title: An innovative strategy for the molecular diagnosis of Usher syndrome identifies causal biallelic mutations in 93% of European patients.
abstract: Usher syndrome (USH), the most prevalent cause of hereditary deafness-blindness, is an autosomal recessive and genetically heterogeneous disorder. Three clinical subtypes (USH1-3) are distinguishable based on the severity of the sensorineural hearing impairment, the presence or absence of vestibular dysfunction, and the age of onset of the retinitis pigmentosa. A total of 10 causal genes, 6 for USH1, 3 for USH2, and 1 for USH3, and an USH2 modifier gene, have been identified. A robust molecular diagnosis is required not only to improve genetic counseling, but also to advance gene therapy in USH patients. Here, we present an improved diagnostic strategy that is both cost- and time-effective. It relies on the sequential use of three different techniques to analyze selected genomic regions: targeted exome sequencing, comparative genome hybridization, and quantitative exon amplification. We screened a large cohort of 427 patients (139 USH1, 282 USH2, and six of undefined clinical subtype) from various European medical centers for mutations in all USH genes and the modifier gene. We identified a total of 421 different sequence variants predicted to be pathogenic, about half of which had not been previously reported. Remarkably, we detected large genomic rearrangements, most of which were novel and unique, in 9% of the patients. Thus, our strategy led to the identification of biallelic and monoallelic mutations in 92.7% and 5.8% of the USH patients, respectively. With an overall 98.5% mutation characterization rate, the diagnosis efficiency was substantially improved compared with previously reported methods.
authors.affiliation: INSERM UMRS 1120, Institut de la Vision, Paris, France.|UPMC-Sorbonnes Universités Paris VI, Paris, France.
authors.forename: Crystel
authors.initials: C
authors.lastname: Bonnet
authors.affiliation: INSERM UMRS 1120, Institut de la Vision, Paris, France.|UPMC-Sorbonnes Universités Paris VI, Paris, France.
authors.forename: Zied
authors.initials: Z
authors.lastname: Riahi
authors.affiliation: Service de Génétique et d'Embryologie Médicales, APHP Hôpital Armand Trousseau, Paris, France.|INSERM U933, Hôpital Armand Trousseau, Paris, France.
authors.forename: Sandra
authors.initials: S
authors.lastname: Chantot-Bastaraud
authors.affiliation: INSERM UMRS 1120, Institut de la Vision, Paris, France.|UPMC-Sorbonnes Universités Paris VI, Paris, France.
authors.forename: Luce
authors.initials: L
authors.lastname: Smagghe
authors.affiliation: IntegraGen SA, Genopole CAMPUS 1 bât. G8, EVRY, Paris, France.
authors.forename: Mélanie
authors.initials: M
authors.lastname: Letexier
authors.affiliation: IntegraGen SA, Genopole CAMPUS 1 bât. G8, EVRY, Paris, France.
authors.forename: Charles
authors.initials: C
authors.lastname: Marcaillou
authors.affiliation: INSERM UMRS 1120, Institut de la Vision, Paris, France.|UPMC-Sorbonnes Universités Paris VI, Paris, France.
authors.forename: Gaëlle M
authors.initials: GM
authors.lastname: Lefèvre
authors.affiliation: Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris, France.
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Hardelin
authors.affiliation: Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris, France.
authors.forename: Aziz
authors.initials: A
authors.lastname: El-Amraoui
authors.affiliation: INSERM UMRS 1120, Institut de la Vision, Paris, France.|UPMC-Sorbonnes Universités Paris VI, Paris, France.
authors.forename: Amrit
authors.initials: A
authors.lastname: Singh-Estivalet
authors.affiliation: UPMC-Sorbonnes Universités Paris VI, Paris, France.|INSERM UMRS968, Institut de la Vision, Paris, France.|Centre d'Investigation Clinique, Direction de l'Hospitalisation et de l'Organisation des Soins, Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Paris, France.
authors.forename: Saddek
authors.initials: S
authors.lastname: Mohand-Saïd
authors.affiliation: Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany.
authors.forename: Susanne
authors.initials: S
authors.lastname: Kohl
authors.affiliation: Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany.
authors.forename: Anne
authors.initials: A
authors.lastname: Kurtenbach
authors.affiliation: Centre d'Investigation Clinique, Direction de l'Hospitalisation et de l'Organisation des Soins, Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Paris, France.|Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany.
authors.forename: Ieva
authors.initials: I
authors.lastname: Sliesoraityte
authors.affiliation: Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany.
authors.forename: Ditta
authors.initials: D
authors.lastname: Zobor
authors.affiliation: Centre de référence des Surdités Génétiques, Service de Génétique, APHP Hôpital Necker, Paris, France.
authors.forename: Souad
authors.initials: S
authors.lastname: Gherbi
authors.affiliation: Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences Second University of Naples, Naples, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Testa
authors.affiliation: Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences Second University of Naples, Naples, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Simonelli
authors.affiliation: TIGEM (Telethon Institute of Genetics and Medicine), Pozzuoli, Italy.|Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Naples, Italy.
authors.forename: Sandro
authors.initials: S
authors.lastname: Banfi
authors.affiliation: Eye Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia.
authors.forename: Ana
authors.initials: A
authors.lastname: Fakin
authors.affiliation: Department of Molecular Genetics, Institute of Pathology, University of Ljubljana, Korytkova, Ljubljana.
authors.forename: Damjan
authors.initials: D
authors.lastname: Glavač
authors.affiliation: Eye Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia.
authors.forename: Martina
authors.initials: M
authors.lastname: Jarc-Vidmar
authors.affiliation: Department of Molecular Genetics, Institute of Pathology, University of Ljubljana, Korytkova, Ljubljana.
authors.forename: Andrej
authors.initials: A
authors.lastname: Zupan
authors.affiliation: Department of Otorhinolaryngology and Cervicofacial Surgery, University Medical Centre Ljubljana, Zaloska 2, University of Ljubljana, Ljubljana, Slovenia.
authors.forename: Saba
authors.initials: S
authors.lastname: Battelino
authors.affiliation: Hospital Sant Joan de Déu, Barcelona, Spain.
authors.forename: Loreto
authors.initials: L
authors.lastname: Martorell Sampol
authors.affiliation: Hospital Sant Joan de Déu, Barcelona, Spain.
authors.forename: Maria Antonia
authors.initials: MA
authors.lastname: Claveria
authors.affiliation: Hospital Sant Joan de Déu, Barcelona, Spain.
authors.forename: Jaume
authors.initials: J
authors.lastname: Catala Mora
authors.affiliation: Kennedy Center, Gl. Landevej, Glostrup, Denmark.
authors.forename: Shzeena
authors.initials: S
authors.lastname: Dad
authors.affiliation: Kennedy Center, Gl. Landevej, Glostrup, Denmark.
authors.forename: Lisbeth B
authors.initials: LB
authors.lastname: Møller
authors.affiliation: Hospital Sant Joan de Déu, Barcelona, Spain.
authors.forename: Jesus
authors.initials: J
authors.lastname: Rodriguez Jorge
authors.affiliation: Eye Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia.
authors.forename: Marko
authors.initials: M
authors.lastname: Hawlina
authors.affiliation: TIGEM (Telethon Institute of Genetics and Medicine), Pozzuoli, Italy.|Department of Translational Medicine, "Federico II" University, Napoli, Italy.
authors.forename: Alberto
authors.initials: A
authors.lastname: Auricchio
authors.affiliation: UPMC-Sorbonnes Universités Paris VI, Paris, France.|INSERM UMRS968, Institut de la Vision, Paris, France.|Centre d'Investigation Clinique, Direction de l'Hospitalisation et de l'Organisation des Soins, Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Paris, France.
authors.forename: José-Alain
authors.initials: JA
authors.lastname: Sahel
authors.affiliation: Centre de référence des Surdités Génétiques, Service de Génétique, APHP Hôpital Necker, Paris, France.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Marlin
authors.affiliation: Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany.|Werner Reichardt Centre for Integrative Neuroscience (CIN), University of Tuebingen, Tuebingen, Germany.
authors.forename: Eberhart
authors.initials: E
authors.lastname: Zrenner
authors.affiliation: UPMC-Sorbonnes Universités Paris VI, Paris, France.|INSERM UMRS968, Institut de la Vision, Paris, France.|Centre d'Investigation Clinique, Direction de l'Hospitalisation et de l'Organisation des Soins, Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Paris, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Audo
authors.affiliation: INSERM UMRS 1120, Institut de la Vision, Paris, France.|UPMC-Sorbonnes Universités Paris VI, Paris, France.|Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris, France.|Collège de France, Paris, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Petit
mesh_terms: D000483:Alleles; D055028:Comparative Genomic Hybridization / Q000379:methods; D005060:Europe; D059472:Exome; D016326:Extracellular Matrix Proteins / Q000235:genetics; D060045:Genes, Modifier; D005820:Genetic Testing / Q000379:methods*; D006801:Humans; D009154:Mutation; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods; D052245:Usher Syndromes / Q000175:diagnosis / Q000235:genetics*
chemical_list: D016326:Extracellular Matrix Proteins; C112735:USH2A protein, human