Application of chromosome microarray analysis in 489 children with developmental delay/intellectual disability

Abstract

To assess the value of chromosome microarray analysis (CMA) for identifying the etiology of developmental delay/intellectual disability (DD/ID). A total of 489 children referred for DD/ID with or without other abnormalities were recruited. All patients showed a normal karyotype. DNA was extracted and hybridized with Affymetrix CytoScan 750K array by following the manufacturer's protocol. The data was analyzed with CHAS v2.0 software. The children were classified as with isolated DD/ID (n=358), DD/ID with epilepsy (n=49), and DD/ID with other structural anomalies (n=82). Pathogenic copy number variants (CNVs) were identified in 126 cases (25.8%), which included 89 (24.9%, 89/358) of whose with isolated DD/ID, 13 (26.5%, 13/49) of those with DD/ID and epilepsy, and 24 (29.3%, 24/82) of whose with DD/ID and other structural anomalies [P=0.064 (24.9% vs. 26.5%), P=0.679 (24.9% vs. 29.3%), and P=0.113 (26.5% vs. 29.3%), respectively]. Among the 126 cases, 79 were identified as microdeletion/microduplication syndromes, which included 15q24 microdeletion syndrome, Xq28 microduplication syndrome, and Lowe syndrome. Forty-seven cases had de novo pathogenic CNVs. ABAT, PMM2, FTSJ1, DYNC1H1 and SETBP1 were considered as candidate genes for DD/ID. CMA is an effective method for identifying the etiology of DD/ID and is capable of identifying microdeletion/microduplication syndromes as well as de novo pathogenic CNVs which may be missed by conventional karyotyping. Based on the results, candidate genes for DD/ID may be identified.