Dataset Information

Three new single nucleotide polymorphisms identified by a genome-wide association study in Korean patients with vitiligo.

ABSTRACT: Genetic susceptibility is involved in the pathogenesis of vitiligo. Association studies with a whole genome-based approach instead of a single or a few candidate genes may be useful for discovering new susceptible genes. Although the etiology of non-segmental and segmental types is different, the association between gene polymorphisms and vitiligo has been reported, without defining types or in non-segmental type. Whole genome-based single nucleotide polymorphisms (SNPs) were examined in patients with non-segmental and segmental types of vitiligo using the Affymetrix GeneChip 500K mapping array, and 10 functional classes of significant SNPs were selected. Genotyping and data analysis of selected 10 SNPs was performed using real-time PCR. Genotype and allele frequencies were significantly different between both types of vitiligo and three of the target SNPs, DNAH5 (rs2277046), STRN3 (rs2273171), and KIAA1005 (rs3213758). A stronger association was suggested between the mutation in KIAA1005 (rs3213758) and the segmental type compared to the non-segmental type of vitiligo. DNAH5 (rs2277046), STRN3 (rs2273171), and KIAA1005 (rs3213758) may be new vitiligo-related SNPs in Korean patients, either non-segmental or segmental type.

SUBMITTER: Cheong KA

PROVIDER: S-EPMC3653093 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

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Three new single nucleotide polymorphisms identified by a genome-wide association study in Korean patients with vitiligo.

Cheong Kyung Ah KA Kim Nan-Hyung NH Noh Minsoo M Lee Ai-Young AY

Journal of Korean medical science 20130502 5

Genetic susceptibility is involved in the pathogenesis of vitiligo. Association studies with a whole genome-based approach instead of a single or a few candidate genes may be useful for discovering new susceptible genes. Although the etiology of non-segmental and segmental types is different, the association between gene polymorphisms and vitiligo has been reported, without defining types or in non-segmental type. Whole genome-based single nucleotide polymorphisms (SNPs) were examined in patient ...[more]

PMID: 23678272

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Project description:Study questionAre the single nucleotide polymorphisms (SNPs) rs2075230, rs6259 and rs727428 at the sex hormone-binding globulin (SHBG) locus, which were identified by genome-wide association studies (GWASs) for testosterone levels, associated with testosterone levels in Japanese men?Summary answerThe SNP rs2075230, but not rs6259 and rs727428, is significantly associated with testosterone levels in Japanese men.What is already knownPrevious GWASs have revealed that rs2075230 is associated with serum testosterone levels in 3495 Chinese men and rs6259 and rs727428 are associated with serum testosterone levels in 3225 men of European ancestry.Study design size and durationThis is an independent validation study of 1687 Japanese men (901 in Cohort 1 and 786 in Cohort 2).Participants/materials setting and methodCohort 1 (20.7 ± 1.7 years old, mean ± SD) and Cohort 2 (31.2 ± 4.8 years) included samples obtained from university students and partners of pregnant women, respectively. The three SNPs were genotyped using either TaqMan probes or restriction fragment length polymorphism PCR. Blood samples were drawn from the cubital vein of the study participants in the morning, and total testosterone and SHBG levels were measured using a time-resolved immunofluorometric assay. Association between each SNP and testosterone levels was evaluated by meta-analysis of the two Japanese male cohorts.Main results and the role of chanceThe age of the two cohorts was significantly different (P < 0.0001). We found that rs2075230 was significantly associated with serum testosterone levels (β STD = 0.15, P = 7.2 × 10-6); however, rs6259 and rs727428 were not (β STD = 0.17, P = 0.071; β STD = 0.082, P = 0.017, respectively), after adjusting for multiple testing in a combined analysis of two Japanese male cohorts. Moreover, rs2075230, rs6259 and rs727428 were significantly associated with high SHBG levels (β STD = 0.22, P = 3.4 × 10-12; β STD = 0.23, P = 6.5 × 10-6 and β STD = 0.21, P = 3.4 × 10-10, respectively).Large scale dataNot applicable.Limitations reasons for cautionThis study had differences in the age and background parameters of participants compared to those observed in previous GWASs. In addition, the average age of participants in the two cohorts in our study also differed from one another. Therefore, the average testosterone levels, which decrease with age, between studies or the two cohorts were different.Wider implications of the findingsThe three SNPs have a considerable effect on SHBG levels and hence may indirectly affect testosterone levels.Study funding/competing interestsThis study was supported partly by the Ministry of Health and Welfare of Japan (1013201) (to T.I.), Grant-in-Aids for Scientific Research (C) (26462461) (to Y.S.) and (23510242) (to A.Ta.) from the Japan Society for the Promotion of Science, the European Union (BMH4-CT96-0314) (to T.I.) and the Takeda Science Foundation (to A.Ta.). There are no conflicts of interest to declare.

Dataset Information

Three new single nucleotide polymorphisms identified by a genome-wide association study in Korean patients with vitiligo.

Publications

Three new single nucleotide polymorphisms identified by a genome-wide association study in Korean patients with vitiligo.

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