title: DNA Diagnostics of Hereditary Hearing Loss: A Targeted Resequencing Approach Combined with a Mutation Classification System.
abstract: Although there are nearly 100 different causative genes identified for nonsyndromic hearing loss (NSHL), Sanger sequencing-based DNA diagnostics usually only analyses three, namely, GJB2, SLC26A4, and OTOF. As this is seen as inadequate, there is a need for high-throughput diagnostic methods to detect disease-causing variations, including single-nucleotide variations (SNVs), insertions/deletions (Indels), and copy-number variations (CNVs). In this study, a targeted resequencing panel for hearing loss was developed including 79 genes for NSHL and selected forms of syndromic hearing loss. One-hundred thirty one presumed autosomal-recessive NSHL (arNSHL) patients of Western-European ethnicity were analyzed for SNVs, Indels, and CNVs. In addition, we established a straightforward variant classification system to deal with the large number of variants encountered. We estimate that combining prescreening of GJB2 with our panel leads to a diagnosis in 25%-30% of patients. Our data show that after GJB2, the most commonly mutated genes in a Western-European population are TMC1, MYO15A, and MYO7A (3.1%). CNV analysis resulted in the identification of causative variants in two patients in OTOA and STRC. One of the major challenges for diagnostic gene panels is assigning pathogenicity for variants. A collaborative database collecting all identified variants from multiple centers could be a valuable resource for hearing loss diagnostics.
authors.affiliation: Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.
authors.forename: Manou
authors.initials: M
authors.lastname: Sommen
authors.affiliation: Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.|Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Schrauwen
authors.affiliation: Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.
authors.forename: Geert
authors.initials: G
authors.lastname: Vandeweyer
authors.affiliation: Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.
authors.forename: Nele
authors.initials: N
authors.lastname: Boeckx
authors.affiliation: Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona.
authors.forename: Jason J
authors.initials: JJ
authors.lastname: Corneveaux
authors.affiliation: Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.|Antwerp University Hospital, Antwerp, Belgium.
authors.forename: Jenneke
authors.initials: J
authors.lastname: van den Ende
authors.affiliation: Department of Otorhinolaryngology, Head & Neck Surgery, Antwerp University Hospital, Antwerp, Belgium.
authors.forename: An
authors.initials: A
authors.lastname: Boudewyns
authors.affiliation: Center of Medical Genetics, Ghent University, Ghent, Belgium.
authors.forename: Els
authors.initials: E
authors.lastname: De Leenheer
authors.affiliation: Center of Medical Genetics, Ghent University, Ghent, Belgium.
authors.forename: Sandra
authors.initials: S
authors.lastname: Janssens
authors.affiliation: Center of Medical Genetics, Ghent University, Ghent, Belgium.
authors.forename: Kathleen
authors.initials: K
authors.lastname: Claes
authors.affiliation: University Department Otolaryngology, St. Augustinus Hospital, Antwerp, Belgium.
authors.forename: Margriet
authors.initials: M
authors.lastname: Verstreken
authors.affiliation: Inner Ear Lab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany.
authors.forename: Nicola
authors.initials: N
authors.lastname: Strenzke
authors.affiliation: Inner Ear Lab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany.
authors.forename: Friederike
authors.initials: F
authors.lastname: Predöhl
authors.affiliation: Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.|Antwerp University Hospital, Antwerp, Belgium.
authors.forename: Wim
authors.initials: W
authors.lastname: Wuyts
authors.affiliation: Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.|Antwerp University Hospital, Antwerp, Belgium.
authors.forename: Geert
authors.initials: G
authors.lastname: Mortier
authors.affiliation: Clinical and Molecular Genetics Unit, UCL Institute of Child Health and Great Ormond Street Hospital NHS Trust, London, UK.
authors.forename: Maria
authors.initials: M
authors.lastname: Bitner-Glindzicz
authors.affiliation: Inner Ear Lab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany.|Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany.
authors.forename: Tobias
authors.initials: T
authors.lastname: Moser
authors.affiliation: Center of Medical Genetics, Ghent University, Ghent, Belgium.
authors.forename: Paul
authors.initials: P
authors.lastname: Coucke
authors.affiliation: Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Huentelman
authors.affiliation: Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.
authors.forename: Guy
authors.initials: G
authors.lastname: Van Camp
mesh_terms: D000072259:Connexin 26; D017630:Connexins / Q000235:genetics; D056915:DNA Copy Number Variations; D059472:Exome; D058851:GPI-Linked Proteins / Q000235:genetics; D020022:Genetic Predisposition to Disease; D006319:Hearing Loss, Sensorineural / Q000175:diagnosis* / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D054643:INDEL Mutation; D036341:Intercellular Signaling Peptides and Proteins; D008565:Membrane Proteins / Q000235:genetics; D009154:Mutation; D000081412:Myosin VIIa; D009218:Myosins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D017630:Connexins; C000607042:GJB2 protein, human; D058851:GPI-Linked Proteins; D036341:Intercellular Signaling Peptides and Proteins; C485245:MYO15A protein, human; C000631455:MYO7A protein, human; D008565:Membrane Proteins; D000081412:Myosin VIIa; C456027:OTOA protein, human; C499079:STRC protein, human; C451751:TMC1 protein, human; D000072259:Connexin 26; D009218:Myosins
keywords: hereditary hearing loss; mutation classification system; targeted resequencing