Targeted comparative genomic hybridization array for the detection of single- and multiexon gene deletions and duplications.

Purpose: To develop a high resolution microarray based method to detect single- and multiexons gene deletions and duplications. Methods: We have developed a high-resolution comparative genomic hybridization array to detect single- and multiexon deletions and duplications in a large set of genes on a single microarray, using the NimbleGen 385K array with an exon-centric design. Results: We have successfully developed, validated, and implemented a targeted gene comparative genomic hybridization arrays for detecting single- and multiexon deletions and duplication in autosomal and X-linked diseaseassociated genes. Conclusion: The comparative genomic hybridization arrays can be adopted readily by clinical molecular diagnostic laboratories as a rapid, cost-effective, highly sensitive, and accurate approach for the detection of single- and multiexon deletions or duplications, particularly in cases where direct sequencing fails to identify a mutation. Genet Med 2009:11(4):232–240. Clinical molecular testing is getting more comprehensive, yet more complicated, with the burgeoning number of known disease-causing genes. Most clinical laboratories develop assays for mutation detection in disease-associated genes based on the reported mutation spectrum (Fig. 1). The mutation spectrum associated with genetic disease ranges from point mutations and small deletions and insertions, which can be detected by direct DNA sequencing, to single- and multiexon deletions and duplications. The gene mutation spectrum and comprehensive genetic testing vary between genes; for instance, 65% of Duchenne and Becker muscular dystrophy cases are due to deletions or duplications of single or multiple exons of the dystrophin gene.1–3 In contrast, 90% of cystic fibrosis cases are due to single base-pair substitutions, microinsertions, or microdeletions in the CFTR gene4,5; 80% of the familial adenomatous polyposis cases are due to point mutations, whereas, only 20% are due to APC gene deletions or duplications6; and around 75% of the Sotos syndrome cases are due to point mutations in the NDS1 gene, while 25% of cases are due to deletions and duplications.7 The current available techniques for detecting single- and multiexon deletions and duplications in a single gene include multiplex polymerase chain reaction (PCR), quantitative PCR, Southern blotting,8 multiplex ligation-dependent probe amplification (MLPA), 9 detection of virtually all mutations-SSCP (DOVAM-S),10,11 and single condition amplification/internal primer sequencing (SCAIP).12 Clinical assays based on multiplex PCR and quantitative real-time PCR have been used traditionally to detect intragenic deletions and duplications for a small number of genes. Importantly, multiplex PCR can detect deletions but cannot detect duplications accurately or examine multiple genes simultaneously. Quantitative real-time PCR methods are more accurate than multiplex PCR, but detection of intragenic duplications is still a challenge. 13,14 In addition, PCR efficiency and PCR product saturation may adversely impact the sensitivity and accuracy of real-time fluorescent PCR, whereas spectral overlap limits the use of real-time fluorescent PCR in multiplex as