Abstract
Capillary electrophoresis-based analysis does not reflect the exact allele number variation at the STR loci due to the non-availability of the data on sequence variation in the repeat region and the SNPs in flanking regions. Herein, this study reports the length-based and sequence-based allelic data of 138 central Indian individuals at 31 autosomal STR loci by NGS. The sequence data at each allele was compared to the reference hg19 sequence. The length-based allelic results were found in concordance with the CE-based results. 20 out of 31 autosomal STR loci showed an increase in the number of alleles by the presence of sequence variation and/or SNPs in the flanking regions. The highest gain in the heterozygosity and allele numbers was observed in D5S2800, D1S1656, D16S539, D5S818, and vWA. rs25768 (A/G) at D5S818 was found to be the most frequent SNP in the studied population. Allele no. 15 of D3S1358, allele no. 19 of D2S1338, and allele no. 22 of D12S391 showed 5 isoalleles each with the same size and with different intervening sequences. Length-based determination of the alleles showed Penta E to be the most useful marker in the central Indian population among 31 STRs studied; however, sequence-based analysis advocated D2S1338 to be the most useful marker in terms of various forensic parameters. Population genetics analysis showed a shared genetic ancestry of the studied population with other Indian populations. This first-ever study to the best of our knowledge on sequence-based STR analysis in the central Indian population is expected to prove the use of NGS in forensic case-work and in forensic DNA laboratories.
Highlights
Exploration of the targeted STRs using capillary electrophoresis (CE) has been currently considered as the gold standard technology in the forensic DNA analysis
Next-generation sequencing (NGS) is useful in mtDNA sequencing which is expedient in degraded samples due to the presence of thousands of copies of mtDNA per c ell[3]
The major advantage of NGS over CE technology is that there exists no limitation in the number of STR markers to be multiplexed in a single reaction
Summary
Exploration of the targeted STRs using capillary electrophoresis (CE) has been currently considered as the gold standard technology in the forensic DNA analysis. In context to abovesaid drawbacks associated with CE, Next-generation sequencing (NGS) appears to be a suitable alternative technique It provides information from numerous STRs and SNPs simultaneously. Many new STR marker sets have been included in the commercially available sequencing kits besides the recommended 20 core CODIS STR loci Before their forensic application, these loci and their aptness at the population level should be understood utterly. A limited number of genetic markers can be accommodated in a single multiplex reaction due to the involvement of different dye sets and limited channels for detection This could be overcome by NGS analysis where numerous genetic markers can be analyzed simultaneously. The study aimed to generate sequence-based allele frequency data, population-specific characteristics, sequence variations, and SNPs in the flanking regions for the forensic casework applications in the studied population
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