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Development of a genotyping microarray for Usher syndrome

Identifieur interne : 001546 ( Main/Exploration ); précédent : 001545; suivant : 001547

Development of a genotyping microarray for Usher syndrome

Auteurs : Frans P M. Cremers [Pays-Bas] ; William J. Kimberling [États-Unis] ; Maigi Külm [Estonie] ; Arjan P. De Brouwer [Pays-Bas] ; Erwin Van Wijk [Pays-Bas] ; Heleen Te Brinke [Pays-Bas] ; Cor W R J. Cremers [Pays-Bas] ; Lies H. Hoefsloot [Pays-Bas] ; Sandro Banfi [Italie] ; Francesca Simonelli [Italie] ; Johannes C. Fleischhauer [Suisse] ; Wolfgang Berger [Suisse] ; Phil M. Kelley [États-Unis] ; Elene Haralambous [Royaume-Uni] ; Maria Bitner-Glindzicz [Royaume-Uni] ; Andrew R. Webster [Royaume-Uni] ; Zubin Saihan [Royaume-Uni] ; Elfride De Baere [Belgique] ; Bart P. Leroy [Belgique] ; Giuliana Silvestri [Royaume-Uni] ; Gareth J. Mckay [Royaume-Uni] ; Robert K. Koenekoop [Canada] ; Jose M. Millan [Espagne] ; Thomas Rosenberg [Danemark] ; Tarja Joensuu [Finlande] ; Eeva-Marja Sankila [Finlande] ; Dominique Weil [France] ; Mike D. Weston [États-Unis] ; Bernd Wissinger [Allemagne] ; Hannie Kremer [Belgique]

Source :

RBID : ISTEX:85BCC45536CF1BDE4E585D34AB33ED062254F920

English descriptors

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.

Url:
DOI: 10.1136/jmg.2006.044784


Affiliations:


Links toward previous steps (curation, corpus...)


Le document en format XML

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<name sortKey="Fleischhauer, Johannes C" sort="Fleischhauer, Johannes C" uniqKey="Fleischhauer J" first="Johannes C" last="Fleischhauer">Johannes C. Fleischhauer</name>
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<author>
<name sortKey="Wissinger, Bernd" sort="Wissinger, Bernd" uniqKey="Wissinger B" first="Bernd" last="Wissinger">Bernd Wissinger</name>
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<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Molecular Genetics Laboratory, University Eye Hospital, Tübingen</wicri:regionArea>
<placeName>
<region type="land" nuts="1">Bade-Wurtemberg</region>
<region type="district" nuts="2">District de Tübingen</region>
<settlement type="city">Tübingen</settlement>
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</author>
<author>
<name sortKey="Kremer, Hannie" sort="Kremer, Hannie" uniqKey="Kremer H" first="Hannie" last="Kremer">Hannie Kremer</name>
<affiliation wicri:level="1">
<country xml:lang="fr">Belgique</country>
<wicri:regionArea>Center for Medical Genetics, Ghent University Hospital, Ghent</wicri:regionArea>
<wicri:noRegion>Ghent</wicri:noRegion>
</affiliation>
</author>
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<monogr></monogr>
<series>
<title level="j">Journal of Medical Genetics</title>
<title level="j" type="abbrev">J Med Genet</title>
<idno type="ISSN">0022-2593</idno>
<idno type="eISSN">1468-6244</idno>
<imprint>
<publisher>BMJ Publishing Group Ltd</publisher>
<date type="published" when="2007-02">2007-02</date>
<biblScope unit="volume">44</biblScope>
<biblScope unit="issue">2</biblScope>
<biblScope unit="page" from="153">153</biblScope>
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<idno type="ISSN">0022-2593</idno>
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<idno type="istex">85BCC45536CF1BDE4E585D34AB33ED062254F920</idno>
<idno type="DOI">10.1136/jmg.2006.044784</idno>
<idno type="href">jmedgenet-44-153.pdf</idno>
<idno type="PMID">16963483</idno>
<idno type="PII">1468-6422</idno>
<idno type="local">0440153</idno>
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<idno type="ISSN">0022-2593</idno>
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<keywords scheme="KwdEn" xml:lang="en">
<term>APEX, arrayed primer extension</term>
<term>RP, retinitis pigmentosa</term>
<term>SSCP, single strand conformation polymorphism</term>
<term>USH, Usher syndrome</term>
<term>USHA, atypical USH</term>
<term>Usher syndrome</term>
<term>arRP, autosomal recessive retinitis pigmentosa</term>
<term>arrayed primer extension</term>
<term>mutation analysis</term>
<term>retinitis pigmentosa</term>
<term>sensorineural deafness</term>
</keywords>
</textClass>
<langUsage>
<language ident="en">en</language>
</langUsage>
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<front>
<div type="abstract" xml:lang="en">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.</div>
</front>
</TEI>
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<li>Zurich</li>
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<li>Université de Zurich</li>
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<region name="Québec">
<name sortKey="Koenekoop, Robert K" sort="Koenekoop, Robert K" uniqKey="Koenekoop R" first="Robert K" last="Koenekoop">Robert K. Koenekoop</name>
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<name sortKey="Millan, Jose M" sort="Millan, Jose M" uniqKey="Millan J" first="Jose M" last="Millan">Jose M. Millan</name>
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