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Title: Demonstration of protein-based human identification using the hair shaft proteome [Protein-based human identification: A proof of concept using the hair shaft proteome]

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 Africanmore » population. Genetically variant peptides were also identified in hair shaft datasets from six archaeological skeletal remains (up to 260 years old). Furthermore, 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.« less

Authors:
ORCiD logo [1];  [2];  [3];  [4];  [5];  [5];  [5];  [5];  [6];  [6];  [5];  [7];  [8];  [6];  [9];  [4];  [3];  [5];  [10]
  1. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Utah Valley Univ., Orem, UT (United States); Protein-Based Identification Technologies, L.L.C., Orem, UT (United States)
  2. Protein-Based Identification Technologies, L.L.C., Orem, UT (United States)
  3. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  4. Montana State Univ., Bozeman, MT (United States)
  5. Univ. of Utah, Salt Lake City, UT (United States)
  6. Univ. of California, Davis, CA (United States)
  7. Utah Valley Univ., Orem, UT (United States)
  8. Univ. of Bradford, Bradford (United Kingdom)
  9. Sorenson Molecular Genealogical Foundation, Salt Lake City, UT (United States)
  10. Univ. Pompeu Fabra (Spain)
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1337466
Report Number(s):
LLNL-JRNL-665656
Journal ID: ISSN 1932-6203
Grant/Contract Number:
AC52-07NA27344; B601942; B607766; #121668; #132043
Resource Type:
Journal Article: Published Article
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 11; Journal Issue: 9; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; peptides; proteomic databases; membrane proteins; genetic loci; alleles; proteomes; archaeology; haplotypes

Citation Formats

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, and Calafell, Francesc. Demonstration of protein-based human identification using the hair shaft proteome [Protein-based human identification: A proof of concept using the hair shaft proteome]. United States: N. p., 2016. Web. doi: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, & Calafell, Francesc. Demonstration of protein-based human identification using the hair shaft proteome [Protein-based human identification: A proof of concept using the hair shaft proteome]. United States. doi: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, and Calafell, Francesc. 2016. "Demonstration of protein-based human identification using the hair shaft proteome [Protein-based human identification: A proof of concept using the hair shaft proteome]". United States. doi:10.1371/journal.pone.0160653.
@article{osti_1337466,
title = {Demonstration of protein-based human identification using the hair shaft proteome [Protein-based human identification: A proof of concept using the hair shaft proteome]},
author = {Parker, Glendon J. and Leppert, Tami and Anex, Deon S. and Hilmer, Jonathan K. and Matsunami, Nori and Baird, Lisa and Stevens, Jeffery and Parsawar, Krishna and Durbin-Johnson, Blythe P. and Rocke, David M. and Nelson, Chad and Fairbanks, Daniel J. and Wilson, Andrew S. and Rice, Robert H. and Woodward, Scott R. and Bothner, Brian and Hart, Bradley R. and Leppert, Mark and Calafell, Francesc},
abstractNote = {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). Furthermore, 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.},
doi = {10.1371/journal.pone.0160653},
journal = {PLoS ONE},
number = 9,
volume = 11,
place = {United States},
year = 2016,
month = 9
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1371/journal.pone.0160653

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Cited by: 3works
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