To examine the contribution of the MHC region to immune-related pathway enrichment, we extracted genes within the MHC from the hg38 annotation (GENCODE v.25). Specifically, we extracted genes from the MHC region (chromosome 6: 28510120–33480577) and the extended MHC region (chromosome 6: 25726063–33400644) using PyRanges (v.0.0.127)74 and gtfparse (v.2.0.1). We further subset the extended MHC region for any gene names that started with HLA. After this, we assessed enrichment for the MHC regions (that is, the MHC region, the extended MHC region and the HLA genes) using a two-sided Fisher’s exact test. We corrected for multiple testing with the Benjamini–Hochberg method.
