Proteomic genotyping of fingermark donors with genetically variant peptides. (September 2019)

• Record Type: Journal Article
• Authors: Borja, Trevor; Karim, Noreen; Goecker, Zachary; Salemi, Michelle; Phinney, Brett; Naeem, Muhammad; Rice, Robert; Parker, Glendon
• Is Part Of: Forensic science international. Volume 42(2019)
• Page Start: 21
• Page End: 30
• Publication Date: 2019-09
• Subjects: GVPs genetically variant peptides -- SNP single nucleotide polymorphism -- RMP random match probability; Fingermarks -- Genetically variant peptide -- Non-synonymous SNPs -- Epidermal corneocytes -- Proteomics -- Mass spectrometry -- Proteomic genotyping -- Genetically variable peptide; Forensic genetics -- Periodicals; Génétique légale -- Périodiques; Forensic genetics; Electronic journals; Periodicals; 614.1
• DOI: 10.1016/j.fsigen.2019.05.005
• Languages: English
• ISSNs: 1872-4973

Abstract

Highlights: Proteomic discovery, characterization and validation of identifying genetically variant peptides from human skin cells. Demonstration of random match probabilities from corneocyte proteomes. Demonstration of exome analysis to discover a rare personal genetically variant peptide. Abstract: Proteomic genotyping detects single amino acid polymorphisms to infer the genotype of corresponding non-synonymous SNPs. Like any DNA genotype, these inferences can be used to estimate random match probability. Fingermarks are a common source of biological evidence that is sample limited and a highly variable source of identifying DNA. Genetically variant peptides from fingermarks, that contain single amino acid polymorphisms, are an additional source of identifying genetic information. To discover these peptide biomarkers epidermal corneocytes from 9 subjects were isolated, processed, digested with trypsin and applied to mass spectrometry. The resulting proteomic and matching exome datasets were used to discover, characterize and validate 60 genetically variant peptides. An average of 28.8 ± 4.4 genetically variant peptides were detected from each subject resulting in a total of 264 SNP allele inferences with 260 true and 4 false positives, a false discovery rate of 1.5%. Random match probabilities were estimated using the genotype frequencies from the matching major populations in the 1000 Genomes Project. Estimates ranged up to a value of 1 in 1.7 × 10 8, with a median probability of 1 in 2.4 × 10 6 . Furthermore, the proteomically-inferred genotypes are likely to be compatible with the STR-based random match probability estimates since the closest STR locus was 2.2 Mb from the nearest GVP-inferred SNP. This project represents a novel mode of genetic information that can be obtained from fingermarks and has the potential to complement other methods of human identification including analysis of ridge patterns or touch DNA.