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Acs-Szabo L, Papp LA, Miklos I. Understanding the molecular mechanisms of human diseases: the benefits of fission yeasts. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:288-311. [PMID: 39104724 PMCID: PMC11299203 DOI: 10.15698/mic2024.08.833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/04/2024] [Accepted: 07/10/2024] [Indexed: 08/07/2024]
Abstract
The role of model organisms such as yeasts in life science research is crucial. Although the baker's yeast (Saccharomyces cerevisiae) is the most popular model among yeasts, the contribution of the fission yeasts (Schizosaccharomyces) to life science is also indisputable. Since both types of yeasts share several thousands of common orthologous genes with humans, they provide a simple research platform to investigate many fundamental molecular mechanisms and functions, thereby contributing to the understanding of the background of human diseases. In this review, we would like to highlight the many advantages of fission yeasts over budding yeasts. The usefulness of fission yeasts in virus research is shown as an example, presenting the most important research results related to the Human Immunodeficiency Virus Type 1 (HIV-1) Vpr protein. Besides, the potential role of fission yeasts in the study of prion biology is also discussed. Furthermore, we are keen to promote the uprising model yeast Schizosaccharomyces japonicus, which is a dimorphic species in the fission yeast genus. We propose the hyphal growth of S. japonicus as an unusual opportunity as a model to study the invadopodia of human cancer cells since the two seemingly different cell types can be compared along fundamental features. Here we also collect the latest laboratory protocols and bioinformatics tools for the fission yeasts to highlight the many possibilities available to the research community. In addition, we present several limiting factors that everyone should be aware of when working with yeast models.
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Affiliation(s)
- Lajos Acs-Szabo
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of DebrecenDebrecen, 4032Hungary
| | - Laszlo Attila Papp
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of DebrecenDebrecen, 4032Hungary
| | - Ida Miklos
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of DebrecenDebrecen, 4032Hungary
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2
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Ellwanger K, Brill JA, de Boer E, Efthymiou S, Elgersma Y, Icmat M, Lecoquierre F, Lobato AG, Morleo M, Ori M, Schaffer AE, Vitobello A, Wells S, Yalcin B, Zhai RG, Sturm M, Zurek B, Graessner H, Bermejo-Sánchez E, Evangelista T, Hoogerbrugge N, Nigro V, Schüle R, Verloes A, Brunner H, Campeau PM, Lasko P, Riess O. Model matchmaking via the Solve-RD Rare Disease Models & Mechanisms Network (RDMM-Europe). Lab Anim (NY) 2024; 53:161-165. [PMID: 38914824 PMCID: PMC11216991 DOI: 10.1038/s41684-024-01395-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Affiliation(s)
- Kornelia Ellwanger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
| | - Julie A Brill
- The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Elke de Boer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Ype Elgersma
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Marynelle Icmat
- The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - François Lecoquierre
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics, FHU G4 Génomique, Rouen, France
| | - Amanda G Lobato
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA
- Graduate Program in Human Genetics and Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Neurology, University of Chicago, Chicago, IL, USA
| | - Manuela Morleo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (Na), Italy
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy
| | - Michela Ori
- Department of Biology, University of Pisa, Pisa, Italy
| | - Ashleigh E Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Antonio Vitobello
- INSERM-Université de Bourgogne UMR1231 GAD «Génétique Des Anomalies du Développement», FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France
- Dijon University Hospital- UF innovation en diagnostic génomique, Dijon, France
| | - Sara Wells
- The Mary Lyon Centre at MRC Harwell, Harwell Science Campus, Oxon, UK
| | - Binnaz Yalcin
- Inserm Unit 1231, University of Bourgogne Franche-Comté, Dijon, France
| | - R Grace Zhai
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Neurology, University of Chicago, Chicago, IL, USA
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Birte Zurek
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Holm Graessner
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Eva Bermejo-Sánchez
- Institute of Rare Diseases Research (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Teresinha Evangelista
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (Na), Italy
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy
| | - Rebecca Schüle
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research (HIH), University of Tübingen, Tübingen, Germany
| | - Alain Verloes
- Department of Genetics, Assistance Publique-Hôpitaux de Paris - Université de Paris, Robert DEBRE University Hospital, Paris, France
| | - Han Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Philippe M Campeau
- Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, Quebec, Canada
| | - Paul Lasko
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
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3
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Hills S, Li Q, Madden JA, Genetti CA, Brownstein CA, Schmitz-Abe K, Beggs AH, Agrawal PB. High number of candidate gene variants are identified as disease-causing in a period of 4 years. Am J Med Genet A 2024; 194:e63509. [PMID: 38158391 DOI: 10.1002/ajmg.a.63509] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/15/2023] [Accepted: 12/09/2023] [Indexed: 01/03/2024]
Abstract
Advances in bioinformatic tools paired with the ongoing accumulation of genetic knowledge and periodic reanalysis of genomic sequencing data have led to an improvement in genetic diagnostic rates. Candidate gene variants (CGVs) identified during sequencing or on reanalysis but not yet implicated in human disease or associated with a phenotypically distinct condition are often not revisited, leading to missed diagnostic opportunities. Here, we revisited 33 such CGVs from our previously published study and determined that 16 of them are indeed disease-causing (novel or phenotype expansion) since their identification. These results emphasize the need to focus on previously identified CGVs during sequencing or reanalysis and the importance of sharing that information with researchers around the world, including relevant functional analysis to establish disease causality.
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Affiliation(s)
- Sonia Hills
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Qifei Li
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Jackson Health System, Miami, Florida, USA
| | - Jill A Madden
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Casie A Genetti
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Catherine A Brownstein
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Klaus Schmitz-Abe
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Jackson Health System, Miami, Florida, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alan H Beggs
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Jackson Health System, Miami, Florida, USA
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4
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Faundes V, Repetto GM, Valdivia LE. Discovery of novel genetic syndromes in Latin America: Opportunities and challenges. Genet Mol Biol 2024; 47Suppl 1:e20230318. [PMID: 38466870 DOI: 10.1590/1678-4685-gmb-2023-0318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/06/2024] [Indexed: 03/13/2024] Open
Abstract
Latin America (LatAm) has a rich and historically significant role in delineating both novel and well-documented genetic disorders. However, the ongoing advancements in the field of human genetics pose challenges to the relatively slow adaption of LatAm in the field. Here, we describe past and present contributions of LatAm to the discovery of novel genetic disorders, often referred as novel gene-disease associations (NGDA). We also describe the current methodologies for discovery of NGDA, taking into account the latest developments in genomics. We provide an overview of opportunities and challenges for NGDA research in LatAm considering the steps currently performed to identify and validate such associations. Given the multiple and diverse needs of populations and countries in LatAm, it is imperative to foster collaborations amongst patients, indigenous people, clinicians and scientists. Such collaborative effort is essential for sustaining and enhancing the LatAm´s contributions to the field of NGDA.
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Affiliation(s)
- Víctor Faundes
- Universidad de Chile, Instituto de Nutrición y Tecnología de los Alimentos, Laboratorio de Genética y Enfermedades Metabólicas, Santiago, Chile
| | - Gabriela M Repetto
- Universidad del Desarrollo, Facultad de Medicina, Instituto de Ciencias e Innovación en Medicina, Centro de Genética y Genómica, Programa de Enfermedades Raras, Santiago, Chile
| | - Leonardo E Valdivia
- Universidad Mayor, Facultad de Ciencias, Centro de Biología Integrativa, Santiago, Chile
- Universidad Mayor, Facultad de Ciencias, Escuela de Biotecnología, Santiago, Chile
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5
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Shalash R, Levi-Ferber M, Cohen C, Dori A, Brodie C, Henis-Korenblit S. Cross-species modeling of muscular dystrophy in Caenorhabditis elegans using patient-derived extracellular vesicles. Dis Model Mech 2024; 17:dmm050412. [PMID: 38501170 PMCID: PMC11007864 DOI: 10.1242/dmm.050412] [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: 07/25/2023] [Accepted: 03/04/2024] [Indexed: 03/20/2024] Open
Abstract
Reliable disease models are critical for medicine advancement. Here, we established a versatile human disease model system using patient-derived extracellular vesicles (EVs), which transfer a pathology-inducing cargo from a patient to a recipient naïve model organism. As a proof of principle, we applied EVs from the serum of patients with muscular dystrophy to Caenorhabditis elegans and demonstrated their capability to induce a spectrum of muscle pathologies, including lifespan shortening and robust impairment of muscle organization and function. This demonstrates that patient-derived EVs can deliver disease-relevant pathologies between species and can be exploited for establishing novel and personalized models of human disease. Such models can potentially be used for disease diagnosis, prognosis, analyzing treatment responses, drug screening and identification of the disease-transmitting cargo of patient-derived EVs and their cellular targets. This system complements traditional genetic disease models and enables modeling of multifactorial diseases and of those not yet associated with specific genetic mutations.
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Affiliation(s)
- Rewayd Shalash
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Mor Levi-Ferber
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Coral Cohen
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Amir Dori
- Department of Neurology, Sheba Medical Center, Ramat-Gan 52621, Israel
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Chaya Brodie
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Sivan Henis-Korenblit
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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6
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Yamamoto S, Kanca O, Wangler MF, Bellen HJ. Integrating non-mammalian model organisms in the diagnosis of rare genetic diseases in humans. Nat Rev Genet 2024; 25:46-60. [PMID: 37491400 DOI: 10.1038/s41576-023-00633-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2023] [Indexed: 07/27/2023]
Abstract
Next-generation sequencing technology has rapidly accelerated the discovery of genetic variants of interest in individuals with rare diseases. However, showing that these variants are causative of the disease in question is complex and may require functional studies. Use of non-mammalian model organisms - mainly fruitflies (Drosophila melanogaster), nematode worms (Caenorhabditis elegans) and zebrafish (Danio rerio) - enables the rapid and cost-effective assessment of the effects of gene variants, which can then be validated in mammalian model organisms such as mice and in human cells. By probing mechanisms of gene action and identifying interacting genes and proteins in vivo, recent studies in these non-mammalian model organisms have facilitated the diagnosis of numerous genetic diseases and have enabled the screening and identification of therapeutic options for patients. Studies in non-mammalian model organisms have also shown that the biological processes underlying rare diseases can provide insight into more common mechanisms of disease and the biological functions of genes. Here, we discuss the opportunities afforded by non-mammalian model organisms, focusing on flies, worms and fish, and provide examples of their use in the diagnosis of rare genetic diseases.
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Affiliation(s)
- Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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7
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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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8
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Muñoz-Pujol G, Ugarteburu O, Segur-Bailach E, Moliner S, Jurado S, Garrabou G, Guitart-Mampel M, García-Villoria J, Artuch R, Fons C, Ribes A, Tort F. CRISPR/Cas9-based functional genomics strategy to decipher the pathogenicity of genetic variants in inherited metabolic disorders. J Inherit Metab Dis 2023; 46:1029-1042. [PMID: 37718653 DOI: 10.1002/jimd.12681] [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: 07/08/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/19/2023]
Abstract
The determination of the functional impact of variants of uncertain significance (VUS) is one of the major bottlenecks in the diagnostic workflow of inherited genetic diseases. To face this problem, we set up a CRISPR/Cas9-based strategy for knock-in cellular model generation, focusing on inherited metabolic disorders (IMDs). We selected variants in seven IMD-associated genes, including seven reported disease-causing variants and four benign/likely benign variants. Overall, 11 knock-in cell models were generated via homology-directed repair in HAP1 haploid cells using CRISPR/Cas9. The functional impact of the variants was determined by analyzing the characteristic biochemical alterations of each disorder. Functional studies performed in knock-in cell models showed that our approach accurately distinguished the functional effect of pathogenic from non-pathogenic variants in a reliable manner in a wide range of IMDs. Our study provides a generic approach to assess the functional impact of genetic variants to improve IMD diagnosis and this tool could emerge as a promising alternative to invasive tests, such as muscular or skin biopsies. Although the study has been performed only in IMDs, this strategy is generic and could be applied to other genetic disorders.
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Affiliation(s)
- Gerard Muñoz-Pujol
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Olatz Ugarteburu
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Eulàlia Segur-Bailach
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Sonia Moliner
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Susana Jurado
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Glòria Garrabou
- Inherited Metabolic diseases and Muscle Disorder's lab, Cellex-IDIBAPS, Faculty of Medicine and Health Sciences, University of Barcelona, Internal Medicine Service-Hospital Clinic of Barcelona and CIBERER, Barcelona, Spain
| | - Mariona Guitart-Mampel
- Inherited Metabolic diseases and Muscle Disorder's lab, Cellex-IDIBAPS, Faculty of Medicine and Health Sciences, University of Barcelona, Internal Medicine Service-Hospital Clinic of Barcelona and CIBERER, Barcelona, Spain
| | - Judit García-Villoria
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Rafael Artuch
- Clinical Biochemistry and Molecular Medicine and Genetics Departments, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, and CIBERER, Esplúgues de Llobregat, Barcelona, Spain
| | - Carme Fons
- Neurology Department, Fetal, Neonatal Neurology and Early Epilepsy Unit, Institut de Recerca, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Antonia Ribes
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Frederic Tort
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
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9
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Fu MP, Merrill SM, Sharma M, Gibson WT, Turvey SE, Kobor MS. Rare diseases of epigenetic origin: Challenges and opportunities. Front Genet 2023; 14:1113086. [PMID: 36814905 PMCID: PMC9939656 DOI: 10.3389/fgene.2023.1113086] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023] Open
Abstract
Rare diseases (RDs), more than 80% of which have a genetic origin, collectively affect approximately 350 million people worldwide. Progress in next-generation sequencing technology has both greatly accelerated the pace of discovery of novel RDs and provided more accurate means for their diagnosis. RDs that are driven by altered epigenetic regulation with an underlying genetic basis are referred to as rare diseases of epigenetic origin (RDEOs). These diseases pose unique challenges in research, as they often show complex genetic and clinical heterogeneity arising from unknown gene-disease mechanisms. Furthermore, multiple other factors, including cell type and developmental time point, can confound attempts to deconvolute the pathophysiology of these disorders. These challenges are further exacerbated by factors that contribute to epigenetic variability and the difficulty of collecting sufficient participant numbers in human studies. However, new molecular and bioinformatics techniques will provide insight into how these disorders manifest over time. This review highlights recent studies addressing these challenges with innovative solutions. Further research will elucidate the mechanisms of action underlying unique RDEOs and facilitate the discovery of treatments and diagnostic biomarkers for screening, thereby improving health trajectories and clinical outcomes of affected patients.
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Affiliation(s)
- Maggie P. Fu
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Sarah M. Merrill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Mehul Sharma
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada,Department of Pediatrics, Faculty of Medicine, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - William T. Gibson
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Stuart E. Turvey
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada,Department of Pediatrics, Faculty of Medicine, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Michael S. Kobor
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada,*Correspondence: Michael S. Kobor,
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10
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Ediae GU, Lemire G, Chisholm C, Hartley T, Eaton A, Osmond M, Rojas SK, Huang L, Gillespie M, Sawyer SL, Boycott KM. The implementation of an enhanced clinical model to improve the diagnostic yield of exome sequencing for patients with a rare genetic disease: A Canadian experience. Am J Med Genet A 2023; 191:338-347. [PMID: 36331261 DOI: 10.1002/ajmg.a.63022] [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: 09/08/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
The introduction of clinical exome sequencing (ES) has provided a unique opportunity to decrease the diagnostic odyssey for patients living with a rare genetic disease (RGD). ES has been shown to provide a diagnosis in 29%-57% of patients with a suspected RGD, with as many as 70% remaining undiagnosed. There is a need to advance the clinical model of care by more formally integrating approaches that were previously considered research into an enhanced diagnostic workflow. We developed an Exome Clinic, which set out to evaluate a workflow for improving the diagnostic yield of ES for patients with an undiagnosed RGD. Here, we report the outcomes of 47 families who underwent clinical ES in the first year of the clinic. The diagnostic yield from clinical ES was 40% (19/47). Families who remained undiagnosed after ES had the opportunity for follow-up studies that included phenotyping and candidate variant segregation in relatives, genomic matchmaking, and ES reanalysis. This enhanced diagnostic workflow increased the diagnostic yield to 55% (26/47), predominantly through the resolution of variants and genes of uncertain significance. We advocate that this approach be integrated into mainstream clinical practice and highlight the importance of a coordinated translational approach for patients with RGD.
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Affiliation(s)
- Grace Uwaila Ediae
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Regional Genetics Program, Children's Hospital of Eastern Ontario Ottawa, Ottawa, Ontario, Canada
| | - Gabrielle Lemire
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Regional Genetics Program, Children's Hospital of Eastern Ontario Ottawa, Ottawa, Ontario, Canada
| | - Caitlin Chisholm
- Regional Genetics Program, Children's Hospital of Eastern Ontario Ottawa, Ottawa, Ontario, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Alison Eaton
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Regional Genetics Program, Children's Hospital of Eastern Ontario Ottawa, Ottawa, Ontario, Canada
| | - Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Samantha K Rojas
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Regional Genetics Program, Children's Hospital of Eastern Ontario Ottawa, Ottawa, Ontario, Canada
| | - Lijia Huang
- Regional Genetics Program, Children's Hospital of Eastern Ontario Ottawa, Ottawa, Ontario, Canada.,Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Meredith Gillespie
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Sarah L Sawyer
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Regional Genetics Program, Children's Hospital of Eastern Ontario Ottawa, Ottawa, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Regional Genetics Program, Children's Hospital of Eastern Ontario Ottawa, Ottawa, Ontario, Canada
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11
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Boycott KM, Hartley T, Kernohan KD, Dyment DA, Howley H, Innes AM, Bernier FP, Brudno M. Care4Rare Canada: Outcomes from a decade of network science for rare disease gene discovery. Am J Hum Genet 2022; 109:1947-1959. [PMID: 36332610 PMCID: PMC9674964 DOI: 10.1016/j.ajhg.2022.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
The past decade has witnessed a rapid evolution in rare disease (RD) research, fueled by the availability of genome-wide (exome and genome) sequencing. In 2011, as this transformative technology was introduced to the research community, the Care4Rare Canada Consortium was launched: initially as FORGE, followed by Care4Rare, and Care4Rare SOLVE. Over what amounted to three eras of diagnosis and discovery, the Care4Rare Consortium used exome sequencing and, more recently, genome and other 'omic technologies to identify the molecular cause of unsolved RDs. We achieved a diagnostic yield of 34% (623/1,806 of participating families), including the discovery of deleterious variants in 121 genes not previously associated with disease, and we continue to study candidate variants in novel genes for 145 families. The Consortium has made significant contributions to RD research, including development of platforms for data collection and sharing and instigating a Canadian network to catalyze functional characterization research of novel genes. The Consortium was instrumental to implementing genome-wide sequencing as a publicly funded test for RD diagnosis in Canada. Despite the successes of the past decade, the challenge of solving all RDs remains enormous, and the work is far from over. We must leverage clinical and 'omic data for secondary use, develop tools and policies to support safe data sharing, continue to explore the utility of new and emerging technologies, and optimize research protocols to delineate complex disease mechanisms. Successful approaches in each of these realms is required to offer diagnostic clarity to all families with RDs.
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Affiliation(s)
- Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada,Corresponding author
| | - Taila Hartley
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Kristin D. Kernohan
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - David A. Dyment
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Heather Howley
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - A. Micheil Innes
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Francois P. Bernier
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
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12
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Harnish JM, Li L, Rogic S, Poirier-Morency G, Kim SY, Boycott KM, Wangler MF, Bellen HJ, Hieter P, Pavlidis P, Liu Z, Yamamoto S. ModelMatcher: A scientist-centric online platform to facilitate collaborations between stakeholders of rare and undiagnosed disease research. Hum Mutat 2022; 43:743-759. [PMID: 35224820 PMCID: PMC9133126 DOI: 10.1002/humu.24364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/12/2022] [Accepted: 02/23/2022] [Indexed: 11/08/2022]
Abstract
Next-generation sequencing is a prevalent diagnostic tool for undiagnosed diseases and has played a significant role in rare disease gene discovery. Although this technology resolves some cases, others are given a list of possibly damaging genetic variants necessitating functional studies. Productive collaborations between scientists, clinicians, and patients (affected individuals) can help resolve such medical mysteries and provide insights into in vivo function of human genes. Furthermore, facilitating interactions between scientists and research funders, including nonprofit organizations or commercial entities, can dramatically reduce the time to translate discoveries from bench to bedside. Several systems designed to connect clinicians and researchers with a shared gene of interest have been successful. However, these platforms exclude some stakeholders based on their role or geography. Here we describe ModelMatcher, a global online matchmaking tool designed to facilitate cross-disciplinary collaborations, especially between scientists and other stakeholders of rare and undiagnosed disease research. ModelMatcher is integrated into the Rare Diseases Models and Mechanisms Network and Matchmaker Exchange, allowing users to identify potential collaborators in other registries. This living database decreases the time from when a scientist or clinician is making discoveries regarding their genes of interest, to when they identify collaborators and sponsors to facilitate translational and therapeutic research.
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Affiliation(s)
- J. Michael Harnish
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
| | - Lucian Li
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, TX, 77030, USA
| | - Sanja Rogic
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Guillaume Poirier-Morency
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Seon-Young Kim
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, TX, 77030, USA
| | | | - Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H8L1, Canada
| | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, 77030, USA
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, 77030, USA
- Department of Neuroscience, BCM, Houston, TX, 77030, USA
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, TX, 77030, USA
- Quantitative and Computational Biosciences Graduate Program, BCM, Houston, TX, 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, 77030, USA
- Department of Neuroscience, BCM, Houston, TX, 77030, USA
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13
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Boycott KM, Azzariti DR, Hamosh A, Rehm HL. Seven years since the launch of the Matchmaker Exchange: The evolution of genomic matchmaking. Hum Mutat 2022; 43:659-667. [PMID: 35537081 PMCID: PMC9133175 DOI: 10.1002/humu.24373] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 11/09/2022]
Abstract
The Matchmaker Exchange (MME) was launched in 2015 to provide a robust mechanism to discover novel disease-gene relationships. It operates as a federated network connecting databases holding relevant data using a common application programming interface, where two or more users are looking for a match for the same gene (two-sided matchmaking). Seven years from its launch, it is clear that the MME is making outstanding contributions to understanding the morbid anatomy of the genome. The number of unique genes present across the MME has steadily increased over time; there are currently >13,520 unique genes (~68% of all protein-coding genes) connected across the MME's eight genomic matchmaking nodes, GeneMatcher, DECIPHER, PhenomeCentral, MyGene2, seqr, Initiative on Rare and Undiagnosed Disease, PatientMatcher, and the RD-Connect Genome-Phenome Analysis Platform. The collective data set accessible across the MME currently includes more than 120,000 cases from over 12,000 contributors in 98 countries. The discovery of potential new disease-gene relationships is happening daily and international collaborative teams are moving these advances forward to publication, now numbering well over 500. Expansion of data sharing into routine clinical practice by clinicians, genetic counselors, and clinical laboratories has ensured access to discovery for even more individuals with undiagnosed rare genetic diseases. Tens of thousands of patients and their family members have been directly or indirectly impacted by the discoveries facilitated by two-sided genomic matchmaking. MME supports further connections to the literature (PubCaseFinder) and to human and model organism resources (Monarch Initiative) and scientists (ModelMatcher). Efforts are now underway to explore additional approaches to matchmaking at the gene or variant level where there is only one querier (one-sided matchmaking). Genomic matchmaking has proven its utility over the past 7 years and will continue to facilitate discoveries in the years to come.
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Affiliation(s)
- Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Danielle R. Azzariti
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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14
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Abstract
Six years ago, DMM launched a subject collection called ‘Drosophila as a Disease Model’. This collection features Review-type articles and original research that highlight the power of Drosophila research in many aspects of human disease modeling. In the ensuing years, Drosophila research has further expanded to capitalize on genome editing, development of resources, and further interest in studying rare disease mechanisms. In the current issue of DMM, we again highlight the versatility, breadth, and scope of Drosophila research in human disease modeling and translational medicine. While many researchers have embraced the power of the fly, many more could still be encouraged to appreciate the strengths of Drosophila and how such research can integrate across species in a multi-pronged approach. Only when we truly acknowledge that all models contribute to our understanding of human biology, can we take advantage of the scope of current research endeavors. Summary: This Editorial encourages us to embrace the power of the fly in studying human disease and highlights how Drosophila studies can be integrated with research in other species to further our understanding of human biology.
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Affiliation(s)
- Esther M Verheyen
- Department of Molecular Biology and Biochemistry, Centre for Cell Biology, Development and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, CanadaV5A 1S6
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15
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Lee JH. Invertebrate Model Organisms as a Platform to Investigate Rare Human Neurological Diseases. Exp Neurobiol 2022; 31:1-16. [PMID: 35256540 PMCID: PMC8907251 DOI: 10.5607/en22003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 01/16/2023] Open
Abstract
Patients suffering from rare human diseases often go through a painful journey for finding a definite molecular diagnosis prerequisite of appropriate cures. With a novel variant isolated from a single patient, determination of its pathogenicity to end such "diagnostic odyssey" requires multi-step processes involving experts in diverse areas of interest, including clinicians, bioinformaticians and research scientists. Recent efforts in building large-scale genomic databases and in silico prediction platforms have facilitated identification of potentially pathogenic variants causative of rare human diseases of a Mendelian basis. However, the functional significance of individual variants remains elusive in many cases, thus requiring incorporation of versatile and rapid model organism (MO)-based platforms for functional analyses. In this review, the current scope of rare disease research is briefly discussed. In addition, an overview of invertebrate MOs for their key features relevant to rare neurological diseases is provided, with the characteristics of two representative invertebrate MOs, Drosophila melanogaster and Caenorhabditis elegans, as well as the challenges against them. Finally, recently developed research networks integrating these MOs in collaborative research are portraited with an array of bioinformatical analyses embedded. A comprehensive survey of MO-based research activities provided in this review will help us to design a wellstructured analysis of candidate genes or potentially pathogenic variants for their roles in rare neurological diseases in future.
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Affiliation(s)
- Ji-Hye Lee
- Department of Oral Pathology & Life Science in Dentistry, School of Dentistry, Pusan National University, Yangsan 50612, Korea.,Dental Life Science Institute, Pusan National University, Yangsan 50612, Korea.,Periodontal Disease Signaling Network Research Center, Pusan National University, Yangsan 50612, Korea
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16
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Marwaha S, Knowles JW, Ashley EA. A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. Genome Med 2022; 14:23. [PMID: 35220969 PMCID: PMC8883622 DOI: 10.1186/s13073-022-01026-w] [Citation(s) in RCA: 105] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/10/2022] [Indexed: 02/07/2023] Open
Abstract
AbstractRare diseases affect 30 million people in the USA and more than 300–400 million worldwide, often causing chronic illness, disability, and premature death. Traditional diagnostic techniques rely heavily on heuristic approaches, coupling clinical experience from prior rare disease presentations with the medical literature. A large number of rare disease patients remain undiagnosed for years and many even die without an accurate diagnosis. In recent years, gene panels, microarrays, and exome sequencing have helped to identify the molecular cause of such rare and undiagnosed diseases. These technologies have allowed diagnoses for a sizable proportion (25–35%) of undiagnosed patients, often with actionable findings. However, a large proportion of these patients remain undiagnosed. In this review, we focus on technologies that can be adopted if exome sequencing is unrevealing. We discuss the benefits of sequencing the whole genome and the additional benefit that may be offered by long-read technology, pan-genome reference, transcriptomics, metabolomics, proteomics, and methyl profiling. We highlight computational methods to help identify regionally distant patients with similar phenotypes or similar genetic mutations. Finally, we describe approaches to automate and accelerate genomic analysis. The strategies discussed here are intended to serve as a guide for clinicians and researchers in the next steps when encountering patients with non-diagnostic exomes.
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17
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Personalized medicine for rare neurogenetic disorders: can we make it happen? Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006200. [PMID: 35332073 PMCID: PMC8958924 DOI: 10.1101/mcs.a006200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Rare neurogenetic disorders are collectively common, affecting 3% of the population, and often manifest with complex multiorgan comorbidity. With advances in genetic, -omics, and computational analysis, more children can be diagnosed and at an earlier age. Innovations in translational research facilitate the identification of treatment targets and development of disease-modifying drugs such as gene therapy, nutraceuticals, and drug repurposing. This increasingly allows targeted therapy to prevent the often devastating manifestations of rare neurogenetic disorders. In this perspective, successes in diagnosis, prevention, and treatment are discussed with a focus on inherited disorders of metabolism. Barriers for the identification, development, and implementation of rare disease-specific therapies are discussed. New methodologies, care networks, and collaborative frameworks are proposed to optimize the potential of personalized genomic medicine to decrease morbidity and improve lives of these vulnerable patients.
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18
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Yang SA, Salazar JL, Li-Kroeger D, Yamamoto S. Functional Studies of Genetic Variants Associated with Human Diseases in Notch Signaling-Related Genes Using Drosophila. Methods Mol Biol 2022; 2472:235-276. [PMID: 35674905 PMCID: PMC9396741 DOI: 10.1007/978-1-0716-2201-8_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Rare variants in the many genes related to Notch signaling cause diverse Mendelian diseases that affect myriad organ systems. In addition, genome- and exome-wide association studies have linked common and rare variants in Notch-related genes to common diseases and phenotypic traits. Moreover, somatic mutations in these genes have been observed in many types of cancer, some of which are classified as oncogenic and others as tumor suppressive. While functional characterization of some of these variants has been performed through experimental studies, the number of "variants of unknown significance" identified in patients with diverse conditions keeps increasing as high-throughput sequencing technologies become more commonly used in the clinic. Furthermore, as disease gene discovery efforts identify rare variants in human genes that have yet to be linked to a disease, the demand for functional characterization of variants in these "genes of unknown significance" continues to increase. In this chapter, we describe a workflow to functionally characterize a rare variant in a Notch signaling related gene that was found to be associated with late-onset Alzheimer's disease. This pipeline involves informatic analysis of the variant of interest using diverse human and model organism databases, followed by in vivo experiments in the fruit fly Drosophila melanogaster. The protocol described here can be used to study variants that affect amino acids that are not conserved between human and fly. By "humanizing" the almondex gene in Drosophila with mutant alleles and heterologous genomic rescue constructs, a missense variant in TM2D3 (TM2 Domain Containing 3) was shown to be functionally damaging. This, and similar approaches, greatly facilitate functional interpretations of genetic variants in the human genome and propel personalized medicine.
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Affiliation(s)
- Sheng-An Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Jose L Salazar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - David Li-Kroeger
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA.
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
- Development, Disease Models and Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX, USA.
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19
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Cloney T, Gallacher L, Pais LS, Tan NB, Yeung A, Stark Z, Brown NJ, McGillivray G, Delatycki MB, de Silva MG, Downie L, Stutterd CA, Elliott J, Compton AG, Lovgren A, Oertel R, Francis D, Bell KM, Sadedin S, Lim SC, Helman G, Simons C, Macarthur DG, Thorburn DR, O'Donnell-Luria AH, Christodoulou J, White SM, Tan TY. Lessons learnt from multifaceted diagnostic approaches to the first 150 families in Victoria's Undiagnosed Diseases Program. J Med Genet 2021; 59:748-758. [PMID: 34740920 DOI: 10.1136/jmedgenet-2021-107902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 09/14/2021] [Indexed: 01/18/2023]
Abstract
BACKGROUND Clinical exome sequencing typically achieves diagnostic yields of 30%-57.5% in individuals with monogenic rare diseases. Undiagnosed diseases programmes implement strategies to improve diagnostic outcomes for these individuals. AIM We share the lessons learnt from the first 3 years of the Undiagnosed Diseases Program-Victoria, an Australian programme embedded within a clinical genetics service in the state of Victoria with a focus on paediatric rare diseases. METHODS We enrolled families who remained without a diagnosis after clinical genomic (panel, exome or genome) sequencing between 2016 and 2018. We used family-based exome sequencing (family ES), family-based genome sequencing (family GS), RNA sequencing (RNA-seq) and high-resolution chromosomal microarray (CMA) with research-based analysis. RESULTS In 150 families, we achieved a diagnosis or strong candidate in 64 (42.7%) (37 in known genes with a consistent phenotype, 3 in known genes with a novel phenotype and 24 in novel disease genes). Fifty-four diagnoses or strong candidates were made by family ES, six by family GS with RNA-seq, two by high-resolution CMA and two by data reanalysis. CONCLUSION We share our lessons learnt from the programme. Flexible implementation of multiple strategies allowed for scalability and response to the availability of new technologies. Broad implementation of family ES with research-based analysis showed promising yields post a negative clinical singleton ES. RNA-seq offered multiple benefits in family ES-negative populations. International data sharing strategies were critical in facilitating collaborations to establish novel disease-gene associations. Finally, the integrated approach of a multiskilled, multidisciplinary team was fundamental to having diverse perspectives and strategic decision-making.
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Affiliation(s)
- Thomas Cloney
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lyndon Gallacher
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lynn S Pais
- Center for Mendelian Genomics, Eli and Edythe L Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Natalie B Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Martin B Delatycki
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Michelle G de Silva
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Lilian Downie
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Chloe A Stutterd
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Justine Elliott
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Alison G Compton
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia.,Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Alysia Lovgren
- Center for Mendelian Genomics, Eli and Edythe L Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Analytic and Translational Genomics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Ralph Oertel
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Katrina M Bell
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Bioinformatics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Simon Sadedin
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sze Chern Lim
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Guy Helman
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Cas Simons
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Translational Bioinformatics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Daniel G Macarthur
- Center for Mendelian Genomics, Eli and Edythe L Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - David R Thorburn
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia.,Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Anne H O'Donnell-Luria
- Center for Mendelian Genomics, Eli and Edythe L Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - John Christodoulou
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia.,Neurodevelopmental Genomics Research Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia .,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
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20
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Brown SDM. Advances in mouse genetics for the study of human disease. Hum Mol Genet 2021; 30:R274-R284. [PMID: 34089057 PMCID: PMC8490014 DOI: 10.1093/hmg/ddab153] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 01/11/2023] Open
Abstract
The mouse is the pre-eminent model organism for studies of mammalian gene function and has provided an extraordinarily rich range of insights into basic genetic mechanisms and biological systems. Over several decades, the characterization of mouse mutants has illuminated the relationship between gene and phenotype, providing transformational insights into the genetic bases of disease. However, if we are to deliver the promise of genomic and precision medicine, we must develop a comprehensive catalogue of mammalian gene function that uncovers the dark genome and elucidates pleiotropy. Advances in large-scale mouse mutagenesis programmes allied to high-throughput mouse phenomics are now addressing this challenge and systematically revealing novel gene function and multi-morbidities. Alongside the development of these pan-genomic mutational resources, mouse genetics is employing a range of diversity resources to delineate gene-gene and gene-environment interactions and to explore genetic context. Critically, mouse genetics is a powerful tool for assessing the functional impact of human genetic variation and determining the causal relationship between variant and disease. Together these approaches provide unique opportunities to dissect in vivo mechanisms and systems to understand pathophysiology and disease. Moreover, the provision and utility of mouse models of disease has flourished and engages cumulatively at numerous points across the translational spectrum from basic mechanistic studies to pre-clinical studies, target discovery and therapeutic development.
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21
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Zurek B, Ellwanger K, Vissers LELM, Schüle R, Synofzik M, Töpf A, de Voer RM, Laurie S, Matalonga L, Gilissen C, Ossowski S, 't Hoen PAC, Vitobello A, Schulze-Hentrich JM, Riess O, Brunner HG, Brookes AJ, Rath A, Bonne G, Gumus G, Verloes A, Hoogerbrugge N, Evangelista T, Harmuth T, Swertz M, Spalding D, Hoischen A, Beltran S, Graessner H. Solve-RD: systematic pan-European data sharing and collaborative analysis to solve rare diseases. Eur J Hum Genet 2021; 29:1325-1331. [PMID: 34075208 PMCID: PMC8440542 DOI: 10.1038/s41431-021-00859-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 02/08/2021] [Accepted: 03/04/2021] [Indexed: 11/28/2022] Open
Abstract
For the first time in Europe hundreds of rare disease (RD) experts team up to actively share and jointly analyse existing patient's data. Solve-RD is a Horizon 2020-supported EU flagship project bringing together >300 clinicians, scientists, and patient representatives of 51 sites from 15 countries. Solve-RD is built upon a core group of four European Reference Networks (ERNs; ERN-ITHACA, ERN-RND, ERN-Euro NMD, ERN-GENTURIS) which annually see more than 270,000 RD patients with respective pathologies. The main ambition is to solve unsolved rare diseases for which a molecular cause is not yet known. This is achieved through an innovative clinical research environment that introduces novel ways to organise expertise and data. Two major approaches are being pursued (i) massive data re-analysis of >19,000 unsolved rare disease patients and (ii) novel combined -omics approaches. The minimum requirement to be eligible for the analysis activities is an inconclusive exome that can be shared with controlled access. The first preliminary data re-analysis has already diagnosed 255 cases form 8393 exomes/genome datasets. This unprecedented degree of collaboration focused on sharing of data and expertise shall identify many new disease genes and enable diagnosis of many so far undiagnosed patients from all over Europe.
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Affiliation(s)
- Birte Zurek
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Kornelia Ellwanger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rebecca Schüle
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research (HIH), University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Matthis Synofzik
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research (HIH), University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Richarda M de Voer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Steven Laurie
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Leslie Matalonga
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Peter A C 't Hoen
- Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Anthony J Brookes
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Ana Rath
- INSERM, US14-Orphanet, Plateforme Maladies Rares, Paris, France
| | - Gisèle Bonne
- Sorbonne Université, INSERM UMRS 974, Center of Research in Myology, Paris, France
| | | | - Alain Verloes
- Genetics Department, APHP-Robert Debré University Hospital, Université de Paris, Paris, France
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | | | - Tina Harmuth
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Morris Swertz
- Department of Genetics, Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Dylan Spalding
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain
| | - Holm Graessner
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany.
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22
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Ganguly P, Madonsela L, Chao JT, Loewen CJR, O’Connor TP, Verheyen EM, Allan DW. A scalable Drosophila assay for clinical interpretation of human PTEN variants in suppression of PI3K/AKT induced cellular proliferation. PLoS Genet 2021; 17:e1009774. [PMID: 34492006 PMCID: PMC8448351 DOI: 10.1371/journal.pgen.1009774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 09/17/2021] [Accepted: 08/10/2021] [Indexed: 12/28/2022] Open
Abstract
Gene variant discovery is becoming routine, but it remains difficult to usefully interpret the functional consequence or disease relevance of most variants. To fill this interpretation gap, experimental assays of variant function are becoming common place. Yet, it remains challenging to make these assays reproducible, scalable to high numbers of variants, and capable of assessing defined gene-disease mechanism for clinical interpretation aligned to the ClinGen Sequence Variant Interpretation (SVI) Working Group guidelines for 'well-established assays'. Drosophila melanogaster offers great potential as an assay platform, but was untested for high numbers of human variants adherent to these guidelines. Here, we wished to test the utility of Drosophila as a platform for scalable well-established assays. We took a genetic interaction approach to test the function of ~100 human PTEN variants in cancer-relevant suppression of PI3K/AKT signaling in cellular growth and proliferation. We validated the assay using biochemically characterized PTEN mutants as well as 23 total known pathogenic and benign PTEN variants, all of which the assay correctly assigned into predicted functional categories. Additionally, function calls for these variants correlated very well with our recent published data from a human cell line. Finally, using these pathogenic and benign variants to calibrate the assay, we could set readout thresholds for clinical interpretation of the pathogenicity of 70 other PTEN variants. Overall, we demonstrate that Drosophila offers a powerful assay platform for clinical variant interpretation, that can be used in conjunction with other well-established assays, to increase confidence in the accurate assessment of variant function and pathogenicity.
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Affiliation(s)
- Payel Ganguly
- Department of Cellular and Physiological Sciences, Life Sciences Institute, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Landiso Madonsela
- Department of Molecular Biology and Biochemistry, Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jesse T. Chao
- Department of Cellular and Physiological Sciences, Life Sciences Institute, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher J. R. Loewen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Timothy P. O’Connor
- Department of Cellular and Physiological Sciences, Life Sciences Institute, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Esther M. Verheyen
- Department of Molecular Biology and Biochemistry, Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Douglas W. Allan
- Department of Cellular and Physiological Sciences, Life Sciences Institute, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
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23
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Yeast as a Tool to Understand the Significance of Human Disease-Associated Gene Variants. Genes (Basel) 2021; 12:genes12091303. [PMID: 34573285 PMCID: PMC8465565 DOI: 10.3390/genes12091303] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/23/2021] [Accepted: 08/23/2021] [Indexed: 02/05/2023] Open
Abstract
At present, the great challenge in human genetics is to provide significance to the growing amount of human disease-associated gene variants identified by next generation DNA sequencing technologies. Increasing evidences suggest that model organisms are of pivotal importance to addressing this issue. Due to its genetic tractability, the yeast Saccharomyces cerevisiae represents a valuable model organism for understanding human genetic variability. In the present review, we show how S. cerevisiae has been used to study variants of genes involved in different diseases and in different pathways, highlighting the versatility of this model organism.
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24
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Baldridge D, Wangler MF, Bowman AN, Yamamoto S, Schedl T, Pak SC, Postlethwait JH, Shin J, Solnica-Krezel L, Bellen HJ, Westerfield M. Model organisms contribute to diagnosis and discovery in the undiagnosed diseases network: current state and a future vision. Orphanet J Rare Dis 2021; 16:206. [PMID: 33962631 PMCID: PMC8103593 DOI: 10.1186/s13023-021-01839-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022] Open
Abstract
Decreased sequencing costs have led to an explosion of genetic and genomic data. These data have revealed thousands of candidate human disease variants. Establishing which variants cause phenotypes and diseases, however, has remained challenging. Significant progress has been made, including advances by the National Institutes of Health (NIH)-funded Undiagnosed Diseases Network (UDN). However, 6000-13,000 additional disease genes remain to be identified. The continued discovery of rare diseases and their genetic underpinnings provides benefits to affected patients, of whom there are more than 400 million worldwide, and also advances understanding the mechanisms of more common diseases. Platforms employing model organisms enable discovery of novel gene-disease relationships, help establish variant pathogenicity, and often lead to the exploration of underlying mechanisms of pathophysiology that suggest new therapies. The Model Organism Screening Center (MOSC) of the UDN is a unique resource dedicated to utilizing informatics and functional studies in model organisms, including worm (Caenorhabditis elegans), fly (Drosophila melanogaster), and zebrafish (Danio rerio), to aid in diagnosis. The MOSC has directly contributed to the diagnosis of challenging cases, including multiple patients with complex, multi-organ phenotypes. In addition, the MOSC provides a framework for how basic scientists and clinicians can collaborate to drive diagnoses. Customized experimental plans take into account patient presentations, specific genes and variant(s), and appropriateness of each model organism for analysis. The MOSC also generates bioinformatic and experimental tools and reagents for the wider scientific community. Two elements of the MOSC that have been instrumental in its success are (1) multidisciplinary teams with expertise in variant bioinformatics and in human and model organism genetics, and (2) mechanisms for ongoing communication with clinical teams. Here we provide a position statement regarding the central role of model organisms for continued discovery of disease genes, and we advocate for the continuation and expansion of MOSC-type research entities as a Model Organisms Network (MON) to be funded through grant applications submitted to the NIH, family groups focused on specific rare diseases, other philanthropic organizations, industry partnerships, and other sources of support.
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Affiliation(s)
- Dustin Baldridge
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA.
- Department of Pediatrics, BCM, Houston, TX, 77030, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA.
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, 77030, USA.
| | - Angela N Bowman
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, 77030, USA
- Department of Neuroscience, BCM, Houston, TX, 77030, USA
| | - Tim Schedl
- Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Stephen C Pak
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | | | - Jimann Shin
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, 77030, USA
- Department of Neuroscience, BCM, Houston, TX, 77030, USA
- Howard Hughes Medical Institute, Houston, TX, 77030, USA
| | - Monte Westerfield
- Institute of Neuroscience, University of Oregon, Eugene, OR, 97403, USA
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25
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26
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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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27
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Link N, Bellen HJ. Using Drosophila to drive the diagnosis and understand the mechanisms of rare human diseases. Development 2020; 147:dev191411. [PMID: 32988995 PMCID: PMC7541339 DOI: 10.1242/dev.191411] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing has greatly accelerated the discovery of rare human genetic diseases. Nearly 45% of patients have variants associated with known diseases but the unsolved cases remain a conundrum. Moreover, causative mutations can be difficult to pinpoint because variants frequently map to genes with no previous disease associations and, often, only one or a few patients with variants in the same gene are identified. Model organisms, such as Drosophila, can help to identify and characterize these new disease-causing genes. Importantly, Drosophila allow quick and sophisticated genetic manipulations, permit functional testing of human variants, enable the characterization of pathogenic mechanisms and are amenable to drug tests. In this Spotlight, focusing on microcephaly as a case study, we highlight how studies of human genes in Drosophila have aided our understanding of human genetic disorders, allowing the identification of new genes in well-established signaling pathways.
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Affiliation(s)
- Nichole Link
- Howard Hughes Medical Institute, BCM, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics (MHG), BCM, Houston, TX, 77030, USA
- Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Hugo J Bellen
- Howard Hughes Medical Institute, BCM, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics (MHG), BCM, Houston, TX, 77030, USA
- Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
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28
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Pridie C, Ueda K, Simmonds AJ. Rosy Beginnings: Studying Peroxisomes in Drosophila. Front Cell Dev Biol 2020; 8:835. [PMID: 32984330 PMCID: PMC7477296 DOI: 10.3389/fcell.2020.00835] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 08/04/2020] [Indexed: 12/19/2022] Open
Abstract
Research using the fruit fly Drosophila melanogaster has traditionally focused on understanding how mutations affecting gene regulation or function affect processes linked to animal development. Accordingly, flies have become an essential foundation of modern medical research through repeated contributions to our fundamental understanding of how their homologs of human genes function. Peroxisomes are organelles that metabolize lipids and reactive oxygen species like peroxides. However, despite clear linkage of mutations in human genes affecting peroxisomes to developmental defects, for many years fly models were conspicuously absent from the study of peroxisomes. Now, the few early studies linking the Rosy eye color phenotype to peroxisomes in flies have been joined by a growing body of research establishing novel roles for peroxisomes during the development or function of specific tissues or cell types. Similarly, unique properties of cultured fly Schneider 2 cells have advanced our understanding of how peroxisomes move on the cytoskeleton. Here, we profile how those past and more recent Drosophila studies started to link specific effects of peroxisome dysfunction to organ development and highlight the utility of flies as a model for human peroxisomal diseases. We also identify key differences in the function and proliferation of fly peroxisomes compared to yeast or mammals. Finally, we discuss the future of the fly model system for peroxisome research including new techniques that should support identification of additional tissue specific regulation of and roles for peroxisomes.
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Affiliation(s)
- C Pridie
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Kazuki Ueda
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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29
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Atalaia A, Thompson R, Corvo A, Carmody L, Piscia D, Matalonga L, Macaya A, Lochmuller A, Fontaine B, Zurek B, Hernandez-Ferrer C, Reinhard C, Gómez-Andrés D, Desaphy JF, Schon K, Lohmann K, Jennings MJ, Synofzik M, Riess O, Yaou RB, Evangelista T, Ratnaike T, Bros-Facer V, Gumus G, Horvath R, Chinnery P, Laurie S, Graessner H, Robinson P, Lochmuller H, Beltran S, Bonne G. A guide to writing systematic reviews of rare disease treatments to generate FAIR-compliant datasets: building a Treatabolome. Orphanet J Rare Dis 2020; 15:206. [PMID: 32787960 PMCID: PMC7424983 DOI: 10.1186/s13023-020-01493-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 08/05/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Rare diseases are individually rare but globally affect around 6% of the population, and in over 70% of cases are genetically determined. Their rarity translates into a delayed diagnosis, with 25% of patients waiting 5 to 30 years for one. It is essential to raise awareness of patients and clinicians of existing gene and variant-specific therapeutics at the time of diagnosis to avoid that treatment delays add up to the diagnostic odyssey of rare diseases' patients and their families. AIMS This paper aims to provide guidance and give detailed instructions on how to write homogeneous systematic reviews of rare diseases' treatments in a manner that allows the capture of the results in a computer-accessible form. The published results need to comply with the FAIR guiding principles for scientific data management and stewardship to facilitate the extraction of datasets that are easily transposable into machine-actionable information. The ultimate purpose is the creation of a database of rare disease treatments ("Treatabolome") at gene and variant levels as part of the H2020 research project Solve-RD. RESULTS Each systematic review follows a written protocol to address one or more rare diseases in which the authors are experts. The bibliographic search strategy requires detailed documentation to allow its replication. Data capture forms should be built to facilitate the filling of a data capture spreadsheet and to record the application of the inclusion and exclusion criteria to each search result. A PRISMA flowchart is required to provide an overview of the processes of search and selection of papers. A separate table condenses the data collected during the Systematic Review, appraised according to their level of evidence. CONCLUSIONS This paper provides a template that includes the instructions for writing FAIR-compliant systematic reviews of rare diseases' treatments that enables the assembly of a Treatabolome database that complement existing diagnostic and management support tools with treatment awareness data.
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Affiliation(s)
- Antonio Atalaia
- Sorbonne Universite - Inserm UMRS 974, Center of Research in Myology, Institut de Myologie, G.H. Pitié-Salpêtrière Paris, 47, boulevard de l'Hopital, F-75 651, Paris Cedex 13, France.
| | - Rachel Thompson
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Alberto Corvo
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Leigh Carmody
- The Jackson Laboratory For Genomic Medicine, Farmington, CT, 06032, USA
| | - Davide Piscia
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Leslie Matalonga
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Alfons Macaya
- Paediatric Neurology, Vall d'Hebron University Hospital and VHIR (Euro-NMD, ERN-RND), 08035, Barcelona, Spain
| | - Angela Lochmuller
- Department of Clinical Neurosciences, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Bertrand Fontaine
- Sorbonne Universite - Inserm UMRS 974, Center of Research in Myology, Institut de Myologie, G.H. Pitié-Salpêtrière Paris, 47, boulevard de l'Hopital, F-75 651, Paris Cedex 13, France
| | - Birte Zurek
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany
| | - Carles Hernandez-Ferrer
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Carola Reinhard
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany
| | - David Gómez-Andrés
- Paediatric Neurology, Vall d'Hebron University Hospital and VHIR (Euro-NMD, ERN-RND), 08035, Barcelona, Spain
| | - Jean-François Desaphy
- Department of Biomedical Sciences and Human Oncology, School of Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Katherine Schon
- Department of Clinical Neurosciences, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, 23538, Lübeck, Germany
| | - Matthew J Jennings
- Department of Clinical Neurosciences, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Matthis Synofzik
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany
| | - Rabah Ben Yaou
- Sorbonne Universite - Inserm UMRS 974, Center of Research in Myology, Institut de Myologie, G.H. Pitié-Salpêtrière Paris, 47, boulevard de l'Hopital, F-75 651, Paris Cedex 13, France
| | - Teresinha Evangelista
- Unité de Morphologie Neuromusculaire, Institut de Myologie, GHU Pitié-Salpêtrière, Paris, France
- Sorbonne Université, AP-HP, INSERM, Centre de référence Des Maladies Neuromusculaires Nord/Est, Ile de France, Paris, France
| | - Thiloka Ratnaike
- Department of Paediatrics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, England
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | | | | | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Patrick Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge and MRC Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge, UK
| | - Steven Laurie
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Holm Graessner
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany
| | - Peter Robinson
- The Jackson Laboratory For Genomic Medicine, Farmington, CT, 06032, USA
| | - Hanns Lochmuller
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Department of Neuropediatrics and Muscle Disorders, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
- Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Gisèle Bonne
- Sorbonne Universite - Inserm UMRS 974, Center of Research in Myology, Institut de Myologie, G.H. Pitié-Salpêtrière Paris, 47, boulevard de l'Hopital, F-75 651, Paris Cedex 13, France
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Azzariti DR, Hamosh A. Genomic Data Sharing for Novel Mendelian Disease Gene Discovery: The Matchmaker Exchange. Annu Rev Genomics Hum Genet 2020; 21:305-326. [PMID: 32339034 DOI: 10.1146/annurev-genom-083118-014915] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the last decade, exome and/or genome sequencing has become a common test in the diagnosis of individuals with features of a rare Mendelian disorder. Despite its success, this test leaves the majority of tested individuals undiagnosed. This review describes the Matchmaker Exchange (MME), a federated network established to facilitate the solving of undiagnosed rare-disease cases through data sharing. MME supports genomic matchmaking, the act of connecting two or more parties looking for cases with similar phenotypes and variants in the same candidate genes. An application programming interface currently connects six matchmaker nodes-the Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources (DECIPHER), GeneMatcher, PhenomeCentral, seqr, MyGene2, and the Initiative on Rare and Undiagnosed Diseases (IRUD) Exchange-resulting in a collective data set spanning more than 150,000 cases from more than 11,000 contributors in 88 countries. Here, we describe the successes and challenges of MME, its individual matchmaking nodes, plans for growing the network, and considerations for future directions.
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Affiliation(s)
- Danielle R Azzariti
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA;
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21287, USA;
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32
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Abstract
The Canadian Genomics Partnership for Rare Diseases, spearheaded by Genome Canada, will integrate genome-wide sequencing to rare disease clinical care in Canada. Centralized and tiered models of data stewardship are proposed to ensure that the data generated can be shared for secondary clinical, research, and quality assurance purposes in compliance with ethics and law. The principal ethico-legal obligations of clinicians, researchers, and institutions are synthesized. Governance infrastructures such as registered access platforms, data access compliance offices, and Beacon systems are proposed as potential organizational and technical foundations of responsible rare disease data sharing. The appropriate delegation of responsibilities, the transparent communication of rights and duties, and the integration of data privacy safeguards into infrastructure design are proposed as the cornerstones of rare disease data stewardship.
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Affiliation(s)
- Alexander Bernier
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, QC H3A 0G1, Canada
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