All genotype data were generated using Illumina iSelect at the Oklahoma Medical Research Foundation (OMRF) genotyping facility. For this project, ten PTPN22 SNPs were generated using Illumina Genome Studio (http://www.illumina.com/software/genomestudio_software.ilmn). Following genotype scoring, SNP clusters were evaluated electronically using the Illumina BEADSTUDIO® software package (http://www.illumina.com). Ambiguous SNP clusters were evaluated manually and SNPs with poor cluster characteristics were not analyzed. All samples had 350 AIMs (ancestry informative markers) and >6000 “null” SNPs (not selected based on P-values, or known associated with any autoimmune disease, http://www.gwascentral.org [37]) genotyped to facilitate adjustment for genetic ancestry and population sub-structure.
