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Cormack M, Irving KB, Cunningham F, Fennell AP. Mainstreaming genomic testing: pre-test counselling and informed consent. Med J Aust 2024; 220:403-406. [PMID: 38479398 DOI: 10.5694/mja2.52254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/29/2024] [Indexed: 05/06/2024]
Affiliation(s)
| | - Kathryn B Irving
- Royal Children's Hospital, Melbourne, VIC
- University of Melbourne, Melbourne, VIC
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Roberts AM, DiStefano MT, Riggs ER, Josephs KS, Alkuraya FS, Amberger J, Amin M, Berg JS, Cunningham F, Eilbeck K, Firth HV, Foreman J, Hamosh A, Hay E, Leigh S, Martin CL, McDonagh EM, Perrett D, Ramos EM, Robinson PN, Rath A, Sant DW, Stark Z, Whiffin N, Rehm HL, Ware JS. Toward robust clinical genome interpretation: Developing a consistent terminology to characterize Mendelian disease-gene relationships-allelic requirement, inheritance modes, and disease mechanisms. Genet Med 2024; 26:101029. [PMID: 37982373 PMCID: PMC11039201 DOI: 10.1016/j.gim.2023.101029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/21/2023] Open
Abstract
PURPOSE The terminology used for gene-disease curation and variant annotation to describe inheritance, allelic requirement, and both sequence and functional consequences of a variant is currently not standardized. There is considerable discrepancy in the literature and across clinical variant reporting in the derivation and application of terms. Here, we standardize the terminology for the characterization of disease-gene relationships to facilitate harmonized global curation and to support variant classification within the ACMG/AMP framework. METHODS Terminology for inheritance, allelic requirement, and both structural and functional consequences of a variant used by Gene Curation Coalition members and partner organizations was collated and reviewed. Harmonized terminology with definitions and use examples was created, reviewed, and validated. RESULTS We present a standardized terminology to describe gene-disease relationships, and to support variant annotation. We demonstrate application of the terminology for classification of variation in the ACMG SF 2.0 genes recommended for reporting of secondary findings. Consensus terms were agreed and formalized in both Sequence Ontology (SO) and Human Phenotype Ontology (HPO) ontologies. Gene Curation Coalition member groups intend to use or map to these terms in their respective resources. CONCLUSION The terminology standardization presented here will improve harmonization, facilitate the pooling of curation datasets across international curation efforts and, in turn, improve consistency in variant classification and genetic test interpretation.
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Affiliation(s)
- Angharad M Roberts
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London, United Kingdom.
| | - Marina T DiStefano
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Katherine S Josephs
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia
| | - Joanna Amberger
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
| | - Helen V Firth
- Dept of Medical Genetics, Cambridge University Hospitals, Cambridge, United Kingdom; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Julia Foreman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Eleanor Hay
- Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London, United Kingdom
| | - Sarah Leigh
- Genomics England, Queen Mary University of London, Dawson Hall, London, United Kingdom
| | | | - Ellen M McDonagh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom; Open Targets, Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Daniel Perrett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | | | - Ana Rath
- INSERM, US14-Orphanet, Paris, France
| | - David W Sant
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
| | - Zornitza Stark
- Australian Genomics, Melbourne 3052, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne 3052, Australia; University of Melbourne, Melbourne 3052, Australia
| | - Nicola Whiffin
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Big Data Institute and Wellcome Centre for Human Genetics, University of Oxford, United Kingdom
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - James S Ware
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
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Harrison PW, Amode MR, Austine-Orimoloye O, Azov A, Barba M, Barnes I, Becker A, Bennett R, Berry A, Bhai J, Bhurji SK, Boddu S, Branco Lins PR, Brooks L, Ramaraju S, Campbell L, Martinez MC, Charkhchi M, Chougule K, Cockburn A, Davidson C, De Silva N, Dodiya K, Donaldson S, El Houdaigui B, Naboulsi T, Fatima R, Giron CG, Genez T, Grigoriadis D, Ghattaoraya G, Martinez JG, Gurbich T, Hardy M, Hollis Z, Hourlier T, Hunt T, Kay M, Kaykala V, Le T, Lemos D, Lodha D, Marques-Coelho D, Maslen G, Merino G, Mirabueno L, Mushtaq A, Hossain S, Ogeh D, Sakthivel MP, Parker A, Perry M, Piližota I, Poppleton D, Prosovetskaia I, Raj S, Pérez-Silva J, Salam A, Saraf S, Saraiva-Agostinho N, Sheppard D, Sinha S, Sipos B, Sitnik V, Stark W, Steed E, Suner MM, Surapaneni L, Sutinen K, Tricomi FF, Urbina-Gómez D, Veidenberg A, Walsh TA, Ware D, Wass E, Willhoft N, Allen J, Alvarez-Jarreta J, Chakiachvili M, Flint B, Giorgetti S, Haggerty L, Ilsley G, Keatley J, Loveland J, Moore B, Mudge J, Naamati G, Tate J, Trevanion S, Winterbottom A, Frankish A, Hunt SE, Cunningham F, Dyer S, Finn R, Martin F, Yates A. Ensembl 2024. Nucleic Acids Res 2024; 52:D891-D899. [PMID: 37953337 PMCID: PMC10767893 DOI: 10.1093/nar/gkad1049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023] Open
Abstract
Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades. In recent years, there has been a dramatic shift in the genomic landscape, with a large increase in the number and phylogenetic breadth of high-quality reference genomes, alongside major advances in the pan-genome representations of higher species. In order to support these efforts and accelerate downstream research, Ensembl continues to focus on scaling for the rapid annotation of new genome assemblies, developing new methods for comparative analysis, and expanding the depth and quality of our genome annotations. This year we have continued our expansion to support global biodiversity research, doubling the number of annotated genomes we support on our Rapid Release site to over 1700, driven by our close collaboration with biodiversity projects such as Darwin Tree of Life. We have also strengthened support for key agricultural species, including the first regulatory builds for farmed animals, and have updated key tools and resources that support the global scientific community, notably the Ensembl Variant Effect Predictor. Ensembl data, software, and tools are freely available.
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Affiliation(s)
- Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - M Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Olanrewaju Austine-Orimoloye
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Andrey G Azov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Matthieu Barba
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Arne Becker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Ruth Bennett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Jyothish Bhai
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Simarpreet Kaur Bhurji
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Sanjay Boddu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Paulo R Branco Lins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Lucy Brooks
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Shashank Budhanuru Ramaraju
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Lahcen I Campbell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Manuel Carbajo Martinez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Mehrnaz Charkhchi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Alexander Cockburn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Nishadi H De Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Kamalkumar Dodiya
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Sarah Donaldson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Bilal El Houdaigui
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Tamara El Naboulsi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Reham Fatima
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Carlos Garcia Giron
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Thiago Genez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Dionysios Grigoriadis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Gurpreet S Ghattaoraya
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Jose Gonzalez Martinez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Tatiana A Gurbich
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Matthew Hardy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Zoe Hollis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Mike Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Vinay Kaykala
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Tuan Le
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Diana Lemos
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Disha Lodha
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Diego Marques-Coelho
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Gareth Maslen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Gabriela Alejandra Merino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Louisse Paola Mirabueno
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Aleena Mushtaq
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Syed Nakib Hossain
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Denye N Ogeh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Manoj Pandian Sakthivel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Malcolm Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Ivana Piližota
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Daniel Poppleton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Irina Prosovetskaia
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Shriya Raj
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - José G Pérez-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Ahamed Imran Abdul Salam
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Shradha Saraf
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Nuno Saraiva-Agostinho
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Dan Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Swati Sinha
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Botond Sipos
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Vasily Sitnik
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - William Stark
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Emily Steed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Likhitha Surapaneni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Kyösti Sutinen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Francesca Floriana Tricomi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - David Urbina-Gómez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Andres Veidenberg
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Thomas A Walsh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Doreen Ware
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
| | - Elizabeth Wass
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Natalie L Willhoft
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Jamie Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Jorge Alvarez-Jarreta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Marc Chakiachvili
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Bethany Flint
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Stefano Giorgetti
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Garth R Ilsley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Jon Keatley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Benjamin Moore
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - John Tate
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Andrea Winterbottom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Sarah Dyer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Andrew D Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Roberts AM, DiStefano MT, Riggs ER, Josephs KS, Alkuraya FS, Amberger J, Amin M, Berg JS, Cunningham F, Eilbeck K, Firth HV, Foreman J, Hamosh A, Hay E, Leigh S, Martin CL, McDonagh EM, Perrett D, Ramos EM, Robinson PN, Rath A, van Sant D, Stark Z, Whiffin N, Rehm HL, Ware JS. Towards robust clinical genome interpretation: developing a consistent terminology to characterize disease-gene relationships - allelic requirement, inheritance modes and disease mechanisms. medRxiv 2023:2023.03.30.23287948. [PMID: 37066232 PMCID: PMC10104222 DOI: 10.1101/2023.03.30.23287948] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
PURPOSE The terminology used for gene-disease curation and variant annotation to describe inheritance, allelic requirement, and both sequence and functional consequences of a variant is currently not standardized. There is considerable discrepancy in the literature and across clinical variant reporting in the derivation and application of terms. Here we standardize the terminology for the characterization of disease-gene relationships to facilitate harmonized global curation, and to support variant classification within the ACMG/AMP framework. METHODS Terminology for inheritance, allelic requirement, and both structural and functional consequences of a variant used by Gene Curation Coalition (GenCC) members and partner organizations was collated and reviewed. Harmonized terminology with definitions and use examples was created, reviewed, and validated. RESULTS We present a standardized terminology to describe gene-disease relationships, and to support variant annotation. We demonstrate application of the terminology for classification of variation in the ACMG SF 2.0 genes recommended for reporting of secondary findings. Consensus terms were agreed and formalized in both sequence ontology (SO) and human phenotype ontology (HPO) ontologies. GenCC member groups intend to use or map to these terms in their respective resources. CONCLUSION The terminology standardization presented here will improve harmonization, facilitate the pooling of curation datasets across international curation efforts and, in turn, improve consistency in variant classification and genetic test interpretation.
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Affiliation(s)
- Angharad M Roberts
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London, UK
- Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London. WC1N 3JH, UK
| | - Marina T DiStefano
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erin Rooney Riggs
- Geisinger Autism & Developmental Medicine Institute, Danville, PA, USA
| | - Katherine S Josephs
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London, UK
- Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia
| | - Joanna Amberger
- Online Mendelian Inheritance in Man (OMIM), Johns Hopkins University School of Medicine, USA
| | | | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill NC, 27599
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah
| | - Helen V Firth
- Dept of Medical Genetics, Cambridge University Hospitals, Cambridge CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Julia Foreman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Ada Hamosh
- Online Mendelian Inheritance in Man (OMIM), Johns Hopkins University School of Medicine, USA
| | - Eleanor Hay
- Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London. WC1N 3JH, UK
| | - Sarah Leigh
- Genomics England, Queen Mary University of London, Dawson Hall, London, EC1M 6BQ, UK
| | | | - Ellen M McDonagh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
- Open Targets, Cambridge, UK
| | - Daniel Perrett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington CT 06032, USA
| | - Ana Rath
- INSERM, US14-Orphanet, Paris, France
| | - David van Sant
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah
| | - Zornitza Stark
- Australian Genomics, Melbourne 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne 3052, Australia
- University of Melbourne, Melbourne 3052, Australia
| | - Nicola Whiffin
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Big Data Institute and Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - James S Ware
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London, UK
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
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6
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Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland J, Mudge J, Sisu C, Wright J, Arnan C, Barnes I, Banerjee A, Bennett R, Berry A, Bignell A, Boix C, Calvet F, Cerdán-Vélez D, Cunningham F, Davidson C, Donaldson S, Dursun C, Fatima R, Giorgetti S, Giron C, Gonzalez J, Hardy M, Harrison P, Hourlier T, Hollis Z, Hunt T, James B, Jiang Y, Johnson R, Kay M, Lagarde J, Martin F, Gómez L, Nair S, Ni P, Pozo F, Ramalingam V, Ruffier M, Schmitt B, Schreiber J, Steed E, Suner MM, Sumathipala D, Sycheva I, Uszczynska-Ratajczak B, Wass E, Yang Y, Yates A, Zafrulla Z, Choudhary J, Gerstein M, Guigo R, Hubbard TJP, Kellis M, Kundaje A, Paten B, Tress M, Flicek P. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res 2022; 51:D942-D949. [PMID: 36420896 PMCID: PMC9825462 DOI: 10.1093/nar/gkac1071] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/15/2022] [Accepted: 11/07/2022] [Indexed: 11/27/2022] Open
Abstract
GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.
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Affiliation(s)
- Adam Frankish
- To whom correspondence should be addressed. Tel: +44 1223 494388; Fax: +44 1223 484696;
| | - Sílvia Carbonell-Sala
- Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Cristina Sisu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA,Department of Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - James C Wright
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Carme Arnan
- Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Abhimanyu Banerjee
- Department of Genetics, Stanford University, Palo Alto, CA, USA,Department of Computer Science, Stanford University, Palo Alto, CA, USA
| | - Ruth Bennett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alexandra Bignell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carles Boix
- MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Ferriol Calvet
- Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
| | - Daniel Cerdán-Vélez
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah Donaldson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Cagatay Dursun
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Reham Fatima
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stefano Giorgetti
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carlos Garcıa Giron
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jose Manuel Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew Hardy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Zoe Hollis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Benjamin James
- MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Yunzhe Jiang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Rory Johnson
- Department of Medical Oncology, Bern University Hospital, Murtenstrasse 35, 3008 Bern, Switzerland,School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland
| | - Mike Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Julien Lagarde
- Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laura Martínez Gómez
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain
| | - Surag Nair
- Department of Genetics, Stanford University, Palo Alto, CA, USA,Department of Computer Science, Stanford University, Palo Alto, CA, USA
| | - Pengyu Ni
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Fernando Pozo
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain
| | - Vivek Ramalingam
- Department of Genetics, Stanford University, Palo Alto, CA, USA,Department of Computer Science, Stanford University, Palo Alto, CA, USA
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bianca M Schmitt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jacob M Schreiber
- Department of Genetics, Stanford University, Palo Alto, CA, USA,Department of Computer Science, Stanford University, Palo Alto, CA, USA
| | - Emily Steed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dulika Sumathipala
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Irina Sycheva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Barbara Uszczynska-Ratajczak
- Computational Biology of Noncoding RNA, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Elizabeth Wass
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Yucheng T Yang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA,Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Andrew Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Zahoor Zafrulla
- Department of Genetics, Stanford University, Palo Alto, CA, USA,Department of Computer Science, Stanford University, Palo Alto, CA, USA
| | - Jyoti S Choudhary
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Roderic Guigo
- Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, E-08003 Catalonia, Spain
| | - Tim J P Hubbard
- Department of Medical and Molecular Genetics, King's College London, Guys Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Palo Alto, CA, USA,Department of Computer Science, Stanford University, Palo Alto, CA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Michael L Tress
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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7
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Sollis E, Mosaku A, Abid A, Buniello A, Cerezo M, Gil L, Groza T, Güneş O, Hall P, Hayhurst J, Ibrahim A, Ji Y, John S, Lewis E, MacArthur JL, McMahon A, Osumi-Sutherland D, Panoutsopoulou K, Pendlington Z, Ramachandran S, Stefancsik R, Stewart J, Whetzel P, Wilson R, Hindorff L, Cunningham F, Lambert S, Inouye M, Parkinson H, Harris L. The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource. Nucleic Acids Res 2022; 51:D977-D985. [PMID: 36350656 PMCID: PMC9825413 DOI: 10.1093/nar/gkac1010] [Citation(s) in RCA: 235] [Impact Index Per Article: 117.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022] Open
Abstract
The NHGRI-EBI GWAS Catalog (www.ebi.ac.uk/gwas) is a FAIR knowledgebase providing detailed, structured, standardised and interoperable genome-wide association study (GWAS) data to >200 000 users per year from academic research, healthcare and industry. The Catalog contains variant-trait associations and supporting metadata for >45 000 published GWAS across >5000 human traits, and >40 000 full P-value summary statistics datasets. Content is curated from publications or acquired via author submission of prepublication summary statistics through a new submission portal and validation tool. GWAS data volume has vastly increased in recent years. We have updated our software to meet this scaling challenge and to enable rapid release of submitted summary statistics. The scope of the repository has expanded to include additional data types of high interest to the community, including sequencing-based GWAS, gene-based analyses and copy number variation analyses. Community outreach has increased the number of shared datasets from under-represented traits, e.g. cancer, and we continue to contribute to awareness of the lack of population diversity in GWAS. Interoperability of the Catalog has been enhanced through links to other resources including the Polygenic Score Catalog and the International Mouse Phenotyping Consortium, refinements to GWAS trait annotation, and the development of a standard format for GWAS data.
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Affiliation(s)
- Elliot Sollis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Abayomi Mosaku
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ala Abid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Annalisa Buniello
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Maria Cerezo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laurent Gil
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK,Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Tudor Groza
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Osman Güneş
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peggy Hall
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James Hayhurst
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Arwa Ibrahim
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Yue Ji
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sajo John
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Elizabeth Lewis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jacqueline A L MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David Osumi-Sutherland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kalliope Panoutsopoulou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Zoë Pendlington
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Santhi Ramachandran
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ray Stefancsik
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan Stewart
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Patricia Whetzel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Robert Wilson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lucia Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Samuel A Lambert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK,Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK,British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK,Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK,British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK,Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK,Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Helen Parkinson
- To whom correspondence should be addressed. Tel: +44 1223 49 4672;
| | - Laura W Harris
- Correspondence may also be addressed to Laura W. Harris. Tel: +44 1223 49 4354;
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8
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Cerezo M, Buniello A, Abid A, Hall P, Hayhurst J, Ibrahim A, John S, Lewis E, McMahon A, Mosaku A, Ramachandran S, Sollis E, Cunningham F, Flicek P, Hindorff L, Harris L, Parkinson H. 64. FAIR sharing of cancer GWAS data via the NHGRI-EBI GWAS catalog. Cancer Genet 2022. [DOI: 10.1016/j.cancergen.2022.10.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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9
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Martin FJ, Amode MR, Aneja A, Austine-Orimoloye O, Azov A, Barnes I, Becker A, Bennett R, Berry A, Bhai J, Bhurji S, Bignell A, Boddu S, Branco Lins PR, Brooks L, Ramaraju SB, Charkhchi M, Cockburn A, Da Rin Fiorretto L, Davidson C, Dodiya K, Donaldson S, El Houdaigui B, El Naboulsi T, Fatima R, Giron CG, Genez T, Ghattaoraya GS, Martinez JG, Guijarro C, Hardy M, Hollis Z, Hourlier T, Hunt T, Kay M, Kaykala V, Le T, Lemos D, Marques-Coelho D, Marugán JC, Merino G, Mirabueno L, Mushtaq A, Hossain S, Ogeh DN, Sakthivel MP, Parker A, Perry M, Piližota I, Prosovetskaia I, Pérez-Silva JG, Salam A, Saraiva-Agostinho N, Schuilenburg H, Sheppard D, Sinha S, Sipos B, Stark W, Steed E, Sukumaran R, Sumathipala D, Suner MM, Surapaneni L, Sutinen K, Szpak M, Tricomi F, Urbina-Gómez D, Veidenberg A, Walsh T, Walts B, Wass E, Willhoft N, Allen J, Alvarez-Jarreta J, Chakiachvili M, Flint B, Giorgetti S, Haggerty L, Ilsley G, Loveland J, Moore B, Mudge J, Tate J, Thybert D, Trevanion S, Winterbottom A, Frankish A, Hunt SE, Ruffier M, Cunningham F, Dyer S, Finn R, Howe K, Harrison PW, Yates AD, Flicek P. Ensembl 2023. Nucleic Acids Res 2022; 51:D933-D941. [PMID: 36318249 PMCID: PMC9825606 DOI: 10.1093/nar/gkac958] [Citation(s) in RCA: 148] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/06/2022] [Accepted: 10/14/2022] [Indexed: 11/22/2022] Open
Abstract
Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years. During that time, our resources, services and tools have continually evolved in line with both the publicly available genome data and the downstream research and applications that utilise the Ensembl platform. In recent years we have witnessed a dramatic shift in the genomic landscape. There has been a large increase in the number of high-quality reference genomes through global biodiversity initiatives. In parallel, there have been major advances towards pangenome representations of higher species, where many alternative genome assemblies representing different breeds, cultivars, strains and haplotypes are now available. In order to support these efforts and accelerate downstream research, it is our goal at Ensembl to create high-quality annotations, tools and services for species across the tree of life. Here, we report our resources for popular reference genomes, the dramatic growth of our annotations (including haplotypes from the first human pangenome graphs), updates to the Ensembl Variant Effect Predictor (VEP), interactive protein structure predictions from AlphaFold DB, and the beta release of our new website.
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Affiliation(s)
- Fergal J Martin
- To whom correspondence should be addressed. Tel: +44 1223 49 44 44;
| | - M Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Alisha Aneja
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Olanrewaju Austine-Orimoloye
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Andrey G Azov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Arne Becker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Ruth Bennett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Jyothish Bhai
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Simarpreet Kaur Bhurji
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Alexandra Bignell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Sanjay Boddu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Paulo R Branco Lins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Lucy Brooks
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Shashank Budhanuru Ramaraju
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Mehrnaz Charkhchi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Alexander Cockburn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Luca Da Rin Fiorretto
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Kamalkumar Dodiya
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Sarah Donaldson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Bilal El Houdaigui
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Tamara El Naboulsi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Reham Fatima
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Carlos Garcia Giron
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Thiago Genez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Gurpreet S Ghattaoraya
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Jose Gonzalez Martinez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Cristi Guijarro
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Matthew Hardy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Zoe Hollis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Mike Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Vinay Kaykala
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Tuan Le
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Diana Lemos
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Diego Marques-Coelho
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - José Carlos Marugán
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Gabriela Alejandra Merino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Louisse Paola Mirabueno
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Aleena Mushtaq
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Syed Nakib Hossain
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Denye N Ogeh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Manoj Pandian Sakthivel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Malcolm Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Ivana Piližota
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Irina Prosovetskaia
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - José G Pérez-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Ahamed Imran Abdul Salam
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Nuno Saraiva-Agostinho
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Dan Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Swati Sinha
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Botond Sipos
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - William Stark
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Emily Steed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Ranjit Sukumaran
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Dulika Sumathipala
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Likhitha Surapaneni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Kyösti Sutinen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Michal Szpak
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Francesca Floriana Tricomi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - David Urbina-Gómez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Andres Veidenberg
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Thomas A Walsh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Brandon Walts
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Elizabeth Wass
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Natalie Willhoft
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Jamie Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Jorge Alvarez-Jarreta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Marc Chakiachvili
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Bethany Flint
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Stefano Giorgetti
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Garth R Ilsley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Benjamin Moore
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - John Tate
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - David Thybert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Andrea Winterbottom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Sarah Dyer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Kevin L Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Andrew D Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK
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Cunningham F, Caldwell E, Mayer-Hamblett N, Goss CH, Muhlebach MS. Eradication of early MRSA infection in cystic fibrosis – a novel study design for “STAR-ter” trial. ERJ Open Res 2022; 8:00190-2022. [DOI: 10.1183/23120541.00190-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/15/2022] [Indexed: 11/05/2022] Open
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DiStefano MT, Goehringer S, Babb L, Alkuraya FS, Amberger J, Amin M, Austin-Tse C, Balzotti M, Berg JS, Birney E, Bocchini C, Bruford EA, Coffey AJ, Collins H, Cunningham F, Daugherty LC, Einhorn Y, Firth HV, Fitzpatrick DR, Foulger RE, Goldstein J, Hamosh A, Hurles MR, Leigh SE, Leong IUS, Maddirevula S, Martin CL, McDonagh EM, Olry A, Puzriakova A, Radtke K, Ramos EM, Rath A, Riggs ER, Roberts AM, Rodwell C, Snow C, Stark Z, Tahiliani J, Tweedie S, Ware JS, Weller P, Williams E, Wright CF, Yates TM, Rehm HL. The Gene Curation Coalition: A global effort to harmonize gene-disease evidence resources. Genet Med 2022; 24:1732-1742. [PMID: 35507016 PMCID: PMC7613247 DOI: 10.1016/j.gim.2022.04.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 01/04/2023] Open
Abstract
PURPOSE Several groups and resources provide information that pertains to the validity of gene-disease relationships used in genomic medicine and research; however, universal standards and terminologies to define the evidence base for the role of a gene in disease and a single harmonized resource were lacking. To tackle this issue, the Gene Curation Coalition (GenCC) was formed. METHODS The GenCC drafted harmonized definitions for differing levels of gene-disease validity on the basis of existing resources, and performed a modified Delphi survey with 3 rounds to narrow the list of terms. The GenCC also developed a unified database to display curated gene-disease validity assertions from its members. RESULTS On the basis of 241 survey responses from the genetics community, a consensus term set was chosen for grading gene-disease validity and database submissions. As of December 2021, the database contained 15,241 gene-disease assertions on 4569 unique genes from 12 submitters. When comparing submissions to the database from distinct sources, conflicts in assertions of gene-disease validity ranged from 5.3% to 13.4%. CONCLUSION Terminology standardization, sharing of gene-disease validity classifications, and resolution of curation conflicts will facilitate collaborations across international curation efforts and in turn, improve consistency in genetic testing and variant interpretation.
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Affiliation(s)
- Marina T DiStefano
- Geisinger Health System, Danville, PA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Lawrence Babb
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Joanna Amberger
- Online Mendelian Inheritance in Man (OMIM), Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Christina Austin-Tse
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Pathology, Massachusetts General Hospital, Boston, MA; Mass General Brigham Laboratory for Molecular Medicine, Cambridge, MA
| | | | - Jonathan S Berg
- Department of Genetics, UNC School of Medicine, University of North Carolina, Chapel Hill, NC
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Carol Bocchini
- Online Mendelian Inheritance in Man (OMIM), Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Elspeth A Bruford
- HUGO Gene Nomenclature Committee (HGNC), European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom; Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Alison J Coffey
- Illumina Clinical Services Laboratory, Illumina Inc, San Diego, CA
| | - Heather Collins
- National Library of Medicine, Bethesda, MD; ICF International Inc, Fairfax, VA
| | - Fiona Cunningham
- Genome Interpretation, Genome Assembly and Annotation (GAA), European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Louise C Daugherty
- Genomics England, Queen Mary University of London, London, United Kingdom; Healx Ltd, Cambridge, United Kingdom
| | | | - Helen V Firth
- Department of Medical Genetics, Addenbrooke's Treatment Centre, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
| | - David R Fitzpatrick
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, College of Medicine & Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Rebecca E Foulger
- Genomics England, Queen Mary University of London, London, United Kingdom; SciBite Limited, BioData Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jennifer Goldstein
- Department of Genetics, UNC School of Medicine, University of North Carolina, Chapel Hill, NC
| | - Ada Hamosh
- Online Mendelian Inheritance in Man (OMIM), Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Sarah E Leigh
- Genomics England, Queen Mary University of London, London, United Kingdom
| | - Ivone U S Leong
- Genomics England, Queen Mary University of London, London, United Kingdom
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | | | - Ellen M McDonagh
- Genomics England, Queen Mary University of London, London, United Kingdom; Open Targets, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | | | - Arina Puzriakova
- Genomics England, Queen Mary University of London, London, United Kingdom
| | | | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health Bethesda, MD
| | - Ana Rath
- INSERM, US14 - Orphanet, Paris, France
| | | | - Angharad M Roberts
- National Heart and Lung Institute & MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom; Great Ormond Street Hospital, London, United Kingdom
| | | | - Catherine Snow
- Genomics England, Queen Mary University of London, London, United Kingdom
| | | | | | - Susan Tweedie
- HUGO Gene Nomenclature Committee (HGNC), European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - James S Ware
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; National Heart and Lung Institute & MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Phillip Weller
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA
| | - Eleanor Williams
- Genomics England, Queen Mary University of London, London, United Kingdom
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, United Kingdom
| | - Thabo Michael Yates
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, College of Medicine & Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA.
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Morales J, Pujar S, Loveland JE, Astashyn A, Bennett R, Berry A, Cox E, Davidson C, Ermolaeva O, Farrell CM, Fatima R, Gil L, Goldfarb T, Gonzalez JM, Haddad D, Hardy M, Hunt T, Jackson J, Joardar VS, Kay M, Kodali VK, McGarvey KM, McMahon A, Mudge JM, Murphy DN, Murphy MR, Rajput B, Rangwala SH, Riddick LD, Thibaud-Nissen F, Threadgold G, Vatsan AR, Wallin C, Webb D, Flicek P, Birney E, Pruitt KD, Frankish A, Cunningham F, Murphy TD. A joint NCBI and EMBL-EBI transcript set for clinical genomics and research. Nature 2022; 604:310-315. [PMID: 35388217 PMCID: PMC9007741 DOI: 10.1038/s41586-022-04558-8] [Citation(s) in RCA: 125] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/07/2022] [Indexed: 12/25/2022]
Abstract
Comprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, the absence of a standard for clinical reporting and browser display complicates the process of consistent interpretation and reporting. To address these challenges, Ensembl/GENCODE1 and RefSeq2 launched a joint initiative, the Matched Annotation from NCBI and EMBL-EBI (MANE) collaboration, to converge on human gene and transcript annotation and to jointly define a high-value set of transcripts and corresponding proteins. Here, we describe the MANE transcript sets for use as universal standards for variant reporting and browser display. The MANE Select set identifies a representative transcript for each human protein-coding gene, whereas the MANE Plus Clinical set provides additional transcripts at loci where the Select transcripts alone are not sufficient to report all currently known clinical variants. Each MANE transcript represents an exact match between the exonic sequences of an Ensembl/GENCODE transcript and its counterpart in RefSeq such that the identifiers can be used synonymously. We have now released MANE Select transcripts for 97% of human protein-coding genes, including all American College of Medical Genetics and Genomics Secondary Findings list v3.0 (ref. 3) genes. MANE transcripts are accessible from major genome browsers and key resources. Widespread adoption of these transcript sets will increase the consistency of reporting, facilitate the exchange of data regardless of the annotation source and help to streamline clinical interpretation.
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Affiliation(s)
- Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Shashikant Pujar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Alex Astashyn
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Ruth Bennett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Eric Cox
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Olga Ermolaeva
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Catherine M Farrell
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Reham Fatima
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Tamara Goldfarb
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jose M Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Diana Haddad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Matthew Hardy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - John Jackson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Vinita S Joardar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Michael Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Vamsi K Kodali
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Kelly M McGarvey
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Michael R Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Bhanu Rajput
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Sanjida H Rangwala
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Lillian D Riddick
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Glen Threadgold
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Anjana R Vatsan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Craig Wallin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - David Webb
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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Foreman J, Brent S, Perrett D, Bevan AP, Hunt SE, Cunningham F, Hurles ME, Firth HV. DECIPHER: Supporting the interpretation and sharing of rare disease phenotype-linked variant data to advance diagnosis and research. Hum Mutat 2022; 43:682-697. [PMID: 35143074 PMCID: PMC9303633 DOI: 10.1002/humu.24340] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/17/2022] [Accepted: 02/07/2022] [Indexed: 11/12/2022]
Abstract
DECIPHER (https://www.deciphergenomics.org) is a free web platform for sharing anonymised phenotype-linked variant data from rare disease patients. Its dynamic interpretation interfaces contextualise genomic and phenotypic data to enable more informed variant interpretation, incorporating international standards for variant classification. DECIPHER supports almost all types of germline and mosaic variation in the nuclear and mitochondrial genome: sequence variants, short tandem repeats, copy-number variants and large structural variants. Patient phenotypes are deposited using Human Phenotype Ontology (HPO) terms, supplemented by quantitative data, which is aggregated to derive gene-specific phenotypic summaries. It hosts data from >250 projects from ~40 countries, openly sharing >40,000 patient records containing >51,000 variants and >172,000 phenotype terms. The rich phenotype-linked variant data in DECIPHER drives rare disease research and diagnosis by enabling patient matching within DECIPHER and with other resources, and has been cited in >2,600 publications. In this paper, we describe the types of data deposited to DECIPHER, the variant interpretation tools, and patient matching interfaces which make DECIPHER an invaluable rare disease resource. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Julia Foreman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Simon Brent
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Daniel Perrett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Andrew P Bevan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Matthew E Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Helen V Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom.,East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, United Kingdom
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Bailie J, Cunningham F, Abimbola S, Laycock A, Bainbridge R, Bailie R, Conte K, Passey M, Peiris D. Methodological pluralism for better evaluations of complex interventions: lessons from evaluating an innovation platform in Australia. Health Res Policy Syst 2022; 20:14. [PMID: 35090472 PMCID: PMC8796351 DOI: 10.1186/s12961-022-00814-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/10/2022] [Indexed: 11/10/2022] Open
Abstract
Complex interventions, such as innovation platforms, pose challenges for evaluators. A variety of methodological approaches are often required to build a more complete and comprehensive understanding of how complex interventions work. In this paper, we outline and critically appraise a methodologically pluralist evaluation of an innovation platform to strengthen primary care for Aboriginal and Torres Strait Islander Australians. In doing so, we aim to identify lessons learned from the approach taken and add to existing literature on implementing evaluations in complex settings, such as innovation platforms. The pluralist design used four evaluation approaches-developmental evaluation, principles-focused evaluation, network analysis, and framework analysis-with differing strengths and challenges. Taken together, the multiple evaluation approaches yielded a detailed description and nuanced understanding of the formation, functioning and outcomes of the innovation platform that would be difficult to achieve with any single evaluation method. While a methodologically pluralist design may place additional pressure on logistical and analytic resources available, it enables a deeper understanding of the mechanisms that underlie complex interventions.
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Affiliation(s)
- J Bailie
- The University Centre for Rural Health, The University of Sydney, 61 Uralba Street, Lismore, NSW, 2480, Australia.
- The School of Public Health, The University of Sydney, Sydney, Australia.
| | - F Cunningham
- Menzies School of Health Research, Charles Darwin University, Brisbane, Australia
| | - S Abimbola
- The School of Public Health, The University of Sydney, Sydney, Australia
- The George Institute for Global Health, The University of New South Wales, Sydney, Australia
| | - A Laycock
- The University Centre for Rural Health, The University of Sydney, 61 Uralba Street, Lismore, NSW, 2480, Australia
| | - R Bainbridge
- School of Health, Medical and Applied Sciences, Central Queensland University, Cairns, Australia
| | - R Bailie
- The University Centre for Rural Health, The University of Sydney, 61 Uralba Street, Lismore, NSW, 2480, Australia
| | - K Conte
- The University Centre for Rural Health, The University of Sydney, 61 Uralba Street, Lismore, NSW, 2480, Australia
- The School of Public Health, De Paul University, Chicago, USA
| | - M Passey
- The University Centre for Rural Health, The University of Sydney, 61 Uralba Street, Lismore, NSW, 2480, Australia
| | - D Peiris
- The School of Public Health, The University of Sydney, Sydney, Australia
- The George Institute for Global Health, The University of New South Wales, Sydney, Australia
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15
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Cunningham F, Allen JE, Allen J, Alvarez-Jarreta J, Amode M, Armean I, Austine-Orimoloye O, Azov A, Barnes I, Bennett R, Berry A, Bhai J, Bignell A, Billis K, Boddu S, Brooks L, Charkhchi M, Cummins C, Da Rin Fioretto L, Davidson C, Dodiya K, Donaldson S, El Houdaigui B, El Naboulsi T, Fatima R, Giron CG, Genez T, Martinez J, Guijarro-Clarke C, Gymer A, Hardy M, Hollis Z, Hourlier T, Hunt T, Juettemann T, Kaikala V, Kay M, Lavidas I, Le T, Lemos D, Marugán JC, Mohanan S, Mushtaq A, Naven M, Ogeh D, Parker A, Parton A, Perry M, Piližota I, Prosovetskaia I, Sakthivel M, Salam A, Schmitt B, Schuilenburg H, Sheppard D, Pérez-Silva J, Stark W, Steed E, Sutinen K, Sukumaran R, Sumathipala D, Suner MM, Szpak M, Thormann A, Tricomi FF, Urbina-Gómez D, Veidenberg A, Walsh T, Walts B, Willhoft N, Winterbottom A, Wass E, Chakiachvili M, Flint B, Frankish A, Giorgetti S, Haggerty L, Hunt S, IIsley G, Loveland J, Martin F, Moore B, Mudge J, Muffato M, Perry E, Ruffier M, Tate J, Thybert D, Trevanion S, Dyer S, Harrison P, Howe K, Yates A, Zerbino D, Flicek P. Ensembl 2022. Nucleic Acids Res 2022; 50:D988-D995. [PMID: 34791404 PMCID: PMC8728283 DOI: 10.1093/nar/gkab1049] [Citation(s) in RCA: 837] [Impact Index Per Article: 418.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 12/29/2022] Open
Abstract
Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed to efficiently deliver annotation at scale for all eukaryotic life, and it also provides deep comprehensive annotation for key species. Genomes representing a greater diversity of species are increasingly being sequenced. In response, we have focussed our recent efforts on expediting the annotation of new assemblies. Here, we report the release of the greatest annual number of newly annotated genomes in the history of Ensembl via our dedicated Ensembl Rapid Release platform (http://rapid.ensembl.org). We have also developed a new method to generate comparative analyses at scale for these assemblies and, for the first time, we have annotated non-vertebrate eukaryotes. Meanwhile, we continually improve, extend and update the annotation for our high-value reference vertebrate genomes and report the details here. We have a range of specific software tools for specific tasks, such as the Ensembl Variant Effect Predictor (VEP) and the newly developed interface for the Variant Recoder. All Ensembl data, software and tools are freely available for download and are accessible programmatically.
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Affiliation(s)
- Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James E Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jamie Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jorge Alvarez-Jarreta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - M Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Irina M Armean
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Olanrewaju Austine-Orimoloye
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrey G Azov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ruth Bennett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jyothish Bhai
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alexandra Bignell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sanjay Boddu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lucy Brooks
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mehrnaz Charkhchi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Luca Da Rin Fioretto
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kamalkumar Dodiya
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah Donaldson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bilal El Houdaigui
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tamara El Naboulsi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Reham Fatima
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carlos Garcia Giron
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thiago Genez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jose Gonzalez Martinez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Cristina Guijarro-Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Arthur Gymer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew Hardy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Zoe Hollis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Juettemann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Vinay Kaikala
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mike Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ilias Lavidas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tuan Le
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Diana Lemos
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - José Carlos Marugán
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Shamika Mohanan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aleena Mushtaq
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marc Naven
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Denye N Ogeh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Parton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Malcolm Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ivana Piližota
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Irina Prosovetskaia
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Manoj Pandian Sakthivel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ahamed Imran Abdul Salam
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bianca M Schmitt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dan Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - José G Pérez-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - William Stark
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Steed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kyösti Sutinen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ranjit Sukumaran
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dulika Sumathipala
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michal Szpak
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Francesca Floriana Tricomi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David Urbina-Gómez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andres Veidenberg
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas A Walsh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Brandon Walts
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Natalie Willhoft
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrea Winterbottom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Elizabeth Wass
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marc Chakiachvili
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bethany Flint
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stefano Giorgetti
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Garth R IIsley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Benjamin Moore
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - John Tate
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David Thybert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah Dyer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kevin L Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew D Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Cezard T, Cunningham F, Hunt SE, Koylass B, Kumar N, Saunders G, Shen A, Silva A, Tsukanov K, Venkataraman S, Flicek P, Parkinson H, Keane T. The European Variation Archive: a FAIR resource of genomic variation for all species. Nucleic Acids Res 2022; 50:D1216-D1220. [PMID: 34718739 PMCID: PMC8728205 DOI: 10.1093/nar/gkab960] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/23/2021] [Accepted: 10/14/2021] [Indexed: 12/13/2022] Open
Abstract
The European Variation Archive (EVA; https://www.ebi.ac.uk/eva/) is a resource for sharing all types of genetic variation data (SNPs, indels, and structural variants) for all species. The EVA was created in 2014 to provide FAIR access to genetic variation data and has since grown to be a primary resource for genomic variants hosting >3 billion records. The EVA and dbSNP have established a compatible global system to assign unique identifiers to all submitted genetic variants. The EVA is active within the Global Alliance of Genomics and Health (GA4GH), maintaining, contributing and implementing standards such as VCF, Refget and Variant Representation Specification (VRS). In this article, we describe the submission and permanent accessioning services along with the different ways the data can be retrieved by the scientific community.
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Affiliation(s)
- Timothe Cezard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Baron Koylass
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nitin Kumar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Gary Saunders
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - April Shen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Andres F Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kirill Tsukanov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sundararaman Venkataraman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Thomas M Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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17
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Hunt SE, Moore B, Amode RM, Armean IM, Lemos D, Mushtaq A, Parton A, Schuilenburg H, Szpak M, Thormann A, Perry E, Trevanion SJ, Flicek P, Yates AD, Cunningham F. Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor-A tutorial. Hum Mutat 2021; 43:986-997. [PMID: 34816521 PMCID: PMC7613081 DOI: 10.1002/humu.24298] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 11/02/2021] [Accepted: 11/14/2021] [Indexed: 11/05/2022]
Abstract
The Ensembl Variant Effect Predictor (VEP) is a freely available, open-source tool for the annotation and filtering of genomic variants. It predicts variant molecular consequences using the Ensembl/GENCODE or RefSeq gene sets. It also reports phenotype associations from databases such as ClinVar, allele frequencies from studies including gnomAD, and predictions of deleteriousness from tools such as Sorting Intolerant From Tolerant and Combined Annotation Dependent Depletion. Ensembl VEP includes filtering options to customize variant prioritization. It is well supported and updated roughly quarterly to incorporate the latest gene, variant, and phenotype association information. Ensembl VEP analysis can be performed using a highly configurable, extensible command-line tool, a Representational State Transfer application programming interface, and a user-friendly web interface. These access methods are designed to suit different levels of bioinformatics experience and meet different needs in terms of data size, visualization, and flexibility. In this tutorial, we will describe performing variant annotation using the Ensembl VEP web tool, which enables sophisticated analysis through a simple interface.
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Affiliation(s)
- Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Benjamin Moore
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ridwan M Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Irina M Armean
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Diana Lemos
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Aleena Mushtaq
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Andrew Parton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Michał Szpak
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Andrew D Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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Rehm HL, Page AJ, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJ, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SO, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Guidry Auvil JM, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CW, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJ, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen R, Li S, Lin MF, Linden M, Liu X, Liyanage IU, Lopez J, Lucassen AM, Lukowski M, Mann AL, Marshall J, Mattioni M, Metke-Jimenez A, Middleton A, Milne RJ, Molnár-Gábor F, Mulder N, Munoz-Torres MC, Nag R, Nakagawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyrönen TH, O’Connor BD, Oesterle S, Ogishima S, Ota Wang V, Paglione LA, Palumbo E, Parkinson HE, Philippakis AA, Pizarro AD, Prlic A, Rambla J, Rendon A, Rider RA, Robinson PN, Rodarmer KW, Rodriguez LL, Rubin AF, Rueda M, Rushton GA, Ryan RS, Saunders GI, Schuilenburg H, Schwede T, Scollen S, Senf A, Sheffield NC, Skantharajah N, Smith AV, Sofia HJ, Spalding D, Spurdle AB, Stark Z, Stein LD, Suematsu M, Tan P, Tedds JA, Thomson AA, Thorogood A, Tickle TL, Tokunaga K, Törnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Vamathevan J, Varma S, Vears DF, Viner C, Voisin C, Wagner AH, Wallace SE, Walsh BP, Williams MS, Winkler EC, Wold BJ, Wood GM, Woolley JP, Yamasaki C, Yates AD, Yung CK, Zass LJ, Zaytseva K, Zhang J, Goodhand P, North K, Birney E. GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genom 2021; 1:100029. [PMID: 35072136 PMCID: PMC8774288 DOI: 10.1016/j.xgen.2021.100029] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
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Affiliation(s)
- Heidi L. Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Angela J.H. Page
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - Lindsay Smith
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jeremy B. Adams
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gil Alterovitz
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | - Michael Baudis
- University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michael J.S. Beauvais
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | - Tim Beck
- University of Leicester, Leicester, UK
| | | | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - David Bernick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Tiffany F. Boughtwood
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Guillaume Bourque
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
| | | | | | - Michael Brudno
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | - David Bujold
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | - Daniel L. Cameron
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | | | | | | | - Bimal P. Chaudhari
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | - Shu Hui Chen
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Justina Chung
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Melissa Cline
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | | | - Mélanie Courtot
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | | | | | | | - L. Jonathan Dursi
- University Health Network, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | | | | | | | - Susan Fairley
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Khalid A. Fakhro
- Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Helen V. Firth
- Wellcome Sanger Institute, Hinxton, UK
- Addenbrooke’s Hospital, Cambridge, UK
| | | | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ian M. Fore
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mallory A. Freeberg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Lauren A. Fromont
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Clara L. Gaff
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Weiniu Gan
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elena M. Ghanaim
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Glazer
- Verily Life Sciences, South San Francisco, CA, USA
| | - Robert C. Green
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Malachi Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Obi L. Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | | | | | - Roderic Guigó
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Dipayan Gupta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Ada Hamosh
- Johns Hopkins University, Baltimore, MD, USA
| | - David P. Hansen
- Australian Genomics, Parkville, VIC, Australia
- The Australian e-Health Research Centre, CSIRO, Herston, QLD, Australia
| | - Reece K. Hart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Invitae, San Francisco, CA, USA
- MyOme, Inc, San Bruno, CA, USA
| | | | - David Haussler
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | - Michael M. Hoffman
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - Oliver M. Hofmann
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Petr Holub
- BBMRI-ERIC, Graz, Austria
- Masaryk University, Brno, Czech Republic
| | | | | | - Sarah E. Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ammar Husami
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | | | - Saumya S. Jamuar
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Republic of Singapore
| | - Elizabeth L. Janes
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- University of Waterloo, Waterloo, ON, Canada
| | | | - Aina Jené
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Amber L. Johns
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Yann Joly
- McGill University, Montreal, QC, Canada
| | - Steven J.M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Alexander Kanitz
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Thomas M. Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- University of Nottingham, Nottingham, UK
| | - Kristina Kekesi-Lafrance
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | | | - Giselle Kerry
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Seik-Soon Khor
- National Center for Global Health and Medicine Hospital, Tokyo, Japan
- University of Tokyo, Tokyo, Japan
| | | | | | | | | | | | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Stephanie Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | | | - Mikael Linden
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Isuru Udara Liyanage
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Alice L. Mann
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Wellcome Sanger Institute, Hinxton, UK
| | | | | | | | - Anna Middleton
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | - Richard J. Milne
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | | | - Nicola Mulder
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | | | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Hidewaki Nakagawa
- Japan Agency for Medical Research & Development (AMED), Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Arcadi Navarro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
| | | | - Ania Niewielska
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Amy Nisselle
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
| | - Jeffrey Niu
- University Health Network, Toronto, ON, Canada
| | - Tommi H. Nyrönen
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Sabine Oesterle
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Vivian Ota Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Emilio Palumbo
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Helen E. Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Jordi Rambla
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Renee A. Rider
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter N. Robinson
- The Jackson Laboratory, Farmington, CT, USA
- University of Connecticut, Farmington, CT, USA
| | - Kurt W. Rodarmer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Alan F. Rubin
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Manuel Rueda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | | | | | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Torsten Schwede
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | | | | | - Neerjah Skantharajah
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Heidi J. Sofia
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dylan Spalding
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Zornitza Stark
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Lincoln D. Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | | | - Patrick Tan
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- Precision Health Research Singapore, Singapore, Republic of Singapore
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | | | - Alastair A. Thomson
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adrian Thorogood
- McGill University, Montreal, QC, Canada
- University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Katsushi Tokunaga
- University of Tokyo, Tokyo, Japan
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Juha Törnroos
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | - David Torrents
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Sean Upchurch
- California Institute of Technology, Pasadena, CA, USA
| | - Alfonso Valencia
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Jessica Vamathevan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Susheel Varma
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- Health Data Research UK, London, UK
| | - Danya F. Vears
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
- Melbourne Law School, University of Melbourne, Parkville, VIC, Australia
| | - Coby Viner
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
| | | | - Alex H. Wagner
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | | | | | | | - Eva C. Winkler
- Section of Translational Medical Ethics, University Hospital Heidelberg, Heidelberg, Germany
| | | | | | | | | | - Andrew D. Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Christina K. Yung
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Indoc Research, Toronto, ON, Canada
| | - Lyndon J. Zass
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | - Ksenia Zaytseva
- McGill University, Montreal, QC, Canada
- Canadian Centre for Computational Genomics, Montreal, QC, Canada
| | - Junjun Zhang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Peter Goodhand
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Kathryn North
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- European Molecular Biology Laboratory, Heidelberg, Germany
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Cunningham F, Cahyadi S, Lengyel I. A Potential New Role for Zinc in Age-Related Macular Degeneration through Regulation of Endothelial Fenestration. Int J Mol Sci 2021; 22:ijms222111974. [PMID: 34769404 PMCID: PMC8584935 DOI: 10.3390/ijms222111974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/21/2021] [Accepted: 11/02/2021] [Indexed: 12/01/2022] Open
Abstract
Age-related macular degeneration (AMD) is a common blinding disease in the western world that is linked to the loss of fenestration in the choriocapillaris that sustains the retinal pigment epithelium and photoreceptors in the back of the eye. Changes in ocular and systemic zinc concentrations have been associated with AMD; therefore, we hypothesized that these changes might be directly involved in fenestrae formation. To test this hypothesis, an endothelial cell (bEND.5) model for fenestrae formation was treated with different concentrations of zinc sulfate (ZnSO4) solution for up to 20 h. Fenestrae were visualized by staining for Plasmalemmal Vesicle Associated Protein-1 (PV-1), the protein that forms the diaphragms of the fenestrated endothelium. Size and distribution were monitored by transmission electron microscopy (TEM). We found that zinc induced the redistribution of PV-1 into areas called sieve plates containing ~70-nm uniform size and typical morphology fenestrae. As AMD is associated with reduced zinc concentrations in the serum and in ocular tissues, and dietary zinc supplementation is recommended to slow disease progression, we propose here that the elevation of zinc concentration may restore choriocapillaris fenestration resulting in improved nutrient flow and clearance of waste material in the retina.
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Affiliation(s)
- Fiona Cunningham
- Wellcome-Wolfson Institute of Experimental Medicine, Queen’s University, Belfast BT9 7BL, UK;
| | - Sabrina Cahyadi
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK;
| | - Imre Lengyel
- Wellcome-Wolfson Institute of Experimental Medicine, Queen’s University, Belfast BT9 7BL, UK;
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK;
- Correspondence:
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Muhlebach MS, Cunningham F, LiPuma JJ, Zhou JJ, Saiman L. Impact of the SARS-CoV-2 pandemic on cystic fibrosis centres and care: survey results from US centres. ERJ Open Res 2021; 7:00249-2021. [PMID: 34646879 PMCID: PMC8364745 DOI: 10.1183/23120541.00249-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 07/15/2021] [Indexed: 11/30/2022] Open
Abstract
The COVID-19 pandemic has affected patients with cystic fibrosis in multiple ways, including fear of becoming infected, the risk of severe disease from SARS-CoV-2 and the need to maintain medical care. As part of an ongoing infection prevention and control (IP&C) study in cystic fibrosis that began in 2019, we assessed how large US cystic fibrosis centres adapted to and perceived effects of the COVID-19 pandemic on care delivery options. The IP&C parent study included two or three centres from each US census region, which followed >300 adult and paediatric patients. Lessons learnt from the pandemic show that telehealth for cystic fibrosis allows multidisciplinary visits but better means for monitoring of lung function and microbiology are neededhttps://bit.ly/2V7g09x
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Affiliation(s)
- Marianne S Muhlebach
- Dept of Pediatrics, Division Pulmonology CB#7217, University of North Carolina, Chapel Hill, NC, USA.,Marsico Lung Institute, Chapel Hill, NC, USA
| | - Fiona Cunningham
- Dept of Pediatrics, Division Pulmonology CB#7217, University of North Carolina, Chapel Hill, NC, USA
| | - John J LiPuma
- Dept of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Juyan J Zhou
- Dept of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Lisa Saiman
- Dept of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Dept of Infection Prevention and Control, NewYork Presbyterian Hospital, New York, NY, USA
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Morales J, McMahon AC, Loveland J, Perry E, Frankish A, Hunt S, Armean IM, Flicek P, Cunningham F. The value of primary transcripts to the clinical and non-clinical genomics community: Survey results and roadmap for improvements. Mol Genet Genomic Med 2021; 9:e1786. [PMID: 34435752 PMCID: PMC8683622 DOI: 10.1002/mgg3.1786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 11/21/2022] Open
Abstract
Background Variant interpretation is dependent on transcript annotation and remains time consuming and challenging. There are major obstacles for historical data reuse and for interpretation of new variants. First, both RefSeq and Ensembl/GENCODE produce transcript sets in common use, but there is currently no easy way to translate between the two. Second, the resources often used for variant interpretation (e.g. ClinVar, gnomAD, UniProt) do not use the same transcript set, nor default transcript or protein sequence. Method Ensembl ran a survey in 2018 to sample attitudes to choosing one default transcript per locus, and to gather data on reference sequences used by the scientific community. This was publicised on the Ensembl and UCSC genome browsers, by email and on social media. Results The survey had 788 responses from 32 different countries, the results of which we report here. Conclusions We present our roadmap to create an effective default set of transcripts for resources, and for reporting interpretation of clinical variants.
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Affiliation(s)
- Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Aoife C McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jane Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sarah Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Irina M Armean
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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Martyn M, McClaren B, Janinski M, Lynch E, Cunningham F, Gaff C. "It's something I've committed to longer term": The impact of an immersion program for physicians on adoption of genomic medicine. Patient Educ Couns 2021; 104:480-488. [PMID: 33268232 DOI: 10.1016/j.pec.2020.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 09/29/2020] [Accepted: 10/07/2020] [Indexed: 06/12/2023]
Abstract
OBJECTIVE To foster implementation of genomic testing in medical care by providing a cadre of physicians with 'hands on' experience in genomics, positioning them as opinion leaders in their medical speciality. This paper presents qualitative evaluation of immediate outcomes, in particular its impact on peer interactions. METHODS Program design and delivery was informed by implementation science, behavior change and experiential learning theories. Inductive content analysis of transcribed audio-recordings from semi-structured post-project interviews with all participants (n = 12) was conducted. RESULTS Participants reported the immersion experience improved their genomic capability, established them as credible genomic experts within their speciality and altered their practice in genomic medicine. Participants reported strengthening and widening of peer-to-peer and interdisciplinary communication, with both passive diffusion and active dissemination of information to peers. Some also became a resource for genetic professionals. CONCLUSIONS Genomic immersion participants described elements which support sustained integration of an innovation, including immediate changes (e.g. use of genomic tests) and wider impacts (e.g. professional networks). PRACTICE IMPLICATIONS This study supports a role for immersion as a successful strategy for enhancing engagement of non-geneticist physicians in genomics. Additional study is needed to understand how immersion experiences change the delivery of genomic services at the provider, practice and health system level.
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Affiliation(s)
- Melissa Martyn
- Murdoch Children's Research Institute, Parkville, Australia; Melbourne Genomics Health Alliance, c/o Walter and Eliza Hall Institute, Parkville, Australia; Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Belinda McClaren
- Murdoch Children's Research Institute, Parkville, Australia; Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Monika Janinski
- Murdoch Children's Research Institute, Parkville, Australia; Melbourne Genomics Health Alliance, c/o Walter and Eliza Hall Institute, Parkville, Australia
| | - Elly Lynch
- Murdoch Children's Research Institute, Parkville, Australia; Melbourne Genomics Health Alliance, c/o Walter and Eliza Hall Institute, Parkville, Australia; Victorian Clinical Genetics Services, The Royal Children's Hospital, Parkville, Australia
| | - Fiona Cunningham
- Melbourne Genomics Health Alliance, c/o Walter and Eliza Hall Institute, Parkville, Australia; Monash Genetics, Monash Health, Clayton, Australia
| | - Clara Gaff
- Murdoch Children's Research Institute, Parkville, Australia; Melbourne Genomics Health Alliance, c/o Walter and Eliza Hall Institute, Parkville, Australia; Department of Paediatrics, University of Melbourne, Parkville, Australia.
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23
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Howe KL, Achuthan P, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Charkhchi M, Cummins C, Da Rin Fioretto L, Davidson C, Dodiya K, El Houdaigui B, Fatima R, Gall A, Garcia Giron C, Grego T, Guijarro-Clarke C, Haggerty L, Hemrom A, Hourlier T, Izuogu OG, Juettemann T, Kaikala V, Kay M, Lavidas I, Le T, Lemos D, Gonzalez Martinez J, Marugán JC, Maurel T, McMahon AC, Mohanan S, Moore B, Muffato M, Oheh DN, Paraschas D, Parker A, Parton A, Prosovetskaia I, Sakthivel MP, Salam AIA, Schmitt BM, Schuilenburg H, Sheppard D, Steed E, Szpak M, Szuba M, Taylor K, Thormann A, Threadgold G, Walts B, Winterbottom A, Chakiachvili M, Chaubal A, De Silva N, Flint B, Frankish A, Hunt SE, IIsley GR, Langridge N, Loveland JE, Martin FJ, Mudge JM, Morales J, Perry E, Ruffier M, Tate J, Thybert D, Trevanion SJ, Cunningham F, Yates AD, Zerbino DR, Flicek P. Ensembl 2021. Nucleic Acids Res 2021; 49:D884-D891. [PMID: 33137190 PMCID: PMC7778975 DOI: 10.1093/nar/gkaa942] [Citation(s) in RCA: 929] [Impact Index Per Article: 309.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (http://rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large biodiversity sequencing projects. Our SARS-CoV-2 genome browser (https://covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.
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Affiliation(s)
- Kevin L Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Premanand Achuthan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jamie Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jorge Alvarez-Jarreta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - M Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Irina M Armean
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrey G Azov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ruth Bennett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jyothish Bhai
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sanjay Boddu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mehrnaz Charkhchi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Luca Da Rin Fioretto
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kamalkumar Dodiya
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bilal El Houdaigui
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Reham Fatima
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carlos Garcia Giron
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tiago Grego
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Cristina Guijarro-Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anmol Hemrom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Osagie G Izuogu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Juettemann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Vinay Kaikala
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mike Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ilias Lavidas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tuan Le
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Diana Lemos
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jose Gonzalez Martinez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - José Carlos Marugán
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aoife C McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Shamika Mohanan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Benjamin Moore
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Denye N Oheh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dimitrios Paraschas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Parton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Irina Prosovetskaia
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Manoj P Sakthivel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ahamed I Abdul Salam
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bianca M Schmitt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dan Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Steed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michal Szpak
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marek Szuba
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Glen Threadgold
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Brandon Walts
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrea Winterbottom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marc Chakiachvili
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ameya Chaubal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nishadi De Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bethany Flint
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Garth R IIsley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nick Langridge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Joanella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - John Tate
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David Thybert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew D Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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24
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Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Howe KL, Hunt T, Izuogu OG, Johnson R, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Riera FC, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Wolf MY, Xu J, Yang YT, Yates A, Zerbino D, Zhang Y, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Tress ML, Flicek P. GENCODE 2021. Nucleic Acids Res 2021; 49:D916-D923. [PMID: 33270111 PMCID: PMC7778937 DOI: 10.1093/nar/gkaa1087] [Citation(s) in RCA: 500] [Impact Index Per Article: 166.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/21/2020] [Accepted: 10/24/2020] [Indexed: 12/14/2022] Open
Abstract
The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis generated both within the consortium and externally to support the creation of transcript structures and the determination of their function. Here, we present improvements to our annotation infrastructure, bioinformatics tools, and analysis, and the advances they support in the annotation of the human and mouse genomes including: the completion of first pass manual annotation for the mouse reference genome; targeted improvements to the annotation of genes associated with SARS-CoV-2 infection; collaborative projects to achieve convergence across reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.
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Affiliation(s)
- Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Julien Lagarde
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Cristina Sisu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.,Department of Bioscience, Brunel University London, Uxbridge UB8 3PH, UK
| | - James C Wright
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Joel Armstrong
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alexandra Bignell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carles Boix
- MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.,Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Silvia Carbonell Sala
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tomás Di Domenico
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Sarah Donaldson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ian T Fiddes
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Carlos García Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jose Manuel Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tiago Grego
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew Hardy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kevin L Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Osagie G Izuogu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, University Hospital, University of Bern, Bern, Switzerland.,Department of Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laura Martínez
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Shamika Mohanan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Muir
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA.,Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Fabio C P Navarro
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Baikang Pei
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Fernando Pozo
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ferriol Calvet Riera
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bianca M Schmitt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eloise Stapleton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Irina Sycheva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Maxim Y Wolf
- Department of Biomedical Informatics at Harvard Medical School, 10 Shattuck Street, Suite 514, Boston, MA 02115, USA
| | - Jinuri Xu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Yucheng T Yang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.,Program in Computational Biology & Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Andrew Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Yan Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.,Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Jyoti S Choudhary
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.,Program in Computational Biology & Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA.,Department of Computer Science, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, E-08003 Catalonia, Spain
| | - Tim J P Hubbard
- Department of Medical and Molecular Genetics, King's College London, Guys Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Michael L Tress
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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25
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McSweeney SM, Christou EAA, Dand N, Boalch A, Holmes S, Harries M, Palamaras I, Cunningham F, Parkins G, Kaur M, Farrant P, McDonagh A, Messenger A, Jones J, Jolliffe V, Ali I, Ardern-Jones M, Mitchell C, Burrows N, Atkar R, Banfield C, Alexandroff A, Champagne C, Cooper HL, Patel GK, Macbeth A, Page M, Bryden A, Mowbray M, Wahie S, Armstrong K, Cooke N, Goodfield M, Man I, de Berker D, Dunnil G, Takwale A, Rao A, Siah TW, Sinclair R, Wade MS, Bhargava K, Fenton DA, McGrath JA, Tziotzios C. Frontal fibrosing alopecia: a descriptive cross-sectional study of 711 cases in female patients from the UK. Br J Dermatol 2020; 183:1136-1138. [PMID: 32652611 DOI: 10.1111/bjd.19399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- S M McSweeney
- St John's Institute of Dermatology, Guy's Hospital, London, SE1 9RT, UK
| | - E A A Christou
- St John's Institute of Dermatology, Guy's Hospital, London, SE1 9RT, UK
| | - N Dand
- Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London, SE1 9RT, UK
| | - A Boalch
- Greenwich and Lewisham NHS Foundation Trust, London, SE13 6LH, UK
| | - S Holmes
- Alan Lyell Centre for Dermatology, Queen Elizabeth University Hospital, Glasgow, G51 4TF, UK.,UK FFA Consortium
| | | | | | - F Cunningham
- Alan Lyell Centre for Dermatology, Queen Elizabeth University Hospital, Glasgow, G51 4TF, UK.,UK FFA Consortium
| | - G Parkins
- Alan Lyell Centre for Dermatology, Queen Elizabeth University Hospital, Glasgow, G51 4TF, UK.,UK FFA Consortium
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - K Bhargava
- St John's Institute of Dermatology, Guy's Hospital, London, SE1 9RT, UK.,UK FFA Consortium
| | - D A Fenton
- St John's Institute of Dermatology, Guy's Hospital, London, SE1 9RT, UK.,UK FFA Consortium
| | - J A McGrath
- St John's Institute of Dermatology, Guy's Hospital, London, SE1 9RT, UK
| | - C Tziotzios
- St John's Institute of Dermatology, Guy's Hospital, London, SE1 9RT, UK
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26
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Buniello A, MacArthur JAL, Cerezo M, Harris LW, Hayhurst J, Malangone C, McMahon A, Morales J, Mountjoy E, Sollis E, Suveges D, Vrousgou O, Whetzel PL, Amode R, Guillen JA, Riat HS, Trevanion SJ, Hall P, Junkins H, Flicek P, Burdett T, Hindorff LA, Cunningham F, Parkinson H. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res 2020; 47:D1005-D1012. [PMID: 30445434 PMCID: PMC6323933 DOI: 10.1093/nar/gky1120] [Citation(s) in RCA: 2310] [Impact Index Per Article: 577.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 10/25/2018] [Indexed: 02/06/2023] Open
Abstract
The GWAS Catalog delivers a high-quality curated collection of all published genome-wide association studies enabling investigations to identify causal variants, understand disease mechanisms, and establish targets for novel therapies. The scope of the Catalog has also expanded to targeted and exome arrays with 1000 new associations added for these technologies. As of September 2018, the Catalog contains 5687 GWAS comprising 71673 variant-trait associations from 3567 publications. New content includes 284 full P-value summary statistics datasets for genome-wide and new targeted array studies, representing 6 × 109 individual variant-trait statistics. In the last 12 months, the Catalog's user interface was accessed by ∼90000 unique users who viewed >1 million pages. We have improved data access with the release of a new RESTful API to support high-throughput programmatic access, an improved web interface and a new summary statistics database. Summary statistics provision is supported by a new format proposed as a community standard for summary statistics data representation. This format was derived from our experience in standardizing heterogeneous submissions, mapping formats and in harmonizing content. Availability: https://www.ebi.ac.uk/gwas/.
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Affiliation(s)
- Annalisa Buniello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jacqueline A L MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Maria Cerezo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laura W Harris
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James Hayhurst
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Cinzia Malangone
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Edward Mountjoy
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, University of Oxford, NIHR Oxford Biomedical Research Centre, Nuffield Department of Medicine, Oxford, UK
| | - Elliot Sollis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Suveges
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Olga Vrousgou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Patricia L Whetzel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jose A Guillen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Harpreet S Riat
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peggy Hall
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Heather Junkins
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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27
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Cunningham F, Achuthan P, Akanni W, Allen J, Amode MR, Armean IM, Bennett R, Bhai J, Billis K, Boddu S, Cummins C, Davidson C, Dodiya KJ, Gall A, Girón CG, Gil L, Grego T, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, Kay M, Laird MR, Lavidas I, Liu Z, Loveland JE, Marugán JC, Maurel T, McMahon AC, Moore B, Morales J, Mudge JM, Nuhn M, Ogeh D, Parker A, Parton A, Patricio M, Abdul Salam AI, Schmitt BM, Schuilenburg H, Sheppard D, Sparrow H, Stapleton E, Szuba M, Taylor K, Threadgold G, Thormann A, Vullo A, Walts B, Winterbottom A, Zadissa A, Chakiachvili M, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Yates AD, Zerbino DR, Flicek P. Ensembl 2019. Nucleic Acids Res 2020; 47:D745-D751. [PMID: 30407521 PMCID: PMC6323964 DOI: 10.1093/nar/gky1113] [Citation(s) in RCA: 631] [Impact Index Per Article: 157.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 10/23/2018] [Indexed: 01/28/2023] Open
Abstract
The Ensembl project (https://www.ensembl.org) makes key genomic data sets available to the entire scientific community without restrictions. Ensembl seeks to be a fundamental resource driving scientific progress by creating, maintaining and updating reference genome annotation and comparative genomics resources. This year we describe our new and expanded gene, variant and comparative annotation capabilities, which led to a 50% increase in the number of vertebrate genomes we support. We have also doubled the number of available human variants and added regulatory regions for many mouse cell types and developmental stages. Our data sets and tools are available via the Ensembl website as well as a through a RESTful webservice, Perl application programming interface and as data files for download.
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Affiliation(s)
- Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Premanand Achuthan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Wasiu Akanni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - M Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Irina M Armean
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ruth Bennett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jyothish Bhai
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sanjay Boddu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kamalkumar Jayantilal Dodiya
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carlos García Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tiago Grego
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Erin Haskell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Osagie G Izuogu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sophie H Janacek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Juettemann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mike Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew R Laird
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ilias Lavidas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Zhicheng Liu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - José C Marugán
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aoife C McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Benjamin Moore
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michael Nuhn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Denye Ogeh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Parton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ahamed Imran Abdul Salam
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bianca M Schmitt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dan Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helen Sparrow
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eloise Stapleton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marek Szuba
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Glen Threadgold
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alessandro Vullo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Brandon Walts
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrea Winterbottom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Amonida Zadissa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marc Chakiachvili
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Myrto Kostadima
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nick Langridge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel M Staines
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bronwen L Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew D Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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28
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Yates AD, Achuthan P, Akanni W, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Marugán JC, Cummins C, Davidson C, Dodiya K, Fatima R, Gall A, Giron CG, Gil L, Grego T, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, Kay M, Lavidas I, Le T, Lemos D, Martinez JG, Maurel T, McDowall M, McMahon A, Mohanan S, Moore B, Nuhn M, Oheh DN, Parker A, Parton A, Patricio M, Sakthivel MP, Abdul Salam AI, Schmitt BM, Schuilenburg H, Sheppard D, Sycheva M, Szuba M, Taylor K, Thormann A, Threadgold G, Vullo A, Walts B, Winterbottom A, Zadissa A, Chakiachvili M, Flint B, Frankish A, Hunt SE, IIsley G, Kostadima M, Langridge N, Loveland JE, Martin FJ, Morales J, Mudge JM, Muffato M, Perry E, Ruffier M, Trevanion SJ, Cunningham F, Howe KL, Zerbino DR, Flicek P. Ensembl 2020. Nucleic Acids Res 2020; 48:D682-D688. [PMID: 31691826 PMCID: PMC7145704 DOI: 10.1093/nar/gkz966] [Citation(s) in RCA: 694] [Impact Index Per Article: 173.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 12/11/2022] Open
Abstract
The Ensembl (https://www.ensembl.org) is a system for generating and distributing genome annotation such as genes, variation, regulation and comparative genomics across the vertebrate subphylum and key model organisms. The Ensembl annotation pipeline is capable of integrating experimental and reference data from multiple providers into a single integrated resource. Here, we present 94 newly annotated and re-annotated genomes, bringing the total number of genomes offered by Ensembl to 227. This represents the single largest expansion of the resource since its inception. We also detail our continued efforts to improve human annotation, developments in our epigenome analysis and display, a new tool for imputing causal genes from genome-wide association studies and visualisation of variation within a 3D protein model. Finally, we present information on our new website. Both software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license) and data updates made available four times a year.
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Affiliation(s)
- Andrew D Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Premanand Achuthan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Wasiu Akanni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jamie Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jorge Alvarez-Jarreta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - M Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Irina M Armean
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrey G Azov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ruth Bennett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jyothish Bhai
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sanjay Boddu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - José Carlos Marugán
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kamalkumar Dodiya
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Reham Fatima
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carlos Garcia Giron
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tiago Grego
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Erin Haskell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Osagie G Izuogu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sophie H Janacek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Juettemann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mike Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ilias Lavidas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tuan Le
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Diana Lemos
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jose Gonzalez Martinez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mark McDowall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Shamika Mohanan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Benjamin Moore
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michael Nuhn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Denye N Oheh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Parton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Manoj Pandian Sakthivel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ahamed Imran Abdul Salam
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bianca M Schmitt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dan Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mira Sycheva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marek Szuba
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Glen Threadgold
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alessandro Vullo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Brandon Walts
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrea Winterbottom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Amonida Zadissa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marc Chakiachvili
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bethany Flint
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Garth IIsley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Myrto Kostadima
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nick Langridge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kevin L Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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29
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Ayon RJ, Hawn MB, Aoun J, Wiwchar M, Forrest AS, Cunningham F, Singer CA, Valencik ML, Greenwood IA, Leblanc N. Molecular mechanism of TMEM16A regulation: role of CaMKII and PP1/PP2A. Am J Physiol Cell Physiol 2019; 317:C1093-C1106. [PMID: 31461344 DOI: 10.1152/ajpcell.00059.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This study explored the mechanism by which Ca2+-activated Cl- channels (CaCCs) encoded by the Tmem16a gene are regulated by calmodulin-dependent protein kinase II (CaMKII) and protein phosphatases 1 (PP1) and 2A (PP2A). Ca2+-activated Cl- currents (IClCa) were recorded from HEK-293 cells expressing mouse TMEM16A. IClCa were evoked using a pipette solution in which free Ca2+ concentration was clamped to 500 nM, in the presence (5 mM) or absence of ATP. With 5 mM ATP, IClCa decayed to <50% of the initial current magnitude within 10 min after seal rupture. IClCa rundown seen with ATP-containing pipette solution was greatly diminished by omitting ATP. IClCa recorded after 20 min of cell dialysis with 0 ATP were more than twofold larger than those recorded with 5 mM ATP. Intracellular application of autocamtide-2-related inhibitory peptide (5 µM) or KN-93 (10 µM), two specific CaMKII inhibitors, produced a similar attenuation of TMEM16A rundown. In contrast, internal application of okadaic acid (30 nM) or cantharidin (100 nM), two nonselective PP1 and PP2A blockers, promoted the rundown of TMEM16A in cells dialyzed with 0 ATP. Mutating serine 528 of TMEM16A to an alanine led to a similar inhibition of TMEM16A rundown to that exerted by either one of the two CaMKII inhibitors tested, which was not observed for three putative CaMKII consensus sites for phosphorylation (T273, T622, and S730). Our results suggest that TMEM16A-mediated CaCCs are regulated by CaMKII and PP1/PP2A. Our data also suggest that serine 528 of TMEM16A is an important contributor to the regulation of IClCa by CaMKII.
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Affiliation(s)
- Ramon J Ayon
- Division of Translational and Regenerative Medicine, Department of Medicine, College of Medicine, The University of Arizona College of Medicine, Arizona Health Sciences Center, Tucson, Arizona
| | - Matthew B Hawn
- Department of Pharmacology, Center of Biomedical Research Excellence for Molecular and Cellular Signal Transduction in the Cardiovascular System, University of Nevada, Reno School of Medicine, Reno, Nevada.,The Center for Cardiovascular Research, Center of Biomedical Research Excellence for Molecular and Cellular Signal Transduction in the Cardiovascular System, University of Nevada, Reno School of Medicine, Reno, Nevada
| | - Joydeep Aoun
- Department of Pharmacology, Center of Biomedical Research Excellence for Molecular and Cellular Signal Transduction in the Cardiovascular System, University of Nevada, Reno School of Medicine, Reno, Nevada.,The Center for Cardiovascular Research, Center of Biomedical Research Excellence for Molecular and Cellular Signal Transduction in the Cardiovascular System, University of Nevada, Reno School of Medicine, Reno, Nevada
| | - Michael Wiwchar
- Department of Pharmacology, Center of Biomedical Research Excellence for Molecular and Cellular Signal Transduction in the Cardiovascular System, University of Nevada, Reno School of Medicine, Reno, Nevada
| | - Abigail S Forrest
- Department of Pharmacology, Center of Biomedical Research Excellence for Molecular and Cellular Signal Transduction in the Cardiovascular System, University of Nevada, Reno School of Medicine, Reno, Nevada
| | - Fiona Cunningham
- Department of Pharmacology, Center of Biomedical Research Excellence for Molecular and Cellular Signal Transduction in the Cardiovascular System, University of Nevada, Reno School of Medicine, Reno, Nevada
| | - Cherie A Singer
- Department of Pharmacology, Center of Biomedical Research Excellence for Molecular and Cellular Signal Transduction in the Cardiovascular System, University of Nevada, Reno School of Medicine, Reno, Nevada
| | - Maria L Valencik
- Department of Pharmacology, Center of Biomedical Research Excellence for Molecular and Cellular Signal Transduction in the Cardiovascular System, University of Nevada, Reno School of Medicine, Reno, Nevada
| | - Iain A Greenwood
- Institute of Molecular and Clinical Sciences, St. George's University of London, London, United Kingdom
| | - Normand Leblanc
- Department of Pharmacology, Center of Biomedical Research Excellence for Molecular and Cellular Signal Transduction in the Cardiovascular System, University of Nevada, Reno School of Medicine, Reno, Nevada.,The Center for Cardiovascular Research, Center of Biomedical Research Excellence for Molecular and Cellular Signal Transduction in the Cardiovascular System, University of Nevada, Reno School of Medicine, Reno, Nevada
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30
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Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, Billis K, Cummins C, Gall A, Girón CG, Gil L, Gordon L, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, To JK, Laird MR, Lavidas I, Liu Z, Loveland JE, Maurel T, McLaren W, Moore B, Mudge J, Murphy DN, Newman V, Nuhn M, Ogeh D, Ong CK, Parker A, Patricio M, Riat HS, Schuilenburg H, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Zadissa A, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Cunningham F, Yates A, Flicek P. Ensembl 2018. Nucleic Acids Res 2019; 46:D754-D761. [PMID: 29155950 PMCID: PMC5753206 DOI: 10.1093/nar/gkx1098] [Citation(s) in RCA: 1903] [Impact Index Per Article: 380.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 10/21/2017] [Indexed: 01/29/2023] Open
Abstract
The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of the draft human genome, with the aim of accelerating genomics research through rapid open distribution of public data. Large amounts of raw data are thus transformed into knowledge, which is made available via a multitude of channels, in particular our browser (http://www.ensembl.org). Over time, we have expanded in multiple directions. First, our resources describe multiple fields of genomics, in particular gene annotation, comparative genomics, genetics and epigenomics. Second, we cover a growing number of genome assemblies; Ensembl Release 90 contains exactly 100. Third, our databases feed simultaneously into an array of services designed around different use cases, ranging from quick browsing to genome-wide bioinformatic analysis. We present here the latest developments of the Ensembl project, with a focus on managing an increasing number of assemblies, supporting efforts in genome interpretation and improving our browser.
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Affiliation(s)
- Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Premanand Achuthan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Wasiu Akanni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - M Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Barrell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Eagle Genomics Ltd., Wellcome Genome Campus, Hinxton, Cambridge CB10 1DR, UK
| | - Jyothish Bhai
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carlos García Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Leo Gordon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Erin Haskell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Osagie G Izuogu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sophie H Janacek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Juettemann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jimmy Kiang To
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew R Laird
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ilias Lavidas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Zhicheng Liu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Benjamin Moore
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Victoria Newman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michael Nuhn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Denye Ogeh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Chuang Kee Ong
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Harpreet Singh Riat
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dan Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helen Sparrow
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alessandro Vullo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Brandon Walts
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Amonida Zadissa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Myrto Kostadima
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nicholas Langridge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dan M Staines
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bronwen L Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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31
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Mignot C, McMahon AC, Bar C, Campeau PM, Davidson C, Buratti J, Nava C, Jacquemont ML, Tallot M, Milh M, Edery P, Marzin P, Barcia G, Barnerias C, Besmond C, Bienvenu T, Bruel AL, Brunga L, Ceulemans B, Coubes C, Cristancho AG, Cunningham F, Dehouck MB, Donner EJ, Duban-Bedu B, Dubourg C, Gardella E, Gauthier J, Geneviève D, Gobin-Limballe S, Goldberg EM, Hagebeuk E, Hamdan FF, Hančárová M, Hubert L, Ioos C, Ichikawa S, Janssens S, Journel H, Kaminska A, Keren B, Koopmans M, Lacoste C, Laššuthová P, Lederer D, Lehalle D, Marjanovic D, Métreau J, Michaud JL, Miller K, Minassian BA, Morales J, Moutard ML, Munnich A, Ortiz-Gonzalez XR, Pinard JM, Prchalová D, Putoux A, Quelin C, Rosen AR, Roume J, Rossignol E, Simon MEH, Smol T, Shur N, Shelihan I, Štěrbová K, Vyhnálková E, Vilain C, Soblet J, Smits G, Yang SP, van der Smagt JJ, van Hasselt PM, van Kempen M, Weckhuysen S, Helbig I, Villard L, Héron D, Koeleman B, Møller RS, Lesca G, Helbig KL, Nabbout R, Verbeek NE, Depienne C. Correction: IQSEC2-related encephalopathy in males and females: a comparative study including 37 novel patients. Genet Med 2019; 21:1897-1898. [PMID: 30279470 PMCID: PMC7608434 DOI: 10.1038/s41436-018-0327-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
This Article was originally published under Nature Research's License to Publish, but has now been made available under a CC BY 4.0 license. The PDF and HTML versions of the Article have been modified accordingly.
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Affiliation(s)
- Cyril Mignot
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universites, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle epiniere, ICM, Paris, France. .,APHP, Hôpital Pitie-Salpetriere, Departement de Genetique et de Cytogenetique; Centre de Reference Deficience Intellectuelle de Causes Rares, GRC UPMC «Deficience Intellectuelle et Autisme», Paris, France.
| | - Aoife C McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Claire Bar
- APHP, Reference Centre for Rare Epilepsies, Necker-Enfants Malades Hospital, Imagine Institute, Paris Descartes University, Paris, France.,INSERM U1163, Imagine Institute, Paris, France.,Paris Descartes University, Paris, France
| | - Philippe M Campeau
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Julien Buratti
- APHP, Hôpital Pitie-Salpetriere, Departement de Genetique et de Cytogenetique; Centre de Reference Deficience Intellectuelle de Causes Rares, GRC UPMC «Deficience Intellectuelle et Autisme», Paris, France
| | - Caroline Nava
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universites, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle epiniere, ICM, Paris, France.,APHP, Hôpital Pitie-Salpetriere, Departement de Genetique et de Cytogenetique; Centre de Reference Deficience Intellectuelle de Causes Rares, GRC UPMC «Deficience Intellectuelle et Autisme», Paris, France
| | | | - Marilyn Tallot
- CHU La Reunion-Groupe Hospitalier Sud Reunion, La Reunion, France
| | - Mathieu Milh
- APHM, Hôpital d'Enfants de La Timone, Service de Neurologie Pediatrique, centre de reference deficiences intellectuelles de cause rare, Marseille, France.,Aix Marseille University, INSERM, MMG, UMR-S 1251, Faculte de medecine, Marseille, France
| | - Patrick Edery
- Service de Genetique, Centre de Reference Anomalies du Developpement, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, Universite Claude Bernard Lyon 1, Bron, France.,Claude Bernard Lyon I University, Lyon, France
| | - Pauline Marzin
- APHP, Hôpital Pitie-Salpetriere, Departement de Genetique et de Cytogenetique; Centre de Reference Deficience Intellectuelle de Causes Rares, GRC UPMC «Deficience Intellectuelle et Autisme», Paris, France
| | - Giulia Barcia
- INSERM U1163, Imagine Institute, Paris, France.,Paris Descartes University, Paris, France.,APHP, Service de genetique medicale, Necker- Enfants Malades Hospital, Imagine Institute, Paris Descartes University, Paris, France
| | - Christine Barnerias
- APHP, Unite fonctionnelle de Neurologie, Necker-Enfants Malades Hospital, Imagine Institute, Paris Descartes University, Paris, France
| | - Claude Besmond
- INSERM U1163, Imagine Institute, Paris, France.,Paris Descartes University, Paris, France
| | - Thierry Bienvenu
- APHP, Laboratoire de Genetique et Biologie Moleculaires, Hôpital Cochin, HUPC, Paris, France.,Universite Paris Descartes Paris, Institut de Psychiatrie et de Neurosciences de Paris, Inserm U894, Paris, France
| | - Ange-Line Bruel
- FHU-TRANSLAD, Universite de Bourgogne/CHU Dijon, Dijon, France.,INSERM UMR 1231 GAD team, Genetics of Developmental disorders, Universite de Bourgogne-Franche Comte, Dijon, France
| | - Ledia Brunga
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Berten Ceulemans
- Department of Pediatric Neurology, University Hospital and University of Antwerp, Antwerp, Belgium
| | - Christine Coubes
- Departement de Genetique Medicale, Maladies rares et Medecine Personnalisee, CHU de Montpellier, Montpellier, France
| | - Ana G Cristancho
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Elizabeth J Donner
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Bénédicte Duban-Bedu
- Centre de Genetique Chromosomique, Hôpital St-Vincent-de-Paul, GHICL, Lille, France
| | - Christèle Dubourg
- CHU Rennes, Service de Genetique Moleculaire et Genomique, Rennes, France
| | - Elena Gardella
- Danish Epilepsy Centre Filadelfia, Dianalund, Denmark.,Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Julie Gauthier
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - David Geneviève
- Departement de Genetique Medicale, Maladies rares et Medecine Personnalisee, CHU de Montpellier, Montpellier, France.,INSERM, U1183, Montpellier, France
| | - Stéphanie Gobin-Limballe
- APHP, Service de genetique medicale, Necker- Enfants Malades Hospital, Imagine Institute, Paris Descartes University, Paris, France
| | - Ethan M Goldberg
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eveline Hagebeuk
- Stichting Epilepsie Instellingen Nederland, SEIN, Zwolle, The Netherlands
| | - Fadi F Hamdan
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Miroslava Hančárová
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Laurence Hubert
- INSERM U1163, Imagine Institute, Paris, France.,Paris Descartes University, Paris, France
| | - Christine Ioos
- APHP, University Hospital of Paris ïle-de-France ouest, Raymond Poincare Hospital, Garches, France
| | - Shoji Ichikawa
- Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Sandra Janssens
- Centre for Medical Genetics Ghent, Ghent University Hospital, C. Heymanslaan 10, Ghent, Belgium
| | - Hubert Journel
- Service de Genetique Medicale, Hôpital Chubert, Vannes, France
| | - Anna Kaminska
- APHP, Department of Clinical Neurophysiology, Necker-Enfants Malades Hospital, Paris, France
| | - Boris Keren
- APHP, Hôpital Pitie-Salpetriere, Departement de Genetique et de Cytogenetique; Centre de Reference Deficience Intellectuelle de Causes Rares, GRC UPMC «Deficience Intellectuelle et Autisme», Paris, France
| | - Marije Koopmans
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Caroline Lacoste
- Departement de Genetique Medicale, APHM, Hopital d'Enfants de La Timone, Marseille, France
| | - Petra Laššuthová
- Child Neurology Department, 2nd Faculty of Medicine, Charles University and Motol Hospital, Prague, Czech Republic
| | - Damien Lederer
- Centre de Genetique Humaine, Institut de Pathologie et de Genetique, Gosselies, Belgium
| | - Daphné Lehalle
- FHU-TRANSLAD, Universite de Bourgogne/CHU Dijon, Dijon, France.,Unite fonctionnelle de genetique clinique, Centre Hospitalier Intercommunal de Creteil, Creteil, France
| | | | - Julia Métreau
- APHP, Service de neurologie pediatrique, Hôpital Universitaire Bicetre, Le Kremlin-Bicetre, France
| | - Jacques L Michaud
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Kathryn Miller
- Department of Pediatrics, Albany Medical Center, Albany, NY, USA
| | - Berge A Minassian
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Marie-Laure Moutard
- APHP, Hôpital Trousseau, service de neuropediatrie, Paris, France.,Sorbonne Universite, GRC n°19, pathologies Congenitales du Cervelet-LeucoDystrophies, APHP, Hôpital Armand Trousseau, Paris, France
| | - Arnold Munnich
- INSERM U1163, Imagine Institute, Paris, France.,Paris Descartes University, Paris, France.,APHP, Service de genetique medicale, Necker- Enfants Malades Hospital, Imagine Institute, Paris Descartes University, Paris, France
| | | | - Jean-Marc Pinard
- Division of Neuropediatrics, CHU Raymond Poincare (APHP), Garches, France
| | - Darina Prchalová
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Audrey Putoux
- Service de Genetique, Centre de Reference Anomalies du Developpement, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, Universite Claude Bernard Lyon 1, Bron, France.,Claude Bernard Lyon I University, Lyon, France
| | - Chloé Quelin
- Service de Genetique Medicale, CLAD Ouest CHU Hôpital Sud, Rennes, France
| | - Alyssa R Rosen
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joelle Roume
- Unite de Genetique Medicale, Centre de Reference des Maladies rares du Developpement (AnD DI Rares), CHI Poissy-St Germain en Laye, Poissy, France
| | - Elsa Rossignol
- Departments of Pediatrics and Neurosciences, CHU Sainte-Justine and University of Montreal, Montreal, Canada
| | - Marleen E H Simon
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Thomas Smol
- Institut de Genetique Medicale, CHRU Lille, Universite de Lille, Lille, France
| | - Natasha Shur
- Department of Pediatrics, Albany Medical Center, Albany, NY, USA
| | - Ivan Shelihan
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Katalin Štěrbová
- Child Neurology Department, 2nd Faculty of Medicine, Charles University and Motol Hospital, Prague, Czech Republic
| | - Emílie Vyhnálková
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Catheline Vilain
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics, Universite Libre de Bruxelles, Brussels, Belgium.,Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Universite Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Universite Libre de Bruxelles, Brussels, Belgium
| | - Julie Soblet
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics, Universite Libre de Bruxelles, Brussels, Belgium.,Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Universite Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Universite Libre de Bruxelles, Brussels, Belgium
| | - Guillaume Smits
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics, Universite Libre de Bruxelles, Brussels, Belgium.,Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Universite Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Universite Libre de Bruxelles, Brussels, Belgium
| | - Samuel P Yang
- Clinical Genomics & Predictive Medicine, Providence Medical Group, Dayton, WA, USA
| | | | - Peter M van Hasselt
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center, Utrecht, The Netherlands
| | - Marjan van Kempen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sarah Weckhuysen
- Neurogenetics Group, Center of Molecular Neurology, VIB, Antwerp, Belgium.,Neurology Department, University Hospital Antwerp, Antwerp, Belgium
| | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laurent Villard
- Aix Marseille University, INSERM, MMG, UMR-S 1251, Faculte de medecine, Marseille, France.,Departement de Genetique Medicale, APHM, Hopital d'Enfants de La Timone, Marseille, France
| | - Delphine Héron
- APHP, Hôpital Pitie-Salpetriere, Departement de Genetique et de Cytogenetique; Centre de Reference Deficience Intellectuelle de Causes Rares, GRC UPMC «Deficience Intellectuelle et Autisme», Paris, France
| | - Bobby Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rikke S Møller
- CHU Rennes, Service de Genetique Moleculaire et Genomique, Rennes, France.,Danish Epilepsy Centre Filadelfia, Dianalund, Denmark
| | - Gaetan Lesca
- Service de Genetique, Centre de Reference Anomalies du Developpement, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, Universite Claude Bernard Lyon 1, Bron, France.,Claude Bernard Lyon I University, Lyon, France
| | - Katherine L Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rima Nabbout
- APHP, Reference Centre for Rare Epilepsies, Necker-Enfants Malades Hospital, Imagine Institute, Paris Descartes University, Paris, France.,INSERM U1163, Imagine Institute, Paris, France.,Paris Descartes University, Paris, France
| | - Nienke E Verbeek
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Christel Depienne
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universites, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle epiniere, ICM, Paris, France. .,IGBMC, CNRS UMR 7104/INSERM U964/Universite de Strasbourg, Illkirch, France. .,Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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32
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Thormann A, Halachev M, McLaren W, Moore DJ, Svinti V, Campbell A, Kerr SM, Tischkowitz M, Hunt SE, Dunlop MG, Hurles ME, Wright CF, Firth HV, Cunningham F, FitzPatrick DR. Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP. Nat Commun 2019; 10:2373. [PMID: 31147538 PMCID: PMC6542828 DOI: 10.1038/s41467-019-10016-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 04/15/2019] [Indexed: 12/31/2022] Open
Abstract
We aimed to develop an efficient, flexible and scalable approach to diagnostic genome-wide sequence analysis of genetically heterogeneous clinical presentations. Here we present G2P ( www.ebi.ac.uk/gene2phenotype ) as an online system to establish, curate and distribute datasets for diagnostic variant filtering via association of allelic requirement and mutational consequence at a defined locus with phenotypic terms, confidence level and evidence links. An extension to Ensembl Variant Effect Predictor (VEP), VEP-G2P was used to filter both disease-associated and control whole exome sequence (WES) with Developmental Disorders G2P (G2PDD; 2044 entries). VEP-G2PDD shows a sensitivity/precision of 97.3%/33% for de novo and 81.6%/22.7% for inherited pathogenic genotypes respectively. Many of the missing genotypes are likely false-positive pathogenic assignments. The expected number and discriminative features of background genotypes are defined using control WES. Using only human genetic data VEP-G2P performs well compared to other freely-available diagnostic systems and future phenotypic matching capabilities should further enhance performance.
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Affiliation(s)
- Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Mihail Halachev
- MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh, EH4 2XU, UK
- South East Scotland Regional Genetics Services, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - David J Moore
- South East Scotland Regional Genetics Services, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Victoria Svinti
- MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Usher Institute for Population Health Sciences and Informatics, The University of Edinburgh, Nine Edinburgh BioQuarter, 9 Little France Road, Edinburgh, EH16 4UX, UK
| | - Shona M Kerr
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Marc Tischkowitz
- Clinical Genetic Department, Addenbrooke's Hospital Cambridge University Hospitals, Cambridge, CB2 0QQ, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Malcolm G Dunlop
- MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh, EH4 2XU, UK
- Edinburgh Cancer Research Centre, Institute of Genetics & Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Matthew E Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Caroline F Wright
- University of Exeter Medical School, RILD Level 4, Royal Devon & Exeter Hospital, Barrack Road, Exeter, UK
| | - Helen V Firth
- Clinical Genetic Department, Addenbrooke's Hospital Cambridge University Hospitals, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - David R FitzPatrick
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh, EH4 2XU, UK.
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33
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Cunningham F, Van Bergen T, Canning P, Lengyel I, Feyen JHM, Stitt AW. The Placental Growth Factor Pathway and Its Potential Role in Macular Degenerative Disease. Curr Eye Res 2019; 44:813-822. [PMID: 31055948 DOI: 10.1080/02713683.2019.1614197] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
There is growing evidence that placental growth factor (PlGF) is an important player in multiple pathologies, including tumorigenesis, inflammatory disorders and degenerative retinopathies. PlGF is a member of the vascular endothelial growth factor (VEGF) family and in the retina, binding of this growth factor to specific receptors is associated with pathological angiogenesis, vascular leakage, neurodegeneration and inflammation. Although they share some receptor signalling pathways, many of the actions of PlGF are distinct from VEGF and this has revealed the enticing prospect that it could be a useful therapeutic target for treating early and late stages of diabetic retinopathy (DR) and neovascular age-related macular degeneration (AMD). Recent research suggests that modulation of PlGF could also be important in the geographic atrophy (GA) form of late AMD by protecting the outer retina and the retinal pigment epithelium (RPE). This review discusses PlGF and its signalling pathways and highlights the potential of blocking the bioactivity of this growth factor to treat irreversible visual loss due to the two main forms of AMD.
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Affiliation(s)
- Fiona Cunningham
- a Centre for Experimental Medicine, Queen's University Belfast , Belfast , Northern Ireland
| | | | - Paul Canning
- a Centre for Experimental Medicine, Queen's University Belfast , Belfast , Northern Ireland
| | - Imre Lengyel
- a Centre for Experimental Medicine, Queen's University Belfast , Belfast , Northern Ireland
| | | | - Alan W Stitt
- a Centre for Experimental Medicine, Queen's University Belfast , Belfast , Northern Ireland
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34
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Martyn M, Kanga-Parabia A, Lynch E, James PA, Macciocca I, Trainer AH, Halliday J, Keogh L, Wale J, Winship I, Bogwitz M, Valente G, Walsh M, Downie L, Amor D, Wallis M, Cunningham F, Burgess M, Brown NJ, Jarmolowicz A, Lunke S, Goranitis I, Gaff CL. A novel approach to offering additional genomic findings-A protocol to test a two-step approach in the healthcare system. J Genet Couns 2019; 28:388-397. [DOI: 10.1002/jgc4.1102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/14/2019] [Accepted: 01/21/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Melissa Martyn
- Melbourne Genomics Health Alliance; Melbourne Australia
- University of Melbourne; Melbourne Australia
- Murdoch Children’s Research Institute; Melbourne Australia
| | - Anaita Kanga-Parabia
- Melbourne Genomics Health Alliance; Melbourne Australia
- University of Melbourne; Melbourne Australia
- Murdoch Children’s Research Institute; Melbourne Australia
| | - Elly Lynch
- Melbourne Genomics Health Alliance; Melbourne Australia
- Murdoch Children’s Research Institute; Melbourne Australia
- Victorian Clinical Genetics Services; Melbourne Australia
| | - Paul A. James
- Peter MacCallum Cancer Institute; Melbourne Australia
- The Royal Melbourne Hospital; Melbourne Australia
| | - Ivan Macciocca
- Murdoch Children’s Research Institute; Melbourne Australia
- Victorian Clinical Genetics Services; Melbourne Australia
| | - Alison H. Trainer
- Peter MacCallum Cancer Institute; Melbourne Australia
- The Royal Melbourne Hospital; Melbourne Australia
| | - Jane Halliday
- University of Melbourne; Melbourne Australia
- Murdoch Children’s Research Institute; Melbourne Australia
| | | | - Janney Wale
- Melbourne Genomics Health Alliance; Melbourne Australia
| | | | | | | | - Maie Walsh
- Peter MacCallum Cancer Institute; Melbourne Australia
- The Royal Melbourne Hospital; Melbourne Australia
| | - Lilian Downie
- University of Melbourne; Melbourne Australia
- Murdoch Children’s Research Institute; Melbourne Australia
- Victorian Clinical Genetics Services; Melbourne Australia
| | - David Amor
- University of Melbourne; Melbourne Australia
- Royal Children’s Hospital; Melbourne Australia
| | | | - Fiona Cunningham
- Murdoch Children’s Research Institute; Melbourne Australia
- Monash Health; Melbourne Australia
| | | | - Natasha J. Brown
- University of Melbourne; Melbourne Australia
- Murdoch Children’s Research Institute; Melbourne Australia
- Victorian Clinical Genetics Services; Melbourne Australia
- Austin Health; Melbourne Australia
- Royal Children’s Hospital; Melbourne Australia
| | - Anna Jarmolowicz
- Murdoch Children’s Research Institute; Melbourne Australia
- Victorian Clinical Genetics Services; Melbourne Australia
| | - Sebastian Lunke
- Murdoch Children’s Research Institute; Melbourne Australia
- Victorian Clinical Genetics Services; Melbourne Australia
| | - Ilias Goranitis
- University of Melbourne; Melbourne Australia
- Murdoch Children’s Research Institute; Melbourne Australia
| | - Clara L. Gaff
- Melbourne Genomics Health Alliance; Melbourne Australia
- University of Melbourne; Melbourne Australia
- Murdoch Children’s Research Institute; Melbourne Australia
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35
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Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Hunt T, Izuogu OG, Lagarde J, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FC, Parker A, Pei B, Pozo F, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Xu J, Yates A, Zerbino D, Zhang Y, Aken B, Choudhary JS, Gerstein M, Guigó R, Hubbard TJ, Kellis M, Paten B, Reymond A, Tress ML, Flicek P. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res 2019; 47:D766-D773. [PMID: 30357393 PMCID: PMC6323946 DOI: 10.1093/nar/gky955] [Citation(s) in RCA: 1713] [Impact Index Per Article: 342.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/20/2018] [Accepted: 10/08/2018] [Indexed: 02/06/2023] Open
Abstract
The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource. The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend the GENCODE gene annotation. Specifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines. In addition, manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard. GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.
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Affiliation(s)
- Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Anne-Maud Ferreira
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, University Hospital, University of Bern, Bern, Switzerland
- Department of Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, 32 Vasser St, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Jane Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Cristina Sisu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Bioscience, Brunel University London, Uxbridge UB8 3PH, UK
| | - James Wright
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 123 Old Brompton Road, London SW7 3RP, UK
| | - Joel Armstrong
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alexandra Bignell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Silvia Carbonell Sala
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain
| | - Jacqueline Chrast
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tomás Di Domenico
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Sarah Donaldson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ian T Fiddes
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Carlos García Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jose Manuel Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tiago Grego
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew Hardy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Osagie G Izuogu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Julien Lagarde
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laura Martínez
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Shamika Mohanan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Muir
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Fabio C P Navarro
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Baikang Pei
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Fernando Pozo
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bianca M Schmitt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eloise Stapleton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Irina Sycheva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Jinuri Xu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Andrew Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Yan Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Bronwen Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jyoti S Choudhary
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 123 Old Brompton Road, London SW7 3RP, UK
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Program in Computational Biology & Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, E-08003 Catalonia, Spain
| | - Tim J P Hubbard
- Department of Medical and Molecular Genetics, King's College London, Guys Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, 32 Vasser St, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Michael L Tress
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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36
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Spooner W, McLaren W, Slidel T, Finch DK, Butler R, Campbell J, Eghobamien L, Rider D, Kiefer CM, Robinson MJ, Hardman C, Cunningham F, Vaughan T, Flicek P, Huntington CC. Haplosaurus computes protein haplotypes for use in precision drug design. Nat Commun 2018; 9:4128. [PMID: 30297836 PMCID: PMC6175845 DOI: 10.1038/s41467-018-06542-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 09/07/2018] [Indexed: 01/08/2023] Open
Abstract
Selecting the most appropriate protein sequences is critical for precision drug design. Here we describe Haplosaurus, a bioinformatic tool for computation of protein haplotypes. Haplosaurus computes protein haplotypes from pre-existing chromosomally-phased genomic variation data. Integration into the Ensembl resource provides rapid and detailed protein haplotypes retrieval. Using Haplosaurus, we build a database of unique protein haplotypes from the 1000 Genomes dataset reflecting real-world protein sequence variability and their prevalence. For one in seven genes, their most common protein haplotype differs from the reference sequence and a similar number differs on their most common haplotype between human populations. Three case studies show how knowledge of the range of commonly encountered protein forms predicted in populations leads to insights into therapeutic efficacy. Haplosaurus and its associated database is expected to find broad applications in many disciplines using protein sequences and particularly impactful for therapeutics design.
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Affiliation(s)
- William Spooner
- Eagle Genomics Ltd., Biodata Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridge, CB10 3DR UK
- Genomics England, QMUL Dawson Hall, London, EC1M 6BQ UK
| | - William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | | | | | - Robin Butler
- MedImmune Ltd., Granta Park, Cambridge, CB21 4QR UK
| | | | | | - David Rider
- MedImmune Ltd., Granta Park, Cambridge, CB21 4QR UK
| | | | | | | | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
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37
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Mignot C, McMahon AC, Bar C, Campeau PM, Davidson C, Buratti J, Nava C, Jacquemont ML, Tallot M, Milh M, Edery P, Marzin P, Barcia G, Barnerias C, Besmond C, Bienvenu T, Bruel AL, Brunga L, Ceulemans B, Coubes C, Cristancho AG, Cunningham F, Dehouck MB, Donner EJ, Duban-Bedu B, Dubourg C, Gardella E, Gauthier J, Geneviève D, Gobin-Limballe S, Goldberg EM, Hagebeuk E, Hamdan FF, Hančárová M, Hubert L, Ioos C, Ichikawa S, Janssens S, Journel H, Kaminska A, Keren B, Koopmans M, Lacoste C, Laššuthová P, Lederer D, Lehalle D, Marjanovic D, Métreau J, Michaud JL, Miller K, Minassian BA, Morales J, Moutard ML, Munnich A, Ortiz-Gonzalez XR, Pinard JM, Prchalová D, Putoux A, Quelin C, Rosen AR, Roume J, Rossignol E, Simon MEH, Smol T, Shur N, Shelihan I, Štěrbová K, Vyhnálková E, Vilain C, Soblet J, Smits G, Yang SP, van der Smagt JJ, van Hasselt PM, van Kempen M, Weckhuysen S, Helbig I, Villard L, Héron D, Koeleman B, Møller RS, Lesca G, Helbig KL, Nabbout R, Verbeek NE, Depienne C. IQSEC2-related encephalopathy in males and females: a comparative study including 37 novel patients. Genet Med 2018; 21:837-849. [PMID: 30206421 PMCID: PMC6752297 DOI: 10.1038/s41436-018-0268-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/31/2018] [Indexed: 12/19/2022] Open
Abstract
Purpose Variants in IQSEC2, escaping X inactivation, cause X-linked intellectual disability with frequent epilepsy in males and females. We aimed to investigate sex-specific differences. Methods We collected the data of 37 unpublished patients (18 males and 19 females) with IQSEC2 pathogenic variants and 5 individuals with variants of unknown significance and reviewed published variants. We compared variant types and phenotypes in males and females and performed an analysis of IQSEC2 isoforms. Results IQSEC2 pathogenic variants mainly led to premature truncation and were scattered throughout the longest brain-specific isoform, encoding the synaptic IQSEC2/BRAG1 protein. Variants occurred de novo in females but were either de novo (2/3) or inherited (1/3) in males, with missense variants being predominantly inherited. Developmental delay and intellectual disability were overall more severe in males than in females. Likewise, seizures were more frequently observed and intractable, and started earlier in males than in females. No correlation was observed between the age at seizure onset and severity of intellectual disability or resistance to antiepileptic treatments. Conclusion This study provides a comprehensive overview of IQSEC2-related encephalopathy in males and females, and suggests that an accurate dosage of IQSEC2 at the synapse is crucial during normal brain development.
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Affiliation(s)
- Cyril Mignot
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universites, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle epiniere, ICM, Paris, France. .,APHP, Hôpital Pitie-Salpetriere, Departement de Genetique et de Cytogenetique; Centre de Reference Deficience Intellectuelle de Causes Rares; GRC UPMC «Deficience Intellectuelle et Autisme», Paris, France.
| | - Aoife C McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Claire Bar
- APHP, Reference Centre for Rare Epilepsies, Necker-Enfants Malades Hospital, Imagine Institute, Paris Descartes University, Paris, France.,INSERM U1163, Imagine Institute, Paris, France.,Paris Descartes University, Paris, France
| | - Philippe M Campeau
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Julien Buratti
- APHP, Hôpital Pitie-Salpetriere, Departement de Genetique et de Cytogenetique; Centre de Reference Deficience Intellectuelle de Causes Rares; GRC UPMC «Deficience Intellectuelle et Autisme», Paris, France
| | - Caroline Nava
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universites, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle epiniere, ICM, Paris, France.,APHP, Hôpital Pitie-Salpetriere, Departement de Genetique et de Cytogenetique; Centre de Reference Deficience Intellectuelle de Causes Rares; GRC UPMC «Deficience Intellectuelle et Autisme», Paris, France
| | | | - Marilyn Tallot
- CHU La Reunion-Groupe Hospitalier Sud Reunion, La Reunion, France
| | - Mathieu Milh
- APHM, Hôpital d'Enfants de La Timone, Service de Neurologie Pediatrique, centre de reference deficiences intellectuelles de cause rare, Marseille, France.,Aix Marseille University, INSERM, MMG, UMR-S 1251, Faculte de medecine, Marseille, France
| | - Patrick Edery
- Service de Genetique, Centre de Reference Anomalies du Developpement, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, Universite Claude Bernard Lyon 1, Bron, France.,Claude Bernard Lyon I University, Lyon, France
| | - Pauline Marzin
- APHP, Hôpital Pitie-Salpetriere, Departement de Genetique et de Cytogenetique; Centre de Reference Deficience Intellectuelle de Causes Rares; GRC UPMC «Deficience Intellectuelle et Autisme», Paris, France
| | - Giulia Barcia
- INSERM U1163, Imagine Institute, Paris, France.,Paris Descartes University, Paris, France.,APHP, Service de genetique medicale, Necker-Enfants Malades Hospital, Imagine Institute, Paris Descartes University, Paris, France
| | - Christine Barnerias
- APHP, Unite fonctionnelle de Neurologie, Necker-Enfants Malades Hospital, Imagine Institute, Paris Descartes University, Paris, France
| | - Claude Besmond
- INSERM U1163, Imagine Institute, Paris, France.,Paris Descartes University, Paris, France
| | - Thierry Bienvenu
- APHP, Laboratoire de Genetique et Biologie Moleculaires, Hôpital Cochin, HUPC, Paris, France.,Universite Paris Descartes Paris, Institut de Psychiatrie et de Neurosciences de Paris, Inserm U894, Paris, France
| | - Ange-Line Bruel
- FHU-TRANSLAD, Universite de Bourgogne/CHU Dijon, Dijon, France.,INSERM UMR 1231 GAD team, Genetics of Developmental disorders, Universite de Bourgogne-Franche Comte, Dijon, France
| | - Ledia Brunga
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Berten Ceulemans
- Department of Pediatric Neurology, University Hospital and University of Antwerp, Antwerp, Belgium
| | - Christine Coubes
- Departement de Genetique Medicale, Maladies rares et Medecine Personnalisee, CHU de Montpellier, Montpellier, France
| | - Ana G Cristancho
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Elizabeth J Donner
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Bénédicte Duban-Bedu
- Centre de Genetique Chromosomique, Hôpital St-Vincent-de-Paul, GHICL, Lille, France
| | - Christèle Dubourg
- CHU Rennes, Service de Genetique Moleculaire et Genomique, Rennes, France
| | - Elena Gardella
- Danish Epilepsy Centre Filadelfia, Dianalund, Denmark.,Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Julie Gauthier
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - David Geneviève
- Departement de Genetique Medicale, Maladies rares et Medecine Personnalisee, CHU de Montpellier, Montpellier, France.,INSERM U1183, Montpellier, France
| | - Stéphanie Gobin-Limballe
- APHP, Service de genetique medicale, Necker-Enfants Malades Hospital, Imagine Institute, Paris Descartes University, Paris, France
| | - Ethan M Goldberg
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eveline Hagebeuk
- Stichting Epilepsie Instellingen Nederland, SEIN, Zwolle, The Netherlands
| | - Fadi F Hamdan
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Miroslava Hančárová
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Laurence Hubert
- INSERM U1163, Imagine Institute, Paris, France.,Paris Descartes University, Paris, France
| | - Christine Ioos
- APHP, University Hospital of Paris ïle-de-France ouest, Raymond Poincare Hospital, Garches, France
| | - Shoji Ichikawa
- Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Sandra Janssens
- Centre for Medical Genetics Ghent, Ghent University Hospital, C. Heymanslaan 10, Ghent, Belgium
| | - Hubert Journel
- Service de Genetique Medicale, Hôpital Chubert, Vannes, France
| | - Anna Kaminska
- APHP, Department of Clinical Neurophysiology, Necker-Enfants Malades Hospital, Paris, France
| | - Boris Keren
- APHP, Hôpital Pitie-Salpetriere, Departement de Genetique et de Cytogenetique; Centre de Reference Deficience Intellectuelle de Causes Rares; GRC UPMC «Deficience Intellectuelle et Autisme», Paris, France
| | - Marije Koopmans
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Caroline Lacoste
- Departement de Genetique Medicale, APHM, Hopital d'Enfants de La Timone, Marseille, France
| | - Petra Laššuthová
- Child Neurology Department, 2nd Faculty of Medicine, Charles University and Motol Hospital, Prague, Czech Republic
| | - Damien Lederer
- Centre de Genetique Humaine, Institut de Pathologie et de Genetique, Gosselies, Belgium
| | - Daphné Lehalle
- FHU-TRANSLAD, Universite de Bourgogne/CHU Dijon, Dijon, France.,Unite fonctionnelle de genetique clinique, Centre Hospitalier Intercommunal de Creteil, Creteil, France
| | | | - Julia Métreau
- APHP, Service de neurologie pediatrique, Hôpital Universitaire Bicetre, Le Kremlin-Bicetre, France
| | - Jacques L Michaud
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Kathryn Miller
- Department of Pediatrics, Albany Medical Center, Albany, NY, USA
| | - Berge A Minassian
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Marie-Laure Moutard
- APHP, Hôpital Trousseau, service de neuropediatrie, Paris, France.,Sorbonne Universite, GRC n°19, pathologies Congenitales du Cervelet-LeucoDystrophies, APHP, Hôpital Armand Trousseau, Paris, France
| | - Arnold Munnich
- INSERM U1163, Imagine Institute, Paris, France.,Paris Descartes University, Paris, France.,APHP, Service de genetique medicale, Necker-Enfants Malades Hospital, Imagine Institute, Paris Descartes University, Paris, France
| | | | - Jean-Marc Pinard
- Division of Neuropediatrics, CHU Raymond Poincare (APHP), Garches, France
| | - Darina Prchalová
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Audrey Putoux
- Service de Genetique, Centre de Reference Anomalies du Developpement, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, Universite Claude Bernard Lyon 1, Bron, France.,Claude Bernard Lyon I University, Lyon, France
| | - Chloé Quelin
- Service de Genetique Medicale, CLAD Ouest CHU Hôpital Sud, Rennes, France
| | - Alyssa R Rosen
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joelle Roume
- Unite de Genetique Medicale, Centre de Reference des Maladies rares du Developpement (AnD DI Rares), CHI Poissy-St Germain en Laye, Poissy, France
| | - Elsa Rossignol
- Departments of Pediatrics and Neurosciences, CHU Sainte-Justine and University of Montreal, Montreal, Canada
| | - Marleen E H Simon
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Thomas Smol
- Institut de Genetique Medicale, CHRU Lille, Universite de Lille, Lille, France
| | - Natasha Shur
- Department of Pediatrics, Albany Medical Center, Albany, NY, USA
| | - Ivan Shelihan
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Katalin Štěrbová
- Child Neurology Department, 2nd Faculty of Medicine, Charles University and Motol Hospital, Prague, Czech Republic
| | - Emílie Vyhnálková
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Catheline Vilain
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics, Universite Libre de Bruxelles, Brussels, Belgium.,Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Universite Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Universite Libre de Bruxelles, Brussels, Belgium
| | - Julie Soblet
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics, Universite Libre de Bruxelles, Brussels, Belgium.,Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Universite Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Universite Libre de Bruxelles, Brussels, Belgium
| | - Guillaume Smits
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics, Universite Libre de Bruxelles, Brussels, Belgium.,Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Universite Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Universite Libre de Bruxelles, Brussels, Belgium
| | - Samuel P Yang
- Clinical Genomics & Predictive Medicine, Providence Medical Group, Dayton, WA, USA
| | | | - Peter M van Hasselt
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center, Utrecht, The Netherlands
| | - Marjan van Kempen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sarah Weckhuysen
- Neurogenetics Group, Center of Molecular Neurology, VIB, Antwerp, Belgium.,Neurology Department, University Hospital Antwerp, Antwerp, Belgium
| | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laurent Villard
- Aix Marseille University, INSERM, MMG, UMR-S 1251, Faculte de medecine, Marseille, France.,Departement de Genetique Medicale, APHM, Hopital d'Enfants de La Timone, Marseille, France
| | - Delphine Héron
- APHP, Hôpital Pitie-Salpetriere, Departement de Genetique et de Cytogenetique; Centre de Reference Deficience Intellectuelle de Causes Rares; GRC UPMC «Deficience Intellectuelle et Autisme», Paris, France
| | - Bobby Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rikke S Møller
- CHU Rennes, Service de Genetique Moleculaire et Genomique, Rennes, France.,Danish Epilepsy Centre Filadelfia, Dianalund, Denmark
| | - Gaetan Lesca
- Service de Genetique, Centre de Reference Anomalies du Developpement, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, Universite Claude Bernard Lyon 1, Bron, France.,Claude Bernard Lyon I University, Lyon, France
| | - Katherine L Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rima Nabbout
- APHP, Reference Centre for Rare Epilepsies, Necker-Enfants Malades Hospital, Imagine Institute, Paris Descartes University, Paris, France.,INSERM U1163, Imagine Institute, Paris, France.,Paris Descartes University, Paris, France
| | - Nienke E Verbeek
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Christel Depienne
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universites, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle epiniere, ICM, Paris, France. .,IGBMC, CNRS UMR 7104/INSERM U964/Universite de Strasbourg, Illkirch, France. .,Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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Lee K, Famiglietti ML, McMahon A, Wei CH, MacArthur JAL, Poux S, Breuza L, Bridge A, Cunningham F, Xenarios I, Lu Z. Scaling up data curation using deep learning: An application to literature triage in genomic variation resources. PLoS Comput Biol 2018; 14:e1006390. [PMID: 30102703 PMCID: PMC6107285 DOI: 10.1371/journal.pcbi.1006390] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 08/23/2018] [Accepted: 07/24/2018] [Indexed: 11/18/2022] Open
Abstract
Manually curating biomedical knowledge from publications is necessary to build a knowledge based service that provides highly precise and organized information to users. The process of retrieving relevant publications for curation, which is also known as document triage, is usually carried out by querying and reading articles in PubMed. However, this query-based method often obtains unsatisfactory precision and recall on the retrieved results, and it is difficult to manually generate optimal queries. To address this, we propose a machine-learning assisted triage method. We collect previously curated publications from two databases UniProtKB/Swiss-Prot and the NHGRI-EBI GWAS Catalog, and used them as a gold-standard dataset for training deep learning models based on convolutional neural networks. We then use the trained models to classify and rank new publications for curation. For evaluation, we apply our method to the real-world manual curation process of UniProtKB/Swiss-Prot and the GWAS Catalog. We demonstrate that our machine-assisted triage method outperforms the current query-based triage methods, improves efficiency, and enriches curated content. Our method achieves a precision 1.81 and 2.99 times higher than that obtained by the current query-based triage methods of UniProtKB/Swiss-Prot and the GWAS Catalog, respectively, without compromising recall. In fact, our method retrieves many additional relevant publications that the query-based method of UniProtKB/Swiss-Prot could not find. As these results show, our machine learning-based method can make the triage process more efficient and is being implemented in production so that human curators can focus on more challenging tasks to improve the quality of knowledge bases. As the volume of literature on genomic variants continues to grow at an increasing rate, it is becoming more difficult for a curator of a variant knowledge base to keep up with and curate all the published papers. Here, we suggest a deep learning-based literature triage method for genomic variation resources. Our method achieves state-of-the-art performance on the triage task. Moreover, our model does not require any laborious preprocessing or feature engineering steps, which are required for traditional machine learning triage methods. We applied our method to the literature triage process of UniProtKB/Swiss-Prot and the NHGRI-EBI GWAS Catalog for genomic variation by collaborating with the database curators. Both the manual curation teams confirmed that our method achieved higher precision than their previous query-based triage methods without compromising recall. Both results show that our method is more efficient and can replace the traditional query-based triage methods of manually curated databases. Our method can give human curators more time to focus on more challenging tasks such as actual curation as well as the discovery of novel papers/experimental techniques to consider for inclusion.
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Affiliation(s)
- Kyubum Lee
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | | | - Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Chih-Hsuan Wei
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Jacqueline Ann Langdon MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sylvain Poux
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Lionel Breuza
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Alan Bridge
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ioannis Xenarios
- Center for Integrative Genomics, University of Lausanne, Lausanne Switzerland.,Department of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland
| | - Zhiyong Lu
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
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39
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40
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Morales J, Welter D, Bowler EH, Cerezo M, Harris LW, McMahon AC, Hall P, Junkins HA, Milano A, Hastings E, Malangone C, Buniello A, Burdett T, Flicek P, Parkinson H, Cunningham F, Hindorff LA, MacArthur JAL. A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog. Genome Biol 2018; 19:21. [PMID: 29448949 PMCID: PMC5815218 DOI: 10.1186/s13059-018-1396-2] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/19/2018] [Indexed: 12/23/2022] Open
Abstract
The accurate description of ancestry is essential to interpret, access, and integrate human genomics data, and to ensure that these benefit individuals from all ancestral backgrounds. However, there are no established guidelines for the representation of ancestry information. Here we describe a framework for the accurate and standardized description of sample ancestry, and validate it by application to the NHGRI-EBI GWAS Catalog. We confirm known biases and gaps in diversity, and find that African and Hispanic or Latin American ancestry populations contribute a disproportionately high number of associations. It is our hope that widespread adoption of this framework will lead to improved analysis, interpretation, and integration of human genomics data.
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Affiliation(s)
- Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Danielle Welter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Emily H Bowler
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Maria Cerezo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Laura W Harris
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Aoife C McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Peggy Hall
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892-9305, USA
| | - Heather A Junkins
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892-9305, USA
| | - Annalisa Milano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Emma Hastings
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Cinzia Malangone
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Annalisa Buniello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892-9305, USA
| | - Jacqueline A L MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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Petrof G, Cuell A, Rajkomar VV, Harries MJ, Takwale A, Holmes S, Cunningham F, Kaur MR. Retrospective review of 18 British South Asian women with frontal fibrosing alopecia. Int J Dermatol 2018; 57:490-491. [PMID: 29384198 DOI: 10.1111/ijd.13929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/02/2018] [Accepted: 01/03/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Gabriela Petrof
- Solihull Hospital, Heart of England NHS Foundation Trust, Solihull, UK
| | - Alexis Cuell
- Solihull Hospital, Heart of England NHS Foundation Trust, Solihull, UK
| | - Vikram V Rajkomar
- The Dermatology Centre, University of Manchester, Salford Royal NHS Foundation Trust, Salford, UK
| | - Matthew J Harries
- The Dermatology Centre, University of Manchester, Salford Royal NHS Foundation Trust, Salford, UK
| | - Anita Takwale
- Gloucestershire Hospitals NHS Foundation trust, Gloucester, UK
| | - Susan Holmes
- Queen Elizabeth University Hospital, Glasgow, UK
| | | | - Manjit R Kaur
- Solihull Hospital, Heart of England NHS Foundation Trust, Solihull, UK
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42
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Hunt SE, McLaren W, Gil L, Thormann A, Schuilenburg H, Sheppard D, Parton A, Armean IM, Trevanion SJ, Flicek P, Cunningham F. Ensembl variation resources. Database (Oxford) 2018; 2018:5255129. [PMID: 30576484 PMCID: PMC6310513 DOI: 10.1093/database/bay119] [Citation(s) in RCA: 274] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/04/2018] [Indexed: 12/31/2022]
Abstract
The major goal of sequencing humans and many other species is to understand the link between genomic variation, phenotype and disease. There are numerous valuable and well-established variation resources, but collating and making sense of non-homogeneous, often large-scale data sets from disparate sources remains a challenge. Without a systematic catalogue of these data and appropriate query and annotation tools, understanding the genome sequence of an individual and assessing their disease risk is impossible. In Ensembl, we substantially solve this problem: we develop methods to facilitate data integration and broad access; aggregate information in a consistent manner and make it available a variety of standard formats, both visually and programmatically; build analysis pipelines to compare variants to comprehensive genomic annotation sets; and make all tools and data publicly available.
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Affiliation(s)
- Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dan Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Andrew Parton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Irina M Armean
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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Tziotzios C, Ainali C, Onoufriadis A, Cunningham F, Palamaras I, Stefanato C, Kirkpatrick N, Vano-Galvan S, Fenton D, McGrath J. 261 Tissue and circulating microRNA co-expression analysis reveals potential involvement of miRNAs in the pathobiology of frontal fibrosing alopecia. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.07.259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Brett FM, Looby S, Chalissery A, Chen D, Heaney C, Heffernan J, Cunningham F, Howley R, Loftus T, Kearney H, Farrell MA. Brain biopsies requiring Creutzfeldt-Jakob disease precautions in the Republic of Ireland 2005-2016. Ir J Med Sci 2017; 187:515-520. [PMID: 28803271 DOI: 10.1007/s11845-017-1673-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/04/2017] [Indexed: 10/19/2022]
Abstract
AIMS Creutzfeldt-Jakob disease (CJD) risk precautions are required when performing brain biopsies on patients with a dementing illness and in 'risk' groups. The impact on a diagnostic neuropathology service is considerable. We sought to determine if better case selection might reduce the necessity for application of CJD risk precautions. METHODS We reviewed the clinical information, contributory investigations and final neuropathologic diagnosis in a cohort of patients (n = 21), referred to the National CJD Surveillance Centre between January 1, 2005, and December 31, 2016. RESULTS Of this 21-patient cohort, five were positive for CJD, four belonged to the 'at risk of CJD' category requiring brain surgery, while the remaining 12 were referred to the National CJD Surveillance Unit with CJD as part of their differential diagnosis. CJD was confirmed in 5/21 (three sporadic [s]CJD, one variant [v]CJD and one iatrogenic [i] CJD). CJD was clinically probable in 4/5 proven CJD patients (80%). The patients (n = 4) in the 'at risk of CJD' group were diagnosed with tumour (n = 2), inflammation (n = 1) and non-specific changes (n = 1). Of the remaining 12 patients (in whom CJD was included in the differential diagnosis), the final neuropathologic diagnoses included tumour (n = 2), neurodegenerative (n = 2), inflammatory (n = 1), metabolic (n = 2), vascular (n = 2) and non-specific gliosis (n = 3). CONCLUSIONS More often than not, the clinical suspicion of CJD was not borne out by the final neuropathological diagnosis. Failure by clinicians to adhere to the recommended CJD investigation algorithm impacts adversely on the neuropathology workload and causes unnecessary concern among operating theatre, laboratory and nursing personnel.
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Affiliation(s)
- F M Brett
- Department of Clinical Neurological Sciences, Royal College of Surgeons, Beaumont Hospital, Dublin 9, Ireland.
| | - S Looby
- Department of Clinical Neurological Sciences, Royal College of Surgeons, Beaumont Hospital, Dublin 9, Ireland
| | - A Chalissery
- Department of Clinical Neurological Sciences, Royal College of Surgeons, Beaumont Hospital, Dublin 9, Ireland
| | - D Chen
- Department of Clinical Neurological Sciences, Royal College of Surgeons, Beaumont Hospital, Dublin 9, Ireland
| | - C Heaney
- Department of Clinical Neurological Sciences, Royal College of Surgeons, Beaumont Hospital, Dublin 9, Ireland
| | - J Heffernan
- Department of Clinical Neurological Sciences, Royal College of Surgeons, Beaumont Hospital, Dublin 9, Ireland
| | - F Cunningham
- Department of Clinical Neurological Sciences, Royal College of Surgeons, Beaumont Hospital, Dublin 9, Ireland
| | - R Howley
- Department of Clinical Neurological Sciences, Royal College of Surgeons, Beaumont Hospital, Dublin 9, Ireland
| | - T Loftus
- Department of Clinical Neurological Sciences, Royal College of Surgeons, Beaumont Hospital, Dublin 9, Ireland
| | - H Kearney
- Department of Clinical Neurological Sciences, Royal College of Surgeons, Beaumont Hospital, Dublin 9, Ireland
| | - M A Farrell
- Department of Clinical Neurological Sciences, Royal College of Surgeons, Beaumont Hospital, Dublin 9, Ireland
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Tziotzios C, Ainali C, Holmes S, Cunningham F, Lwin SM, Palamaras I, Bhargava K, Rymer J, Stefanato CM, Kirkpatrick N, Vano-Galvan S, Petridis C, Fenton DA, Simpson MA, Onoufriadis A, McGrath JA. Tissue and Circulating MicroRNA Co-expression Analysis Shows Potential Involvement of miRNAs in the Pathobiology of Frontal Fibrosing Alopecia. J Invest Dermatol 2017; 137:2440-2443. [PMID: 28774594 DOI: 10.1016/j.jid.2017.06.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/27/2017] [Accepted: 06/27/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Christos Tziotzios
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Chrysanthi Ainali
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Susan Holmes
- Alan Lyell Centre for Dermatology, Queen Elizabeth University Hospital, Glasgow, UK
| | - Fiona Cunningham
- Alan Lyell Centre for Dermatology, Queen Elizabeth University Hospital, Glasgow, UK
| | - Su M Lwin
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Ioulios Palamaras
- Department of Dermatology, Barnet General Hospital, Royal Free Foundation Trust, London, UK
| | - Kapil Bhargava
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Janice Rymer
- King's College London School of Medicine, King's College London, London, UK
| | - Catherine M Stefanato
- Department of Dermatopathology, St. John's Institute of Dermatology, St. Thomas' Hospital, London, UK
| | | | | | - Christos Petridis
- Department of Genetics, Division of Genetics and Molecular Medicine, King's College London, Guy's Hospital, London, UK
| | - David A Fenton
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Michael A Simpson
- Department of Genetics, Division of Genetics and Molecular Medicine, King's College London, Guy's Hospital, London, UK
| | - Alexandros Onoufriadis
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - John A McGrath
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine, King's College London, London, UK.
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Zamora C, Lopez M, Cunningham F, Collichio F, Castillo M. Imaging Manifestations of Pseudoprogression in Metastatic Melanoma Nodes Injected with Talimogene Laherparepvec: Initial Experience. AJNR Am J Neuroradiol 2017; 38:1218-1222. [PMID: 28428211 DOI: 10.3174/ajnr.a5206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/25/2017] [Indexed: 12/22/2022]
Abstract
Talimogene laherparepvec is an oncolytic virus recently approved for targeted treatment of advanced melanoma. Because of an inflammatory reaction, treated lesions may increase in size and develop infiltrative margins that can be construed as disease progression or extracapsular spread. In this report, we describe our initial experience imaging the response of metastatic nodes injected with talimogene laherparepvec. Six of 12 nodes (50%) showed growth from baseline followed by decreased size, 5 of 12 nodes (42%) showed a downward size trend, and 1 node showed continued increase in size. Seven of 9 nodes (78%) developed infiltrative margins at a median of 79 days, and 6 of 9 (67%) nodes became necrotic at a median of 76 days after injection, all showing decreased size at final follow-up. An increase in the size of nodes injected with talimogene laherparepvec does not necessarily indicate progression. Infiltrative margins are also frequently seen and may be confused with extracapsular disease.
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Affiliation(s)
- C Zamora
- From the Division of Neuroradiology, Department of Radiology (C.Z., M.L., M.C.)
| | - M Lopez
- From the Division of Neuroradiology, Department of Radiology (C.Z., M.L., M.C.)
| | - F Cunningham
- the Division of Hematology and Oncology, Department of Medicine (F. Cunningham, F. Collichio), University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - F Collichio
- the Division of Hematology and Oncology, Department of Medicine (F. Cunningham, F. Collichio), University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - M Castillo
- From the Division of Neuroradiology, Department of Radiology (C.Z., M.L., M.C.)
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Cunningham F, Darling MI, Gangopadhyay M, Jackson R, McKay P, Bilsland D. An isolated ulcerated forehead lesion in a 70-year-old man. Clin Exp Dermatol 2017; 42:554-557. [PMID: 28517031 DOI: 10.1111/ced.13093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2016] [Indexed: 11/30/2022]
Affiliation(s)
- F Cunningham
- Alan Lyell Centre for Dermatology, Queen Elizabeth University Hospital, Glasgow, UK
| | - M I Darling
- Alan Lyell Centre for Dermatology, Queen Elizabeth University Hospital, Glasgow, UK
| | - M Gangopadhyay
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow, UK
| | - R Jackson
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow, UK
| | - P McKay
- Beatson West of Scotland Cancer Centre, Glasgow, UK
| | - D Bilsland
- Alan Lyell Centre for Dermatology, Queen Elizabeth University Hospital, Glasgow, UK
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Cunningham F, Wylie G. Comment on standardized laboratory monitoring with use of isotretinoin in acne. J Am Acad Dermatol 2017; 76:e133. [DOI: 10.1016/j.jaad.2016.10.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 10/25/2016] [Indexed: 10/19/2022]
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Cunningham F, Gupta P, Becher G, Magro CM. Necrotizing eosinophilic folliculitis: a new manifestation of the atopic diathesis? Clin Exp Dermatol 2016; 42:100-101. [PMID: 27910130 DOI: 10.1111/ced.12994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2016] [Indexed: 11/27/2022]
Affiliation(s)
- F Cunningham
- Department of Dermatology, Western Ambulatory Care Hospital, Dalnair Street, Yorkhill, Glasgow, G3 8SJ
| | - P Gupta
- Department of Dermatology, Western Ambulatory Care Hospital, Dalnair Street, Yorkhill, Glasgow, G3 8SJ
| | - G Becher
- Department of Dermatology, Western Ambulatory Care Hospital, Dalnair Street, Yorkhill, Glasgow, G3 8SJ
| | - C M Magro
- Department of Pathology, New York Hospital Cornell Medical Centre, New York, USA
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MacArthur J, Bowler E, Cerezo M, Gil L, Hall P, Hastings E, Junkins H, McMahon A, Milano A, Morales J, Pendlington ZM, Welter D, Burdett T, Hindorff L, Flicek P, Cunningham F, Parkinson H. The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog). Nucleic Acids Res 2016; 45:D896-D901. [PMID: 27899670 PMCID: PMC5210590 DOI: 10.1093/nar/gkw1133] [Citation(s) in RCA: 1388] [Impact Index Per Article: 173.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 11/02/2016] [Indexed: 02/02/2023] Open
Abstract
The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality and an improved curation interface. These developments have improved the data release frequency by increasing automation of curation and providing scaling improvements. The range of available Catalog data has also been extended with structured ancestry and recruitment information added for all studies. The infrastructure improvements also support scaling for larger arrays, exome and sequencing studies, allowing the Catalog to adapt to the needs of evolving study design, genotyping technologies and user needs in the future.
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Affiliation(s)
- Jacqueline MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Emily Bowler
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Maria Cerezo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Peggy Hall
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emma Hastings
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Heather Junkins
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Annalisa Milano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Zoe May Pendlington
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Danielle Welter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Lucia Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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