Immuno beadchip array

Genotyping was performed at Cedars-Sinai Medical Center using Illumina whole genome arrays (Human610-Quad; HumanOmniExpress) and the Immuno-BeadChip array as previously described^{16 (link), 18 (link)}. For the Immuno-BeadChip, average genotyping call rate for samples that passed quality control (QC) was 99.98%. Average concordance rate across 83 samples genotyped in replicate was 99.99%. Single-nucleotide polymorphisms (SNPs) underwent methodological review and were evaluated using several SNP statistic parameters, including SNP call frequency, cluster separation, replicate and heritability error rates, heterozygous excess, theta mean and deviation, and R intensity mean. A total of 135,252 autosomal SNPs passed genotyping QC measures and were common across datasets. For the Human OmniExpress and Human610-Quad, average genotyping call rates for samples that passed QC were 99.85% and 99.83%, respectively. Average concordance rate across 19 samples genotyped in replicate was >99.99%. Genotyping of three control trios yielded a heritability frequency of 99.53%. Optimal allele-calling was verified by manual review of top associated SNPs.

Genotyping was at Cedars-Sinai Medical Center using the Illumina Immuno-BeadChip array as previously described (2 (link), 19 (link)). All human subjects were homozygous non-risk for the 3 common CD-associated NOD2 variants (tagged by rs2066842-GG, rs2066844-GG, rs2066845-CC. rs5743293-DD) and then stratified by ATG16L1 CD-associated T300A variant status dividing the study subjects into those that were either homozygous non-risk or homozygous risk (as defined by rs2241880). Written informed consent was received from participants prior to inclusion in the study. All study subjects were identified by number and not by name, had not used antibiotics for at least 6 months. Stool, blood samples, and genetic data were obtained from Material and Information Resources for Inflammatory And Digestive Diseases (MIRIAD) IBD Biobank and approved under IRB #3358 and #Pro00027495.