Identification of Large Rearrangements of the PCDH15 Gene by Combined MLPA and a CGH: Large Duplications Are Responsible for Usher Syndrome

PURPOSE. PCDH15, encoding protocadherin 15, is mutated in Usher syndrome type 1F (USH1F) patients. Not only point mutations, but also large deletions have been detected within this gene. However, the detection and characterization of gross deletions in the USH1F locus have been difficult. The purpose of the present work was to identify large genomic rearrangements of PCDH15 in a cohort of patients and to accurately identify the location of the junction breakpoints of the detected rearrangements. METHODS. A PCDH15 MLPA (multiplex ligation-dependent probe amplification) commercial kit was used, combined with a customized oligonucleotide array-based CGH analysis (aCGH), containing almost 20,000 probes tiling the nonrepetitive sequence of the PCDH15 gene. RESULTS. Two large intragenic rearrangements were identified-one deletion of 55 kb and one direct duplication of 82 kb-in 3 (13%) families from a cohort of 23 USH cases. The patients had been screened for mutations in the five known USH1 genes and were found to carry one or none of the pathogenic mutations in PCDH15. The exact breakpoints of both rearrangements were identified. CONCLUSIONS. This is the first time that large duplications have been associated with Usher syndrome. USH patients have not been extensively tested for large genomic rearrangements such as duplications and deletions. This type of mutation easily escapes detection by traditional PCR-based methods. Thus, a combination of PCR-based mutation screening, together with deletion and duplication analysis, is mandatory for the accurate screening of the PCDH15 gene in Usher patients. (Invest Ophthalmol Vis Sci. 2010; 51: 5480-5485) DOI: 10.1167/iovs.105359