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Fellner A, Wali GM, Mahant N, Grosz BR, Ellis M, Narayanan RK, Ng K, Davis RL, Tchan MC, Kotschet K, Yeow D, Rudaks LI, Siow SF, Wali G, Yiannikas C, Hobbs M, Copty J, Geaghan M, Darveniza P, Liang C, Williams LJ, Chang FCF, Morales-Briceño H, Tisch S, Hayes M, Whyte S, Kummerfeld S, Kennerson ML, Cowley MJ, Fung VSC, Sue CM, Kumar KR. Genome sequencing reanalysis increases the diagnostic yield in dystonia. Parkinsonism Relat Disord 2024; 124:107010. [PMID: 38772265 DOI: 10.1016/j.parkreldis.2024.107010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/15/2024] [Accepted: 05/12/2024] [Indexed: 05/23/2024]
Abstract
PURPOSE We investigated the contribution of genomic data reanalysis to the diagnostic yield of dystonia patients who remained undiagnosed after prior genome sequencing. METHODS Probands with heterogeneous dystonia phenotypes who underwent initial genome sequencing (GS) analysis in 2019 were included in the reanalysis, which was performed through gene-specific discovery collaborations and systematic genomic data reanalysis. RESULTS Initial GS analysis in 2019 (n = 111) identified a molecular diagnosis in 11.7 % (13/111) of cases. Reanalysis between 2020 and 2023 increased the diagnostic yield by 7.2 % (8/111); 3.6 % (4/111) through focused gene-specific clinical correlation collaborative efforts [VPS16 (two probands), AOPEP and POLG], and 3.6 % (4/111) by systematic reanalysis completed in 2023 [NUS1 (two probands) and DDX3X variants, and a microdeletion encompassing VPS16]. Seven of these patients had a high phenotype-based dystonia score ≥3. Notable unverified findings in four additional cases included suspicious variants of uncertain significance in FBXL4 and EIF2AK2, and potential phenotypic expansion associated with SLC2A1 and TREX1 variants. CONCLUSION GS data reanalysis increased the diagnostic yield from 11.7 % to 18.9 %, with potential extension up to 22.5 %. While optimal timing for diagnostic reanalysis remains to be determined, this study demonstrates that periodic re-interrogation of dystonia GS datasets can provide additional genetic diagnoses, which may have significant implications for patients and their families.
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Affiliation(s)
- Avi Fellner
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; The Neurogenetics Clinic, Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel.
| | | | - Neil Mahant
- Movement Disorders Unit, Neurology Department, Westmead Hospital, Westmead, NSW, Australia
| | - Bianca R Grosz
- Northcott Neuroscience Laboratory, ANZAC Research Institute SLHD, Concord, NSW, Australia
| | - Melina Ellis
- Northcott Neuroscience Laboratory, ANZAC Research Institute SLHD, Concord, NSW, Australia
| | - Ramesh K Narayanan
- Northcott Neuroscience Laboratory, ANZAC Research Institute SLHD, Concord, NSW, Australia
| | - Karl Ng
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Department of Neurology, Royal North Shore Hospital, Northern Sydney Local Health District, Sydney, NSW, Australia
| | - Ryan L Davis
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Department of Neurogenetics, Kolling Institute, Faculty of Medicine and Health, University of Sydney and Northern Sydney Local Health District, St. Leonards, NSW, Australia
| | - Michel C Tchan
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Department of Genetic Medicine, Westmead Hospital, Westmead, NSW, Australia
| | - Katya Kotschet
- Clinical Neurosciences, St. Vincent's Hospital, Melbourne, Australia
| | - Dennis Yeow
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Department of Neurology, Concord Repatriation General Hospital, Sydney, NSW, Australia; Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, NSW, Australia; Neuroscience Research Australia, Sydney, NSW, Australia
| | - Laura I Rudaks
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Department of Neurology, Concord Repatriation General Hospital, Sydney, NSW, Australia; Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, NSW, Australia; Department of Clinical Genetics, Royal North Shore Hospital, St. Leonards, NSW, Australia
| | - Sue-Faye Siow
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Department of Clinical Genetics, Royal North Shore Hospital, St. Leonards, NSW, Australia
| | - Gautam Wali
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Department of Neurogenetics, Kolling Institute, Faculty of Medicine and Health, University of Sydney and Northern Sydney Local Health District, St. Leonards, NSW, Australia; Neuroscience Research Australia, Sydney, NSW, Australia
| | - Con Yiannikas
- Department of Neurology, Royal North Shore Hospital, Northern Sydney Local Health District, Sydney, NSW, Australia; Department of Neurology, Concord Repatriation General Hospital, Sydney, NSW, Australia
| | - Matthew Hobbs
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Joseph Copty
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Michael Geaghan
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Paul Darveniza
- Department of Neurology, St. Vincent's Hospital, Darlinghurst, NSW, Australia
| | - Christina Liang
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Department of Neurology, Royal North Shore Hospital, Northern Sydney Local Health District, Sydney, NSW, Australia; Neuroscience Research Australia, Sydney, NSW, Australia
| | - Laura J Williams
- Movement Disorders Unit, Neurology Department, Westmead Hospital, Westmead, NSW, Australia
| | - Florence C F Chang
- Movement Disorders Unit, Neurology Department, Westmead Hospital, Westmead, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Hugo Morales-Briceño
- Movement Disorders Unit, Neurology Department, Westmead Hospital, Westmead, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Stephen Tisch
- Department of Neurology, St. Vincent's Hospital, Darlinghurst, NSW, Australia; School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Michael Hayes
- Department of Neurology, Concord Repatriation General Hospital, Sydney, NSW, Australia
| | - Scott Whyte
- Department of Neurology, Gosford Hospital, Gosford, Australia
| | - Sarah Kummerfeld
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute SLHD, Concord, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, NSW, Australia
| | - Mark J Cowley
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia; Children's Cancer Institute, University of New South Wales, Sydney, Australia
| | - Victor S C Fung
- Movement Disorders Unit, Neurology Department, Westmead Hospital, Westmead, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Carolyn M Sue
- Department of Neurology, Royal North Shore Hospital, Northern Sydney Local Health District, Sydney, NSW, Australia; Department of Neurogenetics, Kolling Institute, Faculty of Medicine and Health, University of Sydney and Northern Sydney Local Health District, St. Leonards, NSW, Australia; Neuroscience Research Australia, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Kishore R Kumar
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Department of Neurology, Concord Repatriation General Hospital, Sydney, NSW, Australia; Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, NSW, Australia; School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia.
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2
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Robertson AJ, Mallett AJ, Stark Z, Sullivan C. It Is in Our DNA: Bringing Electronic Health Records and Genomic Data Together for Precision Medicine. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2024; 5:e55632. [PMID: 38935958 PMCID: PMC11211701 DOI: 10.2196/55632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/08/2024] [Accepted: 04/09/2024] [Indexed: 06/29/2024]
Abstract
Health care is at a turning point. We are shifting from protocolized medicine to precision medicine, and digital health systems are facilitating this shift. By providing clinicians with detailed information for each patient and analytic support for decision-making at the point of care, digital health technologies are enabling a new era of precision medicine. Genomic data also provide clinicians with information that can improve the accuracy and timeliness of diagnosis, optimize prescribing, and target risk reduction strategies, all of which are key elements for precision medicine. However, genomic data are predominantly seen as diagnostic information and are not routinely integrated into the clinical workflows of electronic medical records. The use of genomic data holds significant potential for precision medicine; however, as genomic data are fundamentally different from the information collected during routine practice, special considerations are needed to use this information in a digital health setting. This paper outlines the potential of genomic data integration with electronic records, and how these data can enable precision medicine.
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Affiliation(s)
- Alan J Robertson
- Faculty of Medicine, University of Queensland, Hertson, Australia
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Queensland Digital Health Centre, University of Queensland, Brisbane, Australia
- The Genomic Institute, Department of Health, Queensland Government, Brisbane, Australia
| | - Andrew J Mallett
- Department of Renal Medicine, Townsville University Hospital, Townsville, Australia
- College of Medicine and Dentistry, James Cook University, Townsville, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Australian Genomics, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
| | - Clair Sullivan
- Queensland Digital Health Centre, University of Queensland, Brisbane, Australia
- Centre for Health Services Research, Faculty of Medicine, University of Queensland, Woolloongabba, Australia
- Metro North Hospital and Health Service, Department of Health, Queensland Government, Brisbane, Australia
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3
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Best S, Fehlberg Z, Richards C, Quinn MCJ, Lunke S, Spurdle AB, Kassahn KS, Patel C, Vears DF, Goranitis I, Lynch F, Robertson A, Tudini E, Christodoulou J, Scott H, McGaughran J, Stark Z. Reanalysis of genomic data in rare disease: current practice and attitudes among Australian clinical and laboratory genetics services. Eur J Hum Genet 2024:10.1038/s41431-024-01633-8. [PMID: 38796577 DOI: 10.1038/s41431-024-01633-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/19/2024] [Accepted: 05/09/2024] [Indexed: 05/28/2024] Open
Abstract
Reanalyzing stored genomic data over time is highly effective in increasing diagnostic yield in rare disease. Automation holds the promise of delivering the benefits of reanalysis at scale. Our study aimed to understand current reanalysis practices among Australian clinical and laboratory genetics services and explore attitudes towards large-scale automated re-analysis. We collected audit data regarding testing and reanalysis volumes, policies and procedures from all Australian diagnostic laboratories providing rare disease genomic testing. A genetic health professionals' survey explored current practices, barriers to reanalysis, preferences and attitudes towards automation. Between 2018 and 2021, Australian diagnostic laboratories performed over 25,000 new genomic tests and 950 reanalyses, predominantly in response to clinician requests. Laboratory and clinical genetic health professionals (N = 134) identified workforce capacity as the principal barrier to reanalysis. No specific laboratory or clinical guidelines for genomic data reanalysis or policies were identified nationally. Perceptions of acceptability and feasibility of automating reanalysis were positive, with professionals emphasizing clinical and workflow benefits. In conclusion, there is a large and rapidly growing unmet need for reanalysis of existing genomic data. Beyond developing scalable automated reanalysis pipelines, leadership and policy are needed to successfully transform service delivery models and maximize clinical benefit.
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Affiliation(s)
- Stephanie Best
- Australian Genomics, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Victorian Comprehensive Cancer Centre Alliance, Melbourne, VIC, Australia
| | - Zoe Fehlberg
- Australian Genomics, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Christopher Richards
- Centre for Population Genomics, Garvan Institute of Medical Research, University of New South Wales Sydney, Sydney, NSW, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Michael C J Quinn
- Australian Genomics, Melbourne, VIC, Australia
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Sebastian Lunke
- University of Melbourne, Melbourne, VIC, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Karin S Kassahn
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Danya F Vears
- University of Melbourne, Melbourne, VIC, Australia
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Ilias Goranitis
- Australian Genomics, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Fiona Lynch
- University of Melbourne, Melbourne, VIC, Australia
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Alan Robertson
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- The University of Queensland, Brisbane, QLD, Australia
- The Genomic Institute, Department of Health, Queensland Government, Brisbane, QLD, Australia
| | - Emma Tudini
- Australian Genomics, Melbourne, VIC, Australia
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - John Christodoulou
- University of Melbourne, Melbourne, VIC, Australia
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Hamish Scott
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Julie McGaughran
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
- The University of Queensland, Brisbane, QLD, Australia
| | - Zornitza Stark
- Australian Genomics, Melbourne, VIC, Australia.
- University of Melbourne, Melbourne, VIC, Australia.
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.
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4
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Kumar KR, Cowley MJ, Davis RL. The Next, Next-Generation of Sequencing, Promising to Boost Research and Clinical Practice. Semin Thromb Hemost 2024. [PMID: 38733978 DOI: 10.1055/s-0044-1786756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024]
Affiliation(s)
- Kishore R Kumar
- Molecular Medicine Laboratory and Department of Neurology, Concord Repatriation General Hospital, Concord Clinical School, University of Sydney, Concord, NSW, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- School of Clinical Medicine, UNSW Sydney, Randwick, NSW, Australia
| | - Mark J Cowley
- School of Clinical Medicine, UNSW Sydney, Randwick, NSW, Australia
- Children's Cancer Institute, UNSW Sydney, Randwick, NSW, Australia
| | - Ryan L Davis
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Neurogenetics Research Group, Kolling Institute, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney and Northern Sydney Local Health District, St Leonards, NSW, Australia
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5
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van der Geest MA, Maeckelberghe ELM, van Gijn ME, Lucassen AM, Swertz MA, van Langen IM, Plantinga M. Systematic reanalysis of genomic data by diagnostic laboratories: a scoping review of ethical, economic, legal and (psycho)social implications. Eur J Hum Genet 2024; 32:489-497. [PMID: 38480795 PMCID: PMC11061183 DOI: 10.1038/s41431-023-01529-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 05/02/2024] Open
Abstract
With the introduction of Next Generation Sequencing (NGS) techniques increasing numbers of disease-associated variants are being identified. This ongoing progress might lead to diagnoses in formerly undiagnosed patients and novel insights in already solved cases. Therefore, many studies suggest introducing systematic reanalysis of NGS data in routine diagnostics. Introduction will, however, also have ethical, economic, legal and (psycho)social (ELSI) implications that Genetic Health Professionals (GHPs) from laboratories should consider before possible implementation of systematic reanalysis. To get a first impression we performed a scoping literature review. Our findings show that for the vast majority of included articles ELSI aspects were not mentioned as such. However, often these issues were raised implicitly. In total, we identified nine ELSI aspects, such as (perceived) professional responsibilities, implications for consent and cost-effectiveness. The identified ELSI aspects brought forward necessary trade-offs for GHPs to consciously take into account when considering responsible implementation of systematic reanalysis of NGS data in routine diagnostics, balancing the various strains on their laboratories and personnel while creating optimal results for new and former patients. Some important aspects are not well explored yet. For example, our study shows GHPs see the values of systematic reanalysis but also experience barriers, often mentioned as being practical or financial only, but in fact also being ethical or psychosocial. Engagement of these GHPs in further research on ELSI aspects is important for sustainable implementation.
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Affiliation(s)
- Marije A van der Geest
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| | - Els L M Maeckelberghe
- Institute for Medical Education, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marielle E van Gijn
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anneke M Lucassen
- Faculty of Medicine, Clinical Ethics and Law, University of Southampton, Southampton, UK
- Centre for Personalised Medicine, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Morris A Swertz
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Irene M van Langen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mirjam Plantinga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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6
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Robertson AJ, Tran KA, Bennett C, Sullivan C, Stark Z, Vadlamudi L, Waddell N. Clinically significant changes in genes and variants associated with epilepsy over time: implications for re-analysis. Sci Rep 2024; 14:7717. [PMID: 38565608 PMCID: PMC10987647 DOI: 10.1038/s41598-024-57976-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/23/2024] [Indexed: 04/04/2024] Open
Abstract
Despite the significant advances in understanding the genetic architecture of epilepsy, many patients do not receive a molecular diagnosis after genomic testing. Re-analysing existing genomic data has emerged as a potent method to increase diagnostic yields-providing the benefits of genomic-enabled medicine to more individuals afflicted with a range of different conditions. The primary drivers for these new diagnoses are the discovery of novel gene-disease and variants-disease relationships; however, most decisions to trigger re-analysis are based on the passage of time rather than the accumulation of new knowledge. To explore how our understanding of a specific condition changes and how this impacts re-analysis of genomic data from epilepsy patients, we developed Vigelint. This approach combines the information from PanelApp and ClinVar to characterise how the clinically relevant genes and causative variants available to laboratories change over time, and this approach to five clinical-grade epilepsy panels. Applying the Vigelint pipeline to these panels revealed highly variable patterns in new, clinically relevant knowledge becoming publicly available. This variability indicates that a more dynamic approach to re-analysis may benefit the diagnosis and treatment of epilepsy patients. Moreover, this work suggests that Vigelint can provide empirical data to guide more nuanced, condition-specific approaches to re-analysis.
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Affiliation(s)
- Alan J Robertson
- Faculty of Medicine, University of Queensland, Brisbane, Australia.
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
- Queensland Digital Health Centre, University of Queensland, Brisbane, Australia.
- The Genomic Institute, Department of Health, Queensland Government, Brisbane, Australia.
| | - Khoa A Tran
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, Australia
| | - Carmen Bennett
- UQ Centre for Clinical Research, Herston, Brisbane, QLD, 4029, Australia
- Department of Neurology, Royal Brisbane & Women's Hospital, Herston, Brisbane, QLD, 4029, Australia
| | - Clair Sullivan
- Faculty of Medicine, University of Queensland, Brisbane, Australia
- Queensland Digital Health Centre, University of Queensland, Brisbane, Australia
- Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Woolloongabba, Australia
- Department of Health, Metro North Hospital and Health Service, Queensland Government, Brisbane, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Australian Genomics, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
| | - Lata Vadlamudi
- UQ Centre for Clinical Research, Herston, Brisbane, QLD, 4029, Australia
- Department of Neurology, Royal Brisbane & Women's Hospital, Herston, Brisbane, QLD, 4029, Australia
| | - Nicola Waddell
- Faculty of Medicine, University of Queensland, Brisbane, Australia.
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
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7
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Krenn M, Wagner M, Zulehner G, Weng R, Jäger F, Keritam O, Sener M, Brücke C, Milenkovic I, Langer A, Buchinger D, Habersam R, Mayerhanser K, Brugger M, Brunet T, Jacob M, Graf E, Berutti R, Cetin H, Hoefele J, Winkelmann J, Zimprich F, Rath J. Next-generation sequencing and comprehensive data reassessment in 263 adult patients with neuromuscular disorders: insights into the gray zone of molecular diagnoses. J Neurol 2024; 271:1937-1946. [PMID: 38127101 PMCID: PMC10972933 DOI: 10.1007/s00415-023-12101-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/03/2023] [Accepted: 11/04/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Neuromuscular disorders (NMDs) are heterogeneous conditions with a considerable fraction attributed to monogenic defects. Despite the advancements in genomic medicine, many patients remain without a diagnosis. Here, we investigate whether a comprehensive reassessment strategy improves the diagnostic outcomes. METHODS We analyzed 263 patients with NMD phenotypes that underwent diagnostic exome or genome sequencing at our tertiary referral center between 2015 and 2023. We applied a comprehensive reassessment encompassing variant reclassification, re-phenotyping and NGS data reanalysis. Multivariable logistic regression was performed to identify predictive factors associated with a molecular diagnosis. RESULTS Initially, a molecular diagnosis was identified in 53 cases (20%), while an additional 23 (9%) had findings of uncertain significance. Following comprehensive reassessment, the diagnostic yield increased to 23%, revealing 44 distinct monogenic etiologies. Reasons for newly obtained molecular diagnoses were variant reclassifications in 7 and NGS data reanalysis in 3 cases including one recently described disease-gene association (DNAJB4). Male sex reduced the odds of receiving a molecular diagnosis (OR 0.42; 95%CI 0.21-0.82), while a positive family history (OR 5.46; 95%CI 2.60-11.76) and a myopathy phenotype (OR 2.72; 95%CI 1.11-7.14) increased the likelihood. 7% were resolved through targeted genetic testing or classified as acquired etiologies. CONCLUSION Our findings reinforce the use of NGS in NMDs of suspected monogenic origin. We show that a comprehensive reassessment enhances diagnostic accuracy. However, one needs to be aware that genetic diagnoses are often made with uncertainty and can even be downgraded based on new evidence.
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Affiliation(s)
- Martin Krenn
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Matias Wagner
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Gudrun Zulehner
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Rosa Weng
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Fiona Jäger
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Omar Keritam
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Merve Sener
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Christof Brücke
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Ivan Milenkovic
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Agnes Langer
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Dominic Buchinger
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Richard Habersam
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Katharina Mayerhanser
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Dr. Von Hauner's Children's Hospital, University of Munich, Munich, Germany
| | - Maureen Jacob
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Hakan Cetin
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Juliane Winkelmann
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Jakob Rath
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria.
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8
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Sahin I, Erdem HB, Bahsi T, Saat H. Expanding the Genotype-Phenotype Correlations and Mutational Spectrum in Inherited Retinal Diseases: Novel and Recurrent Mutations. Cureus 2024; 16:e53742. [PMID: 38465142 PMCID: PMC10920963 DOI: 10.7759/cureus.53742] [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] [Accepted: 02/06/2024] [Indexed: 03/12/2024] Open
Abstract
Background Inherited retinal diseases (IRD) represent a prominent etiology of visual impairment on a global scale. The lack of a clear definition of the etiology and genotypic spectrum of IRD is attributed to the significant genetic variability seen. Additionally, there is a scarcity of available data about the correlations between genotypes and phenotypes in this context. This study aimed to clarify the range of mutations and the associations between genotypes and phenotypes in IRD. Methods This cohort consists of 223 patients who have been diagnosed with a range of retinal illnesses, such as retinitis pigmentosa (RP), Stargardt (STGD)/STGD-like disease, Usher syndrome, and Leber congenital amaurosis (LCA). The validation of each mutation and its pathogenicity was conducted by bioinformatics analysis, Sanger sequencing-based co-segregation testing, and computational assessment. The link between genotype and phenotype was analyzed in all patients who possessed mutations as described in the recommendations established by the American College of Medical Genetics. Results A total of 223 cases, comprising Turkish and Syrian families, were examined, revealing the presence of 175 distinct mutations in the IRD gene. Among these mutations, 58 were identified as unique, indicating that they had not been previously reported. A total of 119 mutations were identified to be likely pathogenic, while 104 mutations were classified as pathogenic. The study identified patterns of heredity, namely autosomal recessive, dominant, and X-linked inheritance. Conclusions The findings of this study broaden the clinical and molecular aspects of IRD and further enhance our understanding of its complex nature. The discovery of previously unknown relationships between genetic variations and observable traits, as well as the wide range of genetic variants associated with IRD, significantly contributes to our existing understanding of the diverse phenotypic and genotypic characteristics of IRD. This new information will prove invaluable in facilitating accurate clinical diagnoses as well as personalized therapeutic interventions for individuals affected by IRD.
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Affiliation(s)
- Ibrahim Sahin
- Department of Molecular Medicine, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, BHR
- Department of Medical Genetics, University of Health Sciences, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara, TUR
| | - Haktan B Erdem
- Department of Medical Genetics, Ankara Etlik City Hospital, Ankara, TUR
| | - Taha Bahsi
- Department of Medical Genetics, Ankara Etlik City Hospital, Ankara, TUR
| | - Hanife Saat
- Department of Medical Genetics, Ankara Etlik City Hospital, Ankara, TUR
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9
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Coghlan S, Gyngell C, Vears DF. Ethics of artificial intelligence in prenatal and pediatric genomic medicine. J Community Genet 2024; 15:13-24. [PMID: 37796364 PMCID: PMC10857992 DOI: 10.1007/s12687-023-00678-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/27/2023] [Indexed: 10/06/2023] Open
Abstract
This paper examines the ethics of introducing emerging forms of artificial intelligence (AI) into prenatal and pediatric genomic medicine. Application of genomic AI to these early life settings has not received much attention in the ethics literature. We focus on three contexts: (1) prenatal genomic sequencing for possible fetal abnormalities, (2) rapid genomic sequencing for critically ill children, and (3) reanalysis of genomic data obtained from children for diagnostic purposes. The paper identifies and discusses various ethical issues in the possible application of genomic AI in these settings, especially as they relate to concepts of beneficence, nonmaleficence, respect for autonomy, justice, transparency, accountability, privacy, and trust. The examination will inform the ethically sound introduction of genomic AI in early human life.
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Affiliation(s)
- Simon Coghlan
- School of Computing and Information Systems (CIS), Centre for AI and Digital Ethics (CAIDE), The University of Melbourne, Grattan St, Melbourne, Victoria, 3010, Australia.
- Australian Research Council Centre of Excellence for Automated Decision Making and Society (ADM+S), Melbourne, Victoria, Australia.
| | - Christopher Gyngell
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, The Royal Children's Hospital, 50 Flemington Rd, Parkville, Victoria, 3052, Australia
- University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Danya F Vears
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, The Royal Children's Hospital, 50 Flemington Rd, Parkville, Victoria, 3052, Australia
- University of Melbourne, Parkville, Victoria, 3052, Australia
- Centre for Biomedical Ethics and Law, KU Leuven, Kapucijnenvoer 35, 3000, Leuven, Belgium
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10
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Dueñas Rey A, Del Pozo Valero M, Bouckaert M, Wood KA, Van den Broeck F, Daich Varela M, Thomas HB, Van Heetvelde M, De Bruyne M, Van de Sompele S, Bauwens M, Lenaerts H, Mahieu Q, Josifova D, Rivolta C, O'Keefe RT, Ellingford J, Webster AR, Arno G, Ayuso C, De Zaeytijd J, Leroy BP, De Baere E, Coppieters F. Combining a prioritization strategy and functional studies nominates 5'UTR variants underlying inherited retinal disease. Genome Med 2024; 16:7. [PMID: 38184646 PMCID: PMC10771650 DOI: 10.1186/s13073-023-01277-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/15/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND 5' untranslated regions (5'UTRs) are essential modulators of protein translation. Predicting the impact of 5'UTR variants is challenging and rarely performed in routine diagnostics. Here, we present a combined approach of a comprehensive prioritization strategy and functional assays to evaluate 5'UTR variation in two large cohorts of patients with inherited retinal diseases (IRDs). METHODS We performed an isoform-level re-analysis of retinal RNA-seq data to identify the protein-coding transcripts of 378 IRD genes with highest expression in retina. We evaluated the coverage of their 5'UTRs by different whole exome sequencing (WES) kits. The selected 5'UTRs were analyzed in whole genome sequencing (WGS) and WES data from IRD sub-cohorts from the 100,000 Genomes Project (n = 2397 WGS) and an in-house database (n = 1682 WES), respectively. Identified variants were annotated for 5'UTR-relevant features and classified into seven categories based on their predicted functional consequence. We developed a variant prioritization strategy by integrating population frequency, specific criteria for each category, and family and phenotypic data. A selection of candidate variants underwent functional validation using diverse approaches. RESULTS Isoform-level re-quantification of retinal gene expression revealed 76 IRD genes with a non-canonical retina-enriched isoform, of which 20 display a fully distinct 5'UTR compared to that of their canonical isoform. Depending on the probe design, 3-20% of IRD genes have 5'UTRs fully captured by WES. After analyzing these regions in both cohorts, we prioritized 11 (likely) pathogenic variants in 10 genes (ARL3, MERTK, NDP, NMNAT1, NPHP4, PAX6, PRPF31, PRPF4, RDH12, RD3), of which 7 were novel. Functional analyses further supported the pathogenicity of three variants. Mis-splicing was demonstrated for the PRPF31:c.-9+1G>T variant. The MERTK:c.-125G>A variant, overlapping a transcriptional start site, was shown to significantly reduce both luciferase mRNA levels and activity. The RDH12:c.-123C>T variant was found in cis with the hypomorphic RDH12:c.701G>A (p.Arg234His) variant in 11 patients. This 5'UTR variant, predicted to introduce an upstream open reading frame, was shown to result in reduced RDH12 protein but unaltered mRNA levels. CONCLUSIONS This study demonstrates the importance of 5'UTR variants implicated in IRDs and provides a systematic approach for 5'UTR annotation and validation that is applicable to other inherited diseases.
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Affiliation(s)
- Alfredo Dueñas Rey
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Marta Del Pozo Valero
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Manon Bouckaert
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Katherine A Wood
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Filip Van den Broeck
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Malena Daich Varela
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Huw B Thomas
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Mattias Van Heetvelde
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Stijn Van de Sompele
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Hanne Lenaerts
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Quinten Mahieu
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | | | - Carlo Rivolta
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Raymond T O'Keefe
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Jamie Ellingford
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
- Genomics England, London, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew R Webster
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
- Division of Ophthalmology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elfride De Baere
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Frauke Coppieters
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium.
- Department of Pharmaceutics, Ghent University, Ghent, Belgium.
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11
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van Slobbe M, van Haeringen A, Vissers LELM, Bijlsma EK, Rutten JW, Suerink M, Nibbeling EAR, Ruivenkamp CAL, Koene S. Reanalysis of whole-exome sequencing (WES) data of children with neurodevelopmental disorders in a standard patient care context. Eur J Pediatr 2024; 183:345-355. [PMID: 37889289 PMCID: PMC10858114 DOI: 10.1007/s00431-023-05279-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/20/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023]
Abstract
This study aims to inform future genetic reanalysis management by evaluating the yield of whole-exome sequencing (WES) reanalysis in standard patient care in the Netherlands. Single-center data of 159 patients with a neurodevelopmental disorder (NDD), in which WES analysis and reanalysis were performed between January 1, 2014, and December 31, 2021, was retrospectively collected. Patients were included if they were under the age of 18 years at initial analysis and if this initial analysis did not result in a diagnosis. Demographic, phenotypic, and genotypic characteristics of patients were collected and analyzed. The primary outcomes of our study were (i) diagnostic yield at reanalysis, (ii) reasons for detecting a new possibly causal variant at reanalysis, (iii) unsolicited findings, and (iv) factors associated with positive result of reanalysis. In addition, we conducted a questionnaire study amongst the 7 genetic department in the Netherlands creating an overview of used techniques, yield, and organization of WES reanalysis. The single-center data show that in most cases, WES reanalysis was initiated by the clinical geneticist (65%) or treating physician (30%). The mean time between initial WES analysis and reanalysis was 3.7 years. A new (likely) pathogenic variant or VUS with a clear link to the phenotype was found in 20 initially negative cases, resulting in a diagnostic yield of 12.6%. In 75% of these patients, the diagnosis had clinical consequences, as for example, a screening plan for associated signs and symptoms could be devised. Most (32%) of the (likely) causal variants identified at WES reanalysis were discovered due to a newly described gene-disease association. In addition to the 12.6% diagnostic yield based on new diagnoses, reclassification of a variant of uncertain significance found at initial analysis led to a definite diagnosis in three patients. Diagnostic yield was higher in patients with dysmorphic features compared to patients without clear dysmorphic features (yield 27% vs. 6%; p = 0.001). CONCLUSIONS Our results show that WES reanalysis in patients with NDD in standard patient care leads to a substantial increase in genetic diagnoses. In the majority of newly diagnosed patients, the diagnosis had clinical consequences. Knowledge about the clinical impact of WES reanalysis, clinical characteristics associated with higher yield, and the yield per year after a negative WES in larger clinical cohorts is warranted to inform guidelines for genetic reanalysis. These guidelines will be of great value for pediatricians, pediatric rehabilitation specialists, and pediatric neurologists in daily care of patients with NDD. WHAT IS KNOWN • Whole exome sequencing can cost-effectively identify a genetic cause of intellectual disability in about 30-40% of patients. • WES reanalysis in a research setting can lead to a definitive diagnosis in 10-20% of previously exome negative cases. WHAT IS NEW • WES reanalysis in standard patient care resulted in a diagnostic yield of 13% in previously exome negative children with NDD. • The presence of dysmorphic features is associated with an increased diagnostic yield of WES reanalysis.
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Affiliation(s)
- Michelle van Slobbe
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Julie W Rutten
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Esther A R Nibbeling
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Saskia Koene
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands.
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12
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Racine C, Denommé-Pichon AS, Engel C, Tran Mau-Them F, Bruel AL, Vitobello A, Safraou H, Sorlin A, Nambot S, Delanne J, Garde A, Colin E, Moutton S, Thevenon J, Jean-Marçais N, Willems M, Geneviève D, Pinson L, Perrin L, Laffargue F, Lespinasse J, Lacaze E, Molin A, Gerard M, Lambert L, Benigni C, Patat O, Bourgeois V, Poe C, Chevarin M, Couturier V, Garret P, Philippe C, Duffourd Y, Faivre L, Thauvin-Robinet C. Multiple molecular diagnoses in the field of intellectual disability and congenital anomalies: 3.5% of all positive cases. J Med Genet 2023; 61:36-46. [PMID: 37586840 DOI: 10.1136/jmg-2023-109170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 07/27/2023] [Indexed: 08/18/2023]
Abstract
PURPOSE Wide access to clinical exome/genome sequencing (ES/GS) enables the identification of multiple molecular diagnoses (MMDs), being a long-standing but underestimated concept, defined by two or more causal loci implicated in the phenotype of an individual with a rare disease. Only few series report MMDs rates (1.8% to 7.1%). This study highlights the increasing role of MMDs in a large cohort of individuals addressed for congenital anomalies/intellectual disability (CA/ID). METHODS From 2014 to 2021, our diagnostic laboratory rendered 880/2658 positive ES diagnoses for CA/ID aetiology. Exhaustive search on MMDs from ES data was performed prospectively (January 2019 to December 2021) and retrospectively (March 2014 to December 2018). RESULTS MMDs were identified in 31/880 individuals (3.5%), responsible for distinct (9/31) or overlapping (22/31) phenotypes, and potential MMDs in 39/880 additional individuals (4.4%). CONCLUSION MMDs are frequent in CA/ID and remain a strong challenge. Reanalysis of positive ES data appears essential when phenotypes are partially explained by the initial diagnosis or atypically enriched overtime. Up-to-date clinical data, clinical expertise from the referring physician, strong interactions between clinicians and biologists, and increasing gene discoveries and improved ES bioinformatics tools appear all the more fundamental to enhance chances of identifying MMDs. It is essential to provide appropriate patient care and genetic counselling.
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Affiliation(s)
- Caroline Racine
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Camille Engel
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Frederic Tran Mau-Them
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Ange-Line Bruel
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Antonio Vitobello
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Hana Safraou
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Arthur Sorlin
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Sophie Nambot
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Julian Delanne
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Aurore Garde
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Estelle Colin
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Sébastien Moutton
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Julien Thevenon
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Nolwenn Jean-Marçais
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Marjolaine Willems
- Centre de Référence "Anomalies du Développement syndromes malformatifs" Occitanie, Service de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - David Geneviève
- Centre de Référence "Anomalies du Développement syndromes malformatifs" Occitanie, Service de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
- INSERM U1183, Université de Montpellier, Montpellier, France
| | - Lucile Pinson
- Centre de Référence "Anomalies du Développement syndromes malformatifs" Occitanie, Service de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Laurence Perrin
- Genetic Department, Robert-Debré Hospital Department of Genetics, Paris, France
| | - Fanny Laffargue
- Service de Génétique médicale, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - James Lespinasse
- Unité de Génétique médicale, Centre Hospitalier Métropole Savoie, Chambery, France
| | - Elodie Lacaze
- Department of Medical Genetics, Hospital Group Le Havre, Le Havre, France
| | - Arnaud Molin
- Service de Génétique, University Hospital Centre Caen, Caen, France
| | - Marion Gerard
- Service de Génétique, University Hospital Centre Caen, Caen, France
| | | | | | - Olivier Patat
- Department of Medical Genetics, University Hospital Centre Toulouse, Toulouse, France
| | - Valentin Bourgeois
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Charlotte Poe
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Martin Chevarin
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Victor Couturier
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Philippine Garret
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Christophe Philippe
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Yannis Duffourd
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Christel Thauvin-Robinet
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
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13
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Roman-Naranjo P, Parra-Perez AM, Lopez-Escamez JA. A systematic review on machine learning approaches in the diagnosis and prognosis of rare genetic diseases. J Biomed Inform 2023:104429. [PMID: 37352901 DOI: 10.1016/j.jbi.2023.104429] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 06/05/2023] [Accepted: 06/17/2023] [Indexed: 06/25/2023]
Abstract
BACKGROUND The diagnosis of rare genetic diseases is often challenging due to the complexity of the genetic underpinnings of these conditions and the limited availability of diagnostic tools. Machine learning (ML) algorithms have the potential to improve the accuracy and speed of diagnosis by analyzing large amounts of genomic data and identifying complex multiallelic patterns that may be associated with specific diseases. In this systematic review, we aimed to identify the methodological trends and the ML application areas in rare genetic diseases. METHODS We performed a systematic review of the literature following the PRISMA guidelines to search studies that used ML approaches to enhance the diagnosis of rare genetic diseases. Studies that used DNA-based sequencing data and a variety of ML algorithms were included, summarized, and analyzed using bibliometric methods, visualization tools, and a feature co-occurrence analysis. FINDINGS Our search identified 22 studies that met the inclusion criteria. We found that exome sequencing was the most frequently used sequencing technology (59%), and rare neoplastic diseases were the most prevalent disease scenario (59%). In rare neoplasms, the most frequent applications of ML models were the differential diagnosis or stratification of patients (38.5%) and the identification of somatic mutations (30.8%). In other rare diseases, the most frequent goals were the prioritization of rare variants or genes (55.5%) and the identification of biallelic or digenic inheritance (33.3%). The most employed method was the random forest algorithm (54.5%). In addition, the features of the datasets needed for training these algorithms were distinctive depending on the goal pursued, including the mutational load in each gene for the differential diagnosis of patients, or the combination of genotype features and sequence-derived features (such as GC-content) for the identification of somatic mutations. CONCLUSIONS ML algorithms based on sequencing data are mainly used for the diagnosis of rare neoplastic diseases, with random forest being the most common approach. We identified key features in the datasets used for training these ML models according to the objective pursued. These features can support the development of future ML models in the diagnosis of rare genetic diseases.
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Affiliation(s)
- P Roman-Naranjo
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain; Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer, University of Granada, Junta de Andalucía, PTS, Granada, Spain; Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain.
| | - A M Parra-Perez
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain; Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer, University of Granada, Junta de Andalucía, PTS, Granada, Spain; Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
| | - J A Lopez-Escamez
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain; Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer, University of Granada, Junta de Andalucía, PTS, Granada, Spain; Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain; Meniere's Disease Neuroscience Research Program, Faculty of Medicine & Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, New South Wales, Australia
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14
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Ravel JM, Renaud M, Muller J, Becker A, Renard É, Remen T, Lefort G, Dexheimer M, Jonveaux P, Leheup B, Bonnet C, Lambert L. Clinical utility of periodic reinterpretation of CNVs of uncertain significance: an 8-year retrospective study. Genome Med 2023; 15:39. [PMID: 37221613 DOI: 10.1186/s13073-023-01191-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/15/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND Array-CGH is the first-tier genetic test both in pre- and postnatal developmental disorders worldwide. Variants of uncertain significance (VUS) represent around 10~15% of reported copy number variants (CNVs). Even though VUS reanalysis has become usual in practice, no long-term study regarding CNV reinterpretation has been reported. METHODS This retrospective study examined 1641 CGH arrays performed over 8 years (2010-2017) to demonstrate the contribution of periodically re-analyzing CNVs of uncertain significance. CNVs were classified using AnnotSV on the one hand and manually curated on the other hand. The classification was based on the 2020 American College of Medical Genetics (ACMG) criteria. RESULTS Of the 1641 array-CGH analyzed, 259 (15.7%) showed at least one CNV initially reported as of uncertain significance. After reinterpretation, 106 of the 259 patients (40.9%) changed categories, and 12 of 259 (4.6%) had a VUS reclassified to likely pathogenic or pathogenic. Six were predisposing factors for neurodevelopmental disorder/autism spectrum disorder (ASD). CNV type (gain or loss) does not seem to impact the reclassification rate, unlike the length of the CNV: 75% of CNVs downgraded to benign or likely benign are less than 500 kb in size. CONCLUSIONS This study's high rate of reinterpretation suggests that CNV interpretation has rapidly evolved since 2010, thanks to the continuous enrichment of available databases. The reinterpreted CNV explained the phenotype for ten patients, leading to optimal genetic counseling. These findings suggest that CNVs should be reinterpreted at least every 2 years.
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Affiliation(s)
- Jean-Marie Ravel
- Service de génétique médicale, CHRU de Nancy, Nancy, France
- Laboratoire de génétique médicale, CHRU Nancy, Nancy, France
- Université de Lorraine, NGERE, F-54000Nancy, Inserm, France
| | - Mathilde Renaud
- Service de génétique médicale, CHRU de Nancy, Nancy, France
- Université de Lorraine, NGERE, F-54000Nancy, Inserm, France
| | - Jean Muller
- Laboratoires de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Laboratoire de Génétique Médicale, INSERM, UMRS_1112, Institut de Génétique Médicale d'Alsace (IGMA), Université de Strasbourg Faculté de Médecine de Strasbourg, 67000, Strasbourg, France
- Unité Fonctionnelle de Bioinformatique Médicale Appliquée au Diagnostic (UF7363), Hôpitaux Universitaires de Strasbourg, 67000, Strasbourg, France
| | - Aurélie Becker
- Laboratoire de génétique médicale, CHRU Nancy, Nancy, France
| | - Émeline Renard
- Department of pediatrics, Regional University Hospital of Nancy, Allée du Morvan, 54511, Vandoeuvre-Lès-Nancy, France
| | | | | | | | | | - Bruno Leheup
- Service de génétique médicale, CHRU de Nancy, Nancy, France
- Université de Lorraine, NGERE, F-54000Nancy, Inserm, France
| | - Céline Bonnet
- Laboratoire de génétique médicale, CHRU Nancy, Nancy, France.
- Université de Lorraine, NGERE, F-54000Nancy, Inserm, France.
| | - Laëtitia Lambert
- Service de génétique médicale, CHRU de Nancy, Nancy, France.
- Université de Lorraine, NGERE, F-54000Nancy, Inserm, France.
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15
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Martinez-Barrios E, Sarquella-Brugada G, Perez-Serra A, Fernandez-Falgueras A, Cesar S, Alcalde M, Coll M, Puigmulé M, Iglesias A, Ferrer-Costa C, del Olmo B, Picó F, Lopez L, Fiol V, Cruzalegui J, Hernandez C, Arbelo E, Díez-Escuté N, Cerralbo P, Grassi S, Oliva A, Toro R, Brugada J, Brugada R, Campuzano O. Reevaluation of ambiguous genetic variants in sudden unexplained deaths of a young cohort. Int J Legal Med 2023; 137:345-351. [PMID: 36693943 PMCID: PMC9902310 DOI: 10.1007/s00414-023-02951-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/16/2023] [Indexed: 01/26/2023]
Abstract
Sudden death cases in the young population remain without a conclusive cause of decease in almost 40% of cases. In these situations, cardiac arrhythmia of genetic origin is suspected as the most plausible cause of death. Molecular autopsy may reveal a genetic defect in up to 20% of families. Most than 80% of rare variants remain classified with an ambiguous role, impeding a useful clinical translation. Our aim was to update rare variants originally classified as of unknown significance to clarify their role. Our cohort included fifty-one post-mortem samples of young cases who died suddenly and without a definite cause of death. Five years ago, molecular autopsy identified at least one rare genetic alteration classified then as ambiguous following the American College of Medical Genetics and Genomics' recommendations. We have reclassified the same rare variants including novel data. About 10% of ambiguous variants change to benign/likely benign mainly because of improved population frequencies. Excluding cases who died before one year of age, almost 21% of rare ambiguous variants change to benign/likely benign. This fact makes it important to discard these rare variants as a cause of sudden unexplained death, avoiding anxiety in relatives' carriers. Twenty-five percent of the remaining variants show a tendency to suspicious deleterious role, highlighting clinical follow-up of carriers. Periodical reclassification of rare variants originally classified as ambiguous is crucial, at least updating frequencies every 5 years. This action aids to increase accuracy to enable and conclude a cause of death as well as translation into the clinic.
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Affiliation(s)
- Estefanía Martinez-Barrios
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, 08950 Barcelona, Spain ,Low Prevalence and Complex Diseases of the Heart (ERN GUARD-Heart), European Reference Network for Rare, 1105 AZ Amsterdam, The Netherlands ,Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Georgia Sarquella-Brugada
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, 08950 Barcelona, Spain ,Low Prevalence and Complex Diseases of the Heart (ERN GUARD-Heart), European Reference Network for Rare, 1105 AZ Amsterdam, The Netherlands ,Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Esplugues de Llobregat, 08950 Barcelona, Spain ,Medical Science Department, School of Medicine, University of Girona, 17003 Girona, Spain
| | - Alexandra Perez-Serra
- Cardiovascular Genetics Center, University of Girona-IDIBGI, 17190 Girona, Spain ,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Anna Fernandez-Falgueras
- Cardiovascular Genetics Center, University of Girona-IDIBGI, 17190 Girona, Spain ,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Sergi Cesar
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, 08950 Barcelona, Spain ,Low Prevalence and Complex Diseases of the Heart (ERN GUARD-Heart), European Reference Network for Rare, 1105 AZ Amsterdam, The Netherlands ,Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Mireia Alcalde
- Cardiovascular Genetics Center, University of Girona-IDIBGI, 17190 Girona, Spain ,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Mónica Coll
- Cardiovascular Genetics Center, University of Girona-IDIBGI, 17190 Girona, Spain ,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Marta Puigmulé
- Cardiovascular Genetics Center, University of Girona-IDIBGI, 17190 Girona, Spain ,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Anna Iglesias
- Cardiovascular Genetics Center, University of Girona-IDIBGI, 17190 Girona, Spain ,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Carles Ferrer-Costa
- Cardiovascular Genetics Center, University of Girona-IDIBGI, 17190 Girona, Spain ,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Bernat del Olmo
- Cardiovascular Genetics Center, University of Girona-IDIBGI, 17190 Girona, Spain ,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Ferran Picó
- Cardiovascular Genetics Center, University of Girona-IDIBGI, 17190 Girona, Spain ,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Laura Lopez
- Cardiovascular Genetics Center, University of Girona-IDIBGI, 17190 Girona, Spain ,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Victoria Fiol
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, 08950 Barcelona, Spain ,Low Prevalence and Complex Diseases of the Heart (ERN GUARD-Heart), European Reference Network for Rare, 1105 AZ Amsterdam, The Netherlands ,Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - José Cruzalegui
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, 08950 Barcelona, Spain ,Low Prevalence and Complex Diseases of the Heart (ERN GUARD-Heart), European Reference Network for Rare, 1105 AZ Amsterdam, The Netherlands ,Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Clara Hernandez
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, 08950 Barcelona, Spain ,Low Prevalence and Complex Diseases of the Heart (ERN GUARD-Heart), European Reference Network for Rare, 1105 AZ Amsterdam, The Netherlands ,Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Elena Arbelo
- Low Prevalence and Complex Diseases of the Heart (ERN GUARD-Heart), European Reference Network for Rare, 1105 AZ Amsterdam, The Netherlands ,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain ,Arrhythmias Unit, Hospital Clinic, University of Barcelona-IDIBAPS, 08036 Barcelona, Spain
| | - Nuria Díez-Escuté
- Arrhythmias Unit, Hospital Clinic, University of Barcelona-IDIBAPS, 08036 Barcelona, Spain
| | - Patricia Cerralbo
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, 08950 Barcelona, Spain ,Low Prevalence and Complex Diseases of the Heart (ERN GUARD-Heart), European Reference Network for Rare, 1105 AZ Amsterdam, The Netherlands ,Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Simone Grassi
- Department of Health Sciences, Section of Forensic Medical Sciences, University of Florence, Largo Brambilla 3, 50134 Florence, Italy ,Department of Health Surveillance and Bioethics, Section of Legal Medicine, Fondazione Policlinico A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Antonio Oliva
- Department of Health Surveillance and Bioethics, Section of Legal Medicine, Fondazione Policlinico A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Rocío Toro
- Medicine Department, School of Medicine, 11003 Cadiz, Spain
| | - Josep Brugada
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, 08950 Barcelona, Spain ,Low Prevalence and Complex Diseases of the Heart (ERN GUARD-Heart), European Reference Network for Rare, 1105 AZ Amsterdam, The Netherlands ,Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Esplugues de Llobregat, 08950 Barcelona, Spain ,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain ,Arrhythmias Unit, Hospital Clinic, University of Barcelona-IDIBAPS, 08036 Barcelona, Spain
| | - Ramon Brugada
- Medical Science Department, School of Medicine, University of Girona, 17003, Girona, Spain. .,Cardiovascular Genetics Center, University of Girona-IDIBGI, 17190, Girona, Spain. .,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), 28029, Madrid, Spain. .,Cardiology Service, Hospital Josep Trueta, University of Girona, 17007, Girona, Spain.
| | - Oscar Campuzano
- Medical Science Department, School of Medicine, University of Girona, 17003, Girona, Spain. .,Cardiovascular Genetics Center, University of Girona-IDIBGI, 17190, Girona, Spain. .,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), 28029, Madrid, Spain.
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16
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Tran Mau-Them F, Overs A, Bruel AL, Duquet R, Thareau M, Denommé-Pichon AS, Vitobello A, Sorlin A, Safraou H, Nambot S, Delanne J, Moutton S, Racine C, Engel C, De Giraud d’Agay M, Lehalle D, Goldenberg A, Willems M, Coubes C, Genevieve D, Verloes A, Capri Y, Perrin L, Jacquemont ML, Lambert L, Lacaze E, Thevenon J, Hana N, Van-Gils J, Dubucs C, Bizaoui V, Gerard-Blanluet M, Lespinasse J, Mercier S, Guerrot AM, Maystadt I, Tisserant E, Faivre L, Philippe C, Duffourd Y, Thauvin-Robinet C. Combining globally search for a regular expression and print matching lines with bibliographic monitoring of genomic database improves diagnosis. Front Genet 2023; 14:1122985. [PMID: 37152996 PMCID: PMC10157399 DOI: 10.3389/fgene.2023.1122985] [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: 12/13/2022] [Accepted: 02/13/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction: Exome sequencing has a diagnostic yield ranging from 25% to 70% in rare diseases and regularly implicates genes in novel disorders. Retrospective data reanalysis has demonstrated strong efficacy in improving diagnosis, but poses organizational difficulties for clinical laboratories. Patients and methods: We applied a reanalysis strategy based on intensive prospective bibliographic monitoring along with direct application of the GREP command-line tool (to "globally search for a regular expression and print matching lines") in a large ES database. For 18 months, we submitted the same five keywords of interest [(intellectual disability, (neuro)developmental delay, and (neuro)developmental disorder)] to PubMed on a daily basis to identify recently published novel disease-gene associations or new phenotypes in genes already implicated in human pathology. We used the Linux GREP tool and an in-house script to collect all variants of these genes from our 5,459 exome database. Results: After GREP queries and variant filtration, we identified 128 genes of interest and collected 56 candidate variants from 53 individuals. We confirmed causal diagnosis for 19/128 genes (15%) in 21 individuals and identified variants of unknown significance for 19/128 genes (15%) in 23 individuals. Altogether, GREP queries for only 128 genes over a period of 18 months permitted a causal diagnosis to be established in 21/2875 undiagnosed affected probands (0.7%). Conclusion: The GREP query strategy is efficient and less tedious than complete periodic reanalysis. It is an interesting reanalysis strategy to improve diagnosis.
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Affiliation(s)
- Frédéric Tran Mau-Them
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
- *Correspondence: Frédéric Tran Mau-Them,
| | - Alexis Overs
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | - Ange-Line Bruel
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Romain Duquet
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | - Mylene Thareau
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Arthur Sorlin
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Hana Safraou
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Sophie Nambot
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Julian Delanne
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Sebastien Moutton
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Caroline Racine
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Camille Engel
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | | | - Daphne Lehalle
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Alice Goldenberg
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Marjolaine Willems
- Département de Génétique Médicale Maladies Rares et Médecine Personnalisée, Centre de Référence Maladies Rares Anomalies du Développement, Hôpital Arnaud de Villeneuve, Université Montpellier, Montpellier, France
| | - Christine Coubes
- Département de Génétique Médicale Maladies Rares et Médecine Personnalisée, Centre de Référence Maladies Rares Anomalies du Développement, Hôpital Arnaud de Villeneuve, Université Montpellier, Montpellier, France
| | - David Genevieve
- Département de Génétique Médicale Maladies Rares et Médecine Personnalisée, Centre de Référence Maladies Rares Anomalies du Développement, Hôpital Arnaud de Villeneuve, Université Montpellier, Montpellier, France
| | - Alain Verloes
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Department of Medical Genetics, AP-HPNord- Université de Paris, Hôpital Robert Debré, Paris, France
- INSERM UMR 1141, Paris, France
| | - Yline Capri
- Service de Génétique Clinique, CHU Robert Debré, Paris, France
| | - Laurence Perrin
- Service de Génétique Clinique, CHU Robert Debré, Paris, France
| | - Marie-Line Jacquemont
- Unité de Génétique Médicale, Pole Femme-Mère-Enfant, Groupe Hospitalier Sud Réunion, CHU de La Réunion, La Réunion, France
| | | | - Elodie Lacaze
- Unité de Génétique Médicale, Groupe Hospitalier du Havre, Le Havre, France
| | - Julien Thevenon
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Nadine Hana
- Département de Génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat, Paris, France
- INSERM U1148, Laboratory for Vascular Translational Science, Université Paris de Paris, Hôpital Bichat, Paris, France
| | - Julien Van-Gils
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Charlotte Dubucs
- Department of Medical Genetics, Toulouse University Hospital, Toulouse, France
| | - Varoona Bizaoui
- Service de Génétique, Centre Hospitalier Universitaire Caen Normandie, Caen, France
| | | | | | - Sandra Mercier
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Anne-Marie Guerrot
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Rouen, France
- Inserm U1245, FHU G4 Génomique, Rouen, France
| | - Isabelle Maystadt
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Gosselies, Belgium
| | - Emilie Tisserant
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | - Laurence Faivre
- INSERM UMR1231 GAD, Dijon, France
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Yannis Duffourd
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Christel Thauvin-Robinet
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
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The Diagnostic Yield of Next Generation Sequencing in Inherited Retinal Diseases: A Systematic Review and Meta-analysis. Am J Ophthalmol 2022; 249:57-73. [PMID: 36592879 DOI: 10.1016/j.ajo.2022.12.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/16/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023]
Abstract
PURPOSE Accurate genotyping of individuals with inherited retinal diseases (IRD) is essential for patient management and identifying suitable candidates for gene therapies. This study evaluated the diagnostic yield of next generation sequencing (NGS) in IRDs. DESIGN Systematic review and meta-analysis. METHODS This systematic review was prospectively registered (CRD42021293619). Ovid MEDLINE and Ovid Embase were searched on 6 June 2022. Clinical studies evaluating the diagnostic yield of NGS in individuals with IRDs were eligible for inclusion. Risk of bias assessment was performed. Studies were pooled using a random...effects inverse variance model. Sources of heterogeneity were explored using stratified analysis, meta-regression, and sensitivity analysis. RESULTS This study included 105 publications from 28 countries. Most studies (90 studies) used targeted gene panels. The diagnostic yield of NGS was 61.3% (95% confidence interval: 57.8-64.7%; 51 studies) in mixed IRD phenotypes, 58.2% (51.6-64.6%; 41 studies) in rod-cone dystrophies, 57.7% (46.8-68.3%; eight studies) in macular and cone/cone-rod dystrophies, and 47.6% (95% CI: 41.0-54.3%; four studies) in familial exudative vitreoretinopathy. For mixed IRD phenotypes, a higher diagnostic yield was achieved pooling studies published between 2018-2022 (64.2% [59.5-68.7%]), studies using exome sequencing (73.5% [58.9-86.1%]), and studies using the American College of Medical Genetics variant interpretation standards (65.6% [60.8-70.4%]). CONCLUSION The current diagnostic yield of NGS in IRDs is between 52-74%. The certainty of the evidence was judged as low or very low. A key limitation of the current evidence is the significant heterogeneity between studies. Adoption of standardized reporting guidelines could improve confidence in future meta-analyses.
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Halfmeyer I, Bartolomaeus T, Popp B, Radtke M, Helms T, Hentschel J, Popp D, Jamra RA. Approach to Cohort-Wide Re-Analysis of Exome Data in 1000 Individuals with Neurodevelopmental Disorders. Genes (Basel) 2022; 14:genes14010030. [PMID: 36672771 PMCID: PMC9858523 DOI: 10.3390/genes14010030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/02/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
The re-analysis of nondiagnostic exome sequencing (ES) has the potential to increase diagnostic yields in individuals with rare diseases, but its implementation in the daily routines of laboratories is limited due to restricted capacities. Here, we describe a systematic approach to re-analyse the ES data of a cohort consisting of 1040 diagnostic and nondiagnostic samples. We applied a strict filter cascade to reveal the most promising single-nucleotide variants (SNVs) of the whole cohort, which led to an average of 0.77 variants per individual that had to be manually evaluated. This variant set revealed seven novel diagnoses (0.8% of all nondiagnostic cases) and two secondary findings. Thirteen additional variants were identified by a scientific approach prior to this re-analysis and were also present in this variant set. This resulted in a total increase in the diagnostic yield of 2.3%. The filter cascade was optimised during the course of the study and finally resulted in sensitivity of 85%. After applying the filter cascade, our re-analysis took 20 h and enabled a workflow that can be used repeatedly. This work is intended to provide a practical recommendation for other laboratories wishing to introduce a resource-efficient re-analysis strategy into their clinical routine.
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Affiliation(s)
- Insa Halfmeyer
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
| | - Tobias Bartolomaeus
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
- Center of Functional Genomics, Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Hessische Straße 4A, 10115 Berlin, Germany
| | - Maximilian Radtke
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
| | - Tobias Helms
- Limbus Medical Technologies GmbH, Neuer Markt 9/10, 18055 Rostock, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
| | - Denny Popp
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
- Correspondence:
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