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Betzler IR, Hempel M, Mütze U, Kölker S, Winkler E, Dikow N, Garbade SF, Schaaf CP, Brennenstuhl H. Comparative analysis of gene and disease selection in genomic newborn screening studies. J Inherit Metab Dis 2024. [PMID: 38757337 DOI: 10.1002/jimd.12750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/19/2024] [Accepted: 04/30/2024] [Indexed: 05/18/2024]
Abstract
Genomic newborn screening (gNBS) is on the horizon given the decreasing costs of sequencing and the advanced understanding of the impact of genetic variants on health and diseases. Key to ongoing gNBS pilot studies is the selection of target diseases and associated genes to be included. In this study, we present a comprehensive analysis of seven published gene-disease lists from gNBS studies, evaluating gene-disease count, composition, group proportions, and ClinGen curations of individual disorders. Despite shared selection criteria, we observe substantial variation in total gene count (median 480, range 237-889) and disease group composition. An intersection was identified for 53 genes, primarily inherited metabolic diseases (83%, 44/53). Each study investigated a subset of exclusive gene-disease pairs, and the total number of exclusive gene-disease pairs was positively correlated with the total number of genes included per study. While most pairs receive "Definitive" or "Strong" ClinGen classifications, some are labeled as "Refuted" (n = 5) or "Disputed" (n = 28), particularly in genetic cardiac diseases. Importantly, 17%-48% of genes lack ClinGen curation. This study underscores the current absence of consensus recommendations for selection criteria for target diseases for gNBS resulting in diversity in proposed gene-disease pairs, their coupling with gene variations and the use of ClinGen curation. Our findings provide crucial insights into the selection of target diseases and accompanying gene variations for future gNBS program, emphasizing the necessity for ongoing collaboration and discussion about criteria harmonization for panel selection to ensure the screening's objectivity, integrity, and broad acceptance.
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Affiliation(s)
- Isabel R Betzler
- Institute of Human Genetics, Heidelberg University and University Hospital Heidelberg, Heidelberg, Germany
| | - Maja Hempel
- Institute of Human Genetics, Heidelberg University and University Hospital Heidelberg, Heidelberg, Germany
| | - Ulrike Mütze
- Centre for Child and Adolescent Medicine, Division of Child Neurology and Metabolic Medicine, Heidelberg University and University Hospital Heidelberg, Heidelberg, Germany
| | - Stefan Kölker
- Centre for Child and Adolescent Medicine, Division of Child Neurology and Metabolic Medicine, Heidelberg University and University Hospital Heidelberg, Heidelberg, Germany
| | - Eva Winkler
- Section of Translational Medical Ethics, National Center for Tumour Diseases, Heidelberg University and University Hospital Heidelberg, Heidelberg, Germany
| | - Nicola Dikow
- Institute of Human Genetics, Heidelberg University and University Hospital Heidelberg, Heidelberg, Germany
| | - Sven F Garbade
- Centre for Child and Adolescent Medicine, Division of Child Neurology and Metabolic Medicine, Heidelberg University and University Hospital Heidelberg, Heidelberg, Germany
| | - Christian P Schaaf
- Institute of Human Genetics, Heidelberg University and University Hospital Heidelberg, Heidelberg, Germany
| | - Heiko Brennenstuhl
- Institute of Human Genetics, Heidelberg University and University Hospital Heidelberg, Heidelberg, Germany
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El Naofal M, Ramaswamy S, Alsarhan A, Nugud A, Sarfraz F, Janbaz H, Taylor A, Jain R, Halabi N, Yaslam S, Alfalasi R, Shenbagam S, Rabea F, Bitzan M, Yavuz L, Wafadari D, Abulhoul H, Shankar S, Al Maazmi M, Rizk R, Alloub Z, Elbashir H, Babiker MOE, Chencheri N, AlBanna A, Sultan M, El Bitar M, Kherani S, Thalange N, Alshryda S, Di Donato R, Tzivinikos C, Majid I, Freeman AF, Gonzalez C, Khan AO, Hamdan H, Abuhammour W, AlAwadhi M, AlKhayat A, Alsheikh-Ali A, Abou Tayoun AN. The genomic landscape of rare disorders in the Middle East. Genome Med 2023; 15:5. [PMID: 36703223 PMCID: PMC9881316 DOI: 10.1186/s13073-023-01157-8] [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: 09/02/2022] [Accepted: 01/19/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Rare diseases collectively impose a significant burden on healthcare systems, especially in underserved regions, like the Middle East, which lack access to genomic diagnostic services and the associated personalized management plans. METHODS We established a clinical genomics and genetic counseling facility, within a multidisciplinary tertiary pediatric center, in the United Arab Emirates to locally diagnose and manage patients with rare diseases. Clinical genomic investigations included exome-based sequencing, chromosomal microarrays, and/or targeted testing. We assessed the diagnostic yield and implications for clinical management among this population. Variables were compared using the Fisher exact test. Tests were 2-tailed, and P < .05 was considered statistically significant. RESULTS We present data on 1000 patients with rare diseases (46.2% females; average age, 4.6 years) representing 47 countries primarily from the Arabian Peninsula, the Levant, Africa, and Asia. The cumulative diagnostic yield was 32.5% (95% CI, 29.7-35.5%) and was higher for genomic sequencing-based testing than chromosomal microarrays (37.9% versus 17.2%, P = 0.0001) across all indications, consistent with the higher burden of single gene disorders. Of the 221 Mendelian disorders identified in this cohort, the majority (N = 184) were encountered only once, and those with recessive inheritance accounted for ~ 62% of sequencing diagnoses. Of patients with positive genetic findings (N = 325), 67.7% were less than 5 years of age, and 60% were offered modified management and/or intervention plans. Interestingly, 24% of patients with positive genetic findings received delayed diagnoses (average age, 12.4 years; range 7-37 years), most likely due to a lack of access to genomic investigations in this region. One such genetic finding ended a 15-year-long diagnostic odyssey, leading to a life-threatening diagnosis in one patient, who was then successfully treated using an experimental allogenic bone marrow transplant. Finally, we present cases with candidate genes within regions of homozygosity, likely underlying novel recessive disorders. CONCLUSIONS Early access to genomic diagnostics for patients with suspected rare disorders in the Middle East is likely to improve clinical outcomes while driving gene discovery in this genetically underrepresented population.
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Affiliation(s)
- Maha El Naofal
- Al Jalila Genomics Center of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Sathishkumar Ramaswamy
- Al Jalila Genomics Center of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Ali Alsarhan
- General Pediatrics Department, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Ahmed Nugud
- General Pediatrics Department, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Fatima Sarfraz
- General Pediatrics Department, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Hiba Janbaz
- General Pediatrics Department, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Alan Taylor
- Al Jalila Genomics Center of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Ruchi Jain
- Al Jalila Genomics Center of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Nour Halabi
- Al Jalila Genomics Center of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Sawsan Yaslam
- Al Jalila Genomics Center of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Roudha Alfalasi
- Al Jalila Genomics Center of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Shruti Shenbagam
- Al Jalila Genomics Center of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Fatma Rabea
- grid.510259.a0000 0004 5950 6858College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Martin Bitzan
- Kidney Center of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Lemis Yavuz
- General Pediatrics Department, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Deena Wafadari
- General Pediatrics Department, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Hamda Abulhoul
- Department of Metabolic Medicine, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Shiva Shankar
- Critical Care Centre of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Munira Al Maazmi
- Critical Care Centre of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Ruba Rizk
- Adolescent Medicine, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Zeinab Alloub
- Neurodevelopment Section, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Haitham Elbashir
- Neuroscience Center of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Mohamed O. E. Babiker
- Neurology Department, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Nidheesh Chencheri
- Neurology Department, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Ammar AlBanna
- Mental Health Center of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Meshal Sultan
- Mental Health Center of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Mohamed El Bitar
- ENT Department, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Safeena Kherani
- ENT Department, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Nandu Thalange
- Endocrinology Department, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Sattar Alshryda
- Orthopedics Department, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Roberto Di Donato
- Cardiology Department, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Christos Tzivinikos
- Gastroenterology Department, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Ibrar Majid
- Orthopedics Department, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Alexandra F. Freeman
- grid.419681.30000 0001 2164 9667National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD USA
| | - Corina Gonzalez
- grid.48336.3a0000 0004 1936 8075Immune Deficiency Cellular Therapy Program, National Cancer Institute, NIH, Bethesda, MD USA
| | - Arif O. Khan
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Hisham Hamdan
- Pulmonology and Sleep Medicine Department, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Walid Abuhammour
- Infectious Diseases Department, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Mohamed AlAwadhi
- Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Abdulla AlKhayat
- Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Alawi Alsheikh-Ali
- grid.510259.a0000 0004 5950 6858College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates ,grid.414167.10000 0004 1757 0894Dubai Health Authority, Dubai, United Arab Emirates
| | - Ahmad N. Abou Tayoun
- Al Jalila Genomics Center of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates ,grid.510259.a0000 0004 5950 6858Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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Le Nabec A, Blotas C, Briset A, Collobert M, Férec C, Moisan S. 3D Chromatin Organization Involving MEIS1 Factor in the cis-Regulatory Landscape of GJB2. Int J Mol Sci 2022; 23:ijms23136964. [PMID: 35805969 PMCID: PMC9266880 DOI: 10.3390/ijms23136964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 02/04/2023] Open
Abstract
The human genome is covered by 8% of candidate cis-regulatory elements. The identification of distal acting regulatory elements and an understanding of their action are crucial to determining their key role in gene expression. Disruptions of such regulatory elements and/or chromatin conformation are likely to play a critical role in human genetic diseases. Non-syndromic hearing loss (i.e., DFNB1) is mostly due to GJB2 (Gap Junction Beta 2) variations and DFNB1 large deletions. Although several GJB2 cis-regulatory elements (CREs) have been described, GJB2 gene regulation remains not well understood. We investigated the endogenous effect of these CREs with CRISPR (clustered regularly interspaced short palindromic repeats) disruptions and observed GJB2 expression. To decipher the GJB2 regulatory landscape, we used the 4C-seq technique and defined new chromatin contacts inside the DFNB1 locus, which permit DNA loops and long-range regulation. Moreover, through ChIP-PCR, we determined the involvement of the MEIS1 transcription factor in GJB2 expression. Taken together, the results of our study enable us to describe the 3D DFNB1 regulatory landscape.
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Affiliation(s)
- Anaïs Le Nabec
- University Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (C.B.); (A.B.); (M.C.); (C.F.)
- Correspondence: or twitter@anaisnabec (A.L.N.); (S.M.); Tel.: +33-2-98-01-65-84 (A.L.N.); +33-2-98-01-65-67 (S.M.)
| | - Clara Blotas
- University Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (C.B.); (A.B.); (M.C.); (C.F.)
| | - Alinéor Briset
- University Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (C.B.); (A.B.); (M.C.); (C.F.)
| | - Mégane Collobert
- University Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (C.B.); (A.B.); (M.C.); (C.F.)
| | - Claude Férec
- University Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (C.B.); (A.B.); (M.C.); (C.F.)
| | - Stéphanie Moisan
- University Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (C.B.); (A.B.); (M.C.); (C.F.)
- Laboratoire de Génétique Moléculaire et d’Histocompatibilité, CHRU Brest, UMR 1078, F-29200 Brest, France
- Correspondence: or twitter@anaisnabec (A.L.N.); (S.M.); Tel.: +33-2-98-01-65-84 (A.L.N.); +33-2-98-01-65-67 (S.M.)
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4
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Chen J, Chen P, He B, Gong T, Li Y, Zhang J, Lv J, Mammano F, Hou S, Yang J. Connexin30-Deficiency Causes Mild Hearing Loss With the Reduction of Endocochlear Potential and ATP Release. Front Cell Neurosci 2022; 15:819194. [PMID: 35110999 PMCID: PMC8802669 DOI: 10.3389/fncel.2021.819194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 12/22/2021] [Indexed: 12/26/2022] Open
Abstract
GJB2 and GJB6 are adjacent genes encoding connexin 26 (Cx26) and connexin 30 (Cx30), respectively, with overlapping expressions in the inner ear. Both genes are associated with the commonest monogenic hearing disorder, recessive isolated deafness DFNB1. Cx26 plays an important role in auditory development, while the role of Cx30 in hearing remains controversial. Previous studies found that Cx30 knockout mice had severe hearing loss along with a 90% reduction in Cx26, while another Cx30 knockout mouse model showed normal hearing with nearly half of Cx26 preserved. In this study, we used CRISPR/Cas9 technology to establish a new Cx30 knockout mouse model (Cx30−/−), which preserves approximately 70% of Cx26. We found that the 1, 3, and 6-month-old Cx30−/− mice showed mild hearing loss at full frequency. Immunofluorescence and HE staining suggested no significant differences in microstructure of the cochlea between Cx30−/− mice and wild-type mice. However, transmission electron microscopy showed slight cavity-like damage in the stria vascularis of Cx30−/− mice. And Cx30 deficiency reduced the production of endocochlear potential (EP) and the release of ATP, which may have induced hearing loss. Taken together, this study showed that lack of Cx30 can lead to hearing loss with an approximately 30% reduction of Cx26 in the present Cx30 knockout model. Hence, Cx30 may play an important rather than redundant role in hearing development.
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Affiliation(s)
- Junmin Chen
- Department of Otorhinolaryngology—Head & Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Penghui Chen
- Department of Otorhinolaryngology—Head & Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Baihui He
- Department of Otorhinolaryngology—Head & Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Tianyu Gong
- Department of Otorhinolaryngology—Head & Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Yue Li
- Department of Otorhinolaryngology—Head & Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Jifang Zhang
- Department of Otorhinolaryngology—Head & Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Jingrong Lv
- Department of Otorhinolaryngology—Head & Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Fabio Mammano
- Department of Physics and Astronomy “G. Galilei”, University of Padua, Padua, Italy
- Department of Biomedical Sciences, Institute of Cell Biology and Neurobiology, Italian National Research Council, Monterotondo, Italy
| | - Shule Hou
- Department of Otorhinolaryngology—Head & Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
- *Correspondence: Shule Hou Jun Yang
| | - Jun Yang
- Department of Otorhinolaryngology—Head & Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
- *Correspondence: Shule Hou Jun Yang
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5
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Moon IS, Grant AR, Sagi V, Rehm HL, Stankovic KM. TMPRSS3 Gene Variants With Implications for Auditory Treatment and Counseling. Front Genet 2021; 12:780874. [PMID: 34868270 PMCID: PMC8641783 DOI: 10.3389/fgene.2021.780874] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 10/18/2021] [Indexed: 11/24/2022] Open
Abstract
Objective: To identify and report novel variants in the TMPRSS3 gene and their clinical manifestations related to hearing loss as well as intervention outcomes. This information will be helpful for genetic counseling and treatment planning for these patients. Methods: Literature review of previously reported TMPRSS3 variants was conducted. Reported variants and associated clinical information was compiled. Additionally, cohort data from 18 patients, and their families, with a positive result for TMPRSS3-associated hearing loss were analyzed. Genetic testing included sequencing and copy number variation (CNV) analysis of TMPRSS3 and the Laboratory for Molecular Medicine’s OtoGenome-v1, -v2, or -v3 panels. Clinical data regarding patient hearing rehabilitation was interpreted along with their genetic testing results and in the context of previously reported cochlear implant outcomes in individuals with TMPRSS3 variants. Results: There have been 87 previously reported TMPRSS3 variants associated with non-syndromic hearing loss in more than 20 ancestral groups worldwide. Here we report occurrences of known variants as well as one novel variant: deletion of Exons 1–5 and 13 identified from our cohort of 18 patients. The hearing impairment in many of these families was consistent with that of previously reported patients with TMPRSS3 variants (i.e., typical down-sloping audiogram). Four patients from our cohort underwent cochlear implantation. Conclusion: Bi-allelic variants of TMPRSS3 are associated with down-sloping hearing loss regardless of ancestry. The outcome following cochlear implantation in patients with variants of TMPRSS3 is excellent. Therefore, cochlear implantation is strongly recommended for hearing rehabilitation in these patients.
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Affiliation(s)
- In Seok Moon
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear and Harvard Medical School, Boston, MA, United States.,Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - Andrew R Grant
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States.,New York Medical College, Valhalla, NY, United States
| | - Varun Sagi
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, United States.,University of Minnesota Medical School, Minneapolis, MN, United States
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States.,Center for Genomic Medicine and Departments of Pathology and Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Konstantina M Stankovic
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear and Harvard Medical School, Boston, MA, United States.,Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, United States
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6
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Evaluation of copy number variants for genetic hearing loss: a review of current approaches and recent findings. Hum Genet 2021; 141:387-400. [PMID: 34811589 DOI: 10.1007/s00439-021-02365-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/02/2021] [Indexed: 01/22/2023]
Abstract
Structural variation includes a change in copy number, orientation, or location of a part of the genome. Copy number variants (CNVs) are a common cause of genetic hearing loss, comprising nearly 20% of diagnosed cases. While large deletions involving the gene STRC are the most common pathogenic CNVs, a significant proportion of known hearing loss genes also contain pathogenic CNVs. In this review, we provide an overview of currently used methods for detection of CNVs in genes known to cause hearing loss including molecular techniques such as multiplex ligation probe amplification (MLPA) and digital droplet polymerase chain reaction (ddPCR), array-CGH and single-nucleotide polymorphism (SNP) arrays, as well as techniques for detection of CNVs using next-generation sequencing data analysis including targeted gene panel, exome, and genome sequencing data. In addition, in this review, we compile published data on pathogenic hearing loss CNVs to provide an up-to-date overview. We show that CNVs have been identified in 29 different non-syndromic hearing loss genes. An understanding of the contribution of CNVs to genetic hearing loss is critical to the current diagnosis of hearing loss and is crucial for future gene therapies. Thus, evaluation for CNVs is required in any modern pipeline for genetic diagnosis of hearing loss.
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7
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Le Nabec A, Collobert M, Le Maréchal C, Marianowski R, Férec C, Moisan S. Whole-Genome Sequencing Improves the Diagnosis of DFNB1 Monoallelic Patients. Genes (Basel) 2021; 12:1267. [PMID: 34440441 PMCID: PMC8391926 DOI: 10.3390/genes12081267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022] Open
Abstract
Hearing loss is the most common sensory defect, due in most cases to a genetic origin. Variants in the GJB2 gene are responsible for up to 30% of non-syndromic hearing loss. Today, several deafness genotypes remain incomplete, confronting us with a diagnostic deadlock. In this study, whole-genome sequencing (WGS) was performed on 10 DFNB1 patients with incomplete genotypes. New variations on GJB2 were identified for four patients. Functional assays were realized to explore the function of one of them in the GJB2 promoter and confirm its impact on GJB2 expression. Thus, in this study WGS resolved patient genotypes, thus unlocking diagnosis. WGS afforded progress and bridged some gaps in our research.
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Affiliation(s)
- Anaïs Le Nabec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.C.); (C.L.M.); (C.F.)
| | - Mégane Collobert
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.C.); (C.L.M.); (C.F.)
| | - Cédric Le Maréchal
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.C.); (C.L.M.); (C.F.)
- Laboratoire de Génétique Moléculaire et d’Histocompatibilité, CHRU Brest, UMR 1078, F-29200 Brest, France
| | - Rémi Marianowski
- Service ORL et Chirurgie Cervicofaciale du CHRU Brest, F-29200 Brest, France;
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.C.); (C.L.M.); (C.F.)
- Laboratoire de Génétique Moléculaire et d’Histocompatibilité, CHRU Brest, UMR 1078, F-29200 Brest, France
| | - Stéphanie Moisan
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.C.); (C.L.M.); (C.F.)
- Laboratoire de Génétique Moléculaire et d’Histocompatibilité, CHRU Brest, UMR 1078, F-29200 Brest, France
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8
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Posukh OL. Genetic etiology of hearing loss in Russia. Hum Genet 2021; 141:649-663. [PMID: 34363095 DOI: 10.1007/s00439-021-02327-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022]
Abstract
Prevalence and locus/allelic heterogeneity of the hereditary hearing loss (HL) vary significantly in different human populations. Investigation of the hereditary HL diversity and the evaluation of the factors determining the region-specific landscapes of genetic HL are important for local healthcare and medical genetic services. This review presents the summarized data from the published studies concerning the genetic etiology of HL in different populations of Russia. Multiethnic population of Russia (in total, about 146 million on 2021) includes over 180 different ethnic groups, the number of which varies from millions to just several thousand people. Among them, Russians are the largest group (about 111 million). The contribution of GJB2 gene in the HL etiology in patients of different ethnicities and ethnic-specific prevalence of the GJB2 pathogenic variants were studied in many local populations of Russia. However, the investigation of other "deafness" genes is still limited to a relatively small number of studies on patients with HL of unsolved etiology.
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Affiliation(s)
- Olga L Posukh
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia, 630090. .,Novosibirsk State University, Novosibirsk, Russia, 630090.
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9
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Lin YH, Wu PC, Tsai CY, Lin YH, Lo MY, Hsu SJ, Lin PH, Erdenechuluun J, Wu HP, Hsu CJ, Wu CC, Chen PL. Hearing Impairment with Monoallelic GJB2 Variants: A GJB2 Cause or Non-GJB2 Cause? J Mol Diagn 2021; 23:1279-1291. [PMID: 34325055 DOI: 10.1016/j.jmoldx.2021.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/23/2021] [Accepted: 07/07/2021] [Indexed: 12/26/2022] Open
Abstract
Recessive variants in GJB2 are the most common genetic cause of sensorineural hearing impairment. However, in many patients, only one variant in the GJB2 coding region is identified using conventional sequencing strategy (eg, Sanger sequencing), resulting in nonconfirmative diagnosis. Conceivably, there might be other unidentified pathogenic variants in the noncoding region of GJB2 or other deafness-causing genes in these patients. To address this, a next-generation sequencing-based diagnostic panel targeting the entire GJB2 gene and the coding regions of 158 other known deafness-causing genes was designed and applied to 95 patients with nonsyndromic sensorineural hearing impairment (including 81 Han Taiwanese and 14 Mongolian patients) in whom only a single GJB2 variant had been detected using conventional Sanger sequencing. The panel confirmed the genetic diagnosis in 24 patients (25.3%). Twenty-two of them had causative variants in several deafness-causing genes other than GJB2, including MYO15A, MYO7A, TECTA, POU4F3, KCNQ4, SLC26A4, OTOF, MT-RNR1, MITF, WFS1, and USH2A. The other two patients had causative variants in GJB2, including a Taiwanese patient with a mosaic maternal uniparental disomy c.235delC variant (approximately 69% mosaicism) and a Mongolian patient with compound heterozygous c.35dupG and c.35delG variants, which occurred at the same site. This study demonstrates the utility of next-generation sequencing in clarifying the genetic diagnosis of hearing-impaired patients with nonconfirmative GJB2 genotypes on conventional genetic examinations.
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Affiliation(s)
- Yi-Hsin Lin
- Department of Otolaryngology, National Taiwan University Hospital, National Taiwan University Hospital, Taipei, Taiwan; Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ping-Che Wu
- College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Cheng-Yu Tsai
- Department of Otolaryngology, National Taiwan University Hospital, National Taiwan University Hospital, Taipei, Taiwan; Graduate Institutes of Medical Genomic, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yin-Hung Lin
- Department of Otolaryngology, National Taiwan University Hospital, National Taiwan University Hospital, Taipei, Taiwan; Graduate Institutes of Medical Genomic, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ming-Yu Lo
- Department of Otolaryngology, National Taiwan University Hospital, National Taiwan University Hospital, Taipei, Taiwan; Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shu-Jui Hsu
- Graduate Institutes of Medical Genomic, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pei-Hsuan Lin
- Department of Otolaryngology, National Taiwan University Hospital Yunlin Branch, Yunlin, Taiwan
| | - Jargalkhuu Erdenechuluun
- Department of Otolaryngology, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia; The EMJJ Otolaryngology Hospital, Ulaanbaatar, Mongolia
| | - Hung-Pin Wu
- Department of Otolaryngology Head and Neck Surgery, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan; School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Chuan-Jen Hsu
- Department of Otolaryngology, National Taiwan University Hospital, National Taiwan University Hospital, Taipei, Taiwan; Department of Otolaryngology Head and Neck Surgery, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan
| | - Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, National Taiwan University Hospital, Taipei, Taiwan; Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan.
| | - Pei-Lung Chen
- Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei, Taiwan; Graduate Institutes of Medical Genomic, National Taiwan University College of Medicine, Taipei, Taiwan; Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University Hospital, Taipei, Taiwan.
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10
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Taylor A, Alloub Z, Tayoun AA. A Simple Practical Guide to Genomic Diagnostics in a Pediatric Setting. Genes (Basel) 2021; 12:genes12060818. [PMID: 34071827 PMCID: PMC8228870 DOI: 10.3390/genes12060818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 11/16/2022] Open
Abstract
With limited access to trained clinical geneticists and/or genetic counselors in the majority of healthcare systems globally, and the expanding use of genetic testing in all specialties of medicine, many healthcare providers do not receive the relevant support to order the most appropriate genetic test for their patients. Therefore, it is essential to educate all healthcare providers about the basic concepts of genetic testing and how to properly utilize this testing for each patient. Here, we review the various genetic testing strategies and their utilization based on different clinical scenarios, and test characteristics, such as the types of genetic variation identified by each test, turnaround time, and diagnostic yield for different clinical indications. Additional considerations such as test cost, insurance reimbursement, and interpretation of variants of uncertain significance are also discussed. The goal of this review is to aid healthcare providers in utilizing the most appropriate, fastest, and most cost-effective genetic test for their patients, thereby increasing the likelihood of a timely diagnosis and reducing the financial burden on the healthcare system by eliminating unnecessary and redundant testing.
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Affiliation(s)
- Alan Taylor
- Al Jalila Genomics Center, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates;
- Correspondence:
| | - Zeinab Alloub
- Neurodevelopment Department, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates;
| | - Ahmad Abou Tayoun
- Al Jalila Genomics Center, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates;
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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11
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Bowles B, Ferrer A, Nishimura CJ, Pinto E Vairo F, Rey T, Leheup B, Sullivan J, Schoch K, Stong N, Agolini E, Cocciadiferro D, Williams A, Cummings A, Loddo S, Genovese S, Roadhouse C, McWalter K, Wentzensen IM, Li C, Babovic-Vuksanovic D, Lanpher BC, Dentici ML, Ankala A, Hamm JA, Dallapiccola B, Radio FC, Shashi V, Gérard B, Bloch-Zupan A, Smith RJ, Klee EW. TSPEAR variants are primarily associated with ectodermal dysplasia and tooth agenesis but not hearing loss: A novel cohort study. Am J Med Genet A 2021; 185:2417-2433. [PMID: 34042254 PMCID: PMC8361973 DOI: 10.1002/ajmg.a.62347] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 04/12/2021] [Accepted: 04/22/2021] [Indexed: 12/30/2022]
Abstract
Biallelic loss‐of‐function variants in the thrombospondin‐type laminin G domain and epilepsy‐associated repeats (TSPEAR) gene have recently been associated with ectodermal dysplasia and hearing loss. The first reports describing a TSPEAR disease association identified this gene is a cause of nonsyndromic hearing loss, but subsequent reports involving additional affected families have questioned this evidence and suggested a stronger association with ectodermal dysplasia. To clarify genotype–phenotype associations for TSPEAR variants, we characterized 13 individuals with biallelic TSPEAR variants. Individuals underwent either exome sequencing or panel‐based genetic testing. Nearly all of these newly reported individuals (11/13) have phenotypes that include tooth agenesis or ectodermal dysplasia, while three newly reported individuals have hearing loss. Of the individuals displaying hearing loss, all have additional variants in other hearing‐loss‐associated genes, specifically TMPRSS3, GJB2, and GJB6, that present competing candidates for their hearing loss phenotype. When presented alongside previous reports, the overall evidence supports the association of TSPEAR variants with ectodermal dysplasia and tooth agenesis features but creates significant doubt as to whether TSPEAR variants are a monogenic cause of hearing loss. Further functional evidence is needed to evaluate this phenotypic association.
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Affiliation(s)
- Bradley Bowles
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Alejandro Ferrer
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Carla J Nishimura
- Molecular Otolaryngology and Renal Research Laboratories, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Tristan Rey
- Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France.,Laboratoires de Diagnostic génétique, Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Illkirch, France
| | - Bruno Leheup
- Département de Médecine Infantile, CHRU de Nancy, Nancy, France
| | - Jennifer Sullivan
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Kelly Schoch
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA.,Brystol Myers Squibb, New York, New York, USA
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Dario Cocciadiferro
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Abigail Williams
- Department of Pediatrics, East Tennessee Children's Hospital, Knoxville, Tennessee, USA
| | - Alex Cummings
- Department of Pediatrics, East Tennessee Children's Hospital, Knoxville, Tennessee, USA.,University of Wisconsin Hospitals and Clinics, Madison, Wisconsin, USA
| | - Sara Loddo
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Silvia Genovese
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chelsea Roadhouse
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | | | | | | | - Chumei Li
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Maria Lisa Dentici
- Genetics and Rare Diseases Research Division, Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Arun Ankala
- EGL Genetics LLC, Tucker, Georgia, USA.,Emory University School of Medicine, Atlanta, Georgia, USA
| | - J Austin Hamm
- Department of Pediatrics, East Tennessee Children's Hospital, Knoxville, Tennessee, USA
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Vandana Shashi
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Benedicte Gérard
- Laboratoires de Diagnostic génétique, Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace, Strasbourg, France
| | - Agnes Bloch-Zupan
- Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France.,Centre de référence des maladies rares orales et dentaires O-Rares, Filière Santé Maladies rares TETE COU, European Reference Network CRANIO, Pôle de Médecine et Chirurgie Bucco-dentaires, Hôpital Civil, Hôpitaux Universitaires de Strasbourg (HUS), Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Illkirch, France
| | - Richard J Smith
- Molecular Otolaryngology and Renal Research Laboratories, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
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12
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Safka Brozkova D, Uhrova Meszarosova A, Lassuthova P, Varga L, Staněk D, Borecká S, Laštůvková J, Čejnová V, Rašková D, Lhota F, Gašperíková D, Seeman P. The Cause of Hereditary Hearing Loss in GJB2 Heterozygotes-A Comprehensive Study of the GJB2/DFNB1 Region. Genes (Basel) 2021; 12:genes12050684. [PMID: 34062854 PMCID: PMC8147375 DOI: 10.3390/genes12050684] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/14/2022] Open
Abstract
Hearing loss is a genetically heterogeneous sensory defect, and the frequent causes are biallelic pathogenic variants in the GJB2 gene. However, patients carrying only one heterozygous pathogenic (monoallelic) GJB2 variant represent a long-lasting diagnostic problem. Interestingly, previous results showed that individuals with a heterozygous pathogenic GJB2 variant are two times more prevalent among those with hearing loss compared to normal-hearing individuals. This excess among patients led us to hypothesize that there could be another pathogenic variant in the GJB2 region/DFNB1 locus. A hitherto undiscovered variant could, in part, explain the cause of hearing loss in patients and would mean reclassifying them as patients with GJB2 biallelic pathogenic variants. In order to detect an unknown causal variant, we examined 28 patients using NGS with probes that continuously cover the 0.4 Mb in the DFNB1 region. An additional 49 patients were examined by WES to uncover only carriers. We did not reveal a second pathogenic variant in the DFNB1 region. However, in 19% of the WES-examined patients, the cause of hearing loss was found to be in genes other than the GJB2. We present evidence to show that a substantial number of patients are carriers of the GJB2 pathogenic variant, albeit only by chance.
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Affiliation(s)
- Dana Safka Brozkova
- Neurogenetic laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, 15006 Prague, Czech Republic; (A.U.M.); (P.L.); (D.S.); (P.S.)
- Correspondence:
| | - Anna Uhrova Meszarosova
- Neurogenetic laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, 15006 Prague, Czech Republic; (A.U.M.); (P.L.); (D.S.); (P.S.)
| | - Petra Lassuthova
- Neurogenetic laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, 15006 Prague, Czech Republic; (A.U.M.); (P.L.); (D.S.); (P.S.)
| | - Lukáš Varga
- Department of Otorhinolaryngology–Head and Neck Surgery, Faculty of Medicine and University Hospital, Comenius University, 85107 Bratislava, Slovakia;
- Diabgene Laboratory, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, 84505 Bratislava, Slovakia; (S.B.); (D.G.)
| | - David Staněk
- Neurogenetic laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, 15006 Prague, Czech Republic; (A.U.M.); (P.L.); (D.S.); (P.S.)
| | - Silvia Borecká
- Diabgene Laboratory, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, 84505 Bratislava, Slovakia; (S.B.); (D.G.)
| | - Jana Laštůvková
- Department of Medical Genetics, Masaryk Hospital in Usti nad Labem, Regional Health Corporation, 40011 Ústí nad Labem, Czech Republic; (J.L.); (V.Č.)
| | - Vlasta Čejnová
- Department of Medical Genetics, Masaryk Hospital in Usti nad Labem, Regional Health Corporation, 40011 Ústí nad Labem, Czech Republic; (J.L.); (V.Č.)
| | - Dagmar Rašková
- Centre for Medical Genetics and Reproductive Medicine GENNET, 17000 Prague, Czech Republic; (D.R.); (F.L.)
| | - Filip Lhota
- Centre for Medical Genetics and Reproductive Medicine GENNET, 17000 Prague, Czech Republic; (D.R.); (F.L.)
| | - Daniela Gašperíková
- Diabgene Laboratory, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, 84505 Bratislava, Slovakia; (S.B.); (D.G.)
| | - Pavel Seeman
- Neurogenetic laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, 15006 Prague, Czech Republic; (A.U.M.); (P.L.); (D.S.); (P.S.)
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13
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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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14
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Fathalla BM, Alsarhan A, Afzal S, El Naofal M, Abou Tayoun A. The genomic landscape of pediatric rheumatology disorders in the Middle East. Hum Mutat 2021; 42:e1-e14. [PMID: 33440462 DOI: 10.1002/humu.24165] [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] [Received: 10/03/2020] [Revised: 12/09/2020] [Accepted: 12/31/2020] [Indexed: 12/27/2022]
Abstract
The landscape and clinical utility of comprehensive genomic investigations for a wide range of pediatric rheumatic disorders have not been fully characterized in the Middle East. Here, 71 pediatric patients, of diverse Arab origins, were clinically and genetically assessed for a spectrum of rheumatology-related diseases at the only dedicated tertiary children's hospital in the United Arab Emirates. Clinical genomic investigations included mainly (76%) next-generation sequencing-based gene panels and whole-exome sequencing, along with rapid sequencing in the intensive care unit and urgent setting. The overall positive yield was 46.5%, whereas dual diagnoses were made in two cases (3%). Although the majority (21/33, 64%) of positive findings involved the MEFV gene, the remaining (12/33, 36%) alterations were attributed to 11 other genes/loci. Copy number variants (CNVs) contributed substantially (5/33, 15.2%) to the overall diagnostic yield. Sequencing-based testing, specifically rapid sequencing, had a high positive rate and delivered timely results. Genetic findings guided clinical management plans and interventions in most cases (27/33, 81.8%). We highlight unique findings and provide additional evidence that heterozygous loss of function of the IFIH1 gene increases susceptibility to recurrent fevers. Our study provides new insights into the pathogenic variation landscape in pediatric rheumatic disorders.
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Affiliation(s)
- Basil M Fathalla
- Rheumatology Department, Al Jalila Children's Specialty Hospital, Dubai, UAE
| | - Ali Alsarhan
- Pediatric Residency Program, Al Jalila Children's Specialty Hospital, Dubai, UAE
| | - Samina Afzal
- Oncology & Hematology Department, Al Jalila Children's Specialty Hospital, Dubai, UAE
| | - Maha El Naofal
- Al Jalila Genomics Center, Al Jalila Children's Specialty Hospital, Dubai, UAE
| | - Ahmad Abou Tayoun
- Al Jalila Genomics Center, Al Jalila Children's Specialty Hospital, Dubai, UAE.,Genetics Department, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
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15
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Adadey SM, Quaye O, Amedofu GK, Awandare GA, Wonkam A. Screening for GJB2-R143W-Associated Hearing Impairment: Implications for Health Policy and Practice in Ghana. Public Health Genomics 2020; 23:184-189. [PMID: 33302283 DOI: 10.1159/000512121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/23/2020] [Indexed: 11/19/2022] Open
Abstract
Genetic factors significantly contribute to the burden of hearing impairment (HI) in Ghana as there is a high carrier frequency (1.5%) of the connexin 26 gene founder variant GJB2-R143W in the healthy Ghanaian population. GJB2-R143W mutation accounts for nearly 26% of causes in families segregating congenital non-syndromic HI. With HI associated with high genetic fitness, this indicates that Ghana will likely sustain an increase in the number of individuals living with inheritable HI. There is a universal newborn hearing screening (UNHS) program in Ghana. However, this program does not include genetic testing. Adding genetic testing of GJB2-R143W mutation for the population, prenatal and neonatal stages may lead to guiding genetic counseling for individual and couples, early detection of HI for at-risk infants, and improvement of medical management, including speech therapy and audiologic intervention, as well as provision of the needed social service to enhance parenting and education for children with HI. Based on published research on the genetics of HI in Ghana, we recommend that the UNHS program should include genetic screening for the GJB2-R143W gene variant for newborns who did not pass the initial UNHS tests. This will require an upgrade and resourcing of public health infrastructures to implement the rapid and cost-effective GJB2-R143W testing, followed by appropriate genetic and anticipatory guidance for medical care.
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Affiliation(s)
- Samuel M Adadey
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.,Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Geoffrey K Amedofu
- Department of Eye Ear Nose & Throat, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa,
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16
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Adadey SM, Wonkam-Tingang E, Twumasi Aboagye E, Nayo-Gyan DW, Boatemaa Ansong M, Quaye O, Awandare GA, Wonkam A. Connexin Genes Variants Associated with Non-Syndromic Hearing Impairment: A Systematic Review of the Global Burden. Life (Basel) 2020; 10:life10110258. [PMID: 33126609 PMCID: PMC7693846 DOI: 10.3390/life10110258] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/18/2020] [Accepted: 10/27/2020] [Indexed: 12/21/2022] Open
Abstract
Mutations in connexins are the most common causes of hearing impairment (HI) in many populations. Our aim was to review the global burden of pathogenic and likely pathogenic (PLP) variants in connexin genes associated with HI. We conducted a systematic review of the literature based on targeted inclusion/exclusion criteria of publications from 1997 to 2020. The databases used were PubMed, Scopus, Africa-Wide Information, and Web of Science. The protocol was registered on PROSPERO, the International Prospective Register of Systematic Reviews, with the registration number “CRD42020169697”. The data extracted were analyzed using Microsoft Excel and SPSS version 25 (IBM, Armonk, New York, United States). A total of 571 independent studies were retrieved and considered for data extraction with the majority of studies (47.8% (n = 289)) done in Asia. Targeted sequencing was found to be the most common technique used in investigating connexin gene mutations. We identified seven connexin genes that were associated with HI, and GJB2 (520/571 publications) was the most studied among the seven. Excluding PLP in GJB2, GJB6, and GJA1 the other connexin gene variants (thus GJB3, GJB4, GJC3, and GJC1 variants) had conflicting association with HI. Biallelic GJB2 PLP variants were the most common and widespread variants associated with non-syndromic hearing impairment (NSHI) in different global populations but absent in most African populations. The most common GJB2 alleles found to be predominant in specific populations include; p.Gly12ValfsTer2 in Europeans, North Africans, Brazilians, and Americans; p.V37I and p.L79Cfs in Asians; p.W24X in Indians; p.L56Rfs in Americans; and the founder mutation p.R143W in Africans from Ghana, or with putative Ghanaian ancestry. The present review suggests that only GJB2 and GJB3 are recognized and validated HI genes. The findings call for an extensive investigation of the other connexin genes in many populations to elucidate their contributions to HI, in order to improve gene-disease pair curations, globally.
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Affiliation(s)
- Samuel Mawuli Adadey
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. Box LG 54, Legon GA184, Accra, Greater Accra Region, Ghana; (S.M.A.); (O.Q.); (G.A.A.)
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P.O. Box LG 54, Legon Accra GA184, Greater Accra Region, Ghana; (E.T.A.); (M.B.A.)
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa;
| | - Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa;
| | - Elvis Twumasi Aboagye
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P.O. Box LG 54, Legon Accra GA184, Greater Accra Region, Ghana; (E.T.A.); (M.B.A.)
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa;
| | - Daniel Wonder Nayo-Gyan
- Department of Applied Chemistry and Biochemistry, C. K. Tedam University of Technology and Applied Sciences, P.O. Box 24, Navrongo 00000, Upper East Region, Ghana;
| | - Maame Boatemaa Ansong
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P.O. Box LG 54, Legon Accra GA184, Greater Accra Region, Ghana; (E.T.A.); (M.B.A.)
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. Box LG 54, Legon GA184, Accra, Greater Accra Region, Ghana; (S.M.A.); (O.Q.); (G.A.A.)
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P.O. Box LG 54, Legon Accra GA184, Greater Accra Region, Ghana; (E.T.A.); (M.B.A.)
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. Box LG 54, Legon GA184, Accra, Greater Accra Region, Ghana; (S.M.A.); (O.Q.); (G.A.A.)
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P.O. Box LG 54, Legon Accra GA184, Greater Accra Region, Ghana; (E.T.A.); (M.B.A.)
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa;
- Correspondence: ; Tel.: +27-21-4066307
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17
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Buonfiglio P, Bruque CD, Luce L, Giliberto F, Lotersztein V, Menazzi S, Paoli B, Elgoyhen AB, Dalamón V. GJB2 and GJB6 Genetic Variant Curation in an Argentinean Non-Syndromic Hearing-Impaired Cohort. Genes (Basel) 2020; 11:E1233. [PMID: 33096615 PMCID: PMC7589744 DOI: 10.3390/genes11101233] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Genetic variants in GJB2 and GJB6 genes are the most frequent causes of hereditary hearing loss among several deaf populations worldwide. Molecular diagnosis enables proper genetic counseling and medical prognosis to patients. In this study, we present an update of testing results in a cohort of Argentinean non-syndromic hearing-impaired individuals. A total of 48 different sequence variants were detected in genomic DNA from patients referred to our laboratory. They were manually curated and classified based on the American College of Medical Genetics and Genomics/Association for Molecular Pathology ACMG/AMP standards and hearing-loss-gene-specific criteria of the ClinGen Hearing Loss Expert Panel. More than 50% of sequence variants were reclassified from their previous categorization in ClinVar. These results provide an accurately interpreted set of variants to be taken into account by clinicians and the scientific community, and hence, aid the precise genetic counseling to patients.
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Affiliation(s)
- Paula Buonfiglio
- Laboratorio de Fisiología y Genética de la Audición, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas—INGEBI/CONICET, C1428ADN Ciudad Autónoma de Buenos Aires, Argentina; (P.B.); (A.B.E.)
| | - Carlos D. Bruque
- Centro Nacional de Genética Médica, ANLIS-Malbrán, C1425 Ciudad Autónoma de Buenos Aires, Argentina;
- Instituto de Biología y Medicina Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas—IBYME/CONICET, C1428ADN Ciudad Autónoma de Buenos Aires, Argentina
| | - Leonela Luce
- Laboratorio de Distrofinopatías, Cátedra de Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, C1113AAD Ciudad Autónoma de Buenos Aires, Argentina; (L.L.); (F.G.)
- Instituto de Inmunología, Genética y Metabolismo—INIGEM/CONICET, Universidad de Buenos Aires, C1113AAD Ciudad Autónoma de Buenos Aires, Argentina
| | - Florencia Giliberto
- Laboratorio de Distrofinopatías, Cátedra de Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, C1113AAD Ciudad Autónoma de Buenos Aires, Argentina; (L.L.); (F.G.)
- Instituto de Inmunología, Genética y Metabolismo—INIGEM/CONICET, Universidad de Buenos Aires, C1113AAD Ciudad Autónoma de Buenos Aires, Argentina
| | - Vanesa Lotersztein
- Servicio de Genética, Hospital Militar Central “Dr. Cosme Argerich”, C1426 Ciudad Autónoma de Buenos Aires, Argentina;
| | - Sebastián Menazzi
- Servicio de Genética, Hospital de Clínicas “José de San Martín”, C1120AAR Ciudad Autónoma de Buenos Aires, Argentina;
| | - Bibiana Paoli
- Servicio de Otorrinolaringología Infantil, Hospital de Clínicas “José de San Martín”, C1120AAR Ciudad Autónoma de Buenos Aires, Argentina;
| | - Ana Belén Elgoyhen
- Laboratorio de Fisiología y Genética de la Audición, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas—INGEBI/CONICET, C1428ADN Ciudad Autónoma de Buenos Aires, Argentina; (P.B.); (A.B.E.)
- Departamento de Farmacología, Facultad de Medicina, Universidad de Buenos Aires, C1121ABG Ciudad Autónoma de Buenos Aires, Argentina
| | - Viviana Dalamón
- Laboratorio de Fisiología y Genética de la Audición, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas—INGEBI/CONICET, C1428ADN Ciudad Autónoma de Buenos Aires, Argentina; (P.B.); (A.B.E.)
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18
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McIntyre KJ, Murphy E, Mertens L, Dubuc AM, Heim RA, Mason-Suares H. A Role for Chromosomal Microarray Testing in the Workup of Male Infertility. J Mol Diagn 2020; 22:1189-1198. [PMID: 32615168 DOI: 10.1016/j.jmoldx.2020.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 04/28/2020] [Accepted: 06/18/2020] [Indexed: 12/23/2022] Open
Abstract
Genetic analysis is a critical component in the male infertility workup. For male infertility due to oligospermia/azoospermia, standard guidelines recommend karyotype and Y-chromosome microdeletion analyses. A karyotype is used to identify structural and numerical chromosome abnormalities, whereas Y-chromosome microdeletions are commonly evaluated by multiplex PCR analysis because of their submicroscopic size. Because these assays often require different Vacutainer tubes to be sent to different laboratories, ordering is prone to errors. In addition, this workflow limits the ability for sequential testing and a comprehensive test result. A potential solution includes performing Y-microdeletion and numerical chromosome analysis-the most common genetic causes of oligospermia/azoospermia-by chromosomal microarray (CMA) and reflexing to karyotype as both assays are often offered in the cytogenetics laboratory. Such analyses can be performed using one sodium heparin Vacutainer tube sample. To determine the effectiveness of CMA for the detection of clinically significant Y-chromosome microdeletions, 21 cases with known Y microdeletions were tested by CytoScan HD platform. CMA studies identified all known Y-chromosome microdeletions, and in 11 cases (52%) identified additional clinically important cytogenetic anomalies, including six cases of 46, XX males, one case of isodicentric Y, two cases of a dicentric Y, and three cases of terminal Yq deletions. These findings demonstrate that this testing strategy would simplify ordering and allow for an integrated interpretation of test results.
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Affiliation(s)
- Kelsey J McIntyre
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts; Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Elissa Murphy
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts
| | - Lauren Mertens
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
| | - Adrian M Dubuc
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
| | - Ruth A Heim
- Division of Integrated Genetics, LabCorp, Westborough, Massachusetts
| | - Heather Mason-Suares
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts; Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts.
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M. Adadey S, Tingang Wonkam E, Twumasi Aboagye E, Quansah D, Asante-Poku A, Quaye O, K. Amedofu G, A. Awandare G, Wonkam A. Enhancing Genetic Medicine: Rapid and Cost-Effective Molecular Diagnosis for a GJB2 Founder Mutation for Hearing Impairment in Ghana. Genes (Basel) 2020; 11:genes11020132. [PMID: 32012697 PMCID: PMC7074138 DOI: 10.3390/genes11020132] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 12/17/2022] Open
Abstract
In Ghana, gap-junction protein β 2 (GJB2) variants account for about 25.9% of familial hearing impairment (HI) cases. The GJB2-p.Arg143Trp (NM_004004.6:c.427C>T/OMIM: 121011.0009/rs80338948) variant remains the most frequent variant associated with congenital HI in Ghana, but has not yet been investigated in clinical practice. We therefore sought to design a rapid and cost-effective test to detect this variant. We sampled 20 hearing-impaired and 10 normal hearing family members from 8 families segregating autosomal recessive non syndromic HI. In addition, a total of 111 unrelated isolated individuals with HI were selected, as well as 50 normal hearing control participants. A restriction fragment length polymorphism (RFLP) test was designed, using the restriction enzyme NciI optimized and validated with Sanger sequencing, for rapid genotyping of the common GJB2-p.Arg143Trp variant. All hearing-impaired participants from 7/8 families were homozygous positive for the GJB2-p.Arg143Trp mutation using the NciI-RFLP test, which was confirmed with Sanger sequencing. The investigation of 111 individuals with isolated non-syndromic HI that were previously Sanger sequenced found that the sensitivity of the GJB2-p.Arg143Trp NciI-RFLP testing was 100%. All the 50 control subjects with normal hearing were found to be negative for the variant. Although the test is extremely valuable, it is not 100% specific because it cannot differentiate between other mutations at the recognition site of the restriction enzyme. The GJB2-p.Arg143Trp NciI-RFLP-based diagnostic test had a high sensitivity for genotyping the most common GJB2 pathogenic and founder variant (p.Arg143Trp) within the Ghanaian populations. We recommend the adoption and implementation of this test for hearing impairment genetic clinical investigations to complement the newborn hearing screening program in Ghana. The present study is a practical case scenario of enhancing genetic medicine in Africa.
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Affiliation(s)
- Samuel M. Adadey
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra P. O. Box LG 54, Ghana; (S.M.A.); (E.T.A.); (D.Q.); (A.A.-P.); (O.Q.); (G.A.A.)
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa;
| | - Edmond Tingang Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa;
| | - Elvis Twumasi Aboagye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra P. O. Box LG 54, Ghana; (S.M.A.); (E.T.A.); (D.Q.); (A.A.-P.); (O.Q.); (G.A.A.)
| | - Darius Quansah
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra P. O. Box LG 54, Ghana; (S.M.A.); (E.T.A.); (D.Q.); (A.A.-P.); (O.Q.); (G.A.A.)
| | - Adwoa Asante-Poku
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra P. O. Box LG 54, Ghana; (S.M.A.); (E.T.A.); (D.Q.); (A.A.-P.); (O.Q.); (G.A.A.)
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra P. O. Box LG 54, Ghana; (S.M.A.); (E.T.A.); (D.Q.); (A.A.-P.); (O.Q.); (G.A.A.)
| | - Geoffrey K. Amedofu
- Department of Eye Ear Nose & Throat, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi AK-039-5028, Ghana;
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra P. O. Box LG 54, Ghana; (S.M.A.); (E.T.A.); (D.Q.); (A.A.-P.); (O.Q.); (G.A.A.)
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa;
- Correspondence: ; Tel.: +27-21-4066-307
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20
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Moisan S, Le Nabec A, Quillévéré A, Le Maréchal C, Férec C. Characterization of GJB2 cis-regulatory elements in the DFNB1 locus. Hum Genet 2019; 138:1275-1286. [PMID: 31586237 DOI: 10.1007/s00439-019-02068-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/29/2019] [Indexed: 11/28/2022]
Abstract
Although most disease-causing variants are within coding region of genes, it is now well established that cis-acting regulatory sequences, depending on 3D-chromatin organization, are required for temporal and spatial control of gene expression. Disruptions of such regulatory elements and/or chromatin conformation are likely to play a critical role in human genetic disease. Hence, recurrent monoallelic cases, who present the most common hereditary type of nonsyndromic hearing loss (i.e., DFNB1), carry only one identified pathogenic allele. This strongly suggests the presence of uncharacterized distal cis-acting elements in the missing allele. Here within, we study the spatial organization of a large DFNB1 locus encompassing the gap junction protein beta 2 (GJB2) gene, the most frequently mutated gene in this inherited hearing loss phenotype, with the chromosome conformation capture carbon copy technology (5C). By combining this approach with functional activity reporter assays and mapping of CCCTC-binding factor (CTCF) along the DFNB1 locus, we identify a novel set of cooperating GJB2 cis-acting elements and suggest a DFNB1 three-dimensional looping regulation model.
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Affiliation(s)
- Stéphanie Moisan
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHRU de Brest, Bretagne, Brest, France. .,Univ Brest, Inserm, EFS UMR 1078, GGB, 29200, Brest, France.
| | - Anaïs Le Nabec
- Univ Brest, Inserm, EFS UMR 1078, GGB, 29200, Brest, France
| | | | - Cédric Le Maréchal
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHRU de Brest, Bretagne, Brest, France.,Univ Brest, Inserm, EFS UMR 1078, GGB, 29200, Brest, France
| | - Claude Férec
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHRU de Brest, Bretagne, Brest, France. .,Univ Brest, Inserm, EFS UMR 1078, GGB, 29200, Brest, France.
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21
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Posukh OL, Zytsar MV, Bady-Khoo MS, Danilchenko VY, Maslova EA, Barashkov NA, Bondar AA, Morozov IV, Maximov VN, Voevoda MI. Unique Mutational Spectrum of the GJB2 Gene and its Pathogenic Contribution to Deafness in Tuvinians (Southern Siberia, Russia): A High Prevalence of Rare Variant c.516G>C (p.Trp172Cys). Genes (Basel) 2019; 10:E429. [PMID: 31195736 PMCID: PMC6627114 DOI: 10.3390/genes10060429] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/30/2019] [Accepted: 06/03/2019] [Indexed: 01/09/2023] Open
Abstract
Mutations in the GJB2 gene are the main cause for nonsyndromic autosomal recessive deafness 1A (DFNB1A) in many populations. GJB2 mutational spectrum and pathogenic contribution are widely varying in different populations. Significant efforts have been made worldwide to define DFNB1A molecular epidemiology, but this issue still remains open for some populations. The main aim of study is to estimate the DFNB1A prevalence and GJB2 mutational spectrum in Tuvinians-an indigenous population of the Tyva Republic (Southern Siberia, Russia). Sanger sequencing was applied to analysis of coding (exon 2) and non-coding regions of GJB2 in a cohort of Tuvinian patients with hearing impairments (n = 220) and ethnically matched controls (n = 157). Diagnosis of DFNB1A was established for 22.3% patients (28.8% of familial vs 18.6% of sporadic cases). Our results support that patients with monoallelic GJB2 mutations (8.2%) are coincidental carriers. Recessive mutations p.Trp172Cys, c.-23+1G>A, c.235delC, c.299_300delAT, p.Val37Ile and several benign variants were found in examined patients. A striking finding was a high prevalence of rare variant p.Trp172Cys (c.516G>C) in Tuvinians accounting for 62.9% of all mutant GJB2 alleles and a carrier frequency of 3.8% in controls. All obtained data provide important targeted information for genetic counseling of affected Tuvinian families and enrich current information on variability of GJB2 worldwide.
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Affiliation(s)
- Olga L Posukh
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Marina V Zytsar
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Marita S Bady-Khoo
- Research Institute of Medical-Social Problems and Management of the Republic of Tyva, 667000 Kyzyl, Russia.
- Perinatal Center of the Republic of Tyva, 667000 Kyzyl, Russia.
| | - Valeria Yu Danilchenko
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Ekaterina A Maslova
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Nikolay A Barashkov
- Yakut Scientific Centre of Complex Medical Problems, 677019 Yakutsk, Russia.
- M.K. Ammosov North-Eastern Federal University, 677027 Yakutsk, Russia.
| | - Alexander A Bondar
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Igor V Morozov
- Novosibirsk State University, 630090 Novosibirsk, Russia.
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Vladimir N Maximov
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Michael I Voevoda
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Novosibirsk State University, 630090 Novosibirsk, Russia.
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22
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Shebanits K, Günther T, Johansson ACV, Maqbool K, Feuk L, Jakobsson M, Larhammar D. Copy number determination of the gene for the human pancreatic polypeptide receptor NPY4R using read depth analysis and droplet digital PCR. BMC Biotechnol 2019; 19:31. [PMID: 31164119 PMCID: PMC6549351 DOI: 10.1186/s12896-019-0523-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/30/2019] [Indexed: 01/08/2023] Open
Abstract
Background Copy number variation (CNV) plays an important role in human genetic diversity and has been associated with multiple complex disorders. Here we investigate a CNV on chromosome 10q11.22 that spans NPY4R, the gene for the appetite-regulating pancreatic polypeptide receptor Y4. This genomic region has been challenging to map due to multiple repeated elements and its precise organization has not yet been resolved. Previous studies using microarrays were interpreted to show that the most common copy number was 2 per genome. Results We have investigated 18 individuals from the 1000 Genomes project using the well-established method of read depth analysis and the new droplet digital PCR (ddPCR) method. We find that the most common copy number for NPY4R is 4. The estimated number of copies ranged from three to seven based on read depth analyses with Control-FREEC and CNVnator, and from four to seven based on ddPCR. We suggest that the difference between our results and those published previously can be explained by methodological differences such as reference gene choice, data normalization and method reliability. Three high-quality archaic human genomes (two Neanderthal and one Denisova) display four copies of the NPY4R gene indicating that a duplication occurred prior to the human-Neanderthal/Denisova split. Conclusions We conclude that ddPCR is a sensitive and reliable method for CNV determination, that it can be used for read depth calibration in CNV studies based on already available whole-genome sequencing data, and that further investigation of NPY4R copy number variation and its consequences are necessary due to the role of Y4 receptor in food intake regulation. Electronic supplementary material The online version of this article (10.1186/s12896-019-0523-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kateryna Shebanits
- Department of Neuroscience, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Anna C V Johansson
- Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Khurram Maqbool
- Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Lars Feuk
- Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, SciLifeLab, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Johannesburg, South Africa
| | - Dan Larhammar
- Department of Neuroscience, SciLifeLab, Uppsala University, Uppsala, Sweden.
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ClinGen expert clinical validity curation of 164 hearing loss gene-disease pairs. Genet Med 2019; 21:2239-2247. [PMID: 30894701 PMCID: PMC7280024 DOI: 10.1038/s41436-019-0487-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/01/2019] [Indexed: 01/08/2023] Open
Abstract
PURPOSE Proper interpretation of genomic variants is critical to successful medical decision making based on genetic testing results. A fundamental prerequisite to accurate variant interpretation is the clear understanding of the clinical validity of gene-disease relationships. The Clinical Genome Resource (ClinGen) has developed a semiquantitative framework to assign clinical validity to gene-disease relationships. METHODS The ClinGen Hearing Loss Gene Curation Expert Panel (HL GCEP) uses this framework to perform evidence-based curations of genes present on testing panels from 17 clinical laboratories in the Genetic Testing Registry. The HL GCEP curated and reviewed 142 genes and 164 gene-disease pairs, including 105 nonsyndromic and 59 syndromic forms of hearing loss. RESULTS The final outcome included 82 Definitive (50%), 12 Strong (7%), 25 Moderate (15%), 32 Limited (20%), 10 Disputed (6%), and 3 Refuted (2%) classifications. The summary of each curation is date stamped with the HL GCEP approval, is live, and will be kept up-to-date on the ClinGen website ( https://search.clinicalgenome.org/kb/gene-validity ). CONCLUSION This gene curation approach serves to optimize the clinical sensitivity of genetic testing while reducing the rate of uncertain or ambiguous test results caused by the interrogation of genes with insufficient evidence of a disease link.
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Abe S, Nishio S, Yokota Y, Moteki H, Kumakawa K, Usami S. Diagnostic pitfalls for GJB2-related hearing loss: A novel deletion detected by Array-CGH analysis in a Japanese patient with congenital profound hearing loss. Clin Case Rep 2018; 6:2111-2116. [PMID: 30455902 PMCID: PMC6230644 DOI: 10.1002/ccr3.1800] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/05/2018] [Accepted: 08/12/2018] [Indexed: 11/10/2022] Open
Abstract
Here, we report a novel deletion (copy number variation: CNV) in the GJB2 gene observed in a Japanese hearing loss patient. The deleted segment started in the middle of the GJB2 gene, but the GJB6 gene remained intact. This partial deletion in the GJB2 gene highlights the need for further improvements in GJB2 screening.
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Affiliation(s)
- Satoko Abe
- Department of OtorhinolaryngologyToranomon HospitalTokyoJapan
| | - Shin‐ya Nishio
- Department of OtolaryngologyShinshu University School of MedicineNaganoJapan
- Department of Hearing Implant SciencesShinshu University School of MedicineNaganoJapan
| | - Yoh Yokota
- Department of OtolaryngologyShinshu University School of MedicineNaganoJapan
| | - Hideaki Moteki
- Department of OtolaryngologyShinshu University School of MedicineNaganoJapan
- Department of Hearing Implant SciencesShinshu University School of MedicineNaganoJapan
| | - Kozo Kumakawa
- Department of OtorhinolaryngologyToranomon HospitalTokyoJapan
| | - Shin‐ichi Usami
- Department of OtolaryngologyShinshu University School of MedicineNaganoJapan
- Department of Hearing Implant SciencesShinshu University School of MedicineNaganoJapan
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25
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Shebanits K, Andersson-Assarsson JC, Larsson I, Carlsson LMS, Feuk L, Larhammar D. Copy number of pancreatic polypeptide receptor gene NPY4R correlates with body mass index and waist circumference. PLoS One 2018; 13:e0194668. [PMID: 29621259 PMCID: PMC5886410 DOI: 10.1371/journal.pone.0194668] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/07/2018] [Indexed: 01/14/2023] Open
Abstract
Multiple genetic studies have linked copy number variation (CNV) in different genes to body mass index (BMI) and obesity. A CNV on chromosome 10q11.22 has been associated with body weight. This CNV region spans NPY4R, the gene encoding the pancreatic polypeptide receptor Y4, which has been described as a satiety-stimulating receptor. We have investigated CNV of the NPY4R gene and analysed its relationship to BMI, waist circumference and self-reported dietary intake from 558 individuals (216 men and 342 women) representing a wide BMI range. The copy number for NPY4R ranged from 2 to 8 copies (average 4.6±0.8). Rather than the expected negative correlation, we observed a positive correlation between NPY4R copy number and BMI as well as waist circumference in women (Pearson’s r = 0.267, p = 2.65×10−7 and r = 0.256, p = 8×10−7, respectively). Each additional copy of NPY4R correlated with 2.6 kg/m2 increase in BMI and 5.67 cm increase in waist circumference (p = 2.8×10−5 and p = 6.2×10−5, respectively) for women. For men, there was no statistically significant correlation between CNV and BMI. Our results suggest that NPY4R genetic variation influences body weight in women, but the exact role of this receptor appears to be more complex than previously proposed.
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Affiliation(s)
| | | | - Ingrid Larsson
- Dept. of Gastroenterology and Hepatology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Lena M. S. Carlsson
- Dept. of Molecular and Clinical Medicine, Sahlgrenska Academy at Gothenburg University, Gothenburg, Sweden
| | - Lars Feuk
- Dept. of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Dan Larhammar
- Dept. of Neuroscience, Uppsala University, Uppsala, Sweden
- * E-mail:
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26
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Mittal R, Patel AP, Nguyen D, Pan DR, Jhaveri VM, Rudman JR, Dharmaraja A, Yan D, Feng Y, Chapagain P, Lee DJ, Blanton SH, Liu XZ. Genetic basis of hearing loss in Spanish, Hispanic and Latino populations. Gene 2018; 647:297-305. [PMID: 29331482 PMCID: PMC5806531 DOI: 10.1016/j.gene.2018.01.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 01/02/2018] [Accepted: 01/06/2018] [Indexed: 12/13/2022]
Abstract
Hearing loss (HL) is the most common neurosensory disorder affecting humans. The screening, prevention and treatment of HL require a better understanding of the underlying molecular mechanisms. Genetic predisposition is one of the most common factors that leads to HL. Most HL studies include few Spanish, Hispanic and Latino participants, leaving a critical gap in our understanding about the prevalence, impact, unmet health care needs, and genetic factors associated with hearing impairment among Spanish, Hispanic and Latino populations. The few studies which have been performed show that the gene variants commonly associated with HL in non-Spanish and non-Hispanic populations are infrequently responsible for hearing impairment in Spanish as well as Hispanic and Latino populations (hereafter referred to as Hispanic). To design effective screening tools to detect HL in Spanish and Hispanic populations, studies must be conducted to determine the gene variants that are most commonly associated with hearing impairment in this racial/ethnic group. In this review article, we summarize gene variants and loci associated with HL in Spanish and Hispanic populations. Identifying new genetic variants associated with HL in Spanish and Hispanic populations will pave the way to develop effective screening tools and therapeutic strategies for HL.
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Affiliation(s)
- Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Amit P Patel
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Desiree Nguyen
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Debbie R Pan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Vasanti M Jhaveri
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jason R Rudman
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Arjuna Dharmaraja
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Yong Feng
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, China
| | - Prem Chapagain
- Department of Physics and Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - David J Lee
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Susan H Blanton
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA; Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, China; Tsinghua University School of Medicine, Beijing 10084, China; Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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Amr SS, Murphy E, Duffy E, Niazi R, Balciuniene J, Luo M, Rehm HL, Abou Tayoun AN. Allele-Specific Droplet Digital PCR Combined with a Next-Generation Sequencing-Based Algorithm for Diagnostic Copy Number Analysis in Genes with High Homology: Proof of Concept Using Stereocilin. Clin Chem 2018; 64:705-714. [PMID: 29339441 DOI: 10.1373/clinchem.2017.280685] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 12/08/2017] [Indexed: 11/06/2022]
Abstract
BACKGROUND Copy number variants (CNVs) can substantially contribute to the pathogenic variant spectrum in several disease genes. The detection of this type of variant is complicated in genes with high homology to other genomic sequences, yet such genomics regions are more likely to lead to CNVs, making it critical to address detection in these settings. METHODS We developed a copy number analysis approach for high homology genes/regions that consisted of next-generation sequencing (NGS)-based dosage analysis accompanied by allele-specific droplet digital PCR (ddPCR) confirmatory testing. We applied this approach to copy number analysis in STRC, a gene with 98.9% homology to a nonfunctional pseudogene, pSTRC, and characterized its accuracy in detecting different copy number states by use of known samples. RESULTS Using a cohort of 517 patients with hearing loss, we prospectively demonstrated the clinical utility of the approach, which contributed 30 of the 122 total positives (6%) to the diagnostic yield, increasing the overall yield from 17.6% to 23.6%. Positive STRC genotypes included homozygous (n = 15) or compound heterozygous (n = 8) deletions, or heterozygous deletions in trans with pathogenic sequence variants (n = 7). Finally, this approach limited ddPCR testing to cases with NGS copy number findings, thus markedly reducing the number of costly and laborious, albeit specific, ddPCR tests. CONCLUSIONS NGS-based CNV detection followed by allele-specific ddPCR confirmatory testing is a reliable and affordable approach for copy number analysis in medically relevant genes with homology issues.
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Affiliation(s)
- Sami S Amr
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA.,Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA
| | - Elissa Murphy
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA
| | - Elizabeth Duffy
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA
| | - Rojeen Niazi
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jorune Balciuniene
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Minjie Luo
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA.,The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA.,Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA.,The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ahmad N Abou Tayoun
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA; .,The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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28
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del Castillo FJ, del Castillo I. DFNB1 Non-syndromic Hearing Impairment: Diversity of Mutations and Associated Phenotypes. Front Mol Neurosci 2017; 10:428. [PMID: 29311818 PMCID: PMC5743749 DOI: 10.3389/fnmol.2017.00428] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/07/2017] [Indexed: 02/02/2023] Open
Abstract
The inner ear is a very complex sensory organ whose development and function depend on finely balanced interactions among diverse cell types. The many different kinds of inner ear supporting cells play the essential roles of providing physical and physiological support to sensory hair cells and of maintaining cochlear homeostasis. Appropriately enough, the gene most commonly mutated among subjects with hereditary hearing impairment (HI), GJB2, encodes the connexin-26 (Cx26) gap-junction channel protein that underlies both intercellular communication among supporting cells and homeostasis of the cochlear fluids, endolymph and perilymph. GJB2 lies at the DFNB1 locus on 13q12. The specific kind of HI associated with this locus is caused by recessively-inherited mutations that inactivate the two alleles of the GJB2 gene, either in homozygous or compound heterozygous states. We describe the many diverse classes of genetic alterations that result in DFNB1 HI, such as large deletions that either destroy the GJB2 gene or remove a regulatory element essential for GJB2 expression, point mutations that interfere with promoter function or splicing, and small insertions or deletions and nucleotide substitutions that target the GJB2 coding sequence. We focus on how these alterations disrupt GJB2 and Cx26 functions and on their different effects on cochlear development and physiology. We finally discuss the diversity of clinical features of DFNB1 HI as regards severity, age of onset, inner ear malformations and vestibular dysfunction, highlighting the areas where future research should be concentrated.
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Affiliation(s)
- Francisco J. del Castillo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Ignacio del Castillo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
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29
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Almontashiri NAM, Alswaid A, Oza A, Al-Mazrou KA, Elrehim O, Tayoun AA, Rehm HL, Amr SS. Recurrent variants in OTOF are significant contributors to prelingual nonsydromic hearing loss in Saudi patients. Genet Med 2017; 20:536-544. [PMID: 29048421 PMCID: PMC5929117 DOI: 10.1038/gim.2017.143] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/03/2017] [Indexed: 12/01/2022] Open
Abstract
Purpose Hearing loss is more prevalent in the Saudi Arabian population than in other populations; however, the full range of genetic etiologies in this population is unknown. We report the genetic findings from 33 Saudi hearing-loss probands of tribal ancestry, with predominantly prelingual severe to profound hearing loss. Methods Testing was performed over the course of 2012–2016, and involved initial GJB2 sequence and GJB6-D13S1830 deletion screening, with negative cases being reflexed to a next-generation sequencing panel with 70, 71, or 87 hearing-loss genes. Results A “positive” result was reached in 63% of probands, with two recurrent OTOF variants (p.Glu57* and p.Arg1792His) accountable for a third of all “positive” cases. The next most common cause was pathogenic variants in MYO7A and SLC26A4, each responsible for three “positive” cases. Interestingly, only one “positive” diagnosis had a DFNB1-related cause, due to a homozygous GJB6-D13S1830 deletion, and no sequence variants in GJB2 were detected. Conclusion Our findings implicate OTOF as a potential major contributor to hearing loss in the Saudi population, while highlighting the low contribution of GJB2, thus offering important considerations for clinical testing strategies for Saudi patients. Further screening of Saudi patients is needed to characterize the genetic spectrum in this population.
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Affiliation(s)
- Naif A M Almontashiri
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | | | - Andrea Oza
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA
| | - Khalid A Al-Mazrou
- Department of Otolaryngology, King Saud University, Riyadh, Saudi Arabia
| | - Omnia Elrehim
- Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Ahmad Abou Tayoun
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sami S Amr
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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30
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Bliznetz EA, Lalayants MR, Markova TG, Balanovsky OP, Balanovska EV, Skhalyakho RA, Pocheshkhova EA, Nikitina NV, Voronin SV, Kudryashova EK, Glotov OS, Polyakov AV. Update of the GJB2/DFNB1 mutation spectrum in Russia: a founder Ingush mutation del(GJB2-D13S175) is the most frequent among other large deletions. J Hum Genet 2017; 62:789-795. [PMID: 28405014 PMCID: PMC5584515 DOI: 10.1038/jhg.2017.42] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Revised: 03/05/2017] [Accepted: 03/05/2017] [Indexed: 11/09/2022]
Abstract
Although mutations in the GJB2 gene sequence make up the majority of variants causing autosomal-recessive non-syndromic hearing loss, few large deletions have been shown to contribute to DFNB1 deafness. Currently, genetic testing for DFNB1 hearing loss includes GJB2 sequencing and DFNB1 deletion analysis for two common large deletions, del(GJB6-D13S1830) and del(GJB6-D13S1854). Here, we report frequency in Russia, clinical significance and evolutionary origins of a 101 kb deletion, del(GJB2-D13S175), recently identified by us. In multiethnic cohort of 1104 unrelated hearing loss patients with biallelic mutations at the DFNB1 locus, the del(GJB2-D13S175) allele frequency of up to 0.5% (11/2208) was determined and this allele was shown to be predominantly associated with profound sensorineural hearing loss. Additionally, eight previously unpublished GJB2 mutations were described in this study. All patients carrying del(GJB2-D13S175) were of the Ingush ancestry. Among normal hearing individuals, del(GJB2-D13S175) was observed in Russian Republic of Ingushetia with a carrier rate of ~1% (2/241). Analysis of haplotypes associated with the deletion revealed a common founder in the Ingushes, with age of the deletion being ~3000 years old. Since del(GJB2-D13S175) was missed by standard methods of GJB2 analysis, del(GJB2-D13S175) detection has been added to our routine testing strategy for DFNB1 hearing loss.
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Affiliation(s)
- Elena A Bliznetz
- The Federal Agency for Scientific Organizations, Federal State Budgetary Institution, Research Centre for Medical Genetics, Moscow, Russia
| | - Maria R Lalayants
- Federal Medical and Biological Agency, Federal State-Funded Institution of Science, National Research Center for Audiology and Hearing Rehabilitation, Moscow, Russia
| | - Tatiana G Markova
- Federal Medical and Biological Agency, Federal State-Funded Institution of Science, National Research Center for Audiology and Hearing Rehabilitation, Moscow, Russia
| | - Oleg P Balanovsky
- The Federal Agency for Scientific Organizations, Federal State Budgetary Institution, Research Centre for Medical Genetics, Moscow, Russia
- The Russian Academy of Sciences, Federal State-Funded Institution of Science, Vavilov Institute of General Genetics, Moscow, Russia
| | - Elena V Balanovska
- The Federal Agency for Scientific Organizations, Federal State Budgetary Institution, Research Centre for Medical Genetics, Moscow, Russia
| | - Roza A Skhalyakho
- The Federal Agency for Scientific Organizations, Federal State Budgetary Institution, Research Centre for Medical Genetics, Moscow, Russia
- The Russian Academy of Sciences, Federal State-Funded Institution of Science, Vavilov Institute of General Genetics, Moscow, Russia
| | - Elvira A Pocheshkhova
- The Ministry of Health, Federal State-Funded Educational Institution of Higher Education, Kuban State Medical University, Krasnodar, Russia
| | - Natalya V Nikitina
- The Ministry of Health, State Budgetary Healthcare Institution, Clinical-Diagnostic Center of Mother and Child Health Protection, Yekaterinburg, Russia
| | - Sergey V Voronin
- State Autonomous Healthcare Institution, Regional Clinical Center of Specialized Medical Care, Vladivostok, Russia
| | - Elena K Kudryashova
- The Ministry of Health, State Budgetary Healthcare Institution, Leningrad Regional Clinical Hospital, Saint Petersburg, Russia
| | - Oleg S Glotov
- Federal State Budgetary Educational Institution of Higher Education, Saint Petersburg University, Saint Petersburg, Russia
| | - Alexander V Polyakov
- The Federal Agency for Scientific Organizations, Federal State Budgetary Institution, Research Centre for Medical Genetics, Moscow, Russia
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31
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Bliznetz EA, Kanivets IV, Polyakov AV. DNA copy number analysis of the DFNB1 hereditary hearing loss locus. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417050027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Butchbach MER. Applicability of digital PCR to the investigation of pediatric-onset genetic disorders. BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 10:9-14. [PMID: 27990344 PMCID: PMC5154671 DOI: 10.1016/j.bdq.2016.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/08/2016] [Accepted: 06/21/2016] [Indexed: 12/12/2022]
Abstract
Early-onset rare diseases have a strong impact on child healthcare even though the incidence of each of these diseases is relatively low. In order to better manage the care of these children, it is imperative to quickly diagnose the molecular bases for these disorders as well as to develop technologies with prognostic potential. Digital PCR (dPCR) is well suited for this role by providing an absolute quantification of the target DNA within a sample. This review illustrates how dPCR can be used to identify genes associated with pediatric-onset disorders, to identify copy number status of important disease-causing genes and variants and to quantify modifier genes. It is also a powerful technology to track changes in genomic biomarkers with disease progression. Based on its capability to accurately and reliably detect genomic alterations with high sensitivity and a large dynamic detection range, dPCR has the potential to become the tool of choice for the verification of pediatric disease-associated mutations identified by next generation sequencing, copy number determination and noninvasive prenatal screening.
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Affiliation(s)
- Matthew E R Butchbach
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Department of Biological Sciences, University of Delaware, Newark, DE, USA; Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, USA
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