9/17/2018 Protein-based forensic identification using genetically variant peptides in human bone - ScienceDirect

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Forensic Science International

Volume 288, July 2018, Pages 89-96

Protein-based forensic identification using genetically variant

peptides in human bone
Katelyn Elizabeth Mason a , Deon Anex a, Todd Grey b, Bradley Hart a, Glendon Parker a, c, 1

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https://doi.org/10.1016/j.forsciint.2018.04.016 Get rights and content

Highlights
• Extraction of human bone proteins are applicable to forensic analysis.

• Genetically variant peptides constitute human identification markers.

• Bone genetically variant peptides confirmed with sequenced DNA.

• Random match probabilities obtained as low as 1 in 42 thousand.

• Ancestral information gained from genetically variant peptide profiles.

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

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9/17/2018 Protein-based forensic identification using genetically variant peptides in human bone - ScienceDirect

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 ( ) 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. 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.

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Keywords
Human identification; Genetically variant peptide; Bone; Proteomics; Random match
probability; Single amino acid polymorphism

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1
Environmental Toxicology Department, University of California at Davis, Davis, CA 95616, United States.

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