J Med Genet 44:153-160 doi:10.1136/jmg.2006.044784
  • Letters to JMG

Development of a genotyping microarray for Usher syndrome

  1. Frans P M Cremers1,
  2. William J Kimberling2,
  3. Maigi Külm3,
  4. Arjan P de Brouwer1,
  5. Erwin van Wijk4,
  6. Heleen te Brinke4,
  7. Cor W R J Cremers4,
  8. Lies H Hoefsloot1,
  9. Sandro Banfi5,
  10. Francesca Simonelli6,
  11. Johannes C Fleischhauer7,
  12. Wolfgang Berger8,
  13. Phil M Kelley2,
  14. Elene Haralambous9,
  15. Maria Bitner-Glindzicz9,
  16. Andrew R Webster10,
  17. Zubin Saihan10,
  18. Elfride De Baere11,
  19. Bart P Leroy12,
  20. Giuliana Silvestri13,
  21. Gareth J McKay13,
  22. Robert K Koenekoop14,
  23. Jose M Millan15,
  24. Thomas Rosenberg16,
  25. Tarja Joensuu17,
  26. Eeva-Marja Sankila17,
  27. Dominique Weil18,
  28. Mike D Weston2,
  29. Bernd Wissinger19,
  30. Hannie Kremer11
  1. 1Department of Human Genetics, and Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
  2. 2The Usher Syndrome Center, Boys Town National Research Hospital, Omaha, Nebraska, USA
  3. 3Asper Biotech, Tartu, Estonia
  4. 4Department of Otorhinolaryngology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
  5. 5Téléthon Institute of Genetics and Medicine, Naples, Italy
  6. 6Department of Ophthalmology, Second University of Naples, Naples, Italy
  7. 7Department of Ophthalmology, University Hospital Zurich, Zurich, Switzerland
  8. 8Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
  9. 9Clinical and Molecular Genetics Unit, Institute of Child Health, London, UK
  10. 10Molecular Genetics, Institute of Ophthalmology, UCL, London, UK
  11. 11Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
  12. 12Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
  13. 13Centre for Vision Science, School of Biomedical Science, Queen’s University Belfast, Belfast, Northern Ireland, UK
  14. 14Ocular Genetics Laboratory, McGill University Health Center, Montreal, Canada
  15. 15Unidad de Genetica y Diagnostico Prenatal, Hospital Universitario La Fe, Valencia, Spain
  16. 16Gordon Norrie Centre for Genetic Eye Diseases, National Eye Clinic for the Visually Impaired, Hellerup, Denmark
  17. 17The Folkhalsan Institute of Genetics, Biomedicum Helsinki, and Department of Ophthalmology, University of Helsinki, Helsinki, Finland
  18. 18Unité de Génétique des Deficits Sensoriels, Institut Pasteur, Paris, France
  19. 19Molecular Genetics Laboratory, University Eye Hospital, Tübingen, Germany
  1. Correspondence to:
 F P M Cremers
 Department of Human Genetics, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands; F.Cremers{at}
  • Received 14 June 2006
  • Accepted 22 August 2006
  • Revised 15 August 2006
  • Published Online First 8 September 2006


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.


  • This study was supported by the Forschung contra Blindheit - Initiative Usher Syndrom e.V. (FPMC, CWRJC and HK), Oogfonds Nederland, Gelderse Blinden Vereniging, Stichting Blindenhulp, Algemene Nederlandse Vereniging ter Voorkoming van Blindheid, Rotterdamse Vereniging Blindenbelangen, Stichting voor Ooglijders, the Dr. F.P. Fischer Stichting (CWRJC and HK), the Heinsius-Houbolt Stichting (FPMC, HK and CWRJC,), The Italian Telethon Foundation (SB), the Northern Ireland HPSS R&D Office (GMK), the Deutsche Forschungsgemeinschaft - KFO134 (BW), Paul Schiller Foundation, Zurich, Switzerland (JF an WB), The Danish Society of the Blind (TR), F.I.S. PI04/0918, FAARPEE (JMM), the Big Lottery Fund, the British Retinitis Pigmentosa Society and Deafness Research UK (MB-G), Fonds voor Wetenschappelijk Onderzoek Vlaanderen FWO 3G004306 (BPL and EDB) and the Ulla Hjelt Foundation (E-MS). The work was partially supported by a grant from the Foundation Fighting Blindness and by a grant from the NIH-NIDCD/5P01DC01813 (WJK).

  • Competing interests: None declared.

  • Published Online First 14 November 2006