Infinium 2 iselect custom genotyping beadchip

Inflammation-related gene definitions and SNP identification were described previously(10 (link)). Briefly, inflammatory-related genes were defined based on a pre-defined inflammation panel, and refined through database exploration (T1DBase [http://www.t1dbase.org]; University of Cambridge, Cambridge, UK). Tagging SNPs within a 10kb flanking region of each candidate gene region were identified using the Tagger pairwise method(11 (link)) with an r² threshold of 0.8 and minor allele frequency ≥0.05 based on genotyping data from the Caucasian population of the International HapMap Project. The final SNP list was used to build a customized Infinium II iSelect Custom Genotyping BeadChip (Illumina, San Diego, CA, USA). Genomic DNA was extracted from peripheral blood using the QIAamp DNA extraction kit (Qiagen, CA, USA). SNP genotyping was performed following the standard Infinium II assay protocol. Only SNPs that had genotype data from ≥95% of all samples and samples with genotype data from ≥95% of all SNPs were included in final data report. The genotyping for validation phase was performed using Illumina 300k BeadChips following the same quality control criteria as in discovery phase(12 (link)). We defined any association with a P-value less than 0.05 as statistical significant.