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Genome-wide association study for vitiligo identifies susceptibility loci at 6q27 and the MHC


We conducted a genome-wide association study of generalized vitiligo in the Chinese Han population by genotyping 1,117 cases and 1,429 controls. The 34 most promising SNPs were carried forward for replication in samples from individuals of the Chinese Han (5,910 cases and 9,916 controls) and Chinese Uygur (713 cases and 824 controls) populations. We identified two independent association signals within the major histocompatibility complex (MHC) region (rs11966200, Pcombined = 1.48 × 10−48, OR = 1.90; rs9468925, Pcombined = 2.21 × 10−33, OR = 0.74). Further analyses suggested that the strong association at rs11966200 might reflect the reported association of the HLA-A*3001, HLA-B*1302, HLA-C*0602 and HLA-DRB1*0701 alleles and that the association at rs9468925 might represent a previously unknown HLA susceptibility allele. We also identified one previously undescribed risk locus at 6q27 (rs2236313, Pcombined = 9.72 × 10−17, OR = 1.20), which contains three genes: RNASET2, FGFR1OP and CCR6. Our study provides new insights into the genetic basis of vitiligo.

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Figure 1: Genome-wide association results from the initial GWAS.
Figure 2: Scatter plot of the evidence of association at 6q27 for vitiligo.


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We thank all study participants. We also thank J.-J. Liu, J.-M. Chen and K. Seng Sim at the Genome Institute of Singapore for performing the imputation, association and LD analyses of HLA alleles. This study was supported in part by the Key Project of the Chinese National Natural Science Foundation (No. 30530670), the Cooperation Project of the Chinese Key National Natural Science Foundation for Overseas Youth (No. 30628021) and the Anhui Provincial Special Scientific Program (2007-7).

Author information




X.-J.Z. conceived this study and obtained financial support; X.-J.Z., Y.Z. and S.Y. designed the study; C.Q., Y.-Q.R., L.-H.X. and L.-D.S. participated in the design and were responsible for sample selection, genotyping and project management; S.-M.Z., D.-Y.H., Yang Li, X.-F.T., S.-X.X., Y.-M.L., Q.X., J.-P.G., W.-L.H., C.N., T.-M.P., Yun Li, Y.-S.L. and Z.-Y.Y. conducted sample selection and managed data; A.-E.X., X.-H.G., H.-D.C., X.-M.P., R.-N.W., C.-Z.L., J.-B.L., T.-W.G., J.-Z.Z., X.-L.W., J.W., R.-Y.Y., L.L., J.-B.Y., Y.-W.L., X.-D.W., W.-S.H., Y.Y., Y.Z., W.-S.W., P.-L.D., K.L., X.-J.K., Y.-Q.L., L.S., Z.-F.L. and S.-Q.X. undertook recruitment, collected phenotype data, undertook related data handling and calculation and obtained biological samples; H.-Q.J., M.S., C.-Y.Z., Y.W., G.C., P.L., J.Z., H.C., M.L., X.Z., H.-Y.T., S.-M.H., S.Y. and C.-F.H. performed genotyping analyses; X.-B.Z., S.-Q.Z., X.-D.Z., X.-Y.Y. and F.-Y.Z. undertook data processing, statistical analysis and bioinformatics investigations; all the authors contributed to the final paper.

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Correspondence to Youwen Zhou or Xue-Jun Zhang.

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The authors declare no competing financial interests.

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Supplementary Figures 1–3 and Supplementary Tables 1–4 (PDF 495 kb)

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Quan, C., Ren, YQ., Xiang, LH. et al. Genome-wide association study for vitiligo identifies susceptibility loci at 6q27 and the MHC. Nat Genet 42, 614–618 (2010).

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