Dataset Information

Variant datasets from 330 chestnut accessions

ABSTRACT: The dataset contains genetic variant information derived from 330 chestnut accessions

INSTRUMENT(S): -

ORGANISM(S): Castanea Mollissima

SUBMITTER: College of Plant Science and Technology

PROVIDER: PRJEB87510 | EVA | 2025-03-27

REPOSITORIES: EVA

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	variants_data.GBS173.0.85.0.01.accessioned.vcf.gz	Vcf
	variants_data.GBS173.0.85.0.01.accessioned.vcf.gz.csi	Vcf
	variants_data.GBS173.0.85.0.01.vcf.csi	Other
	variants_data.GBS173.0.85.0.01.vcf.gz	Vcf
	variants_data.RS61.0.7_0.03.accessioned.vcf.gz	Vcf

Items per page:

1 - 5 of 12

Similar Datasets

Project 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.

Dataset Information

Variant datasets from 330 chestnut accessions

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets