PXD012628

PXD012628 is an original dataset announced via ProteomeXchange.

Title	Genetically Variant Peptide Biomarkers from Fingermarks
Description	This dataset results from the discovery, characterization and validation of 74 genetically variant peptides from fingermark protein. These peptides contain single amino acid polymorphisms, the result of non-synonymous SNPs. Detection of these peptide markers in fingermark proteomic datasets allows inferences to be made about the genotype status of corresponding SNP alleles. These inferences provide an individual genetic profile that may be used to calculate random match probabilities and provide information about potential genetic background. Epidermal corneocytes from five European and four South Asian subjects were isolated, processed, proteolytically digested with trypsin and 0.75 µg applied to a Q ExactiveTM hybrid quadrupole-Orbitrap mass spectrometer. The resulting datasets were used for discovery of genetically variant peptides by a “bottom-up” analysis of potential variants identified in X!Tandem datasets (thegpm.org) or by a “top-down” proteomic confirmation of non-synonymous SNP variants shown to be present in corresponding subject exome datasets. The later method resulted in discovery of a rare allele that was not observed in the 1000 Genome Project. The cumulative profiles of detected genetically variant peptides were obtained for each subject. Candidate genetically variant peptides were then validated by comparing proteomically inferred SNP alleles with matching genotypes in exome datasets. An average of 28.8 ± 4.4 genetically variant peptides were detected from each subject. Across the 9 subjects a total of 264 SNP allele inferences were made resulting in 260 true positives and 4 false positives, a false positive rate of 1.5%. Random match probabilities were calculated using the genotype frequencies of common genetically variant peptides from the matching major populations in the 1000 genome project. Estimates ranged up to a value of 1 in 1.7 x 108, with a median probability of 1 in 2.4 x 106. When probabilities were recalculated using values from other major genetic population groups African values were considerably less conservative, with resulting likelihood ratios (AFR/other populations) ranging up to 6 orders of magnitude. Conversely there was no resolution among estimates obtained from all non-African population groups, where resulting random match probabilities were within an order of magnitude. These genetically variant peptides are a starting point for the development of targeted mass spectrometry-based proteomic analyses that will increase the sensitivity of peptide detection. This project represents a novel mode of genetic information that can be obtained from fingermarks and has the potential to complement or confirm other methods of human identification including analysis of ridge patterns or touch DNA.
HostingRepository	PRIDE
AnnounceDate	2019-06-19
AnnouncementXML	Submission_2019-06-19_05:39:55.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Glendon Parker
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-02-08 02:09:30	ID requested
⏵ 1	2019-06-19 05:39:56	announced

Borja T, Karim N, Goecker Z, Salemi M, Phinney B, Naeem M, Rice R, Parker G, Proteomic genotyping of fingermark donors with genetically variant peptides. Forensic Sci Int Genet, 42():21-30(2019) [pubmed]

curator keyword: Technical

submitter keyword: Forensic Science, Fingermarks, Proteomics, Genetically Variant Peptides, Epidermal Corneocytes

Glendon John Parker
contact affiliation	University of California Davis, College of Agricultural and Envirnmental Sciences, Environmental Toxicology
contact email	gjparker@ucdavis.edu
lab head
Glendon Parker
contact affiliation	UC Davis
contact email	gjparker@ucdavis.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD012628
     1. Label: PRIDE project
     2. Name: Genetically Variant Peptide Biomarkers from Fingermarks