Genotyping was preformed on the Illumina Infinium HumanOmniExpressExome 8 v 1.1b chip (Catalog #: WG-351–2301) using the manufacturer’s protocol. Samples for genotyping were aliquoted onto 96 well plates, where each plate had an internal control from the HapMap project (NA12878 - Coriell Institute) in two unique locations. Initial QC was preformed using PLINK 57 to remove markers with: zero alternate alleles, genotyping call rate ≤ 0.98, Hardy-Weinberg P value < 5 × 10−5, and individuals with genotyping call rate < 0.90. This removed 2 samples from the analysis. After QC, 668 individuals genotyped at 767,368 markers were used for imputation. Phasing was performed on each chromosome using ShapeIt v2.r79058, and variants were imputed in 5 Mb segments by Impute v2.3.159 with the 1000 Genomes Phase 1 integrated reference panel11 excluding singleton variants. Note that, in addition to the 22 autosomes, we also included chromosome X, split out into pseudoautosomal (PAR) and non-PAR genomic regions to properly handle male haploidy in the non-PAR regions.
