Development of a genotyping microarray for Usher syndrome

Publisher DOI
PubMed ID
16963483
Abstract
BACKGROUND: Usher syndrome, a combination of retinitis pigmentosa (RP) and sensorineural hearing loss with or without vestibular dysfunction, displays a high degree of clinical and genetic heterogeneity. Three clinical subtypes can be distinguished, based on the age of onset and severity of the hearing impairment, and the presence or absence of vestibular abnormalities. Thus far, eight genes have been implicated in the syndrome, together comprising 347 protein-coding exons. METHODS: To improve DNA diagnostics for patients with Usher syndrome, we developed a genotyping microarray based on the arrayed primer extension (APEX) method. Allele-specific oligonucleotides corresponding to all 298 Usher syndrome-associated sequence variants known to date, 76 of which are novel, were arrayed. RESULTS: Approximately half of these variants were validated using original patient DNAs, which yielded an accuracy of >98%. The efficiency of the Usher genotyping microarray was tested using DNAs from 370 unrelated European and American patients with Usher syndrome. Sequence variants were identified in 64/140 (46%) patients with Usher syndrome type I, 45/189 (24%) patients with Usher syndrome type II, 6/21 (29%) patients with Usher syndrome type III and 6/20 (30%) patients with atypical Usher syndrome. The chip also identified two novel sequence variants, c.400C>T (p.R134X) in PCDH15 and c.1606T>C (p.C536S) in USH2A. CONCLUSION: The Usher genotyping microarray is a versatile and affordable screening tool for Usher syndrome. Its efficiency will improve with the addition of novel sequence variants with minimal extra costs, making it a very useful first-pass screening tool.
Date Issued
2007
Publication Type
Article
Language(s)
en
Author(s)
Cremers, Frans P M
Kimberling, William J
Külm, Maigi
de Brouwer, Arjan P
van Wijk, Erwin
te Brinke, Heleen
Cremers, Cor W R J
Hoefsloot, Lies H
Banfi, Sandro
Simonelli, Francesca
Berger, Wolfgang
Kelley, Phil M
Haralambous, Elene
Bitner-Glindzicz, Maria
Webster, Andrew R
Saihan, Zubin
De Baere, Elfride
Leroy, Bart P
Silvestri, Giuliana
McKay, Gareth J
Koenekoop, Robert K
Millan, Jose M
Rosenberg, Thomas
Joensuu, Tarja
Sankila, Eeva-Marja
Weil, Dominique
Weston, Mike D
Wissinger, Bernd
Kremer, Hannie
Additional Credits
Journal
Journal of medical genetics
Publisher
BMJ Publishing Group
ISSN
0022-2593
ISBN
16963483
Access(Rights)
Unknown
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