Preservation of proteomic and genomic genotypes in skeletal material from forensically treated cadavers

Abstract

Skeletal material is often the only remaining evidence in missing persons cases, for mass burials, or disaster victim identification. Nuclear DNA can be highly degraded in these samples making it difficult to recover quality profiles for human identification or to deconvolute comingled remains. Proteins are chemically more stable than DNA and contain genetic information in the form of genetically variant peptides (GVPs) that can be used to infer non-synonymous SNP genotypes. To test chemical and genetic preservation of both biomolecular types, eight cadavers were examined using five treatments: embalming, burning, burial, and surface decomposition with and without subsequent formalin treatment (0–66 h in 36 % (w/v) formalin). Across the study DNA recoveries ranged from 210 ng to 0.08 ng in 50 mg of processed bone, a 2,600-fold range. Peptide recoveries, ranged from 22,000 ng to 5900 ng from the same amount of bone, a 3.7-fold range. At the information level the same peptide input (750 ng) could be obtained for all samples, and nucleotide level (0.8 ng) for most samples, although this consumed more sample than proteomic analysis. Of the 18 STR-profiles analyzed, 9 were CODIS-ineligible, yet all samples contained GVPs. This indicated that GVPs can be used to construct non-synonymous SNP genotypes in degraded bone samples that cannot provide usable STR-profiles. The relative quality of proteomic and genomic genetic data had a linear relationship (P < 0.0001) with a loss of 1 GVP for a 14 % loss of STR-alleles (97 % CI = 10–22 %), indicating that even correcting for chemical loss, information quality still decreased. SNaPshot™ genotyping of non-synonymous SNPs was less sensitive than GVP inference. Proteomic analysis of individual proteins in the sample indicated that collagen degradation was responsible for most protein loss, and chemical modifications were modest. Future studies are required to examine the stability of both DNA and protein in specific cadaver treatments, for further GVP discovery and validation, and optimization of proteomic sample processing. However, given the stability of GVP detection, even at this preliminary stage, protein-based genotyping is a valid option for extracting genetic information from samples with minimal or even no usable DNA detected. This is the first example of successful proteomic genotyping in forensically degraded bone and demonstrates that proteomic genotyping can be used for human identification and potential deconvolution of comingled remains.