Array-based identification of copy number changes in a diagnostic setting. Simultaneous gene-focused and low resolution whole human genome analysis

ABSTRACT

The aim of this study was to develop and validate a comparative genomic hybridisation [CGH] array that would allow simultaneous targeted analysis of a panel of disease genes and low resolution whole genome analysis. A bespoke Roche NimbleGen 12x135K CGH array [Roche NimbleGen Inc., Madison, Wisconsin, USA] was designed to interrogate the coding regions of 66 genes of interest, with additional widelyspaced backbone probes providing coverage across the whole genome. We analysed genomic deoxyribonucleic acid [DNA] from 20 patients with a range of previously characterised copy number changes and from 8 patients who had not previously undergone any form of dosage analysis. The custom-designed Roche NimbleGen CGH array was able to detect known copy number changes in all 20 patients. A molecular diagnosis was also made for one of the additional 4 patients with a clinical diagnosis that had not been confirmed by sequence analysis, and carrier testing for familial copy number variants was successfully completed for the remaining four patients. The custom-designed CGH array described here is ideally suited for use in a small diagnostic laboratory. The method is robust, accurate, and cost-effective, and offers an ideal alternative to more conventional targeted assays such as multiplex ligation-dependent probe amplification