SNP assays for DVI: cost, time, and performance information for decision-makers

Abstract

In mass disaster events, forensic DNA laboratories may be called upon to quickly pivot their operations toward identifying bodies and reuniting remains with family members. Ideally, laboratories have considered this possibility in advance and have a plan in place. Compared with traditional short tandem repeat (STR) typing, single nucleotide polymorphisms (SNPs) may be better suited to these disaster victim identification (DVI) scenarios due to their small genomic target size, resulting in an improved success rate in degraded DNA samples. As the landscape of technology has shifted toward DNA sequencing, many forensic laboratories now have benchtop instruments available for massively parallel sequencing (MPS), facilitating this operational pivot from routine forensic STR casework to DVI SNP typing. Herein, we review the commercially available SNP sequencing assays amenable to DVI, we use data simulations to explore the potential for kinship prediction from SNP panels of varying size, and we give an example DVI scenario as context for presenting the matrix of considerations: kinship predictive potential, cost, and throughput of current SNP assay options. This information is intended to assist laboratories in choosing a SNP system for disaster preparedness.

Benchmarking for genotyping and imputation using degraded DNA for forensic applications across diverse populations

“…These data were used to examine the impacts of genome mapping and genotyping for five SNP panels commonly used in forensics and ancient DNA studies ( Figure 2A; Supplementary Section 1 ). We used SNP panels, rather than low-coverage sequencing data, as they are more commonly used in the forensic field due to greater privacy concerns, efforts to maintain consistency with previously validated workflows, and to reduce costs 47,48 . The five SNP panels tested include: (a) the MPS-plex panel (1,270 SNPs 28 ) that consists of tri-allelic loci and was developed to increase power for individualization with less SNPs for application with degraded DNA, (b) the FORCE panel (5,422 SNPs 27 ) that was developed as an “all-in-one” panel for wide-spread use in the forensic field and covers loci informative for phenotyping, genetic ancestry, kinship and individualization, (c-d) the 95K and 25K panels 29 were developed for identifying distant kinship (up to 4th degree relatives with 94,752 and 24,999 SNPs respectively) and (e) the Affymetrix Human Origins array 30 that contains 1.2 million SNPs ascertained in diverse populations and is widely used in ancient DNA and population genetics studies.…”

“…In the United States, CODIS STRs were selected in part due their being medically uninformative 54,55 , although this has since been called into question 56 . There are currently multiple NGS kits or SNP panels available for forensic analyses (94 - 9,959 SNPs 48 ), but most target relatively few SNPs compared to SNP panels in other fields (widely used commercial SNP arrays for medical and population genetic studies contain ∼700,000–3.7 millions SNPs 57–59 ). Low coverage whole genome sequencing combined with refinement and imputation has become increasingly popular in place of high coverage sequencing in genomic studies to decrease sequencing costs.…”

“…These data were used to examine the impacts of genome mapping and genotyping for five SNP panels commonly used in forensics and ancient DNA studies (Figure 2A; Supplementary Section 1). We used SNP panels, rather than low-coverage sequencing data, as they are more commonly used in the forensic field due to greater privacy concerns, efforts to maintain consistency with previously validated workflows, and to reduce costs 47,48…”