CMA was carried out following standard procedures. We used a consensus microarray design, focusing on unique genomic regions and avoiding repetitive sequences.7 The arrays were either 44K or 105K custom-designed 60-mer oligonucleotide arrays (Agilent Technologies, Santa Clara, CA) with a whole-genome backbone plus targeted, higher density coverage of known disease-causing regions.7 The backbone coverage included probes spaced every ~35–75 kb, allowing for CNVs of approximately 250 kb and greater to be detected. All clinically relevant CNVs ≥500 kb in the backbone are reported in this study. The 500kb threshold in the backbone regions was used since this size limit was consistently used as the reporting criteria by the ISCA laboratories. For the targeted regions, we could identify imbalances of ~20–50 kb.
