Demonstration of protein-based human identification using the hair shaft proteome

Glendon J. Parker, Tami Leppert, Deon S. Anex, Jonathan K. Hilmer, Nori Matsunami, Lisa Baird, Jeffery Stevens, Krishna Parsawar, Blythe P. Durbin-Johnson, David M Rocke, Chad Nelson, Daniel J. Fairbanks, Andrew S. Wilson, Robert H. Rice, Scott R. Woodward, Brian Bothner, Bradley R. Hart, Mark Leppert

Research output: Contribution to journalArticle

35 Citations (Scopus)

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.

Original languageEnglish (US)
Article numbere0160653
JournalPLoS One
Volume11
Issue number9
DOIs
StatePublished - Sep 1 2016

Fingerprint

Forensic Anthropology
Proteome
proteome
Polymorphism
Hair
hairs
Demonstrations
single nucleotide polymorphism
Single Nucleotide Polymorphism
Nucleotides
DNA
Proteins
proteins
Alleles
genetic polymorphism
peptides
Population
alleles
Peptides
Firearms

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Parker, G. J., Leppert, T., Anex, D. S., Hilmer, J. K., Matsunami, N., Baird, L., ... Leppert, M. (2016). Demonstration of protein-based human identification using the hair shaft proteome. PLoS One, 11(9), [e0160653]. https://doi.org/10.1371/journal.pone.0160653

Demonstration of protein-based human identification using the hair shaft proteome. / Parker, Glendon J.; Leppert, Tami; Anex, Deon S.; Hilmer, Jonathan K.; Matsunami, Nori; Baird, Lisa; Stevens, Jeffery; Parsawar, Krishna; Durbin-Johnson, Blythe P.; Rocke, David M; Nelson, Chad; Fairbanks, Daniel J.; Wilson, Andrew S.; Rice, Robert H.; Woodward, Scott R.; Bothner, Brian; Hart, Bradley R.; Leppert, Mark.

In: PLoS One, Vol. 11, No. 9, e0160653, 01.09.2016.

Research output: Contribution to journalArticle

Parker, GJ, Leppert, T, Anex, DS, Hilmer, JK, Matsunami, N, Baird, L, Stevens, J, Parsawar, K, Durbin-Johnson, BP, Rocke, DM, Nelson, C, Fairbanks, DJ, Wilson, AS, Rice, RH, Woodward, SR, Bothner, B, Hart, BR & Leppert, M 2016, 'Demonstration of protein-based human identification using the hair shaft proteome', PLoS One, vol. 11, no. 9, e0160653. https://doi.org/10.1371/journal.pone.0160653
Parker GJ, Leppert T, Anex DS, Hilmer JK, Matsunami N, Baird L et al. Demonstration of protein-based human identification using the hair shaft proteome. PLoS One. 2016 Sep 1;11(9). e0160653. https://doi.org/10.1371/journal.pone.0160653
Parker, Glendon J. ; Leppert, Tami ; Anex, Deon S. ; Hilmer, Jonathan K. ; Matsunami, Nori ; Baird, Lisa ; Stevens, Jeffery ; Parsawar, Krishna ; Durbin-Johnson, Blythe P. ; Rocke, David M ; Nelson, Chad ; Fairbanks, Daniel J. ; Wilson, Andrew S. ; Rice, Robert H. ; Woodward, Scott R. ; Bothner, Brian ; Hart, Bradley R. ; Leppert, Mark. / Demonstration of protein-based human identification using the hair shaft proteome. In: PLoS One. 2016 ; Vol. 11, No. 9.
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