Immunochip

The Immunochip, a custom Illumina Infinium High-Density array, contains 196,524 polymorphisms (718 small insertion/deletions, 195,806 SNPs). It was initiated by the Welcome Trust Case-Control Consortium and designed for deep replication of established autoimmune and inflammatory disease loci identified by GWAS of common variants using data from the 1000 Genomes Project and any other available disease-specific resequencing data. The Immunochip Consortium selected 186 distinct loci containing markers reaching genome-wide significance (P < 5 × 10⁻⁸) from 12 diseases (autoimmune thyroid disease, ankylosing spondylitis, Crohn's disease, celiac disease, IgA deficiency, multiple sclerosis, primary biliary cirrhosis, psoriasis, rheumatoid arthritis, systemic lupus erythematosus, type 1 diabetes, and ulcerative colitis). For each disease, ~3,000 SNPs were selected from available GWAS data for deep replication, as well as to cover strong candidate genes. Samples were genotyped using the Immunochip according to Illumina's protocols at laboratories at Emory University and The Feinstein Institute for Medical Research and Cincinnati Children's Hospital Medical Center (Utah samples and Cincinnati controls).

All the case–control subjects were genotyped using the ImmunoChip, an Illumina 200K Infinium high-density array. Summary statistics, including P-values and MAF, were downloaded from ImmunoBase (http://www.immunobase.org, accessed 04 May 2014). The number of participants for each disease is shown in Table 1. Samples were of European ancestry and are described in detail in the original papers (5 (link)–13 ).

To determine the accuracy of imputation, TPMT imputed haplotypes were compared to those obtained by other genotyping platforms covering TPMT variation. Of the 87,979 samples, 583 also had genotyping data on Illumina Infinium Immunochip (Immunochip), and HumanOmni1-Quad version 1 (Omni), which captured both rs1800460 and rs1142345. Additionally, Sanger sequencing of rs1800460 in exon 7 and rs1142345 in exon 10 was used to validate the imputation results (primers previously described in Schaeffeler et al., 2001 (link)). The sample selected for Sanger sequencing consisted of 59 individuals predicted to carry one or two defective alleles by imputation that had been exposed to a TPMT medication based on the EMR.

SNP analysis was performed by the Center for Public Health Genomics at University of Virginia, using the Illumina ImmunoChip. The ImmunoChip is a custom array for genotyping of SNPs selected from regions of the human genome firmly associated with autoimmune diseases. The final selection of SNPs containing ~186 000 SNPs in 186 regions, for 12 autoimmune diseases was decided by the ImmunoChip Consortium. The 9- month sample was used for SNP genotyping after DNA extraction done by Roche Molecular Systems (Pleasanton, CA). Quality control (QC) steps to assure high quality of the reported SNPs comprised the exclusion of subjects due to low call rate (>5% SNPs missing) and discordance with reported sex and prior genotyping. Secondly, SNPs were removed from analysis due to low call rate (<95%), Hardy-Weinberg equilibrium (HWE) p-value <10⁻⁶ (except for chromosome 6 due to HLA eligibility requirements) as well as being monomorphic or an insertion-deletion.
A total of 17 SNPs residing in loci within genes coding for complement factors were present on the ImmunoChip. Of these 17 SNPs, two did not pass QC (rs1061170 in CFH and rs2274567 in CD35). In the TEDDY study, we have previously performed a confirmation study of 41 SNPs associated with type 1 diabetes and risk of autoantibody positivity39 (link).

The procedures for genotyping, genetic data filtering and genotype imputation of the 500FG cohort had been previously described (6 (link)). Extracted DNA was genotyped using the commercially available SNP chip, Illumina HumanOmniExpressExome-8 v1.0. Following pre-imputation filtering steps for both markers and individuals, the remaining dataset SNP genotypes were imputed with GoNL as reference panel (16 ).
For Lifelines Deep cohort, genotyping and imputation was performed as previously described (17 ). Both the HumanCytoSNP-12 BeadChip and the ImmunoChip platforms (Illumina, San Diego, CA, USA) were used to genotype the isolated DNA. Independent markers quality control was performed for both platforms and subsequently merged into one dataset. After merging, genotype SNPs were imputed using IMPUTE2 (18 ) against the GoNL reference panel.