Hybridization capture and low-coverage SNP profiling for extended kinship analysis and forensic identification of historical remains

Abstract

DNA-assisted identification of historical remains requires the genetic analysis of highly degraded DNA, along with a comparison to DNA from known relatives. This can be achieved by targeting single nucleotide polymorphisms (SNPs) using a hybridization capture and next-generation sequencing approach suitable for degraded skeletal samples. In the present study, two SNP capture panels were designed to target ~25,000 (25K) and ~95,000 (95K) nuclear SNPs, respectively, to enable distant kinship estimation (up to 4th degree relatives). Low-coverage SNP data were successfully recovered from 14 skeletal elements 75 years postmortem, with captured DNA having mean insert sizes ranging from 32-170 bp across the 14 samples. SNP comparison with DNA from known family references was performed in the Parabon Fx Forensic Analysis Platform, which utilizes a likelihood approach for kinship prediction that was optimized for low-coverage sequencing data with cytosine deamination. The 25K panel produced 15,000 SNPs on average, which allowed for accurate kinship prediction in 17 of the 21 pairwise comparisons. The 95K panel increased the average SNPs to 42,000 and resulted in two additional pairwise comparisons (19 of 21). This study provides the groundwork for the expansion of research involving compromised samples to include SNP hybridization capture.