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Forensic characterization of 124 SNPs in the central Indian population using precision ID Identity Panel through next-generation sequencing

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Abstract

With the advent of next-generation sequencing technology, SNP markers are being explored as a useful alternative to conventional capillary electrophoresis–based STR typing. Low mutation rate and short-sized amplicons are added advantages of SNP markers over the STRs. However, to achieve a sufficient level of discrimination among individuals, a higher number of SNPs need to be characterized simultaneously. Hence, the NGS technique is highly useful to analyze a sufficiently higher number of SNPs simultaneously. Though the technique is in its nascent stage, an attempt has been made to assess its usability in the central Indian population by analyzing 124 SNPs (90 autosomal and 34 Y-chromosome) in 95 individuals. Various quality parameters such as locus balance, locus strand balance, heterozygosity balance, and noise level showed a good quality sequence obtained from the Ion GeneStudio S5 instrument. Obtained frequency of SNP alleles ranged from 0.001 to 0.377 in autosomal SNPs. rs9951171 was found to be the most informative SNP in the studied population with the highest PD and lowest MP value. The cumulative MP of 90 SNPs was found to be 4.76698 × 10–37. Analysis of 34 Y-chromosome SNPs reveals 11 unique haplogroups in 54 male samples with R1a1 as the most frequent haplogroup found in 22.22% of samples. Interpopulation comparison by FST analysis, PCA plot, and STRUCTURE analysis showed genetic stratification of the studied population suggesting the utility of SNP markers present in the Precision ID Identity Panel for forensic demands of the Indian population.

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Acknowledgements

The authors are highly acknowledged to Director, State Forensic Science Laboratory, Sagar, M. P., India, and Joint Director, Regional Forensic Science Laboratory, Bhopal, M. P., India for providing infrastructure to carry out the research work. Our sincere thanks to Dr. Atima Agrawal, Dr. Neeraj Chauhan, Dr. Sanjib Dey, and the entire technical team of Thermo Scientific for their constant technical support during the research work.

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Authors and Affiliations

  1. DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India

    Hirak Ranjan Dash, Kamlesh Kaitholia, Radhika Agarwal & Anil Kumar Singh

  2. Pontifical Catholic University of Rio Grande Do Sul, Porto Alegre, Brazil

    Eduardo Avila & Clarice Sampaio Alho

  3. Department of Zoology, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India

    Soumya Ranjan Jena

  4. Institute of Forensic Science and Criminology, Bundelkhand University, Jhansi, UP, India

    Ankit Srivastava

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  1. Hirak Ranjan Dash
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Correspondence to Hirak Ranjan Dash.

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Ethical

The samples used in this study were collected from the sample donors after obtaining written informed consent from them. During sample collection and experimentations, the ethical principles mentioned in the Helsinki Declaration were followed strictly. Before commencing this study, approval was obtained from the Ethics Committee at the Maharani Laxmi Bai Medical College, Jhansi, India (Ref. No. 4648/IEC/2020/SC-1).

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Dash, H.R., Avila, E., Jena, S.R. et al. Forensic characterization of 124 SNPs in the central Indian population using precision ID Identity Panel through next-generation sequencing. Int J Legal Med 136, 465–473 (2022). https://doi.org/10.1007/s00414-021-02742-5

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