Comprehensive analysis via exome sequencing uncovers genetic etiology in autosomal recessive nonsyndromic deafness in a large multiethnic cohort

Original Research Article © American College of Medical Genetics and Genomics Comprehensive analysis via exome sequencing uncovers genetic etiology in autosomal recessive nonsyndromic deafness in a large multiethnic cohort Guney Bademci, MD1, Joseph Foster II, BSc1, Nejat Mahdieh, PhD2, Mortaza Bonyadi, PhD3, Duygu Duman, PhD4, F.Basak Cengiz, PhD4, Ibis Menendez, MD1, Oscar Diaz-Horta, PhD1, Atefeh Shirkavand, PhD5, Sirous Zeinali, PhD5,6, Asli Subasioglu, MD7, Suna Tokgoz-Yilmaz, PhD8, Fabiola Huesca-Hernandez, BSc9, Maria de la Luz Arenas-Sordo, MD9, Juan Dominguez-Aburto, BSc9, Edgar Hernandez-Zamora, PhD9, Paola Montenegro, PhD10, Rosario Paredes, MD10, Germania Moreta, MD10, Rodrigo Vinueza, BSc10, Franklin Villegas, BSc10, Santiago Mendoza-Benitez, MD11, Shengru Guo, MSc1, Nazim Bozan, MD12, Tulay Tos, MD13, Armagan Incesulu, MD14, Gonca Sennaroglu, PhD8, Susan H. Blanton, PhD1, Hatice Ozturkmen-Akay, MD15, Muzeyyen Yildirim-Baylan, MD16, and Mustafa Tekin, MD1 Purpose: Autosomal recessive nonsyndromic deafness (ARNSD) is characterized by a high degree of genetic heterogeneity, with reported mutations in 58 different genes. This study was designed to detect deafness-causing variants in a multiethnic cohort with ARNSD by using whole-exome sequencing (WES). Methods: After excluding mutations in the most common gene, GJB2, we performed WES in 160 multiplex families with ARNSD from Turkey, Iran, Mexico, Ecuador, and Puerto Rico to screen for mutations in all known ARNSD genes. Results: We detected ARNSD-causing variants in 90 (56%) families, 54% of which had not been previously reported. Identified mutations were located in 31 known ARNSD genes. The most common genes with mutations were MYO15A (13%), MYO7A (11%), SLC26A4 INTRODUCTION Deafness is a global public health concern that affects 1 to 3 per 1,000 newborns.1 In more than half of the cases of congenital or prelingual deafness, the cause is genetic, and most demonstrate an autosomal recessive inheritance pattern.1 Mutations in 58 different genes have been reported to cause autosomal recessive nonsyndromic deafness (ARNSD) (http:// hereditaryhearingloss.org). (10%), TMPRSS3 (9%), TMC1 (8%), ILDR1 (6%), and CDH23 (4%). Nine mutations were detected in multiple families with shared haplotypes, suggesting founder effects. Conclusion: We report on a large multiethnic cohort with ARNSD in which comprehensive analysis of all known ARNSD genes identifies causative DNA variants in 56% of the families. In the remaining families, WES allows us to search for causative variants in novel genes, thus improving our ability to explain the underlying etiology in more families. Genet Med advance online publication 30 July 2015 Key Words: autosomal recessive; deafness; exome; next-generation sequencing Except for one relatively common gene, GJB2 (MIM 121011), most reported mutations are present in only a single or a small number of families.2 Whole-exome sequencing (WES) allows resequencing of nearly all exons of the protein-coding genes in the genome.3 A growing number of research and clinical diagnostic laboratories are successfully using WES for gene/variant identification because of its comprehensive analysis advantages.4,5 In this study, we 1 Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA; 2Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran; 3Faculty of Natural Sciences, Center of Excellence for Biodiversity, University of Tabriz, Tabriz, Iran; 4Division of Genetics, Department of Pediatrics, Ankara University School of Medicine, Ankara, Turkey; 5Kawsar’s Human Genetic Research Center, Tehran, Iran; 6Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran; 7Department of Medical Genetics, Izmir Katip Celebi University, Ataturk Training and Research Hospital, Izmir, Turkey; 8Department of Audiology, Hacettepe University Health Sciences Faculty, Ankara, Turkey; 9Genetic Service, National Institute of Rehabilitation, Mexico D.F., Mexico; 10Molecular Genetic Lab, FFAA Hospital, Quito, Ecuador; 11Audiology Department, Cuernavaca General Hospital, Morelos, Mexico; 12Department of Otolaryngology, Faculty of Medicine, Yuzuncu Yıl University, Van, Turkey; 13Department of Medical Genetics, Dr. Sami Ulus Research and Training Hospital of Women’s and Children’s Health and Diseases, Ankara, Turkey; 14Department of Otolaryngology, Head and Neck Surgery, Eskisehir Osmangazi University, Eskisehir, Turkey; 15Department of Radiology, Istanbul Zeynep Kamil Maternity and Children Training and Research Hospital, Istanbul, Turkey; 16Department of Otorhinolaryngology, Dicle University School of Medicine, Diyarbakir, Turkey. Correspondence: Mustafa Tekin () Submitted 27 March 2015; accepted 19 May 2015; advance online publication 30 July 2015. doi:10.1038/gim.2015.89 364 Volume 18 | Number 4 | April 2016 | Genetics in medicine Original Research Article Exome sequencing in autosomal recessive nonsyndromic deafness | BADEMCI et al present the results of WES in a large multiethnic cohort consisting of 160 families with ARNSD who were negative for GJB2 mutations. MATERIALS AND METHODS Statement of ethics This study was approved by the University of Miami Institutional Review Board (USA), the Ankara University Medical School Ethics Committee (Turkey), the Growth and Development Research Ethics Committee (Iran), the Bioethics Committee of FFAA (HE-1) in Quito (Ecuador), and the Ethics Committee of National Institute of Rehabilitation (Mexico). A signed informed-consent form was obtained from each participant or, in the case of a minor, from the parents. Subjects We included 160 families with at least two members with nonsyndromic sensorineural hearing loss with a pedigree structure suggestive of autosomal recessive inheritance (affected siblings born to unaffected parents with or without parental consanguinity); GJB2 mutations were negative. Hearing loss was congenital or prelingual-onset with a severity ranging from mild to profound. The study comprised 101 families from Turkey, 54 from Iran, 2 from Mexico, 2 from Ecuador, and 1 from Puerto Rico. Sensorineural hearing loss was diagnosed via standard audiometry in a soundproof room according to standard clinical practice. Clinical evaluation of all affected individuals by a geneticist and an otolaryngologist included a thorough physical examination, otoscopy, and ophthalmoscopy. Tandem walking and the Romberg test were used for initial vestibular evaluation, with more detailed tests if needed based on symptoms and findings. Laboratory investigation included, but was not limited to, an electrocardiogram, urinalysis, and, when available, a high-resolution computed tomography (CT) scan of the temporal bone or magnetic resonance imaging (MRI) to identify inner e (...truncated)