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PLoS One. 2016 Sep 7;11(9):e0160653. doi: 10.1371/journal.pone.0160653. eCollection 2016.

Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome.

Author information

1
Department of Biology, Utah Valley University, Orem, Utah, United States of America.
2
Protein-Based Identification Technologies L.L.C., Orem, Utah, United States of America.
3
Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America.
4
Forensic Science Center, Lawrence Livermore National Laboratory, Livermore, California, United States of America.
5
Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America.
6
Mass Spectrometry and Proteomics Core Facility, University of Utah, Salt Lake City, Utah, United States of America.
7
Department of Public Health Sciences, University of California, Davis, California, United States of America.
8
School of Archaeological Sciences, University of Bradford, Bradford, United Kingdom.
9
Department of Environmental Toxicology, University of California, Davis, California, United States of America.
10
Sorenson Molecular Genealogical Foundation, Salt Lake City, Utah, United States of America.

Abstract

Human identification from biological material is largely dependent on the ability to characterize genetic polymorphisms in DNA. Unfortunately, DNA can degrade in the environment, sometimes below the level at which it can be amplified by PCR. Protein however is chemically more robust than DNA and can persist for longer periods. Protein also contains genetic variation in the form of single amino acid polymorphisms. These can be used to infer the status of non-synonymous single nucleotide polymorphism alleles. To demonstrate this, we used mass spectrometry-based shotgun proteomics to characterize hair shaft proteins in 66 European-American subjects. A total of 596 single nucleotide polymorphism alleles were correctly imputed in 32 loci from 22 genes of subjects' DNA and directly validated using Sanger sequencing. Estimates of the probability of resulting individual non-synonymous single nucleotide polymorphism allelic profiles in the European population, using the product rule, resulted in a maximum power of discrimination of 1 in 12,500. Imputed non-synonymous single nucleotide polymorphism profiles from European-American subjects were considerably less frequent in the African population (maximum likelihood ratio = 11,000). The converse was true for hair shafts collected from an additional 10 subjects with African ancestry, where some profiles were more frequent in the African population. Genetically variant peptides were also identified in hair shaft datasets from six archaeological skeletal remains (up to 260 years old). This study demonstrates that quantifiable measures of identity discrimination and biogeographic background can be obtained from detecting genetically variant peptides in hair shaft protein, including hair from bioarchaeological contexts.

PMID:
27603779
PMCID:
PMC5014411
DOI:
10.1371/journal.pone.0160653
[Indexed for MEDLINE]
Free PMC Article

Conflict of interest statement

Patent based on the concept and some data presented in this study have been awarded (US 8,877,455 B2, Australian Patent 2011229918, Canadian Patent CA 2794248, and European Patent EP11759843.3, GJP inventor). The patent is owned by Parker Proteomics LLC. Protein-Based Identification Technologies LLC has an exclusive license to develop the intellectual property and is co-owned by Utah Valley University and GJP. This ownership of PBIT and associated intellectual property does not alter our adherence to PLOS ONE policies on sharing data and materials.

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