1
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Sullivan PJ, Quinn JMW, Wu W, Pinese M, Cowley MJ. SpliceVarDB: A comprehensive database of experimentally validated human splicing variants. Am J Hum Genet 2024; 111:2164-2175. [PMID: 39226898 PMCID: PMC11480807 DOI: 10.1016/j.ajhg.2024.08.002] [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: 10/09/2023] [Revised: 08/03/2024] [Accepted: 08/06/2024] [Indexed: 09/05/2024] Open
Abstract
Variants that alter gene splicing are estimated to comprise up to a third of all disease-causing variants, yet they are hard to predict from DNA sequencing data alone. To overcome this, many groups are incorporating RNA-based analyses, which are resource intensive, particularly for diagnostic laboratories. There are thousands of functionally validated variants that induce mis-splicing; however, this information is not consolidated, and they are under-represented in ClinVar, which presents a barrier to variant interpretation and can result in duplication of validation efforts. To address this issue, we developed SpliceVarDB, an online database consolidating over 50,000 variants assayed for their effects on splicing in over 8,000 human genes. We evaluated over 500 published data sources and established a spliceogenicity scale to standardize, harmonize, and consolidate variant validation data generated by a range of experimental protocols. According to the strength of their supporting evidence, variants were classified as "splice-altering" (∼25%), "not splice-altering" (∼25%), and "low-frequency splice-altering" (∼50%), which correspond to weak or indeterminate evidence of spliceogenicity. Importantly, 55% of the splice-altering variants in SpliceVarDB are outside the canonical splice sites (5.6% are deep intronic). These variants can support the variant curation diagnostic pathway and can be used to provide the high-quality data necessary to develop more accurate in silico splicing predictors. The variants are accessible through an online platform, SpliceVarDB, with additional features for visualization, variant information, in silico predictions, and validation metrics. SpliceVarDB is a very large collection of splice-altering variants and is available at https://splicevardb.org.
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Affiliation(s)
- Patricia J Sullivan
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia; UNSW Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Julian M W Quinn
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Weilin Wu
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Mark Pinese
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia.
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2
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Kwon S, Safer J, Nguyen DT, Hoksza D, May P, Arbesfeld JA, Rubin AF, Campbell AJ, Burgin A, Iqbal S. Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures. Nat Methods 2024; 21:1947-1957. [PMID: 39294369 PMCID: PMC11466821 DOI: 10.1038/s41592-024-02409-0] [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: 01/03/2024] [Accepted: 08/09/2024] [Indexed: 09/20/2024]
Abstract
Recent advances in AI-based methods have revolutionized the field of structural biology. Concomitantly, high-throughput sequencing and functional genomics have generated genetic variants at an unprecedented scale. However, efficient tools and resources are needed to link disparate data types-to 'map' variants onto protein structures, to better understand how the variation causes disease, and thereby design therapeutics. Here we present the Genomics 2 Proteins portal ( https://g2p.broadinstitute.org/ ): a human proteome-wide resource that maps 20,076,998 genetic variants onto 42,413 protein sequences and 77,923 structures, with a comprehensive set of structural and functional features. Additionally, the Genomics 2 Proteins portal allows users to interactively upload protein residue-wise annotations (for example, variants and scores) as well as the protein structure beyond databases to establish the connection between genomics to proteins. The portal serves as an easy-to-use discovery tool for researchers and scientists to hypothesize the structure-function relationship between natural or synthetic variations and their molecular phenotypes.
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Affiliation(s)
- Seulki Kwon
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jordan Safer
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Duyen T Nguyen
- PATTERN, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Hoksza
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jeremy A Arbesfeld
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Alan F Rubin
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Arthur J Campbell
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alex Burgin
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sumaiya Iqbal
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Cancer Data Sciences, Dana-Farber/Harvard Cancer Center, Boston, MA, USA.
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3
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Ridsdale AM, Dickerson A, Chundru VK, Firth HV, Wright CF. Phenotypic spectrum of dual diagnoses in developmental disorders. Am J Hum Genet 2024:S0002-9297(24)00335-5. [PMID: 39353430 DOI: 10.1016/j.ajhg.2024.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 08/30/2024] [Accepted: 08/30/2024] [Indexed: 10/04/2024] Open
Abstract
As more patients receive genome-wide sequencing, the number of individuals diagnosed with multiple monogenic conditions is increasing. We sought to investigate the relative phenotypic contribution of dual diagnoses using both manual curation and computational approaches. First, we computed 1,003,236 semantic similarity scores for all possible pairs of 1,417 genes in the Developmental Disorder Gene2Phenotype (DDG2P) database using Human Phenotype Ontology terms. Next, for 62 probands with two molecular diagnoses in the Deciphering Developmental Disorders study, we computed semantic similarity scores between the probands' phenotypes and DDG2P phenotypes associated with the two disorders and compared the results with manual attribution of proband phenotypes to none, one, or both of the genes. We found a spectrum of phenotypic similarity for dual diagnoses, both across all DDG2P genes and within dual diagnosed probands, from phenotypically distinct through blended to indistinguishable conditions. Pairwise semantic similarity scores between two DDG2P genes were a good predictor of the extent of phenotypic blending observed in probands. Dual diagnoses involving genes linked with synergistic phenotypes can result in more extreme presentations while those involving antagonistic phenotypes have spuriously high pairwise semantic similarity scores despite a potentially milder atypical presentation. We suggest that the phenotypic contribution of two molecular diagnoses may contain discrete, synergistic, or antagonistic elements. Conceptual recognition of this phenotypic spectrum is important for making a final clinico-molecular diagnosis and providing accurate genetic counseling.
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Affiliation(s)
- Alys M Ridsdale
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, St Luke's Campus, Magdalen Road, Exeter EX1 2LU, UK
| | - Anna Dickerson
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, St Luke's Campus, Magdalen Road, Exeter EX1 2LU, UK
| | - V Kartik Chundru
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, St Luke's Campus, Magdalen Road, Exeter EX1 2LU, UK
| | - Helen V Firth
- East Anglian Medical Genetics Service, Clinical Genetics, Box 134, Addenbrooke's Treatment Centre, Level 6, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Saffron Walden CB10 1RQ, UK
| | - Caroline F Wright
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, St Luke's Campus, Magdalen Road, Exeter EX1 2LU, UK.
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4
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Abbott M, Ryan M, Hernández R, McKenzie L, Heidenreich S, Hocking L, Clark C, Ansari M, Moore D, Lampe A, McGowan R, Berg J, Miedzybrodzka Z. Should Scotland provide genome-wide sequencing for the diagnosis of rare developmental disorders? A cost-effectiveness analysis. THE EUROPEAN JOURNAL OF HEALTH ECONOMICS : HEPAC : HEALTH ECONOMICS IN PREVENTION AND CARE 2024:10.1007/s10198-024-01717-8. [PMID: 39249625 DOI: 10.1007/s10198-024-01717-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 08/07/2024] [Indexed: 09/10/2024]
Abstract
AIMS This study aims to evaluate the cost effectiveness of genetic and genomic testing strategies for the diagnosis of rare developmental disorders in NHS Scotland. METHODS Six genetic and genomic testing strategies were evaluated using a decision tree model. First-line, second-line and last-resort trio genome sequencing (GS), and second-line and last-resort trio exome sequencing (ES) were compared with standard genetic testing. The cost effectiveness of each strategy was expressed in terms of incremental cost per additional diagnosis. The impact of uncertainty on cost-effectiveness results was explored using deterministic and probabilistic sensitivity analysis. RESULTS 2nd-line ES was a cost-saving option, increasing diagnostic yield by 13.9% and decreasing cost by £1027 per trio compared to standard genetic testing. Compared to ES, strategies involving GS increased costs significantly, with only a moderate or zero improvement in diagnostic yield. Sensitivity analysis indicated that significant reductions in cost or improvements in diagnostic yield are required before 1st-line GS becomes cost effective. CONCLUSION 2nd-line ES (after chromosomal microarray; replacing gene panel testing) for the diagnosis of developmental disorders is a cost-saving option for the Scottish NHS. Ongoing economic evaluation is required to monitor the evolving cost and diagnostic yield of GS and ES over time.
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Affiliation(s)
- Michael Abbott
- Health Economics Research Unit, University of Aberdeen, Aberdeen, UK.
| | - Mandy Ryan
- Health Economics Research Unit, University of Aberdeen, Aberdeen, UK
| | - Rodolfo Hernández
- Health Economics Research Unit, University of Aberdeen, Aberdeen, UK
| | - Lynda McKenzie
- Health Economics Research Unit, University of Aberdeen, Aberdeen, UK
| | | | - Lynne Hocking
- Department of Medical Genetics, University of Aberdeen, Aberdeen, UK
- NHS Grampian Regional Genetics Service, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Caroline Clark
- NHS Grampian Regional Genetics Service, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Morad Ansari
- South East Scotland Genetic Service, NHS Lothian, Edinburgh, UK
| | - David Moore
- South East Scotland Genetic Service, NHS Lothian, Edinburgh, UK
| | - Anne Lampe
- South East Scotland Genetic Service, NHS Lothian, Edinburgh, UK
| | - Ruth McGowan
- West of Scotland Centre for Genomic Medicine, QEUH, Glasgow, UK
| | | | - Zosia Miedzybrodzka
- Department of Medical Genetics, University of Aberdeen, Aberdeen, UK
- NHS Grampian Regional Genetics Service, Aberdeen Royal Infirmary, Aberdeen, UK
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5
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Razuvayevskaya O, Lopez I, Dunham I, Ochoa D. Genetic factors associated with reasons for clinical trial stoppage. Nat Genet 2024; 56:1862-1867. [PMID: 39075208 PMCID: PMC11387188 DOI: 10.1038/s41588-024-01854-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/02/2024] [Indexed: 07/31/2024]
Abstract
Many drug discovery projects are started but few progress fully through clinical trials to approval. Previous work has shown that human genetics support for the therapeutic hypothesis increases the chance of trial progression. Here, we applied natural language processing to classify the free-text reasons for 28,561 clinical trials that stopped before their endpoints were met. We then evaluated these classes in light of the underlying evidence for the therapeutic hypothesis and target properties. We found that trials are more likely to stop because of a lack of efficacy in the absence of strong genetic evidence from human populations or genetically modified animal models. Furthermore, certain trials are more likely to stop for safety reasons if the drug target gene is highly constrained in human populations and if the gene is broadly expressed across tissues. These results support the growing use of human genetics to evaluate targets for drug discovery programs.
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Affiliation(s)
- Olesya Razuvayevskaya
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Irene Lopez
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Ian Dunham
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - David Ochoa
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
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6
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Jensen M, Smolen C, Tyryshkina A, Pizzo L, Banerjee D, Oetjens M, Shimelis H, Taylor CM, Pounraja VK, Song H, Rohan L, Huber E, El Khattabi L, van de Laar I, Tadros R, Bezzina C, van Slegtenhorst M, Kammeraad J, Prontera P, Caberg JH, Fraser H, Banka S, Van Dijck A, Schwartz C, Voorhoeve E, Callier P, Mosca-Boidron AL, Marle N, Lefebvre M, Pope K, Snell P, Boys A, Lockhart PJ, Ashfaq M, McCready E, Nowacyzk M, Castiglia L, Galesi O, Avola E, Mattina T, Fichera M, Bruccheri MG, Mandarà GML, Mari F, Privitera F, Longo I, Curró A, Renieri A, Keren B, Charles P, Cuinat S, Nizon M, Pichon O, Bénéteau C, Stoeva R, Martin-Coignard D, Blesson S, Le Caignec C, Mercier S, Vincent M, Martin C, Mannik K, Reymond A, Faivre L, Sistermans E, Kooy RF, Amor DJ, Romano C, Andrieux J, Girirajan S. Genetic modifiers and ascertainment drive variable expressivity of complex disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.27.24312158. [PMID: 39252907 PMCID: PMC11383473 DOI: 10.1101/2024.08.27.24312158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Variable expressivity of disease-associated variants implies a role for secondary variants that modify clinical features. We assessed the effects of modifier variants towards clinical outcomes of 2,252 individuals with primary variants. Among 132 families with the 16p12.1 deletion, distinct rare and common variant classes conferred risk for specific developmental features, including short tandem repeats for neurological defects and SNVs for microcephaly, while additional disease-associated variants conferred multiple genetic diagnoses. Within disease and population cohorts of 773 individuals with the 16p12.1 deletion, we found opposing effects of secondary variants towards clinical features across ascertainments. Additional analysis of 1,479 probands with other primary variants, such as 16p11.2 deletion and CHD8 variants, and 1,084 without primary variants, showed that phenotypic associations differed by primary variant context and were influenced by synergistic interactions between primary and secondary variants. Our study provides a paradigm to dissect the genomic architecture of complex disorders towards personalized treatment.
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Affiliation(s)
- Matthew Jensen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Bioinformatics and Genomics Graduate program, Pennsylvania State University, University Park, PA 16802, USA
| | - Corrine Smolen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Bioinformatics and Genomics Graduate program, Pennsylvania State University, University Park, PA 16802, USA
| | - Anastasia Tyryshkina
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Lucilla Pizzo
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Deepro Banerjee
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew Oetjens
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA 17837, USA
| | - Hermela Shimelis
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA 17837, USA
| | - Cora M. Taylor
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA 17837, USA
| | - Vijay Kumar Pounraja
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Bioinformatics and Genomics Graduate program, Pennsylvania State University, University Park, PA 16802, USA
| | - Hyebin Song
- Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA
| | - Laura Rohan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Emily Huber
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Laila El Khattabi
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France
| | - Ingrid van de Laar
- Department of Clinical Genetics, Erasmus MC, Univ. Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rafik Tadros
- Department of Clinical Genetics, Erasmus MC, Univ. Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Connie Bezzina
- Department of Clinical Genetics, Erasmus MC, Univ. Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC, Univ. Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Janneke Kammeraad
- Department of Clinical Genetics, Erasmus MC, Univ. Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Paolo Prontera
- Medical Genetics Unit, Hospital Santa Maria della Misericordia, Perugia, Italy
| | - Jean-Hubert Caberg
- Centre Hospitalier Universitaire de Liège. Domaine Universitaire du Sart Tilman, Liège, Belgium
| | - Harry Fraser
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Siddhartha Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Central Manchester University Hospitals, NHS Foundation Trust Manchester Academic Health Sciences Centre, Manchester, UK
| | - Anke Van Dijck
- Department of Medical Genetics, University and University Hospital Antwerp, Antwerp, Belgium
| | | | - Els Voorhoeve
- Department of Clinical Genetics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Patrick Callier
- Center for Rare Diseases and Reference Developmental Anomalies and Malformation Syndromes, CHU Dijon, Dijon, France
| | - Anne-Laure Mosca-Boidron
- Center for Rare Diseases and Reference Developmental Anomalies and Malformation Syndromes, CHU Dijon, Dijon, France
| | - Nathalie Marle
- Center for Rare Diseases and Reference Developmental Anomalies and Malformation Syndromes, CHU Dijon, Dijon, France
| | - Mathilde Lefebvre
- Laboratoire de Genetique Chromosomique et Moleculaire, CHU Dijon, France
| | - Kate Pope
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Penny Snell
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Amber Boys
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Paul J. Lockhart
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Myla Ashfaq
- Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Margaret Nowacyzk
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Lucia Castiglia
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy
| | - Ornella Galesi
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy
| | - Emanuela Avola
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy
| | - Teresa Mattina
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy
| | - Marco Fichera
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy
- Section of Clinical Biochemistry and Medical Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania School of Medicine, Catania, Italy
| | - Maria Grazia Bruccheri
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy
| | | | - Francesca Mari
- Laboratory of Clinical Molecular Genetics and Cytogenetics, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Flavia Privitera
- Laboratory of Clinical Molecular Genetics and Cytogenetics, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ilaria Longo
- Laboratory of Clinical Molecular Genetics and Cytogenetics, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Aurora Curró
- Laboratory of Clinical Molecular Genetics and Cytogenetics, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandra Renieri
- Laboratory of Clinical Molecular Genetics and Cytogenetics, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Boris Keren
- Département de Génétique, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Sorbonne Université, 75019 Paris, France
| | - Perrine Charles
- Département de Génétique, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Sorbonne Université, 75019 Paris, France
| | | | | | | | | | - Radka Stoeva
- CHU Nantes, Medical Genetics Department, Nantes, France
| | | | - Sophia Blesson
- Department of Genetics, Bretonneau University Hospital, Tours, France
| | - Cedric Le Caignec
- CHU Toulouse, Department of Medical Genetics, Toulouse, France
- Toulouse Neuro Imaging, Center, Inserm, UPS, Université de Toulouse, Toulouse, France
| | - Sandra Mercier
- Department of Genetics, Bretonneau University Hospital, Tours, France
| | - Marie Vincent
- Department of Genetics, Bretonneau University Hospital, Tours, France
| | - Christa Martin
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA 17837, USA
| | - Katrin Mannik
- Institute of Genomics, University of Tartu, Estonia
- Health2030 Genome Center, Fondation Campus Biotech, Geneva, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Switzerland
| | - Laurence Faivre
- Center for Rare Diseases and Reference Developmental Anomalies and Malformation Syndromes, CHU Dijon, Dijon, France
- Laboratoire de Genetique Chromosomique et Moleculaire, CHU Dijon, France
| | - Erik Sistermans
- Department of Clinical Genetics, Amsterdam UMC, Amsterdam, The Netherlands
| | - R. Frank Kooy
- Department of Medical Genetics, University and University Hospital Antwerp, Antwerp, Belgium
| | - David J. Amor
- Department of Clinical Genetics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Corrado Romano
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy
- Section of Clinical Biochemistry and Medical Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania School of Medicine, Catania, Italy
| | - Joris Andrieux
- Institut de Genetique Medicale, Hopital Jeanne de Flandre, CHRU de Lille, Lille, France
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Bioinformatics and Genomics Graduate program, Pennsylvania State University, University Park, PA 16802, USA
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
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7
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McDonagh EM, Trynka G, McCarthy M, Holzinger ER, Khader S, Nakic N, Hu X, Cornu H, Dunham I, Hulcoop D. Human Genetics and Genomics for Drug Target Identification and Prioritization: Open Targets' Perspective. Annu Rev Biomed Data Sci 2024; 7:59-81. [PMID: 38608311 DOI: 10.1146/annurev-biodatasci-102523-103838] [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: 04/14/2024]
Abstract
Open Targets, a consortium among academic and industry partners, focuses on using human genetics and genomics to provide insights to key questions that build therapeutic hypotheses. Large-scale experiments generate foundational data, and open-source informatic platforms systematically integrate evidence for target-disease relationships and provide dynamic tooling for target prioritization. A locus-to-gene machine learning model uses evidence from genome-wide association studies (GWAS Catalog, UK BioBank, and FinnGen), functional genomic studies, epigenetic studies, and variant effect prediction to predict potential drug targets for complex diseases. These predictions are combined with genetic evidence from gene burden analyses, rare disease genetics, somatic mutations, perturbation assays, pathway analyses, scientific literature, differential expression, and mouse models to systematically build target-disease associations (https://platform.opentargets.org). Scored target attributes such as clinical precedence, tractability, and safety guide target prioritization. Here we provide our perspective on the value and impact of human genetics and genomics for generating therapeutic hypotheses.
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Affiliation(s)
- Ellen M McDonagh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
- Open Targets, Wellcome Genome Campus, Hinxton, UK;
| | - Gosia Trynka
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Open Targets, Wellcome Genome Campus, Hinxton, UK;
| | | | | | - Shameer Khader
- Precision Medicine & Computational Biology, Sanofi, Cambridge, Massachusetts, USA
| | | | - Xinli Hu
- Inflammation and Immunology, Pfizer Research and Development, Inc., Cambridge, Massachusetts, USA
| | - Helena Cornu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
- Open Targets, Wellcome Genome Campus, Hinxton, UK;
| | - Ian Dunham
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
- Open Targets, Wellcome Genome Campus, Hinxton, UK;
| | - David Hulcoop
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
- Open Targets, Wellcome Genome Campus, Hinxton, UK;
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Chen Y, Dawes R, Kim HC, Ljungdahl A, Stenton SL, Walker S, Lord J, Lemire G, Martin-Geary AC, Ganesh VS, Ma J, Ellingford JM, Delage E, D'Souza EN, Dong S, Adams DR, Allan K, Bakshi M, Baldwin EE, Berger SI, Bernstein JA, Bhatnagar I, Blair E, Brown NJ, Burrage LC, Chapman K, Coman DJ, Compton AG, Cunningham CA, D'Souza P, Danecek P, Délot EC, Dias KR, Elias ER, Elmslie F, Evans CA, Ewans L, Ezell K, Fraser JL, Gallacher L, Genetti CA, Goriely A, Grant CL, Haack T, Higgs JE, Hinch AG, Hurles ME, Kuechler A, Lachlan KL, Lalani SR, Lecoquierre F, Leitão E, Fevre AL, Leventer RJ, Liebelt JE, Lindsay S, Lockhart PJ, Ma AS, Macnamara EF, Mansour S, Maurer TM, Mendez HR, Metcalfe K, Montgomery SB, Moosajee M, Nassogne MC, Neumann S, O'Donoghue M, O'Leary M, Palmer EE, Pattani N, Phillips J, Pitsava G, Pysar R, Rehm HL, Reuter CM, Revencu N, Riess A, Rius R, Rodan L, Roscioli T, Rosenfeld JA, Sachdev R, Shaw-Smith CJ, Simons C, Sisodiya SM, Snell P, St Clair L, Stark Z, Stewart HS, Tan TY, Tan NB, Temple SEL, Thorburn DR, Tifft CJ, Uebergang E, VanNoy GE, Vasudevan P, Vilain E, Viskochil DH, Wedd L, Wheeler MT, White SM, Wojcik M, Wolfe LA, Wolfenson Z, Wright CF, Xiao C, Zocche D, Rubenstein JL, Markenscoff-Papadimitriou E, Fica SM, Baralle D, Depienne C, MacArthur DG, Howson JMM, Sanders SJ, O'Donnell-Luria A, Whiffin N. De novo variants in the RNU4-2 snRNA cause a frequent neurodevelopmental syndrome. Nature 2024; 632:832-840. [PMID: 38991538 PMCID: PMC11338827 DOI: 10.1038/s41586-024-07773-7] [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: 04/07/2024] [Accepted: 07/02/2024] [Indexed: 07/13/2024]
Abstract
Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes1. Large genome-sequenced cohorts are improving our ability to discover new diagnoses in the non-coding genome. Here we identify the non-coding RNA RNU4-2 as a syndromic NDD gene. RNU4-2 encodes the U4 small nuclear RNA (snRNA), which is a critical component of the U4/U6.U5 tri-snRNP complex of the major spliceosome2. We identify an 18 base pair region of RNU4-2 mapping to two structural elements in the U4/U6 snRNA duplex (the T-loop and stem III) that is severely depleted of variation in the general population, but in which we identify heterozygous variants in 115 individuals with NDD. Most individuals (77.4%) have the same highly recurrent single base insertion (n.64_65insT). In 54 individuals in whom it could be determined, the de novo variants were all on the maternal allele. We demonstrate that RNU4-2 is highly expressed in the developing human brain, in contrast to RNU4-1 and other U4 homologues. Using RNA sequencing, we show how 5' splice-site use is systematically disrupted in individuals with RNU4-2 variants, consistent with the known role of this region during spliceosome activation. Finally, we estimate that variants in this 18 base pair region explain 0.4% of individuals with NDD. This work underscores the importance of non-coding genes in rare disorders and will provide a diagnosis to thousands of individuals with NDD worldwide.
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Affiliation(s)
- Yuyang Chen
- Big Data Institute, University of Oxford, Oxford, UK
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ruebena Dawes
- Big Data Institute, University of Oxford, Oxford, UK
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Hyung Chul Kim
- Big Data Institute, University of Oxford, Oxford, UK
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alicia Ljungdahl
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Sarah L Stenton
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Jenny Lord
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Gabrielle Lemire
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexandra C Martin-Geary
- Big Data Institute, University of Oxford, Oxford, UK
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Vijay S Ganesh
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jialan Ma
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jamie M Ellingford
- Genomics England, London, UK
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Erwan Delage
- Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Elston N D'Souza
- Big Data Institute, University of Oxford, Oxford, UK
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Shan Dong
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - David R Adams
- Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA
| | - Kirsten Allan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Madhura Bakshi
- Department of Clinical Genetics, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Erin E Baldwin
- Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Seth I Berger
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA
- Division of Genetics and Metabolism, Children's National Hospital, Washington, DC, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Ishita Bhatnagar
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Ed Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kimberly Chapman
- Division of Genetics and Metabolism, Children's National Hospital, Washington, DC, USA
| | - David J Coman
- Department of Metabolic Medicine, Queensland Children's Hospital, Brisbane, Queensland, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- School of Medicine, Griffith university, Gold Coast, Queensland, Australia
| | - Alison G Compton
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Chloe A Cunningham
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Precilla D'Souza
- Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA
| | - Petr Danecek
- Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Emmanuèle C Délot
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA
| | - Kerith-Rae Dias
- Neuroscience Research Australia, Sydney, New South Wales, Australia
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Ellen R Elias
- Department of Pediatrics, Children's Hospital Colorado, Aurora, CO, USA
- University of Colorado School of Medicine, University of Colorado, Aurora, CO, USA
| | - Frances Elmslie
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Care-Anne Evans
- Neuroscience Research Australia, Sydney, New South Wales, Australia
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Lisa Ewans
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Centre for Clinical Genetics, Sydney Children's Hospitals Network, Randwick, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Darlinghurst, North South Wales, Australia
| | - Kimberly Ezell
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jamie L Fraser
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA
- Division of Genetics and Metabolism, Children's National Hospital, Washington, DC, USA
| | - Lyndon Gallacher
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Casie A Genetti
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anne Goriely
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, Oxford, UK
| | - Christina L Grant
- Division of Genetics and Metabolism, Children's National Hospital, Washington, DC, USA
| | - Tobias Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Rare Diseases Tübingen, University of Tübingen, Tübingen, Germany
| | - Jenny E Higgs
- Liverpool Centre for Genomic Medicine, Liverpool Women's Hospital, Liverpool, UK
| | - Anjali G Hinch
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Alma Kuechler
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Katherine L Lachlan
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Trust, Southampton, UK
- Department of Human Genetics and Genomic Medicine, Southampton University, Southampton, UK
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - François Lecoquierre
- University of Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, Rouen, France
| | - Elsa Leitão
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Anna Le Fevre
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Richard J Leventer
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Jan E Liebelt
- Paediatric and Reproductive Genetics Unit, South Australian Clinical Genetics Service, Women's and Children's Hospital, North Adelaide, South Australia, Australia
- Repromed, Dulwich, South Australia, Australia
| | - Sarah Lindsay
- Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Paul J Lockhart
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Alan S Ma
- Department of Clinical Genetics, Sydney Children's Hospitals Network Westmead, Sydney, New South Wales, Australia
- Specialty of Genomic Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Ellen F Macnamara
- Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA
| | - Sahar Mansour
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Taylor M Maurer
- GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Hector R Mendez
- GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine - Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Kay Metcalfe
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Stephen B Montgomery
- GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Department of Genetics, Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Mariya Moosajee
- UCL Institute of Ophthalmology, London, UK
- The Francis Crick Institute, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Marie-Cécile Nassogne
- Service de Neurologie Pédiatrique, Cliniques Universitaires Saint-Luc, UCLouvain, Brussels, Belgium
- Institut des Maladies Rares, Cliniques Universitaires Saint-Luc, UCLouvain, Brussels, Belgium
| | - Serena Neumann
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Melanie O'Leary
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elizabeth E Palmer
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Centre for Clinical Genetics, Sydney Children's Hospitals Network, Randwick, New South Wales, Australia
| | - Nikhil Pattani
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - John Phillips
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Georgia Pitsava
- Institute for Clinical and Translational Research, University of California Irvine, Irvine, CA, USA
| | - Ryan Pysar
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Centre for Clinical Genetics, Sydney Children's Hospitals Network, Randwick, New South Wales, Australia
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Heidi L Rehm
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Chloe M Reuter
- GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine - Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicole Revencu
- Center for Human Genetics, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Angelika Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Rocio Rius
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Lance Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Tony Roscioli
- Neuroscience Research Australia, Sydney, New South Wales, Australia
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rani Sachdev
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Centre for Clinical Genetics, Sydney Children's Hospitals Network, Randwick, New South Wales, Australia
| | - Charles J Shaw-Smith
- Department of Clinical Genetics, Peninsula Regional Clinical Genetics Service, Royal Devon University Hospital, Exeter, UK
| | - Cas Simons
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK
- UK and Chalfont Centre for Epilepsy, Chalfont St Peter, UK
| | - Penny Snell
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Laura St Clair
- Department of Clinical Genetics, Sydney Children's Hospitals Network Westmead, Sydney, New South Wales, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Helen S Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Natalie B Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Suzanna E L Temple
- Department of Clinical Genetics, Liverpool Hospital, Sydney, New South Wales, Australia
- School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - David R Thorburn
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Cynthia J Tifft
- Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA
| | - Eloise Uebergang
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Grace E VanNoy
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pradeep Vasudevan
- Medical Genetics, University of Leicester, Leicester Royal Infirmary, Leicester, UK
| | - Eric Vilain
- Institute for Clinical and Translational Science, University of California Irvine, Irvine, CA, USA
| | - David H Viskochil
- Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Laura Wedd
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Matthew T Wheeler
- GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine - Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Monica Wojcik
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lynne A Wolfe
- Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA
| | - Zoe Wolfenson
- Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA
| | - Caroline F Wright
- Department of Clinical and Biomedical Sciences, University of Exeter, Exeter, UK
| | - Changrui Xiao
- Department of Neurology, University of California Irvine, Irvine, CA, USA
| | - David Zocche
- North West Thames Regional Genetics Service, Northwick Park and St Mark's Hospitals, London, UK
| | - John L Rubenstein
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Eirene Markenscoff-Papadimitriou
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | | | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Joanna M M Howson
- Human Genetics Centre of Excellence, Novo Nordisk Research Centre, Oxford, UK
| | - Stephan J Sanders
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Anne O'Donnell-Luria
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicola Whiffin
- Big Data Institute, University of Oxford, Oxford, UK.
- Centre for Human Genetics, University of Oxford, Oxford, UK.
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Murthy S, Nongthomba U. Role of the BCL11A/B Homologue Chronophage (Cph) in Locomotor Behaviour of Drosophila melanogaster. Neuroscience 2024; 551:1-16. [PMID: 38763224 DOI: 10.1016/j.neuroscience.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/21/2024]
Abstract
Functioning of the nervous system requires proper formation and specification of neurons as well as accurate connectivity and signalling between them. Locomotor behaviour depends upon these events that occur during neural development, and any aberration in them could result in motor disorders. Transcription factors are believed to be master regulators that control these processes, but very few linked to behaviour have been identified so far. The Drosophila homologue of BCL11A (CTIP1) and BCL11B (CTIP2), Chronophage (Cph), was recently shown to be involved in temporal patterning of neural stem cells but its role in post-mitotic neurons is not known. We show that knockdown of Cph in neurons during development results in animals with locomotor defects at both larval and adult stages. The defects are more severe in adults, with inability to stand, uncoordinated behaviour and complete loss of ability to walk, climb, or fly. These defects are similar to the motor difficulties observed in some patients with mutations in BCL11A and BCL11B. Electrophysiological recordings showed reduced evoked activity and irregular neuronal firing. All Cph-expressing neurons in the ventral nerve cord are glutamatergic. Our results imply that Cph modulates primary locomotor activity through configuration of glutamatergic neurons. Thus, this study ascribes a hitherto unknown role to Cph in locomotor behaviour of Drosophila melanogaster.
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Affiliation(s)
- Smrithi Murthy
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru 560 012, India.
| | - Upendra Nongthomba
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru 560 012, India.
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Zhang X, Theotokis PI, Li N, Wright CF, Samocha KE, Whiffin N, Ware JS. Genetic constraint at single amino acid resolution in protein domains improves missense variant prioritisation and gene discovery. Genome Med 2024; 16:88. [PMID: 38992748 PMCID: PMC11238507 DOI: 10.1186/s13073-024-01358-9] [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: 09/18/2023] [Accepted: 06/26/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND One of the major hurdles in clinical genetics is interpreting the clinical consequences associated with germline missense variants in humans. Recent significant advances have leveraged natural variation observed in large-scale human populations to uncover genes or genomic regions that show a depletion of natural variation, indicative of selection pressure. We refer to this as "genetic constraint". Although existing genetic constraint metrics have been demonstrated to be successful in prioritising genes or genomic regions associated with diseases, their spatial resolution is limited in distinguishing pathogenic variants from benign variants within genes. METHODS We aim to identify missense variants that are significantly depleted in the general human population. Given the size of currently available human populations with exome or genome sequencing data, it is not possible to directly detect depletion of individual missense variants, since the average expected number of observations of a variant at most positions is less than one. We instead focus on protein domains, grouping homologous variants with similar functional impacts to examine the depletion of natural variations within these comparable sets. To accomplish this, we develop the Homologous Missense Constraint (HMC) score. We utilise the Genome Aggregation Database (gnomAD) 125 K exome sequencing data and evaluate genetic constraint at quasi amino-acid resolution by combining signals across protein homologues. RESULTS We identify one million possible missense variants under strong negative selection within protein domains. Though our approach annotates only protein domains, it nonetheless allows us to assess 22% of the exome confidently. It precisely distinguishes pathogenic variants from benign variants for both early-onset and adult-onset disorders. It outperforms existing constraint metrics and pathogenicity meta-predictors in prioritising de novo mutations from probands with developmental disorders (DD). It is also methodologically independent of these, adding power to predict variant pathogenicity when used in combination. We demonstrate utility for gene discovery by identifying seven genes newly significantly associated with DD that could act through an altered-function mechanism. CONCLUSIONS Grouping variants of comparable functional impacts is effective in evaluating their genetic constraint. HMC is a novel and accurate predictor of missense consequence for improved variant interpretation.
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Affiliation(s)
- Xiaolei Zhang
- National Heart & Lung Institute, Imperial College London, London, UK.
- MRC Laboratory of Medical Sciences, Imperial College London, London, UK.
- Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK.
- Present address: European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Pantazis I Theotokis
- National Heart & Lung Institute, Imperial College London, London, UK
- MRC Laboratory of Medical Sciences, Imperial College London, London, UK
- Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Nicholas Li
- National Heart & Lung Institute, Imperial College London, London, UK
- MRC Laboratory of Medical Sciences, Imperial College London, London, UK
- Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Caroline F Wright
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Kaitlin E Samocha
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicola Whiffin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Centre for Human Genetics, University of Oxford, Oxford, UK.
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
| | - James S Ware
- National Heart & Lung Institute, Imperial College London, London, UK.
- MRC Laboratory of Medical Sciences, Imperial College London, London, UK.
- Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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11
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Low KJ, Watford A, Blair P, Nabney I, Powell J, Wynn SL, Foreman J, Firth H, Ingram J. Improving the care of children with GENetic Rare disease: Observational Cohort study (GenROC)-a study protocol. BMJ Open 2024; 14:e085237. [PMID: 38760043 PMCID: PMC11103197 DOI: 10.1136/bmjopen-2024-085237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/18/2024] [Indexed: 05/19/2024] Open
Abstract
INTRODUCTION Around 2000 children are born in the UK per year with a neurodevelopmental genetic syndrome with significantly increased morbidity and mortality. Often little is known about expected growth and phenotypes in these children. Parents have responded by setting up social media groups to generate data themselves. Given the significant clinical evidence gaps, this research will attempt to identify growth patterns, developmental profiles and phenotypes, providing data on long-term medical and educational outcomes. This will guide clinicians when to investigate, monitor or treat symptoms and when to search for additional or alternative diagnoses. METHODS AND ANALYSIS This is an observational, multicentre cohort study recruiting between March 2023 and February 2026. Children aged 6 months up to 16 years with a pathogenic or likely pathogenic variant in a specified gene will be eligible. Children will be identified through the National Health Service and via self-recruitment. Parents or carers will complete a questionnaire at baseline and again 1 year after recruitment. The named clinician (in most cases a clinical geneticist) will complete a clinical proforma which will provide data from their most recent clinical assessment. Qualitative interviews will be undertaken with a subset of parents partway through the study. Growth and developmental milestone curves will be generated through the DECIPHER website (https://deciphergenomics.org) where 5 or more children have the same genetic syndrome (at least 10 groups expected). ETHICS AND DISSEMINATION The results will be presented at national and international conferences concerning the care of children with genetic syndromes. Results will also be submitted for peer review and publication.
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Affiliation(s)
- Karen Jaqueline Low
- Centre for Academic Child Health, University of Bristol, Bristol, UK
- Department of Clinical Genetics, University Hospitals Bristol and Weston NHS Trust, Bristol, UK
| | - Amy Watford
- Department of Clinical Genetics, University Hospitals Bristol and Weston NHS Trust, Bristol, UK
| | - Peter Blair
- Centre for Academic Child Health, University of Bristol, Bristol, UK
| | - Ian Nabney
- School of Computer Science, Electrical and Electronic Engineering and Engineering Maths, University of Bristol, Bristol, UK
| | - John Powell
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Sarah L Wynn
- Unique Rare Chromosome Disorder Support Group, Oxted, UK
| | - Julia Foreman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Helen Firth
- Clinical Genetics, Cambridge University Hospitals, Cambridge, UK
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, UK
| | - Jenny Ingram
- Centre for Academic Child Health, School of Social & Community Medicine, Bristol University, Bristol, UK
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12
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Chao KR, Wang L, Panchal R, Liao C, Abderrazzaq H, Ye R, Schultz P, Compitello J, Grant RH, Kosmicki JA, Weisburd B, Phu W, Wilson MW, Laricchia KM, Goodrich JK, Goldstein D, Goldstein JI, Vittal C, Poterba T, Baxter S, Watts NA, Solomonson M, Tiao G, Rehm HL, Neale BM, Talkowski ME, MacArthur DG, O'Donnell-Luria A, Karczewski KJ, Radivojac P, Daly MJ, Samocha KE. The landscape of regional missense mutational intolerance quantified from 125,748 exomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.588920. [PMID: 38645134 PMCID: PMC11030311 DOI: 10.1101/2024.04.11.588920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Missense variants can have a range of functional impacts depending on factors such as the specific amino acid substitution and location within the gene. To interpret their deleteriousness, studies have sought to identify regions within genes that are specifically intolerant of missense variation 1-12 . Here, we leverage the patterns of rare missense variation in 125,748 individuals in the Genome Aggregation Database (gnomAD) 13 against a null mutational model to identify transcripts that display regional differences in missense constraint. Missense-depleted regions are enriched for ClinVar 14 pathogenic variants, de novo missense variants from individuals with neurodevelopmental disorders (NDDs) 15,16 , and complex trait heritability. Following ClinGen calibration recommendations for the ACMG/AMP guidelines, we establish that regions with less than 20% of their expected missense variation achieve moderate support for pathogenicity. We create a missense deleteriousness metric (MPC) that incorporates regional constraint and outperforms other deleteriousness scores at stratifying case and control de novo missense variation, with a strong enrichment in NDDs. These results provide additional tools to aid in missense variant interpretation.
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13
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Kingdom R, Beaumont RN, Wood AR, Weedon MN, Wright CF. Genetic modifiers of rare variants in monogenic developmental disorder loci. Nat Genet 2024; 56:861-868. [PMID: 38637616 PMCID: PMC11096126 DOI: 10.1038/s41588-024-01710-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/06/2024] [Indexed: 04/20/2024]
Abstract
Rare damaging variants in a large number of genes are known to cause monogenic developmental disorders (DDs) and have also been shown to cause milder subclinical phenotypes in population cohorts. Here, we show that carrying multiple (2-5) rare damaging variants across 599 dominant DD genes has an additive adverse effect on numerous cognitive and socioeconomic traits in UK Biobank, which can be partially counterbalanced by a higher educational attainment polygenic score (EA-PGS). Phenotypic deviators from expected EA-PGS could be partly explained by the enrichment or depletion of rare DD variants. Among carriers of rare DD variants, those with a DD-related clinical diagnosis had a substantially lower EA-PGS and more severe phenotype than those without a clinical diagnosis. Our results suggest that the overall burden of both rare and common variants can modify the expressivity of a phenotype, which may then influence whether an individual reaches the threshold for clinical disease.
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Affiliation(s)
- Rebecca Kingdom
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Robin N Beaumont
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Andrew R Wood
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Michael N Weedon
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Caroline F Wright
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK.
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14
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Beaumont RN, Hawkes G, Gunning AC, Wright CF. Clustering of predicted loss-of-function variants in genes linked with monogenic disease can explain incomplete penetrance. Genome Med 2024; 16:64. [PMID: 38671509 PMCID: PMC11046769 DOI: 10.1186/s13073-024-01333-4] [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: 10/19/2023] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Genetic variants that severely alter protein products (e.g. nonsense, frameshift) are often associated with disease. For some genes, these predicted loss-of-function variants (pLoFs) are observed throughout the gene, whilst in others, they occur only at specific locations. We hypothesised that, for genes linked with monogenic diseases that display incomplete penetrance, pLoF variants present in apparently unaffected individuals may be limited to regions where pLoFs are tolerated. To test this, we investigated whether pLoF location could explain instances of incomplete penetrance of variants expected to be pathogenic for Mendelian conditions. METHODS We used exome sequence data in 454,773 individuals in the UK Biobank (UKB) to investigate the locations of pLoFs in a population cohort. We counted numbers of unique pLoF, missense, and synonymous variants in UKB in each quintile of the coding sequence (CDS) of all protein-coding genes and clustered the variants using Gaussian mixture models. We limited the analyses to genes with ≥ 5 variants of each type (16,473 genes). We compared the locations of pLoFs in UKB with all theoretically possible pLoFs in a transcript, and pathogenic pLoFs from ClinVar, and performed simulations to estimate the false-positive rate of non-uniformly distributed variants. RESULTS For most genes, all variant classes fell into clusters representing broadly uniform variant distributions, but genes in which haploinsufficiency causes developmental disorders were less likely to have uniform pLoF distribution than other genes (P < 2.2 × 10-6). We identified a number of genes, including ARID1B and GATA6, where pLoF variants in the first quarter of the CDS were rescued by the presence of an alternative translation start site and should not be reported as pathogenic. For other genes, such as ODC1, pLoFs were located approximately uniformly across the gene, but pathogenic pLoFs were clustered only at the end, consistent with a gain-of-function disease mechanism. CONCLUSIONS Our results suggest the potential benefits of localised constraint metrics and that the location of pLoF variants should be considered when interpreting variants.
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Affiliation(s)
- Robin N Beaumont
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX1 2LU, UK.
| | - Gareth Hawkes
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX1 2LU, UK
| | - Adam C Gunning
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX1 2LU, UK
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, EX2 5DW, UK
| | - Caroline F Wright
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX1 2LU, UK.
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15
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Claussnitzer M, Parikh VN, Wagner AH, Arbesfeld JA, Bult CJ, Firth HV, Muffley LA, Nguyen Ba AN, Riehle K, Roth FP, Tabet D, Bolognesi B, Glazer AM, Rubin AF. Minimum information and guidelines for reporting a multiplexed assay of variant effect. Genome Biol 2024; 25:100. [PMID: 38641812 PMCID: PMC11027375 DOI: 10.1186/s13059-024-03223-9] [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: 06/18/2023] [Accepted: 03/25/2024] [Indexed: 04/21/2024] Open
Abstract
Multiplexed assays of variant effect (MAVEs) have emerged as a powerful approach for interrogating thousands of genetic variants in a single experiment. The flexibility and widespread adoption of these techniques across diverse disciplines have led to a heterogeneous mix of data formats and descriptions, which complicates the downstream use of the resulting datasets. To address these issues and promote reproducibility and reuse of MAVE data, we define a set of minimum information standards for MAVE data and metadata and outline a controlled vocabulary aligned with established biomedical ontologies for describing these experimental designs.
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Affiliation(s)
- Melina Claussnitzer
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, 02142, USA
| | - Victoria N Parikh
- Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alex H Wagner
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43215, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43210, USA
| | - Jeremy A Arbesfeld
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43215, USA
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Carol J Bult
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Helen V Firth
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Dept of Medical Genetics, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | - Lara A Muffley
- Department of Genome Sciences, University of Washington, Seattle, WA, 98105, USA
| | - Alex N Nguyen Ba
- Department of Biology, University of Toronto at Mississauga, Mississauga, ON, Canada
| | - Kevin Riehle
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Frederick P Roth
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Daniel Tabet
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Benedetta Bolognesi
- Institute for Bioengineering of Catalunya (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Andrew M Glazer
- Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
| | - Alan F Rubin
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
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16
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Lopez Soriano V, Dueñas Rey A, Mukherjee R, Coppieters F, Bauwens M, Willaert A, De Baere E. Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci. Nat Commun 2024; 15:1600. [PMID: 38383453 PMCID: PMC10881467 DOI: 10.1038/s41467-024-45381-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
Cross-species genome comparisons have revealed a substantial number of ultraconserved non-coding elements (UCNEs). Several of these elements have proved to be essential tissue- and cell type-specific cis-regulators of developmental gene expression. Here, we characterize a set of UCNEs as candidate CREs (cCREs) during retinal development and evaluate the contribution of their genomic variation to rare eye diseases, for which pathogenic non-coding variants are emerging. Integration of bulk and single-cell retinal multi-omics data reveals 594 genes under potential cis-regulatory control of UCNEs, of which 45 are implicated in rare eye disease. Mining of candidate cis-regulatory UCNEs in WGS data derived from the rare eye disease cohort of Genomics England reveals 178 ultrarare variants within 84 UCNEs associated with 29 disease genes. Overall, we provide a comprehensive annotation of ultraconserved non-coding regions acting as cCREs during retinal development which can be targets of non-coding variation underlying rare eye diseases.
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Affiliation(s)
- Victor Lopez Soriano
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Alfredo Dueñas Rey
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | | | - Frauke Coppieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Andy Willaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
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17
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Hall HN, Parry D, Halachev M, Williamson KA, Donnelly K, Campos Parada J, Bhatia S, Joseph J, Holden S, Prescott TE, Bitoun P, Kirk EP, Newbury-Ecob R, Lachlan K, Bernar J, van Heyningen V, FitzPatrick DR, Meynert A. Short-read whole genome sequencing identifies causative variants in most individuals with previously unexplained aniridia. J Med Genet 2024; 61:250-261. [PMID: 38050128 PMCID: PMC7615962 DOI: 10.1136/jmg-2023-109181] [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: 03/12/2023] [Accepted: 09/25/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Classic aniridia is a highly penetrant autosomal dominant disorder characterised by congenital absence of the iris, foveal hypoplasia, optic disc anomalies and progressive opacification of the cornea. >90% of cases of classic aniridia are caused by heterozygous, loss-of-function variants affecting the PAX6 locus. METHODS Short-read whole genome sequencing was performed on 51 (39 affected) individuals from 37 different families who had screened negative for mutations in the PAX6 coding region. RESULTS Likely causative mutations were identified in 22 out of 37 (59%) families. In 19 out of 22 families, the causative genomic changes have an interpretable deleterious impact on the PAX6 locus. Of these 19 families, 1 has a novel heterozygous PAX6 frameshift variant missed on previous screens, 4 have single nucleotide variants (SNVs) (one novel) affecting essential splice sites of PAX6 5' non-coding exons and 2 have deep intronic SNV (one novel) resulting in gain of a donor splice site. In 12 out of 19, the causative variants are large-scale structural variants; 5 have partial or whole gene deletions of PAX6, 3 have deletions encompassing critical PAX6 cis-regulatory elements, 2 have balanced inversions with disruptive breakpoints within the PAX6 locus and 2 have complex rearrangements disrupting PAX6. The remaining 3 of 22 families have deletions encompassing FOXC1 (a known cause of atypical aniridia). Seven of the causative variants occurred de novo and one cosegregated with familial aniridia. We were unable to establish inheritance status in the remaining probands. No plausibly causative SNVs were identified in PAX6 cis-regulatory elements. CONCLUSION Whole genome sequencing proves to be an effective diagnostic test in most individuals with previously unexplained aniridia.
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Affiliation(s)
- Hildegard Nikki Hall
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - David Parry
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
- Illumina United Kingdom, Edinburgh, UK
| | - Mihail Halachev
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Kathleen A Williamson
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Kevin Donnelly
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Jose Campos Parada
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Shipra Bhatia
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Jeffrey Joseph
- MRC Human Genetics Unit, The University of Edinburgh, Edinburgh, UK
| | - Simon Holden
- East Anglia Regional Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Trine E Prescott
- Department of Medical Genetics, Telemark Hospital, Skien, Norway
| | - Pierre Bitoun
- Consultations de Génétique médicale, Service de Pédiatrie, CHU Paris-Nord, Hôpital Jean Verdier, Bondy, France
| | - Edwin P Kirk
- Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Randwick, New South Wales, Australia
| | - Ruth Newbury-Ecob
- Department of Clinical Genetics, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Katherine Lachlan
- University Hospital Southampton, NHS Foundation Trust Wessex Clinical Genetics Service, Southampton, UK
| | - Juan Bernar
- Department of Genetics, Hospital Ruber Internacional, Madrid, Spain
| | - Veronica van Heyningen
- MRC Human Genetics Unit, The University of Edinburgh, Edinburgh, UK
- Institute of Ophthalmology, University College London, London, UK
| | - David R FitzPatrick
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
| | - Alison Meynert
- Institute of Genetics and Cancer, The University of Edinburgh MRC Human Genetics Unit, Edinburgh, UK
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18
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Ball G, Oldham S, Kyriakopoulou V, Williams LZJ, Karolis V, Price A, Hutter J, Seal ML, Alexander-Bloch A, Hajnal JV, Edwards AD, Robinson EC, Seidlitz J. Molecular signatures of cortical expansion in the human fetal brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580198. [PMID: 38405710 PMCID: PMC10888819 DOI: 10.1101/2024.02.13.580198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The third trimester of human gestation is characterised by rapid increases in brain volume and cortical surface area. A growing catalogue of cells in the prenatal brain has revealed remarkable molecular diversity across cortical areas.1,2 Despite this, little is known about how this translates into the patterns of differential cortical expansion observed in humans during the latter stages of gestation. Here we present a new resource, μBrain, to facilitate knowledge translation between molecular and anatomical descriptions of the prenatal developing brain. Built using generative artificial intelligence, μBrain is a three-dimensional cellular-resolution digital atlas combining publicly-available serial sections of the postmortem human brain at 21 weeks gestation3 with bulk tissue microarray data, sampled across 29 cortical regions and 5 transient tissue zones.4 Using μBrain, we evaluate the molecular signatures of preferentially-expanded cortical regions during human gestation, quantified in utero using magnetic resonance imaging (MRI). We find that differences in the rates of expansion across cortical areas during gestation respect anatomical and evolutionary boundaries between cortical types5 and are founded upon extended periods of upper-layer cortical neuron migration that continue beyond mid-gestation. We identify a set of genes that are upregulated from mid-gestation and highly expressed in rapidly expanding neocortex, which are implicated in genetic disorders with cognitive sequelae. Our findings demonstrate a spatial coupling between areal differences in the timing of neurogenesis and rates of expansion across the neocortical sheet during the prenatal epoch. The μBrain atlas is available from: https://garedaba.github.io/micro-brain/ and provides a new tool to comprehensively map early brain development across domains, model systems and resolution scales.
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Affiliation(s)
- G Ball
- Developmental Imaging, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - S Oldham
- Developmental Imaging, Murdoch Children's Research Institute, Melbourne, Australia
| | - V Kyriakopoulou
- Centre for the Developing Brain, King's College London, London, UK
- School of Biomedical Engineering & Imaging Science, King's College London, London, UK
| | - L Z J Williams
- Centre for the Developing Brain, King's College London, London, UK
- School of Biomedical Engineering & Imaging Science, King's College London, London, UK
| | - V Karolis
- Centre for the Developing Brain, King's College London, London, UK
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - A Price
- Centre for the Developing Brain, King's College London, London, UK
- School of Biomedical Engineering & Imaging Science, King's College London, London, UK
| | - J Hutter
- Centre for the Developing Brain, King's College London, London, UK
- School of Biomedical Engineering & Imaging Science, King's College London, London, UK
| | - M L Seal
- Developmental Imaging, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - A Alexander-Bloch
- Department of Child and Adolescent Psychiatry and Behavioral Sciences, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA
| | - J V Hajnal
- Centre for the Developing Brain, King's College London, London, UK
- School of Biomedical Engineering & Imaging Science, King's College London, London, UK
| | - A D Edwards
- Centre for the Developing Brain, King's College London, London, UK
- School of Biomedical Engineering & Imaging Science, King's College London, London, UK
| | - E C Robinson
- Centre for the Developing Brain, King's College London, London, UK
- School of Biomedical Engineering & Imaging Science, King's College London, London, UK
| | - J Seidlitz
- Department of Child and Adolescent Psychiatry and Behavioral Sciences, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA
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19
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Farzan R. Artificial intelligence in Immuno-genetics. Bioinformation 2024; 20:29-35. [PMID: 38352901 PMCID: PMC10859949 DOI: 10.6026/973206300200029] [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: 01/01/2024] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024] Open
Abstract
Rapid advancements in the field of artificial intelligence (AI) have opened up unprecedented opportunities to revolutionize various scientific domains, including immunology and genetics. Therefore, it is of interest to explore the emerging applications of AI in immunology and genetics, with the objective of enhancing our understanding of the dynamic intricacies of the immune system, disease etiology, and genetic variations. Hence, the use of AI methodologies in immunological and genetic datasets, thereby facilitating the development of innovative approaches in the realms of diagnosis, treatment, and personalized medicine is reviewed.
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Affiliation(s)
- Raed Farzan
- Department of Clinical Laboratory Sciences, College of Applied Medical Scienecs, King Saud University, Riyadh - 11433, Saudi Arabia
- Center of Excellence in Biotechnology Research, King Saud University, Riyadh - 11433, Saudi Arabia
- Medical and Molecular Genetics Research, King Saud University, Riyadh-11433, Saudi Arabia
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20
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Templeton KM, Thompson L, Tobias ES, Ahmed SF, McGowan R. Coloboma in a family with Tonne-Kalsheuer syndrome: extending the phenotype of RLIM variants. Clin Dysmorphol 2024; 33:38-42. [PMID: 38038056 DOI: 10.1097/mcd.0000000000000478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Affiliation(s)
- Kerra M Templeton
- West of Scotland Clinical Genetics Service, Queen Elizabeth University Hospital, Glasgow
| | - Louise Thompson
- South East of Scotland Genetics Service, Western General Hospital, Edinburgh
| | - Edward S Tobias
- West of Scotland Clinical Genetics Service, Queen Elizabeth University Hospital, Glasgow
- Academic Unit of Medical Genetics and Clinical Pathology, University of Glasgow, Queen Elizabeth University Hospital
| | - S Faisal Ahmed
- Child Health, School of Medicine, Dentistry and Nursing Studies, University of Glasgow, Royal Hospital for Children, Glasgow, UK
| | - Ruth McGowan
- West of Scotland Clinical Genetics Service, Queen Elizabeth University Hospital, Glasgow
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21
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Wang S, Wang B, Drury V, Drake S, Sun N, Alkhairo H, Arbelaez J, Duhn C, Bal VH, Langley K, Martin J, Hoekstra PJ, Dietrich A, Xing J, Heiman GA, Tischfield JA, Fernandez TV, Owen MJ, O'Donovan MC, Thapar A, State MW, Willsey AJ. Rare X-linked variants carry predominantly male risk in autism, Tourette syndrome, and ADHD. Nat Commun 2023; 14:8077. [PMID: 38057346 PMCID: PMC10700338 DOI: 10.1038/s41467-023-43776-0] [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: 09/29/2022] [Accepted: 11/18/2023] [Indexed: 12/08/2023] Open
Abstract
Autism spectrum disorder (ASD), Tourette syndrome (TS), and attention-deficit/hyperactivity disorder (ADHD) display strong male sex bias, due to a combination of genetic and biological factors, as well as selective ascertainment. While the hemizygous nature of chromosome X (Chr X) in males has long been postulated as a key point of "male vulnerability", rare genetic variation on this chromosome has not been systematically characterized in large-scale whole exome sequencing studies of "idiopathic" ASD, TS, and ADHD. Here, we take advantage of informative recombinations in simplex ASD families to pinpoint risk-enriched regions on Chr X, within which rare maternally-inherited damaging variants carry substantial risk in males with ASD. We then apply a modified transmission disequilibrium test to 13,052 ASD probands and identify a novel high confidence ASD risk gene at exome-wide significance (MAGEC3). Finally, we observe that rare damaging variants within these risk regions carry similar effect sizes in males with TS or ADHD, further clarifying genetic mechanisms underlying male vulnerability in multiple neurodevelopmental disorders that can be exploited for systematic gene discovery.
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Affiliation(s)
- Sheng Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Vanessa Drury
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Sam Drake
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Nawei Sun
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Hasan Alkhairo
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Juan Arbelaez
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Clif Duhn
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Vanessa H Bal
- Graduate School of Applied and Professional Psychology, Rutgers University, New Brunswick, NJ, USA
| | - Kate Langley
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
- School of Psychology, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Joanna Martin
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Pieter J Hoekstra
- University of Groningen, University Medical Center Groningen, Department of Child and Adolescent Psychiatry, Groningen, The Netherlands
- Accare Child Study Center, Groningen, The Netherlands
| | - Andrea Dietrich
- University of Groningen, University Medical Center Groningen, Department of Child and Adolescent Psychiatry, Groningen, The Netherlands
- Accare Child Study Center, Groningen, The Netherlands
| | - Jinchuan Xing
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Gary A Heiman
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Jay A Tischfield
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Thomas V Fernandez
- Yale Child Study Center and Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Michael J Owen
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Michael C O'Donovan
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Anita Thapar
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - A Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA.
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94143, USA.
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22
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Campbell L, Fredericks J, Mathivha K, Moshesh P, Coovadia A, Chirwa P, Dillon B, Ghoor A, Lawrence D, Nair L, Mabaso N, Mokwele D, Novellie M, Krause A, Carstens N. The implementation and utility of clinical exome sequencing in a South African infant cohort. Front Genet 2023; 14:1277948. [PMID: 38028619 PMCID: PMC10665497 DOI: 10.3389/fgene.2023.1277948] [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: 08/15/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Genetic disorders are significant contributors to infant hospitalization and mortality globally. The early diagnosis of these conditions in infants remains a considerable challenge. Clinical exome sequencing (CES) has shown to be a successful tool for the early diagnosis of genetic conditions, however, its utility in African infant populations has not been investigated. The impact of the under-representation of African genomic data, the cost of testing, and genomic workforce shortages, need to be investigated and evidence-based implementation strategies accounting for locally available genetics expertise and diagnostic infrastructure need to be developed. We evaluated the diagnostic utility of singleton CES in a cohort of 32 ill, South African infants from two State hospitals in Johannesburg, South Africa. We analysed the data using a series of filtering approaches, including a curated virtual gene panel consisting of genes implicated in neonatal-and early childhood-onset conditions and genes with known founder and common variants in African populations. We reported a diagnostic yield of 22% and identified seven pathogenic variants in the NPHS1, COL2A1, OCRL, SHOC2, TPRV4, MTM1 and STAC3 genes. This study demonstrates the utility value of CES in the South African State healthcare setting, providing a diagnosis to patients who would otherwise not receive one and allowing for directed management. We anticipate an increase in the diagnostic yield of our workflow with further refinement of the study inclusion criteria. This study highlights important considerations for the implementation of genomic medicine in under-resourced settings and in under-represented African populations where variant interpretation remains a challenge.
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Affiliation(s)
- L. Campbell
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - J. Fredericks
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - K. Mathivha
- Department of Paediatrics and Child Health, School of Clinical Medicine, Nelson Mandela Children’s Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - P. Moshesh
- Department of Paediatrics and Child Health, School of Clinical Medicine, Nelson Mandela Children’s Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Coovadia
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - P. Chirwa
- Nelson Mandela Children’s Hospital, Johannesburg, South Africa
| | - B. Dillon
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Ghoor
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - D. Lawrence
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - L. Nair
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - N. Mabaso
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - D. Mokwele
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - M. Novellie
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Krause
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - N. Carstens
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
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23
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Levitin MO, Rawlins LE, Sanchez-Andrade G, Arshad OA, Collins SC, Sawiak SJ, Iffland PH, Andersson MHL, Bupp C, Cambridge EL, Coomber EL, Ellis I, Herkert JC, Ironfield H, Jory L, Kretz PF, Kant SG, Neaverson A, Nibbeling E, Rowley C, Relton E, Sanderson M, Scott EM, Stewart H, Shuen AY, Schreiber J, Tuck L, Tonks J, Terkelsen T, van Ravenswaaij-Arts C, Vasudevan P, Wenger O, Wright M, Day A, Hunter A, Patel M, Lelliott CJ, Crino PB, Yalcin B, Crosby AH, Baple EL, Logan DW, Hurles ME, Gerety SS. Models of KPTN-related disorder implicate mTOR signalling in cognitive and overgrowth phenotypes. Brain 2023; 146:4766-4783. [PMID: 37437211 PMCID: PMC10629792 DOI: 10.1093/brain/awad231] [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: 11/02/2022] [Revised: 05/31/2023] [Accepted: 06/18/2023] [Indexed: 07/14/2023] Open
Abstract
KPTN-related disorder is an autosomal recessive disorder associated with germline variants in KPTN (previously known as kaptin), a component of the mTOR regulatory complex KICSTOR. To gain further insights into the pathogenesis of KPTN-related disorder, we analysed mouse knockout and human stem cell KPTN loss-of-function models. Kptn -/- mice display many of the key KPTN-related disorder phenotypes, including brain overgrowth, behavioural abnormalities, and cognitive deficits. By assessment of affected individuals, we have identified widespread cognitive deficits (n = 6) and postnatal onset of brain overgrowth (n = 19). By analysing head size data from their parents (n = 24), we have identified a previously unrecognized KPTN dosage-sensitivity, resulting in increased head circumference in heterozygous carriers of pathogenic KPTN variants. Molecular and structural analysis of Kptn-/- mice revealed pathological changes, including differences in brain size, shape and cell numbers primarily due to abnormal postnatal brain development. Both the mouse and differentiated induced pluripotent stem cell models of the disorder display transcriptional and biochemical evidence for altered mTOR pathway signalling, supporting the role of KPTN in regulating mTORC1. By treatment in our KPTN mouse model, we found that the increased mTOR signalling downstream of KPTN is rapamycin sensitive, highlighting possible therapeutic avenues with currently available mTOR inhibitors. These findings place KPTN-related disorder in the broader group of mTORC1-related disorders affecting brain structure, cognitive function and network integrity.
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Affiliation(s)
- Maria O Levitin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Evox Therapeutics Limited, Oxford OX4 4HG, UK
| | - Lettie E Rawlins
- RILD Wellcome Wolfson Medical Research Centre, University of Exeter, Exeter EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon University Healthcare NHS Foundation Trust, Exeter EX1 2ED, UK
| | | | - Osama A Arshad
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Stephan C Collins
- INSERM Unit 1231, Université de Bourgogne Franche-Comté, Dijon 21078, France
| | - Stephen J Sawiak
- Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge CB2 3EB, UK
- Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Phillip H Iffland
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Malin H L Andersson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Caleb Bupp
- Spectrum Health, Helen DeVos Children’s Hospital, Grand Rapids, MI 49503, USA
| | - Emma L Cambridge
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Eve L Coomber
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Ian Ellis
- Department of Clinical Genetics, Alder Hey Children’s Hospital, Liverpool L14 5AB, UK
| | - Johanna C Herkert
- Department of Genetics, University Medical Centre, University of Groningen, Groningen 9713 GZ, The Netherlands
| | - Holly Ironfield
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Logan Jory
- Haven Clinical Psychology Practice Ltd, Bude, Cornwall EX23 9HP, UK
| | | | - Sarina G Kant
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3015 GD, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Alexandra Neaverson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Esther Nibbeling
- Laboratory for Diagnostic Genome Analysis, Department of Clinical Genetics, Leiden University Medical Center, Leiden 3015 GD, The Netherlands
| | - Christine Rowley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Institute of Metabolic Science, Cambridge University, Cambridge CB2 0QQ, UK
| | - Emily Relton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Faculty of Health and Medical Science, University of Surrey, Guildford GU2 7YH, UK
| | - Mark Sanderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Ethan M Scott
- New Leaf Center, Clinic for Special Children, Mount Eaton, OH 44659, USA
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Trust, Oxford OX3 7HE, UK
| | - Andrew Y Shuen
- London Health Sciences Centre, London, ON N6A 5W9, Canada
- Division of Medical Genetics, Department of Pediatrics, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5W9, Canada
| | - John Schreiber
- Department of Neurology, Children’s National Medical Center, Washington DC 20007, USA
| | - Liz Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - James Tonks
- Haven Clinical Psychology Practice Ltd, Bude, Cornwall EX23 9HP, UK
| | - Thorkild Terkelsen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus DK-8200, Denmark
| | - Conny van Ravenswaaij-Arts
- Department of Genetics, University Medical Centre, University of Groningen, Groningen 9713 GZ, The Netherlands
| | - Pradeep Vasudevan
- Department of Clinical Genetics, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester LE1 7RH, UK
| | - Olivia Wenger
- New Leaf Center, Clinic for Special Children, Mount Eaton, OH 44659, USA
| | - Michael Wright
- Institute of Human Genetics, International Centre for Life, Newcastle upon Tyne NE1 7RU, UK
| | - Andrew Day
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Qkine Ltd., Cambridge CB5 8HW, UK
| | - Adam Hunter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Minal Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Christopher J Lelliott
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Institute of Metabolic Science, Cambridge University, Cambridge CB2 0QQ, UK
| | - Peter B Crino
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Binnaz Yalcin
- INSERM Unit 1231, Université de Bourgogne Franche-Comté, Dijon 21078, France
| | - Andrew H Crosby
- RILD Wellcome Wolfson Medical Research Centre, University of Exeter, Exeter EX2 5DW, UK
| | - Emma L Baple
- RILD Wellcome Wolfson Medical Research Centre, University of Exeter, Exeter EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon University Healthcare NHS Foundation Trust, Exeter EX1 2ED, UK
| | - Darren W Logan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Waltham Petcare Science Institute, Waltham on the Wolds LE14 4RT, UK
| | - Matthew E Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sebastian S Gerety
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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24
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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: 6] [Impact Index Per Article: 6.0] [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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25
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Liu Z, Huang YF. Deep multiple-instance learning accurately predicts gene haploinsufficiency and deletion pathogenicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555384. [PMID: 37693607 PMCID: PMC10491176 DOI: 10.1101/2023.08.29.555384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Copy number losses (deletions) are a major contributor to the etiology of severe genetic disorders. Although haploinsufficient genes play a critical role in deletion pathogenicity, current methods for deletion pathogenicity prediction fail to integrate multiple lines of evidence for haploinsufficiency at the gene level, limiting their power to pinpoint deleterious deletions associated with genetic disorders. Here we introduce DosaCNV, a deep multiple-instance learning framework that, for the first time, models deletion pathogenicity jointly with gene haploinsufficiency. By integrating over 30 gene-level features potentially predictive of haploinsufficiency, DosaCNV shows unmatched performance in prioritizing pathogenic deletions associated with a broad spectrum of genetic disorders. Furthermore, DosaCNV outperforms existing methods in predicting gene haploinsufficiency even though it is not trained on known haploinsufficient genes. Finally, DosaCNV leverages a state-of-the-art technique to quantify the contributions of individual gene-level features to haploinsufficiency, allowing for human-understandable explanations of model predictions. Altogether, DosaCNV is a powerful computational tool for both fundamental and translational research.
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Affiliation(s)
- Zhihan Liu
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Molecular, Cellular, and Integrative Biosciences Program, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
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26
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Cheng J, Novati G, Pan J, Bycroft C, Žemgulytė A, Applebaum T, Pritzel A, Wong LH, Zielinski M, Sargeant T, Schneider RG, Senior AW, Jumper J, Hassabis D, Kohli P, Avsec Ž. Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science 2023; 381:eadg7492. [PMID: 37733863 DOI: 10.1126/science.adg7492] [Citation(s) in RCA: 326] [Impact Index Per Article: 326.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 08/23/2023] [Indexed: 09/23/2023]
Abstract
The vast majority of missense variants observed in the human genome are of unknown clinical significance. We present AlphaMissense, an adaptation of AlphaFold fine-tuned on human and primate variant population frequency databases to predict missense variant pathogenicity. By combining structural context and evolutionary conservation, our model achieves state-of-the-art results across a wide range of genetic and experimental benchmarks, all without explicitly training on such data. The average pathogenicity score of genes is also predictive for their cell essentiality, capable of identifying short essential genes that existing statistical approaches are underpowered to detect. As a resource to the community, we provide a database of predictions for all possible human single amino acid substitutions and classify 89% of missense variants as either likely benign or likely pathogenic.
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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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Lenassi E, Carvalho A, Thormann A, Abrahams L, Arno G, Fletcher T, Hardcastle C, Lopez J, Hunt SE, Short P, Sergouniotis PI, Michaelides M, Webster A, Cunningham F, Ramsden SC, Kasperaviciute D, Fitzpatrick DR, Black GC, Ellingford JM. EyeG2P: an automated variant filtering approach improves efficiency of diagnostic genomic testing for inherited ophthalmic disorders. J Med Genet 2023; 60:810-818. [PMID: 36669873 PMCID: PMC10423522 DOI: 10.1136/jmg-2022-108618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 12/16/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND Genomic variant prioritisation is one of the most significant bottlenecks to mainstream genomic testing in healthcare. Tools to improve precision while ensuring high recall are critical to successful mainstream clinical genomic testing, in particular for whole genome sequencing where millions of variants must be considered for each patient. METHODS We developed EyeG2P, a publicly available database and web application using the Ensembl Variant Effect Predictor. EyeG2P is tailored for efficient variant prioritisation for individuals with inherited ophthalmic conditions. We assessed the sensitivity of EyeG2P in 1234 individuals with a broad range of eye conditions who had previously received a confirmed molecular diagnosis through routine genomic diagnostic approaches. For a prospective cohort of 83 individuals, we assessed the precision of EyeG2P in comparison with routine diagnostic approaches. For 10 additional individuals, we assessed the utility of EyeG2P for whole genome analysis. RESULTS EyeG2P had 99.5% sensitivity for genomic variants previously identified as clinically relevant through routine diagnostic analysis (n=1234 individuals). Prospectively, EyeG2P enabled a significant increase in precision (35% on average) in comparison with routine testing strategies (p<0.001). We demonstrate that incorporation of EyeG2P into whole genome sequencing analysis strategies can reduce the number of variants for analysis to six variants, on average, while maintaining high diagnostic yield. CONCLUSION Automated filtering of genomic variants through EyeG2P can increase the efficiency of diagnostic testing for individuals with a broad range of inherited ophthalmic disorders.
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Affiliation(s)
- Eva Lenassi
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Ana Carvalho
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Medical Genetic Unit, Pediatric Hospital, Coimbra Hospital and Universitary Centre (CHUC), Coimbra, Portugal
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | | | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Tracy Fletcher
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Claire Hardcastle
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | | | - Panagiotis I Sergouniotis
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Michel Michaelides
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Andrew Webster
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - David R Fitzpatrick
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Graeme C Black
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Jamie M Ellingford
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Genomics England Ltd, London, UK
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Tuncay IO, DeVries D, Gogate A, Kaur K, Kumar A, Xing C, Goodspeed K, Seyoum-Tesfa L, Chahrour MH. The genetics of autism spectrum disorder in an East African familial cohort. CELL GENOMICS 2023; 3:100322. [PMID: 37492102 PMCID: PMC10363748 DOI: 10.1016/j.xgen.2023.100322] [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: 11/16/2022] [Revised: 03/09/2023] [Accepted: 04/16/2023] [Indexed: 07/27/2023]
Abstract
Autism spectrum disorder (ASD) is a group of complex neurodevelopmental conditions affecting communication and social interaction in 2.3% of children. Studies that demonstrated its complex genetic architecture have been mainly performed in populations of European ancestry. We investigate the genetics of ASD in an East African cohort (129 individuals) from a population with higher prevalence (5%). Whole-genome sequencing identified 2.13 million private variants in the cohort and potentially pathogenic variants in known ASD genes (including CACNA1C, CHD7, FMR1, and TCF7L2). Admixture analysis demonstrated that the cohort comprises two ancestral populations, African and Eurasian. Admixture mapping discovered 10 regions that confer ASD risk on the African haplotypes, containing several known ASD genes. The increased ASD prevalence in this population suggests decreased heterogeneity in the underlying genetic etiology, enabling risk allele identification. Our approach emphasizes the power of African genetic variation and admixture analysis to inform the architecture of complex disorders.
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Affiliation(s)
- Islam Oguz Tuncay
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Darlene DeVries
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashlesha Gogate
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kiran Kaur
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kimberly Goodspeed
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Maria H Chahrour
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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30
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Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich ASD, Fiziev PP, Kuderna LFK, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Bataillon T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O'Donnell-Luria A, Rehm HL, Xu J, Rogers J, Marques-Bonet T, Farh KKH. The landscape of tolerated genetic variation in humans and primates. Science 2023; 380:eabn8153. [PMID: 37262156 DOI: 10.1126/science.abn8197] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/22/2023] [Indexed: 06/03/2023]
Abstract
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.
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Affiliation(s)
- Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Tobias Hamp
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Jeffrey Ede
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Jeremy McRae
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
| | - Yanshen Yang
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | | | - Petko P Fiziev
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Yibing Wu
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Aashish Adhikari
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Yair Field
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Chen Chen
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Serafim Batzoglou
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Rebecca Reimers
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Daniel Balick
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
| | - Joseph D Orkin
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Département d'anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Alejandro Valenzuela
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, 8000 Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, Tefé, Amazonas, CEP 69553-225, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels, Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City, UT 84102, USA
| | - Iracilda Sampaio
- Universidade Federal do Para, Guamá, Belém - PA, 66075-110, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
| | - João Valsecchi do Amaral
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, 69553-225, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia - RedeFauna, Manaus, Amazonas, 69080-900, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica - ComFauna, Iquitos, Loreto, 16001, Peru
| | - Mariluce Messias
- Universidade Federal de Rondonia, Porto Velho, Rondônia, 78900-000, Brazil
- PPGREN - Programa de Pós-Graduação "Conservação e Uso dos Recursos Naturais and BIONORTE - Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Rede BIONORTE, Universidade Federal de Rondonia, Porto Velho, Rondônia, 78900-000, Brazil
| | - Maria N F da Silva
- Instituto Nacional de Pesquisas da Amazonia, Petrópolis, Manaus - AM, 69067-375, Brazil
| | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Rogerio Rossi
- Universidade Federal do Mato Grosso, Boa Esperança, Cuiabá - MT, 78060-900, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
- Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | | | | | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eduardo Fernandez-Duque
- Yale University, New Haven, CT 06520, USA
- Universidad Nacional de Formosa, Argentina Fundacion ECO, Formosa, Argentina
| | | | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, PoB 16316, Addis Ababa 1000, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Long Zhou
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Shangcheng District, Hangzhou 310006, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office, P.O. Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald - Insei Riems, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi 100000, Vietnam
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, 70191 Stuttgart, Germany
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Av. Doctor Aiguader, N88, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C. Wellington 30, 08005 Barcelona, Spain
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province 430000, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Jessica Lee
- Mandai Nature, 80 Mandai Lake Road, Singapore 729826, Republic of Singapore
| | - Patrick Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 168582, Republic of Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 168582, Republic of Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore 168582, Republic of Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz Science Campus Primate Cognition, 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Pg. Luís Companys 23, 08010 Barcelona, Spain
| | - Amanda Melin
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH8 9XP, UK
| | | | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shamil Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jinbo Xu
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
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31
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Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich A, Fiziev P, Kuderna L, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath J, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Batallion T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O’Donnell A, Rehm H, Xu J, Rogers J, Marques-Bonet T, Kai-How Farh K. The landscape of tolerated genetic variation in humans and primates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.01.538953. [PMID: 37205491 PMCID: PMC10187174 DOI: 10.1101/2023.05.01.538953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases. One Sentence Summary Deep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.
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Affiliation(s)
- Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Tobias Hamp
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Jeffrey Ede
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Joshua G. Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Jeremy McRae
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
| | - Yanshen Yang
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Anastasia Dietrich
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Petko Fiziev
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Lukas Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Yibing Wu
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Aashish Adhikari
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Yair Field
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Chen Chen
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Serafim Batzoglou
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Rebecca Reimers
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Daniel Balick
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Mareike C. Janiak
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna; Djerassiplatz 1, 1030, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna; 1030, Vienna, Austria
| | - Joseph D. Orkin
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Département d’anthropologie, Université de Montréal; 3150 Jean-Brillant, Montréal, QC, H3T 1N8, Canada
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR); Ghaziabad, 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Alejandro Valenzuela
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University; Aarhus, 8000, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University; Aarhus, 8000, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development; Estrada da Bexiga 2584, Tefé, Amazonas, CEP 69553-225, Brazil
- Faculty of Sciences, Department of Organismal Biology, Unit of Evolutionary Biology and Ecology, Université Libre de Bruxelles (ULB); Avenue Franklin D. Roosevelt 50, 1050, Brussels, Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University; SE-75236, Uppsala, Sweden
| | | | - Julie Horvath
- North Carolina Museum of Natural Sciences; Raleigh, North Carolina, 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University; Durham, North Carolina , 27707, USA
- Department of Biological Sciences, North Carolina State University; Raleigh, North Carolina , 27695, USA
- Department of Evolutionary Anthropology, Duke University; Durham, North Carolina , 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | | | - Fabricio Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah; Salt Lake City, Utah, 84102, USA
| | - Iracilda Sampaio
- Universidade Federal do Para; Guamá, Belém - PA, 66075-110, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
| | - João Valsecchi do Amaral
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development; Tefé, Amazonas, 69553-225, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia – RedeFauna; Manaus, Amazonas, 69080-900, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica – ComFauna; Iquitos, Loreto, 16001, Peru
| | - Mariluce Messias
- Universidade Federal de Rondonia; Porto Velho, Rondônia, 78900-000, Brazil
- PPGREN - Programa de Pós-Graduação “Conservação e Uso dos Recursos Naturais and BIONORTE - Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Rede BIONORTE, Universidade Federal de Rondonia; Porto Velho, Rondônia, 78900-000, Brazil
| | - Maria N. F. da Silva
- Instituto Nacional de Pesquisas da Amazonia; Petrópolis, Manaus - AM, 69067-375, Brazil
| | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Rogerio Rossi
- Universidade Federal do Mato Grosso; Boa Esperança, Cuiabá - MT, 78060-900, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
- Department of Biology, Trinity University; San Antonio, Texas, 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | - Clément J. Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | | | | | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center; Houston, Texas, 77030, USA
| | | | - Joe H. Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center; Houston, Texas, 77030, USA
| | - Eduardo Fernandez-Duque
- Yale University; New Haven, Connecticut, 06520, USA
- Universidad Nacional de Formosa, Argentina Fundacion ECO, Formosa, Argentina
| | | | | | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming, Yunnan, 650223, China
| | - Long Zhou
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming, Yunnan, 650223, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen; Copenhagen, DK-2100, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center; 1369 West Wenyi Road, Hangzhou, 311121, China
- Women’s Hospital, School of Medicine, Zhejiang University; 1 Xueshi Road, Shangcheng District, Hangzhou, 310006, China
| | - Julius D. Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office; P.O.Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health; 17493 Greifswald - Isle of Riems, Germany
| | - Minh D. Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University; Hanoi, 100000, Vietnam
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart; 70191 Stuttgart, Germany
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology; Av. Doctor Aiguader, N88, Barcelona, 08003, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation; C. Wellington 30, Barcelona, 08005, Spain
| | - Thomas Batallion
- Bioinformatics Research Centre, Aarhus University; Aarhus, 8000, Denmark
| | - Tilo Nadler
- Cuc Phuong Commune; Nho Quan District, Ninh Binh Province, 430000, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Jessica Lee
- Mandai Nature; 80 Mandai Lake Road, Singapore 729826, Republic of Singapore
| | - Patrick Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM); Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School; Singapore 168582, Republic of Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM); Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School; Singapore 168582, Republic of Singapore
- SingHealth Duke-NUS Genomic Medicine Centre; Singapore 168582, Republic of Singapore
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland; Chambers Street, Edinburgh, EH1 1JF, UK
- School of Geosciences, University of Edinburgh; Drummond Street, Edinburgh, EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research; 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen; 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
- Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
| | - Amanda Melin
- Leibniz Science Campus Primate Cognition; 37077 Göttingen, Germany
- Department of Anthropology & Archaeology and Department of Medical Genetics
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University; SE-75236, Uppsala, Sweden
- Alberta Children’s Hospital Research Institute; University of Calgary; 2500 University Dr NW T2N 1N4, Calgary, Alberta, Canada
| | | | - Robin M. D. Beck
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR); Ghaziabad, 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Christian Roos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh; Edinburgh, EH8 9XP, UK
| | - Jean P. Boubli
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Monkol Lek
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research; Kellnerweg 4, 37077 Göttingen, Germany
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- Department of Genetics, Yale School of Medicine; New Haven, Connecticut, 06520, USA
| | - Anne O’Donnell
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Heidi Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Jinbo Xu
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
- Toyota Technological Institute at Chicago; Chicago, Illinois, 60637, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
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Wright CF, Campbell P, Eberhardt RY, Aitken S, Perrett D, Brent S, Danecek P, Gardner EJ, Chundru VK, Lindsay SJ, Andrews K, Hampstead J, Kaplanis J, Samocha KE, Middleton A, Foreman J, Hobson RJ, Parker MJ, Martin HC, FitzPatrick DR, Hurles ME, Firth HV. Genomic Diagnosis of Rare Pediatric Disease in the United Kingdom and Ireland. N Engl J Med 2023; 388:1559-1571. [PMID: 37043637 PMCID: PMC7614484 DOI: 10.1056/nejmoa2209046] [Citation(s) in RCA: 71] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
BACKGROUND Pediatric disorders include a range of highly penetrant, genetically heterogeneous conditions amenable to genomewide diagnostic approaches. Finding a molecular diagnosis is challenging but can have profound lifelong benefits. METHODS We conducted a large-scale sequencing study involving more than 13,500 families with probands with severe, probably monogenic, difficult-to-diagnose developmental disorders from 24 regional genetics services in the United Kingdom and Ireland. Standardized phenotypic data were collected, and exome sequencing and microarray analyses were performed to investigate novel genetic causes. We developed an iterative variant analysis pipeline and reported candidate variants to clinical teams for validation and diagnostic interpretation to inform communication with families. Multiple regression analyses were performed to evaluate factors affecting the probability of diagnosis. RESULTS A total of 13,449 probands were included in the analyses. On average, we reported 1.0 candidate variant per parent-offspring trio and 2.5 variants per singleton proband. Using clinical and computational approaches to variant classification, we made a diagnosis in approximately 41% of probands (5502 of 13,449). Of 3599 probands in trios who received a diagnosis by clinical assertion, approximately 76% had a pathogenic de novo variant. Another 22% of probands (2997 of 13,449) had variants of uncertain significance in genes that were strongly linked to monogenic developmental disorders. Recruitment in a parent-offspring trio had the largest effect on the probability of diagnosis (odds ratio, 4.70; 95% confidence interval [CI], 4.16 to 5.31). Probands were less likely to receive a diagnosis if they were born extremely prematurely (i.e., 22 to 27 weeks' gestation; odds ratio, 0.39; 95% CI, 0.22 to 0.68), had in utero exposure to antiepileptic medications (odds ratio, 0.44; 95% CI, 0.29 to 0.67), had mothers with diabetes (odds ratio, 0.52; 95% CI, 0.41 to 0.67), or were of African ancestry (odds ratio, 0.51; 95% CI, 0.31 to 0.78). CONCLUSIONS Among probands with severe, probably monogenic, difficult-to-diagnose developmental disorders, multimodal analysis of genomewide data had good diagnostic power, even after previous attempts at diagnosis. (Funded by the Health Innovation Challenge Fund and Wellcome Sanger Institute.).
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Affiliation(s)
- Caroline F. Wright
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter UK, EX2 5DW
| | - Patrick Campbell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- Cambridge University Hospitals Foundation Trust, Addenbrooke’s Hospital, Cambridge UK, CB2 0QQ
| | - Ruth Y. Eberhardt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Stuart Aitken
- MRC Human Genetics Unit, Institute of Genetic and Cancer, University of Edinburgh, Edinburgh UK, EH4 2XU
| | - Daniel Perrett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SD
| | - Simon Brent
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SD
| | - Petr Danecek
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Eugene J. Gardner
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - V. Kartik Chundru
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Sarah J. Lindsay
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Katrina Andrews
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Juliet Hampstead
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Joanna Kaplanis
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Kaitlin E. Samocha
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Anna Middleton
- Wellcome Connecting Science, Wellcome Genome Campus, Hinxton, Cambridge, UK, CB10 1SA
| | - Julia Foreman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SD
| | - Rachel J. Hobson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Michael J. Parker
- Wellcome Centre for Ethics and Humanities/Ethox Centre, Oxford Population Health, University of Oxford, Big Data Institute, Old Road Campus, Oxford, UK, OX3 7LF
| | - Hilary C. Martin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - David R. FitzPatrick
- MRC Human Genetics Unit, Institute of Genetic and Cancer, University of Edinburgh, Edinburgh UK, EH4 2XU
| | - Matthew E. Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Helen V. Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- Cambridge University Hospitals Foundation Trust, Addenbrooke’s Hospital, Cambridge UK, CB2 0QQ
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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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Whole Genome Analysis of Dizygotic Twins With Autism Reveals Prevalent Transposon Insertion Within Neuronal Regulatory Elements: Potential Implications for Disease Etiology and Clinical Assessment. J Autism Dev Disord 2023; 53:1091-1106. [PMID: 35759154 DOI: 10.1007/s10803-022-05636-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2022] [Indexed: 10/17/2022]
Abstract
Transposable elements (TEs) have been implicated in autism spectrum disorder (ASD). However, our understanding of their roles is far from complete. Herein, we explored de novo TE insertions (dnTEIs) and de novo variants (DNVs) across the genomes of dizygotic twins with ASD and their parents. The neuronal regulatory elements had a tendency to harbor dnTEIs that were shared between twins, but ASD-risk genes had dnTEIs that were unique to each twin. The dnTEIs were 4.6-fold enriched in enhancers that are active in embryonic stem cell (ESC)-neurons (p < 0.001), but DNVs were 1.5-fold enriched in active enhancers of astrocytes (p = 0.0051). Our findings suggest that dnTEIs and DNVs play a role in ASD etiology by disrupting enhancers of neurons and astrocytes.
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Wang N, Li Y, Zhou X, Wang X, Yang G. Comprehensive analysis identifies ARHGEF6 as a potential prognostic and immunological biomarker in lung adenocarcinoma. Comput Biol Med 2023; 153:106448. [PMID: 36586227 DOI: 10.1016/j.compbiomed.2022.106448] [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: 08/14/2022] [Revised: 12/11/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Lung adenocarcinoma (LUAD), the most common histological type in lung cancer, is one of leading cancers with considerable morbidity/mortality worldwide. Treating LUAD remains an outstanding challenge due to the lack of early diagnosis and the poor therapeutic effects. Rac/Cdc42 guanine nucleotide exchange factor 6 (ARHGEF6), one of cytoskeletal regulators, exerts crucial biological functions in T cell migration. The potential biological role of ARHGEF6 in LUAD has yet to be established. Using multiple bioinformatics tools and statistical methods, we discovered that the mRNA and protein expression level of ARHGEF6 was significantly downregulated in tumor tissues comparing to normal controls. Moreover, ARHGEF6 presented high diagnostic value in LUAD patients (AUC = 0.949), and the patients with low ARHGEF6 expression had more somatic mutations and poor T stage, N stage, clinical prognosis. Experimental validation indicated that ARHGEF6 was low expressed in A549 and PC-9 cells comparing to the normal lung epithelial cells. The overexpression of ARHGEF6 remarkably attenuated the abilities of cell proliferation and colony formation. Furthermore, the immune landscape analysis in TME revealed that ARHGEF6 expression was positively associated with immune cell infiltration and immune checkpoints. Single-cell transcriptome analysis indicated that ARHGEF6 expression was also distributed in immune cell types in TME based on TISCH database. Additionally, differentially expressed genes (DEGs) and functional enrichment analyses uncovered that ARHGEF6 was involved in T cell activation. Finally, LUAD samples were classified two clusters based on DEGs for subgroups analysis. In summary, this study comprehensively uncovered that ARHGEF6 could be identified as a potential prognostic and immunological biomarker in lung adenocarcinoma.
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Affiliation(s)
- Ning Wang
- The Third Central Hospital of Tianjin, Tianjin, 300170, China.
| | - Yuanyuan Li
- Department of Oncology, The Third Central Hospital of Tianjin, Tianjin, 300170, China
| | - Xue Zhou
- Department of Nephrology, Tianjin Haihe Hospital, Tianjin, 300350, China
| | - Xue Wang
- Department of Respiratory Medicine, The Third Central Hospital of Tianjin, Tianjin, 300170, China
| | - Guoyue Yang
- The Third Central Hospital of Tianjin, Tianjin, 300170, China
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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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Eberhardt RY, Wright CF, FitzPatrick DR, Hurles ME, Firth HV. Detection of mosaic chromosomal alterations in children with severe developmental disorders recruited to the DDD study. GENETICS IN MEDICINE OPEN 2023; 1:100836. [PMID: 39346101 PMCID: PMC11436381 DOI: 10.1016/j.gimo.2023.100836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/01/2024]
Abstract
Purpose Structural mosaicism has been previously implicated in developmental disorders. We aimed to identify rare mosaic chromosomal alterations (MCAs) in probands with severe undiagnosed developmental disorders. Methods We identified MCAs in genotyping array data from 12,530 probands in the Deciphering Developmental Disorders study using mosaic chromosome alterations caller (MoChA). Results We found 61 MCAs in 57 probands, many of these were tissue specific. In 23 of 26 (88.5%) cases for which the MCA was detected in saliva in which blood was also available for analysis, the MCA could not be detected in blood. The MCAs included 20 polysomies, comprising either 1 arm of a chromosome or a whole chromosome, for which we were able to show the timing of the error (25% mitosis, 40% meiosis I, and 35% meiosis II). Only 2 of 57 (3.5%) of the probands in whom we found MCAs had another likely genetic diagnosis identified by exome sequencing, despite an overall diagnostic yield of ∼40% across the cohort. Conclusion Our results show that identification of MCAs provides candidate diagnoses for previously undiagnosed patients with developmental disorders, potentially explaining ∼0.45% of cases in the Deciphering Developmental Disorders study. Nearly 90% of these MCAs would have remained undetected by analyzing DNA from blood and no other tissue.
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Affiliation(s)
- Ruth Y Eberhardt
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, United Kingdom
| | - Caroline F Wright
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Matthew E Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, United Kingdom
| | - Helen V Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Clinical Genetics, Addenbrooke's Hospital, Cambridge, United Kingdom
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Nagirnaja L, Lopes AM, Charng WL, Miller B, Stakaitis R, Golubickaite I, Stendahl A, Luan T, Friedrich C, Mahyari E, Fadial E, Kasak L, Vigh-Conrad K, Oud MS, Xavier MJ, Cheers SR, James ER, Guo J, Jenkins TG, Riera-Escamilla A, Barros A, Carvalho F, Fernandes S, Gonçalves J, Gurnett CA, Jørgensen N, Jezek D, Jungheim ES, Kliesch S, McLachlan RI, Omurtag KR, Pilatz A, Sandlow JI, Smith J, Eisenberg ML, Hotaling JM, Jarvi KA, Punab M, Rajpert-De Meyts E, Carrell DT, Krausz C, Laan M, O'Bryan MK, Schlegel PN, Tüttelmann F, Veltman JA, Almstrup K, Aston KI, Conrad DF. Diverse monogenic subforms of human spermatogenic failure. Nat Commun 2022; 13:7953. [PMID: 36572685 PMCID: PMC9792524 DOI: 10.1038/s41467-022-35661-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 12/16/2022] [Indexed: 12/27/2022] Open
Abstract
Non-obstructive azoospermia (NOA) is the most severe form of male infertility and typically incurable. Defining the genetic basis of NOA has proven challenging, and the most advanced classification of NOA subforms is not based on genetics, but simple description of testis histology. In this study, we exome-sequenced over 1000 clinically diagnosed NOA cases and identified a plausible recessive Mendelian cause in 20%. We find further support for 21 genes in a 2-stage burden test with 2072 cases and 11,587 fertile controls. The disrupted genes are primarily on the autosomes, enriched for undescribed human "knockouts", and, for the most part, have yet to be linked to a Mendelian trait. Integration with single-cell RNA sequencing data shows that azoospermia genes can be grouped into molecular subforms with synchronized expression patterns, and analogs of these subforms exist in mice. This analysis framework identifies groups of genes with known roles in spermatogenesis but also reveals unrecognized subforms, such as a set of genes expressed across mitotic divisions of differentiating spermatogonia. Our findings highlight NOA as an understudied Mendelian disorder and provide a conceptual structure for organizing the complex genetics of male infertility, which may provide a rational basis for disease classification.
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Affiliation(s)
- Liina Nagirnaja
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Alexandra M Lopes
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Wu-Lin Charng
- Department of Neurology, Washington University, St. Louis, MO, USA
| | - Brian Miller
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Rytis Stakaitis
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Laboratory of Molecular Neurooncology, Neuroscience Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Ieva Golubickaite
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alexandra Stendahl
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Tianpengcheng Luan
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Corinna Friedrich
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Eisa Mahyari
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Eloise Fadial
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Laura Kasak
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Katinka Vigh-Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Manon S Oud
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Miguel J Xavier
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Samuel R Cheers
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Emma R James
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jingtao Guo
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Timothy G Jenkins
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Antoni Riera-Escamilla
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Catalonia, Spain
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB Sant Pau), Universitat Autònoma de Barcelona, Barcelona, Catalonia, 08025, Spain
| | - Alberto Barros
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Filipa Carvalho
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Susana Fernandes
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - João Gonçalves
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal
- Centre for Toxicogenomics and Human Health, Nova Medical School, Lisbon, Portugal
| | | | - Niels Jørgensen
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Davor Jezek
- Department of Histology and Embryology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Emily S Jungheim
- Department of Obstetrics and Gynecology at Northwestern University, Division of Reproductive Endocrinology, Chicago, IL, USA
| | - Sabine Kliesch
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - Robert I McLachlan
- Hudson Institute of Medical Research and the Department of Obstetrics and Gynecology, Monash University, Clayton, VIC, Australia
| | - Kenan R Omurtag
- Department of Obstetrics and Gynecology at Washington University, Division of Reproductive Endocrinology, St. Louis, MO, USA
| | - Adrian Pilatz
- Clinic for Urology, Pediatric Urology and Andrology, Justus Liebig University, Giessen, Germany
| | - Jay I Sandlow
- Department of Urology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - James Smith
- Department of Urology, University California San Francisco, San Francisco, CA, USA
| | - Michael L Eisenberg
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
| | - James M Hotaling
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Keith A Jarvi
- Division of Urology, Department of Surgery, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Margus Punab
- Andrology Center, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Ewa Rajpert-De Meyts
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Douglas T Carrell
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Csilla Krausz
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Maris Laan
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Moira K O'Bryan
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Peter N Schlegel
- Department of Urology, Weill Cornell Medicine, New York, NY, USA
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Joris A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Kristian Almstrup
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Kenneth I Aston
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Donald F Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA.
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Cormier MJ, Pedersen BS, Bayrak-Toydemir P, Quinlan AR. Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies. BMC Bioinformatics 2022; 23:482. [PMID: 36376793 PMCID: PMC9664736 DOI: 10.1186/s12859-022-05041-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Despite numerous molecular and computational advances, roughly half of patients with a rare disease remain undiagnosed after exome or genome sequencing. A particularly challenging barrier to diagnosis is identifying variants that cause deleterious alternative splicing at intronic or exonic loci outside of canonical donor or acceptor splice sites. RESULTS Several existing tools predict the likelihood that a genetic variant causes alternative splicing. We sought to extend such methods by developing a new metric that aids in discerning whether a genetic variant leads to deleterious alternative splicing. Our metric combines genetic variation in the Genome Aggregate Database with alternative splicing predictions from SpliceAI to compare observed and expected levels of splice-altering genetic variation. We infer genic regions with significantly less splice-altering variation than expected to be constrained. The resulting model of regional splicing constraint captures differential splicing constraint across gene and exon categories, and the most constrained genic regions are enriched for pathogenic splice-altering variants. Building from this model, we developed ConSpliceML. This ensemble machine learning approach combines regional splicing constraint with multiple per-nucleotide alternative splicing scores to guide the prediction of deleterious splicing variants in protein-coding genes. ConSpliceML more accurately distinguishes deleterious and benign splicing variants than state-of-the-art splicing prediction methods, especially in "cryptic" splicing regions beyond canonical donor or acceptor splice sites. CONCLUSION Integrating a model of genetic constraint with annotations from existing alternative splicing tools allows ConSpliceML to prioritize potentially deleterious splice-altering variants in studies of rare human diseases.
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Affiliation(s)
- Michael J Cormier
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Brent S Pedersen
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | | | - Aaron R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
- Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA.
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.
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40
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Halliday BJ, Baynam G, Ewans L, Greenhalgh L, Leventer RJ, Pilz DT, Sachdev R, Scheffer IE, Markie DM, McGillivray G, Robertson SP, Mandelstam S. Distinctive Brain Malformations in Zhu-Tokita-Takenouchi-Kim Syndrome. AJNR Am J Neuroradiol 2022; 43:1660-1666. [PMID: 36229163 PMCID: PMC9731255 DOI: 10.3174/ajnr.a7663] [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: 02/24/2022] [Accepted: 08/08/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND AND PURPOSE Zhu-Tokita-Takenouchi-Kim syndrome is a severe multisystem malformation disorder characterized by developmental delay and a diverse array of congenital abnormalities. However, these currently identified phenotypic components provide limited guidance in diagnostic situations, due to both the nonspecificity and variability of these features. Here we report a case series of 7 individuals with a molecular diagnosis of Zhu-Tokita-Takenouchi-Kim syndrome, 5 ascertained by their presentation with the neuronal migration disorder, periventricular nodular heterotopia. MATERIALS AND METHODS Individuals with a molecular diagnosis of Zhu-Tokita-Takenouchi-Kim syndrome were recruited from 2 sources, a high-throughput sequencing study of individuals with periventricular nodular heterotopia or from clinical diagnostic sequencing studies. We analyzed available brain MR images of recruited individuals to characterize periventricular nodular heterotopia distribution and to identify the presence of any additional brain abnormalities. RESULTS Pathogenic variants in SON, causative of Zhu-Tokita-Takenouchi-Kim syndrome, were identified in 7 individuals. Brain MR images from these individuals were re-analyzed. A characteristic set of imaging anomalies in addition to periventricular nodular heterotopia was identified, including the elongation of the pituitary stalk, cerebellar enlargement with an abnormally shaped posterior fossa, rounding of the caudate nuclei, hippocampal malformations, and cortical anomalies including polymicrogyria or dysgyria. CONCLUSIONS The recurrent neuroradiologic changes identified here represent an opportunity to guide diagnostic formulation of Zhu-Tokita-Takenouchi-Kim syndrome on the basis of brain MR imaging evaluation.
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Affiliation(s)
- B J Halliday
- From the Departments of Women's and Children's Health (B.J.H., S.P.R.)
| | - G Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia (G.B.), Undiagnosed Diseases Program, King Edward Memorial Hospital, Perth, Australia
| | - L Ewans
- Centre for Population Genomics (L.E.), Garvan Institute of Medical Research, Sydney, Australia
- Centre for Clinical Genetics (L.E., R.S.), Sydney Children's Hospital, Sydney, Australia
| | - L Greenhalgh
- Liverpool Centre for Genomic Medicine (L.G.), Liverpool Women's Hospital, Liverpool, England
| | - R J Leventer
- Murdoch Children's Research Institute (R.J.L., I.E.S., G.M., S.M.), Melbourne, Australia
- Department of Paediatrics (R.J.L., I.E.S., S.M.), Epilepsy Research Centre
- Departments of Neurology (R.J.L., I.E.S.)
| | - D T Pilz
- West of Scotland Genetics Service (D.T.P.), Queen Elizabeth University Hospital, Glasgow, UK
| | - R Sachdev
- Centre for Clinical Genetics (L.E., R.S.), Sydney Children's Hospital, Sydney, Australia
| | - I E Scheffer
- Murdoch Children's Research Institute (R.J.L., I.E.S., G.M., S.M.), Melbourne, Australia
- Department of Paediatrics (R.J.L., I.E.S., S.M.), Epilepsy Research Centre
- Austin Health (I.E.S.)
- Florey Institute (I.E.S.), University of Melbourne, Melbourne, Australia
- Departments of Neurology (R.J.L., I.E.S.)
| | - D M Markie
- Pathology (D.M.M.), OtagoMedical School, University of Otago, Dunedin, New Zealand
| | - G McGillivray
- Murdoch Children's Research Institute (R.J.L., I.E.S., G.M., S.M.), Melbourne, Australia
- Victorian Clinical Genetics Services (G.M.), Murdoch Children's Research Institute, Melbourne, Australia
| | - S P Robertson
- From the Departments of Women's and Children's Health (B.J.H., S.P.R.)
| | - S Mandelstam
- Murdoch Children's Research Institute (R.J.L., I.E.S., G.M., S.M.), Melbourne, Australia
- Department of Paediatrics (R.J.L., I.E.S., S.M.), Epilepsy Research Centre
- Radiology (S.M.), Royal Children's Hospital, Melbourne, Australia
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41
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Motelow JE, Lippa NC, Hostyk J, Feldman E, Nelligan M, Ren Z, Alkelai A, Milner JD, Gharavi AG, Tang Y, Goldstein DB, Kernie SG. Risk Variants in the Exomes of Children With Critical Illness. JAMA Netw Open 2022; 5:e2239122. [PMID: 36306130 PMCID: PMC9617179 DOI: 10.1001/jamanetworkopen.2022.39122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IMPORTANCE Diagnostic genetic testing can lead to changes in management in the pediatric intensive care unit. Genetic risk in children with critical illness but nondiagnostic exome sequencing (ES) has not been explored. OBJECTIVE To assess the association between loss-of-function (LOF) variants and pediatric critical illness. DESIGN, SETTING, AND PARTICIPANTS This genetic association study examined ES first screened for causative variants among 267 children at the Morgan Stanley Children's Hospital of NewYork-Presbyterian, of whom 22 were otherwise healthy with viral respiratory failure; 18 deceased children with bronchiolitis from the Office of the Chief Medical Examiner of New York City, of whom 14 were previously healthy; and 9990 controls from the Institute for Genomic Medicine at Columbia University Irving Medical Center. The ES data were generated between January 1, 2015, and December 31, 2020, and analyzed between January 1, 2017, and September 2, 2022. EXPOSURE Critical illness. MAIN OUTCOMES AND MEASURES Odds ratios and P values for genes and gene-sets enriched for rare LOF variants and the loss-of-function observed/expected upper bound fraction (LOEUF) score at which cases have a significant enrichment. RESULTS This study included 285 children with critical illness (median [range] age, 4.1 [0-18.9] years; 148 [52%] male) and 9990 controls. A total of 228 children (80%) did not receive a genetic diagnosis. After quality control (QC), 231 children harbored excess rare LOF variants in genes with a LOEUF score of 0.680 or less (intolerant genes) (P = 1.0 × 10-5). After QC, 176 children without a diagnosis harbored excess ultrarare LOF variants in intolerant genes but only in those without a known disease association (odds ratio, 1.8; 95% CI, 1.3-2.5). After QC, 25 children with viral respiratory failure harbored excess ultrarare LOF variants in intolerant genes but only in those without a known disease association (odds ratio, 2.8; 95% CI, 1.1-6.6). A total of 114 undiagnosed children were enriched for de novo LOF variants in genes without a known disease association (observed, 14; expected, 6.8; enrichment, 2.05). CONCLUSIONS AND RELEVANCE In this genetic association study, excess LOF variants were observed among critically ill children despite nondiagnostic ES. Variants lay in genes without a known disease association, suggesting future investigation may connect phenotypes to causative genes.
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Affiliation(s)
- Joshua E. Motelow
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
| | - Natalie C. Lippa
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Joseph Hostyk
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Evin Feldman
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
| | - Matthew Nelligan
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
| | - Zhong Ren
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York
| | | | - Ali G. Gharavi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, NewYork-Presbyterian, New York, New York
| | - Yingying Tang
- Molecular Genetics Laboratory, New York City Office of Chief Medical Examiner, New York, New York
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Steven G. Kernie
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
- NewYork-Presbyterian Hospital, New York, New York
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42
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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: 34] [Impact Index Per Article: 17.0] [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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43
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Beaumont RN, Wright CF. Estimating diagnostic noise in panel-based genomic analysis. Genet Med 2022; 24:2042-2050. [PMID: 35920826 DOI: 10.1016/j.gim.2022.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 11/26/2022] Open
Abstract
PURPOSE Gene panels with a series of strict variant filtering rules are often used for clinical analysis of exomes and genomes. Panel sizes vary, affecting the test's sensitivity and specificity. We investigated the background rate of candidate variants in a population setting using gene panels developed to diagnose a range of heterogeneous monogenic diseases. METHODS We used the Gene2Phenotype database with the Variant Effect Predictor plugin to identify rare nonsynonymous variants in exome sequence data from 200,643 individuals in UK Biobank. We evaluated 5 clinically curated gene panels of varying sizes (50-1700 genes). RESULTS Bigger gene panels resulted in more prioritized variants, varying from an average of approximately 0.3 to 3.5 variants per person. The number of individuals with prioritized variants varied linearly with coding sequence length for monoallelic genes (∼300 individuals per 1000 base pairs) and quadratically for biallelic genes, with notable outliers. CONCLUSION Although large gene panels may be the best strategy to maximize diagnostic yield in genetically heterogeneous diseases, they frequently prioritize likely benign variants requiring follow up. Most individuals have ≥1 rare nonsynonymous variant in panels containing >500 disease genes. Extreme caution should be applied when interpreting candidate variants, particularly in the absence of relevant phenotypes.
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Affiliation(s)
- Robin N Beaumont
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom.
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44
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Riggs ER, Bingaman TI, Barry CA, Behlmann A, Bluske K, Bostwick B, Bright A, Chen CA, Clause AR, Dharmadhikari AV, Ganapathi M, Gonzaga-Jauregui C, Grant AR, Hughes MY, Kim SR, Krause A, Liao J, Lumaka A, Mah M, Maloney CM, Mohan S, Osei-Owusu IA, Reble E, Rennie O, Savatt JM, Shimelis H, Siegert RK, Sneddon TP, Thaxton C, Toner KA, Tran KT, Webb R, Wilcox EH, Yin J, Zhuo X, Znidarsic M, Martin CL, Betancur C, Vorstman JAS, Miller DT, Schaaf CP. Clinical validity assessment of genes frequently tested on intellectual disability/autism sequencing panels. Genet Med 2022; 24:1899-1908. [PMID: 35616647 PMCID: PMC10200330 DOI: 10.1016/j.gim.2022.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/28/2022] [Accepted: 05/02/2022] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Neurodevelopmental disorders (NDDs), such as intellectual disability (ID) and autism spectrum disorder (ASD), exhibit genetic and phenotypic heterogeneity, making them difficult to differentiate without a molecular diagnosis. The Clinical Genome Resource Intellectual Disability/Autism Gene Curation Expert Panel (GCEP) uses systematic curation to distinguish ID/ASD genes that are appropriate for clinical testing (ie, with substantial evidence supporting their relationship to disease) from those that are not. METHODS Using the Clinical Genome Resource gene-disease validity curation framework, the ID/Autism GCEP classified genes frequently included on clinical ID/ASD testing panels as Definitive, Strong, Moderate, Limited, Disputed, Refuted, or No Known Disease Relationship. RESULTS As of September 2021, 156 gene-disease pairs have been evaluated. Although most (75%) were determined to have definitive roles in NDDs, 22 (14%) genes evaluated had either Limited or Disputed evidence. Such genes are currently not recommended for use in clinical testing owing to the limited ability to assess the effect of identified variants. CONCLUSION Our understanding of gene-disease relationships evolves over time; new relationships are discovered and previously-held conclusions may be questioned. Without periodic re-examination, inaccurate gene-disease claims may be perpetuated. The ID/Autism GCEP will continue to evaluate these claims to improve diagnosis and clinical care for NDDs.
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Affiliation(s)
| | | | | | | | | | - Bret Bostwick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | | | - Chun-An Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | | | - Avinash V Dharmadhikari
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA; Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Mythily Ganapathi
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Claudia Gonzaga-Jauregui
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, Mexico
| | - Andrew R Grant
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; New York Medical College, Valhalla, NY
| | | | - Se Rin Kim
- National Human Genome Research Institute, Bethesda, MD
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jun Liao
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Aimé Lumaka
- Laboratoire de Génétique Humaine, University of Liège, Liège, Belgium
| | - Michelle Mah
- Trillium Health Partners, Mississauga, Ontario, Canada
| | | | | | - Ikeoluwa A Osei-Owusu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Emma Reble
- St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Olivia Rennie
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Juliann M Savatt
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA
| | - Hermela Shimelis
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA
| | - Rebecca K Siegert
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Tam P Sneddon
- Department of Pathology and Laboratory Medicine, School of Medicine, The University of North Carolina, Chapel Hill, NC
| | - Courtney Thaxton
- Department of Pathology and Laboratory Medicine, School of Medicine, The University of North Carolina, Chapel Hill, NC
| | - Kelly A Toner
- Drexel University College of Medicine, Philadelphia, PA
| | - Kien Trung Tran
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Ryan Webb
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Emma H Wilcox
- The Warren Alpert Medical School of Brown University, Providence, RI
| | - Jiani Yin
- Department of Neurology, University of California Los Angeles, Los Angeles, CA
| | - Xinming Zhuo
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Masa Znidarsic
- University Medical Center Ljubljana, Ljubljana, Slovenia
| | | | - Catalina Betancur
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France
| | - Jacob A S Vorstman
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
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45
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Warrier V, Zhang X, Reed P, Havdahl A, Moore TM, Cliquet F, Leblond CS, Rolland T, Rosengren A, Rowitch DH, Hurles ME, Geschwind DH, Børglum AD, Robinson EB, Grove J, Martin HC, Bourgeron T, Baron-Cohen S. Genetic correlates of phenotypic heterogeneity in autism. Nat Genet 2022; 54:1293-1304. [PMID: 35654973 PMCID: PMC9470531 DOI: 10.1038/s41588-022-01072-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 04/01/2022] [Indexed: 12/27/2022]
Abstract
The substantial phenotypic heterogeneity in autism limits our understanding of its genetic etiology. To address this gap, here we investigated genetic differences between autistic individuals (nmax = 12,893) based on core and associated features of autism, co-occurring developmental disabilities and sex. We conducted a comprehensive factor analysis of core autism features in autistic individuals and identified six factors. Common genetic variants were associated with the core factors, but de novo variants were not. We found that higher autism polygenic scores (PGS) were associated with lower likelihood of co-occurring developmental disabilities in autistic individuals. Furthermore, in autistic individuals without co-occurring intellectual disability (ID), autism PGS are overinherited by autistic females compared to males. Finally, we observed higher SNP heritability for autistic males and for autistic individuals without ID. Deeper phenotypic characterization will be critical in determining how the complex underlying genetics shape cognition, behavior and co-occurring conditions in autism.
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Affiliation(s)
- Varun Warrier
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK.
| | - Xinhe Zhang
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Patrick Reed
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Alexandra Havdahl
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway
- PROMENTA Research Center, Department of Psychology, University of Oslo, Oslo, Norway
| | - Tyler M Moore
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Lifespan Brain Institute of the Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA, USA
| | - Freddy Cliquet
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris Cité, Paris, France
| | - Claire S Leblond
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris Cité, Paris, France
| | - Thomas Rolland
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris Cité, Paris, France
| | - Anders Rosengren
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Institute of Biological Psychiatry, MHC Sct Hans, Copenhagen University Hospital, Copenhagen, Denmark
| | - David H Rowitch
- Department of Paediatrics, Cambridge University Clinical School, Cambridge, UK
| | - Matthew E Hurles
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Daniel H Geschwind
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine (CGPM), Aarhus University, Aarhus, Denmark
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, Aarhus, Denmark
| | - Elise B Robinson
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine (CGPM), Aarhus University, Aarhus, Denmark
- Department of Biomedicine (Human Genetics) and iSEQ Center, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Hilary C Martin
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris Cité, Paris, France
| | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK.
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46
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Blakes AJM, Wai HA, Davies I, Moledina HE, Ruiz A, Thomas T, Bunyan D, Thomas NS, Burren CP, Greenhalgh L, Lees M, Pichini A, Smithson SF, Taylor Tavares AL, O'Donovan P, Douglas AGL, Whiffin N, Baralle D, Lord J. A systematic analysis of splicing variants identifies new diagnoses in the 100,000 Genomes Project. Genome Med 2022; 14:79. [PMID: 35883178 PMCID: PMC9327385 DOI: 10.1186/s13073-022-01087-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/13/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Genomic variants which disrupt splicing are a major cause of rare genetic diseases. However, variants which lie outside of the canonical splice sites are difficult to interpret clinically. Improving the clinical interpretation of non-canonical splicing variants offers a major opportunity to uplift diagnostic yields from whole genome sequencing data. METHODS Here, we examine the landscape of splicing variants in whole-genome sequencing data from 38,688 individuals in the 100,000 Genomes Project and assess the contribution of non-canonical splicing variants to rare genetic diseases. We use a variant-level constraint metric (the mutability-adjusted proportion of singletons) to identify constrained functional variant classes near exon-intron junctions and at putative splicing branchpoints. To identify new diagnoses for individuals with unsolved rare diseases in the 100,000 Genomes Project, we identified individuals with de novo single-nucleotide variants near exon-intron boundaries and at putative splicing branchpoints in known disease genes. We identified candidate diagnostic variants through manual phenotype matching and confirmed new molecular diagnoses through clinical variant interpretation and functional RNA studies. RESULTS We show that near-splice positions and splicing branchpoints are highly constrained by purifying selection and harbour potentially damaging non-coding variants which are amenable to systematic analysis in sequencing data. From 258 de novo splicing variants in known rare disease genes, we identify 35 new likely diagnoses in probands with an unsolved rare disease. To date, we have confirmed a new diagnosis for six individuals, including four in whom RNA studies were performed. CONCLUSIONS Overall, we demonstrate the clinical value of examining non-canonical splicing variants in individuals with unsolved rare diseases.
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Affiliation(s)
- Alexander J M Blakes
- Faculty of Medicine, Human Development and Health, University of Southampton, Southampton, UK
- Faculty of Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Htoo A Wai
- Faculty of Medicine, Human Development and Health, University of Southampton, Southampton, UK
| | - Ian Davies
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Hassan E Moledina
- Faculty of Medicine, Human Development and Health, University of Southampton, Southampton, UK
| | - April Ruiz
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Tessy Thomas
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - David Bunyan
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - N Simon Thomas
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Christine P Burren
- Department of Paediatric Endocrinology and Diabetes, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
- Bristol Medical School, Department of Translational Health Sciences, University of Bristol, Bristol, UK
| | - Lynn Greenhalgh
- Liverpool Centre for Genomic Medicine, Crown Street, Liverpool, UK
| | - Melissa Lees
- North East Thames Regional Genomics Service, Great Ormond Street Hospital, London, UK
| | - Amanda Pichini
- Department of Clinical Genetics, University Hospitals Bristol and Weston Foundation Trust, Bristol, UK
- Genomics England, Dawson Hall, Charterhouse Square, London, UK
| | - Sarah F Smithson
- Department of Clinical Genetics, University Hospitals Bristol and Weston Foundation Trust, Bristol, UK
| | - Ana Lisa Taylor Tavares
- Genomics England, Dawson Hall, Charterhouse Square, London, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
| | - Peter O'Donovan
- Genomics England, Dawson Hall, Charterhouse Square, London, UK
| | - Andrew G L Douglas
- Faculty of Medicine, Human Development and Health, University of Southampton, Southampton, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Nicola Whiffin
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Diana Baralle
- Faculty of Medicine, Human Development and Health, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Jenny Lord
- Faculty of Medicine, Human Development and Health, University of Southampton, Southampton, UK.
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47
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Ellingford JM, Ahn JW, Bagnall RD, Baralle D, Barton S, Campbell C, Downes K, Ellard S, Duff-Farrier C, FitzPatrick DR, Greally JM, Ingles J, Krishnan N, Lord J, Martin HC, Newman WG, O'Donnell-Luria A, Ramsden SC, Rehm HL, Richardson E, Singer-Berk M, Taylor JC, Williams M, Wood JC, Wright CF, Harrison SM, Whiffin N. Recommendations for clinical interpretation of variants found in non-coding regions of the genome. Genome Med 2022; 14:73. [PMID: 35850704 PMCID: PMC9295495 DOI: 10.1186/s13073-022-01073-3] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/16/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The majority of clinical genetic testing focuses almost exclusively on regions of the genome that directly encode proteins. The important role of variants in non-coding regions in penetrant disease is, however, increasingly being demonstrated, and the use of whole genome sequencing in clinical diagnostic settings is rising across a large range of genetic disorders. Despite this, there is no existing guidance on how current guidelines designed primarily for variants in protein-coding regions should be adapted for variants identified in other genomic contexts. METHODS We convened a panel of nine clinical and research scientists with wide-ranging expertise in clinical variant interpretation, with specific experience in variants within non-coding regions. This panel discussed and refined an initial draft of the guidelines which were then extensively tested and reviewed by external groups. RESULTS We discuss considerations specifically for variants in non-coding regions of the genome. We outline how to define candidate regulatory elements, highlight examples of mechanisms through which non-coding region variants can lead to penetrant monogenic disease, and outline how existing guidelines can be adapted for the interpretation of these variants. CONCLUSIONS These recommendations aim to increase the number and range of non-coding region variants that can be clinically interpreted, which, together with a compatible phenotype, can lead to new diagnoses and catalyse the discovery of novel disease mechanisms.
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Affiliation(s)
- Jamie M Ellingford
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, M13 9PT, UK.
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK.
- Genomics England, London, UK.
| | - Joo Wook Ahn
- Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Richard D Bagnall
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Sydney, Australia
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Stephanie Barton
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Chris Campbell
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Kate Downes
- Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
- South West Genomic Laboratory Hub, Exeter Genomic Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Celia Duff-Farrier
- South West NHS Genomic Laboratory Hub, Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - John M Greally
- Department of Pediatrics, Division of Pediatric Genetic, Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert, Einstein College of Medicine, Bronx, NY, USA
| | - Jodie Ingles
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Neesha Krishnan
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Jenny Lord
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Hilary C Martin
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - William G Newman
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, M13 9PT, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Ebony Richardson
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jenny C Taylor
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Maggie Williams
- South West NHS Genomic Laboratory Hub, Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - Jordan C Wood
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Steven M Harrison
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ambry Genetics, Aliso Viejo, CA, USA
| | - Nicola Whiffin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
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48
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Kingdom R, Tuke M, Wood A, Beaumont RN, Frayling TM, Weedon MN, Wright CF. Rare genetic variants in genes and loci linked to dominant monogenic developmental disorders cause milder related phenotypes in the general population. Am J Hum Genet 2022; 109:1308-1316. [PMID: 35700724 PMCID: PMC9300873 DOI: 10.1016/j.ajhg.2022.05.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/19/2022] [Indexed: 12/02/2022] Open
Abstract
Many rare monogenic diseases are known to be caused by deleterious variants in thousands of genes, however the same variants can also be found in people without the associated clinical phenotypes. The penetrance of these monogenic variants is generally unknown in the wider population, as they are typically identified in small clinical cohorts of affected individuals and families with highly penetrant variants. Here, we investigated the phenotypic effect of rare, potentially deleterious variants in genes and loci where similar variants are known to cause monogenic developmental disorders (DDs) in a large population cohort. We used UK Biobank to investigate phenotypes associated with rare protein-truncating and missense variants in 599 monoallelic DDG2P genes by using whole-exome-sequencing data from ∼200,000 individuals and rare copy-number variants overlapping known DD loci by using SNP-array data from ∼500,000 individuals. We found that individuals with these likely deleterious variants had a mild DD-related phenotype, including lower fluid intelligence, slower reaction times, lower numeric memory scores, and longer pairs matching times compared to the rest of the UK Biobank cohort. They were also shorter, had a higher BMI, and had significant socioeconomic disadvantages: they were less likely to be employed or be able to work and had a lower income and higher deprivation index. Our findings suggest that many genes routinely tested within pediatric genetics have deleterious variants with intermediate penetrance that may cause lifelong sub-clinical phenotypes in the general adult population.
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Affiliation(s)
- Rebecca Kingdom
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Marcus Tuke
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Andrew Wood
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Robin N Beaumont
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Timothy M Frayling
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, RILD Building, Barrack Road, Exeter EX2 5DW, UK.
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49
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McGurk KA, Halliday BP. Dilated cardiomyopathy - details make the difference. Eur J Heart Fail 2022; 24:1197-1199. [PMID: 35717623 DOI: 10.1002/ejhf.2586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/16/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Kathryn A McGurk
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Brian P Halliday
- National Heart and Lung Institute, Imperial College London, London, UK.,Cardiovascular Research Centre at Royal Brompton and Harefield Hospitals, part of Guy's and St Thomas' NHS Foundation Trust, London, UK
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50
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Han Y, Klinger K, Rajpal DK, Zhu C, Teeple E. Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform. BMC Bioinformatics 2022; 23:232. [PMID: 35710324 PMCID: PMC9202116 DOI: 10.1186/s12859-022-04753-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/26/2022] [Indexed: 11/10/2022] Open
Abstract
Background The Open Targets (OT) Platform integrates a wide range of data sources on target-disease associations to facilitate identification of potential therapeutic drug targets to treat human diseases. However, due to the complexity that targets are usually functionally pleiotropic and efficacious for multiple indications, challenges in identifying novel target to indication associations remain. Specifically, persistent need exists for new methods for integration of novel target-disease association evidence and biological knowledge bases via advanced computational methods. These offer promise for increasing power for identification of the most promising target-disease pairs for therapeutic development. Here we introduce a novel approach by integrating additional target-disease features with machine learning models to further uncover druggable disease to target indications. Results We derived novel target-disease associations as supplemental features to OT platform-based associations using three data sources: (1) target tissue specificity from GTEx expression profiles; (2) target semantic similarities based on gene ontology; and (3) functional interactions among targets by embedding them from protein–protein interaction (PPI) networks. Machine learning models were applied to evaluate feature importance and performance benchmarks for predicting targets with known drug indications. The evaluation results show the newly integrated features demonstrate higher importance than current features in OT. In addition, these also show superior performance over association benchmarks and may support discovery of novel therapeutic indications for highly pursued targets. Conclusion Our newly generated features can be used to represent additional underlying biological relatedness among targets and diseases to further empower improved performance for predicting novel indications for drug targets through advanced machine learning models. The proposed methodology enables a powerful new approach for systematic evaluation of drug targets with novel indications. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04753-4.
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Affiliation(s)
- Yingnan Han
- Translational Sciences, Sanofi US, Framingham, MA, 01701, USA
| | | | - Deepak K Rajpal
- Translational Sciences, Sanofi US, Framingham, MA, 01701, USA
| | - Cheng Zhu
- Translational Sciences, Sanofi US, Framingham, MA, 01701, USA.
| | - Erin Teeple
- Translational Sciences, Sanofi US, Framingham, MA, 01701, USA.
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