We analyzed data from 15,749 whole-genome oligonucleotide arrays on individuals who presented for diagnostic array testing with abnormal clinical phenotypes, including DD/ID, ASD and/or MCA. We detected 4,628 imbalances consistent with our reporting criteria (defined in Methods) and classified 2,691 (17.1%) as pathogenic (pCNVs), in line with prior reports of the yield from CMA in diagnostic testing.5 Since a single individual may have had multiple pCNVs (i.e., unbalanced translocations), the diagnostic yield for this dataset was 14.7% (2,321 cases with pCNV/15,749 total cases). Excluding 106 whole-chromosome aneuploidies, there were 2,585 pCNVs with a mean size of ~6.5 Mb (median of ~2.8 Mb) and a mean of ~69 genes per CNV (median of 44 genes). Deletions were more commonly interpreted as pathogenic than duplications, accounting for 67.9% of the imbalances.
