Methods for detecting single nucleotide polymorphisms (SNPS) associated with pre-term delivery and kits therefor

Abstract

The present disclosure provides a method for detecting single nucleotide polymorphisms (SNPs) in a biological sample, said method comprising sequencing DNA from the biological sample and genotyping at least 40 SNPs located at a set of SNP loci in the biological sample. The genotyping is carried out for both copies of each locus. The method of the present disclosure may help in predicting susceptibility of a subject to a pre-term delivery. The present disclosure also provides a kit for performing the methods described herein.

Description

[0001] METHODS FOR DETECTING SINGLE NUCLEOTIDE POLYMORPHISMS (SNPs) AND KITS THEREOF CROSS-REFERENCE TO RELATED APPLICATIONS

[0002] This application claims the benefit of priority to Indian Provisional Application No.

[0003] 202531001584, filed on January 7, 2025, the contents of which are incorporated by reference herein in their entirety.

[0004] REFERENCE TO SEQUENCE LISTING

[0005] This application includes an electronically submitted sequence listing in XML format. The XML file contains a sequence listing entitled “IP83183_SeqList_ST26” created on January 7, 2026, and having a size of -71KB. The sequence listing contained in this XML file is part of the specification and is incorporated herein by reference in its entirety.

[0006] TECHNICAL FIELD

[0007] The present disclosure relates generally to the field of genomics. More particularly, the present disclosure relates to detection of single nucleotide polymorphisms (SNPs) in biological samples.

[0008] BACKGROUND OF THE DISCLOSURE

[0009] Preterm birth (PTB) (birth before 37 weeks) poses a global health challenge and is the largest cause of neonatal mortality and is linked to various health adversities in childhood and adult life. There has been no improvement in the PTB rates over the past decade (2010-20), especially in the regions with the highest burdens despite global improvement in socioeconomic conditions. India is currently among the top five countries with a high rate of PTB. In 2020, an estimated 13.4 million live births were preterm, of which India recorded the highest number of PTBs, accounting for over 23% of all PTBs worldwide. Majority of PTBs are spontaneous, with no known etiology. The multifactorial nature of spontaneous preterm birth (sPTB) involves complex interactions between genetic, environmental, and physiological factors. Genetic predisposition plays a significant role in influencing sPTB risk. However, the extent of genetic influence is known to vary across different populations emphasizing the need for population-specific genomic studies for sPTB.Although India and other south Asian countries contribute the highest numbers of PTBs, investigations on genomic triggers of this adverse birth outcome are lacking, except for a limited nested-case control analysis. Thus, there is an urgent need to devise methods that can assess the genetic predisposition of women to PTB. This information alone may not accurately predict the chances of delivering pre-term in a pregnant woman. This information could then be used along with other factors determining pre-term birth such as environmental factors, physiological factors, family history, etc. to assess the risk of women to PTB. The present disclosure attempts to address this need.

[0010] SUMMARY OF THE DISCLOSURE

[0011] The present disclosure provides a method for detecting single nucleotide polymorphisms (SNPs) in a biological sample, said method comprising sequencing DNA from the biological sample and genotyping at least 40 SNPs located at a set of SNP loci in the biological sample, wherein the set of SNP loci comprises: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rsl2414133 (A / G), rs43870 (T / C), rs280179 (G / A), rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsl 1967047 (T / C), rsl516501 (C / T), rs3104369 (C / T), and rs972544 (A / C).

[0012] In another aspect, the present disclosure provides a method for identifying susceptibility of a subject to a pre-term delivery, said method comprising:

[0013] sequencing DNA from a biological sample of the subject and genotyping at least 40 SNPs at a set of SNP loci in the biological sample, wherein the set of SNP loci comprises: rs!43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rs!6827662 (G / A), rs73158515(G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rsl2414133 (A / G), rs43870 (T / C), rs280179 (G / A), rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsll967047 (T / C), rsl 516501 (C / T), rs3104369 (C / T), and rs972544 (A / C);

[0014] wherein the presence of risk alleles at one or more SNP loci indicates the susceptibility of the individual to pre-term delivery.

[0015] In some embodiments, the present disclosure provides a kit for detecting single nucleotide polymorphisms (SNPs) in a biological sample, said kit comprising primers for genotyping at least 40 SNPs located at a set of SNP loci in the biological sample, wherein the set of SNP loci comprises: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rsl2414133 (A / G), rs43870 (T / C), rs280179 (G / A), rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsll967047 (T / C), rsl 516501 (C / T), rs3104369 (C / T), and rs972544 (A / C).BRIEF DESCRIPTION OF THE ACCOMPANYING FIGURES

[0016] In order that the disclosure may be readily understood and put into practical effect, reference will now be made to exemplary embodiments as illustrated with reference to the accompanying figures. The figures together with description below, are incorporated in and form part of the specification, and serve to further illustrate the embodiments and explain various principles and advantages, where:

[0017] Figure 1 is a Manhattan plot depicting association of the maternal nuclear genomic variants with spontaneous preterm birth. Blue line indicates the suggestive significance threshold of lx IO'5, and the red line indicates the genome-wide significance threshold of 5xl0'8.

[0018] Figure 2 is a Manhattan plot of the results of transethnic meta-analysis of preterm birth. The red dots above the genome-wide significance threshold (red line) indicate 25 SNPs those were associated with sPTB in Indian women and European cohorts. The blue dots indicate other 110 SNPs those were associated with sPTB in only European cohorts.

[0019] Figure 3 shows a schematic of library preparation and sequencing according to one embodiment.

[0020] DETAILED DESCRIPTION OF THE DISCLOSURE

[0021] Before describing the invention in greater detail, it is important to take note of the common terms and phrases that are employed throughout the present disclosure for better understanding of the technology provided herein.

[0022] As used herein, the term ‘comprising’ when placed before the recitation of steps in a method means that the method encompasses one or more steps that are additional to those expressly recited, and that the additional one or more steps may be performed before, between, and / or after the recited steps. For example, a method comprising steps a, b, and c encompasses a method of steps a, b, x, and c, a method of steps a, b, c, and x, as well as a method of steps x, a, b, and c. Furthermore, the term “comprising” when placed before the recitation of steps in a method does not (although it may) require sequential performance of the listed steps, unless the content clearly dictates otherwise. For example, a method comprising steps a, b, and c encompasses, for example, a method of performing steps in the order of steps a, c, and b, the order of steps c, b, and a, and the order of steps c, a, and b, etc.With respect to the use of substantially any plural and / or singular terms herein, those having skill in the art can translate from the plural to the singular and / or from the singular to the plural as is appropriate to the context and / or application. The various singular / plural permutations may be expressly set forth herein for sake of clarity. The use of the expression “at least” or “at least one” suggests the use of one or more elements or ingredients or quantities, as the use may be in the embodiment of the disclosure to achieve one or more of the desired objects or results.

[0023] Throughout this specification, the word “comprise”, or variations such as “comprises” or “comprising” or “containing” or “has” or “having”, or “including but not limited to” wherever used, will be understood to imply the inclusion of a stated element, integer or step, or group of elements, integers or steps, but not the exclusion of any other element, integer or step, or group of elements, integers or steps.

[0024] Reference throughout this specification to “some embodiments”, “one embodiment” or “an embodiment” means that a particular feature, structure or characteristic described in connection with the embodiment may be included in at least one embodiment of the present disclosure. Thus, the appearances of the phrases “in some embodiments”, “in one embodiment” or “in an embodiment” in various places throughout this specification may not necessarily all refer to the same embodiment. It is appreciated that certain features of the disclosure, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the disclosure, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable sub-combination.

[0025] The term “about” as used herein encompasses variations of + / -5% and more preferably + / -2.5%, as such variations are appropriate for practicing the present invention.

[0026] As used herein, the term "risk allele" refers to one of the alternative forms of the same SNP or an alternative form at the same genetic locus that increases the risk of PTB.

[0027] The use of any and all examples, or exemplary language (e.g., “such as”) provided with respect to certain embodiments herein is intended merely to better illustrate the disclosure and does not pose a limitation on the scope of the disclosure otherwise claimed.The present disclosure provides a method for detecting single nucleotide polymorphisms (SNPs) in a biological sample, said method comprising:

[0028] sequencing DNA from the biological sample and genotyping at least 40 SNPs located at a set of SNP loci in the biological sample, wherein the set of SNP loci comprises: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rsl2414133 (A / G), rs43870 (T / C), rs280179 (G / A), rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsll967047 (T / C), rsl 516501 (C / T), rs3104369 (C / T), and rs972544 (A / C).

[0029] In some embodiments, the present disclosure provides a method for detecting single nucleotide polymorphisms (SNPs) in a biological sample, said method comprising:

[0030] sequencing DNA from the biological sample and genotyping at least 40 SNPs in both copies of a set of SNP loci in the biological sample, wherein the set of SNP loci comprises: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A),rs825082 (A / G), rs825084 (C / T), rsl2414133 (A / G), rs43870 (T / C), rs280179 (G / A), rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsll967047 (T / C), rsl 516501 (C / T), rs3104369 (C / T), and rs972544 (A / C).

[0031] In some embodiments, the method comprises sequencing DNA from the biological sample and genotyping at least 45, at least 50, at least 55, at least 60, at least 65 or all 68 SNPs from the above set of SNP loci.

[0032] In some embodiments, the method for detecting SNPs in a biological sample comprises sequencing DNA from the biological sample and genotyping the following SNPs in the biological sample: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), and rs35362309 (A / G).

[0033] In some embodiments, the method for detecting SNPs in a biological sample comprises sequencing DNA from the biological sample and genotyping the following SNPs in the biological sample: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rs!2414133 (A / G),rs43870 (T / C), rs280179 (G / A), rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsl 1967047 (T / C), rsl516501 (C / T), rs3104369 (C / T), and rs972544 (A / C).

[0034] In some exemplary, non-limiting embodiments, the method comprises genotyping all 68 SNPs from the above set of SNP loci.

[0035] In some exemplary, non-limiting embodiments, the method comprises genotyping all 68 SNPs in both copies of the above set of SNP loci.

[0036] Accordingly, in some exemplary embodiments, the present disclosure provides a method for detecting single nucleotide polymorphisms (SNPs) in a biological sample, said method comprising:

[0037] sequencing DNA from the biological sample and genotyping 68 SNPs located at a set of SNP loci in the biological sample, wherein the set of SNP loci comprises: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl 6949470 (A / G), rsl 0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rsl2414133 (A / G), rs43870 (T / C), rs280179 (G / A), rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsll967047 (T / C), rsl 516501 (C / T), rs3104369 (C / T), and rs972544 (A / C).

[0038] The step of genotyping provides information on the presence of risk allele at a given SNP locus.

[0039] In some embodiments, the risk allele may be present in the SNP in a single copy or both copies of the locus.In some embodiments, the genotype at the SNP loci described above may be determined by any number of methods, such as, but not limited to, analyzing the DNA sequence directly, analyzing an RNA transcript (e.g., mRNA) or a gene expression product (e.g., a protein).

[0040] In some embodiments, the biological sample is selected from blood (e.g., peripheral blood or dry blood spot obtained from peripheral blood or finger pricking), buccal swab, urine, saliva, or any combination thereof.

[0041] In some embodiments, the biological sample is a dry blood sample.

[0042] In some embodiments, the step of sequencing DNA from the biological sample comprises:

[0043] • preparing a DNA library from the biological sample; and

[0044] • sequencing the DNA library to obtain sequence information to determine the genotype at a given locus.

[0045] In some exemplary embodiments, the step of sequencing DNA from the biological sample comprises:

[0046] • preparing a DNA library from the biological sample; and

[0047] • sequencing the DNA library to obtain sequence information to determine the genotype in both copies of a given locus.

[0048] There are several methods known in the art and many commercial kits are available to prepare DNA libraries for sequencing purposes. For example, a DNA library can be prepared by primer extension target enrichment that employs a hybridization capture technology designed to employ primer extension reactions to specifically capture and release target library molecules for sequencing. After library preparation, a biotinylated target specific capture primer anneals with the target region / fragment and is extended on the target library fragments. A bead wash is employed to remove the off-target library fragments. Then a target specific release primer anneals upstream to the same strand and while it is extended, releases the target library molecules from the capture-extension hybrids into the supernatant. The supernatant is then highly enriched with high specificity to the targeted regions. A final short universal primed library amplification provides libraries ready for quality check (QC), prior to sequencing in 6-8 hours. An exemplary schematic of library preparation and sequencing / genotyping is shown in Figure 3.

[0049] In some embodiments, determining the genotype may be direct or indirect. While the direct method involves analyzing the DNA sequence directly, the indirect method may involve analyzing an RNA transcript, such as but not limiting to messenger RNA transcripts or analyzing gene expression products, such as polypeptides / proteins.

[0050] Accordingly, in some embodiments, the method of the present disclosure involves sequencing RNA transcript or gene expression products to determine the genotype at a given SNP locus.

[0051] In some exemplary, non-limiting embodiments, the method of the present disclosure involves sequencing RNA transcript or gene expression products to determine the genotype in both copies of a given SNP locus.

[0052] Accordingly, in some exemplary embodiments, the present disclosure provides a method for detecting single nucleotide polymorphisms (SNPs) in a biological sample, said method comprising:

[0053] sequencing a gene expression product from the biological sample and genotyping the presence of at least 40 SNPs in the gene expression product, wherein the 40 SNPs are selected from a set of SNP loci wherein the set of SNP loci comprises: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rs!2414133 (A / G), rs43870 (T / C), rs280179 (G / A), rs!2212888 (G / A),rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsl 1967047 (T / C), rsl 516501 (C / T), rs3104369 (C / T), and rs972544 (A / C).

[0054] In some embodiments, the method for detecting SNPs in a biological sample comprises sequencing a gene expression product from the biological sample and genotyping the presence of the following SNPs in the gene expression product: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), and rs35362309 (A / G),

[0055] In some other exemplary, non-limiting embodiments, the present disclosure provides a method for detecting single nucleotide polymorphisms (SNPs) in a biological sample, said method comprising:

[0056] sequencing a gene expression product from the biological sample and genotyping the presence of the following 68 SNPs in the gene expression product: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rsl2414133 (A / G), rs43870 (T / C), rs280179 (G / A), rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsll967047 (T / C), rsl 516501 (C / T), rs3104369 (C / T), and rs972544 (A / C).In some embodiments, the gene expression product is RNA. In some embodiments, the RNA includes messenger RNA (mRNA) transcript, tRNA or both. In some embodiments, the gene expression product is a protein / polypeptide.

[0057] In some embodiments, the sequencing is carried out by next generation sequencing.

[0058] In some embodiments, the next generation sequencing is selected from a group comprising Illumina (Solexa) sequencing, Lynx therapeutics’ massively parallel signature sequencing (MPSS), Polony sequencing, Pyrosequencing, Solid sequencing, DNA nanoball sequencing, Helioscope single molecule sequencing, Single molecule long read sequencing and Single molecule real time (RNAP) sequencing.

[0059] The method of the present disclosure is carried out in vitro.

[0060] In some embodiments, the present disclosure provides a method that predicts / identifies the susceptibility of a subject to pre-term delivery / pre-term birth. One of ordinary skill in the art understands that prediction is different from diagnosis. In particular, prediction refers to chance or a possibility that a person may have a specific condition / disorder / disease in future,' i.e., at the time of prediction, the person is not suffering from any symptom or a condition / disorder / disease whereas diagnosis refers to identification by a doctor / clinician / radiologist that a person has the condition / disorder / disease at the time of diagnosis.

[0061] Accordingly, in some embodiments, provided herein is a method for predicting / identifying susceptibility of a subject to a pre-term delivery, said method comprising: sequencing DNA from a biological sample of the subject and genotyping at least 40 SNPs at a set of SNP loci in the biological sample, wherein the set of SNP loci comprises: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rs!7307967 (C / T), rs!0917151 (G / A), rs!2345249 (C / T), rs!374927 (C / T), rs!40281307(C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rsl2414133 (A / G), rs43870 (T / C), rs280179 (G / A), rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsl 1967047 (T / C), rsl 516501 (C / T), rs3104369 (C / T), and rs972544 (A / C), wherein the presence of a risk allele at one or more loci from the set of SNP loci indicates the susceptibility of the individual to preterm delivery.

[0062] In some embodiments, the method for predicting / identifying susceptibility of a subject to a preterm delivery comprises: sequencing DNA from a biological sample of the subject and genotyping the following SNPs in the biological sample: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), and rs35362309 (A / G), wherein the presence of a risk allele at one or more loci indicates the susceptibility of the individual to pre-term delivery.

[0063] In some embodiments, the method for predicting / identifying susceptibility of a subject to a preterm delivery comprises: sequencing DNA from a biological sample of the subject and genotyping the following 68 SNPs in the biological sample: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307(C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rsl2414133 (A / G), rs43870 (T / C), rs280179 (G / A), rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsl 1967047 (T / C), rsl 516501 (C / T), rs3104369 (C / T), and rs972544 (A / C), wherein the presence of a risk allele at one or more loci indicates the susceptibility of the individual to pre-term delivery.

[0064] In some embodiments, the presence of risk allele in one or both copies of at least 2, at least 5, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55, at least 60, at least 65, at least 66, or all 68 of the above set of SNP loci indicates the susceptibility of the individual to pre-term delivery.

[0065] Accordingly, while the present embodiments relate to a method for identifying susceptibility of a subject to a pre-term delivery, all aspects of the method, including the steps involved are as described in any of the previous embodiments and are not being reiterated for the sake of brevity.

[0066] For some SNP loci, the presence of risk allele in both copies may indicate greater susceptibility to pre-term delivery compared to the presence of risk allele in one copy. For some other SNP loci, the presence of risk allele in just one copy may be sufficient to increase the susceptibility of the individual to pre-term delivery.

[0067] In some embodiments, the subject is a human female.

[0068] In some exemplary embodiments, the subject is an Indian female.

[0069] Accordingly, in some exemplary non-limiting embodiments, the method of the present disclosure predicts / identifies susceptibility of an Indian female to a pre-term delivery.

[0070] In some embodiments, the method of the present disclosure is only one of the ways to help a clinician predict the risk or genetic susceptibility of a female individual to pre-term birth.However, since pre-term birth is caused by a multitude of factors such as environmental, physiological, family history, etc., each of those factors must be considered in combination with the method of the present disclosure for ascertaining susceptibility to pre-term birth with high accuracy and accordingly help initiate targeted interventions and improve maternal and neonatal health outcomes.

[0071] The present disclosure also relates to a kit for carrying out the method described in any one of the previous embodiments.

[0072] In some embodiments, the kit comprises components such as, but not limited to, one or more of primers, probes, antibodies, protein-capture agent(s), reagent(s), reaction buffer(s), instruction sheet(s) and any other elements useful to determine the genotype and identify the alleles present in the SNP loci described herein.

[0073] In some embodiments, the reagent(s) may be specific for detecting / determining the genotype at one or more of the 68 SNP loci, as described herein. Accordingly, depending on whether genotyping is direct or indirect, the reagent may be a polynucleotide, or an array of polynucleotides, or an antibody or a panel of antibodies.

[0074] In some embodiments, the present disclosure provides a kit for detecting single nucleotide polymorphisms (SNPs) in a biological sample, said kit comprising primers for genotyping at least 40 SNPs located at a set of SNP loci in the biological sample, wherein the set of SNP loci comprises: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rs!0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rs!2414133 (A / G), rs43870 (T / C), rs280179 (G / A),rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsll967047 (T / C), rsl 516501 (C / T), rs3104369 (C / T), and rs972544 (A / C).

[0075] In some embodiments, the present disclosure provides a kit for detecting single nucleotide polymorphisms (SNPs) in a biological sample, said kit comprising primers for genotyping at least 40 SNPs in both copies of a set of SNP loci in the biological sample, wherein the set of SNP loci comprises: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rsl2414133 (A / G), rs43870 (T / C), rs280179 (G / A), rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsl 1967047 (T / C), rsl516501 (C / T), rs3104369 (C / T), and rs972544 (A / C).

[0076] In some embodiments, the kit for detecting SNPs in a biological sample comprises primers for genotyping the following SNPs: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), and rs35362309 (A / G),In some embodiments, the kit comprises primers for genotyping at least 45, at least 50, at least 55, at least 60, at least 65, at least 66, or all 68 SNPs from the above set of SNP loci.

[0077] In some exemplary, non-limiting embodiments, the kit comprises primers for genotyping all 68 SNPs in one or both copies of the above set of SNP loci.

[0078] Accordingly, in some exemplary embodiments, the present disclosure provides a kit for detecting single nucleotide polymorphisms (SNPs) in a biological sample, said kit comprising primers for genotyping 68 SNPs in one or both copies of a set of SNP loci in the biological sample, wherein the set of SNP loci comprises: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rsl2414133 (A / G), rs43870 (T / C), rs280179 (G / A), rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsl 1967047 (T / C), rsl516501 (C / T), rs3104369 (C / T), and rs972544 (A / C).

[0079] In some embodiments, the kit comprises components selected from:

[0080] • Reagents for preparing DNA libraries: reagents for DNA fragmentation, end repair and A-tailing, adapter ligation, and library amplification;

[0081] • Universal adapter oligonucleotides with T tails;

[0082] • DNA purification beads;

[0083] • Dual indexed primers for genotyping one or more SNPs located at the SNP loci mentioned above;

[0084] • Biotinylated hybridization oligonucleotide probes;

[0085] • Reagents for primer extension and target enrichment (e.g., labeled nucleotides);• Beads for capturing hybridized samples and post capture purification;

[0086] and any combination thereof.

[0087] In some embodiments, the kit comprises the following components:

[0088] • Oligonucleotide primers for capturing and amplifying specific regions in the genome harbouring the SNPs being genotyped (exemplary primers are listed in Table 1), universal adapter oligonucleotides with T tails;

[0089] • Reagents for DNA fragmentation, end repair, A tailing, adapter ligation and library amplification;

[0090] • Beads for DNA purification, capturing of hybridized sample and post capture purification; and

[0091] • An instruction manual comprising instructions to perform the method of the present disclosure (processing and sequencing of samples) and an analysis workflow.

[0092]

[0093]

[0094] A person of ordinary skill in the art would understand that the sequence of the primers for detecting SNPs can vary from those disclosed in Table 1; however, as long as the primers can amplify the regions in the genome harbouring the SNPs identified in the present disclosure, the primers are encompassed by the present invention.

[0095] In some embodiments, the kit may also comprise one or more containers, lancets, and instruction manual for carrying out the method and / or interpreting the result.

[0096] The foregoing descriptive matter is illustrative of the disclosure and not a limitation. While the present disclosure is susceptible to various modifications and alternative forms, specific aspects thereof have been shown by way of examples and drawings and are described in detail below. However, it should be understood that it is not intended to limit the invention to the particular forms disclosed, but on the contrary, the intention is to cover all modifications, equivalents, and alternatives falling within the spirit and the scope of the invention as defined by the embodiments of the disclosure.

[0097] EXAMPLES

[0098] Example 1: Identification of SNPs associated with pre-term birth

[0099] Methods

[0100] Cohort description

[0101] A prospective hospital -based pregnancy cohort termed as GARBH-Ini (Interdisciplinary Group for Advanced Research on Birth Outcomes - DBT India Initiative) was initiated in May, 2015 at Gurugram Civil Hospital in Haryana, India. Pregnant women, who visited the antenatal clinic before 20 weeks of gestational age (according to ultrasonography dating) and provided written informed consent, were enrolled in the cohort. These women were followed up during the prenatal period (11-14 weeks, 18-20 weeks, 26-28 weeks, 30-32 weeks), at delivery, and once within six months after delivery. Clinical and demographic details were collected from the enrolled participants using standardised case records forms during their visits to Gurugram Civil Hospital in Haryana, India, by a dedicated and well-trained research team. In addition to the collection of epidemiological details of the enrolled women, biospecimens were collected and ultrasonography scans were performed at defined time-points. Women less than 18 years old, having multiple pregnancies, stillbirths, or caregiver initiated preterm deliveries were excluded. The study was approved by the Institutional Ethics Committees of Gurugram CivilHospital, BRIC-Translational Health Science and Technology Institute (BRIC-THSTI) and BRIC -National Institute of Biomedical Genomics (BRIC -NIB MG).

[0102] Peripheral blood from the enrolled women was collected at each time point by phlebotomists during the visits. EDTA-stabilized maternal peripheral blood samples were stored at -20°C within 24 hours of the collection and subsequent DNA extraction was performed followed by genomic data generation and analyses.

[0103] DNA isolated from peripheral blood, dried blood spot, and / or saliva from the study participants were genotyped using Infmium Global Screening Array version 3.0 multi-disease drop-in panel at 700,604 loci, and genotypes were called using inhouse developed cluster file and quality was assessed as mentioned below.

[0104] Genotyping and imputation quality control

[0105] PLINK vl.9 was used for quality control of the genome-wide genotype data. From the genotyped data, only biallelic autosomal and X chromosomal loci were selected (n = 677,695). For the quality control, loci with call rate <95% (numbers excluded, ne= 4,551), minor allele frequency <5% (ne= 348,443), loci that significantly deviated from Hardy-Weinberg equilibrium (FDR-BH q-value <0.05, ne=2, 840). Individuals were excluded if they showed sex discrepancy (ne=l), cryptic relatedness upto second degree (ne=118), had call rate <95% (ne=47) and high or low heterozygosity (±3 -84 standard deviations from the mean) (ne=78). Finally, 322,428 biallelic SNPs and 5,967 individuals passed all the genotyping quality criteria. For quality control of the mitochondrial variants, mitochondrial chromosome was extracted from the genotyped data (n = 1,138) and loci with call rate <95% (ne= 11), minor allele frequency <1% (ne= 963) were excluded. Moreover, the heterozygous calls for the mitochondrial variants were set as missing to remove heteroplasmy. Finally, after removing duplicated SNPs present in the array (ne= 39), 125 mitochondrial SNPs passed the quality criteria.

[0106] Further, the genotypes of the nuclear variants were statistically phased using SHAPEIT2, and the untyped SNPs in the array were imputed with IMPUTE2, using reference haplotypes from 1000 Genomes Phase 3 and Genome Asia 100K Project Pilot phase. After imputing missing genotypes, quality control of the imputed loci was performed. Variants with ambiguity in determining genotypes (A / T or C / G), minor allele frequency <5%, deviating from Hardy-Weinberg equilibrium (FDR-BH q-value < 0.05) and imputation accuracy score (INFO) <90% were excluded to enhance the accuracy of the imputed data.

[0107] Logistic regression under additive model was performed to identify the SNPs associated with sPTB adjusting for age, BMI, parity, occupational status and top seven principal components of genotype data as covariates.

[0108] Prediction analysis was performed with ten-fold cross validation using Least Absolute Shrinkage and Selection Operator (LASSO) regression to correct for overfitting, and the best combination of SNPs was identified that can predict sPTB in the Indian population. To determine 95% confidence interval of area under the curve, bootstrapping was performed 10,000 times.

[0109] Results:

[0110] Association of maternal genetic variants with spontaneous preterm birth

[0111] Among 6,211 women, 4,682 women passed genotype quality control, out of which 521 women delivered preterm (<37 weeks) and 4,161 women delivered at term (37-<42 weeks).

[0112] Among 4,177,599 SNPs tested, 40 SNPs were significantly associated with sPTB (p<L10'5), of which association with rs57480735 was significant at the genome-wide level (p=2.3><10'8) (Figure 1). Minor allele G at rs57480735 increased the risk for sPTB (OR=1.57 (1.34 - 1.84)) and decreased gestational age at delivery ( = -1.12, p=1.16><10'3).

[0113] Identification of transethnic variants associated with sPTB

[0114] On comparing the association results from GARBH-Ini with the top 10,000 associated variants from 23andMe, 190 SNPs were found to be associated in both the studies. rs35760881 exhibited the most significant association with sPTB (p=2.87xl0‘5) and its minor allele A increased the risk for sPTB in both Indian (OR=1.45) and European women (OR=1.14). Transethnic meta-analysis of sPTB with the other two recently published European studies identified 135 genome-wide significant SNPs. Of 135 SNPs, 132 SNPs showed no or little heterogeneity in allelic effects across the studies (I2<0.5 and Cochran’s Q p-value>0.1). Among these, 25 SNPs from three chromosomal regions were associated in Indian women (p<0.05) (Figure 5).Predictive ability of the identified SNPs in Indian women

[0115] The SNPs significantly associated in the present cohort and the transethnic SNPs identified (n= 252; 40 significantly associated SNPs from GARBH-Ini, 190 transethnic SNPs from comparative analysis and 25 transethnic SNPs from meta-analysis; 3 SNPs were common between comparative analysis and meta-analysis), were able to predict sPTB with an AUC of 0.80 (CI: 0.78-0.82). Addition of covariates (age, BMI at enrolment, parity and occupational status) in the model did not alter that ability significantly (AUC: 0.81(0.79-0.83)). Finally, 68 out of the 252 SNPs shown in Table 2 below were found to predict sPTB with an AUC of 0.78, after correction for overfitting.

[0116] Table 2: List of 68 SNPs used to prepare the SNP panel

[0117]

[0118]

[0119] Example 2: Methods and results for SNP Panel verificationTo verify the efficiency and accuracy of the SNP Panel of the present disclosure containing 68 SNPs described herein, three women were randomly selected from a pool of women from the GARBH-INi cohort known to have a high number of risk alleles.

[0120] DNA was isolated from peripheral blood of the three selected women from the GARBH-INi cohort and from the cell line HTR8 / SVNeo (Trophoblast cell line) as a positive control. DNA quantification was performed using both Nanodrop and Qubit. Pre-capture input libraries were first generated from the genomic DNA using the SNP panel of the present disclosure, and their quality was assessed using the Agilent TapeStation High Sensitivity DNA assay. This was followed by enrichment of the target from the pre-capture input libraries, which involved pooling of the pre-capture libraries, capture extension, binding to capture beads, and release primer extension using the SNP panel of the present disclosure. Following enrichment, the final library quality control was conducted and sequenced using the SNP panel of the present disclosure on the MiSeq sequencing equipment at 1000X. The raw fastq files were aligned to GRCh38 reference genome and variant calling was performed. The read depth was checked at all the 68 SNP positions in Integrative Genomics Viewer (James T. Robinson, Helga Thorvaldsdottir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov. Integrative Genomics Viewer. Nature Biotechnology 29, 24-26 (2011). and the genotypes of the selected individuals were verified using orthogonal datasets from the same individuals.

[0121] We obtained an overall mean depth of 191 OX and we found genotype concordance of 100%, indicating that this SNP panel can capture the variant genotype information accurately. The results are shown in Table 3 below:

[0122]

[0123]

[0124]

[0125] Example 3: Kit for detecting SNPs

[0126] A kit is prepared in accordance with the requirements of the present disclosure to extract DNA from a sample (e.g., whole blood, dried blood spot or saliva) and to generate targeted sequencing libraries which are then subjected to next generation sequencing by employing commercially available sequencing platforms. An exemplary kit comprises of the following components:

[0127] • Oligonucleotide primers for capturing and amplifying specific regions in the genome harbouring the SNPs being genotyped (exemplary primers are listed in Table 1), universal adapter oligonucleotides with T tails;

[0128] • Reagents for DNA fragmentation, end repair, A tailing, adapter ligation and library amplification;

[0129] • Beads for DNA purification, capturing of hybridized sample and post capture purification; and

[0130] • An instruction manual comprising instructions to perform the method of the present disclosure (processing and sequencing of samples) and an analysis workflow.

[0131] The kit may include blood collection tubes and / or lancets for finger pricking.

[0132] Additional embodiments and features of the present disclosure will be apparent to one of ordinary skill in art based on the description provided herein. The embodiments herein provide various features and advantageous details thereof in the description. Descriptions of well-known / conventional methods and techniques are omitted so as to not unnecessarily obscure the embodiments herein.

[0133] The foregoing description of the specific embodiments fully reveals the general nature of the embodiments herein that others can, by applying current knowledge, readily modify and / or adapt for various applications such specific embodiments without departing from the generic concept, and, therefore, such adaptations and modifications should and are intended to be comprehended within the meaning and range of equivalents of the disclosed embodiments. It is to be understood that the phraseology or terminology employed herein is for the purpose of description and not of limitation. Therefore, while the embodiments in this disclosure have been described in terms of preferred embodiments, those skilled in the art will recognize thatthe embodiments herein can be practiced with modification within the spirit and scope of the embodiments as described herein.

[0134] While considerable emphasis has been placed herein on the particular features of this disclosure, it will be appreciated that various modifications can be made, and that many changes can be made in the preferred embodiments without departing from the principles of the disclosure. These and other modifications in the nature of the disclosure or the preferred embodiments will be apparent to those skilled in the art from the disclosure herein, whereby it is to be distinctly understood that the foregoing descriptive matter is to be interpreted merely as illustrative of the disclosure and not as a limitation.

[0135] All references, articles, publications, general disclosures etc. cited herein are incorporated by reference in their entireties for all purposes. However, mention of any reference, article, publication, general methodologies etc. cited herein is not, and should not be taken as, an acknowledgment or any form of suggestion that they constitute valid prior art or form part of the common general knowledge in any country in the world.

Claims

We claim:

1. A method for detecting single nucleotide polymorphisms (SNPs) in a biological sample, said method comprising:sequencing DNA from the biological sample and genotyping at least 40 SNPs located at a set of SNP loci in the biological sample, wherein the set of SNP loci comprises: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rsl2414133 (A / G), rs43870 (T / C), rs280179 (G / A), rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsl 1967047 (T / C), rsl 516501 (C / T), rs3104369 (C / T), and rs972544 (A / C).

2. The method of claim 1, wherein the method comprises genotyping the following SNPs in the biological sample: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), and rs35362309 (A / G).

3. The method of claim 1, wherein the method comprises genotyping the following SNPs in the biological sample: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C),rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rsl2414133 (A / G), rs43870 (T / C), rs280179 (G / A), rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsl 1967047 (T / C), rsl516501 (C / T), rs3104369 (C / T), and rs972544 (A / C).

4. The method of claim 1, wherein the method comprises genotyping at least 45, at least 50, at least 55, at least 60, at least 66, or all 68 SNPs from the set of SNP loci.

5. The method of any one of claims 1-4, wherein the biological sample is selected from blood, buccal swab, urine, saliva, or any combination thereof.

6. The method of any one of claims 1-5, wherein the step of sequencing DNA from the biological sample comprises:• preparing a DNA library from the biological sample; and• sequencing the DNA library to obtain sequence information to determine the genotype at a given locus.

7. The method of claim 6, wherein the sequencing is carried out by next generation sequencing.

8. A method for identifying susceptibility of a subject to a pre-term delivery, said method comprising: sequencing DNA from a biological sample of the subject and genotyping at least 40 SNPs at a set of SNP loci in the biological sample, wherein the set of SNP loci comprises: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437(C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rsl2414133 (A / G), rs43870 (T / C), rs280179 (G / A), rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsll967047 (T / C), rsl516501 (C / T), rs3104369 (C / T), and rs972544 (A / C);wherein the presence of risk allele at one or more SNP loci from the set of SNP loci indicates the susceptibility of the individual to pre-term delivery.

9. The method of claim 8, wherein the method comprises genotyping SNPs present at the following SNP loci in the biological sample: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), and rs35362309 (A / G),wherein the presence of risk allele at one or more SNP loci indicates the susceptibility of the individual to pre-term delivery.

10. The method of claim 8, wherein the method comprises genotyping SNPs present at the following SNP loci in the biological sample: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317(T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rsl2414133 (A / G), rs43870 (T / C), rs280179 (G / A), rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsl 1967047 (T / C), rsl 516501 (C / T), rs3104369 (C / T), and rs972544 (A / C),wherein the presence of risk allele at one or more SNP loci indicates the susceptibility of the individual to pre-term delivery.

11. The method of any one of claims 8-10, wherein the presence of risk allele in at least 1, at least 2, at least 5, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55, at least 60, at least 65, at least 66, or all 68 SNPs at the set of SNP loci indicates the susceptibility of the individual to a pre-term delivery.

12. The method of any one of claims 8-11, wherein the biological sample is selected from blood, buccal swab, urine, saliva, or any combination thereof.

13. The method of any one of claims 8-12, wherein the step of sequencing DNA from the biological sample comprises:• preparing a DNA library from the biological sample; and• sequencing the DNA library to obtain sequence information to determine the genotype at a given locus.

14. The method of claim 13, wherein the sequencing is carried out by next generation sequencing.

15. A kit for detecting single nucleotide polymorphisms (SNPs) in a biological sample, said kit comprising primers for genotyping at least 40 SNPs located at a set of SNP loci in the biological sample, wherein the set of SNP loci comprises: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294(A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rsl2414133 (A / G), rs43870 (T / C), rs280179 (G / A), rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsll967047 (T / C), rsl 516501 (C / T), rs3104369 (C / T), and rs972544 (A / C).

16. The kit of claim 15, wherein the kit comprises primers for genotyping at least 45, at least 50, at least 55, at least 60, at least 65, at least 66, or all 68 SNPs from the set of SNP loci.

17. The kit of claim 15, wherein the kit comprises primers for genotyping SNPs present at the following SNP loci in the biological sample: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), and rs35362309 (A / G).

18. The kit of claim 15, wherein the kit comprises primers for genotyping SNPs present at the following SNP loci in the biological sample: rsl43317895 (G / A), rs72682514 (G / T), rs2194899 (G / A), rsl6827662 (G / A), rs73158515 (G / T), rsl0057007 (A / G), rs34249845 (C / A), rsl0867297 (T / C), rsl45930268 (T / G), rs76537358 (T / G), rs9652325 (C / T), rsl 1854711 (T / C), rs57480735 (A / G), rs2009779 (C / T), rs6032856 (A / C), rs6032857 (T / C), rs6039883 (A / G), rs6030979 (G / T), rs3818215 (C / T), rs2839040 (A / G), rs35760881 (G / A), rs3820282 (C / T), rsl6949470 (A / G), rsl0894808 (C / T), rsl3439896 (A / G), rsl7307967 (C / T), rsl0917151 (G / A), rsl2345249 (C / T), rsl374927 (C / T), rsl40281307 (C / T), rsl026885 (C / T), rs628437 (C / A), rs2999572 (T / G), rs6440003 (G / A), rsl046276 (T / C), rs2594217 (A / G), rs3753803 (A / G), rs2695637 (G / A), rs705791 (G / T), rs35362309 (A / G), rsl317886 (A / G), rs9503335 (G / A), rs7578396 (T / G), rs9503336 (C / A), rs975317 (T / C), rsl628377 (G / A), rsl 133359 (G / A), rs8061852 (A / G), rs9940294 (A / C), rs8046177 (T / C), rs701112 (C / T), rsl 1178234 (G / A), rsl 1078931 (C / T), rs7800751 (G / A), rs825082 (A / G), rs825084 (C / T), rsl2414133 (A / G), rs43870 (T / C), rs280179 (G / A), rsl2212888 (G / A), rsl0926412 (C / T), rs280185 (C / T), rs4944847 (G / A), rs280158 (G / A), rsl 1967047 (T / C), rsl 516501 (C / T), rs3104369 (C / T), and rs972544 (A / C).

19. The kit of any one of claims 15-18, wherein the kit comprises components selected from a group comprising:• Reagents for preparing DNA libraries: reagents for DNA fragmentation, end repair and A-tailing, adapter ligation, and library amplification;• Universal adapter oligonucleotides with T tails;• DNA purification beads;• Biotinylated hybridization oligonucleotide probes;• Reagents for primer extension and target enrichment (e.g., labeled nucleotides);• Beads for capturing hybridized samples and post capture purification;and any combination thereof;• instruction manual; andany combination thereof.

20. The kit as claimed in any one of claims 15-19, wherein the kit comprises:• Oligonucleotide primers for capturing and amplifying specific regions in the genome harbouring the SNPs being genotyped, universal adapter oligonucleotides with T tails;• Reagents for DNA fragmentation, end repair, A tailing, adapter ligation and library amplification;• Beads for DNA purification, capturing of hybridized sample and post capture purification; and• An instruction manual comprising instructions to perform the method of the present disclosure (processing and sequencing of samples) and an analysis workflow.

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