTTTTTACAAATCCAGGTACATTTATAACCGGCATCT 97 TTTACTTTACAGAAGAGTTGAATTCTAGCAAAGCTAACTCGTAGTAGATT 98 CTGTTTCCAAGGGAAGCCTATTGTTTTTCTCTTAATTTTCTTTGTAAAAT 99 TGAAAACGCTTTCTCTGCTTCTCACAGTCTTTTTAAAGTCTGGGTTTCGA 100 AAGTAACAATCAAGAGGCATTTCCATTCCTCCTAGGCATTTTGTCTTCAA 101 TTAGAATAATTACCACCATTTGGATAGTAATGCTTCATGATTCCACCACC 102 CAAGCTTCTCATAGGGTCCTTGCCCCAAAGAAAAAGGAACACAATTCTTT 103 AGATGTACCTTTGAAAGGTAAAAGCCTTAACATTGGTTATGACCACAAAG 104 CAAGAGTCCCAAAGAAGAAAATTATAAGAAAAATAAATCTAGATAAAAAT 105 TTGGAACTTTTCCACAAACTCTTTTTTATTATTAATCAATGCTTAAGATA 106 GTTCTGACTTTGGTTTTCCTCCAGGGTGAAAGAAGGGTCTCTTTTAACTC 107 ACCCTTGATGTGAACACTTCCTCAAGTCAAAAGCCTTTCCTGGGGCTGCT 108 ACTGGTGACTTCAATCTTCATCTGAGCTGGGCATTAAAAACAAAAACAAA 109 IgK Plateau2 >clir2:88857361-88858361110 CTAACACTCTCCCCTGTTGAAGCTCTTTGTGACGGGCGAGCTCAGGCCCT111 GATGGGTGACTTCGCAGGCGTAGACTTTGTGTTTCTCGTAGTCTGCTTTGDOCKET NO. STFD-015-PCT PATENT APPLICATION112 CTCAGCGTCAGGGTGCTGCTGAGGCTGTAGGTGCTGTCCTTGCTGTCCTG 113 CTCTGTGACACTCTCCTGGGAGTTACCCGATTGGAGGGCGTTATCCACCT 114 TCCACTGTACTTTGGCCTCTCTGGGATAGAAGTTATTCAGCAGGCACACA 115 ACAGAGGCAGTTCCAGATTTCAACTGCTCATCAGATGGCGGGAAGATGAA 116 GACAGATGGTGCAGCCACAGTTCCTGAGGAAAGAAGCAAACAGGATGGTG 117 TTTAAGTAACAAAGTTCTGCCCTTGGGTGTGTTGTTTGCGGATAATCACA 118 GGGCATGTTAGGGACAGACAGAAAACAGCATGCTTATCCCAGATAATTAT 119 AGCAAGGAGACCAAGAAGCGTATTTAAAATCTTGATGTTTTGAGTTTCTT 120 CCTAGCTTCCCCCTATTCCTTAATAAAGTTCTAAATTGTTTTGTTGGAGC 121 TCTTTGCAGCCATTCTGAGGGCTTTGCATGCTTTTCTGACCTTGCAGTAA 122 ACTCAATGCTTTAGGCAAAGAATGGCCACGTCATCCGACCCCCTCAGAGT 123 TTAGAATTCAGAACAGGTCTGAAGAAGACCAGGCAGCGGCTGAGTCAAGG 124 AAAGCCTCCGTCCGCTTTTATTTCCCCTGTGCCTCTTCCAGGACTGTGCT 125 GGGATAACAGGCTCCCGGGGGTTACTTTGGCTGGGCTGGGCTAAAACCTC 126 CCTGCAGAGCAGGCCCTGAGCCCTGCCTCTGCGCCTGGGTGGTGTCAGCC 127 CCTCCACCTTCTGACTGTTCCAGCA\CTCTCTAAGCCCTCCCAAAGGCCT 128 CAAGGCCTGTAACCATATGCAGCAATTTTCAGCCATACCAGGAGAGGTCA 129 ACTGTAATCTTGGCCACCTGCCTAAGAGGAAGTGGCTAGCTTCACTTCTG 130 A131 Igx LMR >chr2:88861923-88885450132 CCACAGTGAGAGCTCTCCATTGTCTTGCTGAACAAAAACCCTTCTCACCA 133 AAGGGGAACAGAGTCCTGGGTCAGCTGCTGAAGCTCAACTCCCTTTTCGA 134 GCAGGTGTGGAAGCCCTGAGGCTTCTCTGACATAGCATGTGTTTATTTTC 135 TTAGGTGAGACCTAAAATCCAAGAAGAGAATATATTTACGTCTATGGCCT 136 GATGGTTCCTTTCTTTAGCAACTTGCCACATCTGGACTGCTTATTATTTA 137 TTTATTTTTTAGAAAGTAGACTGAATGTTAATTACAAAGAAAAACAAGCA 138 ATTAAAAAAAATGGCCAGTTTTTTTGTACTTTCTTTTGGGGTGGGCTGGG 139 GGGGCTTTTGCAAAGGATAAACTTCATTTAGTGTAATTATGGAAATCATC 140 AGCTTCTCAATGAGTAATAATTACAGGTTGTCTTACTATTTTATCTTCTC 141 CTTTGCTGCAATGTTATTTA. AAA. AAAGGTAGACTAAATATATATCAACTT 142 AAGGCTCATAACTTTGAAATGCATTTTGAAATGTAGCTCCAGATGGTATA 143 CGAAACCAAAGTGAAGACTAATAGAGTAGAAAAGTAGACTTTACTTGGTT 144 GGTTTGTCTGTTTTCACAGCACAGGAAGAGCTCAGCTCTTACTGAGCTGG 145 ACCAGGCGCATGCCATCTTTGGAGCTGCCATGGAGTCCCAGTGTTCCATA 146 GTGTTTCCATAGTAATCTCATCAACAACACTGAAGACCTTTTCAGTATTT 147 TCI " ITTGAGlCCAGCrCCATlTl T'GCAgccttgtatctctcttaaccttc148 catctccaccccttccatacattactcccacctccctacactccttagaa149 tttttctatggcctccagctttcacaagcactccctctacttaaggaacat150 ctttctccacctgggttagccttgtgaactgctaatctctttcaaaattcDOCKET NO. STFD-015-PCT PATENT APPLICATION151 aactgaagagagaccttctctcagattagccctgagcaggtgacctgaat152 ttacagagtacagagacaggtcactgggcctagagtacctaattattttt153 tattttatttatttatttttttgagacggagtctcgctctgtcgcccag154 gctggagtgcagtggtgcgatettggctcactgcaagctccgcctcccgg155 gttcacaccattctcctgcctcagcctcccgactagctgggactaaaggc156 gcccgccaccacgcctcgctaattttttgtattttagtagagacggggt157 ttcaccgtgttagccaggatggtctcgatctcctgacctcgtgatccgcc158 cacctcggcctcccaaagtgctgggattacaggcgtgagccaccgcgccc159 agccgagtgcctgtttattttacctgctttcagattctcttctaccctt160 ctaaattataagctgtttgatgttttatttgccctgtatttgggaggctc161 cgtccagtatctttacttagcaaatgcttaacaaacattttcagaataaa162 taaaAAAAAATACCTAATTGAAAGTCAATAATAGATCAGAGATGCTATCA 163 TAGACCAAAGACTAATACTGACTGCCACAACAGTAACTTTTACAACAGAA 164 ATCATAACTACAATTCTAAAGATTAGGGGTAGGTTTATTTGATTCTGTCA 165 CTGGCAGCTTTGCTAGTTGCCTTGAATAGCAGAATTAGCATTTGGTCTCA 166 CCAGAAGATGAGGAAGGAGAGGGATCAAGTTAGAGGTGGAGAGTTAACAT 167 TGGCAAGTGAAATTTAATGTGCAAAATAGCTGACCAAGGGCATAGTCCTT 168 TTTTAAAGGGGACACAAAGTGATTTTCTCTGCAGACATACACGCAATACC 169 AATCATAAAGGGTGacatttattgagcacttactaagtgccagacattgt170 acatggatcatcacatttaattattcccaagactctatgaactaggaact171 aatattatcccctactttgtaggtgcaaaaacttgagggcagagaggtca172 aggaactggcttatggcagtaagtggcagagctgtgacctaaactcagAT173 CCCATGTTTTTAACTGAACTATATGCAGATTATACTCCAGGAGTAAAGTC 174 ACTCAACGGAAGCAACAAGCGTGACAGGGAATGCTGGGATGGGGGAAGGT 175 AAAAGG AACTCCTta ga ctgggataagtgtgtacagacgtatgtataaga176 ctacacatggaaatattgtttaaagagtgaaaaataactaaaatcctcat177 taataggagtttggttaaactgtgctagagctttacaatgtagcacaaag178 cagacattaaggggaagacgtagacttctatataGTTACGTGGAAGGTGT179 TTGTGAAAATGCAGGTCACTGAAGAGTATGTGTGGTGAGATATCATGATC 180 CCATCTACATTGAATATATATGTATATAAATACGGGCTGAATTTTAAAAG 181 ACATAAATTGTGCTTGGTAGTTATCTCCTGGGATTGCAGAGGAGGAACAA 182 TGACACTTTATGCCATCTCCTCCTACTCTTCTGTATGGTGATGTGAATAT 183 ATTCATTTTATAGTTTTTAGAAATAATAAAACTGTACTAATTTTGAAAAA 184 CAGTAAACTCTGACATTGCCTATTAGCATTCTCGATATTCCTGTGCAATG 185 CATAAACATAACTTTTTAAAAGATATGTACACACATGTGTGAGTTTTCTT 186 TGTCAAATACTTTCTATAAATCTTTAAATCAAGCATGCCAAAAAGGTAAA 187 AGCTTTCCTGTTTCAGTGTAGGAGATAGTCGTCTGCAAAGGAAAGAGATG 188 TAGGGGATAGAAACAGGAATGAAAAAGATGACTGAGCTGTTCGAGGGACT189 TATGTTCCTAAGTGAGCTAATTGGAAATCTAATATGAACAGTGCAACCGADOCKET NO. STFD-015-PCT PATENT APPLICATION190 ATAACTATTGTAAAGCAGTATTTGTAAACAATAAAAGATGATTATCATAA 191 GTACCATTGTTGCAAAAACTATTTTATTGATCACATGCAGTGGTGATCTG 192 TAGGAATGATTGTTGTGATGTTTGCTGTAACATAAAATGAAACATGGGAA 193 GTGGCTGAGATCTTTAGGATGTGTGTGGTTCATTTTTTGAAAGCAAATGT 194 TGTCTCAGAAGCATCTGTGAGACTCTGCCAGGATCCACCGTTCTACAAAA 195 TATCTGTGATGGACATTGATAAGATTGATCTGTTGAGGAAAGGCAAGGTG 196 TCAGTAAGATAGTCTGAGAGCTTCTTGGATTTCATGTAAAAGAGTGCTGG 197 AAATAGAATTTCTTGGGGAACATTCCAACTAACTCATCACTGAAGGTGCT 198 TTACATTGAACCCTCAGCAAAGTTAGATTATCAGAAAAAAAATATAAACT 199 GCTGTggaggggacaggaaggaaagtcagggagggaggggggcaaggaga200 gaaagagcgagagagaggagagaaagagagagagagaggagagagagagC201 ACAAGTACACACTTCAATGCACATCTATAAATCATCCTGAAAACTACTGA 202 TAAATTATTTTAGCAATGTTCCTCAGATGTAACATTTCAAGAAATATCAT 203 TTTTGCTTTTTATTTGGCATAATTTACTAGCCAATTTAGGAAGTTCCCCT 204 CACATCAGTAACATACAGTACATCACCCAGTATGTCAGAGGACACAATGG 205 CATAAGTTTGCCTTTTGCAAGGTTTGAGGGATGGCCATTTCCCTACCTGA 206 CTCAGGAAAGTCTGTAGCTGATATCCATCTTCAAGTTTGTGGTTCTTTCT 207 CTCTATATATATATTTGAGCTCAGCAGTCATGCTGGAGTCCAGAGTAGGT 208 GATTCTTTCTGCTTTAGCTTGACTCCTCCTTAAGATTGTAACTCTCTCAG 209 TTTTACATTTTTTGTCAGACGTAAGCTGACATTCCACAAGGAGAGGAGGA 210 AATTCTGTGGTTCACATCCAGTGGTGCTTGGAACCTGATTGGTTGTCATT 211 CTTCCAGCTAGTTTGTCACGAGTGGATATCTGTCCTGGATTCCCAAGGAT 212 CAAGGCTGCCCCATTAGCCAGGAAGTAGGGAGATAGAGGAGGTCACTTGA 213 GAAAGAGCTGCTTCTTTGCCGCCTCCAGGTTGTGTCTGTTTCCTCTCATA 214 TCTGAAGACAGATGTGCTGGCAGAAGCAAAGTCCTTTGTCCGGCCACGTG 215 CAAATGCATGGGACATAAATATGAACAGAGATTCTTGTCCCACTCTAGAA 216 AATGTAGATGTTCATCTTGTTTCCAAGGGGACAGTAAGGCTGCAGGTGTT 217 TTTTGACTTCCTTGAGAGAAAGAGAAGATAGCAGCAATTGTATCAGGGCT 218 TACTATCCTAGGAGGGGTTCAGCCACCGAGATTTACATATTCAGTGCTGT 219 GGTTTTTGTTTCATTTTGCAAGAGGAACGAGCCCCTCAAGCTCTGTCTTA 220 GAGTTCCCTGCCCTCCCTGTCTACCTACTTGGCACCCAGCCCCTATGTTC 221 TCTTCTCGTATTAAGGCATAGAAATCATGGGCAACTACTGTTCAGGCTGG 222 CTCTGGATGAAGTTGTGAAATCGATGAGTTGGGGCTTAGTTTTGCAGACC 223 CCCAAATGCCCTGATAATCCTGGCTCgaaggggtgtccagcccctccaca224 cctgtgggtatttctcgtcaggtgggacgagagactgagaaaagaaataa225 gacacagagacaaagtatagagaaggaacagtgggcccaagggaccgtca226 ctcagcatacggaggacccgcgctggcaccggtctctgagtccctcagt227 atttattgattactattttcactacctcagcaaggggaatgcggcaggag228 a acagggtgata gtagggagaaggtcagca agaaa acatgtgagca aaggDOCKET NO. STFD-015-PCT PATENT APPLICATION229 aatctgtgtcacaagtaaattcaagggaaggtactatgcctggatgtgca230 cgtaggccagatttatgcttctctcacccaaacatctcagtgtagtaaag231 aacaacagagcagcattgccgccagcatatctcgcctccagccacagagc232 ggttttctcctatctcagaatagaacgaatgtacaatcaggttttacact233 gagacatgccgttcccaggggcatgcaggagacagagggcttcctcttat234 ctcaaccgcaagaggcctcctcttttactaatcctcctcagcgcagacc235 cttcacgggtgtcaggctgggggacggtcagatctttcccatcccgcaag236 gccatatctcaggctgtctcagtggggagaaaccttggacaatacccagt237 tttcctgggcagaggtccctgcggctttccgcagtgcactgtgcccctag238 ttaatcgagaatggagaatggcgatgacttttaccaagcatactgcctgt239 aaacatgttgttaacaaggcacattctgcacagccctagatcccttaaat240 cttgattccatacaacacatgtttctgtgagcacaaggttggggctaaag241 ttacagattaacagcatctcaaggcaaaacaattgttcaggatacagatc242 aaaatggagtttcttatgtcttccttttctacatagacaaagtaacagtc243 tgatctctcttttccctaTCCTGGCTGAGGCTAGAGCTCCAAGTCTAAGA244 AGGAGGATAGGAGGCGGACAGGCCAATGGAAACAATGAATGAACAACAGA 245 TGGAAACAAGGAATAGTGTGGATTTTTGAGTTCATTAGcgcgtcctccac 246 tctttcaaaacctcctttgcaatgacagaagaaatataaaaatgataatg247 aatttatttcgtggttggagaatcatgagaggtcctattagaagaaaaaa248 ctttgaagaacaccacagagatttaaaccatgtcattgaattcatagaga249 aactggaatttagaaacattttttccattgcaaaaacaggaggtgtcctt250 gaagcagccagttctagttttccccacagagccccagaaaagcCGTACTT251 CAGAGCTATCGGGCTGGGAATGGTGATAGGTGGACAGTGGAGAGTGGAAT 252 AACACCTGGGTCATCTCTCTGCTGGTTACAGACAGCTTGGCCCTCATGCT 253 TCAGGCCGTGGGAATAGAGATTGAAAGAAAAAGGGGGCAAGTTAATAGGC 254 ATTCAATAGTAATGGGATTTAAAAAACCCTCCCAAACCACTAGAAGGAAA 255 AGAAATAGACAAAAATAATAAACCAATCCAGCAAAGTTTAGGAAAAGTGA 256 ATAAAAAATTGAGGTAAGCACGATACATAAAAGTACAAATTAAGTTTGAA 257 GGACCAAGTCAAAATATACAGTCACAAACTATTGTGAATGTTAAATTATT 258 TAAAACTTTAAATAATTTATCTAAAAATAAAAATAAACCAAAAAGATGAC 259 TATGTATGTTTTCAAGGATATTTGATTCACTAGAGAAACAGTTCATTTGC 260 TTCCTATTTATGATGATTAAAAACTAGATTGCAAAAGTTAGATGTTAATG 261 TAAAGAAAACTTTATGAAAATGATAATGgatttttatctagtagaaaaga262 taaccccaatgcttatggttttattgctctgtaggacattaacaagttgt263 gcatcttatttagcaaacttattctaacattAGTAGAtgtgagtgtgtgt264 gtgtgcgtgtgtgtgtgtgtacgtatacatataggtgtgtgcaggtatgt265 gtatatgtatgtatgtaggtatatatgtatataCTAGCAAATGATAAAGT266 TGGTTCAAAGGACGATGTAcagtagtacctccttatccacaattttgctt267 tctggggtttcagttacctgtaggcaactgtagtctgaaaatattaaaaaDOCKET NO. STFD-015-PCT PATENT APPLICATION268 gaaatttctagaaataagaatttactcattttaaatgtgtgccttagta269 gcgtgatgacatatcatgcccttccgctccataccagcctgggactgaat270 catccctttgtccagcgtctccatgctgtctacacttaccctcctgttta271 gatgcttagtagccctcttggtcatcagattgactgtcatgatatcctag272 tgtttgtgctcaagtaactctattttactgaatgttctattttatac273 tagttattgttgttaacctcttactgtgactaattaatgcattttatcat274 aggtaagtgtgtataggaaaaaacatagcatatgtagggttgtgcaatag275 catccactgggggGAGAATTTTGCTGAAGttagaacagagaagactgtcc276 agaagaaagaatttctatacttgccaccttttctgtttggtgtcctc277 atgtaagtctcagtgttacgatctgtctccccacctCAATCACTGCCCTC278 TGTCTCTGGAAGGAAATTCCCCTTGGGCTGAGGCCAGCATGGTGCCAGAC 279 AGGAGAGATCCAGTACCCACTCTGGAAAATTTCATAAGATAACTGGTTCT 280 CCACCTTCTTCAGGGACCTTTTATCATATCTCATGTGCCCATGGCATTTG 281 TCACTGCCATCTGCACAACACTGAACTCCAGCAACATCAACTgagaagaa 282 agagagagagagggagaaagagaaagagagagagagaAAAGTCGTTTGTT283 GATTGAGCCACACAAAATTTTTTTTCTAATTAAATTATATATCCAGGTAG 284 CTGCAATATGCTACAATCCCAAATACACATATTTATTAAATATGATTCAA 285 AGAGCATTCATTGAGTACTCTGTATCAAGGCACAATGTAAAATAAGTGCA 286 AAATTACTGGTGATTGTTACGCCTTTCTGTGGGACTCGACTCTCTCTGGT 287 TGGAGGTACTGTGTGGGAGCACGTGAGCTCCAATCAGGTGGTCTGGAGGG 288 AGCAAAATGCAGCTGTTGGAGGTTAAATATGAAGGGAAATAGCAGTAGGC 289 ATCGGATAGCATAGAATGAAAATAAAAGTGCATATACTTCCAGTGCCTGT 290 TTTACAGATTCCTTGTCtttttttttttttttgaagacggagtctccctc291 tgtcgcccaggctggagtgcaatgctgtgatcttggctcactgcaacctc292 cgccttctgggttcaagcgattctcctgcctcagcctgctgagtagctga293 gattacaggtgcgcaccatcacgcccggctaatttttgtatttttagtag294 aggcggtgtttcactatgttggtaaggctggtctcgagctcctgacctcg295 tgatccacctgcctcagcctcccaaagtgctgggattacaggcatgagcc296 agtgcgcctggccTCCTTGTTTTTTAAAACTAGTTCAAACCCTCAACTCA 297 TAATTTGGGAAATTCAGGTCATAGGATGCCCTGTTATTTATAAGGTATCC 298 AGCAATGCATGGAACAGAATATTTAACTTTTAAAAAACTTATATTAGGTT 299 GTTGCAAAAGTAATTGCTGTCATtttctcctttcttttcttttctttc300 tttctttctttttctttctttctctttcttcttttctttctttttctttc301 tttctctttctttcctttctttcttttctttctctttcttttctttcctt302 tttctttcttgtctttctctttctttctctttctttttctttctttctct303 ttctttcctttctttcttttctttctttctctttctttcctcttcttt304 ctttcccctttctttctttctttctttcttgtctttctttctttcttctt305 tctttcttttttctttccttctctttccttcctttcctttccttcctt306 cctccctctctccctcccttccttccttttccttccttccttcccttccaDOCKET NO. STFD-015-PCT PATENT APPLICATION307 ttcccttcccttccccttccttccttccctccctccctcccttccttcct308 tctctctCtctttctttctttcttcctttctttctttctctttcctttct309 tcttcGTTGTTGTGTTCCAGAACGATTTAGTGTTACCTACAGTTCCCAG 310 AGAAAGAATCCTGTCTTGAGGGGTGGCTGGGGCAGGGCTACTACTCTCCC 311 TGCTCTGTGCTCTAGTGGCCAGGTGGATCAGCTCCAGCTGCCAGGCCAAA 312313 TAGTAAATATAAGATGCCTTCAGCTTTTAGTATATGCATAATCATAAATA 314 TAAATTTGTTTAAAACCTGAACTATTCTGATGTTCTCACTGGCTAGCCAA 315 ACTTAAAATGTGTATTTGGACTTGAATTTCCCACCAAGGGTGTTACTAGC 316 TTCTTTACTGTTGCAGCTGCCTTTTGTTTTGTTTTTGAAAGTTTAAaaaa 317 atacacaagggggcttttgcttcctgaaagatggagtagaattactttta318 cctatttctctcaagtaaagtaaaaaccccggacattgtacgtaaagcaa319 acttatgaagactctggaagctggagagaagaaggcagaccagttaggaa320 cattgggacccaaggagcgacccagcagtgcattccacggggtttctttt321 tgcctcatccattccagacttggttctggagaagtttgtcaacccagaaa322 caccaacaggcccagaaaaacataaagccctaataaaaagctggctctct323 ctagtcaaaggagaaagaaaggggaagcccagtaaaacaattcttaggca324 gtaacggctctgctccattcaaacaccCAActtctccttcctgagtggca325 agagaggaaattcgctgagatgagtttaaatgagatccaaagcctcataa326 cacaatactccaaagtccagatttcaaatgaaaaccacacatcccaacag327 gaaccaggggaaccaggaaaatctcagctttgatgagacagttaagaggc328 gctaatactgacatgacagagacgttagaattacctgacaagaatgttaa329 agctgccatcgtaagaacacatcaaactcaacaccaccatcaatgagtaa330 gatcataaatcaacatttctggaaaactccaaccagcaccagcagaattc331 gcattcttttcaagtgctcatggaacatataccaaaattgccatatactg332 ggccatgtaacaaacctcaacaaatttaatagaactgaaatcacatgaag333 tgtgttctctgaccacctggaatcaaactggaaatcgataatagaaaaat334 aatgggaaaaatgccaaacccltggaaacaaaacaacacacttctaaaca335 atccatgggagatttcaaggaaaataaaagattatatattgaatagaata336 aaactgaagatgtaacatattataatatcaaggatacagtaaaagcCCAA337 AGAAATGAAAACttatcccagaaaaatgaaaacttagcacaaaaacgtat338 acaatacacaactattcatagtggttttatttgtattaaaaaaaaactgg339 aatcagtcaaaatgtcctacaatagattaatggtaaaacaaactgcggta340 catccatcccatggaataattagtaataaaaagtagtgagttgggcacgg341 tggttcatacctacaatccatacctacatacctacagcactttgtgaagt342 agaggtgggagaatcgcttgacctaggagtttgagaccagcgtaggcaac343 atagtgagaccatgtctctaaaaaaaatttaaaaaaattagctgtgtgtt344 gtgtcccatgcctgtagtcctagctacttgggaggctgaggcaggaggaa345 gcttgagcccaggagttcgaggctgctagagagagttatgatctcgccacDOCKET NO. STFD-015-PCT PATENT APPLICATION346 tgcactccaccctgtgtgacagagtgagactctgtctctaaaaaaaatta347 aaaaaaaaatagtgagctgttgatacacatgacttgaatggatctgaggg348 gcattatgctgagtataaaggtcacatattgcatgattccatttacataa349 cgtttttgTCTTTTCAAAAATATTGCAAGGGGtactggttgcagggtgt350 gcgcatttttcaatttacaaattggcctcaaattcgtgtattaagtttca351 ttcccacatttgcaatgataagtcctccatggagttcctcactctacat352 cctctccaatacttgatattatcaggctttttaatttttttccactcaaa353 tggtcaatacgttgtattttatttttggtttaaaatacatattgtgttt354 tctgatcactcatgaggttgaccatttaaaaatgtttattggctattggg355 gtctcatctgttgtgaattgcctgtttttaaggtatgcccacttttttat356 tgagtttcttatttttttcactattgcataggagttttCAATCTTTCTTC357 CCTCCTCTTATTCTTTAATAACAGAATCCCAATTTTTTTACAGGGCAACA 358 GTGTCCCAGCCAAAAATCTAATTCCTCAGCTTCTTTGCAGTTAGGACTGT 359 TGAGACATCATCTGAAATCTATTGTGCATTTCTGGAAAAATTTTGCTTGA 360 TGGACAGAGGCACCACTGCTTATTTCTCCTTTGTGTTCTATCTTCTTCTA 361 Tctggaacttggcagaagcacccatcttgcaggatgaaagtcacaagcta362 gagtggaggagcaggcagggaaagga cctgggtcctgcagcagctgtcta363 gctctgaaccacctgcctccagaGTCCGCCTTGGTGAGAAAAATGTATCT364 CTTTATCTGATCAAGCTCCTCTAGTTAGATTTCAACTACATATAGCTGAG 365 TGAATACTGATGAATACTGAATAATGAAtgctggtacaactttctaatat366 cttctcttagagttctgcattgaagtttttaaataagtttagtctatacc367 tttcttttccattttcagtcttcaattttgacttcaagataattctagtc368 ctatgatgtgatttatgtttctaaataatggcatttaccctctttcacta369 ttccctggaaTTGGAAAAAATAGGttatttattatttatttattattt370 atttatttatttatttGGGTTTGGGTAAAACTTAACCATATGTTTAACAG371 G ACCtggactttgatttaagca aactta gggtaaagacagtttaaagaca372 atcaaggaaattggaatagaaaatgggtattggatattagggaattactc373 tcaattatgctgggaatcataatggaatggtggttgttttttaaaagтcc374 ttatcagttggcaacgtattaatgattggctgaaaaatactgccagtgtc375 tgtgtgtgaggaggtgagagaacagagtaattggatgaggggggaggcgg376 tagttgaaacaagattagcaaaatgttaatttgtgaagcttagggttcat377 tatactatttgtgtatattcatatttctataaacactaaaaatgaaaata378 aaGTGGTCTCGTGTTGCTGACTGTGACTGTCACACTCTGTCAGCAGATGG 379 CAGTGTTGTATAAACCATGAGCCTACATAGGCCTAATGGATCATTGTGCT 380 TGCTAAGTAACAAAATCAATGATACGATATAAACcaggtcagatttat 381 gcttttagacaaaagggcaaggtaagatttgcagagtaaagaacaggtac382 agagtaataataaatatTTTAAAAATTCTAAGTGATTCATTAAAGTCTT383 ATAGACAAGTTGGGTAGAAAAGTACGTAAAAACCCCATAAACCTATAAC384 TTACTAGAATTATAAAATCATTTGGtctctctctctctctcaaactctcCDOCKET NO. STFD-015-PCT PATENT APPLICATION385 CCTTATTTGCATTTTAAATCAGTATTTTCATACATATATATTTGCAAAAC 386 CTTATTGATTTCATTGATGAAAATGACTTGGAGTTTGCTTTAAAACCTTA 387 CACGATAAACATAAATATTATTCTGTAGTTCTTTTTACCCAACTTTTAAC 388 TGGCATAGTTTAATCTATGAAAACAGCTCCATATTTTAAAAGATTCTCTA 389 ACTATGACAACAGGCAACATTTCATAGATGATAAAATGTCTTATCAACTA 390 ATACCTAATATTTTAACTTAGGTTATGTACAGTAGCTTTAAGAACCAGTT 391 GTAGAATTTGATATATAGAAAATAATATAGACCCTGTCACTGGGCAAACT 392 TATGGTGGAATCATTTTTTGTGTTGTTGTGGACAAATTAGTTATTCTTTC 393 TGAACCCCTGTTTGGATATATATTTTTTAAAGCCCATAATTTGGGCATCC 394 TCATAAAGTAGTGACGTCTGAAATTAAACAATCAATGTAAGAGAGCTAGT 395 TTCCTTTCTCGGCAAGAGAATATGACTCTAAAATTTATGCCCAAGTTAGA 396 CTATTTTTATCTTGCCTCTTTCCCCTAGAATATTTGGGTTTaattaaaaa 397 tttacaatgaaattagaaaaataaaaataaaaatcgaaaatcaaaTGGAG398 ATAAAATAACAGTGGTAATCAAAATAGACCCCTATTTTGATCTAAAAAAG 399 Aaaagaaaaaaagataatttggacatcataaaattaaacttctgctcttc400 acatggcacgttaagaaaataaaaggcgccacacattgggagaacatatt401 cataaaacacaaatgtgagaaaaaaatcatatgcagaatatacaaagaac402 tctcacagtccatagtaacaacaccccaataaaaacttgaccaaaaattt403 gaaaggatatgtcatcaaagaaggtatatagTGAAGTTAAAATACTAGGC404 TCgagcaagtggaaccctcattcactgctgatgggagtgcaaaagagcac405 agcaactttggaaaacagtttggcagtttcttataaagttcaacatacac406 ctaccagatgactcagcagtcccaaagctaggaatttacccaagtgaaat407 gaaatcctgagttcacacaaaaacctgcattggaaagcttacagcaactt408 tattcttagcagctaaaaattagaaatgaccaaatggctttaaattgtta409 actagataaacaatctgtggcatatccacacaatggaatactactcaaca410 atagacagtgaactagtgctacacgaaacagcaaggatgaatctcaaatg411 cattctcctaagtgaacaagtgaacaaagccagactcaaaaggcttcaca412 ttgcatggctctatttacatgacattcaggaagaggcaaacgattggatc413 agacaaaaaccagtggttgccaagggctggggtgaaggaaggggcataaa414 ggaactttaaaggatgagggacttgtcctatatcttgaatgtggttgtgg415 ttacacagctatgcatttgccaaaacttatagaaatatacacgaaaaggt416 ggcttttattgtaatttatacctcagtaaacctcacttaaaaTAAGCAGT417 TTTTgattgaacataaaatctggttctgagcttcttggaaaccgactaaa418 tgaagataatgtgttatgttacataactttcatctaggggaaaaatttct419 agtttctacgtgtgactgaaggttttcctgggataaaagttgaagacaat420 ttctatcttggggcattgcataggagctgctaaatggataatATTGGGGG421 CACTGCATAGAAACGGCATTGGATAATACTCTCAGTAGTAATTTCATAGA 422 GAATAAAAAACAGAATTCGTATGATCTtttttttacttgtataaatttaa423 gcaatacaggtgcaattttgctacata gctata ctgtgtagtggtga agtDOCKET NO. STFD-015-PCT PATENT APPLICATION424 ctgggcttttagtgtatctatcgcctgaatcatgtatattgtatccattt425 agtattttctcatcactcaacctccttccacccttccacccatctcaatc426 tccagtgtttatcataccacactctatgtccatgtgtacacatcatttag427 ctcccactataagtgagaacatgtgacatttgaccttctgtttttgaat428 tatccacttaagataatggcctccagttccaaccacattgctgcaaaaga429 catgatttcattcttttctttatagctgaatagtatttcattgtggtatg430 tgtatacacacacacacacacacacacaccacgttttctttatccaatca431 tctgttgatggacacttgggttgattccatatctttgctattgtgaatag432 tgctgcaataaacaagtgagtgcagatatcttttttatataataatttat433 ttccctttgggtagatacccagttgtggtattgctgaaccacatggtagt434 tctatttctagttctttgagaaatctccatagtgttttccacagaagctg435 tactagtttacattcccactaataatgtgtaagtattcccttttctctgc436 atccttgccaacatgttattttttggtgttttaataataggcattctgac437 tgctgtaagataatatctcattgtggttttaacttgcgattctctagtga438 ttagtgatttgagcatttgttttttgtacgcttcttggccatttgtata439 ctgtattagtctgttcttatgctgctaataaagacatacccaagattggg440 taatttacaaagaaaaagtggtttaattgactcagttccatatggctgga441 gaggcctcacaatcatggcagaaggcaaaggagaagcaaaggcacatatt442 acatggaggcaggcaagagagtgtgtgcaggggaactcccctttataaaa443 tcatcagatctcataggacttattcagtatcatgagaacagcatgggaca444 aacctgcccccatgattcaattacctcccaccgggtctctcccatgatat445 gtggggattattacaatttagggtgagatctgggtggagacacagagcca446 aaccatatcatataccttctttgaaaaatgtctattcatgtcctttgcc447 cacttttttggtggggttattttgctgttgttgttgaattgtttgagttc448 cttctaaattctggacattatttccctgtaggatgcatagtttgcaaata449 ttttcacccattctgcagattatctgttcactctattgattatttctctt450 gctgttcagaagcgttctagttaattaagtcctgtttgtctatttttgt451 tttggtgcttgtgcttttgatatcttagtcctgagttcttcacctagatt452 aattccagaagcattttccctaggttttcttctagtgtttttgtagttac453 aggtcttatatgtaagtctttaatctgtctgagttaacttttgtatttg454 gtgagagatagaggtctagttccattcttctgcatatggcaattcaattt455 ccccagtactgtctattgaaaaggatccatatgactatttcttgtataaa456 tgttgaatgtgaatagagaacatcagatggcaaagctggtatgtggcttt457 aCCATCTGTAAACAGATGGTGGACTGTCCATCTGGTGGTCTCAGAGGGTG 458 GCCTCCTAGGTATTCACCTTGATGAAGTTAGCAGAGCTGAGGCCACACTT 459 TTAGACTTGTGTGCTCACAAACCCTTGGATGCAAATTCAGAGCTGGATAG 460 ATTCATTCTATTGCA. AACCA. ACATGTTGATTTATTCATCTGTGCCTAGAA 461 ATCT. AACCATTCTGTAAACTTGATGACAGCATCCTCTGGCCAGCATGTTT462 CTTCCTAGTTggaggcgtggtgtgtttgatggagcatcaacttagacacaDOCKET NO. STFD-015-PCT PATENT APPLICATION463 gaattagaatcttaactctgcatctatgaactgggtgtgacattaggta464 aattacttiactttccccaagcctcaaatttctcatctgaaatgtggaaa465 taataacgtttctcttataaacttgctgtgagga gtaaataaaatagtgt466 ttatgaattacttagcatagtccctgggcatgtaatttcttagtaagtac467 taattttTGTTGGTTAGATCCAGTTACAGGGGAAGCAAATTTACAGATAT 468 GTGGTTCATGAGCAACAGATTTTCTGGATTATTGTCTTACACACAGTAAC 469 CAGACTGATCTTTAAAAATCACAAACAAGAAACAAATCAAATTATTCCCC 470 TGCTTAAACTCTCTGGAGGTTTCTTATTGCACTTAGAAACTCATTGTCAT 471 GATCCCTAGGCCAACACCTgtggttcccacccttggctggtgtgcataga472 atcttctggagaactttgaaaactactggtgcccaaattgatgcctagag473 attccgaagagtctggtccatgtggggactgggcactgtgacttttatta474 gctctctagttgttccagtataATCTTGCCCTGACCCCTCCCTCCTGTC475 TGTGTTTCTTATTGGGCCTTCTCTCCTTCCCTGCTCCTATGACTGGGACC 476 TCCCTTCTAATCTTTGAATGTGCTGAGCTCTTCCTTCAGGACCGAAAGCC 477 TCTTCATTACTGAGCCAGGTGCTACCACCCCTTCTATGTCAAGCTCACAT 478 TCCATCTTCGTTATGACTCTGGCCTCTGGTCAGAACTTGGGGTGCTCTTT 479 CCCTTCAGGAAGTTGGGACTTGGAGGGCTGGGACTTCACCATCAGAGTCT 480 TTTGTGCCTGGTTGTAGTTGGAATCTCGTGCATTTTCATGTAGAGGTTAC 481 ACTGTTTGCAGGGCCCATCTGGTCTTCACAGTGAAGAGAGAAGTCTTAGC 482 TGTTCAAAAGTCATGTTGCTTGCTATTGGAGCCCCTGATATGTggcccag 483 attatggtaaggcgagtgagtgaggcattgccttggtcataaattttaag484 gaggtcccgcaaactcagtagtcaagataaataatattttaatgcaatat485 ttaaacaatcaaaattaatgcaaaaaatccatgatgaaaaaaaaatcaga486 attCAGGTCAATTCCAGGTTGATTTAGTGAATAAAGAGATATCAATAGGG 487 ACTGCTTTAtttttttatatttatttacttaatttttttttttaagat488 ggaagtctcgctctgttgcccaggctggagtgcactggcacaatcttggc489 tcactacaacctccacctcctgggttcaagtgattctcctgcctcagcct490 cccaagtagctgggattacaactgcctgccacaactcctgaataatttтg491 tatttttaatagggacggggtttcaccatgttggccaggctggtcttgaa492 ctcctgagctcaagtaatccacccgccttggcctcccaaagtgctgggat493 tacaggtgtaagccaacacgcccagtcACGGACTGTTTTATATTTGTGGT494 TAAGGGGGATTTAAGGGATAATTTGAGTCTGTTCTGCTTTCTTGGGTTGT 495 GTTTCTCAAACTGGCTTATGGGGATTTCCAGCGATGTAAATTTTGTGATG 496 AAAATATTTTATAGTAAAGCACACATGGCCATATTGTGGAAAGAAATGCC 497 AAAATTTTATGAAACTTTAAAATAAATCAAGCTCaactactggagaagct 498 gaggtaggaggatcgcttgagcccgggagttggaggttacagtgagccat499 gCATTCGAAAGCAGAACAGAATCGAATTATCCCTCGAATGCGCTACAGCC 500 ACAATATAAAACAGTCATTACTGATATCTCTTTATTCACTAGATAGATCC501 TGAATTgtctcgctctgtctcccaggctggagtgcagtgcgagaccttgtDOCKET NO. STFD-015-PCT PATENT APPLICATION502 ctcTAaaacaaataaataaataaatacaaacaaaaacaaGCTCAAGACTT503 TGAAGAAATGATACCCCGGAGCTTTCAGACCAGAGACTCCCGAGTTACAC 504 ACATTTTCTTCTTTCTGCCACTAGGTGGAGGCAGTGGAGCAGGTTGAGAA 505 TCACTGTCATAAAGCTTGTAATTAAAGAACATCAGAGTGCCAGACAGTGG 506 AGCTGCTATAAAGTGCAGAATAACTACTCCTGTCCTATACTTGGTCGCGT 507 ATGAGCGGGAAGTGAATGGAAGGGAGGCTCGAAACAATGGGAAGAGCCGT 508 AAGAATCAGGTCTGATAAACTTACATAAACGGCCTTGCACACAACTTTTC 509 TGGCTGAACCTGCACTTCCCATAAGTCAAATGCAAATGTTGGAAGGAATA 510 TCTTGCGAGGTTCTTTCTAGCTTGTACAGCCTGAGCTATTTTAAAGGAGA 511 AAAGCTGACGAGCAATCGTCCTTGGAATTTGCAGTGCATAAACTTGACCA 512 GCAAAGGGCAGCAGTGCACACACCTTTTAAAAAGTAACTTTCCAAATTTT 513 CTACTGCCATGAGAGAGTTCTGATTCTACAAATAGGAGACAGTGTTTGGA 514 CCACTTAATAACAACCAACCATAAAAGTAAATTTTCTTTTTATTAAACCT 515 TTTAATTTTACATTTGTAAACAGAAAAgaaatccttattttgttggctct516 gggacatcactttcttggttcaactccttcctcctgaccactgcttctaa517 gtctcctgtgctgttttcttctcatctcttcgacctctacttgttgggtt518 acctgccaggtcccagcctgccttcattgatttaactcattgctagtaac519 ctcgccctgtttcccaaatttgcatctccacccggactatttcccgaact520 ccagaatcacgcatattcatccacctgtccaagggatattgccaattaga521 ggtctagcaggcatctcaaatgtctaatatgttcaactctaatccctgat522 tcccgcctgccttccccatctcagaaaatgtccttccaaattctctagtt523 gctcaggttaaacacttgcaaccaccttgatttcacgtttctcccacgcc524 tcacatccaatatgtaacaaattctattttttctacctttgaaacatga525 ccagaatctgacacttttcaccacagttgccactgAGCCTCTTGACTATT526 ATCAAGAAAGGAGATGTGTTCTGTTTTGTAAAGATTATTAAAAGATGTTA 527 AATTGGGACTTTTTTTGTATTTGTTTTGTAAGGTATCTCAAAGGCCAAGA 528 ATAATATAATGGATATTGTGTTCTCTAATGGAACAATTCATTTTCTCTCC 529 TCCTCCACTGCATTTTTGGGGATGGTGGAAGTATTGGAGGATTTTCAGAA 530 TAAGAAACAATTTTATTGCTGTTCACCAGATGTCAGGAGGGTATGGTGTG 531 GTGGGCCTGGGAGTGGACTGTTTAACCCTAGAACTTAGAAACCAGTGTCC 532 CTGTGGAGCACAAACCCTAATAGGTCTTGGTGAGTAACAGAATAGATAAA 533 AGAGAGCTCAGTCTGGTCATAAATCCTTTGGCCAGTTGCCATTCATTGCC 534 ATGAGAAATTCCCCAAGAAGACACCCACCTCTTTTTCAGGCAATTCTGTT 535 TACTAGATTCTGGAGGATTCGTTATCATCGAAGAACCCTGCCTTCTAGTC 536 AGATGGtgcattagtcagaattctttttgcaagtaacataagtcagctgt537 aacacatacaagtagaaaaggaattagaaaaagaaaagtagttatactaa538 tgtgaaagaaaaaataaacctcaggaccccaaaaatcactaagccaaaag539 ggaaagtcaagctgggaattgcatcaggcaaacctgcctcccattttatt540 cctaaataagatagctacaaagaaaaaaaagctacatacctccctcacaaDOCKET NO. STFD-015-PCT PATENT APPLICATION541 tttgcccacaaggtaattccttgtggacaaagaaaggacagagctcaaag542 tcatccctctgttcacttcagacaaatgcatatgcaatgcttcttctgcc543 ctactgtttcaataagccagactaaggcataaatgactatttctctacct544 gcctttcacatgtgaaaggctgatcagagactcaaaacaatgcaacccca545 gcaggaagcccccttccctgccttgagttgtcacacctttccagaccaaa546 gcgatgcacatcttctacatatcgattgatgtttcttgtctccctaaaat547 gtataacaccaagctgtgccccgacccccttgggcacatatatcaggacc548 tctggagactttatcatgggcttgtccttaatcttgggaaaataaacttt549 ctaaattaattgagatctgtctcatactttgagttcacactaggttgttc550 acaaagacacaaggaaggctatagatccaggatggggctatgcaggtgga551 aaatgtacctttgatcatgtcaccaaaccagtccagggaTACGCCCAAAA552 CATGCTTGGCAGCATGAGGCTGCAGTGTGCACTGATGACATTAGTGCTTA 553 TGGACTTGGTCTCACTGCTAGTGAGAGTCATTTTCTTGATTATTTTTCTC 554 AAATTTGGGTGAGGTGAATGTGTAGCTCCACAAGATGGTGTAGAGGGGGC 555 AATGTGAAGCCATGTAACCTTATTGAACATCTTTTTGGAGTGTCCATTTT 556 ACTTGAATGGTTCATGGAAAAAAATTATATTAAAATTTATACACACATAA 557 AAGGCACAAGTTGTAGTATTTACTACGAGAAGAAAACATGATTTAAGAGA 558 TAAGCTTCAAACTGCACAAATAGCAGTAGGGGAGACGAAGATAGTTATTC 559 ACTTCCCTCTGCTGCTTATTGTGAACCATGAGAAGCCCCATCTTAAAGCG 560 TCTGAGGAAGTACATGGACTTATAATAGCAAATCTATGCATATATCTTAT 561 TTTAGCCTTTTCTGCTAGACTTTGGGTtggagaagtgatgtgagaagtg562 taaagagcacaaaattaggagtcaaaaggcctggttttagcctcagctct563 gccacgaactaagtgacctgggttaagatatttctatctgtgccctctaa564 gatatttccttacatcaaagaatgcaatagataatttctaaggttctttt565 tggctttTAGTCTCTAGGTCATTGGAATGGAGACGTTAGGCGAGCATTCT 566 TCTTTGGAGCTGTAGAACATTAGTTTGATCACCAGAAGGCACAGGATCCC 567 ATGGTGATATAGGATTATAGGAAATGAACAAAACACAGtcttctctcatg 568 cacttctctcacagtcttctctcacttctctctctctttctgtttтgtg569 tatttatattttcCATAatagggtaggttataccactgccccaaatctca570 tggcctagctccaacaaatgctatatcttgctcatgctacaatcttcac571 cagggccagaaaggtgctctgctccatgcagccactcaaggatccaggca572 gacagaggctctaccatctTGTATTTGCACCATTTGGAGCACATGGCCTC 573 TTAAGTTGCTTATACAGATAAAGGATAGACTGGAAAATTCCGTAAGATCT 574 TTTTCCTGCCTCAGCCTGCAAAGGATGTATGTATGCCTATTTCTTTGGCC 575 ATAGCATTTGT. AAGGAGACTGGGACATATAGGTGAGCAAATGGAACATAT 576 ACAAAGTAATAATGTCTCTAAGATAAATATTTACAATTCACAAATGTACA 577 AAGAATTTTATAGATGCATCCATAATTCACATTTTGTGTCATTATCACCA 578 TTTTCTCCTAAATTACATAAAACTTATTTTATTTATTGACATGTGCTTCA579 TATTTATCATTTATCACTGCCTGCTAATTTTCATCAGGAGCATCAATGGCDOCKET NO. STFD-015-PCT PATENT APPLICATION580 TATTCAATATCCTATTTATGTACCATAGTTTATAAATGTATTGACATTTA 581 AGTGATAATTTATTATGGTTTTTTGCTATTATAACTTATTGAATTGATGA 582 AATGACATACTTTTATTAACTGATTTTTCTAATATTAATTTCTAGTTCCA 583 TGAGGCTTTCCACTTTGGATGGTAAAAAGGGAGATAGCATTTCTACTTAT 584 ATGCATAAATTAATTCTAGGTAGTGAATTTTATTTATCTGGGAATAATTT 585 TTAGATATGGCAACTCTCATTCATTTTGACAAGAAAAATCTAAAGCTCAT 586 AAACCCTGAATCCTATATGCTTACTCTCACAAAAATCTCTAATGTCCTGC 587 TGGGATTTATCCACAGTTTAGATTAGACCTGGAATACATATGGTCATGCA 588 ACAATGATCTTAGAACAGGACTTTAACTTGGCTTTAGGAACTGAGGCTGA 589 GAGTAATAGAATTGATTTTTTTGTGTGTGTGTGAAGCTCCTATTATAATA 590 ATGAGAATACTTTGATTCACTCAGTTAAAGTTTTCCCCTGATTTATTGTG 591 TACATACAATGAAGGATCAAGAAAGAGAAATTTTTAAATGGAAGCATTAG 592 CCAGACAAGTTTGACCTCACAGTTTTACTAGGGGATATATCACCTAGTTT 593 TGGATCTATTTCTAACATCTTAACATTGTGAAAAGAGTCTTGGGAAACTG 594 GTTAAATCCCAAAGAATGCTGCAATAGGAGGTTGGCCCTTATGAGTTATT 595 TAATATCTTGAGCTGCCTTCGGAAAATGTTGCTGAGCAGGCATTGAAGAG 596 TATCGATAAAATTTATTGAGAATTTGTTTATTATGATTAACAGAGGTAAA 597 AGCCAGTATATTACTGATTAATATAGGTAAAAGGCAGTTAAGAAATTGGG 598 AATGCTTTCTCTTCTGCTTTCTTCTACGATGCACAAGGCGTTTCACATTT 599 ATGCCCCTATGAAAATTACTAGGCTGTCCTAGTCATTAGATCTTTCAGCA 600 GTTTGTAGTTTTAGAGCTTCTAAGTTGACTTCTGTCTTTTCTATTCATAC 601 AATTACACATTCTGTGATGATATTTTTGGCTCTTGATTTACATTGGGTAC 602 TTTCACAACCCACTGCTCATGAAATTTG603 TCRy Platcau2 >chr7:37884197-37887670604 ATGAGAATAAAGTGCATTGTATGCCCTCATGATAGTATATTATGTATTGT 605 GTACATAACCAGTAATCTACCAGTTTAAAACTTATTATGTAACTGTTTTT 606 ATTTAGATGATGTTTTGCGTATTATTAAAGATGAAGACTTCAAAATACTG 607 GAGCAAAGACAAGTAGTATTATCGGAAAAAGAAGCACAAGCACTGTGCAA 608 GGAATATGAAAATGAAGACTATTTTAATAAACTTATAGAAAACATGACCA 609 GGTAGAATCCAGGTTGAGAAAATTCAGTCTGATTTATTTTTGAATCATGT 610 AAACTTTCTCTTAAGTCTGGTTTCTATTTAAGCTGCCAAACTCCTCAAGT 611 CTGTAAACATGTTCTGAGTTTACTTCTCTACCAGTCCTGCTCCCATCCCA 612 ATCCTCTGCTCACCTGCCTGTCTTCTCTAGTCTTCCTGGAATGTTACTGG 613 AATAGTAGGAAGGTCTCAGAGGAAGTTACTGGAGTCCCATTGAGTTGAAC 614 ACCAGAAGTCCAGGGTGTACAATACTATGAAGTTTAAGCAGAGAACTGAC 615 TGACTCTGAAGAGCTTTTGTAATCTTATAGTTAACTAGTTCTAGGAAAGA 616 ATGAGTTGCTAGAAATGTGCTGGGTTTCTTTCTAGAAGAATGACTGAAAT 617 AGCAATTGAGGCTGAAATCCTGCAAGGGCATATAAACCAGCAGGACCATG618 GGAACAATGAAAGAAACATCTACAAGAATCATGGCACTCCCCTTCCCTTCDOCKET NO. STFD-015-PCT PATENT APPLICATION619 CTTTCCCTGCTTCTATTCTTTTATAGATATGCTCTTGAAAACATATCAAC 620 GGAAAAAAATCACAGACCTCTGTTAAAAGATTATTTTACATGTTACATGT 621 TTTTGATCTATTTAACAATATGCATTTGTATTGCCTATACATAATTAGCT 622 ACTGAGCTACACTTCTTATTACCTCTTCTTTGTTTTCTTTTCTAATAGTG 623 GTCCATCTCTAGCCCTTGTTTTATTGAGAGACAATGGCTTGCAATACTGG 624 AAACAATTACTGGGACCAAGAACTGTTGAAGAAGCCATTGAATATTTTCC 625 AGAGAGGTAGGATTCATACCATGGGTCACTATCTGTTTTCGTGGGCTCCA 626 TTTTAAACACCTTTTTAGATGTAGAGTATTGGAACCACAGCTCTAGTCCA 627 AGGGAGCTTCTCAGGAAAGCTACCTTTCCTGGGGACGGAGTGGACTGCTT 628 ATGACTGGAGGTCCAACCCAGTGACAGCCTGAGGATGGCCAAAGATTTTC 629 AAGAAACCACTGTGAGGTGCTAGGCTTGGGGCTGGGAGCTAAGAGGTGTA 630 TATTTCAGTCAACAGGTCATCTCTTGGGAGAAATATCCACCCTACCCGCT 631 ATTTAGGAGAAATTCCTTTGAGAAGGTTATGGTGGCAGCTGTAGCTTCTT 632 TAACTGATCATGAGTTTTAAGACAATGATGACTAATTGAATATGTACTCT 633 ACAATTCAGGGGGAACATTTATTGACTTAGCTTACTGATTAATCTTAGAA 634 GTCAGCTAAACTTTGTAATCAACTTGACCCCTGGCATATTACCTGGCACA 635 TAGGGGGAACTCTTTCAATATTTTCTGAGCTTACCTGCTAGGCTTAGTAT 636 CATCTGCAGGATAGAAATAGTATCTCACGCATCTCCATATTTGGCATGAA 637 GCTGATGGAAACAAATTGAATTTCAATTCCCTTGAATTCTTCTTGCTGAT 638 TTTAGGGTAGGATTCAATTCAAAGGAAGAAAGGACACCCCTCATACTCCC 639 TTCAGGTGTGCAAGAATATAGATGCTCTTTAAGGTACTGCAAACATGACA 640 TACATGTTGACACAATAAATAACAATAGTTATGAAGCCTCACTTACATGA 641 AAGCTGAAGTGCTTTCTTTTGGGTGGGATACACTTAAATCTGACTTGTGT 642 TGCATTAACATGTATTGCCCCTTAGTTAGCCCTACTCAATTATGTCTTTG 643 CTTATGTGCCAATGACTGTGAAGGATAATAAGCATAGAACCTCTGCAAGT 644 GGTGTGAGCAGAGTGCCATGGAATCATTTAATAAAATGTGGCATAGAGTG 645 CAATGCATGCTACCAGAGAGAGGGATTGCTATCAACACAAGGCCTGTGCC 646 AGTAGGCACACTGGTCTAGACACTGTGGCACCAAGTGTGGAGGCTCTCAG 647 TTACTGCCCCATCTCCACCCCACTATCATACTGAAAATTGCCCCATGTTC 648 ACAATTAATCTTAATCTTTATTTCTAATTGATCCCCACTTTTCCACTTTC 649 CTTGGCTCCACCCACCACTTACGGTTGCTTTAGGAATAACTCTTCAAATG 650 GAACTTCACCCCTTTCCTGTGCCTGAATATCAGATTCTATGCTGGCATTG 651 TTTTACCCAAAATATGATAATTTGCATAGAAGAGAAGCACAGCAACCCCT 652 CGTTGTTACCTGTTACTCCCTCTATCCCACAATTCCTCCCCGGACATTTT 653 CCAATAATCATGTTTAACAGCAT. AACAGGGGTTGGGAGAATGCTCTGCAT 654 TGAGTAGAGTAAGTGCTCAGGATGACTCAGGCTGTTTCATTCAATCATTG 655 TCCAAATCCCTAACCCCTGGCAATCACAGAGTCCAAGGGACTAGGGCTGA 656 AGGTATCTCCAAATTAGAGGTGTGGGAACAGCCAAGGGCAGAATGGAAAG657 GTCAAGGTGATAAGGCaaaaaaaaaacaaaaacaaacaa acaaaaCCCTGDOCKET NO. STFD-015-PCT PATENT APPLICATION658 AATGAGTCATTGAGACTAGAGAGAAAAGAAGAGGATCTGGAAGCTGGGGA 659 CAGAAAACCAAGTTTCCAGTGATGTGGAGAATCCACATCAGTGTTAGCAG 660 GAAGGAACATTATTCACCACAGCTGGAATTTGTTGGGTTGATTGCCCTGG 661 ACTGTTTAAAGGGAAAAAAGTGAAATGAGCAGTGAGCATTATTTGCTACT 662 GAAATATGCATAGATAGATAGAAAAACAGATAAAAAGGACAACTGAAAAA 663 ATACCAAAGAGCAACAACTGATTCAAGAGATGCATGCTTATTTATAGGAA 664 AGAAAGCATAACAATAAACTGTCTAATGTGGATGGTCTGGTATTATCAGC 665 ATCACTCCTGCCTCTTCCCACAAAGCTGTCCTGTCTACTTCTCTTTTATT 666 GCTGTTGTTGCTCACCTGGAGGTTTCCCTTCAGTATCTTCTGGATTTAAT 667 GTTTATAATTTTATATCTTTGGTCTAGAGTCAAATGCCATGTAATGCTTG 668 ATAATGTGAAGCATTATCACATGGTGAAAGCCACAGAAGaaaatttattt 669 agagttcaatacacacaccatatatttcaaaggcatcatctgattgcatc670 tgcaaaatcaccttctgaaacaggttttattgttgtatttatatttgaga671 caactaaagcacaaagaagttaagcagctccctaatatcacacagctagc672 aagtagtgcaacaaggattctaccctctgagctttttcactgcaCAGGGC673 ATCtatatcagtctgttctcatgc674 TCRy Plateau 1 >ehr7:38231857-38233162675 aACTTCTATCTGTGCTTGTTCTAAGAGTGGATCAGATCTCAACAGTGCAA 676 CAGGGAGGCTTGCTGGGAGGCTGGAGTCTAACCAGGATGAGCGTCTCATA 677 GTGGAGAAGGGGCAAGGAAAGTCTCAAATGTCTGGCCTTGAGACTAAAAC 678 CTTAGAACTCAATGGTGTTATGGGAGTGAGAATCTCCTGTTTCAGGATTG 679 GAGTTGCATATACACCAACCTCATAGATGATGCTTAAGTTGCCAATCAGG 680 TTGTTAATTTAACCTGAGAAGGAGCTCTCACCCAGACATGCTGGGGGAAC 681 CGGTAGGATGTTGCCAATCCTCAGAGGAAGCCAAGTCTGGCTCAGAAGTC 682 TTACCTCTCTAAGCACAGACCAAGCGGAATGAGGTATAGTATTTGAATAT 683 GCTAGGAAGTCAGACTGTGGGAGCCTACAGTGATTATCTCAACGATTGAG 684 TTATATATTCTCCTGGGACTGCATAGATTCAGCCCAGGGGCATGGGCACC 685 CACTCTGCCATGTTTCGGTGGGGTAGGAGTGGAGACATTTGTCCTTTATG 686 CTCACATTGCTGAGCAATCCTCTGATGGACCCTTATCACTCATTTATCTG 687 ATGTTATTGTCCTCTAGTAATCCTTGGTCTGGTTGATGCTGAAATCATTT 688 TGTCTCTGTAGAGGGACTTGATGTGATTCCATTTATGACATTTGTTACAC 689 AGTTGAACTCAGGGCTTCTATATCCCTGGTTTCCTGTGGAGAAAGAAGCA 690 CATCACTGTTGCCCACATCTGTGATCTACCTGTGCTAATAGGTTCATGAG 691 TCTTGTGTCACCCTGTTTACACTGAGGAAATGAAACCAAAGGTATTAGTG 692 TCTCTGAATCAGGTGCCTCTGGAAGGTACAGATACTGGGTGGAATGTTAG 693 GATCATCTCCGTGCTGCAAGATGTCCTCTGGTCTTCAGGACAGTGTCATG 694 GGAGTGGACCGAAGGTGCCATGTCTGAACAGTCCTGGGCATCAGATTCCC 695 AACTCACCTGGTAGCTAATGAACCTTGAATATCAAATGCAGGGAGCCCCA696 CCTACCCACAGGGTGGAGAGTGTGTTTGATAGTAATCTTGTATGTGTGAADOCKET NO. STFD-015-PCT PATENT APPLICATION697 GATGGATATTTTATTTCCATTAGCTGTGGGCTCTTGAAAGTGAGCAAAGT 698 TGGTTGTGGTTTAACTGTCCTCGTTTTGTCTTACAACACCCTAGCCACCC 699 CATGCACAGCCCCAACCAGTAGGGGCCGGTTTGACTTTGAGCATTTTCCA 700 TGAATCAACCACATTTGCCAGAGCACGTAAACAAAAGAAGCCTGAG. AAAA 701 TAAAAc702 TCRγ_LMR >chr7:38276318-38291616703 TCACACCGGTCTAAGCTTCTACAAAAATCTCAGCCTTCTGATCCTCGGGA 704 CACGACTAGCAATCCAACAACTTTGAACTAGCAATTTCATCTTCTGGCTT 705 TTTTGGAAGTCCTTGAATATAGGTTTTGTGACATGTGATAGTTTGTAATT 706 TTTCCTCATAAATTGCCTGTTTTCTTCTAAGGCAGTAATTCTTGAAAAGC 707 ACCAACAGAAAAGGGAAATGGAAAAAAAAAAGCAGGAAGAGAAAACAGCA 708 GGTTTAATGGGTCAACCCACTGCTTTTCTAAATTACCAGG. AAAAGTATTC 709 AGAGAATTGTCTTTTTTTTTTCCAGGGGTTCAATTGTGTTGAAACTGCTT 710 TGAGATTACATCAAAGGAAAAGCCCTTCTGTTCCCACAAACACCAGAGCC 711 TCTCTGCTAGCAATTTGGGAAGATACTTCTGAAAGGAGGAAGCTCTTTAG 712 TAACTGAAAATGCAAATGTGTCAATGCAGATATACTTGAGAAATTTGAAC 713 AACGGTCTCCACTTTCAAAAAGCCACTTTTATCATTTGGCAACATGATGC 714 TTTACCAAGGCAATGCCAAATGAAAAAATGTGTTCTGCAATGACTTATTA 715 TTTCTCCTGGAATAATAGAAGAAATTTGTAGAATTCTATCTCCCATGAAA 716 TAATACATTCTTTAATTATACTGAGGCATGACCAAAAAAAACAAATCCAG 717 TTATCTAATATGTTGAAAAATCTGCCATCTTAAGCCGGGGTCAGCTGTGT 718 GATCTCCTGAGTACAGATGAGGTGTTCACTTGCAAGGGCTGAGGAGGACA 719 AGCCTTGACAACCTCCATGTCCACTCCAGATCCACCCTGCTCCAGCCTAA 720 GTCCCCTGAGTCCTCATTCAGGAAGATATGAATGAGGTCACAGAGGGTAC 721 CTGTCCATACACAGCAGCTCACAGCCCCCAATTCAATGGAGAGGACAATG 722 GGGCTGGGTGAAAATTATGTTTGGAAAGGGTTTCTTCTTAATAGAAAATT 723 CAAAATTATTATGTGGCGCTGTCAATGACCCTTTACACCTGTGATAGATG 724 GAATGACGCCCGCTCAATCTCTTCTTGTCCTCTGGCCTTCCTTATTTCAG 725 GACCATGAGGCGAAGCATCAGAAGTCTTAGCAGCTGTCAATATTTCAAGA 726 GCCATGAAGGATTTAACTAATAAAATGTGGA. AAAGTAATGAATTATAAAA 727 TCTTTTATtaaatttaccaaaaaaatacaagaatgatatgaagaacacag728 tgtttagttttcctaagggcataaaataaaacctaaataaatggagaaac729 atacattgatgaataaaaagctcctatcataaagaggccaatacatccta730 aattcatctataaatttccagcaattccagtcagaattactacgacatgt731 tgttgttgttctaggctgtgaggtttaatgttgggctagataagttgatt732 ttaaattctacaggagtgaataaatatgagatgattgaaaaagattttct733 gaaaaatggtacagtgaatagacatttggcatagtagatcttaattttta734 tcacaaagctactgagataatatgataatgatgtaagaataatgaaacag735 acaaataaaacagaaATTCTCCAGAAAATGTGTCAAATATGTGTGCATATDOCKET NO. STFD-015-PCT PATENT APPLICATION736 TTAAAACACGCTGCAGCATTTTTAAATTGAAAGGAAATGATGGATTGTTT 737 GGAAACGGGCATTAGGAAAATAATTACCTTAGAAAATAAAAATACCACTC 738 TACCTCATCCCAGATAACACAGGGTCCAAATAGATTAAAATTAAAATTAC 739 AAAGCAACACGTGGCCAGAAGGAACATATTGGAGATTTATTGTATCCATT 740 GAGTAAAGGGGCATGGGATGGAAATGGGGTAGGAGAAACTTAACACATTA 741 ATTTTTAGGAAGTAAGCATGTGG AAAATTTTCTATTTTT AT AGTATTTTC 742 AAATAAATGTTTTTGAAAGAATAGACAATGAGGACTTGCTAAAAAATTTA 743 GAGAGGAAAGTGACATGATCACATTTGCACTGGAGAAAGATAGATGTGCA 744 AGCAGAAAGGAAGGGGCGCTCCCCAGGACAGCAATTTGGCTGAAGCAGAT 745 GGTTTTATAGGTGGTCGCCATAATCCAATAAGAGGCAACCAGGACCTGAA 746 TTGTTGCAGTGATGGTGGAGATGGACAGAGTGGCTGCAGCAATAAACATT 747 AACAAGTTTACTCGAGCTTTTAAAGGATTCTTATGAAATAAATTATTATC 748 TCAGGAAGTTGGGAATGAAgaaaaagacactttaaaattggaaaacccag749 gttcagattccagttcttccactcctggtgatgtgcccttgggcacacac750 acttctcagagcctgggtttcctcatcttttaaatggagagaattagacc751 tatttcccaggacttttgtACGATATTTATAATCGAGCATGGGACACAGT752 AGGGGCTAAAAACTGTTTAATTTTCTCTTATCATTTATGTAATAATTCAG 753 ACAGAGAGACTTCACTTCATAAGGTAGAATGGAAAGATCTTATTTCTGTG 754 TCTTTTTATCTGAAAATAATAAGTTATTGTTACTTCGTACTGTCAATTAC 755 CCTTTGCACCTGTCATAGATGGGATGATGCCCATTCAATCCCTCTTTGTC 756 CTCTGCTTTTCCTTATTCCAGAACCATGTGGGGAAGTATCAGAAGTCTTA 757 GAAGCTGTCTACATTTCAACAGCCATGAAAGATTTAAGTAATACAATGTA 758 AAAAGTAAGTAATGAATTATAACATATTTTATTAAGTTTACAAAAAAAAA 759 GAACTATGTGAAGACCATGATGTTCAGTTTTACTAAAGGCGTAAAATGAA 760 ACCCAAATGAATGTGTATAAAGATAAGCAGTTTCGCCTCTAACCCTGTGT 761 TTTGGAACACATACATCCTCCCCGCCACATTTGTCATGTCTTGAGTTAAC 762 AAACTGAGGCAACTTAAATCCTGCTTCCAAGAAGATGGGTTATGAATGAA 763 CAAATATATAAATAACAAGTAAGTCAAGTGAGGTAAAGCACAAGTTGATA 764 CTGCATTGCTTGAAGTTTTGCATCACTTTTTCAAGTCTGATGataataat 765 tttcatagagaacagcttcaaccaaatttgttagaccatcaaaagatacg766 aaaatatatctcacatttcatttcagggttggttgccaacatgaaccaa767 aataataatttgcacatttttttcacattggttatctttcagaaattgt768 agtggatcttaattaaatcaggtacaGCAGTAAGTTAAGACACTTCTGAG769 AGAGACCACCCTCTGAAGCAAAAAAAAACACATTATCTGACATGTACAAG 770 AGATAAAAAAATCACATACTGACAATCTGTGGACCACTAACTTTCATAAA 771 TTAGCATAATTTGATTCACATATGTCATCACTTAGA TAATATCAGACAT 772 GTTACAATATAGTCCAGTGGATCTTCACTTGTTTCTAAAAACACCAGGGC 773 AGTGTTTGGGAGAGGCCGGGTCACTGCACTTTCAATCAGATTCTCCCTTT774 TAGCAATTGTGCCACCTGTCTTCATTCTTAACCTGAAGATTTAGTCTTTTDOCKET NO. STFD-015-PCT PATENT APPLICATION775 AGGGTTTCTTTTGCACTTGGGGTACTTAACATGCCACTATGCATATTGTA 776 GATTTATAGATACTTTTCAACTGATACTGCTCCCACAGGCAAACATGCCT 777 GGTGAAACACTTGTTTCTTTTTGGCAAACAAGAAATGTTTGCATAAAAGA 778 CTCGTGTCTGGAAAAATGTCTTGAGAAATTGATATGCTACTCTAAGCCCC 779 AAATCTCCTTTTCACTTACCTTCCCCCTGCTGCAGGATGACAATCCATGG 780 GCCTGTGCTTTCTGATAGTGAAAGAGAAGAAAACTCATAAATATAGTGTC 781 TACCATGAGTCAGGCACTAACTATGCATTTATCTCTTTCTGCTTTACCCT 782 ATAAATGGTTATTACCATTAAAAGTCATGTGAGGAAACAGAATTAGGGAG 783 TTCAAACTGAGCCAGGATTTCAGTTCAAGTTTTCCAGATCCCAAACCCTG 784 TTCATCAATTACTTCACAGTTGGAGAGATATGTGTGGAAGGAACGCAGTT 785 CCCAAGTATAGTCTAGGTCTGTATAATATAGAGAATCTGTATCTCAAATG 786 GCCATATAGAGGATGCTGGGTATTGCTTTCTAGGAATCACAGAACATATT 787 AAACGAAATAAAAAGCAGATGAAATGGTTGATTTGCATATTCTAAAAAGC 788 ATTGAGTAGTCAGTGACAACACCTAGCAAAATAATCTGTGAGGAGCGGGG 789 CTAGTTGAATCTGAATATCAAATTATATCTCACAATTTACTTTCTTTTTA 790 TTTGTCTTTCAGTGACACCAGGAGATTATACATCCATGGGGCCATTTGGG 791 CCATGCACTTCAGAATGACAATCATTGCCGTCATGGCTGGCCTATTGCCC 792 TGCACATGTCAGGGGGAACACAAAGAGTTTCTAAACCTGCAGTAAGTTAG 793 AGAGAAGACTGGGTCTTCCCTGCATTGGGTCTGTAGTGTTTCGGTCAGGG 794 GCTCTGTTGAGACAGCCTACTCCAGTCTCAGATTGGACCACACAGGGTTG 795 GGCCTGGTTTGTGGGTGTCTTTCTCGCAGGTGAAACCATAGCTTCAAGAG 796 CTCCTGTAAACTCCCTTCAGATCTCATATCACAGGAAACTCAGTAATAGT 797 TGGGTCTCTGCACTCTTCTCTCATTACTAGGAGAAACAAAAAACACAGAA 798 GTCAACAAAACACTATCTGCTTGAGAAAACACCCTTGCCATTCCATCAGA 799 TGATACAATATACTGTTGCCATTTACTGCAATAGGAAAGTCTGGGGAGGA 800 AAATAATACATGCTTGGAGATTGGGGGAAGGGAGTGGAATTGGAATCAAT 801 AATTTTTTTGGCTACTTGTCAGACATCCAAAAAGAGAGGTACTGAGCTAA 802 ATGTAATGGTATAGATATGGTTGCTACTATTGTTCTTGCTATTTTCTAGG 803 TGTGGCTGGTAAGGCCTTGGACATGAACAAGTCCTAGGTCACTCTAAGAA 804 GGCAGAAAGCAGGCCAGGACTACCCAATTTGAACCAAGTGTGTGGCCAGC 805 CCCTTGGGATTGGTTCCAGCTTTCAGAGTGAAGAGTAGGAAATTCCAGCC 806 TTGGTTCAGCAGGTCCTTCTATTATAAGAATTTACTAATCTAGTCAGAAA 807 AAAAGCTAATCTCTATGTCCCACATGCCCATATGTGTGATGGGCATACCA 808 GGGAAACTGCTCTGATTAGTAAGGGATTTCAGAACAGTTAGGAAGCTGTA 809 GAAACAAAGGGCAGTAAATAGCTATGGGAAGACAACATGGGTAGATGGGT 810 CAGaaagaaatgcagagaaaacagtcactttttgtccccaccaaccagag811 acaactactattaacaotttaatatittcccttacaaoctAATATCTGCT812 CATCTTTTTCATTTGCTTCACATAGATATAATATGTGTGCTCGATTTTAA813 GCTCTGTCTTTAT. AACTTAAGGTAACACCAGGAATATTTTTCTGCTCTGTDOCKET NO. STFD-015-PCT PATENT APPLICATION814 GGTTACTTTCTTATCACGTTCTGACACTTAGCAAGATTCCCTGGTTCACT 815 ACCACACTAACCATCAGATCACATAGGGGTCTGCAGATTTTATTTATTTT 816 ACATGGCCAGTCCCACGAATTAAAGGAACAGAAAAACAAGAAATTATGAT 817 TTAATTGATCTGTTAGGTTTTGAACTTCTATGAGGTTCCTGTTGCTCATT 818 TAGTATCTAATTAATGAAAGTAATtaatatctgccttcctttcttaa819 catcatctcctcactctcctactagtctcctgtgtctcccaaacaaact820 agctgtcctcaaagcctgaggctcacttcctgggggaactcaaactaaga821 cCGGTTGGCTGTGTCCCTTTCAATACAGATACCCTCCCGGTTGTTATAAC 822 AGTTCCATGTCCCTCCAGACTTAAGAGTAGCAAGGActtttgtgttgcaa 823 tagcccatttgtgtagttacaacagagactatgttgtccaccaacgtaga824 atatatttactattgggtcctttgcaaaaatagtttgccaactcctgTTt825 taga gcaattaa ggtttaaaggactatgttttaccttcatttattttatt826 tccagttcttatcatttccttgtgtgaattcaagtttttgacccatatca827 ttttttttttttttgcctgaataacttcagacatttcttgtgaagtgcaa828 ctgctggcaatgaattctctcagttttattttgtctgaagctgtcttta829 tgccaagtgacagttttttcatttaacactttgtagatttcactccaatg830 tcttcttgcttgcgtggtttcagatggaaaatctgcttttttccctctag831 ctaccttcaagagtttctctttattttggttttcaacagtttaaatcta832 atatgtctaggtattttgttctgttttaatatttatcctggttggtgtt833 ttcctagcttttttgttctgtggtttggtatctatcactacatttggaat834 actctcagccattattttttcaaatatttgttctgctctttgtctctttt835 gtttcagggattctagttacaaatatgtttgaaaatatgatattgtccac836 agttctgttcttccatgaagatatgctttctctcctgttctttctttctc837 atctccttgcattgcagttgggtcatatctagtggcctatctttatgtt838 aaccaaatctttccttatctccatagggtctactggtgagcccttcaaag839 gcattcttgatttctgttactgtgttttttttttatgtcttgcattttca840 ttgaattttttatgtaattgctgtctctttgctgaaattctctgtctg841 accttgcatgttgtctaccttttccattagagcctttaacatactcatca842 gttattttaaactccctgcctgacagctcaaacatctgagtcatatcaga843 gtccgatgcgtatgattgctttgtggcttcaagactgtgttccttctgt844 tttggggtaaggtacttagatttttttattgaaaggggacgatgttgtat845 aacacagtagatactgagataactatatttgatgcttaaaaatgcctaca846 ttggccaggcacgctggttcatgcctgtaatcccagcactttgggaggcc847 aaggtgggcagatcacgaggtcaagagattgagaccatcctggccaatat848 ggtaaaaaccccgtctctactaaaaatagaaagattagccaggcatggtg849 acgcatgcctatagtcccagctactcgggaggctgaggcaggtaaatcac850 tcgaacccgggaggtagaggttgcagtgagctgagatcagccactgcact851 ctagcctgggtgacagagcaagactccgcctcaaaaaaaaaaaaaaaaag852 aaaaaagaaaaaagaaaaaaaaaatgcctgcatctttctttctgccagacDOCKET NO. STFD-015-PCT PATENT APPLICATION853 ctttagtgtgggagtttgtgttaatctagttaggagttagactgggttag854 aagtttgttgttgctaCTAAGTTGTCTGGATTGGAGTTTGTTCTTCATAG855 GACATTAGAGACTTTAGATTTCTCTAATCATCCCTTGTTCTTGGCTTTGA 856 GCCATCCCTTTGTTCTGCTCCCCAGAGACAGTCTGTCTTTTGAAGCTCTC 857 TTCACTGCATTCTACTGTTGCTTTTGCTCAAGGTAGTATGGTGGTGAGGT 858 GAGGAAGGGAGCCATTCTCTGCTATTTTCATTCAGCTTCTGTCTTAAACA 859 GGCAGGGTCAAACCGGGACTTGAGAATGTAACTTCACAACTGTTGCTGCT 860 CTTATTCCAGAGGTGGCACATTTCCAGTCATAGGAGGCACCCACCAGTGT 861 CCTTGGGCTATGATTTTGACACCCACCCTTCTGCACATTAAAACTCATTA 862 CTCTGTGGAGATAGGGATAAAGTATTGGGCAGAGTTGATGGTGGCTTCCT 863 TTTCCCTCCCTCAACTAAAATGAAATTCCATAGAAACCTTCTCTTGCAGA 864 TTAAGTCCTTCTACAGTGGAGAAGAGGTGGGGTAGGtctgggtgaattta 865 gacagtggctactgttccccttctaagccagtaccaaaaaggggagcttt866 ctctggattctccatgctcttccctgcaagagcctgcatagggttcctgg867 agaaaaagtctaaaagatggtgggaaattccctaaaattttggcccccag868 cggctcacactctcccactagtctgcattcagcctttataatttcactaa869 aatgtctagtttaatttcctatcagtttTCTTTCTAGCCGTAGAGACCAC870 ATATTAGATGCTATTTTTACCTCCTCTCTCAGAGTCAGGACACAGCgtgg 871 ttacgaggacagacgctgaagccagaaccccagcccctccccccccccag872 ttaagaactctgaccacaaagtaaatcacatcgctctgcctctgtttcct873 cccccgtaagatgagaatcacaacagaccaatgtgaaaagatgtcccaag874 gatgagatgagttacatgtaaaggatttagagcagtgcccaagagggagc875 agagtaccctgaataaacggctgctGCAATCACAGGCAGAAGCCGGGAAG876 AGGATCCATCCTGGTGGGGATCCACCTTGTCGGTGGATCATCTAATGCCC 877 CCTCCCTTCCCTAGGAGGATCTGAGACCTGTGCAAAGGAAGTGTGCTGGC 878 TGGACTGTAGGAGGATCCCTCAGAGTGGAATGAGCCTGAGGAGAGGGCAG 879 GAGCTTCATTTCACACTCACCCCCAACATGAGTGGAGCAAATGAATGCTA 880 ACTTCTTCAAGGTCACAGGACACAGCTGAGGAAACATGGGCATTTGGGGT 881 TTAAGAAGGTATTTTATCTTTCAAATTATTTCATATTAAAGTGGAAAAAA 882 ATGAAGATGACATTGCGAAAGTATTGCAATGGTTATATAAGATGTGTAAG 883 ATACCCAGCACGTTTCCTGCCACTCAGTGATTCCCTCTTTGAGTCTGGAT 884 CATATAAACTTTCAGGTAATCCCTGGACCTTGAGCACAGAGTACACTGAT 885 TTCTGTATGTCCTAATGTGTGAACATAATCAAGTTTCCAGAGGTTGAAGG 886 GGAAGTCCTGGGAGGTGCAGTCCAACCCTGACAACCCTGCTAAGCCTATG 887 CTCCTGTTGGAAGGGGGCTGGTACACACAGACCTAAAGAGGGATTCTGTG 888 CGGGTGTCCTGACATCTCTCATCTGTGArTCCAGCAAGCACATAACTATC 889 TCCATTTCCTTTTTCCTGAGAATTTATCTTGTAGGTCAAAACAGATCTAG 890 GAACATCATTTTCAGCTACAGCCCCTAAGTGAATTGAGAGGGTCATGTTG891 TTGAGGAAAATGCATCAAGTTATGTCTCAGCCAGTATAAGCGGCTAGATADOCKET NO. STFD-015-PCT PATENT APPLICATION892 CCACCCCAGATAGTATTTGGACTTTTAATATTTTTCTCTGGAAATTAATA 893 TTTCAGGTTGCTCCAATTTCTTGTATCCAAAACAAGCTGTAAGCAAAGAA 894 GAGAAATCCATATGAAGACCTGAGGTATAAAGATGCACCATTAAATAATT 895 TACTTGCTCTCTCCTCAAGAGTCAAAATGATGGGGAACCCGTAAGAGTCC 896 AGAGAGAGGAAAAGATGATGCTTCCAGCAACGACATCCTGCTGTGTCCCA 897 AGGAGAAGGCAGGGAAGTGTGTGCTTGATGCCCAGTGGGCTCAATAATCA 898 CAGCAGTAAATGACCTCATCTTCATGTTTGTGAAATTTACTTTCAAGGTT 899 GAAGTGGAAGGATGAGCATCATTGTAAGCCACAACACCTAATGGACCCTG 900 AGCAGGTGCGATTGTCAACACACATCCAATGCCGACTTAGGTTTCAGCTG 901 ACACCAGTATTTGACTTCATTTTTAGTCTTGGCTGGATATTTTACAAGGT 902 ATAAAAGCATCCTTATCTTTTGCCCTGGGTATTTTAAATTTGTGCCAACT 903 TTAACGCCCTGAGAATAACTGTAAGCAAAGAAAATTAATTCTCATGAACA 904 CCTGATATGTAAAGATGAAGTGATAAAGAATTTCTTCACCTGATATACAA 905 AGTGAAATGACTGGAGCAAACCCCAAGGTGAATCCCTACATGCTCCTGGT 906 GCTGACATGCTCTGGTCTGCCAGGCTGTGTTCCCAAGAAGAAGCAGGAAA 907 GTGAGGATGCCTGTGCCTAGAATGTTTAGTGTGTGGCAAGGGTAGCTTGG 908 TCTGAGCAGGTGTCAGGGAAAGAAGTAGTGGGTCACAGTGATTCCCTGAC 909 AACCCTTTCTGTAGAGTGCAGCGTTGTCAGATCTGAAATGGCTGGCCCTC 910 TAAATACTCCAGTGCCCAGGAGATCTGGCAATATGGTGATGGTTAGAGGA 911 GAACTCTTCCTATGAAGGGTGAGGTGTGGGTGAGTGGTGACAGTGGCAAT 912 TAACTTCAATTTCTCTCCCCTTCCCTGTTGCCTCCTATTTCGTTTTTCAG 913 TAGCCCTAGTGATATGAGGATATGTGATATGTGGATATGAGGATACAGTG 914 ATATGTATTTTGTACTCAAAGCAAAAATTACTCTTCCTGTGGGTTGAATG 915 TGGATCTAAAACTCAAGGTTATAAAACACCTGTATTTCTCACTATATAAA 916 ATACTGAAAATTTGTGCTGATTTTATAACAAATTTTATAAATGAAAATAA 917 AAGTACATATACGTGGACAATTGAGTATATTTGTTTAATTAATTGGGAGG 918 ATGCCATCTATTTCAGCCCCAGAGAGGCCAAATATCAGTTCAATATTGCT 919 CTCCAGAAATTAGAGAGGACACTAGACACAACCATCCTATGGAAATGGGA 920 TTGGCTTGCACTTGTACCAGACTGTGGAGCTTATATCTTGAACAGTTTGG 921 CCCTTAGACTCCCACTCCCCACACCATAGTATGTAGGAgggaccttctga 922 aaagagcttctgacgcagtaggcctgggctgaggcttgactgactggatt923 taaaagaagctcctaagtgaagccaatgctgctggttcacaaatcaaact924 ttgagtaccaaggACTTAGAGTATTAGTCTAAATAATTTTATTTTCTAAT 925 ATGCAATAATAACTCATATGATTAATGTAGTGCTTCAatttgttgagcat 926 taggcatgccccaagcacttgcaagaactttatttgtattatttaagtta927 cttttctcaacagtttatttgagtaatcattattatgttctccattttac928 aattaggaaaatgaatcaaatatatgctaactaatttatctgaagtcaca929 cagctaataTGGGGAGGGTGGATGTGTAACAAAGGGTCATTAAAGAAAAA930 TTGAGAAATTGGGAAACACTAAATATGAATAAATGTCACTCATGAGTCTADOCKET NO. STFD-015-PCT PATENT APPLICATION931 TCACTCTAGGACAGTGACTGAAAATCAttttctgtaaagacccaaataat932 aaatattttgggctttgtgggtctctgttatagctacagtcatctctcag933 aatcttcaggggatttgttccaggatccccga cagataccaaaatccatg934 tatgctcaagtccctgatataaaatggcatagtacctgcatataacaaat935 gcacatcctcctctacacttcaaatcatctctaattatgtataataccta936 atacaatgtaaatactatgtatgtagttgctatattatattgtttttatt937 tgtattatttttattgctgtattgtaattttttatttttttcaaatattt938 ttgatccactgttggttgaattcgcaggtatttaatgcacagatagtgaa939 gactgactgaatgtactctaccattcaagtgcaaaagcagctagcaaaag940 cagccataaacaatatataaataaataggcatggttgtatttcaataaaa941 ctttatttacaaaactggagactgctggtcatagacatagtttgctgacc942 TTCTGCTCAATAGTAACCAGTATTAACATGAAGGTTGGTATTTTTGTTTT 943 TTTTTTTCTGAGAGGTATAGAGTAGTGATATGATTAAGTGGAAAAAGATA 944 AAAATAATTTTAAGTGTGCCATATATAGTTATATTTTATGTTGTTATATA 945 AACAGTTTCATTATTAAATGCATGAATCAATAAAATATTGAAGCCATTAT 946 GGCATACATCTTtaaaagtagtagcagctttttgttacaatgtgtaaaat947 ctgtgcaagtaccaagaagatgttaaaatcacccatcctttcagagacac948 ccactctttaaacttggagaatttttttccttttgctcgttcttcaata949 tatacatgtatgtacatGAGAGCTTACTATTTAAATCAGTTCTGTGTTCA950 ATATCCTCCTGCTAAATACATGGTGAATATTTTCAATTTTACTTATAGTT 951 CTTCAAAAACACTGCTTAATTGCTACATAGTATTTCATTACTTTAAATTC 952 ACACAGATACGGTGTCTCTTTCCTTCCTCTTCCTCACTCTAGTGTGTCTC 953 TAAGTTTTCTTCCCCATAAATCTCCCAGGAGTCTCTTAAAAAGTCAAAGT 954 GACTGCATCTTCTAAGACCTGACCTTGTGTGGCCACTACAGTCACTCTAC 955 ACTGCTCttttgaggattaaataaaataatccatgtaaaatacttaacac956 TGACATTGTGAAAAGCTGAATTCCATCTTTTCATTCACCTATTTCTTGAA 957 AAGTTCATGTTCTCAGGCTCTGTATTTCCTTAACAATCTTCTTCCCTTTG 958 CTTTTATGTATGCATCAGGTGAGAGGTGAGGTCTGTTGAGGACTCACTCA 959 GGCGCTCAGGTCATTCTCCCTGTGGACCACCATGGTCAGGAATCATGGCG 960 GACAGGATGCGGGACTCCAGATTCTGAGTCTGCACCTGGAAAGGGGCTGA 961 CCTGCCATGGAGGCTCCTGGTATTCCCTCATTGGGCTTTCAATAGCATTT 962 CTCCTCTTATCCTATCAGGATGGTACAAGCTGATTCTCAGAAGGGAGAAT 963 GGAGAAAAAATACGTTGCAATTACTTCAAGGACTGTAAGTAGACTGCATG 964 TATGGCAATATGCTGTCAGATATCCATAGTACTAAAGGTATAAATAGGAG 965 AAAATCTTTGAAACTCCGGATTTTTCATCATTAATTTGTTGTTTGAAAGT 966 TTCAAAGAAGTGAGAGAGGACTTTTAGAGTTTTACAGTTTTATATTTTGT 967 TTCATTATTTTTTGAAAGTTCCCAACCACCCAATGATTAATCATGGAATA 968 AACATAAAATAATTGTCAATCATTATTTCTTATTTATTAATTTCTGAGGG969 GTATTATTATGGTTATTTCCTTTACCGATGCAGGAAGCATGTATTATCTTDOCKET NO. STFD-015-PCT PATENT APPLICATION970 TCTTCTTAACTATCTAATCCTATTTTACTCAGGATTTTTAGTTTTCTTTG 971 CAGAACCCTGAAAGACAAGATCTCCAAAGCATAGCCCCCATCCTGAGATC 972 CCCCACTGTGCCTAGGAGCTGGGTTCCACTGCACAGTGCTTGTTTTGTCC 973 CAGCACTGAGCCCTGAGTGTGAAGTGAGCTGCATGCTCTTCCTCTAGGAC 974 ACAGGATTTATACTTTCATCTCTCATATACCCCAAACAGGTGATTGTTTA 975 CTTACAGATCTACTTACTTGTCCCTAGATTTCTTCAGGATGGCCTCAGGT 976 GCGAATAAAAAGCACACAGTTACTATGTTTGACAGATCACTCTAACTTTG 977 AAAACCTCCAATGCTCATGAACCAAATGGGAAAATAATGATAACAGCAGG 978 GAATATCTATGTAAAATATATACTGCTTCCTACTTTCATTCTGAACCAGT 979 TACTAGAAATCTCTACGTAGCGAATTACTAGACAGATGAATTTTGCTCTA 980 AGCCACCCACTCTGTATTTTCAGAGTTCCCAGATATCCTAATGTTGTAGG 981 AAATAGTGTCAAAATGTCCCTAATTTGGATCCTAATTGCTGACACtgata 982 tgggatgggggagggaagtgcagggaaaggaaggacgtggtccctgteg983 agggccccactcccaggcctgtgcccacggacctaggtgaggacaggcac984 tcctgcctccacgcccaaatgttgcatttcccaagaccaccctggcccgc985 cacgcctccatcttgtgcctataaaacccctgagaccctagtgggcacac986 acacaagtggctggacatcgagaggaacactaatgtggaaaagcacacct987 acagagactggcgggctgcaggccatcgactggcagaacaaagcagagtt988 tggcgagactggcgggctgcaggccatcgactggcagaacaaagcagagt989 ttggcggggtggttggaggaaagcctggccgctgagcagtcaactccagg990 ggaaaaccaccttcccactccatctcccgtctggctcccccatctgctaa991 gagctacttccactcaataaaaccttgcactcggccaggcgcggtggctc992 acacctgtaatcccagcactttgggaggccgaggtgggcagatcacgagg993 tcaggagtcgagacaatcctggctaacacggtgaaaccccgtctctact994 aaaaatacaaaaaattagccaggcatggtggggggcgcctgtagtcccag995 ctactcgggagactgcccaggagaatggcgtgaacccgggaggcggagct996 tgcgtgagccgagattgcgccactgcactccagcccaggcgacaaagcga997 gactccgtctcaaaacaaaaacaaaaataaaaaacttgcactcattctcc998 aagcccacatgttatccaattctttcagtacaccaaggcaagaaacccag999 ggatacagaaagccctccgtccttgcaataaggcagggggtctaattgag1000 ctggctaaagcaagtcacctatggacagccaaactaaaaggacaccttgt1001 aacacaggcccactggggcctcaggagttataagcattcacccctagaca1002 ctgctgtggggtcggagccccacaacctgcacgtgtgcatgctcccccta1003 gaggtttgaggagaggggcaccaagaagggagccacatccttatcgcacg1004 ccctgagagggaacaagaaaacttttcccgtttGGACACCATGAATCACC1005 AATGTGATTCTGCACACCAAGGGAGCAGAATCTAAGATGTCTTCCTGCAA 1006 CATTCCAGAAGAGCTGCAGGGAGGGCAGGCTCCGGCTGGGCACCCAGCTG 1007 AGCAAACCGCTGTGGTTGCCCACATGGAGAAGGATGTGGACAGGCACAGA1008 CTCGGAGATAGTTTCTGTGTAGGTTATCTTGACAACTCTAACACTGTGGDOCKET NO. STFD-015-PCT PATENT APPLICATION1009 TCRγ Plateau3 >chr7:38379851-383814201010 aCATGTGGACTTGGAAGCAATAATTGGACACTCCAAAGGCAACATTCCTT 1011 GGACAACTGGAACACAAATTGAAGGACAGGTCGCTATTGCCCCACCCCAC 1012 TTCCAGCAACCACAGGAAGGAGGAAAAAAAATTAGGAACAGTAACAGAGA 1013 AGGAACAACAAGAGAGGTAAGAAAACAAGGAAAGTTCGTATCTTGGAATC 1014 TTGGGGGAGAATTGGAAGTTTGGTGGCATCTCCAAATGCCACAGACAGCA 1015 CTTTGTGATCACTGGTAGGGTTTTGGAGAGCAGAGCATAATGACACAGAG 1016 TTTAATATTTACTGGTGGGAGAGGGTGTAGGGTATCAGCCATGTGGCAAG 1017 GTGCGTATGGACAAGGCACTCCTGGGCTGGACTGGTTTTACAGGGCATCA 1018 GAGTGCAGCAGGGAGGGAAATAAGCATGCAATTCTGACCCAACCCTCAAG 1019 AATCAAACAACCTGAGTGTTTGACCTGAGATCGGGGGGACTGGGAATTAA 1020 CTGGATTTTAGGAAACAAAGATAAAATTTAGATTTCTTTGGAAAGAGCTT 1021 CAGGGTACCTACCTGGCCTTCCTCTCAATTTGCATAGATGTAAGGGTTAT 1022 GTCTCAAATATCTTTTAAGTGGAAAAAGTCACTATTTGCTGCTGCTTGTT 1023 AAGTGATCCTTAAAAGGTATTACCAATGAGTCACAAAATATTTGGATGGA 1024 ATATTAAGCTTATTCGCGCATGGTTTATTTGGCTTTATGAACAACTTATC 1025 AACCCCCTACTGTGTGCCTTGAAGAACGCTGCCCGTGAACATCCAGGCGG 1026 TCTCCTCCTGGTGATTCAGGACAGGATCATCATCAAACAGGGATGCACCT 1027 GCAGGGCTCAAAGATGAACAAAACCACCTGGATCTCCATTTTCTAAGTCT 1028 TCCAAGAGAATATTGGTCATTGTCTTCTCTGTGCTGTTACCAAATGTCCG 1029 ATTCCATTTACTGAAGTCCTAGGAAAGTCTCACACCAGGAAGACGGTAGC 1030 TACAGCACTGTGTAGAAAAGCTGTGCGATCTGCTCATCTCCAAGTTCTGA 1031 CACGTTTGTAAGGTTTTTAGTTGAGTTCCAAGTAAAAACCAGAAGGCAGC 1032 TGTTAGTTGGGCTCCTTTGAAAAGAGGAGTAGAGTCCTATCAAGGCCAAT 1033 CCATTGGCCAGTCTATTTCTAAGGCTTCAAGGTGTTCAGCCATGCAATTT 1034 TGCATGGAATAAAGCACTGAGCTTCCGCCATCTTT. AAACTCATTGAGTTC 1035 TCATAACTTTTGTAGTTTCCCGAAGGCATTTTCTTTAATGGGCCATCTGA 1036 ATGGGCCATGGGGTCATGCTGGGATTGTTCCAATGACCTGGTTAGAGGCT 1037 TCTTTATGTAAGAAAAGAGGGCTCAGAATTCTAAACGTGCACACTCCACT 1038 GGGCAGCCTAAGATGTGATGGATATGGTTTTCTGGCTGACTCCAAAGCCA 1039 CCCCAGCTTTGTCAGGAAGAGCAGGCGTGGTGGAAGCAATGCAACAGCAT 1040 GGTATGGGAGCTTTTACCTGTCCCAGGGGCCCTGGCTACCCTGAGATAGT 1041 GTTAAAAATTGAAATTGCTg1042 TCRβ Plateau > chr7: 142218210- 1422233761043 attattatgtatcaataaaaaTTTAAATACATAAATAGAAATAGCAAACT1044 AATATAACAAAAGTA AAT1 TAGGl L l(i 11 AATATT1 TAATATGGACCATA 1045 GTCTATCAACAATATGTTATGTATTCTTTTCTCTTTATAAATTCTTTATA 1046 GAACATCCTGCAAATCCAGACCATACACAATAAGTATTTGAGTGACTCGA1047 ATCCACTAAAAGTTGGGTATATTAGAATCTGGGGTGTGAATACCTATGTGDOCKET NO. STFD-015-PCT PATENT APPLICATION1048 ACACAAGTCAGTTTCACCTATGACAACCGGCAATTTATGGAGACAAATTT 1049 CAAGAGTGAACCTTATAATCAGGTAGGTCTGAAAGGAATATTAGCATATC 1050 ACAAGTAAATTTTATCATTCTGCAAAATTATCACCAATAATTTTGCTAAC 1051 AATTAAAATTATCATTGTTAAATTTTCATGTATTAGATGGTTATAAATAC 1052 GTGCAATAGATATGTTCCTGAAAAGTTGCAAATGTTGAATCATATTGTAA 1053 AATATGCAACATTAATGGTCTTTCCAGTATGGCCTAGGGGTCAGTGATCA 1054 CTGGCCTGATGAGATCCTCTCCATGTATTTACCAAAGAGACTGTGCTATG 1055 TTTTGATAGGTTAGTCTTCCACATTAGCAAAATAAAACTTATTTCTGCTG 1056 CAGAGGCTAAAACAAAGGAAAGGGTGATTCCCTAAAGCTGTTGAAGGTTG 1057 CCCCCATGCTTCCTGCAGTTATTCATGTCCCTGGTCAAATTGATGGATCT 1058 TATAGGTAGACGAAAATTGGCAGTAAACTGTGGTAATCTTCGAATGAATA 1059 CATCCCACCTGTGGTATAGGATAAAAGGTTGATAAAACAGGGGGACATAA 1060 ATAGCAGGCCCTACTAGAGGATTCTAGAATCAACTAAACCAGAATTTTGG 1061 AAGATGAAATACCAATAGTTACCAAAGGCAACCACAAAGAAAAAAGTATC 1062 TCACTTTTAGAACATAAGACAACATAAATACGGAACCAGCAACCCAAAAG 1063 GGATGGTTTAGAAAAGTGAAAATGGATAACCATAGTTCTTGTTTTCTAAA 1064 ACGTGAAATGAGTGCCCTGATGGTATTTGGACTTTGGAAAATGGCCCCTC 1065 TGAGCACTCAAATAGATCTTCTCCCTCTAGGCTCTTCTGGGTATTTACCT 1066 TAAAGCATTTTACCTGGACTATTGAGTTCAAAACCACTCTTTGCAAGTAA 1067 TTGCTTCTAGTTAAGATTGTGCAGAAAATCCTTGAATACCTTCTTTTTAA 1068 AAACTCTATGGCATATCTGATGCCTATTATGTGCCAGACACCATACTGTT 1069 TGAAATGAGGAAAACATGAAACTAACCTGCTGTCAAGAGGACTAAAACCC 1070 AATGGCAAAGCAAAGAGATTTTAATAAATGTTGGTTTTAATCACAGCTAC 1071 AAATATTTGTAAACAATAAGGTTCTGACTAAATGAAGTGAAAAGAAAAGA 1072 TTTCCAGCATAGGGATTATGCACACAGAGCATCTCTCTGTATTTATCTGA 1073 CCAAAATCAACATGACCTAACCCAAAAAGGAATGTTTATATCCTATTACT 1074 GGAAAGGAATGAATCCATCATTTTTTGTTAAATTGTAATTTAAGAGGTGA 1075 GCTACATGTGAGGTTTAAGAAGTTCTAAAATACCCATTTATATCTCTTCT 1076 TTTCTGGCAGATACTAACTATTCAATTGACTGACAAGACTATCAACCTGG 1077 AAAAGTTAACTGAGGTTACTTGGATTGATGGTGGTCCTGTACTTCCTACT 1078 CCAACTAAGACAAGTACCATCCCAATGAGTTCTCATCCTTCTCCATCTAC 1079 TACCAATGCCACCAGTTCTGAGACAATCACCAGTTCTGCCAGTGCAAATA 1080 CTACCACTGGCACTACTGATACTGTTCCTATCACAACCACATCTTTCCCA 1081 AGTACTACTAGTGTTACAACTAATACTACTGTTCCTGATACAACTTCTCC 1082 TTTCCCTACAAGTACTACTAATGCTAGCACTAATGCTACTGTTCCTATCA 1083 CAACCACACCTTTTCCCAACAAGTACTATTGGTGTTACAACTAATGCTACT 1084 GTTCCCAATACAACTGCCCCTTTCCCAACAAATGCTAGTACTGCTAGCAC 1085 TAATGCTACTGTTCCTATCACAACCACATGTTTTGCAACAAGTACTATTG1086 GTGTTACAACTAATGCTACTGTTCCCGATACAACTGCCCCTTTCCCAACADOCKET NO. STFD-015-PCT PATENT APPLICATION1087 AATACTACTACTGCTAGCACTAATGCTACTATTCCTATCACAACCACACC 1088 TTTTGCAACAAGTACTATTAGTGTTACAACTAGTACTACTGTTCCTGATA 1089 CAACTGCTCCTTTCCCTACAAGTACTACTAGTGCTAGCACTAATGCTACC 1090 CCTGTTCCTATCACAACCACACTTTTTGCAACAAGTACTATTGGTGTTAC 1091 AACTGGTACTACTGTTCCTGATACAACTGCTCCTTTCCCTACAAGTACTA 1092 CTAGTACTAGCACTAGTGCTACTGTTCCTATTACAACCACACCTTCCCCT 1093 ACAAATACTGCTGATGCTAACACTAGTAATACTGTTCCTAATACCACTAT 1094 GCCTTCTCCTACAAGTAGTACTACTGTGAGTACTATTGCTACCGTTCCCA 1095 TTTCAGTGACTCCTTCTCTGACAAGTACTGCTGATGCCACCATTAGTACT 1096 ACTGTACTTATTGCCACTACTTCTTCTCTAACAGGTACTACTGATGTTAG 1097 CACTAGTACTACTATTAATAATATAAGTACTCCTGTTCAAACAAATACTA 1098 CTAATGCTAGCACTAGTACTAATGTTGCTAATATAACTGCTACCTCTCAT 1099 ACAAGTACTGATGATACTGTTCCTAATAATACTGTTCCAGTTACAGCTAT 1100 TCCTTCTCTTGCAAATACTGGTGTTGACACTACTAGCAACAGTTTTTCCA 1101 TTATGACCACTTCTTTCTCTGAAAGTACTAATGCTATGAACACTACTGTT 1102 ATTATGGCAACTACTTCTCCTACAAGTACTGATGTTGCTAGCACAAATAA 1103 TGATGCTTCTATGACAAATTTTCTTTTAGCTACAATGTCTGCTGGTAATA 1104 TAACTAGTAATAGTATTTCCATAACAACTACTTCTTTTGGTAATAGTGTT 1105 CCTTTTGTGACTACTCCTTCTCCAAGTACTGATGCTACTACTACAAGTAA 1106 TAATACTAATCCTGGCATGACTACTTATTACCAGACTTCTCCTACCATTC 1107 CTACCCATACTCTTACTTCTATTCCTAGCTCTATTACTTCTATTTTGAGC 1108 ATGTTTCCAACAAGTAATACATTCACTACTGATAAAATTACTAATTTTAC 1109 TACCCCTACAAATGCAAACACCATTATTTTCAACACTCTTGATACAAAAA 1110 GTACCATGGTAATAGATGCTACGGTCACTACTACCAGCACCAAAGATAAT 1111 ACCATGAGTCCAGATACAACAGTTACTTCCATAGACAAATTCACCACACA 1112 CATCACACAGTTCGCTACTCCCCATTCTGCTACTACTACAACACTGGCCT 1113 TAAGCCACACCTCATTAGCTCCTACAAATCTTTCTAATCTAGGCACCATG 1114 GATATTACTGATGCAGATAACTCCAGCAGTGTTACAGGTAACACGACACA 1115 CATTTCTGTTTCAAATCTCACAACAGCCTCAGTCACAATAACAGCCACTG 1116 GTCTAGATTCACAAACTCCCCATATGGTAATAAATTCTGTGGCTACTTAT 1117 TTACCTATTACTGCAACTAGTGCTACCACAGATACTACAAATATTACAAA 1118 ATATGCTTTAAATACTACCACTCCTGATAGTACAGTACATACCTCTGCTA 1119 CTGCACCTACTTATATTGCAAATGCCATAAATGCTACTCAAGTTCCATGA 1120 TTACTACTCAAGGCAGGATAGTTACCTCAGATAACGCCTACAAACAACTA 1121 TTACAGATATAGAAAATCAGTTACGAGACACTCTATCTATCTTATGCTAC 1122 TTAAGTTTCACGGATATTAGTACTCTAGCCATAAAAGACACAGCTACTC 1123 CAAACACTCTCGTCATTGCAGACATGTTTAGGAAGGTTTACAAACCTTAT 1124 AGGTTTCACCAAAGAAGCTGTGGGTACTTATTTTGCAACCATAGTATGTG1125 CTCTTATTCTTTTAAATTATAGTTATTACTCCTATAACCTCATCAGTTAADOCKET NO. STFD-015-PCT PATENT APPLICATION1126 ACTACAGATGTTTTATATATCCTATATATCCTTGCTACAGATTTCACAGG 1127 TAATTTTGGTATCTCAGATAACACCACATTAGGCTCTGTAAATACTATTG 1128 CCTTAGATTTAGTTACTGAAATAGCCCAACTTGTTTCTTGGGTCACATGA 1129 CGTACCATAACTGAGAGTACTGGTGATACCCCCAGCACTCAAATGGTTTC 1130 TATACCAACAGTTATTGATATTACAGGAGAGTATGTAATTAGTAATGCTA 1131 AAAAAATGCACTTTATTATCCTATGGACTTTTCCAAATGCCATAGCTACC 1132 AATAGAGTCATTTGCATTACACATACTAATAGTATTATTTCTTCTGAGGA 1133 GATCCTAGCTGTAGCTACAGATATAGAAAATTCTACCATTGAAGATCTTG 1134 TATAACCTTACTTCAGCCACTGAAATAATTTAAATTATAAATATTACATG 1135 TGGGTTTGACTATCACAGAAAATAAAATGATTATAGATCCTAAAAACATA 1136 AATTCCTGAACTTTGCAACCATTAATTCATAGGTACTACTAATACTCTTA 1137 CTACAGATTTTATAAGTACTTCCACTTATAGACAGAAGAGCATTCTCAGA 1138 AAATTAGAATTAATCTAAATTATGAGATAGTCTTAAAGCCTCACTGTTAC 1139 CACCAATGACTGGCTCTGACTCTAGTATAAATCAGAAATTATCCAGACAG 1140 AGGTGAGAATGTAAATATACAGCATGAGGAAGACAGCCTCCACATTGGAA 1141 TCAGAGTTCATAATCTTATTTGCATTTTCTTCTATTAATACAAGCTTTTC 1142 CCTTATAATTTCACTGTTCAGACTCCCCTTCATTGTGTTAGGGTTTTCAG 1143 TCTATTCCTGGTTTTTCATATCCAAATTCATCATCCATCCTTGATCCATT 1144 GTTTTCTTAGATCACTCAAACCCCCATGAGTAGACCCATGGTCATTACCA 1145 AATCTGGTCATTTGGGTACTATTGTAGGTTTAACCCTAGGGCAATAttct 1146 cgaagtttagttcaggg1147 TCRβ_LMR >chr7: 142774538-1427862131148 CAATAAAGTGACCCTGCTCTCACTGTCTGTGTCTGTGCCTCCTCCTTCAC 1149 ACTCCTTCACATTGGAAAGCATCCTCCAACCTCAGGTCAGACAGGGCTCT 1150 CCCCCTTAAACATAAGAAGAGCCTCCAGCTCCCAAATGTGTTCCATGGTA 1151 CACTAGATTAACACATACAAAGAGGTGGAATCCAAAAATAAGAAGCTTGG 1152 GAGAAAGGGGGGCACTGTTTTCTAGAGAAACGTGTGTTTCAGAAAGGTGG 1153 TCTTCGGCAGGGGCTATTGTTTTATTTGGGCTTCTCAGAGTGGTTAGAGC 1154 TACTCTGCCTTCAGAACAATCACAGTACAGAAAATGTGTCAGCATCTTCG 1155 AGGTGGCCCAAAATATTTGACCAGCTGAAACTTCTTGCTAAAATACAACA 1156 ATAATTACAAATGCTGCTGGTGATGACGTGACTCTCCCAGGAATGTGTCG 1157 GCACCAAACCCTCGACCAAGCCCTCCCTTCTCATTCGCCTGGAAAATCAG 1158 ACTCAAATAAATCTTCCTGGCCCTCCGACTCTTCCCTTAATTCCCTAGTT 1159 CCATCTCTGTGAGCAGGCTAGAGAGATGTTCCACCTACCACAGCGGGAGC 1160 CAGACTGCGACTTGGGAATCAAGCCCAGCTCTTCATGCTGCATTTTTATC 1161 TTCTTTGCCTTTGGGGTAGGATGCCACAGTGAATCCCACAGCTAACACCA 1162 GCTCCTCACTCTGACCAGGGAAAGAAACTACAGAGGGTCAGGATTCACCC 1163 ATTTGATCAATTAACTGAGAAAGGATTCATTTTCATAAAACTTGCTTGAC1164 TTTGAGACACTTCAAGTGAGTTATTTGGGATTCTTTAAAAAAGGTGGAAGDOCKET NO. STFD-015-PCT PATENT APPLICATION1165 GAAAGATCTGAGGACTGTGACACAACCAGCCACTCTGACCACACATTGAC 1166 TGGCTTGCACCCACTGGACACAGCAGAGGGAGGCAGGCTTCATGGCACTT 1167 GCGGCACCTGCCAAAGCCTCCTTCTGGCAATTCTGAGAGGGCCTAAGTTG 1168 GGGCCGTAGCTCATCCAAGCTTGTCACCCAAGATCCAAGCAAGCTTCTCT 1169 TTGAAATTCCACCTTCACCTTCTGTCCCAAGTGGTTGTGGACATCCCTGG 1170 GAGCTGGCGCTAAGGGCCAGGAGCAGCCAAGGGAGACAGACAAGTTCAGA 1171 GCACATTTCCAGTTACAGGGAACAGAGCACAGGCCTCCAAGTGTCCATGG 1172 AGCAGCGTGCAAATTGCAGGGATGAGTAGAGTAAAACCTCTACATGCAGC 1173 ACAGCATTCCTGGCAAACACAGGGGACCACAGTACACATGCTGTGGAATA 1174 CACCCAAGTATGCATCAGACACTTGTTTGGTAAACAGTAAATGTGTAAGA 1175 TCAATTACCTTGAGAGGGCCATCTGTGCTCCAGACATGTGGTTTGTGTGA 1176 GGAGACGGCTACCACTCACTATCTTCAGAGGAAAACAGGGCTCAGGGCTT 1177 GCACACAATGGACAGATACACATGGGTCACCCAAAACGTCACTGCATACA 1178 AACATCACTTTGTTCAACATGGATTTTGTTTTTATGGAGTCCAAATGCAG 1179 ACCCTAGTTCACCTTACAGCCTTGGGTTTGTCTGCTTTGGGAGATATATA 1180 TCCAGTTGATAGACAGACAAGACAGATACATTTTTTCCCTTTCTTACCAC 1181 AATGTCAATGCCTCATCTGAATATCATCATTACTCAAGAGTCAAGGGAAG 1182 AACCAAACGCTTCATATAAACAGGGCTGGGCTGGGCTAGATGGGGAGTGT 1183 TAGTTTCCAGTGTTTTCTGTCTCCATTCAGATCATTCCTATCAAAGCCCA 1184 GCTGGTCACCTCAAGCCAAGACACAGACATAAGGATCCCAATGGCCTTCC 1185 AGATGGCTGCTTCCACCTCCCATCTTGGCCACTAAGACTCTTTACACAGG 1186 AAAGTGAGTCACCCCAGTGAGAAGGGTTGCCAGCGGAAATAGGGCATGAA 1187 AATCACAGATAACCATGGGATTTCTTCCAAGTGGTCAGTGTAAAATAAac 1188 caccaccaccaccaccGAAAACACAAAAGAAGCAAAAAAAGTGCTTATTC 1189 AAAATCCAAGACAAAATACTGTGTGAGAGTCAGGCCACGGGGTTGCCTTT 1190 TCTCAGGCCACACAGCTTTCCCAGTCCGTTTGCTCGCATGGAACCGTAAG 1191 ATGTGAAGGCCTGCAGAGCGTGTGCTTGGGATGGAGGCTGGTACTGTTCA 1192 CCTGTGGGTCCAGACCAAAGGGCAAAGAGGCAGAAAACTGAAACTCTGTC 1193 CACCGGCACAGCTTAGGCCCTTCTGCTCATAGAGGCTCTGAAGAACCCCC 1194 ACCTCAGCCTTCACACATATCCTTCTGGCTGAACTACAGccagactggag 1195 tgccatggcatgatctctgctcactacaacctctgcctccagggttcaag1196 tgattcagcctcccaagtagctggaattacaggcacccaccactgtgccc1197 agctaatttattttttattttatttatttatttatttitttatttattta1198 tttatttattttgtatttttagcagagacagggtttcaccatgttggcca1199 gactggttttgaactcctgacctcaagtgatccaaagtgctgggattaca1200 ggcgtgagctaccgctcctggcTCAGACCCCATTTTTAAAAAATAttttc1201 aacatttattttagattcatggggtacatgtgcagatttgttacatgggt1202 atattgtgtgatgctgaggtctggggcacaaatgatctcctcactcaggc1203 agtgaccatagtacccaataggtatttttttagctctatccaccctccttDOCKET NO. STFD-015-PCT PATENT APPLICATION1204 ctctcttccctctagtagttgcagtgtctagtcttcccatctttatatcc1205 atgtgtacccaatgctcagctcccacttatacatgagaacgtgatatttg1206 gttttctgttcttatgttaatttgcttatgattatggtctccagctccat1207 ccatgttgctgtaaaggacatgatttcattcttttcatggctgcatagta1208 ttccatggtgtatatgtaccacatttccttcatccagtctaccgctgatg1209 gccacctaggtcattccatggctttgctactgtgaatagtgatgtgatg1210 gacatgtgagagcatgtgtctttttggcagaacaattattttcctttggg1211 taaatgcccagtaatggaattgctgggtggaatcgtagttctgttttaaa1212 ttatttcagaaatctccaaactgctttctgcattaatttttccatgaact1213 cattacactctgaccaacagtgtataggtgttccatttcctctgcagcc1214 tcaccagcatcttctgttttttgacattttaataatagccactctgCAGC1215 CAAGCTCTTTCAAGGCCAATGTGGAGAAGAGCCACAAACATTCCTTTTCC 1216 CGAAGAGAATTCTTGCCTGCCCACTGGTAGATTTCTTGGTTTCATCTGTC 1217 TTTCATTGTTTGTTTTTCAAAGAAAAACCAAAGGTAAAGTGATAATGATC 1218 TTCCACACCTGAACCAGTTTGTAGCCACCAGAGCCTGCTGGGAAGGGGCC 1219 CCTCACGCATGCATTGATCTTGTGACCTGGAATTTGAGAGATCAATAAGC 1220 CCCGTAGCAACCTACCATACAACTGCCCATCAGCGCTGATCCTTTCATGG 1221 GATTAGCTCAATTCTGGCTCTGCAGACACTGGCAGCCACAGTTGACAAAC 1222 CCTGGGCCTCTGTGGGCTTCCTTTGTCACCCAGGGCCACAGTGGGCTGCC 1223 TGTCCTAGGCAGAGACGCAGCAACATTCTCTTAAACTGAAATTAAGCATA 1224 AATCCACTTCACCGATAATCATCTGAGGGCTCAGTCCCTGCCTCCTTCCT 1225 CGGGGATTTTAAAACACACATTTCTCTGACCAAACAGGTAGGTGAGATCT 1226 GACTTTAAAAGGAGGGAAAATCGGGTTGAATTGGGGTATCAGGAATGAAT 1227 CCCAAGCATTTTTGTGTGGCGAGAGGCATCCACATCCCAAGCTGTACCTG 1228 GAGATGGAGAAAAATGCAGGAGAGAAGAAGAGAAAACAAAGGGGGACAAC 1229 GAGCCCTGGTTGCTTTGCCAAGGTCTTGGGCACAGACAGGGCCGGCTCTG 1230 GCTGGGAGCTGCTGCTCTAGGGGTTGGGAGAGTTCTGTTCATCCATGGTG 1231 CTCAGCAGCAGGGACTGGGGGCCGTGGTAGGTGCAGATGCCCAGACTCTC 1232 AAGCTTGCTCCTTGCATGGCTGGCAGGGGCATTGCTCCTTGTCACCAGGT 1233 GACTGCACAGGGCAGCTGTCATGGACATCCAGGGGGCCATCCAGAGCATC 1234 ACTGATGAGCATGTTGAATGCTTTGGGGCCATCGTCATGTTGGCCCCAGT 1235 TGCACACATGGTATCTTCTCTTTGCTTGGGGCGAAGGGGGCGGGGAGGGG 1236 CGGGGATAGTCTGCCATGCTCAGAGTTGTAATCATTCAGCAGCTGCTCCA 1237 TATATTCTAAATCCTTGCACAGGAAGGCTCCTCGGCCCAACTCCCCCAGG 1238 CTGGCCACACAGACACTGGGCTCCATTCCCAAGTCTTTGGTGGCTGCTGT 1239 GTCAGCTGGTGTCAGAGGCCCCAGGGTCAGCAATGAGTGGGGGTCTTGTG 1240 CTGCTTCTGCTAGGCCCAGCCAAGGGGCTGCTCTGTGCCTCCTGGGAGTC 1241 CCAGGGTCACTGCCACCTTAAGGGCCACATGCCATAGCTGG. AAGTCACTA1242 TATGTTTGGGGAAGAGTTGGAGATCGGGAAACCATTCCCTCATAACAAGGDOCKET NO. STFD-015-PCT PATENT APPLICATION1243 TAGTAAATAGTTTGGCAAAAAACTGAAGATAAAGTGGCAGTGCTGAGTAA 1244 TCATGGGCTTCCTACAGGTGATCGGGTTGATTTCTTGTTGCCACTGCCTG 1245 GCCTGAAGACAGTGCTTGGCTCAGCGGTGGCAGCAGACGAAGCAGCAGCT 1246 CAAGAGGATGATGATGGTGGCCCACACCAGCCAGAGCCACAGCAGTGTTT 1247 TTTGTCACAGGTGTAGCTTGGATTGTTGGTACCACACAGGCTTATCCCAT 1248 GGGGGTTCACCCTGGGTTGACAGGGGCTGGGCAGCACCTGGAGGACCAGG 1249 AacaccacccacacccccacacacacaccacccagaccATCTCCTCTGCA1250 AGCCCctcctgctcctgctcctccatcacagcactgccctccttctgctt1251 cctctcctcctctgccctCCAGAACAGTGGTCTTAAAGAGGTTTCTTGGC1252 CTTGGCACTTCTGTGGGCTCCCAATGTGCTGATGTGTGACACGCTGGCAT 1253 GCTTGGCAAGACCTCACTGCTGCCTTTGACTACACAGGGTCCTCTCTGTA 1254 CCCAGAGCAAACATATGCAAGGAAACCCCAGCACTGACCGAATCAGCTTC 1255 CTCGGAGGCCCCTCTCCACATGTGCTCCTGCTAACCCAGTCTGTACTCCC 1256 CACAAGCTGATGTCCTGCTTGGAGATGATCGTGCTGGCCCTCTTGCCCAA 1257 CAACTGGCTCCTGTGTCTGGAGGGGAGAAGACAAATCCTTGGTCTCCATC 1258 CCTCATGTTCTTGAGAAGTCTGCCTTTTATTCCTCCACAGAATAATACCA 1259 ACATGTTTACACTATTCCTATGtatagacattttcccatttagttttctc1260 tcccctccggagtggttattaatccagcggtacagataagaaaacaggtt1261 caaagaggcttattagtttacccacgtcccaagcccagcagatggtaggt1262 ctggggttgactcctcatttgcctggcttcaaagcccacgctctctgtgc1263 cccgcCTCACATCCCGCTATGACTGTGGTCTGAGGTGATGACAAGTCCGT 1264 CAGCGCTGACCTCTGATGTTTCTCCAGCCCCCTGTCACTATCACCCATTC 1265 CCTTCCTCCCTGCATCTCCTGAGGGGCACCTCCCAATTGTCCCATTCCAT 1266 GCGGCAAGACGACTGCTCTCAGAGAGCTCCTGGTTATGGCATTGCTCCCT 1267 ACCCTCCCACAGTGATCAAACTAGAATTCAAGCTCCCTGGGGAAATGTAG 1268 GGTTCTCCTGGCACCACCCTTGCCCCCACTCCCAGTCTCATGCCTCTTCA 1269 CTGCTCTCCTCCCCTGTCCCCTCCCCTGCTCAGAAGCCCTGGTGGCCCAT 1270 CCAACAAGCCATGCGCCTCCTGCCTCTGTCTCTGGACACTATGGCACTCT 1271 CAGACTGGAAGCCGTTCCTAACCTCCCCTTCACCCTTTTCAGAAAAGTCT 1272 TCCTGATTCTTCCTTGTCCCCACCTCCCTTGGGTCTGGCTCTGCTGGCCC 1273 TCCCTCGGGTCTGAGGCAGCCATCCTCCTCCTGTCTCCGCTTGCCTCTGT 1274 CCTAGTCCTGCTCAGGTGCTCAGGTGCAATAGATGCGTCCATCCTGGCAA 1275 TCAACTGTGTGCTCCTCAAGCGGGTACATCTTGTCTTACATATCCTGATA 1276 TCTCCAGTGATTAAGCAAAGCCTGGGATGTAATAAGCACCCAGTGAGTGG 1277 AGGAATAAACATGGAGTGGAGGGAAATGTGCTGAGAAAAGAAAGACCCTT 1278 CCAGAAGaatgattctcaaagagtggtccctaagccagcaacaccaaaat1279 ctcctgggaatttaggagaaacacaaaagctaggccctaccccacaccca1280 ccgagtcagatctcctgggacagggcccaacaaacagcatatttttttat1281 ttgagatagggtcttgctctgttgcccaggctgaagtgcaatggcatgatDOCKET NO. STFD-015-PCT PATENT APPLICATION1282 cactgctcactgcagccttgacctcccaagctcaagtgatcctcccacct1283 cagcctcccaagtagctaggaccacaggcgcacaccacaaacccagctaa1284 tattattattatttgtagagatggcaacctcatatgtcgctcaggctggt1285 ctcaaactcctaggctaaagtgatcgcctgcccctttgcctcccaaggtg1286 ctgggattacaggcgtgagccaccacacccagacagcaacctgcatttta1287 acatatcttccaggtcttctgatgcccgctgaaaacttgagaTTGGATAC1288 GGTAATGACATCCTTAGGCCAGTATtgaaaccgccattgcaaaattgtaa1289 ctgagacagtgaaacagatctgacccaaccaactctatcttgcggttttt1290 ttgtttttggttttgttttttttttttttttggagccggagtctcaa1291 tctgttgccaggctggagtgcagtggctcgatcttggctcactgctacct1292 ccacctcccaggttcaagtgattcccctgcctcagcctccccagtagctg1293 gaactacaggtgcacaccaccatgcctggctaattttttgtattttagta1294 gaggcggggtttcaccatgttggccgggctggtctcaaactcctgacctc1295 atgatccacctgcctctgcctaccaaagtactgggattatgggcgtgaac1296 aaccgcgcctggcctccatcttgcttttaacctccaagctgtccttattc1297 cttccccagcataggctgaactaactttgggaagaacttagtttctagtt1298 tgaaacaaagacggtaacagtccttgcccaaaacaaacctcctttttgcc1299 tggagactagactgtcttataggactaacaaatttgccaaaagattagaa1300 attatggtttaggagtcacgtagctggagtctgcaagattccaaacctcc1301 ccaaattgctcctggggataacgtcactattgtaaaacctaagatcagtg1302 cttgagatattttaaagaccctgcacttgatgcatcagctggcacaacgc1303 agatcgataaactagttcatctgatcttgtggcccccactcaggaaccga1304 ctcagcacaagaaagcagctggggtttcatctccaacccaacggatcagc1305 actcccgactcactgctttcccctccgcccaccaaattatcctctaaaac1306 tcggatcctcgaattcccggggagacggcaagatttgatttgagtaatag1307 taaaactccagtctcccacacagtctgctctgggtgaattactctttctc1308 tatgtcaattcccctgtcttgataaatcggttctgtctatacagcaggca1309 aggtgaacctattgggcagttacGATATCTCTCTGAAAACAAGTCACTAT1310 TTtttgttgtttttgttttgttttgtttttgagacagagtctctctct1311 gtcgccaggctggagtgcaatggtgcgatctcggctcactgcaacctccg1312 cctcccgggttcaagctattctcctgcctcagcctcccaagtagctggga1313 ttacaggcaagcgccaccacgcccggctaattttttgtatttttagtaga1314 gacagggtttcaccatgttagccaggctggtctcgaactcctgacctcag1315 gtgatccacccgcgtccgcctcccaaagtgctgggattacagacgtgagc1316 caccgcgcccggcTTCAGTCACTAACATTTTTACTGACTCTTCTggcacc 1317 atgattaaccccgacacgcactatcgcatgcaattctcacaaccccatga1318 ggtaggtattattattgctcctagcttacagataaagagacagagtttaa1319 gaggtttagCCACGCTACGGGGCTGCTGGGAGCCCGGCAGTCTGGCCACA1320 GGAGGTCGGTTTCACGGAAGGGCAGGATGTGGCGGCATCTCCTGAATTTADOCKET NO. STFD-015-PCT PATENT APPLICATION1321 AGGAGTCTTGGGGGCGCGGTGCTTCTCTGTCAttgggcaactcattttag 1322 cctcttggggtttcagttcctcaactgagaacaaggaatttaggttgaaa1323 tgaACATGCTGGAAAGCTTTCAAGAATTGCACACGTGAAATGCTCTTTGC 1324 GTGTCTCCCGGTCTCCCACCCGCCCCCGACACAGAGGCGCAGGAGTAACC 1325 CTGCTCCCTTCCGCGTCCTCGCCCCACCACGAGCTGCGCATTCTTCTCGC 1326 CCCCTCAAGTGGCCGAGCTCAGATTGCAGTTACTTAGGTCTAAAAAAATA 1327 AGGAAAGGCTGCCCCCTGCTGCCCACATGGATGCATGACCCCAACCTGAT 1328 ACCTGCCTAACTGGTCTTCCTAGCTTTTATGGAAAAAACGCTGCATATGA 1329 GCTTGGGCATACCGTCCAGAGAGGCAAAACTGGGACAAACTCCATCGGAA 1330 TTCTAAAAAACCATGATGCCAAGACAGAGTGGCA...

Claims

DOCKET NO. STFD-015-PCT PATENT APPLICATION CLAIMS1. A composition comprising:(i) a first set of capture probes comprising at least a first nucleic acid molecule comprising a first nucleic acid sequence comprising a maximal rearrangement domain of TRA, TRB, TRG, IGH, IGK, or IGL; and(ii) a second set of capture probes comprising at least a second nucleic acid molecule comprising a second nucleic acid sequence comprising a low recombination domain at or proximal to TRA, TRB. TRG. IGH. IGK. or IGL.

2. The composition of claim 1, wherein the first nucleic acid sequence comprises one or a combination of at least two of: SEQ ID NO: 1 or a functional variant thereof, SEQ ID NO: 2 or a functional variant thereof. SEQ ID NO: 3 or a functional variant thereof, SEQ ID NO: 4 or a functional variant thereof, SEQ ID NO: 5 or a functional variant thereof, SEQ ID NO: 6 or a functional variant thereof, SEQ ID NO: 7 or a functional variant thereof, SEQ ID NO: 8 or a functional variant thereof, SEQ ID NO: 9 or a functional variant thereof, SEQ ID NO: 10 or a functional variant thereof, SEQ ID NO: 11 or a functional variant thereof, SEQ ID NO: 12 or a functional variant thereof, SEQ ID NO: 13 or a functional variant thereof, SEQ ID NO: 14 or a functional variant thereof, SEQ ID NO: 15 or a functional variant thereof, SEQ ID NO: 16 or a functional variant thereof, and SEQ ID NO: 17 or a functional variant thereof.

3. The composition of either of claims 1 or 2, wherein the second nucleic acid sequence comprises one or a combination of at least two of: SEQ ID NO: 18 or a functional variant thereof, SEQ ID NO: 19 or a functional variant thereof, SEQ ID NO: 20 or a functional variant thereof, SEQ ID NO: 21 or a functional variant thereof, SEQ ID NO: 22 or a functional variant thereof, SEQ ID NO: 23 or a functional variant thereof, SEQ ID NO: 24 or a functional variant thereof, SEQ ID NO: 25 or a functional variant thereof, SEQ ID NO: 26 or a functional variant thereof, SEQ ID NO: 27 or a functional variant thereof, SEQ ID NO: 28 or a functional variant thereof, SEQ ID NO: 29 or a functional variant thereof, SEQ ID NO: 30 or a functional variant thereof, SEQ ID NO: 31 or a functional variant thereof, SEQ ID NO: 32 or a functional variant thereof, SEQ ID NO: 33 or a functional variant thereof, SEQ ID NO: 34 or a functional variantDOCKET NO. STFD-015-PCT PATENT APPLICATIONthereof, SEQ ID NO: 35 or a functional variant thereof, and SEQ ID NO: 36 or a functional variant thereof.

4. The composition of claim 1, wherein each first nucleic acid sequence independently comprises a sequence comprising at least a portion of SEQ ID NOS: 1-17, 131-602, 702-108, 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034, or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 1-17, 131-602, 702-108, 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010- 7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034.

5. The composition of claim 4, wherein the at least a portion is up to about 120 nucleotides.

6. The composition of claim 1, wherein each first nucleic acid sequence independently comprises a sequence of SEQ ID NOS: 1-17, 131-602, 702-108, 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034, or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 1-17. 131-602, 702-108, 1147— 1381, 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034.

7. The composition of claim 1 or 6, wherein each second nucleic acid sequence independently comprises a sequence comprising at least a portion of SEQ ID NOS: 18-36, 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752-5762. 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009. 7682-8205, 8264-8378, 8417-8492, 8557-8570. orDOCKET NO. STFD-015-PCT PATENT APPLICATION8573-8642, or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 18-36, 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716- 5737, 5738, 5739, 5741, 5742. 5744, 5745, 5747, 5748, 5752-5762, 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642.

8. The composition of claim 7, wherein the at least a portion is up to about 120 nucleotides.

9. The composition of any one of claims 1 through 8, wherein each second nucleic acid sequence independently comprises a sequence of SEQ ID NOS: 18-36, 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752-5762. 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009. 7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642, or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 18-36, 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752-5762, 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570. or 8573-8642.

10. The composition of any of claims 1 through 9, wherein the first set of capture probes comprises two nucleic acid molecules, and the second set of capture probes comprises two nucleic acid molecules; wherein each of the two nucleic acid molecules of the first set of capture probes comprises a nucleic acid sequence targeting a different maximal rearrangement domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL; and wherein each of the two nucleic acid molecules of the second set of capture probes comprises a nucleic acid sequence targeting a different low recombination domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL; orwherein the first set of capture probes comprises three nucleic acid molecules, and the second set of capture probes comprises three nucleic acid molecules, wherein each of the three nucleic acid molecules of the first set of capture probes comprises a nucleic acid sequence targeting a different maximal rearrangement domain selected from: TRA, TRB, TRG, IGH,DOCKET NO. STFD-015-PCT PATENT APPLICATION IGK, or IGL; and wherein each of the three nucleic acid molecules of the second set of capture probes comprises a nucleic acid sequence targeting a different low recombination domain selected from: TRA, TRB, TRG. IGH. IGK, or IGL; orwherein the first set of capture probes comprises four nucleic acid molecules, and the second set of capture probes comprises four nucleic acid molecules, wherein each of the four nucleic acid molecules of the first set of capture probes comprises a nucleic acid sequence targeting a different maximal rearrangement domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL; and wherein each of the four nucleic acid molecules of the second set of capture probes comprises a nucleic acid sequence targeting a different low recombination domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL; orwherein the first set of capture probes comprises five nucleic acid molecules, and the second set of capture probes comprises five nucleic acid molecules, wherein each of the five nucleic acid molecules of the first set of capture probes comprises a nucleic acid sequence targeting a different maximal rearrangement domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL; and wherein each of the five nucleic acid molecules of the second set of capture probes comprises a nucleic acid sequence targeting a different low recombination domain selected from: TRA, TRB, TRG. IGH. IGK. or IGL; orwherein the first set of capture probes comprises six nucleic acid molecules, and the second set of capture probes comprises six nucleic acid molecules, wherein each of the six nucleic acid molecules of the first set of capture probes comprises a nucleic acid sequence targeting a different maximal rearrangement domain selected from: TRA, TRB, TRG, IGH, IGK. or IGL; and wherein each of the six nucleic acid molecules of the second set of capture probes comprises a nucleic acid sequence targeting a different low recombination domain selected from: TRA, TRB, TRG, IGH, IGK, or IGL.

11. The composition of any one of claims 1 through 10 further comprising a third set of capture probes comprising at least a third nucleic acid molecule comprising a third nucleic acid sequence targeting V, D, or J domain from at least one of: TRA, TRB, TRG, IGH, IGK, or IGL.DOCKET NO. STFD-015-PCT PATENT APPLICATION12. The composition of claim 11, wherein each third nucleic acid sequence independently comprises a sequence comprising at least a portion ofSEQ ID NOS: 9035-9553, or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 9035-9553.

13. The composition of claim 12, wherein the at least a portion is up to about 120 nucleotides.

14. The composition of claim 11, wherein each third nucleic acid sequence independently comprises a sequence of SEQ ID NOS: 9035-9553, or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 9035-9553.

15. The composition of any one of claims 1 through 14 further comprising a fourth set of capture probes comprising at least a fourth nucleic acid sequence targeting (i) recurrently mutated genes in tumor DNA and (ii) TCR and BCR V and J regions.

16. The composition of claim 15, wherein each fourth nucleic acid sequence targeting (i) recurrently mutated genes in tumor DNA independently comprises a sequence comprising at least a portion of SEQ ID NOS: 11,815-13,436, or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 11,815-13,436.

17. The composition of claim 16, wherein the at least a portion is up to about 120 nucleotides.

18. The composition of claim 15, wherein each fourth nucleic acid sequence targeting (i) recurrently mutated genes in tumor DNA independently comprises one of SEQ ID NOS: 11,815-13.436, or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 11,815-13,436.

19. The composition of any one of claims 15 through 18, wherein the fourth nucleic acid sequence targeting (i) recurrently mutated genes in tumor DNA targets a recurrent mutated gene of a lymphoma.DOCKET NO. STFD-015-PCT PATENT APPLICATION20. The composition of any one of claims 15 through 19, wherein each fourth nucleic acid sequence targeting (ii) TCR and BCR V and J regions independently comprises a sequence comprising at least a portion of SEQ ID NOS: 9,554-11,814, or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 9,554-11,814.

21. The composition of claim 20, wherein the at least a portion is up to about 120 nucleotides.

22. The composition of any one of claims 15 through 19, wherein each fourth nucleic acid sequence targeting (ii) TCR and BCR V and J regions independently comprises one of SEQ ID NOS: 9,554-11,814, or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 9,554-11,814.

23. A kit comprising at least one of:a first set of capture probes, and / or a second set of capture probes, and / or a third set of capture probes, and / or a fourth set of capture probes;wherein the first set of capture probes comprises a plurality of nucleic acid sequences comprising SEQ ID NO: 1 or a functional variant thereof, SEQ ID NO: 2 or a functional variant thereof, SEQ ID NO: 3 or a functional variant thereof, SEQ ID NO: 4 or a functional variant thereof, SEQ ID NO: 5 or a functional variant thereof, SEQ ID NO: 6 or a functional variant thereof, SEQ ID NO: 7 or a functional variant thereof, SEQ ID NO: 8 or a functional variant thereof, SEQ ID NO: 9 or a functional variant thereof, SEQ ID NO: 10 or a functional variant thereof, SEQ ID NO: 11 or a functional variant thereof, SEQ ID NO: 12 or a functional variant thereof, SEQ ID NO: 13 or a functional variant thereof, SEQ ID NO: 14 or a functional variant thereof, SEQ ID NO: 15 or a functional variant thereof, SEQ ID NO: 16 or a functional variant thereof, and SEQ ID NO: 17 or a functional variant thereof;wherein the second set of capture probes comprises one or a plurality' of nucleic acids sequences comprising SEQ ID NO: 18 or a functional variant thereof, SEQ ID NO: 19 or a functional variant thereof, SEQ ID NO: 20 or a functional variant thereof, SEQ ID NO: 21 or a functional variant thereof, SEQ ID NO: 22 or a functional variant thereof, SEQ ID NO: 23 orDOCKET NO. STFD-015-PCT PATENT APPLICATIONa functional variant thereof, SEQ ID NO: 24 or a functional variant thereof, SEQ ID NO: 25 or a functional variant thereof, SEQ ID NO: 26 or a functional variant thereof, SEQ ID NO: 27 or a functional variant thereof, SEQ ID NO: 28 or a functional variant thereof, SEQ ID NO: 29 or a functional variant thereof, SEQ ID NO: 30 or a functional variant thereof. SEQ ID NO: 31 or a functional variant thereof, SEQ ID NO: 32 or a functional variant thereof, SEQ ID NO: 33 or a functional variant thereof, SEQ ID NO: 34 or a functional variant thereof, SEQ ID NO: 35 or a functional variant thereof, and SEQ ID NO: 36 or a functional variant thereof;wherein the third set of capture probes comprises one or a plurality of nucleic acid sequences selected from SEQ ID NOS: 9035-9553; andwherein the fourth set of capture probes comprises one or a plurality of nucleic acid sequences comprising sequences selected from Table 4.

24. A kit comprising at least one of:a first set of capture probes, and / or a second set of capture probes, and / or a third set of capture probes, and / or a fourth set of capture probes;wherein the first set of capture probes comprises a plurality of first nucleic acid sequences, each of the plurality’ of first nucleic acid sequence independently selected from SEQ ID NOS: 1-17, 131-602, 702-108, 1147-1381, 1515-3882, 5054-5530, 5586-5715, 5740, 5743, 5746, 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034 or a functional variant thereof having at least about 75% sequence identity to 1-17, 131-602, 702-108. 1147-1381, 1515-3882, 5054-5530. 5586-5715, 5740, 5743, 5746, 5749-5751, 5763, 5764, 5767, 5769-6048, 6573-6630, 6746-6783, 6860-6923, 6938, 6939, 7010-7079, 7080-7479, 7480-7619, 7620-7681, 8206-8263, 8379-8416, 8493-8556, 8571-8572, or 8643-9034;wherein the second set of capture probes comprises one or a plurality of second nucleic acids sequences, each of the second nucleic acid nucleic acid sequences independently selected from SEQ ID NOS: 18-36, 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752-5762, 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492, 8557-8570, or 8573-8642 or a functional variant thereof having at least aboutDOCKET NO. STFD-015-PCT PATENT APPLICATION75% sequence identity to SEQ ID NOS: 18-36, 37-130, 603-701, 1009-1146, 1382-1514, 3883-5053, 5531-5585, 5716-5737, 5738, 5739, 5741, 5742, 5744, 5745, 5747, 5748, 5752- 5762, 5965, 5966, 5768, 6049-6572, 6631-6745, 6784-6859, 6924-6937, 6940-7009, 7682-8205, 8264-8378, 8417-8492. 8557-8570, or 8573-8642;wherein the third set of capture probes comprises one or a plurality of third nucleic acid sequences, each third nucleic acid sequence independently selected from SEQ ID NOS: 9035-9553 or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 9035-9553; andwherein the fourth set of capture probes comprises one or a plurality of fourth nucleic acid sequences, each fourth nucleic acid sequence independently selected from SEQ ID NOS: 9554–13,436 or a functional variant thereof having at least about 75% sequence identity to SEQ ID NOS: 9554–13,436.

25. The kit of claim 23 or 24, wherein at least one nucleic acid sequence from the capture probes is immobilized to one or a plurality’ of solid supports.

26. The kit of either of any one of claims 23 through 25. wherein the kit comprises a single solid support comprising a series of vessels, each vessel comprising a bottom surface and side walls, wherein the at least one nucleic acid sequence from the capture probes is immobilized to the solid support at the bottom surface.

27. The kit of claim 23 or 24, wherein the kit comprises a plurality of solid supports, each solid support comprising a vessel, wherein at least one nucleic acid sequence of a set of capture probes is positioned within at least one vessel.

28. The kit of claim 27, wherein the at least one nucleic acid sequence is in solid phase, and, optionally, lyophilized in the at least one vessel.

29. The kit of claim 27, wherein the kit comprises the at least one nucleic acid sequence in solution and, optionally, immobilized to a surface of the vessel.DOCKET NO. STFD-015-PCT PATENT APPLICATION30. A system comprising a solid support, and a first set of probes, a second set of probes and a third set of probes;wherein the first set of probes are complementary to a maximal rearrangement domain of one or a combination of two or more of TRA. TRB. TRG, IGH, IGK. or IGL; the second set of probes are complementary to a low recombination domain of one or a combination of two or more of TRA, TRB, TRG, IGH, IGK, or IGL; and the third set of probes are complementary to a V, D, or J domain from at least one of: TRA, TRB, TRG, IGH, IGK, or IGL.

31. A system comprising a solid support comprising a plurality of vessels, wherein each vessel comprises: (i) at least a first set of capture probes and / or a second set of capture probes; and (ii) a set of sequencing primers;wherein each sequencing primer in the set of sequencing primers comprises a nucleic acid sequence complementary to a maximal rearrangement domain of TRA, TRB, TRG. IGH, IGK, or IGL; or complementary to one of a plateau domain to the respective genes for TRA, TRB, TRG, IGH, IGK, or IGL; andwherein the first set of probes are complementary to a maximal rearrangement domain of one or a combination of two or more of TRA, TRB, TRG, IGH, IGK, or IGL;wherein the second set of probes are complementary to a low recombination domain of one or a combination of two or more of TRA, TRB, TRG, IGH, IGK, or IGL; and wherein the third set of probes are complementary to a V, D, or J domains from at least one of: TRA, TRB, TRG, IGH, IGK, or IGL.

32. A method of preparing a sample comprising:exposing the sample to:(i) the composition of any one of claims 1 through 22; or(ii) the system of claims 30 or 31;wherein the sample comprises DNA from a subject.

33. The method of claim 32, wherein the sample is a blood, saliva or urine sample from a healthy subject; or wherein the sample is a blood, saliva, or urine sample from a patient diagnosed with or suspected of having a hyperproliferative disorder.DOCKET NO. STFD-015-PCT PATENT APPLICATION34. The method of claim 32, wherein the sample is from a test subject and the DNA is cell-free DNA.

35. The method of claim 32, wherein the subject is receiving CAR-T therapy.

36. The method of claim 34, wherein the test subject is selected from a peripheral T-cell lymphoma patient, a myeloma patient, a patient receiving CAR-T therapy, or a bladder cancer patient.

37. The method of any one of claim 32 through 36 further comprising subjecting the sample to hybridization conditions in the presence of at least one of the first set of capture probes, the second set of capture probes, the third set of capture probes, and / or the fourth set of capture probes.

38. The method of any one of claims 32 through 37 further comprising a step of obtaining the sample prior to the step of exposing.

39. The method of any one of claims 32 through 38 further comprising extracting the DNA from the sample prior to the step of exposing.

40. The method of any one of claims 32 through 39 further comprising sequencing the DNA to produce sequence data.

41. The method of claim 40, wherein the sequencing comprises polymerization from a set of sequencing primers, wherein each sequencing primer in the set of sequencing primers comprises sequencing nucleic acid sequence complementary to one of the location of maximal rearrangement for a different one of the genes for TRA, TRB, TRG, IGH, IGK, or IGL or one of the location of low recombination close to the respective genes for TRA, TRB, TRG, IGH, IGK, or IGL.DOCKET NO. STFD-015-PCT PATENT APPLICATION42. A method of determining the total amount of T-cells and / or B-cells in a subject or a fraction of the T cells and / or B cells in a sample, the method comprising:exposing a sample to:(i) the composition of any one of claims 1 through 22; or(ii) the system of claims 30 or 31;wherein the sample comprises DNA from a subject.

43. The method of claim 42 further comprising sequencing at least a portion of the DNA.

44. The method of claims 42 or 43, wherein the location of maximal rearrangement for a gene for one of TRA, TRB, TRG, IGH, IGK, or IGL is a valley region and the location of low recombination close to the gene for TRA, TRB, TRG, IGH. IGK, or IGL is a shoulder region; andwherein the method further comprises determining a median sequence depth for each valley region and a median sequence depth for each shoulder region, subtracting the median sequence depth for each valley region from the median sequence depth for each respective shoulder region to obtain a respective depth of valley for each valley region, and dividing each respective depth of valley by the median depth for the respective shoulder region to obtain a fraction of the T-cells and / or B-cells.

45. The method of any of claims 42 through 44, wherein the DNA is cfDNA and the method further comprises extracting genomic DNA from the cfDNA prior to the step of exposing.

46. A method of determining the total amount of T-cells and / or B-cells in a subject or determining a fraction of the T cells and / or B cells in a sample, the method comprising:(a) extracting genomic DNA from a sample from the subject;(b) sequencing at least a portion of the genomic DNA;(c) exposing the genomic DNA to the composition of any of claims 1 through 22 or the system of claims 30 or 31.DOCKET NO. STFD-015-PCT PATENT APPLICATION47. The method of claim 46 further comprising a step of obtaining baseline read depth of at least the portion of the genomic data.

48. The method of claim 46 or claim 47 further comprising determining the total amount of T-cells and / or B-cells in the subject or determining a fraction of the T cells and / or B cells in the sample by one or more of:(a) determining the number and / or sequence of maximal rearranged domain (MRD or LMR) in the genomic DNA;(b) calculating the ratio of αβTcells to γδTcells from the genomic DNA;(c) calculating the number and / or sequence of an LMR in an IgH portion of the genomic DNA; (d) calculating the ratio of Igκ to Igλ in the genomic DNA; and(e) quantifying the number Ig class switches in the genomic DNA.

49. The method of claim 48 further comprising correlating the number and / or sequence of LMR in an IgH portion of the genomic DNA and / or to the number Ig class switches in the genomic DNA to the number of B cells in sample.

50. The method of claim 48 or claim 49 further comprising correlating one or more of: (i) the number and / or sequence of maximal rearranged regions (LMRs) in the genomic DNA; (ii) the ratio of αβT cells to γδT cells; and(iii) the ratio of Igκ to Igλ in the genomic DNA; to the number of T cells in the sample.

51. A computer-implemented method of determining the total amount of T-cells and / or B-cells in a subject or in a sample, the method comprising:sequencing the genomic DNA to produce sequence data;executing processor executable instructions for determining a median sequence depth across at least a portion of the DNA.

52. The method of claim 51 further comprising:(i) extracting genomic DNA from a sample comprising DNA from the subject; andDOCKET NO. STFD-015-PCT PATENT APPLICATION(ii) contacting the genomic DNA with the composition of any of claims 1 through 22 or the system of claims 30 or 31.

53. The method of claim 52, wherein the location of maximal rearrangement for a gene for one of TRA, TRB, TRG, IGH, IGK, or IGL is a valley region and the location of low recombination proximate to TRA, TRB, TRG, IGH, IGK, or IGL is a shoulder region; and wherein the step of determining a median sequence depth comprises subtracting the median sequence depth for each valley region from the median sequence depth for each respective shoulder region to obtain a respective depth of valley for each valley region, and dividing each respective depth of valley by the median depth for the respective shoulder region to obtain a fraction of the T-cells and / or B-cells.

54. A computer program product encoded on a computer-readable storage medium, the computer program product comprising instructions for:(a) determining, from sequence data comprising valley region sequence, reads for a location of maximal rearrangement for one or more gene selected from V, D, and J genes in a DNA; and(b) determining, from the sequence data, shoulder region sequence reads for a location of low recombination proximate to the one or more gene,(c) determining a median sequence depth for each valley region and a median sequence depth for each shoulder region, the median sequence depth calculated by subtracting the median sequence depth for each valley region from the median sequence depth for each respective shoulder region to obtain a respective depth of valley for each valley region; and dividing each respective depth of valley by the median depth for the respective shoulder region.

55. The computer program product of claim 54 further comprising instructions for:(d) determining a fraction of the T-cells and / or B-cells by correlating the values of any of steps (a), (b), (c), or combination thereof.

56. The computer program product of claim 54 or 55, wherein the DNA is genomic DNA from a cfDNA sample or genomic DNA from a saliva, urine or blood sample.DOCKET NO. STFD-015-PCT PATENT APPLICATION57. A method of monitoring disease progression of a subject comprising determining the total amount of T-cells and / or B-cells in the subject, the method comprising:(a) obtaining sequence data from DNA from the subject; and(b) determining a median sequence depth of a set of genomic DNA within the DNA sample by subtracting the median sequence depth for each valley region from the median sequence depth for each respective shoulder region to obtain a respective depth of valley for each valley region, and subsequently dividing each respective depth of valley by the median depth for the respective shoulder region.

58. The method of claim 57 further comprising:a step of (c) exposing at least a portion of the genomic DNA to a set of primers complementary to the DNA and specific, such that sequence data are generated for one or more of:(i) determining the number and / or sequence of LMRs in the genomic DNA;(ii) calculating the ratio of αβTcells to γδTcells from the genomic DNA;(iii) calculating the number and / or sequence of LMRs in an IgH portion of the genomic DNA; (iv) calculating the ratio of Igκ to Igλ in the genomic DNA; and(v) quantifying the number Ig class switches in the genomic DNA; anda step of (d) of correlating the sequence data across a portion of genomic DNA in the cfDNA to a fraction of the T-cells and / or B-cells in the subject.

59. The method of claim 57 or 58, wherein, if monitoring the number of B cells in the subject, the method further comprises correlating the number and / or sequence of LMRs in an IgH portion of the genomic DNA and / or to the number Ig class switches in the genomic DNA to the number of B cells in the subject.

60. The method of any of claims 57 through 59, wherein, if the monitoring the number of T cells, the method further comprises correlating one or more of:(i) the number and / or sequence of maximal rearranged regions (LMR) in the genomic DNA; (ii) the ratio of αβT cells to γδT cells; and(iii) the ratio of Igκ to Igλ in the genomic DNA;DOCKET NO. STFD-015-PCT PATENT APPLICATIONto the number of T cells in the subject.

61. The method of any of claims 57 through 60, wherein the subject has been diagnosed with or is suspected of having a hyperproliferative disorder.

62. The method of any of claims 57 through 61, wherein the genomic DNAis from a cfDNA sample.

63. The method of claim 61, wherein the subject is a peripheral T-cell lymphoma patient, a myeloma patient, a patient receiving CAR-T therapy, or a bladder cancer patient.

64. The method of any of claims 57 through 63, the sequence data comprises valley region sequence reads for a location of maximal rearrangement for one or more gene selected from V, D, and J genes and shoulder region sequence reads for a location of low recombination proximate to the one or more genes.

65. The method of any of claims 57 through 64 further comprising a step of correlating the sequence data to the number of T cells and / or B cells in the subject; and subsequently correlating the number of T cells and / or B cells in the subject with disease progression.

66. The method of claim 65, wherein, if the number of T cells and / or B cells are elevated in the subject, the disease progression is negligible or limited; and wherein, if the number of T cells and / or B cells are not elevated in the subject, the disease has likely progressed.

67. 5A method of determining whether a subject is a responder or non-responder to a therapeutic agent comprising:(a) obtaining sequence data from DNA from the subject exposed to a therapeutic agent; and(b) determining a median sequence depth of a set of genomic DNA within the DNA sample by subtracting the median sequence depth for each valley region from the median sequence depth for each respective shoulder region to obtain a respective depth of valley for each valleyDOCKET NO. STFD-015-PCT PATENT APPLICATIONregion, and subsequently dividing each respective depth of valley by the median depth for the respective shoulder region; and(c) determining the number of T cells and / or B cells in the subject by comparing the sequence data and the median sequence depth of the DNA to the number of T cells and or B cells in a control subject.

68. The method of claim 67, wherein:(i) if the number of T cells and / or B cells in the subject is higher than a control subject and the control subject is a non-responder to the therapeutic agent, then determining that the subject is a responder to the therapeutic agent; or(ii) if the number of T cells and / or B cells in the subject is about equivalent to a control subject and the control subject is a responder to the therapeutic agent, then determining that the subject is a responder to the therapeutic agent; or(iii) if the number of T cells and / or B cells in the subject is lower than a control subject and the control subject is a responder to the therapeutic agent, then determining that the subject is a non-responder to the therapeutic agent; or(iv) if the number of T cells and / or B cells in the subject is about equivalent to a control subject and the control subject is a non-responder to the therapeutic agent, then determining that the subject is a non-responder to the therapeutic agent.

69. The method of claim 67 or 68. wherein the step of obtaining sequence data comprises exposing at least a portion of the cfDNAto a set of primers complementary to the cfDNA and specific, such that sequence data are generated for one or more of:(i) determining the number and / or sequence of maximal rearranged regions (LMRs or MRDs) in the genomic DNA;(ii) calculating the ratio of otPTcells to γδTcells from the genomic DNA;(iii) calculating the number and / or sequence of LMRs or MRDs in an IgH portion of the genomic DNA;(iv) calculating the ratio of Igκ to Igλ in the genomic DNA; and(v) quantifying the number Ig class switches in the genomic DNA; andDOCKET NO. STFD-015-PCT PATENT APPLICATIONwherein the method further comprises a step (c) of correlating the sequence data across a portion of genomic DNA in the DNA to a fraction of the T-cells and / or B-cells in the subject.

70. The method of any of claims 67 through 69, wherein, if monitoring the number of B cells in the subject, the method comprises correlating the number and / or sequence of LMR in an IgH portion of the genomic DNA and / or to the number Ig class switches in the genomic DNA to the number of B cells in the subject.

71. The method of any of claims 67 through 70, wherein, if the monitoring the number of T cells from a sample, the method further comprises correlating one or more of:(i) the number and / or sequence of maximal rearranged regions (LMR) in the genomic DNA; (ii) the ratio of αβT cells to γδT cells; and(iii) the ratio of Igκ to Igλ, in the genomic DNA;to the number of T cells in the subject.

72. The method of any of claims 67 through 71, wherein the subject has been diagnosed with or is suspected of having a hyperproliferative disorder.

73. The method of claim 72, wherein the subject has cancer.

74. The method of claim 73, wherein the subject is subject with peripheral T-cell lymphoma, myeloma, or bladder cancer patient.

75. The method of any of claims 67 through 74, wherein the sequence data comprises valley region sequence reads for a location of maximal rearrangement for one or more gene selected from V, D, and J genes and shoulder region sequence reads for a location of low recombination proximate to the one or more genes.

76. The method of any of claims 67 through 75, wherein the therapeutic agent is CAR-T therapy.DOCKET NO. STFD-015-PCT PATENT APPLICATION77. The method of any of claims 67 through 76 further comprising a step of correlating the sequence data to the number of T cells and / or B cells in the subject.

78. The method of claims any of claims 67 through 77. wherein, if the number of T cells and / or B cells are elevated in the subject and the subject has been diagnosed with a hyperproliferative disorder, then the therapeutic agent is likely therapeutically effective.

79. The method of any of claims 67 through 78, wherein the DNA sample is a cfDNA sample or a DNA sample from bodily fluid.

80. The method of claim 79, wherein the bodily fluid is saliva, cell free plasma or urine.

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