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Decomposition of Individual SNP Patterns from Mixed DNA Samples

Faculty of Engineering, Bar Ilan University, Ramat Gan 5290002, Israel
Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
Author to whom correspondence should be addressed.
Academic Editor: Ricardo Jorge Dinis-Oliveira
Forensic Sci. 2022, 2(3), 455-472;
Received: 1 November 2021 / Revised: 17 May 2022 / Accepted: 22 June 2022 / Published: 5 July 2022
(This article belongs to the Special Issue Feature Papers in Forensic Sciences in 2022)
Single-nucleotide polymorphism (SNP) markers have great potential to identify individuals, family relations, biogeographical ancestry, and phenotypic traits. In many forensic situations, DNA mixtures of a victim and an unknown suspect exist. Extracting SNP profiles from suspect’s samples can be used to assist investigation or gather intelligence. Computational tools to determine inclusion/exclusion of a known individual from a mixture exist, but no algorithm for extraction of an unknown SNP profile without a list of suspects is available. Here, we present an advanced haplotype-based HMM algorithm (AH-HA), a novel computational approach for extracting an unknown SNP profile from whole genome sequencing (WGS) of a two-person mixture. AH-HA utilizes techniques similar to the ones used in haplotype phasing. It constructs the inferred genotype as an imperfect mosaic of haplotypes from a reference panel of the target population. It outperforms more simplistic approaches, maintaining high performance through a wide range of sequencing depths (500×–5×). AH-HA can be applied in cases of victim–suspect mixtures and improves the capabilities of the investigating forces. This approach can be extended to more complex mixtures with more donors and less prior information, further motivating the development of SNP-based forensics technologies. View Full-Text
Keywords: forensics; mixtures; SNP forensics; mixtures; SNP
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MDPI and ACS Style

Azhari, G.; Waldman, S.; Ofer, N.; Keller, Y.; Carmi, S.; Yaari, G. Decomposition of Individual SNP Patterns from Mixed DNA Samples. Forensic Sci. 2022, 2, 455-472.

AMA Style

Azhari G, Waldman S, Ofer N, Keller Y, Carmi S, Yaari G. Decomposition of Individual SNP Patterns from Mixed DNA Samples. Forensic Sciences. 2022; 2(3):455-472.

Chicago/Turabian Style

Azhari, Gabriel, Shamam Waldman, Netanel Ofer, Yosi Keller, Shai Carmi, and Gur Yaari. 2022. "Decomposition of Individual SNP Patterns from Mixed DNA Samples" Forensic Sciences 2, no. 3: 455-472.

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