Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus

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We performed a genome-wide association study (GWAS) of systemic lupus erythematosus (SLE) in a Chinese Han population by genotyping 1,047 cases and 1,205 controls using Illumina Human610-Quad BeadChips and replicating 78 SNPs in two additional cohorts (3,152 cases and 7,050 controls). We identified nine new susceptibility loci (ETS1, IKZF1, RASGRP3, SLC15A4, TNIP1, 7q11.23, 10q11.22, 11q23.3 and 16p11.2; 1.77 × 10−25Pcombined ≤ 2.77 × 10−8) and confirmed seven previously reported loci (BLK, IRF5, STAT4, TNFAIP3, TNFSF4, 6q21 and 22q11.21; 5.17 × 10−42Pcombined ≤ 5.18 × 10−12). Comparison with previous GWAS findings highlighted the genetic heterogeneity of SLE susceptibility between Chinese Han and European populations. This study not only advances our understanding of the genetic basis of SLE but also highlights the value of performing GWAS in diverse ancestral populations.

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Figure 1: Summary of genome-wide association results for 1,047 cases and 1,205 controls.

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  • 04 December 2009

    In the version of this article initially published, there were two errors in the author affiliations and corresponding author details. Jian-Jun Liu is also affiliated with footnote 17, and Sen Yang and Xue-Jun Zhang are the corresponding authors. These errors have been corrected in the HTML and PDF versions of the article.


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We thank all study participants. This study was funded by the National Natural Science Foundation (30972727), the Key Project of National Natural Science Foundation (30530670 and 30830089), the Anhui Provincial Special Scientific Program (2007-7) and the Anhui Skin Genetic Study Innovative Research Team Program (TD200701).

Author information




X.-J.Z. conceived of this study and obtained financial support. X.-J.Z., J.-J.L. and S.Y. designed the study. J.-W.H., H.-F.Z., Y.C. and L.-D.S. participated in the design and were responsible for sample selection, genotyping and project management. D.-Q.Y., Z.H., Jin-Hua Xu, Z.-M.C., H.-F.X., H.F., Q.-J.L., Jian-Hua Xu, X.-P.L., Y.-F.P., D.-Q.D., F.-Q.Z., Z.-Z.Y., X.-Y.Z., Q.-W.W., F.H., L.M., X.-X.Z., W.-F.Z., F.G., P.-L.Z., Q.G., B.L., M.G., F.-L.X., J.-L.H., S.-X.L., H.L., Z.-X.W., C.-J.Y., P.-G.W., W.-M.Z., A.-P.Z., D.L. and Z.-F.Z. conducted sample selection and data management. W.-H.D., J.-Q.Y., S.-K.S., J.L., Y.-J.S., K.-J.Z., Yang Li, D.-Y.H. and Y.-M.L. undertook recruitment, collected phenotype data, undertook related data handling and calculation, managed recruitment and obtained biological samples. W.H., G.-P.Z., F.-S.Z., Y.-L.C., C.Q., C.Z., Z.Z., W.-S.L., Y.-Q.R., S.-Q.Z., M.S. and Y.W. performed genotyping analysis. H.-F.Z., X.-B.Z., Yi Li, H.Q.L. and F.-Y.Z. undertook data processing, statistical analysis and bioinformatics investigations. All the authors contributed to the final paper, with X.-J.Z., J.-J.L., S.Y., J.-W.H., H.-F.Z., Y.C. and L.-D.S playing key roles.

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Correspondence to Sen Yang or Xue-Jun Zhang.

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Han, JW., Zheng, HF., Cui, Y. et al. Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. Nat Genet 41, 1234–1237 (2009).

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