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Alkhidir S, El-Akouri K, Al-Dewik N, Khodjet-El-Khil H, Okashah S, Islam N, Ben-Omran T, Al-Shafai M. The genetic basis and the diagnostic yield of genetic testing related to nonsyndromic hearing loss in Qatar. Sci Rep 2024; 14:4202. [PMID: 38378725 PMCID: PMC10879212 DOI: 10.1038/s41598-024-52784-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
Hearing loss is the most predominant sensory defect occurring in pediatrics, of which, 66% cases are attributed to genetic factors. The prevalence of hereditary hearing loss increases in consanguineous populations, and the prevalence of hearing loss in Qatar is 5.2%. We aimed to investigate the genetic basis of nonsyndromic hearing loss (NSHL) in Qatar and to evaluate the diagnostic yield of different genetic tests available. A retrospective chart review was conducted for 59 pediatric patients with NSHL referred to the Department of Adult and Pediatric Medical Genetics at Hamad Medical Corporation in Qatar, and who underwent at least one genetic test. Out of the 59 patients, 39 were solved cases due to 19 variants in 11 genes and two copy number variants that explained the NSHL phenotype. Of them 2 cases were initially uncertain and were reclassified using familial segregation. Around 36.8% of the single variants were in GJB2 gene and c.35delG was the most common recurrent variant seen in solved cases. We detected the c.283C > T variant in FGF3 that was seen in a Qatari patient and found to be associated with NSHL for the first time. The overall diagnostic yield was 30.7%, and the diagnostic yield was significantly associated with genetic testing using GJB2 sequencing and using the hearing loss (HL) gene panel. The diagnostic yield for targeted familial testing was 60% (n = 3 patients) and for gene panel was 50% (n = 5). Thus, we recommend using GJB2 gene sequencing as a first-tier genetic test and HL gene panel as a second-tier genetic test for NSHL. Our work provided new insights into the genetic pool of NSHL among Arabs and highlights its unique diversity, this is believed to help further in the diagnostic and management options for NSHL Arab patients.
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Affiliation(s)
- Shaza Alkhidir
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
- Department of Adult and Pediatric Medical Genetics, Hamad Medical Corporation, Doha, Qatar
| | - Karen El-Akouri
- Department of Adult and Pediatric Medical Genetics, Hamad Medical Corporation, Doha, Qatar
- Division of Genetic and Genomic Medicine, Sidra Medicine, Doha, Qatar
| | - Nader Al-Dewik
- Department of Adult and Pediatric Medical Genetics, Hamad Medical Corporation, Doha, Qatar
| | - Houssein Khodjet-El-Khil
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Sarah Okashah
- Department of Adult and Pediatric Medical Genetics, Hamad Medical Corporation, Doha, Qatar
- Department of Public Health, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Nazmul Islam
- Department of Public Health, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Tawfeg Ben-Omran
- Department of Adult and Pediatric Medical Genetics, Hamad Medical Corporation, Doha, Qatar.
- Division of Genetic and Genomic Medicine, Sidra Medicine, Doha, Qatar.
| | - Mashael Al-Shafai
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar.
- Biomedical Research Center, Qatar University, Doha, Qatar.
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2
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Jin X, Huang S, An L, Zhang C, Dai P, Gao H, Ma X. Variant analysis of 92 Chinese Han families with hearing loss. BMC Med Genomics 2022; 15:12. [PMID: 35062939 PMCID: PMC8781451 DOI: 10.1186/s12920-022-01158-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/07/2022] [Indexed: 01/31/2024] Open
Abstract
Abstract
Background
Hearing loss (HL) is the most frequent sensory deficit in humans, HL has strong genetic heterogeneity. The genetic diagnosis of HL is very important to aid treatment decisions and to provide prognostic information and genetic counseling for the patient’s family.
Methods
We undertook pedigree analysis in 92 Chinese non-syndromic HL patients by targeted next-generation sequencing and Sanger sequencing.
Results
Among the 92 HL patients, 18 were assigned a molecular diagnosis with 33 different variants in 14 deafness genes. Eighteen of the variants in 12 deafness genes were novel. Variants in TMC1, CDH23, LOXHD1 and USH2A were each detected in two probands, and variants in POU3F4, OTOA, GPR98, GJB6, TRIOBP, SLC26A4, MYO15A, TNC, STRC and TMPRSS3 were each detected in one proband.
Conclusion
Our findings expand the spectrum of deafness gene variation, which will inform genetic diagnosis of deafness and add to the theoretical basis for the prevention of deafness.
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3
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Nishio SY, Usami SI. Frequency of the STRC-CATSPER2 deletion in STRC-associated hearing loss patients. Sci Rep 2022; 12:634. [PMID: 35022556 PMCID: PMC8755823 DOI: 10.1038/s41598-021-04688-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/21/2021] [Indexed: 01/14/2023] Open
Abstract
The STRC gene, located on chromosome 15q15.3, is one of the genetic causes of autosomal recessive mild-to-moderate sensorineural hearing loss. One of the unique characteristics of STRC-associated hearing loss is the high prevalence of long deletions or copy number variations observed on chromosome 15q15.3. Further, the deletion of chromosome 15q15.3 from STRC to CATSPER2 is also known to be a genetic cause of deafness infertility syndrome (DIS), which is associated with not only hearing loss but also male infertility, as CATSPER2 plays crucial roles in sperm motility. Thus, information regarding the deletion range for each patient is important to the provision of appropriate genetic counselling for hearing loss and male infertility. In the present study, we performed next-generation sequencing (NGS) analysis for 9956 Japanese hearing loss patients and analyzed copy number variations in the STRC gene based on NGS read depth data. In addition, we performed Multiplex Ligation-dependent Probe Amplification analysis to determine the deletion range including the PPIP5K1, CKMT1B, STRC and CATSPER2 genomic region to estimate the prevalence of the STRC-CATSPER deletion, which is causative for DIS among the STRC-associated hearing loss patients. As a result, we identified 276 cases with STRC-associated hearing loss. The prevalence of STRC-associated hearing loss in Japanese hearing loss patients was 2.77% (276/9956). In addition, 77.1% of cases with STRC homozygous deletions carried a two copy loss of the entire CKMT1B-STRC-CATSPER2 gene region. This information will be useful for the provision of more appropriate genetic counselling regarding hearing loss and male infertility for the patients with a STRC deletion.
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Affiliation(s)
- Shin-Ya Nishio
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
| | - Shin-Ichi Usami
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan.
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Evaluation of copy number variants for genetic hearing loss: a review of current approaches and recent findings. Hum Genet 2021; 141:387-400. [PMID: 34811589 DOI: 10.1007/s00439-021-02365-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/02/2021] [Indexed: 01/22/2023]
Abstract
Structural variation includes a change in copy number, orientation, or location of a part of the genome. Copy number variants (CNVs) are a common cause of genetic hearing loss, comprising nearly 20% of diagnosed cases. While large deletions involving the gene STRC are the most common pathogenic CNVs, a significant proportion of known hearing loss genes also contain pathogenic CNVs. In this review, we provide an overview of currently used methods for detection of CNVs in genes known to cause hearing loss including molecular techniques such as multiplex ligation probe amplification (MLPA) and digital droplet polymerase chain reaction (ddPCR), array-CGH and single-nucleotide polymorphism (SNP) arrays, as well as techniques for detection of CNVs using next-generation sequencing data analysis including targeted gene panel, exome, and genome sequencing data. In addition, in this review, we compile published data on pathogenic hearing loss CNVs to provide an up-to-date overview. We show that CNVs have been identified in 29 different non-syndromic hearing loss genes. An understanding of the contribution of CNVs to genetic hearing loss is critical to the current diagnosis of hearing loss and is crucial for future gene therapies. Thus, evaluation for CNVs is required in any modern pipeline for genetic diagnosis of hearing loss.
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Rentas S, Abou Tayoun A. Utility of droplet digital PCR and NGS-based CNV clinical assays in hearing loss diagnostics: current status and future prospects. Expert Rev Mol Diagn 2021; 21:213-221. [PMID: 33554673 DOI: 10.1080/14737159.2021.1887731] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Genetic variants in over 100 genes can cause non-syndromic hearing loss (NSHL). Comprehensive diagnostic testing of these genes requires detecting pathogenic sequence and copy number alterations with economical, scalable and sensitive assays. Here we discuss best practices and effective testing algorithms for hearing-loss-related genes with special emphasis on detection of copy number variants.Areas covered: We review studies that used next-generation sequencing (NGS), chromosomal microarrays, droplet digital PCR (ddPCR), and multiplex ligation-dependent probe amplification (MLPA) for the diagnosis of NSHL. We specifically focus on unique and recurrent copy number changes that affect the GJB2 and STRC genes, two of the most common causes of NSHL.Expert opinion: NGS panels and exome sequencing can detect most pathogenic sequence and copy number variants that cause NSHL; however, GJB2 and STRC currently require additional assays to capture all pathogenic copy number variants. Adoption of genome sequencing may simplify diagnostic workflows, but further investigational studies will be required to evaluate its clinical efficacy.
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Affiliation(s)
- Stefan Rentas
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ahmad Abou Tayoun
- Al Jalila Genomics Center, Al Jalila Children's Specialty Hospital, Dubai, UAE.,Department of Genetics, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
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Jimenez JE, Nourbakhsh A, Colbert B, Mittal R, Yan D, Green CL, Nisenbaum E, Liu G, Bencie N, Rudman J, Blanton SH, Zhong Liu X. Diagnostic and therapeutic applications of genomic medicine in progressive, late-onset, nonsyndromic sensorineural hearing loss. Gene 2020; 747:144677. [PMID: 32304785 PMCID: PMC7244213 DOI: 10.1016/j.gene.2020.144677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/12/2020] [Accepted: 04/14/2020] [Indexed: 02/06/2023]
Abstract
The progressive, late-onset, nonsyndromic, sensorineural hearing loss (PNSHL) is the most common cause of sensory impairment globally, with presbycusis affecting greater than a third of individuals over the age of 65. The etiology underlying PNSHL include presbycusis, noise-induced hearing loss, drug ototoxicity, and delayed-onset autosomal dominant hearing loss (AD PNSHL). The objective of this article is to discuss the potential diagnostic and therapeutic applications of genomic medicine in PNSHL. Genomic factors contribute greatly to PNSHL. The heritability of presbycusis ranges from 25 to 75%. Current therapies for PNSHL range from sound amplification to cochlear implantation (CI). PNSHL is an excellent candidate for genomic medicine approaches as it is common, has well-described pathophysiology, has a wide time window for treatment, and is amenable to local gene therapy by currently utilized procedural approaches. AD PNSHL is especially suited to genomic medicine approaches that can disrupt the expression of an aberrant protein product. Gene therapy is emerging as a potential therapeutic strategy for the treatment of PNSHL. Viral gene delivery approaches have demonstrated promising results in human clinical trials for two inherited causes of blindness and are being used for PNSHL in animal models and a human trial. Non-viral gene therapy approaches are useful in situations where a transient biologic effect is needed or for delivery of genome editing reagents (such as CRISPR/Cas9) into the inner ear. Many gene therapy modalities that have proven efficacious in animal trials have potential to delay or prevent PNSHL in humans. The development of new treatment modalities for PNSHL will lead to improved quality of life of many affected individuals and their families.
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Affiliation(s)
- Joaquin E Jimenez
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Aida Nourbakhsh
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Brett Colbert
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Human Genetics and John P. Hussman Institute of Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Medical Scientist Training Program, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Carlos L Green
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Eric Nisenbaum
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - George Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Nicole Bencie
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jason Rudman
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Susan H Blanton
- Department of Human Genetics and John P. Hussman Institute of Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Human Genetics and John P. Hussman Institute of Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.
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7
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Spectrum of Genetic Variants Associated with Anterior Segment Dysgenesis in South Florida. Genes (Basel) 2020; 11:genes11040350. [PMID: 32224865 PMCID: PMC7230952 DOI: 10.3390/genes11040350] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 12/02/2022] Open
Abstract
Anterior segment dysgenesis (ASD) comprises a wide spectrum of developmental conditions affecting the cornea, iris, and lens, which may be associated with abnormalities of other organs. To identify disease-causing variants, we performed exome sequencing in 24 South Florida families with ASD. We identified 12 likely causative variants in 10 families (42%), including single nucleotide or small insertion–deletion variants in B3GLCT, BMP4, CYP1B1, FOXC1, FOXE3, GJA1, PXDN, and TP63, and a large copy number variant involving PAX6. Four variants were novel. Each variant was detected only in one family. Likely causative variants were detected in 1 out of 7 black and 9 out of 17 white families. In conclusion, exome sequencing for ASD allows us to identify a wide spectrum of rare DNA variants in South Florida. Further studies will explore missing variants, especially in the black communities.
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Downie L, Halliday J, Burt R, Lunke S, Lynch E, Martyn M, Poulakis Z, Gaff C, Sung V, Wake M, Hunter MF, Saunders K, Rose E, Lewis S, Jarmolowicz A, Phelan D, Rehm HL, Amor DJ. Exome sequencing in infants with congenital hearing impairment: a population-based cohort study. Eur J Hum Genet 2019; 28:587-596. [PMID: 31827275 DOI: 10.1038/s41431-019-0553-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 10/30/2019] [Accepted: 11/07/2019] [Indexed: 12/11/2022] Open
Abstract
Congenital hearing impairment (HI) is the most common sensory impairment and can be isolated or part of a syndrome. Diagnosis through newborn hearing screening and management through early intervention, hearing aids and cochlear implantation is well established in the Australian setting; however understanding the genetic basis of congenital HI has been missing. This population-derived cohort comprised infants with moderate-profound bilateral HI born in the 2016-2017 calendar years, detected through newborn hearing screening. Participants were recruited through an integrated paediatric, otolaryngology and genetics HI clinic and offered whole exome sequencing (WES) on a HiSeq4000 or NextSeq500 (Illumina) platform with a targeted average sequencing depth of 100x and chromosome microarray on the Illumina Infinium core exome-24v1.2 platform. Of those approached, 68% (106/156) consented to participate. The rate of genetic diagnosis was 56% (59/106), significantly higher than standard of care (GJB2/6 sequencing only), 21% (22/106). There were clinical implications for the 106 participants: 36% required no further screening, 9% had tailored screening initiated, 2% were offered treatment and 4% had informed care for a complex neurodevelopmental syndrome. WES in this cohort demonstrates the range of diagnoses associated with congenital HI and confirms the genetic heterogeneity of congenital HI. The high diagnostic yield and clinical implications emphasises the need for genomic sequencing to become standard of care.
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Affiliation(s)
- Lilian Downie
- Victorian Clinical Genetics Services, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Royal Children's Hospital, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Jane Halliday
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Rachel Burt
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Elly Lynch
- Victorian Clinical Genetics Services, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Melbourne Genomics Health Alliance, Melbourne, VIC, Australia
| | - Melissa Martyn
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.,Melbourne Genomics Health Alliance, Melbourne, VIC, Australia
| | - Zeffie Poulakis
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Royal Children's Hospital, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Clara Gaff
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.,Melbourne Genomics Health Alliance, Melbourne, VIC, Australia
| | - Valerie Sung
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Royal Children's Hospital, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Melissa Wake
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Matthew F Hunter
- Monash Health, Melbourne, VIC, Australia.,Monash University, Melbourne, VIC, Australia
| | - Kerryn Saunders
- Monash Health, Melbourne, VIC, Australia.,Monash University, Melbourne, VIC, Australia
| | - Elizabeth Rose
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Royal Children's Hospital, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Sharon Lewis
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Anna Jarmolowicz
- Victorian Clinical Genetics Services, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Dean Phelan
- Victorian Clinical Genetics Services, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Heidi L Rehm
- Massachusetts General Hospital and the Broad Institute of MIT and Harvard, Boston, MA, USA
| | | | - David J Amor
- Victorian Clinical Genetics Services, Melbourne, VIC, Australia. .,Murdoch Children's Research Institute, Melbourne, VIC, Australia. .,Royal Children's Hospital, Melbourne, VIC, Australia. .,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.
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9
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Mid-Frequency Hearing Loss Is Characteristic Clinical Feature of OTOA-Associated Hearing Loss. Genes (Basel) 2019; 10:genes10090715. [PMID: 31527525 PMCID: PMC6770988 DOI: 10.3390/genes10090715] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/09/2019] [Accepted: 09/12/2019] [Indexed: 12/03/2022] Open
Abstract
The OTOA gene (Locus: DFNB22) is reported to be one of the causative genes for non-syndromic autosomal recessive hearing loss. The copy number variations (CNVs) identified in this gene are also known to cause hearing loss, but have not been identified in Japanese patients with hearing loss. Furthermore, the clinical features of OTOA-associated hearing loss have not yet been clarified. In this study, we performed CNV analyses of a large Japanese hearing loss cohort, and identified CNVs in 234 of 2262 (10.3%, 234/2262) patients with autosomal recessive hearing loss. Among the identified CNVs, OTOA gene-related CNVs were the second most frequent (0.6%, 14/2262). Among the 14 cases, 2 individuals carried OTOA homozygous deletions, 4 carried heterozygous deletions with single nucleotide variants (SNVs) in another allele. Additionally, 1 individual with homozygous SNVs in the OTOA gene was also identified. Finally, we identified 7 probands with OTOA-associated hearing loss, so that its prevalence in Japanese patients with autosomal recessive hearing loss was calculated to be 0.3% (7/2262). As novel clinical features identified in this study, the audiometric configurations of patients with OTOA-associated hearing loss were found to be mid-frequency. This is the first study focused on the detailed clinical features of hearing loss caused by this gene mutation and/or gene deletion.
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10
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Bademci G, Abad C, Incesulu A, Elian F, Reyahi A, Diaz-Horta O, Cengiz FB, Sineni CJ, Seyhan S, Atli EI, Basmak H, Demir S, Nik AM, Footz T, Guo S, Duman D, Fitoz S, Gurkan H, Blanton SH, Walter MA, Carlsson P, Walz K, Tekin M. FOXF2 is required for cochlear development in humans and mice. Hum Mol Genet 2019; 28:1286-1297. [PMID: 30561639 DOI: 10.1093/hmg/ddy431] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 11/14/2022] Open
Abstract
Molecular mechanisms governing the development of the human cochlea remain largely unknown. Through genome sequencing, we identified a homozygous FOXF2 variant c.325A>T (p.I109F) in a child with profound sensorineural hearing loss (SNHL) associated with incomplete partition type I anomaly of the cochlea. This variant is not found in public databases or in over 1000 ethnicity-matched control individuals. I109 is a highly conserved residue in the forkhead box (Fox) domain of FOXF2, a member of the Fox protein family of transcription factors that regulate the expression of genes involved in embryogenic development as well as adult life. Our in vitro studies show that the half-life of mutant FOXF2 is reduced compared to that of wild type. Foxf2 is expressed in the cochlea of developing and adult mice. The mouse knockout of Foxf2 shows shortened and malformed cochleae, in addition to altered shape of hair cells with innervation and planar cell polarity defects. Expressions of Eya1 and Pax3, genes essential for cochlear development, are reduced in the cochleae of Foxf2 knockout mice. We conclude that FOXF2 plays a major role in cochlear development and its dysfunction leads to SNHL and developmental anomalies of the cochlea in humans and mice.
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Affiliation(s)
- Guney Bademci
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Clemer Abad
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Armagan Incesulu
- Department of Otolaryngology-Head and Neck Surgery, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Fahed Elian
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Azadeh Reyahi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Oscar Diaz-Horta
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Filiz B Cengiz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Claire J Sineni
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Serhat Seyhan
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Medical Genetics, Bakirkoy Dr Sadi Konuk Research and Training Hospital, Istanbul, Turkey
| | - Emine Ikbal Atli
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Hikmet Basmak
- Department of Ophthalmology, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Selma Demir
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Ali Moussavi Nik
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Tim Footz
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Shengru Guo
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Duygu Duman
- Division of Pediatric Genetics, Ankara University School of Medicine, Ankara, Turkey
| | - Suat Fitoz
- Department of Radiology, Ankara University School of Medicine, Ankara, Turkey
| | - Hakan Gurkan
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Susan H Blanton
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA.,Dr John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael A Walter
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Peter Carlsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Katherina Walz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Dr John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mustafa Tekin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA.,Dr John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
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12
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Tassano E, Ronchetto P, Calcagno A, Fiorio P, Gimelli G, Capra V, Scala M. 'Distal 16p12.2 microdeletion' in a patient with autosomal recessive deafness-22. J Genet 2019; 98:56. [PMID: 31204719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The 16p12.2 chromosome band contains three large segmental duplications: BP1, BP2 and BP3, providing a substrate for recombination and recurrent chromosomal rearrangements. The '16p12.2 microdeletion' is a recurrent deletion comprised between BP2 and BP3, associated with variable clinical findings. We identified a heterozygous 16p12.2 microdeletion spanning between BP1 and BP2 in a child evaluated for short stature and mild dyslexia. Unexpectedly, the mother carried the same deletion in the homozygous state and suffered from severe hearing loss. Detailed family history revealed consanguinity of the maternal grandparents. The 16p12.2 microdeletion is a rare condition and contains only three genes: METTL9, IGSF6 and OTOA of which the OTOA is considered responsible for DFNB22 hearing loss (MIM: 607039) under its homozygous condition. A number of OTOA mutations have been described, whereas very few cases of a 16p12.2 microdeletion similar to that observed in our family have been reported. In conclusion, we describe a rare 'distal 16p12.2microdeletion' widening the phenotypic spectrum associated with the recurrent 16p12.2 microdeletion and support the causative role of OTOA microdeletion in hearing impairment.
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Affiliation(s)
- Elisa Tassano
- Laboratorio di Citogenetica, Istituto Giannina Gaslini, 16147 Genova, Italy.
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14
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Kim BJ, Kim DK, Han JH, Oh J, Kim AR, Lee C, Kim NK, Park HR, Kim MY, Lee S, Lee S, Oh DY, Park WY, Park S, Choi BY. Clarification of glycosylphosphatidylinositol anchorage of OTOANCORIN and human OTOA variants associated with deafness. Hum Mutat 2019; 40:525-531. [PMID: 30740825 DOI: 10.1002/humu.23719] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/23/2019] [Accepted: 02/06/2019] [Indexed: 12/22/2022]
Abstract
Otoancorin (OTOA), encoded by OTOA, is required for the development of the tectorial membrane in the inner ear. Mutations in this gene cause nonsyndromic hearing loss (DFNB22). The molecular mechanisms underlying most DFNB22 remain poorly understood. Disruption of glycosylphosphatidylinositol (GPI) anchorage has been assumed to be the pathophysiology mandating experimental validation. From a Korean deaf family, we identified two trans OTOA variants (c.1320 + 5 G > C and p.Gln589ArgfsX55 [NM_144672.3]) . The pathogenic potential of c.1320 + 5 G > C was confirmed by a minigene splicing assay. To experimentally determine the GPI anchorage, wild-type (WT) and mutant OTOA harboring p.Gln589ArgfsX55 were expressed in HEK293T cells. The mutant OTOA with p.Gln589ArgfsX55 resulted in an uncontrolled release of OTOA into the medium in contrast with phosphatidylinositol-specific phospholipase C-induced controlled release of WT OTOA from the cell surface. Together, the results of this reverse translational study confirmed GPI-anchorage of OTOA and showed that downstream sequences from the 589th amino acid are critical for GPI-anchorage.
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Affiliation(s)
- Bong Jik Kim
- Department of Otolaryngology - Head and Neck Surgery, Chungnam National University College of Medicine, Daejeon, South Korea.,Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Dong-Kyu Kim
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, Utah
| | - Jin Hee Han
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Jayoung Oh
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Ah Reum Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Chung Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Nayoung Kd Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Hye-Rim Park
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Min Young Kim
- Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Sejoon Lee
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Seungmin Lee
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Doo Yi Oh
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea.,Department of Molecular Cell Biology, School of Medicine, Sungkyunkwan University, Seoul, South Korea
| | - Sungjin Park
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, Utah
| | - Byung Yoon Choi
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
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Mahfood M, Kamal Eddine Ahmad Mohamed W, Al Mutery A, Tlili A. Clinical Exome Sequencing Identifies a Frameshift Mutation Within the STRC Gene in a United Arab Emirates Family with Profound Nonsyndromic Hearing Loss. Genet Test Mol Biomarkers 2019; 23:204-208. [PMID: 30758234 DOI: 10.1089/gtmb.2018.0264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AIMS Autosomal recessive nonsyndromic hearing loss (ARNSHL) is the most common form of hereditary deafness. Despite its frequency, the diagnosis of this disorder continues to be a challenging task given its extreme genetic heterogeneity. The purpose of this study was to identify the causative mutation in a consanguineous United Arab Emirates (UAE) family with ARNSHL. MATERIALS AND METHODS Clinical exome sequencing (CES) followed by segregation analysis via Sanger sequencing was used to identify the causative mutation. In addition, 109 deaf individuals and 50 deafness-free controls from the UAE population were screened for the identified mutation. RESULTS AND DISCUSSION CES identified the STRC frameshift mutation c.4510del (p.Glu1504Argfs*32) as the causative mutation in this family. Moreover, segregation analysis confirmed the above finding. In addition, the absence of this variant in 109 unrelated deaf individuals and 50 healthy controls indicates that it is rare in the UAE population. CONCLUSION The present study represents the first STRC mutation reported in the UAE population. It also reinforces the power of next-generation sequencing in the diagnosis of heterogenous disorders such as nonsyndromic hearing loss.
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Affiliation(s)
- Mona Mahfood
- 1 Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | | | - Abdullah Al Mutery
- 1 Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates.,2 Molecular Genetics Research Laboratory, University of Sharjah, Sharjah, United Arab Emirates
| | - Abdelaziz Tlili
- 1 Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates.,2 Molecular Genetics Research Laboratory, University of Sharjah, Sharjah, United Arab Emirates.,3 Human Genetics and Stem Cell Laboratory, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates
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Dysfunction of GRAP, encoding the GRB2-related adaptor protein, is linked to sensorineural hearing loss. Proc Natl Acad Sci U S A 2019; 116:1347-1352. [PMID: 30610177 DOI: 10.1073/pnas.1810951116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have identified a GRAP variant (c.311A>T; p.Gln104Leu) cosegregating with autosomal recessive nonsyndromic deafness in two unrelated families. GRAP encodes a member of the highly conserved growth factor receptor-bound protein 2 (GRB2)/Sem-5/drk family of proteins, which are involved in Ras signaling; however, the function of the growth factor receptor-bound protein 2 (GRB2)-related adaptor protein (GRAP) in the auditory system is not known. Here, we show that, in mouse, Grap is expressed in the inner ear and the protein localizes to the neuronal fibers innervating cochlear and utricular auditory hair cells. Downstream of receptor kinase (drk), the Drosophila homolog of human GRAP, is expressed in Johnston's organ (JO), the fly hearing organ, and the loss of drk in JO causes scolopidium abnormalities. drk mutant flies present deficits in negative geotaxis behavior, which can be suppressed by human wild-type but not mutant GRAP. Furthermore, drk specifically colocalizes with synapsin at synapses, suggesting a potential role of such adaptor proteins in regulating actin cytoskeleton dynamics in the nervous system. Our findings establish a causative link between GRAP mutation and nonsyndromic deafness and suggest a function of GRAP/drk in hearing.
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Identification of candidate gene FAM183A and novel pathogenic variants in known genes: High genetic heterogeneity for autosomal recessive intellectual disability. PLoS One 2018; 13:e0208324. [PMID: 30500859 PMCID: PMC6267965 DOI: 10.1371/journal.pone.0208324] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 11/15/2018] [Indexed: 11/19/2022] Open
Abstract
The etiology of intellectual disability (ID) is heterogeneous including a variety of genetic and environmental causes. Historically, most research has not focused on autosomal recessive ID (ARID), which is a significant cause of ID, particularly in areas where parental consanguinity is common. Identification of genetic causes allows for precision diagnosis and improved genetic counseling. We performed whole exome sequencing to 21 Turkish families, seven multiplex and 14 simplex, with nonsyndromic ID. Based on the presence of multiple affected siblings born to unaffected parents and/or shared ancestry, we consider all families as ARID. We revealed the underlying causative variants in seven families in MCPH1 (c.427dupA, p.T143Nfs*5), WDR62 (c.3406C>T, p.R1136*), ASPM (c.5219_5225delGAGGATA, p.R1740Tfs*7), RARS (c.1588A>G, p.T530A), CC2D1A (c.811delG, p.A271Pfs*30), TUSC3 (c.793C>T, p.Q265*) and ZNF335 (c.808C>T, p.R270C and c.3715C>A, p.Q1239K) previously linked with ARID. Besides ARID genes, in one family, affected male siblings were hemizygous for PQBP1 (c.459_462delAGAG, p.R153Sfs*41) and in one family the proband was female and heterozygous for X-chromosomal SLC9A6 (c.1631+1G>A) variant. Each of these variants, except for those in MCPH1 and PQBP1, have not been previously published. Additionally in one family, two affected children were homozygous for the c.377G>A (p.W126*) variant in the FAM183A, a gene not previously associated with ARID. No causative variants were found in the remaining 11 families. A wide variety of variants explain half of families with ARID. FAM183A is a promising novel candidate gene for ARID.
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Vona B, Hofrichter MAH, Schröder J, Shehata-Dieler W, Nanda I, Haaf T. Hereditary hearing loss SNP-microarray pilot study. BMC Res Notes 2018; 11:391. [PMID: 29903040 PMCID: PMC6003021 DOI: 10.1186/s13104-018-3466-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/01/2018] [Indexed: 02/08/2023] Open
Abstract
Objectives Despite recent advancements in diagnostic tools, the genomic landscape of hereditary hearing loss remains largely uncharacterized. One strategy to understand genome-wide aberrations includes the analysis of copy number variation that can be mapped using SNP-microarray technology. A growing collection of literature has begun to uncover the importance of copy number variation in hereditary hearing loss. This pilot study underpins a larger effort that involves the stage-wise analysis of hearing loss patients, many of whom have advanced to high-throughput sequencing analysis. Data description Our data originate from the Infinium HumanOmni1-Quad v1.0 SNP-microarrays (Illumina) that provide useful markers for genome-wide association studies and copy number variation analysis. This dataset comprises a cohort of 108 individuals (99 with hearing loss, 9 normal hearing family members) for the purpose of understanding the genetic contribution of copy number variations to hereditary hearing loss. These anonymized SNP-microarray data have been uploaded to the NCBI Gene Expression Omnibus and are intended to benefit other investigators interested in aggregating platform-matched array patient datasets or as part of a supporting reference tool for other laboratories to better understand recurring copy number variations in other genetic disorders.
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Affiliation(s)
- Barbara Vona
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany.
| | | | - Jörg Schröder
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Wafaa Shehata-Dieler
- Department of ORL, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, Comprehensive Hearing Center, Würzburg, Germany
| | - Indrajit Nanda
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
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STRC Deletion is a Frequent Cause of Slight to Moderate Congenital Hearing Impairment in the Czech Republic. Otol Neurotol 2018; 38:e393-e400. [PMID: 28984810 DOI: 10.1097/mao.0000000000001571] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE This study aimed to clarify the molecular epidemiology of hearing loss by identifying the responsible genes in patients without GJB2 mutations. STUDY DESIGN Prospective genetic study. SETTING Tertiary referral hospital. PATIENTS Fifty one patients with bilateral sensorineural hearing loss, 20 men, and 31 women, mean age 24.9 years, range 3 to 64 years, from 49 families. GJB2 and deltaGJB6-D13S1830 mutations were excluded previously. INTERVENTION Diagnostic. Sixty-nine genes reported to be causative of hearing loss were analyzed. Sequence capture technology, next-generation sequencing, and multiplex ligation-dependent probe amplification (MLPA) were used. Coverage of STRC was screened in Integrative Genomics Viewer software. MAIN OUTCOME MEASURE Identification of causal pathogenic mutations in genes related to deafness. RESULTS Five families (10%) had recessive STRC deletions or mutations. Five unrelated patients (10%) had recessive mutations in TMPRSS3, USH2A, PCDH15, LOXHD1, and MYO15A. Three families (6%) had autosomal dominant mutations in MYO6A, KCNQ4, and SIX1. One family (2%) had an X-linked POU3F4 mutation. Thus, we identified the cause of hearing loss in 28% of the families studied. CONCLUSIONS Following GJB2, STRC was the second most frequently mutated gene in patients from the Czech Republic with hearing loss. To decrease the cost of testing, we recommend STRC deletion screening with MLPA before next-generation sequencing. The existence of a pseudogene and polymorphic STRC regions can lead to false-positive or false-negative results when copy number variation analysis is based on next-generation sequencing data.
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Fontana P, Morgutti M, Pecile V, Lenarduzzi S, Cappellani S, Falco M, Scarano F, Lonardo F. A novel OTOA mutation in an Italian family with hearing loss. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Tlili A, Fahd Al Mutery A, Mahfood M, Kamal Eddine Ahmad Mohamed W, Bajou K. Identification of a novel frameshift mutation in the ILDR1 gene in a UAE family, mutations review and phenotype genotype correlation. PLoS One 2017; 12:e0185281. [PMID: 28945813 PMCID: PMC5612695 DOI: 10.1371/journal.pone.0185281] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/08/2017] [Indexed: 12/17/2022] Open
Abstract
Autosomal recessive non-syndromic hearing loss is one of the most common monogenic diseases. It is characterized by high allelic and locus heterogeneities that make a precise diagnosis difficult. In this study, whole-exome sequencing was performed for an affected patient allowing us to identify a new frameshift mutation (c.804delG) in the Immunoglobulin-Like Domain containing Receptor-1 (ILDR1) gene. Direct Sanger sequencing and segregation analysis were performed for the family pedigree. The mutation was homozygous in all affected siblings but heterozygous in the normal consanguineous parents. The present study reports a first ILDR1 gene mutation in the UAE population and confirms that the whole-exome sequencing approach is a robust tool for the diagnosis of monogenic diseases with high levels of allelic and locus heterogeneity. In addition, by reviewing all reported ILDR1 mutations, we attempt to establish a genotype phenotype correlation to explain the phenotypic variability observed at low frequencies.
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Affiliation(s)
- Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Human Genetics and Stem cell laboratory, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates
- * E-mail:
| | - Abdullah Fahd Al Mutery
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Mona Mahfood
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | | | - Khalid Bajou
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Human Genetics and Stem cell laboratory, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates
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22
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Yao R, Zhang C, Yu T, Li N, Hu X, Wang X, Wang J, Shen Y. Evaluation of three read-depth based CNV detection tools using whole-exome sequencing data. Mol Cytogenet 2017; 10:30. [PMID: 28852425 PMCID: PMC5569469 DOI: 10.1186/s13039-017-0333-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/15/2017] [Indexed: 12/16/2022] Open
Abstract
Background Whole exome sequencing (WES) has been widely accepted as a robust and cost-effective approach for clinical genetic testing of small sequence variants. Detection of copy number variants (CNV) within WES data have become possible through the development of various algorithms and software programs that utilize read-depth as the main information. The aim of this study was to evaluate three commonly used, WES read-depth based CNV detection programs using high-resolution chromosomal microarray analysis (CMA) as a standard. Methods Paired CMA and WES data were acquired for 45 samples. A total of 219 CNVs (size ranged from 2.3 kb – 35 mb) identified on three CMA platforms (Affymetrix, Agilent and Illumina) were used as standards. CNVs were called from WES data using XHMM, CoNIFER, and CNVnator with modified settings. Results All three software packages detected an elevated proportion of small variants (< 20 kb) compared to CMA. XHMM and CoNIFER had poor detection sensitivity (22.2 and 14.6%), which correlated with the number of capturing probes involved. CNVnator detected most variants and had better sensitivity (87.7%); however, suffered from an overwhelming detection of small CNVs below 20 kb, which required further confirmation. Size estimation of variants was exaggerated by CNVnator and understated by XHMM and CoNIFER. Conclusion Low concordances of CNV, detected by three different read-depth based programs, indicate the immature status of WES-based CNV detection. Low sensitivity and uncertain specificity of WES-based CNV detection in comparison with CMA based CNV detection suggests that CMA will continue to play an important role in detecting clinical grade CNV in the NGS era, which is largely based on WES. Electronic supplementary material The online version of this article (doi:10.1186/s13039-017-0333-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ruen Yao
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127 China
| | - Cheng Zhang
- Boston Children's Hospital, Boston, MA 02115 USA
| | - Tingting Yu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127 China
| | - Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127 China
| | - Xuyun Hu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127 China.,Boston Children's Hospital, Boston, MA 02115 USA
| | - Xiumin Wang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127 China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127 China
| | - Yiping Shen
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127 China.,Boston Children's Hospital, Boston, MA 02115 USA
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The diagnostic yield of whole-exome sequencing targeting a gene panel for hearing impairment in The Netherlands. Eur J Hum Genet 2016; 25:308-314. [PMID: 28000701 DOI: 10.1038/ejhg.2016.182] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 10/19/2016] [Accepted: 11/22/2016] [Indexed: 12/12/2022] Open
Abstract
Hearing impairment (HI) is genetically heterogeneous which hampers genetic counseling and molecular diagnosis. Testing of several single HI-related genes is laborious and expensive. In this study, we evaluate the diagnostic utility of whole-exome sequencing (WES) targeting a panel of HI-related genes. Two hundred index patients, mostly of Dutch origin, with presumed hereditary HI underwent WES followed by targeted analysis of an HI gene panel of 120 genes. We found causative variants underlying the HI in 67 of 200 patients (33.5%). Eight of these patients have a large homozygous deletion involving STRC, OTOA or USH2A, which could only be identified by copy number variation detection. Variants of uncertain significance were found in 10 patients (5.0%). In the remaining 123 cases, no potentially causative variants were detected (61.5%). In our patient cohort, causative variants in GJB2, USH2A, MYO15A and STRC, and in MYO6 were the leading causes for autosomal recessive and dominant HI, respectively. Segregation analysis and functional analyses of variants of uncertain significance will probably further increase the diagnostic yield of WES.
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Variations in Multiple Syndromic Deafness Genes Mimic Non-syndromic Hearing Loss. Sci Rep 2016; 6:31622. [PMID: 27562378 PMCID: PMC4999867 DOI: 10.1038/srep31622] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/20/2016] [Indexed: 12/18/2022] Open
Abstract
The genetics of both syndromic (SHL) and non-syndromic hearing loss (NSHL) is characterized by a high degree of genetic heterogeneity. We analyzed whole exome sequencing data of 102 unrelated probands with apparently NSHL without a causative variant in known NSHL genes. We detected five causative variants in different SHL genes (SOX10, MITF, PTPN11, CHD7, and KMT2D) in five (4.9%) probands. Clinical re-evaluation of these probands shows that some of them have subtle syndromic findings, while none of them meets clinical criteria for the diagnosis of the associated syndrome (Waardenburg (SOX10 and MITF), Kallmann (CHD7 and SOX10), Noonan/LEOPARD (PTPN11), CHARGE (CHD7), or Kabuki (KMT2D). This study demonstrates that individuals who are evaluated for NSHL can have pathogenic variants in SHL genes that are not usually considered for etiologic studies.
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25
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Rosenberg C, Freitas ÉL, Uehara DT, Auricchio MTBM, Costa SS, Oiticica J, Silva AG, Krepischi AC, Mingroni-Netto RC. Genomic copy number alterations in non-syndromic hearing loss. Clin Genet 2015; 89:473-477. [DOI: 10.1111/cge.12683] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 10/06/2015] [Accepted: 10/06/2015] [Indexed: 11/30/2022]
Affiliation(s)
- C. Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - É. L. Freitas
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - D. T. Uehara
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - M. T. B. M. Auricchio
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - S. S. Costa
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - J. Oiticica
- Department of Otorhinolaryngology, Medical School; University of São Paulo; São Paulo Brazil
| | - A. G. Silva
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - A. C. Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - R. C. Mingroni-Netto
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
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26
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Uehara DT, Freitas ÉL, Alves LU, Mazzeu JF, Auricchio MT, Tabith A, Monteiro ML, Rosenberg C, Mingroni-Netto RC. A novel KCNQ4 mutation and a private IMMP2L-DOCK4 duplication segregating with nonsyndromic hearing loss in a Brazilian family. Hum Genome Var 2015; 2:15038. [PMID: 27081546 PMCID: PMC4785540 DOI: 10.1038/hgv.2015.38] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 08/17/2015] [Accepted: 08/24/2015] [Indexed: 02/07/2023] Open
Abstract
Here we describe a novel missense variant in the KCNQ4 gene and a private duplication at 7q31.1 partially involving two genes (IMMP2L and DOCK4). Both mutations segregated with nonsyndromic hearing loss in a family with three affected individuals. Initially, we identified the duplication in a screening of 132 unrelated cases of hearing loss with a multiplex ligation-dependent probe amplification panel of genes that are candidates to have a role in hearing, including IMMP2L. Mapping of the duplication by array-CGH revealed that the duplication also encompassed the 3′-end of DOCK4. Subsequently, whole-exome sequencing identified the breakpoint of the rearrangement, thereby confirming the existence of a fusion IMMP2L-DOCK4 gene. Transcription products of the fusion gene were identified, indicating that they escaped nonsense-mediated messenger RNA decay. A missense substitution (c.701A>T) in KCNQ4 (a gene at the DFNA2A locus) was also identified by whole-exome sequencing. Because the substitution is predicted to be probably damaging and KCNQ4 has been implicated in hearing loss, this mutation might explain the deafness in the affected individuals, although a hypothetical effect of the product of the fusion gene on hearing cannot be completely ruled out.
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Affiliation(s)
- Daniela T Uehara
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo , São Paulo, Brazil
| | - Érika L Freitas
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo , São Paulo, Brazil
| | - Leandro U Alves
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo , São Paulo, Brazil
| | | | - Maria Tbm Auricchio
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo , São Paulo, Brazil
| | - Alfredo Tabith
- DERDIC, Pontifical Catholic University of São Paulo , São Paulo, Brazil
| | - Mário Lr Monteiro
- Department of Ophthalmology and Otorhinolaryngology, Faculty of Medicine, University of São Paulo , São Paulo, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo , São Paulo, Brazil
| | - Regina C Mingroni-Netto
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo , São Paulo, Brazil
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Basit S, Malibari OI, Al-Balawi AM, Afzal S, Eldardear AEM, Ramzan K. Xq21.31-q21.32 duplication underlies intellectual disability in a large family with five affected males. Am J Med Genet A 2015; 170A:87-93. [DOI: 10.1002/ajmg.a.37372] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 08/31/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Sulman Basit
- Center for Genetics and Inherited Diseases; Taibah University Almadinah Almunawwarah; Saudi Arabia
| | - Omhani I. Malibari
- Department of Metabolic Diseases; King Abdulla Medical City-Madinah Maternity and Children Hospital; Almadinah Almunawwarah Saudi Arabia
| | - Alia M. Al-Balawi
- Center for Genetics and Inherited Diseases; Taibah University Almadinah Almunawwarah; Saudi Arabia
| | - Sibtain Afzal
- Prince Naif Centre for Immunology Research; College of Medicine; King Saud University; Riyadh Saudi Arabia
| | | | - Khushnooda Ramzan
- Department of Genetics; Research Centre; King Faisal Specialist Hospital and Research Centre; Riyadh Saudi Arabia
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Bademci G, Foster J, Mahdieh N, Bonyadi M, Duman D, Cengiz FB, Menendez I, Diaz-Horta O, Shirkavand A, Zeinali S, Subasioglu A, Tokgoz-Yilmaz S, Huesca-Hernandez F, de la Luz Arenas-Sordo M, Dominguez-Aburto J, Hernandez-Zamora E, Montenegro P, Paredes R, Moreta G, Vinueza R, Villegas F, Mendoza-Benitez S, Guo S, Bozan N, Tos T, Incesulu A, Sennaroglu G, Blanton SH, Ozturkmen-Akay H, Yildirim-Baylan M, Tekin M. Comprehensive analysis via exome sequencing uncovers genetic etiology in autosomal recessive nonsyndromic deafness in a large multiethnic cohort. Genet Med 2015. [PMID: 26226137 PMCID: PMC4733433 DOI: 10.1038/gim.2015.89] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Purpose Autosomal recessive non-syndromic 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 (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.
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Affiliation(s)
- Guney Bademci
- 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
| | - Joseph Foster
- 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
| | - Nejat Mahdieh
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mortaza Bonyadi
- Faculty of Natural Sciences, Center of Excellence for Biodiversity, University of Tabriz, Tabriz, Iran
| | - Duygu Duman
- Division of Genetics, Department of Pediatrics, Ankara University School of Medicine, Ankara, Turkey
| | - F Basak Cengiz
- Division of Genetics, Department of Pediatrics, Ankara University School of Medicine, Ankara, Turkey
| | - Ibis Menendez
- 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
| | - Oscar Diaz-Horta
- 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
| | | | - Sirous Zeinali
- Kawsar's Human Genetic Research Center, Tehran, Iran.,Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Asli Subasioglu
- Department of Medical Genetics, Izmir Katip Celebi University, Ataturk Training and Research Hospital, Izmir, Turkey
| | - Suna Tokgoz-Yilmaz
- Department of Audiology, Hacettepe University Health Sciences Faculty, Ankara, Turkey
| | | | | | | | | | | | | | | | | | | | | | - Shengru Guo
- 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
| | - Nazim Bozan
- Department of Otolaryngology, Faculty of Medicine, Yuzuncu Yıl University, Van, Turkey
| | - Tulay Tos
- Department of Medical Genetics, Dr. Sami Ulus Research and Training Hospital of Women's and Children's Health and Diseases, Ankara, Turkey
| | - Armagan Incesulu
- Department of Otolaryngology, Head and Neck Surgery, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Gonca Sennaroglu
- Department of Audiology, Hacettepe University Health Sciences Faculty, Ankara, Turkey
| | - Susan H Blanton
- 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
| | - Hatice Ozturkmen-Akay
- Department of Radiology, Istanbul Zeynep Kamil Maternity and Children Training and Research Hospital, Istanbul, Turkey
| | | | - Mustafa Tekin
- 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
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Ji H, Lu J, Wang J, Li H, Lin X. Combined examination of sequence and copy number variations in human deafness genes improves diagnosis for cases of genetic deafness. BMC EAR, NOSE, AND THROAT DISORDERS 2014; 14:9. [PMID: 25342930 PMCID: PMC4194081 DOI: 10.1186/1472-6815-14-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 08/26/2014] [Indexed: 11/11/2022]
Abstract
Background Copy number variations (CNVs) are the major type of structural variation in the human genome, and are more common than DNA sequence variations in populations. CNVs are important factors for human genetic and phenotypic diversity. Many CNVs have been associated with either resistance to diseases or identified as the cause of diseases. Currently little is known about the role of CNVs in causing deafness. CNVs are currently not analyzed by conventional genetic analysis methods to study deafness. Here we detected both DNA sequence variations and CNVs affecting 80 genes known to be required for normal hearing. Methods Coding regions of the deafness genes were captured by a hybridization-based method and processed through the standard next-generation sequencing (NGS) protocol using the Illumina platform. Samples hybridized together in the same reaction were analyzed to obtain CNVs. A read depth based method was used to measure CNVs at the resolution of a single exon. Results were validated by the quantitative PCR (qPCR) based method. Results Among 79 sporadic cases clinically diagnosed with sensorineural hearing loss, we identified previously-reported disease-causing sequence mutations in 16 cases. In addition, we identified a total of 97 CNVs (72 CNV gains and 25 CNV losses) in 27 deafness genes. The CNVs included homozygous deletions which may directly give rise to deleterious effects on protein functions known to be essential for hearing, as well as heterozygous deletions and CNV gains compounded with sequence mutations in deafness genes that could potentially harm gene functions. Conclusions We studied how CNVs in known deafness genes may result in deafness. Data provided here served as a basis to explain how CNVs disrupt normal functions of deafness genes. These results may significantly expand our understanding about how various types of genetic mutations cause deafness in humans.
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Affiliation(s)
- Haiting Ji
- Department of Otolaryngology, Eye & ENT Hospital, Fudan University, #83 Fenyang Road, Shanghai 200031, P.R China
| | - Jingqiao Lu
- Department of Otolaryngology, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322-3030, USA
| | - Jianjun Wang
- Department of Otolaryngology, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322-3030, USA
| | - Huawei Li
- Department of Otolaryngology, Eye & ENT Hospital, Fudan University, #83 Fenyang Road, Shanghai 200031, P.R China
| | - Xi Lin
- Department of Otolaryngology, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322-3030, USA
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