1. Unveiling Genetic Variants Underlying Vitamin D Deficiency in Multiple Korean Cohorts by a Genome-Wide Association Study
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Young Chul Lee, Heejin Jin, Seung-Hyun Kwon, Je Hyun Seo, Hyuk Jin Choi, Ji Won Yoon, Ye An Kim, Ah-Ra Do, Chan Soo Shin, Jae Won Yun, So Eun Ahn, Do Joon Park, Sungho Won, and Eunsin Bae
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Calcium & Bone Metabolism ,Endocrinology, Diabetes and Metabolism ,Single-nucleotide polymorphism ,Genome-wide association study ,Diseases of the endocrine glands. Clinical endocrinology ,vitamin D deficiency ,Endocrinology ,Asian People ,Vitamin D and neurology ,Humans ,Medicine ,SNP ,Vitamin D ,Allele ,genetic predisposition to disease ,Genetics ,genome-wide association study ,business.industry ,polymorphism, single nucleotide ,Heritability ,RC648-665 ,medicine.disease ,vitamin d deficiency ,Expression quantitative trait loci ,Original Article ,asians ,business - Abstract
Background: Epidemiological data have shown that vitamin D deficiency is highly prevalent in Korea. Genetic factors influencing vitamin D deficiency in humans have been studied in Europe but are less known in East Asian countries, including Korea. We aimed to investigate the genetic factors related to vitamin D levels in Korean people using a genome-wide association study (GWAS).Methods: We included 12,642 subjects from three different genetic cohorts consisting of Korean participants. The GWAS was performed on 7,590 individuals using linear or logistic regression meta- and mega-analyses. After identifying significant single nucleotide polymorphisms (SNPs), we calculated heritability and performed replication and rare variant analyses. In addition, expression quantitative trait locus (eQTL) analysis for significant SNPs was performed.Results: rs12803256, in the actin epsilon 1, pseudogene (ACTE1P) gene, was identified as a novel polymorphism associated with vitamin D deficiency. SNPs, such as rs11723621 and rs7041, in the group-specific component gene (GC) and rs11023332 in the phosphodiesterase 3B (PDE3B) gene were significantly associated with vitamin D deficiency in both meta- and mega-analyses. The SNP heritability of the vitamin D concentration was estimated to be 7.23%. eQTL analysis for rs12803256 for the genes related to vitamin D metabolism, including glutamine-dependent NAD(+) synthetase (NADSYN1) and 7-dehydrocholesterol reductase (DHCR7), showed significantly different expression according to alleles.Conclusion: The genetic factors underlying vitamin D deficiency in Korea included polymorphisms in the GC, PDE3B, NADSYN1, and ACTE1P genes. The biological mechanism of a non-coding SNP (rs12803256) for DHCR7/NADSYN1 on vitamin D concentrations is unclear, warranting further investigations.
- Published
- 2021
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