Demonstration of Protein-Based Human Identification 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 »
- Publication Date:
- Research Org.:
- Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1337466
- Alternate Identifier(s):
- OSTI ID: 1335793
- Report Number(s):
- LLNL-JRNL-665656
Journal ID: ISSN 1932-6203; 10.1371/journal.pone.0160653
- Grant/Contract Number:
- B601942; B607766; #121668; #132043; AC52-07NA27344
- Resource Type:
- Published Article
- Journal Name:
- PLoS ONE
- Additional Journal Information:
- Journal Name: PLoS ONE Journal Volume: 11 Journal Issue: 9; Journal ID: ISSN 1932-6203
- Publisher:
- Public Library of Science (PLoS)
- 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, ed., Francesc. Demonstration of Protein-Based Human Identification 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, ed., Francesc. Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome. United States. 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, and Calafell, ed., Francesc. Wed .
"Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome". United States. https://doi.org/10.1371/journal.pone.0160653.
@article{osti_1337466,
title = {Demonstration of Protein-Based Human Identification 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, ed., 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 = {Wed Sep 07 00:00:00 EDT 2016},
month = {Wed Sep 07 00:00:00 EDT 2016}
}
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Works referenced in this record:
Ancient DNA Reveals Prehistoric Gene-Flow from Siberia in the Complex Human Population History of North East Europe
journal, February 2013
- Der Sarkissian, Clio; Balanovsky, Oleg; Brandt, Guido
- PLoS Genetics, Vol. 9, Issue 2
Forensic trace DNA: a review
journal, January 2010
- van Oorschot, Roland AH; Ballantyne, Kaye N.; Mitchell, R. John
- Investigative Genetics, Vol. 1, Issue 1
Protein deamidation
journal, April 2002
- Robinson, N. E.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 8
A molecular basis for classic blond hair color in Europeans
journal, June 2014
- Guenther, Catherine A.; Tasic, Bosiljka; Luo, Liqun
- Nature Genetics, Vol. 46, Issue 7
Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes
journal, May 2012
- Tennessen, Jacob A.; Bigham, Abigail W.; O’Connor, Timothy D.
- Science, Vol. 337, Issue 6090
Developing a novel panel of genome-wide ancestry informative markers for bio-geographical ancestry estimates
journal, January 2014
- Jia, Jing; Wei, Yi-Liang; Qin, Cui-Jiao
- Forensic Science International: Genetics, Vol. 8, Issue 1
Proteomics methods to study methionine oxidation: methionine sulfoxide proteomics
journal, October 2013
- Ghesquière, Bart; Gevaert, Kris
- Mass Spectrometry Reviews, Vol. 33, Issue 2
Correlation of Microscopic and Mitochondrial DNA Hair Comparisons
journal, September 2002
- Houck, Max M.; Budowle, Bruce
- Journal of Forensic Sciences, Vol. 47, Issue 5
Proteins help solve taxonomy riddle
journal, November 2013
- Callaway, Ewen
- Nature, Vol. 503, Issue 7474
Short tandem repeat (STR) genotyping of keratinised hair Part 2. An optimised genomic DNA extraction procedure reveals donor dependence of STR profiles
journal, October 2005
- McNevin, Dennis; Wilson-Wilde, Linzi; Robertson, James
- Forensic Science International, Vol. 153, Issue 2-3
Protein Identification Using Customized Protein Sequence Databases Derived from RNA-Seq Data
journal, December 2011
- Wang, Xiaojing; Slebos, Robbert J. C.; Wang, Dong
- Journal of Proteome Research, Vol. 11, Issue 2
Logical implications of applying the principles of population genetics to the interpretation of DNA profiling evidence
journal, August 2002
- Triggs, Christopher M.; Buckleton, John S.
- Forensic Science International, Vol. 128, Issue 3
Development of a novel forensic STR multiplex for ancestry analysis and extended identity testing: Nucleic acids
journal, March 2013
- Phillips, Chris; Fernandez-Formoso, Luis; Gelabert-Besada, Miguel
- ELECTROPHORESIS, Vol. 34, Issue 8
Short tandem repeat (STR) genotyping of keratinised hair
journal, October 2005
- McNevin, Dennis; Wilson-Wilde, Linzi; Robertson, James
- Forensic Science International, Vol. 153, Issue 2-3
Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine
journal, April 1993
- Zweig, M. H.; Campbell, G.
- Clinical Chemistry, Vol. 39, Issue 4
Current algorithmic solutions for peptide-based proteomics data generation and identification
journal, February 2013
- Hoopmann, Michael R.; Moritz, Robert L.
- Current Opinion in Biotechnology, Vol. 24, Issue 1
On Human Hair as a Race-Character, Examined by the Aid of the Microscope
journal, February 1864
- Pruner-Bey, Dr.
- Anthropological Review, Vol. 2, Issue 4
STR genotyping of exogenous hair shaft DNA
journal, December 2007
- Robertson, Kate S.; McNevin, Dennis; Robertson, James
- Australian Journal of Forensic Sciences, Vol. 39, Issue 2
Linkage disequilibrium in the human genome
journal, May 2001
- Reich, David E.; Cargill, Michele; Bolk, Stacey
- Nature, Vol. 411, Issue 6834
Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics
journal, August 2011
- Lam, Henry; Aebersold, Ruedi
- Methods, Vol. 54, Issue 4
Preservation of key biomolecules in the fossil record: current knowledge and future challenges
journal, January 1999
- Bada, Jeffrey L.; Wang, Xueyun S.; Hamilton, Healy
- Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, Vol. 354, Issue 1379
An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia
journal, September 2011
- Rasmussen, M.; Guo, X.; Wang, Y.
- Science, Vol. 334, Issue 6052
The human type I keratin gene family: Characterization of new hair follicle specific members and evaluation of the chromosome 17q21.2 gene domain
journal, December 2004
- Rogers, Michael A.; Winter, Hermelita; Langbein, Lutz
- Differentiation, Vol. 72, Issue 9-10
Scientific Working Group on Materials Analysis Position on Hair Evidence
journal, September 2009
- Lanning, Karen A.; Michaud, Amy L.; Bisbing, Richard E.
- Journal of Forensic Sciences, Vol. 54, Issue 5
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
journal, June 2013
- Orlando, Ludovic; Ginolhac, Aurélien; Zhang, Guojie
- Nature, Vol. 499, Issue 7456
Structural basis for heteromeric assembly and perinuclear organization of keratin filaments
journal, June 2012
- Lee, Chang-Hun; Kim, Min-Sung; Chung, Byung Min
- Nature Structural & Molecular Biology, Vol. 19, Issue 7
The Human Type II Keratin Gene Cluster on Chromosome 12q13.13: Final Count or Hidden Secrets?
journal, March 2005
- Bowden, Paul E.
- Journal of Investigative Dermatology, Vol. 124, Issue 3
TANDEM: matching proteins with tandem mass spectra
journal, February 2004
- Craig, R.; Beavis, R. C.
- Bioinformatics, Vol. 20, Issue 9
Generalized Method for Probability-based Peptide and Protein Identification from Tandem Mass Spectrometry Data and Sequence Database Searching
journal, May 2008
- Ramos-Fernández, Antonio; Paradela, Alberto; Navajas, Rosana
- Molecular & Cellular Proteomics, Vol. 7, Issue 9
The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils
journal, October 2012
- Allentoft, Morten E.; Collins, Matthew; Harker, David
- Proceedings of the Royal Society B: Biological Sciences, Vol. 279, Issue 1748
The Archaeogenetics of Europe
journal, February 2010
- Soares, Pedro; Achilli, Alessandro; Semino, Ornella
- Current Biology, Vol. 20, Issue 4
An invariant form for the prior probability in estimation problems
journal, September 1946
- Jeffreys, Harold
- Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences, Vol. 186, Issue 1007, p. 453-461
Methods and Future Prospects for Forensic Identification of Hairs by Electrophoresis
journal, January 1985
- Marshall, R. C.; Gillespie, J. M.; Klement, V.
- Journal of the Forensic Science Society, Vol. 25, Issue 1
Novel Oxidative Modifications in Redox-Active Cysteine Residues
journal, December 2010
- Jeong, Jaeho; Jung, Yongsik; Na, Seungjin
- Molecular & Cellular Proteomics, Vol. 10, Issue 3
Ancient human genome sequence of an extinct Palaeo-Eskimo
journal, February 2010
- Rasmussen, Morten; Li, Yingrui; Lindgreen, Stinus
- Nature, Vol. 463, Issue 7282
Preservation of ancient DNA in thermally damaged archaeological bone
journal, November 2008
- Ottoni, Claudio; Koon, Hannah E. C.; Collins, Matthew J.
- Naturwissenschaften, Vol. 96, Issue 2
Characterization of New Members of the Human Type II Keratin Gene Family and a General Evaluation of the Keratin Gene Domain on Chromosome 12q13.13
journal, March 2005
- Rogers, Michael A.; Edler, Lutz; Winter, Hermelita
- Journal of Investigative Dermatology, Vol. 124, Issue 3
Selective biodegradation in hair shafts derived from archaeological, forensic and experimental contexts
journal, September 2007
- Wilson, A. S.; Dodson, H. I.; Janaway, R. C.
- British Journal of Dermatology, Vol. 157, Issue 3
A Human Genome Diversity Cell Line Panel
journal, April 2002
- Cann, H. M.
- Science, Vol. 296, Issue 5566
Discovery and genotyping of genome structural polymorphism by sequencing on a population scale
journal, February 2011
- Handsaker, Robert E.; Korn, Joshua M.; Nemesh, James
- Nature Genetics, Vol. 43, Issue 3
Statistics Notes: Diagnostic tests 2: predictive values
journal, July 1994
- Altman, D. G.; Bland, J. M.
- BMJ, Vol. 309, Issue 6947
Proteomic tools for the investigation of human hair structural proteins and evidence of weakness sites on hair keratin coil segments
journal, February 2012
- Barthélemy, Nicolas R.; Bednarczyk, Audrey; Schaeffer-Reiss, Christine
- Analytical Biochemistry, Vol. 421, Issue 1
‘Hard’ and ‘soft’ principles defining the structure, function and regulation of keratin intermediate filaments
journal, February 2002
- Coulombe, Pierre A.; Omary, M. Bishr
- Current Opinion in Cell Biology, Vol. 14, Issue 1
Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants
journal, November 2012
- Fu, Wenqing; O’Connor, Timothy D.; Jun, Goo
- Nature, Vol. 493, Issue 7431
Forensic Mitochondrial DNA Analysis of 691 Casework Hairs
journal, January 2005
- Melton, Terry; Dimick, Gloria; Higgins, Bonnie
- Journal of Forensic Sciences, Vol. 50, Issue 1
Bayesian Data Analysis
book, July 2003
- Gelman, Andrew; Carlin, John B.; Stern, Hal S.
- Chapman and Hall/CRC
Development of SNP-based human identification system
journal, November 2009
- Kim, Jae-Jung; Han, Bok-Ghee; Lee, Hae-In
- International Journal of Legal Medicine, Vol. 124, Issue 2
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
journal, October 2010
- Nesvizhskii, Alexey I.
- Journal of Proteomics, Vol. 73, Issue 11
A Simplified Method for Mitochondrial DNA Extraction from Head Hair Shafts
journal, January 2005
- Graffy, Elizabeth A.; Foran, David R.
- Journal of Forensic Sciences, Vol. 50, Issue 5
Common DNA variants predict tall stature in Europeans
journal, November 2013
- Liu, Fan; Hendriks, A. Emile J.; Ralf, Arwin
- Human Genetics, Vol. 133, Issue 5
Integrating common and rare genetic variation in diverse human populations
journal, September 2010
- ,
- Nature, Vol. 467, Issue 7311, p. 52-58
Exponentially Modified Protein Abundance Index (emPAI) for Estimation of Absolute Protein Amount in Proteomics by the Number of Sequenced Peptides per Protein
journal, June 2005
- Ishihama, Yasushi; Oda, Yoshiya; Tabata, Tsuyoshi
- Molecular & Cellular Proteomics, Vol. 4, Issue 9
Archaic human genomics
journal, January 2012
- Disotell, Todd R.
- American Journal of Physical Anthropology, Vol. 149, Issue S55
Genetic Analyses from Ancient DNA
journal, December 2004
- Pääbo, Svante; Poinar, Hendrik; Serre, David
- Annual Review of Genetics, Vol. 38, Issue 1
The Divergence of Neandertal and Modern Human Y Chromosomes
journal, April 2016
- Mendez, Fernando L.; Poznik, G. David; Castellano, Sergi
- The American Journal of Human Genetics, Vol. 98, Issue 4
Developing a SNP panel for forensic identification of individuals
journal, December 2006
- Kidd, Kenneth K.; Pakstis, Andrew J.; Speed, William C.
- Forensic Science International, Vol. 164, Issue 1
Proteome degradation in fossils: investigating the longevity of protein survival in ancient bone: Proteome degradation in fossils
journal, February 2014
- Wadsworth, Caroline; Buckley, Mike
- Rapid Communications in Mass Spectrometry, Vol. 28, Issue 6
Large-Scale Mass Spectrometric Detection of Variant Peptides Resulting from Nonsynonymous Nucleotide Differences
journal, November 2013
- Sheynkman, Gloria M.; Shortreed, Michael R.; Frey, Brian L.
- Journal of Proteome Research, Vol. 13, Issue 1
Science and the law: scientific evidence, causation, admissibility, reliability “Daubert” decision revisited
journal, July 1999
- Brautbar, Nachman
- Toxicology and Industrial Health, Vol. 15, Issue 6
Revised age of late Neanderthal occupation and the end of the Middle Paleolithic in the northern Caucasus
journal, May 2011
- Pinhasi, R.; Higham, T. F. G.; Golovanova, L. V.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 21
Combining Results of Multiple Search Engines in Proteomics
journal, May 2013
- Shteynberg, David; Nesvizhskii, Alexey I.; Moritz, Robert L.
- Molecular & Cellular Proteomics, Vol. 12, Issue 9
Genome-wide patterns of population structure and admixture in West Africans and African Americans
journal, December 2009
- Bryc, K.; Auton, A.; Nelson, M. R.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 2
Protein identification using MS/MS data
journal, September 2011
- Cottrell, John S.
- Journal of Proteomics, Vol. 74, Issue 10
Protein preservation and DNA retrieval from ancient tissues
journal, July 1999
- Poinar, H. N.; Stankiewicz, B. A.
- Proceedings of the National Academy of Sciences, Vol. 96, Issue 15
Ancient human genomes suggest three ancestral populations for present-day Europeans
journal, September 2014
- Lazaridis, Iosif; Patterson, Nick; Mittnik, Alissa
- Nature, Vol. 513, Issue 7518
Comprehensive proteomics
journal, February 2011
- Beck, Martin; Claassen, Manfred; Aebersold, Ruedi
- Current Opinion in Biotechnology, Vol. 22, Issue 1
Proteome Analysis of Human Hair Shaft: From Protein Identification to Posttranslational Modification
journal, January 2006
- Lee, Young Jin; Rice, Robert H.; Lee, Young Moo
- Molecular & Cellular Proteomics, Vol. 5, Issue 5
Detection and Validation of Non-synonymous Coding SNPs from Orthogonal Analysis of Shotgun Proteomics Data
journal, June 2007
- Bunger, Maureen K.; Cargile, Benjamin J.; Sevinsky, Joel R.
- Journal of Proteome Research, Vol. 6, Issue 6
Differentiating Inbred Mouse Strains from Each Other and Those with Single Gene Mutations Using Hair Proteomics
journal, December 2012
- Rice, Robert H.; Bradshaw, Katie M.; Durbin-Johnson, Blythe P.
- PLoS ONE, Vol. 7, Issue 12
DNA from keratinous tissue. Part I: Hair and nail
journal, January 2012
- Bengtsson, Camilla Friis; Olsen, Maia E.; Brandt, Luise Ørsted
- Annals of Anatomy - Anatomischer Anzeiger, Vol. 194, Issue 1
Modeling Deamidation in Sheep α-Keratin Peptides and Application to Archeological Wool Textiles
journal, December 2013
- Solazzo, Caroline; Wilson, Julie; Dyer, Jolon M.
- Analytical Chemistry, Vol. 86, Issue 1
Instability and decay of the primary structure of DNA
journal, April 1993
- Lindahl, Tomas
- Nature, Vol. 362, Issue 6422
A quantitative assessment of a reliable screening technique for the STR analysis of telogen hair roots
journal, January 2013
- Edson, Janette; Brooks, Elizabeth M.; McLaren, Carolyn
- Forensic Science International: Genetics, Vol. 7, Issue 1
Assessing uncertainty in DNA evidence caused by sampling effects
journal, January 2002
- Curran, J. M.; Buckleton, J. S.; Triggs, C. M.
- Science & Justice, Vol. 42, Issue 1