Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

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

Journal Article · · Forensic Science International
 [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)
+ Show Author Affiliations

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.

Research Organization:
Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
Sponsoring Organization:
USDOE National Nuclear Security Administration (NNSA)
Grant/Contract Number:
AC52-07NA27344
OSTI ID:
1512602
Report Number(s):
LLNL-JRNL-743520; 898379
Journal Information:
Forensic Science International, Vol. 288, Issue C; ISSN 0379-0738
Publisher:
ElsevierCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 22 works
Citation information provided by
Web of Science

References (38)

Method Development of Efficient Protein Extraction in Bone Tissue for Proteome Analysis journal June 2007
The forensic evaluation of burned skeletal remains: A synthesis journal January 2009
Ancient DNA: Methodological challenges journal June 1994
Preservation of ancient DNA in thermally damaged archaeological bone journal November 2008
Instability and decay of the primary structure of DNA journal April 1993
Collagen Fingerprinting: A New Screening Technique for Radiocarbon Dating Ancient Bone journal March 2016
Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne journal September 2016
Ancient proteins resolve the evolutionary history of Darwin’s South American ungulates journal March 2015
Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome journal September 2016
Research potential and limitations of trace analyses of cremated remains journal January 2011
Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. canadensis journal April 2009
Identification of a new hominin bone from Denisova Cave, Siberia using collagen fingerprinting and mitochondrial DNA analysis journal March 2016
Distinguishing between archaeological sheep and goat bones using a single collagen peptide journal January 2010
Comparing ancient DNA survival and proteome content in 69 archaeological cattle tooth and bone samples from multiple European sites journal March 2017
Bone protein “extractomics”: comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics journal January 2016
New techniques for the recovery of small amounts of mature enamel proteins journal December 2011
Novel Oxidative Modifications in Redox-Active Cysteine Residues journal December 2010
Modeling Deamidation in Sheep α-Keratin Peptides and Application to Archeological Wool Textiles journal December 2013
Proteomics methods to study methionine oxidation: methionine sulfoxide proteomics journal October 2013
Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation journal May 2011
Unlocking Ancient Protein Palimpsests journal March 2014
Mass Spectrometric Protein Identification Using the Global Proteome Machine book January 2010
Biochemistry of bone journal April 1988
Bone matrix proteins: their function, regulation, and relationship to osteoporosis journal March 2003
THE MATERIAL BONE: Structure-Mechanical Function Relations journal August 1998
Species Identification of Bovine, Ovine and Porcine Type 1 Collagen; Comparing Peptide Mass Fingerprinting and LC-Based Proteomics Methods journal March 2016
Mid-Pliocene warm-period deposits in the High Arctic yield insight into camel evolution journal March 2013
A new procedure for extraction of collagen from modern and archaeological bones for 14C dating journal July 2011
An acetic acid-based extraction method to obtain high quality collagen from archeological bone remains journal February 2012
Revised age of late Neanderthal occupation and the end of the Middle Paleolithic in the northern Caucasus journal May 2011
Intra- and Interskeletal Proteome Variations in Fresh and Buried Bones journal April 2017
Recovery and identification of mature enamel proteins in ancient teeth: Protein recovery from ancient dental enamel journal December 2011
Equilibrium and kinetic constants for the thiol-disulfide interchange reaction between glutathione and dithiothreitol. journal September 1992
Effects of amino acid sequence, buffers, and ionic strength on the rate and mechanism of deamidation of asparagine residues in small peptides. journal November 1991
Mass spectrometry data from proteomic analysis of human skin keratins after exposure to UV radiation journal June 2016
Improving SRM Assay Development: A Global Comparison between Triple Quadrupole, Ion Trap, and Higher Energy CID Peptide Fragmentation Spectra journal September 2011
Collagen Structure and Stability journal June 2009
Cleavage N-Terminal to Proline:  Analysis of a Database of Peptide Tandem Mass Spectra journal May 2003

Cited By (5)

Artificial fingerprints for cross-comparison of forensic DNA and protein recovery methods journal October 2019
Beyond Genes: Re-Identifiability of Proteomic Data and Its Implications for Personalized Medicine journal September 2019
Rotator Cuff Tenocytes Differentiate into Hypertrophic Chondrocyte-Like Cells to Produce Calcium Deposits in an Alkaline Phosphatase-Dependent Manner journal September 2019
Artificial fingerprints for cross-comparison of forensic DNA and protein recovery methods journal October 2019
Beyond Genes: Re-Identifiability of Proteomic Data and Its Implications for Personalized Medicine journal September 2019

Figures / Tables (11)

Fig. 1(p. 5)figure Fig. 1
Table 1(p. 8)table Table 1
Fig. 2(p. 10)figure Fig. 2
Fig. 3(p. 11)figure Fig. 3
Fig. 4(p. 12)figure Fig. 4
Supplemental Fig 1.(p. 17)figure Supplemental Fig 1.
Supplemental Table 1(p. 18)figure Supplemental Table 1
Supplemental table 2(p. 19)figure Supplemental table 2
Supplemental Table 2 (continued)(p. 20)figure Supplemental Table 2 (continued)
Supplemental Table 2 (Continued)(p. 21)figure Supplemental Table 2 (Continued)
Supplemental Table 3(p. 22)figure Supplemental Table 3

Similar Records

Related Subjects

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