Whole genome sequencing data was obtained on all fibroblasts and iPSCs for members of all families in this study. Data were analyzed with CNVnator (Abyzov et al., 2011) for copy number variations (CNVs) discovery and with a GATK-based pipeline for single nucleotide variation (SNV) discovery (see Supplemental Experimental Procedures). For three families with both parents participating in the study (03, 07, and 1123), we predicted de novo CNVs and SNVs. Of the putative de novo CNVs, only one 4.8 kb deletion (chr14:39987476-39992327) found in the 1123 proband could be validated by qPCR. For this event, qPCR validation showed roughly 30% copy-number decrease in the proband relative to either of the parent, suggesting that the deletion is possibly a somatic mosaic variant. This deletion did not overlap any known genes. Proband 07-03 carries a previously uncharacterized deletion involving exon 2 in the PTEN gene (chr10:89,641,498-89,658,394), which was also found in his unaffected father. Proband 1120 and 03 did not carry any deleterious CNVs that could potentially be pathogenic. On average, each proband had ~112,000 rare SNVs not previously detected by the
