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Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome
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...
Autores principales: | , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5014411/ https://www.ncbi.nlm.nih.gov/pubmed/27603779 http://dx.doi.org/10.1371/journal.pone.0160653 |
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author | 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 |
author_facet | 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 |
author_sort | Parker, Glendon J. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-5014411 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-50144112016-09-27 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 PLoS One Research Article 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. Public Library of Science 2016-09-07 /pmc/articles/PMC5014411/ /pubmed/27603779 http://dx.doi.org/10.1371/journal.pone.0160653 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication. |
spellingShingle | Research Article 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 |
title | Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome |
title_full | Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome |
title_fullStr | Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome |
title_full_unstemmed | Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome |
title_short | Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome |
title_sort | demonstration of protein-based human identification using the hair shaft proteome |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5014411/ https://www.ncbi.nlm.nih.gov/pubmed/27603779 http://dx.doi.org/10.1371/journal.pone.0160653 |
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