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Decomposition of Individual SNP Patterns From Mixed DNA Samples

16 Pages Posted: 25 Nov 2020 Publication Status: Review Complete

See all articles by Gabriel Azhari

Gabriel Azhari

Bar Ilan University - Faculty of Engineering

Shamam Waldman

The Hebrew University of Jerusalem - Braun School of Public Health and Community Medicine

Netanel Ofer

Bar Ilan University - Faculty of Engineering

Yosi Keller

Bar Ilan University - Faculty of Engineering

Shai Carmi

The Hebrew University of Jerusalem - Braun School of Public Health and Community Medicine

Gur Yaari

Bar Ilan University - Faculty of Engineering

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Abstract

Single Nucleotide Polymorphism markers (SNPs) 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 from such samples the suspect's SNP profile can be used to assist investigation and gather intelligence. Computational tools to determine inclusion/exclusion of a known individual from a mixture exist, but no algorithm to extract an unknown SNP profile without a list of suspects is available. We present here AH-HA, a novel computational approach for extracting an unknown SNP profile from a whole genome sequencing (WGS) of a two person mixture. It 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 is shown to outperform more simplistic approaches, maintaining high performance through a wide range of sequencing depths (500x - 5x). AH-HA can be applied in cases of victim-suspect mixtures and improve 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.

Suggested Citation

Azhari, Gabriel and Waldman, Shamam and Ofer, Netanel and Keller, Yosi and Carmi, Shai and Yaari, Gur, Decomposition of Individual SNP Patterns From Mixed DNA Samples. Available at SSRN: https://ssrn.com/abstract=3737807 or http://dx.doi.org/10.2139/ssrn.3737807
This version of the paper has not been formally peer reviewed.

Gabriel Azhari

Bar Ilan University - Faculty of Engineering ( email )

Ramat Gan
Israel

Shamam Waldman

The Hebrew University of Jerusalem - Braun School of Public Health and Community Medicine ( email )

P.O.B. 12000
Jerusalem, 91120
Israel

Netanel Ofer

Bar Ilan University - Faculty of Engineering ( email )

Ramat Gan
Israel

Yosi Keller

Bar Ilan University - Faculty of Engineering ( email )

Ramat Gan
Israel

Shai Carmi

The Hebrew University of Jerusalem - Braun School of Public Health and Community Medicine ( email )

P.O.B. 12000
Jerusalem, 91120
Israel

Gur Yaari (Contact Author)

Bar Ilan University - Faculty of Engineering ( email )

Ramat Gan
Israel

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