title: Development of a genotyping microarray for Usher syndrome.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Human Genetics, and Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands. F.Cremers@antrg.umcn.nl
authors.forename: Frans P M
authors.initials: FP
authors.lastname: Cremers
authors.forename: William J
authors.initials: WJ
authors.lastname: Kimberling
authors.forename: Maigi
authors.initials: M
authors.lastname: Külm
authors.forename: Arjan P
authors.initials: AP
authors.lastname: de Brouwer
authors.forename: Erwin
authors.initials: E
authors.lastname: van Wijk
authors.forename: Heleen
authors.initials: H
authors.lastname: te Brinke
authors.forename: Cor W R J
authors.initials: CW
authors.lastname: Cremers
authors.forename: Lies H
authors.initials: LH
authors.lastname: Hoefsloot
authors.forename: Sandro
authors.initials: S
authors.lastname: Banfi
authors.forename: Francesca
authors.initials: F
authors.lastname: Simonelli
authors.forename: Johannes C
authors.initials: JC
authors.lastname: Fleischhauer
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Berger
authors.forename: Phil M
authors.initials: PM
authors.lastname: Kelley
authors.forename: Elene
authors.initials: E
authors.lastname: Haralambous
authors.forename: Maria
authors.initials: M
authors.lastname: Bitner-Glindzicz
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Webster
authors.forename: Zubin
authors.initials: Z
authors.lastname: Saihan
authors.forename: Elfride
authors.initials: E
authors.lastname: De Baere
authors.forename: Bart P
authors.initials: BP
authors.lastname: Leroy
authors.forename: Giuliana
authors.initials: G
authors.lastname: Silvestri
authors.forename: Gareth J
authors.initials: GJ
authors.lastname: McKay
authors.forename: Robert K
authors.initials: RK
authors.lastname: Koenekoop
authors.forename: Jose M
authors.initials: JM
authors.lastname: Millan
authors.forename: Thomas
authors.initials: T
authors.lastname: Rosenberg
authors.forename: Tarja
authors.initials: T
authors.lastname: Joensuu
authors.forename: Eeva-Marja
authors.initials: EM
authors.lastname: Sankila
authors.forename: Dominique
authors.initials: D
authors.lastname: Weil
authors.forename: Mike D
authors.initials: MD
authors.lastname: Weston
authors.forename: Bernd
authors.initials: B
authors.lastname: Wissinger
authors.forename: Hannie
authors.initials: H
authors.lastname: Kremer
mesh_terms: D004247:DNA / Q000235:genetics; D017931:DNA Primers; D005060:Europe; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D052245:Usher Syndromes / Q000235:genetics*
chemical_list: D017931:DNA Primers; D004247:DNA