Array-based Identifcation of Copy Number Changes in a Diagnostic Setting Simultaneous gene-focused and low resolution whole human genome analysis
Journal Title: Sultan Qaboos University Medical Journal - Year 2013, Vol 13, Issue 1
Abstract
Objectives: Te 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. Methods: 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. Results: Te 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 confrmed by sequence analysis, and carrier testing for familial copy number variants was successfully completed for the remaining four patients. Conclusion: Te custom-designed CGH array described here is ideally suited for use in a small diagnostic laboratory. Te method is robust, accurate, and cost-effective, and offers an ideal alternative to more conventional targeted assays such as multiplex ligation-dependent probe amplifcation.
Authors and Affiliations
Renate Marquis-Nicholson| Diagnostic Genetics, LabPLUS, Auckland City Hospital, Auckland, New Zealand, Elaine Doherty| Diagnostic Genetics, LabPLUS, Auckland City Hospital, Auckland, New Zealand, Jennifer M. Love| Diagnostic Genetics, LabPLUS, Auckland City Hospital, Auckland, New Zealand, Chuan-Ching Lan| Diagnostic Genetics, LabPLUS, Auckland City Hospital, Auckland, New Zealand, Alice M. George| Diagnostic Genetics, LabPLUS, Auckland City Hospital, Auckland, New Zealand, Anthony Trush| Roche Diagnostics New Zealand Ltd., Auckland, New Zealand, Donald R. Love| Diagnostic Genetics, LabPLUS, Auckland City Hospital, Auckland, New Zealand& School of Biological Sciences, University of Auckland, Auckland, New Zealand
Keywords
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