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Palmer EE, Cederroth H, Cederroth M, Delgado-Vega AM, Roberts N, Taylan F, Nordgren A, Botto LD. Equity in action: The Diagnostic Working Group of The Undiagnosed Diseases Network International. NPJ Genom Med 2024; 9:37. [PMID: 38965249 PMCID: PMC11224220 DOI: 10.1038/s41525-024-00422-y] [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: 11/30/2023] [Accepted: 05/29/2024] [Indexed: 07/06/2024] Open
Abstract
Rare diseases are recognized as a global public health priority. A timely and accurate diagnosis is a critical enabler for precise and personalized health care. However, barriers to rare disease diagnoses are especially steep for those from historically underserved communities, including low- and middle-income countries. The Undiagnosed Diseases Network International (UDNI) was launched in 2015 to help fill the knowledge gaps that impede diagnosis for rare diseases, and to foster the translation of research into medical practice, aided by active patient involvement. To better pursue these goals, in 2021 the UDNI established the Diagnostic Working Group of the UDNI (UDNI DWG) as a community of practice that would (a) accelerate diagnoses for more families; (b) support and share knowledge and skills by developing Undiagnosed Diseases Programs, particularly those in lower resource areas; and (c) promote discovery and expand global medical knowledge. This Perspectives article documents the initial establishment and iterative co-design of the UDNI DWG.
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Affiliation(s)
- Elizabeth Emma Palmer
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia.
- Centre for Clinical Genetics, Sydney Childrens' Hospitals Network, Sydney, NSW, Australia.
| | | | | | - Angelica Maria Delgado-Vega
- 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
| | - Natalie Roberts
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, 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
| | - 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
- Institute of Biomedicine, Department of Laboratory Medicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Lorenzo D Botto
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
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2
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Rubin AF. A new way of looking at transcription factor assays. Mol Syst Biol 2024; 20:741-743. [PMID: 38849564 PMCID: PMC11219719 DOI: 10.1038/s44320-024-00044-7] [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: 03/22/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
AF Rubin discusses a new high-throughput functional assay for transcription factors applied for a deep mutational scanning study of the transcription factor PAX6 by Kudla and colleagues (McDonnell et al, 2023 ) in this issue of Molecular Systems Biology .
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Affiliation(s)
- Alan F Rubin
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
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3
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Chong JX, Berger SI, Baxter S, Smith E, Xiao C, Calame DG, Hawley MH, Rivera-Munoz EA, DiTroia S, Bamshad MJ, Rehm HL. Considerations for reporting variants in novel candidate genes identified during clinical genomic testing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.579012. [PMID: 38370830 PMCID: PMC10871197 DOI: 10.1101/2024.02.05.579012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Since the first novel gene discovery for a Mendelian condition was made via exome sequencing (ES), the rapid increase in the number of genes known to underlie Mendelian conditions coupled with the adoption of exome (and more recently, genome) sequencing by diagnostic testing labs has changed the landscape of genomic testing for rare disease. Specifically, many individuals suspected to have a Mendelian condition are now routinely offered clinical ES. This commonly results in a precise genetic diagnosis but frequently overlooks the identification of novel candidate genes. Such candidates are also less likely to be identified in the absence of large-scale gene discovery research programs. Accordingly, clinical laboratories have both the opportunity, and some might argue a responsibility, to contribute to novel gene discovery which should in turn increase the diagnostic yield for many conditions. However, clinical diagnostic laboratories must necessarily balance priorities for throughput, turnaround time, cost efficiency, clinician preferences, and regulatory constraints, and often do not have the infrastructure or resources to effectively participate in either clinical translational or basic genome science research efforts. For these and other reasons, many laboratories have historically refrained from broadly sharing potentially pathogenic variants in novel genes via networks like Matchmaker Exchange, much less reporting such results to ordering providers. Efforts to report such results are further complicated by a lack of guidelines for clinical reporting and interpretation of variants in novel candidate genes. Nevertheless, there are myriad benefits for many stakeholders, including patients/families, clinicians, researchers, if clinical laboratories systematically and routinely identify, share, and report novel candidate genes. To facilitate this change in practice, we developed criteria for triaging, sharing, and reporting novel candidate genes that are most likely to be promptly validated as underlying a Mendelian condition and translated to use in clinical settings.
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Affiliation(s)
- Jessica X. Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
| | - Seth I. Berger
- Center for Genetic Medicine Research, Children’s National Research Institute, 111 Michigan Ave, NW, Washington, DC, 20010, USA
| | - Samantha Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02141, USA
| | - Erica Smith
- Department of Clinical Diagnostics, Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | - Changrui Xiao
- Department of Neurology, University of California Irvine, 200 South Manchester Ave. St 206E, Orange, CA, 92868, USA
| | - Daniel G. Calame
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Neurosciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Megan H. Hawley
- Clinical Operations, Invitae, 485F US-1 Suite 110, Iselin, NJ, 08830, USA
| | - E. Andres Rivera-Munoz
- Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza T605, Houston, TX, 77030, USA
| | - Stephanie DiTroia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02141, USA
| | | | - Michael J. Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
- Department of Pediatrics, Division of Genetic Medicine, Seattle Children’s Hospital, Seattle, WA, 98195, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02141, USA
- Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge St, Boston, MA, 02114, USA
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4
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Brown CM, Amendola LM, Chandrasekhar A, Hagelstrom RT, Halter G, Kesari A, Thorpe E, Perry DL, Taft RJ, Coffey AJ. A framework for the evaluation and reporting of incidental findings in clinical genomic testing. Eur J Hum Genet 2024; 32:665-672. [PMID: 38565640 PMCID: PMC11153510 DOI: 10.1038/s41431-024-01575-1] [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: 10/16/2023] [Revised: 12/29/2023] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
Currently, there are no widely accepted recommendations in the genomics field guiding the return of incidental findings (IFs), defined here as unexpected results that are unrelated to the indication for testing. Consequently, reporting policies for IFs among laboratories offering genomic testing are variable and may lack transparency. Herein we describe a framework developed to guide the evaluation and return of IFs encountered in probands undergoing clinical genome sequencing (cGS). The framework prioritizes clinical significance and actionability of IFs and follows a stepwise approach with stopping points at which IFs may be recommended for return or not. Over 18 months, implementation of the framework in a clinical laboratory facilitated the return of actionable IFs in 37 of 720 (5.1%) individuals referred for cGS, which is reduced to 3.1% if glucose-6-phosphate dehydrogenase (G6PD) deficiency is excluded. This framework can serve as a model to standardize reporting of IFs identified during genomic testing.
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Affiliation(s)
- Carolyn M Brown
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA.
| | - Laura M Amendola
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | | | | | - Gillian Halter
- Scripps MD Anderson Cancer Center, San Diego, CA, 92121, USA
| | - Akanchha Kesari
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Erin Thorpe
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Denise L Perry
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Ryan J Taft
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Alison J Coffey
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA.
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5
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Kernohan KD, Boycott KM. The expanding diagnostic toolbox for rare genetic diseases. Nat Rev Genet 2024; 25:401-415. [PMID: 38238519 DOI: 10.1038/s41576-023-00683-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2023] [Indexed: 05/23/2024]
Abstract
Genomic technologies, such as targeted, exome and short-read genome sequencing approaches, have revolutionized the care of patients with rare genetic diseases. However, more than half of patients remain without a diagnosis. Emerging approaches from research-based settings such as long-read genome sequencing and optical genome mapping hold promise for improving the identification of disease-causal genetic variants. In addition, new omic technologies that measure the transcriptome, epigenome, proteome or metabolome are showing great potential for variant interpretation. As genetic testing options rapidly expand, the clinical community needs to be mindful of their individual strengths and limitations, as well as remaining challenges, to select the appropriate diagnostic test, correctly interpret results and drive innovation to address insufficiencies. If used effectively - through truly integrative multi-omics approaches and data sharing - the resulting large quantities of data from these established and emerging technologies will greatly improve the interpretative power of genetic and genomic diagnostics for rare diseases.
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Affiliation(s)
- Kristin D Kernohan
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
- Newborn Screening Ontario, CHEO, Ottawa, ON, Canada
| | - Kym M Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada.
- Department of Genetics, CHEO, Ottawa, ON, Canada.
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6
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Ozisik O, Gorokhova S, Cerino M, Bartoli M, Baudot A. System-level analysis of genes mutated in muscular dystrophies reveals a functional pattern associated with muscle weakness distribution. Sci Rep 2024; 14:11225. [PMID: 38755190 PMCID: PMC11099060 DOI: 10.1038/s41598-024-60761-9] [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: 01/18/2024] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
Muscular dystrophies (MDs) are inherited genetic diseases causing weakness and degeneration of muscles. The distribution of muscle weakness differs between MDs, involving distal muscles or proximal muscles. While the mutations in most of the MD-associated genes lead to either distal or proximal onset, there are also genes whose mutations can cause both types of onsets. We hypothesized that the genes associated with different MD onsets code proteins with distinct cellular functions. To investigate this, we collected the MD-associated genes and assigned them to three onset groups: genes mutated only in distal onset dystrophies, genes mutated only in proximal onset dystrophies, and genes mutated in both types of onsets. We then systematically evaluated the cellular functions of these gene sets with computational strategies based on functional enrichment analysis and biological network analysis. Our analyses demonstrate that genes mutated in either distal or proximal onset MDs code proteins linked with two distinct sets of cellular processes. Interestingly, these two sets of cellular processes are relevant for the genes that are associated with both onsets. Moreover, the genes associated with both onsets display high centrality and connectivity in the network of muscular dystrophy genes. Our findings support the hypothesis that the proteins associated with distal or proximal onsets have distinct functional characteristics, whereas the proteins associated with both onsets are multifunctional.
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Affiliation(s)
- Ozan Ozisik
- Aix Marseille University, INSERM, MMG, Marseille, France.
- Université Paris Cité, INSERM U976, Paris, France.
| | - Svetlana Gorokhova
- Aix Marseille University, INSERM, MMG, Marseille, France
- Department of Medical Genetics, La Timone Hospital, AP-HM, Marseille, France
| | - Mathieu Cerino
- Aix Marseille University, INSERM, MMG, Marseille, France
- Department of Medical Genetics, La Timone Hospital, AP-HM, Marseille, France
- Laboratory of Biochemistry, La Conception Hospital, AP-HM, Marseille, France
| | - Marc Bartoli
- Aix Marseille University, INSERM, MMG, Marseille, France
- CNRS, Marseille, France
| | - Anaïs Baudot
- Aix Marseille University, INSERM, MMG, Marseille, France.
- CNRS, Marseille, France.
- Barcelona Supercomputing Center, Barcelona, Spain.
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7
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Orlic-Milacic M, Rothfels K, Matthews L, Wright A, Jassal B, Shamovsky V, Trinh Q, Gillespie ME, Sevilla C, Tiwari K, Ragueneau E, Gong C, Stephan R, May B, Haw R, Weiser J, Beavers D, Conley P, Hermjakob H, Stein LD, D’Eustachio P, Wu G. Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes. Database (Oxford) 2024; 2024:baae031. [PMID: 38713862 PMCID: PMC11184451 DOI: 10.1093/database/baae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/23/2024] [Accepted: 04/01/2024] [Indexed: 05/09/2024]
Abstract
Germline and somatic mutations can give rise to proteins with altered activity, including both gain and loss-of-function. The effects of these variants can be captured in disease-specific reactions and pathways that highlight the resulting changes to normal biology. A disease reaction is defined as an aberrant reaction in which a variant protein participates. A disease pathway is defined as a pathway that contains a disease reaction. Annotation of disease variants as participants of disease reactions and disease pathways can provide a standardized overview of molecular phenotypes of pathogenic variants that is amenable to computational mining and mathematical modeling. Reactome (https://reactome.org/), an open source, manually curated, peer-reviewed database of human biological pathways, in addition to providing annotations for >11 000 unique human proteins in the context of ∼15 000 wild-type reactions within more than 2000 wild-type pathways, also provides annotations for >4000 disease variants of close to 400 genes as participants of ∼800 disease reactions in the context of ∼400 disease pathways. Functional annotation of disease variants proceeds from normal gene functions, described in wild-type reactions and pathways, through disease variants whose divergence from normal molecular behaviors has been experimentally verified, to extrapolation from molecular phenotypes of characterized variants to variants of unknown significance using criteria of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Reactome's data model enables mapping of disease variant datasets to specific disease reactions within disease pathways, providing a platform to infer pathway output impacts of numerous human disease variants and model organism orthologs, complementing computational predictions of variant pathogenicity. Database URL: https://reactome.org/.
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Affiliation(s)
- Marija Orlic-Milacic
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Karen Rothfels
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Lisa Matthews
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Adam Wright
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Bijay Jassal
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Veronica Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Quang Trinh
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Marc E Gillespie
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
- College of Pharmacy and Health Sciences, St. John’s University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Cristoffer Sevilla
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Krishna Tiwari
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Eliot Ragueneau
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Chuqiao Gong
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Ralf Stephan
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
- Institute for Globally Distributed Open Research and Education (IGDORE)
| | - Bruce May
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Robin Haw
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Joel Weiser
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Deidre Beavers
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Rd., Portland, OR 97239, USA
| | - Patrick Conley
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Rd., Portland, OR 97239, USA
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Lincoln D Stein
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Room 4386, Toronto, ON M5S 1A8, Canada
| | - Peter D’Eustachio
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Guanming Wu
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Rd., Portland, OR 97239, USA
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8
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Stenton SL, O'Leary MC, Lemire G, VanNoy GE, DiTroia S, Ganesh VS, Groopman E, O'Heir E, Mangilog B, Osei-Owusu I, Pais LS, Serrano J, Singer-Berk M, Weisburd B, Wilson MW, Austin-Tse C, Abdelhakim M, Althagafi A, Babbi G, Bellazzi R, Bovo S, Carta MG, Casadio R, Coenen PJ, De Paoli F, Floris M, Gajapathy M, Hoehndorf R, Jacobsen JOB, Joseph T, Kamandula A, Katsonis P, Kint C, Lichtarge O, Limongelli I, Lu Y, Magni P, Mamidi TKK, Martelli PL, Mulargia M, Nicora G, Nykamp K, Pejaver V, Peng Y, Pham THC, Podda MS, Rao A, Rizzo E, Saipradeep VG, Savojardo C, Schols P, Shen Y, Sivadasan N, Smedley D, Soru D, Srinivasan R, Sun Y, Sunderam U, Tan W, Tiwari N, Wang X, Wang Y, Williams A, Worthey EA, Yin R, You Y, Zeiberg D, Zucca S, Bakolitsa C, Brenner SE, Fullerton SM, Radivojac P, Rehm HL, O'Donnell-Luria A. Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project. Hum Genomics 2024; 18:44. [PMID: 38685113 PMCID: PMC11057178 DOI: 10.1186/s40246-024-00604-w] [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: 08/11/2023] [Accepted: 04/02/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND A major obstacle faced by families with rare diseases is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five years and causal variants are identified in under 50%, even when capturing variants genome-wide. To aid in the interpretation and prioritization of the vast number of variants detected, computational methods are proliferating. Knowing which tools are most effective remains unclear. To evaluate the performance of computational methods, and to encourage innovation in method development, we designed a Critical Assessment of Genome Interpretation (CAGI) community challenge to place variant prioritization models head-to-head in a real-life clinical diagnostic setting. METHODS We utilized genome sequencing (GS) data from families sequenced in the Rare Genomes Project (RGP), a direct-to-participant research study on the utility of GS for rare disease diagnosis and gene discovery. Challenge predictors were provided with a dataset of variant calls and phenotype terms from 175 RGP individuals (65 families), including 35 solved training set families with causal variants specified, and 30 unlabeled test set families (14 solved, 16 unsolved). We tasked teams to identify causal variants in as many families as possible. Predictors submitted variant predictions with estimated probability of causal relationship (EPCR) values. Model performance was determined by two metrics, a weighted score based on the rank position of causal variants, and the maximum F-measure, based on precision and recall of causal variants across all EPCR values. RESULTS Sixteen teams submitted predictions from 52 models, some with manual review incorporated. Top performers recalled causal variants in up to 13 of 14 solved families within the top 5 ranked variants. Newly discovered diagnostic variants were returned to two previously unsolved families following confirmatory RNA sequencing, and two novel disease gene candidates were entered into Matchmaker Exchange. In one example, RNA sequencing demonstrated aberrant splicing due to a deep intronic indel in ASNS, identified in trans with a frameshift variant in an unsolved proband with phenotypes consistent with asparagine synthetase deficiency. CONCLUSIONS Model methodology and performance was highly variable. Models weighing call quality, allele frequency, predicted deleteriousness, segregation, and phenotype were effective in identifying causal variants, and models open to phenotype expansion and non-coding variants were able to capture more difficult diagnoses and discover new diagnoses. Overall, computational models can significantly aid variant prioritization. For use in diagnostics, detailed review and conservative assessment of prioritized variants against established criteria is needed.
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Affiliation(s)
- Sarah L Stenton
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Melanie C O'Leary
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabrielle Lemire
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grace E VanNoy
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie DiTroia
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vijay S Ganesh
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Emily Groopman
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emily O'Heir
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brian Mangilog
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ikeoluwa Osei-Owusu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lynn S Pais
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jillian Serrano
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael W Wilson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina Austin-Tse
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Marwa Abdelhakim
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Azza Althagafi
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Computer Science Department, College of Computers and Information Technology, Taif University, Taif, Saudi Arabia
| | - Giulia Babbi
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Riccardo Bellazzi
- enGenome Srl, Pavia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Maria Giulia Carta
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Rita Casadio
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | | | - Matteo Floris
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Manavalan Gajapathy
- Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
- Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert Hoehndorf
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Julius O B Jacobsen
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, UK
| | - Thomas Joseph
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Akash Kamandula
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Structural and Computational Biology and Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, USA
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Yulan Lu
- Center for Molecular Medicine, Pediatric Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Paolo Magni
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Tarun Karthik Kumar Mamidi
- Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
- Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Pier Luigi Martelli
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Marta Mulargia
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Giovanna Nicora
- enGenome Srl, Pavia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | | | - Vikas Pejaver
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yisu Peng
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | | | - Maurizio S Podda
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
- University of Siena, Siena, Italy
- CTGLab, Institute of Informatics and Telematics (IIT), CNR, ViaMoruzzi 1, 56124, Pisa, Italy
| | - Aditya Rao
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | | | - Vangala G Saipradeep
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Castrense Savojardo
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Peter Schols
- Invitae, San Francisco, CA, USA
- Codon One, Louvain, EU, Belgium
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, USA
| | - Naveen Sivadasan
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Damian Smedley
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, UK
| | | | - Rajgopal Srinivasan
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Yuanfei Sun
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Uma Sunderam
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Wuwei Tan
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Naina Tiwari
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Xiao Wang
- Center for Molecular Medicine, Pediatric Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Yaqiong Wang
- Center for Molecular Medicine, Pediatric Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Amanda Williams
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elizabeth A Worthey
- Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
- Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rujie Yin
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Yuning You
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Daniel Zeiberg
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | | | - Constantina Bakolitsa
- Department of Plant and Microbial Biology and Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Steven E Brenner
- Department of Plant and Microbial Biology and Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA, USA
| | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anne O'Donnell-Luria
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
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9
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Livesey BJ, Badonyi M, Dias M, Frazer J, Kumar S, Lindorff-Larsen K, McCandlish DM, Orenbuch R, Shearer CA, Muffley L, Foreman J, Glazer AM, Lehner B, Marks DS, Roth FP, Rubin AF, Starita LM, Marsh JA. Guidelines for releasing a variant effect predictor. ARXIV 2024:arXiv:2404.10807v1. [PMID: 38699161 PMCID: PMC11065047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Computational methods for assessing the likely impacts of mutations, known as variant effect predictors (VEPs), are widely used in the assessment and interpretation of human genetic variation, as well as in other applications like protein engineering. Many different VEPs have been released to date, and there is tremendous variability in their underlying algorithms and outputs, and in the ways in which the methodologies and predictions are shared. This leads to considerable challenges for end users in knowing which VEPs to use and how to use them. Here, to address these issues, we provide guidelines and recommendations for the release of novel VEPs. Emphasising open-source availability, transparent methodologies, clear variant effect score interpretations, standardised scales, accessible predictions, and rigorous training data disclosure, we aim to improve the usability and interpretability of VEPs, and promote their integration into analysis and evaluation pipelines. We also provide a large, categorised list of currently available VEPs, aiming to facilitate the discovery and encourage the usage of novel methods within the scientific community.
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Affiliation(s)
- Benjamin J. Livesey
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Mihaly Badonyi
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Mafalda Dias
- Centre for Genomic Regulation (CRG),The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jonathan Frazer
- Centre for Genomic Regulation (CRG),The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sushant Kumar
- Department of Medical Biophysics, University of Toronto; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - David M. McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Rose Orenbuch
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Lara Muffley
- Department of Genome Sciences, University of Washington and the Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Julia Foreman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Ben Lehner
- Wellcome Sanger Institute, Cambridge, UK; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Debora S. Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Frederick P. Roth
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Alan F. Rubin
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington and the Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Joseph A. Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
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10
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Seaby EG, Leggatt G, Cheng G, Thomas NS, Ashton JJ, Stafford I, Baralle D, Rehm HL, O'Donnell-Luria A, Ennis S. A gene pathogenicity tool "GenePy" identifies missed biallelic diagnoses in the 100,000 Genomes Project. Genet Med 2024; 26:101073. [PMID: 38245859 DOI: 10.1016/j.gim.2024.101073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/22/2024] Open
Abstract
PURPOSE The 100,000 Genomes Project diagnosed a quarter of affected participants, but 26% of diagnoses were not on the applied gene panel(s); with many being de novo variants. Assessing biallelic variants without a gene panel is more challenging. METHODS We sought to identify missed biallelic diagnoses using GenePy, which incorporates allele frequency, zygosity, and a user-defined deleterious metric, generating an aggregate GenePy score per gene, per participant. We calculated GenePy scores for 2862 recessive disease genes in 78,216 100,000 Genomes Project participants. For each gene, we ranked participant GenePy scores and scrutinized affected participants without a diagnosis, whose scores ranked among the top 5 for each gene. In cases which participant phenotypes overlapped with the disease gene of interest, we extracted rare variants and applied phase, ClinVar, and ACMG classification. RESULTS 3184 affected individuals without a molecular diagnosis had a top-5-ranked GenePy score and 682 of 3184 (21%) had phenotypes overlapping with a top-ranking gene. In 122 of 669 (18%) phenotype-matched cases (excluding 13 withdrawn participants), we identified a putative missed diagnosis (2.2% of all undiagnosed participants). A further 334 of 669 (50%) cases have a possible missed diagnosis but require functional validation. CONCLUSION Applying GenePy at scale has identified 456 potential diagnoses, demonstrating the value of novel diagnostic strategies.
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Affiliation(s)
- Eleanor G Seaby
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton, Hampshire, United Kingdom; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA; Paediatric Infectious Diseases, Imperial College London, London, United Kingdom.
| | - Gary Leggatt
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton, Hampshire, United Kingdom
| | - Guo Cheng
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton, Hampshire, United Kingdom
| | - N Simon Thomas
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton, Hampshire, United Kingdom; Wessex Regional Genomics Laboratory, Salisbury NHS Foundation Trust, Salisbury, United Kingdom
| | - James J Ashton
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton, Hampshire, United Kingdom
| | | | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton, Hampshire, United Kingdom
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Sarah Ennis
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton, Hampshire, United Kingdom
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11
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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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12
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Hwang SM. Genomic testing for germline predisposition to hematologic malignancies. Blood Res 2024; 59:12. [PMID: 38485837 PMCID: PMC10923764 DOI: 10.1007/s44313-024-00012-y] [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: 01/25/2024] [Accepted: 02/27/2024] [Indexed: 03/18/2024] Open
Abstract
Germline predisposition (GPD) to hematological malignancies has gained interest because of the increased use of genetic testing in this field. Recent studies have suggested that GPD is underrecognized and requires appropriate genomic testing for an accurate diagnosis. Identification of GPD significantly affects patient management and has diverse implications for family members. This review discusses the reasons for testing GPD in hematologic malignancies and explores the considerations necessary for appropriate genomic testing. The aim is to provide insights into how these genetic insights can inform treatment strategies and genetic counseling, ultimately enhancing patient care.
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Affiliation(s)
- Sang Mee Hwang
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Gumiro 173 Beongil-82, Bundanggu, Seongnam, Gyeonggido, 13620, South Korea.
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13
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Stenton SL, Pejaver V, Bergquist T, Biesecker LG, Byrne AB, Nadeau E, Greenblatt MS, Harrison S, Tavtigian S, Radivojac P, Brenner SE, O’Donnell-Luria A. Assessment of the evidence yield for the calibrated PP3/BP4 computational recommendations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.05.24303807. [PMID: 38496501 PMCID: PMC10942508 DOI: 10.1101/2024.03.05.24303807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Purpose To investigate the number of rare missense variants observed in human genome sequences by ACMG/AMP PP3/BP4 evidence strength, following the calibrated PP3/BP4 computational recommendations. Methods Missense variants from the genome sequences of 300 probands from the Rare Genomes Project with suspected rare disease were analyzed using computational prediction tools able to reach PP3_Strong and BP4_Moderate evidence strengths (BayesDel, MutPred2, REVEL, and VEST4). The numbers of variants at each evidence strength were analyzed across disease-associated genes and genome-wide. Results From a median of 75.5 rare (≤1% allele frequency) missense variants in disease-associated genes per proband, a median of one reached PP3_Strong, 3-5 PP3_Moderate, and 3-5 PP3_Supporting. Most were allocated BP4 evidence (median 41-49 per proband) or were indeterminate (median 17.5-19 per proband). Extending the analysis to all protein-coding genes genome-wide, the number of PP3_Strong variants increased approximately 2.6-fold compared to disease-associated genes, with a median per proband of 1-3 PP3_Strong, 8-16 PP3_Moderate, and 10-17 PP3_Supporting. Conclusion A small number of variants per proband reached PP3_Strong and PP3_Moderate in 3,424 disease-associated genes, and though not the intended use of the recommendations, also genome-wide. Use of PP3/BP4 evidence as recommended from calibrated computational prediction tools in the clinical diagnostic laboratory is unlikely to inappropriately contribute to the classification of an excessive number of variants as Pathogenic or Likely Pathogenic by ACMG/AMP rules.
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Affiliation(s)
- Sarah L. Stenton
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vikas Pejaver
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Timothy Bergquist
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Leslie G. Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alicia B. Byrne
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Emily Nadeau
- Department of Medicine and University of Vermont Cancer Center, University of Vermont, Larner College of Medicine, Burlington, VT 05405, USA
| | - Marc S. Greenblatt
- Department of Medicine and University of Vermont Cancer Center, University of Vermont, Larner College of Medicine, Burlington, VT 05405, USA
| | - Steven Harrison
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Ambry Genetics, Aliso Viejo, CA, USA
| | - Sean Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, MA 02115, USA
| | - Steven E. Brenner
- Department of Plant and Microbial Biology and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Anne O’Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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14
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Jefferis J, Mallett AJ. Exploring the impact and utility of genomic sequencing in established CKD. Clin Kidney J 2024; 17:sfae043. [PMID: 38464959 PMCID: PMC10921391 DOI: 10.1093/ckj/sfae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Indexed: 03/12/2024] Open
Abstract
Clinical genetics is increasingly recognized as an important area within nephrology care. Clinicians require awareness of genetic kidney disease to recognize clinical phenotypes, consider use of genomics to aid diagnosis, and inform treatment decisions. Understanding the broad spectrum of clinical phenotypes and principles of genomic sequencing is becoming increasingly required in clinical nephrology, with nephrologists requiring education and support to achieve meaningful patient outcomes. Establishment of effective clinical resources, multi-disciplinary teams and education is important to increase application of genomics in clinical care, for the benefit of patients and their families. Novel applications of genomics in chronic kidney disease include pharmacogenomics and clinical translation of polygenic risk scores. This review explores established and emerging impacts and utility of genomics in kidney disease.
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Affiliation(s)
- Julia Jefferis
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Andrew J Mallett
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Department of Renal Medicine, Townsville University Hospital, Douglas, Australia
- College of Medicine and Dentistry, James Cook University, Douglas, Australia
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15
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Ross JE, Mohan S, Zhang J, Sullivan MJ, Bury L, Lee K, Futchi I, Frantz A, McDougal D, Perez Botero J, Cattaneo M, Cooper N, Downes K, Gresele P, Keenan C, Lee AI, Megy K, Morange PE, Morgan NV, Schulze H, Zimowski K, Freson K, Lambert MP. Evaluating the clinical validity of genes related to hemostasis and thrombosis using the Clinical Genome Resource gene curation framework. J Thromb Haemost 2024; 22:645-665. [PMID: 38016518 PMCID: PMC10922649 DOI: 10.1016/j.jtha.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND Inherited bleeding, thrombotic, and platelet disorders (BTPDs) are a heterogeneous set of diseases, many of which are very rare globally. Over the past 5 decades, the genetic basis of some of these disorders has been identified, and recently, high-throughput sequencing has become the primary means of identifying disease-causing genetic variants. OBJECTIVES Knowledge of the clinical validity of a gene-disease relationship is essential to provide an accurate diagnosis based on results of diagnostic gene panel tests and inform the construction of such panels. The Scientific and Standardization Committee for Genetics in Thrombosis and Hemostasis undertook a curation process for selecting 96 TIER1 genes for BTPDs. The purpose of the process was to evaluate the evidence supporting each gene-disease relationship and provide an expert-reviewed classification for the clinical validity of genes associated with BTPDs. METHODS The Clinical Genome Resource (ClinGen) Hemostasis/Thrombosis Gene Curation Expert Panel assessed the strength of evidence for TIER1 genes using the semiquantitative ClinGen gene-disease clinical validity framework. ClinGen Lumping and Splitting guidelines were used to determine the appropriate disease entity or entities for each gene, and 101 gene-disease relationships were identified for curation. RESULTS The final outcome included 68 Definitive (67%), 26 Moderate (26%), and 7 Limited (7%) classifications. The summary of each curation is available on the ClinGen website. CONCLUSION Expert-reviewed assignment of gene-disease relationships by the ClinGen Hemostasis/Thrombosis Gene Curation Expert Panel facilitates accurate molecular diagnoses of BTPDs by clinicians and diagnostic laboratories. These curation efforts can allow genetic testing to focus on genes with a validated role in disease.
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Affiliation(s)
- Justyne E Ross
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shruthi Mohan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jing Zhang
- KingMed Diagnostics, Guangzhou, Guangdong, China
| | - Mia J Sullivan
- Versiti Blood Center of Wisconsin, Milwaukee, Wisconsin, USA
| | - Loredana Bury
- Department of Medicine, Section of Internal and Cardiovascular Medicine, University of Perugia, Perugia, Italy
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Isabella Futchi
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Annabelle Frantz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dara McDougal
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Juliana Perez Botero
- Versiti Blood Center of Wisconsin, Milwaukee, Wisconsin, USA; Division of Hematology/Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Marco Cattaneo
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milan, Italy
| | - Nichola Cooper
- Centre for Haematology, Imperial College London, London, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Paolo Gresele
- Department of Medicine, Section of Internal and Cardiovascular Medicine, University of Perugia, Perugia, Italy
| | - Catriona Keenan
- Haemostasis Molecular Diagnostic Laboratory, National Coagulation Centre, St James's Hospital, Dublin, Ireland
| | - Alfred I Lee
- Section of Hematology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Karyn Megy
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Pierre-Emmanuel Morange
- INSERM, INRAE, C2VN, Aix Marseille University, Marseille, France; Hematology Laboratory, La Timone Hospital, APHM, Marseille, France
| | - Neil V Morgan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Harald Schulze
- Institute of Experimental Biomedicine, Julius-Maximilians-University Wuerzburg, Wuerzburg, Germany
| | - Karen Zimowski
- Aflac Cancer and Blood Disorders Center, Emory University/Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium.
| | - Michele P Lambert
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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16
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Roberts AM, DiStefano MT, Riggs ER, Josephs KS, Alkuraya FS, Amberger J, Amin M, Berg JS, Cunningham F, Eilbeck K, Firth HV, Foreman J, Hamosh A, Hay E, Leigh S, Martin CL, McDonagh EM, Perrett D, Ramos EM, Robinson PN, Rath A, Sant DW, Stark Z, Whiffin N, Rehm HL, Ware JS. Toward robust clinical genome interpretation: Developing a consistent terminology to characterize Mendelian disease-gene relationships-allelic requirement, inheritance modes, and disease mechanisms. Genet Med 2024; 26:101029. [PMID: 37982373 PMCID: PMC11039201 DOI: 10.1016/j.gim.2023.101029] [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: 04/21/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/21/2023] Open
Abstract
PURPOSE The terminology used for gene-disease curation and variant annotation to describe inheritance, allelic requirement, and both sequence and functional consequences of a variant is currently not standardized. There is considerable discrepancy in the literature and across clinical variant reporting in the derivation and application of terms. Here, we standardize the terminology for the characterization of disease-gene relationships to facilitate harmonized global curation and to support variant classification within the ACMG/AMP framework. METHODS Terminology for inheritance, allelic requirement, and both structural and functional consequences of a variant used by Gene Curation Coalition members and partner organizations was collated and reviewed. Harmonized terminology with definitions and use examples was created, reviewed, and validated. RESULTS We present a standardized terminology to describe gene-disease relationships, and to support variant annotation. We demonstrate application of the terminology for classification of variation in the ACMG SF 2.0 genes recommended for reporting of secondary findings. Consensus terms were agreed and formalized in both Sequence Ontology (SO) and Human Phenotype Ontology (HPO) ontologies. Gene Curation Coalition member groups intend to use or map to these terms in their respective resources. CONCLUSION The terminology standardization presented here will improve harmonization, facilitate the pooling of curation datasets across international curation efforts and, in turn, improve consistency in variant classification and genetic test interpretation.
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Affiliation(s)
- Angharad M Roberts
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London, United Kingdom.
| | - Marina T DiStefano
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Katherine S Josephs
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia
| | - Joanna Amberger
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
| | - Helen V Firth
- Dept of Medical Genetics, Cambridge University Hospitals, Cambridge, United Kingdom; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Julia Foreman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Eleanor Hay
- Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London, United Kingdom
| | - Sarah Leigh
- Genomics England, Queen Mary University of London, Dawson Hall, London, United Kingdom
| | | | - Ellen M McDonagh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom; Open Targets, Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Daniel Perrett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | | | - Ana Rath
- INSERM, US14-Orphanet, Paris, France
| | - David W Sant
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
| | - Zornitza Stark
- Australian Genomics, Melbourne 3052, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne 3052, Australia; University of Melbourne, Melbourne 3052, Australia
| | - Nicola Whiffin
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Big Data Institute and Wellcome Centre for Human Genetics, University of Oxford, United Kingdom
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - James S Ware
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
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Gargano MA, Matentzoglu N, Coleman B, Addo-Lartey EB, Anagnostopoulos A, Anderton J, Avillach P, Bagley AM, Bakštein E, Balhoff JP, Baynam G, Bello SM, Berk M, Bertram H, Bishop S, Blau H, Bodenstein DF, Botas P, Boztug K, Čady J, Callahan TJ, Cameron R, Carbon S, Castellanos F, Caufield JH, Chan LE, Chute C, Cruz-Rojo J, Dahan-Oliel N, Davids JR, de Dieuleveult M, de Souza V, de Vries BBA, de Vries E, DePaulo JR, Derfalvi B, Dhombres F, Diaz-Byrd C, Dingemans AJM, Donadille B, Duyzend M, Elfeky R, Essaid S, Fabrizzi C, Fico G, Firth HV, Freudenberg-Hua Y, Fullerton JM, Gabriel DL, Gilmour K, Giordano J, Goes FS, Moses RG, Green I, Griese M, Groza T, Gu W, Guthrie J, Gyori B, Hamosh A, Hanauer M, Hanušová K, He Y(O, Hegde H, Helbig I, Holasová K, Hoyt CT, Huang S, Hurwitz E, Jacobsen JOB, Jiang X, Joseph L, Keramatian K, King B, Knoflach K, Koolen DA, Kraus M, Kroll C, Kusters M, Ladewig MS, Lagorce D, Lai MC, Lapunzina P, Laraway B, Lewis-Smith D, Li X, Lucano C, Majd M, Marazita ML, Martinez-Glez V, McHenry TH, McInnis MG, McMurry JA, Mihulová M, Millett CE, Mitchell PB, Moslerová V, Narutomi K, Nematollahi S, Nevado J, Nierenberg AA, Čajbiková NN, Nurnberger JI, Ogishima S, Olson D, Ortiz A, Pachajoa H, Perez de Nanclares G, Peters A, Putman T, Rapp CK, Rath A, Reese J, Rekerle L, Roberts A, Roy S, Sanders SJ, Schuetz C, Schulte EC, Schulze TG, Schwarz M, Scott K, Seelow D, Seitz B, Shen Y, Similuk MN, Simon ES, Singh B, Smedley D, Smith CL, Smolinsky JT, Sperry S, Stafford E, Stefancsik R, Steinhaus R, Strawbridge R, Sundaramurthi JC, Talapova P, Tenorio Castano JA, Tesner P, Thomas RH, Thurm A, Turnovec M, van Gijn ME, Vasilevsky NA, Vlčková M, Walden A, Wang K, Wapner R, Ware JS, Wiafe AA, Wiafe SA, Wiggins LD, Williams AE, Wu C, Wyrwoll MJ, Xiong H, Yalin N, Yamamoto Y, Yatham LN, Yocum AK, Young AH, Yüksel Z, Zandi PP, Zankl A, Zarante I, Zvolský M, Toro S, Carmody LC, Harris NL, Munoz-Torres MC, Danis D, Mungall CJ, Köhler S, Haendel MA, Robinson PN. The Human Phenotype Ontology in 2024: phenotypes around the world. Nucleic Acids Res 2024; 52:D1333-D1346. [PMID: 37953324 PMCID: PMC10767975 DOI: 10.1093/nar/gkad1005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/12/2023] [Accepted: 10/19/2023] [Indexed: 11/14/2023] Open
Abstract
The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs.
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Affiliation(s)
| | | | - Ben Coleman
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | - Joel Anderton
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Anita M Bagley
- Shriners Children's Northern California, Sacramento, CA, USA
| | - Eduard Bakštein
- National Institute of Mental Health, Klecany, Czech Republic
| | - James P Balhoff
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC 27517, USA
| | - Gareth Baynam
- Rare Care Centre, Perth Children's Hospital, Perth, Australia
| | | | - Michael Berk
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia
| | - Holli Bertram
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Somer Bishop
- Department of Psychiatry and Behavioral Sciences, UCSF Weil Institute for Neuroscience, San Francisco, CA, USA
| | - Hannah Blau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - David F Bodenstein
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | | | - Kaan Boztug
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Jolana Čady
- Institute of Health Information and Statistics of the Czech Republic, Prague, Czech Republic
| | - Tiffany J Callahan
- Department of Biomedical Informatics, Columbia University Irving Medical Center, NY, NY, USA
| | | | - Seth J Carbon
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - J Harry Caufield
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lauren E Chan
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Christopher G Chute
- Schools of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Jaime Cruz-Rojo
- UDISGEN (Dysmorphology and Genetics Unit), 12 de Octubre Hospital, Madrid, Spain
| | - Noémi Dahan-Oliel
- Department of Clinical Research, Shriners Hospitals for Children, Montreal, Quebec, Canada
| | - Jon R Davids
- Shriners Children's Northern California, Sacramento, CA, USA
| | - Maud de Dieuleveult
- Département I&D, AP-HP, Banque Nationale de Données Maladies Rares, Paris, France
| | - Vinicius de Souza
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - J Raymond DePaulo
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Beata Derfalvi
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Ferdinand Dhombres
- Fetal Medicine Department, Armand Trousseau Hospital, Sorbonne University, GRC26, INSERM, Limics, Paris, France
| | - Claudia Diaz-Byrd
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Alexander J M Dingemans
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Bruno Donadille
- St Antoine Hospital, Reference Center for Rare Growth Endocrine Disorders, Sorbonne University, AP-HP, INSERM, US14 - Orphanet, Plateforme Maladies Rares, Paris, France
| | | | - Reem Elfeky
- Department of Immunology, GOS Hospital for Children NHS Foundation Trust, University College London, London, UK
| | - Shahim Essaid
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Giovanna Fico
- Bipolar and Depressive Disorders Unit, Institute of Neuroscience, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERSAM, Barcelona, Catalonia, Spain
| | - Helen V Firth
- Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK
| | - Yun Freudenberg-Hua
- Department of Psychiatry, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | | | - Davera L Gabriel
- School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | | | - Jessica Giordano
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Rachel Gore Moses
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ian Green
- SNOMED International, London W2 6BD, UK
| | - Matthias Griese
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, German center for Lung research (DZL), Munich, Germany
| | - Tudor Groza
- Rare Care Centre, Perth Children's Hospital, Perth, Australia
| | | | - Julia Guthrie
- Department of Structural and Computational Biology, University of Vienna; Max Perutz Labs, Vienna, Austria
| | - Benjamin Gyori
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Marc Hanauer
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, Paris, France
| | - Kateřina Hanušová
- Institute of Health Information and Statistics of the Czech Republic, Prague, Czech Republic
| | | | - Harshad Hegde
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ingo Helbig
- Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kateřina Holasová
- Institute of Health Information and Statistics of the Czech Republic, Prague, Czech Republic
| | - Charles Tapley Hoyt
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | | | - Eric Hurwitz
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Julius O B Jacobsen
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - Lisa Joseph
- Neurodevelopmental and Behavioral Phenotyping Service, National Institute of Mental Health, Bethesda, MD, USA
| | - Kamyar Keramatian
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Bryan King
- Department of Psychiatry and Behavioral Sciences, UCSF Weil Institute for Neuroscience, San Francisco, CA, USA
| | - Katrin Knoflach
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, German center for Lung research (DZL), Munich, Germany
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Megan L Kraus
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Carlo Kroll
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Maaike Kusters
- Immunology, NIHR Great Ormond Street Hospital BRC, London, UK
| | - Markus S Ladewig
- Department of Ophthalmology, University Clinic Marburg - Campus Fulda, Fulda, Germany
| | - David Lagorce
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, Paris, France
| | - Meng-Chuan Lai
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Pablo Lapunzina
- Institute of Medical and Molecular Genetics, Hospital Univ. La Paz, Madrid, Spain
| | - Bryan Laraway
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - David Lewis-Smith
- Translational and Clinical Research Institute, Henry Wellcome Building, Framlington Place, Newcastle University, Newcastle-Upon-Tyne NE14LP, UK
| | | | - Caterina Lucano
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, Paris, France
| | - Marzieh Majd
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Victor Martinez-Glez
- Center for Genomic Medicine, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí (I3PT-CERCA), Sabadell, Spain
| | - Toby H McHenry
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Melvin G McInnis
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Julie A McMurry
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michaela Mihulová
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - Caitlin E Millett
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Philip B Mitchell
- Discipline of Psychiatry & Mental Health, School of Clinical Medicine, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW, Australia
| | - Veronika Moslerová
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - Kenji Narutomi
- Okinawa Prefectural Nanbu Medical Center & Children's Medical Center
| | - Shahrzad Nematollahi
- School of Physical and Occupational Therapy, McGill University, Montreal, Quebec, Canada
| | - Julian Nevado
- Institute of Medical and Molecular Genetics, Hospital Univ. La Paz, Madrid, Spain
| | - Andrew A Nierenberg
- Dauten Family Center for Bipolar Treatment Innovation, Massachusetts General Hospital, Boston, MA, USA
| | - Nikola Novák Čajbiková
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - John I Nurnberger
- Stark Neurosciences Research Institute, Departments of Psychiatry and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Daniel Olson
- Data Collaboration Center, Data Science, Critical Path Institute, Tucson, AZ, USA
| | - Abigail Ortiz
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Harry Pachajoa
- Centro de Investigaciones en Anomalías Congénitas y Enfermedades Raras (CIACER), Universidad Icesi, Cali, Colombia
| | - Guiomar Perez de Nanclares
- Molecular (epi) genetics lab, Bioaraba Health Research Institute, Araba University Hospital, Vitoria-Gasteiz, Spain
| | - Amy Peters
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Tim Putman
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Christina K Rapp
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, German center for Lung research (DZL), Munich, Germany
| | - Ana Rath
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, Paris, France
| | - Justin Reese
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lauren Rekerle
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Angharad M Roberts
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London W12 0HS, UK
| | - Suzy Roy
- SNOMED International, London W2 6BD, UK
| | - Stephan J Sanders
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
| | - Catharina Schuetz
- Universitätsklinikum Carl Gustav Carus, Medizinische Fakultät, TU, Dresden, Germany
| | - Eva C Schulte
- Institute of Psychiatric Phenomics and Genomics (IPPG), LMU University Hospital, LMU Munich, Munich, Germany
| | - Thomas G Schulze
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Martin Schwarz
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - Katie Scott
- Department of Psychiatry, Dalhousie University, Halifax, NS, Canada
| | - Dominik Seelow
- Exploratory Diagnostic Sciences, Berliner Institut für Gesundheitsforschung - Charité, Berlin, Germany
| | - Berthold Seitz
- Department of Ophthalmology, Saarland University Medical Center UKS, Homburg/Saar, Germany
| | | | - Morgan N Similuk
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eric S Simon
- Eisenberg Family Depression Center, University of Michigan, Ann Arbor, MI, USA
| | - Balwinder Singh
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - Jake T Smolinsky
- Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Sarah Sperry
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | | | - Ray Stefancsik
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Robin Steinhaus
- Exploratory Diagnostic Sciences, Berliner Institut für Gesundheitsforschung - Charité, Berlin, Germany
| | - Rebecca Strawbridge
- Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | | | - Polina Talapova
- Institute for Research and Health Policy Studies, Tufts Medicine, Boston, MA 2111, USA
| | | | - Pavel Tesner
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - Rhys H Thomas
- Translational and Clinical Research Institute, Henry Wellcome Building, Framlington Place, Newcastle University, Newcastle-Upon-Tyne NE14LP, UK
| | - Audrey Thurm
- Neurodevelopmental and Behavioral Phenotyping Service, National Institute of Mental Health, Bethesda, MD, USA
| | - Marek Turnovec
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - Marielle E van Gijn
- Department of Genetics, University Medical Center Groningen, Groningen, Netherlands
| | | | - Markéta Vlčková
- Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic
| | - Anita Walden
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kai Wang
- Chinese HPO Consortium, Beijing, China
| | - Ron Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - James S Ware
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London W12 0HS, UK
| | | | | | - Lisa D Wiggins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Andrew E Williams
- Institute for Research and Health Policy Studies, Tufts Medicine, Boston, MA 2111, USA
| | - Chen Wu
- Chinese HPO Consortium, Beijing, China
| | - Margot J Wyrwoll
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, Edinburgh, UK
| | - Hui Xiong
- Chinese HPO Consortium, Beijing, China
| | - Nefize Yalin
- Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Yasunori Yamamoto
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Japan
| | - Lakshmi N Yatham
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Anastasia K Yocum
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Allan H Young
- Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London & South London and Maudsley NHS Foundation Trust, Bethlem Royal Hospital, Monks Orchard Road, Beckenham, Kent, London SE5 8AF, UK
| | - Zafer Yüksel
- Department of Human Genetics, Bioscientia Healthcare GmbH, Ingelheim, Germany
| | - Peter P Zandi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Andreas Zankl
- Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
| | - Ignacio Zarante
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Miroslav Zvolský
- Institute of Health Information and Statistics of the Czech Republic, Prague, Czech Republic
| | - Sabrina Toro
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Leigh C Carmody
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Nomi L Harris
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Monica C Munoz-Torres
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Daniel Danis
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Christopher J Mungall
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Melissa A Haendel
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
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Wang Z, Zhao G, Zhu Z, Wang Y, Xiang X, Zhang S, Luo T, Zhou Q, Qiu J, Tang B, Xia K, Li B, Li J. VarCards2: an integrated genetic and clinical database for ACMG-AMP variant-interpretation guidelines in the human whole genome. Nucleic Acids Res 2024; 52:D1478-D1489. [PMID: 37956311 PMCID: PMC10767961 DOI: 10.1093/nar/gkad1061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/21/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
VarCards, an online database, combines comprehensive variant- and gene-level annotation data to streamline genetic counselling for coding variants. Recognising the increasing clinical relevance of non-coding variations, there has been an accelerated development of bioinformatics tools dedicated to interpreting non-coding variations, including single-nucleotide variants and copy number variations. Regrettably, most tools remain as either locally installed databases or command-line tools dispersed across diverse online platforms. Such a landscape poses inconveniences and challenges for genetic counsellors seeking to utilise these resources without advanced bioinformatics expertise. Consequently, we developed VarCards2, which incorporates nearly nine billion artificially generated single-nucleotide variants (including those from mitochondrial DNA) and compiles vital annotation information for genetic counselling based on ACMG-AMP variant-interpretation guidelines. These annotations include (I) functional effects; (II) minor allele frequencies; (III) comprehensive function and pathogenicity predictions covering all potential variants, such as non-synonymous substitutions, non-canonical splicing variants, and non-coding variations and (IV) gene-level information. Furthermore, VarCards2 incorporates 368 820 266 documented short insertions and deletions and 2 773 555 documented copy number variations, complemented by their corresponding annotation and prediction tools. In conclusion, VarCards2, by integrating over 150 variant- and gene-level annotation sources, significantly enhances the efficiency of genetic counselling and can be freely accessed at http://www.genemed.tech/varcards2/.
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Affiliation(s)
- Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhaopo Zhu
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Yijing Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xudong Xiang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Shiyu Zhang
- Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Tengfei Luo
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Qiao Zhou
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jian Qiu
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Beisha Tang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, & Multi-Omics Research Center for Brain Disorders, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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19
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Carvalho NDAD, Santiago KM, Maia JML, Costa FD, Formiga MN, Soares DCDQ, Paixão D, Mello CALD, Costa CMLD, Rocha JCCD, Rivera B, Carraro DM, Torrezan GT. Prevalence and clinical implications of germline pathogenic variants in cancer predisposing genes in young patients across sarcoma subtypes. J Med Genet 2023; 61:61-68. [PMID: 37536918 PMCID: PMC10803955 DOI: 10.1136/jmg-2023-109269] [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: 03/10/2023] [Accepted: 07/11/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Sarcomas are a rare and diverse group of cancers occurring mainly in young individuals for which an underlying germline genetic cause remains unclear in most cases. METHODS Germline DNA from 177 children, adolescents and young adults with soft tissue or bone sarcomas was tested using multigene panels with 113 or 126 cancer predisposing genes (CPGs) to describe the prevalence of germline pathogenic/likely pathogenic variants (GPVs). Subsequent testing of a subset of tumours for loss of heterozygosity (LOH) evaluation was performed to investigate the clinical and molecular significance of these variants. RESULTS GPVs were detected in 21.5% (38/177) of the patients (15.8% in children and 21.6% in adolescents and young adults), with dominant CPGs being altered in 15.2% overall. These variants were found in genes previously associated with the risk of developing sarcomas (TP53, RB1, NF1, EXT1/2) but also in genes where that risk is still emerging/limited (ERCC2, TSC2 and BRCA2) or unknown (PALB2, RAD50, FANCM and others). The detection rates of GPVs varied from 0% to 33% across sarcoma subtypes and GPV carriers were more likely to present more than one primary tumour than non-carriers (21.1%×6.5%; p=0.012). Loss of the wild-type allele was detected in 48% of tumours from GPV carriers, mostly in genes definitively associated with sarcoma risk. CONCLUSION Our findings reveal that a high proportion of young patients with sarcomas presented a GPV in a CPG, underscoring the urgency of establishing appropriate genetic screening strategies for these individuals and their families.
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Affiliation(s)
| | - Karina Miranda Santiago
- Clinical and Functional Genomics Group, ACCamargo Cancer Center, Sao Paulo, São Paulo, Brazil
| | | | | | | | | | - Daniele Paixão
- Oncogenetics Department, ACCamargo Cancer Center, Sao Paulo, Brazil
| | | | | | | | - Barbara Rivera
- Molecular Mechanisms and Experimental Therapy in Oncology Program, IDIBELL, Barcelona, Spain
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Québec, Canada
| | - Dirce Maria Carraro
- Clinical and Functional Genomics Group, ACCamargo Cancer Center, Sao Paulo, São Paulo, Brazil
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, Sao Paulo, Brazil
| | - Giovana Tardin Torrezan
- Clinical and Functional Genomics Group, ACCamargo Cancer Center, Sao Paulo, São Paulo, Brazil
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, Sao Paulo, Brazil
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20
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Seaby EG, Thomas NS, Hunt D, Baralle D, Rehm HL, O’Donnell-Luria A, Ennis S. A Panel-Agnostic Strategy 'HiPPo' Improves Diagnostic Efficiency in the UK Genomic Medicine Service. Healthcare (Basel) 2023; 11:3179. [PMID: 38132069 PMCID: PMC10742528 DOI: 10.3390/healthcare11243179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Genome sequencing is available as a clinical test in the UK through the Genomic Medicine Service (GMS). The GMS analytical strategy predominantly filters genome data on preselected gene panels. Whilst this reduces variants requiring assessment by reporting laboratories, pathogenic variants outside applied panels may be missed, and variants in genes without established disease-gene relationships are largely ignored. This study compares the analysis of a research exome to a GMS clinical genome for the same patients. For the research exome, we applied a panel-agnostic approach filtering for variants with High Pathogenic Potential (HiPPo) using ClinVar, allele frequency, and in silico prediction tools. We then restricted HiPPo variants to Gene Curation Coalition (GenCC) disease genes. These results were compared with the GMS genome panel-based approach. Twenty-four participants from eight families underwent parallel research exome and GMS genome sequencing. Exome HiPPo analysis identified a similar number of variants as the GMS panel-based approach. GMS genome analysis returned two pathogenic variants and one de novo variant. Exome HiPPo analysis returned the same variants plus an additional pathogenic variant and three further de novo variants in novel genes, where case series are underway. When HiPPo was restricted to GenCC disease genes, statistically fewer variants required assessment to identify more pathogenic variants than reported by the GMS, giving a diagnostic rate per variant assessed of 20% for HiPPo versus 3% for the GMS. With UK plans to sequence 5 million genomes, strategies are needed to optimise genome analysis beyond gene panels whilst minimising the burden of variants requiring clinical assessment.
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Affiliation(s)
- Eleanor G. Seaby
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton SO16 6YD, Hampshire, UK; (D.H.); (D.B.); (S.E.)
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; (H.L.R.); (A.O.-L.)
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Paediatric Infectious Diseases, Imperial College London, London W2 1NY, UK
| | - N. Simon Thomas
- Wessex Regional Genomics Laboratory, Salisbury NHS Foundation Trust, Salisbury SP2 8BJ, UK;
| | - David Hunt
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton SO16 6YD, Hampshire, UK; (D.H.); (D.B.); (S.E.)
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton SO16 6YD, Hampshire, UK; (D.H.); (D.B.); (S.E.)
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; (H.L.R.); (A.O.-L.)
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Anne O’Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; (H.L.R.); (A.O.-L.)
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sarah Ennis
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton SO16 6YD, Hampshire, UK; (D.H.); (D.B.); (S.E.)
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21
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Abstract
Rare diseases are a leading cause of infant mortality and lifelong disability. To improve outcomes, timely diagnosis and effective treatments are needed. Genomic sequencing has transformed the traditional diagnostic process, providing rapid, accurate and cost-effective genetic diagnoses to many. Incorporating genomic sequencing into newborn screening programmes at the population scale holds the promise of substantially expanding the early detection of treatable rare diseases, with stored genomic data potentially benefitting health over a lifetime and supporting further research. As several large-scale newborn genomic screening projects launch internationally, we review the challenges and opportunities presented, particularly the need to generate evidence of benefit and to address the ethical, legal and psychosocial issues that genomic newborn screening raises.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics, Melbourne, Victoria, Australia.
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.
| | - Richard H Scott
- Great Ormond Street Hospital for Children, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
- Genomics England, London, UK
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22
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Josephs KS, Roberts AM, Theotokis P, Walsh R, Ostrowski PJ, Edwards M, Fleming A, Thaxton C, Roberts JD, Care M, Zareba W, Adler A, Sturm AC, Tadros R, Novelli V, Owens E, Bronicki L, Jarinova O, Callewaert B, Peters S, Lumbers T, Jordan E, Asatryan B, Krishnan N, Hershberger RE, Chahal CAA, Landstrom AP, James C, McNally EM, Judge DP, van Tintelen P, Wilde A, Gollob M, Ingles J, Ware JS. Beyond gene-disease validity: capturing structured data on inheritance, allelic requirement, disease-relevant variant classes, and disease mechanism for inherited cardiac conditions. Genome Med 2023; 15:86. [PMID: 37872640 PMCID: PMC10594882 DOI: 10.1186/s13073-023-01246-8] [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: 04/04/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND As the availability of genomic testing grows, variant interpretation will increasingly be performed by genomic generalists, rather than domain-specific experts. Demand is rising for laboratories to accurately classify variants in inherited cardiac condition (ICC) genes, including secondary findings. METHODS We analyse evidence for inheritance patterns, allelic requirement, disease mechanism and disease-relevant variant classes for 65 ClinGen-curated ICC gene-disease pairs. We present this information for the first time in a structured dataset, CardiacG2P, and assess application in genomic variant filtering. RESULTS For 36/65 gene-disease pairs, loss of function is not an established disease mechanism, and protein truncating variants are not known to be pathogenic. Using the CardiacG2P dataset as an initial variant filter allows for efficient variant prioritisation whilst maintaining a high sensitivity for retaining pathogenic variants compared with two other variant filtering approaches. CONCLUSIONS Access to evidence-based structured data representing disease mechanism and allelic requirement aids variant filtering and analysis and is a pre-requisite for scalable genomic testing.
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Affiliation(s)
- Katherine S Josephs
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Angharad M Roberts
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Great Ormond Street Hospital, NHS Foundation Trust, London, UK
| | - Pantazis Theotokis
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Roddy Walsh
- Amsterdam University Medical Centre, University of Amsterdam, Heart Center, Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | | | - Matthew Edwards
- Clinical Genetics & Genomics Lab, Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Andrew Fleming
- Clinical Genetics & Genomics Lab, Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Courtney Thaxton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason D Roberts
- Population Health Research Institute, McMaster University, and Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Melanie Care
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Division of Cardiology, Toronto General Hospital, Toronto, Canada
| | - Wojciech Zareba
- Clinical Cardiovascular Research Center, University of Rochester, Rochester, NY, USA
| | - Arnon Adler
- Division of Cardiology, Peter Munk Cardiac Centre, University Health Network and Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | - Rafik Tadros
- Cardiovascular Genetics Center, Montreal Heart Institute, and Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Valeria Novelli
- Unit of Immunology and Functional Genomics, Centro Cardiologico Monzino IRCCS, Milano, Italy
| | - Emma Owens
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lucas Bronicki
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Department of Genetics, CHEO, Ottawa, Ontario, Canada
| | - Olga Jarinova
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Department of Genetics, CHEO, Ottawa, Ontario, Canada
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Stacey Peters
- Department of Cardiology and Genomic Medicine, Royal Melbourne Hospital, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
| | - Tom Lumbers
- Barts Health & University College London Hospitals NHS Trusts, London, UK
- Institute of Health Informatics, University College London, London, UK
| | - Elizabeth Jordan
- Divisions of Human Genetics and Cardiovascular Medicine, The Ohio State University, Columbus, OH, USA
| | - Babken Asatryan
- Department of Cardiology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Neesha Krishnan
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
| | - Ray E Hershberger
- Divisions of Human Genetics and Cardiovascular Medicine, The Ohio State University, Columbus, OH, USA
| | - C Anwar A Chahal
- Center for Inherited Cardiovascular Diseases, WellSpan Health, Lancaster, PA, USA
- Cardiac Electrophysiology and Inherited Cardiovascular Diseases, Cardiovascular Division, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
| | - Andrew P Landstrom
- Department of Pediatrics and Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Cynthia James
- Johns Hopkins Center for Inherited Heart Diseases, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Elizabeth M McNally
- Center for Genetic Medicine, Dept of Medicine (Cardiology), Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Daniel P Judge
- Medical University of South Carolina, Charleston, SC, USA
| | - Peter van Tintelen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Arthur Wilde
- Department of Cardiology, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
| | - Michael Gollob
- Inherited Arrhythmia and Cardiomyopathy Program, Division of Cardiology, University of Toronto, Toronto, ON, Canada
| | - Jodie Ingles
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK.
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK.
- MRC London Institute of Medical Sciences, Imperial College London, London, UK.
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23
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Tesi B, Boileau C, Boycott KM, Canaud G, Caulfield M, Choukair D, Hill S, Spielmann M, Wedell A, Wirta V, Nordgren A, Lindstrand A. Precision medicine in rare diseases: What is next? J Intern Med 2023; 294:397-412. [PMID: 37211972 DOI: 10.1111/joim.13655] [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] [Indexed: 05/23/2023]
Abstract
Molecular diagnostics is a cornerstone of modern precision medicine, broadly understood as tailoring an individual's treatment, follow-up, and care based on molecular data. In rare diseases (RDs), molecular diagnoses reveal valuable information about the cause of symptoms, disease progression, familial risk, and in certain cases, unlock access to targeted therapies. Due to decreasing DNA sequencing costs, genome sequencing (GS) is emerging as the primary method for precision diagnostics in RDs. Several ongoing European initiatives for precision medicine have chosen GS as their method of choice. Recent research supports the role for GS as first-line genetic investigation in individuals with suspected RD, due to its improved diagnostic yield compared to other methods. Moreover, GS can detect a broad range of genetic aberrations including those in noncoding regions, producing comprehensive data that can be periodically reanalyzed for years to come when further evidence emerges. Indeed, targeted drug development and repurposing of medicines can be accelerated as more individuals with RDs receive a molecular diagnosis. Multidisciplinary teams in which clinical specialists collaborate with geneticists, genomics education of professionals and the public, and dialogue with patient advocacy groups are essential elements for the integration of precision medicine into clinical practice worldwide. It is also paramount that large research projects share genetic data and leverage novel technologies to fully diagnose individuals with RDs. In conclusion, GS increases diagnostic yields and is a crucial step toward precision medicine for RDs. Its clinical implementation will enable better patient management, unlock targeted therapies, and guide the development of innovative treatments.
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Affiliation(s)
- Bianca Tesi
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Catherine Boileau
- Département de Génétique, APHP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Guillaume Canaud
- INSERM U1151, Unité de médecine translationnelle et thérapies ciblées, Hôpital Necker-Enfants Malades, Université Paris Cité, AP-HP, Paris, France
| | - Mark Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Daniela Choukair
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Sue Hill
- Chief Scientific Officer, NHS England, London, UK
| | - Malte Spielmann
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, 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
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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24
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Hayesmoore JB, Bhuiyan ZA, Coviello DA, du Sart D, Edwards M, Iascone M, Morris-Rosendahl DJ, Sheils K, van Slegtenhorst M, Thomson KL. EMQN: Recommendations for genetic testing in inherited cardiomyopathies and arrhythmias. Eur J Hum Genet 2023; 31:1003-1009. [PMID: 37443332 PMCID: PMC10474043 DOI: 10.1038/s41431-023-01421-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Inherited cardiomyopathies and arrhythmias (ICAs) are a prevalent and clinically heterogeneous group of genetic disorders that are associated with increased risk of sudden cardiac death and heart failure. Making a genetic diagnosis can inform the management of patients and their at-risk relatives and, as such, molecular genetic testing is now considered an integral component of the clinical care pathway. However, ICAs are characterised by high genetic and allelic heterogeneity, incomplete / age-related penetrance, and variable expressivity. Therefore, despite our improved understanding of the genetic basis of these conditions, and significant technological advances over the past two decades, identifying and recognising the causative genotype remains challenging. As clinical genetic testing for ICAs becomes more widely available, it is increasingly important for clinical laboratories to consolidate existing knowledge and experience to inform and improve future practice. These recommendations have been compiled to help clinical laboratories navigate the challenges of ICAs and thereby facilitate best practice and consistency in genetic test provision for this group of disorders. General recommendations on internal and external quality control, referral, analysis, result interpretation, and reporting are described. Also included are appendices that provide specific information pertinent to genetic testing for hypertrophic, dilated, and arrhythmogenic right ventricular cardiomyopathies, long QT syndrome, Brugada syndrome, and catecholaminergic polymorphic ventricular tachycardia.
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Affiliation(s)
- Jesse B Hayesmoore
- Oxford Regional Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Zahurul A Bhuiyan
- Division of Genetic Medicine, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | | | - Desirée du Sart
- Biological Sciences and Genomics, Monash University, Melbourne, VIC, Australia
| | - Matthew Edwards
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Deborah J Morris-Rosendahl
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | | | | | - Kate L Thomson
- Oxford Regional Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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25
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Krishnan AR, Schwartz ML, Somerville C, Ding Q, Kim RH. Using whole genome sequence findings to assess gene-disease causality in cardiomyopathy and arrhythmia patients. Future Cardiol 2023; 19:583-592. [PMID: 37830358 DOI: 10.2217/fca-2023-0082] [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] [Indexed: 10/14/2023] Open
Abstract
Aim: The genetic etiologies of cardiomyopathies and arrhythmias have not been fully elucidated. Materials & methods: Research findings from genome analyses in a cardiomyopathy and arrhythmia cohort were gathered. Gene-disease relationships from two databases were compared with patient phenotypes. A literature review was conducted for genes with limited evidence. Results: Of 43 genes with candidate findings from 18 cases, 23.3% of genes had never been curated, 15.0% were curated for cardiomyopathies, 16.7% for arrhythmias and 31.3% for other conditions. 25.5% of candidate findings were curated for the patient's specific phenotype with 11.8% having definitive evidence. MYH6 and TPCN1 were flagged for recuration. Conclusion: Findings from genome sequencing in disease cohorts may be useful to guide gene-curation efforts.
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Affiliation(s)
- Aishwarya Rajesh Krishnan
- Division of Clinical & Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
| | - Marci Lb Schwartz
- Division of Clinical & Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, M5G 1X8, Canada
| | - Cherith Somerville
- Division of Clinical & Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, M5G 1X8, Canada
| | - Qiliang Ding
- Division of Clinical & Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, M5G 1X8, Canada
| | - Raymond H Kim
- Division of Clinical & Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, M5G 1X8, Canada
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Sinai Health System, Department of Medicine, Toronto, Ontario, M5T 3L9, Canada
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AlAbdi L, Maddirevula S, Shamseldin HE, Khouj E, Helaby R, Hamid H, Almulhim A, Hashem MO, Abdulwahab F, Abouyousef O, Alqahtani M, Altuwaijri N, Jaafar A, Alshidi T, Alzahrani F, Alkuraya FS. Diagnostic implications of pitfalls in causal variant identification based on 4577 molecularly characterized families. Nat Commun 2023; 14:5269. [PMID: 37644014 PMCID: PMC10465531 DOI: 10.1038/s41467-023-40909-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
Despite large sequencing and data sharing efforts, previously characterized pathogenic variants only account for a fraction of Mendelian disease patients, which highlights the need for accurate identification and interpretation of novel variants. In a large Mendelian cohort of 4577 molecularly characterized families, numerous scenarios in which variant identification and interpretation can be challenging are encountered. We describe categories of challenges that cover the phenotype (e.g. novel allelic disorders), pedigree structure (e.g. imprinting disorders masquerading as autosomal recessive phenotypes), positional mapping (e.g. double recombination events abrogating candidate autozygous intervals), gene (e.g. novel gene-disease assertion) and variant (e.g. complex compound inheritance). Overall, we estimate a probability of 34.3% for encountering at least one of these challenges. Importantly, our data show that by only addressing non-sequencing-based challenges, around 71% increase in the diagnostic yield can be expected. Indeed, by applying these lessons to a cohort of 314 cases with negative clinical exome or genome reports, we could identify the likely causal variant in 54.5%. Our work highlights the need to have a thorough approach to undiagnosed diseases by considering a wide range of challenges rather than a narrow focus on sequencing technologies. It is hoped that by sharing this experience, the yield of undiagnosed disease programs globally can be improved.
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Affiliation(s)
- Lama AlAbdi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ebtissal Khouj
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana Helaby
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Halima Hamid
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Aisha Almulhim
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Omar Abouyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Norah Altuwaijri
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amal Jaafar
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa Alshidi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fatema Alzahrani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.
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27
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Foreman J, Perrett D, Mazaika E, Hunt SE, Ware JS, Firth HV. DECIPHER: Improving Genetic Diagnosis Through Dynamic Integration of Genomic and Clinical Data. Annu Rev Genomics Hum Genet 2023; 24:151-176. [PMID: 37285546 PMCID: PMC7615097 DOI: 10.1146/annurev-genom-102822-100509] [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] [Indexed: 06/09/2023]
Abstract
DECIPHER (Database of Genomic Variation and Phenotype in Humans Using Ensembl Resources) shares candidate diagnostic variants and phenotypic data from patients with genetic disorders to facilitate research and improve the diagnosis, management, and therapy of rare diseases. The platform sits at the boundary between genomic research and the clinical community. DECIPHER aims to ensure that the most up-to-date data are made rapidly available within its interpretation interfaces to improve clinical care. Newly integrated cardiac case-control data that provide evidence of gene-disease associations and inform variant interpretation exemplify this mission. New research resources are presented in a format optimized for use by a broad range of professionals supporting the delivery of genomic medicine. The interfaces within DECIPHER integrate and contextualize variant and phenotypic data, helping to determine a robust clinico-molecular diagnosis for rare-disease patients, which combines both variant classification and clinical fit. DECIPHER supports discovery research, connecting individuals within the rare-disease community to pursue hypothesis-driven research.
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Affiliation(s)
- Julia Foreman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom; ,
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Daniel Perrett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom; ,
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Erica Mazaika
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; ,
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom; ,
| | - James S Ware
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; ,
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Helen V Firth
- Wellcome Sanger Institute, Hinxton, United Kingdom
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom;
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28
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Stenton SL, O’Leary M, Lemire G, VanNoy GE, DiTroia S, Ganesh VS, Groopman E, O’Heir E, Mangilog B, Osei-Owusu I, Pais LS, Serrano J, Singer-Berk M, Weisburd B, Wilson M, Austin-Tse C, Abdelhakim M, Althagafi A, Babbi G, Bellazzi R, Bovo S, Carta MG, Casadio R, Coenen PJ, De Paoli F, Floris M, Gajapathy M, Hoehndorf R, Jacobsen JO, Joseph T, Kamandula A, Katsonis P, Kint C, Lichtarge O, Limongelli I, Lu Y, Magni P, Mamidi TKK, Martelli PL, Mulargia M, Nicora G, Nykamp K, Pejaver V, Peng Y, Pham THC, Podda MS, Rao A, Rizzo E, Saipradeep VG, Savojardo C, Schols P, Shen Y, Sivadasan N, Smedley D, Soru D, Srinivasan R, Sun Y, Sunderam U, Tan W, Tiwari N, Wang X, Wang Y, Williams A, Worthey EA, Yin R, You Y, Zeiberg D, Zucca S, Bakolitsa C, Brenner SE, Fullerton SM, Radivojac P, Rehm HL, O’Donnell-Luria A. Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.02.23293212. [PMID: 37577678 PMCID: PMC10418577 DOI: 10.1101/2023.08.02.23293212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Background A major obstacle faced by rare disease families is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five years, and causal variants are identified in under 50%. The Rare Genomes Project (RGP) is a direct-to-participant research study on the utility of genome sequencing (GS) for diagnosis and gene discovery. Families are consented for sharing of sequence and phenotype data with researchers, allowing development of a Critical Assessment of Genome Interpretation (CAGI) community challenge, placing variant prioritization models head-to-head in a real-life clinical diagnostic setting. Methods Predictors were provided a dataset of phenotype terms and variant calls from GS of 175 RGP individuals (65 families), including 35 solved training set families, with causal variants specified, and 30 test set families (14 solved, 16 unsolved). The challenge tasked teams with identifying the causal variants in as many test set families as possible. Ranked variant predictions were submitted with estimated probability of causal relationship (EPCR) values. Model performance was determined by two metrics, a weighted score based on rank position of true positive causal variants and maximum F-measure, based on precision and recall of causal variants across EPCR thresholds. Results Sixteen teams submitted predictions from 52 models, some with manual review incorporated. Top performing teams recalled the causal variants in up to 13 of 14 solved families by prioritizing high quality variant calls that were rare, predicted deleterious, segregating correctly, and consistent with reported phenotype. In unsolved families, newly discovered diagnostic variants were returned to two families following confirmatory RNA sequencing, and two prioritized novel disease gene candidates were entered into Matchmaker Exchange. In one example, RNA sequencing demonstrated aberrant splicing due to a deep intronic indel in ASNS, identified in trans with a frameshift variant, in an unsolved proband with phenotype overlap with asparagine synthetase deficiency. Conclusions By objective assessment of variant predictions, we provide insights into current state-of-the-art algorithms and platforms for genome sequencing analysis for rare disease diagnosis and explore areas for future optimization. Identification of diagnostic variants in unsolved families promotes synergy between researchers with clinical and computational expertise as a means of advancing the field of clinical genome interpretation.
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Affiliation(s)
- Sarah L. Stenton
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Melanie O’Leary
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabrielle Lemire
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grace E. VanNoy
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie DiTroia
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vijay S. Ganesh
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Emily Groopman
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emily O’Heir
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brian Mangilog
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ikeoluwa Osei-Owusu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lynn S. Pais
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jillian Serrano
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Wilson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina Austin-Tse
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Marwa Abdelhakim
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Azza Althagafi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computer Science Department, College of Computers and Information Technology, Taif University, Taif, Saudi Arabia
| | - Giulia Babbi
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Riccardo Bellazzi
- enGenome Srl, Pavia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Maria Giulia Carta
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Rita Casadio
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | | | - Matteo Floris
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Manavalan Gajapathy
- Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
- Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert Hoehndorf
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Julius O.B. Jacobsen
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, UK
| | - Thomas Joseph
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Akash Kamandula
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Panagiotis Katsonis
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Olivier Lichtarge
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Structural and Computational Biology & Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, USA
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Yulan Lu
- Center for molecular medicine, Pediatric Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Paolo Magni
- enGenome Srl, Pavia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Tarun Karthik Kumar Mamidi
- Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
- Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Pier Luigi Martelli
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Marta Mulargia
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | | | | | - Vikas Pejaver
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yisu Peng
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Thi Hong Cam Pham
- Anatomy and Surgical Training Department, University of Medicine and Pharmacy, Hue University, Vietnam
| | - Maurizio S. Podda
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Aditya Rao
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | | | - Vangala G Saipradeep
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Castrense Savojardo
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, Texas, USA
| | - Naveen Sivadasan
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Damian Smedley
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, UK
| | | | - Rajgopal Srinivasan
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Yuanfei Sun
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Uma Sunderam
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Wuwei Tan
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Naina Tiwari
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Xiao Wang
- Center for molecular medicine, Pediatric Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Yaqiong Wang
- Center for molecular medicine, Pediatric Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Amanda Williams
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elizabeth A. Worthey
- Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
- Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rujie Yin
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Yuning You
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Daniel Zeiberg
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | | | - Constantina Bakolitsa
- Department of Plant and Microbial Biology and Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Steven E. Brenner
- Department of Plant and Microbial Biology and Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Stephanie M Fullerton
- Department of Bioethics & Humanities, University of Washington School of Medicine, Seattle, WA, USA
| | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anne O’Donnell-Luria
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
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Geoffroy V, Lamouche JB, Guignard T, Nicaise S, Kress A, Scheidecker S, Le Béchec A, Muller J. The AnnotSV webserver in 2023: updated visualization and ranking. Nucleic Acids Res 2023:7175348. [PMID: 37216590 DOI: 10.1093/nar/gkad426] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/20/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023] Open
Abstract
Much of the human genetics variant repertoire is composed of single nucleotide variants (SNV) and small insertion/deletions (indel) but structural variants (SV) remain a major part of our modified DNA. SV detection has often been a complex question to answer either because of the necessity to use different technologies (array CGH, SNP array, Karyotype, Optical Genome Mapping…) to detect each category of SV or to get an appropriate resolution (Whole Genome Sequencing). Thanks to the deluge of pangenomic analysis, Human geneticists are accumulating SV and their interpretation remains time consuming and challenging. The AnnotSV webserver (https://www.lbgi.fr/AnnotSV/) aims at being an efficient tool to (i) annotate and interpret SV potential pathogenicity in the context of human diseases, (ii) recognize potential false positive variants from all the SV identified and (iii) visualize the patient variants repertoire. The most recent developments in the AnnotSV webserver are: (i) updated annotations sources and ranking, (ii) three novel output formats to allow diverse utilization (analysis, pipelines), as well as (iii) two novel user interfaces including an interactive circos view.
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Affiliation(s)
- Véronique Geoffroy
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
- Laboratoire de Génétique Médicale, UMR 1112, INSERM, IGMA, Université de Strasbourg, Strasbourg, France
| | - Jean-Baptiste Lamouche
- Laboratoire de Génétique Médicale, UMR 1112, INSERM, IGMA, Université de Strasbourg, Strasbourg, France
- Unité Fonctionnelle de Bioinformatique Médicale appliquée au diagnostic (UF7363), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | | | - Samuel Nicaise
- Unité Fonctionnelle de Bioinformatique Médicale appliquée au diagnostic (UF7363), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Arnaud Kress
- Complex Systems and Translational Bioinformatics, ICube, UMR 7357, University of Strasbourg, CNRS, FMTS, Strasbourg, France
| | - Sophie Scheidecker
- Laboratoire de Génétique Médicale, UMR 1112, INSERM, IGMA, Université de Strasbourg, Strasbourg, France
- Laboratoires de Diagnostic Génétique, IGMA, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Antony Le Béchec
- Unité Fonctionnelle de Bioinformatique Médicale appliquée au diagnostic (UF7363), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jean Muller
- Laboratoire de Génétique Médicale, UMR 1112, INSERM, IGMA, Université de Strasbourg, Strasbourg, France
- Unité Fonctionnelle de Bioinformatique Médicale appliquée au diagnostic (UF7363), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Laboratoires de Diagnostic Génétique, IGMA, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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30
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Brock DC, Abbott M, Reed L, Kammeyer R, Gibbons M, Angione K, Bernard TJ, Gaskell A, Demarest S. Epilepsy panels in clinical practice: Yield, variants of uncertain significance, and treatment implications. Epilepsy Res 2023; 193:107167. [PMID: 37230012 DOI: 10.1016/j.eplepsyres.2023.107167] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023]
Abstract
OBJECTIVE There has been increasing utilization of genetic testing for pediatric epilepsy in recent years. Little systematic data is available examining how practice changes have impacted testing yields, diagnostic pace, incidence of variants of uncertain significance (VUSs), or therapeutic management. METHODS A retrospective chart review was performed at Children's Hospital Colorado from February 2016 through February 2020. All patients under 18 years for whom an epilepsy gene panel was sent were included. RESULTS A total of 761 epilepsy gene panels were sent over the study period. During the study period, there was a 292% increase in the average number of panels sent per month. The time from seizure onset to panel result decreased over the study period from a median of 2.9 years to 0.7 years. Despite the increase in testing, the percentage of panels yielding a disease-causing result remained stable at 11-13%. A total of 90 disease-causing results were identified, > 75% of which provided guidance in management. Children were more likely to have a disease-causing result if they were < 3 years old at seizure onset (OR 4.4, p < 0.001), had neurodevelopmental concerns (OR 2.2, p = 0.002), or had a developmentally abnormal MRI (OR 3.8, p < 0.001). A total of 1417 VUSs were identified, equating to 15.7 VUSs per disease-causing result. Non-Hispanic white patients had a lower average number of VUSs than patients of all other races/ethnicities (1.7 vs 2.1, p < 0.001). SIGNIFICANCE Expansion in the volume of genetic testing corresponded to a decrease in the time from seizure onset to testing result. Diagnostic yield remained stable, resulting in an increase in the absolute number of disease-causing results annually-most of which have implications for management. However, there has also been an increase in total VUSs, which likely resulted in additional clinical time spent on VUS resolution.
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Affiliation(s)
- Dylan C Brock
- Children's Hospital Colorado Anschutz Medical Campus, Aurora 13123 East 16th Avenue, Aurora, CO 80045; University of Colorado, Anschutz Medical Campus School of Medicine, Department of Pediatrics, Section of Neurology Anschutz Medical Campus, Aurora 13001 E 17th Pl, Aurora, CO 80045.
| | - Megan Abbott
- Children's Hospital Colorado Anschutz Medical Campus, Aurora 13123 East 16th Avenue, Aurora, CO 80045; University of Colorado, Anschutz Medical Campus School of Medicine, Department of Pediatrics, Section of Neurology Anschutz Medical Campus, Aurora 13001 E 17th Pl, Aurora, CO 80045.
| | - Laurel Reed
- Children's Hospital Colorado Anschutz Medical Campus, Aurora 13123 East 16th Avenue, Aurora, CO 80045; University of Colorado, Anschutz Medical Campus School of Medicine, Department of Pediatrics, Section of Neurology Anschutz Medical Campus, Aurora 13001 E 17th Pl, Aurora, CO 80045.
| | - Ryan Kammeyer
- Children's Hospital Colorado Anschutz Medical Campus, Aurora 13123 East 16th Avenue, Aurora, CO 80045; University of Colorado, Anschutz Medical Campus School of Medicine, Department of Pediatrics, Section of Neurology Anschutz Medical Campus, Aurora 13001 E 17th Pl, Aurora, CO 80045.
| | - Melissa Gibbons
- Children's Hospital Colorado Anschutz Medical Campus, Aurora 13123 East 16th Avenue, Aurora, CO 80045; University of Colorado, Anschutz Medical Campus School of Medicine, Department of Pediatrics, Section of Neurology Anschutz Medical Campus, Aurora 13001 E 17th Pl, Aurora, CO 80045.
| | - Katie Angione
- Precision Medicine Institute, Children's Hospital Colorado Anschutz Medical Campus, Aurora 1312 East 16th Avenue, Aurora, CO 80045, USA; University of Colorado, Anschutz Medical Campus School of Medicine, Department of Pediatrics, Section of Neurology Anschutz Medical Campus, Aurora 13001 E 17th Pl, Aurora, CO 80045.
| | - Timothy J Bernard
- Children's Hospital Colorado Anschutz Medical Campus, Aurora 13123 East 16th Avenue, Aurora, CO 80045; University of Colorado, Anschutz Medical Campus School of Medicine, Department of Pediatrics, Section of Neurology Anschutz Medical Campus, Aurora 13001 E 17th Pl, Aurora, CO 80045.
| | - Alisa Gaskell
- Precision Medicine Institute, Children's Hospital Colorado Anschutz Medical Campus, Aurora 1312 East 16th Avenue, Aurora, CO 80045, USA; University of Colorado, Anschutz Medical Campus School of Medicine, Department of Pediatrics, Section of Neurology Anschutz Medical Campus, Aurora 13001 E 17th Pl, Aurora, CO 80045.
| | - Scott Demarest
- Precision Medicine Institute, Children's Hospital Colorado Anschutz Medical Campus, Aurora 1312 East 16th Avenue, Aurora, CO 80045, USA; University of Colorado, Anschutz Medical Campus School of Medicine, Department of Pediatrics, Section of Neurology Anschutz Medical Campus, Aurora 13001 E 17th Pl, Aurora, CO 80045.
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31
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Seal RL, Tweedie S, Bruford EA. A standardised nomenclature for long non-coding RNAs. IUBMB Life 2023; 75:380-389. [PMID: 35880706 PMCID: PMC9877250 DOI: 10.1002/iub.2663] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/08/2022] [Indexed: 01/29/2023]
Abstract
The HUGO Gene Nomenclature Committee (HGNC) is the sole group with the authority to approve symbols for human genes, including long non-coding RNA (lncRNA) genes. Use of approved symbols ensures that publications and biomedical databases are easily searchable and reduces the risks of confusion that can be caused by using the same symbol to refer to different genes or using many different symbols for the same gene. Here, we describe how the HGNC names lncRNA genes and review the nomenclature of the seven lncRNA genes most mentioned in the scientific literature.
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Affiliation(s)
- Ruth L. Seal
- HUGO Gene Nomenclature Committee, European Molecular Biology LaboratoryEuropean Bioinformatics Institute, Wellcome Genome CampusHinxtonUK
- Department of HaematologyUniversity of Cambridge School of Clinical MedicineCambridgeUK
| | - Susan Tweedie
- HUGO Gene Nomenclature Committee, European Molecular Biology LaboratoryEuropean Bioinformatics Institute, Wellcome Genome CampusHinxtonUK
| | - Elspeth A. Bruford
- HUGO Gene Nomenclature Committee, European Molecular Biology LaboratoryEuropean Bioinformatics Institute, Wellcome Genome CampusHinxtonUK
- Department of HaematologyUniversity of Cambridge School of Clinical MedicineCambridgeUK
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32
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King JR, Grill K, Hammarström L. Genomic-Based Newborn Screening for Inborn Errors of Immunity: Practical and Ethical Considerations. Int J Neonatal Screen 2023; 9:ijns9020022. [PMID: 37092516 PMCID: PMC10123688 DOI: 10.3390/ijns9020022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/25/2023] Open
Abstract
Inborn errors of immunity (IEI) are a group of over 450 genetically distinct conditions associated with significant morbidity and mortality, for which early diagnosis and treatment improve outcomes. Newborn screening for severe combined immunodeficiency (SCID) is currently underway in several countries, utilising a DNA-based technique to quantify T cell receptor excision circles (TREC) and kappa-deleting recombination excision circles (KREC). This strategy will only identify those infants with an IEI associated with T and/or B cell lymphopenia. Other severe forms of IEI will not be detected. Up-front, first-tier genomic-based newborn screening has been proposed as a potential approach by which to concurrently screen infants for hundreds of monogenic diseases at birth. Given the clinical, phenotypic and genetic heterogeneity of IEI, a next-generation sequencing-based newborn screening approach would be suitable. There are, however, several ethical, legal and social issues which must be evaluated in detail prior to adopting a genomic-based newborn screening approach, and these are discussed herein in the context of IEI.
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Affiliation(s)
- Jovanka R King
- Department of Allergy & Clinical Immunology, Women's and Children's Hospital Network, North Adelaide, SA 5006, Australia
- Immunology Directorate, SA Pathology, Adelaide, SA 5000, Australia
- Robinson Research Institute and Discipline of Paediatrics, School of Medicine, University of Adelaide, North Adelaide, SA 5006, Australia
| | - Kalle Grill
- Department of Historical, Philosophical and Religious Studies, Umeå University, SE-90187 Umeå, Sweden
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet, SE-14183 Huddinge, Sweden
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33
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Josephs KS, Roberts AM, Theotokis P, Walsh R, Ostrowski PJ, Edwards M, Fleming A, Thaxton C, Roberts JD, Care M, Zareba W, Adler A, Sturm AC, Tadros R, Novelli V, Owens E, Bronicki L, Jarinova O, Callewaert B, Peters S, Lumbers T, Jordan E, Asatryan B, Krishnan N, Hershberger RE, Chahal CAA, Landstrom AP, James C, McNally EM, Judge DP, van Tintelen P, Wilde A, Gollob M, Ingles J, Ware JS. Beyond gene-disease validity: capturing structured data on inheritance, allelic-requirement, disease-relevant variant classes, and disease mechanism for inherited cardiac conditions. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.03.23287612. [PMID: 37066275 PMCID: PMC10104233 DOI: 10.1101/2023.04.03.23287612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Background As availability of genomic testing grows, variant interpretation will increasingly be performed by genomic generalists, rather than domain-specific experts. Demand is rising for laboratories to accurately classify variants in inherited cardiac condition (ICC) genes, including as secondary findings. Methods We analyse evidence for inheritance patterns, allelic requirement, disease mechanism and disease-relevant variant classes for 65 ClinGen-curated ICC gene-disease pairs. We present this information for the first time in a structured dataset, CardiacG2P, and assess application in genomic variant filtering. Results For 36/65 gene-disease pairs, loss-of-function is not an established disease mechanism, and protein truncating variants are not known to be pathogenic. Using CardiacG2P as an initial variant filter allows for efficient variant prioritisation whilst maintaining a high sensitivity for retaining pathogenic variants compared with two other variant filtering approaches. Conclusions Access to evidence-based structured data representing disease mechanism and allelic requirement aids variant filtering and analysis and is pre-requisite for scalable genomic testing.
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Affiliation(s)
- Katherine S Josephs
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London UK
| | - Angharad M Roberts
- National Heart and Lung Institute, Imperial College London, London, UK
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | | | - Roddy Walsh
- Amsterdam University Medical Centre, University of Amsterdam, Heart Center, Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | | | - Matthew Edwards
- Clinical Genetics & Genomics Lab, Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London UK
| | - Andrew Fleming
- Clinical Genetics & Genomics Lab, Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London UK
| | - Courtney Thaxton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason D Roberts
- Population Health Research Institute, McMaster University, and Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Melanie Care
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Division of Cardiology, Toronto General Hospital, Toronto, Canada
| | - Wojciech Zareba
- Clinical Cardiovascular Research Center, University of Rochester, Rochester, New York, USA
| | - Arnon Adler
- Division of Cardiology, Peter Munk Cardiac Centre, University Health Network and Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Amy C Sturm
- 23andMe, Sunnyvale, California, Genomic Health
| | - Rafik Tadros
- Cardiovascular Genetics Center, Montreal Heart Institute, and Faculty of Medicine, Université de Montréal
| | - Valeria Novelli
- Unit of Immunology and Functional Genomics, Centro Cardiologico Monzino IRCCS, Milano, Italy
| | - Emma Owens
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lucas Bronicki
- CHEO Research Institute, University of Ottawa, Ontario, Canada
| | - Olga Jarinova
- CHEO Research Institute, University of Ottawa, Ontario, Canada
- Department of Genetics, CHEO, Ontario, Canada
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital
- Department of Biomolecular Medicine, Ghent University
| | - Stacey Peters
- Department of Cardiology and Genomic Medicine, Royal Melbourne Hospital, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
| | - Tom Lumbers
- Barts Health & University College London Hospitals NHS Trusts, London, UK
- Institute of Health Informatics, University College London, London, UK
| | - Elizabeth Jordan
- Division of Human Genetics, The Ohio State University, Columbus, Ohio USA
| | - Babken Asatryan
- Department of Cardiology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Neesha Krishnan
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
| | - Ray E Hershberger
- Division of Human Genetics, The Ohio State University, Columbus, Ohio USA
| | - C Anwar A Chahal
- Center for Inherited Cardiovascular Diseases, WellSpan Health, Lancaster, PA USA
- Cardiac Electrophysiology and Inherited Cardiovascular Diseases, Cardiovascular Division, Hospital of the University of Pennsylvania, Philadelphia, PA USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN USA
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
| | - Andrew P Landstrom
- Department of Pediatrics and Cell Biology, Duke University School of Medicine, Durham, North Carolina, US
| | - Cynthia James
- Johns Hopkins Center for Inherited Heart Diseases, Department of Medicine, Johns Hopkins
| | - Elizabeth M McNally
- Center for Genetic Medicine, Dept of Medicine (Cardiology), Northwestern University Feinberg School of Medicine, Chicago, IL US
| | - Daniel P Judge
- Medical University of South Carolina, Charleston, SC USA
| | - Peter van Tintelen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Arthur Wilde
- Amsterdam UMC location University of Amsterdam, Department of Cardiology, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Cardiovascular Sciences, Heart Failure and arrhythmias, Amsterdam, the Netherlands
| | - Michael Gollob
- Inherited Arrhythmia and Cardiomyopathy Program, Division of Cardiology, University of Toronto, Toronto ON Canada
| | - Jodie Ingles
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London UK
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
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34
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Roberts AM, DiStefano MT, Riggs ER, Josephs KS, Alkuraya FS, Amberger J, Amin M, Berg JS, Cunningham F, Eilbeck K, Firth HV, Foreman J, Hamosh A, Hay E, Leigh S, Martin CL, McDonagh EM, Perrett D, Ramos EM, Robinson PN, Rath A, van Sant D, Stark Z, Whiffin N, Rehm HL, Ware JS. Towards robust clinical genome interpretation: developing a consistent terminology to characterize disease-gene relationships - allelic requirement, inheritance modes and disease mechanisms. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.30.23287948. [PMID: 37066232 PMCID: PMC10104222 DOI: 10.1101/2023.03.30.23287948] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
PURPOSE The terminology used for gene-disease curation and variant annotation to describe inheritance, allelic requirement, and both sequence and functional consequences of a variant is currently not standardized. There is considerable discrepancy in the literature and across clinical variant reporting in the derivation and application of terms. Here we standardize the terminology for the characterization of disease-gene relationships to facilitate harmonized global curation, and to support variant classification within the ACMG/AMP framework. METHODS Terminology for inheritance, allelic requirement, and both structural and functional consequences of a variant used by Gene Curation Coalition (GenCC) members and partner organizations was collated and reviewed. Harmonized terminology with definitions and use examples was created, reviewed, and validated. RESULTS We present a standardized terminology to describe gene-disease relationships, and to support variant annotation. We demonstrate application of the terminology for classification of variation in the ACMG SF 2.0 genes recommended for reporting of secondary findings. Consensus terms were agreed and formalized in both sequence ontology (SO) and human phenotype ontology (HPO) ontologies. GenCC member groups intend to use or map to these terms in their respective resources. CONCLUSION The terminology standardization presented here will improve harmonization, facilitate the pooling of curation datasets across international curation efforts and, in turn, improve consistency in variant classification and genetic test interpretation.
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Affiliation(s)
- Angharad M Roberts
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London, UK
- Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London. WC1N 3JH, UK
| | - Marina T DiStefano
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erin Rooney Riggs
- Geisinger Autism & Developmental Medicine Institute, Danville, PA, USA
| | - Katherine S Josephs
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London, UK
- Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia
| | - Joanna Amberger
- Online Mendelian Inheritance in Man (OMIM), Johns Hopkins University School of Medicine, USA
| | | | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill NC, 27599
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah
| | - Helen V Firth
- Dept of Medical Genetics, Cambridge University Hospitals, Cambridge CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Julia Foreman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Ada Hamosh
- Online Mendelian Inheritance in Man (OMIM), Johns Hopkins University School of Medicine, USA
| | - Eleanor Hay
- Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London. WC1N 3JH, UK
| | - Sarah Leigh
- Genomics England, Queen Mary University of London, Dawson Hall, London, EC1M 6BQ, UK
| | | | - Ellen M McDonagh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
- Open Targets, Cambridge, UK
| | - Daniel Perrett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington CT 06032, USA
| | - Ana Rath
- INSERM, US14-Orphanet, Paris, France
| | - David van Sant
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah
| | - Zornitza Stark
- Australian Genomics, Melbourne 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne 3052, Australia
- University of Melbourne, Melbourne 3052, Australia
| | - Nicola Whiffin
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Big Data Institute and Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - James S Ware
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London, UK
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
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35
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Homan CC, Scott HS, Brown AL. Hereditary platelet disorders associated with germ line variants in RUNX1, ETV6, and ANKRD26. Blood 2023; 141:1533-1543. [PMID: 36626254 PMCID: PMC10651873 DOI: 10.1182/blood.2022017735] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/22/2022] [Accepted: 12/24/2022] [Indexed: 01/11/2023] Open
Abstract
Hereditary platelet disorders (HPDs) are a group of blood disorders with variable severity and clinical impact. Although phenotypically there is much overlap, known genetic causes are many, prompting the curation of multigene panels for clinical use, which are being deployed in increasingly large-scale populations to uncover missing heritability more efficiently. For some of these disorders, in particular RUNX1, ETV6, and ANKRD26, pathogenic germ line variants in these genes also come with a risk of developing hematological malignancy (HM). Although they may initially present as similarly mild-moderate thrombocytopenia, each of these 3 disorders have distinct penetrance of HM and a different range of somatic alterations associated with malignancy development. As our ability to diagnose HPDs has improved, we are now faced with the challenges of integrating these advances into routine clinical practice for patients and how to optimize management and surveillance of patients and carriers who have not developed malignancy. The volume of genetic information now being generated has created new challenges in how to accurately assess and report identified variants. The answers to all these questions involve international initiatives on rare diseases to better understand the biology of these disorders and design appropriate models and therapies for preclinical testing and clinical trials. Partnered with this are continued technological developments, including the rapid sharing of genetic variant information and automated integration with variant classification relevant data, such as high-throughput functional data. Collective progress in this area will drive timely diagnosis and, in time, leukemia preventive therapeutic interventions.
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Affiliation(s)
- Claire C. Homan
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Hamish S. Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
- Australian Cancer Research Foundation (ACRF) Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Anna L. Brown
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
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36
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Stark Z, Boughtwood T, Haas M, Braithwaite J, Gaff CL, Goranitis I, Spurdle AB, Hansen DP, Hofmann O, Laing N, Metcalfe S, Newson AJ, Scott HS, Thorne N, Ward RL, Dinger ME, Best S, Long JC, Grimmond SM, Pearson J, Waddell N, Barnett CP, Cook M, Field M, Fielding D, Fox SB, Gecz J, Jaffe A, Leventer RJ, Lockhart PJ, Lunke S, Mallett AJ, McGaughran J, Mileshkin L, Nones K, Roscioli T, Scheffer IE, Semsarian C, Simons C, Thomas DM, Thorburn DR, Tothill R, White D, Dunwoodie S, Simpson PT, Phillips P, Brion MJ, Finlay K, Quinn MC, Mattiske T, Tudini E, Boggs K, Murray S, Wells K, Cannings J, Sinclair AH, Christodoulou J, North KN. Australian Genomics: Outcomes of a 5-year national program to accelerate the integration of genomics in healthcare. Am J Hum Genet 2023; 110:419-426. [PMID: 36868206 PMCID: PMC10027474 DOI: 10.1016/j.ajhg.2023.01.018] [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] [Received: 11/20/2022] [Accepted: 01/27/2023] [Indexed: 03/05/2023] Open
Abstract
Australian Genomics is a national collaborative partnership of more than 100 organizations piloting a whole-of-system approach to integrating genomics into healthcare, based on federation principles. In the first five years of operation, Australian Genomics has evaluated the outcomes of genomic testing in more than 5,200 individuals across 19 rare disease and cancer flagship studies. Comprehensive analyses of the health economic, policy, ethical, legal, implementation and workforce implications of incorporating genomics in the Australian context have informed evidence-based change in policy and practice, resulting in national government funding and equity of access for a range of genomic tests. Simultaneously, Australian Genomics has built national skills, infrastructure, policy, and data resources to enable effective data sharing to drive discovery research and support improvements in clinical genomic delivery.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia.
| | - Tiffany Boughtwood
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Childhood Dementia Initiative, Sydney, NSW, Australia
| | - Matilda Haas
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Jeffrey Braithwaite
- Centre for Healthcare Resilience and Implementation Science, Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia; International Society for Quality in Health Care, Dublin, Ireland
| | - Clara L Gaff
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Melbourne Genomics Health Alliance, Melbourne, VIC, Australia; Walter and Eliza Hall Institute, Melbourne, VIC, Australia
| | - Ilias Goranitis
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - David P Hansen
- Australian e-Health Research Centre, CSIRO Health and Biosecurity, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Oliver Hofmann
- University of Melbourne Centre for Cancer Research, Melbourne, VIC, Australia
| | - Nigel Laing
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | - Sylvia Metcalfe
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Ainsley J Newson
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; The University of Sydney, Faculty of Medicine and Health, Sydney School of Public Health, Sydney Health Ethics, Sydney, NSW, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Natalie Thorne
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Melbourne Genomics Health Alliance, Melbourne, VIC, Australia; Walter and Eliza Hall Institute, Melbourne, VIC, Australia
| | - Robyn L Ward
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Stephanie Best
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Centre for Healthcare Resilience and Implementation Science, Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia; Department of Health Services Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia
| | - Janet C Long
- Centre for Healthcare Resilience and Implementation Science, Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia
| | - Sean M Grimmond
- University of Melbourne Centre for Cancer Research, Melbourne, VIC, Australia
| | - John Pearson
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Nicola Waddell
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Christopher P Barnett
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, SA, Australia
| | - Matthew Cook
- Centre for Personalised Immunology, Australian National University, Canberra, ACT, Australia; Department of Medicine, University of Cambridge, Puddicombe Way, Cambridge, UK
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Newcastle, NSW, Australia
| | - David Fielding
- Department of Thoracic Medicine, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Stephen B Fox
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia; Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Adam Jaffe
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; Sydney Children's Hospital Network, Randwick, Sydney, NSW, Australia
| | - Richard J Leventer
- University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Neurology, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Paul J Lockhart
- University of Melbourne, Melbourne, VIC, Australia; Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Sebastian Lunke
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Andrew J Mallett
- KidGen Collaborative, Australian Genomics, Melbourne, VIC, Australia; Department of Renal Medicine, Townsville University Hospital, Townsville, QLD, Australia; College of Medicine and Dentistry, James Cook University, Townsville, QLD, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Julie McGaughran
- Genetic Health Queensland, Royal Brisbane & Women's Hospital, Brisbane, QLD, Australia; School of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Linda Mileshkin
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Katia Nones
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Tony Roscioli
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia; Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia; Neuroscience Research Australia (NeuRA) and Prince of Wales Clinical School, UNSW, Sydney, NSW, Australia
| | - Ingrid E Scheffer
- University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Neurology, Royal Children's Hospital, Melbourne, VIC, Australia; Department of Medicine, University of Melbourne, Austin Health, Melbourne, VIC, Australia; Florey Institute of Neuroscience and Mental Health, Melbourne, VIC, Australia
| | - Christopher Semsarian
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia; Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Cas Simons
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Centre for Population Genomics, Garvan Institute of Medical Research, and University of New South Wales, Sydney, NSW, Australia
| | - David M Thomas
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - David R Thorburn
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Richard Tothill
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia; Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Deborah White
- Blood Cancer Program, Precision Cancer Medicine Theme, The South Australian Medical Research Institute, Adelaide, SA, Australia; Faculty of Health and Medical Science, The University of Adelaide, Adelaide, SA, Australia
| | - Sally Dunwoodie
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | - Peter T Simpson
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Peta Phillips
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Marie-Jo Brion
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Keri Finlay
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Michael Cj Quinn
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; College of Medicine and Dentistry, James Cook University, Townsville, QLD, Australia
| | - Tessa Mattiske
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Emma Tudini
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Kirsten Boggs
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Sydney Children's Hospital Network, Randwick, Sydney, NSW, Australia; Sydney Children's Hospital Network, Westmead, NSW, Australia
| | - Sean Murray
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Mito Foundation, Sydney, NSW, Australia
| | - Kathy Wells
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Breast Cancer Network Australia, Melbourne, VIC, Australia
| | - John Cannings
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Thoracic Oncology Group of Australasia, Melbourne, VIC, Australia; ProCan, Children's Medical Research Institute, The University of Sydney, Sydney, NSW, Australia
| | - Andrew H Sinclair
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - John Christodoulou
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Kathryn N North
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia.
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Reactive gene curation to support interpretation and reporting of a clinical genome test for rare disease: Experience from over 1,000 cases. CELL GENOMICS 2023; 3:100258. [PMID: 36819666 PMCID: PMC9932986 DOI: 10.1016/j.xgen.2023.100258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/13/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023]
Abstract
Current standards in clinical genetics recognize the need to establish the validity of gene-disease relationships as a first step in the interpretation of sequence variants. We describe our experience incorporating the ClinGen Gene-Disease Clinical Validity framework in our interpretation and reporting workflow for a clinical genome sequencing (cGS) test for individuals with rare and undiagnosed genetic diseases. This "reactive" gene curation is completed upon identification of candidate variants during active case analysis and within the test turn-around time by focusing on the most impactful evidence and taking advantage of the broad applicability of the framework to cover a wide range of disease areas. We demonstrate that reactive gene curation can be successfully implemented in support of cGS in a clinical laboratory environment, enabling robust clinical decision making and allowing all variants to be fully and appropriately considered and their clinical significance confidently interpreted.
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38
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Hendriks WJAJ, van Cruchten RTP, Pulido R. Hereditable variants of classical protein tyrosine phosphatase genes: Will they prove innocent or guilty? Front Cell Dev Biol 2023; 10:1051311. [PMID: 36755664 PMCID: PMC9900141 DOI: 10.3389/fcell.2022.1051311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life-if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest 'guilt by association' for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.
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Affiliation(s)
- Wiljan J. A. J. Hendriks
- Department of Cell Biology, Radboud University Medical Centre, Nijmegen, The Netherlands,*Correspondence: Wiljan J. A. J. Hendriks,
| | | | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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39
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Ochoa D, Hercules A, Carmona M, Suveges D, Baker J, Malangone C, Lopez I, Miranda A, Cruz-Castillo C, Fumis L, Bernal-Llinares M, Tsukanov K, Cornu H, Tsirigos K, Razuvayevskaya O, Buniello A, Schwartzentruber J, Karim M, Ariano B, Martinez Osorio R, Ferrer J, Ge X, Machlitt-Northen S, Gonzalez-Uriarte A, Saha S, Tirunagari S, Mehta C, Roldán-Romero J, Horswell S, Young S, Ghoussaini M, Hulcoop D, Dunham I, McDonagh E. The next-generation Open Targets Platform: reimagined, redesigned, rebuilt. Nucleic Acids Res 2023; 51:D1353-D1359. [PMID: 36399499 PMCID: PMC9825572 DOI: 10.1093/nar/gkac1046] [Citation(s) in RCA: 81] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 11/19/2022] Open
Abstract
The Open Targets Platform (https://platform.opentargets.org/) is an open source resource to systematically assist drug target identification and prioritisation using publicly available data. Since our last update, we have reimagined, redesigned, and rebuilt the Platform in order to streamline data integration and harmonisation, expand the ways in which users can explore the data, and improve the user experience. The gene-disease causal evidence has been enhanced and expanded to better capture disease causality across rare, common, and somatic diseases. For target and drug annotations, we have incorporated new features that help assess target safety and tractability, including genetic constraint, PROTACtability assessments, and AlphaFold structure predictions. We have also introduced new machine learning applications for knowledge extraction from the published literature, clinical trial information, and drug labels. The new technologies and frameworks introduced since the last update will ease the introduction of new features and the creation of separate instances of the Platform adapted to user requirements. Our new Community forum, expanded training materials, and outreach programme support our users in a range of use cases.
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Affiliation(s)
- David Ochoa
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Andrew Hercules
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Miguel Carmona
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Daniel Suveges
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jarrod Baker
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Cinzia Malangone
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Irene Lopez
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Alfredo Miranda
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Carlos Cruz-Castillo
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Luca Fumis
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Manuel Bernal-Llinares
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Kirill Tsukanov
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Helena Cornu
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Konstantinos Tsirigos
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Olesya Razuvayevskaya
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Annalisa Buniello
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jeremy Schwartzentruber
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Mohd Karim
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Bruno Ariano
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Ricardo Esteban Martinez Osorio
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Javier Ferrer
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Xiangyu Ge
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Sandra Machlitt-Northen
- GlaxoSmithKline plc, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Asier Gonzalez-Uriarte
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Shyamasree Saha
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Santosh Tirunagari
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Chintan Mehta
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Juan María Roldán-Romero
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Stuart Horswell
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Sarah Young
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Maya Ghoussaini
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - David G Hulcoop
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- GlaxoSmithKline plc, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Ian Dunham
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Ellen M McDonagh
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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40
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David KL, Deignan JL. Moving toward more consistency in variant classification and clinical action. Genet Med 2023; 25:12-15. [PMID: 36399133 DOI: 10.1016/j.gim.2022.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/19/2022] Open
Affiliation(s)
- Karen L David
- Department of Medicine, NewYork-Presbyterian Brooklyn Methodist Hospital, Brooklyn, NY.
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA
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41
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Genome screening, reporting, and genetic counseling for healthy populations. Hum Genet 2023; 142:181-192. [PMID: 36331656 PMCID: PMC9638226 DOI: 10.1007/s00439-022-02480-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/16/2022] [Indexed: 11/06/2022]
Abstract
Rapid advancements of genome sequencing (GS) technologies have enhanced our understanding of the relationship between genes and human disease. To incorporate genomic information into the practice of medicine, new processes for the analysis, reporting, and communication of GS data are needed. Blood samples were collected from adults with a PCR-confirmed SARS-CoV-2 (COVID-19) diagnosis (target N = 1500). GS was performed. Data were filtered and analyzed using custom pipelines and gene panels. We developed unique patient-facing materials, including an online intake survey, group counseling presentation, and consultation letters in addition to a comprehensive GS report. The final report includes results generated from GS data: (1) monogenic disease risks; (2) carrier status; (3) pharmacogenomic variants; (4) polygenic risk scores for common conditions; (5) HLA genotype; (6) genetic ancestry; (7) blood group; and, (8) COVID-19 viral lineage. Participants complete pre-test genetic counseling and confirm preferences for secondary findings before receiving results. Counseling and referrals are initiated for clinically significant findings. We developed a genetic counseling, reporting, and return of results framework that integrates GS information across multiple areas of human health, presenting possibilities for the clinical application of comprehensive GS data in healthy individuals.
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42
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Data-driven historical characterization of epilepsy-associated genes. Eur J Paediatr Neurol 2023; 42:82-87. [PMID: 36586220 DOI: 10.1016/j.ejpn.2022.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Many epilepsy-associated genes have been identified over the last three decades, revealing a remarkable molecular heterogeneity with the shared outcome of recurrent seizures. Information about the genetic landscape of epilepsies is scattered throughout the literature and answering the simple question of how many genes are associated with epilepsy is not straightforward. Here, we present a computationally driven analytical review of epilepsy-associated genes using the complete scientific literature in PubMed. Based on our search criteria, we identified a total of 738 epilepsy-associated genes. We further classified these genes into two Tiers. A broad gene list of 738 epilepsy-associated genes (Tier 2) and a narrow gene list composed of 143 epilepsy-associated genes (Tier 1). Our search criteria do not reflect the degree of association. The average yearly number of identified epilepsy-associated genes between 1992 and 2021 was 4.8. However, most of these genes were only identified in the last decade (2010-2019). Ion channels represent the largest class of epilepsy-associated genes. For many of these, both gain- and loss-of-function effects have been associated with epilepsy in recent years. We identify 28 genes frequently reported with heterogenous variant effects which should be considered for variant interpretation. Overall, our study provides an updated and manually curated list of epilepsy-related genes together with additional annotations and classifications reflecting the current genetic landscape of epilepsy.
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43
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Dyskeratosis congenita and telomere biology disorders. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2022; 2022:637-648. [PMID: 36485133 PMCID: PMC9821046 DOI: 10.1182/hematology.2022000394] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Numerous genetic discoveries and the advent of clinical telomere length testing have led to the recognition of a spectrum of telomere biology disorders (TBDs) beyond the classic dyskeratosis congenita (DC) triad of nail dysplasia, abnormal skin pigmentation, and oral leukoplakia occurring with pediatric bone marrow failure. Patients with DC/TBDs have very short telomeres for their age and are at high risk of bone marrow failure, cancer, pulmonary fibrosis (PF), pulmonary arteriovenous malformations, liver disease, stenosis of the urethra, esophagus, and/or lacrimal ducts, avascular necrosis of the hips and/or shoulders, and other medical problems. However, many patients with TBDs do not develop classic DC features; they may present in middle age and/or with just 1 feature, such as PF or aplastic anemia. TBD-associated clinical manifestations are progressive and attributed to aberrant telomere biology caused by the X-linked recessive, autosomal dominant, autosomal recessive, or de novo occurrence of pathogenic germline variants in at least 18 different genes. This review describes the genetics and clinical manifestations of TBDs and highlights areas in need of additional clinical and basic science research.
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44
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Nassar LR, Barber GP, Benet-Pagès A, Casper J, Clawson H, Diekhans M, Fischer C, Gonzalez JN, Hinrichs A, Lee B, Lee C, Muthuraman P, Nguy B, Pereira T, Nejad P, Perez G, Raney B, Schmelter D, Speir M, Wick B, Zweig A, Haussler D, Kuhn R, Haeussler M, Kent W. The UCSC Genome Browser database: 2023 update. Nucleic Acids Res 2022; 51:D1188-D1195. [PMID: 36420891 PMCID: PMC9825520 DOI: 10.1093/nar/gkac1072] [Citation(s) in RCA: 137] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/14/2022] [Accepted: 10/25/2022] [Indexed: 11/26/2022] Open
Abstract
The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve the community as it enters its 23rd year. This year has seen an emphasis in clinical data, with new tracks and an expanded Recommended Track Sets feature on hg38 as well as the addition of a single cell track group. SARS-CoV-2 continues to remain a focus, with regular annotation updates to the browser and continued curation of our phylogenetic sequence placing tool, hgPhyloPlace, whose tree has now reached over 12M sequences. Our GenArk resource has also grown, offering over 2500 hubs and a system for users to request any absent assemblies. We have expanded our bigBarChart display type and created new ways to visualize data via bigRmsk and dynseq display. Displaying custom annotations is now easier due to our chromAlias system which eliminates the requirement for renaming sequence names to the UCSC standard. Users involved in data generation may also be interested in our new tools and trackDb settings which facilitate the creation and display of their custom annotations.
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Affiliation(s)
- Luis R Nassar
- To whom correspondence should be addressed. Tel: +1 305 205 9160;
| | - Galt P Barber
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Anna Benet-Pagès
- Institute of Neurogenomics, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, 85764Neuherberg, Germany,Medical Genetics Center (Medizinisch Genetisches Zentrum), Munich 80335, Germany
| | - Jonathan Casper
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Hiram Clawson
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mark Diekhans
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Clay Fischer
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Angie S Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brian T Lee
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Christopher M Lee
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Pranav Muthuraman
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Beagan Nguy
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tiana Pereira
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Parisa Nejad
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Gerardo Perez
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brian J Raney
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Daniel Schmelter
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Matthew L Speir
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brittney D Wick
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ann S Zweig
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Haussler
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Robert M Kuhn
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Maximilian Haeussler
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - W James Kent
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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45
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Tudini E, Andrews J, Lawrence DM, King-Smith SL, Baker N, Baxter L, Beilby J, Bennetts B, Beshay V, Black M, Boughtwood TF, Brion K, Cheong PL, Christie M, Christodoulou J, Chong B, Cox K, Davis MR, Dejong L, Dinger ME, Doig KD, Douglas E, Dubowsky A, Ellul M, Fellowes A, Fisk K, Fortuno C, Friend K, Gallagher RL, Gao S, Hackett E, Hadler J, Hipwell M, Ho G, Hollway G, Hooper AJ, Kassahn KS, Krishnaraj R, Lau C, Le H, San Leong H, Lundie B, Lunke S, Marty A, McPhillips M, Nguyen LT, Nones K, Palmer K, Pearson JV, Quinn MC, Rawlings LH, Sadedin S, Sanchez L, Schreiber AW, Sigalas E, Simsek A, Soubrier J, Stark Z, Thompson BA, U J, Vakulin CG, Wells AV, Wise CA, Woods R, Ziolkowski A, Brion MJ, Scott HS, Thorne NP, Spurdle AB. Shariant platform: Enabling evidence sharing across Australian clinical genetic-testing laboratories to support variant interpretation. Am J Hum Genet 2022; 109:1960-1973. [PMID: 36332611 PMCID: PMC9674965 DOI: 10.1016/j.ajhg.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Sharing genomic variant interpretations across laboratories promotes consistency in variant assertions. A landscape analysis of Australian clinical genetic-testing laboratories in 2017 identified that, despite the national-accreditation-body recommendations encouraging laboratories to submit genotypic data to clinical databases, fewer than 300 variants had been shared to the ClinVar public database. Consultations with Australian laboratories identified resource constraints limiting routine application of manual processes, consent issues, and differences in interpretation systems as barriers to sharing. This information was used to define key needs and solutions required to enable national sharing of variant interpretations. The Shariant platform, using both the GRCh37 and GRCh38 genome builds, was developed to enable ongoing sharing of variant interpretations and associated evidence between Australian clinical genetic-testing laboratories. Where possible, two-way automated sharing was implemented so that disruption to laboratory workflows would be minimized. Terms of use were developed through consultation and currently restrict access to Australian clinical genetic-testing laboratories. Shariant was designed to store and compare structured evidence, to promote and record resolution of inter-laboratory classification discrepancies, and to streamline the submission of variant assertions to ClinVar. As of December 2021, more than 14,000 largely prospectively curated variant records from 11 participating laboratories have been shared. Discrepant classifications have been identified for 11% (28/260) of variants submitted by more than one laboratory. We have demonstrated that co-design with clinical laboratories is vital to developing and implementing a national variant-interpretation sharing effort. This approach has improved inter-laboratory concordance and enabled opportunities to standardize interpretation practices.
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Affiliation(s)
- Emma Tudini
- Australian Genomics, Melbourne, VIC 3052, Australia,Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - James Andrews
- Australian Genomics, Melbourne, VIC 3052, Australia,Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - David M. Lawrence
- Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Sarah L. King-Smith
- Australian Genomics, Melbourne, VIC 3052, Australia,Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Naomi Baker
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia
| | | | - John Beilby
- PathWest Laboratory Medicine Western Australia, Perth, WA 6009, Australia,School of Biomedical Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Bruce Bennetts
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia,Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW 2145, Australia
| | - Victoria Beshay
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Michael Black
- Department of Diagnostic Genomics, PathWest Laboratory Medicine Western Australia, Perth, WA 6009, Australia
| | - Tiffany F. Boughtwood
- Australian Genomics, Melbourne, VIC 3052, Australia,Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | | | - Pak Leng Cheong
- Department of Medical Genomics, Royal Prince Alfred Hospital, NSW Health Pathology, Sydney, NSW 2050, Australia,University of Sydney, Sydney, NSW 2006, Australia
| | - Michael Christie
- Department of Pathology, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - John Christodoulou
- Australian Genomics, Melbourne, VIC 3052, Australia,Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW 2145, Australia,Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Kathy Cox
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Mark R. Davis
- Department of Diagnostic Genomics, PathWest Laboratory Medicine Western Australia, Perth, WA 6009, Australia,Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia
| | - Lucas Dejong
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Marcel E. Dinger
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Kenneth D. Doig
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Evelyn Douglas
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Andrew Dubowsky
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Melissa Ellul
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Andrew Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Katrina Fisk
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Cristina Fortuno
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kathryn Friend
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | | | - Song Gao
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Emma Hackett
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Johanna Hadler
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Michael Hipwell
- Division of Molecular Medicine, NSW Health Pathology North, Newcastle, NSW 2305, Australia
| | - Gladys Ho
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia,Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW 2145, Australia
| | - Georgina Hollway
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia,Cancer Research, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Amanda J. Hooper
- Department of Clinical Biochemistry, PathWest Laboratory Medicine Western Australia, Fiona Stanley Hospital Network, Perth, WA 6150, Australia,School of Medicine, The University of Western Australia, Perth, WA 6009, Australia
| | - Karin S. Kassahn
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia,Adelaide Medical School, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Rahul Krishnaraj
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Chiyan Lau
- Pathology Queensland, Brisbane, QLD 4006, Australia,The University of Queensland, Brisbane, QLD 4072, Australia
| | - Huong Le
- Department of Medical Genomics, Royal Prince Alfred Hospital, NSW Health Pathology, Sydney, NSW 2050, Australia
| | - Huei San Leong
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Ben Lundie
- Pathology Queensland, Brisbane, QLD 4006, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia
| | - Anthony Marty
- Melbourne Genomics Health Alliance, Melbourne, VIC 3052, Australia
| | - Mary McPhillips
- Division of Molecular Medicine, NSW Health Pathology North, Newcastle, NSW 2305, Australia
| | - Lan T. Nguyen
- Department of Clinical Biochemistry, PathWest Laboratory Medicine Western Australia, Fiona Stanley Hospital Network, Perth, WA 6150, Australia
| | - Katia Nones
- Cancer Research, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kristen Palmer
- Genomics Statewide Services, New South Wales Health Pathology, Newcastle, NSW 2300, Australia
| | - John V. Pearson
- Genome Informatics, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Michael C.J. Quinn
- Australian Genomics, Melbourne, VIC 3052, Australia,Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4006, Australia
| | - Lesley H. Rawlings
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Simon Sadedin
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia,Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Louisa Sanchez
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Andreas W. Schreiber
- Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia,School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Emanouil Sigalas
- Department of Pathology, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - Aygul Simsek
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Julien Soubrier
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia,School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Zornitza Stark
- Australian Genomics, Melbourne, VIC 3052, Australia,Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia
| | - Bryony A. Thompson
- Department of Pathology, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - James U
- Melbourne Genomics Health Alliance, Melbourne, VIC 3052, Australia
| | | | - Amanda V. Wells
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Cheryl A. Wise
- Department of Diagnostic Genomics, PathWest Laboratory Medicine Western Australia, Perth, WA 6009, Australia
| | - Rick Woods
- Pathology Queensland, Brisbane, QLD 4006, Australia
| | - Andrew Ziolkowski
- Division of Molecular Medicine, NSW Health Pathology North, Newcastle, NSW 2305, Australia
| | - Marie-Jo Brion
- Australian Genomics, Melbourne, VIC 3052, Australia,Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Hamish S. Scott
- Australian Genomics, Melbourne, VIC 3052, Australia,Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia,Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia,Adelaide Medical School, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Natalie P. Thorne
- Australian Genomics, Melbourne, VIC 3052, Australia,University of Melbourne, Melbourne, VIC 3052, Australia,Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia,Melbourne Genomics Health Alliance, Melbourne, VIC 3052, Australia,Walter and Eliza Hall Institute, Melbourne, VIC 3052, Australia
| | - Amanda B. Spurdle
- Australian Genomics, Melbourne, VIC 3052, Australia,Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia,Corresponding author
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46
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Which patients with CKD will benefit from genomic sequencing? Synthesizing progress to illuminate the future. Curr Opin Nephrol Hypertens 2022; 31:541-547. [PMID: 36093902 PMCID: PMC9594128 DOI: 10.1097/mnh.0000000000000836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
PURPOSE OF REVIEW This review will summarize and synthesize recent findings in regard to monogenic kidney disorders, including how that evidence is being translated into practice. It will add to existing key knowledge to provide context for clinicians in consolidating existing practice and approaches. RECENT FINDINGS Whilst there are long established factors, which indicate increased likelihood of identifying a monogenic cause for kidney disease, these can now be framed in terms of the identification of new genes, new indications for genomic testing and new evidence for clinical utility of genomic testing in nephrology. Further, inherent in the use of genomics in nephrology are key concepts including robust informed consent, variant interpretation and return of results. Recent findings of variants in genes related to complex or broader kidney phenotypes are emerging in addition to understanding of de novo variants. Phenocopy phenomena are indicating a more pragmatic use of broader gene panels whilst evidence is emerging of a role in unexplained kidney disease. Clinical utility is evolving but is being successfully demonstrated across multiple domains of outcome and practice. SUMMARY We provide an updated framework of evidence to guide application of genomic testing in chronic kidney disease (CKD), building upon existing principles and knowledge to indicate how the practice and implementation of this can be applied today. There are clearly established roles for genomic testing for some patients with CKD, largely those with suspected heritable forms, with these continuing to expand as new evidence emerges.
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Wang Y, Ling Y, Gong J, Zhao X, Zhou H, Xie B, Lou H, Zhuang X, Jin L, Fan S, Zhang G, Xu S. PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform. Nucleic Acids Res 2022; 51:D1109-D1116. [PMID: 36243989 PMCID: PMC9825616 DOI: 10.1093/nar/gkac905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/21/2022] [Accepted: 10/04/2022] [Indexed: 01/30/2023] Open
Abstract
Structural variations (SVs) play important roles in human evolution and diseases, but there is a lack of data resources concerning representative samples, especially for East Asians. Taking advantage of both next-generation sequencing and third-generation sequencing data at the whole-genome level, we developed the database PGG.SV to provide a practical platform for both regionally and globally representative structural variants. In its current version, PGG.SV archives 584 277 SVs obtained from whole-genome sequencing data of 6048 samples, including 1030 long-read sequencing genomes representing 177 global populations. PGG.SV provides (i) high-quality SVs with fine-scale and precise genomic locations in both GRCh37 and GRCh38, covering underrepresented SVs in existing sequencing and microarray data; (ii) hierarchical estimation of SV prevalence in geographical populations; (iii) informative annotations of SV-related genes, potential functions and clinical effects; (iv) an analysis platform to facilitate SV-based case-control association studies and (v) various visualization tools for understanding the SV structures in the human genome. Taken together, PGG.SV provides a user-friendly online interface, easy-to-use analysis tools and a detailed presentation of results. PGG.SV is freely accessible via https://www.biosino.org/pggsv.
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Affiliation(s)
| | | | | | - Xiaohan Zhao
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China,Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | - Hanwen Zhou
- Key Laboratory of Computational Biology, National Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bo Xie
- Key Laboratory of Computational Biology, National Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Haiyi Lou
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xinhao Zhuang
- Key Laboratory of Computational Biology, National Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China,Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | | | - Shaohua Fan
- Correspondence may also be addressed to Shaohua Fan.
| | - Guoqing Zhang
- Correspondence may also be addressed to Guoqing Zhang.
| | - Shuhua Xu
- To whom correspondence should be addressed. Tel: +86 21 31246617; Fax: +86 21 31246617;
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48
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Seal RL, Braschi B, Gray K, Jones TEM, Tweedie S, Haim-Vilmovsky L, Bruford EA. Genenames.org: the HGNC resources in 2023. Nucleic Acids Res 2022; 51:D1003-D1009. [PMID: 36243972 PMCID: PMC9825485 DOI: 10.1093/nar/gkac888] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 01/30/2023] Open
Abstract
The HUGO Gene Nomenclature Committee (HGNC) assigns unique symbols and names to human genes. The HGNC database (www.genenames.org) currently contains over 43 000 approved gene symbols, over 19 200 of which are assigned to protein-coding genes, 14 000 to pseudogenes and nearly 9000 to non-coding RNA genes. The public website, www.genenames.org, displays all approved nomenclature within Symbol Reports that contain data curated by HGNC nomenclature advisors and links to related genomic, clinical, and proteomic information. Here, we describe updates to our resource, including improvements to our search facility and new download features.
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Affiliation(s)
- Ruth L Seal
- To whom correspondence should be addressed. Tel: +44 1223 494444; Fax: +44 1223 494446;
| | - Bryony Braschi
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Kristian Gray
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK,Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge CB2 0PT, UK
| | - Tamsin E M Jones
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Susan Tweedie
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Liora Haim-Vilmovsky
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Elspeth A Bruford
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK,Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge CB2 0PT, UK
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49
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Frangione E, Chung M, Casalino S, MacDonald G, Chowdhary S, Mighton C, Faghfoury H, Bombard Y, Strug L, Pugh T, Simpson J, Hao L, Lebo M, Lane WJ, Taher J, Lerner‐Ellis J. Genome Reporting for Healthy Populations-Pipeline for Genomic Screening from the GENCOV COVID-19 Study. Curr Protoc 2022; 2:e534. [PMID: 36205462 PMCID: PMC9874607 DOI: 10.1002/cpz1.534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Genome sequencing holds the promise for great public health benefits. It is currently being used in the context of rare disease diagnosis and novel gene identification, but also has the potential to identify genetic disease risk factors in healthy individuals. Genome sequencing technologies are currently being used to identify genetic factors that may influence variability in symptom severity and immune response among patients infected by SARS-CoV-2. The GENCOV study aims to look at the relationship between genetic, serological, and biochemical factors and variability of SARS-CoV-2 symptom severity, and to evaluate the utility of returning genome screening results to study participants. Study participants select which results they wish to receive with a decision aid. Medically actionable information for diagnosis, disease risk estimation, disease prevention, and patient management are provided in a comprehensive genome report. Using a combination of bioinformatics software and custom tools, this article describes a pipeline for the analysis and reporting of genetic results to individuals with COVID-19, including HLA genotyping, large-scale continental ancestry estimation, and pharmacogenomic analysis to determine metabolizer status and drug response. In addition, this pipeline includes reporting of medically actionable conditions from comprehensive gene panels for Cardiology, Neurology, Metabolism, Hereditary Cancer, and Hereditary Kidney, and carrier screening for reproductive planning. Incorporated into the genome report are polygenic risk scores for six diseases-coronary artery disease; atrial fibrillation; type-2 diabetes; and breast, prostate, and colon cancer-as well as blood group genotyping analysis for ABO and Rh blood types and genotyping for other antigens of clinical relevance. The genome report summarizes the findings of these analyses in a way that extensively communicates clinically relevant results to patients and their physicians. © 2022 Wiley Periodicals LLC. Basic Protocol 1: HLA genotyping and disease association Basic Protocol 2: Large-scale continental ancestry estimation Basic Protocol 3: Dosage recommendations for pharmacogenomic gene variants associated with drug response Support Protocol: System setup.
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Affiliation(s)
- Erika Frangione
- Mount Sinai HospitalSinai HealthTorontoOntarioCanada,Lunenfeld‐Tanenbaum Research InstituteSinai HealthTorontoOntarioCanada
| | - Monica Chung
- Mount Sinai HospitalSinai HealthTorontoOntarioCanada,Lunenfeld‐Tanenbaum Research InstituteSinai HealthTorontoOntarioCanada
| | - Selina Casalino
- Mount Sinai HospitalSinai HealthTorontoOntarioCanada,Lunenfeld‐Tanenbaum Research InstituteSinai HealthTorontoOntarioCanada
| | - Georgia MacDonald
- Mount Sinai HospitalSinai HealthTorontoOntarioCanada,Lunenfeld‐Tanenbaum Research InstituteSinai HealthTorontoOntarioCanada
| | - Sunakshi Chowdhary
- Mount Sinai HospitalSinai HealthTorontoOntarioCanada,Lunenfeld‐Tanenbaum Research InstituteSinai HealthTorontoOntarioCanada
| | - Chloe Mighton
- Mount Sinai HospitalSinai HealthTorontoOntarioCanada,Lunenfeld‐Tanenbaum Research InstituteSinai HealthTorontoOntarioCanada,University of TorontoTorontoOntarioCanada,Unity Health TorontoTorontoOntarioCanada
| | | | - Yvonne Bombard
- University of TorontoTorontoOntarioCanada,Unity Health TorontoTorontoOntarioCanada
| | - Lisa Strug
- The Hospital for Sick ChildrenTorontoOntarioCanada
| | - Trevor Pugh
- University Health NetworkTorontoOntarioCanada,Ontario Institute for Cancer ResearchTorontoOntarioCanada
| | - Jared Simpson
- Ontario Institute for Cancer ResearchTorontoOntarioCanada
| | - Limin Hao
- Laboratory of Molecular MedicinePartners Personalized MedicineBostonMassachusetts
| | - Matthew Lebo
- Laboratory of Molecular MedicinePartners Personalized MedicineBostonMassachusetts,Harvard Medical School & Brigham and Women's HospitalBostonMassachusetts
| | - William J. Lane
- Harvard Medical School & Brigham and Women's HospitalBostonMassachusetts
| | - Jennifer Taher
- Mount Sinai HospitalSinai HealthTorontoOntarioCanada,University of TorontoTorontoOntarioCanada
| | - Jordan Lerner‐Ellis
- Mount Sinai HospitalSinai HealthTorontoOntarioCanada,Lunenfeld‐Tanenbaum Research InstituteSinai HealthTorontoOntarioCanada,University of TorontoTorontoOntarioCanada
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50
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Krey I, Platzer K, Esterhuizen A, Berkovic SF, Helbig I, Hildebrand MS, Lerche H, Lowenstein D, Møller RS, Poduri A, Sadleir L, Sisodiya SM, Weckhuysen S, Wilmshurst JM, Weber Y, Lemke JR. Current practice in diagnostic genetic testing of the epilepsies. Epileptic Disord 2022; 24:765-786. [PMID: 35830287 PMCID: PMC10752379 DOI: 10.1684/epd.2022.1448] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/10/2022] [Indexed: 01/19/2023]
Abstract
Epilepsy genetics is a rapidly developing field, in which novel disease-associated genes, novel mechanisms associated with epilepsy, and precision medicine approaches are continuously being identified. In the past decade, advances in genomic knowledge and analysis platforms have begun to make clinical genetic testing accessible for, in principle, people of all ages with epilepsy. For this reason, the Genetics Commission of the International League Against Epilepsy (ILAE) presents this update on clinical genetic testing practice, including current techniques, indications, yield of genetic testing, recommendations for pre- and post-test counseling, and follow-up after genetic testing is completed. We acknowledge that the resources vary across different settings but highlight that genetic diagnostic testing for epilepsy should be prioritized when the likelihood of an informative finding is high. Results of genetic testing, in particular the identification of causative genetic variants, are likely to improve individual care. We emphasize the importance of genetic testing for individuals with epilepsy as we enter the era of precision therapy.
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Affiliation(s)
- Ilona Krey
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Alina Esterhuizen
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| | - Samuel F. Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne (Austin Health), Heidelberg, VIC, Australia
| | - Ingo Helbig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian-Albrechts-University, Building C, Arnold-Heller-Straße 3, 24105 Kiel, Germany
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 USA
- Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104 USA
| | - Michael S. Hildebrand
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg and Murdoch Children’s Research Institute, Royal Children’s Hospital, Victoria, Australia
| | - Holger Lerche
- Department of Epileptology and Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Germany
| | - Daniel Lowenstein
- Department of Neurology, University of California, San Francisco, USA
| | - Rikke S. Møller
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Annapurna Poduri
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lynette Sadleir
- Department of Paediatrics and Child Health, University of Otago, Wellington, New Zealand
| | - Sanjay M. Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology London, UK and Chalfont Centre for Epilepsy, Buckinghamshire, UK
| | - Sarah Weckhuysen
- Center for Molecular Neurology, VIB-University of Antwerp, VIB, Antwerp, Belgium; Department of Neurology, University Hospital Antwerp, Antwerp, Belgium
| | - Jo M. Wilmshurst
- Department of Paediatric Neurology, Paediatric and Child Health, Red Cross War Memorial Children’s Hospital, Neuroscience Institute, University of Cape Town, South Africa
| | - Yvonne Weber
- Department of Epileptology and Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Germany
- Department of Epileptology and Neurology, University of Aachen, Germany
| | - Johannes R. Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig, Germany
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