Development of a SNP-based panel for human identification for Indian populations

Sarkar, Anujit (2017) Development of a SNP-based panel for human identification for Indian populations. Forensic Science International: Genetics, 27. pp. 58-66. ISSN 1872-4973

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Abstract

The widely employed short tandem repeat (STR)-based panels for forensic human identification (HID) have limitations while dealing with challenging forensic samples involving DNAdegradation, resulting in dropping-out of higher molecular weight alleles/loci. To address this issue, bialleic markers like single nucleotide polymorph isms (SNPs) and insertion-deletions (indels), which can be scored even when the template DNAis heavily degraded «100 bp), have been suggested as alternative markers for HIDtesting. Recent studies have highlighted their utility in forensic HIDand several panels based on biallelic markers have been described for worldwide populations. However, there has been very little information about the behavior of such DNA markers in Indian populations, which is known to possess great genetic diversity. This study describes a two-step approach for designing a SNP-based panel consisting of70 SNPs for HID testing in Indian populations. In the first step, candidate SNPs were shortlisted from public databases by screening them for several criteria including allelic distribution, genomic location, potential phenotypic expression or functionality and species specificity. The second step involved genotyping the shortlisted SNPs in various Indian populations followed by shortlisting of the best performers for identity-testing. Starting with 592,652 SNPs listed in Human660W-Quad Beadchip (lIIumina Inc.), we shortlisted 275 candidate SNPs for identity-testing and genotyped them in 462 unrelated individuals from different population groups in India. Post genotyping and statistical analyses based on biogeographic regions, 206 SNPs demonstrated desired allelic distribution (Heterozygosity ~ 0.4 and FsT:;; 0.02), from which 2-4 widely separated (>20 Mb apart) SNPs from each chromosome were finally selected to construct a panel of 70 SNPs.This panel on average possessed match probability 10e-29 and probability of paternity of 0.99999997, which was orders of magnitude higher than most of the currently employed STR-based chemistries and SNP-based panels that were proposed previously for HIDtesting. For comparison purpose, genotyping previously reported SNPs for HIDin our samples led us to conclude that the panel developed in this study is much more efficient and robust and better suited for the Indian populations.

Item Type: Article
Uncontrolled Keywords: SNP-panel ; Forensic human identification ; Indian populations.
Subjects: Research > Research Center - Health Sciences
Depositing User: KMC Library
Date Deposited: 22 Jul 2017 09:05
Last Modified: 22 Jul 2017 09:05
URI: http://eprints.manipal.edu/id/eprint/149410

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