Demonstration of a mitochondrial DNA-compatible workflow for genetically variant peptide identification from human hair samples

Abstract

Hair is an evidentiary sample that typically does not provide sufficient nuclear DNA for forensic analysis. Therefore, state-of-the-art forensic examination for hair samples include subjective microscopic evaluation, mitochondrial DNA (mtDNA) analysis, and more recently, proteomic genotyping that uses protein variation in the form of genetically variant peptides (GVPs) to infer single nucleotide polymorphism (SNP) alleles. Since many cases involve limited sample amounts (approximately 2 cm or less), any additional destructive testing (besides mtDNA) would be excluded. If a mtDNA-compatible protein extraction workflow could be developed, GVPs would provide additional forensic value without sacrificing any portion of the original hair sample. Here, we demonstrate an optimized method that can be used to obtain both whole genome mtDNA and putative GVP profiles from a single limited hair sample. The method involves urea-based extraction of proteins from hair, followed by buffer exchange and protease digestion. Peptides are eluted through a 30 kDa membrane and analyzed using traditional proteomic techniques. DNA is subsequently extracted from the filter and analyzed using whole mt-genome analysis. The method was verified with a range of hair sample types (head, pubic, and arm hair) from a diverse cohort of 22 individuals. Specifically, putative GVP profiles and mtDNA haplotypes concordant with buccal swab samples from the same donor were obtained from 22 individuals. Further, the utility of the method was verified across two different laboratories. The method is applicable for proteomic-based GVP analysis and mt-genome analysis for forensic research applications.

Keywords: Genetically variant peptides; Hair; Human identification; Mitochondrial DNA; Non-synonymous single nucleotide polymorphisms.