Compositions and methods for simultaneous genetic analysis of multiple libraries - Patents.com

Abstract

The present disclosure provides compositions and methods that combine the benefits of different genetic analysis methods by performing simultaneous genetic analysis on a single pool of different libraries generated for different approaches, such as a combinatorial library including an LPWG library and a target-enriched library.

Description

[Technical Field]

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS This application claims priority to U.S. Provisional Patent Application No. 63 / 311,041, filed February 16, 2022, and U.S. Provisional Patent Application No. 63 / 167,914, filed March 30, 2021, both of which are incorporated by reference herein in their entirety for all purposes.

[0002] The present invention relates to compositions and methods for genetic analysis.

[0003] Sequence Listing This application contains a Sequence Listing that has been submitted electronically in ASCII format and is incorporated herein by reference in its entirety. The ASCII copy, created on March 28, 2022, is named CLFK_007_02WO_SeqList_ST25 and is approximately 21.4 KB in size. [Background technology]

[0004] Next-generation sequencing (NGS) is rapidly gaining popularity in clinical settings for identifying genetic alterations. As the number of genetic abnormalities and predictive biomarkers leading to new drug development increases, NGS technology is increasingly replacing traditional techniques, such as single-gene testing, by simultaneously analyzing a wide range of genomic alterations. Current applications of NGS approaches include targeted gene panels and whole-genome sequencing, with most applications choosing to utilize only one of the two approaches or to pursue both approaches in parallel. The ability to combine libraries specific to different NGS approaches in a single sequencing analysis would integrate the advantages of each approach, thereby improving data quality, cost, and turnaround time. Therefore, compositions and methods for simultaneously analyzing multiple libraries are highly desirable. Summary of the Invention

[0005] In some embodiments of the kits of the present disclosure, the kit includes one or more capture probe modules, each capture probe module including a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample, and the one or more capture probe modules have passed a probe quality control (QC) process. In some embodiments of the kits of the present disclosure, the kit further includes a set of adapters, each adapter including an adapter module. In some embodiments of the kits of the present disclosure, the set of adapters has passed an adapter QC process.

[0006] In some embodiments of the kits of the present disclosure, the kit includes a set of adapters, each adapter including an adapter module, and the set of adapters has passed an adapter QC process. In some embodiments of the kits of the present disclosure, the kit further includes one or more capture probe modules, each capture probe module including a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample.

[0007] In some embodiments of the kits of the present disclosure, the adapter QC process includes a test for adapter ligation, wherein the test for adapter ligation includes (a) ligating a set of adapters to a predetermined amount of end-repaired DNA fragments to generate a library of adapter-tagged DNA fragments (LIBS); and (b) amplifying the LIBS to generate library postamplification (LPA); the set of adapters is considered to have passed the test for adapter ligation if the concentration of LPA is greater than the predetermined concentration.

[0008] In some embodiments of the kits of the present disclosure, the adapter QC process includes a test for adapter distribution that includes: (a) ligating a set of adapters to a predetermined amount of end-repaired DNA fragments to generate a library of adapter-tagged DNA fragments (LIBS); (b) amplifying the LIBS using a primer pair that includes at least one primer that includes an index sequence to generate a library post-index amplification (LPIA); and (c) performing quantitative genetic analysis on the LPIA, wherein the set of adapters is considered to have passed the test for adapter distribution if one or more pass / fail criteria for the quantitative genetic analysis are met.

[0009] In some embodiments of the kits of the present disclosure, the predetermined pass / fail criteria for the adapter QC process include one or more of: (a) barcode crosstalk is present in 0.05% to 5% or less of the reads; (b) unknown adapters are present in 1% to 50% or less of the reads; (c) 10% to 80% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads for all unique adapter sequences; (d) at least 60% to 99.9% of all unique adapter sequences are present; and (e) 5% to 50% or less of the unique adapter sequences have reads that are more than twice the average number of reads for all unique adapter sequences.

[0010] In some embodiments of the kits of the present disclosure, a set of adapters is considered to have passed the adapter QC process if it passes the test for adapter ligation and / or the test for adapter distribution. In some embodiments of the kits of the present disclosure, a set of adapters is considered to have passed the adapter QC process if it passes the test for adapter ligation. In some embodiments of the kits of the present disclosure, a set of adapters is considered to have passed the adapter QC process if it passes the test for adapter distribution. In some embodiments of the kits of the present disclosure, a set of adapters is considered to have passed the adapter QC process if it passes the test for adapter ligation and the test for adapter distribution.

[0011] In some embodiments of the kits of the present disclosure, the probe QC process involves: (a) ligating a set of adapters to a DNA sample containing end-repaired DNA fragments to generate a library of adapter-tagged DNA fragments (LIBS); (b) amplifying the LIBS to generate library postamplification (LPA); (c) dividing or diluting the LPA to generate target capture LPA (TC LPA) and whole genome LPA (WG LPA); (d) amplifying the WG LPA to generate an amplified whole genome library (WGLA); and (e) ligating one or more capture probe modules to be tested to the TC LPA. (f) isolating the adapter-tagged DNA fragment-capture probe module complexes to form isolated adapter-tagged DNA fragment-capture probe module complexes; (g) enzymatically treating the isolated adapter-tagged DNA fragment-capture probe module complexes to produce hybrid molecules, each hybrid molecule comprising a capture probe module and a complement of the adapter-tagged DNA fragment; (h) amplifying the hybrid molecules to produce an amplified target capture library (TCLA); (i) combining the WGLA and TCLA to form a sequence-matched library (SRL); and (j) performing quantitative genetic analysis on the SRL; wherein the DNA sample contains a plurality of single nucleotide polymorphisms (SNPs), and the one or more capture probe modules are deemed to have passed the probe QC process if one or more predetermined pass / fail criteria for the quantitative genetic analysis are met.

[0012] In some embodiments of the kits of the present disclosure, the predetermined pass / fail criteria for the probe QC process include one or more of: (a) at least 60% to 99.9% of the capture probes have at least 1 total read; (b) at least 60% to 99.9% of the capture probes have at least 10 to at least 200 on-target total reads; and (c) at least 60% to 99.9% of the expected SNPs are detected in the DNA sample.

[0013] In some embodiments of the kits of the present disclosure, the kit comprises a first primer pair comprising a first F primer and a first R primer, wherein each adapter module comprises an amplification region; the first F primer comprises an amplification region binding region and a sequencing primer binding region; and the first R primer comprises a tail sequence binding region and a sequencing primer binding region.

[0014] In some embodiments of the kits of the present disclosure, the kit comprises a second primer pair comprising a second F primer and a second R primer, wherein each adapter module comprises an amplification region; and each of the second F primer and the second R primer comprises an amplification region binding region and a sequencing primer binding region.

[0015] In some embodiments of the kits of the present disclosure, the tail sequence of each capture probe module comprises a library tag.

[0016] In some embodiments of kits of the present disclosure, the kit includes: (a) a set of adapters comprising adapter modules, each adapter comprising an amplified region; (b) one or more capture probe modules, each capture probe module comprising a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample, wherein the tail sequence of each capture probe module comprises a library tag; (c) a first primer pair comprising a first F primer and a first R primer, wherein the first F primer comprises an amplified region binding region and a sequencing primer binding region, and the first R primer comprises a library tag binding region and a sequencing primer binding region; and (d) a second primer pair, wherein the second F primer and the second R primer each comprise an amplified region binding region and a sequencing primer binding region, and wherein neither primer of the second primer pair binds to a library tag.

[0017] In some embodiments of the kits of the present disclosure, the library tag comprises a nucleic acid sequence or an amino acid sequence.

[0018] In some embodiments of the kits of the present disclosure, a first primer pair is used to generate a first modified library and a second primer pair is used to generate a second modified library, wherein the first modified library and the second modified library are configured to be combined into a sequence-matched library (SRL).

[0019] In some embodiments of the kits of the present disclosure, both the first modified library and the second modified library are generated from a test sample.

[0020] In some embodiments of the kits of the present disclosure, the first modified library or the second modified library comprises a library tag, wherein the library tag is configured to distinguish the first modified library from the second modified library.

[0021] In some embodiments of the kit of the present disclosure, each library fragment of the first modified library is an adapter-tagged DNA fragment comprising an adapter, a capture probe module, and at least a portion of the DNA sequence of the test sample; and each library fragment of the second modified library is an adapter-tagged DNA fragment comprising an adapter and at least a portion of the DNA sequence of the test sample, wherein none of the adapter-tagged DNA fragments of the second modified library comprises a capture probe module.

[0022] In some embodiments of the kits of the present disclosure, the kit comprises one or more capture probe modules, wherein each capture probe module comprises a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample.

[0023] In some embodiments of the kits of the present disclosure, the kit comprises one or more capture probe modules, wherein each capture probe module comprises a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample, and wherein the one or more capture probe modules have passed a probe quality control (QC) process.

[0024] In some embodiments of the kits of the present disclosure, the kit comprises a set of adaptors, each adaptor comprising an adaptor module.

[0025] In some embodiments of the kits of the present disclosure, the kit comprises a set of adapters, each adapter comprising an adapter module, and the set of adapters has passed an adapter quality control (QC) process.

[0026] In some embodiments of the kits of the present disclosure, the kit comprises: (a) one or more capture probe modules, each capture probe module comprising a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample; and (b) a set of adapters, each adapter comprising an adapter module.

[0027] In some embodiments of the kits of the present disclosure, the kit comprises: (a) one or more capture probe modules, each capture probe module comprising a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample; and (b) a set of adapters, each adapter comprising an adapter module, wherein the set of adapters has passed an adapter quality control (QC) process.

[0028] In some embodiments of the kits of the present disclosure, the kit includes: (a) one or more capture probe modules, each capture probe module including a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample, wherein one or more capture probe modules have passed a probe quality control (QC) process; and (b) a set of adapters, each adapter including an adapter module.

[0029] In some embodiments of the kits of the present disclosure, the kit includes: (a) one or more capture probe modules, each capture probe module including a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample, wherein one or more capture probe modules have passed a probe quality control (QC) process; and (b) a set of adapters, each adapter including an adapter module, wherein the set of adapters have passed an adapter quality control (QC) process.

[0030] In some embodiments of the kits of the present disclosure, the adapter QC process includes a test for adapter ligation, wherein the test for adapter ligation includes (a) ligating a set of adapters to a predetermined amount of end-repaired DNA fragments to generate a library of adapter-tagged DNA fragments (LIBS); and (b) amplifying the LIBS to generate library postamplification (LPA); and the set of adapters is considered to have passed the test for adapter ligation if the concentration of LPA is higher than the predetermined concentration.

[0031] In some embodiments of the kit of the present disclosure, the end-repaired DNA fragments in step (a) of the adapter ligation test are generated from a DNA sample. In some embodiments, the DNA sample is a blended DNA sample of at least two different cell lines. In some embodiments, the DNA sample is a blended DNA sample of two different cell lines. In some embodiments, the two different cell lines are blended at a 50:50 ratio. In some embodiments, the two different cell lines are NA09596 and NA12878. In some embodiments, the DNA sample is the 50:50 blend sample described in Example 15.

[0032] In some embodiments of the kits of the present disclosure, the DNA sample used in the test for adapter ligation is different from the DNA sample used in the test for adapter distribution.

[0033] In some embodiments of the kit of the present disclosure, the predetermined amount of the end-repaired DNA fragments is about 5 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of the end-repaired DNA fragments is about 10 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of the end-repaired DNA fragments is about 15 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of the end-repaired DNA fragments is about 20 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of the end-repaired DNA fragments is about 25 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of the end-repaired DNA fragments is about 30 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of the end-repaired DNA fragments is about 35 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of the end-repaired DNA fragments is about 40 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of the end-repaired DNA fragments is about 50 ng.

[0034] In some embodiments of the kit of the present disclosure, the predetermined amount of the end-repaired DNA fragments is 5 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of the end-repaired DNA fragments is 10 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of the end-repaired DNA fragments is 15 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of the end-repaired DNA fragments is 20 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of the end-repaired DNA fragments is 25 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of the end-repaired DNA fragments is 30 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of the end-repaired DNA fragments is 35 ng. In some embodiments of the kit of the present disclosure, the predetermined amount is 40 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of the end-repaired DNA fragments is 50 ng.

[0035] In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 1 ng to about 100 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 1 ng to about 50 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 50 ng to about 100 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 5 ng to about 90 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 10 ng to about 80 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 20 ng to about 60 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 20 ng to about 50 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 20 ng to about 40 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 30 ng to about 50 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 40 ng to about 50 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 30 ng to about 40 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 20 ng to about 30 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is greater than about 100 ng.

[0036] In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is 1 ng to 100 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is 1 ng to 50 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is 50 ng to 100 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is 5 ng to 90 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is 10 ng to 80 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is 20 ng to 60 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is 20 ng to 50 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is 20 ng to 40 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is 30 ng to 50 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is 40 ng to 50 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is 30 ng to 40 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is 20 ng to 30 ng. In some embodiments of the kit of the present disclosure, the predetermined amount of end-repaired DNA fragments is greater than 100 ng.

[0037] In some embodiments of the kits of the present disclosure, the predetermined concentration of LPA is about 1 ng / μL. In some embodiments of the kits of the present disclosure, the predetermined concentration of LPA is about 5 ng / μL. In some embodiments of the kits of the present disclosure, the predetermined concentration of LPA is about 10 ng / μL. In some embodiments of the kits of the present disclosure, the predetermined concentration of LPA is about 20 ng / μL. In some embodiments of the kits of the present disclosure, the predetermined concentration of LPA is about 30 ng / μL. In some embodiments of the kits of the present disclosure, the predetermined concentration of LPA is about 40 ng / μL. In some embodiments of the kits of the present disclosure, the predetermined concentration of LPA is about 50 ng / μL. In some embodiments of the kits of the present disclosure, the predetermined concentration of LPA is about 60 ng / μL. In some embodiments of the kits of the present disclosure, the predetermined concentration of LPA is about 70 ng / μL. In some embodiments of the kits of the present disclosure, the predetermined concentration of LPA is about 80 ng / μL. In some embodiments of the kits of the present disclosure, the predetermined concentration of LPA is about 90 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is about 100 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is about 150 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is about 200 ng / μL.

[0038] In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 1 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 5 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 10 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 20 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 30 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 40 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 50 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 60 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 70 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 80 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 90 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 100 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 150 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 200 ng / μL.

[0039] In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is about 1 ng / μL to about 200 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is greater than about 200 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is about 10 ng / μL to about 100 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is about 10 ng / μL to about 90 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is about 20 ng / μL to about 80 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is about 10 ng / μL to about 80 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is about 30 ng / μL to about 80 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is about 40 ng / μL to about 80 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is about 50 ng / μL to about 80 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is about 50 ng / μL to about 70 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is about 60 ng / μL to about 70 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is about 50 ng / μL to about 60 ng / μL.

[0040] In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 1 ng / μL to 200 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 10 ng / μL to 100 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 10 ng / μL to 90 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 20 ng / μL to 80 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 30 ng / μL to 80 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 10 ng / μL to 80 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 40 ng / μL to 80 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 50 ng / μL to 80 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 50 ng / μL to 70 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 60 ng / μL to 70 ng / μL. In some embodiments of the kit of the present disclosure, the predetermined concentration of LPA is 50 ng / μL to 60 ng / μL.

[0041] In some embodiments of the kits of the present disclosure, the predetermined concentration of LPA is greater than about 200 ng / μL.In some embodiments of the kits of the present disclosure, the predetermined concentration of LPA is greater than 200 ng / μL.

[0042] In some embodiments of the kits of the present disclosure, a set of adapters is considered to have passed the adapter QC process if it passes the test for adapter ligation.

[0043] In some embodiments of the kits of the present disclosure, the adapter QC process includes a test for adapter distribution that includes: (a) ligating a set of adapters to a predetermined amount of end-repaired DNA fragments to generate a library of adapter-tagged DNA fragments (LIBS); (b) amplifying the LIBS using a primer pair that includes at least one primer that includes an index sequence to generate a library post-index amplification (LPIA); and (c) performing quantitative genetic analysis on the LPIA, wherein the set of adapters is considered to have passed the test for adapter distribution if one or more predetermined pass / fail criteria for the quantitative genetic analysis are met.

[0044] In some embodiments of the kit of the present disclosure, the end-repaired DNA fragments in step (a) of the adapter distribution test are generated from a DNA sample. In some embodiments, the DNA sample comprises wild-type (wt) cell-free DNA (cfDNA). In some embodiments, the DNA sample consists of wt cfDNA. In some embodiments, the DNA sample comprises wt cfDNA obtained from a healthy human. In some embodiments, the DNA sample is the wt cfDNA sample described in Example 16.

[0045] In some embodiments of the kits of the present disclosure, the DNA sample used in the test for adapter distribution is different from the DNA sample used in the test for adapter ligation.

[0046] In some embodiments of the kits of the present disclosure, the predetermined acceptance criteria for the adapter QC process include criterion (a). In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.05% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.1% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.2% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.3% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.4% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.5% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.6% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.7% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.8% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.9% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 1% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 2% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 3% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 4% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 5% or less of the reads.

[0047] In some embodiments, criterion (a) is that barcode crosstalk is present in 0.05% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.1% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.2% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.3% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.4% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.5% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.6% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.7% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.8% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.9% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 1% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 2% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 3% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 4% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 5% or less of the reads.

[0048] In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.05% to about 10% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.05% to about 5% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.1% to about 5% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.1% to about 2% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.05% to about 2% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.1% to about 1% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.05% to about 1% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.1% to about 0.5% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.1% to about 0.4% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.1% to about 0.3% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.2% to about 0.3% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.1% to about 0.2% or less of the reads.

[0049] In some embodiments, criterion (a) is that barcode crosstalk is present in 0.05% to 10% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.05% to 5% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.1% to 5% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.1% to 2% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.05% to 2% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.1% to 1% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.05% to 1% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.1% to 0.5% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.1% to 0.4% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in no more than 0.1%-0.3% of reads. In some embodiments, criterion (a) is that barcode crosstalk is present in no more than 0.2%-0.3% of reads. In some embodiments, criterion (a) is that barcode crosstalk is present in no more than 0.1%-0.2% of reads.

[0050] In some embodiments of the kits of the present disclosure, the predetermined pass / fail criteria for the adapter QC process include criterion (b). In some embodiments, criterion (b) is that unknown adapters are present in no more than about 1% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than about 5% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than about 10% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than about 15% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than about 20% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than about 25% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than about 30% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than about 35% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than about 40% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than about 45% of the reads. In some embodiments, criterion (b) is that the unknown adaptor is present in no more than about 50% of the reads.

[0051] In some embodiments, criterion (b) is that the unknown adapter is present in no more than 1% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 5% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 10% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 15% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 20% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 25% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 30% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 35% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 40% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 45% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 50% of the reads.

[0052] In some embodiments, criterion (b) is that the unknown adapter is present in no more than about 1% to about 50% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than about 1% to about 20% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than about 1% to about 15% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than about 1% to about 10% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than about 5% to about 20% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than about 5% to about 15% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than about 5% to about 10% of the reads.

[0053] In some embodiments, criterion (b) is that unknown adapters are present in no more than 1%-50% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than 1%-20% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than 1%-15% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than 1%-10% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than 5%-20% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than 5%-15% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than 5%-10% of the reads.

[0054] In some embodiments of the kits of the present disclosure, the predetermined pass / fail criteria for the adapter QC process include criterion (c). In some embodiments, criterion (c) is that no more than about 10% of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that no more than about 20% of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that no more than about 30% of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that no more than about 40% of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that no more than about 50% of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that about 60% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that about 70% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that about 80% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that about 90% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences.

[0055] In some embodiments of the kits of the present disclosure, the predetermined pass / fail criteria for the adapter QC process include criterion (c). In some embodiments, criterion (c) is that no more than 10% of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that no more than 20% of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that no more than 30% of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that no more than 40% of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that no more than 50% of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that no more than 60% of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that 70% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that 80% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that 90% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences.

[0056] In some embodiments, criterion (c) is that about 10% to about 90% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that about 10% to about 80% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that about 20% to about 80% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that about 30% to about 70% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that about 40% to about 60% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that about 40% to about 50% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that about 50% to about 60% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences.

[0057] In some embodiments, criterion (c) is that 10% to 90% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that 10% to 80% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that 20% to 80% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that 30% to 70% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that 40% to 60% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that 40% to 50% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that 50% to 60% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences.

[0058] In some embodiments of the kits of the present disclosure, the predetermined pass / fail criteria for the adapter QC process include criterion (d). In some embodiments, criterion (d) is the presence of at least about 60% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 65% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 70% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 75% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 80% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 85% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 90% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 95% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 96% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 97% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 98% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 99% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 99.5% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of about 100% of all unique adapter sequences.

[0059] In some embodiments, criterion (d) is the presence of at least 60% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 65% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 70% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 75% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 80% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 85% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 90% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 95% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 96% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 97% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 98% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 99% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 99.5% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of 100% of all unique adapter sequences.

[0060] In some embodiments, criterion (d) is the presence of at least about 60% to about 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 70% to about 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 80% to about 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 90% to about 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 95% to about 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 96% to about 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 97% to about 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 98% to about 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is that at least about 99% to about 99.9% of all unique adapter sequences are present.

[0061] In some embodiments, criterion (d) is the presence of at least about 60% to about 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 70% to about 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 80% to about 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 90% to about 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 95% to about 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 96% to about 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 97% to about 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 98% to about 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 99% to about 100% of all unique adapter sequences. In some embodiments, criterion (d) is that at least about 99.9% to about 100% of all unique adapter sequences are present.

[0062] In some embodiments, criterion (d) is the presence of at least 60% to 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 70% to 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 80% to 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 90% to 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 95% to 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 96% to 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 97% to 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 98% to 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 99% to 99.9% of all unique adapter sequences.

[0063] In some embodiments, criterion (d) is the presence of at least 60% to 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 70% to 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 80% to 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 90% to 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 95% to 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 96% to 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 97% to 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 98% to 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 99% to 100% of all unique adapter sequences. In some embodiments, criterion (d) is that at least 99.9% to 100% of all unique adapter sequences are present.

[0064] In some embodiments of the kits of the present disclosure, the predetermined pass / fail criteria for the adapter QC process include criterion (e). In some embodiments, criterion (e) is that no more than about 1% of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 5% of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 10% of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 15% of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 20% of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 25% of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 30% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 35% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 40% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 45% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 50% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences.

[0065] In some embodiments, criterion (e) is that 1% or less of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that 5% or less of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that 10% or less of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that 15% or less of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that 20% or less of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that 25% or less of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that 30% or less of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than 35% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than 40% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than 45% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than 50% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences.

[0066] In some embodiments, criterion (e) is that about 10% to about 50% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that about 5% to about 50% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that about 5% to about 40% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that about 10% to about 30% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that about 10% to about 20% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that about 20% to about 40% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 20% to about 30% of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences. In some embodiments, criterion (e) is that no more than about 15% to about 25% of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences. In some embodiments, criterion (e) is that no more than about 15% to about 20% of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences.

[0067] In some embodiments, criterion (e) is that 1% to 50% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences. In some embodiments, criterion (e) is that 5% to 50% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences. In some embodiments, criterion (e) is that 5% to 40% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences. In some embodiments, criterion (e) is that 10% to 30% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences. In some embodiments, criterion (e) is that 10% to 20% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences. In some embodiments, criterion (e) is that 20% to 40% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences. In some embodiments, criterion (e) is that no more than 20%-30% of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences. In some embodiments, criterion (e) is that no more than 15%-25% of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences. In some embodiments, criterion (e) is that no more than 15%-20% of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences.

[0068] In some embodiments of the kits of the present disclosure, the predetermined pass / fail criteria for the adapter QC process include criterion (a) and criterion (b). In some embodiments, the predetermined pass / fail criteria include criterion (c), criterion (d), and criterion (e). In some embodiments, the predetermined pass / fail criteria include criterion (a), criterion (b), and criterion (c). In some embodiments, the predetermined pass / fail criteria include criterion (a), criterion (b), and criterion (d). In some embodiments, the predetermined pass / fail criteria include criterion (a), criterion (b), and criterion (e). In some embodiments, the predetermined pass / fail criteria include criterion (a), criterion (b), criterion (c), and criterion (d). In some embodiments, the predetermined pass / fail criteria include criterion (a), criterion (b), criterion (c), and criterion (e ...d), and criterion (e). In some embodiments, the predetermined pass / fail criteria include criterion (a), criterion (b), criterion (c), criterion (d), and criterion (e). In some embodiments, the predetermined pass / fail criteria include at least one criterion selected from criteria (a), (b), (c), (d), and (e).

[0069] In some embodiments of the kits of the present disclosure, a set of adapters is considered to have passed the adapter QC process if it passes the test for adapter distribution.

[0070] In some embodiments of the kits of the present disclosure, a set of adapters is considered to have passed the adapter QC process if it passes both the test for adapter ligation and the test for adapter distribution.

[0071] In some embodiments of the kits of the present disclosure, the probe QC process includes: (a) ligating a set of adapters to a DNA sample containing end-repaired DNA fragments to generate a library of adapter-tagged DNA fragments (LIBS); (b) amplifying the LIBS to generate library postamplification (LPA); (c) dividing or diluting the LPA to generate target capture LPA (TC LPA) and whole genome LPA (WG LPA); (d) amplifying the WG LPA to generate an amplified whole genome library (WGLA); and (e) ligating one or more capture probe modules to be tested to the TC LPA. (f) isolating the adapter-tagged DNA fragment-capture probe module complexes to form isolated adapter-tagged DNA fragment-capture probe module complexes; (g) enzymatically treating the isolated adapter-tagged DNA fragment-capture probe module complexes to produce hybrid molecules, each hybrid molecule comprising a capture probe module and a complement of the adapter-tagged DNA fragment; (h) amplifying the hybrid molecules to produce an amplified target capture library (TCLA); (i) combining the WGLA and TCLA to form a sequence-matched library (SRL); and (j) performing quantitative genetic analysis on the SRL.

[0072] In some embodiments, the terms LPA and adaptor-tagged parent library are used interchangeably. In some embodiments, the terms WGLA and LPWG library are used interchangeably. In some embodiments, the terms SRL and combinatorial library are used interchangeably.

[0073] In some embodiments of the kits of the present disclosure, the TC LPA is at least about 1 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least about 5 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least about 10 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least about 15 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least about 20 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least about 25 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least about 30 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least about 35 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least about 40 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least about 45 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least about 50 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least about 55 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least about 60 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least about 65 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least about 70 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least about 75 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least about 80 ng / μL.

[0074] In some embodiments of the kits of the present disclosure, the TC LPA is at least 1 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least 5 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least 10 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least 15 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least 20 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least 25 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least 30 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least 35 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least 40 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least 45 ng / μL. In some embodiments of the kits of the present disclosure, the TC LPA is at least 50 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least 55 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least 60 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least 65 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least 70 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least 75 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least 80 ng / μL.

[0075] In some embodiments of the kit of the present disclosure, the TC LPA is at least about 1 ng / μL to about 100 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least about 1 ng / μL to about 80 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least about 10 ng / μL to about 80 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least about 10 ng / μL to about 70 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least about 10 ng / μL to about 60 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least about 20 ng / μL to about 60 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least about 20 ng / μL to about 50 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least about 20 ng / μL to about 40 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least about 30 ng / μL to about 50 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least about 30 ng / μL to about 40 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least about 20 ng / μL to about 30 ng / μL.

[0076] In some embodiments of the kit of the present disclosure, the TC LPA is at least 1 ng / μL to 100 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least 1 ng / μL to 80 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least 10 ng / μL to 80 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least 10 ng / μL to 70 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least 10 ng / μL to 60 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least 20 ng / μL to 60 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least 20 ng / μL to 50 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least 20 ng / μL to 40 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least 30 ng / μL to 50 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least 30 ng / μL to 40 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least 20 ng / μL to 30 ng / μL.

[0077] In some embodiments of the kits of the present disclosure, the WG LPA is at least about 0.1 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least about 0.5 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least about 1 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least about 1.5 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least about 2 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least about 2.5 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least about 3 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least about 3.5 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least about 4 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least about 4.5 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least about 5 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least about 5.5 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least about 6 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least about 6.5 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least about 7 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least about 7.5 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least about 8 ng / μL.

[0078] In some embodiments of the kits of the present disclosure, the WG LPA is at least 0.1 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least 0.5 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least 1 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least 1.5 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least 2 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least 2.5 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least 3 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least 3.5 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least 4 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least 4.5 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least 5 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least 5.5 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least 6 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least 6.5 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least 7 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least 7.5 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least 8 ng / μL.

[0079] In some embodiments of the kit of the present disclosure, the WG LPA is at least about 0.1 ng / μL to about 10 ng / μL. In some embodiments of the kit of the present disclosure, the WG LPA is at least about 0.1 ng / μL to about 8 ng / μL. In some embodiments of the kit of the present disclosure, the WG LPA is at least about 1 ng / μL to about 10 ng / μL. In some embodiments of the kit of the present disclosure, the WG LPA is at least about 1 ng / μL to about 5 ng / μL. In some embodiments of the kit of the present disclosure, the WG LPA is at least about 2 ng / μL to about 10 ng / μL. In some embodiments of the kit of the present disclosure, the WG LPA is at least about 2 ng / μL to about 6 ng / μL. In some embodiments of the kit of the present disclosure, the WG LPA is at least about 3 ng / μL to about 5 ng / μL. In some embodiments of the kit of the present disclosure, the WG LPA is at least about 3 ng / μL to about 4 ng / μL. In some embodiments of the kits of the present disclosure, the WG LPA is at least about 2 ng / μL to about 3 ng / μL.

[0080] In some embodiments of the kit of the present disclosure, the WG LPA is at least 0.1 ng / μL to 10 ng / μL. In some embodiments of the kit of the present disclosure, the WG LPA is at least 0.1 ng / μL to 8 ng / μL. In some embodiments of the kit of the present disclosure, the WG LPA is at least 1 ng / μL to 10 ng / μL. In some embodiments of the kit of the present disclosure, the WG LPA is at least 1 ng / μL to 5 ng / μL. In some embodiments of the kit of the present disclosure, the WG LPA is at least 2 ng / μL to 10 ng / μL. In some embodiments of the kit of the present disclosure, the WG LPA is at least 2 ng / μL to 6 ng / μL. In some embodiments of the kit of the present disclosure, the WG LPA is at least 3 ng / μL to 5 ng / μL. In some embodiments of the kit of the present disclosure, the WG LPA is at least 3 ng / μL to 4 ng / μL. In some embodiments of the kit of the present disclosure, the WG LPA is at least 2 ng / μL to 3 ng / μL.

[0081] In some embodiments of the kits of the present disclosure, the TCLA is at least about 1.0 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 1.5 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 2.0 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 2.5 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 3.0 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 3.5 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 4.0 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 4.5 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 5.0 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 5.5 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 6.0 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 6.5 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 7.0 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 7.5 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 8.0 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 8.5 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 9.0 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 9.5 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 10 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 15 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 20 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 25 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 30 ng / μL.In some embodiments of the kits of the present disclosure, the TCLA is at least about 35 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 40 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 45 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 50 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 55 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 60 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 65 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 70 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 75 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 80 ng / μL.

[0082] In some embodiments of the kits of the present disclosure, the TCLA is at least 1.0 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 1.5 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 2.0 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 2.5 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 3.0 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 3.5 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 4.0 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least about 4.5 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 5.0 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 5.5 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 6.0 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 6.5 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 7.0 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 7.5 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 8.0 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 8.5 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 9.0 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 9.5 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 10 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 15 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 20 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 25 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 30 ng / μL.In some embodiments of the kits of the present disclosure, the TCLA is at least 35 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 40 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 45 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 50 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 55 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 60 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 65 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 70 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 75 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 80 ng / μL.

[0083] In some embodiments of the kit of the present disclosure, the TCLA is at least about 1 ng / μL to about 200 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least about 100 ng / μL to about 200 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least about 1 ng / μL to about 100 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least about 1 ng / μL to about 80 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least about 1 ng / μL to about 50 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least about 1 ng / μL to about 40 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least about 1 ng / μL to about 30 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least about 1 ng / μL to about 20 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least about 1 ng / μL to about 10 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least about 5 ng / μL to about 10 ng / μL.

[0084] In some embodiments of the kit of the present disclosure, the TCLA is at least 1 ng / μL to 200 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least 100 ng / μL to 200 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least 1 ng / μL to 100 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least 1 ng / μL to 80 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least 1 ng / μL to 50 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least 1 ng / μL to 40 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least 1 ng / μL to 30 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least 1 ng / μL to 20 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least 1 ng / μL to 10 ng / μL. In some embodiments of the kits of the present disclosure, the TCLA is at least 5 ng / μL to 10 ng / μL.

[0085] In some embodiments of the kits of the present disclosure, the WGLA is at least about 1.0 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 1.5 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 2.0 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 2.5 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 3.0 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 3.5 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 4.0 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 4.5 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 5.0 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 5.5 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 6.0 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 6.5 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 7.0 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 7.5 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 8.0 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 8.5 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 9.0 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 9.5 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 10 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 15 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 20 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 25 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 30 ng / μL.In some embodiments of the kits of the present disclosure, the WGLA is at least about 35 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 40 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 45 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 50 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 55 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 60 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 65 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 70 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 75 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 80 ng / μL.

[0086] In some embodiments of the kits of the present disclosure, the WGLA is at least 1.0 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 1.5 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 2.0 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 2.5 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 3.0 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 3.5 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 4.0 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 4.5 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 5.0 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 5.5 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 6.0 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 6.5 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 7.0 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 7.5 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 8.0 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 8.5 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 9.0 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 9.5 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 10 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 15 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 20 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 25 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 30 ng / μL.In some embodiments of the kits of the present disclosure, the WGLA is at least 35 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 40 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 45 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 50 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 55 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 60 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 65 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 70 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 75 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 80 ng / μL.

[0087] In some embodiments of the kit of the present disclosure, WGLA is at least about 1 ng / μL to about 200 ng / μL. In some embodiments of the kit of the present disclosure, WGLA is at least about 100 ng / μL to about 200 ng / μL. In some embodiments of the kit of the present disclosure, WGLA is at least about 1 ng / μL to about 100 ng / μL. In some embodiments of the kit of the present disclosure, WGLA is at least about 1 ng / μL to about 80 ng / μL. In some embodiments of the kit of the present disclosure, WGLA is at least about 1 ng / μL to about 50 ng / μL. In some embodiments of the kit of the present disclosure, WGLA is at least about 1 ng / μL to about 40 ng / μL. In some embodiments of the kit of the present disclosure, WGLA is at least about 1 ng / μL to about 30 ng / μL. In some embodiments of the kit of the present disclosure, WGLA is at least about 1 ng / μL to about 20 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 1 ng / μL to about 10 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least about 5 ng / μL to about 10 ng / μL.

[0088] In some embodiments of the kit of the present disclosure, WGLA is at least 1 ng / μL to 200 ng / μL. In some embodiments of the kit of the present disclosure, WGLA is at least 100 ng / μL to 200 ng / μL. In some embodiments of the kit of the present disclosure, WGLA is at least 1 ng / μL to 100 ng / μL. In some embodiments of the kit of the present disclosure, WGLA is at least 1 ng / μL to 80 ng / μL. In some embodiments of the kit of the present disclosure, WGLA is at least 1 ng / μL to 50 ng / μL. In some embodiments of the kit of the present disclosure, WGLA is at least 1 ng / μL to 40 ng / μL. In some embodiments of the kit of the present disclosure, WGLA is at least 1 ng / μL to 30 ng / μL. In some embodiments of the kit of the present disclosure, WGLA is at least 1 ng / μL to 20 ng / μL. In some embodiments of the kit of the present disclosure, WGLA is at least 1 ng / μL to 10 ng / μL. In some embodiments of the kits of the present disclosure, the WGLA is at least 5 ng / μL to 10 ng / μL.

[0089] In some embodiments of the kits of the present disclosure, one or more capture probe modules are considered to have passed the probe QC process if one or more predetermined pass / fail criteria for quantitative genetic analysis are met.

[0090] In some embodiments of the kits of the present disclosure, one or more capture probe modules are considered to have passed the probe QC process if one or more predetermined pass / fail criteria for quantitative genetic analysis are met.

[0091] In some embodiments of kits of the present disclosure, the predetermined acceptance criteria for the probe QC process include criterion (a). In some embodiments, criterion (a) is that about 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.8% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.7% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.6% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.5% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.4% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.3% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.2% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.1% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98.8% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98.7% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98.6% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98.5% of the capture probes have at least one total read.In some embodiments, criterion (a) is that at least about 98.4% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98.3% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98.2% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98.1% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 97% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 96% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least about 95% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least about 90% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least about 85% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least about 80% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least about 75% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least about 70% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least about 65% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least about 60% of the capture probes have at least one total read.

[0092] In some embodiments, criterion (a) is that 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 99.8% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 99.7% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 99.6% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 99.5% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 99.4% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 99.3% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 99.2% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 99.1% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 99% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 98.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 98.8% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 98.7% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 98.6% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 98.5% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 98.4% of the capture probes have at least one total read.In some embodiments, criterion (a) is that at least 98.3% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 98.2% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 98.1% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 98% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 97% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 96% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least 95% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least 90% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least 85% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least 80% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least 75% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least 70% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least 65% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least 60% of the capture probes have at least one total read.

[0093] In some embodiments, criterion (a) is that at least about 60% to about 99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 70% to about 99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 80% to about 99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 90% to about 99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 95% to about 99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 96% to about 99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 97% to about 99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98% to about 99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99% to about 99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99% to about 100% of the capture probes have at least one total read.

[0094] In some embodiments, criterion (a) is that at least 60%-99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 70%-99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 80%-99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 90%-99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 95%-99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 96%-99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 97%-99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 98%-99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 99% to 99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 99% to 100% of the capture probes have at least one total read.

[0095] In some embodiments, criterion (a) is that at least about 60% to about 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 70% to about 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 80% to about 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 90% to about 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 95% to about 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 96% to about 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 97% to about 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98% to about 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99% to about 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.5% to about 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.9% to about 100% of the capture probes have at least one total read.

[0096] In some embodiments, criterion (a) is that at least 60% to 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 70% to 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 80% to 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 90% to 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 95% to 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 96% to 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 97% to 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 98% to 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 99% to 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 99.5% to 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least 99.9% to 100% of the capture probes have at least one total read.

[0097] In some embodiments of the kits of the present disclosure, the predetermined acceptance criteria for the probe QC process include criterion (b). In some embodiments, criterion (b) is that about 100% of the capture probes have at least 10-200 on-target total reads. In some embodiments, criterion (b) is that at least about 99.9% of the capture probes have at least 10-200 on-target total reads. In some embodiments, criterion (b) is that at least about 99.5% of the capture probes have at least 10-200 on-target total reads. In some embodiments, criterion (b) is that at least about 99% of the capture probes have at least 10-200 on-target total reads. In some embodiments, criterion (b) is that at least about 98.5% of the capture probes have at least 10-200 on-target total reads. In some embodiments, criterion (b) is that at least about 98% of the capture probes have at least 10-200 on-target total reads. In some embodiments, criterion (b) is that at least about 97.5% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 97% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 96.5% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 96% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 95.5% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 95% of the capture probes have an on-target total read of at least 10-200. In some embodiments, the predetermined pass / fail criteria for the probe QC process include criterion (b) that at least about 90% of the capture probes have at least 10-200 on-target total reads.In some embodiments, criterion (b) is that at least about 85% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 80% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 75% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 70% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 65% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 60% of the capture probes have an on-target total read of at least 10-200.

[0098] In some embodiments, criterion (b) is that 100% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 99.9% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 99.5% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 99% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 98.5% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 98% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 97.5% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 97% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 96.5% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 96% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 95.5% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 95% of the capture probes have an on-target total read of at least 10-200. In some embodiments of the kits of the present disclosure, the predetermined acceptance criteria for the probe QC process include criterion (b) that at least 90% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 85% of the capture probes have an on-target total read of at least 10-200.In some embodiments, criterion (b) is that at least 80% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 75% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 70% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 65% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 60% of the capture probes have an on-target total read of at least 10-200.

[0099] In some embodiments, criterion (b) is that about 100% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 99.9% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 99.5% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 99% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 98.5% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 98% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 97.5% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 97% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 96.5% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 96% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 95.5% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 95% of the capture probes have an on-target total read of at least 50. In some embodiments, the predetermined pass / fail criteria for the probe QC process include criterion (b) that at least about 90% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 85% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 80% of the capture probes have an on-target total read of at least 50.In some embodiments, criterion (b) is that at least about 75% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 70% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 65% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 60% of the capture probes have an on-target total read of at least 50.

[0100] In some embodiments, criterion (b) is that 100% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 99.9% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 99.5% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 99% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 98.5% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 98% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 97.5% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 97% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 96.5% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 96% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 95.5% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 95% of the capture probes have an on-target total read of at least 50. In some embodiments of the kits of the present disclosure, the predetermined acceptance criteria for the probe QC process include criterion (b) that at least 90% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 85% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 80% of the capture probes have an on-target total read of at least 50.In some embodiments, criterion (b) is that at least 75% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 70% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 65% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 60% of the capture probes have an on-target total read of at least 50.

[0101] In some embodiments, criterion (b) is that about 100% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 99.9% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 99.5% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 99% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 98.5% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 98% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 97.5% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 97% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 96.5% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 96% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 95.5% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 95% of the capture probes have an on-target total read of at least 60. In some embodiments, the predetermined pass / fail criteria for the probe QC process include criterion (b) that at least about 90% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 85% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 80% of the capture probes have an on-target total read of at least 60.In some embodiments, criterion (b) is that at least about 75% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 70% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 65% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 60% of the capture probes have an on-target total read of at least 60.

[0102] In some embodiments, criterion (b) is that 100% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 99.9% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 99.5% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 99% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 98.5% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 98% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 97.5% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 97% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 96.5% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 96% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 95.5% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 95% of the capture probes have an on-target total read of at least 60. In some embodiments of the kits of the present disclosure, the predetermined acceptance criteria for the probe QC process include criterion (b) that at least 90% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 85% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 80% of the capture probes have an on-target total read of at least 60.In some embodiments, criterion (b) is that at least 75% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 70% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 65% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 60% of the capture probes have an on-target total read of at least 60.

[0103] In some embodiments, criterion (b) is that about 100% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 99.9% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 99.5% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 99% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 98.5% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 98% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 97.5% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 97% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 96.5% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 96% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 95.5% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 95% of the capture probes have an on-target total read of at least 70. In some embodiments, the predetermined pass / fail criteria for the probe QC process include criterion (b) that at least about 90% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 85% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 80% of the capture probes have an on-target total read of at least 70.In some embodiments, criterion (b) is that at least about 75% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 70% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 65% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 60% of the capture probes have an on-target total read of at least 70.

[0104] In some embodiments, criterion (b) is that 100% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 99.9% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 99.5% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 99% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 98.5% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 98% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 97.5% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 97% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 96.5% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 96% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 95.5% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 95% of the capture probes have an on-target total read of at least 70. In some embodiments of the kits of the present disclosure, the predetermined acceptance criteria for the probe QC process include criterion (b) that at least 90% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 85% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 80% of the capture probes have an on-target total read of at least 70.In some embodiments, criterion (b) is that at least 75% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 70% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 65% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 60% of the capture probes have an on-target total read of at least 60.

[0105] In some embodiments, criterion (b) is that about 100% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 99.9% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 99.5% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 99% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 98.5% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 98% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 97.5% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 97% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 96.5% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 96% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 95.5% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 95% of the capture probes have an on-target total read of at least 80. In some embodiments, the predetermined pass / fail criteria for the probe QC process include criterion (b) that at least about 90% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 85% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 80% of the capture probes have an on-target total read of at least 80.In some embodiments, criterion (b) is that at least about 75% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 70% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 65% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 60% of the capture probes have an on-target total read of at least 60.

[0106] In some embodiments, criterion (b) is that 100% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 99.9% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 99.5% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 99% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 98.5% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 98% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 97.5% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 97% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 96.5% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 96% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 95.5% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 95% of the capture probes have an on-target total read of at least 80. In some embodiments of the kits of the present disclosure, the predetermined acceptance criteria for the probe QC process include criterion (b) that at least 90% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 85% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 80% of the capture probes have an on-target total read of at least 80.In some embodiments, criterion (b) is that at least 75% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 70% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 65% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 60% of the capture probes have an on-target total read of at least 80.

[0107] In some embodiments, criterion (b) is that at least about 60% to about 99.9% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 70% to about 99.9% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 80% to about 99.9% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 90% to about 99.9% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 95% to about 99.9% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 99% to about 99.9% of the capture probes have an on-target total read of at least 10-200.

[0108] In some embodiments, criterion (b) is that at least 60%-99.9% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 70%-99.9% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 80%-99.9% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 90%-99.9% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 95%-99.9% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 99%-99.9% of the capture probes have an on-target total read of at least 10-200.

[0109] In some embodiments, criterion (b) is that at least about 60% to about 100% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 70% to about 100% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 80% to about 100% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 90% to about 100% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 95% to about 100% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least about 99% to about 100% of the capture probes have an on-target total read of at least 10-200.

[0110] In some embodiments, criterion (b) is that at least 60%-100% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 70%-100% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 80%-100% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 90%-100% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 95%-100% of the capture probes have an on-target total read of at least 10-200. In some embodiments, criterion (b) is that at least 99%-100% of the capture probes have an on-target total read of at least 10-200.

[0111] In some embodiments, criterion (b) is that at least about 60% to about 100% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 70% to about 100% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 80% to about 100% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 90% to about 100% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 95% to about 100% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least about 99% to about 100% of the capture probes have an on-target total read of at least 50.

[0112] In some embodiments, criterion (b) is that at least 60%-100% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 70%-100% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 80%-100% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 90%-100% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 95%-100% of the capture probes have an on-target total read of at least 50. In some embodiments, criterion (b) is that at least 99%-100% of the capture probes have an on-target total read of at least 50.

[0113] In some embodiments, criterion (b) is that at least about 60% to about 100% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 70% to about 100% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 80% to about 100% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 90% to about 100% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 95% to about 100% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least about 99% to about 100% of the capture probes have an on-target total read of at least 60.

[0114] In some embodiments, criterion (b) is that at least 60%-100% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 70%-100% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 80%-100% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 90%-100% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 95%-100% of the capture probes have an on-target total read of at least 60. In some embodiments, criterion (b) is that at least 99%-100% of the capture probes have an on-target total read of at least 60.

[0115] In some embodiments, criterion (b) is that at least about 60% to about 100% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 70% to about 100% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 80% to about 100% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 90% to about 100% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 95% to about 100% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least about 99% to about 100% of the capture probes have an on-target total read of at least 70.

[0116] In some embodiments, criterion (b) is that at least 60%-100% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 70%-100% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 80%-100% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 90%-100% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 95%-100% of the capture probes have an on-target total read of at least 70. In some embodiments, criterion (b) is that at least 99%-100% of the capture probes have an on-target total read of at least 70.

[0117] In some embodiments, criterion (b) is that at least about 60% to about 100% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 70% to about 100% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 80% to about 100% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 90% to about 100% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 95% to about 100% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least about 99% to about 100% of the capture probes have an on-target total read of at least 80.

[0118] In some embodiments, criterion (b) is that at least 60%-100% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 70%-100% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 80%-100% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 90%-100% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 95%-100% of the capture probes have an on-target total read of at least 80. In some embodiments, criterion (b) is that at least 99%-100% of the capture probes have an on-target total read of at least 80.

[0119] In some embodiments of the kits of the present disclosure, the predetermined pass / fail criteria for the probe QC process include criterion (c). In some embodiments, criterion (c) is the detection of at least about 99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least about 99.5% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least about 99% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least about 98% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least about 97% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least about 96% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least about 95% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least about 90% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least about 85% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 80% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 75% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 70% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 65% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 60% of the expected SNPs in the DNA sample.

[0120] In some embodiments, criterion (c) is the detection of at least 99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least 99.5% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least 99% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least 98% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least 97% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least 96% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least 95% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least 90% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least 85% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least 80% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least 75% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least 70% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least 65% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least 60% of the expected SNPs in the DNA sample.

[0121] In some embodiments, criterion (c) is detecting at least about 60% to about 99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 70% to about 99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 80% to about 99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 90% to about 99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 95% to about 99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 96% to about 99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 97% to about 99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 98% to about 99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 99% to about 99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 100% of the expected SNPs in the DNA sample.

[0122] In some embodiments, criterion (c) is the detection of at least 60%-99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least 70%-99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least 80%-99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least 90%-99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least 95%-99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least 96%-99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least 97%-99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is the detection of at least 98%-99.9% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 99% to 99.9% of the expected SNPs in the DNA sample, hi some embodiments, criterion (c) is detecting at least 100% of the expected SNPs in the DNA sample.

[0123] In some embodiments, criterion (c) is detecting at least about 60% to about 100% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 70% to about 100% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 80% to about 100% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 90% to about 100% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 95% to about 100% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 96% to about 100% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 97% to about 100% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 98% to about 100% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 99% to about 100% of the expected SNPs in the DNA sample, hi some embodiments, criterion (c) is detecting about 100% of the expected SNPs in the DNA sample.

[0124] In some embodiments, criterion (c) is detecting at least 60%-100% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least 70%-100% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least 80%-100% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least 90%-100% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least 95%-100% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least 96%-100% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least 97%-100% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least 98%-100% of the expected SNPs in the DNA sample. In some embodiments, criterion (c) is detecting at least about 99%-100% of the expected SNPs in the DNA sample, hi some embodiments, criterion (c) is detecting 100% of the expected SNPs in the DNA sample.

[0125] In some embodiments of the kits of the present disclosure, the predetermined pass / fail criteria for the adapter QC process include criterion (a) and criterion (b). In some embodiments of the kits of the present disclosure, the predetermined pass / fail criteria for the probe QC process include criterion (a) and criterion (c). In some embodiments of the kits of the present disclosure, the predetermined pass / fail criteria for the probe QC process include criterion (b) and criterion (c). In some embodiments of the kits of the present disclosure, the predetermined pass / fail criteria for the probe QC process include criterion (a), criterion (b), and criterion (c).

[0126] In some embodiments of the kits of the present disclosure, the DNA sample used in the probe QC process comprises human wild-type DNA. In some embodiments of the kits of the present disclosure, the DNA sample used in the probe QC process comprises a plurality of single nucleotide polymorphisms (SNPs). In some embodiments of the kits of the present disclosure, the DNA sample used in the probe QC process comprises any suitable DNA.

[0127] In some embodiments of the kits of the present disclosure, the kit includes a DNA sample used as a positive control sample specific for a capture probe module of the same kit. In some embodiments, the positive control sample includes human wild-type DNA. In some embodiments, the positive control sample includes multiple SNPs. In some embodiments, the positive control sample includes a DNA sample used in a probe QC process for a capture probe module of the kit. In some embodiments, the positive control sample includes any suitable DNA.

[0128] In some embodiments of the kits of the present disclosure, the adapter QC process is performed according to any one of the methods of performing an adapter QC process of the present disclosure.

[0129] In some embodiments of the kits of the present disclosure, the probe QC process is performed according to any one of the methods of performing a probe QC process of the present disclosure.

[0130] In some embodiments of the kits of the present disclosure, the kit includes: (a) one or more capture probe modules, each capture probe module including a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample; (b) a set of adapters, each adapter including an adapter module including an amplification region; and (c) a first primer pair including a first F primer and a first R primer, wherein the first F primer includes an amplification region binding region and a sequencing primer binding region, and the first R primer includes a tail sequence binding region and a sequencing primer binding region.

[0131] In some embodiments of the kits of the present disclosure, the kit includes: (a) one or more capture probe modules, each capture probe module including a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample; (b) a set of adapters, each adapter including an adapter module including an amplification region; and (c) a first primer pair including a first F primer and a first R primer, wherein the first F primer includes an amplification region binding region and a sequencing primer binding region, and the first R primer includes a tail sequence binding region and a sequencing primer binding region; wherein the capture probe modules have passed a probe QC process.

[0132] In some embodiments of the kits of the present disclosure, the kit includes: (a) one or more capture probe modules, each capture probe module including a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample; (b) a set of adapters, each adapter including an adapter module including an amplification region; and (c) a first primer pair including a first F primer and a first R primer, wherein the first F primer includes an amplification region binding region and a sequencing primer binding region, and the first R primer includes a tail sequence binding region and a sequencing primer binding region; wherein the set of adapters has passed an adapter QC process.

[0133] In some embodiments of the kits of the present disclosure, the kit includes: (a) one or more capture probe modules, each capture probe module including a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample; (b) a set of adapters, each adapter including an adapter module including an amplification region; and (c) a first primer pair including a first F primer and a first R primer, wherein the first F primer includes an amplification region binding region and a sequencing primer binding region, and the first R primer includes a tail sequence binding region and a sequencing primer binding region; wherein the set of adapters has passed an adapter QC process and the capture probe module has passed a probe QC process.

[0134] In some embodiments of the kits of the present disclosure, the kit includes (a) a set of adapters, each adapter including an adapter module comprising an amplification region; and (b) a second primer pair comprising a second F primer and a second R primer, wherein each of the second F primer and the second R primer comprises an amplification region binding region and a sequencing primer binding region.

[0135] In some embodiments of the kits of the present disclosure, the kit includes (a) a set of adapters, each adapter including an adapter module comprising an amplified region; and (b) a second primer pair including a second F primer and a second R primer, wherein each of the second F primer and the second R primer comprises an amplified region binding region and a sequencing primer binding region; and wherein the set of adapters has passed an adapter QC process.

[0136] In some embodiments of the kits of the present disclosure, the kit includes: (a) one or more capture probe modules, each capture probe module including a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample; (b) an adapter set, each adapter including an adapter module including an amplification region; (c) a first primer pair including a first F primer and a first R primer, wherein the first F primer includes an amplification region binding region and a sequencing primer binding region, and the first R primer includes a tail sequence binding region and a sequencing primer binding region; and (d) a second primer pair including a second F primer and a second R primer, wherein the second F primer and the second R primer include an amplification region binding region and a sequencing primer binding region, respectively.

[0137] In some embodiments of the kits of the present disclosure, the kit comprises: (a) one or more capture probe modules, each capture probe module comprising a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample; (b) an adapter set comprising adapter modules, each adapter comprising an amplified region; (c) a first primer pair comprising a first F primer and a first R primer, wherein the first F primer comprises an amplified region binding region and a sequencing primer binding region, and the first R primer comprises a tail sequence binding region and a sequencing primer binding region; and (d) a second primer pair comprising a second F primer and a second R primer, wherein the second F primer and the second R primer comprise an amplified region binding region and a sequencing primer binding region, respectively; wherein the capture probe modules have passed a probe QC process.

[0138] In some embodiments of the kits of the present disclosure, the kit comprises: (a) one or more capture probe modules, each capture probe module comprising a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample; (b) an adapter set, each adapter comprising an adapter module comprising an amplified region; (c) a first primer pair comprising a first F primer and a first R primer, wherein the first F primer comprises an amplified region binding region and a sequencing primer binding region, and the first R primer comprises a tail sequence binding region and a sequencing primer binding region; and (d) a second primer pair comprising a second F primer and a second R primer, wherein the second F primer and the second R primer comprise an amplified region binding region and a sequencing primer binding region, respectively; wherein the set of adapters has passed an adapter QC process.

[0139] In some embodiments of the kits of the present disclosure, the kit comprises: (a) one or more capture probe modules, each capture probe module comprising a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample; (b) an adapter set, each adapter comprising an adapter module comprising an amplified region; (c) a first primer pair comprising a first F primer and a first R primer, wherein the first F primer comprises an amplified region binding region and a sequencing primer binding region, and the first R primer comprises a tail sequence binding region and a sequencing primer binding region; and (d) a second primer pair comprising a second F primer and a second R primer, wherein the second F primer and the second R primer comprise an amplified region binding region and a sequencing primer binding region, respectively; wherein the set of adapters has passed an adapter QC process and the capture probe module has passed a probe QC process.

[0140] In some embodiments of the kits of the present disclosure, the kit comprises: (a) one or more capture probe modules, each capture probe module comprising a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample, wherein the tail sequence of each capture probe module comprises a library tag; and (b) a set of adapters, each adapter comprising an adapter module comprising an amplified region.

[0141] In some embodiments of the kits of the present disclosure, the kit includes: (a) one or more capture probe modules, each capture probe module including a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample, wherein the tail sequence of each capture probe module includes a library tag; and (b) a set of adapters, each adapter including an adapter module including an amplified region; and the set of adapters has passed an adapter QC process.

[0142] In some embodiments of the kits of the present disclosure, the kit includes: (a) one or more capture probe modules, each capture probe module including a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample, wherein the tail sequence of each capture probe module includes a library tag; and (b) a set of adapters, each adapter including an adapter module including an amplified region; and the one or more capture probe modules have passed a probe QC process.

[0143] In some embodiments of the kits of the present disclosure, the kit includes: (a) one or more capture probe modules, each capture probe module including a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample, wherein the tail sequence of each capture probe module includes a library tag; and (b) a set of adapters, each adapter including an adapter module including an amplified region; one or more of the capture probe modules have passed a probe QC process, and the set of adapters has passed an adapter QC process.

[0144] In some embodiments of kits of the present disclosure, the kit includes: (a) one or more capture probe modules, each capture probe module including a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample, wherein the tail sequence of each capture probe module includes a library tag; (b) a set of adapters, each adapter including an adapter module including an amplification region; (c) a first primer pair including a first F primer and a first R primer, wherein the first F primer includes an amplification region binding region and a sequencing primer binding region, and the first R primer includes a library tag binding region and a sequencing primer binding region; and (d) a second primer pair including a second F primer and a second R primer, wherein the second F primer and the second R primer each include an amplification region binding region and a sequencing primer binding region, and wherein neither primer of the second primer pair binds to a library tag.

[0145] In some embodiments of the kits of the present disclosure, the kit comprises: (a) one or more capture probe modules, each capture probe module comprising a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample, wherein the tail sequence of each capture probe module comprises a library tag; (b) an adapter set comprising adapter modules, each adapter comprising an amplified region; (c) a first primer pair comprising a first F primer and a first R primer, wherein the first F primer comprises an amplification region binding region and a sequencing primer binding region, and the first R primer comprises a library tag binding region and a sequencing primer binding region; and (d) a second primer pair comprising a second F primer and a second R primer, wherein the second F primer and the second R primer each comprise an amplification region binding region and a sequencing primer binding region, and wherein neither primer of the second primer pair binds to a library tag; wherein the one or more capture probe modules have passed a probe QC process.

[0146] In some embodiments of the kits of the present disclosure, the kit includes: (a) one or more capture probe modules, each capture probe module including a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample, wherein the tail sequence of each capture probe module includes a library tag; (b) an adapter set including adapter modules each including an amplified region; (c) a first primer pair including a first F primer and a first R primer, wherein the first F primer includes an amplified region binding region and a sequencing primer binding region, and the first R primer includes a library tag binding region and a sequencing primer binding region; and (d) a second primer pair including a second F primer and a second R primer, wherein the second F primer and the second R primer each include an amplified region binding region and a sequencing primer binding region, and wherein neither primer of the second primer pair binds to a library tag; wherein the set of adapters has passed an adapter QC process.

[0147] In some embodiments of the kits of the present disclosure, the kit comprises: (a) one or more capture probe modules, each capture probe module comprising a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample, wherein the tail sequence of each capture probe module comprises a library tag; (b) an adapter set comprising adapter modules each comprising an amplified region; (c) a first primer pair comprising a first F primer and a first R primer, wherein the first F primer comprises an amplified region binding region and a sequencing primer binding region, and the first R primer comprises a library tag binding region and a sequencing primer binding region; and (d) a second primer pair comprising a second F primer and a second R primer, wherein the second F primer and the second R primer comprise an amplified region binding region and a sequencing primer binding region, respectively, and wherein neither primer of the second primer pair binds to a library tag; wherein the one or more capture probe modules have passed a probe QC process and the set of adapters has passed an adapter QC process.

[0148] In some embodiments of the kits of the present disclosure, a first primer pair is used to generate a first modified library.

[0149] In some embodiments of the kits of the present disclosure, a second primer pair is used to generate a second modified library.

[0150] In some embodiments of the kits of the present disclosure, a first primer pair is used to generate a first modified library and a second primer pair is used to generate a second modified library, hi some embodiments, the first modified library and the second modified library are configured to be combined into a sequence-matched library (SRL).

[0151] In some embodiments of the kits of the present disclosure, the tail sequence of each capture probe module comprises a library tag.

[0152] In some embodiments of the kits of the present disclosure, the library tag comprises a nucleic acid sequence or an amino acid sequence, hi some embodiments, the library tag comprises one or more of DNA, RNA, PNA, or a non-naturally occurring nucleic acid, a synthetic nucleic acid, a modified nucleic acid, a non-naturally occurring amino acid, a synthetic amino acid, and a modified amino acid.

[0153] In some embodiments of the kits of the present disclosure, the library tag comprises a detectable label, hi some embodiments, the detectable label comprises one or more of a fluorescent moiety, a magnetic or paramagnetic moiety, an enzymatic moiety, a binding moiety, an epitope, and a radioactive moiety.

[0154] In some embodiments of the kits of the present disclosure, the library tag selectively or specifically binds to a detectable moiety, hi some embodiments, the detectable moiety comprises one or more of a fluorescent moiety, a magnetic or paramagnetic moiety, an enzymatic moiety, a binding moiety, an epitope, and a radioactive moiety.

[0155] In some embodiments of the kits of the present disclosure, the library tag comprises a unique polynucleotide sequence, which in some embodiments has 70% or less sequence identity to any DNA fragment in the test sample.

[0156] In some embodiments of kits of the present disclosure, the kit includes: (a) an adapter set comprising an adapter module, each adapter comprising an amplified region; (b) one or more capture probe modules, each capture probe module comprising a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample, wherein the tail sequence of each capture probe module comprises a library tag; (c) a first primer pair comprising a first F primer and a first R primer, wherein the first F primer comprises an amplified region binding region and a sequencing primer binding region, and the first R primer comprises a library tag binding region and a sequencing primer binding region; and (d) a second primer pair comprising a second F primer and a second R primer, wherein the second F primer and the second R primer each comprise an amplified region binding region and a sequencing primer binding region, and wherein neither primer of the second primer pair binds to a library tag.

[0157] In some embodiments of the kits of the present disclosure, the kit is used to generate a first modified library and a second modified library, wherein the kit includes: (a) a set of adapters, each adapter including an adapter module; and (b) one or more capture probe modules, each capture probe module including a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample, the tail sequence of each capture probe module including a library tag. In some embodiments, the first modified library includes DNA fragments including the adapters, the capture probe module, and the target sequence of the capture probe module. In some embodiments, the second modified library includes DNA fragments including the adapters and at least a portion of the DNA sequence of the test sample. In some embodiments, both the first modified library and the second modified library are generated from the same test sample.

[0158] In some embodiments of the kits of the present disclosure, a first primer pair is used to generate a first modified library and a second primer pair is used to generate a second modified library.

[0159] In some embodiments of the kits of the present disclosure, the first modified library comprises first DNA fragments that comprise adaptors, capture probe modules, and target sequences of the capture probe modules.

[0160] In some embodiments of the kits of the present disclosure, the second modified library comprises second DNA fragments comprising the adaptors and at least a portion of the DNA sequence of the test sample.

[0161] In some embodiments of the kits of the present disclosure, the first modified library and the second modified library are configured to be combined into a sequence-matched library (SRL), which in some embodiments is also referred to as a combinatorial library.

[0162] In some embodiments of the kits of the present disclosure, each library fragment of the first modified library is an adaptor-tagged DNA fragment comprising an adaptor, a capture probe module, and at least a portion of a DNA sequence of the test sample.

[0163] In some embodiments of the kits of the present disclosure, each library fragment of the second modified library is an adaptor-tagged DNA fragment comprising an adaptor and at least a portion of a DNA sequence of the test sample.

[0164] In some embodiments of the kits of the present disclosure, none of the adaptor-tagged DNA fragments of the second modified library comprise a capture probe module.

[0165] In some embodiments of the kits of the present disclosure, the first modified library is a target capture library (TCL) or an amplified target capture library (TCLA).

[0166] In some embodiments of the kits of the present disclosure, the second modified library is a whole genomic library (WGL) or an amplified whole genomic library (WGLA).

[0167] In some embodiments of the kits of the present disclosure, the first modified library or the second modified library comprises a library tag, wherein the library tag is configured to distinguish the first modified library from the second modified library.

[0168] In some embodiments of the kits of the present disclosure, the first modified library comprises a first library tag and the second modified library comprises a second library tag, and the first library tag and the second library tag are not identical.

[0169] In some embodiments of the kit of the present disclosure, each library fragment of the first modified library comprises, from 5' to 3', a 5' oligonucleotide (A1), a first 5' adaptor module, at least a portion of the DNA sequence of the test sample, and a 3' oligonucleotide (A2); or a 5' oligonucleotide (A1), at least a portion of the DNA sequence of the test sample, a first 3' adaptor module, and a 3' oligonucleotide (A2); and each fragment of the second modified library comprises, from 5' to 3', a 5' oligonucleotide (B1), a second 5' adaptor module, at least a portion of the DNA sequence of the test sample, a second 3' adaptor module, and a 3' oligonucleotide (B2). In some embodiments, at least one of A1, A2, B1, and B2 contains at least one library tag. In some embodiments, the library tag comprises a unique polynucleotide sequence, wherein the unique polynucleotide sequence has 70% or less identity to a sequence selected from the list consisting of A1, B1, A2, B2, a first 5' adaptor module, a target sequence, a first 3' adaptor module, a second 5' adaptor module, any DNA fragment of the test sample, and a second 3' adaptor module.

[0170] In some embodiments of the kit of the present disclosure, each library fragment of the first modified library comprises, from 5' to 3', a 5' oligonucleotide (A1), a first 5' adaptor module, at least a portion of the DNA sequence of the test sample, and a 3' oligonucleotide (A2), or a 5' oligonucleotide (A1), at least a portion of the DNA sequence of the test sample, a first 3' adaptor module, and a 3' oligonucleotide (A2); wherein each fragment of the second modified library comprises, from 5' to 3', a 5' oligonucleotide (B1), a second 5' adaptor module, and a 3' oligonucleotide (B2). and a 3' oligonucleotide (B2); wherein at least one of A1, A2, B1, and B2 comprises a library tag, the library tag comprising a unique polynucleotide sequence, the unique polynucleotide sequence having 70% or less sequence identity to a sequence selected from the list consisting of A1, B1, A2, B2, the first 5' adaptor module, the target sequence, the first 3' adaptor module, the second 5' adaptor module, any DNA fragment of the test sample, and the second 3' adaptor module.

[0171] In some embodiments of the kits of the present disclosure, each adaptor of the set of adaptors comprises a linker oligonucleotide and a non-linker oligonucleotide.

[0172] In some embodiments of the kits of the present disclosure, the non-ligated strand oligonucleotide is capable of hybridizing to a region at the 3' end of the ligated strand oligonucleotide and forming a duplex therewith.

[0173] In some embodiments of the kits of the present disclosure, the linker oligonucleotide comprises an adaptor module.

[0174] In some embodiments of the kits of the present disclosure, the linking strand oligonucleotide comprises an overhang of dT, dA, dC, or dG at the 3' end.

[0175] In some embodiments of the kits of the present disclosure, the non-ligated strand oligonucleotide comprises a modification at its 3' end that prevents ligation to the 5' end of the dsDNA fragment and / or adapter dimer formation, whereby the non-ligated strand is configured to be displaced from the double strand.

[0176] In some embodiments of the kits of the present disclosure, each adapter of the set of adapters comprises an ID region selected from a pool of unique ID regions, wherein the pool is selected from a plurality of pools, and the selected pool is unique to the test sample.

[0177] In some embodiments of the kits of the present disclosure, the adapter module comprises: (a) an amplification region comprising a primer binding site; (b) an ID region; and (c) an anchor region.

[0178] In some embodiments of the kits of the present disclosure, the amplification region comprises primer binding sites, wherein the primer binding sites allow for amplification using PCR (polymerase chain reaction), LAMP (loop-mediated isothermal amplification), NASBA (nucleic acid sequence-based amplification), SDA (standard displacement amplification), RCA (rolling circle replication), or LCR (ligase chain reaction).

[0179] In some embodiments of the kits of the present disclosure, the amplified region comprises or consists of between 10 and 50 nucleotides. In some embodiments, the amplified region comprises or consists of between 20 and 30 nucleotides. In some embodiments, the amplified region comprises or consists of 25 nucleotides.

[0180] In some embodiments of the kits of the present disclosure, the amplified region comprises or consists of about 10 to about 50 nucleotides, in some embodiments, about 20 to about 30 nucleotides, and in some embodiments, about 25 nucleotides.

[0181] In some embodiments of the kits of the present disclosure, the anchor region comprises an overhang at the 3' end.

[0182] In some embodiments of the kits of the present disclosure, the anchor region comprises or consists of between 1 and 50 nucleotides. In some embodiments, the anchor region comprises or consists of between 5 and 25 nucleotides. In some embodiments, the anchor region comprises or consists of 10 nucleotides.

[0183] In some embodiments of the kits of the present disclosure, the anchor region comprises or consists of about 10 to about 50 nucleotides. In some embodiments, the anchor region comprises or consists of about 5 to about 25 nucleotides. In some embodiments, the anchor region comprises or consists of about 10 nucleotides.

[0184] In some embodiments of the kits of the present disclosure, the ID region comprises or consists of between 3 and 50 nucleotides. In some embodiments, the ID region comprises or consists of between 3 and 15 nucleotides. In some embodiments, the ID region comprises or consists of 8 nucleotides.

[0185] In some embodiments of the kits of the present disclosure, the ID region comprises or consists of about 3 to about 50 nucleotides. In some embodiments, the ID region comprises or consists of about 3 to about 15 nucleotides. In some embodiments, the ID region comprises or consists of about 8 nucleotides.

[0186] In some embodiments of the kits of the present disclosure, the adaptor module further comprises a unique molecular identifier (UMI) multiplication factor.

[0187] In some embodiments of the kits of the present disclosure, the UMI multiplier is adjacent to or contained within the ID region.

[0188] In some embodiments of the kits of the present disclosure, the UMI multiplication factor comprises or consists of between 1 and 5 nucleotides.

[0189] In some embodiments of the kits of the present disclosure, the UMI multiplier comprises or consists of about 1 to about 5 nucleotides.

[0190] In some embodiments of the kits of the present disclosure, the UMI multiplier is 3 nucleotides in length and comprises a nucleic acid sequence selected from a group of 64 unique nucleotide sequences.

[0191] In some embodiments of the kits of the present disclosure, the pool of ID regions comprises between 2 and 10,000 unique ID region sequences. In some embodiments, the pool of ID regions comprises between 10 and 500 unique ID region sequences. In some embodiments, the pool of ID regions comprises between 50 and 300 unique ID region sequences. In some embodiments of the kits of the present disclosure, the pool of ID regions comprises 60 unique ID region sequences.

[0192] In some embodiments of the kits of the present disclosure, the pool of ID regions comprises about 2 to about 10,000 unique ID region sequences. In some embodiments, the pool of ID regions comprises about 10 to about 300 unique ID region sequences. In some embodiments of the kits of the present disclosure, the pool of ID regions comprises about 50 to about 300 unique ID region sequences. In some embodiments of the kits of the present disclosure, the pool of ID regions comprises about 60 unique ID region sequences.

[0193] In some embodiments of the kits of the present disclosure, each ID region of the pool of ID regions is 8 nucleotides in length.

[0194] In some embodiments of the kits of the present disclosure, each ID region of the pool of ID regions is about 8 nucleotides in length.

[0195] In some embodiments of the kits of the present disclosure, each ID region sequence is at least a Hamming distance of 2 from any other ID region sequence.

[0196] In some embodiments of the kits of the present disclosure, each ID region is configured to identify the DNA fragment bound thereto.

[0197] In some embodiments of the kits of the present disclosure, each adaptor module of the set of adaptor modules is selected from the group consisting of between 64 and 2,560,000 unique nucleotide sequences.

[0198] In some embodiments of the kits of the present disclosure, each adaptor module of the set of adaptor modules is selected from the group consisting of about 64 to about 2,560,000 unique nucleotide sequences.

[0199] In some embodiments of the kits of the present disclosure, each adaptor module of the set of adaptor modules comprises a unique nucleotide sequence selected from 3840 unique nucleotide sequences, wherein each sequence of the 3840 unique nucleotide sequences is separated from any other sequence by a Hamming distance of at least 2.

[0200] In some embodiments of the kits of the present disclosure, the anchor region of each adapter of the set of adapters comprises one of four nucleotide sequences, and each ID region of a given sequence pairs with only one of the four anchor regions of the given sequence.

[0201] In some embodiments of the kits of the present disclosure, the amplification region of each adapter of the set of adapters comprises identical primer binding sites.

[0202] In some embodiments of the kits of the present disclosure, each ID region of the pool of ID regions is 8 nucleotides in length, and each ID region sequence is separated from any other ID region sequence by a Hamming distance of at least 2; each adapter of the set of adapters comprises a UMI multiplier adjacent to or contained within the ID region, and the UMI multiplier of each adapter of the set of adapters is 3 nucleotides in length; the UMI multiplier of a given sequence pairs with one ID region of the given sequence; the anchor region of each adapter of the set of adapters comprises one of four nucleotide sequences, and each ID region of the given sequence pairs with only one of the four anchor regions of the given sequence; and the amplification region of each adapter of the set of adapters comprises identical primer binding sites.

[0203] In some embodiments of the kits of the present disclosure, the kit comprises one adaptor set, hi some embodiments, the kit comprises more than one set of adaptor modules.

[0204] In some embodiments, the kits include between 2 and 1000 sets of adapter modules. In some embodiments, the kits include between 2 and 500 sets of adapter modules. In some embodiments, the kits include between 2 and 100 sets of adapter modules. In some embodiments, the kits include between 2 and 50 sets of adapter modules. In some embodiments, the kits include between 50 and 100 sets of adapter modules. In some embodiments, the kits include between 5 and 50 sets of adapter modules. In some embodiments, the kits include between 10 and 50 sets of adapter modules. In some embodiments, the kits include between 15 and 50 sets of adapter modules. In some embodiments, the kits include between 20 and 50 sets of adapter modules. In some embodiments, the kits include between 30 and 50 sets of adapter modules. In some embodiments, the kits include between 40 and 50 sets of adapter modules. In some embodiments, the kits include between 45 and 50 sets of adapter modules. In some embodiments, the kits include 48 sets of adapter modules.

[0205] In some embodiments, the kit includes about 2 to about 1000 sets of adaptor modules. In some embodiments, the kit includes about 2 to about 500 sets of adaptor modules. In some embodiments, the kit includes about 2 to about 100 sets of adaptor modules. In some embodiments, the kit includes about 2 to about 50 sets of adaptor modules. In some embodiments, the kit includes about 50 to about 100 sets of adaptor modules. In some embodiments, the kit includes about 5 to about 50 sets of adaptor modules. In some embodiments, the kit includes about 10 to about 50 sets of adaptor modules. In some embodiments, the kit includes about 15 to about 50 sets of adaptor modules. In some embodiments, the kit includes about 20 to about 50 sets of adaptor modules. In some embodiments, the kit includes about 30 to about 50 sets of adaptor modules. In some embodiments, the kit includes about 40 to about 50 sets of adaptor modules. In some embodiments, the kit includes about 45 to about 50 sets of adaptor modules. In some embodiments, the kit includes about 48 sets of adaptor modules.

[0206] In some embodiments of the kits of the present disclosure, each set of adapter modules is unique to a given test sample.

[0207] In some embodiments of the kits of the present disclosure, the kit includes one or more reagents for ligating adapters of an adapter set to DNA fragments of a test sample to generate an adapter-tagged DNA library. In some embodiments, the one or more reagents for ligating adapters include a DNA ligase. In some embodiments, the DNA ligase is T4 DNA ligase.

[0208] In some embodiments of the kits of the present disclosure, the set of adaptors is configured to be ligated to DNA fragments of the test sample using a method comprising: (a) ligating the set of adaptors to the DNA fragments to generate a plurality of adaptor / DNA fragment complexes; and (b) contacting the plurality of adaptor / DNA fragment complexes with one or more enzymes to form an adaptor-tagged DNA library comprising a plurality of adaptor-tagged DNA fragments. In some embodiments, each adaptor / DNA fragment complex comprises a ligation strand oligonucleotide ligated to each end of the DNA fragment. In some embodiments, non-ligation strand oligonucleotides are displaced from the adaptor / DNA fragment complexes in step (b).

[0209] In some embodiments of the kits of the present disclosure, the kit includes one or more reagents for amplifying an adapter-tagged DNA library to create a library postamplification (LPA). In some embodiments, the one or more reagents for amplifying the adapter-tagged DNA library include a DNA polymerase. In some embodiments, the one or more reagents for amplifying the adapter-tagged DNA library include one or more primers for PCR. In some embodiments, the one or more primers include a single primer sequence that is complementary to a primer binding site of the adapter amplification region.

[0210] In some embodiments of the kits of the present disclosure, the kit includes one or more reagents for generating an amplified whole genome library (WGLA) from an LPA. In some embodiments, the one or more reagents for generating the WGLA include one or more primers that hybridize to primer binding sites of the adapter amplification region. In some embodiments, the one or more primers include a sequencing adapter capable of binding to a flow cell. In some embodiments, the sequencing adapter includes a sequencing primer binding site. In some embodiments, the one or more reagents for generating the WGLA include a DNA polymerase.

[0211] In some embodiments of the kits of the present disclosure, the WGLA is sequence-matched.

[0212] In some embodiments of the kits of the present disclosure, the tail sequence of the capture probe module comprises a primer binding site.

[0213] In some embodiments of the kits of the present disclosure, the tail sequence comprises a sequencing primer binding site.

[0214] In some embodiments of the kits of the present disclosure, the tail sequence is configured to hybridize with a partner oligonucleotide.

[0215] In some embodiments of the kits of the present disclosure, each capture probe module is selected from a capture probe panel comprising a plurality of capture probe modules.

[0216] In some embodiments of the kits of the present disclosure, at least one capture probe module is configured to hybridize downstream of a specific DNA target region and at least one capture probe module is configured to hybridize upstream of a specific DNA target region.

[0217] In some embodiments of kits of the present disclosure, each capture probe of a plurality of capture probe modules is configured to hybridize to its target sequence within about 200 bp of any other capture probe.

[0218] In some embodiments of the kits of the present disclosure, each capture probe module of the capture probe panel hybridizes to an adaptor-tagged DNA fragment to form a plurality of adaptor-tagged DNA fragment-capture probe module complexes.

[0219] In some embodiments of the kits of the present disclosure, the partner oligonucleotide comprises a specific member of a binding pair that allows for isolation of the adaptor-tagged DNA fragment-capture probe module complex.

[0220] In some embodiments of the kits of the present disclosure, the partner oligonucleotide comprises a biotin molecule.

[0221] In some embodiments of the kits of the present disclosure, each capture probe module comprises a specific member of a binding pair that allows for isolation of the adaptor-tagged DNA fragment-capture probe module complex.

[0222] In some embodiments of the kits of the present disclosure, the capture probe module comprises a biotin molecule.

[0223] In some embodiments of the kits of the present disclosure, each capture probe module comprises a capture probe less than about 60 nucleotides in length.

[0224] In some embodiments of the kits of the present disclosure, each capture probe module comprises a capture probe less than 60 nucleotides in length.

[0225] In some embodiments of the kits of the present disclosure, each capture probe module comprises a capture probe less than about 40 nucleotides in length.

[0226] In some embodiments of the kits of the present disclosure, each capture probe module comprises a capture probe that is 40 nucleotides in length.

[0227] In some embodiments of the kits of the present disclosure, the kit comprises a component for isolating adaptor-tagged DNA fragment-capture probe module complexes, hi some embodiments, the component for isolating adaptor-tagged DNA fragment-capture probe module complexes comprises streptavidin.

[0228] In some embodiments of kits of the present disclosure, the kit includes one or more enzymes for enzymatically treating isolated adaptor-tagged DNA fragment-capture probe module complexes. In some embodiments, the one or more enzymes include a 5'-3' polymerase configured to extend each capture probe of the adaptor-tagged DNA fragment-capture probe module complexes using the adaptor-tagged DNA fragments as templates to create a plurality of hybrid molecules (a target capture library), wherein each hybrid molecule comprises a capture probe module and the complement of an adaptor-tagged DNA fragment.

[0229] In some embodiments of the kits of the present disclosure, the kit includes one or more reagents for amplifying hybrid molecules to create an amplified target capture library (TCLA), wherein the first modified library is a TCLA. In some embodiments, the one or more reagents for amplifying hybrid molecules include one or more primers comprising a sequencing adaptor capable of binding to a flow cell. In some embodiments, the sequencing adaptor comprises a sequencing primer binding site. In some embodiments, the one or more reagents for amplifying hybrid molecules includes a DNA polymerase.

[0230] In some embodiments of the kits of the present disclosure, the SRLs are configured to be sequenced in a single flow cell of a sequencing instrument.

[0231] In some embodiments of the kits of the present disclosure, the kit includes components for performing quantitative genetic analysis of the SRL. In some embodiments, the components for performing quantitative genetic analysis include one or more sequencing primers. In some embodiments, quantitative genetic analysis is used to detect nucleotide transitions or transversions, nucleotide insertions or deletions, genomic rearrangements, or copy number changes in test sample DNA fragments.

[0232] In some embodiments of the kits of the present disclosure, the test sample is obtained from a tissue biopsy. In some embodiments, the tissue biopsy is obtained from a tumor or tissue suspected to be a tumor. In some embodiments, the tissue biopsy is obtained from a malignant tumor or a tumor suspected to be malignant.

[0233] In some embodiments of the kits of the present disclosure, the DNA fragments of the test sample comprise cell-free DNA (cfDNA), genomic DNA (gDNA), complementary DNA (cDNA), mitochondrial DNA, methylated DNA, demethylated DNA, or a combination thereof.

[0234] In some embodiments of the kits of the present disclosure, the DNA fragments of the test sample comprise epigenetic marks.

[0235] In some embodiments of the kits of the present disclosure, the DNA fragments of the test sample are obtained from a library selected from the list consisting of a whole genome library, an amplicon library, a whole exome library, a cDNA library, or a methylated DNA library.

[0236] In some embodiments of the kits of the present disclosure, the test sample is obtained from a biological sample selected from the group consisting of an amniotic fluid sample, a blood sample, a skin sample, a hair sample, a hair follicle sample, a saliva sample, a mucus sample, a sweat sample, a tear sample, an epithelial tissue sample, a urine sample, a semen sample, a seminal plasma sample, a serum sample, a prostatic fluid sample, a pre-ejaculate (Cowper's fluid) sample, an ocular fluid sample, a stool sample, a biopsy sample, an ascites sample, a cerebrospinal fluid sample, a lymph sample, a tissue extract sample, a feces sample, and a formalin-fixed, paraffin-embedded (FFPE) sample.

[0237] In some embodiments of the kits of the present disclosure, the DNA fragments of the test sample are end-repaired prior to ligation to the adapters.

[0238] In some embodiments of the kits of the present disclosure, the kit includes one or more reagents for performing end repair. In some embodiments, the one or more reagents for performing end repair include one or more enzymes selected from DNA polymerase, kinase, and Klenow fragment. In some embodiments, the one or more reagents for performing end repair include DNA polymerase I, T4 DNA polymerase, T4 polynucleotide kinase, and Klenow fragment. In some embodiments, the one or more reagents for performing end repair include an end repair buffer. In some embodiments, the end repair buffer includes MgCl2, NaCl, Tris-HCl, DTT, KCL, and dNTPs.

[0239] Some embodiments of the present disclosure provide a method for performing an adapter quality control (QC) process on a set of adapters, where each adapter includes an adapter module.

[0240] In some embodiments of methods of performing an adapter QC process of the present disclosure, the adapter QC process includes a test for adapter ligation, wherein the test for adapter ligation includes (a) ligating a set of adapters to a predetermined amount of end-repaired DNA fragments to generate a library of adapter-tagged DNA fragments (LIBS); and (b) amplifying the LIBS to generate library postamplification (LPA); wherein the set of adapters is considered to have passed the test for adapter ligation if the concentration of LPA is greater than a predetermined concentration.

[0241] In some embodiments of the method of performing the adapter QC process of the present disclosure, the end-repaired DNA fragments of step (a) of the adapter ligation test are generated from a DNA sample. In some embodiments, the DNA sample is a blended DNA sample of at least two different cell lines. In some embodiments, the DNA sample is a blended DNA sample of two different cell lines. In some embodiments, the two different cell lines are blended at a 50:50 ratio. In some embodiments, the two different cell lines are NA09596 and NA12878. In some embodiments, the DNA sample is the 50:50 blend sample described in Example 15.

[0242] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the DNA sample used in the test for adapter ligation is different from the DNA sample used in the test for adapter distribution.

[0243] In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 5 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 10 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 15 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 20 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 25 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 30 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 35 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 40 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 50 ng.

[0244] In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is 5 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is 10 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is 15 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is 20 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is 25 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is 30 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is 35 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is 40 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is 50 ng.

[0245] In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between about 1 ng and about 100 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between about 1 ng and about 50 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between about 50 ng and about 100 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between about 5 ng and about 90 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between about 10 ng and about 80 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between about 20 ng and about 60 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between about 20 ng and about 50 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 20 ng to about 40 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 30 ng to about 50 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 40 ng to about 50 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 30 ng to about 40 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is about 20 ng to about 30 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is greater than about 100 ng.

[0246] In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between 1 ng and 100 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between 1 ng and 50 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between 50 ng and 100 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between 5 ng and 90 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between 10 ng and 80 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between 20 ng and 60 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between 20 ng and 50 ng. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between 20 ng and 40 ng. In some embodiments of the methods of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between 30 ng and 50 ng. In some embodiments of the methods of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between 40 ng and 50 ng. In some embodiments of the methods of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between 30 ng and 40 ng. In some embodiments of the methods of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is between 20 ng and 30 ng. In some embodiments of the methods of performing an adapter QC process of the present disclosure, the predetermined amount of end-repaired DNA fragments is greater than 100 ng.

[0247] In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is about 1 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is about 5 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is about 10 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is about 20 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is about 30 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is about 40 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is about 50 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is about 60 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is about 70 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is about 80 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is about 90 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is about 100 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is about 150 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is about 200 ng / μL.

[0248] In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is 1 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is 5 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is 10 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is 20 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is 30 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is 40 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is 50 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is 60 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is 70 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is 80 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is 90 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is 100 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is 150 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is 200 ng / μL.

[0249] In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between about 1 ng / μL and about 200 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is greater than about 200 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between about 10 ng / μL and about 100 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between about 10 ng / μL and about 90 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between about 20 ng / μL and about 80 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between about 10 ng / μL and about 80 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between about 30 ng / μL and about 80 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between about 40 ng / μL and about 80 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between about 50 ng / μL and about 80 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between about 50 ng / μL and about 70 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between about 60 ng / μL and about 70 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between about 50 ng / μL and about 60 ng / μL.

[0250] In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between 1 ng / μL and 200 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between 10 ng / μL and 100 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between 10 ng / μL and 90 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between 20 ng / μL and 80 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between 10 ng / μL and 80 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between 30 ng / μL and 80 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between 40 ng / μL and 80 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between 50 ng / μL and 80 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between 50 ng / μL and 70 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between 60 ng / μL and 70 ng / μL. In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is between 50 ng / μL and 60 ng / μL.

[0251] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is greater than about 200 ng / μL. In some embodiments of the methods of performing an adapter QC process of the present disclosure, the predetermined concentration of LPA is greater than 200 ng / μL.

[0252] In some embodiments of the disclosed methods of performing an adapter QC process, a set of adapters is considered to have passed the adapter QC process if it passes the test for adapter ligation.

[0253] In some embodiments of methods of performing the adapter QC process of the present disclosure, the adapter QC process includes a test for adapter distribution that includes: (a) ligating a set of adapters to a predetermined amount of end-repaired DNA fragments to generate a library of adapter-tagged DNA fragments (LIBS); (b) amplifying the LIBS using at least one primer that includes an index sequence to generate a library post-index amplification (LPIA); and (c) performing quantitative genetic analysis on the LPIA, wherein the set of adapters is considered to have passed the test for adapter distribution if one or more predetermined pass / fail criteria for the quantitative genetic analysis are met.

[0254] In some embodiments of the method of performing the adapter QC process of the present disclosure, the end-repaired DNA fragments of step (a) of testing for adapter distribution are generated from a DNA sample. In some embodiments, the DNA sample comprises wild-type (wt) cell-free DNA (cfDNA). In some embodiments, the DNA sample consists of wt cfDNA. In some embodiments, the DNA sample comprises wt cfDNA obtained from a healthy human. In some embodiments, the DNA sample is the wt cfDNA sample described in Example 16.

[0255] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the DNA sample used in the test for adapter distribution is different from the DNA sample used in the test for adapter ligation.

[0256] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the predetermined pass / fail criteria for the adapter QC process include criterion (a). In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.05% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.1% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.2% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.3% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.4% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.5% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.6% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.7% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.8% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.9% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 1% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 2% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 3% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 4% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 5% or less of the reads.

[0257] In some embodiments, criterion (a) is that barcode crosstalk is present in 0.05% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.1% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.2% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.3% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.4% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.5% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.6% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.7% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.8% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.9% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 1% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 2% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 3% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 4% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 5% or less of the reads.

[0258] In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.05% to about 10% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.05% to about 5% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.1% to about 5% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.05% to about 2% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.1% to about 1% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.1% to about 0.5% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.1% to about 0.4% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in about 0.1% to about 0.2% or less of the reads.

[0259] In some embodiments, criterion (a) is that barcode crosstalk is present in 0.05% to 10% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.05% to 5% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.1% to 5% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.05% to 2% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.1% to 1% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.1% to 0.5% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.1% to 0.4% or less of the reads. In some embodiments, criterion (a) is that barcode crosstalk is present in 0.1% to 0.2% or less of the reads.

[0260] In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined pass / fail criteria for the adapter QC process include criterion (b). In some embodiments, criterion (b) is that an unknown adapter is present in no more than about 1% of the reads. In some embodiments, criterion (b) is that an unknown adapter is present in no more than about 5% of the reads. In some embodiments, criterion (b) is that an unknown adapter is present in no more than about 10% of the reads. In some embodiments, criterion (b) is that an unknown adapter is present in no more than about 15% of the reads. In some embodiments, criterion (b) is that an unknown adapter is present in no more than about 20% of the reads. In some embodiments, criterion (b) is that an unknown adapter is present in no more than about 25% of the reads. In some embodiments, criterion (b) is that an unknown adapter is present in no more than about 30% of the reads. In some embodiments, criterion (b) is that an unknown adapter is present in no more than about 35% of the reads. In some embodiments, criterion (b) is that an unknown adapter is present in no more than about 40% of the reads. In some embodiments, criterion (b) is that an unknown adapter is present in no more than about 45% of the reads. In some embodiments, criterion (b) is that the unknown adaptor is present in no more than about 50% of the reads.

[0261] In some embodiments, criterion (b) is that the unknown adapter is present in no more than 1% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 5% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 10% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 15% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 20% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 25% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 30% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 35% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 40% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 45% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than 50% of the reads.

[0262] In some embodiments, criterion (b) is that the unknown adapter is present in no more than about 1% to about 50% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than about 1% to about 20% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than about 1% to about 15% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than about 1% to about 10% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than about 5% to about 20% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than about 5% to about 15% of the reads. In some embodiments, criterion (b) is that the unknown adapter is present in no more than about 5% to about 10% of the reads.

[0263] In some embodiments, criterion (b) is that unknown adapters are present in no more than 1%-50% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than 1%-20% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than 1%-15% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than 1%-10% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than 5%-20% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than 5%-15% of the reads. In some embodiments, criterion (b) is that unknown adapters are present in no more than 5%-10% of the reads.

[0264] In some embodiments of methods of performing an adapter QC process of the present disclosure, the predetermined pass / fail criteria for the adapter QC process include criterion (c). In some embodiments, criterion (c) is that about 10% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that about 20% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that about 30% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that about 40% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that about 50% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that about 60% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that about 70% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that about 80% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that about 90% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences.

[0265] In some embodiments, the predetermined pass / fail criteria for the adapter QC process include criterion (c). In some embodiments, criterion (c) is that no more than 10% of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that no more than 20% of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that no more than 30% of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that no more than 40% of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that no more than 50% of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that no more than 60% of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that 70% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that 80% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences. In some embodiments, criterion (c) is that 90% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all the unique adapter sequences.

[0266] In some embodiments, criterion (c) is that about 10 to about 90% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that about 10% to about 80% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that about 20% to about 80% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that about 30 to about 70% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that about 40% to about 60% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that about 40% to about 50% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that about 50% to about 60% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences.

[0267] In some embodiments, criterion (c) is that 10% to 90% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that 10% to 80% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that 20% to 80% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that 30% to 70% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that 40% to 60% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that 40% to 50% or less of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences. In some embodiments, criterion (c) is that no more than 50% to 60% of the unique adapter sequences have a number of reads that is 0% to 50% of the average number of reads of all unique adapter sequences.

[0268] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the predetermined pass / fail criteria for the adapter QC process include criterion (d). In some embodiments, criterion (d) is the presence of at least about 60% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 65% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 70% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 75% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 80% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 85% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 90% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 95% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 96% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 97% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 98% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 99% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 99.5% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of about 100% of all unique adapter sequences.

[0269] In some embodiments, criterion (d) is the presence of at least 60% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 65% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 70% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 75% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 80% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 85% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 90% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 95% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 96% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 97% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 98% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 99% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 99.5% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of 100% of all unique adapter sequences.

[0270] In some embodiments, criterion (d) is the presence of at least about 60% to about 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 70% to about 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 80% to about 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 90% to about 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 95% to about 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 96% to about 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 97% to about 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 98% to about 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 99% to about 99.9% of all unique adapter sequences.

[0271] In some embodiments, criterion (d) is the presence of at least 60% to 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 70% to 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 80% to 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 90% to 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 95% to 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 96% to 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 97% to 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 98% to 99.9% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 99% to 99.9% of all unique adapter sequences.

[0272] In some embodiments, criterion (d) is the presence of at least about 60% to about 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 70% to about 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 80% to about 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 90% to about 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 95% to about 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 96% to about 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 97% to about 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 98% to about 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least about 99% to about 100% of all unique adapter sequences.

[0273] In some embodiments, criterion (d) is the presence of at least 60% to 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 70% to 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 80% to 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 90% to 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 95% to 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 96% to 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 97% to 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 98% to 100% of all unique adapter sequences. In some embodiments, criterion (d) is the presence of at least 99% to 100% of all unique adapter sequences.

[0274] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the predetermined pass / fail criteria for the adapter QC process include criterion (e). In some embodiments, criterion (e) is that no more than about 5% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 10% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 15% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 20% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 25% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 30% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 35% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 40% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 45% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 50% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences.

[0275] In some embodiments, criterion (e) is that 5% or less of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that 10% or less of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that 15% or less of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that 20% or less of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that 25% or less of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that 30% or less of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that 35% or less of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than 40% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than 45% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than 50% of the unique adapter sequences have reads that are more than twice the average number of reads of all the unique adapter sequences.

[0276] In some embodiments, criterion (e) is that about 10% to about 50% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that about 5% to about 50% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that about 5% to about 40% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that about 10% to about 30% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that about 10% to about 20% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that about 20% to about 40% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 20% to about 30% of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 15% to about 25% of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences. In some embodiments, criterion (e) is that no more than about 15% to about 20% of the unique adapter sequences have reads that are greater than twice the average number of reads of all the unique adapter sequences.

[0277] In some embodiments, criterion (e) is that 1% to 50% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences. In some embodiments, criterion (e) is that 5% to 50% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences. In some embodiments, criterion (e) is that 5% to 40% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences. In some embodiments, criterion (e) is that 10% to 30% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences. In some embodiments, criterion (e) is that 10% to 20% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences. In some embodiments, criterion (e) is that 20% to 40% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences. In some embodiments, criterion (e) is that 20% to 30% or less of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences. In some embodiments, criterion (e) is that no more than 15%-25% of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences. In some embodiments, criterion (e) is that no more than 15%-20% of the unique adapter sequences have reads that are greater than twice the average number of reads of all unique adapter sequences.

[0278] In some embodiments of the method of performing an adapter QC process of the present disclosure, the predetermined pass / fail criteria for the adapter QC process include criterion (a) and criterion (b). In some embodiments, the predetermined pass / fail criteria include criterion (c), criterion (d), and criterion (e). In some embodiments, the predetermined pass / fail criteria include criterion (a), criterion (b), and criterion (c). In some embodiments, the predetermined pass / fail criteria include criterion (a), criterion (b), and criterion (d). In some embodiments, the predetermined pass / fail criteria include criterion (a), criterion (b), and criterion (e). In some embodiments, the predetermined pass / fail criteria include criterion (a), criterion (b), criterion (c), and criterion (d). In some embodiments, the predetermined pass / fail criteria include criterion (a), criterion (b), criterion (c), and criterion (e ... In some embodiments, the predetermined pass / fail criteria include criterion (a), criterion (b), criterion (c), criterion (d), and criterion (e). In some embodiments, the predetermined pass / fail criteria include at least one criterion selected from criteria (a), (b), (c), (d), and (e).

[0279] In some embodiments of the disclosed method of performing an adapter QC process, a set of adapters is considered to have passed the adapter QC process if it passes the adapter distribution test.

[0280] In some embodiments of the methods of performing an adapter QC process of the present disclosure, a set of adapters is considered to have passed the adapter QC process if it passes the test for adapter ligation and the test for adapter distribution.

[0281] In some embodiments of the methods of performing an adapter QC process of the present disclosure, each adapter of the set of adapters comprises a linker oligonucleotide and a non-linker oligonucleotide.

[0282] In some embodiments of the disclosed methods of performing the adapter QC process, the non-ligated strand oligonucleotide can hybridize to a region at the 3' end of the ligated strand oligonucleotide and form a duplex therewith.

[0283] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the linker oligonucleotide comprises an adapter module.

[0284] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the linker oligonucleotide comprises an overhang of dT, dA, dC, or dG at the 3' end.

[0285] In some embodiments of methods of carrying out the adapter QC process of the present disclosure, the unligated strand oligonucleotide comprises a modification at its 3' end that prevents ligation to the 5' end of the dsDNA fragment and / or adapter dimer formation, whereby the unligated strand is configured to be displaced from the double strand.

[0286] In some embodiments of the methods of performing an adapter QC process of the present disclosure, each adapter of the set of adapters comprises an ID region selected from a pool of unique ID regions, wherein the pool is selected from a plurality of pools, and the selected pool is unique to the test sample.

[0287] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the adapter module comprises: (a) an amplification region comprising a primer binding site; (b) an ID region; and (c) an anchor region.

[0288] In some embodiments of methods of performing an adapter QC process of the present disclosure, the amplification region comprises primer binding sites, wherein the primer binding sites allow for amplification using PCR (polymerase chain reaction), LAMP (loop-mediated isothermal amplification), NASBA (nucleic acid sequence-based amplification), SDA (standard displacement amplification), RCA (rolling circle replication), or LCR (ligase chain reaction).

[0289] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the amplified region comprises or consists of between 10 and 50 nucleotides. In some embodiments, the amplified region comprises or consists of between 20 and 30 nucleotides. In some embodiments, the amplified region comprises or consists of 25 nucleotides.

[0290] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the amplified region comprises or consists of about 10 to about 50 nucleotides. In some embodiments, the amplified region comprises or consists of about 20 to about 30 nucleotides. In some embodiments, the amplified region comprises or consists of about 25 nucleotides.

[0291] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the anchor region comprises an overhang at the 3' end.

[0292] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the anchor region comprises or consists of between 1 and 50 nucleotides. In some embodiments, the anchor region comprises or consists of between 5 and 25 nucleotides. In some embodiments, the anchor region comprises or consists of 10 nucleotides.

[0293] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the anchor region comprises or consists of about 1 to about 50 nucleotides. In some embodiments, the anchor region comprises or consists of about 5 to about 25 nucleotides. In some embodiments, the anchor region comprises or consists of about 10 nucleotides.

[0294] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the ID region comprises or consists of between 3 and 50 nucleotides. In some embodiments, the ID region comprises or consists of between 3 and 15 nucleotides. In some embodiments, the ID region comprises or consists of 8 nucleotides.

[0295] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the ID region comprises or consists of about 3 to about 50 nucleotides. In some embodiments, the ID region comprises or consists of about 3 to about 15 nucleotides. In some embodiments, the ID region comprises or consists of about 8 nucleotides.

[0296] In some embodiments of the method of performing an adapter QC process of the present disclosure, the adapter module further comprises a unique molecular identifier (UMI) multiplication factor.

[0297] In some embodiments of the methods of performing the adapter QC process of the present disclosure, the UMI multiplication factor is adjacent to or contained within the ID region.

[0298] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the UMI multiplication factor comprises or consists of between 1 and 5 nucleotides.

[0299] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the UMI multiplication factor comprises or consists of about 1 to about 5 nucleotides.

[0300] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the UMI multiplication factor is 3 nucleotides in length and comprises a nucleic acid sequence selected from a group of 64 unique nucleotide sequences.

[0301] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the pool of ID regions comprises between 2 and 10,000 unique ID region sequences. In some embodiments, the pool of ID regions comprises between 10 and 500 unique ID region sequences. In some embodiments, the pool of ID regions comprises between 50 and 300 unique ID region sequences. In some embodiments, the pool of ID regions comprises 60 unique ID region sequences.

[0302] In some embodiments of methods of performing an adapter QC process of the present disclosure, the pool of ID regions comprises between about 2 and about 10,000 unique ID region sequences. In some embodiments, the pool of ID regions comprises between about 10 and about 500 unique ID region sequences. In some embodiments, the pool of ID regions comprises between about 50 and about 300 unique ID region sequences. In some embodiments, the pool of ID regions comprises about 60 unique ID region sequences.

[0303] In some embodiments of the methods of performing an adapter QC process of the present disclosure, each ID region of the pool of ID regions is 8 nucleotides in length.

[0304] In some embodiments of the methods of performing an adapter QC process of the present disclosure, each ID region sequence is at least a Hamming distance of 2 from any other ID region sequence.

[0305] In some embodiments of the methods of performing an adapter QC process of the present disclosure, each ID region is configured to identify the DNA fragment bound to it.

[0306] In some embodiments of the methods of performing an adapter QC process of the present disclosure, each adapter module of the set of adapter modules is selected from the group consisting of between 64 and 2,560,000 unique nucleotide sequences.

[0307] In some embodiments of the methods of performing an adapter QC process of the present disclosure, each adapter module of the set of adapter modules is selected from the group consisting of between about 64 and about 2,560,000 unique nucleotide sequences.

[0308] In some embodiments of the methods of performing an adapter QC process of the present disclosure, each adapter module of the set of adapter modules comprises a unique nucleotide sequence selected from 3840 unique nucleotide sequences, wherein each sequence of the 3840 unique nucleotide sequences is separated from any other sequence by a Hamming distance of at least 2.

[0309] In some embodiments of the methods of performing the adapter QC process of the present disclosure, the anchor region of each adapter of the set of adapters comprises one of four nucleotide sequences, and each ID region of a given sequence pairs with only one of the four anchor regions of the given sequence.

[0310] In some embodiments of the methods of performing an adapter QC process of the present disclosure, the amplified region of each adapter of a set of adapters comprises identical primer binding sites.

[0311] In some embodiments of a method of performing an adapter QC process of the present disclosure, each ID region of the pool of ID regions is 8 nucleotides in length, and each ID region sequence is separated from any other ID region sequence by a Hamming distance of at least 2; each adapter of the set of adapters comprises a UMI multiplication factor adjacent to or contained within the ID region, and the UMI multiplication factor of each adapter of the set of adapters is 3 nucleotides in length; the UMI multiplication factor of a given sequence pairs with one ID region of the given sequence; the anchor region of each adapter of the set of adapters comprises one of four nucleotide sequences, and each ID region of the given sequence pairs with only one of the four anchor regions of the given sequence; and the amplification region of each adapter of the set of adapters comprises identical primer binding sites.

[0312] In some embodiments of methods of performing the adapter QC process of the present disclosure, the method includes (a) ligating a set of adapters to DNA fragments of a test sample to generate a plurality of adapter / DNA fragment complexes; and (b) contacting the plurality of adapter / DNA fragment complexes with one or more enzymes to form an adapter-tagged DNA library comprising a plurality of adapter-tagged DNA fragments. In some embodiments, each adapter / DNA fragment complex includes a ligation strand oligonucleotide ligated to each end of the DNA fragment. In some embodiments, non-ligation strand oligonucleotides are displaced from the adapter / DNA fragment complexes in step (b). In some embodiments, the set of adapters is any adapter set of the present disclosure.

[0313] Some embodiments of the present disclosure provide methods for performing a probe quality control (QC) process on one or more capture probe modules.

[0314] In some embodiments of a method for performing the probe QC process of the present disclosure, the method includes: (a) ligating a set of adapters to a DNA sample containing end-repaired DNA fragments to generate a library of adapter-tagged DNA fragments (LIBS); (b) amplifying the LIBS to generate a library postamplification (LPA); (c) dividing or diluting the LPA to generate a target capture LPA (TC LPA) and a whole genome LPA (WG LPA); (d) amplifying the WG LPA to generate an amplified whole genome library (WGLA); and (e) ligating one or more capture probe modules to be tested to a TC LPA. (f) isolating the adapter-tagged DNA fragment-capture probe module complexes to form isolated adapter-tagged DNA fragment-capture probe module complexes; (g) enzymatically treating the isolated adapter-tagged DNA fragment-capture probe module complexes to produce hybrid molecules, each hybrid molecule comprising a capture probe module and a complement of the adapter-tagged DNA fragment; (h) amplifying the hybrid molecules to produce an amplified target capture library (TCLA); (i) combining the WGLA and TCLA to form a sequence-matched library (SRL); and (j) performing quantitative genetic analysis on the SRL.

[0315] In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 1 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 10 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 15 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 20 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least about 25 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 30 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 35 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 40 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 45 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 50 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 55 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 60 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 65 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 70 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 75 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 80 ng / μL.

[0316] In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 1 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 10 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 15 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 20 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 25 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 30 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 35 ng / μL. In some embodiments of the kit of the present disclosure, the TC LPA is at least 40 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 45 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 50 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 55 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 60 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 65 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 70 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 75 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 80 ng / μL.

[0317] In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 1 ng / μL to about 100 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 1 ng / μL to about 80 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 10 ng / μL to about 80 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 10 ng / μL to about 70 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 10 ng / μL to about 60 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 20 ng / μL to about 60 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 20 ng / μL to about 50 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 20 ng / μL to about 40 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 30 ng / μL to about 50 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 30 ng / μL to about 40 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least about 20 ng / μL to about 30 ng / μL.

[0318] In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 1 ng / μL to 100 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 1 ng / μL to 80 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 10 ng / μL to 80 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 10 ng / μL to 70 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 10 ng / μL to 60 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 20 ng / μL to 60 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 20 ng / μL to 50 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 20 ng / μL to about 40 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 30 ng / μL to 50 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 30 ng / μL to 40 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TC LPA is at least 20 ng / μL to 30 ng / μL.

[0319] In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 0.1 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 0.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 1 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 1.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 2 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 2.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 3 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 3.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 4 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 4.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 5.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 6 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 6.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 7 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 7.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 8 ng / μL.

[0320] In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 0.1 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 0.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 1 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 1.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 2 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 2.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 3 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 3.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 4 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 4.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 5.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 6 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 6.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 7 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 7.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 8 ng / μL.

[0321] In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 0.1 ng / μL to about 10 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 0.1 ng / μL to about 8 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 1 ng / μL to about 10 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 1 ng / μL to about 5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 2 ng / μL to about 10 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 2 ng / μL to about 6 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least about 3 ng / μL to about 5 ng / μL. In some embodiments of the disclosed methods of performing a probe QC process, the WG LPA is at least about 3 ng / μL to about 4 ng / μL. In some embodiments of the disclosed methods of performing a probe QC process, the WG LPA is at least about 2 ng / μL to about 3 ng / μL.

[0322] In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 0.1 ng / μL to 10 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 0.1 ng / μL to 8 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 1 ng / μL to 10 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 1 ng / μL to 5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 2 ng / μL to 10 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 2 ng / μL to 6 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WG LPA is at least 3 ng / μL to 5 ng / μL. In some embodiments of the disclosed methods of performing a probe QC process, the WG LPA is at least 3 ng / μL to 4 ng / μL. In some embodiments of the disclosed methods of performing a probe QC process, the WG LPA is at least 2 ng / μL to 3 ng / μL.

[0323] In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 1.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 1.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 2.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 2.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 3.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 3.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 4.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 4.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 5.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 5.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 6.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 6.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 7.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 7.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 8.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 8.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 9.0 ng / μL.In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 9.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 10 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 15 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 20 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 25 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 30 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 35 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 40 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 45 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 50 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 55 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 60 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 65 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 70 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 75 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 80 ng / μL.

[0324] In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 1.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 1.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 2.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 2.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 3.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 3.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 4.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 4.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 5.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 5.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 6.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 6.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 7.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 7.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 8.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 8.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 9.0 ng / μL.In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 9.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 10 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 15 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 20 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 25 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 30 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 35 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 40 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 45 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 50 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 55 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 60 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 65 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 70 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 75 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 80 ng / μL.

[0325] In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 1 ng / μL to about 200 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 100 ng / μL to about 200 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 1 ng / μL to about 100 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least about 1 ng / μL to about 80 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 1 ng / μL to about 50 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 1 ng / μL to about 40 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least about 1 ng / μL to about 30 ng / μL. In some embodiments of the disclosed methods of performing a probe QC process, the TCLA is at least about 1 ng / μL to about 20 ng / μL. In some embodiments of the disclosed methods of performing a probe QC process, the TCLA is at least about 1 ng / μL to about 10 ng / μL. In some embodiments of the disclosed methods of performing a probe QC process, the TCLA is at least about 5 ng / μL to about 10 ng / μL.

[0326] In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 1 ng / μL to 200 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 100 ng / μL to 200 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 1 ng / μL to 100 ng / μL. In some embodiments of the kit of the present disclosure, the TCLA is at least 1 ng / μL to 80 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 1 ng / μL to 50 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 1 ng / μL to 40 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the TCLA is at least 1 ng / μL to 30 ng / μL. In some embodiments of the disclosed method of performing a probe QC process, the TCLA is at least 1 ng / μL to 20 ng / μL. In some embodiments of the disclosed method of performing a probe QC process, the TCLA is at least 1 ng / μL to 10 ng / μL. In some embodiments of the disclosed method of performing a probe QC process, the TCLA is at least 5 ng / μL to 10 ng / μL.

[0327] In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 1.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 1.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 2.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 2.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 3.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 3.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 4.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 4.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 5.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 5.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 6.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 6.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 7.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 7.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 8.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 8.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 9.0 ng / μL.In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 9.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 10 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 15 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 20 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 25 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 30 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 35 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 40 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 45 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 50 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 55 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 60 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 65 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 70 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 75 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 80 ng / μL.

[0328] In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 1.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 1.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 2.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 2.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 3.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 3.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 4.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 4.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 5.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 5.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 6.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 6.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 7.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 7.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 8.0 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 8.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 9.0 ng / μL.In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 9.5 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 10 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 15 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 20 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 25 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 30 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 35 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 40 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 45 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 50 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 55 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 60 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 65 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 70 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 75 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 80 ng / μL.

[0329] In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 1 ng / μL to about 200 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 100 ng / μL to about 200 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 1 ng / μL to about 100 ng / μL. In some embodiments of the kit of the present disclosure, the WGLA is at least about 1 ng / μL to about 80 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 1 ng / μL to about 50 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 1 ng / μL to about 40 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 1 ng / μL to about 30 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 1 ng / μL to about 20 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 1 ng / μL to about 10 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least about 5 ng / μL to about 10 ng / μL.

[0330] In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 1 ng / μL to 200 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 100 ng / μL to 200 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 1 ng / μL to 100 ng / μL. In some embodiments of the kit of the present disclosure, the WGLA is at least 1 ng / μL to 80 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 1 ng / μL to 50 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 1 ng / μL to 40 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 1 ng / μL to 30 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 1 ng / μL to 20 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 1 ng / μL to 10 ng / μL. In some embodiments of the method of performing a probe QC process of the present disclosure, the WGLA is at least 5 ng / μL to 10 ng / μL.

[0331] In some embodiments of the methods of performing a probe QC process of the present disclosure, one or more capture probe modules are considered to have passed the probe QC process if one or more predetermined pass / fail criteria for quantitative genetic analysis are met.

[0332] In some embodiments of the disclosed methods of performing a probe QC process, the predetermined pass / fail criteria for the probe QC process include criterion (a). In some embodiments, criterion (a) is that about 100% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.8% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.7% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.6% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.5% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.4% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.3% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.2% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99.1% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 99% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98.9% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98.8% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98.7% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98.6% of the capture probes have at least one total read.In some embodiments, criterion (a) is that at least about 98.5% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98.4% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98.3% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98.2% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98.1% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 98% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 97% of the capture probes have at least one total read. In some embodiments, criterion (a) is that at least about 96% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least about 95% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least about 90% of the capture probes have at least one total read. In some embodiments of the kits of the present disclosure, criterion (a) is that at least about 85...

Claims

1. A method for simultaneous DNA analysis, comprising: (a) performing a first process on a first adaptor-tagged library comprising a first locus to generate a first modified library; (b) performing a second process on a second adaptor-tagged library that includes a second locus to generate a second modified library; wherein the first process and the second process are not identical; (c) contacting the first modified library with the second modified library to generate a combinatorial library; The method, wherein the first adaptor-tagged library and the second adaptor-tagged library are derived from the same adaptor-tagged parent library.

2. The method of claim 1, wherein the first process includes contacting a first adaptor-tagged library with a capture probe, and the second process includes amplifying or extending DNA fragments of a second adaptor-tagged library.

3. The method of claim 1, wherein the first process generates a target capture library and the second process generates a whole genome library.

4. The method described in claim 1, wherein the first modified library is a target capture library (TCL) or an amplified target capture library (TCLA).

5. The method described in claim 1, wherein the second modified library is a whole genomic library (WGL) or an amplified whole genomic library (WGLA).

6. The method described in claim 1, wherein the first modified library is an amplified target capture library (TCLA) and the second modified library is an amplified whole genome library (WGLA).

7. A method described in any one of claims 1 to 6, further comprising performing targeted genetic analysis and broad coverage whole genome analysis on the combinatorial library.

8. A method according to any one of claims 1 to 6, further comprising an initiation step of dividing the adaptor-tagged parent library into at least two partitions, wherein a first partition is the first adaptor-tagged library and a second partition is the second adaptor-tagged library.

9. The method of claim 1, wherein the first modified library comprises: a first DNA molecule comprising, from 5' to 3', a 5' oligonucleotide (A1), a first 5' adaptor module, a sequence of a first locus, and a 3' oligonucleotide (A2); or a first DNA molecule comprising, from 5' to 3', a 5' oligonucleotide (A1), a sequence of a first locus, a first 3' adaptor module, and a 3' oligonucleotide (A2); or a first DNA molecule comprising, from 5' to 3', a 5' oligonucleotide (A1), a first 5' adaptor module, a sequence of a first locus, a first 3' adaptor module, and a 3' oligonucleotide (A2); the first locus comprises a DNA region; a first test sample comprising a DNA molecule having a sequence identical to or a complementary sequence to a sequence of the first locus; the first 5' adaptor module, the first 3' adaptor module, or both, are attached to the first locus in the first adaptor-tagged library; the second modified library comprising: a second DNA molecule comprising, from 5' to 3', a 5' oligonucleotide (B1), a second 5' adaptor module, a sequence of a second locus, and a 3' oligonucleotide (B2); or a second DNA molecule comprising, from 5' to 3', a 5' oligonucleotide (B1), a sequence of a second locus, a second 3' adaptor module, and a 3' oligonucleotide (B2); or a second DNA molecule comprising, from 5' to 3', a 5' oligonucleotide (B1), a second 5' adaptor module, a sequence of a second locus, a second 3' adaptor module, and a 3' oligonucleotide (B2); the second locus comprises a DNA region; a second test sample comprising a DNA molecule having a sequence identical to or a complement of a sequence at said second locus; the second 5' adaptor module, the second 3' adaptor module, or both, are attached to the second locus within the second adaptor-tagged library; Either the first modified library or the second modified library comprises a library tag; or 7. The method of any one of claims 1 to 6, wherein the first modified library comprises a first library tag and the second modified library comprises a second library tag, and the first library tag and the second library tag are not identical.

10. A method described in any one of claims 1 to 6, wherein the first adaptor-tagged library and the second adaptor-tagged library each contain an adaptor module.

11. The method of any one of claims 1 to 6, wherein each adapter of the first adaptor-tagged library and the second adaptor-tagged library comprises a linking strand oligonucleotide and a non-linking strand oligonucleotide, the non-linking strand oligonucleotide being capable of hybridizing to a region at the 3' end of the linking strand oligonucleotide and forming a duplex therewith.

12. The method of any one of claims 1 to 6, wherein each adapter in the first adaptor-tagged library and the second adaptor-tagged library is selected from a set of adapters, each adapter in the set of adapters comprises an ID region selected from a pool of unique ID regions, the pool being selected from a plurality of pools, and the selected pool being unique to the test sample.

13. The method of any one of claims 1 to 6, wherein each adapter of the first adaptor-tagged library and the second adaptor-tagged library comprises an adaptor module comprising: a. an amplified region comprising a primer binding site; b. an ID region; C. Anchor region.

14. The method of claim 13, wherein the ID region identifies both the sample and the DNA fragment.

15. The first process comprises: (a) contacting said first adaptor-tagged library with one or more capture probes under conditions suitable for hybridization to form one or more capture probe / adaptor-tagged DNA complexes, wherein each capture probe comprises: a first region comprising a primer binding site; a second region capable of hybridizing to a target region within the first locus of the first adaptor-tagged library; (b) isolating the one or more capture probe / adapter-tagged DNA complexes from step (a), wherein each isolated capture probe / adapter-tagged DNA complex comprises a capture probe and an adaptor-tagged DNA molecule; (c) enzymatically treating the one or more isolated capture probe / adapter-tagged DNA complexes from step (b) to generate one or more adaptor-tagged hybrid nucleic acid molecules, wherein each hybrid nucleic acid molecule comprises: (i) at least a portion of the capture probe or its complement; and (ii) at least a portion of the adaptor-tagged DNA molecule or its complement.

16. The method of claim 15, wherein the second process generates a whole genome library.

17. The method of claim 16, further comprising performing targeted genetic analysis and broad coverage whole genome analysis on the combinatorial library.

18. The method of any one of claims 1 to 6 and 15 to 17, wherein the second process comprises amplifying or extending a second locus of the second adaptor-tagged library, wherein the amplifying or extending comprises hybridizing a first primer comprising a 5' oligonucleotide (B1) and a second primer comprising a 3' oligonucleotide (B2) to the adaptor-tagged DNA molecule, at least one of B1 and B2 comprising a library tag, and the amplified or extended locus comprises B1 and B2.

19. The method of any one of claims 1 to 6 and 15 to 17, further comprising performing genetic analysis.

20. The method of any one of claims 1 to 6 and 15 to 17, further comprising combining the first modified library with the second modified library to form a sequence-matched library.

21. The method of any one of claims 1 to 6 and 15 to 17, further comprising: linking an adapter to a DNA fragment of a test sample to generate a plurality of adapter / DNA fragment complexes; and contacting the plurality of adapter / DNA fragment complexes with one or more enzymes to form an adapter-tagged DNA library comprising a plurality of adapter-tagged DNA fragments.

22. The method of claim 21, wherein the plurality of adaptor-tagged DNA fragments form the adaptor-tagged parent library.

23. The method of claim 21, wherein the test sample comprises a biological sample selected from the group consisting of an amniotic fluid sample, a blood sample, a skin sample, a hair sample, a hair follicle sample, a saliva sample, a mucus sample, a sweat sample, a tear sample, an epithelial tissue sample, a urine sample, a semen sample, a seminal plasma sample, a serum sample, a prostatic fluid sample, a pre-ejaculate (Cowper's fluid) sample, an ocular fluid sample, a fecal sample, a biopsy sample, a peritoneal fluid sample, a cerebrospinal fluid sample, a lymphatic fluid sample, a tissue sample, a tissue extract sample, a fecal sample, and a formalin-fixed paraffin-embedded (FFPE) sample.

24. The method of claim 21, wherein the test sample comprises DNA, a DNA fragment, cell-free DNA (cfDNA), genomic DNA (gDNA), complementary DNA (cDNA), mitochondrial DNA, methylated DNA, demethylated DNA, or a DNA molecule containing an epigenetic mark.

25. A set of adaptors, each adaptor comprising an adaptor module comprising an amplified region; b. one or more capture probe modules, each capture probe module comprising a tail sequence and a capture probe sequence capable of hybridizing to a target sequence in a test sample, the tail sequence of each capture probe module comprising a library tag; c. a first primer pair comprising a first F primer and a first R primer, wherein the first F primer comprises an amplification region binding region and a sequencing primer binding region, and the first R primer comprises a library tag binding region and a sequencing primer binding region; d. a second primer pair comprising a second F primer and a second R primer, wherein said second F primer and said second R primer comprise an amplification region binding region and a sequencing primer binding region, respectively, and wherein none of the primers of said second primer pair binds to said library tag.

26. The kit described in claim 25, used to generate a first modified library and a second modified library.

27. The method of claim 27, wherein the first modified library comprises DNA fragments comprising an adaptor, a capture probe module, and a target sequence for the capture probe module; 27. The kit of claim 26, wherein the second modified library comprises DNA fragments comprising adaptors and at least a portion of a DNA sequence of a test sample.

28. The kit of claim 25 used to generate combinatorial sequence-matched DNA libraries (SRLs), target capture libraries (TCLs), amplified target capture libraries (TCLAs), libraries of adaptor-tagged DNA fragments (LIBS), library postamplification (LPA), low pass whole genome (LPWG) libraries, whole genome LPAs (WG LPAs), target capture LPAs (TC LPAs) and amplified whole genome libraries (WGLAs).