Copy number variations (CNVs) have been well documented to contribute significantly to some genetic disorders; however their frequency is currently not well established in many rare conditions. Here we describe the development, validation and clinical implementation of a custom oligonucleotide-based array CGH platform for the detection of exonic deletions and duplications in 54 genes, primarily implicated in neurodevelopmental disorders, for which our laboratory currently offers clinical sequence analysis. For the majority of the genes included in this design, the frequency of pathogenic copy number variation is currently unknown.  Selected genes include brain malformation genes, genes implicated in infantile epileptic encephalopathy, Rett/Atypical Rett syndrome, Angelman syndrome, as well as several other genes associated with orphan Mendelian genetic diseases. This custom array, designed by Agilent technologies and printed in an 8x60K format, contains approximately 50,000 probes more densely distributed across the exons of the genes being tested.  The array has been designed to detect exonic copy number changes as small as 300-400 bp.  The performance of this array and its potential application as a diagnostic tool has been evaluated by testing 48 blinded control samples, 33 of which contained a previously characterized abnormality ranging from multiple exons to single exonic CNVs.  The results of this validation study demonstrated that the array-CGH platform unambiguously detected all the expected aberrations and no copy number changes were identified in the remainder 15 negative samples. As of August 2011 we analyzed 111 clinical samples referred to our clinical laboratory for deletion/duplication testing, however disease-associated copy number variations have not been identified. In one patient with global developmental delay, regression and seizures, we identified a previously unreported gain of exons 13 and 14 in the microcephalin gene (MCPH1) that was also present in his phenotypically normal father.  Duplications of the 8p23.1 region that include the MCPH1 gene have previously been described in some families with an autism spectrum disorder.  These preliminary results obtained from a small cohort of patients with heterogeneous clinical presentation corroborate the presumption that the frequency of CNVs in these conditions is rare, that sequence analysis would still be considered the first tier of testing and that genetic diagnosis is also dependent on accurate clinical assessment of these patients’ phenotypes.

This poster (#460) will be presented at the ACMG Annual Meeting by Yu-Wei Cheng, our molecular fellow, Friday March 30: 10:30-11:30 am. Stop by and learn more.