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).
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).
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