For the MSSM/Penn/Pitt cohorts, genotyping was performed on the Illumina Infinium HumanOmniExpressExome 8 v 1.1b chip (Catalog #: WG-351-2301) using the manufacturer’s protocol as previously described9. The HBCC samples were genotyped on one of 3 different Illumina gene chips: HumanHap650Y, Human1M-Duo, and HumanOmni5M-Quad using the manufacturer’s protocol as follows: Approximately, 400 ng DNA was used and each DNA sample was QC tested for 260/280 ratio by nanodrop and DNA band intactness on 2% agarose gel. Briefly, the samples were whole-genome amplified, fragmented, precipitated and resuspended in appropriate hybridization buffer. Denatured samples were hybridized on prepared Illumina Quad Bead Chips. After hybridization, the Bead Chip oligonucleotides were extended by a single fluorescent labeled base, which was detected by fluorescence imaging with an Illumina Bead Array Reader, iScan.
