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Title: Protein-based forensic identification using genetically variant peptides in human bone

Abstract

Bone tissue contains organic material that is useful for forensic investigations and may contain preserved endogenous protein that can persist in the environment for extended periods of time over a range of conditions. Single amino acid polymorphisms in these proteins reflect genetic information since they result from non-synonymous single nucleotide polymorphisms (SNPs) in DNA. Detection of genetically variant peptides (GVPs) — those peptides that contain amino acid polymorphisms — in digests of bone proteins allows for the corresponding SNP alleles to be inferred. Resulting genetic profiles can be used to calculate statistical measures of association between a bone sample and an individual. In this study proteomic analysis on rib cortical bone samples from 10 recently deceased individuals demonstrates this concept. A straight-forward acidic demineralization protocol yielded proteins that were digested with trypsin. Tryptic digests were analyzed by liquid chromatography mass spectrometry. A total of 1736 different proteins were identified across all resulting datasets. On average, individual samples contained 454 ± 121 ($$\bar{x}$$ ± σ) proteins. Thirty-five genetically variant peptides were identified from 15 observed proteins. Overall, 134 SNP inferences were made based on proteomically detected GVPs, which were confirmed by sequencing of subject DNA. Inferred individual SNP genetic profiles ranged in random match probability (RMP) from 1/6 to 1/42,472 when calculated with European population frequencies in the 1000 Genomes Project, Phase 3. Similarly, RMPs based on African population frequencies were calculated for each SNP genetic profile and likelihood ratios (LR) were obtained by dividing each European RMP by the corresponding African RMP. In conclusion, resulting LR values ranged from 1.4 to 825 with a median value of 16. GVP markers offer a basis for the identification of compromised skeletal remains independent of the presence of DNA template.

Authors:
 [1]; ORCiD logo [1];  [2];  [1];  [3]
  1. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Forensic Science Center
  2. Utah Dept. of Health, Salt Lake City, UT (United States). Utah Office of the Medical Examiner
  3. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Forensic Science Center; Protein-Based Identification Technologies LLC, Orem, UT (United States)
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA)
OSTI Identifier:
1512602
Report Number(s):
LLNL-JRNL-743520
Journal ID: ISSN 0379-0738; 898379
Grant/Contract Number:  
AC52-07NA27344
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Forensic Science International
Additional Journal Information:
Journal Volume: 288; Journal Issue: C; Journal ID: ISSN 0379-0738
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Human identification; Genetically variant peptide; Bone; Proteomics; Random match probability; Single amino acid polymorphism

Citation Formats

Mason, Katelyn Elizabeth, Anex, Deon, Grey, Todd, Hart, Bradley, and Parker, Glendon. Protein-based forensic identification using genetically variant peptides in human bone. United States: N. p., 2018. Web. doi:10.1016/j.forsciint.2018.04.016.
Mason, Katelyn Elizabeth, Anex, Deon, Grey, Todd, Hart, Bradley, & Parker, Glendon. Protein-based forensic identification using genetically variant peptides in human bone. United States. doi:10.1016/j.forsciint.2018.04.016.
Mason, Katelyn Elizabeth, Anex, Deon, Grey, Todd, Hart, Bradley, and Parker, Glendon. Sun . "Protein-based forensic identification using genetically variant peptides in human bone". United States. doi:10.1016/j.forsciint.2018.04.016. https://www.osti.gov/servlets/purl/1512602.
@article{osti_1512602,
title = {Protein-based forensic identification using genetically variant peptides in human bone},
author = {Mason, Katelyn Elizabeth and Anex, Deon and Grey, Todd and Hart, Bradley and Parker, Glendon},
abstractNote = {Bone tissue contains organic material that is useful for forensic investigations and may contain preserved endogenous protein that can persist in the environment for extended periods of time over a range of conditions. Single amino acid polymorphisms in these proteins reflect genetic information since they result from non-synonymous single nucleotide polymorphisms (SNPs) in DNA. Detection of genetically variant peptides (GVPs) — those peptides that contain amino acid polymorphisms — in digests of bone proteins allows for the corresponding SNP alleles to be inferred. Resulting genetic profiles can be used to calculate statistical measures of association between a bone sample and an individual. In this study proteomic analysis on rib cortical bone samples from 10 recently deceased individuals demonstrates this concept. A straight-forward acidic demineralization protocol yielded proteins that were digested with trypsin. Tryptic digests were analyzed by liquid chromatography mass spectrometry. A total of 1736 different proteins were identified across all resulting datasets. On average, individual samples contained 454 ± 121 ($\bar{x}$ ± σ) proteins. Thirty-five genetically variant peptides were identified from 15 observed proteins. Overall, 134 SNP inferences were made based on proteomically detected GVPs, which were confirmed by sequencing of subject DNA. Inferred individual SNP genetic profiles ranged in random match probability (RMP) from 1/6 to 1/42,472 when calculated with European population frequencies in the 1000 Genomes Project, Phase 3. Similarly, RMPs based on African population frequencies were calculated for each SNP genetic profile and likelihood ratios (LR) were obtained by dividing each European RMP by the corresponding African RMP. In conclusion, resulting LR values ranged from 1.4 to 825 with a median value of 16. GVP markers offer a basis for the identification of compromised skeletal remains independent of the presence of DNA template.},
doi = {10.1016/j.forsciint.2018.04.016},
journal = {Forensic Science International},
issn = {0379-0738},
number = C,
volume = 288,
place = {United States},
year = {2018},
month = {4}
}

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