Genome-wide genotyping was carried out using the Illumina Human660W-Quad array (Illumina, Inc., San Diego, CA) according to the manufacturer’s protocol, as described in Li et al (Y. F. Li et al., 2010). This Infinium HD Beadchip required 200ng DNA per sample and contains 657,366 variants, including 95,876 intensity-only markers for calling copy number variants that are not considered here. For quality control purposes, each 96-well plate included DNA from two members of a single three-member Centre d’Etude du Polymorphisme Humain (CEPH) family, with the two members rotating across plates, as well as a duplicate of another randomly-selected sample on that plate. In addition to standard QC filters, we used GenCall scores, metrics of genotype reliability generated by the BeadStudio software, to assess sample quality (Cunningham et al., 2008). Specifically, both the GenCall_10, representing the 10th percentile, and GenCall_50, 50th percentile, scores were used to assess sample quality following standard guidelines. Additionally, each sample was genotyped on a custom 96-plex panel using Illumina VeraCode chemistry (Lin, Yeakley, McDaniel, & Shen, 2009). This panel contains SNPs present on the Human660W-Quad and served as an additional check on quality control.
