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Curic E, Ewans L, Pysar R, Taylan F, Botto LD, Nordgren A, Gahl W, Palmer EE. International Undiagnosed Diseases Programs (UDPs): components and outcomes. Orphanet J Rare Dis 2023; 18:348. [PMID: 37946247 PMCID: PMC10633944 DOI: 10.1186/s13023-023-02966-1] [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: 04/27/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Over the last 15 years, Undiagnosed Diseases Programs have emerged to address the significant number of individuals with suspected but undiagnosed rare genetic diseases, integrating research and clinical care to optimize diagnostic outcomes. This narrative review summarizes the published literature surrounding Undiagnosed Diseases Programs worldwide, including thirteen studies that evaluate outcomes and two commentary papers. Commonalities in the diagnostic and research process of Undiagnosed Diseases Programs are explored through an appraisal of available literature. This exploration allowed for an assessment of the strengths and limitations of each of the six common steps, namely enrollment, comprehensive clinical phenotyping, research diagnostics, data sharing and matchmaking, results, and follow-up. Current literature highlights the potential utility of Undiagnosed Diseases Programs in research diagnostics. Since participants have often had extensive previous genetic studies, research pipelines allow for diagnostic approaches beyond exome or whole genome sequencing, through reanalysis using research-grade bioinformatics tools and multi-omics technologies. The overall diagnostic yield is presented by study, since different selection criteria at enrollment and reporting processes make comparisons challenging and not particularly informative. Nonetheless, diagnostic yield in an undiagnosed cohort reflects the potential of an Undiagnosed Diseases Program. Further comparisons and exploration of the outcomes of Undiagnosed Diseases Programs worldwide will allow for the development and improvement of the diagnostic and research process and in turn improve the value and utility of an Undiagnosed Diseases Program.
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Affiliation(s)
- Ela Curic
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia
| | - Lisa Ewans
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Ryan Pysar
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Lorenzo D Botto
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - William Gahl
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Elizabeth Emma Palmer
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia.
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia.
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Meyer AP, Ma J, Brock G, Hashimoto S, Cottrell CE, Mathew M, Hunter JM, Leung ML, Corsmeier D, Jayaraman V, Waldrop MA, Flanigan KM. Exome sequencing in the pediatric neuromuscular clinic leads to more frequent diagnosis of both neuromuscular and neurodevelopmental conditions. Muscle Nerve 2023; 68:833-840. [PMID: 37789688 DOI: 10.1002/mus.27976] [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: 01/06/2023] [Revised: 09/06/2023] [Accepted: 09/10/2023] [Indexed: 10/05/2023]
Abstract
INTRODUCTION/AIMS Exome sequencing (ES) has proven to be a valuable diagnostic tool for neuromuscular disorders, which often pose a diagnostic challenge. The aims of this study were to investigate the clinical outcomes associated with utilization of ES in the pediatric neuromuscular clinic and to determine if specific phenotypic features or abnormal neurodiagnostic tests were predictive of a diagnostic result. METHODS This was a retrospective medical record review of 76 pediatric neuromuscular clinic patients who underwent ES. Based upon clinical assessment prior to ES, patients were divided into two groups: affected by neuromuscular (n = 53) or non-neuromuscular (n = 23) syndromes. RESULTS A diagnosis was made in 28/76 (36.8%), with 29 unique disorders identified. In the neuromuscular group, a neuromuscular condition was confirmed in 78% of those receiving a genetic diagnosis. Early age of symptom onset was associated with a significantly higher diagnostic yield. The most common reason neuromuscular diagnoses were not detected on prior testing was due to causative genes not being present on disease-specific panels. Changes to medical care were made in 57% of individuals receiving a diagnosis on ES. DISCUSSION These data further support ES as a powerful diagnostic tool in the pediatric neuromuscular clinic and highlight the advantages of ES over gene panels, including the ability to identify diagnoses regardless of etiology, identify genes newly associated with disease, and identify multiple confounding diagnoses. Rapid and accurate diagnosis by ES can not only end the patient's diagnostic odyssey, but often impacts patients' medical management and genetic counseling of families.
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Affiliation(s)
- Alayne P Meyer
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Jianing Ma
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
| | - Guy Brock
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
| | - Sayaka Hashimoto
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Catherine E Cottrell
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Mariam Mathew
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Jesse M Hunter
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Marco L Leung
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Don Corsmeier
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Vijayakumar Jayaraman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Megan A Waldrop
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Department of Neurology, Nationwide Children's Hospital & The Ohio State University, Columbus, Ohio, USA
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kevin M Flanigan
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Department of Neurology, Nationwide Children's Hospital & The Ohio State University, Columbus, Ohio, USA
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, Ohio, USA
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Chung CCY, Hue SPY, Ng NYT, Doong PHL, Chu ATW, Chung BHY. Meta-analysis of the diagnostic and clinical utility of exome and genome sequencing in pediatric and adult patients with rare diseases across diverse populations. Genet Med 2023; 25:100896. [PMID: 37191093 DOI: 10.1016/j.gim.2023.100896] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
PURPOSE This meta-analysis aims to compare the diagnostic and clinical utility of exome sequencing (ES) vs genome sequencing (GS) in pediatric and adult patients with rare diseases across diverse populations. METHODS A meta-analysis was conducted to identify studies from 2011 to 2021. RESULTS One hundred sixty-one studies across 31 countries/regions were eligible, featuring 50,417 probands of diverse populations. Diagnostic rates of ES (0.38, 95% CI 0.36-0.40) and GS (0.34, 95% CI 0.30-0.38) were similar (P = .1). Within-cohort comparison illustrated 1.2-times odds of diagnosis by GS over ES (95% CI 0.79-1.83, P = .38). GS studies discovered a higher range of novel genes than ES studies; yet, the rate of variant of unknown significance did not differ (P = .78). Among high-quality studies, clinical utility of GS (0.77, 95% CI 0.64-0.90) was higher than that of ES (0.44, 95% CI 0.30-0.58) (P < .01). CONCLUSION This meta-analysis provides an important update to demonstrate the similar diagnostic rates between ES and GS and the higher clinical utility of GS over ES. With the newly published recommendations for clinical interpretation of variants found in noncoding regions of the genome and the trend of decreasing variant of unknown significance and GS cost, it is expected that GS will be more widely used in clinical settings.
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Affiliation(s)
| | - Shirley P Y Hue
- Hong Kong Genome Institute, Hong Kong Special Administrative Region
| | - Nicole Y T Ng
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Annie T W Chu
- Hong Kong Genome Institute, Hong Kong Special Administrative Region.
| | - Brian H Y Chung
- Hong Kong Genome Institute, Hong Kong Special Administrative Region; Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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Wong MST, Thomas T, Lim JY, Kam S, Teo JX, Ching J, Goh CYJ, Jamuar SS, Lim WK, Koh AL. DEGS1 -related leukodystrophy: a clinical report and review of literature. Clin Dysmorphol 2023; 32:106-111. [PMID: 37195341 DOI: 10.1097/mcd.0000000000000457] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
BACKGROUND Leukodystrophies are a heterogeneous group of disorders affecting the white matter of the central nervous system, with or without affecting the peripheral nervous system. Biallelic variants in DEGS1 , coding for desaturase 1 (Des1) protein, were recently reported to be associated with hypomyelinating leukodystrophy (HLD), a subclass of leukodystrophies where the formation of the myelin sheath is affected. METHODS Genomic sequencing was performed on our index patient with severe developmental delay, severe failure to thrive, dystonia, seizures, and hypomyelination on brain imaging. Sphingolipid analysis was performed and dihydroceramide/ceramide (dhCer/Cer) ratios were obtained by the measurement of ceramide and dihydroceramide species. RESULTS A homozygous missense variant was identified in DEGS1 (c.565A > G:p Asn189Asp). The identified DEGS1 variant has been annotated as "conflicting reports of pathogenicity" on ClinVar. Follow-up sphingolipid analysis on our patient showed significantly raised dhCer/Cer and this was consistent with dysfunction of the Des1 protein, providing additional evidence to support the pathogenicity of this variant. CONCLUSION While rare, pathogenic variants in DEGS1 should be considered in patients with HLD phenotype. To date, 25 patients have been reported across four studies on DEGS1 -related HLD, and, in this report, we summarize the literature. More such reports will enable deeper phenotypic characterization of this disorder.
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Affiliation(s)
| | - Terrence Thomas
- Neurology Service, Department of Paediatrics, KK Women's and Children's Hospital
- SingHealth Duke-NUS Paediatric Academic Clinical Programme
| | - Jiin Ying Lim
- SingHealth Duke-NUS Paediatric Academic Clinical Programme
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital
- SingHealth Duke-NUS Genomic Medicine Centre
| | - Sylvia Kam
- SingHealth Duke-NUS Paediatric Academic Clinical Programme
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital
- SingHealth Duke-NUS Genomic Medicine Centre
| | | | - Jianhong Ching
- Cardiovascular and Metabolic Disorders Programme, Duke-NUS Medical School
- KK Research Centre, KK Women's and Children's Hospital
| | - Chew Yin Jasmine Goh
- Division of Nursing - Nursing Clinical Services, Genetics Specialty Nurse, KK Women's and Children's Hospital, Singapore, Singapore
| | - Saumya Shekhar Jamuar
- Lee Kong Chian School of Medicine, Nanyang Technological University
- SingHealth Duke-NUS Paediatric Academic Clinical Programme
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital
- SingHealth Duke-NUS Genomic Medicine Centre
- SingHealth Duke-NUS Institute of Precision Medicine
| | - Weng Khong Lim
- SingHealth Duke-NUS Genomic Medicine Centre
- SingHealth Duke-NUS Institute of Precision Medicine
| | - Ai Ling Koh
- Lee Kong Chian School of Medicine, Nanyang Technological University
- SingHealth Duke-NUS Paediatric Academic Clinical Programme
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital
- SingHealth Duke-NUS Genomic Medicine Centre
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Alix T, Chéry C, Josse T, Bronowicki JP, Feillet F, Guéant-Rodriguez RM, Namour F, Guéant JL, Oussalah A. Predictors of the utility of clinical exome sequencing as a first-tier genetic test in patients with Mendelian phenotypes: results from a referral center study on 603 consecutive cases. Hum Genomics 2023; 17:5. [PMID: 36740706 PMCID: PMC9899384 DOI: 10.1186/s40246-023-00455-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 01/28/2023] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Clinical exome sequencing (CES) provides a comprehensive and effective analysis of relevant disease-associated genes in a cost-effective manner compared to whole exome sequencing. Although several studies have focused on the diagnostic yield of CES, no study has assessed predictors of CES utility among patients with various Mendelian phenotypes. We assessed the effectiveness of CES as a first-level genetic test for molecular diagnosis in patients with a Mendelian phenotype and explored independent predictors of the clinical utility of CES. RESULTS Between January 2016 and December 2019, 603 patients (426 probands and 177 siblings) underwent CES at the Department of Molecular Medicine of the University Hospital of Nancy. The median age of the probands was 34 years (IQR, 12-48), and the proportion of males was 46.9% (200/426). Adults and children represented 64.8% (276/426) and 35.2% (150/426), respectively. The median test-to-report time was 5.6 months (IQR, 4.1-7.2). CES revealed 203 pathogenic or likely pathogenic variants in 160 patients, corresponding to a diagnostic yield of 37.6% (160/426). Independent predictors of CES utility were criteria strongly suggestive of an extreme phenotype, including pediatric presentation and patient phenotypes associated with an increased risk of a priori probability of a monogenic disorder, the inclusion of at least one family member in addition to the proband, and a CES prescription performed by an expert in the field of rare genetic disorders. CONCLUSIONS Based on a large dataset of consecutive patients with various Mendelian phenotypes referred for CES as a first-tier genetic test, we report a diagnostic yield of ~ 40% and several independent predictors of CES utility that might improve CES diagnostic efficiency.
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Affiliation(s)
- Tom Alix
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France
| | - Céline Chéry
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France ,grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France
| | - Thomas Josse
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France
| | - Jean-Pierre Bronowicki
- grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Department of Gastroenterology and Liver Diseases, University Hospital of Nancy, 54000 Nancy, France
| | - François Feillet
- grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Department of Pediatrics, University Hospital of Nancy, 54000 Nancy, France
| | - Rosa-Maria Guéant-Rodriguez
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France ,grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France
| | - Farès Namour
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France ,grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France
| | - Jean-Louis Guéant
- Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000, Nancy, France. .,INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000, Nancy, France. .,Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.
| | - Abderrahim Oussalah
- Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000, Nancy, France. .,INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000, Nancy, France. .,Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.
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Fong N, Lim JY, Cham B, Kam S, Goh CY, Wei H, Tan YM, Law HY, Lim WK, Tan ES, Tan EC, Jamuar SS. Rapid exome sequencing to aid diagnostics in genetic disorders: Implementation and challenges in the Singapore context. ANNALS OF THE ACADEMY OF MEDICINE, SINGAPORE 2022. [DOI: 10.47102/annals-acadmedsg.202252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Nikki Fong
- KK Women’s and Children’s Hospital, Singapore
| | | | - Breana Cham
- KK Women’s and Children’s Hospital, Singapore
| | - Sylvia Kam
- KK Women’s and Children’s Hospital, Singapore
| | - Chew Yin Goh
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Heming Wei
- KK Women’s and Children’s Hospital, Singapore
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Nazeha N, Koh AL, Kam S, Lim JY, Goh DLM, Jamuar SS, Graves N. Reduced resource utilization with early use of next-generation sequencing in rare genetic diseases in an Asian cohort. Am J Med Genet A 2022; 188:3482-3491. [PMID: 36156406 DOI: 10.1002/ajmg.a.62974] [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: 05/09/2022] [Revised: 08/22/2022] [Accepted: 09/03/2022] [Indexed: 01/31/2023]
Abstract
Children with genetic diseases endure a prolonged and costly "diagnostic odyssey." The use of whole exome sequencing (WES) and whole genome sequencing (WGS) has improved the diagnosis rate, ending the odyssey. However, the additional costs associated WES/WGS has impeded their adoption in Asian settings. We aim to estimate the expected change to the mean number of diagnostic tests used, and the associated costs from a decision to use WES early in the diagnostic pathways of pediatric phenotypes, as compared to Existing Practice. Retrospective data from a patient cohort recruited under the Singapore Undiagnosed Disease Program from a tertiary hospital in Singapore, for the period October 2004 to September 2020, was analyzed. Four phenotype-specific subgroups were used: multiple congenital anomalies (MCA) without developmental delay; global developmental delay (GDD); neuromuscular disorder (NMD) and primary immunodeficiency disorder (PID). Patients had undergone a traditional diagnostic pathway and received a diagnosis either through clinical exome or WES or WGS. A costs only analysis was performed, by tabulating the outcomes "test quantity" and "test costs" incurred by patients. The outcomes were compared with alternate diagnostic pathways which incorporates the early introduction of WES trio testing. To include uncertainty in cost outcomes, simulation studies were done on uncertain parameters. Cost outcomes are reported in Singapore dollars (S$). The 92 included patients had MCA (n = 48), GDD (n = 29), NMD (n = 10), or PID (n = 5). Patients were aged between 18 days and 26 years, 52.2% were males. The majority were of Chinese ethnicity (81.5%). If patients had access to WES directly, test quantity reduced by 97.38% for MCA, 96.98% for GDD, 96.56% for NMD, and 99.84% for PID. The expected cost savings per patient were $5940 for MCA (US$4433), $5342 for GDD (US$3986), $4622 for NMD (US$3449), and $58,497 for PID (US$43,654). Uncertainty assessment for MCA and GDD patients showed a respective likelihood of 86.9% and 97.4% for cost savings. Adoption of alternate diagnostic pathways with early WES in selected pediatric subgroups are likelt to reduce costs, when compared to Existing Practice. Benefits arising from earlier diagnosis, and the potential cost savings could mitigate the large initial cost of implementing WES in Asian settings.
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Affiliation(s)
- Nuraini Nazeha
- Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Ai Ling Koh
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Sylvia Kam
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Jiin Ying Lim
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Denise Li Meng Goh
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Paediatrics, Khoo Teck Puat - National University Children's Medical Institute, National University Hospital, Singapore, Singapore
| | - Saumya Shekhar Jamuar
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore.,SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
| | - Nicholas Graves
- Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
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Kim SY, Lee S, Woo H, Han J, Ko YJ, Shim Y, Park S, Jang SS, Lim BC, Ko JM, Kim KJ, Cho A, Kim H, Hwang H, Choi JE, Kim MJ, Moon J, Seong MW, Park SS, Choi SA, Lee JE, Kwon YS, Sohn YB, Kim JS, Kim WS, Lee YJ, Kwon S, Kim YO, Kook H, Cho YG, Cheon CK, Kang KS, Song MR, Kim YJ, Cha HJ, Choi HJ, Kee Y, Park SG, Baek ST, Choi M, Ryu DS, Chae JH. The Korean undiagnosed diseases program phase I: expansion of the nationwide network and the development of long-term infrastructure. Orphanet J Rare Dis 2022; 17:372. [PMID: 36209187 PMCID: PMC9548182 DOI: 10.1186/s13023-022-02520-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phase I of the Korean Undiagnosed Diseases Program (KUDP), performed for 3 years, has been completed. The Phase I program aimed to solve the problem of undiagnosed patients throughout the country and develop infrastructure, including a data management system and functional core laboratory, for long-term translational research. Herein, we share the clinical experiences of the Phase I program and introduce the activities of the functional core laboratory and data management system. RESULTS During the program (2018-2020), 458 patients were enrolled and classified into 3 groups according to the following criteria: (I) those with a specific clinical assessment which can be verified by direct testing (32 patients); (II) those with a disease group with genetic and phenotypic heterogeneity (353 patients); and (III) those with atypical presentations or diseases unknown to date (73 patients). All patients underwent individualized diagnostic processes based on the decision of an expert consortium. Confirmative diagnoses were obtained for 242 patients (52.8%). The diagnostic yield was different for each group: 81.3% for Group I, 53.3% for Group II, and 38.4% for Group III. Diagnoses were made by next-generation sequencing for 204 patients (84.3%) and other genetic testing for 35 patients (14.5%). Three patients (1.2%) were diagnosed with nongenetic disorders. The KUDP functional core laboratory, with a group of experts, organized a streamlined research pipeline covering various resources, including animal models, stem cells, structural modeling and metabolic and biochemical approaches. Regular data review was performed to screen for candidate genes among undiagnosed patients, and six different genes were identified for functional research. We also developed a web-based database system that supports clinical cohort management and provides a matchmaker exchange protocol based on a matchbox, likely to reinforce the nationwide clinical network and further international collaboration. CONCLUSIONS The KUDP evaluated the unmet needs of undiagnosed patients and established infrastructure for a data-sharing system and future functional research. The advancement of the KUDP may lead to sustainable bench-to-bedside research in Korea and contribute to ongoing international collaboration.
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Affiliation(s)
- Soo Yeon Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seungbok Lee
- Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, National University College of Medicine, 101 Daehakro Jongno-gu, Seoul, 110-744, Republic of Korea
| | - Hyewon Woo
- Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, National University College of Medicine, 101 Daehakro Jongno-gu, Seoul, 110-744, Republic of Korea
| | - Jiyeon Han
- Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, National University College of Medicine, 101 Daehakro Jongno-gu, Seoul, 110-744, Republic of Korea
| | - Young Jun Ko
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Youngkyu Shim
- Department of Pediatrics, Korea University Ansan Hospital, Ansan, Republic of Korea
| | - Soojin Park
- Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, National University College of Medicine, 101 Daehakro Jongno-gu, Seoul, 110-744, Republic of Korea
| | - Se Song Jang
- Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, National University College of Medicine, 101 Daehakro Jongno-gu, Seoul, 110-744, Republic of Korea
| | - Byung Chan Lim
- Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, National University College of Medicine, 101 Daehakro Jongno-gu, Seoul, 110-744, Republic of Korea
| | - Jung Min Ko
- Division of Clinical Genetics, Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ki Joong Kim
- Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, National University College of Medicine, 101 Daehakro Jongno-gu, Seoul, 110-744, Republic of Korea
| | - Anna Cho
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Hunmin Kim
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Hee Hwang
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Ji Eun Choi
- Department of Pediatrics, SMG-SNU Boramae Hospital, Seoul, Republic of Korea
| | - Man Jin Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jangsup Moon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sun Ah Choi
- Department of Pediatrics, Ehwa Womans University Mokdong Hospital, Ehwa Womans University College of Medicine, Seoul, Republic of Korea
| | - Ji Eun Lee
- Department of Pediatric, Inha University College of Medicine, Inha University Hospital, Incheon, Republic of Korea
| | - Young Se Kwon
- Department of Pediatric, Inha University College of Medicine, Inha University Hospital, Incheon, Republic of Korea
| | - Young Bae Sohn
- Department of Medical Genetics, Ajou University Hospital, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Jon Soo Kim
- Department of Pediatrics, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Won Seop Kim
- Department of Pediatrics, Chungbuk National University Hospital, Cheongju, Republic of Korea.,Department of Pediatrics, College of Medicine, Chungbuk National University, Cheongju, Republic of Korea
| | - Yun Jeong Lee
- Department of Pediatrics, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Soonhak Kwon
- Department of Pediatrics, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Young Ok Kim
- Departmentof Pediatrics, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Hoon Kook
- Departmentof Pediatrics, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Yong Gon Cho
- Department of Laboratory Medicine, Jeonbuk National University Medical School, Jeonju, Republic of Korea
| | - Chong Kun Cheon
- Department of Pediatrics, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea
| | - Ki-Soo Kang
- Department of Pediatrics, Jeju National University Hospital, Jeju, Republic of Korea
| | - Mi-Ryoung Song
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Young-Joon Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Hyuk-Jin Cha
- Collage of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Hee-Jung Choi
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yun Kee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Sung-Gyoo Park
- Collage of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Seung Tae Baek
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | - Jong-Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea. .,Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, National University College of Medicine, 101 Daehakro Jongno-gu, Seoul, 110-744, Republic of Korea.
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9
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Schuermans N, Hemelsoet D, Terryn W, Steyaert S, Van Coster R, Coucke PJ, Steyaert W, Callewaert B, Bogaert E, Verloo P, Vanlander AV, Debackere E, Ghijsels J, LeBlanc P, Verdin H, Naesens L, Haerynck F, Callens S, Dermaut B, Poppe B. Shortcutting the diagnostic odyssey: the multidisciplinary Program for Undiagnosed Rare Diseases in adults (UD-PrOZA). Orphanet J Rare Dis 2022; 17:210. [PMID: 35606766 PMCID: PMC9128245 DOI: 10.1186/s13023-022-02365-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/13/2022] [Indexed: 11/23/2022] Open
Abstract
Background In order to facilitate the diagnostic process for adult patients suffering from a rare disease, the Undiagnosed Disease Program (UD-PrOZA) was founded in 2015 at the Ghent University Hospital in Belgium. In this study we report the five-year results of our multidisciplinary approach in rare disease diagnostics. Methods Patients referred by a healthcare provider, in which an underlying rare disease is likely, qualify for a UD-PrOZA evaluation. UD-PrOZA uses a multidisciplinary clinical approach combined with state-of-the-art genomic technologies in close collaboration with research facilities to diagnose patients. Results Between 2015 and 2020, 692 patients (94% adults) were referred of which 329 (48%) were accepted for evaluation. In 18% (60 of 329) of the cases a definite diagnosis was made. 88% (53 of 60) of the established diagnoses had a genetic origin. 65% (39 of 60) of the genetic diagnoses were made through whole exome sequencing (WES). The mean time interval between symptom-onset and diagnosis was 19 years. Key observations included novel genotype–phenotype correlations, new variants in known disease genes and the identification of three new disease genes. In 13% (7 of 53), identifying the molecular cause was associated with therapeutic recommendations and in 88% (53 of 60), gene specific genetic counseling was made possible. Actionable secondary findings were reported in 7% (12 of 177) of the patients in which WES was performed. Conclusion UD-PrOZA offers an innovative interdisciplinary platform to diagnose rare diseases in adults with previously unexplained medical problems and to facilitate translational research. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02365-y.
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Affiliation(s)
- Nika Schuermans
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium. .,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
| | | | - Wim Terryn
- Department of Nephrology, Jan Yperman Hospital, Ieper, Belgium
| | - Sanne Steyaert
- Department of General Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - Rudy Van Coster
- Department of Pediatrics, Division of Pediatric Neurology and Metabolic Diseases, Ghent University Hospital, Ghent, Belgium
| | - Paul J Coucke
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Wouter Steyaert
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Elke Bogaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Patrick Verloo
- Department of Pediatrics, Division of Pediatric Neurology and Metabolic Diseases, Ghent University Hospital, Ghent, Belgium
| | - Arnaud V Vanlander
- Department of Pediatrics, Division of Pediatric Neurology and Metabolic Diseases, Ghent University Hospital, Ghent, Belgium
| | - Elke Debackere
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Jody Ghijsels
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Pontus LeBlanc
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Hannah Verdin
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Leslie Naesens
- Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium.,Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Filomeen Haerynck
- Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium
| | - Steven Callens
- Department of General Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - Bart Dermaut
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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10
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Sheidley BR, Malinowski J, Bergner AL, Bier L, Gloss DS, Mu W, Mulhern MM, Partack EJ, Poduri A. Genetic testing for the epilepsies: A systematic review. Epilepsia 2021; 63:375-387. [PMID: 34893972 DOI: 10.1111/epi.17141] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/29/2022]
Abstract
OBJECTIVE Numerous genetic testing options for individuals with epilepsy have emerged over the past decade without clear guidelines regarding optimal testing strategies. We performed a systematic evidence review (SER) and conducted meta-analyses of the diagnostic yield of genetic tests commonly utilized for patients with epilepsy. We also assessed nonyield outcomes (NYOs) such as changes in treatment and/or management, prognostic information, recurrence risk determination, and genetic counseling. METHODS We performed an SER, in accordance with PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses), using PubMed, Embase, CINAHL, and Cochrane Central through December of 2020. We included studies that utilized genome sequencing (GS), exome sequencing (ES), multigene panel (MGP), and/or genome-wide comparative genomic hybridization/chromosomal microarray (CGH/CMA) in cohorts (n ≥ 10) ascertained for epilepsy. Quality assessment was undertaken using ROBINS-I (Risk of Bias in Non-Randomized Studies of Interventions). We estimated diagnostic yields and 95% confidence intervals with random effects meta-analyses and narratively synthesized NYOs. RESULTS From 5985 nonduplicated articles published through 2020, 154 met inclusion criteria and were included in meta-analyses of diagnostic yield; 43 of those were included in the NYO synthesis. The overall diagnostic yield across all test modalities was 17%, with the highest yield for GS (48%), followed by ES (24%), MGP (19%), and CGH/CMA (9%). The only phenotypic factors that were significantly associated with increased yield were (1) the presence of developmental and epileptic encephalopathy and/or (2) the presence of neurodevelopmental comorbidities. Studies reporting NYOs addressed clinical and personal utility of testing. SIGNIFICANCE This comprehensive SER, focused specifically on the literature regarding patients with epilepsy, provides a comparative assessment of the yield of clinically available tests, which will help shape clinician decision-making and policy regarding insurance coverage for genetic testing. We highlight the need for prospective assessment of the clinical and personal utility of genetic testing for patients with epilepsy and for standardization in reporting patient characteristics.
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Affiliation(s)
- Beth R Sheidley
- Epilepsy Genetics Program, Division of Epilepsy and Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | | | - Amanda L Bergner
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Louise Bier
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - David S Gloss
- Department of Neurology, Charleston Area Medical Center, Charleston, West Virginia, USA
| | - Weiyi Mu
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Maureen M Mulhern
- Department of Pathology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA.,Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Emily J Partack
- Genomics Services, Quest Diagnostics, Marlborough, Massachusetts, USA
| | - Annapurna Poduri
- Epilepsy Genetics Program, Division of Epilepsy and Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA
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11
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Álvaro-Sánchez S, Abreu-Rodríguez I, Abulí A, Serra-Juhe C, Garrido-Navas MDC. Current Status of Genetic Counselling for Rare Diseases in Spain. Diagnostics (Basel) 2021; 11:2320. [PMID: 34943558 PMCID: PMC8700506 DOI: 10.3390/diagnostics11122320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 12/29/2022] Open
Abstract
Genetic Counselling is essential for providing personalised information and support to patients with Rare Diseases (RD). Unlike most other developed countries, Spain does not recognize geneticists or genetic counsellors as healthcare professionals Thus, patients with RD face not only challenges associated with their own disease but also deal with lack of knowledge, uncertainty, and other psychosocial issues arising as a consequence of diagnostic delay. In this review, we highlight the importance of genetic counsellors in the field of RD as well as evaluate the current situation in which rare disease patients receive genetic services in Spain. We describe the main units and strategies at the national level assisting patients with RD and we conclude with a series of future perspectives and unmet needs that Spain should overcome to improve the management of patients with RD.
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Affiliation(s)
| | - Irene Abreu-Rodríguez
- Genetics Service, Hospital del Mar Research Institute, IMIM, 08003 Barcelona, Spain;
| | - Anna Abulí
- Department of Clinical and Molecular Genetics, Hospital Vall d’Hebron, 08035 Barcelona, Spain;
- Medicine Genetics Group, Vall d’Hebron Research Institute (VHIR), 08035 Barcelona, Spain
| | - Clara Serra-Juhe
- U705 CIBERER, Genetics Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain;
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Maria del Carmen Garrido-Navas
- CONGEN, Genetic Counselling Services, C/Albahaca 4, 18006 Granada, Spain;
- Genetics Department, Faculty of Sciences, Universidad de Granada, 18071 Granada, Spain
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12
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Shickh S, Mighton C, Uleryk E, Pechlivanoglou P, Bombard Y. The clinical utility of exome and genome sequencing across clinical indications: a systematic review. Hum Genet 2021; 140:1403-1416. [PMID: 34368901 DOI: 10.1007/s00439-021-02331-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/31/2021] [Indexed: 12/15/2022]
Abstract
Exome sequencing and genome sequencing have the potential to improve clinical utility for patients undergoing genetic investigations. However, evidence of clinical utility is limited to pediatric populations; we aimed to fill this gap by conducting a systematic review of the literature on the clinical utility of exome/genome sequencing across disease indications in pediatric and adult populations. MEDLINE, EMBASE and Cochrane Library were searched between 2016 and 2020. Quantitative studies evaluating diagnostic yield were included; other measures of clinical utility such as changes to clinical management were documented if reported. Two reviewers screened, extracted data, and appraised risk of bias. Fifty studies met our inclusion criteria. All studies reported diagnostic yield, which ranged from 3 to 70%, with higher range of yields reported for neurological indications and acute illness ranging from 22 to 68% and 37-70%, respectively. Diagnoses triggered a range of clinical management changes including surveillance, reproductive-risk counseling, and identifying at-risk relatives in 4-100% of patients, with higher frequencies reported for acute illness ranging from 67 to 95%. The frequency of variants of uncertain significance ranged from 5 to 85% across studies with a potential trend of decreasing frequency over time and higher rates identified in patients of non-European ancestry. This review provides evidence for a higher range of diagnostic yield of exome/genome sequencing compared to standard genetic tests, particularly in neurological and acute indications. However, we identified significant heterogeneity in study procedures and outcomes, precluding a meaningful meta-analysis and certainty in the evidence available for decision-making. Future research that incorporates a comprehensive and consistent approach in capturing clinical utility of exome/genome sequencing across broader ancestral groups is necessary to improve diagnostic accuracy and yield and allow for analysis of trends over time.Prospero registration CRD42019094101.
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Affiliation(s)
- Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | | | - Petros Pechlivanoglou
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,The Hospital for Sick Children, Toronto, ON, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada. .,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada. .,Li Ka Shing Knowledge Institute of St. Michael's Hospital, University of Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada.
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13
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Yahia A, Stevanin G. The History of Gene Hunting in Hereditary Spinocerebellar Degeneration: Lessons From the Past and Future Perspectives. Front Genet 2021; 12:638730. [PMID: 33833777 PMCID: PMC8021710 DOI: 10.3389/fgene.2021.638730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/02/2021] [Indexed: 01/02/2023] Open
Abstract
Hereditary spinocerebellar degeneration (SCD) encompasses an expanding list of rare diseases with a broad clinical and genetic heterogeneity, complicating their diagnosis and management in daily clinical practice. Correct diagnosis is a pillar for precision medicine, a branch of medicine that promises to flourish with the progressive improvements in studying the human genome. Discovering the genes causing novel Mendelian phenotypes contributes to precision medicine by diagnosing subsets of patients with previously undiagnosed conditions, guiding the management of these patients and their families, and enabling the discovery of more causes of Mendelian diseases. This new knowledge provides insight into the biological processes involved in health and disease, including the more common complex disorders. This review discusses the evolution of the clinical and genetic approaches used to diagnose hereditary SCD and the potential of new tools for future discoveries.
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Affiliation(s)
- Ashraf Yahia
- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
- Department of Biochemistry, Faculty of Medicine, National University, Khartoum, Sudan
- Institut du Cerveau, INSERM U1127, CNRS UMR7225, Sorbonne Université, Paris, France
- Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
| | - Giovanni Stevanin
- Institut du Cerveau, INSERM U1127, CNRS UMR7225, Sorbonne Université, Paris, France
- Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
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14
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Affiliation(s)
- Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Vardha Ismail
- Clinical Genetics, Southampton University Hospitals NHS Trust, Southampton, UK
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