Yukinori Okada 1 , 2 , 3 , 4 , 5 , 21 , Buhm Han 3 , 4 , 5 , 21 , Lam C. Tsoi 6 , Philip E. Stuart 7 , Eva Ellinghaus 8 , Trilokraj Tejasvi 7 , Vinod Chandran 9 , 10 , Fawnda Pellett 10 , Remy Pollock 10 , Anne M. Bowcock 11 , Gerald G. Krueger 12 , Michael Weichenthal 13 , John J. Voorhees 7 , Proton Rahman 14 , Peter K. Gregersen 15 , Andre Franke 8 , Rajan P. Nair 7 , Gonçalo R. Abecasis 6 , Dafna D. Gladman 9 , 10 , 16 , James T. Elder 7 , 17 , Paul I.W. de Bakker 18 , 19 , ∗ , Soumya Raychaudhuri 3 , 4 , 5 , 20 , ∗∗
07 August 2014
Psoriasis vulgaris (PsV) risk is strongly associated with variation within the major histocompatibility complex (MHC) region, but its genetic architecture has yet to be fully elucidated. Here, we conducted a large-scale fine-mapping study of PsV risk in the MHC region in 9,247 PsV-affected individuals and 13,589 controls of European descent by imputing class I and II human leukocyte antigen (HLA) genes from SNP genotype data. In addition, we imputed sequence variants for MICA, an MHC HLA-like gene that has been associated with PsV, to evaluate association at that locus as well. We observed that HLA-C ∗06:02 demonstrated the lowest p value for overall PsV risk (p = 1.7 × 10 −364). Stepwise analysis revealed multiple HLA-C ∗06:02 -independent risk variants in both class I and class II HLA genes for PsV susceptibility ( HLA-C ∗12:03 , HLA-B amino acid positions 67 and 9, HLA-A amino acid position 95, and HLA-DQα1 amino acid position 53; p < 5.0 × 10 −8), but no apparent risk conferred by MICA. We further evaluated risk of two major clinical subtypes of PsV, psoriatic arthritis (PsA; n = 3,038) and cutaneous psoriasis (PsC; n = 3,098). We found that risk heterogeneity between PsA and PsC might be driven by HLA-B amino acid position 45 (p omnibus = 2.2 × 10 −11), indicating that different genetic factors underlie the overall risk of PsV and the risk of specific PsV subphenotypes. Our study illustrates the value of high-resolution HLA and MICA imputation for fine mapping causal variants in the MHC.