Targeted enrichment of whole‐genome SNPs from highly burned skeletal remains

• Published in: Journal of forensic sciences 2024-09, Vol.69 (5), p.1558-1577
• Main Authors: Emery, Matthew V., Bolhofner, Katelyn, Spake, Laure, Ghafoor, Suhail, Versoza, Cyril J., Rawls, Erin M., Winingear, Stevie, Buikstra, Jane E., Loreille, Odile, Fulginiti, Laura C., Stone, Anne C.
• Format: Article
• Language: English
• Subjects: ancient DNA; Bones; burnt human remains; cremains; Deoxyribonucleic acid; DNA; forensic DNA; Gene sequencing; Genomes; Human remains; Impact analysis; Nucleotides; Polymorphism; pyrolysis; single‐nucleotide polymorphisms; SNP genotyping; targeted capture; Thermal degradation
• ISSN: 0022-1198; 1556-4029; 1556-4029
• DOI: 10.1111/1556-4029.15482

Genetic assessment of highly incinerated and/or degraded human skeletal material is a persistent challenge in forensic DNA analysis, including identifying victims of mass disasters. Few studies have investigated the impact of thermal degradation on whole‐genome single‐nucleotide polymorphism (SNP) quality and quantity using next‐generation sequencing (NGS). We present whole‐genome SNP data obtained from the bones and teeth of 27 fire victims using two DNA extraction techniques. Extracts were converted to double‐stranded DNA libraries then enriched for whole‐genome SNPs using unpublished biotinylated RNA baits and sequenced on an Illumina NextSeq 550 platform. Raw reads were processed using the EAGER (Efficient Ancient Genome Reconstruction) pipeline, and the SNPs filtered and called using FreeBayes and GATK (v. 3.8). Mixed‐effects modeling of the data suggest that SNP variability and preservation is predominantly determined by skeletal element and burn category, and not by extraction type. Whole‐genome SNP data suggest that selecting long bones, hand and foot bones, and teeth subjected to temperatures 350°C. Our data complement previous analyses of burned human remains that compare extraction methods for downstream forensic applications and support the idea of adopting a modified Dabney extraction technique when traditional forensic methods fail to produce DNA yields sufficient for genetic identification.