CNVs were detected using Birdsuite (version 1.6)31. Events with LOD score >/= 10 kb and size >/= 10kb were lifted onto HG19 using the UCSC browser’s lift over tool. These spanned ~16 loci. One of these events (HG19:chr6:78973201-79029367) overlaps a region of common CNVs in HapMap32. CNVs were validated with either commercially available or custom designed TaqMan probes. Probes were - 6p22.1, HG19:chr6:29859709-29896421, Hs03587795_cn (LifeTech), context sequence CAGGAGAATGTTCCTGCTGAGGACA; Chr9,HG19:chr9:7734481-7770942, Hs06879643_cn, context sequence AATAGCCTCATTACACCTTGCAAAT; 6q16.1, HG19:chr6:95486777-95578465, probe primer TCCATAATCAGCGTGGCATA, 5’ 6-FAM ZEN 3’Iowa Black FQ, forward primer TCAGGGTTGGTTTGCTTATTG, reverse primer CACCAATATATGTTCAAAGGGTCA. Assays were carried out using digital droplet PCR (Bio-Rad) according to the manufacturer’s instructions.
