Development of a genotyping microarray for Usher syndrome

Frans P.M. Cremers, William J. Kimberling, Maigi Külm, Arjan P. De Brouwer, Erwin Van Wijk, Heleen Te Brinke, Cor W.R.J. Cremers, Lies H. Hoefsloot, Sandro Banfi, Francesca Simonelli, Johannes C. Fleischhauer, Wolfgang Berger, Phil M. Kelley, Elene Haralambous, Maria Bitner-Glindzicz, Andrew R. Webster, Zubin Saihan, Elfride De Baere, Bart P. Leroy, Giuliana SilvestriGareth J. McKay, Robert K. Koenekoop, Jose M. Millan, Thomas Rosenberg, Tarja Joensuu, Eeva Marja Sankila, Dominique Weil, Mike D. Weston, Bernd Wissinger, Hannie Kremer

Research output: Contribution to journalArticle

87 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)153-160
Number of pages8
JournalJournal of medical genetics
Volume44
Issue number2
DOIs
StatePublished - Feb 2007

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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    Cremers, F. P. M., Kimberling, W. J., Külm, M., De Brouwer, A. P., Van Wijk, E., Te Brinke, H., Cremers, C. W. R. J., Hoefsloot, L. H., Banfi, S., Simonelli, F., Fleischhauer, J. C., Berger, W., Kelley, P. M., Haralambous, E., Bitner-Glindzicz, M., Webster, A. R., Saihan, Z., De Baere, E., Leroy, B. P., ... Kremer, H. (2007). Development of a genotyping microarray for Usher syndrome. Journal of medical genetics, 44(2), 153-160. https://doi.org/10.1136/jmg.2006.044784