Affy60

All participants were genotyped upon consent using common single nucleotide polymorphism (SNP) arrays including Affymetrix Affy60 and Axiom, and Illumina HumanHap550 (v1, v3), Human610-Quad (v1), and HumanOmniExpress. We applied pre-imputation quality control measures to our genotype data, including removing SNPs with minor allele frequencies (MAF) < 5%, Hardy–Weinberg equilibrium p values < 1.0e − 4, and call rates < 95%. We phased and imputed the genotype data using the Haplotype Reference Consortium reference panel version r1.1 2016 available on the Michigan Imputation server [40 (link)]. After imputation, we further removed duplicated and strand-ambiguous SNPs, as well as SNPs with MAF < 0.01 or an imputation quality score below 0.8. Samples genotyped using different arrays were processed in separate batches.

Genomic DNA was extracted from blood using the Puregene DNA Isolation Kit (Gentra Systems, Minneapolis, USA). Four hundred and thirty seven samples were genotyped using the Affy 5.0 (Affymetrix, Santa Clara, CA, USA) and the Illumina 550 K chips (Illumina, San Diego, CA, USA). Two hundred fourteen of these samples were also genotyped using the Affy 6.0 chip. The Affy 5.0 chip contains 31,393 SNPs on chromosome 6 among 488,756 SNPs across 22 chromosomes. The Affy 6.0 chip contains 56,202 SNPs on chromosome 6 among 906,600 SNPs across 22 chromosomes. The Illumina 550 K chip contains 36,591 SNPs on chromosome 6 among 546,401 SNPs across 22 chromosomes. The National Center for Genome Medicine at Academia Sinica carried out all genotyping. All of the sample call rates were > 97%, and the mean individual-sample call rate was 98.4 ± 0.7%.
Within the extended human MHC region, which includes ~6 megabases (Mb) on chromosome 6p (position 28–34 Mb), the Affy 6.0 chip contains 2,203 SNPs, the Affy 5.0 chip contains 1,406 SNPs, and the Illumina 550 K chip contains 1,939 SNPs (Additional file 1). The intra-MHC region spanning the HLA-A gene at the telomeric end and the HLA-DPB1 gene at the centromeric end actually harbors class III genes (which are also termed complement genes), in addition to both class I loci (HLA-A, HLA-B, HLA–C) and class II loci (HLA-DRB1, HLA-DQB1, HLA-DPB1).