Development of a genotyping microarray for Usher syndrome

• Published in: Journal of medical genetics Vol. 44; no. 2; pp. 153 - 160
• Main Authors: 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, Fleischhauer, Johannes C, 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
• Format: Journal Article
• Language: English
• Published: London BMJ Publishing Group Ltd 01-02-2007; BMJ; BMJ Publishing Group LTD; BMJ Group
• Subjects: APEX; arrayed primer extension; arRP; atypical USH; autosomal recessive retinitis pigmentosa; Biological and medical sciences; DNA - genetics; DNA polymerase; DNA Primers; Efficiency; Europe; Fundamental and applied biological sciences. Psychology; General aspects. Genetic counseling; Genes; Genetic Variation; Genetics of eukaryotes. Biological and molecular evolution; Genomes; Genotype; Hearing loss; Humans; Letter to JMG; Medical genetics; Medical sciences; Molecular and cellular biology; Mutation; mutation analysis; Oligonucleotide Array Sequence Analysis; Ophthalmology; Proteins; retinitis pigmentosa; Retinopathies; sensorineural deafness; single strand conformation polymorphism; SSCP; USH; USHA; Usher syndrome; Usher Syndromes - genetics; Europe; United Kingdom > UK; United States > US; Human; Eye disease; Retinopathy; Usher syndrome; Development; ENT disease; Genotype; Genetics; Genetic disease
• ISSN: 0022-2593; 1468-6244; 1468-6244
• DOI: 10.1136/jmg.2006.044784

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.