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

To perform genome-wide association testing, we coded JIA samples with uveitis as cases and JIA samples without uveitis as controls. First, we performed a genome-wide association study (GWAS) in Phase 1 and Phase 2 individually, to check the overall behavior of the genome-wide test statistics (lambda Phase1 = 1.008, lambda Phase2 = 1.017). GWAS were performed using PLINK 1.9 31 using an additive logistic regression model, correcting for the top two principal components and sex. Data were then meta-analyzed using METAL. 32 To ensure we were analyzing SNPs with high-quality imputation, we only analyzed common . CC-BY-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/140954 doi: bioRxiv preprint SNPs (MAF > 1%) with imputation quality (info) score > 0.7. In the Phase 1 data, additional GWAS were performed comparing samples with JIA and uveitis to unaffected controls, as well as JIA samples without uveitis to unaffected controls; results were concordant with studies previously performed in these phenotypes (Supplementary Table 6 ).