Genotyping was performed at Cedars-Sinai Medical Center using Illumina whole-genome arrays per manufacturer’s protocol (Illumina, San Diego, CA). The discovery cohort was genotyped on 3 platforms, including Illumina HumanCNV370-Quad (830 subjects), Human610-Quad (1037 subjects), and HumanOmniExpress (1243 subjects) arrays (total 3110 independent subjects). Average genotyping call rates for samples that passed quality control (QC) were 99.86% (HumanCNV370-Quad), 99.83% (Human610-Quad), and 99.85% (HumanOmniExpress). One to two percent of samples were genotyped in replicate and yielded average 99.99% concordance for genotypes called. Optimal allele-calling was verified by manual review of top associated single-nucleotide polymorphisms (SNPs).
A stringent QC procedure was applied to the GWAS data. Of the 3110 subjects genotyped, 10 were removed because of high missing rate (>2%), 27 were removed because of cryptic relatedness (Pi_Hat > 0.05), 3 were removed because sample either withdrew from the study or was later reclassified as non-IBD, leaving 3070 individuals for further analysis. Seventy-six individuals identified as nonwhites by principal component analysis were also removed. A total of 2959 of the 2994 genotyped subjects had ANCA status and were thereby included in the analyses.
A stringent QC procedure was applied to the GWAS data. Of the 3110 subjects genotyped, 10 were removed because of high missing rate (>2%), 27 were removed because of cryptic relatedness (Pi_Hat > 0.05), 3 were removed because sample either withdrew from the study or was later reclassified as non-IBD, leaving 3070 individuals for further analysis. Seventy-six individuals identified as nonwhites by principal component analysis were also removed. A total of 2959 of the 2994 genotyped subjects had ANCA status and were thereby included in the analyses.