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 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.
Department of Biology, Utah Valley University, Orem, Utah, United States of America.|Protein-Based Identification Technologies L.L.C., Orem, Utah, United States of America.
Glendon J
http://orcid.org/0000-0003-2937-5853
GJ
Parker
Protein-Based Identification Technologies L.L.C., Orem, Utah, United States of America.|Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America.
Tami
T
Leppert
Forensic Science Center, Lawrence Livermore National Laboratory, Livermore, California, United States of America.
Deon S
DS
Anex
Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America.
Jonathan K
JK
Hilmer
Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America.
Nori
N
Matsunami
Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America.
Lisa
L
Baird
Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America.
Jeffery
J
Stevens
Mass Spectrometry and Proteomics Core Facility, University of Utah, Salt Lake City, Utah, United States of America.
Krishna
K
Parsawar
Department of Public Health Sciences, University of California, Davis, California, United States of America.
Blythe P
BP
Durbin-Johnson
Department of Public Health Sciences, University of California, Davis, California, United States of America.
David M
DM
Rocke
Mass Spectrometry and Proteomics Core Facility, University of Utah, Salt Lake City, Utah, United States of America.
Chad
C
Nelson
Department of Biology, Utah Valley University, Orem, Utah, United States of America.
Daniel J
DJ
Fairbanks
School of Archaeological Sciences, University of Bradford, Bradford, United Kingdom.
Andrew S
AS
Wilson
Department of Environmental Toxicology, University of California, Davis, California, United States of America.
Robert H
RH
Rice
Sorenson Molecular Genealogical Foundation, Salt Lake City, Utah, United States of America.
Scott R
SR
Woodward
Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America.
Brian
B
Bothner
Forensic Science Center, Lawrence Livermore National Laboratory, Livermore, California, United States of America.
Bradley R
BR
Hart
Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America.
Mark
M
Leppert
D000483:Alleles; D044383:Black People / Q000235:genetics; D018732:Forensic Anthropology / Q000379:methods*; D005838:Genotype; D006197:Hair / Q000737:chemistry*; D006801:Humans; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040901:Proteomics; D044465:White People / Q000235:genetics