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Genomic Landscape of Genetic Variants in Healthy Kazakh Individuals: Insights from a GWAS Study

ABSTRACT: This project presents a comprehensive genotyping dataset for 224 healthy Kazakh individuals. Genomic DNA was collected from local medical stations across Kazakhstan and genotyped using the Illumina Infinium SNP Genotyping Array GSA MG v2. The study contributes to understanding the genetic variation of the Kazakh population and highlights single nucleotide variants with biomedical significance.

INSTRUMENT(S): -

ORGANISM(S): Homo Sapiens

SUBMITTER: Center for Life Sciences, National Laboratory Astana, Nazarbayev University

PROVIDER: PRJEB89820 | EVA | 2025-05-26

REPOSITORIES: EVA

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Project description:BACKGROUND:There are now over 2000 loci in the human genome where genome wide association studies (GWAS) have found one or more SNPs to be associated with altered risk of a complex trait disease. At each of these loci, there must be some molecular level mechanism relevant to the disease. What are these mechanisms and how do they contribute to disease? RESULTS:Here we consider the roles of three primary mechanism classes: changes that directly alter protein function (missense SNPs), changes that alter transcript abundance as a consequence of variants close-by in sequence, and changes that affect splicing. Missense SNPs are divided into those predicted to have a high impact on in vivo protein function, and those with a low impact. Splicing is divided into SNPs with a direct impact on splice sites, and those with a predicted effect on auxiliary splicing signals. The analysis was based on associations found for seven complex trait diseases in the classic Wellcome Trust Case Control Consortium (WTCCC1) GWA study and subsequent studies and meta-analyses, collected from the GWAS catalog. Linkage disequilibrium information was used to identify possible candidate SNPs for involvement in disease mechanism in each of the 356 loci associated with these seven diseases. With the parameters used, we find that 76% of loci have at least of these mechanisms. Overall, except for the low incidence of direct impact on splice sites, the mechanisms are found at similar frequencies, with changes in transcript abundance the most common. But the distribution of mechanisms over diseases varies markedly, as does the fraction of loci with assigned mechanisms. Many of the implicated proteins have previously been suggested as relevant, but the specific mechanism assignments are new. In addition, a number of new disease relevant proteins are proposed. CONCLUSIONS:The high fraction of GWAS loci with proposed mechanisms suggests that these classes of mechanism play a major role. Other mechanism types, such as variants affecting expression of genes remote in the DNA sequence, will contribute in other loci. Each of the identified putative mechanisms provides a hypothesis for further investigation.

			Action	DRS
	sample_1.snv.vcf.csi	Other
	sample_1.snv.vcf.gz	Vcf
	sample_1.snv.vcf.gz.csi	Vcf
	sample_101.snv.vcf.csi	Other
	sample_101.snv.vcf.gz	Vcf

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Genomic Landscape of Genetic Variants in Healthy Kazakh Individuals: Insights from a GWAS Study

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