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Genetic characterization of variants and population inference through multiple independent pool-seq: The Cyprus Genome Project

ABSTRACT: The Cyprus Genome project, the first large-scale study of human genetic variation in Cyprus, addresses the island’s complex genetic makeup resulting from its unique geographic location and historical immigration. This intricate genetic heritage, combined with the limitations of existing genetic data in representing the full spectrum of population-level diversity in Cyprus, necessitates a more comprehensive approach to studying the Cypriot gene pool. Here, we present a genetically diverse population study which demonstrates the power of pool-sequencing (pool-seq methodology) using DNA from 10,000 randomly selected healthy bone marrow donors collected over a period of several years. This study highlights the use of pool-seq as a viable way to elucidate both rare and common variants specific to the population which is also a proven, cost-effective and time-efficient method. DNA samples were pooled for whole exome and gene panel sequencing enabling statistical analysis of variant frequencies and read numbers between pools, resulting in confidence intervals. The resulting variant database was validated across established resources like gnomAD and published Cypriot clinical research cohort data, ensuring fidelity. Enhanced sensitivity in (rare) variant detection was achieved by combining WES and gene panel sequencing to maximise read depth. The results, including an interactive genome map with annotations from gnomAD and ClinVar, are publicly accessible at www.cyprusgenome.org, facilitating clinical research.

INSTRUMENT(S): Illumina

ORGANISM(S): Homo Sapiens

SUBMITTER: Karaiskakio Foundation

PROVIDER: PRJEB89856 | EVA | 2025-05-26

REPOSITORIES: EVA

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			Action	DRS
	CyGenome_Whole_Exome_VCF_4.3_02052025.vcf.csi	Other
	CyGenome_Whole_Exome_VCF_4.3_02052025.vcf.gz	Vcf
	CyGenome_Whole_Exome_VCF_4.3_02052025.vcf.gz.csi	Vcf

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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.

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Genetic characterization of variants and population inference through multiple independent pool-seq: The Cyprus Genome Project

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