An amino acid motif in HLA-DRß1 distinguishes patients with uveitis in juvenile idiopathic arthritis

A.J.W. Haasnoot; M.W. Schilham; S.S.M. Kamphuis; P.C.E. Hissink Muller; A. Heiligenhaus; D. Foell; R.A. Ophoff; T.R.D.J. Radstake; A.I. Den Hollander; T.H.C.M. Reinards; S. Hiddingh; N. Schalij-Delfos; E.P.A.H. Hoppenreijs; M.A.J. van Rossum; C. Wouters; R.K. Saurenmann; N. Wulffraat; R. ten Cate; J.H. de Boer; S.L. Pulit; J.J.W. Kuiper

We performed genome-wide association testing across the autosomal genome, using a logistic regression framework assuming an additive model in PLINK 1.9 30, 31 , correcting for sex and the first two principal components (Supplementary Figures 1 and 2 ). Our data enabled three possible comparison groups: (a) JIA cases and population-level controls, (b) JIA-associated uveitis cases and population-level controls, and (c) JIA-associated uveitis cases and non-uveitis JIA. As the goal of our analysis was to investigate similarities and differences in the genetic architecture of JIA and uveitis, and because far larger GWAS of JIA and population-level controls have already been performed, 20 we performed the first two genome-wide association studies (GWAS) as a means of data quality control only (Supplementary Figure 3) and account for them when considering multiple testing burden. We focus here on the results of the last comparison: JIA-associated uveitis cases and non-uveitis JIA samples.