Genotyping and Analysis of Immunochip Data

The blood of all cases was previously collected at the time of diagnosis of the disease and subsequently DNA was extracted and genotyped for 186 K SNPs using the Illumina Immunochip version 1 platform. The genotyped data of cases is described in the study by Rivera et al.^{8 (link)}. Similarly, the blood of all healthy controls was collected by the dedicated research nurses immediately next to the time of receiving response to questionnaire. DNA of controls was also genotyped on the Illumina Immunochip version 1 and is further described elsewhere^{65 (link),66 (link)}. In this study, 1,058 controls from EIMS, 1,905 controls from EIRA and 731 cases (290 LS and 441 non-LS) that passed genotyping quality control filtering were analyzed throughout the study.