System for telomere measurement and methods of using the same

Abstract

The disclosure relates to a system, composition and computer program products for determining the length of a telomere in a sample. Methods of diagnosing a subject with a telomeric disorder are also disclosed herein with steps of correlating the telomere length with the diagnosis of disease and, optionally, in connection with the detection of other information such as the presence of mutations at certain genes with the chromosomal DNA of the subject or the methylation frequency of the chromosomal DNA.

Description

ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION SYSTEM FOR TELOMERE MEASUREMENT AND METHODS OF USING THE SAME STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

[0001] This invention was made with Government support under contracts AG033747 and CA197563 awarded by the National Institutes of Health. The Government has certain rights in the invention. CROSS REFERENCE TO RELATED APPLICATIONS

[0002] This application claims the benefit of U.S. Provisional Application No. 63 / 604,168, which was filed November 29, 2023, entitled, “SYSTEM FOR TELOMERE MEASUREMENT AND METHODS OF USING THE SAME,” and U.S. Provisional Application No. 63 / 720,726, which was filed November 14, 2024, entitled, “SYSTEM FOR TELOMERE MEASUREMENT AND METHODS OF USING THE SAME,” each of which are incorporated by reference in their entireties. SEQUENCE LISTING

[0003] The Sequence Listing filed herewith has the filename STFD-006-PCT Sequence Listing.xml, was created on November 29, 2024, has a file size of 737,000 bytes, and is incorporated herein by reference in its entirety. FIELD

[0004] The disclosure relates to a system, device and software program product for measuring telomere length in isolated cell samples from subjects. The disclosure relates to methods of predicting age of a subject or health of a subject by measuring distribution of telomere length across a plurality of samples from a subject. BACKGROUND

[0005] Telomeres are nucleoprotein structures at the ends of all linear chromosomes which act to prevent the recognition of chromosome ends by the cell’s double-strand break repair machinery (1,2). Telomeric repeats––stretches of non-coding, stereotypical repeats––are requiredATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION for the function of shelterin, the protein complex (TIN2, TPP1, POT1, TRF1, TRF2, RAP1) which suppresses double-strand break repair and serves as the recruitment complex for telomerase, the ribonucleoprotein holoenzyme responsible for maintaining telomere length in cells (3,4). In non-malignant cells lacking telomerase, telomeres erode by several dozens of basepairs during each cell division due to the inability of DNA polymerase II to replicate the entire length of linear chromosomes (5,6). Eventually, in the presence of competent DNA- damage response (DDR) machinery, telomere erosion leads to replicative senescence and apoptosis; and in cells with defective DDR, telomere crisis––a process characterized by rampant chromosomal instability stemming from end-to-end fusions at chromosomal termini lacking functional telomeres (7,8). The end-to-end fusions and chromosomal instability seen in crisis can be replicated by sabotaging the shelterin complex via deletion or destabilization of TRF2 (9). In self-renewing cells––such as stem, germ, and cancer cells––telomerase is responsible for elongating telomeres during mitosis and is recruited to telomeres by the shelterin component TPP1 and retained at the elongating telomere end by POT1 resulting in stable telomere length over time (10). In a minority of cancers, an alternative, homologous recombination dependent telomere lengthening mechanism (ALT) is responsible for maintaining telomere length (11). Therefore, telomere length is an important biomarker for the replicative potential as well as the replicative history of a cell in cells with insufficient telomerase to indefinitely maintain telomere length, and, consequently, ensuring telomere maintenance by upregulation of telomerase or initiating ALT is required for any cell aspiring towards indefinite self-renewal. Current telomere measurement techniques are incapable of measuring enriched populations of telomere length in a sample; are incapable of reaching resolution sufficient for diagnosis of human health, and are incapable of simultaneously measuring DNA methylation or frequency of mutation across chromosomal DNA. SUMMARY OF EMBODIMENTS

[0006] The disclosure relates to a method of determining telomere length comprising: (a) detecting primer alignment within a chromosome in a sample; (b) determining telomere length of the chromosome in the sample.

[0007] In some embodiments, the step of detecting the primer alignment comprises utilizing T2T-CHM13 assembly and determining a score corresponding to the percent identity of theATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION chromosome in the sample. In some embodiments, the step of determining telomere length comprises calculating an average telomere length after repeating steps (a) and (b) on the sample and comparing the average telomere length to the length of a control sample or control dataset.

[0008] In some embodiments, the method further comprises a step of (c) performing a sequencing analysis before or after step (b). In some embodiments, the step of determining telomere length comprises extending a single stranded portion of the telomere, exposing the telomere to a probe and quantifying the amount of the probe based upon the intensity of signal on an image of the sample. In some embodiments, the step of determining telomere length is performed by sequencing chromosomal DNA from a sample by performing Nanopore or single- molecule real time sequencing or long-read sequencing; generating a computer-readable file comprising sequence information from the chromosomal DNA; and analyzing the sequence information by a computer implemented method of (i) identifying an end of a telomere and a telomeric boundary associated with the end of the telomere; and (ii) calculating the number of nucleotides between and including the end of a telomere and a telomeric boundary associated with the end of the telomere. In some embodiments, the method further comprises a step of utilizing the telomere length to determine whether the subject has a telomeric disorder as compared to known lengths of control sequences and correlating the telomeric length to the likelihood that the subject has the telomeric disorder. In some embodiments, the method is free of performing polymerase chain reaction and long-read sequencing during the analysis of the telomer region within the chromosomal DNA.

[0009] In some embodiments, the disclosure relates to a method of determining the length of a telomere, wherein the step of performing a sequencing analysis is a computer-implemented step in which a computer program product executes the instruction for: (a) compiling nucleic acid information from the sample; (b) aligning sequences against a control sequence; (c) calculating a score based upon the percent identity of the nucleic acid information as compared to a control; and, optionally, (d) displaying the score or percent identity on a display; or (a) compiling nucleic acid information from the sample; (b) aligning sequences against a control sequence to identify a telomer sequence within the nucleic acid information;ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION (c) estimating a location of a telomeric boundary to determine the beginning of a non- telomeric sequence within the nucleic acid information; (d) determining the length of the telomere after measuring the number of nucleotides between the end of 5’ or 3’ end of the telomere sequence and the telomeric boundary; ad optionally calculating and / or displaying a score based upon the percent identity of the nucleic acid information relative to a control sequence. In some embodiments, the methods further comprise a step of obtaining a sample from the subject prior to performance of the sequencing or the analyzing of the sequence information. Furthermore, in some embodiments, the method comprises a step of isolating chromosomal DNA from the sample of a subject prior to sequencing the chromosomal DNA.

[0010] The disclosure also relates to a method of determining telomere length distribution from a plurality of samples comprising: (a) detecting primer alignment within a chromosome in a sample; (b) determining telomere length of the chromosome in the sample.

[0011] In some embodiments, the step of determining telomere length comprises calculating an average telomere length after repeating steps (a) and (b) on the sample and comparing the average telomere length to the length of a control sample or control dataset. In some embodiments, the method further comprises a step obrieff (c) performing a sequencing analysis before or after step (b).

[0012] In some embodiments, the step of determining telomere length comprises extending a single stranded portion of the telomere, exposing the telomere to a probe and quantifying the amount of the probe based upon the intensity of signal on an image of the sample. In some embodiments, the probe is a capture oligonucleotide comprising a barcode region and the probe associates with the barcode region associates with the telomere in the chromosomal DNA, covalently or non-covalently.

[0013] The disclosure also provides a method comprising a step of determining telomere length comprising generating a computer-readable file comprising sequence data of chromosomal DNA within the sample by performing nanopore sequencing prior to generating the computer readable file. In some embodiments, the method is free of performing polymerase chain reaction and long-read sequencing. In some embodiments, the step of performing aATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION sequencing analysis is a computer-implemented step in which a computer program product executes the instruction for: (a) compiling nucleic acid information from the sample; (b) aligning sequences against a control sequence; (c) calculating a score based upon the percent identity of the nucleic acid information as compared to a control; and, optionally, (d) displaying the score or percent identity on a display.

[0014] The disclosure further relates to a computer-implemented method of determining telomere length or telomere length distribution among one or a plurality of samples, on a device that accesses a computer memory, the method comprising: (a) detecting a presence of a telomere at the end of genetic material from the sample; (b) detecting a presence of a telomere boundary from the sample distal from the telomere end; and (c) measuring the length of the telomere from the end of the genetic material to the telomere boundary. In some embodiments, the method comprises the steps of Figure 10.

[0015] In some embodiments, the method further comprises a step of (d) determining a score based upon the length of the telomere and compared to the distribution of telomere lengths from a control population of samples. In some embodiments, the method further comprises a step (e) comparing the length of the telomere from the sample to a population distribution of telomere lengths samples of the same or substantially the same age. In some embodiments, in a system comprising a controller and processor in operable communication to a microscope, camera, display and computer memory, the method comprises: capturing a digital image of the sample, displaying the digital image on the display prior to performing steps (a) through (c); and performing steps (a) through (c) on the digital image; wherein the digital image is captured through the microscope at a magnification sufficient for a user to visualize the telomere on the display.

[0016] In some embodiments, the method further comprises a step of collecting additional data on the sample prior to, subsequent to or contemporaneous with performing step (c). In some embodiments, the additional data collection comprises the step of identifying one or a plurality of mutations in the chromosomal DNA of the sample by comparing the sequence of a telomere and / or exon within the chromosomal DNA to control sequences known to be free ofATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION one or a plurality of mutations. In some embodiments, the method further comprises the step of performing a sequencing reaction of the sample prior to performing steps (a) through (c).

[0017] The disclosure relates to methods of determining telomere length wherein the telomere length is at least about 3,000 basepairs, 4,000 basepairs, 5,000 basepairs, or 6,000 basepairs of DNA. In some embodiments, the telomere length is from about 3,500 to about 6,000 basepairs of DNA. In some embodiments, the methods are free of determining telomere length with an average telomere length above about 7.1 kilobases (kb), 7.2kb, 7.3 kb, 7.4 kb, 7.5 kb, 7.6 kb, 7.7 kb, 7.8 kb, 7.9 kb, 8.0 kb, 8.1 kb, 8.2 kb, 8.3 kb, 8.4 kb, 8.5 kb, 8.6 kb, or about 8.7 kb. In some embodiments, the methods associated therewith are free of a step of registering a portion of a chromosome that is over about 11 kb in length, about 12 kb in length, about 13 kb in length, about 14 kb in length, or about 15 kb in length. In some embodiments, the methods associated therewith are free of a step of determining telomere length of telomeres over about 9 kb in length, about 10 kb in length, about 11 kb in length, about 12 kb in length, or about 13 kb in length, over about 14 kb in length, about 15 kb in length, about 16 kb in length, about 17 kb in length, about 18 kb in length, about 19 kb in length, or about 20 kb in length.

[0018] The disclosure also relates to a computer program product encoded on a computer- readable storage medium comprising instructions for: (a) registering at least a portion of a chromosome sequence of a sample comprising a telomere; (b) aligning the telomere of the sample to identify the end of the chromosome; (c) identifying a telomere boundary on the chromosome; (d) measuring a length of the telomere from about the end of the chromosome to the boundary of the telomere. In some embodiments, the computer program product further comprises instructions for sequencing at least a portion of the chromosome free of the telomere. In some embodiments, the computer program instructions and the methods associated therewith are free of a step of identifying a telomere boundary or measuring a length of a telomere with a average telomere length above about 7.1 kilobases (kb), 7.2kb, 7.3 kb, 7.4 kb, 7.5 kb, 7.6 kb, 7.7 kb, 7.8 kb, 7.9 kb, 8.0 kb, 8.1 kb, 8.2 kb, 8.3 kb, 8.4 kb, 8.5 kb, 8.6 kb, or about 8.7 kb. In some embodiments, the computer program instructions and the methods associated therewith are free of a step of registering a portion of a chromosome that is over about 11 kb in length, about 12 kb in length, about 13 kb in length, about 14 kb in length, or about 15 kb in length. In someATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION embodiments, the methods associated therewith are free of a step of determining telomere length of telomeres over about 9 kb in length, about 10 kb in length, about 11 kb in length, about 12 kb in length, or about 13 kb in length, over about 14 kb in length, about 15 kb in length, about 16 kb in length, about 17 kb in length, about 18 kb in length, about 19 kb in length, or about 20 kb in length. In some embodiments, the computer program instructions and the methods associated therewith are free of a step of measuring telomere length wherein, in about 75% of the telomeres measured, the length of the telomeres are above about 8.5 kb in length, are above about 8.6 kb in length, are above about 8.7 kb in length, are above about 8.8 kb in length, are above about 8.9 kb in length, are above about 9 kb in length, are above about 10 kb in length, are above about 11 kb in length, are above about 12 kb in length, are above about 13 kb in length, are above about 14 kb in length, are above about 15 kb in length, are above about 16 kb in length, are above about 17 kb in length, are above about 19 kb in length, are above about 20 kb in length, are above about 21 kb in length. In some embodiments, the computer program instructions and the methods associated therewith are free of a step of filtering chromosomes or telomeres from the sample or data from the same where the chromosomes or telomeres are above about 8.5 kb in length, are above about 8.6 kb in length, are above about 8.7 kb in length, are above about 8.8 kb in length, are above about 8.9 kb in length, are above about 9 kb in length, are above about 10 kb in length, are above about 11 kb in length, are above about 12 kb in length, are above about 13 kb in length, are above about 14 kb in length, are above about 15 kb in length, are above about 16 kb in length, are above about 17 kb in length, are above about 19 kb in length, are above about 20 kb in length, are above about 21 kb in length.

[0019] In some embodiments, the computer program product further comprises instructions for collecting data associated with the subject comprising one or a combination of: the sequence of an exon within the sample, the sequence of a non-coding region of a chromosome, the sequence of a mutation, the identity of one or a plurality of chromosome copy number alterations, the quantity of DNA methylation on the chromosome, and the presence or quantity of a barcode; and optionally, the data collection is performed simultaneously with the step of determining telomere length or sequentially before or after such step but with the same sample, such that the data generated are multiplexed to include telomere length and the additional data through same analysis. In some embodiments, the analysis is performed in 10 minutes or less. In some embodiments, the computer program product further comprisesATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION instructions for: calculating a score associated with the telomere length as compared to a known telomere length of a control sample.

[0020] In some embodiments, the step of sequencing at least a portion of a chromosome in the sample or the step of generating a computer-readable file comprises producing a FASTQ file comprising the nucleotide sequence of at least a portion of the chromosome; and subsequently analyzing the FASTQ file to identify the telomere sequence within he portion of chromosome.

[0021] In some embodiments, the computer program product further comprises a step of imaging produced by a camera in operable communication with a microscope.

[0022] The disclosure also relates to a system comprising any disclosed computer program product, a controller and / or processor, and a computer memory. In some embodiments, the system further comprises a display in operable communication to a microscope, camera, the controller and the computer memory. In some embodiments, the system further comprises a vessel addressable by the microscope and comprising a volume of from about 10 microliters to about 1000 microliters. In some embodiments, the system comprises (i) a vessel positioned at or proximate to a nanoporus membrane; (ii) reagents for nanopore sequencing or single-molecule real time sequencing.

[0023] The disclosure relates to a method of diagnosing a subject with a hyperproliferative disorder or a telomeric disorder comprising: determining the length of a telomere in a sample from the subject. In some embodiments, the method further comprises the step of diagnosing the subject with a hyperproliferative disorder if the telomere comprises less than about 2,500 base pairs of DNA. In some embodiments, the step of detecting is preceded by a step of acquiring the sample from the subject. In some embodiments, the method further comprises exposing a sample from a subject to at least one nucleic acid probe or functional fragment thereof prior to performing a step of determining telomere length of chromosomal DNA within the sample. In some embodiments, the probe comprises at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 1 through 768, or a functional fragment or variant thereof comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 1 through 768. In some embodiments, the method is free of biochemical intervention to remove or reduce a number of nucleic acid molecules prior to step (a). In some embodiments, the method is free of biochemical intervention to remove or reduce a number of nucleic acidATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION molecules prior to determining the length of the telomere. In some embodiments, the biochemical intervention is use of a filter. In some embodiments, the biochemical intervention is use of an enzyme to digest DNA or RNA in the sample. In some embodiments, the method is free of intervention to reduce the number of nucleic acids in the sample to less than or equal to about 10 kilobases to about 12 kilobases prior to sequencing. In some embodiments, the method is free of methods of filtering library nucleic acid lengths to less than or equal to about 10 kilobases to about 15 kilobases prior to determining telomere length. In some embodiment, the method is free of methods of filtering library nucleic acid lengths to less than or equal to about 10 kilobases to about 12 kilobases prior to determining telomere length. In some embodiments, the step of determining the length of the telomere comprises: (a) sequencing at least a portion of a chromosome in the sample comprising the telomere; (b) aligning the telomere of the sample to identify the end of the chromosome; (c) identifying a telomere boundary on the chromosome; (d) measuring the length of the telomere from about the end of the chromosome to the boundary of the telomere. In some embodiments, steps (b) through (d) are performed on a system comprising a computer program product disclosed herein and the steps (b) through (d) are performed by a computer implemented method after sequencing is performed. In some embodiments, the step of determining telomere length further comprises: preparing an image of the telomere with a camera in operable communication with a microscope position at or proximate to the sample. In some embodiments, the step of sequencing at least a portion of the chromosome comprises performing long-read sequencing before or after steps (b), (c) and (d). In some embodiments, the method further comprises a step of collecting data from the sample associated with the subject comprising one or a combination of: the sequence of an exon within the sample, the sequence of a non-coding region of a chromosome, the sequence of a mutation, the identity of one or a plurality of chromosome copy number alterations, the quantity of DNA methylation on the chromosome, and the presence or quantity of a barcode annealed to the sample; and diagnosing the subject with a hyperproliferative disorder if the data from the sample comprises a mutation relative to a control sample. In each of the aforementioned steps, the steps are performed by a computer-implemented method in some embodiments. In some embodiments, the method further comprises a step of calculating a score based upon the telomere length and the age of the subject.ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION

[0024] The disclosure also relates to a method of determining the age of a sample or the health of a subject comprising: determining the length of a telomere in a sample from the subject. In some embodiments, the method is free of a step of removing DNA molecules from the sample, wherein the DNA molecules are from about 10 kilobases to about 15 kilobases in length.

[0025] In some embodiments, the method is free of a step of removing DNA molecules from the sample, wherein the DNA molecules are greater than about 10 kilobases in length. In some embodiments, the method is free of a step of removing DNA molecules from the sample, wherein the DNA molecules are greater than about 11 kilobases in length. In some embodiments, the method is free of a step of removing DNA molecules from the sample, wherein the DNA molecules are greater than about 12 kilobases in length. In some embodiments, the method is free of a step of removing DNA molecules from the sample, wherein the DNA molecules are greater than about 13 kilobases in length. In some embodiments, the method is free of a step of removing DNA molecules from the sample, wherein the DNA molecules are greater than about 14 kilobases in length. In some embodiments, the method is free of a step of removing DNA molecules from the sample, wherein the DNA molecules are greater than about 15 kilobases in length.

[0026] In some embodiments, the method further comprises the step of diagnosing the subject with a hyperproliferative disorder if the telomere comprises less than a threshold number of base pairs of DNA. In some embodiments, the threshold number is about 2,500, 3,000, 3,500, 4,000 or less base pairs of DNA. In some embodiments, the step of detecting is preceded by a step of acquiring the sample from the subject. In some embodiments, the method further comprises exposing a sample from a subject to at least one capture oligonucleotide or functional fragment thereof. In some embodiments, the capture oligonucleotide comprises at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 1 through 768, or a functional fragment or variant thereof comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 1 through 768. In some embodiments, the step of determining the length of the telomere comprises: (a) sequencing at least a portion of a chromosome in the sample comprising the telomere; (b) aligning the telomere of the sample to identify the end of the chromosome; (c) identifying a telomere boundary on the chromosome;ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION (d) measuring the length of the telomere from about the end of the chromosome to the boundary of the telomere.

[0027] In some embodiments, the method is free of biochemical intervention to reduce length of nucleic acids prior to sequencing. In some embodiments, the method further comprises exposing a sample from a subject to at least one nucleic acid probe or functional fragment thereof prior to performing a step of determining telomere length of chromosomal DNA within the sample, but the method is free of biochemical intervention to remove or reduce a number DNA of certain size prior to step (a). In some embodiments, the method is free of intervention to reduce the nucleic acid sizes retained for analysis prior to sequencing. In some embodiments, the method is free of intervention to reduce the nucleic acid size to less than or equal to about 10 to about 15 kb prior to sequencing. In some embodiments, the method is free of intervention to reduce the nucleic acid size to less than or equal to about 10 to about 12 kb prior to sequencing. In some embodiments, the method is free of methods of filtering library nucleic acid lengths to less than or equal to about 10 kb to about 15 kb prior to determining telomere length. In some embodiment, the method is free of methods of filtering library nucleic acid lengths to less than or equal to about 10 kb to about 12 kb prior to determining telomere length. In some embodiments, the method is free of intervention to reduce analyzed telomere length prior to sequencing. In some embodiments, the method is free of intervention to reduce analyzed maximum telomere length to less than or equal to about 6 kb, 7 kb, 8 kb, about 9 kb or about 10 kb prior to sequencing. In some embodiments, the method is free of intervention to reduce analyzed telomere length to less than or equal to about 9 kb to about 10 kb prior to sequencing.

[0028] The disclosure also relates to a method of determining or identifying a mutation in genomic DNA of a subject, such as a single nucleotide polymorphism, comprising mixing a sample comprising at least a portion of a telomere from the subject with a sample comprising whole genomic DNA comprising a known variant at a particular locus or a known control; sequencing at least a portion of genomic DNA with at least a portion of the telomere; comparing the sequence length of the telomere and chromosomal DNA from the subject to a control; and identifying the presence, absence or quantity of a variant in the genomic DNA of the subject. In some embodiments, the subject has cancer, has a hyperproliferative disorder, a telomeric disorder or is suspected of having any of the foregoing.ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION

[0029] The disclosure also relates to a composition comprising any one or plurality of nucleotide sequences comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 1 through 768, or a functional fragment or variant thereof comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 1 through 768. The disclosure also relates to a kit for performing any of the methods disclosed herein comprising any one or plurality of nucleotide sequences comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 1 through 768, or a functional fragment or variant thereof comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 1 through 768. BRIEF DESCRIPTION OF DRAWINGS

[0030] FIGS.1A through 1J depict high-resolution telomere measurement by nanopore long- read sequencing. (1A) Schematic representation of DNA sequencing library preparation for telomere measurement by telomere capture or whole genome long-read sequencing. (1B) Head- to-head comparison of telomere length distributions obtained through either telomere capture or whole genome sequencing library preparation from a single source of HEK 293T DNA. (1C) Telomeres per gigabase sequenced for both library preparation methods. (1D) Correlation between mean telomere lengths from matched samples determined by sequencing or TRF (n=14). (1E) Difference in bp between mean telomere length of matched samples measured by both TRF and sequencing (n=14). (1F) Correlation between mean telomere lengths from matched samples of RTEL1 mutant individuals determined by sequencing or flow-FISH (n=7). (1G) Difference in bp between mean telomere length of matched samples measured by both flow-FISH and sequencing (n=7). (1H) Bootstrapping analysis of the change in standard error of the mean telomere length as a function of the total number of telomeres measured. (1I-1J) Comparison of digital and analog telomere measurement in hESCs. (1I) Digital telomere measurement by sequencing of wild-type and PARN KO hESCs. (1J) Analog telomere measurement by TRF of wild-type and PARN KO hESC clones.

[0031] FIGS.2 through FIG.2H depict telomere attrition and de novo elongation in cultured human cells. (2A) Telomere length distributions of hESCs 66 to 108 days post Cre-mediatedATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION TERT knock-out. (Left) Box and violin plots of telomere lengths (p-values given by Wilcoxon rank-sum test). (Right) Density distributions of telomere lengths. (2B) Linear regression of telomere length distribution summary statistics versus days post TERT knock-out. (2C) Telomere length distributions of wild-type, 284R heterozygous or homozygous TIN2 mutants. (2D) Stacked bar graphs of telomere length fractions from hESCs with TIN2 mutations by genotype (Top) or days post TERT-knockout (Bottom). (2E) Schematic representation of experiment to measure de novo telomere elongation in HEK293T cells. (2F) TRAP assay for telomerase activity in transiently transfected HEK293T cells. (2G) Telomere length distributions as box or violin plots (Top) and density distributions (Bottom) for transiently transfected HEK293T cells as measured by both canonical and variant telomere capture sequencing. (2H) Chromosome-specific telomere length distributions following transient transfection with both hTERT and hTR / TSQ1 or GFP arranged by ascending chromosomal 25th percentile telomere length.

[0032] FIGS.3A through 3J depict telomere length distributions in healthy human aging and a cohort of RTEL1 mutant individuals. (3A) Telomere length distributions from PBLs of 14 healthy individuals aged 18 to 77 years. (3B) Telomere length distributions from PBLs of 7 RTEL1 mutant individuals (healthy carriers = solid outline; diseased carriers = dashed outline). (3C) Telomere length distributions from PBLs or DNA obtained from bone marrow biopsy sample of individual under evaluation for a potential telomere biology disorder at Stanford hospital. (3D) Telomere length distributions from PBLs of 14 healthy individuals aggregated into young (18-20; n=5), middle (35-65; n=6), and elder (>70; n=3) aged cohorts (p-value calculated by Wilcoxon rank-sum test). (3E) Linear regressions of telomere length summary statistics vs. donor age in 14 healthy individuals (mean = blue, median = purple, q1 / 25th percentile = maroon, q3 / 75th percentile = yellow). (3F) Linear regressions of telomere length summary statistics vs. donor age in 7 samples from RTEL1 mutant individuals (labeled colors as in E). (3G) Principal component analysis of telomere length distributions of healthy aging (n=14, unlabeled) and TBD samples (n=9, labeled). (3H) Stacked bar graph representing telomere length fractions in 1000 bp bins from 0-1000 to 15000-16000 in young, middle, and elder aged cohorts. (3I) Stacked bar graph representing telomere length fractions in 1000 bp bins from 0-1000 to 15000-16000 in 9 samples from individuals with mutations associated with, or being evaluated for, telomere biology disorders. (3J) Receiver operator characteristic curve for binary classification of healthyATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION vs carrier or diseased telomere phenotype utilizing an MLP model trained on the data in A-H (AUC=0.97).

[0033] FIGS.4A through 4C. Telomere length distributions from patient-matched benign and malignant colonic tissue in a cohort of colorectal carcinoma patients. (4A) Grid box and violin plots of telomere length distributions for twenty individuals in the cohort showing matched benign (red) and malignant (blue) colonic tissue by patient ID (p-value calculated by Wilcoxon rank-sum test). (4B) Linear regression of telomere length distribution summary statistics for benign colonic epithelia versus patient age. (4C) Linear regression of telomere length distribution summary statistics for malignant colonic epithelia versus patient age.

[0034] FIGS.5A and 5B depict Variant telomere capture only produces successful libraries in HEK293T cells transiently transfected with a variant telomerase RNA component template (TSQ1). FIG.5A depicts Pore occupancy vs. time as produced by ONT MinKNOW software during sequencing of GFP in 293T cells. FIG.5B depicts Pore occupancy vs. time as produced by ONT MinKNOW software during sequencing of hTERT in 293T cells.

[0035] FIGS.6A and 6B depict telomere restriction fragment Southern Blot analysis of twelve healthy donors and Stanford Hospital patient. (Left, 6A) Phosphor image of TRF from twelve healthy donors and Stanford hospital patient aligned to ethidium bromide image of corresponding DNA ladder from gel. (Right, 6B) Quantitative analysis of signal from TRF Southern Blot using R (4.1.0), analysis code available on github.

[0036] FIGS.7A and 7B. Subtelomere lengths measured from telomeric reads in samples digested by single or combination restriction enzyme digest. (Top Panel, 7A) Subtelomeric lengths, aggregate and chromosome-specific (left, right, respectively) measured in telomeric reads from previously published PacBio data sequencing DNA previously digested by HinfI / RsaI / EcoRV (12). (Bottom Panel, 7B) Subtelomeric lengths, aggregate and chromosome- specific (left, right, respectively) measured in telomeric reads from nanopore sequencing in DNA previously digested with EcoRV alone (original data).

[0037] FIGS.8A through 8F depict PacBio but not Oxford nanopore telomere length measurements are bottle-necked by read length. HEK293T telomere length distributions representing sample of 1000 telomere measurements randomly selected from telomeric reads with a read-length longer than incrementally increasing cutoffs, as measured by PacBio (8A, 12) or ONT long-reads (8B, original data). Correlation between measured telomere length and readATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION length from PacBio (8C, 12) or ONT (8D, original data) long-read sequencing digital telomere length measurement. (8E) Read length density distributions for PacBio or ONT data previously demonstrated. (8F) Aggregate subtelomere length measured following single or combination restriction digestion in telomeric reads by ONT (left, original data), or PacBio (right, 12).

[0038] FIGS.9A through 9C depict data displaying simultaneous measure of telomere lengths of a sample and detection of mutations, copy number alterations, assess genome methylation and structural variation in humans from the same input DNA, in a single experiment.

[0039] FIG.10 depicts a flowchart showing steps in a software computer program product in which telomere sequence is determined using alignment tools to identify the end of a telomere, the telomere boundary and measuring the telomere nucleotide sequence number by adding the number of nucleotide bases between and including the end of the telomere and the telomere boundary.

[0040] FIG.11 depicts a schematic of computational pipeline for telomere measurement from long-read sequencing data. Reads are first aligned to a telomere-to-telomere human genome assembly (e.g. CHM13v2.0) using minimap2 (https: / / github.com / lh3 / minimap2). All subsequent steps up to the generation of a summary tab-delimited file containing chromosome arm-specific telomere measurements (e.g. tels.tsv) are performed by Telometer (https: / / github.com / santiago- es / Telometer). TeloScore calculation and further integration with other clinically descriptive datasets can be carried out in R (code unpublished).

[0041] FIGS.12A and 12B provide a demonstration of TeloScore sensitivity and specificity for short telomere syndromes in an expanded, unpublished dataset of telomere measurements made from peripheral blood from healthy adults and short telomere syndrome patients using Telometer. (FIG.12A) Boxplots showing the distributions of TeloScores across both healthy and affected individuals used to determine the optimal TeloScore threshold of 3.3 using a brute force maximization of the Kolmogorov-Smirnov statistic. (FIG.12B) AUC of the optimal TeloScore threshold as a binary classifier for short telomere syndromes using the same data as in (FIG. 12A).

[0042] FIG.13 depicts chromosome arm-specific telomere measurements of the wild-type WA01 human embryonic stem cell line demonstratng that telomere measurement by long-read sequencing can reveal previously inaccessible differences in telomere length at the chromosome arm level (red dotted line denotes the global mean telomere length in this cell line).ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION

[0043] FIG.14 depicts comparison of linear regressions of various summary statistics of the telomere length distribution versus age in healthy adults using a telomere capture method which requires biotin pulldown of telomeres (Karimian et al Science 2024, Red) or does not use biotin pulldown of telomeres in the library preparation method (Sanchez et al Nature Communications 2024, Blue) as analyzed by the Telometer computational pipeline. Raw sequencing data from the Karimian et al 2024 dataset was downloaded from a public repository and analyzed using the Telometer computational pipeline. This figure demonstrates that data generated using a library preparation method which requires the use of biotinylated DNA oligos to pulldown telomere ends results in a final sequencing output which systematically underestimates telomere length.

[0044] FIG.15 depicts a demonstration that Telomere measurement by long-read sequencing can be successfully applied in a tissue-agnostic manor, here comparing the telomere length distribution obtained from peripheral blood (Blood) and various regions of the central nervous system (all others) from tissue collected from an individual at autopsy. The only difference in the protocols followed to generate these data for the samples obtained from central nervous system tissue is that a DNA extraction method tailored to the preservation of DNA from solid tissues (New England Biolabs, HMW DNA Extraction Kit for Cells and Tissue) was followed prior to Telometer library preparation.6 samples were multiplexed on a single flow cell using DNA from a non-blood source (in this case, Blood + different regions of the brain) and we are able to measure telomeres and detect heterogeneity in these samples (competitor flow-FISH can only measure from blood).

[0045] FIGS.16 and 17 depict simultaneously measuring telomeres and identifying TERT mutations and structural variants from PBMC and blood marrow aspirate DNA in a patient with very short telomeres for their age group. These figures demonstrate that using compound whole- genome and Telometer libraries premixed prior to sequencing allows us to generate both whole genomic information and high-resolution telomere length measurements in the same experiment. In this case, telomeres from either the peripheral blood or bone marrow of an individual with a suspected short telomere syndrome were analyzed (right) alongside single nucleotide variant, structural variant data generated by the whole-genome sequencing library (left, variants in the TERT gene encoding telomerase reverse transcriptase provided as an example).

[0046] FIG.18 depicts a test whether biotinylated telomere capture DNA oligos can potentially bias telomere length measurement by long-read sequencing, DNA extracted fromATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION HEK293T cells was prepared for telomere length measurement by Telometer using either standard (Non-Biotin) DNA telomere capture oligos or biotinylated oligos which contain an additional biotin on the end opposite the telomere overhang annealing sequence to facilitate streptavidin bead pulldown of DNA molecules which were successfully ligated to the telomere capture probe. Streptavidin pull-down and subsequent washing prior to proceeding with sequencing library preparation was performed as described in Karimian et al Science 2024 using the ThermoFisher KILObase binder Streptavidin bead kit. DETAILED DESCRIPTION OF EMBODIMENTS

[0047] Before the present systems and methods are described, it is to be understood that the present disclosure is not limited to the particular processes, compositions, or methodologies described, as these may vary. It is also to be understood that the terminology used in the description is for the purposes of describing the particular versions or embodiments only, and is not intended to limit the scope of the present disclosure. Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the present disclosure, the methods, devices, and materials in some embodiments are now described. All publications mentioned herein are incorporated by reference in their entirety. Nothing herein is to be construed as an admission that the present disclosure is not entitled to antedate such disclosure by virtue of prior invention. Definitions

[0048] Unless otherwise defined herein, scientific and technical terms used in connection with the present disclosure shall have the meanings that are commonly understood by those of ordinary skill in the art. The meaning and scope of the terms should be clear, however, in the event of any latent ambiguity, definitions provided herein take precedent over any dictionary or extrinsic definition. Further, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular.

[0049] The indefinite articles “a” and “an,” as used herein in the specification and in the claims, unless clearly indicated to the contrary, should be understood to mean “at least one.”ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION 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 one embodiment, to A without B (optionally including elements other than B); in another embodiment, to B without A (optionally including elements other than A); in yet another embodiment, to both A and B (optionally including other elements); etc.

[0050] 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.

[0051] The term “about” is used herein to mean within the typical ranges of tolerances in the art. For example, “about” can be understood as about 2 standard deviations from the mean. According to certain embodiments, when referring to a measurable value such as an amount and the like, “about” is meant to encompass variations of ±20%, ±10%, ±5%, ±1%, ±0.9%, ±0.8%, ±0.7%, ±0.6%, ±0.5%, ±0.4%, ±0.3%, ±0.2% or ±0.1% from the specified value as such variations are appropriate to perform the disclosed methods. When “about” is present before a series of numbers or a range, it is understood that “about” can modify each of the numbers in the series or range.

[0052] 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 beforeATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION a series of numbers or a range, it is understood that “at least” can modify 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.

[0053] As used herein, the terms “patient,” “individual diagnosed with …,” and “individual suspected of having …” all refer to an individual who has been diagnosed with a particular disease or a disorder (e.g., telomere disorder and / or cancer) has been given a probable diagnosis of a particular disease or disorder (e.g., (e.g., telomere disorder and / or cancer) or an individual who has positive scans (e.g., PET scans) but otherwise lacks major symptoms of a particular disease or disorder and is without a clinical diagnosis of a disease disorder.

[0054] As used herein, the term “animal” includes, but is not limited to, humans and non- human 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.

[0055] 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.

[0056] 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”). InATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION 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.

[0057] The term “hyperproliferative cell” refers to a cell located in a tissue or organ having or exhibiting a “hyperproliferative disorder,” 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 hyperplasia, neoplasia, and cancer. In some embodiments, a hyperproliferative cell comprises at least one or a plurality of genetic mutation that confer a co-opt or dysregulation event of existing growth regulatory pathways within the cell. In some embodiments, the hyperproliferative cells cancer cells adopt one or a plurality of myriad strategies, such as somatic mutations, gene fusions, epigenetic modifications, and regulatory mechanism disruptions to over-activate oncogenic and to down-regulate tumor suppressive pathways. In some embodiments, the hyperproliferative disease is a cancer derived from the gastrointestinal tract or urinary system. In some embodiments, a hyperproliferative disease is a cancer of the adrenal gland, bile ducts, bladder, blood, bone, bone marrow, brain, breast, cervix, colon, esophagus, eye, gall bladder, ganglia, gastrointestinal tract, heart, lymphatic system, liver, lung, kidney, muscle, ovary, pancreas, parathyroid, penis, prostate, prostate glands, rectum, salivary glands, skin, spine, stomach, spleen, testis, thymus, thyroid, or uterus. In some embodiments, the term hyperproliferative disease is a cancer chosen from: lung cancer, bone cancer, blood cancer, chronic myelomonocytic leukemia (CMML), bile duct cancer, cervical cancer, liver cancer, pancreatic cancer, skin cancer, cancer of the head and neck, cancer of the eye, 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 ofATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION 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).

[0058] By “fragment” is meant a portion of a polypeptide or nucleic acid molecule. This portion contains, preferably, at least about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 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.

[0059] “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.

[0060] 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.

[0061] 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). In some embodiments, the subject in need thereof is a human diagnosed with a telomere disease or telomere disorder. In some embodiments, the subject in need thereof is a human seeking treatment for a disease or disorder. In some embodiments, the subject in need thereof is a human undergoing treatment for a telomere disease or disorder.

[0062] 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 singleATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION 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 4 kilobases 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.

[0063] 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 non- human mammal. 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. 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.

[0064] 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.

[0065] The nucleic acid molecule and / or sequences of each embodiment 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. A single strand provides a probeATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION 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 or double 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 ο- 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 he 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 C1-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.ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION 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., to increase 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.

[0066] As used herein, the term “nucleic acid molecule” is a molecule that comprises one or more nucleotide sequences that encode one or more proteins. In some embodiments, a nucleic acid molecule comprises initiation and termination signals operably linked to regulatory elements including a promoter and polyadenylation signal capable of directing expression in the cells of the individual to whom the nucleic acid molecule is administered. In some embodiments, the nucleic acid molecule also includes a plasmid containing one or more telomeres from a sample. In some embodiments, methods of the disclosure comprise a step of sequencing chromosomal DNA from a sample and such DNA is circularized prior to sequencing during long-read sequencing by ligating an adaptor sequence on either end of the chromosomal DNA. Such circularization enables sequencing data to be generated after exposing such chromosomal DNA to an immobilization tether and a DNA polymerase in the presence of a light source and a light detection equipment.

[0067] As used herein, the term “kit” refers to a set of components provided in the context of a system for long-sequencing of a telomeric nucleic acid molecules, generating a computer-readble file comprising a nucleic acid sequence comprising a telomere from a sample, delivering materials or diagnosing a subject with having a telomere disorder. Such delivery systems may include, for example, systems that allow for storage, transport, or delivery of various diagnostic or therapeutic 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) containingATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION relevant reaction reagents and / or supporting materials. As used herein, the term “fragmented kit” refers to a diagnostic 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. As another example, the kit may comprise a first container comprising a solid support such as a chip or slide with one or a plurality of tethers or oligonucleotides with affinities to one or a plurality of telomeric DNA and / or barcodes disclosed herein and a second container comprising any one or plurality of reagents necessary for the detection and / or quantification of the amount of barcode in a sample. 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 vial or plurality of vials comprising one or a combination of capture probes to bind telomeric DNA such as those nucleotide sequences from Table X or a functional fragment thereof comprising at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to a sequence of Table X.

[0068] 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 protease disclosed herein. In some embodiments, the probe comprises an amino acid sequence that is a substrate of an enzyme 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 leastATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION 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 antibodies or antibody fragments that bind to any one or more molecules identified in Table Y below. A probe may be immobilized, adsorbed, or otherwise non-covalently bound to a solid surface, such that upon exposure to light or an enzyme for a time period sufficient to perform an enzymatic reaction, it can be enzymatically cleaved. In some embodiments, cleavage of the substrate causes a biological change in the nature or chemical availability of one or more probes such that cleavage enables detection of the reaction product. For instance, if the step of detecting comprises use of FRET, cleavage of the substrate 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.

[0069] As used herein, the term “predicting” refers to making a finding that an individual has a significantly enhanced probability or likelihood of benefiting from and / or responding to a treatment for a telomere disease or disorder.

[0070] A “score” is a numerical value that may be assigned or generated after normalization of the value corresponding to the telomere sequence and telomere length associated with a particular disorder. In some embodiments, the score is normalized in respect to a control data value, such as a value corresponding to a sample from a subject not exhibiting a mutation (e.g wildtype gene or protein from subject) or a subject that falls within a distribution telomere length considered normal for the age and condition of the subject.

[0071] 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 inATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION both sequences to yield 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 negative-scoring 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 inATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION comparison 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, and less than about 0.001.

[0072] As used herein, the term “stratifying” refers to sorting individuals into different classes or strata based on the features of the particular disease or telomere disorder. For example, stratifying a population of individuals with a telomere disorder involves assigning the individuals on the basis of the severity of the disease and / or presence of a mutation associated with the severity of the disorder.

[0073] As used herein, the term “subject,” “individual,” or “patient,” used interchangeably, means any animal, including mammals, such as mice, rats, other rodents, rabbits, dogs, cats, swine, cattle, sheep, horses, or primates, such as humans. In some embodiments, the subject is a human seeking treatment for a particular telomere disorder. In some embodiments, the subject is a human diagnosed with a particular disease or disorder, such as cancer. In some embodiments, the subject is a human suspected of having a particular telomere disease or disorder. In some embodiments, the subject is a healthy human being. For diagnosis of those conditions which are specific for a type of subject, such as a human being, the term "patient" may be interchangeably used. In some instances, in the description of the present invention, the term "patient" will refer to human patients suffering from a particular disease or disorder. In some embodiments, the subject may be a human suspected of having or being identified as at risk to develop a type of cancer or telomere disorder more severe or invasive than initially diagnosed. In some embodiments, the subject may be diagnosed as having at resistance to one or a plurality of treatments to treat a disease or disorder afflicting the subject. In some embodiments, the subject is suspected of having or has been diagnosed with stage I, II, III or greater stage of cancer. In some embodiments, the subject may be a human suspected of having or being identified as at risk to a terminal condition or disorder. In some embodiments, the subject may be a mammal which functions as a source of the isolated sample of biopsy or bodily fluid. In some embodiments, the subject may be a non-human animal from which a sample of biopsy or bodily fluid is isolated or provided.

[0074] As used herein, the term “telomere disease or disorder” refers to a hyperproliferative disorder (such as colorectal carcinoma, acute myeloid leukemia, liver cancer, melanoma, lung cancer, Myelodisplastic syndrome (MDS), clonal hematopoiesis, myeloproliferative neoplasms (MPNs); and a telomere biology disorder such as dyskeratosis congenita, idiopathic pulmonaryATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION fibrosis, cryptogenic cirrhosis, aplastic anemia, bone marrow failure, bone marrow transplant failure.

[0075] As used herein, the term “threshold” refers to a defined value by which a normalized score can be categorized. By comparing a measured value to a preset threshold, a normalized score can be classified based upon whether it is above or below the preset threshold.

[0076] As used herein, the terms “treat,” “treated,” or “treating” can refer to therapeutic treatment and / or prophylactic or preventative measures wherein the object is to prevent or slow down (lessen) an undesired physiological condition, disorder or disease, or obtain beneficial or desired clinical results. For purposes of the embodiments described herein, beneficial or desired clinical results include, but are not limited to, alleviation of symptoms; diminishment of extent of condition, disorder or disease; stabilized (i.e., not worsening) state of condition, disorder or disease; delay in onset or slowing of condition, disorder or disease progression; amelioration of the condition, disorder or disease state or remission (whether partial or total), whether detectable or undetectable; an amelioration of at least one measurable physical parameter, not necessarily discernible by the patient; or enhancement or improvement of condition, disorder or disease. Treatment can also include eliciting a clinically significant response without excessive levels of side effects. Treatment also includes prolonging survival as compared to expected survival if not receiving treatment.

[0077] As used herein, the term “therapeutic” means an agent utilized to treat, combat, ameliorate, prevent, or improve an unwanted condition or disease of a patient.

[0078] A “therapeutically effective amount” or “effective amount” of a composition is a predetermined amount calculated to achieve the desired effect, i.e., to treat, combat, ameliorate, prevent, or improve one or more symptoms of a telomere disease or disorder. The activity contemplated by the present methods includes both medical therapeutic and / or prophylactic treatment, as appropriate. The specific dose of a compound administered according to the present disclosure to obtain therapeutic and / or prophylactic effects will, of course, be determined by the particular circumstances surrounding the case, including, for example, the compound administered, the route of administration, and the condition being treated. It will be understood that the effective amount administered will be determined by the physician in the light of the relevant circumstances including the condition to be treated, the choice of compound to be administered, and the chosen route of administration, and therefore the above dosage ranges areATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION not intended to limit the scope of the present disclosure in any way. A therapeutically effective amount of compounds of embodiments of the present disclosure is typically an amount such that when it is administered in a physiologically tolerable excipient composition, it is sufficient to achieve an effective systemic concentration or local concentration in the tissue. Computer Program Product

[0079] The disclosure relates to a computer program product with instructions for: (a) receiving sequence data from a sample comprising a nucleic acid sequence of at least one telomere; (b) determining an end of a telomere and a telomeric boundary of the telomere; and (c) determining a length of the telomere based upon the summation of nucleotides between and including the end of the telomere and the telomeric boundary.

[0080] 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.

[0081] 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.

[0082] 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 pointing devices, 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.

[0083] 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 technologyATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION and may operate according to any suitable protocol and may include wireless networks, wired networks, or fiber optic networks.

[0084] 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.

[0085] 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.

[0086] 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, circuit configurations 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 of the invention disclosed herein. The computer readable medium or media can be transportable, such that the program or programs stored thereon can beATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION loaded onto one or more different computers or other processors to implement various aspects of the present invention as discussed above. In some embodiments, the system comprises cloud- based software that executes one or all of the steps of each disclosed method instruction.

[0087] 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.

[0088] 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. that perform 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.

[0089] 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.

[0090] Also, the disclosure relates to various embodiments in which one or more methods. The acts performed as part of the method may be ordered in any suitable way. Accordingly, embodiments may be constructed in which acts are performed in an order different than illustrated, which may include performing some acts simultaneously, even though shown as sequential acts in illustrative embodiments.

[0091] Computer-implemented embodiments of the disclosure relate to methods of determining a sequence of a telomere, and optionally identifying structural variations in chromosomal DNA (simultaneously or in sequence with the same dataset of a sample),ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION comprising steps of: (d) comparing a first normalized score to a first threshold relative to a first control dataset of a sample and comparing a second normalized score to a second threshold relative to a control dataset of the sample; and (e) classifying the subject as having a telomeric disorder a based upon results of comparing of step (d) relative to the first and / or second threshold; wherein each of steps (d) and (e) are performed after step (c). In some embodiments, structural variations in chromosomal DNA comprise one or a combination of: the sequence of an exon, the sequence of a non-coding region of a chromosome, the identity or sequence of a mutation, the identity of one or a plurality of chromosome copy number alterations, the quantity of DNA methylation on the chromosome, and the presence or quantity of a barcode. In some embodiments, the computer-program product comprises a step of calculating the first normalized score and the second normalized score based upon chromosomal DNA in the sample that is no less than about 10 kilobases in length. In some embodiments, the computer-program product comprises a step of calculating the first normalized score and the second normalized score based upon chromosomal DNA in the sample that is no less than about 11 kilobases in length. In some embodiments, the computer-program product comprises a step of calculating the first normalized score and the second normalized score based upon chromosomal DNA in the sample that is no less than about 12 kilobases in length. In some embodiments, the computer-program product comprises a step of calculating the first normalized score and the second normalized score based upon chromosomal DNA in the sample that is no less than about 13 kilobases in length. In some embodiments, the computer-program product comprises a step of calculating the first normalized score and the second normalized score based upon chromosomal DNA in the sample that is no less than about 14 kilobases in length. In some embodiments, the computer-program product comprises a step of calculating the first normalized score and the second normalized score based upon chromosomal DNA in the sample that is no less than about 15 kilobases in length. In some embodiments, the first and second threshold are determined relative to telomere lengths of a control sample, where the determining of the telomere length within the control sample is calculated free of a step of removing data associated with DNA molecules of greater than about 10 kilobases and / or free of a step of calculating telomere length of DNA molecules in the sample only of those DNA molecules less than 10 kilobases in length.

[0092] In some embodiments, the first and second threshold are determined relative to telomere lengths of a control sample, where the determining of the telomere length within theATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION control sample is calculated free of a step of removing data associated with DNA molecules of greater than about 11 kilobases and / or free of a step of calculating telomere length of DNA molecules in the sample only of those DNA molecules less than 11 kilobases in length.

[0093] In some embodiments, the first and second threshold are determined relative to telomere lengths of a control sample, where the determining of the telomere length within the control sample is calculated free of a step of removing data associated with DNA molecules of greater than about 12 kilobases and / or free of a step of calculating telomere length of DNA molecules in the sample only of those DNA molecules less than 12 kilobases in length. In some embodiments, the first and second threshold are determined relative to telomere lengths of a control sample, where the determining of the telomere length within the control sample is calculated free of a step of removing data associated with DNA molecules of greater than about 13 kilobases and / or free of a step of calculating telomere length of DNA molecules in the sample only of those DNA molecules less than 13 kilobases in length. In some embodiments, the first and second threshold are determined relative to telomere lengths of a control sample, where the determining of the telomere length within the control sample is calculated free of a step of removing data associated with DNA molecules of greater than about 14 kilobases and / or free of a step of calculating telomere length of DNA molecules in the sample only of those DNA molecules less than 14 kilobases in length.

[0094] 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 Network (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 for calculating the alignment of known telomeric repeat sequences to the data from a sample registered with the computer program product. In some embodiments, the system comprises a device that interacts with one or more communication channels or mediums or links, such thatATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION alignment processes for telomere sequences of a sample are compared to control sequences stored on a memory and shared with a network in operable communication with the device.

[0095] 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.

[0096] 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. In some embodiments, the

[0097] 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.

[0098] 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 can contain, store, communicate, propagate, or transport the program for use by or in connection with the instruction execution system, apparatus, or device.

[0099] 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, aATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION 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.

[0100] 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.

[0101] 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.

[0102] 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.

[0103] 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,ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION 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.

[0104] 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.

[0105] In some embodiment, 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 comprise disparate 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 distributedATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION over different locations including over different storage devices, and may exist, at least partially, merely as electronic signals on a system or network.

[0106] 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.

[0107] 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. As also 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 one embodiment, 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-ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION magnetic signal through a fiber optic cable for execution by a processor and stored on RAM storage device for execution by the processor.

[0108] 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 object 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).

[0109] 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.

[0110] Functions, operations, components and / or features described herein with reference to one or more embodiments, may be combined with, or may be utilized in combination with, one or more other functions, operations, components and / or features described herein with reference to one or more other embodiments, or vice versa.

[0111] Although the disclosure has been described with reference to exemplary embodiments, it is not limited thereto. Those skilled in the art will appreciate that numerous changes and modifications may be made to the preferred embodiments of the disclosure and that such changes and modifications may be made without departing from the true spirit of the disclosure. It is therefore intended that the appended claims be construed to cover all such equivalent variations as fall within the true spirit and scope of the disclosure.

[0112] All referenced journal articles, patents, and other publications are incorporated by reference herein in their entireties.ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Nucleic Acid Compositions

[0100] Disclosed are nucleic acid sequences, nucleic acid molecules comprising one or plurality of such nucleic acid sequences, and compositions comprising one or plurality of such nucleic acid sequences and / or nucleic acid molecules, wherein the nucleic acid sequences comprise one or a combination of capture sequence identified in Table X or those functional fragments comprising at least about 75% sequence identity to the sequences identified in Table X (also identified as capture oligonucleotides). The nucleic acid sequence according to the present disclosure comprise a first nucleic acid sequence encoding a capture domain comprising a nucleic acid domain that associates with a telomere, and a second nucleic acid sequence domain comprising a barcode domain. In some embodiments, the nucleic acid sequence further comprises a third nucleic acid sequence encoding a linker domain comprising a linker peptide, wherein the third nucleic acid sequence is positioned between the first nucleic acid sequence and the second nucleic acid sequence in the 5’ to 3’ orientation. In some embodiments, the nucleic acid sequence is operably linked to at least one regulatory sequence and / or forms part of a nucleic acid molecule, such as a plasmid. The disclosure also relates to a composition comprising a nucleic acid sequence from a sample and one or a plurality of nucleic acid sequences comprising one or a plurality of capture sequences identified in Table X or those functional fragments comprising at least about 75% sequence identity to the sequences identified in Table X. In some embodiments, the telomere sequence from a sample is first isolated from the sample and then exposed to a composition comprising one or a plurality of nucleic acid sequences comprising one or a plurality of capture sequences identified in Table X or those functional fragments comprising at least about 75% sequence identity to the sequences identified in Table X.

[0101] The disclosure also relates to a kit for sequencing telomeric DNA of a sample comprising a first container comprising one or a plurality of capture sequences identified in Table X or those functional fragments comprising at least about 75% sequence identity to the sequences identified in Table X. In some embodiments, the capture oligonucleotides comprise a capture domain, complementary to the telomere and a barcode domain. In some embodiments, the oligonucleotide comprising the capture domains comprise one or a combination of nucleotide sequences from Table X or a functional fragment thereof comprising at least about 75%, 80%,ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to a sequence of Table X. In some embodiments, the kits provides instructions for operating a processor and computer memory to execute steps, optionally remotely, of (a) detecting a presence of a 5’ or 3’ end of a telomere from the sample; (b) detecting a presence of a telomere boundary from the sample distal from the telomere end; and (c) measuring the length of the telomere from the end of the genetic material to the telomere boundary. In some embodiments, the kit further comprises a computer program product with steps to execute: a) detection of a 5’ or 3’ end of a telomere from the sample; (b) detection a presence of a telomere boundary from the sample distal from the telomere end; and (c) measuring the length of the telomere from the end of the genetic material to the telomere boundary. In some embodiments, the step of measuring is performed by a computer program product comprising executable step to perform summation of the number of nucleotides in sequence from the data. In some embodiments, the kit further comprises a computer program product with steps to execute: (a) compiling or registering nucleic acid information from the sample; (b) aligning sequences against a control sequence to identify a telomer sequence within the nucleic acid information; (c) estimating a location of a telomeric boundary to determine the beginning of a non-telomeric sequence within the nucleic acid information; (d) determining the length of the telomere after measuring the number of nucleotides between the end of 5’ or 3’ end of the telomere sequence and the telomeric boundary; ad optionally calculating and / or displaying a score based upon the percent identity of the nucleic acid information relative to a control sequence. In some embodiments, the computer program product further comprises an executable step for detection of a structural variation of chromosomal DNA from a sample based upon the presence, absence or quantity of a mutation within telomeric DNA or non-telomeric DNA. Methods

[0102] The disclosure relates to methods of determining telomeric length in chromosomal DNA of a subject. In some embodiments the methods comprise generating a computer-readable file comprising sequence information. In some embodiments, the step of generating a computer- readable file comprises performing a long-reading sequence reaction and generating a report, in computer readable format, that contains the sequence of from about 1, 000 to about 25,000 base pairs of DNA from a sample of the subject. In some embodiments, the step of generating aATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION computer-readable file comprises performing analysis of data from a long-reading sequence reaction and generating a report, in computer readable format, that contains the sequence of from about 1, 000 to about 25,000 base pairs of DNA from a sample of the subject. In some embodiments, the data from the sequencing or the sequencing itself is free of filtering out or removing sequencing data from DNA molecules over about 10 kilobases in length. In some embodiments, the data from the sequencing or the sequencing itself is free of filtering out or removing sequencing data from DNA molecules over about 11 kilobases in length. In some embodiments, the data from the sequencing or the sequencing itself is free of filtering out or removing sequencing data from DNA molecules over about 12 kilobases in length. In some embodiments, the data from the sequencing or the sequencing itself is free of filtering out or removing sequencing data from DNA molecules over about 13 kilobases in length. In some embodiments, the data from the sequencing or the sequencing itself is free of filtering out or removing sequencing data from DNA molecules over about 14 kilobases in length. In some embodiments, the data from the sequencing or the sequencing itself is free of filtering out or removing sequencing data from DNA molecules over about 15 kilobases in length. Generally methods of performing long-reading sequencing are known, as, for, example in Patent Publication WO / 2021 / 225886, and US Patent Application US 20220162690, both of which are incorporated by reference in their entireties. Methods of the disclosure also include performing a sequencing reaction using capture oligos and generating a computer-readable file comprising the sequence information from the chromosomal DNA and registering or compiling that sequence information within a computer program product with executable instructions for: (a) detecting and end of the telomere sequence within the sequence information; (b) determining a telomeric boundary associated with the end of the telomere sequence; and (c) measuring the number of nucleotides between and including the end of the telomeric sequence and the telomeric boundary. In some embodiments, the computer program product comprises steps from the series of steps outlined in Figure 10. I In some embodiments, the steps (a), (b) and / or (c) are performed on chromosomal DNA free of a step of filtering out or removing DNA sequence analysis greater than about 10 kilobases in length. In some embodiments, the steps (a), (b) and / or (c) are performed on chromosomal DNA free of a step of filtering out or removing DNA sequence analysis greater than about 11 kilobases in length. In some embodiments, the steps (a), (b) and / or (c) are performed on chromosomal DNA free of a step of filtering out or removing DNAATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION sequence analysis greater than about 12 kilobases in length. In some embodiments, the steps (a), (b) and / or (c) are performed on chromosomal DNA free of a step of filtering out or removing DNA sequence analysis greater than about 13 kilobases in length. In some embodiments, the steps (a), (b) and / or (c) are performed on chromosomal DNA free of a step of filtering out or removing DNA sequence analysis greater than about 14 kilobases in length. In some embodiments, the steps (a), (b) and / or (c) are performed on chromosomal DNA free of a step of filtering out or removing DNA sequence analysis greater than about 15 kilobases in length.

[0103] In some embodiments, the step of generating a computer readable file comprising sequence information from at least a portion of the chromosomal DNA comprises sequencing at least about 2, 000, 3,000, or 4,00 or more base pairs of DNA from the sample using long-read sequencing techniques and then generating the report from a computer processor operably linked to the equipment on which the long-read sequencing is performed. In some embodiments, the method is free of a step in which polymerase chain reaction is performed. In some embodiments a step of sequencing is performed on chromosomal DNA isolated from a sample from a subject using the capture oligos disclosed in Table X or functional fragments comprising at least about 75% sequence identity to the capture oligos disclosed in Table X. In some embodiments, the method is free of a biochemical intervention removing long-read sequencing of chromosomal DNA over about 11, 12, 13, 14, or 15 kilobases in length.

[0104] The disclosure relates to a method of determining the length of a telomere, the method comprising: (a) annealing a free 3’ end of a telomere in a sample to one or a plurality of nucleotides that are complementary to the 3’ strand of the telomere; and (b) calculating the length of the telomere in a sample. In some embodiments, the disclosure relates to methods of determining the length of a telomere, the method comprising: (a) annealing a free 3’ end of a telomere in a sample to one or a plurality of nucleotides that are complementary to the 3’ strand of the telomere; (b) calculating the length of the telomere in a sample; and (c) correlating the length of the telomere with the diagnosis of a subject with a telomere disorder.

[0105] In some embodiments, the step of annealing the free 3’ end of a telomere with a nucleotide sequence complementary to the 3’ strand of the telomere comprises exposing the telomere in a sample to one or a plurality of capture oligos. In some embodiments, the capture oligonucleotides comprise a capture domain, complementary to the telomere and a barcode domain. In some embodiments, the oligonucleotide comprising the capture domains compriseATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION one or a combination of nucleotide sequences from Table X or a functional fragment thereof comprising at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to a sequence of Table X. In some embodiments, the method is free of a biochemical intervention removing long-read sequencing of chromosomal DNA over about 11, 12, 13, 14, or 15 kilobases in length from any of steps (a), (b) or (c). Table X Barcoded Oligos: 5' Phosphate to 3’ orientation SEQ The sequences are identified for purposes of this application as SEQ ID NO:1 through ID SEQ ID NO:768 (as listed in order from Capture1 to Capture 768). NO. Capture1 TGCTCCGTGCATCTCCAAGGTTCACAAAGACACCGACAACTTTCTTCCCTAAC 1 Capture2 TGCTCCGTGCATCTCCAAGGTTCACAAAGACACCGACAACTTTCTTTAACCCT 2 Capture3TGCTCCGTGCATCTCCAAGGTTCACAAAGACACCGACAACTTTCTTCCTAACC 3Capture4 TGCTCCGTGCATCTCCAAGGTTCACAAAGACACCGACAACTTTCTTCTAACCC 4 Capture5TGCTCCGTGCATCTCCAAGGTTCACAAAGACACCGACAACTTTCTTAACCCTA 5Capture6 TGCTCCGTGCATCTCCAAGGTTCACAAAGACACCGACAACTTTCTTACCCTAA 6 Capture7 TGCTCCGTGCATCTCCAAGGTTCACAAAGACACCGACAACTTTCTTACCCTAA 7 Capture8TGCTCCGTGCATCTCCAAGGTTCACAAAGACACCGACAACTTTCTTCCTAACT 8Capture9 TGCTCCGTGCATCTCCAAGGTTACAGACGACTACAAACGGAATCGACCCTAAC 9 Capture10TGCTCCGTGCATCTCCAAGGTTACAGACGACTACAAACGGAATCGATAACCCT 10Capture11 TGCTCCGTGCATCTCCAAGGTTACAGACGACTACAAACGGAATCGACCTAACC 11 Capture12 TGCTCCGTGCATCTCCAAGGTTACAGACGACTACAAACGGAATCGACTAACCC 12 Capture13TGCTCCGTGCATCTCCAAGGTTACAGACGACTACAAACGGAATCGAAACCCTA 13Capture14 TGCTCCGTGCATCTCCAAGGTTACAGACGACTACAAACGGAATCGAACCCTAA 14 Capture15TGCTCCGTGCATCTCCAAGGTTACAGACGACTACAAACGGAATCGAACCCTAA 15Capture16 TGCTCCGTGCATCTCCAAGGTTACAGACGACTACAAACGGAATCGACCTAACT 16 Capture17 TGCTCCGTGCATCTCCAAGGTTCCTGGTAACTGGGACACAAGACTCCCCTAAC 17 Capture18TGCTCCGTGCATCTCCAAGGTTCCTGGTAACTGGGACACAAGACTCTAACCCT 18Capture19 TGCTCCGTGCATCTCCAAGGTTCCTGGTAACTGGGACACAAGACTCCCTAACC 19 Capture20TGCTCCGTGCATCTCCAAGGTTCCTGGTAACTGGGACACAAGACTCCTAACCC 20Capture21 TGCTCCGTGCATCTCCAAGGTTCCTGGTAACTGGGACACAAGACTCAACCCTA 21 Capture22 TGCTCCGTGCATCTCCAAGGTTCCTGGTAACTGGGACACAAGACTCACCCTAA 22 Capture23TGCTCCGTGCATCTCCAAGGTTCCTGGTAACTGGGACACAAGACTCACCCTAA 23Capture24 TGCTCCGTGCATCTCCAAGGTTCCTGGTAACTGGGACACAAGACTCCCTAACT 24 Capture25TGCTCCGTGCATCTCCAAGGTTTAGGGAAACACGATAGAATCCGAACCCTAAC 25Capture26 TGCTCCGTGCATCTCCAAGGTTTAGGGAAACACGATAGAATCCGAATAACCCT 26 Capture27 TGCTCCGTGCATCTCCAAGGTTTAGGGAAACACGATAGAATCCGAACCTAACC 27 Capture28TGCTCCGTGCATCTCCAAGGTTTAGGGAAACACGATAGAATCCGAACTAACCC 28Capture29 TGCTCCGTGCATCTCCAAGGTTTAGGGAAACACGATAGAATCCGAAAACCCTA 29ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture30 TGCTCCGTGCATCTCCAAGGTTTAGGGAAACACGATAGAATCCGAAACCCTAA 30Capture31TGCTCCGTGCATCTCCAAGGTTTAGGGAAACACGATAGAATCCGAAACCCTAA 31Capture32 TGCTCCGTGCATCTCCAAGGTTTAGGGAAACACGATAGAATCCGAACCTAACT 32Capture33TGCTCCGTGCATCTCCAAGGTTAAGGTTACACAAACCCTGGACAAGCCCTAAC 33Capture34 TGCTCCGTGCATCTCCAAGGTTAAGGTTACACAAACCCTGGACAAGTAACCCT 34 Capture35 TGCTCCGTGCATCTCCAAGGTTAAGGTTACACAAACCCTGGACAAGCCTAACC 35Capture36TGCTCCGTGCATCTCCAAGGTTAAGGTTACACAAACCCTGGACAAGCTAACCC 36Capture37 TGCTCCGTGCATCTCCAAGGTTAAGGTTACACAAACCCTGGACAAGAACCCTA 37Capture38TGCTCCGTGCATCTCCAAGGTTAAGGTTACACAAACCCTGGACAAGACCCTAA 38Capture39 TGCTCCGTGCATCTCCAAGGTTAAGGTTACACAAACCCTGGACAAGACCCTAA 39 Capture40 TGCTCCGTGCATCTCCAAGGTTAAGGTTACACAAACCCTGGACAAGCCTAACT 40Capture41TGCTCCGTGCATCTCCAAGGTTGACTACTTTCTGCCTTTGCGAGAACCCTAAC 41Capture42 TGCTCCGTGCATCTCCAAGGTTGACTACTTTCTGCCTTTGCGAGAATAACCCT 42Capture43TGCTCCGTGCATCTCCAAGGTTGACTACTTTCTGCCTTTGCGAGAACCTAACC 43Capture44 TGCTCCGTGCATCTCCAAGGTTGACTACTTTCTGCCTTTGCGAGAACTAACCC 44 Capture45 TGCTCCGTGCATCTCCAAGGTTGACTACTTTCTGCCTTTGCGAGAAAACCCTA 45Capture46TGCTCCGTGCATCTCCAAGGTTGACTACTTTCTGCCTTTGCGAGAAACCCTAA 46Capture47 TGCTCCGTGCATCTCCAAGGTTGACTACTTTCTGCCTTTGCGAGAAACCCTAA 47Capture48TGCTCCGTGCATCTCCAAGGTTGACTACTTTCTGCCTTTGCGAGAACCTAACT 48Capture49 TGCTCCGTGCATCTCCAAGGTTAAGGATTCATTCCCACGGTAACACCCCTAAC 49 Capture50 TGCTCCGTGCATCTCCAAGGTTAAGGATTCATTCCCACGGTAACACTAACCCT 50Capture51TGCTCCGTGCATCTCCAAGGTTAAGGATTCATTCCCACGGTAACACCCTAACC 51Capture52 TGCTCCGTGCATCTCCAAGGTTAAGGATTCATTCCCACGGTAACACCTAACCC 52Capture53TGCTCCGTGCATCTCCAAGGTTAAGGATTCATTCCCACGGTAACACAACCCTA 53Capture54 TGCTCCGTGCATCTCCAAGGTTAAGGATTCATTCCCACGGTAACACACCCTAA 54 Capture55 TGCTCCGTGCATCTCCAAGGTTAAGGATTCATTCCCACGGTAACACACCCTAA 55Capture56TGCTCCGTGCATCTCCAAGGTTAAGGATTCATTCCCACGGTAACACCCTAACT 56Capture57 TGCTCCGTGCATCTCCAAGGTTACGTAACTTGGTTTGTTCCCTGAACCCTAAC 57Capture58TGCTCCGTGCATCTCCAAGGTTACGTAACTTGGTTTGTTCCCTGAATAACCCT 58Capture59 TGCTCCGTGCATCTCCAAGGTTACGTAACTTGGTTTGTTCCCTGAACCTAACC 59 Capture60 TGCTCCGTGCATCTCCAAGGTTACGTAACTTGGTTTGTTCCCTGAACTAACCC 60Capture61TGCTCCGTGCATCTCCAAGGTTACGTAACTTGGTTTGTTCCCTGAAAACCCTA 61Capture62 TGCTCCGTGCATCTCCAAGGTTACGTAACTTGGTTTGTTCCCTGAAACCCTAA 62Capture63TGCTCCGTGCATCTCCAAGGTTACGTAACTTGGTTTGTTCCCTGAAACCCTAA 63Capture64 TGCTCCGTGCATCTCCAAGGTTACGTAACTTGGTTTGTTCCCTGAACCTAACT 64 Capture65 TGCTCCGTGCATCTCCAAGGTTAACCAAGACTCGCTGTGCCTAGTTCCCTAAC 65Capture66TGCTCCGTGCATCTCCAAGGTTAACCAAGACTCGCTGTGCCTAGTTTAACCCT 66Capture67 TGCTCCGTGCATCTCCAAGGTTAACCAAGACTCGCTGTGCCTAGTTCCTAACC 67Capture68TGCTCCGTGCATCTCCAAGGTTAACCAAGACTCGCTGTGCCTAGTTCTAACCC 68Capture69 TGCTCCGTGCATCTCCAAGGTTAACCAAGACTCGCTGTGCCTAGTTAACCCTA 69 Capture70 TGCTCCGTGCATCTCCAAGGTTAACCAAGACTCGCTGTGCCTAGTTACCCTAA 70ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture71 TGCTCCGTGCATCTCCAAGGTTAACCAAGACTCGCTGTGCCTAGTTACCCTAA 71Capture72TGCTCCGTGCATCTCCAAGGTTAACCAAGACTCGCTGTGCCTAGTTCCTAACT 72Capture73 TGCTCCGTGCATCTCCAAGGTTGAGAGGACAAAGGTTTCAACGCTTCCCTAAC 73Capture74TGCTCCGTGCATCTCCAAGGTTGAGAGGACAAAGGTTTCAACGCTTTAACCCT 74Capture75 TGCTCCGTGCATCTCCAAGGTTGAGAGGACAAAGGTTTCAACGCTTCCTAACC 75 Capture76 TGCTCCGTGCATCTCCAAGGTTGAGAGGACAAAGGTTTCAACGCTTCTAACCC 76Capture77TGCTCCGTGCATCTCCAAGGTTGAGAGGACAAAGGTTTCAACGCTTAACCCTA 77Capture78 TGCTCCGTGCATCTCCAAGGTTGAGAGGACAAAGGTTTCAACGCTTACCCTAA 78Capture79TGCTCCGTGCATCTCCAAGGTTGAGAGGACAAAGGTTTCAACGCTTACCCTAA 79Capture80 TGCTCCGTGCATCTCCAAGGTTGAGAGGACAAAGGTTTCAACGCTTCCTAACT 80 Capture81 TGCTCCGTGCATCTCCAAGGTTTCCATTCCCTCCGATAGATGAAACCCCTAAC 81Capture82TGCTCCGTGCATCTCCAAGGTTTCCATTCCCTCCGATAGATGAAACTAACCCT 82Capture83 TGCTCCGTGCATCTCCAAGGTTTCCATTCCCTCCGATAGATGAAACCCTAACC 83Capture84TGCTCCGTGCATCTCCAAGGTTTCCATTCCCTCCGATAGATGAAACCTAACCC 84Capture85 TGCTCCGTGCATCTCCAAGGTTTCCATTCCCTCCGATAGATGAAACAACCCTA 85 Capture86 TGCTCCGTGCATCTCCAAGGTTTCCATTCCCTCCGATAGATGAAACACCCTAA 86Capture87TGCTCCGTGCATCTCCAAGGTTTCCATTCCCTCCGATAGATGAAACACCCTAA 87Capture88 TGCTCCGTGCATCTCCAAGGTTTCCATTCCCTCCGATAGATGAAACCCTAACT 88Capture89TGCTCCGTGCATCTCCAAGGTTTCCGATTCTGCTTCTTTCTACCTGCCCTAAC 89Capture90 TGCTCCGTGCATCTCCAAGGTTTCCGATTCTGCTTCTTTCTACCTGTAACCCT 90 Capture91 TGCTCCGTGCATCTCCAAGGTTTCCGATTCTGCTTCTTTCTACCTGCCTAACC 91Capture92TGCTCCGTGCATCTCCAAGGTTTCCGATTCTGCTTCTTTCTACCTGCTAACCC 92Capture93 TGCTCCGTGCATCTCCAAGGTTTCCGATTCTGCTTCTTTCTACCTGAACCCTA 93Capture94TGCTCCGTGCATCTCCAAGGTTTCCGATTCTGCTTCTTTCTACCTGACCCTAA 94Capture95 TGCTCCGTGCATCTCCAAGGTTTCCGATTCTGCTTCTTTCTACCTGACCCTAA 95 Capture96 TGCTCCGTGCATCTCCAAGGTTTCCGATTCTGCTTCTTTCTACCTGCCTAACT 96Capture97TGCTCCGTGCATCTCCAAGGTTAGAACGACTTCCATACTCGTGTGACCCTAAC 97Capture98 TGCTCCGTGCATCTCCAAGGTTAGAACGACTTCCATACTCGTGTGATAACCCT 98Capture99TGCTCCGTGCATCTCCAAGGTTAGAACGACTTCCATACTCGTGTGACCTAACC 99Capture100 TGCTCCGTGCATCTCCAAGGTTAGAACGACTTCCATACTCGTGTGACTAACCC 100 Capture101 TGCTCCGTGCATCTCCAAGGTTAGAACGACTTCCATACTCGTGTGAAACCCTA 101Capture102TGCTCCGTGCATCTCCAAGGTTAGAACGACTTCCATACTCGTGTGAACCCTAA 102Capture103 TGCTCCGTGCATCTCCAAGGTTAGAACGACTTCCATACTCGTGTGAACCCTAA 103Capture104TGCTCCGTGCATCTCCAAGGTTAGAACGACTTCCATACTCGTGTGACCTAACT 104Capture105 TGCTCCGTGCATCTCCAAGGTTAACGAGTCTCTTGGGACCCATAGACCCTAAC 105 Capture106 TGCTCCGTGCATCTCCAAGGTTAACGAGTCTCTTGGGACCCATAGATAACCCT 106Capture107TGCTCCGTGCATCTCCAAGGTTAACGAGTCTCTTGGGACCCATAGACCTAACC 107Capture108 TGCTCCGTGCATCTCCAAGGTTAACGAGTCTCTTGGGACCCATAGACTAACCC 108Capture109TGCTCCGTGCATCTCCAAGGTTAACGAGTCTCTTGGGACCCATAGAAACCCTA 109Capture110 TGCTCCGTGCATCTCCAAGGTTAACGAGTCTCTTGGGACCCATAGAACCCTAA 110 Capture111 TGCTCCGTGCATCTCCAAGGTTAACGAGTCTCTTGGGACCCATAGAACCCTAA 111ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture112 TGCTCCGTGCATCTCCAAGGTTAACGAGTCTCTTGGGACCCATAGACCTAACT 112Capture113TGCTCCGTGCATCTCCAAGGTTAGGTCTACCTCGCTAACACCACTGCCCTAAC 113Capture114 TGCTCCGTGCATCTCCAAGGTTAGGTCTACCTCGCTAACACCACTGTAACCCT 114Capture115TGCTCCGTGCATCTCCAAGGTTAGGTCTACCTCGCTAACACCACTGCCTAACC 115Capture116 TGCTCCGTGCATCTCCAAGGTTAGGTCTACCTCGCTAACACCACTGCTAACCC 116 Capture117 TGCTCCGTGCATCTCCAAGGTTAGGTCTACCTCGCTAACACCACTGAACCCTA 117Capture118TGCTCCGTGCATCTCCAAGGTTAGGTCTACCTCGCTAACACCACTGACCCTAA 118Capture119 TGCTCCGTGCATCTCCAAGGTTAGGTCTACCTCGCTAACACCACTGACCCTAA 119Capture120TGCTCCGTGCATCTCCAAGGTTAGGTCTACCTCGCTAACACCACTGCCTAACT 120Capture121 TGCTCCGTGCATCTCCAAGGTTCGTCAACTGACAGTGGTTCGTACTCCCTAAC 121 Capture122 TGCTCCGTGCATCTCCAAGGTTCGTCAACTGACAGTGGTTCGTACTTAACCCT 122Capture123TGCTCCGTGCATCTCCAAGGTTCGTCAACTGACAGTGGTTCGTACTCCTAACC 123Capture124 TGCTCCGTGCATCTCCAAGGTTCGTCAACTGACAGTGGTTCGTACTCTAACCC 124Capture125TGCTCCGTGCATCTCCAAGGTTCGTCAACTGACAGTGGTTCGTACTAACCCTA 125Capture126 TGCTCCGTGCATCTCCAAGGTTCGTCAACTGACAGTGGTTCGTACTACCCTAA 126 Capture127 TGCTCCGTGCATCTCCAAGGTTCGTCAACTGACAGTGGTTCGTACTACCCTAA 127Capture128TGCTCCGTGCATCTCCAAGGTTCGTCAACTGACAGTGGTTCGTACTCCTAACT 128Capture129 TGCTCCGTGCATCTCCAAGGTTACCCTCCAGGAAAGTACCTCTGATCCCTAAC 129Capture130TGCTCCGTGCATCTCCAAGGTTACCCTCCAGGAAAGTACCTCTGATTAACCCT 130Capture131 TGCTCCGTGCATCTCCAAGGTTACCCTCCAGGAAAGTACCTCTGATCCTAACC 131 Capture132 TGCTCCGTGCATCTCCAAGGTTACCCTCCAGGAAAGTACCTCTGATCTAACCC 132Capture133TGCTCCGTGCATCTCCAAGGTTACCCTCCAGGAAAGTACCTCTGATAACCCTA 133Capture134 TGCTCCGTGCATCTCCAAGGTTACCCTCCAGGAAAGTACCTCTGATACCCTAA 134Capture135TGCTCCGTGCATCTCCAAGGTTACCCTCCAGGAAAGTACCTCTGATACCCTAA 135Capture136 TGCTCCGTGCATCTCCAAGGTTACCCTCCAGGAAAGTACCTCTGATCCTAACT 136 Capture137 TGCTCCGTGCATCTCCAAGGTTCCAAACCCAACAACCTAGATAGGCCCCTAAC 137Capture138TGCTCCGTGCATCTCCAAGGTTCCAAACCCAACAACCTAGATAGGCTAACCCT 138Capture139 TGCTCCGTGCATCTCCAAGGTTCCAAACCCAACAACCTAGATAGGCCCTAACC 139Capture140TGCTCCGTGCATCTCCAAGGTTCCAAACCCAACAACCTAGATAGGCCTAACCC 140Capture141 TGCTCCGTGCATCTCCAAGGTTCCAAACCCAACAACCTAGATAGGCAACCCTA 141 Capture142 TGCTCCGTGCATCTCCAAGGTTCCAAACCCAACAACCTAGATAGGCACCCTAA 142Capture143TGCTCCGTGCATCTCCAAGGTTCCAAACCCAACAACCTAGATAGGCACCCTAA 143Capture144 TGCTCCGTGCATCTCCAAGGTTCCAAACCCAACAACCTAGATAGGCCCTAACT 144Capture145TGCTCCGTGCATCTCCAAGGTTGTTCCTCGTGCAGTGTCAAGAGATCCCTAAC 145Capture146 TGCTCCGTGCATCTCCAAGGTTGTTCCTCGTGCAGTGTCAAGAGATTAACCCT 146 Capture147 TGCTCCGTGCATCTCCAAGGTTGTTCCTCGTGCAGTGTCAAGAGATCCTAACC 147Capture148TGCTCCGTGCATCTCCAAGGTTGTTCCTCGTGCAGTGTCAAGAGATCTAACCC 148Capture149 TGCTCCGTGCATCTCCAAGGTTGTTCCTCGTGCAGTGTCAAGAGATAACCCTA 149Capture150TGCTCCGTGCATCTCCAAGGTTGTTCCTCGTGCAGTGTCAAGAGATACCCTAA 150Capture151 TGCTCCGTGCATCTCCAAGGTTGTTCCTCGTGCAGTGTCAAGAGATACCCTAA 151 Capture152 TGCTCCGTGCATCTCCAAGGTTGTTCCTCGTGCAGTGTCAAGAGATCCTAACT 152ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture153 TGCTCCGTGCATCTCCAAGGTTTTGCGTCCTGTTACGAGAACTCATCCCTAAC 153Capture154TGCTCCGTGCATCTCCAAGGTTTTGCGTCCTGTTACGAGAACTCATTAACCCT 154Capture155 TGCTCCGTGCATCTCCAAGGTTTTGCGTCCTGTTACGAGAACTCATCCTAACC 155Capture156TGCTCCGTGCATCTCCAAGGTTTTGCGTCCTGTTACGAGAACTCATCTAACCC 156Capture157 TGCTCCGTGCATCTCCAAGGTTTTGCGTCCTGTTACGAGAACTCATAACCCTA 157 Capture158 TGCTCCGTGCATCTCCAAGGTTTTGCGTCCTGTTACGAGAACTCATACCCTAA 158Capture159TGCTCCGTGCATCTCCAAGGTTTTGCGTCCTGTTACGAGAACTCATACCCTAA 159Capture160 TGCTCCGTGCATCTCCAAGGTTTTGCGTCCTGTTACGAGAACTCATCCTAACT 160Capture161TGCTCCGTGCATCTCCAAGGTTGAGCCTCTCATTGTCCGTTCTCTACCCTAAC 161Capture162 TGCTCCGTGCATCTCCAAGGTTGAGCCTCTCATTGTCCGTTCTCTATAACCCT 162 Capture163 TGCTCCGTGCATCTCCAAGGTTGAGCCTCTCATTGTCCGTTCTCTACCTAACC 163Capture164TGCTCCGTGCATCTCCAAGGTTGAGCCTCTCATTGTCCGTTCTCTACTAACCC 164Capture165 TGCTCCGTGCATCTCCAAGGTTGAGCCTCTCATTGTCCGTTCTCTAAACCCTA 165Capture166TGCTCCGTGCATCTCCAAGGTTGAGCCTCTCATTGTCCGTTCTCTAACCCTAA 166Capture167 TGCTCCGTGCATCTCCAAGGTTGAGCCTCTCATTGTCCGTTCTCTAACCCTAA 167 Capture168 TGCTCCGTGCATCTCCAAGGTTGAGCCTCTCATTGTCCGTTCTCTACCTAACT 168Capture169TGCTCCGTGCATCTCCAAGGTTACCACTGCCATGTATCAAAGTACGCCCTAAC 169Capture170 TGCTCCGTGCATCTCCAAGGTTACCACTGCCATGTATCAAAGTACGTAACCCT 170Capture171TGCTCCGTGCATCTCCAAGGTTACCACTGCCATGTATCAAAGTACGCCTAACC 171Capture172 TGCTCCGTGCATCTCCAAGGTTACCACTGCCATGTATCAAAGTACGCTAACCC 172 Capture173 TGCTCCGTGCATCTCCAAGGTTACCACTGCCATGTATCAAAGTACGAACCCTA 173Capture174TGCTCCGTGCATCTCCAAGGTTACCACTGCCATGTATCAAAGTACGACCCTAA 174Capture175 TGCTCCGTGCATCTCCAAGGTTACCACTGCCATGTATCAAAGTACGACCCTAA 175Capture176TGCTCCGTGCATCTCCAAGGTTACCACTGCCATGTATCAAAGTACGCCTAACT 176Capture177 TGCTCCGTGCATCTCCAAGGTTCTTACTACCCAGTGAACCTCCTCGCCCTAAC 177 Capture178 TGCTCCGTGCATCTCCAAGGTTCTTACTACCCAGTGAACCTCCTCGTAACCCT 178Capture179TGCTCCGTGCATCTCCAAGGTTCTTACTACCCAGTGAACCTCCTCGCCTAACC 179Capture180 TGCTCCGTGCATCTCCAAGGTTCTTACTACCCAGTGAACCTCCTCGCTAACCC 180Capture181TGCTCCGTGCATCTCCAAGGTTCTTACTACCCAGTGAACCTCCTCGAACCCTA 181Capture182 TGCTCCGTGCATCTCCAAGGTTCTTACTACCCAGTGAACCTCCTCGACCCTAA 182 Capture183 TGCTCCGTGCATCTCCAAGGTTCTTACTACCCAGTGAACCTCCTCGACCCTAA 183Capture184TGCTCCGTGCATCTCCAAGGTTCTTACTACCCAGTGAACCTCCTCGCCTAACT 184Capture185 TGCTCCGTGCATCTCCAAGGTTGCATAGTTCTGCATGATGGGTTAGCCCTAAC 185Capture186TGCTCCGTGCATCTCCAAGGTTGCATAGTTCTGCATGATGGGTTAGTAACCCT 186Capture187 TGCTCCGTGCATCTCCAAGGTTGCATAGTTCTGCATGATGGGTTAGCCTAACC 187 Capture188 TGCTCCGTGCATCTCCAAGGTTGCATAGTTCTGCATGATGGGTTAGCTAACCC 188Capture189TGCTCCGTGCATCTCCAAGGTTGCATAGTTCTGCATGATGGGTTAGAACCCTA 189Capture190 TGCTCCGTGCATCTCCAAGGTTGCATAGTTCTGCATGATGGGTTAGACCCTAA 190Capture191TGCTCCGTGCATCTCCAAGGTTGCATAGTTCTGCATGATGGGTTAGACCCTAA 191Capture192 TGCTCCGTGCATCTCCAAGGTTGCATAGTTCTGCATGATGGGTTAGCCTAACT 192 Capture193 TGCTCCGTGCATCTCCAAGGTTGTAAGTTGGGTATGCAACGCAATGCCCTAAC 193ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture194 TGCTCCGTGCATCTCCAAGGTTGTAAGTTGGGTATGCAACGCAATGTAACCCT 194Capture195TGCTCCGTGCATCTCCAAGGTTGTAAGTTGGGTATGCAACGCAATGCCTAACC 195Capture196 TGCTCCGTGCATCTCCAAGGTTGTAAGTTGGGTATGCAACGCAATGCTAACCC 196Capture197TGCTCCGTGCATCTCCAAGGTTGTAAGTTGGGTATGCAACGCAATGAACCCTA 197Capture198 TGCTCCGTGCATCTCCAAGGTTGTAAGTTGGGTATGCAACGCAATGACCCTAA 198 Capture199 TGCTCCGTGCATCTCCAAGGTTGTAAGTTGGGTATGCAACGCAATGACCCTAA 199Capture200TGCTCCGTGCATCTCCAAGGTTGTAAGTTGGGTATGCAACGCAATGCCTAACT 200Capture201 TGCTCCGTGCATCTCCAAGGTTCATACAGCGACTACGCATTCTCATCCCTAAC 201Capture202TGCTCCGTGCATCTCCAAGGTTCATACAGCGACTACGCATTCTCATTAACCCT 202Capture203 TGCTCCGTGCATCTCCAAGGTTCATACAGCGACTACGCATTCTCATCCTAACC 203 Capture204 TGCTCCGTGCATCTCCAAGGTTCATACAGCGACTACGCATTCTCATCTAACCC 204Capture205TGCTCCGTGCATCTCCAAGGTTCATACAGCGACTACGCATTCTCATAACCCTA 205Capture206 TGCTCCGTGCATCTCCAAGGTTCATACAGCGACTACGCATTCTCATACCCTAA 206Capture207TGCTCCGTGCATCTCCAAGGTTCATACAGCGACTACGCATTCTCATACCCTAA 207Capture208 TGCTCCGTGCATCTCCAAGGTTCATACAGCGACTACGCATTCTCATCCTAACT 208 Capture209 TGCTCCGTGCATCTCCAAGGTTCGACGGTTAGATTCACCTCTTACACCCTAAC 209Capture210TGCTCCGTGCATCTCCAAGGTTCGACGGTTAGATTCACCTCTTACATAACCCT 210Capture211 TGCTCCGTGCATCTCCAAGGTTCGACGGTTAGATTCACCTCTTACACCTAACC 211Capture212TGCTCCGTGCATCTCCAAGGTTCGACGGTTAGATTCACCTCTTACACTAACCC 212Capture213 TGCTCCGTGCATCTCCAAGGTTCGACGGTTAGATTCACCTCTTACAAACCCTA 213 Capture214 TGCTCCGTGCATCTCCAAGGTTCGACGGTTAGATTCACCTCTTACAACCCTAA 214Capture215TGCTCCGTGCATCTCCAAGGTTCGACGGTTAGATTCACCTCTTACAACCCTAA 215Capture216 TGCTCCGTGCATCTCCAAGGTTCGACGGTTAGATTCACCTCTTACACCTAACT 216Capture217TGCTCCGTGCATCTCCAAGGTTTGAAACCTAAGAAGGCACCGTATCCCCTAAC 217Capture218 TGCTCCGTGCATCTCCAAGGTTTGAAACCTAAGAAGGCACCGTATCTAACCCT 218 Capture219 TGCTCCGTGCATCTCCAAGGTTTGAAACCTAAGAAGGCACCGTATCCCTAACC 219Capture220TGCTCCGTGCATCTCCAAGGTTTGAAACCTAAGAAGGCACCGTATCCTAACCC 220Capture221 TGCTCCGTGCATCTCCAAGGTTTGAAACCTAAGAAGGCACCGTATCAACCCTA 221Capture222TGCTCCGTGCATCTCCAAGGTTTGAAACCTAAGAAGGCACCGTATCACCCTAA 222Capture223 TGCTCCGTGCATCTCCAAGGTTTGAAACCTAAGAAGGCACCGTATCACCCTAA 223 Capture224 TGCTCCGTGCATCTCCAAGGTTTGAAACCTAAGAAGGCACCGTATCCCTAACT 224Capture225TGCTCCGTGCATCTCCAAGGTTCTAGACACCTTGGGTTGACAGACCCCCTAAC 225Capture226 TGCTCCGTGCATCTCCAAGGTTCTAGACACCTTGGGTTGACAGACCTAACCCT 226Capture227TGCTCCGTGCATCTCCAAGGTTCTAGACACCTTGGGTTGACAGACCCCTAACC 227Capture228 TGCTCCGTGCATCTCCAAGGTTCTAGACACCTTGGGTTGACAGACCCTAACCC 228 Capture229 TGCTCCGTGCATCTCCAAGGTTCTAGACACCTTGGGTTGACAGACCAACCCTA 229Capture230TGCTCCGTGCATCTCCAAGGTTCTAGACACCTTGGGTTGACAGACCACCCTAA 230Capture231 TGCTCCGTGCATCTCCAAGGTTCTAGACACCTTGGGTTGACAGACCACCCTAA 231Capture232TGCTCCGTGCATCTCCAAGGTTCTAGACACCTTGGGTTGACAGACCCCTAACT 232Capture233 TGCTCCGTGCATCTCCAAGGTTTCAGTGAGGATCTACTTCGACCCACCCTAAC 233 Capture234 TGCTCCGTGCATCTCCAAGGTTTCAGTGAGGATCTACTTCGACCCATAACCCT 234ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture235 TGCTCCGTGCATCTCCAAGGTTTCAGTGAGGATCTACTTCGACCCACCTAACC 235Capture236TGCTCCGTGCATCTCCAAGGTTTCAGTGAGGATCTACTTCGACCCACTAACCC 236Capture237 TGCTCCGTGCATCTCCAAGGTTTCAGTGAGGATCTACTTCGACCCAAACCCTA 237Capture238TGCTCCGTGCATCTCCAAGGTTTCAGTGAGGATCTACTTCGACCCAACCCTAA 238Capture239 TGCTCCGTGCATCTCCAAGGTTTCAGTGAGGATCTACTTCGACCCAACCCTAA 239 Capture240 TGCTCCGTGCATCTCCAAGGTTTCAGTGAGGATCTACTTCGACCCACCTAACT 240Capture241TGCTCCGTGCATCTCCAAGGTTTGCGTACAGCAATCAGTTACATTGCCCTAAC 241Capture242 TGCTCCGTGCATCTCCAAGGTTTGCGTACAGCAATCAGTTACATTGTAACCCT 242Capture243TGCTCCGTGCATCTCCAAGGTTTGCGTACAGCAATCAGTTACATTGCCTAACC 243Capture244 TGCTCCGTGCATCTCCAAGGTTTGCGTACAGCAATCAGTTACATTGCTAACCC 244 Capture245 TGCTCCGTGCATCTCCAAGGTTTGCGTACAGCAATCAGTTACATTGAACCCTA 245Capture246TGCTCCGTGCATCTCCAAGGTTTGCGTACAGCAATCAGTTACATTGACCCTAA 246Capture247 TGCTCCGTGCATCTCCAAGGTTTGCGTACAGCAATCAGTTACATTGACCCTAA 247Capture248TGCTCCGTGCATCTCCAAGGTTTGCGTACAGCAATCAGTTACATTGCCTAACT 248Capture249 TGCTCCGTGCATCTCCAAGGTTCCAGTAGAAGTCCGACAACGTCATCCCTAAC 249 Capture250 TGCTCCGTGCATCTCCAAGGTTCCAGTAGAAGTCCGACAACGTCATTAACCCT 250Capture251TGCTCCGTGCATCTCCAAGGTTCCAGTAGAAGTCCGACAACGTCATCCTAACC 251Capture252 TGCTCCGTGCATCTCCAAGGTTCCAGTAGAAGTCCGACAACGTCATCTAACCC 252Capture253TGCTCCGTGCATCTCCAAGGTTCCAGTAGAAGTCCGACAACGTCATAACCCTA 253Capture254 TGCTCCGTGCATCTCCAAGGTTCCAGTAGAAGTCCGACAACGTCATACCCTAA 254 Capture255 TGCTCCGTGCATCTCCAAGGTTCCAGTAGAAGTCCGACAACGTCATACCCTAA 255Capture256TGCTCCGTGCATCTCCAAGGTTCCAGTAGAAGTCCGACAACGTCATCCTAACT 256Capture257 TGCTCCGTGCATCTCCAAGGTTCAGACTTGGTACGGTTGGGTAACTCCCTAAC 257Capture258TGCTCCGTGCATCTCCAAGGTTCAGACTTGGTACGGTTGGGTAACTTAACCCT 258Capture259 TGCTCCGTGCATCTCCAAGGTTCAGACTTGGTACGGTTGGGTAACTCCTAACC 259 Capture260 TGCTCCGTGCATCTCCAAGGTTCAGACTTGGTACGGTTGGGTAACTCTAACCC 260Capture261TGCTCCGTGCATCTCCAAGGTTCAGACTTGGTACGGTTGGGTAACTAACCCTA 261Capture262 TGCTCCGTGCATCTCCAAGGTTCAGACTTGGTACGGTTGGGTAACTACCCTAA 262Capture263TGCTCCGTGCATCTCCAAGGTTCAGACTTGGTACGGTTGGGTAACTACCCTAA 263Capture264 TGCTCCGTGCATCTCCAAGGTTCAGACTTGGTACGGTTGGGTAACTCCTAACT 264 Capture265 TGCTCCGTGCATCTCCAAGGTTGGACGAAGAACTCAAGTCAAAGGCCCCTAAC 265Capture266TGCTCCGTGCATCTCCAAGGTTGGACGAAGAACTCAAGTCAAAGGCTAACCCT 266Capture267 TGCTCCGTGCATCTCCAAGGTTGGACGAAGAACTCAAGTCAAAGGCCCTAACC 267Capture268TGCTCCGTGCATCTCCAAGGTTGGACGAAGAACTCAAGTCAAAGGCCTAACCC 268Capture269 TGCTCCGTGCATCTCCAAGGTTGGACGAAGAACTCAAGTCAAAGGCAACCCTA 269 Capture270 TGCTCCGTGCATCTCCAAGGTTGGACGAAGAACTCAAGTCAAAGGCACCCTAA 270Capture271TGCTCCGTGCATCTCCAAGGTTGGACGAAGAACTCAAGTCAAAGGCACCCTAA 271Capture272 TGCTCCGTGCATCTCCAAGGTTGGACGAAGAACTCAAGTCAAAGGCCCTAACT 272Capture273TGCTCCGTGCATCTCCAAGGTTCTACTTACGAAGCTGAGGGACTGCCCCTAAC 273Capture274 TGCTCCGTGCATCTCCAAGGTTCTACTTACGAAGCTGAGGGACTGCTAACCCT 274 Capture275 TGCTCCGTGCATCTCCAAGGTTCTACTTACGAAGCTGAGGGACTGCCCTAACC 275ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture276 TGCTCCGTGCATCTCCAAGGTTCTACTTACGAAGCTGAGGGACTGCCTAACCC 276Capture277TGCTCCGTGCATCTCCAAGGTTCTACTTACGAAGCTGAGGGACTGCAACCCTA 277Capture278 TGCTCCGTGCATCTCCAAGGTTCTACTTACGAAGCTGAGGGACTGCACCCTAA 278Capture279TGCTCCGTGCATCTCCAAGGTTCTACTTACGAAGCTGAGGGACTGCACCCTAA 279Capture280 TGCTCCGTGCATCTCCAAGGTTCTACTTACGAAGCTGAGGGACTGCCCTAACT 280 Capture281 TGCTCCGTGCATCTCCAAGGTTATGTCCCAGTTAGAGGAGGAAACACCCTAAC 281Capture282TGCTCCGTGCATCTCCAAGGTTATGTCCCAGTTAGAGGAGGAAACATAACCCT 282Capture283 TGCTCCGTGCATCTCCAAGGTTATGTCCCAGTTAGAGGAGGAAACACCTAACC 283Capture284TGCTCCGTGCATCTCCAAGGTTATGTCCCAGTTAGAGGAGGAAACACTAACCC 284Capture285 TGCTCCGTGCATCTCCAAGGTTATGTCCCAGTTAGAGGAGGAAACAAACCCTA 285 Capture286 TGCTCCGTGCATCTCCAAGGTTATGTCCCAGTTAGAGGAGGAAACAACCCTAA 286Capture287TGCTCCGTGCATCTCCAAGGTTATGTCCCAGTTAGAGGAGGAAACAACCCTAA 287Capture288 TGCTCCGTGCATCTCCAAGGTTATGTCCCAGTTAGAGGAGGAAACACCTAACT 288Capture289TGCTCCGTGCATCTCCAAGGTTGCTTGCGATTGATGCTTAGTATCACCCTAAC 289Capture290 TGCTCCGTGCATCTCCAAGGTTGCTTGCGATTGATGCTTAGTATCATAACCCT 290 Capture291 TGCTCCGTGCATCTCCAAGGTTGCTTGCGATTGATGCTTAGTATCACCTAACC 291Capture292TGCTCCGTGCATCTCCAAGGTTGCTTGCGATTGATGCTTAGTATCACTAACCC 292Capture293 TGCTCCGTGCATCTCCAAGGTTGCTTGCGATTGATGCTTAGTATCAAACCCTA 293Capture294TGCTCCGTGCATCTCCAAGGTTGCTTGCGATTGATGCTTAGTATCAACCCTAA 294Capture295 TGCTCCGTGCATCTCCAAGGTTGCTTGCGATTGATGCTTAGTATCAACCCTAA 295 Capture296 TGCTCCGTGCATCTCCAAGGTTGCTTGCGATTGATGCTTAGTATCACCTAACT 296Capture297TGCTCCGTGCATCTCCAAGGTTACCACAGGAGGACGATACAGAGAACCCTAAC 297Capture298 TGCTCCGTGCATCTCCAAGGTTACCACAGGAGGACGATACAGAGAATAACCCT 298Capture299TGCTCCGTGCATCTCCAAGGTTACCACAGGAGGACGATACAGAGAACCTAACC 299Capture300 TGCTCCGTGCATCTCCAAGGTTACCACAGGAGGACGATACAGAGAACTAACCC 300 Capture301 TGCTCCGTGCATCTCCAAGGTTACCACAGGAGGACGATACAGAGAAAACCCTA 301Capture302TGCTCCGTGCATCTCCAAGGTTACCACAGGAGGACGATACAGAGAAACCCTAA 302Capture303 TGCTCCGTGCATCTCCAAGGTTACCACAGGAGGACGATACAGAGAAACCCTAA 303Capture304TGCTCCGTGCATCTCCAAGGTTACCACAGGAGGACGATACAGAGAACCTAACT 304Capture305 TGCTCCGTGCATCTCCAAGGTTCCACAGTGTCAACTAGAGCCTCTCCCCTAAC 305 Capture306 TGCTCCGTGCATCTCCAAGGTTCCACAGTGTCAACTAGAGCCTCTCTAACCCT 306Capture307TGCTCCGTGCATCTCCAAGGTTCCACAGTGTCAACTAGAGCCTCTCCCTAACC 307Capture308 TGCTCCGTGCATCTCCAAGGTTCCACAGTGTCAACTAGAGCCTCTCCTAACCC 308Capture309TGCTCCGTGCATCTCCAAGGTTCCACAGTGTCAACTAGAGCCTCTCAACCCTA 309Capture310 TGCTCCGTGCATCTCCAAGGTTCCACAGTGTCAACTAGAGCCTCTCACCCTAA 310 Capture311 TGCTCCGTGCATCTCCAAGGTTCCACAGTGTCAACTAGAGCCTCTCACCCTAA 311Capture312TGCTCCGTGCATCTCCAAGGTTCCACAGTGTCAACTAGAGCCTCTCCCTAACT 312Capture313 TGCTCCGTGCATCTCCAAGGTTTAGTTTGGATGACCAAGGATAGCCCCCTAAC 313Capture314TGCTCCGTGCATCTCCAAGGTTTAGTTTGGATGACCAAGGATAGCCTAACCCT 314Capture315 TGCTCCGTGCATCTCCAAGGTTTAGTTTGGATGACCAAGGATAGCCCCTAACC 315 Capture316 TGCTCCGTGCATCTCCAAGGTTTAGTTTGGATGACCAAGGATAGCCCTAACCC 316ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture317 TGCTCCGTGCATCTCCAAGGTTTAGTTTGGATGACCAAGGATAGCCAACCCTA 317Capture318TGCTCCGTGCATCTCCAAGGTTTAGTTTGGATGACCAAGGATAGCCACCCTAA 318Capture319 TGCTCCGTGCATCTCCAAGGTTTAGTTTGGATGACCAAGGATAGCCACCCTAA 319Capture320TGCTCCGTGCATCTCCAAGGTTTAGTTTGGATGACCAAGGATAGCCCCTAACT 320Capture321 TGCTCCGTGCATCTCCAAGGTTGGAGTTCGTCCAGAGAAGTACACGCCCTAAC 321 Capture322 TGCTCCGTGCATCTCCAAGGTTGGAGTTCGTCCAGAGAAGTACACGTAACCCT 322Capture323TGCTCCGTGCATCTCCAAGGTTGGAGTTCGTCCAGAGAAGTACACGCCTAACC 323Capture324 TGCTCCGTGCATCTCCAAGGTTGGAGTTCGTCCAGAGAAGTACACGCTAACCC 324Capture325TGCTCCGTGCATCTCCAAGGTTGGAGTTCGTCCAGAGAAGTACACGAACCCTA 325Capture326 TGCTCCGTGCATCTCCAAGGTTGGAGTTCGTCCAGAGAAGTACACGACCCTAA 326 Capture327 TGCTCCGTGCATCTCCAAGGTTGGAGTTCGTCCAGAGAAGTACACGACCCTAA 327Capture328TGCTCCGTGCATCTCCAAGGTTGGAGTTCGTCCAGAGAAGTACACGCCTAACT 328Capture329 TGCTCCGTGCATCTCCAAGGTTCTACGTGTAAGGCATACCTGCCAGCCCTAAC 329Capture330TGCTCCGTGCATCTCCAAGGTTCTACGTGTAAGGCATACCTGCCAGTAACCCT 330Capture331 TGCTCCGTGCATCTCCAAGGTTCTACGTGTAAGGCATACCTGCCAGCCTAACC 331 Capture332 TGCTCCGTGCATCTCCAAGGTTCTACGTGTAAGGCATACCTGCCAGCTAACCC 332Capture333TGCTCCGTGCATCTCCAAGGTTCTACGTGTAAGGCATACCTGCCAGAACCCTA 333Capture334 TGCTCCGTGCATCTCCAAGGTTCTACGTGTAAGGCATACCTGCCAGACCCTAA 334Capture335TGCTCCGTGCATCTCCAAGGTTCTACGTGTAAGGCATACCTGCCAGACCCTAA 335Capture336 TGCTCCGTGCATCTCCAAGGTTCTACGTGTAAGGCATACCTGCCAGCCTAACT 336 Capture337 TGCTCCGTGCATCTCCAAGGTTCTTTCGTTGTTGACTCGACGGTAGCCCTAAC 337Capture338TGCTCCGTGCATCTCCAAGGTTCTTTCGTTGTTGACTCGACGGTAGTAACCCT 338Capture339 TGCTCCGTGCATCTCCAAGGTTCTTTCGTTGTTGACTCGACGGTAGCCTAACC 339Capture340TGCTCCGTGCATCTCCAAGGTTCTTTCGTTGTTGACTCGACGGTAGCTAACCC 340Capture341 TGCTCCGTGCATCTCCAAGGTTCTTTCGTTGTTGACTCGACGGTAGAACCCTA 341 Capture342 TGCTCCGTGCATCTCCAAGGTTCTTTCGTTGTTGACTCGACGGTAGACCCTAA 342Capture343TGCTCCGTGCATCTCCAAGGTTCTTTCGTTGTTGACTCGACGGTAGACCCTAA 343Capture344 TGCTCCGTGCATCTCCAAGGTTCTTTCGTTGTTGACTCGACGGTAGCCTAACT 344Capture345TGCTCCGTGCATCTCCAAGGTTAGTAGAAAGGGTTCCTTCCCACTCCCCTAAC 345Capture346 TGCTCCGTGCATCTCCAAGGTTAGTAGAAAGGGTTCCTTCCCACTCTAACCCT 346 Capture347 TGCTCCGTGCATCTCCAAGGTTAGTAGAAAGGGTTCCTTCCCACTCCCTAACC 347Capture348TGCTCCGTGCATCTCCAAGGTTAGTAGAAAGGGTTCCTTCCCACTCCTAACCC 348Capture349 TGCTCCGTGCATCTCCAAGGTTAGTAGAAAGGGTTCCTTCCCACTCAACCCTA 349Capture350TGCTCCGTGCATCTCCAAGGTTAGTAGAAAGGGTTCCTTCCCACTCACCCTAA 350Capture351 TGCTCCGTGCATCTCCAAGGTTAGTAGAAAGGGTTCCTTCCCACTCACCCTAA 351 Capture352 TGCTCCGTGCATCTCCAAGGTTAGTAGAAAGGGTTCCTTCCCACTCCCTAACT 352Capture353TGCTCCGTGCATCTCCAAGGTTGATCCAACAGAGATGCCTTCAGTGCCCTAAC 353Capture354 TGCTCCGTGCATCTCCAAGGTTGATCCAACAGAGATGCCTTCAGTGTAACCCT 354Capture355TGCTCCGTGCATCTCCAAGGTTGATCCAACAGAGATGCCTTCAGTGCCTAACC 355Capture356 TGCTCCGTGCATCTCCAAGGTTGATCCAACAGAGATGCCTTCAGTGCTAACCC 356 Capture357 TGCTCCGTGCATCTCCAAGGTTGATCCAACAGAGATGCCTTCAGTGAACCCTA 357ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture358 TGCTCCGTGCATCTCCAAGGTTGATCCAACAGAGATGCCTTCAGTGACCCTAA 358Capture359TGCTCCGTGCATCTCCAAGGTTGATCCAACAGAGATGCCTTCAGTGACCCTAA 359Capture360 TGCTCCGTGCATCTCCAAGGTTGATCCAACAGAGATGCCTTCAGTGCCTAACT 360Capture361TGCTCCGTGCATCTCCAAGGTTGCTGTGTTCCACTTCATTCTCCTGCCCTAAC 361Capture362 TGCTCCGTGCATCTCCAAGGTTGCTGTGTTCCACTTCATTCTCCTGTAACCCT 362 Capture363 TGCTCCGTGCATCTCCAAGGTTGCTGTGTTCCACTTCATTCTCCTGCCTAACC 363Capture364TGCTCCGTGCATCTCCAAGGTTGCTGTGTTCCACTTCATTCTCCTGCTAACCC 364Capture365 TGCTCCGTGCATCTCCAAGGTTGCTGTGTTCCACTTCATTCTCCTGAACCCTA 365Capture366TGCTCCGTGCATCTCCAAGGTTGCTGTGTTCCACTTCATTCTCCTGACCCTAA 366Capture367 TGCTCCGTGCATCTCCAAGGTTGCTGTGTTCCACTTCATTCTCCTGACCCTAA 367 Capture368 TGCTCCGTGCATCTCCAAGGTTGCTGTGTTCCACTTCATTCTCCTGCCTAACT 368Capture369TGCTCCGTGCATCTCCAAGGTTGTGCAACTTTCCCACAGGTAGTTCCCCTAAC 369Capture370 TGCTCCGTGCATCTCCAAGGTTGTGCAACTTTCCCACAGGTAGTTCTAACCCT 370Capture371TGCTCCGTGCATCTCCAAGGTTGTGCAACTTTCCCACAGGTAGTTCCCTAACC 371Capture372 TGCTCCGTGCATCTCCAAGGTTGTGCAACTTTCCCACAGGTAGTTCCTAACCC 372 Capture373 TGCTCCGTGCATCTCCAAGGTTGTGCAACTTTCCCACAGGTAGTTCAACCCTA 373Capture374TGCTCCGTGCATCTCCAAGGTTGTGCAACTTTCCCACAGGTAGTTCACCCTAA 374Capture375 TGCTCCGTGCATCTCCAAGGTTGTGCAACTTTCCCACAGGTAGTTCACCCTAA 375Capture376TGCTCCGTGCATCTCCAAGGTTGTGCAACTTTCCCACAGGTAGTTCCCTAACT 376Capture377 TGCTCCGTGCATCTCCAAGGTTCATCTGGAACGTGGTACACCTGTACCCTAAC 377 Capture378 TGCTCCGTGCATCTCCAAGGTTCATCTGGAACGTGGTACACCTGTATAACCCT 378Capture379TGCTCCGTGCATCTCCAAGGTTCATCTGGAACGTGGTACACCTGTACCTAACC 379Capture380 TGCTCCGTGCATCTCCAAGGTTCATCTGGAACGTGGTACACCTGTACTAACCC 380Capture381TGCTCCGTGCATCTCCAAGGTTCATCTGGAACGTGGTACACCTGTAAACCCTA 381Capture382 TGCTCCGTGCATCTCCAAGGTTCATCTGGAACGTGGTACACCTGTAACCCTAA 382 Capture383 TGCTCCGTGCATCTCCAAGGTTCATCTGGAACGTGGTACACCTGTAACCCTAA 383Capture384TGCTCCGTGCATCTCCAAGGTTCATCTGGAACGTGGTACACCTGTACCTAACT 384Capture385 TGCTCCGTGCATCTCCAAGGTTACTGGTGCAGCTTTGAACATCTAGCCCTAAC 385Capture386TGCTCCGTGCATCTCCAAGGTTACTGGTGCAGCTTTGAACATCTAGTAACCCT 386Capture387 TGCTCCGTGCATCTCCAAGGTTACTGGTGCAGCTTTGAACATCTAGCCTAACC 387 Capture388 TGCTCCGTGCATCTCCAAGGTTACTGGTGCAGCTTTGAACATCTAGCTAACCC 388Capture389TGCTCCGTGCATCTCCAAGGTTACTGGTGCAGCTTTGAACATCTAGAACCCTA 389Capture390 TGCTCCGTGCATCTCCAAGGTTACTGGTGCAGCTTTGAACATCTAGACCCTAA 390Capture391TGCTCCGTGCATCTCCAAGGTTACTGGTGCAGCTTTGAACATCTAGACCCTAA 391Capture392 TGCTCCGTGCATCTCCAAGGTTACTGGTGCAGCTTTGAACATCTAGCCTAACT 392 Capture393 TGCTCCGTGCATCTCCAAGGTTATGGACTTTGGTAACTTCCTGCGTCCCTAAC 393Capture394TGCTCCGTGCATCTCCAAGGTTATGGACTTTGGTAACTTCCTGCGTTAACCCT 394Capture395 TGCTCCGTGCATCTCCAAGGTTATGGACTTTGGTAACTTCCTGCGTCCTAACC 395Capture396TGCTCCGTGCATCTCCAAGGTTATGGACTTTGGTAACTTCCTGCGTCTAACCC 396Capture397 TGCTCCGTGCATCTCCAAGGTTATGGACTTTGGTAACTTCCTGCGTAACCCTA 397 Capture398 TGCTCCGTGCATCTCCAAGGTTATGGACTTTGGTAACTTCCTGCGTACCCTAA 398ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture399 TGCTCCGTGCATCTCCAAGGTTATGGACTTTGGTAACTTCCTGCGTACCCTAA 399Capture400TGCTCCGTGCATCTCCAAGGTTATGGACTTTGGTAACTTCCTGCGTCCTAACT 400Capture401 TGCTCCGTGCATCTCCAAGGTTGTTGAATGAGCCTACTGGGTCCTCCCCTAAC 401Capture402TGCTCCGTGCATCTCCAAGGTTGTTGAATGAGCCTACTGGGTCCTCTAACCCT 402Capture403 TGCTCCGTGCATCTCCAAGGTTGTTGAATGAGCCTACTGGGTCCTCCCTAACC 403 Capture404 TGCTCCGTGCATCTCCAAGGTTGTTGAATGAGCCTACTGGGTCCTCCTAACCC 404Capture405TGCTCCGTGCATCTCCAAGGTTGTTGAATGAGCCTACTGGGTCCTCAACCCTA 405Capture406 TGCTCCGTGCATCTCCAAGGTTGTTGAATGAGCCTACTGGGTCCTCACCCTAA 406Capture407TGCTCCGTGCATCTCCAAGGTTGTTGAATGAGCCTACTGGGTCCTCACCCTAA 407Capture408 TGCTCCGTGCATCTCCAAGGTTGTTGAATGAGCCTACTGGGTCCTCCCTAACT 408 Capture409 TGCTCCGTGCATCTCCAAGGTTTGAGAGACAAGATTGTTCGTGGACCCCTAAC 409Capture410TGCTCCGTGCATCTCCAAGGTTTGAGAGACAAGATTGTTCGTGGACTAACCCT 410Capture411 TGCTCCGTGCATCTCCAAGGTTTGAGAGACAAGATTGTTCGTGGACCCTAACC 411Capture412TGCTCCGTGCATCTCCAAGGTTTGAGAGACAAGATTGTTCGTGGACCTAACCC 412Capture413 TGCTCCGTGCATCTCCAAGGTTTGAGAGACAAGATTGTTCGTGGACAACCCTA 413 Capture414 TGCTCCGTGCATCTCCAAGGTTTGAGAGACAAGATTGTTCGTGGACACCCTAA 414Capture415TGCTCCGTGCATCTCCAAGGTTTGAGAGACAAGATTGTTCGTGGACACCCTAA 415Capture416 TGCTCCGTGCATCTCCAAGGTTTGAGAGACAAGATTGTTCGTGGACCCTAACT 416Capture417TGCTCCGTGCATCTCCAAGGTTAGATTCAGACCGTCTCATGCAAAGCCCTAAC 417Capture418 TGCTCCGTGCATCTCCAAGGTTAGATTCAGACCGTCTCATGCAAAGTAACCCT 418 Capture419 TGCTCCGTGCATCTCCAAGGTTAGATTCAGACCGTCTCATGCAAAGCCTAACC 419Capture420TGCTCCGTGCATCTCCAAGGTTAGATTCAGACCGTCTCATGCAAAGCTAACCC 420Capture421 TGCTCCGTGCATCTCCAAGGTTAGATTCAGACCGTCTCATGCAAAGAACCCTA 421Capture422TGCTCCGTGCATCTCCAAGGTTAGATTCAGACCGTCTCATGCAAAGACCCTAA 422Capture423 TGCTCCGTGCATCTCCAAGGTTAGATTCAGACCGTCTCATGCAAAGACCCTAA 423 Capture424 TGCTCCGTGCATCTCCAAGGTTAGATTCAGACCGTCTCATGCAAAGCCTAACT 424Capture425TGCTCCGTGCATCTCCAAGGTTCAAGAGCTTTGACTAAGGAGCATGCCCTAAC 425Capture426 TGCTCCGTGCATCTCCAAGGTTCAAGAGCTTTGACTAAGGAGCATGTAACCCT 426Capture427TGCTCCGTGCATCTCCAAGGTTCAAGAGCTTTGACTAAGGAGCATGCCTAACC 427Capture428 TGCTCCGTGCATCTCCAAGGTTCAAGAGCTTTGACTAAGGAGCATGCTAACCC 428 Capture429 TGCTCCGTGCATCTCCAAGGTTCAAGAGCTTTGACTAAGGAGCATGAACCCTA 429Capture430TGCTCCGTGCATCTCCAAGGTTCAAGAGCTTTGACTAAGGAGCATGACCCTAA 430Capture431 TGCTCCGTGCATCTCCAAGGTTCAAGAGCTTTGACTAAGGAGCATGACCCTAA 431Capture432TGCTCCGTGCATCTCCAAGGTTCAAGAGCTTTGACTAAGGAGCATGCCTAACT 432Capture433 TGCTCCGTGCATCTCCAAGGTTTGGAAGATGAGACCCTGATCTACGCCCTAAC 433 Capture434 TGCTCCGTGCATCTCCAAGGTTTGGAAGATGAGACCCTGATCTACGTAACCCT 434Capture435TGCTCCGTGCATCTCCAAGGTTTGGAAGATGAGACCCTGATCTACGCCTAACC 435Capture436 TGCTCCGTGCATCTCCAAGGTTTGGAAGATGAGACCCTGATCTACGCTAACCC 436Capture437TGCTCCGTGCATCTCCAAGGTTTGGAAGATGAGACCCTGATCTACGAACCCTA 437Capture438 TGCTCCGTGCATCTCCAAGGTTTGGAAGATGAGACCCTGATCTACGACCCTAA 438 Capture439 TGCTCCGTGCATCTCCAAGGTTTGGAAGATGAGACCCTGATCTACGACCCTAA 439ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture440 TGCTCCGTGCATCTCCAAGGTTTGGAAGATGAGACCCTGATCTACGCCTAACT 440Capture441TGCTCCGTGCATCTCCAAGGTTTCACTACTCAACAGGTGGCATGAACCCTAAC 441Capture442 TGCTCCGTGCATCTCCAAGGTTTCACTACTCAACAGGTGGCATGAATAACCCT 442Capture443TGCTCCGTGCATCTCCAAGGTTTCACTACTCAACAGGTGGCATGAACCTAACC 443Capture444 TGCTCCGTGCATCTCCAAGGTTTCACTACTCAACAGGTGGCATGAACTAACCC 444 Capture445 TGCTCCGTGCATCTCCAAGGTTTCACTACTCAACAGGTGGCATGAAAACCCTA 445Capture446TGCTCCGTGCATCTCCAAGGTTTCACTACTCAACAGGTGGCATGAAACCCTAA 446Capture447 TGCTCCGTGCATCTCCAAGGTTTCACTACTCAACAGGTGGCATGAAACCCTAA 447Capture448TGCTCCGTGCATCTCCAAGGTTTCACTACTCAACAGGTGGCATGAACCTAACT 448Capture449 TGCTCCGTGCATCTCCAAGGTTGCTAGGTCAATCTCCTTCGGAAGTCCCTAAC 449 Capture450 TGCTCCGTGCATCTCCAAGGTTGCTAGGTCAATCTCCTTCGGAAGTTAACCCT 450Capture451TGCTCCGTGCATCTCCAAGGTTGCTAGGTCAATCTCCTTCGGAAGTCCTAACC 451Capture452 TGCTCCGTGCATCTCCAAGGTTGCTAGGTCAATCTCCTTCGGAAGTCTAACCC 452Capture453TGCTCCGTGCATCTCCAAGGTTGCTAGGTCAATCTCCTTCGGAAGTAACCCTA 453Capture454 TGCTCCGTGCATCTCCAAGGTTGCTAGGTCAATCTCCTTCGGAAGTACCCTAA 454 Capture455 TGCTCCGTGCATCTCCAAGGTTGCTAGGTCAATCTCCTTCGGAAGTACCCTAA 455Capture456TGCTCCGTGCATCTCCAAGGTTGCTAGGTCAATCTCCTTCGGAAGTCCTAACT 456Capture457 TGCTCCGTGCATCTCCAAGGTTCAGGTTACTCCTCCGTGAGTCTGACCCTAAC 457Capture458TGCTCCGTGCATCTCCAAGGTTCAGGTTACTCCTCCGTGAGTCTGATAACCCT 458Capture459 TGCTCCGTGCATCTCCAAGGTTCAGGTTACTCCTCCGTGAGTCTGACCTAACC 459 Capture460 TGCTCCGTGCATCTCCAAGGTTCAGGTTACTCCTCCGTGAGTCTGACTAACCC 460Capture461TGCTCCGTGCATCTCCAAGGTTCAGGTTACTCCTCCGTGAGTCTGAAACCCTA 461Capture462 TGCTCCGTGCATCTCCAAGGTTCAGGTTACTCCTCCGTGAGTCTGAACCCTAA 462Capture463TGCTCCGTGCATCTCCAAGGTTCAGGTTACTCCTCCGTGAGTCTGAACCCTAA 463Capture464 TGCTCCGTGCATCTCCAAGGTTCAGGTTACTCCTCCGTGAGTCTGACCTAACT 464 Capture465 TGCTCCGTGCATCTCCAAGGTTTCAATCAAGAAGGGAAAGCAAGGTCCCTAAC 465Capture466TGCTCCGTGCATCTCCAAGGTTTCAATCAAGAAGGGAAAGCAAGGTTAACCCT 466Capture467 TGCTCCGTGCATCTCCAAGGTTTCAATCAAGAAGGGAAAGCAAGGTCCTAACC 467Capture468TGCTCCGTGCATCTCCAAGGTTTCAATCAAGAAGGGAAAGCAAGGTCTAACCC 468Capture469 TGCTCCGTGCATCTCCAAGGTTTCAATCAAGAAGGGAAAGCAAGGTAACCCTA 469 Capture470 TGCTCCGTGCATCTCCAAGGTTTCAATCAAGAAGGGAAAGCAAGGTACCCTAA 470Capture471TGCTCCGTGCATCTCCAAGGTTTCAATCAAGAAGGGAAAGCAAGGTACCCTAA 471Capture472 TGCTCCGTGCATCTCCAAGGTTTCAATCAAGAAGGGAAAGCAAGGTCCTAACT 472Capture473TGCTCCGTGCATCTCCAAGGTTCATGTTCAACCAAGGCTTCTATGGCCCTAAC 473Capture474 TGCTCCGTGCATCTCCAAGGTTCATGTTCAACCAAGGCTTCTATGGTAACCCT 474 Capture475 TGCTCCGTGCATCTCCAAGGTTCATGTTCAACCAAGGCTTCTATGGCCTAACC 475Capture476TGCTCCGTGCATCTCCAAGGTTCATGTTCAACCAAGGCTTCTATGGCTAACCC 476Capture477 TGCTCCGTGCATCTCCAAGGTTCATGTTCAACCAAGGCTTCTATGGAACCCTA 477Capture478TGCTCCGTGCATCTCCAAGGTTCATGTTCAACCAAGGCTTCTATGGACCCTAA 478Capture479 TGCTCCGTGCATCTCCAAGGTTCATGTTCAACCAAGGCTTCTATGGACCCTAA 479 Capture480 TGCTCCGTGCATCTCCAAGGTTCATGTTCAACCAAGGCTTCTATGGCCTAACT 480ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture481 TGCTCCGTGCATCTCCAAGGTTAGAGGGTACTATGTGCCTCAGCACCCCTAAC 481Capture482TGCTCCGTGCATCTCCAAGGTTAGAGGGTACTATGTGCCTCAGCACTAACCCT 482Capture483 TGCTCCGTGCATCTCCAAGGTTAGAGGGTACTATGTGCCTCAGCACCCTAACC 483Capture484TGCTCCGTGCATCTCCAAGGTTAGAGGGTACTATGTGCCTCAGCACCTAACCC 484Capture485 TGCTCCGTGCATCTCCAAGGTTAGAGGGTACTATGTGCCTCAGCACAACCCTA 485 Capture486 TGCTCCGTGCATCTCCAAGGTTAGAGGGTACTATGTGCCTCAGCACACCCTAA 486Capture487TGCTCCGTGCATCTCCAAGGTTAGAGGGTACTATGTGCCTCAGCACACCCTAA 487Capture488 TGCTCCGTGCATCTCCAAGGTTAGAGGGTACTATGTGCCTCAGCACCCTAACT 488Capture489TGCTCCGTGCATCTCCAAGGTTCACCCACACTTACTTCAGGACGTACCCTAAC 489Capture490 TGCTCCGTGCATCTCCAAGGTTCACCCACACTTACTTCAGGACGTATAACCCT 490 Capture491 TGCTCCGTGCATCTCCAAGGTTCACCCACACTTACTTCAGGACGTACCTAACC 491Capture492TGCTCCGTGCATCTCCAAGGTTCACCCACACTTACTTCAGGACGTACTAACCC 492Capture493 TGCTCCGTGCATCTCCAAGGTTCACCCACACTTACTTCAGGACGTAAACCCTA 493Capture494TGCTCCGTGCATCTCCAAGGTTCACCCACACTTACTTCAGGACGTAACCCTAA 494Capture495 TGCTCCGTGCATCTCCAAGGTTCACCCACACTTACTTCAGGACGTAACCCTAA 495 Capture496 TGCTCCGTGCATCTCCAAGGTTCACCCACACTTACTTCAGGACGTACCTAACT 496Capture497TGCTCCGTGCATCTCCAAGGTTTTCTGAAGTTCCTGGGTCTTGAACCCCTAAC 497Capture498 TGCTCCGTGCATCTCCAAGGTTTTCTGAAGTTCCTGGGTCTTGAACTAACCCT 498Capture499TGCTCCGTGCATCTCCAAGGTTTTCTGAAGTTCCTGGGTCTTGAACCCTAACC 499Capture500 TGCTCCGTGCATCTCCAAGGTTTTCTGAAGTTCCTGGGTCTTGAACCTAACCC 500 Capture501 TGCTCCGTGCATCTCCAAGGTTTTCTGAAGTTCCTGGGTCTTGAACAACCCTA 501Capture502TGCTCCGTGCATCTCCAAGGTTTTCTGAAGTTCCTGGGTCTTGAACACCCTAA 502Capture503 TGCTCCGTGCATCTCCAAGGTTTTCTGAAGTTCCTGGGTCTTGAACACCCTAA 503Capture504TGCTCCGTGCATCTCCAAGGTTTTCTGAAGTTCCTGGGTCTTGAACCCTAACT 504Capture505 TGCTCCGTGCATCTCCAAGGTTGACAGACACCGTTCATCGACTTTCCCCTAAC 505 Capture506 TGCTCCGTGCATCTCCAAGGTTGACAGACACCGTTCATCGACTTTCTAACCCT 506Capture507TGCTCCGTGCATCTCCAAGGTTGACAGACACCGTTCATCGACTTTCCCTAACC 507Capture508 TGCTCCGTGCATCTCCAAGGTTGACAGACACCGTTCATCGACTTTCCTAACCC 508Capture509TGCTCCGTGCATCTCCAAGGTTGACAGACACCGTTCATCGACTTTCAACCCTA 509Capture510 TGCTCCGTGCATCTCCAAGGTTGACAGACACCGTTCATCGACTTTCACCCTAA 510 Capture511 TGCTCCGTGCATCTCCAAGGTTGACAGACACCGTTCATCGACTTTCACCCTAA 511Capture512TGCTCCGTGCATCTCCAAGGTTGACAGACACCGTTCATCGACTTTCCCTAACT 512Capture513 TGCTCCGTGCATCTCCAAGGTTTTCTCAGTCTTCCTCCAGACAAGGCCCTAAC 513Capture514TGCTCCGTGCATCTCCAAGGTTTTCTCAGTCTTCCTCCAGACAAGGTAACCCT 514Capture515 TGCTCCGTGCATCTCCAAGGTTTTCTCAGTCTTCCTCCAGACAAGGCCTAACC 515 Capture516 TGCTCCGTGCATCTCCAAGGTTTTCTCAGTCTTCCTCCAGACAAGGCTAACCC 516Capture517TGCTCCGTGCATCTCCAAGGTTTTCTCAGTCTTCCTCCAGACAAGGAACCCTA 517Capture518 TGCTCCGTGCATCTCCAAGGTTTTCTCAGTCTTCCTCCAGACAAGGACCCTAA 518Capture519TGCTCCGTGCATCTCCAAGGTTTTCTCAGTCTTCCTCCAGACAAGGACCCTAA 519Capture520 TGCTCCGTGCATCTCCAAGGTTTTCTCAGTCTTCCTCCAGACAAGGCCTAACT 520 Capture521 TGCTCCGTGCATCTCCAAGGTTCCGATCCTTGTGGCTTCTAACTTCCCCTAAC 521ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture522 TGCTCCGTGCATCTCCAAGGTTCCGATCCTTGTGGCTTCTAACTTCTAACCCT 522Capture523TGCTCCGTGCATCTCCAAGGTTCCGATCCTTGTGGCTTCTAACTTCCCTAACC 523Capture524 TGCTCCGTGCATCTCCAAGGTTCCGATCCTTGTGGCTTCTAACTTCCTAACCC 524Capture525TGCTCCGTGCATCTCCAAGGTTCCGATCCTTGTGGCTTCTAACTTCAACCCTA 525Capture526 TGCTCCGTGCATCTCCAAGGTTCCGATCCTTGTGGCTTCTAACTTCACCCTAA 526 Capture527 TGCTCCGTGCATCTCCAAGGTTCCGATCCTTGTGGCTTCTAACTTCACCCTAA 527Capture528TGCTCCGTGCATCTCCAAGGTTCCGATCCTTGTGGCTTCTAACTTCCCTAACT 528Capture529 TGCTCCGTGCATCTCCAAGGTTGTTTGTCATACTCGTGTGCTCACCCCCTAAC 529Capture530TGCTCCGTGCATCTCCAAGGTTGTTTGTCATACTCGTGTGCTCACCTAACCCT 530Capture531 TGCTCCGTGCATCTCCAAGGTTGTTTGTCATACTCGTGTGCTCACCCCTAACC 531 Capture532 TGCTCCGTGCATCTCCAAGGTTGTTTGTCATACTCGTGTGCTCACCCTAACCC 532Capture533TGCTCCGTGCATCTCCAAGGTTGTTTGTCATACTCGTGTGCTCACCAACCCTA 533Capture534 TGCTCCGTGCATCTCCAAGGTTGTTTGTCATACTCGTGTGCTCACCACCCTAA 534Capture535TGCTCCGTGCATCTCCAAGGTTGTTTGTCATACTCGTGTGCTCACCACCCTAA 535Capture536 TGCTCCGTGCATCTCCAAGGTTGTTTGTCATACTCGTGTGCTCACCCCTAACT 536 Capture537 TGCTCCGTGCATCTCCAAGGTTGAATCTAAGCAAACACGAAGGTGGCCCTAAC 537Capture538TGCTCCGTGCATCTCCAAGGTTGAATCTAAGCAAACACGAAGGTGGTAACCCT 538Capture539 TGCTCCGTGCATCTCCAAGGTTGAATCTAAGCAAACACGAAGGTGGCCTAACC 539Capture540TGCTCCGTGCATCTCCAAGGTTGAATCTAAGCAAACACGAAGGTGGCTAACCC 540Capture541 TGCTCCGTGCATCTCCAAGGTTGAATCTAAGCAAACACGAAGGTGGAACCCTA 541 Capture542 TGCTCCGTGCATCTCCAAGGTTGAATCTAAGCAAACACGAAGGTGGACCCTAA 542Capture543TGCTCCGTGCATCTCCAAGGTTGAATCTAAGCAAACACGAAGGTGGACCCTAA 543Capture544 TGCTCCGTGCATCTCCAAGGTTGAATCTAAGCAAACACGAAGGTGGCCTAACT 544Capture545TGCTCCGTGCATCTCCAAGGTTTACAGTCCGAGCCTCATGTGATCTCCCTAAC 545Capture546 TGCTCCGTGCATCTCCAAGGTTTACAGTCCGAGCCTCATGTGATCTTAACCCT 546 Capture547 TGCTCCGTGCATCTCCAAGGTTTACAGTCCGAGCCTCATGTGATCTCCTAACC 547Capture548TGCTCCGTGCATCTCCAAGGTTTACAGTCCGAGCCTCATGTGATCTCTAACCC 548Capture549 TGCTCCGTGCATCTCCAAGGTTTACAGTCCGAGCCTCATGTGATCTAACCCTA 549Capture550TGCTCCGTGCATCTCCAAGGTTTACAGTCCGAGCCTCATGTGATCTACCCTAA 550Capture551 TGCTCCGTGCATCTCCAAGGTTTACAGTCCGAGCCTCATGTGATCTACCCTAA 551 Capture552 TGCTCCGTGCATCTCCAAGGTTTACAGTCCGAGCCTCATGTGATCTCCTAACT 552Capture553TGCTCCGTGCATCTCCAAGGTTACCGAGATCCTACGAATGGAGTGTCCCTAAC 553Capture554 TGCTCCGTGCATCTCCAAGGTTACCGAGATCCTACGAATGGAGTGTTAACCCT 554Capture555TGCTCCGTGCATCTCCAAGGTTACCGAGATCCTACGAATGGAGTGTCCTAACC 555Capture556 TGCTCCGTGCATCTCCAAGGTTACCGAGATCCTACGAATGGAGTGTCTAACCC 556 Capture557 TGCTCCGTGCATCTCCAAGGTTACCGAGATCCTACGAATGGAGTGTAACCCTA 557Capture558TGCTCCGTGCATCTCCAAGGTTACCGAGATCCTACGAATGGAGTGTACCCTAA 558Capture559 TGCTCCGTGCATCTCCAAGGTTACCGAGATCCTACGAATGGAGTGTACCCTAA 559Capture560TGCTCCGTGCATCTCCAAGGTTACCGAGATCCTACGAATGGAGTGTCCTAACT 560Capture561 TGCTCCGTGCATCTCCAAGGTTCCTGGGAGCATCAGGTAGTAACAGCCCTAAC 561 Capture562 TGCTCCGTGCATCTCCAAGGTTCCTGGGAGCATCAGGTAGTAACAGTAACCCT 562ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture563 TGCTCCGTGCATCTCCAAGGTTCCTGGGAGCATCAGGTAGTAACAGCCTAACC 563Capture564TGCTCCGTGCATCTCCAAGGTTCCTGGGAGCATCAGGTAGTAACAGCTAACCC 564Capture565 TGCTCCGTGCATCTCCAAGGTTCCTGGGAGCATCAGGTAGTAACAGAACCCTA 565Capture566TGCTCCGTGCATCTCCAAGGTTCCTGGGAGCATCAGGTAGTAACAGACCCTAA 566Capture567 TGCTCCGTGCATCTCCAAGGTTCCTGGGAGCATCAGGTAGTAACAGACCCTAA 567 Capture568 TGCTCCGTGCATCTCCAAGGTTCCTGGGAGCATCAGGTAGTAACAGCCTAACT 568Capture569TGCTCCGTGCATCTCCAAGGTTTAGCTGACTGTCTTCCATACCGACCCCTAAC 569Capture570 TGCTCCGTGCATCTCCAAGGTTTAGCTGACTGTCTTCCATACCGACTAACCCT 570Capture571TGCTCCGTGCATCTCCAAGGTTTAGCTGACTGTCTTCCATACCGACCCTAACC 571Capture572 TGCTCCGTGCATCTCCAAGGTTTAGCTGACTGTCTTCCATACCGACCTAACCC 572 Capture573 TGCTCCGTGCATCTCCAAGGTTTAGCTGACTGTCTTCCATACCGACAACCCTA 573Capture574TGCTCCGTGCATCTCCAAGGTTTAGCTGACTGTCTTCCATACCGACACCCTAA 574Capture575 TGCTCCGTGCATCTCCAAGGTTTAGCTGACTGTCTTCCATACCGACACCCTAA 575Capture576TGCTCCGTGCATCTCCAAGGTTTAGCTGACTGTCTTCCATACCGACCCTAACT 576Capture577 TGCTCCGTGCATCTCCAAGGTTAAGAAACAGGATGACAGAACCCTCCCCTAAC 577 Capture578 TGCTCCGTGCATCTCCAAGGTTAAGAAACAGGATGACAGAACCCTCTAACCCT 578Capture579TGCTCCGTGCATCTCCAAGGTTAAGAAACAGGATGACAGAACCCTCCCTAACC 579Capture580 TGCTCCGTGCATCTCCAAGGTTAAGAAACAGGATGACAGAACCCTCCTAACCC 580Capture581TGCTCCGTGCATCTCCAAGGTTAAGAAACAGGATGACAGAACCCTCAACCCTA 581Capture582 TGCTCCGTGCATCTCCAAGGTTAAGAAACAGGATGACAGAACCCTCACCCTAA 582 Capture583 TGCTCCGTGCATCTCCAAGGTTAAGAAACAGGATGACAGAACCCTCACCCTAA 583Capture584TGCTCCGTGCATCTCCAAGGTTAAGAAACAGGATGACAGAACCCTCCCTAACT 584Capture585 TGCTCCGTGCATCTCCAAGGTTTACAAGCATCCCAACACTTCCACTCCCTAAC 585Capture586TGCTCCGTGCATCTCCAAGGTTTACAAGCATCCCAACACTTCCACTTAACCCT 586Capture587 TGCTCCGTGCATCTCCAAGGTTTACAAGCATCCCAACACTTCCACTCCTAACC 587 Capture588 TGCTCCGTGCATCTCCAAGGTTTACAAGCATCCCAACACTTCCACTCTAACCC 588Capture589TGCTCCGTGCATCTCCAAGGTTTACAAGCATCCCAACACTTCCACTAACCCTA 589Capture590 TGCTCCGTGCATCTCCAAGGTTTACAAGCATCCCAACACTTCCACTACCCTAA 590Capture591TGCTCCGTGCATCTCCAAGGTTTACAAGCATCCCAACACTTCCACTACCCTAA 591Capture592 TGCTCCGTGCATCTCCAAGGTTTACAAGCATCCCAACACTTCCACTCCTAACT 592 Capture593 TGCTCCGTGCATCTCCAAGGTTGACCATTGTGATGAACCCTGTTGTCCCTAAC 593Capture594TGCTCCGTGCATCTCCAAGGTTGACCATTGTGATGAACCCTGTTGTTAACCCT 594Capture595 TGCTCCGTGCATCTCCAAGGTTGACCATTGTGATGAACCCTGTTGTCCTAACC 595Capture596TGCTCCGTGCATCTCCAAGGTTGACCATTGTGATGAACCCTGTTGTCTAACCC 596Capture597 TGCTCCGTGCATCTCCAAGGTTGACCATTGTGATGAACCCTGTTGTAACCCTA 597 Capture598 TGCTCCGTGCATCTCCAAGGTTGACCATTGTGATGAACCCTGTTGTACCCTAA 598Capture599TGCTCCGTGCATCTCCAAGGTTGACCATTGTGATGAACCCTGTTGTACCCTAA 599Capture600 TGCTCCGTGCATCTCCAAGGTTGACCATTGTGATGAACCCTGTTGTCCTAACT 600Capture601TGCTCCGTGCATCTCCAAGGTTATGCTTGTTACATCAACCCTGGACCCCTAAC 601Capture602 TGCTCCGTGCATCTCCAAGGTTATGCTTGTTACATCAACCCTGGACTAACCCT 602 Capture603 TGCTCCGTGCATCTCCAAGGTTATGCTTGTTACATCAACCCTGGACCCTAACC 603ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture604 TGCTCCGTGCATCTCCAAGGTTATGCTTGTTACATCAACCCTGGACCTAACCC 604Capture605TGCTCCGTGCATCTCCAAGGTTATGCTTGTTACATCAACCCTGGACAACCCTA 605Capture606 TGCTCCGTGCATCTCCAAGGTTATGCTTGTTACATCAACCCTGGACACCCTAA 606Capture607TGCTCCGTGCATCTCCAAGGTTATGCTTGTTACATCAACCCTGGACACCCTAA 607Capture608 TGCTCCGTGCATCTCCAAGGTTATGCTTGTTACATCAACCCTGGACCCTAACT 608 Capture609 TGCTCCGTGCATCTCCAAGGTTCGACCTGTTTCTCAGGGATACAACCCCTAAC 609Capture610TGCTCCGTGCATCTCCAAGGTTCGACCTGTTTCTCAGGGATACAACTAACCCT 610Capture611 TGCTCCGTGCATCTCCAAGGTTCGACCTGTTTCTCAGGGATACAACCCTAACC 611Capture612TGCTCCGTGCATCTCCAAGGTTCGACCTGTTTCTCAGGGATACAACCTAACCC 612Capture613 TGCTCCGTGCATCTCCAAGGTTCGACCTGTTTCTCAGGGATACAACAACCCTA 613 Capture614 TGCTCCGTGCATCTCCAAGGTTCGACCTGTTTCTCAGGGATACAACACCCTAA 614Capture615TGCTCCGTGCATCTCCAAGGTTCGACCTGTTTCTCAGGGATACAACACCCTAA 615Capture616 TGCTCCGTGCATCTCCAAGGTTCGACCTGTTTCTCAGGGATACAACCCTAACT 616Capture617TGCTCCGTGCATCTCCAAGGTTAACAACCGAACCTTTGAATCAGAACCCTAAC 617Capture618 TGCTCCGTGCATCTCCAAGGTTAACAACCGAACCTTTGAATCAGAATAACCCT 618 Capture619 TGCTCCGTGCATCTCCAAGGTTAACAACCGAACCTTTGAATCAGAACCTAACC 619Capture620TGCTCCGTGCATCTCCAAGGTTAACAACCGAACCTTTGAATCAGAACTAACCC 620Capture621 TGCTCCGTGCATCTCCAAGGTTAACAACCGAACCTTTGAATCAGAAAACCCTA 621Capture622TGCTCCGTGCATCTCCAAGGTTAACAACCGAACCTTTGAATCAGAAACCCTAA 622Capture623 TGCTCCGTGCATCTCCAAGGTTAACAACCGAACCTTTGAATCAGAAACCCTAA 623 Capture624 TGCTCCGTGCATCTCCAAGGTTAACAACCGAACCTTTGAATCAGAACCTAACT 624Capture625TGCTCCGTGCATCTCCAAGGTTTCTCGGAGATAGTTCTCACTGCTGCCCTAAC 625Capture626 TGCTCCGTGCATCTCCAAGGTTTCTCGGAGATAGTTCTCACTGCTGTAACCCT 626Capture627TGCTCCGTGCATCTCCAAGGTTTCTCGGAGATAGTTCTCACTGCTGCCTAACC 627Capture628 TGCTCCGTGCATCTCCAAGGTTTCTCGGAGATAGTTCTCACTGCTGCTAACCC 628 Capture629 TGCTCCGTGCATCTCCAAGGTTTCTCGGAGATAGTTCTCACTGCTGAACCCTA 629Capture630TGCTCCGTGCATCTCCAAGGTTTCTCGGAGATAGTTCTCACTGCTGACCCTAA 630Capture631 TGCTCCGTGCATCTCCAAGGTTTCTCGGAGATAGTTCTCACTGCTGACCCTAA 631Capture632TGCTCCGTGCATCTCCAAGGTTTCTCGGAGATAGTTCTCACTGCTGCCTAACT 632Capture633 TGCTCCGTGCATCTCCAAGGTTCGGATGAACATAGGATAGCGATTCCCCTAAC 633 Capture634 TGCTCCGTGCATCTCCAAGGTTCGGATGAACATAGGATAGCGATTCTAACCCT 634Capture635TGCTCCGTGCATCTCCAAGGTTCGGATGAACATAGGATAGCGATTCCCTAACC 635Capture636 TGCTCCGTGCATCTCCAAGGTTCGGATGAACATAGGATAGCGATTCCTAACCC 636Capture637TGCTCCGTGCATCTCCAAGGTTCGGATGAACATAGGATAGCGATTCAACCCTA 637Capture638 TGCTCCGTGCATCTCCAAGGTTCGGATGAACATAGGATAGCGATTCACCCTAA 638 Capture639 TGCTCCGTGCATCTCCAAGGTTCGGATGAACATAGGATAGCGATTCACCCTAA 639Capture640TGCTCCGTGCATCTCCAAGGTTCGGATGAACATAGGATAGCGATTCCCTAACT 640Capture641 TGCTCCGTGCATCTCCAAGGTTCCTCATCTTGTGAAGTTGTTTCGGCCCTAAC 641Capture642TGCTCCGTGCATCTCCAAGGTTCCTCATCTTGTGAAGTTGTTTCGGTAACCCT 642Capture643 TGCTCCGTGCATCTCCAAGGTTCCTCATCTTGTGAAGTTGTTTCGGCCTAACC 643 Capture644 TGCTCCGTGCATCTCCAAGGTTCCTCATCTTGTGAAGTTGTTTCGGCTAACCC 644ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture645 TGCTCCGTGCATCTCCAAGGTTCCTCATCTTGTGAAGTTGTTTCGGAACCCTA 645Capture646TGCTCCGTGCATCTCCAAGGTTCCTCATCTTGTGAAGTTGTTTCGGACCCTAA 646Capture647 TGCTCCGTGCATCTCCAAGGTTCCTCATCTTGTGAAGTTGTTTCGGACCCTAA 647Capture648TGCTCCGTGCATCTCCAAGGTTCCTCATCTTGTGAAGTTGTTTCGGCCTAACT 648Capture649 TGCTCCGTGCATCTCCAAGGTTACGGTATGTCGAGTTCCAGGACTACCCTAAC 649 Capture650 TGCTCCGTGCATCTCCAAGGTTACGGTATGTCGAGTTCCAGGACTATAACCCT 650Capture651TGCTCCGTGCATCTCCAAGGTTACGGTATGTCGAGTTCCAGGACTACCTAACC 651Capture652 TGCTCCGTGCATCTCCAAGGTTACGGTATGTCGAGTTCCAGGACTACTAACCC 652Capture653TGCTCCGTGCATCTCCAAGGTTACGGTATGTCGAGTTCCAGGACTAAACCCTA 653Capture654 TGCTCCGTGCATCTCCAAGGTTACGGTATGTCGAGTTCCAGGACTAACCCTAA 654 Capture655 TGCTCCGTGCATCTCCAAGGTTACGGTATGTCGAGTTCCAGGACTAACCCTAA 655Capture656TGCTCCGTGCATCTCCAAGGTTACGGTATGTCGAGTTCCAGGACTACCTAACT 656Capture657 TGCTCCGTGCATCTCCAAGGTTTGGCTTGATCTAGGTAAGGTCGAACCCTAAC 657Capture658TGCTCCGTGCATCTCCAAGGTTTGGCTTGATCTAGGTAAGGTCGAATAACCCT 658Capture659 TGCTCCGTGCATCTCCAAGGTTTGGCTTGATCTAGGTAAGGTCGAACCTAACC 659 Capture660 TGCTCCGTGCATCTCCAAGGTTTGGCTTGATCTAGGTAAGGTCGAACTAACCC 660Capture661TGCTCCGTGCATCTCCAAGGTTTGGCTTGATCTAGGTAAGGTCGAAAACCCTA 661Capture662 TGCTCCGTGCATCTCCAAGGTTTGGCTTGATCTAGGTAAGGTCGAAACCCTAA 662Capture663TGCTCCGTGCATCTCCAAGGTTTGGCTTGATCTAGGTAAGGTCGAAACCCTAA 663Capture664 TGCTCCGTGCATCTCCAAGGTTTGGCTTGATCTAGGTAAGGTCGAACCTAACT 664 Capture665 TGCTCCGTGCATCTCCAAGGTTGTAGTGGACCTAGAACCTGTGCCACCCTAAC 665Capture666TGCTCCGTGCATCTCCAAGGTTGTAGTGGACCTAGAACCTGTGCCATAACCCT 666Capture667 TGCTCCGTGCATCTCCAAGGTTGTAGTGGACCTAGAACCTGTGCCACCTAACC 667Capture668TGCTCCGTGCATCTCCAAGGTTGTAGTGGACCTAGAACCTGTGCCACTAACCC 668Capture669 TGCTCCGTGCATCTCCAAGGTTGTAGTGGACCTAGAACCTGTGCCAAACCCTA 669 Capture670 TGCTCCGTGCATCTCCAAGGTTGTAGTGGACCTAGAACCTGTGCCAACCCTAA 670Capture671TGCTCCGTGCATCTCCAAGGTTGTAGTGGACCTAGAACCTGTGCCAACCCTAA 671Capture672 TGCTCCGTGCATCTCCAAGGTTGTAGTGGACCTAGAACCTGTGCCACCTAACT 672Capture673TGCTCCGTGCATCTCCAAGGTTAACGGAGGAGTTAGTTGGATGATCCCCTAAC 673Capture674 TGCTCCGTGCATCTCCAAGGTTAACGGAGGAGTTAGTTGGATGATCTAACCCT 674 Capture675 TGCTCCGTGCATCTCCAAGGTTAACGGAGGAGTTAGTTGGATGATCCCTAACC 675Capture676TGCTCCGTGCATCTCCAAGGTTAACGGAGGAGTTAGTTGGATGATCCTAACCC 676Capture677 TGCTCCGTGCATCTCCAAGGTTAACGGAGGAGTTAGTTGGATGATCAACCCTA 677Capture678TGCTCCGTGCATCTCCAAGGTTAACGGAGGAGTTAGTTGGATGATCACCCTAA 678Capture679 TGCTCCGTGCATCTCCAAGGTTAACGGAGGAGTTAGTTGGATGATCACCCTAA 679 Capture680 TGCTCCGTGCATCTCCAAGGTTAACGGAGGAGTTAGTTGGATGATCCCTAACT 680Capture681TGCTCCGTGCATCTCCAAGGTTAGGTGATCCCAACAAGCGTAAGTACCCTAAC 681Capture682 TGCTCCGTGCATCTCCAAGGTTAGGTGATCCCAACAAGCGTAAGTATAACCCT 682Capture683TGCTCCGTGCATCTCCAAGGTTAGGTGATCCCAACAAGCGTAAGTACCTAACC 683Capture684 TGCTCCGTGCATCTCCAAGGTTAGGTGATCCCAACAAGCGTAAGTACTAACCC 684 Capture685 TGCTCCGTGCATCTCCAAGGTTAGGTGATCCCAACAAGCGTAAGTAAACCCTA 685ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture686 TGCTCCGTGCATCTCCAAGGTTAGGTGATCCCAACAAGCGTAAGTAACCCTAA 686Capture687TGCTCCGTGCATCTCCAAGGTTAGGTGATCCCAACAAGCGTAAGTAACCCTAA 687Capture688 TGCTCCGTGCATCTCCAAGGTTAGGTGATCCCAACAAGCGTAAGTACCTAACT 688Capture689TGCTCCGTGCATCTCCAAGGTTTACATGCTCCTGTTGTTAGGGAGGCCCTAAC 689Capture690 TGCTCCGTGCATCTCCAAGGTTTACATGCTCCTGTTGTTAGGGAGGTAACCCT 690 Capture691 TGCTCCGTGCATCTCCAAGGTTTACATGCTCCTGTTGTTAGGGAGGCCTAACC 691Capture692TGCTCCGTGCATCTCCAAGGTTTACATGCTCCTGTTGTTAGGGAGGCTAACCC 692Capture693 TGCTCCGTGCATCTCCAAGGTTTACATGCTCCTGTTGTTAGGGAGGAACCCTA 693Capture694TGCTCCGTGCATCTCCAAGGTTTACATGCTCCTGTTGTTAGGGAGGACCCTAA 694Capture695 TGCTCCGTGCATCTCCAAGGTTTACATGCTCCTGTTGTTAGGGAGGACCCTAA 695 Capture696 TGCTCCGTGCATCTCCAAGGTTTACATGCTCCTGTTGTTAGGGAGGCCTAACT 696Capture697TGCTCCGTGCATCTCCAAGGTTTCTTCTACTACCGATCCGAAGCAGCCCTAAC 697Capture698 TGCTCCGTGCATCTCCAAGGTTTCTTCTACTACCGATCCGAAGCAGTAACCCT 698Capture699TGCTCCGTGCATCTCCAAGGTTTCTTCTACTACCGATCCGAAGCAGCCTAACC 699Capture700 TGCTCCGTGCATCTCCAAGGTTTCTTCTACTACCGATCCGAAGCAGCTAACCC 700 Capture701 TGCTCCGTGCATCTCCAAGGTTTCTTCTACTACCGATCCGAAGCAGAACCCTA 701Capture702TGCTCCGTGCATCTCCAAGGTTTCTTCTACTACCGATCCGAAGCAGACCCTAA 702Capture703 TGCTCCGTGCATCTCCAAGGTTTCTTCTACTACCGATCCGAAGCAGACCCTAA 703Capture704TGCTCCGTGCATCTCCAAGGTTTCTTCTACTACCGATCCGAAGCAGCCTAACT 704Capture705 TGCTCCGTGCATCTCCAAGGTTACAGCATCAATGTTTGGCTAGTTGCCCTAAC 705 Capture706 TGCTCCGTGCATCTCCAAGGTTACAGCATCAATGTTTGGCTAGTTGTAACCCT 706Capture707TGCTCCGTGCATCTCCAAGGTTACAGCATCAATGTTTGGCTAGTTGCCTAACC 707Capture708 TGCTCCGTGCATCTCCAAGGTTACAGCATCAATGTTTGGCTAGTTGCTAACCC 708Capture709TGCTCCGTGCATCTCCAAGGTTACAGCATCAATGTTTGGCTAGTTGAACCCTA 709Capture710 TGCTCCGTGCATCTCCAAGGTTACAGCATCAATGTTTGGCTAGTTGACCCTAA 710 Capture711 TGCTCCGTGCATCTCCAAGGTTACAGCATCAATGTTTGGCTAGTTGACCCTAA 711Capture712TGCTCCGTGCATCTCCAAGGTTACAGCATCAATGTTTGGCTAGTTGCCTAACT 712Capture713 TGCTCCGTGCATCTCCAAGGTTGATGTAGAGGGTACGGTTTGAGGCCCCTAAC 713Capture714TGCTCCGTGCATCTCCAAGGTTGATGTAGAGGGTACGGTTTGAGGCTAACCCT 714Capture715 TGCTCCGTGCATCTCCAAGGTTGATGTAGAGGGTACGGTTTGAGGCCCTAACC 715 Capture716 TGCTCCGTGCATCTCCAAGGTTGATGTAGAGGGTACGGTTTGAGGCCTAACCC 716Capture717TGCTCCGTGCATCTCCAAGGTTGATGTAGAGGGTACGGTTTGAGGCAACCCTA 717Capture718 TGCTCCGTGCATCTCCAAGGTTGATGTAGAGGGTACGGTTTGAGGCACCCTAA 718Capture719TGCTCCGTGCATCTCCAAGGTTGATGTAGAGGGTACGGTTTGAGGCACCCTAA 719Capture720 TGCTCCGTGCATCTCCAAGGTTGATGTAGAGGGTACGGTTTGAGGCCCTAACT 720 Capture721 TGCTCCGTGCATCTCCAAGGTTGGCTCCATAGGAACTCACGCTACTCCCTAAC 721Capture722TGCTCCGTGCATCTCCAAGGTTGGCTCCATAGGAACTCACGCTACTTAACCCT 722Capture723 TGCTCCGTGCATCTCCAAGGTTGGCTCCATAGGAACTCACGCTACTCCTAACC 723Capture724TGCTCCGTGCATCTCCAAGGTTGGCTCCATAGGAACTCACGCTACTCTAACCC 724Capture725 TGCTCCGTGCATCTCCAAGGTTGGCTCCATAGGAACTCACGCTACTAACCCTA 725 Capture726 TGCTCCGTGCATCTCCAAGGTTGGCTCCATAGGAACTCACGCTACTACCCTAA 726ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture727 TGCTCCGTGCATCTCCAAGGTTGGCTCCATAGGAACTCACGCTACTACCCTAA 727Capture728TGCTCCGTGCATCTCCAAGGTTGGCTCCATAGGAACTCACGCTACTCCTAACT 728Capture729 TGCTCCGTGCATCTCCAAGGTTTTGTGAGTGGAAAGATACAGGACCCCCTAAC 729Capture730TGCTCCGTGCATCTCCAAGGTTTTGTGAGTGGAAAGATACAGGACCTAACCCT 730Capture731 TGCTCCGTGCATCTCCAAGGTTTTGTGAGTGGAAAGATACAGGACCCCTAACC 731 Capture732 TGCTCCGTGCATCTCCAAGGTTTTGTGAGTGGAAAGATACAGGACCCTAACCC 732Capture733TGCTCCGTGCATCTCCAAGGTTTTGTGAGTGGAAAGATACAGGACCAACCCTA 733Capture734 TGCTCCGTGCATCTCCAAGGTTTTGTGAGTGGAAAGATACAGGACCACCCTAA 734Capture735TGCTCCGTGCATCTCCAAGGTTTTGTGAGTGGAAAGATACAGGACCACCCTAA 735Capture736 TGCTCCGTGCATCTCCAAGGTTTTGTGAGTGGAAAGATACAGGACCCCTAACT 736 Capture737 TGCTCCGTGCATCTCCAAGGTTAGTTTCCATCACTTCAGACTTGGGCCCTAAC 737Capture738TGCTCCGTGCATCTCCAAGGTTAGTTTCCATCACTTCAGACTTGGGTAACCCT 738Capture739 TGCTCCGTGCATCTCCAAGGTTAGTTTCCATCACTTCAGACTTGGGCCTAACC 739Capture740TGCTCCGTGCATCTCCAAGGTTAGTTTCCATCACTTCAGACTTGGGCTAACCC 740Capture741 TGCTCCGTGCATCTCCAAGGTTAGTTTCCATCACTTCAGACTTGGGAACCCTA 741 Capture742 TGCTCCGTGCATCTCCAAGGTTAGTTTCCATCACTTCAGACTTGGGACCCTAA 742Capture743TGCTCCGTGCATCTCCAAGGTTAGTTTCCATCACTTCAGACTTGGGACCCTAA 743Capture744 TGCTCCGTGCATCTCCAAGGTTAGTTTCCATCACTTCAGACTTGGGCCTAACT 744Capture745TGCTCCGTGCATCTCCAAGGTTGATTGTCCTCAAACTGCCACCTACCCCTAAC 745Capture746 TGCTCCGTGCATCTCCAAGGTTGATTGTCCTCAAACTGCCACCTACTAACCCT 746 Capture747 TGCTCCGTGCATCTCCAAGGTTGATTGTCCTCAAACTGCCACCTACCCTAACC 747Capture748TGCTCCGTGCATCTCCAAGGTTGATTGTCCTCAAACTGCCACCTACCTAACCC 748Capture749 TGCTCCGTGCATCTCCAAGGTTGATTGTCCTCAAACTGCCACCTACAACCCTA 749Capture750TGCTCCGTGCATCTCCAAGGTTGATTGTCCTCAAACTGCCACCTACACCCTAA 750Capture751 TGCTCCGTGCATCTCCAAGGTTGATTGTCCTCAAACTGCCACCTACACCCTAA 751 Capture752 TGCTCCGTGCATCTCCAAGGTTGATTGTCCTCAAACTGCCACCTACCCTAACT 752Capture753TGCTCCGTGCATCTCCAAGGTTCCTGTCTGGAAGAAGAATGGACTTCCCTAAC 753Capture754 TGCTCCGTGCATCTCCAAGGTTCCTGTCTGGAAGAAGAATGGACTTTAACCCT 754Capture755TGCTCCGTGCATCTCCAAGGTTCCTGTCTGGAAGAAGAATGGACTTCCTAACC 755Capture756 TGCTCCGTGCATCTCCAAGGTTCCTGTCTGGAAGAAGAATGGACTTCTAACCC 756 Capture757 TGCTCCGTGCATCTCCAAGGTTCCTGTCTGGAAGAAGAATGGACTTAACCCTA 757Capture758TGCTCCGTGCATCTCCAAGGTTCCTGTCTGGAAGAAGAATGGACTTACCCTAA 758Capture759 TGCTCCGTGCATCTCCAAGGTTCCTGTCTGGAAGAAGAATGGACTTACCCTAA 759Capture760TGCTCCGTGCATCTCCAAGGTTCCTGTCTGGAAGAAGAATGGACTTCCTAACT 760Capture761 TGCTCCGTGCATCTCCAAGGTTCTGAACGGTCATAGAGTCCACCATCCCTAAC 761 Capture762 TGCTCCGTGCATCTCCAAGGTTCTGAACGGTCATAGAGTCCACCATTAACCCT 762Capture763TGCTCCGTGCATCTCCAAGGTTCTGAACGGTCATAGAGTCCACCATCCTAACC 763Capture764 TGCTCCGTGCATCTCCAAGGTTCTGAACGGTCATAGAGTCCACCATCTAACCC 764Capture765TGCTCCGTGCATCTCCAAGGTTCTGAACGGTCATAGAGTCCACCATAACCCTA 765Capture766 TGCTCCGTGCATCTCCAAGGTTCTGAACGGTCATAGAGTCCACCATACCCTAA 766 Capture767 TGCTCCGTGCATCTCCAAGGTTCTGAACGGTCATAGAGTCCACCATACCCTAA 767ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Capture768 TGCTCCGTGCATCTCCAAGGTTCTGAACGGTCATAGAGTCCACCATCCTAACT 768

[0106] In some embodiments, the disclosure relates to a method of determining the length of a telomere, the method comprising: (a) performing long-read sequencing of a nucleotide sequence comprising a telomere from a sample; and (b) calculating the length of the telomere. In some embodiments, the step of performing long-read sequencing comprises performing a sequencing reaction with Nanopore sequencing or single-molecule real time sequencing.

[0107] In some embodiments, the step of calculating the length of the telomere comprises a computer-implemented method of substeps including: receiving a file comprising a nucleotide sequence of DNA isolated from a sample; (a) compiling and / or registering nucleic acid information from the sample; (b) aligning sequences against a control sequence to identify a telomere sequence within the nucleic acid information; (c) estimating a location of a telomeric boundary to determine the beginning of a non-telomeric sequence within the nucleic acid information; (d) determining the length of the telomere after measuring the number of nucleotides between the end of 5’ or 3’ end of the telomere sequence and the telomeric boundary; and (e) optionally calculating and / or displaying a score based upon the percent identity of the nucleic acid information relative to a control sequence. In some embodiments, the step of long-read sequencing comprises: (i) isolating DNA from a sample; (ii) ligating adapter sequences to the chromosomal DNA; (iii) immobilizing the chromosomal DNA to a solid support, optionally performed by associating or binding the chromosomal DNA, covalently or non-covalently, to a tether sequence; exposing the chromosomal DNA to a polymerase and a mixture of dNTPs; measuring light generated from the polymerization of complementary DNA against the chromosomal DNA; and generating a file with sequence information of the chromosomal DNA by correlating sequential measurement of light corresponding to a polymerization event of sequential single dNTP binding to the complementary DNA. In some embodiments, the step of measuring light is performed on a wave guide instrument operably connected to a processor that stores the measurements associated with one or a plurality of polymerization events.

[0108] Methods of the disclosure also include methods disclosed herein comprising a step of detecting the presence of a barcode domain of the capture oligonucleotides comprisingATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION exposing the chromosomal DNA from a sample of a subject to a probe specific for one or a plurality of capture oligonucleotides after annealing the capture oligonucleotides to the isolated chromosomal DNA and the detecting the presence of a capture oligo-specific probe. In some embodiments, this step is performed sequentially to or simultaneously with other steps of analyzing the telomere length disclosed herein.

[0109] In some embodiments, the disclosure relates to methods of diagnosing and / or prognosing subjects comprising correlating the length in a sample to the stage or presence of telomeric disorder. The present disclosure also relates to a method for characterizing the stage of development or pathology of a telomeric disorder in a subject comprising computer implemented method steps of: (a) compiling nucleic acid information from the sample; (b) aligning sequences against a control sequence to identify a telomer sequence within the nucleic acid information;

[0110] (c) estimating a location of a telomeric boundary to determine the beginning of a non- telomeric sequence within the nucleic acid information;

[0111] (d) determining the length of the telomere after measuring the number of nucleotides between the end of 5’ or 3’ end of the telomere sequence and the telomeric boundary; and optionally calculating and / or displaying a score based upon the percent identity of the nucleic acid information relative to a control sequence; and collecting data associated with the subject comprising one or a combination of: the sequence of an exon within the sample, the sequence of a non-coding region of a chromosome, the sequence of a mutation, the identity of one or a plurality of chromosome copy number alterations, the quantity of DNA methylation on the chromosome, and the presence or quantity of a barcode. In some embodiments, the method further comprises the step of correlating the data associated with the subject comprising one or a combination of: the sequence of an exon within the sample, the sequence of a non-coding region of a chromosome, the sequence of a mutation, the identity of one or a plurality of chromosome copy number alterations, the quantity of DNA methylation on the chromosome, and the presence or quantity of a barcode to the probability that the subject has a telomeric disorder.

[0112] Methods of the disclosure also relate to methods of determining whether a subject is has or can be diagnosed with a telomeric disorder comprising the steps (optionally simultaneously performing): collecting data associated with the subject comprising one or a combination of:

[0113] the sequence of an exon within the sample, the sequence of a non-coding region of a chromosome, the sequence of a mutation, the identity of one or a plurality of chromosome copyATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION number alterations, the quantity of DNA methylation on the chromosome, and the presence or quantity of a barcode, and the determination of a sequence of a telomere. In some embodiments, the method comprises isolating chromosomal DNA from a sample from a subject; performing long-reading sequencing of the chromosomal DNA, generating a computer program file comprising sequencing data from the chromosomal DNA; providing the computer-program file to the computer program product with computer-implemented method steps of: a) compiling and / or registering nucleic acid information from the sample; (b) aligning sequences against a control sequence to identify a telomere sequence within the nucleic acid information; (c) estimating a location of a telomeric boundary to determine the beginning of a non-telomeric sequence within the nucleic acid information; (d) determining the length of the telomere after measuring the number of nucleotides between the end of 5’ or 3’ end of the telomere sequence and the telomeric boundary; and (e) optionally calculating and / or displaying a score based upon the percent identity of the nucleic acid information relative to a control sequence. In some embodiment, the method further comprises (f) comparing the nucleic acid information from the sample to a database of structural variants to identify the presence of structural variants in the sample; and (g) correlating the presence of structural variants to the likelihood or probability that the subject has a telomeric disorder. In some embodiments, the method further comprises the step of calculating the probability or likelihood that the presence of a structural variant in the sample correlates to the subject being diagnosed with a telomeric disorder. In some embodiments, the methods of the disclosure comprise the step of identifying the presence of a structural variant of isolated chromosomal DNA and the telomere sequence of the isolated chromosomal DNA from the same sample.

[0114] Structural variants of the disclosure include non-limiting examples of mutations within the sample. In some embodiments, the disclosure relates to a method of detecting a mutation from a sample of a subject comprising: (a) isolating chromosomal DNA from the sample; (b) compiling sequence information from the sample; (c) registering at least a portion of a chromosome sequence of a sample comprising a telomere; (d) aligning the telomere of the sample to identify the end of the chromosome; (e) identifying a telomere boundary on the chromosome; (f) measuring a length of the telomere from about the end of the chromosome to the boundary of the telomere; and (g) identifying a structural variant by comparing the sequence information of telomeric and non-telomeric DNA sequence to control sequence informationATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION known to be free of a mutation, wherein any one or plurality of steps (c) through (g) are performed on a computer-readable storage medium comprising instructions for one or a combination of steps (c) through (g). In some embodiments, the method further comprises correlating the presence of a structural variant to the probability of the subject being diagnosed with having the structural variant.

[0115] In some embodiments, the sample is a population of cells. In some embodiments, the sample is a single cell from which chromosomal DNA is isolated.

[0116] In some embodiments, structural variants are determined based on sequencing the chromosomal DNA from a sample of a subject and comparing that sequence to a known set of genes that encode a protein. In some embodiments, the wild-type or putative human control sequence is identified as a protein identified on Table Y and if there is a mutation in that control sequence, the subject has a likelihood of having or being diagnosed with a telomeric disorder. Such controls sequences associated with telomeric disorders are as follows: TABLE Y: Control Human Sequences upon which chromosomal DNA sequences are compared. >NP_001397813.1 adrenocortical dysplasia protein homolog isoform 3 [Homo sapiens] MAGSGRLVLRPWIRELILGSETPSSPRAGQLLEVLQDAEAAVAGPSHAPDTSDVGATLL VSDGTHSVRCLVTREALDTSDWEEKEFGFRGTEGRLLLLQDCGVHVQVAEGGAPAEFY LQVDRFSLLPTEQPRLRVPGCNQDLDVQKKLYDCLEEHLSESTSSNAGLSLSQLLDEMR EDQEHQGALVCLAESCLTLEGPCTAPPVTHWAASRCKATGEAVYTVPSSMLCISENDQL ILSSLGPCQRTQGTPALPGHMSSEESGTSISLLPALSLAAPDPGQRSSSQPSPAICSAPATLT PRSPHASRTPSSPLQSCTPSLSPRSHVPSPHQALVTRPQKPSLEFKEFVGLPCKNRPPFPRT GATRGAQEPCSVWEPPKRHRDGSAFQYEYEPPCTSLCARVQAVRLPPQLMAWALHFL MDAQPGSEPTPM (SEQ ID NO: 769) >NP_001274177.1 recQ-like DNA helicase BLM isoform 3 [Homo sapiens] MEHICKLIDTIPDDKLKLLDCGNELLQQRNIRRKLLTEVDFNKSDASLLGSLWRYRPDSL DGPMEGDSCPTGNSMKELNFSHLPSNSVSPGDCLLTTTLGKTGFSATRKNLFERPLFNTH LQKSFVSSNWAETPRLGKKNESSYFPGNVLTSTAVKDQNKHTASINDLERETQPSYDID NFDIDDFDDDDDWEDIMHNLAASKSSTAAYQPIKEGRPIKSVSERLSSAKTDCLPVSSTAATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION QNINFSESIQNYTDKSAQNLASRNLKHERFQSLSFPHTKEMMKIFHKKFGLHNFRTNQLE AINAALLGEDCFILMPTGGGKSLCYQLPACVSPGVTVVISPLRSLIVDQVQKLTSLDIPAT YLTGDKTDSEATNIYLQLSKKDPIIKLLYVTPEKICASNRLISTLENLYERKLLARFVIDEA HCVSQWGHDFRQDYKRMNMLRQKFPSVPVMALTATANPRVQKDILTQLKILRPQVFS MSFNRHNLKYYVLPKKPKKVAFDCLEWIRKHHPYDSGIIYCLSRRECDTMADTLQRDG LAALAYHAGLSDSARDEVQQKWINQDGCQVICATIAFGMGIDKPDVRFVIHASLPKSVE GYYQESGRAGRDGEISHCLLFYTYHDVTRLKRLIMMEKDGNHHTRETHFNNLYSMVHY CENITECRRIQLLAYFGENGFNPDFCKKHPDVSCDNCCKTKDYKTRDVTDDVKSIVRFV QEHSSSQGMRNIKHVGPSGRFTMNMLVDIFLGSKSAKIQSGIFGKGSAYSRHNAERLFK KLILDKILDEDLYINANDQAIAYVMLGNKAQTVLNGNLKVDFMETENSSSVKKQKALV AKVSQREEMVKKCLGELTEVCKSLGKVFGVHYFNIFNTVTLKKLAESLSSDPEVLLQID GVTEDKLEKYGAEVISVLQKYSEWTSPAEDSSPGISLSSSRGPGRSAAEELDEEIPVSSHY FASKTRNERKRKKMPASQRSKRRKTASSGSKAKGGSATCRKISSKTKSSSIIGSSSASHTS QATSGANSKLGIMAPPKPINRPFLKPSYAFS (SEQ ID NO: 770) >NP_001397996.1 CST complex subunit CTC1 isoform 2 [Homo sapiens] MAAGRAQVPSSEQAWLEDAQVFIQKTLCPAVKEPNVQLTPLVIDCVKTVWLSQGRNQG STLPLSYSFVSVQDLKTHQRLPCCSHLSWSSSAYQAWAQEAGPNGNPLPREQLLLLGTL TDLSADLEQECRNGSLYVRDNTGVLSCELIDLDLSWLGHLFLFPRWSYLPPARWNSSGE GHLELWDAPVPVFPLTISPGPVTPIPVLYPESASCLLRLRNKLRGVQRNLAGSLVRLSAL VKSKQKAYFILSLGRSHPAVTHVSIIVQVPAQLVWHRALRPGTAYVLTELRVSKIRGQR QHVWMTSQSSRLLLLKPECVQELELELEGPLLEADPKPLPMPSNSEDKKDPESLVRYSR LLSYSGAVTGVLNEPAGLYELDGQLGLCLAYQQFRGLRRVMRPGVCLQLQDVHLLQSV GGGTRRPVLAPCLRGAVLLQSFSRQKPGAHSSRQAYGASLYEQLVWERQLGLPLYLWA TKALEELACKLCPHVLRHHQFLQHSSPGSPSLGLQLLAPTLDLLAPPGSPVRNAHNEILE EPHHCPLQKYTRLQTPSSFPTLATLKEEGQRKAWASFDPKALLPLPEASYLPSCQLNRRL AWSWLCLLPSAFCPAQVLLGVLVASSHKGCLQLRDQSGSLPCLLLAKHSQPLSDPRLIG CLVRAERFQLIVERDVRSSFPSWKELSMPGFIQKQQARVYVQFFLADALILPVPRPCLHS ATPSTPQTDPTGPEGPHLGQSRLFLLCHKEALMKRNFCVPPGASPEVPKPALSFYVLGSW LGGTQRKEGTGWGLPEPQGNDDNDQKVHLIFFGSSVRWFEFLHPGQVYRLIAPGPATP MLFEKDGSSCISRRPLELAGCASCLTVQDNWTLELESSQDIQDVLDANKSLPESSLTDLLATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION SDNFTDSLVSFSAEILSRTLCEPLVASLWMKLGNTGAMRRCVKLTVALETAECEFPPHL DVYIEDPHLPPSLGLLPGARVHFSQLEKRVSRSHNVYCCFRSSTYVQVLSFPPETTISIPLP HIYLAELLQGGQSPFQATASCHIVSVFSLQLFWVCAYCTSICRQSSARVDEPMTMFLWT LCTSPSVLRPIVLSFELERKPSKIVPLEPPRLQRFQCGELPFLTHVNPRLRLSCLSIRESEYS SSLGILASSC (SEQ ID NO: 771) >NP_001350619.15' exonuclease Apollo isoform c [Homo sapiens] MNGVLIPHTPIAVDFWSLRRAGTARLFFLSHMHSDHTVGLSSTWARPLYCSPITAHLLH RHLQVSKQWIQALEVGESHVLPLDEIGQETMTVTLLDANHCPGSVMFLFEGYFGTILYT GDFRYTPSMLKEPALTLGKQIHTLYLDNTNCNPALVLPSRQEAAHQIVQLIRKHPQHNIK IGLYSLGKESLLEQLALEFQTWVVLSPRRLELVQLLGLADVFTVEEKAGRIHAVDHMEIC HSNMLRWNQTHPTIAILPTSRKIHSSHPDIHVIPYSDHSSYSELRAFVAALKPCQVVPIVS RRPCGGFQDSLSPRISVPLIPDSVQQYMSSSSRKPSLLWLLERRLKRPRTQGVVFESPEES ADQSQADRDSKKAKKEKLSPWPADLEKQPSHHPLRIKKQLFPDLYSKEWNKAVPFCRV FFQEI (SEQ ID NO: 772) >NP_001275676.1 H / ACA ribonucleoprotein complex subunit DKC1 isoform 3 [Homo sapiens] MADAEVIILPKKHKKKKERKSLPEEDVAEIQHAEEFLIKPESKVAKLDTSQWPLLLKNFD KLNVRTTHYTPLACGSNPLKREIGDYIRTGFINLDKPSNPSSHEVVAWIRRILRVEKTGHS GTLDPKVTGCLIVCIERATRLVKSQQSAGKEYVGIVRLHNAIEGGTQLSRALETLTGALF QRPPLIAAVKRQLRVRTIYESKMIEYDPERRLGIFWVSCEAGTYIRTLCVHLGLLLGVGG QMQELRRVRSGVMSEKDHMVTMHDVLDAQWLYDNHKDESYLRRVVYPLEKLLTSHK RLVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQEIVVITTKGEAICMAIALMTTAVIST CDHGIVAKIKRVIMERDTYPRKWGLGPKASQKKLMIKQGLLDKHGKPTDSTPATWKQE YVDYR (SEQ ID NO: 773) >NP_001295062.1 Fanconi anemia group M protein isoform 2 [Homo sapiens] MSGRQRTLFQTWGSSISRSSGTPGCSSGTERPQSPGSSKAPLPAAAEAQLESDDDVLLVA AYEAERQLCLENGGFCTSAGALWIYPTNCPVRDYQLHISRAALFCNTLVCLPTGLGKTFI AAVVMYNFYRWFPSGKVVFMAPTKPLVTQQIEACYQVMGIPQSHMAEMTGSTQASTRATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION KEIWCSKRVLFLTPQVMVNDLSRGACPAAEIKCLVIDEAHKALGNYAYCQAVQQVITN LLIGQIELRSEDSPDILTYSHERKVEKLIVPLGEELAAIQKTYIQILESFARSLIQRNVLMRR DIPNLTKYQIILARDQFRKNPSPNIVGIQQGIIEGEFAICISLYHGYELLQQMGMRSLYFFL CGIMDGTKGMTRSKNELGRNEDFMKLYNHLECMFARTRSTSANGISAIQQGDKNKKFV YSHPKLKKLEEVVIEHFKSWNAENTTEKKRDETRVMIFSSFRDSVQEIAEMLSQHQPIIR VMTFVGHASGKSTKGFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLIICFDS QKSPIRLVQRMGRTGRKRQGRIVIILSEGREERIYNQSQSNKRSIYKAISSNRQVLHFYQR SPRMVPDGINPKLHKMFITHGVYEPEKPSRNLQRKSSIFSYRDGMRQSSLKKDWFLSEEE FKLWNRLYRLRDSDEIKEITLPQVQFSSLQNEENKPAQESTTGIHQLSLSEWRLWQDHPL PTHQVDHSDRCRHFIGLMQMIEGMRHEEGECSYELEVESYLQMEDVTSTFIAPRNESNN LASDTFITHKKSSFIKNINQGSSSSVIESDEECAEIVKQTHIKPTKIVSLKKKVSKEIKKDQL KKENNHGIIDSVDNDRNSTVENIFQEDLPNDKRTSDTDEIAATCTINENVIKEPCVLLTEC QFTNKSTSSLAGNVLDSGYNSFNDEKSVSSNLFLPFEEELYIVRTDDQFYNCHSLTKEVL ANVERFLSYSPPPLSGLSDLEYEIAKGTALENLLFLPCAEHLRSDKCTCLLSHSAVNSQQ NLELNSLKCINYPSEKSCLYDIPNDNISDEPSLCDCDVHKHNQNENLVPNNRVQIHRSPA QNLVGENNHDVDNSDLPVLSTDQDESLLLFEDVNTEFDDVSLSPLNSKSESLPVSDKTAI SETPLVSQFLISDELLLDNNSELQDQITRDANSFKSRDQRGVQEEKVKNHEDIFDCSRDLF SVTFDLGFCSPDSDDEILEHTSDSNRPLDDLYGRYLEIKEISDANYVSNQALIPRDHSKNF TSGTVIIPSNEDMQNPNYVHLPLSAAKNEELLSPGYSQFSLPVQKKVMSTPLSKSNTLNS FSKIRKEILKTPDSSKEKVNLQRFKEALNSTFDYSEFSLEKSKSSGPMYLHKSCHSVEDG QLLTSNESEDDEIFRRKVKRAKGNVLNSPEDQKNSEVDSPLHAVKKRRFPINRSELSSSD ESENFPKPCSQLEDFKVCNGNARRGIKVPKRQSHLKHVARKFLDDEAELSEEDAEYVSS DENDESENEQDSSLLDFLNDETQLSQAINDSEMRAIYMKSLRSPMMNNKYKMIHKTHK NINIFSQIPEQDETYLEDSFCVDEEESCKGQSSEEEVCVDFNLITDDCFANSKKYKTRRAV MLKEMMEQNCAHSKKKLSRIILPDDSSEEENNVNDKRESNIAVNPSTVKKNKQQDHCL NSVPSGSSAQSKVRSTPRVNPLAKQSKQTSLNLKDTISEVSDFKPQNHNEVQSTTPPFTT VDSQKDCRKFPVPQKDGSALEDSSTSGASCSKSRPHLAGTHTSLRLPQEGKGTCILVGG HEITSGLEVISSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQ HLQSMFERICVIVEKDREKTGDTSRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLK ELSLVEQRKNVGIHVPTVVNSNKSEALQFYLSIPNISYITALNMCHQFSSVKRMANSSLQ EISMYAQVTHQKAEEIYRYIHYVFDIQMLPNDLNQDRLKSDI (SEQ ID NO: 774)ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION >NP_001366024.1 DNA ligase 4 isoform 1 [Homo sapiens] MAASQTSQTVASHVPFADLCSTLERIQKSKGRAEKIRHFREFLDSWRKFHDALHKNHKD VTDSFYPAMRLILPQLERERMAYGIKETMLAKLYIELLNLPRDGKDALKLLNYRTPTGT HGDAGDFAMIAYFVLKPRCLQKGSLTIQQVNDLLDSIASNNSAKRKDLIKKSLLQLITQS SALEQKWLIRMIIKDLKLGVSQQTIFSVFHNDAAELHNVTTDLEKVCRQLHDPSVGLSDI SITLFSAFKPMLAAIADIEHIEKDMKHQSFYIETKLDGERMQMHKDGDVYKYFSRNGYN YTDQFGASPTEGSLTPFIHNAFKADIQICILDGEMMAYNPNTQTFMQKGTKFDIKRMVE DSDLQTCYCVFDVLMVNNKKLGHETLRKRYEILSSIFTPIPGRIEIVQKTQAHTKNEVIDA LNEAIDKREEGIMVKQPLSIYKPDKRGEGWLKIKPEYVSGLMDELDILIVGGYWGKGSR GGMMSHFLCAVAEKPPPGEKPSVFHTLSRVGSGCTMKELYDLGLKLAKYWKPFHRKA PPSSILCGTEKPEVYIEPCNSVIVQIKAAEIVPSDMYKTGCTLRFPRIEKIRDDKEWHECMT LDDLEQLRGKASGKLASKHLYIGGDDEPQEKKRKAAPKMKKVIGIIEHLKAPNLTNVNK ISNIFEDVEFCVMSGTDSQPKPDLENRIAEFGGYIVQNPGPDTYCVIAGSENIRVKNIILSN KHDVVKPAWLLECFKTKSFVPWQPRFMIHMCPSTKEHFAREYDCYGDSYFIDTDLNQL KEVFSGIKNSNEQTPEEMASLIADLEYRYSWDCSPLSMFRRHTVYLDSYAVINDLSTKNE GTRLAIKALELRFHGAKVVSCLAEGVSHVIIGEDHSRVADFKAFRRTFKRKFKILKESWV TDSIDKCELQEENQYLI (SEQ ID NO: 775) >NP_001030005.1 H / ACA ribonucleoprotein complex subunit 2 isoform b [Homo sapiens] MTKIKADPDGPEAQAEACSGERTYQELLVNQNPIAQPLASRRLTRKLYKCIKKAVKQKQ IRRGVKEVQKFVNKGEKGTWVQPQAPSAPPV (SEQ ID NO: 776) >sp|Q9NPE3.1|NOP10_HUMAN RecName: Full=H / ACA ribonucleoprotein complex subunit 3; AltName: Full=Nucleolar protein 10; AltName: Full=Nucleolar protein family A member 3; AltName: Full=snoRNP protein NOP10 MFLQYYLNEQGDRVYTLKKFDPMGQQTCSAHPARFSPDDKYSRHRITIKKRFKV LMTQQPRPVL (SEQ ID NO: 777) >NP_001341938.1 nucleophosmin isoform 5 [Homo sapiens]ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION MEDSMDMDMSPLRPQNYLFGCELKADKDYHFKVDNDENEHQLSLRTVSLGAGAKDEL HIVEAEAMNYEGSPIKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLV AVEEDAESEDEEEEDVKLLSISGKRSAPGGGSKVPQKKVKLAADEDDDDDDEEDDDED DDDDDFDDEEAEEKAPVKKGQESFKKQEKTPKTPKGPSSVEDIKAKMQASIEKAH (SEQ ID NO: 778) >NP_001127949.1 poly(A)-specific ribonuclease PARN isoform 2 [Homo sapiens] MDFLLFQFGLCTFKYDYTDSKYITKSFNFYVFPKPFNRSSPDVKFVCQSSSIDFLASQGFD FNKVFRNGIPYLNQEEERQLREQYDEKRSQANGAGALSYVSPNTSKCPVTIPEDQKKFID QVVEKIEDLLQSEENKNLDLEPCTGFQRKLIYQTLSWKYPKGIHVETLETEKKERYIVISK VDEEERKRREQQKHAKEQEELNDAVGFSRVIHAIANSGKLVIGHNMLLDVMHTVHQFY CPLPADLSEFKEMTTCVFPRLLDTKLMASTQPFKDIINNTSLAELEKRLKETPFNPPKVES AEGFPSYDTASEQLHEAGYDAYITGLCFISMANYLGSFLSPPKIHVSARSKLIEPFFNKLF LMRVMDIPYLNLEGPDLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDTSAF VSLSQPEQVKIAVNTSKYAESYRIQTYAEYMGRKQEEKQIKRKWTEDSWKEADSKRLN PQCIPYTLQNHYYRNNSFTAPSTVGKRNLSPSQEEAGLEDGVSGEISDTELEQTDSCAEP LSEGRKKAKKLKRMKKELSPAGSISKNSPATLFEVPDTW (SEQ ID NO: 779) >NP_001342050.1 replication protein A 70 kDa DNA-binding subunit isoform 3 [Homo sapiens] MVGQLSEGAIAAIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLATQ LNPLVEEEQLSSNCVCQIHRFIVNTLKDGRRVVILMELEVLKSAEAVGVKIGNPVPYNEG LGQPQVAPPAPAASPAASSRPQPQNGSSGMGSTVSKAYGASKTFGKAAGPSLSHTSGGT QSKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESGEIRATAFNE QVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPCEDDHHLPTV QFDFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTA TLWGEDADKFDGSRQPVLAIKGARVSDFGGRSLSVLSSSTIIANPDIPEAYKLRGWFDAE GQALDGVSISDLKSGGVGGSNTNWKTLYEVKSENLGQGDKVNIADFQENQWVTCFQES AEAILGQNAAYLGELKDKNEQAFEEVFQNANFRSFIFRVRVKVETYNDESRIKATVMDV KPVDYREYGRRLVMSIRRSALM (SEQ ID NO: 780)ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION >NP_001269938.1 regulator of telomere elongation helicase 1 isoform 3 [Homo sapiens] MPKIVLNGVTVDFPFQPYKCQQEYMTKVLECLQQKVNGILESPTGTGKTLCLLCTTLAW REHLRDGISARKIAERAQGELFPDRALSSWGNAAAAAGDPIACYTDIPKIIYASRTHSQLT QVINELRNTSYRPKVCVLGSREQLCIHPEVKKQESNHLQIHLCRKKVASRSCHFYNNVE EKSLEQELASPILDIEDLVKSGSKHRVCPYYLSRNLKQQADIIFMPYNYLLDAKSRRAHN IDLKGTVVIFDEAHNVEKMCEESASFDLTPHDLASGLDVIDQVLEEQTKAAQQGEPHPEF SADSPSPGLNMELEDIAKLKMILLRLEGAIDAVELPGDDSGVTKPGSYIFELFAEAQITFQ TKGCILDSLDQIIQHLAGRAGVFTNTAGLQKLADIIQIVFSVDPSEGSPGSPAGLGALQSY KVHIHPDAGHRRTAQRSDAWSTTAARKRGKVLSYWCFSPGHSMHELVRQGVRSLILTS GTLAPVSSFALEMQIPFPVCLENPHIIDKHQIWVGVVPRGPDGAQLSSAFDRRFSEECLSS LGKALGNIARVVPYGLLIFFPSYPVMEKSLEFWRARDLARKMEALKPLFVEPRSKGSFSE TISAYYARVAAPGSTGATFLAVCRGKASEGLDFSDTNGRGVIVTGLPYPPRMDPRVVLK MQFLDEMKGQGGAGGQFLSGQEWYRQQASRAVNQAIGRVIRHRQDYGAVFLCDHRF AFADARAQLPSWVRPHVRVYDNFGHVIRDVAQFFRVAERTMPAPAPRATAPSVRGEDA VSEAKSPGPFFSTRKAKSLDLHVPSLKQRSSGSPAAGDPESSLCVEYEQEPVPARQRPRG LLAALEHSEQRAGSPGEEQAHSCSTLSLLSEKRPAEEPRGGRKKIRLVSHPEEPVAGAQT DRAKLFMVAVKQELSQANFATFTQALQDYKGSDDFAALAACLGPLFAEDPKKHNLLQ GFYQFVRPHHKQQFEEVCIQLTGRGCGYRPEHSIPRRQRAQPVLDPTGRTAPDPKLTVST AAAQQLDPQEHLNQGRPHLSPRPPPTGDPGSQPQWGSGVPRAGKQGQHAVSAYLADA RRALGSAGCSQLLAALTAYKQDDDLDKVLAVLAALTTAKPEDFPLLHRFSMFVRPHHK QRFSQTCTDLTGRPYPGMEPPGPQEERLAVPPVLTHRAPQPGPSRSEKTGKTQSKISSFLR QRPAGTVGAGGEDAGPSQSSGPPHGPAASEWGEPHGRDIAGQQATGAPGGPLSAGCVC QGCGAEDVVPFQCPACDFQRCQACWQRHLQASRMCPACHTASRKQSVMQVFWPEPQ (SEQ ID NO: 781) >NP_079204.2 CST complex subunit STN1 [Homo sapiens] MQPGSSRCEEETPSLLWGLDPVFLAFAKLYIRDILDMKESRQVPGVFLYNGHPIKQVDV LGTVIGVRERDAFYSYGVDDSTGVINCICWKKLNTESVSAAPSAARELSLTSQLKKLQET IEQKTKIEIGDTIRVRGSIRTYREEREIHATTYYKVDDPVWNIQIARMLELPTIYRKVYDQ PFHSSALEKEEALSNPGALDLPSLTSLLSEKAKEFLMENRVQSFYQQELEMVESLLSLAN QPVIHSASSDQVNFKKDTTSKAIHSIFKNAIQLLQEKGLVFQKDDGFDNLYYVTREDKDLATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION HRKIHRIIQQDCQKPNHMEKGCHFLHILACARLSIRPGLSEAVLQQVLELLEDQSDIVST MEHYYTAF (SEQ ID NO: 782) >NP_001180305.1 telomerase reverse transcriptase isoform 2 [Homo sapiens] MPRAPRCRAVRSLLRSHYREVLPLATFVRRLGPQGWRLVQRGDPAAFRALVAQCLVCV PWDARPPPAAPSFRQVSCLKELVARVLQRLCERGAKNVLAFGFALLDGARGGPPEAFTT SVRSYLPNTVTDALRGSGAWGLLLRRVGDDVLVHLLARCALFVLVAPSCAYQVCGPPL YQLGAATQARPPPHASGPRRRLGCERAWNHSVREAGVPLGLPAPGARRRGGSASRSLP LPKRPRRGAAPEPERTPVGQGSWAHPGRTRGPSDRGFCVVSPARPAEEATSLEGALSGT RHSHPSVGRQHHAGPPSTSRPPRPWDTPCPPVYAETKHFLYSSGDKEQLRPSFLLSSLRPS LTGARRLVETIFLGSRPWMPGTPRRLPRLPQRYWQMRPLFLELLGNHAQCPYGVLLKTH CPLRAAVTPAAGVCAREKPQGSVAAPEEEDTDPRRLVQLLRQHSSPWQVYGFVRACLR RLVPPGLWGSRHNERRFLRNTKKFISLGKHAKLSLQELTWKMSVRDCAWLRRSPGVGC VPAAEHRLREEILAKFLHWLMSVYVVELLRSFFYVTETTFQKNRLFFYRKSVWSKLQSI GIRQHLKRVQLRELSEAEVRQHREARPALLTSRLRFIPKPDGLRPIVNMDYVVGARTFRR EKRAERLTSRVKALFSVLNYERARRPGLLGASVLGLDDIHRAWRTFVLRVRAQDPPPEL YFVKVDVTGAYDTIPQDRLTEVIASIIKPQNTYCVRRYAVVQKAAHGHVRKAFKSHVST LTDLQPYMRQFVAHLQETSPLRDAVVIEQSSSLNEASSGLFDVFLRFMCHHAVRIRGKS YVQCQGIPQGSILSTLLCSLCYGDMENKLFAGIRRDGLLLRLVDDFLLVTPHLTHAKTFL SYARTSIRASLTFNRGFKAGRNMRRKLFGVLRLKCHSLFLDLQVNSLQTVCTNIYKILLL QAYRFHACVLQLPFHQQVWKNPTFFLRVISDTASLCYSILKAKNAGMSLGAKGAAGPL PSEAVQWLCHQAFLLKLTRHRVTYVPLLGSLRTAQTQLSRKLPGTTLTALEAAANPALP SDFKTILD (SEQ ID NO: 783) >NP_001350597.1 TERF1-interacting nuclear factor 2 isoform 3 [Homo sapiens] MATPLVAGPAALRFAAAASWQVVRGRCVEHFPRVLEFLRSLRAVAPGLVRYRHHERLC MGLKAKTKQDLRKILEAQETFYQQVKQLSEAPVDLASKLQELEQEYGEPFLAAMEKLL FEYLCQLEKALPTPQAQQLQDVLSWMQPGVSITSSLAWRQYGVDMGWLLPECSVTDSV NLAEPMEQNPPQQQRLALHNPLPKAKPGTHLPQGPSSRTHPEPLAGRHFNLAPLGRRRV QSQWASTRGGHKERPTVMLFPFRNLGSPTQVISKPESKEEHAIYTADLAMGTRAASTGK SKSPCQTLGGRALKENPVDLPATEQKENCLDCYMDPLRLSLLPPRARKPVCPPSLCSSVIATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION TIGDLVLDSDEEENGQGEGKESLENYQKTKFDTLIPTLCEYLPPSGHGAIPVSSCDCRDSS RPL (SEQ ID NO: 784) >WNK26759.1 thymidylate synthase isoform 1, partial [Homo sapiens] MPVAGSELPRRPLPPAAQERDAEPRPPHGELQYLGQIQHILRCGVRKDDRTGTGTLSVF GMQARYSLR (SEQ ID NO: 785) >NP_001137462.1 telomerase Cajal body protein 1 [Homo sapiens] MKTLETQPLAPDCCPSDQDPAPAHPSPHASPMNKNADSELMPPPPERGDPPRLSPDPVA GSAVSQELREGDPVSLSTPLETEFGSPSELSPRIEEQELSENTSLPAEEANGSLSEEEANGP ELGSGKAMEDTSGEPAAEDEGDTAWNYSFSQLPRFLSGSWSEFSTQPENFLKGCKWAP DGSCILTNSADNILRIYNLPPELYHEGEQVEYAEMVPVLRMVEGDTIYDYCWYSLMSSA QPDTSYVASSSRENPIHIWDAFTGELRASFRAYNHLDELTAAHSLCFSPDGSQLFCGFNR TVRVFSTARPGRDCEVRATFAKKQGQSGIISCIAFSPAQPLYACGSYGRSLGLYAWDDG SPLALLGGHQGGITHLCFHPDGNRFFSGARKDAELLCWDLRQSGYPLWSLGREVTTNQ RIYFDLDPTGQFLVSGSTSGAVSVWDTDGPGNDGKPEPVLSFLPQKDCTNGVSLHPSLPL LATASGQRVFPEPTESGDEGEELGLPLLSTRHVHLECRLQLWWCGGAPDSSIPDDHQGE KGQGGTEGGVGELI (SEQ ID NO: 786) >NP_001337865.1 zinc finger CCHC domain-containing protein 8 isoform 3 [Homo sapiens] MNNAISKQYHQEIEEFVSNLVKRFEEQQKNDVEKTSFNLLPQPSSIVLEEDHKVEESCAI KNNKEAFSVVGSVLYFTNFCLDKLGQPLLNENPQLSEGWEIPKYHQVFSHIVSLEGQEIQ VKAKRPKPHCFNCGSEEHQMKDCPMPRNAARISEKRKEYMDACGEANNQNFQQRYHA EEVEERFGRFKPGVISEELQDALGVTDKSLPPFIYRMRQLGYPPGWLKEAELENSGLALY DGKDGTDGETEVGEIQQNKSVTYDLSKLVNYPGFNISTPRGIPDEWRIFGSIPMQACQQK DVFANYLTSNFQAPGVKSGNKRSSSHSSPGSPKKQKNESNSAGSPADMELDSDMEVPH GSQSSESFQFQPPLPPDTPPLPRGTPPPVFTPPLPKGTPPLTPSDSPQTRTASGAVDEDALT LEELEEQQRRIWAALEQAESVNSDSDVPVDTPLTGNSVASSPCPNELDLPVPEGKTSEKQ TLDEPEVPEIFTKKSEAGHASSPDSEVTSLCQKEKAELAPVNTEGALLDNGSVVPNCDISATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION NGGSQKLFPADTSPSTATKIHSPIPDMSKFATGITPFEFENMAESTGMYLRIRSLLKNSPR NQQKNKKASE (SEQ ID NO: 787)

[0117] In some embodiments the presence of structural variants from within the isolated chromosomal DNA indicates that the subject has a telomeric disease. In some embodiments, the methods of the disclosure comprise the step of identifying the presence or absence of the following mutations of the proteins of Table Y. Table Z: Known structural variants of Genes associated with Telomeric disease. Gene Mutation M455K M429K M458K P454L P457L P454L P457L P454T P457T P428T P452fs P455fs P455S P452S P426S D419N D445N D448N F442S F445S F445L F416L F442L P436S P433S V429A V432A Q430R Q427R Q401R R425Q R428Q R425W R428W A424V A427V A398V T420M T423M P421R P418R P418L P421L P391R P417R P420R Y415N Y418N Y416C Y413C A413V A410V A410S A413S R409H R406H H408Q H379Q H405Q K403R K406R P376L P402L P405L P402T P405T P401H P404H P401L P404L W402* W399* S371C S397C S400C Q396* Q393* R393K R390K G387E G361E G390E P381L P384L R380Q R383Q R380W R383W G374V G377V V347I V373I V376I F375L F372L S340N S366N S369N P365S P368S T360S T363S Q359H Q356H P352S P355S R348H R351H R348C R351C R322C S349L S346L S346fs S349fs S344fs S347fs Q342R Q339R Q342* Q339* P337A P340A S335N S338N R335H R332H R332C R335C A333D A330D A330T A333T T324S T327S T325I T322I T325N T322N A319V A322V S318L S321L S318T S321T P314fs P317fs P317L P314L P312H P315H S311N S308N S282C S308C S311C G308E G305E A301V A304V S292N S295N S290N S293N E288K E285K M282V M285V G254S G283S G280S A277G A280G S271G S274G S271Y S268Y P270L P267L A264S A267S L262V L265V T261I T264I L258V L261V L255P L258P P256L P253L D252G D255G G248D G245D Q247H Q244H Q244K Q247K T246K T243K R242T R245T R245K R242K R245G R242G C240R C243R P239L P242L I233F I236F Q231H Q234H S230F S227F S227Y S230Y C225Y C228Y T218I T221I A215V A218V T215M T212M A214V A211V C212R C209R R208Q R211Q R211* R208* H203P H206P T205A T202A P200fs P203fs P200L P203L P200S P203S A198V A201V T200I T197I G194D G197D G197V G194V E193V E196V T191I T194I G180R G183R A181fs A184fs Q176fs Q179fs R173Q R176Q R173L R176L L169P L172P N160S N163S N160fs N163fs S161L S158L C151* C148* Y146C Y149C L145P L148P D143Y D140Y L139* L142* D118H D121H D118fs D121fs D118fs D121fs Q119H Q116H Y114C Y117C E112Q E115Q A111S A114S A112T A109T G108D G111D Q103* Q106* G99R G102R L94P L97P K84del K81del E80del E83del T75N T78N C66S C69S H62R H65R G60A G63A D59N D62N L56F L59F T54M T57M P46S P49S A45G A48G S43F S46F P42fs P45fs A43G A40G ACD V39I V42I D34N D37N Q36R V34I Q30H G29R R27Q L16MATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION E15Q W12* V8I R6S A2P A72E A70V A70T G67R P63R P63S L60P E59G R53W V13I R12T S7T R4H G3R BLM S778C S403C C1217R L1213P L1136P L1133V L1210V S1207F R1202Q R1202* I1124L I1201L S1200T S1123T L1196fs R1195Q R1195G R1195* R1193G V1190M H1189Q Q1180* R1178P R1178Q R1178* Q1177E R1175Q R1175W P1174L P1097L V1169I S1166L S1089L S1089T S1166T P1165L K1087T K1164T K1164E S1081P S1158P I1155V R1153fs R1153H R1153P L1075V L1152V T1147S C1069R C1146R L1145R L1068R L1142H L1142H F1141L M1140I M1138K P1137S E1136K D1135N V1134F A1132T P1124L G1123R P1114S V1113M V1111I V1111L D1109G L1108P S1106Y R1102K P1101T C1100S G1098E A1096T A1094V A1094T V1093A H1092R H1091Q H1091R H1091Y N1090S V1085L V1085M A1084V E1083K R1074S R1074K I1072V T1066R T1066S T1064M T1064A G1059D G1059V L1058R R1057H R1057C R1051Q R1051W C1046fs A1044V Q1038R Q1038P F1035fs V1034fs S1028F A1027T A1025V Q1020P Q1017* L1016Q I1010L P1008R L1007fs I1005V I1003V T1002A P999fs P999L P999H P998L L995fs Y991* Y991C R987Q R987W C985del N981S R975G R966P R966Q R966W A965V A965T P963fs L961P L961fs L961V P956L P956S L955F H945Q H945fs P944L P944fs P944S P943L C940Y T937S L935F A934T V929M C928Y C928F M925I A924fs A924T G923W T922M N921K M917R M917V L915F A913V A913T P910H R905Q I902V A900V A900T V896L S894Y N890D D885N D885Y K876M V871M Q869* I868V E861* T859I T859S V854fs N857S Q855R T853A A849V A846V P842S R841H R841C R840Q R840W I838V C837S C837Y S836C S836P D833N D833H T826K A825P A825T P824L A821S I820T I820V R818L R818Q G814E P813L P813S H812Q W807C R806H R806C S803A F800S I799V K795E D793E N792S D791N P786T E785K L783fs G782A G778D E777Q K776R G771E W769C W769R V765A Y764fs Y764C A760T P759L V756M P754A S753N P750Q R744C H737R R731Q R731W H726fs P725R P722S G721A G721S D718E D718H Q716R T714I T714P A710T S709* H708Q P705A A697T F692L Q691* A686T Q684E Q682R Q682E F680V G679D M677V S676N S671C P670S R666S V665G V665M D664N E662Q V661I Q658H A654T R653Q R653W V652M L647Q R646Q R646W R646fs S643C Q640P Q640* K637E L635R D625G R624Q R624W C620F C620Y G619V H617L L609V A605fs A601T P599S C596fs W594C S593F R589L R589H R589C N587S N587H L586V Q585* S583N A578V P576L P574L P574S P569L F567S S566F S566C A565T A563V K562* R561H R561P R561S E558del E558G E557fs E557K F549S Q544H R542P R542Q R542fs R542W Q538R H534Q H533Y H533D E530K L529F L529I N526D R522Q R522G R522W P520A P516L D512V T510A P509S P500A S499N H489P R487G K480N K480R Y467C L466H Q461H R460H R460C E459Q E454K E454fs A450T Y448C A447T R445H R445C S444F S443L P439L R436H R436C F434L S433G V429F V429I A428V A428T G427V G427S R426H L425P A422V A422T G414E G414A G414W S411T H407N D405fs Q404H Q404R L403V C400Y V399A V399M G398fs R396Q R396* M395T R393Q R393W L391F R389H R389C Q386* A384G L383F Q378R E374* E374K Y373C Y373H L372P G371S A370T V365A V365M V362D V362L S359L S357fs L355P S353fs Y352H R351Q R351W L349R L349F S348N CTC1 S348fs P346S P346A K343R D342E D342G S340L S340W P337A M336TATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION K332R P331R P331T L327S P325S E317Q P312S L309R R306L R306H V298F Q296H Q296R R295H R295C Q294* G293A R292H R292C R292G I291M V288M R287Q R287* E285D E285Q G278V R276Q R276W R273G W271C W271* W271R V270L Q268fs A267T V263L V259M T257I R251G L249V L249F S248F L247P I246M I246T K242fs R232Q R232* A227V R224Q R224* G221D L219P R216K P206A P200L P200S T199R T199M T199P V198I V198fs P195S V188M V186M V186L P185A D183Y D183N H178Q A169T P168H P168S P167L Y165* R162H R162C F160L L157P H156R H156D W153* S152F S152C D150E D150N D148E I147T I147fs S143R V141I T139S N138S D137E Y134C G131R C128F E125fs D123Y R108Q R108* P107L P107R N102fs P105S N104K A99P A96S A96T Q93R Q93* Y92C S90G S88N S86L H84fs S83N S83T C82R R78H H76Q H76N K74N K74R V68I S66G Y65C S64N G58D Q57R N56H R55K W50* K47E D44fs P40L P34S L27V Q24R Q20* D18H E17G A14T Q13E V4I D14G F28del L26R R46W R46L R60G Q63P E73A E76Q I85V Q87R V92I L94F T114S S126F A132P A6P L16S L16F C149W C23W R158* R32* R170* R44* H175R H49R R80Q R206Q H104R H230R T125M T251M I135V I261V S152F S278F R283C R157C R283H R157H Q167H Q293H V298I V172I R174Q R300Q D308G D182G L184Q L310Q S315C S189C V190M V316M P191R P317R D195N D321N S209N S335N P221L P347L V353A V227A Q239E Q365E A257V A383V Q388R Q262R L394W L268W R395W R269W R269Q R395Q I270M I396M V287A V413A S292F S418F Q419R Q293R T300M T426M T321S T447S E323D E449D G328R G454R P333A DCLRE1 P459A D462N D336N G352V G478V S360fs S486fs S487R S361R T381S B T507S N510Y N384Y A2V I7T P10L K17del K14R E18del R19W K20R S21L L22V E24K E25D Q31E Q31K A33T F36V L37del I38T K39E P40R E41K K43E A45T D48N T49M S50Y L56S F59S N63K V64G R65T T66A T67I H68R H68Q H68Q L72F L72Y C74R E82Q D85N I87V N93Y R111Q S121G A139T R141S S148G R158W A162T I163V I163L G165A G165V I187L V190I D208N E210G S255G H259P S280R S295F S304N K314R M316I L317F L317V L321V R322Q G326S I327V V329I Q331H I336V I343V I347V L349S M350T M350I T352A A353V T357A D359N E372Q R378Q P384S P384L A386T L391M L398P D399H G402R G402E P404A T408I P409S P409L Q414E Y419N E421del E426del E421Q E426Q V427del V432del P435L P430L E440K E435K A445V A440V K448R K443R R449P R444P E445V E450V E445D E450D S446T S451T S446N S451N S446R S451R T453S T458S P463T P458T K472del K467del K473del K478del G482V G477V E479A E484A G486R G481R G486E G481E D486N D491N S489N S494N DKC1 K505del K500del K504N K499N K505N K500N E503D E508D L511F L506F FANCM R1860H R1834H LIG4 K357fs K424fs K436fs T112M S110T P109L Y107fs Y107C Y105C R101Q C98G M97fs M97T M97V E89fs E89A P87S M79I M79T M79L I78N K76N G74R N72K N72S Q68H E66fs V64M G63R R61Q R61W Q59H K58Q K56R V55M K52N K52R Y48C K46N T44S R41fs A39D A39T P37S Q36fs A35V L27Q NHP2 Y24N T23I T23A E21fs C18Y A17V D9N D7HATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION P62L R61C P60L Q58R F52L F52L I48fs Y41fs R43Q R43G R34W P32R H31R H31Y A30D A30G Q26fs Q25H D12E D12H G11R E9D NOP10 L3fs NPM1 D116del D180del D82del D178H D114H D80H W578* W593* W639* T585R T631R T570R T570A T585A T631A N566K N581K N627K N581K N627K N566K S625L S564L S579L I624V I578V I563V G561E G576E G622E P620S P559S P574S E556V E571V E617V K615E K554E K569E M553I M568I M614I M553T M568T M614T K551R K566R K612R K545R K606R K560R E599G E553G E538G C597R C536R C551R S550F S535F S596F D595E D549E D534E D534N D549N D595N D534Y D549Y D595Y T548N T533N T594N E590Q E544Q E529Q D542N D527N D588N D527Y D542Y D588Y G538E G523E G584E E524fs E539fs E585fs G581R G535R G520R L517R L532R L578R S511N S572N S526N N568D N522D N507D R521K R567K R506K K566R K505R K520R V564A V503A V518A V564I V503I V518I S516G S562G S501G A499T A514T A560T F497C F512C F558C R493L R554L R508L R554H R493H R508H R508C R493C R554C Y491C Y506C Y552C Y506H Y491H Y552H H490P H505P H551P N550K N489K N504K Y485C Y546C Y500C C482R C497R C543R Q481* Q496* Q542* R538P R492P R477P R477W R492W R538W R469I R515I R454I M467I M452I M513I M513V M452V M467V E511K E450K E465K R444Q R459Q R505Q R505W R459W R444W Y443C Y504C Y458C A501S A440S A455S K453N K499N K438N S498N S437N S452N T451I T436I T497I V449I V495I V434I K492Q K431Q K446Q Q490R Q429R Q444R S425R S440R S486R D432G D417G D478G S413F S428F S474F Q411* Q426* Q472* Y401C Y416C Y462C L415V L461V L400V D399N D414N D460N P407H P453H P392H T390A T451A T405A R383H R398H R444H R444C R383C R398C L379S L440S L394S D378E D393E D439E L387I L372I L433I L372V L387V L433V D383N D429N D368N M367V M382V M428V V366I V381I V427I R365K R380K R426K K421R K360R K375R N420* N374* N359* F358fs F373fs F419fs P371R P417R P356R H346D H407D H361D I345L I360L I406L K359E K405E K344E F354L F400L F339L G398V G337V G352V M393T M347T M332T I345V I391V I330V F344C F329C F390C F344V F390V F329V Y323C Y338C Y384C A322G A337G A383G A383V A322V A337V Q314fs Q375fs Q329fs E317K E378K E332K Q329* Q375* Q314* S368C S307C S322C G304V G319V G365V E318K E303K E364K K359E K313E K298E K359Q K313Q K298Q P296T P311T P357T N295S N310S N356S L304V L350V L289V R303L R288L R349L R288Q R303Q R349Q R349W R303W R288W A298V A344V A283V N279del N294del N340del N340S N279S N294S T270A T285A T331A V257I V318I V272I V318fs V272fs V257fs T254A T269A T315A E267K E252K E313K L247F L262F L308F D246N D261N D307N A306V A245V A260V P303R P257R P242R Y240C Y301C Y255C V232I V247I V293I M243I M289I M228I N242fs N288fs N227fs N242fs N288fs N227fs I224T I239T I285T I224V I239V I285V V223G V238G V284G G220E G235E G281E S219L S280L S234L H214D H229D H275D I274* I213* I228* E202L E217L E263L Q193L Q208L Q254L E192fs E207fs E253fs R251G R190G R205G R188P R249P R203P R188H R249H R203H R188C R249C R203C E202del E187del E248del D245G D184G D199G D245N D184N D199N K243N K182N K197N S242G S196G S181G V179I V194I V240I Y192* Y177* Y238* Y192H Y238H Y177H R237Q R191Q R176Q R176* R191* R237* E175V PARN E236V E190V E185G E170G E231G L230S L184S L169S P176LATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION P161L P222L P161R P176R P222R P161A P222A P176A Y160C Y221C Y175C W158* W219* W173* W158G W173G W219G Q163E Q148E Q209E G146R G161R G207R L200F L154F L139F S133N S148N S194N L130F L145F L191F E128G E143G E189G E128fs E189fs E143fs V184M V123M V138M I120M I135M I181M Q116R Q131R Q177R Q177* Q116* Q131* T111M T126M T172M T120A T105A T166A N119S N104S N165S Y100C Y115C Y161C G157E G111E G96E A110V A156V A95V A156S A110S A95S A107V A153V A92V R104H R150H R89H R104C R150C R89C Q145P Q99P Q84P E93fs E139fs E78fs R140G R79G R94G Q75L Q136L Q90L I131V I70V I85V G130R G84R G69R R82Q R67Q R128Q R128* R67* R82* D61H D76H D122H G120R G59R G74R A71G A117G A56G I52N I113N I67N V107I V61I V46I S100Y S39Y S54Y P33L P94L F32S F93S Y30F Y91F Y91C Y30C Y91N Y30N T85M T24M I23V I84V K21R K82R S20L S81L T73I T12I D2E D63E M1V M62V L57P K56N Y54F E52D E52Q E51G A42V S41fs S41F S39L P38L P38S S35T A26T F24L E20G I19M I19V H13Q H13Y L12F N11S F8fs N7H I3V RPA1 V227A V214A E240K E227K T257A T270A RTEL1 c.1338+3 A>G STN1 A367V S265R S248C D157Y T151A R135T R133Q TERC g.5714C>T T1129N T1066N T1129S T1066S S1062A S1125A P1124L P1061L L1123V L1060V P1121R P1058R P1121L P1058L N1120H N1057H A1119T A1056T A1055S A1118S A1118T A1055T A1054V A1117V A1054D A1117D A1117S A1054S E1053K E1116K E1116Q E1053Q T1050I T1113I L1049M L1112M T1111M T1048M T1110M T1047M T1110A T1047A G1046E G1109E G1109R G1046R P1045R P1108R P1045L P1108L P1045S P1108S L1044V L1107V K1106R K1043R R1105Q R1042Q R1042W R1105W S1041C S1104C L1040V L1103V Q1102K Q1039K T1101M T1038M Q1100R Q1037R A1036T A1099T P1028R P1091R P1028L P1091L V1027L V1090L V1090M V1027M T1088N T1025N R1086H R1023H R1023C R1086C R1023G R1086G R1021Q R1084Q R1021G R1084G T1083S T1020S L1019V L1082V L1016fs L1079fs A1014P A1077P Q1008H Q1071H Q1008* Q1071* V1007M V1070M E1005D E1068D S1067Y S1004Y S1004A S1067A P1066S P1003S L1065V L1002V P1064L P1001L G1063S G1000S A1062S A999S A1062T A999T A998S A1061S A998T A1061T K1059N K996N K1059R K996R A1058T A995T A1058S A995S S1055L S992L A1052S A989S A1052T A989T K1050N K987N A1049G A986G L1047P L984P S1045C S982C L1042F L979F S978F S1041F A977T A1040T A1040S A977S T1039M T976M T976P T1039P T1039A T976A D1038A D975A S1037C S974C I973T I1036T V1035I V972I R1034H R971H R1034C R971C T1030I T967I T1030R T967R P966A P1029A P1029S P966S W1026G W963G V1025A V962A V962F V1025fs V962fs Q961H Q1024H H1022R H959R H1022L H959L F958C F1021C L954P L1017P A951S A1014S A1009V A946V A1009S A946S L1005F L942F K1003R K940R I938F I1001F I1001V I938V T999I T936I T936A T999A C935fs C998fs T933M T996M T996K T933K L994F L931F S993G S930G L924V L987V F986L F923L S984R S921R S921N S984N H983Y H920Y C919S C982S C982Y C919Y C982F C919F K918fs K981fs R979Q R916Q R979W R916W V914I V977I G976E G913E F912L F975L R909H R972H R908H TERT R971H R908C R971C M907V M970V M907L M970L M907L M970L N906SATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION N969S N906H N969H A903V A966V G900S G963S R962L R899L R962H R899H R962S R899S R962C R899C N898T N961T N961S N898S A956T A893T I891V I954V R951Q R888Q R888W R951W S885R S948R S947P Y946H D945V D945N S944R S944N R938Q R938W G932S C931Y W930L F928C G926A G926S H925Q H925Y P923L M922L V920I F919L A918T T917K T917M G916D G916S G915D G915S A913V A913G E912K E910G V909I P908L K902N K902* R901Q R901W N899T V897L V897M E893Q P892S V891I R889Q R885S F883C T882S K881I A880V A880T H879Q L877fs H876Y H876N L872F L871W F870I D869Y V867M R865H R865C L864P G861R D860G D860N R859Q R859W R858Q A855V N851D D848N D848fs S843G C842Y T839M L837F P832L Q829R V826F V826I Y825H K823E G822D R821fs R821fs R819H R819S R819C V818M A817G A817T H816Y H816N H815R H815P M813T M813V R811H R811C L810V F809fs V808I D807E D807N F806S L805I L805F G804D G804V G804S S803N S802I A801D A801G A801S A801P A801T N799S S796F S796P Q794H Q794R E793K I792V V791I V791I V867M V790I D788G R787K R787M P785L P785R P785S P785A T783I E782D E782A H779R A778T Y772fs Q775* R774Q R774* Y772C T765I S764C S764F H762Y S761N A758S K757R R756L R756H R756C V755I H754Q H752R A751V A751S A751T A750T V747A V747fs V747I V746M R743Q R743W R742H R742C V741L V741M C740Y T738M N737K N737I N737S N737D Q736R K734E I733V I733F I732V S731N A730T I729M I729V V728I E727D T726K T726M R724S R724T Q722R P721R I720M I720V D718N Y717N A716V A716T T714K T714M V713M V711L E705K P704S P703L P702L D701G Q700* A699S A699T R698W V697A R696H R696S L695Q V694A V694E V694M T692N T692I T692A R691H R691S R691C W690C I686M I686T D685N D684V D684G D684N G682D A678T G677C L676R L676V L675R L675V G674V G674D G674C G674S R672H R672C R671Q R671G R671W A670G A670V R669P R669Q R669W E668A E668Q E668K V664M V664L S663N S663R S663G L661Q R657S T655S T655N R653H R653S R653C E652K A651P R650K E648V R646H R646C T644K T644M R643G A642T V640L V640M V639I Y638C D637A D637N M636T M636V N635S V634L I633S P632L R631Q R631W G629R D628N P627R P627A P625fs P625T I624V R622C L621I S619T T618R T618M T618A L616M A615V A615T P614H P614S A612V A612T E611K R610L R610Q R610G R610W H609Y Q608H Q608K R607S A604T S602L S602P R599Q R599W V596G V596L R595K K594R L593F H592L I589V I587M I587T I587V K583T W581C W581* S579R S579I R577Q R577W R572S R572K N571fs K570N T567M T566N T564M V563A Y562fs F560L S559C S559A L557V E555K E555Q V553I V551A V551M S550R S550R S550R M549I W547G H546R A542V A542S A542S E539D E539Q E539K E538* R537H R537C L536Q L536M R535P R535H R535C H534Q H534L H534P H534R H534Y A532V A532T A532S P530Q P530L C528Y G527V V526A V526I G525E G525V P524S P524A S523R S523N R522K R521H R521L R521G R521C L520P L520V A518V A518S D516N D516H V514G S513N S513C T509M Q506R L505R L505Q S504W K502N K502R H500L G498R L497R S496C S496T I495L K493R L488F R486H R486C R485fs E484K E484*ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION E484Q N483S H482N S480P G479D W478* G476S P475L P475fs P474L P474S V473L V473L R471W R470H R470C L469M V465L F464L G463A G463C G463R G463S Q460del Q460fs W459C P458T S457G S456T H455L Q454H Q454R Q454L R453H R453C Q450R R447L R447H R447C R446C R446G R446S P445R D444E D444G T443K T443R T443A T443P E441del D442N E441D E441K E440G E440K E439K E439Q E439fs P438H A437V A437S A436V V435E V435L S434F G433D P431H P431L P431T E429* E429K R428W A427V A427T C426W C426S G424S A422G A422P A422T P421S T420N T420A T420S V419F A418V A417G A417V A417P L415R P414S C413Y H412R H412Y T411M T411A V407M V407L G406V G406R P404L P404R P404S P404A C403S A401V A401S N399S G398E G398R L396V L394Q Y386fs R390P R390Q R390W Y386C R385H R385C Q384H Q384R Q384L L382V R381H R381P R381G P380T P380S T375fs R378S R378K R377H R377C P376L T375S T375I T375A T375fs G374E G374R P373R P373S P370R P370S R369G S368F G367C I364V V361L R358P R358Q R358W R358G A357G G356A R351G L350fs L350M S349F S349C S348R S348N L346P L346V F345Y P343R R342Q Q340K K338R K338Q D337E D337Y D337N G336D S335del S335P Y333fs H330Q H330N K329N E327D E327Q A326S A326T Y325H Y325D V324M P323L P323R P322L P322R P322S P322A P320R P320L P320S T319K T319M D318E D318G D318Y W317S W317R P316L P316H R315H R315C R315S P314R P314L P314S P313S R312Q R312P R312W S311L S311T S309fs P308L P308A P307L P307R P307S G306D A305V A305L A305T H303L H303N Q302R R301L R301H V299M V299L S298Y S298N S298C S298P S298T P297L P297S P297T H296P H296Y S295C S295P H294Q H294L H294Y R293L R293C T292M T292R L289P L289F A288G A288V G287A G287C G287S E286A E286K S284F S284P T283I T283P E280K A279V A279P A279T P278R P278L P278S A276D P275L S274T V273M V272A V272G V272M C271S C271G C271R C271fs R268H R268C D267G D267N P265L P265R G264A R263H R263S T262M R261S R261K R261W G260D P259L H258Q H258Q H258Y A257G A257S W256* S255Y G254E G254A G254R Q253H Q253R Q253* G252E G252R V251L V251F V251I T249K T249M R248Q R248P R248W E247Q P246L P246S E245D E245D A243V A243T A242T A242P G241D R240L R240H R240C R240S P238L P238S R237K K236N K236E L234F P233Q S231N R230L R230Q R230* S229I S229N S229R A228V A228T G226V G226C G225R G225R R224Q R224H R224G R224C R222K R222T R222W A221V A221T A218G A218D A218T P217R P217L P217T P213L P213S V212I A210T E209D R208S V207I S206R S206C H205fs N204K N204I N204Y W203C W203S W203G W203R A202T R201P R201Q R201W E200G E200* G198R G198R L197R R196P R195G R194Q R194* P193S P193T S191N S191T S191G A190V A190T H189Q H189Q H189P H189R H189D P187L P187R P187T P186L P186S R185Q R185L R185W A184T Q183R Q183E T182S T182I T182A T182S A181V A181S A180T G179V G179A G179S L178V Q177R L175P P173S G172E V170M Q169* V162M L158F L158V A157V A154S V150F V148L D147G D146E V144M R143C L141V L139R G138A G138R G135A G135R G135R R132P L131R L131V P124L P124A Y122C S121R S121N R120P R120C S118N S118C F115L E113fs P111R P111S G110D G110fs G110A R108S A107D A107S A107T A107P G106E G106P G106R D105GATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION L103G A102V F101V L97R N95K K94N K94N K94Q A93G A93V R91C R87S R87K P450L P415L S413F S448F D411fs D446fs D446V D411V R410G R445G C409Y C444Y P438L P403L P403A P438A I437V I402V A401V A436V G435D G400D H399D H434D G433R G398R P431fs P396fs P396T P431T P396A P431A P430T P395T P395S P430S L394I L429I L429V L394V E427G E392G T389I T424I P388S P423S F418S F383S K382E K417E E373D E408D E373Q E408Q G369E G404E G369V G404V Q368H Q403H I354K I389K I389T I354T V351D V386D V351I V386I S384N S349N P345L P380L P335S P370S L331I L366I R330G R365G L364fs L329fs P328S P363S D327H D362H M361I M326I M361V M326V Y325C Y360C C324Y C359Y C359S C324S C324fs C359fs C356Y C321Y E354D E319K E354K E319fs E354fs T350A T315A V345L V310L P309S P344S N308fs N343fs E342A E307A L340P L305P A339V A304V R338G R303G G302fs G337fs C297Y C332Y K294R K329R K329E K294E A323P A288P T278S T313S Y312* Y277* I276T I311T A275V A310V A275T A310T E273* E308* E308Q E273Q K306R K271R S305T S270T E304K E269K K267N K302N V264A V299A V299G V264G Q263fs Q298fs G294S G259S R291G R256G P254S P289S L287P L252P T284A T249A T284fs T249fs T284fs T249fs P283H P248H P283S P248S P283A P248A R282H R247H R282C R247C R282S R247S K245fs K280fs K280* K245* K280E K245E R241S R276S R276fs R241fs T240P T275P W272* W237* Q271* Q236* Q269* Q234* V268L V233L R266Q R231Q R230Q R265Q R230* R265* G229S G264S L260V L225V H222Y H257Y R256Q R221Q L253V L218V E216Q E251Q T248M T213M S245Y S210Y P244L P209L P241S P206S L205F L240F H204P H239P G237D G202D P201L P236L P236S P201S P197L P232L H193Q H228Q H228Y H193Y L192F L227F R189G R224G P185L P220L P214T P179T P214S P179S L211V L176V N175K N210K S173P S208P D172E D207E T171I T206I C168R C203R E167fs E202fs L200F L165F G162E G197E M161I M196I M161V M196V R190K R155K S151F S186F S185T S150T M177R M142R W141R W176R V173M V138M Q133R Q168R A132V A167V P130S P165S F117S F152S A110T A145T P142R P107R L135F L100F E99K E134K S130L S95L S95P S130P A124V A89V A89P A124P S122T S87T Q120R Q85R Y80C Y115C F79fs F114fs E77Q E112Q Q76H Q111H L108F L73F K106N K71N K106E K71E K101R K66R V94L I93T P92S P88T H86fs H85D N84S N84H Q78R A77V TINF2 G73D G73R Q72L V67M Q21E R13C A10S A7V A7P A7fs TYMS E87K R115* Q7fs A36T R52W P78T T132N L153V F164L I184L P200R H204R S243F E251G P287L R298W T317I G326S G350fs P359S L360V L373fs H376Y A390T R398W N414S P423L G435R S438F T442M G481S WRAP53 R483H T505M V508I R513G A522fs A522fs G521W A522G G543S ZCCHC8 T419I T258I T397I T496I P186L P87L G184R G85R G170R G71R

[0118] The disclosure relates to a method of determining or identifying a mutation in genomic DNA of a subject, such as a single nucleotide polymorphism, comprising mixing a sample comprising at least a portion of a telomere from the subject with a sample comprising whole genomic DNA comprising a known variant at a particular locus or a known control;ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION sequencing at least a portion of genomic DNA with at least a portion of the telomere; comparing the sequence length of the telomere and chromosomal DNA from the subject to a control; and identifying the presence, absence or quantity of a variant in the genomic DNA of the subject. In some embodiments, the subject has cancer, has a hyperproliferative disorder, a telomeric disorder or is suspected of having any of the foregoing. In some embodiments, the subject comprises at least one mutation identified in Table Z.

[0119] The disclosure relates to methods of diagnosing a subject with a telomeric disease comprising: measuring the telomere length of isolated chromosomal DNA of a sample from the subject; and detecting the presence or absence of one or more of the mutations identified in Table Z based upon alignment or analysis of the chromosomal DNA relative to the control sequences of Table Y. Some embodiments of methods of diagnosis comprise: isolating a chromosomal DNA from a sample of the subject; analyzing the telomere sequence with any one or combination of steps disclosed herein to identify the length of the telomere sequence; detecting the presence of one or more mutations within the chromosomal DNA; and correlating the presence of the mutation and the length of the telomere sequence with the likelihood of the subject having a telomeric disorder. In some embodiments, the method further comprises simultaneously, or in serially, performing a step of genomic DNA sequencing with the analysis of the length and sequencing of the telomere.

[0120] The disclosure relates to methods of identifying the presence, absence or quantity of a mutation in a subject comprising: measuring the telomere length of isolated chromosomal DNA of a sample from the subject; and detecting the presence or absence of one or more of the mutations in the chromosomal DNA based upon alignment or analysis of the chromosomal DNA relative to the control sequences. Some embodiments of methods of diagnosis comprise: isolating a chromosomal DNA from a sample of the subject; analyzing the telomere sequence with any one or combination of steps disclosed herein to identify the length of the telomere sequence; detecting the presence of one or more mutations within the chromosomal DNA; and correlating the presence of the mutation and the length of the telomere sequence with the likelihood of the subject having a telomeric disorder. In some embodiments, the method further comprises simultaneously, or in serially, performing a step of genomic DNA sequencing with the analysis of the length and sequencing of the telomere. In some embodiments, the method comprises detecting the presence or absence of one or more of the mutations identified in TableATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Z based upon alignment or analysis of the chromosomal DNA relative to one or a plurality of control sequences. In some embodiments, the control sequence is chosen from one or a plurality of control sequences from Table Y.

[0121] The disclosure relates to a method of sequencing genomic DNA from a subject comprising mixing genomic DNA from a subject with telomeric DNA from the subject; sequencing whole genomic DNA from the subject simultaneously with sequencing telomeric DNA from the subject; analyzing the genomic DNA from the subject to identify one or a plurality of mutations and analyzing the telomeric DNA from the subject to determine age of the subject; comparing the age of the subject with the identity of the one or plurality of mutations; and assigning a prognosis or diagnosis to the subject based upon the age and the presence of the one or plurality of mutations. In some embodiments the mutation is selected from one or a plurality of the mutations identified in Table Z. In some embodiments, the mutation is a mutation in human TERT. In some embodiments, the method further comprises repeating any one or multiple aforementioned steps across a plurality of sample to generate a distribution of telomeric length across multiple tissues. In some embodiments the distribution of telomeric length is used to calculate an average telomeric length across multiple tissues and the average telomeric length is used to prognose, diagnose or identify the presence, absence, or quantity of mutations in a subject.

[0122] In some embodiments, the sample is from one or more of: cells from isolated blood, cells from isolated bone marrow, isolated cells from lymph node or lymph tissue, PBMCs, T cells, B cells, NK cells, central nervous system cells, cells from the GI tract, cells from the skin, prostate cells, breast cells, pancreas cells, cells from the colon, cells from the head or neck, epithelial cells, lung cells, brain cells, stomach cells, intestinal cells, esophageal cells, ovarian cells, testicular cells, cervical cells, uterine cells, bladder cells, kidney cells, biliary cells, liver cells, thyroid cells or the like.

[0123] The disclosure relates to a computer-implemented method of calculating telomere length comprising measuring telomere length and identifying one or a plurality of mutations in a whole genome sequence scan or sequencing of genomic DNA. In some embodiments, the step of analyzing comprises preparing a distribution of telomeric lengths across multiple sample taken from a subject. In some embodiments, genomic DNA is mixed with telomeric DNA samples prior to the step of analyzing. In some embodiments, the step of analyzing comprisesATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION determining high-resolution telomere length measurements determining genomic DNA sequence from one or a plurality of samples and preparing a distribution based upon an age of the subject. In some embodiments, the method further comprises comparing the age, the telomeric length and the genome sequence with a control to identify or quantify the presence of a mutation associated with a telomeric disorder. In some embodiments, the method further comprises selecting a treatment for the subject based upon the age, the telomeric length and the genomic DNA of the subject. In some embodiments, the method comprises determining a disordered cell type of a cancer cell, a pre-cancerous cell, a cell predisoposed to be a cancerous cell, a myelodisplastic syndrome cell, a clonal hemoatopoiesis cell, a myeloproliferative neoplasm cell, a dyskeratosis congenita cell, an idiopathic pulmonary fibrosis cell, a cryptogenic cirrhosis cell, an aplastic anemia cell, a bone marrow failure cell; and subsequently providing or administering a treatment to the subject based upon the step of determining.

[0124] The disclosure relates to a computer-implemented method of calculating telomere length by analyzing data including chromosomal DNA sequence to determine the end of the telomeric sequence, the telomeric boundary within the telomeric sequences and measuring the number of nucleotides including and between the end of the telomere and the telomeric boundary. In some embodiments, the method further comprises comparing the number of nucleotide in the telomere (telomere length) to the length of a control sample with a known length or health metric, such that variance as between the lengths may be correlated to the presence of a telomeric disorder.

[0125] In some embodiments, the method of identifying the telomeric boundary is a computer- implemented method step of comparing the chromosomal sequence information with the sequence comprising a known boundary to identify where within the chromosomal sequence information telomere repeats are no longer detected and estimating the location of the telomere repeat on where within the chromosomal DNA the last telomeric repeat is detected. In some embodiments, the telomere repeat is a 6 to 12 nucleotide nucleotide sequence (such as TTAGGG) that appears only within the non-coding portion of chromosomal DNA. Other telomeric repeats sequences are known and set forth in Aksenova et al. Genes (Basel).2019 Feb; 10(2): 118, which is incorporated by reference in its entirety.

[0126] In some embodiments, telomere length is a biomarker for a cancer, hematology, bone marrow transplant prognostication, pre-cancer disorders, telomere biological disorders.ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION

[0127] In some embodiments, methods of determining a disordered cell type are provided. In some embodiments, the methods comprise any method of determining telomere length herein. In some embodiments, the method comprises determining a disordered cell type of a cancer cell, a pre-cancerous cell, a cell predisoposed to be a cancerous cell, a myelodisplastic syndrome cell, a clonal hemoatopoiesis cell, a myeloproliferative neoplasm cell, a dyskeratosis congenita cell, an idiopathic pulmonary fibrosis cell, a cryptogenic cirrhosis cell, an aplastic anemia cell, a bone marrow failure cell.

[0128] In some embodiments, methods of diagnosis are provided. In some embodiments, the methods comprise any method of determining telomere length herein. In some embodiments, the method comprises diagnosing a subject as having a cancer cell, a pre-cancerous condition, a predisopostion to cancer, having myelodisplastic syndrome, having clonal hemoatopoiesis, having a myeloproliferative neoplasm, having dyskeratosis congenita, having idiopathic pulmonary fibrosis, having cryptogenic cirrhosis, having aplastic anemia, or having bone marrow failure. In some embodiments, the method comprises prognosticating or prognosing bone marrow transplant success based upon one or more of: the telomeric length, the average telomeric length across multiple samples from the subject, the age of the subject, and at least a portion of the genomic DNA sequence from the subject.

[0129] The disclosure also relates to a method of determining compound risk or probability of developing a telomeric disorder or a hyperproliferative disorder, such as cancer, in a subject, the method comprising calculating at least a partial genomic DNA sequence, calculating telomeric length or a distribution of telomeric length from one or a plurality of samples from the subject; identifying the presence, absence or quantity of one or more mutations in the genomic DNA, and the calculating the probability of developing the telomeric disorder based upon the age, telomeric length and at least partial telomeric sequence. In some embodiments, the method further comprises sequencing whole genomic DNA of the subject and comparing the sequence to a control sequence such that a change in the whole genomic sequence relative to the control indicates a mutation. In some embodiments the whole genome sequencing is performed simultaneously with the calculation of telomer length. In some embodiments, the one or plurality of mutations is a SNP. In some embodiments, the one or plurality of mutations is from a gene associated with telomere regulation, such as POT1 and TIN2. As identified in the reference cited in Example 2, which is incorporated by reference in its entirety. In some embodiments, the oneATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION or plurality of mutations is from a gene position in a mammalian TERT loci, such as human TERT, which contains dozens of SNPs associated with increased cancer risk. Unlike previous methods which can only identify SNPs (and therefore only speculate if they impact the telomere’s tumor suppressive mechanism) or determine leukocyte telomere length (and require additional testing in order to determine the presence of mutations which could impact telomere maintenance), our method is able to directly relate telomere length measurements to the presence or absence of SNPs relevant to both telomere maintenance and cancer risk. In some embodiments, the method further comprises a step of determining the risk of developing a telomeric disorder but comparing one or more of: the age of the subject, at least a portion of the genomic DNA sequence of the subject, the telomere length of a sample of the subject or the distribution of telomeric length across multiple cells of the subject. In some embodiments, the method is a computer-implemented method, in which one or more step of sequencing or sequence analysis is performed in a computer system comprising a memory and a computer program product with instructions for any of the above-identified steps. In some embodiments, the step of calculating telomere length, telomere distribution across multiple samples, the step of comparing genomic DNA sequence of the subject with a control and / or the step of calculating probability of developing a telomeric disorder is performed by a computer-implemented method on a system with a processor, memory and computer program product disclosed herein. References and Notes 1. R. K. Moyzis, J. M. Buckingham, L. S. Cram, M. Dani, L. L. Deaven, M. D. Jones, J. Meyne, R. L. Ratliff, J. R. Wu, A highly conserved repetitive DNA sequence, (TTAGGG)n, present at the telomeres of human chromosomes. Proc Natl Acad Sci U S A.85, 6622–6626 (1988). 2. T. de Lange, L. Shiue, R. M. Myers, D. R. Cox, S. L. Naylor, A. M. Killery, H. E. Varmus, Structure and variability of human chromosome ends. Mol Cell Biol.10, 518–527 (1990). 3. C. W. Greider, E. H. Blackburn, Identification of a specific telomere terminal transferase activity in Tetrahymena extracts. 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Marrone, F. Goldman, A. Dearlove, M. Bessler, P. J. Mason, I. Dokal, The RNA component of telomerase is mutated in autosomal dominant dyskeratosis congenita. Nature.413, 432–435 (2001).ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION 16. C. M. Roake, L. Chen, A. L. Chakravarthy, J. E. Ferrell, G. D. Raffa, S. E. Artandi, Disruption of Telomerase RNA Maturation Kinetics Precipitates Disease. Molecular Cell. 74, 688- 700.e3 (2019). 17. T. Vulliamy, R. Beswick, M. Kirwan, U. Hossain, A. Walne, I. Dokal, Telomere length measurement can distinguish pathogenic from non-pathogenic variants in the shelterin component, TIN2. Clinical Genetics.81, 76–81 (2012). 18. S. Choo, F. K. Lorbeer, S. G. Regalado, S. B. Short, S. Wu, G. Rieser, A. A. Bertuch, D. Hockemeyer, Editing TINF2 as a potential therapeutic approach to restore telomere length in dyskeratosis congenita. Blood.140, 608–618 (2022). 19. G. Cristofari, J. Lingner, Telomere length homeostasis requires that telomerase levels are limiting. EMBO J.25, 565–574 (2006). 20. N. Rufer, W. Dragowska, G. Thornbury, E. Roosnek, P. M. Lansdorp, Telomere length dynamics in human lymphocyte subpopulations measured by flow cytometry. Nat Biotechnol.16, 743–747 (1998). 21. A. Valdes, T. Andrew, J. Gardner, M. Kimura, E. Oelsner, L. Cherkas, A. Aviv, T. Spector, Obesity, cigarette smoking, and telomere length in women. The Lancet. 366, 662–664 (2005). 22. K. Demanelis, F. Jasmine, L. S. Chen, M. Chernoff, L. Tong, D. Delgado, C. Zhang, J. Shinkle, M. Sabarinathan, H. Lin, E. Ramirez, M. Oliva, S. Kim-Hellmuth, B. E. Stranger, T.-P. Lai, A. Aviv, K. G. Ardlie, F. Aguet, H. Ahsan, GTEx Consortium, J. A. Doherty, M. G. Kibriya, B. L. Pierce, Determinants of telomere length across human tissues. Science.369, eaaz6876 (2020).ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION 23. M. M. Ouellette, M. Liao, B. S. Herbert, M. Johnson, S. E. Holt, H. S. Liss, J. W. Shay, W. E. Wright, Subsenescent telomere lengths in fibroblasts immortalized by limiting amounts of telomerase. J Biol Chem.275, 10072–10076 (2000). 24. T.-P. Lai, S. Verhulst, S. A. Savage, S. M. Gadalla, A. Benetos, S. Toupance, P. Factor-Litvak, E. Susser, A. Aviv, Buildup from birth onward of short telomeres in human hematopoietic cells. Aging Cell.22, e13844 (2023). 25. H. A. Raj, T.-P. Lai, M. R. Niewisch, N. Giri, Y. Wang, S. R. Spellman, A. Aviv, S. M. Gadalla, S. A. Savage, The distribution and accumulation of the shortest telomeres in telomere biology disorders. British Journal of Haematology. n / a, doi:10.1111 / bjh.18945. 26. L. Xu, X. Wang, X. Lu, F. Liang, Z. Liu, H. Zhang, X. Li, S. Tian, L. Wang, Z. Wang, Long- read sequencing identifies novel structural variations in colorectal cancer. PLOS Genetics. 19, e1010514 (2023). 27. N. D. Hastie, M. Dempster, M. G. Dunlop, A. M. Thompson, D. K. Green, R. C. Allshire, Telomere reduction in human colorectal carcinoma and with ageing. Nature.346, 866–868 (1990). 28. F. P. Barthel, W. Wei, M. Tang, E. Martinez-Ledesma, X. Hu, S. B. Amin, K. C. Akdemir, S. Seth, X. Song, Q. Wang, T. Lichtenberg, J. Hu, J. Zhang, S. Zheng, R. G. W. Verhaak, Systematic analysis of telomere length and somatic alterations in 31 cancer types. Nat Genet.49, 349–357 (2017). 29. M. T. Teixeira, M. Arneric, P. Sperisen, J. Lingner, Telomere length homeostasis is achieved via a switch between telomerase- extendible and -nonextendible states. Cell.117, 323–335 (2004).ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION 30. M. T. Hemann, M. A. Strong, L. Y. Hao, C. W. Greider, The shortest telomere, not average telomere length, is critical for cell viability and chromosome stability. Cell. 107, 67–77 (2001). 31. J. E. Gorzynski, S. D. Goenka, K. Shafin, T. D. Jensen, D. G. Fisk, M. E. Grove, E. Spiteri, T. Pesout, J. Monlong, G. Baid, J. A. Bernstein, S. Ceresnak, P.-C. Chang, J. W. Christle, H. Chubb, K. P. Dalton, K. Dunn, D. R. Garalde, J. Guillory, J. W. Knowles, A. Kolesnikov, M. Ma, T. Moscarello, M. Nattestad, M. Perez, M. R. Z. Ruzhnikov, M. Samadi, A. Setia, C. Wright, C. J. Wusthoff, K. Xiong, T. Zhu, M. Jain, F. J. Sedlazeck, A. Carroll, B. Paten, E. A. Ashley, Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting. New England Journal of Medicine.386, 700–702 (2022). 32. C. W. Greider, Regulating telomere length from the inside out: the replication fork model. Genes Dev.30, 1483–1491 (2016). 33. N. Stong, Z. Deng, R. Gupta, S. Hu, S. Paul, A. K. Weiner, E. E. Eichler, T. Graves, C. C. Fronick, L. Courtney, R. K. Wilson, P. M. Lieberman, R. V. Davuluri, H. Riethman, Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline. Genome Res.24, 1039–1050 (2014). 34. N. W. Kim, F. Wu, Advances in quantification and characterization of telomerase activity by the telomeric repeat amplification protocol (TRAP). Nucleic Acids Res. 25, 2595–2597 (1997). 1. 35. K.-T. Tan, M. K. Slevin, M. Meyerson, H. Li, Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres. Genome Biology.23, 180 (2022). EXAMPLES Example 1: Digital telomere measurement by long-read sequencing measures intact telomeres at high-resolutionATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION

[0130] Recently, it has been demonstrated that long-read sequencing technologies such as PacBio HiFi and Oxford Nanopore (ONT) sequencing can be used to sequence and measure telomeres at unprecedented resolution (12,13). We developed a sequencing preparation and bioinformatic pipeline capable of reproducibly measuring telomeres from whole-genome or telomere-enriched long reads (Fig.1A). Telomere-containing reads are identified by identifying telomeric repeats aligned to the chromosomal termini of the recently completed telomere-to- telomere human genome (14). Telomeres are then measured from the basepair capping the terminal telomeric repeat to the beginning of the subtelomeric sequence anchoring the telomeric region to its reference chromosome. The ability to measure the distribution of individual telomere lengths from whole-genome long-read sequencing data enables telomere length analysis to be generically accessible without any additional biochemical intervention prior to sequencing library preparation, but the retrieval of telomeric reads from whole genome sequencing data is highly inefficient due to the paucity of telomere content relative to the rest of the human genome. Capturing the telomeric end with an oligo designed to complement both the telomeric 3’ overhang on one end and the ONT sequencing adapter in combination with restriction digestion of genomic DNA, we can biochemically enrich for telomeric reads by several thousand-fold without significantly impacting the measurement of the telomere length distribution (Fig.1B to C).

[0131] To demonstrate digital telomere measurement by long-read sequencing can accurately recapitulate known telomere phenotypes, we sequenced several genetically modified human embryonic stem cell (hESC) lines. First, we sequenced a CDKN2A- / -TERT- / -, AAVSI:hTERTfloxhESC line passaged for 66, 78, 98, and 105 days post Cre recombinase- mediated telomerase inactivation and observed progressive shortening (40 bp per day, on average) over time (Fig.2A to B). Genetic defects in PARN––a critical ribonuclease for the appropriate maturation of the human telomerase RNA component (hTR)––and a gain-of-function mutation (T284R) in TIN2––a shelterin component and negative regulator of telomere length–– are two known genetic etiologies of dyskeratosis congenita (DC), a disease diagnosed by pathologically short mean telomere length in peripheral blood leukocytes (PBLs) (15-18). To determine if digital telomere measurement similarly reflects this phenotype, we measured the telomere length distribution of PARN knock-out (Fig.1I), TIN2 T284R heterozygous or homozygous mutants (Fig.2C), and their corresponding wild-type parental hESCs and foundATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION digital telomere measurement can confidently discriminate between healthy and pathologically short telomere length distributions. The relative shortening of the mean telomere length in genetically edited versus wild-type hESCs is also in broad agreement with analog measurements by Southern blot in these same cells (TRF)(Fig.1J)(18). Finally, to verify that our method captures intact, full-length telomeres we set out to use digital telomere measurement to observe de novo telomere addition by forcing a cell line with stable telomeres to overexpress the catalytic core of telomerase (19). To this end, we transiently transfected HEK293T cells with an hTR encoding a variant telomeric template sequence (TSQ1) or wild-type hTR in addition to telomerase or GFP alone, harvested genomic DNA after three days, and performed telomere capture sequencing using capture oligos designed against either the TSQ1 variant sequence (5’- TTGCGG-3’) or the canonical human telomere sequence (5’-TTAGGG-3’). As expected, attempting telomere capture with variant-targeting oligos on genomic DNA harvested from cells not expressing the TSQ1 variant sequence did not produce a successful sequencing library (Fig. S1). Transient transfection with either hTR or TSQ1 and telomerase substantially increased in vitro telomerase activity and resulted in a 1000 bp increase in the mean telomere length (Fig.2, E to H). Notably, chromosomes with shorter telomeres in the control group (GFP) experienced a greater magnitude of elongation relative to chromosomes with longer telomeres (Fig.2H). The detection of de novo telomere elongation by both wild-type and variant capture confirms that telomere length distributions measured by long-read sequencing are representative of the underlying intact telomere distribution. High-resolution telomere measurement distinguishes human aging and disease

[0132] Mean telomere shortening with age has been observed by all existing methods of telomere measurement, however these methods only produce coarse estimates of the population mean (TRF) or relative measures of total telomeric content (flow-FISH, qPCR) (20-22). Moreover, given the resolution of existing methods and the innate variability of telomere length between individuals of similar age, it remains unclear if telomere length can serve as a predictive biomarker of aging. We sequenced DNA derived from PBLs of fourteen healthy human donors aged 18 to 77 years and found significant correlations between the mean, median, first quartile, and third quartile telomere lengths and donor age (Fig.3A, 3D to E). We observe that the mean and median telomere lengths in peripheral leukocytes decrease by approximately two-dozenATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION basepairs per year, in close agreement with an earlier estimation made from over 1100 TRFs of human PBL DNA (21). Strikingly, the third quartile telomere length shortens nearly twice as fast as the first quartile telomere length (Fig.3E), suggesting that longer telomeres are lost more rapidly than shorter telomeres with age, echoing observations made in TRF measurements of BJ fibroblasts with limiting telomerase activity in serial passage (23). As in BJ fibroblasts, this observation could be explained by insufficient telomerase in the hematopoietic stem cell pool to indefinitely sustain telomere length, or negative selection of cells with increasing fractions of very short telomeres. Quantification of the fraction of telomeres of various sizes in each aging cohort similarly shows that the fraction of the distribution comprised of shorter telomeres increases with age as the longer telomere fraction shrinks with the notable exception of the two shortest fractions which appear to be relatively stable with age in PBLs (Fig.3H). Our observations quantitatively reinforce a recent observation through a PCR-based assay for the amplification of very short telomeres that telomeres significantly shorter than the mean telomere length accumulate and increase in proportion with age (24). If telomerase function in the hematopoietic stem cell compartment is particularly important for preventing the accumulation of the shortest telomere fractions, the differential age-associated telomere attrition rate in telomeres of varying length should be attenuated or disappear. To answer this question, we sequenced 7 the peripheral blood leukocytes of 6 individuals aged 6 to 50 either diagnosed with DC or identified as healthy carriers of a DC-associated RTEL1 mutant (25) as well as genomic DNA from two paired bone marrow (TB32-M) and peripheral blood (TB32-B) samples from one individual currently under evaluation for a possible telomere biology disorder at Stanford Hospital (Table S1). We confirmed telomeres from these individuals were significantly shorter relative to their age group (Fig.3B to C, 3F) and observed a significant correlation (R2=0.84) with measurements made by the clinical gold-standard method for telomere measurement in peripheral blood, flow-FISH (Fig.1H). An analysis of the telomere length fractions in our cohort of individuals with genetic defects in telomere maintenance revealed significant variation between individuals but altogether much higher proportions of the shortest fractions of telomeres compared to healthy donors (Fig.3H, 3I). Strikingly, TBD patient telomere length distributions were enriched for the two shortest fractions of telomeres (0-2000 bp) relative to healthy donors, suggesting that leukocytes thought to be near the replicative limit can persist in the peripheral blood and that shortest telomere fractions in the distribution are particularly sensitive to theATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION underlying state of the cell’s telomere maintenance apparatus. In TERT-null hESCs, the daily rate of telomere shortening was at least double the annual rate of shortening for the corresponding distribution statistic in PBLs but the trend of slower shortening in shorter telomeres was somewhat preserved (Fig.2B), although it is notable that these TERT null hESCs are only weeks away from their empirically observed replicative limit at 110-120 days post TERT inactivation (18). In RTEL1 patients and carriers, we no longer observe slower shortening of the first quartile telomeres relative to the mean or third quartile; in fact, the first quartile telomere appears to shorten more rapidly with age, on average (Fig.3B). These data suggest that information about the integrity of the underlying telomere length machinery in a cell population can be inferred from the telomere length distribution and its change over time. Furthermore, this data supports a model of age-associated telomere attrition where limiting telomerase and not negative selection against cells with very short telomeres is the primary driver of the growth of the short telomere fractions observed in aging PBLs. We additionally performed TRF with DNA from twelve of the fourteen healthy donors and the two samples obtained from the Stanford patient (Fig. S2). TRF was found to systematically overestimate mean telomere length by one to three thousand basepairs in all samples for which both digital and analog telomere measurement were performed, most likely due to undigested subtelomeric sequence biasing the results of the Southern blot (Fig.1F, 1G, S2, S3). Furthermore, while it was not possible to distinguish the telomere lengths from TB32’s blood and marrow samples by TRF, digital telomere measurement revealed the bone marrow telomere length distribution contained longer telomeres than in the same individual’s PBLs (Fig.3C, S2).

[0133] Telomere biology disorders are diagnosed by measuring PBL telomere length by flow- FISH, comparing the result to previously measured population statistics for telomere length for the patient’s age, and subsequent detection of a genetic defect by targeted exon sequencing. Symptomatic patients often have observed mean telomere lengths at or below the first percentile for their age, and, since telomere biology disorders exhibit genetic anticipation and the severity of their clinical presentation is inversely proportional to telomere length, related but asymptomatic individuals carrying the same genetic defect may still have telomere lengths within the lower quintile of the population for their age (17,25). Digital telomere measurement could also be used, therefore, as a tool in the diagnosis of telomere biology disorders. As a proof of concept, we leveraged machine learning to create a binary classification model capable ofATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION distinguishing symptomatic, or both symptomatic and healthy carriers of defects in telomere maintenance using our healthy donor and RTEL1 mutant cohorts as training data. Even in our limited sample, this model was able to predict both symptomatic and healthy mutant carrier status from telomere length distributions and age alone with upwards of 90% accuracy (Fig.3J).

[0134] Finally, to validate our observations about the relationship between age, the telomere length distribution, and telomerase activity, we analyzed previously published, high-coverage (30X, on average) whole genome long-read sequencing data from patient-matched colorectal carcinoma and surrounding benign epithelia obtained from twenty individuals predominantly aged between 50 and 70 years (26). In this independent dataset, we also observed trends between the four summary statistics of the telomere length distribution and age in benign colonic epithelium, including more rapid shortening of the third quartile relative to the first, but found no correlation between age and any summary statistic of the tumor telomere length distributions, as expected for cells immortalized by telomerase (Fig.4A to C). We also find that, in this cohort, tumor telomeres were significantly shorter than those measured in benign epithelia in 75% of samples, in agreement with previous studies utilizing TRF or TelSeq, a short-read sequencing method for estimating relative telomere content (27,28). Therefore, the telomerase activity present in both hematopoietic and colon epithelial stem cells is insufficient to indefinitely maintain telomere length with the consequence of monotonic shortening, on average, and more rapid shortening of longer relative to shorter telomeres with age in their cellular progeny. Discussion

[0135] For decades, human telomere measurement has only been possible with methods which provided either relative quantifications of telomere content or an estimation of the mean telomere length in a population. Long-read sequencing is revolutionizing our ability to explore the genomic landscape of the chromosomal terminus and we have developed a method which produces high-resolution, high-throughput measurements of individual intact telomeres using nanopore sequencing. In this work, our method recapitulates the dramatic telomere shortening observed in three DC genotypes both in culture and in vivo, de novo telomere addition by overexpression of the catalytic core in a cell line with stable telomeres, progressive telomere attrition in human aging and in the presence and absence of functional telomerase. Telomere measurements made by long-read sequencing are comparatively much richer than TRF or flow-ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION FISH while requiring less input DNA than either existing technique. TRF systematically overestimates mean telomere length by up to several thousand basepairs likely due to the extent of genomic digestion, the restriction enzymes selected for then task, and preparation of the DNA for Southern blot. Flow-FISH is comparatively better at estimating the mean telomere length than TRF, but still overestimates by 1500 bp on average, and flow-FISH’s utility is restricted to mean telomere estimation of PBLs. Additionally, the ability to anchor individual telomeres to specific chromosomes enabled us to demonstrate more significant elongation of chromosomes with shorter first quartile telomere lengths prior to overexpression of the telomerase catalytic core, providing novel evidence for the preferential action of telomerase at the shortest telomeres in humans (23,29,30).

[0136] Many studies, including this one, have demonstrated that the mean telomere length shortens with age. We make the additional novel observation that the structure of the telomere length distribution –– interquartile telomere lengths, median, mean, fraction of telomeres within different length ranges –– contains information about the underlying telomere maintenance mechanism of the cell. We also find that the rate of change in telomeres of varying length can vary substantially in some tissues, for example between the first and third quartiles of the length distribution. The function of telomerase is particularly critical for the maintenance of the first quartile telomere length, and inactivating telomerase in vitro or impairing its function in vivo both have a marked impact on the maintenance of the lower end of the telomere length distribution. Although we only study two compartments (peripheral blood and colonic epithelia) in aging cohorts, there appears to be some variation even in healthy aging-associated telomere attrition between the two compartments. This difference could be explained by the dosage of telomerase, the proliferation rate, or perhaps even the dosage of shelterin components within the stem cell compartments of each tissue, but more comprehensive investigation of telomere length evolution in healthy aging is required. Our study is limited by a relatively modest number of human samples, but as the repertoire of long-read genomic data grows, it is possible analysis of telomere length distributions from diverse populations will enable telomere length to become a more robust and perhaps even predictive biomarker of aging in humans. Generating ensembles of high-resolution measurements instead of means from a single noisy signal permitted us to train a machine learning model capable of distinguishing healthy and diseased telomere distributions. Long-read sequencing technologies are already being deployed in the clinical setting for theATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION rapid diagnosis of genetic disorders and as a tool in clinical research (31), and this work demonstrates that digital telomere measurement holds promise as a diagnostic tool for the evaluation of telomere biology disorders.

[0137] Surprisingly, in every sequencing experiment we have performed in either humans or cultured cell lines, including embryonic stem cells, we have measured telomeres as short as dozens of basepairs. Our work demonstrates that the shortest telomere fractions are sensitive to functional perturbation, suggesting that even if some extremely short telomere measurements are somehow artefactual, cells can tolerate some quantity of very short telomeres without triggering replicative senescence or experiencing chromosomal instability, likely due to the critical protective role of shelterin at telomeres. Future work leveraging digital telomere measurement could elucidate the critical mass of very short telomeres or the thresholds at which either shelterin must be impaired or telomeres sufficiently shortened prior to triggering replicative senescence or observing telomere fusions. Access to the complete telomere length distribution of a cell also opens the possibility of more effectively studying the effects of perturbing the cell’s telomeric rheostat (32) on telomere length. For example, in this work we find that in a previously studied cohort of patient-matched colorectal carcinoma and benign colonic epithelia, tumor cells harbored shorter telomeres in approximately 75% of patients. Since telomere length distributions in tumors are known to be stable over time, it follows that the setpoint of a tumor’s telomeric rheostat is somehow related to its unique cellular biology but until now it has not been possible to assess precisely how a certain rate of division, telomerase activity, and concentration of key telomere maintenance machinery like the RNA template, telomerase holoenzyme, or shelterin component proteins individually or quantitatively contribute to stable telomere length distributions. Understanding this dynamic biochemical equilibrium could reveal novel regulators of telomere length as well as new approaches towards therapeutically targeting the telomere maintenance machinery in cancer. Methods High-molecular weight DNA isolation and quantification

[0138] High-molecular weight (HMW) DNA was extracted using the NEB Monarch HMW DNA Extraction kit for Cells and Blood (Catalog #T3050L) according to the kit manufacturer’s instructions. Briefly, for cells maintained in tissue culture, cells were trypsinized until detached and then centrifuged at 1000 g for three minutes before adding prep and lysis solution accordingATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION to the manufacturer’s instructions. Cells were incubated for 10 minutes at 1800 RPM in a thermomixer and DNA from the lysed cells was precipitated onto glass beads, washed twice with 80% ethanol, and finally eluted in Monarch Elution Buffer II according to manufacturer’s instructions. DNA was quantified using a Qubit 4 fluorometer and the Qubit BR dsDNA quantification reagents (Catalog #Q32850). For DNA extraction from peripheral blood, red blood cell lysis was first performed prior to DNA extraction according to the manufacturer’s instructions. DNA quality was assessed by Nanodrop and the average molecular weight was verified to be 60 kb or larger using an Agilent Tapestation (Catalog #5067-5365, 5067-5365). Telomere Restriction Fragment Southern Blot

[0139] Approximately 4 µg of genomic DNA was prepared in a 50 uL total volume restriction digest solution (1X Fast Digest Buffer, 3 µL HinfI, and 3 µL RsaI) and allowed to digest at 37°C overnight. In the morning, 1 µL each of HinfI and RsaI was added to each digestion reaction and allowed to incubate at 37°C for a further three hours. A 1% TAE agarose gel was prepared and 3 µL per sample underwent gel electrophoresis (125V, 70 minutes) to confirm restriction digest completed successfully (Figure SX). A 0.8% TBE agarose gel was then prepared in a 20x27 cm casting tray after adding 15 µL ethidium bromide to the agarose solution. The entire volume of each restriction digest reaction was then loaded into each well with 1X NEB nucleic acid loading dye in addition to NEB 1 kb reference ladder and gel electrophoresis was performed (85V for 16 hours). In the morning, the gel was dried using a BioRad gel dryer (1 hour under vacuum then 1 hour under vacuum and 50°C). A UV-translucent ruler was then overlayed on the dried gel before imaging with UV transillumination to establish reference distances for the ladder markers from the well positions. The dried gel was then incubated in denaturing buffer (1.5M NaCl, 0.5M NaOH) for one hour with gentle shaking. The denatured gel was washed with deionized water twice before a second one-hour incubation in neutralizing buffer (1.5M NaCl, 1M Tris-HCl, pH 7.4) with gentle shaking. The neutralizing buffer was decanted and the neutralized gel was washed twice with deionized water. The gel was then rolled vertically into a glass hybridization tube (Thermo-Fischer Scientific) and incubated with pre-warmed hybridization buffer (Invitrogen #AM8670) at 42°C for 30 minutes with rotation.0.5 µM of γ-32P labeled telomere probe was then added to the hybridization buffer tube and incubated at 42°C overnight with rotation. The gel was washed once with 2X SSC buffer and twice more with 1X SSC buffer (0.15M NaCl, 15 mM sodium citrate) before exposing onto a phosphor screen inside a leadATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION exposure cassette for 24 hours. Following exposure, the phosphor screen was imaged on a Typhoon scanner.

[0140] Both the southern blot images and the ethidium bromide reference ladder were loaded onto ImageJ and aligned. The signal intensities at each position coordinate starting from the bottom of the well in the southern blot image were obtained with the ImageJ line and Measure tools after drawing a line from the bottom of the well to the bottom of the gel through each sample lane. Telomerase repeated amplification protocol (TRAP)

[0141] To measure telomerase activity, a two-step TRAP procedure was performed as previously described (34). Briefly, cell protein extracts (at 1X or 3X dilution with lysis buffer per transient transfection condition) were incubated with telomeric primers for 30 min at 30°C in a PCR machine, followed by 5 min of inactivation at 72°C (cold extension).1 μl of the cold extension reaction was PCR amplified (24 cycle of 30 s at 94°C, followed by 30 s at 59°C) in the presence of32P end-labeled telomeric primers. The radiolabeled PCR reactions were resolved by 9% polyacrylamide gel electrophoresis at room temperature, and the gel was exposed to a phosphor- imager and the phosphor screen was scanned by a Typhoon scanner. Whole-genome sequencing nanopore library preparation

[0142] Nanopore library preparation for whole-genome sequencing was carried out according to Oxford Nanopore Technologies (ONT) protocol for native genomic DNA sequencing (LSK-110) with some modifications. Briefly, approximately 1 µg of DNA per sample was end-prepped using the FFPE DNA repair and Ultra II End-Prep enzyme mixes from the NEBNext companion module for ONT ligation sequencing (Catalog #E7180L). The end-prep reaction was incubated in a thermocycler at 20°C for 30 minutes and then 65°C for 30 minutes. End-prepped DNA was extracted from the reaction using Promega ProNex size selection beads (Catalog #NG2001) at a bead-to-reaction solution ratio of 1.6 and incubated on a Hula mixer at room temperature for five minutes prior to being pelleted on a magnet and then washed twice with 80% ethanol and then allowed to dry on the magnet for 3 minutes. DNA was eluted from the beads using ONT elution buffer at 37°C for 15 minutes. For simplex experiments, sequencing adapters (ONT AMXF) were then ligated to the end-prepped DNA for one hour at room temperature using NEB Quick T4 DNA ligase (Catalog #E7180L). For multiplex experiments, ONT barcodes were ligated using NEB Blunt / TA ligase for one hour at room temperature and barcoded DNA was extracted,ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION pooled up to 1 µg of total DNA, and then ligated to sequencing adapters as described previously. Adapter-ligated DNA was extracted from the ligation reaction using Promega ProNex size selection beads at a bead-to-reaction solution ratio of 1.1 and incubated and eluted as described previously.20-50 fmols of Adapter-ligated DNA was sequenced on R9.4.1 PromethION flow cells on a P2Solo for 24-72 hours. It is advisable to quantify DNA after every bead purification step using a Qubit fluorometer and the Qubit dsDNA BR DNA quantification assay.

[0143] Genetically modified hESCs were sequenced on R10.4 PromethION flow cells on a P2Solo and therefore the sequencing adapter used was changed to pair with the updated flow cell chemistry, per ONT’s standard sequencing protocol (adapter NA instead of AMII for telomere capture). Telomere capture sequencing nanopore library preparation

[0144] Barcoded telomere capture oligos were annealed to sequencing tether (seqTether) by mixing equimolar amounts of both oligos in low TE buffer, heating to 95°C for 2 minutes and then being allowed to cool at room temperature for an hour. Approximately 3 ug of HMW genomic DNA was ligated to barcoded, freshly duplexed oligos in a 100 µL ligation reaction (10 µL 10X rCutSmart buffer, 5 µL 5 µM duplex capture oligos, 2 µL 2000U / µL T4 DNA ligase, 1 µL 10 mM ATP, 3 µg gDNA, nuclease-free H2O up to 100 µL) overnight at 37°C. The following day the ligation reaction was heat inactivated at 65°C for 10 minutes. Potential gaps between the capture oligo and the double-strand / single-strand junction were then filled in using the same reaction tube by adding 2 µL (4U) Sulfolubus DNA Polymerase IV (NEB #M0327S), 12 µL 10X ThermoPol Buffer, 1 µL 20 mM dNTPs, 1 µL 10 mM ATP, and 4 µL of nuclease-free H2O followed by incubation at 56°C for 2 minutes and then 72°C for 15 minutes with shaking (500 RPM). Promega ProNex size selection beads were then added to the ligation reaction at a bead- to-solution ratio of 1.6 and the solution was equilibrated on a rotating mixer for 5 minutes at room temperature. The bead solution was then pelleted on a magnet, washed twice with 80% ethanol, allowed to dry on the magnet for 3 minutes, and then eluted in 60 µL of ONT elution buffer for 15 minutes at 37°C. The complete volume of eluted capture-oligo ligated DNA was then ligated onto the ONT sequencing adapter (AMII for R9, NA for R10 libraries) per ONT’s barcode ligation sequencing protocol (5 µL sequencing adapter mix, 20 µL 5X Quick T4 DNA Ligase Buffer, 10 µL Quick T4 DNA Ligase, 5 µL nuclease-free H2O) at room temperature forATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION one hour. The rest of the library preparation and sequencing protocol is performed as for whole- genome sequencing above. Data Analysis

[0145] Sequencing data was basecalled using Guppy 6.3.0 (ONT) high-accuracy basecalling and aligned to a human telomere-to-telomere reference genome (T2T-CHM13 + Stong 2014 subtelomere assemblies (32)) with minimap2. Aligned BAM files were then sorted and indexed with samtools (v.1.16.0) and telomere measurements were extracted from alignments using a custom script (TBD). The custom script is based on previously published work for telomere measurement from PacBio HiFi reads (12) which was adapted for telomere measurement from Oxford nanopore long reads. In brief, reads mapping to the terminal arms of each chromosome are searched for telomeric repeats by using regular expressions targeted at the sequence patterns corresponding to both the canonical human telomeric repeat (TTAGGG / CCCTAA) and the commonly miscalled motifs previously identified in the literature (35). A check is then performed to ensure that identified telomeric sequences are terminal and telomeres are measured from the read terminus until the sub / telomeric boundary. Conceptually, the sub / telomeric boundary is encountered by moving from the telomere terminus inward until telomeric repeats give way to non-telomeric sequence. We formally define the sub / telomeric boundary as the genomic position corresponding to the starting position of the final two telomeric repeats before encountering non-telomeric motifs. The telomere length is then the length, in basepairs, spanned by consecutive telomeric sequence motifs at the terminus of chromosome arms. Figures were made and statistical analyses performed with R (v4.1.0). Bootstrapping and TRF signal peak analysis code are similarly available on github.

[0146] For samples sequenced on R10.4 PromethION flow cells, raw pod5 files were basecalled using a custom bonito telomere calling model (HG002.k1) provided by Oxford Nanopore Technologies. As the R10 nanopore chemistry differs significantly from R9, the raw signal from the flow cell is substantially changed and telomere identification from basecalled reads with our custom scripts is not possible with data produced from the default guppy R10 basecaller; however, ONT’s custom telomere basecalling model once again makes it possible for our algorithm to accurately identify telomeric reads from R10 data. Training ONT basecalling models to basecall telomeres more accurately has been previously demonstrated in the literature (35). Otherwise, library preparation and data analysis were performed as described above.ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Binary Classification Model

[0147] To develop a predictor of the disease or carrier status of patients based on telomere length and other minimal sequencing data, the Multi-Layer Perceptron Classifier (MLPClassifier) from Scikit-learn 1.2.2 was employed. The MLPClassifier is a feedforward artificial neural network model that maps input data sets to a collection of acceptable outputs. An MLP is made up of numerous layers, each of which is completely connected to the one before it. Except for the input layer, the remaining neurons have nonlinear activation functions. The MLPClassifier used for this study contained three hidden layers of 8 neurons each, the ‘relu’ activation function applied sequentially, the ‘adam’ solver, a maximum of 500 iterations, and early stopping engaged. Two types of classification were pursued: diseased vs. healthy and carrier (both diseased and carrier patients) vs. healthy patients. The ‘telomere length’ and ‘age’ data fields from the telomere measurement analysis pipeline were provided as input to the classifier and the ‘phenotype’ field was utilized as the disease / carrier label. To train both models, a 70:30 training:test data split was used, and randomized validation sets were used during training for validation score calculations at each iteration. In result, the disease vs. healthy classifier achieved 96% accuracy while the carrier vs. healthy classifier achieved 85% accuracy. Tissue Culture Transient Transfection of HEK293T Cells

[0148] HEK293T cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin / streptomycin. Transient transfection was carried using a 3:1 polyethylenimine to plasmid ratio and 3 µg of DNA, equal parts pCDNA-2xStrep-3xFLAG-hTERT and either pBS- U1-hTR or pBS-U1-TSQ1 containing plasmids. Following the addition of PEI and transfection plasmids, cells were maintained in culture for three days. Cells were then trypsinized and collected and approximately one-million cells were set aside for downstream interphase DNA FISH. High molecular weight DNA was collected from the remaining cells for each condition according to the NEB Monarch High Molecular Weight DNA Extraction Kit for Cells and Blood (NEB #T3050L) protocol. Extracted DNA was quantified using the Qubit BR dsDNA assay (Invitrogen #Q32853) and a Qubit 4 fluorometer. TABLE 1 NCI RTEL1 MutantsATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION ed 5Stanford Patient Healthy Donors Sample ID Age Sample ID Age Sample ID Age TB 2 1 4 77ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Table 2A: Characteristics of healthy peripheral blood donors, RTEL1 mutants, and patient at Stanford Hospital CRC Cohort from Xu et al, PLOS Genetics 2012 N=benign / normal; T=tumor Sample ID Age Sample ID AgeATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Table 2B. Sample ID and age at biopsy of patient-matched benign colonic epithelia and tumor biopsies. 5' --> 3'ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION Example 2: Whole-genome sequencing of non-cancerous cells in cancer patients has been / is used for the identification of single-nucleotide polymorphisms (SNPs) in individuals or families suspected of having a genetically inherited predisposition for cancer as mutations in both the coding and non- coding genome can lead to elevated cancer risk. Leukocyte telomere length has independently been demonstrated to play a causal role in the genetic predisposition for cancer in some families with mutations leading to aberrantly long telomeres (De Boyle et al. and Armanios NEJM 2023, Schmutz et al. and deLange eLife 2020). As our method is capable of simultaneously generating high-coverage whole-genome sequencing and telomere length measurements in the same experiment, we can integrate these two distinct data to ascertain the compound risk for cancer from these two sources. This is particularly novel for cancer risk SNPs which may occur in genes associated with telomere regulation, such as POT1 and TIN2 in the paper cited above, but also the TERT loci, which contains dozens of SNPs associated with increased cancer risk. Unlike previous methods which can only identify SNPs (and therefore only speculate if they impact the telomere’s tumor suppressive mechanism) or determine leukocyte telomere length (and require additional testing in order to determine the presence of mutations which could impact telomere maintenance), our method is able to directly relate telomere length measurements to the presence or absence of SNPs relevant to both telomere maintenance and cancer risk.

Claims

ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION CLAIMS 1. A method of determining telomere length comprising: (a) detecting primer alignment within a chromosome in a sample; (b) determining telomere length of the chromosome in the sample.

2. The method of claim 1, wherein the step of detecting the primer alignment comprises utilizing T2T-CHM13 assembly and determining a score corresponding to the percent identity of the chromosome in the sample.

3. The method of claim 1 or 2, wherein the step of determining telomere length comprises calculating an average telomere length after repeating steps (a) and (b) on the sample and comparing the average telomere length to the length of a control sample or control dataset.

4. The method of any of claims 1 through 3, further comprising a step of (c) performing a sequencing analysis before or after step (b).

5. The method of any of claims 1 through 4, wherein the step of determining telomere length comprises extending a single stranded portion of the telomere, exposing the telomere to a probe and quantifying the amount of the probe based upon the intensity of signal on an image of the sample.

6. The method of any of claims 1 through 5, wherein the step of determining telomere length is performed by nanopore sequencing.

7. The method of any of claims 1 through 6, wherein the method is free of performing polymerase chain reaction and long-read sequencing.ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION 8. The method of claim 4, wherein the step of performing a sequencing analysis is a computer-implemented step in which a computer program product executes the instruction for: (a) compiling nucleic acid information from the sample; (b) aligning sequences against a control sequence; (c) calculating a score based upon the percent identity of the nucleic acid information as compared to a control; and, optionally, (d) displaying the score or percent identity on a display; or (a) compiling nucleic acid information from the sample; (b) aligning sequences against a control sequence to identify a telomer sequence within the nucleic acid information; (c) estimating a location of a telomeric boundary to determine the beginning of a non- telomeric sequence within the nucleic acid information; (d) determining the length of the telomere after measuring the number of nucleotides between the end of 5’ or 3’ end of the telomere sequence and the telomeric boundary; ad optionally calculating and / or displaying a score based upon the percent identity of the nucleic acid information relative to a control sequence.

9. The method of any of claims 1 through 8 further comprising a step of obtaining a sample from the subject.

10. A method of determining telomere length distribution from a plurality of samples comprising: (a) detecting primer alignment within a chromosome in a sample; (b) determining telomere length of the chromosome in the sample.

11. The method of claim 10, wherein the step of detecting the primer alignment comprises utilizing T2T-CHM13 assembly and determining a score corresponding to the percent identity of the chromosome in the sample.ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION 12. The method of claim 10 or 11, wherein the step of determining telomere length comprises calculating an average telomere length after repeating steps (a) and (b) on the sample and comparing the average telomere length to the length of a control sample or control dataset.

13. The method of any of claims 10 through 12, further comprising a step of (c) performing a sequencing analysis before or after step (b).

14. The method of any of claims 10 through 13, wherein the step of determining telomere length comprises extending a single stranded portion of the telomere, exposing the telomere to a probe and quantifying the amount of the probe based upon the intensity of signal on an image of the sample.

15. The method of any of claims 10 through 14, wherein the step of determining telomere length is performed by nanopore sequencing.

16. The method of any of claims 10 through 15, wherein the method is free of performing polymerase chain reaction and long-read sequencing.

17. The method of claim 13, wherein the step of performing a sequencing analysis is a computer-implemented step in which a computer program product executes the instruction for: (a) compiling nucleic acid information from the sample; (b) aligning sequences against a control sequence; (c) calculating a score based upon the percent identity of the nucleic acid information as compared to a control; and, optionally, (d) displaying the score or percent identity on a display.

18. A computer-implemented method of determining telomere length or telomere length distribution among one or a plurality of samples, on a device that accesses a computer memory, the method comprising: (a) detecting a presence of a telomere at the end of genetic material from the sample;ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION (b) detecting a presence of a telomere boundary from the sample distal from the telomere end; and (c) measuring the length of the telomere from the end of the genetic material to the telomere boundary.

19. The method of claim 18 further comprising a step of (d) determining a score based upon the length of the telomere and compared to the distribution of telomere lengths from a control population of cells.

20. The method of claim 19 further comprising a step (e) comparing the length of the telomere from the sample to a population distribution of telomere lengths samples of the same or substantially the same age.

21. The method of any of claims 18 through 20 further comprising, in a system comprising a controller in operable communication to a microscope, camera, display and computer memory: capturing a digital image of the sample, displaying the digital image on the display prior to performing steps (a) through (c); and performing steps (a) through (c) on the digital image; wherein the digital image is captured through the microscope at a magnification sufficient for a user to visualize the telomere on the display.

22. The method of any of claims 18 through 21 further comprising collecting additional data on the sample prior to, subsequent to or contemporaneous with performing step (c).

23. The method of claim 22, further comprising the step of identifying one or a plurality of mutations in the chromosomal DNA of the sample by comparing the sequence of a telomere and / or exon within the chromosomal DNA to control sequences known to be free of one or a plurality of mutations.

24. The method of any of claims 18 through 23 further comprising the step of performing a sequencing reaction of the sample prior to performing steps (a) through (c).ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION 25. The method of any of claims 18 through 24 wherein the telomere length is at least about 3,000 basepairs, 4,000 basepairs, 5,000 basepairs, or 6,000 basepairs of DNA.

26. The method of any of claims 18 through 25 wherein the telomere length is from about 3,500 to about 6,000 basepairs of DNA.

27. A computer program product encoded on a computer-readable storage medium comprising instructions for: (a) registering at least a portion of a chromosome sequence of a sample comprising a telomere; (b) aligning the telomere of the sample to identify the end of the chromosome; (c) identifying a telomere boundary on the chromosome; (d) measuring a length of the telomere from about the end of the chromosome to the boundary of the telomere.

28. The computer program product of claim 27 further comprising instructions for sequencing at least a portion of the chromosome free of the telomere.

29. The computer program product of either of claims 27 and 28, further comprising instructions for collecting data associated with the subject comprising one or a combination of: the sequence of an exon within the sample, the sequence of a non-coding region of a chromosome, the sequence of a mutation, the identity of one or a plurality of chromosome copy number alterations, the quantity of DNA methylation on the chromosome, and the presence or quantity of a barcode.

30. The computer program product of any of claims 27 through 29 further comprising instructions for: calculating a score associated with the telomere length as compared to a known telomere length of a control sample.ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION 31. The computer program product of any of claims 27 through 30, wherein the sequencing at least a portion of a chromosome in the sample comprises producing a FASTQ file comprising the nucleotide sequence of at least the portion of the chromosome; 32. The computer program product of any of claims 27 through 31, wherein the imaging is produced by a camera in operable communication with a microscope.

33. The computer program product of any of claims 27 through 32, wherein the sequencing is performed by nanopore sequencing.

34. A system comprising the computer program product of claim 27, a controller and a computer memory.

35. The system of claim 34 further comprising a display in operable communication to a microscope, camera, the controller and the computer memory.

36. The system of claims 34 or 35, further comprising a vessel addressable by the microscope and comprising a volume of from about 10 microliters to about 1000 microliters.

37. The system of claim 36, wherein the vessel is position at or proximate to a nanoporus membrane and reagents for nanopore sequencing.

38. A method of diagnosing a subject with a hypeproliferative disorder comprising: determining the length of a telomere in a sample from the subject.

39. The method of claim 38 further comprising the step of diagnosing the subject with a hyperoliferative disorder if the telomere comprises less than about 2,500 base pairs of DNA.

40. The method of claim 38 or 39, wherein the step of detecting is preceded by a step of acquiring the sample from the subject.ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION 41. The method of any of claims 38 through 40 further comprising exposing a sample from a subject to at least one nucleic acid probe or functional fragment thereof.

42. The method of claim 41, wherein the probe comprises at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 1 through 96, or a functional fragment or variant thereof comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 1 through 96.

43. The method of any of claims 38 through 42, wherein the step of determining the length of the telomere comprises: (a) sequencing at least a portion of a chromosome in the sample comprising the telomere; (b) aligning the telomere of the sample to identify the end of the chromosome; (c) identifying a telomere boundary on the chromosome; (d) measuring the length of the telomere from about the end of the chromosome to the boundary of the telomere.

44. The method of claim 43, wherein the step of determining telomere length further comprises: preparing an image of the telomere with a camera in operable communication with a microscope position at or proximate to the sample.

45. The method of any of claims 43 through 44, wherein the step of sequencing at least a portion of the chromosome comprises performing nanopore sequencing before or after steps (b), (c) and (d).

46. The method of any of claims 37 through 45, wherein the sample is a single cell.

47. The method of any of claims 37 through 46 further comprising collecting data from the sample associated with the subject comprising one or a combination of: the sequence of an exon within the sample, the sequence of a non-coding region of a chromosome, the sequence of a mutation, the identity of one or a plurality of chromosome copyATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION number alterations, the quantity of DNA methylation on the chromosome, and the presence or quantity of a barcode annealed to the sample; and diagnosing the subject with a hyperproliferative disorder if the data from the sample comprises a mutation relative to a control sample.

48. The method of any of claims 37 through 48, wherein the hyperproliferative disorder is cancer.

49. The method of any of claims 37 through 48 further comprising a step of calculating a score based upon the telomere length and the age of the subject.

50. A method of determining the age of a sample or the health of a subject comprising: determining the length of a telomere in a sample from the subject.

51. The method of claim 50 further comprising the step of diagnosing the subject with a hyperoliferative disorder if the telomere comprises less than about 2,500 base pairs of DNA.

52. The method of claim 50 or 51, wherein the step of detecting is preceded by a step of acquiring the sample from the subject.

53. The method of any of claims 50 through 52 further comprising exposing a sample from a subject to at least one nucleic acid probe or functional fragment thereof.

54. The method of claim 53, wherein the probe comprises at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 1 through 768, or a functional fragment or variant thereof comprising at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 1 through 768.

55. The method of any of claims 50 through 54, wherein the step of determining the length of the telomere comprises:ATTORNEY DOCKET NO: STFD-006-PCT PCT APPLICATION (a) sequencing at least a portion of a chromosome in the sample comprising the telomere; (b) aligning the telomere of the sample to identify the end of the chromosome; (c) identifying a telomere boundary on the chromosome; (d) measuring the length of the telomere from about the end of the chromosome to the boundary of the telomere.

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