Validation of the Agilent 244K oligonucleotide array-based comparative genomic hybridization platform for clinical...

High-resolution microarray comparative genomic hybridization (aCGH) is being adopted for diagnostic evaluation of genomic disorders, but validation for clinical diagnosis has not yet been reported. We present validation data for the Agilent Human Genome Microarray Kit 244K for clinical application. The platform contains approximately 240,000 distinct 60-mer oligonucleotide probes spanning the entire human genome. We studied 45 previously characterized samples (43 abnormal, 2 normal), 32 with knowledge of prior results and 13 in a blinded manner with 11 performed in a reference laboratory providing microarray testing. Array analysis confirmed known aberrations in 43 samples and a normal result in 2. The array analysis corrected 1 karyotype and clarified 2 additional cases. Array data from 6 patients with 22q11.2 deletion found an average of 2.56 megabases (Mb; range, 2.49-2.62 Mb) with a common 2.43-Mb deleted region. Approximately 7 copy number variants from 400 base pairs to 1.6 Mb were identified per sample. Results demonstrate the usefulness of the aCGH-244K platform as a powerful diagnostic tool.