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Wener ER, McLennan JD, Papsin BC, Cushing SL, Stavropoulos DJ, Mendoza-Londono R, Quercia N, Gordon KA. Variants in Genes Associated with Hearing Loss in Children: Prevalence in a Large Canadian Cohort. Laryngoscope 2024; 134:3832-3838. [PMID: 38426810 DOI: 10.1002/lary.31373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/17/2024] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
OBJECTIVE The objective of this study was to assess the prevalence of genetic variants associated with hearing loss in a large cohort of children in Canada using high throughput next generation sequencing (NGS). METHODS A total of 485 children with hearing loss underwent NGS testing with an 80 gene panel of syndromic and non-syndromic variants known to be associated with hearing loss. Genetic variants were classified as pathogenic, likely pathogenic, likely benign, benign, or variants of uncertain significance (VUS), according to the American College of Medical Genetics and Genomics guidelines. RESULTS Across the 80 genes tested, 923 variants, predominantly in 28 genes, were identified in 324 children. Pathogenic variants occurred in 19/80 (23.8%) of the hearing loss related genes tested and confirmed the etiology of hearing loss in 73/485 (15.1%) of children. GJB2 was the most prevalent gene, affecting 28/73 (38.4%) children with confirmed genetic hearing loss in our cohort. Most identified variants (748/923, 81.0%, in 76/80 genes) were of uncertain significance. CONCLUSION Genetic testing using NGS identified the etiology in approximately 15% of childhood hearing loss in a Canadian cohort which is lower than what is typically reported. GJB2 was the most common genetic cause of hearing loss. VUS are commonly identified, presenting clinical challenges for counseling. LEVEL OF EVIDENCE 4 Laryngoscope, 134:3832-3838, 2024.
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Affiliation(s)
- Emily R Wener
- Archie's Cochlear Implant Laboratory, Neuroscience & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jacob D McLennan
- Archie's Cochlear Implant Laboratory, Neuroscience & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Blake C Papsin
- Archie's Cochlear Implant Laboratory, Neuroscience & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Otolaryngology-Head and Neck Surgery, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sharon L Cushing
- Archie's Cochlear Implant Laboratory, Neuroscience & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Otolaryngology-Head and Neck Surgery, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Dimitri James Stavropoulos
- Genome Diagnostics Paediatric Laboratory Medicine, Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Roberto Mendoza-Londono
- Genome Diagnostics Paediatric Laboratory Medicine, Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nada Quercia
- Division of Clinical & Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Karen A Gordon
- Archie's Cochlear Implant Laboratory, Neuroscience & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Otolaryngology-Head and Neck Surgery, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada
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Mkaouar R, Riahi Z, Marrakchi J, Mezzi N, Romdhane L, Boujemaa M, Dallali H, Sayeb M, Lahbib S, Jaouadi H, Boudabbous H, Zekri L, Chargui M, Messaoud O, Elyounsi M, Kraoua I, Zaouak A, Turki I, Mokni M, Boucher S, Petit C, Giraudet F, Mbarek C, Besbes G, Halayem S, Zainine R, Turki H, Tounsi A, Bonnet C, Mrad R, Abdelhak S, Trabelsi M, Charfeddine C. Current phenotypic and genetic spectrum of syndromic deafness in Tunisia: paving the way for precision auditory health. Front Genet 2024; 15:1384094. [PMID: 38711914 PMCID: PMC11072975 DOI: 10.3389/fgene.2024.1384094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/15/2024] [Indexed: 05/08/2024] Open
Abstract
Hearing impairment (HI) is a prevalent neurosensory condition globally, impacting 5% of the population, with over 50% of congenital cases attributed to genetic etiologies. In Tunisia, HI underdiagnosis prevails, primarily due to limited access to comprehensive clinical tools, particularly for syndromic deafness (SD), characterized by clinical and genetic heterogeneity. This study aimed to uncover the SD spectrum through a 14-year investigation of a Tunisian cohort encompassing over 700 patients from four referral centers (2007-2021). Employing Sanger sequencing, Targeted Panel Gene Sequencing, and Whole Exome Sequencing, genetic analysis in 30 SD patients identified diagnoses such as Usher syndrome, Waardenburg syndrome, cranio-facial-hand-deafness syndrome, and H syndrome. This latter is a rare genodermatosis characterized by HI, hyperpigmentation, hypertrichosis, and systemic manifestations. A meta-analysis integrating our findings with existing data revealed that nearly 50% of Tunisian SD cases corresponded to rare inherited metabolic disorders. Distinguishing between non-syndromic and syndromic HI poses a challenge, where the age of onset and progression of features significantly impact accurate diagnoses. Despite advancements in local genetic characterization capabilities, certain ultra-rare forms of SD remain underdiagnosed. This research contributes critical insights to inform molecular diagnosis approaches for SD in Tunisia and the broader North-African region, thereby facilitating informed decision-making in clinical practice.
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Affiliation(s)
- Rahma Mkaouar
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Zied Riahi
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Jihene Marrakchi
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Otorhinolaryngology, District Hospital of Menzel Bourguiba, Bizerte, Tunisia
| | - Nessrine Mezzi
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Biology, Faculty of Sciences of Bizerte, Université Tunis Carthage, Tunis, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Biology, Faculty of Sciences of Bizerte, Université Tunis Carthage, Tunis, Tunisia
| | - Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Genetic Typing Service, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Marwa Sayeb
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Saida Lahbib
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hager Jaouadi
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Marseille Medical Genetics (MMG) U1251, Aix Marseille Université, INSERM, Marseille, France
| | - Hela Boudabbous
- Department of Pediatrics, La Rabta Hospital, Tunis, Tunisia
- Laboratory of Hereditary Diseases of the Metabolism Investigation and Patients Management, Faculty of Medicine in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Epidemiology and Public Health, Directorate General of Military Health, Faculty of Medicine in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Lotfi Zekri
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- ICHARA Association (International Research Institute on Sign Language), Tunis, Tunisia
| | - Mariem Chargui
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Olfa Messaoud
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Meriem Elyounsi
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital in Tunis, Tunis, Tunisia
- LR99ES10 Laboratory of Human Genetics, Faculty of Medicine in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Ichraf Kraoua
- Child and Adolescent Neurology Department of Neurology, National Institute of Neurology, Tunis, Tunisia
- LR18SP04 Department of Child Neurology, National Institute Mongi Ben Hmida of Neurology in Tunis. University of Tunis El Manar, Tunis, Tunisia
| | - Anissa Zaouak
- Department of Dermatology, Habib Thameur Hospital, Research Unit Genodermatoses and Cancers LR12SP03, Tunis, Tunisia
| | - Ilhem Turki
- Child and Adolescent Neurology Department of Neurology, National Institute of Neurology, Tunis, Tunisia
- LR18SP04 Department of Child Neurology, National Institute Mongi Ben Hmida of Neurology in Tunis. University of Tunis El Manar, Tunis, Tunisia
| | - Mourad Mokni
- Service de dermatologie, Hôpital La Rabta, Unité de recherche UR 12SP07, Hôpital La Rabta, Tunis, Tunisia
| | - Sophie Boucher
- Service d’ORL et chirurgie cervico-faciale, CHU d’Angers, Angers, France
- Equipe Mitolab, Institut Mitovasc, CNRS UMR6015, UMR Inserm 1083, Université d’Angers, Angers, France
| | - Christine Petit
- Institut Pasteur, Université Paris Cité, Inserm UA06, Institut de l’Audition, Paris, France
- Collège de France, Paris, France
| | - Fabrice Giraudet
- Unité Mixte de Recherche (UMR) 1107, INSERM, Clermont-Ferrand, France
- Centre Auditif SoluSons, Clermont-Ferrand, France
| | - Chiraz Mbarek
- ENT Department, Habib Thameur Hospital, Tunis, Tunisia
| | - Ghazi Besbes
- Department of Otorhinolaryngology and Maxillofacial Surgery - La Rabta Hospital in Tunis, Tunis, Tunisia
| | - Soumeyya Halayem
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Service de pédopsychiatrie, Hôpital Razi, Faculté de Médecine de Tunis, Université Tunis el Manar, Tunis, Tunisia
| | - Rim Zainine
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Otorhinolaryngology and Maxillofacial Surgery - La Rabta Hospital in Tunis, Tunis, Tunisia
| | - Hamida Turki
- Dermatology Department Hedi Chaker University Hospital, Sfax University Sfax Tunisia, Tunis, Tunisia
| | | | - Crystel Bonnet
- Institut Pasteur, Université Paris Cité, Inserm UA06, Institut de l’Audition, Paris, France
| | - Ridha Mrad
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital in Tunis, Tunis, Tunisia
- LR99ES10 Laboratory of Human Genetics, Faculty of Medicine in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Mediha Trabelsi
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital in Tunis, Tunis, Tunisia
- LR99ES10 Laboratory of Human Genetics, Faculty of Medicine in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Cherine Charfeddine
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
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Türk E, Ayaz A, Yüksek A, Süzek BE. DEVOUR: Deleterious Variants on Uncovered Regions in Whole-Exome Sequencing. PeerJ 2023; 11:e16026. [PMID: 37727687 PMCID: PMC10506587 DOI: 10.7717/peerj.16026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/13/2023] [Indexed: 09/21/2023] Open
Abstract
The discovery of low-coverage (i.e. uncovered) regions containing clinically significant variants, especially when they are related to the patient's clinical phenotype, is critical for whole-exome sequencing (WES) based clinical diagnosis. Therefore, it is essential to develop tools to identify the existence of clinically important variants in low-coverage regions. Here, we introduce a desktop application, namely DEVOUR (DEleterious Variants On Uncovered Regions), that analyzes read alignments for WES experiments, identifies genomic regions with no or low-coverage (read depth < 5) and then annotates known variants in the low-coverage regions using clinical variant annotation databases. As a proof of concept, DEVOUR was used to analyze a total of 28 samples from a publicly available Hirschsprung disease-related WES project (NCBI Bioproject: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB19327), revealing the potential existence of 98 disease-associated variants in low-coverage regions. DEVOUR is available from https://github.com/projectDevour/DEVOUR under the MIT license.
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Affiliation(s)
- Erdem Türk
- Department of Computer Engineering, Muğla Sıtkı Koçman University, Muğla, Turkey
- Bioinformatics Graduate Program, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Akif Ayaz
- Department of Medical Genetics, School of Medicine, İstanbul Medipol University, İstanbul, Turkey
| | - Ayhan Yüksek
- Department of Computer Engineering, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Barış E. Süzek
- Department of Computer Engineering, Muğla Sıtkı Koçman University, Muğla, Turkey
- Bioinformatics Graduate Program, Muğla Sıtkı Koçman University, Muğla, Turkey
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Perry J, Redfield S, Oza A, Rouse S, Stewart C, Khela H, Srinivasan T, Albano V, Shearer E, Kenna M. Exome Sequencing Expands the Genetic Diagnostic Spectrum for Pediatric Hearing Loss. Laryngoscope 2023; 133:2417-2424. [PMID: 36515421 DOI: 10.1002/lary.30507] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/29/2022] [Accepted: 11/07/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Genetic testing is the standard-of-care for diagnostic evaluation of bilateral, symmetric, sensorineural hearing loss (HL). We sought to determine the efficacy of a comprehensive genetic testing method, exome sequencing (ES), in a heterogeneous pediatric patient population with bilateral symmetric, bilateral asymmetric, and unilateral HL. METHODS Trio-based ES was performed for pediatric patients with confirmed HL including those with symmetric, asymmetric, and unilateral HL. RESULTS ES was completed for 218 probands. A genetic cause was identified for 31.2% of probands (n = 68). The diagnostic rate was 40.7% for bilateral HL, 23.1% for asymmetric HL, and 18.3% for unilateral HL, with syndromic diagnoses made in 20.8%, 33.3%, and 54.5% of cases in each group, respectively. Secondary or incidental findings were identified in 10 families (5.52%). CONCLUSION ES is an effective method for genetic diagnosis for HL including phenotypically diverse patients and allows the identification of secondary findings, discovery of deafness-causing genes, and the potential for efficient data re-analysis. LEVEL OF EVIDENCE 4 Laryngoscope, 133:2417-2424, 2023.
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Affiliation(s)
- Julia Perry
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Shelby Redfield
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Andrea Oza
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, USA
- Clinical Genomics, Invitae, San Francisco, California, USA
| | - Stephanie Rouse
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Candace Stewart
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Harmon Khela
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Tarika Srinivasan
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts, USA
| | - Victoria Albano
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Eliot Shearer
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts, USA
| | - Margaret Kenna
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts, USA
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Riza AL, Alkhzouz C, Farcaș M, Pîrvu A, Miclea D, Mihuț G, Pleșea RM, Ștefan D, Drodar M, Lazăr C, Study OBOTHINT, Study OBOTFUSE, Ioana M, Popp R. Non-Syndromic Hearing Loss in a Romanian Population: Carrier Status and Frequent Variants in the GJB2 Gene. Genes (Basel) 2022; 14:69. [PMID: 36672810 PMCID: PMC9858611 DOI: 10.3390/genes14010069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
The genetic causes of autosomal recessive nonsyndromic hearing loss (ARNSHL) are heterogeneous and highly ethnic-specific. We describe GJB2 (connexin 26) variants and carrier frequencies as part of our study and summarize previously reported ones for the Romanian population. In total, 284 unrelated children with bilateral congenital NSHL were enrolled between 2009 and 2018 in northwestern Romania. A tiered diagnostic approach was used: all subjects were tested for c.35delG, c.71G>A and deletions in GJB6 (connexin 30) using PCR-based methods. Furthermore, 124 cases undiagnosed at this stage were analyzed by multiplex-ligation-dependent probe amplifications (MLPA), probe mix P163, and sequencing of GJB2 exon 2. Targeted allele-specific PCR/restriction fragment length polymorphism (RFLP) established definite ethio-pathogenical diagnosis for 72/284 (25.35%) of the cohort. Out of the 124 further analyzed, in 12 cases (9.67%), we found compound heterozygous point mutations in GJB2. We identified one case of deletion of exon 1 of the WFS1 (wolframin) gene. Carrier status evaluation used Illumina Infinium Global Screening Array (GSA) genotyping: the HINT cohort-416 individuals in northwest Romania, and the FUSE cohort-472 individuals in southwest Romania. GSA variants yielded a cumulated risk allele presence of 0.0284. A tiered diagnostic approach may be efficient in diagnosing ARNSHL. The summarized contributions to Romanian descriptive epidemiology of ARNSHL shows that pathogenic variants in the GJB2 gene are frequent among NSHL cases and have high carrier rates, especially for c.35delG and c.71G>A. These findings may serve in health strategy development.
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Affiliation(s)
- Anca-Lelia Riza
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Camelia Alkhzouz
- First Pediatric Department, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- Clinical Emergency Hospital for Children, 400394 Cluj-Napoca, Romania
| | - Marius Farcaș
- Molecular Sciences Department, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Andrei Pîrvu
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Diana Miclea
- First Pediatric Department, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- Clinical Emergency Hospital for Children, 400394 Cluj-Napoca, Romania
| | - Gheorghe Mihuț
- ENT Department, Clinical Emergency Hospital for Children, 400394 Cluj-Napoca, Romania
| | - Răzvan-Mihail Pleșea
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Delia Ștefan
- Molecular Sciences Department, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Mihaela Drodar
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Călin Lazăr
- First Pediatric Department, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- Clinical Emergency Hospital for Children, 400394 Cluj-Napoca, Romania
| | | | | | - Mihai Ioana
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Radu Popp
- Molecular Sciences Department, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
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Zeng B, Xu H, Yu Y, Li S, Tian Y, Li T, Yang Z, Wang H, Wang G, Chang M, Tang W. Increased diagnostic yield in a cohort of hearing loss families using a comprehensive stepwise strategy of molecular testing. Front Genet 2022; 13:1057293. [PMID: 36568381 PMCID: PMC9768221 DOI: 10.3389/fgene.2022.1057293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Hearing loss is one of the most common sensory disorders in humans. This study proposes a stepwise strategy of deafness gene detection using multiplex PCR combined with high-throughput sequencing, Sanger sequencing, multiplex ligation-dependent probe amplification (MLPA), and whole-exome sequencing (WES) to explore its application in molecular diagnosis of hearing loss families. A total of 152 families with hearing loss were included in this study, the highest overall diagnosis rate was 73% (111/152). The diagnosis rate of multiplex PCR combined with high-throughput sequencing was 52.6% (80/152). One families was diagnosed by Sanger sequencing of GJB2 exon 1. Two families were diagnosed by MLPA analysis of the STRC gene. The diagnosis rate with additional contribution from WES was 18.4% (28/152). We identified 21 novel variants from 15 deafness genes by WES. Combining WES and deep clinical phenotyping, we diagnosed 11 patients with syndromic hearing loss (SHL). This study demonstrated improved diagnostic yield in a cohort of hearing loss families and confirmed the advantages of a stepwise strategy in the molecular diagnosis of hearing loss.
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Affiliation(s)
- Beiping Zeng
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China,National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Henan Institute of Reproduction Health Science and Technology, Zhengzhou, China
| | - Hongen Xu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China,The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanan Yu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Siqi Li
- Department of Physiology and Neurobiology, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Yongan Tian
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Tiandong Li
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Zengguang Yang
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Haili Wang
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Henan Institute of Reproduction Health Science and Technology, Zhengzhou, China
| | - Guangke Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Mingxiu Chang
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Henan Institute of Reproduction Health Science and Technology, Zhengzhou, China,*Correspondence: Mingxiu Chang, ; Wenxue Tang,
| | - Wenxue Tang
- The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China,*Correspondence: Mingxiu Chang, ; Wenxue Tang,
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Zhu Y, Hu L, Yang L, Wang L, Lu Y, Dong X, Xiao T, Xu Z, Wu B, Zhou W. Association Between Expanded Genomic Sequencing Combined With Hearing Screening and Detection of Hearing Loss Among Newborns in a Neonatal Intensive Care Unit. JAMA Netw Open 2022; 5:e2220986. [PMID: 35816303 PMCID: PMC9274323 DOI: 10.1001/jamanetworkopen.2022.20986] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
IMPORTANCE Hearing loss is a global social burden. Early identification of hearing loss missed by newborn hearing screening tests in the neonatal intensive care unit is crucial. OBJECTIVE To assess the association between expanded genomic sequencing combined with hearing screening and detection of hearing loss as well as improvement in the neonatal intensive care unit. DESIGN, SETTING, AND PARTICIPANTS This cohort study was performed between August 8, 2016, and December 31, 2020, among 8078 newborns admitted to the neonatal intensive care unit of the Children's Hospital of Fudan University in Shanghai, China. Follow-up for hearing status was performed via telephone interviews between September 1 and November 30, 2021. EXPOSURES A hearing screening test and the expanded genomic sequencing targeting 2742 genes were administered to each patient. Those who failed the hearing screening test or had positive genetic findings were referred for diagnostic audiometry at a median of 3 months of age. MAIN OUTCOMES AND MEASURES The primary outcome was hearing loss missed by hearing screening test. Secondary outcomes were genetic findings and benefits associated with the expanded genomic sequencing for clinical management of patients in the neonatal intensive care unit. RESULTS Of 8078 patients (4666 boys [57.8%]; median age, 6.3 days [IQR, 3.0-12.0 days]), 52 of 240 (21.7%) received a diagnosis of hearing loss. Expanded genomic sequencing combined with hearing screening was associated with a 15.6% increase (7 of 45 patients) in cases of diagnosed hearing loss that were missed by hearing screening. Of the 52 patients with hearing loss, genetic factors were identified for 39 patients (75.0%); GJB2 and SLC26A4 were the most common genes identified. Patients with genetic findings experienced a more severe degree of hearing loss than those without genetic findings (21 profound, 4 severe, 7 moderate, and 7 mild vs 2 severe, 4 moderate, and 7 mild; P = .005), with more bilateral hearing loss (39 of 39 [100%] vs 9 of 13 [69.2%]; P = .003). Clinical management strategies were changed for patients who underwent genomic sequencing combined with hearing screening. CONCLUSIONS AND RELEVANCE This study suggests that expanded genomic sequencing combined with hearing screening may be effective at detecting hearing loss among patients in the neonatal intensive care unit.
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Affiliation(s)
- Yunqian Zhu
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Liyuan Hu
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Lin Yang
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Laishuan Wang
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Xinran Dong
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Tiantian Xiao
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Zhengmin Xu
- Department of Otolaryngology–Head and Neck Surgery, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Key Laboratory of Neonatal Diseases, Ministry of Health, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Wenhao Zhou
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Key Laboratory of Neonatal Diseases, Ministry of Health, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
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8
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Xiang J, Zhang H, Sun X, Zhang J, Xu Z, Sun J, Peng Z. Utility of Whole Genome Sequencing for Population Screening of Deafness-Related Genetic Variants and Cytomegalovirus Infection in Newborns. Front Genet 2022; 13:883617. [PMID: 35571039 PMCID: PMC9099144 DOI: 10.3389/fgene.2022.883617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Hearing loss affects approximately two out of every 1,000 newborns. Genetic factors and congenital cytomegalovirus (CMV) infections account for around 90% of the etiology. The purpose of this study was to develop and test a whole genome sequencing (WGS) approach to detect deafness-related genetic variants and CMV infections simultaneously in newborns.Method: Deafness-related genes causing congenital or childhood hearing loss were curated and selected for newborn screening. Nine dried blood spots from newborns with known genetic variants (n = 6) or CMV infections (n = 3) were employed to develop and validate the WGS testing and analytic pipeline. We then pilot tested the WGS analysis on 51 de-identified clinical samples.Results: 92 gene-disease pairs were selected for screening hearing loss in newborns. In the validation test, WGS accurately detected all types of genetic variants, including single nucleotide variations, insertions/deletions, and copy number variations in the nuclear or mitochondrial genome. Sequence reads mapping to the CMV reference genome were discovered in CMV infected samples. In the pilot test, WGS identified nine out of 51 (18%) newborns carrying pathogenic variants associated with deafness.Conclusion: WGS can simultaneously detect genetic variants and CMV infections in dried blood spot specimens from newborns. Our study provides proof of principle that genome sequencing can be a promising alternative for newborn screening of hearing loss.
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Affiliation(s)
- Jiale Xiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | | | - Junqing Zhang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Zhenpeng Xu
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Zhiyu Peng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- *Correspondence: Zhiyu Peng,
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9
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Acharya A, Schrauwen I, Leal SM. Identification of autosomal recessive nonsyndromic hearing impairment genes through the study of consanguineous and non-consanguineous families: past, present, and future. Hum Genet 2022; 141:413-430. [PMID: 34291353 PMCID: PMC10416318 DOI: 10.1007/s00439-021-02309-9] [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: 05/31/2021] [Accepted: 06/24/2021] [Indexed: 10/20/2022]
Abstract
Hearing impairment (HI) is one of the most common sensory disabilities with exceptionally high genetic heterogeneity. Of genetic HI cases, 30% are syndromic and 70% are nonsyndromic. For nonsyndromic (NS) HI, 77% of the cases are due to autosomal recessive (AR) inheritance. ARNSHI is usually congenital/prelingual, severe-to-profound, affects all frequencies and is not progressive. Thus far, 73 ARNSHI genes have been identified. Populations with high rates of consanguinity have been crucial in the identification of ARNSHI genes, and 92% (67/73) of these genes were identified in consanguineous families. Recent changes in genomic technologies and analyses have allowed a shift towards ARNSHI gene discovery in outbred populations. The latter is crucial towards understanding the genetic architecture of ARNSHI in diverse and understudied populations. We present an overview of the 73 ARNSHI genes, the methods used to identify them, including next-generation sequencing which revolutionized the field, and new technologies that show great promise in advancing ARNSHI discoveries.
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Affiliation(s)
- Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA.
- Department of Neurology, Columbia University Medical Center, New York, NY, USA.
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA.
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10
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Calpena E, Wurmser M, McGowan SJ, Atique R, Bertola DR, Cunningham ML, Gustafson JA, Johnson D, Morton JEV, Passos-Bueno MR, Timberlake AT, Lifton RP, Wall SA, Twigg SRF, Maire P, Wilkie AOM. Unexpected role of SIX1 variants in craniosynostosis: expanding the phenotype of SIX1-related disorders. J Med Genet 2022; 59:165-169. [PMID: 33436522 PMCID: PMC8273188 DOI: 10.1136/jmedgenet-2020-107459] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Pathogenic heterozygous SIX1 variants (predominantly missense) occur in branchio-otic syndrome (BOS), but an association with craniosynostosis has not been reported. METHODS We investigated probands with craniosynostosis of unknown cause using whole exome/genome (n=628) or RNA (n=386) sequencing, and performed targeted resequencing of SIX1 in 615 additional patients. Expression of SIX1 protein in embryonic cranial sutures was examined in the Six1nLacZ/+ reporter mouse. RESULTS From 1629 unrelated cases with craniosynostosis we identified seven different SIX1 variants (three missense, including two de novo mutations, and four nonsense, one of which was also present in an affected twin). Compared with population data, enrichment of SIX1 loss-of-function variants was highly significant (p=0.00003). All individuals with craniosynostosis had sagittal suture fusion; additionally four had bilambdoid synostosis. Associated BOS features were often attenuated; some carrier relatives appeared non-penetrant. SIX1 is expressed in a layer basal to the calvaria, likely corresponding to the dura mater, and in the mid-sagittal mesenchyme. CONCLUSION Craniosynostosis is associated with heterozygous SIX1 variants, with possible enrichment of loss-of-function variants compared with classical BOS. We recommend screening of SIX1 in craniosynostosis, particularly when sagittal±lambdoid synostosis and/or any BOS phenotypes are present. These findings highlight the role of SIX1 in cranial suture homeostasis.
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Affiliation(s)
- Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Maud Wurmser
- Institut Cochin, INSERM, CNRS, Université de Paris, Paris, France
| | - Simon J McGowan
- Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rodrigo Atique
- Centro de Estudos do Genoma Humano, Universidade de São Paulo, São Paulo, Brazil
| | - Débora R Bertola
- Unidade de Genética Clínica, Instituto da Criança do Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Michael L Cunningham
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington, USA
- Seattle Children's Craniofacial Center, Seattle Children's Hospital, and Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, Washington, USA
| | - Jonas A Gustafson
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington, USA
| | - David Johnson
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | | | - Andrew T Timberlake
- Hansjörg Wyss Department of Plastic Surgery, New York University Langone Medical Center, New York, New York, USA
| | | | - Steven A Wall
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Stephen R F Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Pascal Maire
- Institut Cochin, INSERM, CNRS, Université de Paris, Paris, France
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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11
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Jain A, Bhoyar RC, Pandhare K, Mishra A, Sharma D, Imran M, Senthivel V, Divakar MK, Rophina M, Jolly B, Batra A, Sharma S, Siwach S, Jadhao AG, Palande NV, Jha GN, Ashrafi N, Mishra PK, A K V, Jain S, Dash D, Kumar NS, Vanlallawma A, Sarma RJ, Chhakchhuak L, Kalyanaraman S, Mahadevan R, Kandasamy S, B M P, Rajagopal RE, Ramya J E, Devi P N, Bajaj A, Gupta V, Mathew S, Goswami S, Mangla M, Prakash S, Joshi K, Meyakumla, S S, Gajjar D, Soraisham R, Yadav R, Devi YS, Gupta A, Mukerji M, Ramalingam S, B K B, Scaria V, Sivasubbu S. Genetic epidemiology of autoinflammatory disease variants in Indian population from 1029 whole genomes. JOURNAL OF GENETIC ENGINEERING AND BIOTECHNOLOGY 2021; 19:183. [PMID: 34905135 PMCID: PMC8671593 DOI: 10.1186/s43141-021-00268-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/13/2021] [Indexed: 11/16/2022]
Abstract
Background Autoinflammatory disorders are the group of inherited inflammatory disorders caused due to the genetic defect in the genes that regulates innate immune systems. These have been clinically characterized based on the duration and occurrence of unprovoked fever, skin rash, and patient’s ancestry. There are several autoinflammatory disorders that are found to be prevalent in a specific population and whose disease genetic epidemiology within the population has been well understood. However, India has a limited number of genetic studies reported for autoinflammatory disorders till date. The whole genome sequencing and analysis of 1029 Indian individuals performed under the IndiGen project persuaded us to perform the genetic epidemiology of the autoinflammatory disorders in India. Results We have systematically annotated the genetic variants of 56 genes implicated in autoinflammatory disorder. These genetic variants were reclassified into five categories (i.e., pathogenic, likely pathogenic, benign, likely benign, and variant of uncertain significance (VUS)) according to the American College of Medical Genetics and Association of Molecular pathology (ACMG-AMP) guidelines. Our analysis revealed 20 pathogenic and likely pathogenic variants with significant differences in the allele frequency compared with the global population. We also found six causal founder variants in the IndiGen dataset belonging to different ancestry. We have performed haplotype prediction analysis for founder mutations haplotype that reveals the admixture of the South Asian population with other populations. The cumulative carrier frequency of the autoinflammatory disorder in India was found to be 3.5% which is much higher than reported. Conclusion With such frequency in the Indian population, there is a great need for awareness among clinicians as well as the general public regarding the autoinflammatory disorder. To the best of our knowledge, this is the first and most comprehensive population scale genetic epidemiological study being reported from India. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-021-00268-2.
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Affiliation(s)
- Abhinav Jain
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Rahul C Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Kavita Pandhare
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Anushree Mishra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Disha Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vigneshwar Senthivel
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mercy Rophina
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Bani Jolly
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Arushi Batra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sumit Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Sanjay Siwach
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Arun G Jadhao
- Department of Zoology, RTM Nagpur University, Nagpur, Maharashtra, 440033, India
| | - Nikhil V Palande
- Department of Zoology, Shri Mathuradas Mohota College of Science, Nagpur, Maharashtra, 440009, India
| | - Ganga Nath Jha
- Department of Anthropology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Nishat Ashrafi
- Department of Anthropology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Prashant Kumar Mishra
- Department of Biotechnology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Vidhya A K
- Department of Biochemistry, Dr. Kongu Science and Art College, Erode, Tamil Nadu, 638107, India
| | - Suman Jain
- Thalassemia and Sickle Cell Society, Hyderabad, Telangana, 500052, India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | | | - Andrew Vanlallawma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Ranjan Jyoti Sarma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | | | | | - Radha Mahadevan
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Sunitha Kandasamy
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Pabitha B M
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | | | - Ezhil Ramya J
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Nirmala Devi P
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Anjali Bajaj
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vishu Gupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Samatha Mathew
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sangam Goswami
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mohit Mangla
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Savinitha Prakash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Kandarp Joshi
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Meyakumla
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Sreedevi S
- Department of Microbiology, St.Pious X Degree & PG College for Women, Hyderabad, Telangana, 500076, India
| | - Devarshi Gajjar
- Department of Microbiology, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, 390002, India
| | - Ronibala Soraisham
- Department of Dermatology, Venereology and Leprology, Regional Institute of Medical Sciences, Imphal, Manipur, 795004, India
| | - Rohit Yadav
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Yumnam Silla Devi
- CSIR- North East Institute of Science and Technology, Jorhat, Assam, 785006, India
| | - Aayush Gupta
- Department of Dermatology, Dr. D.Y. Patil Medical College, Pune, Maharashtra, 411018, India
| | - Mitali Mukerji
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sivaprakash Ramalingam
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Binukumar B K
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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12
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Han S, Zhang D, Guo Y, Fu Z, Guan G. Prevalence and Characteristics of STRC Gene Mutations (DFNB16): A Systematic Review and Meta-Analysis. Front Genet 2021; 12:707845. [PMID: 34621290 PMCID: PMC8491653 DOI: 10.3389/fgene.2021.707845] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Mutations in the STRC (MIM 606440) gene, inducing DFNB16, are considered a major cause of mild–moderate autosomal recessive non-syndromic hearing loss (ARNSHL). We conducted a systematic review and meta-analysis to determine the global prevalence and characteristics of STRC variations, important information required for genetic counseling. Methods: PubMed, Google Scholar, Medline, Embase, and Web of Science were searched for relevant articles published before January 2021. Results: The pooled prevalence of DFNB16 in GJB2-negative patients with hearing loss was 4.08% (95% CI: 0.0289–0.0573), and the proportion of STRC variants in the mild–moderate hearing loss group was 14.36%. Monoallelic mutations of STRC were 4.84% (95% CI: 0.0343–0.0680) in patients with deafness (non-GJB2) and 1.36% (95% CI: 0.0025–0.0696) in people with normal hearing. The DFNB16 prevalence in genetically confirmed patients (non-GJB2) was 11.10% (95% CI: 0.0716–0.1682). Overall pooled prevalence of deafness–infertility syndrome (DIS) was 36.75% (95% CI: 0.2122–0.5563) in DFNB16. The prevalence of biallelic deletions in STRC gene mutations was 70.85% (95% CI: 0.5824–0.8213). Conclusion: Variants in the STRC gene significantly contribute to mild–moderate hearing impairment. Moreover, biallelic deletions are a main feature of STRC mutations. Copy number variations associated with infertility should be seriously considered when investigating DFNB16.
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Affiliation(s)
- Shuang Han
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Dejun Zhang
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Yingyuan Guo
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Zeming Fu
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Guofang Guan
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
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13
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Differential genetic diagnoses of adult post-lingual hearing loss according to the audiogram pattern and novel candidate gene evaluation. Hum Genet 2021; 141:915-927. [PMID: 34519870 PMCID: PMC9034979 DOI: 10.1007/s00439-021-02367-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023]
Abstract
Ski-slope hearing loss (HL), which refers to increased auditory threshold at high frequencies, is common in adults. However, genetic contributions to this post-lingual HL remain largely unknown. Here, we prospectively investigated deafness-associated and novel candidate genes causing ski-slope HL. We analyzed 192 families with post-lingual HL via gene panel and/or exome sequencing. With an overall molecular diagnostic rate of 35.4% (68/192) in post-lingual HL, ski-slope HL showed a lower diagnostic rate (30.7%) compared with other conditions (40.7%). In patients who showed HL onset before the age of 40, genetic diagnostic probability was significantly lower for ski-slope HL than for other conditions. Further analysis of 51 genetically undiagnosed patients in the ski-slope HL group identified three variants in delta-like ligand 1 (DLL1), a Notch ligand, which presented in vitro gain-of-function effects on Notch downstream signaling. In conclusion, genetic diagnostic rates in post-lingual HL varied according to audiogram patterns with age-of-onset as a confounding factor. DLL1 was identified as a candidate gene causing ski-slope HL.
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14
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Jain A, Govindaraj GM, Edavazhippurath A, Faisal N, Bhoyar RC, Gupta V, Uppuluri R, Manakkad SP, Kashyap A, Kumar A, Divakar MK, Imran M, Sawant S, Dalvi A, Chakyar K, Madkaikar M, Raj R, Sivasubbu S, Scaria V. Whole genome sequencing identifies novel structural variant in a large Indian family affected with X-linked agammaglobulinemia. PLoS One 2021; 16:e0254407. [PMID: 34252140 PMCID: PMC8274882 DOI: 10.1371/journal.pone.0254407] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/25/2021] [Indexed: 12/30/2022] Open
Abstract
X-linked agammaglobulinemia (XLA, OMIM #300755) is a primary immunodeficiency disorder caused by pathogenic variations in the BTK gene, characterized by failure of development and maturation of B lymphocytes. The estimated prevalence worldwide is 1 in 190,000 male births. Recently, genome sequencing has been widely used in difficult to diagnose and familial cases. We report a large Indian family suffering from XLA with five affected individuals. We performed complete blood count, immunoglobulin assay, and lymphocyte subset analysis for all patients and analyzed Btk expression for one patient and his mother. Whole exome sequencing (WES) for four patients, and whole genome sequencing (WGS) for two patients have been performed. Carrier screening was done for 17 family members using Multiplex Ligation-dependent Probe Amplification (MLPA) and haplotype ancestry mapping using fineSTRUCTURE was performed. All patients had hypogammaglobulinemia and low CD19+ B cells. One patient who underwent Btk estimation had low expression and his mother showed a mosaic pattern. We could not identify any single nucleotide variants or small insertion/ deletions from the WES dataset that correlates with the clinical feature of the patient. Structural variant analysis through WGS data identifies a novel large deletion of 5,296 bp at loci chrX:100,624,323-100,629,619 encompassing exons 3-5 of the BTK gene. Family screening revealed seven carriers for the deletion. Two patients had a successful HSCT. Haplotype mapping revealed a South Asian ancestry. WGS led to identification of the accurate genetic mutation which could help in early diagnosis leading to improved outcomes, prevention of permanent organ damage and improved quality of life, as well as enabling genetic counselling and prenatal diagnosis in the family.
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Affiliation(s)
- Abhinav Jain
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Geeta Madathil Govindaraj
- Department of Pediatrics, Government Medical College Kozhikode, Kozhikode, Kerala, India
- Department of Pediatrics, FPID Regional Diagnostic Centre, Government Medical College Kozhikode, Kozhikode, Kerala, India
| | - Athulya Edavazhippurath
- Department of Pediatrics, Government Medical College Kozhikode, Kozhikode, Kerala, India
- Multidisciplinary Research Unit, Government College Kozhikode, Kozhikode, Kerala, India
| | - Nabeel Faisal
- Department of Pediatrics, Government Medical College Kozhikode, Kozhikode, Kerala, India
| | - Rahul C Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India
| | - Vishu Gupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Ramya Uppuluri
- Department of Pediatric Hematology, Oncology, Blood and Marrow Transplantation, Apollo Hospitals, Chennai, Tamil Nadu, India
| | | | - Atul Kashyap
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India
| | - Anoop Kumar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India
| | - Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Sneha Sawant
- Department of Pediatric Immunology and Leukocyte Biology, ICMR-National Institute of Immunohaematology, KEM Hospital, Mumbai, Maharashtra, India
| | - Aparna Dalvi
- Department of Pediatric Immunology and Leukocyte Biology, ICMR-National Institute of Immunohaematology, KEM Hospital, Mumbai, Maharashtra, India
| | - Krishnan Chakyar
- Department of Pediatrics, Government Medical College Kozhikode, Kozhikode, Kerala, India
| | - Manisha Madkaikar
- Department of Pediatric Immunology and Leukocyte Biology, ICMR-National Institute of Immunohaematology, KEM Hospital, Mumbai, Maharashtra, India
| | - Revathi Raj
- Department of Pediatric Hematology, Oncology, Blood and Marrow Transplantation, Apollo Hospitals, Chennai, Tamil Nadu, India
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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15
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Molina-Ramírez LP, Burkitt-Wright EM, Saeed H, McDermott JH, Kyle C, Wright R, Campbell C, Bhaskar SS, Taylor A, Dutton L, Forde C, Metcalfe K, Smith A, Clayton-Smith J, Douzgou S, Chandler K, Briggs TA, Banka S, Newman WG, Gokhale D, Bruce IA, Black GC. The diagnostic utility of clinical exome sequencing in 60 patients with hearing loss disorders: A single-institution experience. Clin Otolaryngol 2021; 46:1257-1262. [PMID: 34171171 DOI: 10.1111/coa.13826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/08/2021] [Accepted: 05/08/2021] [Indexed: 11/27/2022]
Affiliation(s)
- Leslie P Molina-Ramírez
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Emma Mm Burkitt-Wright
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Haroon Saeed
- Paediatric ENT Department, Manchester Academic Health Science Centre, Royal Manchester Children's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - John H McDermott
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Claire Kyle
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Ronnie Wright
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Christopher Campbell
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Sanjeev S Bhaskar
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Algy Taylor
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Laura Dutton
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Claire Forde
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Kay Metcalfe
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Audrey Smith
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Jill Clayton-Smith
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Sofia Douzgou
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Kate Chandler
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Tracy A Briggs
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - William G Newman
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - David Gokhale
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Iain A Bruce
- Paediatric ENT Department, Manchester Academic Health Science Centre, Royal Manchester Children's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, UK.,Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine, Health University of Manchester, Manchester, UK
| | - Graeme C Black
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
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16
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Ripen AM, Chear CT, Baharin MF, Nallusamy R, Chan KC, Kassim A, Choo CM, Wong KJ, Fong SM, Tan KK, Nachiappan JP, Teo KR, Chiow MY, Hishamshah M, Ghani H, Muralitharan RR, Mohamad SB. A single-center pilot study in Malaysia on the clinical utility of whole-exome sequencing for inborn errors of immunity. Clin Exp Immunol 2021; 206:119-128. [PMID: 34060650 PMCID: PMC8506128 DOI: 10.1111/cei.13626] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 01/02/2023] Open
Abstract
Primary immunodeficiency diseases refer to inborn errors of immunity (IEI) that affect the normal development and function of the immune system. The phenotypical and genetic heterogeneity of IEI have made their diagnosis challenging. Hence, whole-exome sequencing (WES) was employed in this pilot study to identify the genetic etiology of 30 pediatric patients clinically diagnosed with IEI. The potential causative variants identified by WES were validated using Sanger sequencing. Genetic diagnosis was attained in 46.7% (14 of 30) of the patients and categorized into autoinflammatory disorders (n = 3), diseases of immune dysregulation (n = 3), defects in intrinsic and innate immunity (n = 3), predominantly antibody deficiencies (n = 2), combined immunodeficiencies with associated and syndromic features (n = 2) and immunodeficiencies affecting cellular and humoral immunity (n = 1). Of the 15 genetic variants identified, two were novel variants. Genetic findings differed from the provisional clinical diagnoses in seven cases (50.0%). This study showed that WES enhances the capacity to diagnose IEI, allowing more patients to receive appropriate therapy and disease management.
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Affiliation(s)
- Adiratna Mat Ripen
- Primary Immunodeficiency Unit, Allergy and Immunology Research Centre, Institute for Medical Research, Ministry of Health, Selangor, Malaysia
| | - Chai Teng Chear
- Primary Immunodeficiency Unit, Allergy and Immunology Research Centre, Institute for Medical Research, Ministry of Health, Selangor, Malaysia.,Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Farid Baharin
- Primary Immunodeficiency Unit, Allergy and Immunology Research Centre, Institute for Medical Research, Ministry of Health, Selangor, Malaysia
| | - Revathy Nallusamy
- Pediatric Department, Penang General Hospital, Ministry of Health, Penang, Malaysia
| | - Kwai Cheng Chan
- Pediatric Department, Penang General Hospital, Ministry of Health, Penang, Malaysia
| | - Asiah Kassim
- Pediatric Department, Kuala Lumpur Hospital, Ministry of Health, Kuala Lumpur, Malaysia
| | - Chong Ming Choo
- Pediatric Department, Sultan Abdul Halim Hospital, Ministry of Health, Kedah, Malaysia
| | - Ke Juin Wong
- Pediatric Department, Likas Hospital, Ministry of Health, Sabah, Malaysia
| | - Siew Moy Fong
- Pediatric Department, Likas Hospital, Ministry of Health, Sabah, Malaysia
| | - Kah Kee Tan
- Pediatric Department, Tuanku Ja'afar Hospital, Ministry of Health, Seremban, Malaysia
| | | | - Kai Ru Teo
- Pediatric Department, Sultan Ismail Johor Bahru Hospital, Ministry of Health, Johor, Malaysia
| | - Mei Yee Chiow
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Munirah Hishamshah
- Primary Immunodeficiency Unit, Allergy and Immunology Research Centre, Institute for Medical Research, Ministry of Health, Selangor, Malaysia
| | - Hamidah Ghani
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Rikeish R Muralitharan
- Primary Immunodeficiency Unit, Allergy and Immunology Research Centre, Institute for Medical Research, Ministry of Health, Selangor, Malaysia.,Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science, Monash University, Melbourne, Victoria, Australia
| | - Saharuddin Bin Mohamad
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.,Centre of Research in Systems Biology, Structural Bioinformatics and Human Digital Imaging (CRYSTAL), University of Malaya, Kuala Lumpur, Malaysia
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17
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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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18
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Downie L, Amor DJ, Halliday J, Lewis S, Martyn M, Goranitis I. Exome Sequencing for Isolated Congenital Hearing Loss: A Cost-Effectiveness Analysis. Laryngoscope 2020; 131:E2371-E2377. [PMID: 33382469 DOI: 10.1002/lary.29356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/19/2022]
Abstract
OBJECTIVES/HYPOTHESIS To assess the relative cost-effectiveness of exome sequencing for isolated congenital deafness compared with standard care. STUDY DESIGN Incremental cost-effectiveness and cost-benefit analyses were undertaken from the perspective of the Australian healthcare system using an 18-year time horizon. METHODS A decision tree was used to model the costs and outcomes associated with exome sequencing and standard care for infants presenting with isolated congenital deafness. RESULTS Exome sequencing resulted in an incremental cost of AU$1,000 per child and an additional 30 diagnoses per 100 children tested. The incremental cost-effectiveness ratio was AU$3,333 per additional diagnosis. The mean societal willingness to pay for exome sequencing was estimated at AU$4,600 per child tested relative to standard care, resulting in a positive net benefit of AU$3,600. Deterministic and probabilistic sensitivity analyses confirmed the cost-effectiveness of exome sequencing. CONCLUSIONS Our findings demonstrate the cost-effectiveness of exome sequencing in congenital hearing loss, through increased diagnostic rate and consequent improved process of care by reducing or ceasing diagnostic investigation or facilitating targeted further investigation. We recommend equitable funding for exome sequencing in infants presenting with isolated congenital hearing loss. LEVEL OF EVIDENCE N/A. Laryngoscope, 131:E2371-E2377, 2021.
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Affiliation(s)
- Lilian Downie
- Victorian Clinical Genetics Services, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - David J Amor
- Victorian Clinical Genetics Services, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Jane Halliday
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Sharon Lewis
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Melissa Martyn
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Melbourne Genomics Health Alliance, Melbourne, Victoria, Australia
| | - Ilias Goranitis
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Centre for Health Policy, University of Melbourne, Melbourne, Victoria, Australia.,Australian Genomics Health Alliance, Melbourne, Victoria, Australia
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19
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Genetic Spectrum of Syndromic and Non-Syndromic Hearing Loss in Pakistani Families. Genes (Basel) 2020; 11:genes11111329. [PMID: 33187236 PMCID: PMC7709052 DOI: 10.3390/genes11111329] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/27/2020] [Accepted: 11/09/2020] [Indexed: 12/30/2022] Open
Abstract
The current molecular genetic diagnostic rates for hereditary hearing loss (HL) vary considerably according to the population background. Pakistan and other countries with high rates of consanguineous marriages have served as a unique resource for studying rare and novel forms of recessive HL. A combined exome sequencing, bioinformatics analysis, and gene mapping approach for 21 consanguineous Pakistani families revealed 13 pathogenic or likely pathogenic variants in the genes GJB2, MYO7A, FGF3, CDC14A, SLITRK6, CDH23, and MYO15A, with an overall resolve rate of 61.9%. GJB2 and MYO7A were the most frequently involved genes in this cohort. All the identified variants were either homozygous or compound heterozygous, with two of them not previously described in the literature (15.4%). Overall, seven missense variants (53.8%), three nonsense variants (23.1%), two frameshift variants (15.4%), and one splice-site variant (7.7%) were observed. Syndromic HL was identified in five (23.8%) of the 21 families studied. This study reflects the extreme genetic heterogeneity observed in HL and expands the spectrum of variants in deafness-associated genes.
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20
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Xiang YB, Xu CY, Xu YZ, Li HZ, Zhou LL, Xu XQ, Chen ZH, Tang SH. Next-generation sequencing identifies rare pathogenic and novel candidate variants in a cohort of Chinese patients with syndromic or nonsyndromic hearing loss. Mol Genet Genomic Med 2020; 8:e1539. [PMID: 33095980 PMCID: PMC7767562 DOI: 10.1002/mgg3.1539] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/27/2020] [Accepted: 10/02/2020] [Indexed: 11/15/2022] Open
Abstract
Background Hearing loss (HL) is a common sensory disorder in humans characterized by extreme clinical and genetic heterogeneity. In recent years, next‐generation sequencing (NGS) technologies have proven to be highly effective and powerful tools for population genetic studies of HL. Here, we analyzed clinical and molecular data from 21 Chinese deaf families who did not have hotspot mutations in the common deafness genes GJB2, SLC26A4, GJB3, and MT‐RNR1. Method Targeted next‐generation sequencing (TGS) of 127 known deafness genes was performed in probands of 12 families, while whole‐exome sequencing (WES) or trio‐WES was used for the remaining nine families. Results Potential pathogenic mutations in a total of 12 deafness genes were identified in 13 probands; the mutations were observed in GJB2, CDH23, EDNRB, MYO15A, OTOA, OTOF, TBC1D24, SALL1, TMC1, TWNK, USH1C, and USH1G, with eight of the identified mutations being novel. Further, a copy number variant (CNV) was detected in one proband with heterozygous deletion of chromosome 4p16.3‐4p15.32. Thus, the total diagnostic rate using NGS in our deafness patients reached 66.67% (14/21). Conclusions These results expand the mutation spectrum of deafness‐causing genes and provide support for the use of NGS detection technologies for routine molecular diagnosis in Chinese deaf populations.
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Affiliation(s)
- Yan-Bao Xiang
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Chen-Yang Xu
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Yun-Zhi Xu
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Huan-Zheng Li
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Li-Li Zhou
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Xue-Qin Xu
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Zi-Hui Chen
- Key laboratory of Medical Genetic, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Shao-Hua Tang
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China.,Key laboratory of Medical Genetic, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
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21
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Morgan A, Lenarduzzi S, Spedicati B, Cattaruzzi E, Murru FM, Pelliccione G, Mazzà D, Zollino M, Graziano C, Ambrosetti U, Seri M, Faletra F, Girotto G. Lights and Shadows in the Genetics of Syndromic and Non-Syndromic Hearing Loss in the Italian Population. Genes (Basel) 2020; 11:genes11111237. [PMID: 33105617 PMCID: PMC7690429 DOI: 10.3390/genes11111237] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 11/16/2022] Open
Abstract
Hearing loss (HL), both syndromic (SHL) and non-syndromic (NSHL), is the most common sensory disorder, affecting ~460 million people worldwide. More than 50% of the congenital/childhood cases are attributable to genetic causes, highlighting the importance of genetic testing in this class of disorders. Here we applied a multi-step strategy for the molecular diagnosis of HL in 125 patients, which included: (1) an accurate clinical evaluation, (2) the analysis of GJB2, GJB6, and MT-RNR1 genes, (3) the evaluation STRC-CATSPER2 and OTOA deletions via Multiplex Ligation Probe Amplification (MLPA), (4) Whole Exome Sequencing (WES) in patients negative to steps 2 and 3. Our approach led to the characterization of 50% of the NSHL cases, confirming both the relevant role of the GJB2 (20% of cases) and STRC deletions (6% of cases), and the high genetic heterogeneity of NSHL. Moreover, due to the genetic findings, 4% of apparent NSHL patients have been re-diagnosed as SHL. Finally, WES characterized 86% of SHL patients, supporting the role of already know disease-genes. Overall, our approach proved to be efficient in identifying the molecular cause of HL, providing essential information for the patients’ future management.
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Affiliation(s)
- Anna Morgan
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
- Correspondence:
| | - Stefania Lenarduzzi
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
| | - Beatrice Spedicati
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34125 Trieste, Italy
| | - Elisabetta Cattaruzzi
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
| | - Flora Maria Murru
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
| | - Giulia Pelliccione
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
| | - Daniela Mazzà
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
| | - Marcella Zollino
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, UOC Genetica, 00168 Rome, Italy;
- Istituto di Medicina Genomica, Università Cattolica Sacro Cuore, 00168 Rome, Italy
| | - Claudio Graziano
- Unit of Medical Genetics, S. Orsola-Malpighi Hospital, 40138 Bologna, Italy; (C.G.); (M.S.)
| | - Umberto Ambrosetti
- Audiology and audiophonology, University of Milano/Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy;
| | - Marco Seri
- Unit of Medical Genetics, S. Orsola-Malpighi Hospital, 40138 Bologna, Italy; (C.G.); (M.S.)
| | - Flavio Faletra
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
| | - Giorgia Girotto
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34125 Trieste, Italy
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22
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Vona B, Doll J, Hofrichter MA, Haaf T. Non-syndromic hearing loss: clinical and diagnostic challenges. MED GENET-BERLIN 2020. [DOI: 10.1515/medgen-2020-2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Abstract
Hereditary hearing loss is clinically and genetically heterogeneous. There are presently over 120 genes that have been associated with non-syndromic hearing loss and many more that are associated with syndromic forms. Despite an increasing number of genes that have been implemented into routine molecular genetic diagnostic testing, the diagnostic yield from European patient cohorts with hereditary hearing loss remains around the 50 % mark. This attests to the many gaps of knowledge the field is currently working toward resolving. It can be expected that many more genes await identification. However, it can also be expected, for example, that the mutational signatures of the known genes are still unclear, especially variants in non-coding or regulatory regions influencing gene expression. This review summarizes several challenges in the clinical and diagnostic setting for hereditary hearing loss with emphasis on syndromes that mimic non-syndromic forms of hearing loss in young children and other factors that heavily influence diagnostic rates. A molecular genetic diagnosis for patients with hearing loss opens several additional avenues, such as patient tailored selection of the best currently available treatment modalities, an understanding of the prognosis, and supporting family planning decisions. In the near future, a genetic diagnosis may enable patients to engage in preclinical trials for the development of therapeutics.
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Affiliation(s)
- Barbara Vona
- Tübingen Hearing Research Centre, Department of Otolaryngology – Head & Neck Surgery , Eberhard Karls University , Elfriede-Aulhorn-Strasse 5 , Tübingen , Germany
| | - Julia Doll
- Institute of Human Genetics , Julius Maximilians University , Würzburg , Germany
| | | | - Thomas Haaf
- Institute of Human Genetics , Julius-Maximilians University Würzburg , Biozentrum, Am Hubland , Würzburg , Germany
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Flexible Real-Time Polymerase Chain Reaction-Based Platforms for Detecting Deafness Mutations in Koreans: A Proposed Guideline for the Etiologic Diagnosis of Auditory Neuropathy Spectrum Disorder. Diagnostics (Basel) 2020; 10:diagnostics10090672. [PMID: 32899707 PMCID: PMC7554951 DOI: 10.3390/diagnostics10090672] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/29/2020] [Accepted: 09/01/2020] [Indexed: 01/23/2023] Open
Abstract
Routine application of next-generation sequencing in clinical settings is often limited by time- and cost-prohibitive complex filtering steps. Despite the previously introduced genotyping kit that allows screening of the 11 major recurring variants of sensorineural hearing loss (SNHL) genes in the Korean population, the demand for phenotype- and variant-specific screening kits still remains. Herein, we developed a new real-time PCR-based kit (U-TOP™ HL Genotyping Kit Ver2), comprising six variants from two auditory neuropathy spectrum disorder (ANSD) genes (OTOF and ATP1A3) and five variants from three SNHL genes (MPZL2, COCH, and TMC1), with a distinct auditory phenotype, making this the first genotyping kit dedicated to ANSD. The concordance rate with Sanger sequencing, sensitivity, and specificity of this genotyping kit were all 100%, suggesting reliability. The kit not only allows timely and cost-effective identification of recurring OTOF variants, but it also allows timely detection of cochlear nerve deficiency for those without OTOF variants. Herein, we provide a clinical guideline for an efficient, rapid, and cost-effective etiologic diagnosis of prelingual ANSD. Our study provides a good example of continuing to update new key genetic variants, which will continuously be revealed through NGS, as targets for the newly developed genotyping kit.
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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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Sun Y, Xiang J, Liu Y, Chen S, Yu J, Peng J, Liu Z, Chen L, Sun J, Yang Y, Yang Y, Zhou Y, Peng Z. Increased diagnostic yield by reanalysis of data from a hearing loss gene panel. BMC Med Genomics 2019; 12:76. [PMID: 31138263 PMCID: PMC6540452 DOI: 10.1186/s12920-019-0531-6] [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: 01/29/2019] [Accepted: 05/14/2019] [Indexed: 12/30/2022] Open
Abstract
Background Congenital hearing loss affects approximately 1–2 infants out of every 1000, with 50% of the cases resulting from genetic factors. Targeted gene panels have been widely used for genetic diagnosis of hearing loss. This study aims to reveal new diagnoses via reanalyzing historical data of a multigene panel, and exam the reasons for new diagnoses. Methods A total of 210 samples were enlisted, including clinical reports and sequencing data of patients with congenital/prelingual hearing loss who were referred to clinical genetic testing from October 2014 to June 2017. All variants listed on the original clinical reports were reinterpreted according to the standards and guidelines recommended by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP). Expanded analysis of raw data were performed in undiagnosed cases. Results Re-analysis resulted in nine new diagnoses, improving the overall diagnostic rate from 39 to 43%. New diagnoses were attributed to newly published clinical evidence in the literature, adoption of new interpretation guidelines and expanded analysis range. Conclusion This work demonstrates benefits of reanalysis of targeted gene panel data, indicating that periodical reanalysis should be performed in clinical practice. Electronic supplementary material The online version of this article (10.1186/s12920-019-0531-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu Sun
- Department of Otorhinolaryngology, Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jiale Xiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yidong Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sen Chen
- Department of Otorhinolaryngology, Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jintao Yu
- Department of Otorhinolaryngology, Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jiguang Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zijing Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Lisha Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yun Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,AiLife Diagnostics, 1920 Country Place Pkwy, Pearland, TX, 77584, USA
| | - Yulin Zhou
- United Diagnostic and Research Center for Clinical Genetics, School of Public Health of Xiamen University, Xiamen, Fujian, 361003, China. .,Xiamen Maternal and Child Health Hospital, Xiamen, Fujian, 361003, China.
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
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