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Mainali A, Athey T, Bahl S, Hung C, Caluseriu O, Chan A, Eaton A, Ghai SJ, Kannu P, MacPherson M, Niederhoffer KY, Siriwardena K, Mercimek-Andrews S. Diagnostic yield of clinical exome sequencing in adulthood in medical genetics clinics. Am J Med Genet A 2023; 191:510-517. [PMID: 36401557 DOI: 10.1002/ajmg.a.63053] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/11/2022] [Accepted: 11/08/2022] [Indexed: 11/21/2022]
Abstract
Clinical exome sequencing (ES) is the most comprehensive genomic test to identify underlying genetic diseases in Canada. We performed this retrospective cohort study to investigate the diagnostic yield of clinical ES in adulthood. Inclusion criteria were: (1) Adult patients ≥18 years old; (2) Patients underwent clinical ES between January 1 and December 31, 2021; (3) Patients were seen in the Department of Medical Genetics. We reviewed patient charts. We applied American College of Medical Genetics and Genomics and the Association for Molecular Pathology variant classification guidelines for interpretation of variants. Non-parametric Fisher's exact statistical test was used. Seventy-seven patients underwent clinical ES. Fourteen different genetic diseases were confirmed in 15 patients: FBXO11, MYH7, MED13L, NSD2, ANKRD11 (n = 2), SHANK3, RHOBTB2, CDKL5, TRIO, TCF4, SCN1, SMAD3, POGZ, and EIF2B3 diseases. The diagnostic yield of clinical ES was 19.5%. Patients with a genetic diagnosis had a significantly higher frequency of neurodevelopmental disorders than those with no genetic diagnosis (p = 0.00339). The diagnostic yield of clinical ES was the highest in patients with seizures (35.7%), and with progressive neurodegenerative diseases (33.3%). Clinical ES is a helpful genomic test to provide genetic diagnoses to the patients who are referred to medical genetic clinics due to suspected genetic diseases in adulthood to end their diagnostic odyssey. Targeted next generation sequencing panels for specific phenotypes may decrease the cost of genomic test in adulthood.
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Affiliation(s)
- Apurba Mainali
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Alberta Health Services, Edmonton Zone, Edmonton, Alberta, Canada
| | - Taryn Athey
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Alberta Health Services, Edmonton Zone, Edmonton, Alberta, Canada
| | - Shalini Bahl
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Alberta Health Services, Edmonton Zone, Edmonton, Alberta, Canada.,Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Clara Hung
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Alberta Health Services, Edmonton Zone, Edmonton, Alberta, Canada
| | - Oana Caluseriu
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Alberta Health Services, Edmonton Zone, Edmonton, Alberta, Canada
| | - Alicia Chan
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Alberta Health Services, Edmonton Zone, Edmonton, Alberta, Canada
| | - Alison Eaton
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Alberta Health Services, Edmonton Zone, Edmonton, Alberta, Canada
| | - Shailly Jain Ghai
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Alberta Health Services, Edmonton Zone, Edmonton, Alberta, Canada
| | - Peter Kannu
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Alberta Health Services, Edmonton Zone, Edmonton, Alberta, Canada
| | - Melissa MacPherson
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Alberta Health Services, Edmonton Zone, Edmonton, Alberta, Canada
| | - Karen Y Niederhoffer
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Alberta Health Services, Edmonton Zone, Edmonton, Alberta, Canada
| | - Komudi Siriwardena
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Alberta Health Services, Edmonton Zone, Edmonton, Alberta, Canada
| | - Saadet Mercimek-Andrews
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Alberta Health Services, Edmonton Zone, Edmonton, Alberta, Canada.,Women and Children's Health Research Institute, University of Alberta, Edmonton, Alberta, Canada.,Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta, Canada
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Bessenyei B, Balogh I, Mokánszki A, Ujfalusi A, Pfundt R, Szakszon K. MED13L-related intellectual disability due to paternal germinal mosaicism. Cold Spring Harb Mol Case Stud 2022; 8:a006124. [PMID: 34654706 PMCID: PMC8744498 DOI: 10.1101/mcs.a006124] [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: 06/30/2021] [Accepted: 09/13/2021] [Indexed: 12/03/2022] Open
Abstract
The MED13L-related intellectual disability or MRFACD syndrome (Mental retardation and distinctive facial features with or without cardiac defects; MIM # 616789) is one of the most common forms of syndromic intellectual disability with about a hundred cases reported so far. Affected individuals share overlapping features comprising intellectual disability, hypotonia, motor delay, remarkable speech delay, and a recognizable facial gestalt. De novo disruption of the MED13L gene by deletions, duplications, or sequence variants has been identified as deleterious. Siblings affected by intragenic deletion transmitted from a mosaic parent have been reported once in the literature. We now present the first case of paternal germinal mosaicism for a missense MED13L variant causing MRFACD syndrome in one of the father's children and being the likely cause of intellectual disability and facial dysmorphism in the other. As part of the Mediator complex, the MED proteins have an essential role in regulating transcription. Thirty-two subunits of the Mediator complex genes have been linked to congenital malformations that are now acknowledged as transcriptomopathies. The MRFACD syndrome has been suggested to represent a recognizable phenotype.
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Affiliation(s)
- Beáta Bessenyei
- Division of Clinical Genetics, Department of Laboratory Medicine, University of Debrecen, Debrecen, 4032 Hungary
| | - István Balogh
- Division of Clinical Genetics, Department of Laboratory Medicine, University of Debrecen, Debrecen, 4032 Hungary
| | - Attila Mokánszki
- Institute of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, 4032 Hungary
| | - Anikó Ujfalusi
- Division of Clinical Genetics, Department of Laboratory Medicine, University of Debrecen, Debrecen, 4032 Hungary
| | - Rolph Pfundt
- Genome Diagnostics Nijmegen, Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Katalin Szakszon
- Institute of Paediatrics, Faculty of Medicine, University of Debrecen, Debrecen, 4032 Hungary
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Sabo A, Murdock D, Dugan S, Meng Q, Gingras MC, Hu J, Muzny D, Gibbs R. Community-based recruitment and exome sequencing indicates high diagnostic yield in adults with intellectual disability. Mol Genet Genomic Med 2020; 8:e1439. [PMID: 32767738 PMCID: PMC7549560 DOI: 10.1002/mgg3.1439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/12/2020] [Accepted: 07/01/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Establishing a genetic diagnosis for individuals with intellectual disability (ID) benefits patients and their families as it may inform the prognosis, lead to appropriate therapy, and facilitate access to medical and supportive services. Exome sequencing has been successfully applied in a diagnostic setting, but most clinical exome referrals are pediatric patients, with many adults with ID lacking a comprehensive genetic evaluation. METHODS Our unique recruitment strategy involved partnering with service and education providers for individuals with ID. We performed exome sequencing and analysis, and clinical variant interpretation for each recruited family. RESULTS All five families enrolled in the study opted-in for the return of genetic results. In three out of five families exome sequencing analysis identified pathogenic or likely pathogenic variants in KANSL1, TUSC3, and MED13L genes. Families discussed the results and any potential medical follow-up in an appointment with a board certified clinical geneticist. CONCLUSION Our study suggests high yield of exome sequencing as a diagnostic tool in adult patients with ID who have not undergone comprehensive sequencing-based genetic testing. Research studies including an option of return of results through a genetic clinic could help minimize the disparity in exome diagnostic testing between pediatric and adult patients with ID.
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Affiliation(s)
- Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - David Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
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