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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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2
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Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, Allen J, Asri M, Bzikadze AV, Chen NC, Chin CS, Diekhans M, Flicek P, Formenti G, Fungtammasan A, Garcia Giron C, Garrison E, Gershman A, Gerton JL, Grady PGS, Guarracino A, Haggerty L, Halabian R, Hansen NF, Harris R, Hartley GA, Harvey WT, Haukness M, Heinz J, Hourlier T, Hubley RM, Hunt SE, Hwang S, Jain M, Kesharwani RK, Lewis AP, Li H, Logsdon GA, Lucas JK, Makalowski W, Markovic C, Martin FJ, Mc Cartney AM, McCoy RC, McDaniel J, McNulty BM, Medvedev P, Mikheenko A, Munson KM, Murphy TD, Olsen HE, Olson ND, Paulin LF, Porubsky D, Potapova T, Ryabov F, Salzberg SL, Sauria MEG, Sedlazeck FJ, Shafin K, Shepelev VA, Shumate A, Storer JM, Surapaneni L, Taravella Oill AM, Thibaud-Nissen F, Timp W, Tomaszkiewicz M, Vollger MR, Walenz BP, Watwood AC, Weissensteiner MH, Wenger AM, Wilson MA, Zarate S, Zhu Y, Zook JM, Eichler EE, O'Neill RJ, Schatz MC, Miga KH, Makova KD, Phillippy AM. The complete sequence of a human Y chromosome. Nature 2023; 621:344-354. [PMID: 37612512 PMCID: PMC10752217 DOI: 10.1038/s41586-023-06457-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [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: 12/02/2022] [Accepted: 07/19/2023] [Indexed: 08/25/2023]
Abstract
The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1-3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.
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Affiliation(s)
- Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Oxford Nanopore Technologies Inc., Oxford, UK
| | - Monika Cechova
- Faculty of Informatics, Masaryk University, Brno, Czech Republic
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Savannah J Hoyt
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Dylan J Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Nicolas Altemose
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Paul W Hook
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mikko Rautiainen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ivan A Alexandrov
- Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Center for Algorithmic Biotechnology, Saint Petersburg State University, St Petersburg, Russia
- Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Jamie Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mobin Asri
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Andrey V Bzikadze
- Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego, CA, USA
| | - Nae-Chyun Chen
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Chen-Shan Chin
- GeneDX Holdings Corp, Stamford, CT, USA
- Foundation of Biological Data Science, Belmont, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | | | - Carlos Garcia Giron
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ariel Gershman
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO, USA
- University of Kansas Medical Center, Kansas City, MO, USA
| | - Patrick G S Grady
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Genomics Research Centre, Human Technopole, Milan, Italy
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Reza Halabian
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Nancy F Hansen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robert Harris
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Gabrielle A Hartley
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Jakob Heinz
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Thibaut Hourlier
- 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
| | - Stephen Hwang
- XDBio Program, Johns Hopkins University, Baltimore, MD, USA
| | - Miten Jain
- Department of Bioengineering, Department of Physics, Northeastern University, Boston, MA, USA
| | - Rupesh K Kesharwani
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Julian K Lucas
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Wojciech Makalowski
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Christopher Markovic
- Genome Technology Access Center at the McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ann M Mc Cartney
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Jennifer McDaniel
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Brandy M McNulty
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Paul Medvedev
- Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Saint Petersburg State University, St Petersburg, Russia
- UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Hugh E Olsen
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Nathan D Olson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Luis F Paulin
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Fedor Ryabov
- Masters Program in National Research University Higher School of Economics, Moscow, Russia
| | - Steven L Salzberg
- Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, USA
| | | | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | | | | | - Alaina Shumate
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | - Likhitha Surapaneni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Angela M Taravella Oill
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Marta Tomaszkiewicz
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Department of Biomedical Engineering, Pennsylvania State University, State College, PA, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Brian P Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Allison C Watwood
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Melissa A Wilson
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Samantha Zarate
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Yiming Zhu
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Justin M Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Investigator, Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
| | - Michael C Schatz
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Karen H Miga
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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3
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Foreman J, Perrett D, Mazaika E, Hunt SE, Ware JS, Firth HV. DECIPHER: Improving Genetic Diagnosis Through Dynamic Integration of Genomic and Clinical Data. Annu Rev Genomics Hum Genet 2023; 24:151-176. [PMID: 37285546 PMCID: PMC7615097 DOI: 10.1146/annurev-genom-102822-100509] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DECIPHER (Database of Genomic Variation and Phenotype in Humans Using Ensembl Resources) shares candidate diagnostic variants and phenotypic data from patients with genetic disorders to facilitate research and improve the diagnosis, management, and therapy of rare diseases. The platform sits at the boundary between genomic research and the clinical community. DECIPHER aims to ensure that the most up-to-date data are made rapidly available within its interpretation interfaces to improve clinical care. Newly integrated cardiac case-control data that provide evidence of gene-disease associations and inform variant interpretation exemplify this mission. New research resources are presented in a format optimized for use by a broad range of professionals supporting the delivery of genomic medicine. The interfaces within DECIPHER integrate and contextualize variant and phenotypic data, helping to determine a robust clinico-molecular diagnosis for rare-disease patients, which combines both variant classification and clinical fit. DECIPHER supports discovery research, connecting individuals within the rare-disease community to pursue hypothesis-driven research.
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Affiliation(s)
- Julia Foreman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom; ,
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Daniel Perrett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom; ,
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Erica Mazaika
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; ,
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom; ,
| | - James S Ware
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; ,
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Helen V Firth
- Wellcome Sanger Institute, Hinxton, United Kingdom
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom;
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4
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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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Salz R, Saraiva-Agostinho N, Vorsteveld E, van der Made CI, Kersten S, Stemerdink M, Allen J, Volders PJ, Hunt SE, Hoischen A, 't Hoen PAC. SUsPECT: a pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation. BMC Genomics 2023; 24:305. [PMID: 37280537 PMCID: PMC10245480 DOI: 10.1186/s12864-023-09391-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/19/2023] [Indexed: 06/08/2023] Open
Abstract
Our incomplete knowledge of the human transcriptome impairs the detection of disease-causing variants, in particular if they affect transcripts only expressed under certain conditions. These transcripts are often lacking from reference transcript sets, such as Ensembl/GENCODE and RefSeq, and could be relevant for establishing genetic diagnoses. We present SUsPECT (Solving Unsolved Patient Exomes/gEnomes using Custom Transcriptomes), a pipeline based on the Ensembl Variant Effect Predictor (VEP) to predict variant impact on custom transcript sets, such as those generated by long-read RNA-sequencing, for downstream prioritization. Our pipeline predicts the functional consequence and likely deleteriousness scores for missense variants in the context of novel open reading frames predicted from any transcriptome. We demonstrate the utility of SUsPECT by uncovering potential mutational mechanisms of pathogenic variants in ClinVar that are not predicted to be pathogenic using the reference transcript annotation. In further support of SUsPECT's utility, we identified an enrichment of immune-related variants predicted to have a more severe molecular consequence when annotating with a newly generated transcriptome from stimulated immune cells instead of the reference transcriptome. Our pipeline outputs crucial information for further prioritization of potentially disease-causing variants for any disease and will become increasingly useful as more long-read RNA sequencing datasets become available.
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Affiliation(s)
- Renee Salz
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, 6525 GA, the Netherlands
| | - Nuno Saraiva-Agostinho
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Emil Vorsteveld
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, the Netherlands
| | - Caspar I van der Made
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, the Netherlands
- Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, and Radboud Expertise Center for Immunodeficiency and Autoinflammation, Radboud University Medical Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Simone Kersten
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, the Netherlands
| | - Merel Stemerdink
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Jamie Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Pieter-Jan Volders
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Laboratory of Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, Hasselt, 3500, Belgium
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, the Netherlands
- Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, and Radboud Expertise Center for Immunodeficiency and Autoinflammation, Radboud University Medical Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Peter A C 't Hoen
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, 6525 GA, the Netherlands.
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6
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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: 136] [Impact Index Per Article: 68.0] [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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7
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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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8
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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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9
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Abstract
Ensembl Plants ( http://plants.ensembl.org ) offers genome-scale information for plants, with four releases per year. As of release 47 (April 2020) it features 79 species and includes genome sequence, gene models, and functional annotation. Comparative analyses help reconstruct the evolutionary history of gene families, genomes, and components of polyploid genomes. Some species have gene expression baseline reports or variation across genotypes. While the data can be accessed through the Ensembl genome browser, here we review specifically how our plant genomes can be interrogated programmatically and the data downloaded in bulk. These access routes are generally consistent across Ensembl for other non-plant species, including plant pathogens, pests, and pollinators.
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Affiliation(s)
- Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
| | | | | | | | | | | | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
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10
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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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11
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Wagner AH, Babb L, Alterovitz G, Baudis M, Brush M, Cameron DL, Cline M, Griffith M, Griffith OL, Hunt SE, Kreda D, Lee JM, Li S, Lopez J, Moyer E, Nelson T, Patel RY, Riehle K, Robinson PN, Rynearson S, Schuilenburg H, Tsukanov K, Walsh B, Konopko M, Rehm HL, Yates AD, Freimuth RR, Hart RK. The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification. Cell Genom 2021; 1. [PMID: 35311178 PMCID: PMC8929418 DOI: 10.1016/j.xgen.2021.100027] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Maximizing the personal, public, research, and clinical value of genomic information will require the reliable exchange of genetic variation data. We report here the Variation Representation Specification (VRS, pronounced "verse"), an extensible framework for the computable representation of variation that complements contemporary human-readable and flat file standards for genomic variation representation. VRS provides semantically precise representations of variation and leverages this design to enable federated identification of biomolecular variation with globally consistent and unique computed identifiers. The VRS framework includes a terminology and information model, machine-readable schema, data sharing conventions, and a reference implementation, each of which is intended to be broadly useful and freely available for community use. VRS was developed by a partnership among national information resource providers, public initiatives, and diagnostic testing laboratories under the auspices of the Global Alliance for Genomics and Health (GA4GH).
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Affiliation(s)
- Alex H. Wagner
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Corresponding author
| | - Lawrence Babb
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Corresponding author
| | - Gil Alterovitz
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Michael Baudis
- University of Zurich and Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Matthew Brush
- Oregon Health & Science University, Portland, OR 97239, USA
| | - Daniel L. Cameron
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Melissa Cline
- UC Santa Cruz Genomics Institute, Santa Cruz, CA 95060, USA
| | - Malachi Griffith
- Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Obi L. Griffith
- Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Sarah E. Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David Kreda
- Department of Biomedical Informatics, Harvard Medical School, Boston MA 02115, USA
| | - Jennifer M. Lee
- Essex Management LLC and National Cancer Institute, Rockville, MD 20850, USA
| | - Stephanie Li
- The Global Alliance for Genomics and Health, Toronto, ON, Canada
| | | | - Eric Moyer
- National Center for Biotechnology Information, National Library of Medicine National Institutes of Health, Bethesda, MD 20894, USA
| | | | | | - Kevin Riehle
- Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Shawn Rynearson
- Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA
| | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kirill Tsukanov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Brian Walsh
- Oregon Health & Science University, Portland, OR 97239, USA
| | - Melissa Konopko
- The Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - Heidi L. Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Cambridge, MA 02142, USA
| | - Andrew D. Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Robert R. Freimuth
- Center for Individualized Medicine, Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Reece K. Hart
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- MyOme, Inc., Menlo Park, CA 94070, USA
- Corresponding author
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12
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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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13
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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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14
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Shamsani J, Kazakoff SH, Armean IM, McLaren W, Parsons MT, Thompson BA, O'Mara TA, Hunt SE, Waddell N, Spurdle AB. A plugin for the Ensembl Variant Effect Predictor that uses MaxEntScan to predict variant spliceogenicity. Bioinformatics 2020; 35:2315-2317. [PMID: 30475984 PMCID: PMC6596880 DOI: 10.1093/bioinformatics/bty960] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [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: 10/29/2018] [Revised: 10/29/2018] [Accepted: 11/22/2018] [Indexed: 02/02/2023] Open
Abstract
Summary Assessing the pathogenicity of genetic variants can be a complex and challenging task. Spliceogenic variants, which alter mRNA splicing, may yield mature transcripts that encode non-functional protein products, an important predictor of Mendelian disease risk. However, most variant annotation tools do not adequately assess spliceogenicity outside the native splice site and thus the disease-causing potential of variants in other intronic and exonic regions is often overlooked. Here, we present a plugin for the Ensembl Variant Effect Predictor that packages MaxEntScan and extends its functionality to provide splice site predictions using a maximum entropy model. The plugin incorporates a sliding window algorithm to predict splice site loss or gain for any variant that overlaps a transcript feature. We also demonstrate the utility of the plugin by comparing our predictions to two mRNA splicing datasets containing several cancer-susceptibility genes. Availability and implementation Source code is freely available under the Apache License, Version 2.0: https://github.com/Ensembl/VEP_plugins. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jannah Shamsani
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
| | - Stephen H Kazakoff
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
| | - Irina M Armean
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Will McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
| | - Bryony A Thompson
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne VIC, Australia
| | - Tracy A O'Mara
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nicola Waddell
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
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15
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Howe KL, Contreras-Moreira B, De Silva N, Maslen G, Akanni W, Allen J, Alvarez-Jarreta J, Barba M, Bolser DM, Cambell L, Carbajo M, Chakiachvili M, Christensen M, Cummins C, Cuzick A, Davis P, Fexova S, Gall A, George N, Gil L, Gupta P, Hammond-Kosack KE, Haskell E, Hunt SE, Jaiswal P, Janacek SH, Kersey PJ, Langridge N, Maheswari U, Maurel T, McDowall MD, Moore B, Muffato M, Naamati G, Naithani S, Olson A, Papatheodorou I, Patricio M, Paulini M, Pedro H, Perry E, Preece J, Rosello M, Russell M, Sitnik V, Staines DM, Stein J, Tello-Ruiz MK, Trevanion SJ, Urban M, Wei S, Ware D, Williams G, Yates AD, Flicek P. Ensembl Genomes 2020-enabling non-vertebrate genomic research. Nucleic Acids Res 2020; 48:D689-D695. [PMID: 31598706 PMCID: PMC6943047 DOI: 10.1093/nar/gkz890] [Citation(s) in RCA: 283] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 09/29/2019] [Accepted: 10/02/2019] [Indexed: 12/28/2022] Open
Abstract
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life.
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Affiliation(s)
- Kevin L Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bruno Contreras-Moreira
- 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
| | - Gareth Maslen
- 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
| | - Jorge Alvarez-Jarreta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthieu Barba
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dan M Bolser
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lahcen Cambell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Manuel Carbajo
- 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
| | - Mikkel Christensen
- 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
| | - Alayne Cuzick
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Paul Davis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Silvie Fexova
- 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
| | - Nancy George
- 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
| | - Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Kim E Hammond-Kosack
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Erin Haskell
- 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
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sophie H Janacek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul J Kersey
- 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
| | - Uma Maheswari
- 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 D McDowall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ben 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
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Irene Papatheodorou
- 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
| | - Michael Paulini
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helder Pedro
- 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
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Marc Rosello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew Russell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Vasily Sitnik
- 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
| | - Joshua Stein
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | | | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Martin Urban
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Sharon Wei
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - 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
| | - Gary Williams
- 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
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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16
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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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17
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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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18
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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: 1897] [Impact Index Per Article: 379.4] [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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19
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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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20
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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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21
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Aken BL, Achuthan P, Akanni W, Amode MR, Bernsdorff F, Bhai J, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Juettemann T, Keenan S, Laird MR, Lavidas I, Maurel T, McLaren W, Moore B, Murphy DN, Nag R, Newman V, Nuhn M, Ong CK, Parker A, Patricio M, Riat HS, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Wilder SP, Zadissa A, Kostadima M, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Cunningham F, Yates A, Zerbino DR, Flicek P. Ensembl 2017. Nucleic Acids Res 2016; 45:D635-D642. [PMID: 27899575 PMCID: PMC5210575 DOI: 10.1093/nar/gkw1104] [Citation(s) in RCA: 407] [Impact Index Per Article: 50.9] [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: 10/08/2016] [Revised: 10/25/2016] [Accepted: 10/28/2016] [Indexed: 12/12/2022] Open
Abstract
Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate and integrate a diverse collection of large-scale reference data to create a more comprehensive view of genome biology than would be possible from any individual dataset. Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees. An accompanying suite of tools, infrastructure and programmatic access methods ensure uniform data analysis and distribution for all supported species. Together, these provide a comprehensive solution for large-scale and targeted genomics applications alike. Among many other developments over the past year, we have improved our resources for gene regulation and comparative genomics, and added CRISPR/Cas9 target sites. We released new browser functionality and tools, including improved filtering and prioritization of genome variation, Manhattan plot visualization for linkage disequilibrium and eQTL data, and an ontology search for phenotypes, traits and disease. We have also enhanced data discovery and access with a track hub registry and a selection of new REST end points. All Ensembl data are freely released to the scientific community and our source code is available via the open source Apache 2.0 license.
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Affiliation(s)
- Bronwen L Aken
- 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
| | - Friederike Bernsdorff
- 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
| | - Denise Carvalho-Silva
- 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
| | - Peter Clapham
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Laurent Gil
- 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
| | - Leo Gordon
- 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
| | - Sarah E Hunt
- 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
| | - Stephen Keenan
- 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
| | - 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
| | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rishi Nag
- 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
| | - 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
| | - Daniel 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
| | - Steven P Wilder
- 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
| | - Myrto Kostadima
- 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
| | - 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
| | - 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 .,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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22
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Abstract
The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis. It is open source, free to use, and supports full reproducibility of results. The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.
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Affiliation(s)
- William McLaren
- 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
| | - Sarah E Hunt
- 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
| | - Graham R S Ritchie
- 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
| | - 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.
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23
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McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, Flicek P, Cunningham F. The Ensembl Variant Effect Predictor. Genome Biol 2016; 17:122. [PMID: 27268795 PMCID: PMC4893825 DOI: 10.1186/s13059-016-0974-4] [Citation(s) in RCA: 3871] [Impact Index Per Article: 483.9] [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: 03/18/2016] [Accepted: 05/03/2016] [Indexed: 02/06/2023] Open
Abstract
The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis. It is open source, free to use, and supports full reproducibility of results. The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.
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Affiliation(s)
- William McLaren
- 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
| | - Sarah E Hunt
- 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
| | - Graham R S Ritchie
- 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
| | - 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.
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24
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Hunt SE, Dorfman KD, Segal Y, Barocas VH. A computational model of flow and species transport in the mesangium. Am J Physiol Renal Physiol 2016; 310:F222-9. [PMID: 26831339 DOI: 10.1152/ajprenal.00182.2015] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 10/06/2015] [Indexed: 01/17/2023] Open
Abstract
A variety of macromolecules accumulate in the glomerular mesangium in many different diseases, but the physics of the transport of these molecules within the mesangial matrix has not been extensively studied. We present a computational model of convection and diffusion within the porous mesangial matrix and apply this model to the specific instance of immunoglobulin A (IgA) transport in IgA nephropathy. We examine the influence of physiological factors including glomerular basement membrane (GBM) thickness and mesangial matrix density on the total accumulation of IgA. Our results suggest that IgA accumulation can be understood by relating convection and diffusion, thus demonstrating the importance of intrinsic glomerular factors.
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Affiliation(s)
- Sarah E Hunt
- Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota;
| | - Kevin D Dorfman
- Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota
| | - Yoav Segal
- Division of Renal Diseases and Hypertension, Department of Medicine, University of Minnesota, Minneapolis, Minnesota; and Minneapolis Veterans Affairs Health Care System, Minneapolis, Minnesota
| | - Victor H Barocas
- Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota
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25
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Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Keenan S, Lavidas I, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Nuhn M, Parker A, Patricio M, Pignatelli M, Rahtz M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Birney E, Harrow J, Muffato M, Perry E, Ruffier M, Spudich G, Trevanion SJ, Cunningham F, Aken BL, Zerbino DR, Flicek P. Ensembl 2016. Nucleic Acids Res 2016; 44:D710-6. [PMID: 26687719 PMCID: PMC4702834 DOI: 10.1093/nar/gkv1157] [Citation(s) in RCA: 1066] [Impact Index Per Article: 133.3] [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: 09/19/2015] [Revised: 10/19/2015] [Accepted: 10/19/2015] [Indexed: 01/17/2023] Open
Abstract
The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org). Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. Our data is made available without restriction and all code is available from our GitHub organization site (http://github.com/Ensembl) under an Apache 2.0 license.
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Affiliation(s)
- Andrew Yates
- 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 Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Denise Carvalho-Silva
- 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
| | - Peter Clapham
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen Fitzgerald
- 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
| | - Carlos García Girón
- 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
| | - Thibaut Hourlier
- 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
| | - Sophie H Janacek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nathan Johnson
- 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
| | - Stephen Keenan
- 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
| | - Fergal J Martin
- 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
| | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rishi Nag
- 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
| | - 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
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew Rahtz
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Harpreet Singh Riat
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Sheppard
- 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
| | - Steven P Wilder
- 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
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, 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
| | - Giulietta Spudich
- 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
| | - Bronwen L Aken
- 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 Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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26
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Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Kähäri AK, Keenan S, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Overduin B, Parker A, Patricio M, Perry E, Pignatelli M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Aken BL, Birney E, Harrow J, Kinsella R, Muffato M, Ruffier M, Searle SMJ, Spudich G, Trevanion SJ, Yates A, Zerbino DR, Flicek P. Ensembl 2015. Nucleic Acids Res 2014; 43:D662-9. [PMID: 25352552 PMCID: PMC4383879 DOI: 10.1093/nar/gku1010] [Citation(s) in RCA: 961] [Impact Index Per Article: 96.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Ensembl (http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model organisms. This year we released updated annotation (gene models, comparative genomics, regulatory regions and variation) on the new human assembly, GRCh38, although we continue to support researchers using the GRCh37.p13 assembly through a dedicated site (http://grch37.ensembl.org). Our Regulatory Build has been revamped to identify regulatory regions of interest and to efficiently highlight their activity across disparate epigenetic data sets. A number of new interfaces allow users to perform large-scale comparisons of their data against our annotations. The REST server (http://rest.ensembl.org), which allows programs written in any language to query our databases, has moved to a full service alongside our upgraded website tools. Our online Variant Effect Predictor tool has been updated to process more variants and calculate summary statistics. Lastly, the WiggleTools package enables users to summarize large collections of data sets and view them as single tracks in Ensembl. The Ensembl code base itself is more accessible: it is now hosted on our GitHub organization page (https://github.com/Ensembl) under an Apache 2.0 open source license.
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Affiliation(s)
- Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - M Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Barrell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kathryn Beal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Simon Brent
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Denise Carvalho-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter Clapham
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Guy Coates
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carlos García Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Leo Gordon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sophie H Janacek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nathan Johnson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Juettemann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andreas K Kähäri
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen Keenan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bert Overduin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Harpreet Singh Riat
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alessandro Vullo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Steven P Wilder
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Amonida Zadissa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bronwen L Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Rhoda Kinsella
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen M J Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Giulietta Spudich
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andy Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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27
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Mahajan A, Go MJ, Zhang W, Below JE, Gaulton KJ, Ferreira T, Horikoshi M, Johnson AD, Ng MCY, Prokopenko I, Saleheen D, Wang X, Zeggini E, Abecasis GR, Adair LS, Almgren P, Atalay M, Aung T, Baldassarre D, Balkau B, Bao Y, Barnett AH, Barroso I, Basit A, Been LF, Beilby J, Bell GI, Benediktsson R, Bergman RN, Boehm BO, Boerwinkle E, Bonnycastle LL, Burtt N, Cai Q, Campbell H, Carey J, Cauchi S, Caulfield M, Chan JCN, Chang LC, Chang TJ, Chang YC, Charpentier G, Chen CH, Chen H, Chen YT, Chia KS, Chidambaram M, Chines PS, Cho NH, Cho YM, Chuang LM, Collins FS, Cornelis MC, Couper DJ, Crenshaw AT, van Dam RM, Danesh J, Das D, de Faire U, Dedoussis G, Deloukas P, Dimas AS, Dina C, Doney AS, Donnelly PJ, Dorkhan M, van Duijn C, Dupuis J, Edkins S, Elliott P, Emilsson V, Erbel R, Eriksson JG, Escobedo J, Esko T, Eury E, Florez JC, Fontanillas P, Forouhi NG, Forsen T, Fox C, Fraser RM, Frayling TM, Froguel P, Frossard P, Gao Y, Gertow K, Gieger C, Gigante B, Grallert H, Grant GB, Grrop LC, Groves CJ, Grundberg E, Guiducci C, Hamsten A, Han BG, Hara K, Hassanali N, Hattersley AT, Hayward C, Hedman AK, Herder C, Hofman A, Holmen OL, Hovingh K, Hreidarsson AB, Hu C, Hu FB, Hui J, Humphries SE, Hunt SE, Hunter DJ, Hveem K, Hydrie ZI, Ikegami H, Illig T, Ingelsson E, Islam M, Isomaa B, Jackson AU, Jafar T, James A, Jia W, Jöckel KH, Jonsson A, Jowett JBM, Kadowaki T, Kang HM, Kanoni S, Kao WHL, Kathiresan S, Kato N, Katulanda P, Keinanen-Kiukaanniemi KM, Kelly AM, Khan H, Khaw KT, Khor CC, Kim HL, Kim S, Kim YJ, Kinnunen L, Klopp N, Kong A, Korpi-Hyövälti E, Kowlessur S, Kraft P, Kravic J, Kristensen MM, Krithika S, Kumar A, Kumate J, Kuusisto J, Kwak SH, Laakso M, Lagou V, Lakka TA, Langenberg C, Langford C, Lawrence R, Leander K, Lee JM, Lee NR, Li M, Li X, Li Y, Liang J, Liju S, Lim WY, Lind L, Lindgren CM, Lindholm E, Liu CT, Liu JJ, Lobbens S, Long J, Loos RJF, Lu W, Luan J, Lyssenko V, Ma RCW, Maeda S, Mägi R, Männisto S, Matthews DR, Meigs JB, Melander O, Metspalu A, Meyer J, Mirza G, Mihailov E, Moebus S, Mohan V, Mohlke KL, Morris AD, Mühleisen TW, Müller-Nurasyid M, Musk B, Nakamura J, Nakashima E, Navarro P, Ng PK, Nica AC, Nilsson PM, Njølstad I, Nöthen MM, Ohnaka K, Ong TH, Owen KR, Palmer CNA, Pankow JS, Park KS, Parkin M, Pechlivanis S, Pedersen NL, Peltonen L, Perry JRB, Peters A, Pinidiyapathirage JM, Platou CG, Potter S, Price JF, Qi L, Radha V, Rallidis L, Rasheed A, Rathman W, Rauramaa R, Raychaudhuri S, Rayner NW, Rees SD, Rehnberg E, Ripatti S, Robertson N, Roden M, Rossin EJ, Rudan I, Rybin D, Saaristo TE, Salomaa V, Saltevo J, Samuel M, Sanghera DK, Saramies J, Scott J, Scott LJ, Scott RA, Segrè AV, Sehmi J, Sennblad B, Shah N, Shah S, Shera AS, Shu XO, Shuldiner AR, Sigurđsson G, Sijbrands E, Silveira A, Sim X, Sivapalaratnam S, Small KS, So WY, Stančáková A, Stefansson K, Steinbach G, Steinthorsdottir V, Stirrups K, Strawbridge RJ, Stringham HM, Sun Q, Suo C, Syvänen AC, Takayanagi R, Takeuchi F, Tay WT, Teslovich TM, Thorand B, Thorleifsson G, Thorsteinsdottir U, Tikkanen E, Trakalo J, Tremoli E, Trip MD, Tsai FJ, Tuomi T, Tuomilehto J, Uitterlinden AG, Valladares-Salgado A, Vedantam S, Veglia F, Voight BF, Wang C, Wareham NJ, Wennauer R, Wickremasinghe AR, Wilsgaard T, Wilson JF, Wiltshire S, Winckler W, Wong TY, Wood AR, Wu JY, Wu Y, Yamamoto K, Yamauchi T, Yang M, Yengo L, Yokota M, Young R, Zabaneh D, Zhang F, Zhang R, Zheng W, Zimmet PZ, Altshuler D, Bowden DW, Cho YS, Cox NJ, Cruz M, Hanis CL, Kooner J, Lee JY, Seielstad M, Teo YY, Boehnke M, Parra EJ, Chambers JC, Tai ES, McCarthy MI, Morris AP. Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. Nat Genet 2014; 46:234-44. [PMID: 24509480 PMCID: PMC3969612 DOI: 10.1038/ng.2897] [Citation(s) in RCA: 777] [Impact Index Per Article: 77.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 01/17/2014] [Indexed: 11/18/2022]
Abstract
To further understanding of the genetic basis of type 2 diabetes (T2D) susceptibility, we aggregated published meta-analyses of genome-wide association studies (GWAS) including 26,488 cases and 83,964 controls of European, East Asian, South Asian, and Mexican and Mexican American ancestry. We observed significant excess in directional consistency of T2D risk alleles across ancestry groups, even at SNPs demonstrating only weak evidence of association. By following up the strongest signals of association from the trans-ethnic meta-analysis in an additional 21,491 cases and 55,647 controls of European ancestry, we identified seven novel T2D susceptibility loci. Furthermore, we observed considerable improvements in fine-mapping resolution of common variant association signals at several T2D susceptibility loci. These observations highlight the benefits of trans-ethnic GWAS for the discovery and characterisation of complex trait loci, and emphasize an exciting opportunity to extend insight into the genetic architecture and pathogenesis of human diseases across populations of diverse ancestry.
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Beecham AH, Patsopoulos NA, Xifara DK, Davis MF, Kemppinen A, Cotsapas C, Shah TS, Spencer C, Booth D, Goris A, Oturai A, Saarela J, Fontaine B, Hemmer B, Martin C, Zipp F, D'Alfonso S, Martinelli-Boneschi F, Taylor B, Harbo HF, Kockum I, Hillert J, Olsson T, Ban M, Oksenberg JR, Hintzen R, Barcellos LF, Agliardi C, Alfredsson L, Alizadeh M, Anderson C, Andrews R, Søndergaard HB, Baker A, Band G, Baranzini SE, Barizzone N, Barrett J, Bellenguez C, Bergamaschi L, Bernardinelli L, Berthele A, Biberacher V, Binder TMC, Blackburn H, Bomfim IL, Brambilla P, Broadley S, Brochet B, Brundin L, Buck D, Butzkueven H, Caillier SJ, Camu W, Carpentier W, Cavalla P, Celius EG, Coman I, Comi G, Corrado L, Cosemans L, Cournu-Rebeix I, Cree BAC, Cusi D, Damotte V, Defer G, Delgado SR, Deloukas P, di Sapio A, Dilthey AT, Donnelly P, Dubois B, Duddy M, Edkins S, Elovaara I, Esposito F, Evangelou N, Fiddes B, Field J, Franke A, Freeman C, Frohlich IY, Galimberti D, Gieger C, Gourraud PA, Graetz C, Graham A, Grummel V, Guaschino C, Hadjixenofontos A, Hakonarson H, Halfpenny C, Hall G, Hall P, Hamsten A, Harley J, Harrower T, Hawkins C, Hellenthal G, Hillier C, Hobart J, Hoshi M, Hunt SE, Jagodic M, Jelčić I, Jochim A, Kendall B, Kermode A, Kilpatrick T, Koivisto K, Konidari I, Korn T, Kronsbein H, Langford C, Larsson M, Lathrop M, Lebrun-Frenay C, Lechner-Scott J, Lee MH, Leone MA, Leppä V, Liberatore G, Lie BA, Lill CM, Lindén M, Link J, Luessi F, Lycke J, Macciardi F, Männistö S, Manrique CP, Martin R, Martinelli V, Mason D, Mazibrada G, McCabe C, Mero IL, Mescheriakova J, Moutsianas L, Myhr KM, Nagels G, Nicholas R, Nilsson P, Piehl F, Pirinen M, Price SE, Quach H, Reunanen M, Robberecht W, Robertson NP, Rodegher M, Rog D, Salvetti M, Schnetz-Boutaud NC, Sellebjerg F, Selter RC, Schaefer C, Shaunak S, Shen L, Shields S, Siffrin V, Slee M, Sorensen PS, Sorosina M, Sospedra M, Spurkland A, Strange A, Sundqvist E, Thijs V, Thorpe J, Ticca A, Tienari P, van Duijn C, Visser EM, Vucic S, Westerlind H, Wiley JS, Wilkins A, Wilson JF, Winkelmann J, Zajicek J, Zindler E, Haines JL, Pericak-Vance MA, Ivinson AJ, Stewart G, Hafler D, Hauser SL, Compston A, McVean G, De Jager P, Sawcer SJ, McCauley JL. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat Genet 2013; 45:1353-60. [PMID: 24076602 PMCID: PMC3832895 DOI: 10.1038/ng.2770] [Citation(s) in RCA: 980] [Impact Index Per Article: 89.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 09/03/2013] [Indexed: 12/13/2022]
Abstract
Using the ImmunoChip custom genotyping array, we analyzed 14,498 subjects with multiple sclerosis and 24,091 healthy controls for 161,311 autosomal variants and identified 135 potentially associated regions (P < 1.0 × 10(-4)). In a replication phase, we combined these data with previous genome-wide association study (GWAS) data from an independent 14,802 subjects with multiple sclerosis and 26,703 healthy controls. In these 80,094 individuals of European ancestry, we identified 48 new susceptibility variants (P < 5.0 × 10(-8)), 3 of which we found after conditioning on previously identified variants. Thus, there are now 110 established multiple sclerosis risk variants at 103 discrete loci outside of the major histocompatibility complex. With high-resolution Bayesian fine mapping, we identified five regions where one variant accounted for more than 50% of the posterior probability of association. This study enhances the catalog of multiple sclerosis risk variants and illustrates the value of fine mapping in the resolution of GWAS signals.
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Bradley DT, Hughes AE, Badger SA, Jones GT, Harrison SC, Wright BJ, Bumpstead S, Baas AF, Grétarsdóttir S, Burnand K, Child AH, Clough RE, Cockerill G, Hafez H, Scott DJA, Ariëns RA, Johnson A, Sohrabi S, Smith A, Thompson MM, van Bockxmeer FM, Waltham M, Matthíasson SE, Thorleifsson G, Thorsteinsdottir U, Blankensteijn JD, Teijink JA, Wijmenga C, de Graaf J, Kiemeney LA, Wild JB, Edkins S, Gwilliam R, Hunt SE, Potter S, Lindholt JS, Golledge J, Norman PE, van Rij A, Powell JT, Eriksson P, Stefánsson K, Thompson JR, Humphries SE, Sayers RD, Deloukas P, Samani NJ, Bown MJ. A Variant in
LDLR
Is Associated With Abdominal Aortic Aneurysm. ACTA ACUST UNITED AC 2013; 6:498-504. [DOI: 10.1161/circgenetics.113.000165] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background—
Abdominal aortic aneurysm (AAA) is a common cardiovascular disease among older people and demonstrates significant heritability. In contrast to similar complex diseases, relatively few genetic associations with AAA have been confirmed. We reanalyzed our genome-wide study and carried through to replication suggestive discovery associations at a lower level of significance.
Methods and Results—
A genome-wide association study was conducted using 1830 cases from the United Kingdom, New Zealand, and Australia with infrarenal aorta diameter ≥30 mm or ruptured AAA and 5435 unscreened controls from the 1958 Birth Cohort and National Blood Service cohort from the Wellcome Trust Case Control Consortium. Eight suggestive associations with
P
<1×10
−4
were carried through to in silico replication in 1292 AAA cases and 30 503 controls. One single-nucleotide polymorphism associated with
P
<0.05 after Bonferroni correction in the in silico study underwent further replication (706 AAA cases and 1063 controls from the United Kingdom, 507 AAA cases and 199 controls from Denmark, and 885 AAA cases and 1000 controls from New Zealand). Low-density lipoprotein receptor (
LDLR
) rs6511720 A was significantly associated overall and in 3 of 5 individual replication studies. The full study showed an association that reached genome-wide significance (odds ratio, 0.76; 95% confidence interval, 0.70–0.83;
P
=2.08×10
−10
).
Conclusions—
LDLR rs6511720 is associated with AAA. This finding is consistent with established effects of this variant on coronary artery disease. Shared causal pathways with other cardiovascular diseases may present novel opportunities for preventative and therapeutic strategies for AAA.
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Schafer MA, Robertson RJ, Thekkada SJ, Gallagher M, Hunt SE, Goss FL, Aaron DJ. Validation of the OMNI RPE Seven Day Exertional Recall Questionnaire. Res Q Exerc Sport 2013; 84:363-372. [PMID: 24261016 DOI: 10.1080/02701367.2013.814042] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PURPOSE The present study examined the validity of the Seven Day Recall Questionnaire among recreationally active men and women. METHOD Initially, participants completed a level walk (2.5 mph [4.0 kph]), hill walk (3.5 mph [5.6 kph], 5% grade), and run (5.0 mph [8.0 kph], 2.5% grade). Seven days later, participants were given the Seven Day Recall Questionnaire and rated their perceived exertion associated with the exercise bouts. Participants then repeated the same exercise bouts as in Session 1, and the OMNI rating of perceived exertion (RPE) was estimated. RESULTS Concurrent validity indicated that for both men and women, respectively, the RPE-Overall (r = .48, r = .70), RPE-Leg (r = .43, r = .66), and RPE-Chest (r = .47, r = .66) derived from the Seven Day Recall Questionnaire distributed as a function of oxygen consumption. RPE-Overall (r = .61, r = .76), RPE-Leg (r = .56, r = .72), and RPE-Chest (r = .61, r = .72) from the Seven Day Recall Questionnaire distributed as a function of heart rate. Convergent validity coefficients between the perceptual responses from the Seven Day Recall Questionnaire and the recall/criterion session were: level walk (r = .53-.87, r = .51-.80), hill walk (r = .65-.79, r = .56-.64), and run (r = .60-.68, r = .68-.78) for men and women, respectively. CONCLUSIONS Concurrent and convergent evidence partially supports the utilization of the Seven Day Recall Questionnaire to recall the relative intensity of walking and running exercise sessions conducted 7 days prior.
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Affiliation(s)
- Mark A Schafer
- Western Kentucky University, Bowling Green, KY 42101, USA.
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Ripke S, O'Dushlaine C, Chambert K, Moran JL, Kähler AK, Akterin S, Bergen SE, Collins AL, Crowley JJ, Fromer M, Kim Y, Lee SH, Magnusson PKE, Sanchez N, Stahl EA, Williams S, Wray NR, Xia K, Bettella F, Borglum AD, Bulik-Sullivan BK, Cormican P, Craddock N, de Leeuw C, Durmishi N, Gill M, Golimbet V, Hamshere ML, Holmans P, Hougaard DM, Kendler KS, Lin K, Morris DW, Mors O, Mortensen PB, Neale BM, O'Neill FA, Owen MJ, Milovancevic MP, Posthuma D, Powell J, Richards AL, Riley BP, Ruderfer D, Rujescu D, Sigurdsson E, Silagadze T, Smit AB, Stefansson H, Steinberg S, Suvisaari J, Tosato S, Verhage M, Walters JT, Levinson DF, Gejman PV, Kendler KS, Laurent C, Mowry BJ, O'Donovan MC, Owen MJ, Pulver AE, Riley BP, Schwab SG, Wildenauer DB, Dudbridge F, Holmans P, Shi J, Albus M, Alexander M, Campion D, Cohen D, Dikeos D, Duan J, Eichhammer P, Godard S, Hansen M, Lerer FB, Liang KY, Maier W, Mallet J, Nertney DA, Nestadt G, Norton N, O'Neill FA, Papadimitriou GN, Ribble R, Sanders AR, Silverman JM, Walsh D, Williams NM, Wormley B, Arranz MJ, Bakker S, Bender S, Bramon E, Collier D, Crespo-Facorro B, Hall J, Iyegbe C, Jablensky A, Kahn RS, Kalaydjieva L, Lawrie S, Lewis CM, Lin K, Linszen DH, Mata I, McIntosh A, Murray RM, Ophoff RA, Powell J, Rujescu D, Van Os J, Walshe M, Weisbrod M, Wiersma D, Donnelly P, Barroso I, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin AP, Deloukas P, Duncanson A, Jankowski J, Markus HS, Mathew CG, Palmer CNA, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Spencer CCA, Band G, Bellenguez C, Freeman C, Hellenthal G, Giannoulatou E, Pirinen M, Pearson RD, Strange A, Su Z, Vukcevic D, Donnelly P, Langford C, Hunt SE, Edkins S, Gwilliam R, Blackburn H, Bumpstead SJ, Dronov S, Gillman M, Gray E, Hammond N, Jayakumar A, McCann OT, Liddle J, Potter SC, Ravindrarajah R, Ricketts M, Tashakkori-Ghanbaria A, Waller MJ, Weston P, Widaa S, Whittaker P, Barroso I, Deloukas P, Mathew CG, Blackwell JM, Brown MA, Corvin AP, McCarthy MI, Spencer CCA, Bramon E, Corvin AP, O'Donovan MC, Stefansson K, Scolnick E, Purcell S, McCarroll SA, Sklar P, Hultman CM, Sullivan PF. Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Nat Genet 2013; 45:1150-9. [PMID: 23974872 PMCID: PMC3827979 DOI: 10.1038/ng.2742] [Citation(s) in RCA: 1134] [Impact Index Per Article: 103.1] [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: 12/09/2012] [Accepted: 08/01/2013] [Indexed: 12/11/2022]
Abstract
Schizophrenia is a heritable disorder with substantial public health
impact. We conducted a multi-stage genome-wide association study (GWAS) for
schizophrenia beginning with a Swedish national sample (5,001 cases, 6,243
controls) followed by meta-analysis with prior schizophrenia GWAS (8,832 cases,
12,067 controls) and finally by replication of SNPs in 168 genomic regions in
independent samples (7,413 cases, 19,762 controls, and 581 trios). In total, 22
regions met genome-wide significance (14 novel and one previously implicated in
bipolar disorder). The results strongly implicate calcium signaling in the
etiology of schizophrenia, and include genome-wide significant results for
CACNA1C and CACNB2 whose protein products
interact. We estimate that ∼8,300 independent and predominantly common
SNPs contribute to risk for schizophrenia and that these collectively account
for most of its heritability. Common genetic variation plays an important role
in the etiology of schizophrenia, and larger studies will allow more detailed
understanding of this devastating disorder.
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Affiliation(s)
- Stephan Ripke
- 1] Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA. [2] Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [3]
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Berndt SI, Gustafsson S, Mägi R, Ganna A, Wheeler E, Feitosa MF, Justice AE, Monda KL, Croteau-Chonka DC, Day FR, Esko T, Fall T, Ferreira T, Gentilini D, Jackson AU, Luan J, Randall JC, Vedantam S, Willer CJ, Winkler TW, Wood AR, Workalemahu T, Hu YJ, Lee SH, Liang L, Lin DY, Min JL, Neale BM, Thorleifsson G, Yang J, Albrecht E, Amin N, Bragg-Gresham JL, Cadby G, den Heijer M, Eklund N, Fischer K, Goel A, Hottenga JJ, Huffman JE, Jarick I, Johansson Å, Johnson T, Kanoni S, Kleber ME, König IR, Kristiansson K, Kutalik Z, Lamina C, Lecoeur C, Li G, Mangino M, McArdle WL, Medina-Gomez C, Müller-Nurasyid M, Ngwa JS, Nolte IM, Paternoster L, Pechlivanis S, Perola M, Peters MJ, Preuss M, Rose LM, Shi J, Shungin D, Smith AV, Strawbridge RJ, Surakka I, Teumer A, Trip MD, Tyrer J, Van Vliet-Ostaptchouk JV, Vandenput L, Waite LL, Zhao JH, Absher D, Asselbergs FW, Atalay M, Attwood AP, Balmforth AJ, Basart H, Beilby J, Bonnycastle LL, Brambilla P, Bruinenberg M, Campbell H, Chasman DI, Chines PS, Collins FS, Connell JM, Cookson W, de Faire U, de Vegt F, Dei M, Dimitriou M, Edkins S, Estrada K, Evans DM, Farrall M, Ferrario MM, Ferrières J, Franke L, Frau F, Gejman PV, Grallert H, Grönberg H, Gudnason V, Hall AS, Hall P, Hartikainen AL, Hayward C, Heard-Costa NL, Heath AC, Hebebrand J, Homuth G, Hu FB, Hunt SE, Hyppönen E, Iribarren C, Jacobs KB, Jansson JO, Jula A, Kähönen M, Kathiresan S, Kee F, Khaw KT, Kivimaki M, Koenig W, Kraja AT, Kumari M, Kuulasmaa K, Kuusisto J, Laitinen JH, Lakka TA, Langenberg C, Launer LJ, Lind L, Lindström J, Liu J, Liuzzi A, Lokki ML, Lorentzon M, Madden PA, Magnusson PK, Manunta P, Marek D, März W, Mateo Leach I, McKnight B, Medland SE, Mihailov E, Milani L, Montgomery GW, Mooser V, Mühleisen TW, Munroe PB, Musk AW, Narisu N, Navis G, Nicholson G, Nohr EA, Ong KK, Oostra BA, Palmer CN, Palotie A, Peden JF, Pedersen N, Peters A, Polasek O, Pouta A, Pramstaller PP, Prokopenko I, Pütter C, Radhakrishnan A, Raitakari O, Rendon A, Rivadeneira F, Rudan I, Saaristo TE, Sambrook JG, Sanders AR, Sanna S, Saramies J, Schipf S, Schreiber S, Schunkert H, Shin SY, Signorini S, Sinisalo J, Skrobek B, Soranzo N, Stančáková A, Stark K, Stephens JC, Stirrups K, Stolk RP, Stumvoll M, Swift AJ, Theodoraki EV, Thorand B, Tregouet DA, Tremoli E, Van der Klauw MM, van Meurs JB, Vermeulen SH, Viikari J, Virtamo J, Vitart V, Waeber G, Wang Z, Widén E, Wild SH, Willemsen G, Winkelmann BR, Witteman JC, Wolffenbuttel BH, Wong A, Wright AF, Zillikens MC, Amouyel P, Boehm BO, Boerwinkle E, Boomsma DI, Caulfield MJ, Chanock SJ, Cupples LA, Cusi D, Dedoussis GV, Erdmann J, Eriksson JG, Franks PW, Froguel P, Gieger C, Gyllensten U, Hamsten A, Harris TB, Hengstenberg C, Hicks AA, Hingorani A, Hinney A, Hofman A, Hovingh KG, Hveem K, Illig T, Jarvelin MR, Jöckel KH, Keinanen-Kiukaanniemi SM, Kiemeney LA, Kuh D, Laakso M, Lehtimäki T, Levinson DF, Martin NG, Metspalu A, Morris AD, Nieminen MS, Njølstad I, Ohlsson C, Oldehinkel AJ, Ouwehand WH, Palmer LJ, Penninx B, Power C, Province MA, Psaty BM, Qi L, Rauramaa R, Ridker PM, Ripatti S, Salomaa V, Samani NJ, Snieder H, Sørensen TI, Spector TD, Stefansson K, Tönjes A, Tuomilehto J, Uitterlinden AG, Uusitupa M, van der Harst P, Vollenweider P, Wallaschofski H, Wareham NJ, Watkins H, Wichmann HE, Wilson JF, Abecasis GR, Assimes TL, Barroso I, Boehnke M, Borecki IB, Deloukas P, Fox CS, Frayling T, Groop LC, Haritunian T, Heid IM, Hunter D, Kaplan RC, Karpe F, Moffatt M, Mohlke KL, O’Connell JR, Pawitan Y, Schadt EE, Schlessinger D, Steinthorsdottir V, Strachan DP, Thorsteinsdottir U, van Duijn CM, Visscher PM, Di Blasio AM, Hirschhorn JN, Lindgren CM, Morris AP, Meyre D, Scherag A, McCarthy MI, Speliotes EK, North KE, Loos RJ, Ingelsson E. Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. Nat Genet 2013; 45:501-12. [PMID: 23563607 PMCID: PMC3973018 DOI: 10.1038/ng.2606] [Citation(s) in RCA: 436] [Impact Index Per Article: 39.6] [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: 10/16/2012] [Accepted: 03/14/2013] [Indexed: 12/25/2022]
Abstract
Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.
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Affiliation(s)
- Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA
| | - Stefan Gustafsson
- Department of Medical Sciences, Molecular Epidemiology, Uppsala University, Uppsala, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Reedik Mägi
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Estonian Genome Center, University of Tartu, Tartu 50410, Estonia
| | - Andrea Ganna
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Eleanor Wheeler
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Mary F. Feitosa
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Anne E. Justice
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
| | - Keri L. Monda
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
- Center for Observational Research, Amgen, Thousands Oaks, CA, 91320
| | | | - Felix R. Day
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu 50410, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Tove Fall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Teresa Ferreira
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Davide Gentilini
- Molecular Biology Department, Istituto Auxologico Italiano, Milano, Italy
| | - Anne U. Jackson
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jian’an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK
| | - Joshua C. Randall
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Sailaja Vedantam
- Divisions of Genetics and Endocrinology and Center for Basic and Translational Obesity Research, Children’s Hospital, Boston, Massachusetts 02115, USA
- Metabolism Initiative and Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Cristen J. Willer
- Department of Internal Medicine (Cardiovascular), University of Michigan, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, MI 48109, USA
| | - Thomas W. Winkler
- Public Health and Gender Studies, Institute of Epidemiology and Preventive Medicine, Regensburg University Medical Center, Regensburg, Germany
| | - Andrew R. Wood
- Genetics of Complex Traits, Peninsula College of Medicine and Dentistry, University of Exeter, Exeter, EX1 2LU, UK
| | - Tsegaselassie Workalemahu
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia 30322, USA
| | - Sang Hong Lee
- The Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Liming Liang
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Dan-Yu Lin
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Josine L. Min
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Benjamin M. Neale
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114
| | | | - Jian Yang
- University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4102, Australia
- Queensland Institute of Medical Research, Brisbane 4029, Australia
| | - Eva Albrecht
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, Rotterdam, 3015GE, The Netherlands
| | - Jennifer L. Bragg-Gresham
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Gemma Cadby
- Genetic Epidemiology and Biostatistics Platform, Ontario Institute for Cancer Research. Toronto, Canada, M5G 1L7
- Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Toronto, Canada, M5G 1X5
- Centre for Genetic Epidemiology and Biostatistics, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Martin den Heijer
- Department of Internal Medicine, VU University Medical Centre, Amsterdam, The Netherlands
| | - Niina Eklund
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Unit of Public Health Genomics, 00014, Helsinki, Finland
| | - Krista Fischer
- Estonian Genome Center, University of Tartu, Tartu 50410, Estonia
| | - Anuj Goel
- Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, VU University Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - Jennifer E. Huffman
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Ivonne Jarick
- Institute of Medical Biometry and Epidemiology, University of Marburg, 35037 Marburg, Germany
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
- Uppsala Clinical Research Center, Uppsala university hospital, Sweden
| | - Toby Johnson
- Genome Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary, University of London, London, UK
| | - Stavroula Kanoni
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Marcus E. Kleber
- LURIC Study nonprofit LLC, Freiburg, Germany
- Mannheim Institute of Public Health, Social and Preventive Medicine, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany
| | - Inke R. König
- Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, 23562 Lübeck, Germany
| | - Kati Kristiansson
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Unit of Public Health Genomics, 00014, Helsinki, Finland
| | - Zoltán Kutalik
- Department of Medical Genetics, University of Lausanne, 1005 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Claudia Lamina
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Cecile Lecoeur
- University Lille Nord de France, 59000 Lille, France
- CNRS UMR8199-IBL-Institut Pasteur de Lille, F-59000 Lille, France
| | - Guo Li
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington 98101, USA
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, SE1 7EH, UK
| | - Wendy L. McArdle
- School of Social and Community Medicine, University of Bristol, UK
| | - Carolina Medina-Gomez
- Department of Epidemiology, Erasmus MC, Rotterdam, 3015GE, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, 3015GE, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA)
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, Munich, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology and Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Julius S. Ngwa
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts 02118, USA
| | - Ilja M. Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Lavinia Paternoster
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN, UK
| | - Sonali Pechlivanis
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Markus Perola
- Estonian Genome Center, University of Tartu, Tartu 50410, Estonia
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Unit of Public Health Genomics, 00014, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014, Helsinki, Finland
| | - Marjolein J. Peters
- Department of Epidemiology, Erasmus MC, Rotterdam, 3015GE, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, 3015GE, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA)
| | - Michael Preuss
- Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, 23562 Lübeck, Germany
- Universität zu Lübeck, Medizinische Klinik II, 23538 Lübeck, Germany
| | - Lynda M. Rose
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02215, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA
| | - Dmitry Shungin
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
- Department of Public Health & Clinical Medicine, Umeå University, Umeå, Sweden
- Department of Odontology, Umeå University, Sweden
| | - Albert Vernon Smith
- Icelandic Heart Association, Kopavogur, Iceland
- Department of Medicine, University of Iceland, Reykjavik, Iceland
| | - Rona J. Strawbridge
- Atherosclerosis Research Unit, Department of Medicine, Solna, Karolinska Institutet, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Ida Surakka
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Unit of Public Health Genomics, 00014, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014, Helsinki, Finland
| | - Alexander Teumer
- Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, 17487 Greifswald, Germany
| | - Mieke D. Trip
- Department of Vascular Medicine, Academic Medical Center, Amsterdam, The Netherlands
- Heart Failure Research Centre, Department of Clinical and Experimental Cardiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Jonathan Tyrer
- Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Jana V. Van Vliet-Ostaptchouk
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands
- LifeLines Cohort Study, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Liesbeth Vandenput
- Department of Internal Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 45 Gothenburg, Sweden
| | - Lindsay L. Waite
- Hudson Alpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Jing Hua Zhao
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK
| | - Devin Absher
- Hudson Alpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Folkert W. Asselbergs
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, The Netherlands
| | - Mustafa Atalay
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio Campus, Finland
| | | | - Anthony J. Balmforth
- Division of Epidemiology, Multidisciplinary Cardiovascular Research Centre (MCRC), Leeds Institute of Genetics, Health and Therapeutics (LIGHT), University of Leeds, Leeds LS2 9JT, UK
| | - Hanneke Basart
- Department of Vascular Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - John Beilby
- PathWest Laboratory of Western Australia, Department of Molecular Genetics, J Block, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Department of Surgery and Pathology, University of Western Australia, Nedlands, Australia, 6009
| | - Lori L. Bonnycastle
- Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Paolo Brambilla
- Dipartimento di Medicina Sperimentale. Università degli Studi Milano-Bicocca, Monza, Italy
| | - Marcel Bruinenberg
- LifeLines Cohort Study, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Daniel I. Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02215, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter S. Chines
- Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Francis S. Collins
- Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - John M. Connell
- British Heart Foundation Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, G12 8TA, UK
- University of Dundee, Ninewells Hospital &Medical School, Dundee, DD1 9SY, UK
| | - William Cookson
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Ulf de Faire
- Division of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Femmie de Vegt
- Department of Epidemiology, Biostatistics and HTA, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Mariano Dei
- Istituto di Ricerca Genetica e Biomedicadel del CNR, Monserrato, 09042, Cagliari, Italy
| | - Maria Dimitriou
- Department of Dietetics-Nutrition, Harokopio University, 70 El. Venizelou Str, Athens, Greece
| | - Sarah Edkins
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Karol Estrada
- Department of Epidemiology, Erasmus MC, Rotterdam, 3015GE, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, 3015GE, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA)
| | - David M. Evans
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN, UK
| | - Martin Farrall
- Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Marco M. Ferrario
- Epidemiology and Preventive Medicine Research Center, Department of Clinical and Experimental Medicine, University of Insubria, Varese, Italy
| | - Jean Ferrières
- Department of Cardiology, Toulouse University School of Medicine, Rangueil Hospital, Toulouse, France
| | - Lude Franke
- LifeLines Cohort Study, University Medical Center Groningen, University of Groningen, The Netherlands
- Department of Genetics, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Francesca Frau
- University of Milan, Department of Health Sciences, Ospedale San Paolo, 20139 Milano, Italy
| | - Pablo V. Gejman
- University of Chicago, Chicago, Illinois 60637, USA
- Northshore University HealthSystem, Evanston, Illinois 60201, USA
| | - Harald Grallert
- Research Unit for Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Department of Medicine, University of Iceland, Reykjavik, Iceland
| | - Alistair S. Hall
- Division of Cardiovascular and Neuronal Remodelling, Multidisciplinary Cardiovascular Research Centre, Leeds Institute of Genetics, Health and Therapeutics, University of Leeds, UK
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Anna-Liisa Hartikainen
- Department of Clinical Sciences/Obstetrics and Gynecology, University of Oulu, 90014 Oulu, Finland
| | - Caroline Hayward
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Nancy L. Heard-Costa
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Andrew C. Heath
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, 45147 Essen, Germany
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, 17487 Greifswald, Germany
| | - Frank B. Hu
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Sarah E. Hunt
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Elina Hyppönen
- Centre For Paediatric Epidemiolgy and Biostatistics/MRC Centre of Epidemiology for Child Health, University College of London Institute of Child Health, London, UK
| | - Carlos Iribarren
- Division of Research, Kaiser Permanente Northern California, Oakland, California 94612, USA
| | - Kevin B. Jacobs
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
| | - John-Olov Jansson
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Antti Jula
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Population Studies Unit, 20720 Turku, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, University of Tampere and Tampere University Hospital, 33520 Tampere, Finland
| | - Sekar Kathiresan
- Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Frank Kee
- UKCRC Centre of Excellence for Public Health (NI) Queens University, Belfast
| | - Kay-Tee Khaw
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge, Cambridge CB2 2SR, UK
| | - Mika Kivimaki
- Department of Epidemiology and Public Health, University College London, 1-19 Torrington Place, London WC1E 6BT, UK
| | - Wolfgang Koenig
- Department of Internal Medicine II – Cardiology, University of Ulm Medical Center, Ulm, Germany
| | - Aldi T. Kraja
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Meena Kumari
- Department of Epidemiology and Public Health, University College London, 1-19 Torrington Place, London WC1E 6BT, UK
| | - Kari Kuulasmaa
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Chronic Disease Epidemiology and Prevention Unit, 00271, Helsinki, Finland
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland, Kuopio Campus and Kuopio University Hospital, 70210 Kuopio, Finland
| | | | - Timo A. Lakka
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio Campus, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK
- Department of Epidemiology and Public Health, University College London, 1-19 Torrington Place, London WC1E 6BT, UK
| | - Lenore J. Launer
- Laboratory of Epidemiology, Demography, Biometry, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Akademiska sjukhuset, 751 85 Uppsala, Sweden
| | - Jaana Lindström
- National Institute for Health and Welfare, Diabetes Prevention Unit, 00271 Helsinki, Finland
| | - Jianjun Liu
- Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Antonio Liuzzi
- Department of Internal Medicine, Istituto Auxologico Italiano, Verbania, Italy
| | - Marja-Liisa Lokki
- Transplantation Laboratory, Haartman Institute, University of Helsinki, 00014, Helsinki, Finland
| | - Mattias Lorentzon
- Department of Internal Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 45 Gothenburg, Sweden
| | - Pamela A. Madden
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Patrik K. Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Paolo Manunta
- Università Vita-Salute San Raffaele, Chair of Nephrology San Raffaele Scientific Institute, OU Nephrology and Dialysis, 20132 Milan, Italy
| | - Diana Marek
- Department of Medical Genetics, University of Lausanne, 1005 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Winfried März
- Mannheim Institute of Public Health, Social and Preventive Medicine, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany
- Synlab Academy, Mannheim, Germany
| | - Irene Mateo Leach
- Department of Cardiology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Barbara McKnight
- Departments of Biostatistics, University of Washington, Seattle, Washington 98195, USA
| | - Sarah E. Medland
- Queensland Institute of Medical Research, Brisbane 4029, Australia
| | - Evelin Mihailov
- Estonian Genome Center, University of Tartu, Tartu 50410, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu 50410, Estonia
| | | | - Vincent Mooser
- Genetics Division, GlaxoSmithKline, King of Prussia, Pennsylvania 19406, USA
| | - Thomas W. Mühleisen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Patricia B. Munroe
- Genome Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary, University of London, London, UK
| | - Arthur W. Musk
- School of Population Health, The University of Western Australia, Nedlands WA 6009, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia, 6009
- Busselton Population Medical Research Foundation Inc., Sir Charles Gairdner Hospital, Nedlands, Western Australia 6009, Australia
| | - Narisu Narisu
- Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Gerjan Navis
- Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen
| | - George Nicholson
- MRC Harwell, Harwell, UK
- Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
| | - Ellen A. Nohr
- Department of Public Health, Section of Epidemiology, Aarhus University, Denmark
| | - Ken K. Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK
- MRC Unit for Lifelong Health & Ageing, London, UK
| | - Ben A. Oostra
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA)
- Department of Clinical Genetics, Erasmus MC, Rotterdam, 3015GE, The Netherlands
- Centre for Medical Systems Biology & Netherlands Consortium on Healthy Aging, Leiden, the Netherlands
| | - Colin N.A. Palmer
- Medical Research Institute, University of Dundee, Ninewells Hospital and Medical School. Dundee, DD1 9SY
| | - Aarno Palotie
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014, Helsinki, Finland
| | | | - Nancy Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Annette Peters
- Research Unit for Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Munich Heart Alliance, Munich, Germany
| | | | - Anneli Pouta
- Department of Clinical Sciences/Obstetrics and Gynecology, University of Oulu, 90014 Oulu, Finland
- National Institute for Health and Welfare, 90101 Oulu, Finland
| | - Peter P. Pramstaller
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano/Bozen, 39100, Italy - Affiliated Institute of the University of Lübeck, Lübeck, Germany
- Department of Neurology, General Central Hospital, Bolzano, Italy
- Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LJ, UK
| | - Carolin Pütter
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Aparna Radhakrishnan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK
- NHS Blood and Transplant, Cambridge Centre, Cambridge, CB2 0PT, UK
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520 Turku, Finland
- The Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, 20520 Turku, Finland
| | - Augusto Rendon
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK
- NHS Blood and Transplant, Cambridge Centre, Cambridge, CB2 0PT, UK
- MRC Biostatistics Unit, Institute of Public Health, Cambridge, UK
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus MC, Rotterdam, 3015GE, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, 3015GE, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA)
| | - Igor Rudan
- Centre for Population Health Sciences, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Timo E. Saaristo
- Finnish Diabetes Association, Kirjoniementie 15, 33680, Tampere, Finland
- Pirkanmaa Hospital District, Tampere, Finland
| | - Jennifer G. Sambrook
- Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK
- NHS Blood and Transplant, Cambridge Centre, Cambridge, CB2 0PT, UK
| | - Alan R. Sanders
- University of Chicago, Chicago, Illinois 60637, USA
- Northshore University HealthSystem, Evanston, Illinois 60201, USA
| | - Serena Sanna
- Istituto di Ricerca Genetica e Biomedicadel del CNR, Monserrato, 09042, Cagliari, Italy
| | - Jouko Saramies
- South Karelia Central Hospital, 53130 Lappeenranta, Finland
| | - Sabine Schipf
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Stefan Schreiber
- Institute for Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Heribert Schunkert
- Universität zu Lübeck, Medizinische Klinik II, 23538 Lübeck, Germany
- Deutsches Zentrum für Herz-Kreislaufforschung e. V. (DZHK), Universität zu Lübeck, 23538 Lübeck, Germany
| | - So-Youn Shin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Juha Sinisalo
- Division of Cardiology, Cardiovascular Laboratory, Helsinki University Central Hospital, 00029 Helsinki, Finland
| | - Boris Skrobek
- University Lille Nord de France, 59000 Lille, France
- CNRS UMR8199-IBL-Institut Pasteur de Lille, F-59000 Lille, France
| | - Nicole Soranzo
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, SE1 7EH, UK
| | - Alena Stančáková
- University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Klaus Stark
- Klinik und Poliklinik für Innere Medizin II, Universitätklinikum Regensburg, 93053 Regensburg, Germany
| | - Jonathan C. Stephens
- Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK
- NHS Blood and Transplant, Cambridge Centre, Cambridge, CB2 0PT, UK
| | | | - Ronald P. Stolk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, The Netherlands
- LifeLines Cohort Study, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Michael Stumvoll
- Department of Medicine, University of Leipzig, 04103 Leipzig, Germany
- University of Leipzig, IFB Adiposity Diseases, Leipzig, Germany
| | - Amy J. Swift
- Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Eirini V. Theodoraki
- Department of Dietetics-Nutrition, Harokopio University, 70 El. Venizelou Str, Athens, Greece
| | - Barbara Thorand
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Elena Tremoli
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università di Milano, Centro Cardiologico Monzino, IRCCS, Milan, Italy
| | - Melanie M. Van der Klauw
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands
- LifeLines Cohort Study, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Joyce B.J. van Meurs
- Department of Epidemiology, Erasmus MC, Rotterdam, 3015GE, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, 3015GE, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA)
| | - Sita H. Vermeulen
- Department of Epidemiology, Biostatistics and HTA, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Jorma Viikari
- Department of Medicine, University of Turku and Turku University Hospital, 20520 Turku, Finland
| | - Jarmo Virtamo
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Chronic Disease Epidemiology and Prevention Unit, 00271, Helsinki, Finland
| | - Veronique Vitart
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Gérard Waeber
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois (CHUV) University Hospital, 1011 Lausanne, Switzerland
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
| | - Elisabeth Widén
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014, Helsinki, Finland
| | - Sarah H. Wild
- Centre for Population Health Sciences, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam, 1081 BT Amsterdam, The Netherlands
| | | | - Jacqueline C.M. Witteman
- Department of Epidemiology, Erasmus MC, Rotterdam, 3015GE, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA)
| | - Bruce H.R. Wolffenbuttel
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands
- LifeLines Cohort Study, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Andrew Wong
- MRC Unit for Lifelong Health & Ageing, London, UK
| | - Alan F. Wright
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - M. Carola Zillikens
- Department of Internal Medicine, Erasmus MC, Rotterdam, 3015GE, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA)
| | - Philippe Amouyel
- Institut Pasteur de Lille, INSERM U744, Université Lille Nord de France, F-59000 Lille, France
| | - Bernhard O. Boehm
- Division of Endocrinology and Diabetes, Department of Medicine, University Hospital, Ulm, Germany
| | - Eric Boerwinkle
- Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Dorret I. Boomsma
- Department of Biological Psychology, VU University Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - Mark J. Caulfield
- Genome Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary, University of London, London, UK
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts 02118, USA
| | - Daniele Cusi
- University of Milan, Department of Health Sciences, Ospedale San Paolo, 20139 Milano, Italy
- Fondazione Filarete, Milano, Italy
| | - George V. Dedoussis
- Department of Dietetics-Nutrition, Harokopio University, 70 El. Venizelou Str, Athens, Greece
| | - Jeanette Erdmann
- Universität zu Lübeck, Medizinische Klinik II, 23538 Lübeck, Germany
- Deutsches Zentrum für Herz-Kreislaufforschung e. V. (DZHK), Universität zu Lübeck, 23538 Lübeck, Germany
| | - Johan G. Eriksson
- Department of General Practice and Primary health Care, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, 00271 Helsinki, Finland
- Helsinki University Central Hospital, Unit of General Practice, 00280 Helsinki, Finland
| | - Paul W. Franks
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
- Department of Public Health & Clinical Medicine, Umeå University, Umeå, Sweden
- Department of Nutrition, Harvard School of Public Health, Boston, MA
| | - Philippe Froguel
- University Lille Nord de France, 59000 Lille, France
- CNRS UMR8199-IBL-Institut Pasteur de Lille, F-59000 Lille, France
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, W12 0NN, London, UK
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Anders Hamsten
- Atherosclerosis Research Unit, Department of Medicine, Solna, Karolinska Institutet, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Tamara B. Harris
- Laboratory of Epidemiology, Demography, Biometry, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Christian Hengstenberg
- Klinik und Poliklinik für Innere Medizin II, Universitätklinikum Regensburg, 93053 Regensburg, Germany
| | - Andrew A. Hicks
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano/Bozen, 39100, Italy - Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Aroon Hingorani
- Department of Epidemiology and Public Health, University College London, 1-19 Torrington Place, London WC1E 6BT, UK
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, 45147 Essen, Germany
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, Rotterdam, 3015GE, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA)
| | - Kees G. Hovingh
- Department of Vascular Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Kristian Hveem
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, 7600 Levanger, Norway
| | - Thomas Illig
- Research Unit for Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Hannover Unified Biobank, Hannover Medical School, 30625 Hannover, Germany
| | - Marjo-Riitta Jarvelin
- National Institute for Health and Welfare, 90101 Oulu, Finland
- Department of Epidemiology and Biostatistics, School of Public Health, Faculty of Medicine, Imperial College London, London, W2 1PG, UK
- Institute of Health Sciences, University of Oulu, 90014 Oulu, Finland
- Biocenter Oulu, University of Oulu, 90014 Oulu, Finland
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Sirkka M. Keinanen-Kiukaanniemi
- Institute of Health Sciences, University of Oulu, 90014 Oulu, Finland
- Unit of General Practice, Oulu University Hospital, Oulu, Finland
| | - Lambertus A. Kiemeney
- Department of Epidemiology, Biostatistics and HTA, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen, The Netherlands
- Department of Urology, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen, The Netherlands
- Comprehensive Cancer Center East, 6501 BG Nijmegen, The Netherlands
| | - Diana Kuh
- MRC Unit for Lifelong Health & Ageing, London, UK
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland, Kuopio Campus and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere and Tampere University Hospital, 33520 Tampere, Finland
| | | | | | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu 50410, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Andrew D. Morris
- Medical Research Institute, University of Dundee, Ninewells Hospital and Medical School. Dundee, DD1 9SY
| | - Markku S. Nieminen
- Division of Cardiology, Cardiovascular Laboratory, Helsinki University Central Hospital, 00029 Helsinki, Finland
| | - Inger Njølstad
- Department of Clinical Medicine, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Claes Ohlsson
- Department of Internal Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 45 Gothenburg, Sweden
| | - Albertine J. Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Willem H. Ouwehand
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK
- NHS Blood and Transplant, Cambridge Centre, Cambridge, CB2 0PT, UK
| | - Lyle J. Palmer
- Genetic Epidemiology and Biostatistics Platform, Ontario Institute for Cancer Research. Toronto, Canada, M5G 1L7
- Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Toronto, Canada, M5G 1X5
| | - Brenda Penninx
- Department of Psychiatry, University Medical Centre Groningen, 9713 GZ Groningen, The Netherlands
| | - Chris Power
- Centre For Paediatric Epidemiolgy and Biostatistics/MRC Centre of Epidemiology for Child Health, University College of London Institute of Child Health, London, UK
| | - Michael A. Province
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington 98101, USA
- Departments of Epidemiology, Medicine and Health Services, University of Washington, Seattle, Washington 98195, USA
- Group Health Research Institute, Group Health, Seattle, Washington 98101, USA
| | - Lu Qi
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Rainer Rauramaa
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Paul M. Ridker
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02215, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Samuli Ripatti
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Unit of Public Health Genomics, 00014, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014, Helsinki, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Chronic Disease Epidemiology and Prevention Unit, 00271, Helsinki, Finland
| | - Nilesh J. Samani
- Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, LE3 9QP, UK
- Leicester NIHR Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, The Netherlands
- LifeLines Cohort Study, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Thorkild I.A. Sørensen
- Institute of Preventive Medicine, Bispebjerg University Hospital, Copenhagen, and Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, SE1 7EH, UK
| | - Kari Stefansson
- deCODE Genetics, 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavík, Iceland
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, 04103 Leipzig, Germany
- University of Leipzig, IFB Adiposity Diseases, Leipzig, Germany
| | - Jaakko Tuomilehto
- National Institute for Health and Welfare, Diabetes Prevention Unit, 00271 Helsinki, Finland
- Red RECAVA Grupo RD06/0014/0015, Hospital Universitario La Paz, 28046 Madrid, Spain
- Centre for Vascular Prevention, Danube-University Krems, 3500 Krems, Austria
- South Ostrobothnia Central Hospital, 60220 Seinajoki, Finland
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus MC, Rotterdam, 3015GE, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, 3015GE, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA)
| | - Matti Uusitupa
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Finland
- Research Unit, Kuopio University Hospital, Kuopio, Finland
| | - Pim van der Harst
- Department of Genetics, University Medical Center Groningen, University of Groningen, The Netherlands
- Department of Cardiology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Peter Vollenweider
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois (CHUV) University Hospital, 1011 Lausanne, Switzerland
| | - Henri Wallaschofski
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Nicholas J. Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK
| | - Hugh Watkins
- Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - H.-Erich Wichmann
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
- Klinikum Grosshadern, Munich, Germany
| | - James F. Wilson
- Centre for Population Health Sciences, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Goncalo R. Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Themistocles L. Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- University of Cambridge Metabolic Research Labs, Institute of Metabolic Science Addenbrooke’s Hospital, CB2 OQQ, Cambridge, UK
| | - Michael Boehnke
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Ingrid B. Borecki
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Caroline S. Fox
- Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham Heart Study, Framingham, Massachusetts 01702, USA
| | - Timothy Frayling
- Genetics of Complex Traits, Peninsula College of Medicine and Dentistry, University of Exeter, Exeter, EX1 2LU, UK
| | - Leif C. Groop
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, 20502 Malmö, Sweden
| | - Talin Haritunian
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Iris M. Heid
- Public Health and Gender Studies, Institute of Epidemiology and Preventive Medicine, Regensburg University Medical Center, Regensburg, Germany
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - David Hunter
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Robert C. Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LJ, UK
- Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Old Road Headington, Oxford, OX3 7LJ, UK
| | - Miriam Moffatt
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Jeffrey R. O’Connell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, One Gustave L. Levy Place, Box 1498, New York, NY 10029-6574 USA
- Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, One Gustave L. Levy Place, Box 1498, New York, NY 10029-6574 USA
| | - David Schlessinger
- Laboratory of Genetics, National Institute on Aging, Baltimore, Maryland 21224, USA
| | | | - David P. Strachan
- Division of Population Health Sciences and Education, St George’s, University of London, London, SW17 0RE, UK
| | - Unnur Thorsteinsdottir
- deCODE Genetics, 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavík, Iceland
| | - Cornelia M. van Duijn
- Department of Epidemiology, Erasmus MC, Rotterdam, 3015GE, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA)
- Center of Medical Systems Biology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Peter M. Visscher
- The Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
- University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4102, Australia
| | | | - Joel N. Hirschhorn
- Divisions of Genetics and Endocrinology and Center for Basic and Translational Obesity Research, Children’s Hospital, Boston, Massachusetts 02115, USA
- Metabolism Initiative and Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Cecilia M. Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Andrew P. Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - David Meyre
- University Lille Nord de France, 59000 Lille, France
- CNRS UMR8199-IBL-Institut Pasteur de Lille, F-59000 Lille, France
- Department of Clinical Epidemiology and Biostatistics, McMasterUniversity, Hamilton, Ontario L8S 4L8, Canada
| | - André Scherag
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LJ, UK
- Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Old Road Headington, Oxford, OX3 7LJ, UK
| | - Elizabeth K. Speliotes
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kari E. North
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
| | - Ruth J.F. Loos
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK
- The Charles Bronfman Institute of Personalized Medicine, Mount Sinai School of Medicine, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
- Department of Preventive Medicine, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology, Uppsala University, Uppsala, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
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Fakiola M, Strange A, Cordell HJ, Miller EN, Pirinen M, Su Z, Mishra A, Mehrotra S, Monteiro GR, Band G, Bellenguez C, Dronov S, Edkins S, Freeman C, Giannoulatou E, Gray E, Hunt SE, Lacerda HG, Langford C, Pearson R, Pontes NN, Rai M, Singh SP, Smith L, Sousa O, Vukcevic D, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski J, Markus HS, Mathew CG, Palmer CNA, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Wilson ME, Deloukas P, Peltonen L, Christiansen F, Witt C, Jeronimo SMB, Sundar S, Spencer CCA, Blackwell JM, Donnelly P. Common variants in the HLA-DRB1-HLA-DQA1 HLA class II region are associated with susceptibility to visceral leishmaniasis. Nat Genet 2013; 45:208-13. [PMID: 23291585 PMCID: PMC3664012 DOI: 10.1038/ng.2518] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [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: 08/23/2012] [Accepted: 12/06/2012] [Indexed: 12/18/2022]
Abstract
To identify susceptibility loci for visceral leishmaniasis, we undertook genome-wide association studies in two populations: 989 cases and 1,089 controls from India and 357 cases in 308 Brazilian families (1,970 individuals). The HLA-DRB1-HLA-DQA1 locus was the only region to show strong evidence of association in both populations. Replication at this region was undertaken in a second Indian population comprising 941 cases and 990 controls, and combined analysis across the three cohorts for rs9271858 at this locus showed P(combined) = 2.76 × 10(-17) and odds ratio (OR) = 1.41, 95% confidence interval (CI) = 1.30-1.52. A conditional analysis provided evidence for multiple associations within the HLA-DRB1-HLA-DQA1 region, and a model in which risk differed between three groups of haplotypes better explained the signal and was significant in the Indian discovery and replication cohorts. In conclusion, the HLA-DRB1-HLA-DQA1 HLA class II region contributes to visceral leishmaniasis susceptibility in India and Brazil, suggesting shared genetic risk factors for visceral leishmaniasis that cross the epidemiological divides of geography and parasite species.
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Affiliation(s)
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- Cambridge Institute for Medical Research, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
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Deloukas P, Kanoni S, Willenborg C, Farrall M, Assimes TL, Thompson JR, Ingelsson E, Saleheen D, Erdmann J, Goldstein BA, Stirrups K, König IR, Cazier JB, Johansson A, Hall AS, Lee JY, Willer CJ, Chambers JC, Esko T, Folkersen L, Goel A, Grundberg E, Havulinna AS, Ho WK, Hopewell JC, Eriksson N, Kleber ME, Kristiansson K, Lundmark P, Lyytikäinen LP, Rafelt S, Shungin D, Strawbridge RJ, Thorleifsson G, Tikkanen E, Van Zuydam N, Voight BF, Waite LL, Zhang W, Ziegler A, Absher D, Altshuler D, Balmforth AJ, Barroso I, Braund PS, Burgdorf C, Claudi-Boehm S, Cox D, Dimitriou M, Do R, Doney ASF, El Mokhtari N, Eriksson P, Fischer K, Fontanillas P, Franco-Cereceda A, Gigante B, Groop L, Gustafsson S, Hager J, Hallmans G, Han BG, Hunt SE, Kang HM, Illig T, Kessler T, Knowles JW, Kolovou G, Kuusisto J, Langenberg C, Langford C, Leander K, Lokki ML, Lundmark A, McCarthy MI, Meisinger C, Melander O, Mihailov E, Maouche S, Morris AD, Müller-Nurasyid M, Nikus K, Peden JF, Rayner NW, Rasheed A, Rosinger S, Rubin D, Rumpf MP, Schäfer A, Sivananthan M, Song C, Stewart AFR, Tan ST, Thorgeirsson G, van der Schoot CE, Wagner PJ, Wells GA, Wild PS, Yang TP, Amouyel P, Arveiler D, Basart H, Boehnke M, Boerwinkle E, Brambilla P, Cambien F, Cupples AL, de Faire U, Dehghan A, Diemert P, Epstein SE, Evans A, Ferrario MM, Ferrières J, Gauguier D, Go AS, Goodall AH, Gudnason V, Hazen SL, Holm H, Iribarren C, Jang Y, Kähönen M, Kee F, Kim HS, Klopp N, Koenig W, Kratzer W, Kuulasmaa K, Laakso M, Laaksonen R, Lee JY, Lind L, Ouwehand WH, Parish S, Park JE, Pedersen NL, Peters A, Quertermous T, Rader DJ, Salomaa V, Schadt E, Shah SH, Sinisalo J, Stark K, Stefansson K, Trégouët DA, Virtamo J, Wallentin L, Wareham N, Zimmermann ME, Nieminen MS, Hengstenberg C, Sandhu MS, Pastinen T, Syvänen AC, Hovingh GK, Dedoussis G, Franks PW, Lehtimäki T, Metspalu A, Zalloua PA, Siegbahn A, Schreiber S, Ripatti S, Blankenberg SS, Perola M, Clarke R, Boehm BO, O'Donnell C, Reilly MP, März W, Collins R, Kathiresan S, Hamsten A, Kooner JS, Thorsteinsdottir U, Danesh J, Palmer CNA, Roberts R, Watkins H, Schunkert H, Samani NJ. Large-scale association analysis identifies new risk loci for coronary artery disease. Nat Genet 2012. [PMID: 23202125 DOI: 10.1038/ng.2480] [Citation(s) in RCA: 1227] [Impact Index Per Article: 102.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Coronary artery disease (CAD) is the commonest cause of death. Here, we report an association analysis in 63,746 CAD cases and 130,681 controls identifying 15 loci reaching genome-wide significance, taking the number of susceptibility loci for CAD to 46, and a further 104 independent variants (r(2) < 0.2) strongly associated with CAD at a 5% false discovery rate (FDR). Together, these variants explain approximately 10.6% of CAD heritability. Of the 46 genome-wide significant lead SNPs, 12 show a significant association with a lipid trait, and 5 show a significant association with blood pressure, but none is significantly associated with diabetes. Network analysis with 233 candidate genes (loci at 10% FDR) generated 5 interaction networks comprising 85% of these putative genes involved in CAD. The four most significant pathways mapping to these networks are linked to lipid metabolism and inflammation, underscoring the causal role of these activities in the genetic etiology of CAD. Our study provides insights into the genetic basis of CAD and identifies key biological pathways.
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Eyre S, Bowes J, Diogo D, Lee A, Barton A, Martin P, Zhernakova A, Stahl E, Viatte S, McAllister K, Amos CI, Padyukov L, Toes REM, Huizinga TWJ, Wijmenga C, Trynka G, Franke L, Westra HJ, Alfredsson L, Hu X, Sandor C, de Bakker PIW, Davila S, Khor CC, Heng KK, Andrews R, Edkins S, Hunt SE, Langford C, Symmons D, Concannon P, Onengut-Gumuscu S, Rich SS, Deloukas P, Gonzalez-Gay MA, Rodriguez-Rodriguez L, Ärlsetig L, Martin J, Rantapää-Dahlqvist S, Plenge RM, Raychaudhuri S, Klareskog L, Gregersen PK, Worthington J. High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis. Nat Genet 2012; 44:1336-40. [PMID: 23143596 PMCID: PMC3605761 DOI: 10.1038/ng.2462] [Citation(s) in RCA: 458] [Impact Index Per Article: 38.2] [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: 05/10/2012] [Accepted: 10/10/2012] [Indexed: 12/17/2022]
Abstract
Using the Immunochip custom single nucleotide polymorphism (SNP) array, designed for dense genotyping of 186 genome wide association study (GWAS) confirmed loci we analysed 11,475 rheumatoid arthritis cases of European ancestry and 15,870 controls for 129,464 markers. The data were combined in meta-analysis with GWAS data from additional independent cases (n=2,363) and controls (n=17,872). We identified fourteen novel loci; nine were associated with rheumatoid arthritis overall and 5 specifically in anti-citrillunated peptide antibody positive disease, bringing the number of confirmed European ancestry rheumatoid arthritis loci to 46. We refined the peak of association to a single gene for 19 loci, identified secondary independent effects at six loci and association to low frequency variants (minor allele frequency <0.05) at 4 loci. Bioinformatic analysis of the data generated strong hypotheses for the causal SNP at seven loci. This study illustrates the advantages of dense SNP mapping analysis to inform subsequent functional investigations.
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Affiliation(s)
- Steve Eyre
- Arthritis Research UK Epidemiology Unit, Centre for Musculoskeletal Research, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
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Zeggini E, Panoutsopoulou K, Southam L, Rayner NW, Day-Williams AG, Lopes MC, Boraska V, Esko T, Evangelou E, Hoffman A, Houwing-Duistermaat JJ, Ingvarsson T, Jonsdottir I, Jonnson H, Kerkhof HJ, Kloppenburg M, Bos SD, Mangino M, Metrustry S, Slagboom PE, Thorleifsson G, Raine EVA, Ratnayake M, Ricketts M, Beazley C, Blackburn H, Bumpstead S, Elliott KS, Hunt SE, Potter SC, Shin SY, Yadav VK, Zhai G, Sherburn K, Dixon K, Arden E, Aslam N, Battley PK, Carluke I, Doherty S, Gordon A, Joseph J, Keen R, Koller NC, Mitchell S, O'Neill F, Paling E, Reed MR, Rivadeneira F, Swift D, Walker K, Watkins B, Wheeler M, Birrell F, Ioannidis JPA, Meulenbelt I, Metspalu A, Rai A, Salter D, Stefansson K, Stykarsdottir U, Uitterlinden AG, van Meurs JBJ, Chapman K, Deloukas P, Ollier WER, Wallis GA, Arden N, Carr A, Doherty M, McCaskie A, Willkinson JM, Ralston SH, Valdes AM, Spector TD, Loughlin J. Identification of new susceptibility loci for osteoarthritis (arcOGEN): a genome-wide association study. Lancet 2012; 380:815-23. [PMID: 22763110 PMCID: PMC3443899 DOI: 10.1016/s0140-6736(12)60681-3] [Citation(s) in RCA: 278] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Osteoarthritis is the most common form of arthritis worldwide and is a major cause of pain and disability in elderly people. The health economic burden of osteoarthritis is increasing commensurate with obesity prevalence and longevity. Osteoarthritis has a strong genetic component but the success of previous genetic studies has been restricted due to insufficient sample sizes and phenotype heterogeneity. METHODS We undertook a large genome-wide association study (GWAS) in 7410 unrelated and retrospectively and prospectively selected patients with severe osteoarthritis in the arcOGEN study, 80% of whom had undergone total joint replacement, and 11,009 unrelated controls from the UK. We replicated the most promising signals in an independent set of up to 7473 cases and 42,938 controls, from studies in Iceland, Estonia, the Netherlands, and the UK. All patients and controls were of European descent. FINDINGS We identified five genome-wide significant loci (binomial test p≤5·0×10(-8)) for association with osteoarthritis and three loci just below this threshold. The strongest association was on chromosome 3 with rs6976 (odds ratio 1·12 [95% CI 1·08-1·16]; p=7·24×10(-11)), which is in perfect linkage disequilibrium with rs11177. This SNP encodes a missense polymorphism within the nucleostemin-encoding gene GNL3. Levels of nucleostemin were raised in chondrocytes from patients with osteoarthritis in functional studies. Other significant loci were on chromosome 9 close to ASTN2, chromosome 6 between FILIP1 and SENP6, chromosome 12 close to KLHDC5 and PTHLH, and in another region of chromosome 12 close to CHST11. One of the signals close to genome-wide significance was within the FTO gene, which is involved in regulation of bodyweight-a strong risk factor for osteoarthritis. All risk variants were common in frequency and exerted small effects. INTERPRETATION Our findings provide insight into the genetics of arthritis and identify new pathways that might be amenable to future therapeutic intervention. FUNDING arcOGEN was funded by a special purpose grant from Arthritis Research UK.
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Morris AP, Voight BF, Teslovich TM, Ferreira T, Segrè AV, Steinthorsdottir V, Strawbridge RJ, Khan H, Grallert H, Mahajan A, Prokopenko I, Kang HM, Dina C, Esko T, Fraser RM, Kanoni S, Kumar A, Lagou V, Langenberg C, Luan J, Lindgren CM, Müller-Nurasyid M, Pechlivanis S, Rayner NW, Scott LJ, Wiltshire S, Yengo L, Kinnunen L, Rossin EJ, Raychaudhuri S, Johnson AD, Dimas AS, Loos RJF, Vedantam S, Chen H, Florez JC, Fox C, Liu CT, Rybin D, Couper DJ, Kao WHL, Li M, Cornelis MC, Kraft P, Sun Q, van Dam RM, Stringham HM, Chines PS, Fischer K, Fontanillas P, Holmen OL, Hunt SE, Jackson AU, Kong A, Lawrence R, Meyer J, Perry JRB, Platou CGP, Potter S, Rehnberg E, Robertson N, Sivapalaratnam S, Stančáková A, Stirrups K, Thorleifsson G, Tikkanen E, Wood AR, Almgren P, Atalay M, Benediktsson R, Bonnycastle LL, Burtt N, Carey J, Charpentier G, Crenshaw AT, Doney ASF, Dorkhan M, Edkins S, Emilsson V, Eury E, Forsen T, Gertow K, Gigante B, Grant GB, Groves CJ, Guiducci C, Herder C, Hreidarsson AB, Hui J, James A, Jonsson A, Rathmann W, Klopp N, Kravic J, Krjutškov K, Langford C, Leander K, Lindholm E, Lobbens S, Männistö S, Mirza G, Mühleisen TW, Musk B, Parkin M, Rallidis L, Saramies J, Sennblad B, Shah S, Sigurðsson G, Silveira A, Steinbach G, Thorand B, Trakalo J, Veglia F, Wennauer R, Winckler W, Zabaneh D, Campbell H, van Duijn C, Uitterlinden AG, Hofman A, Sijbrands E, Abecasis GR, Owen KR, Zeggini E, Trip MD, Forouhi NG, Syvänen AC, Eriksson JG, Peltonen L, Nöthen MM, Balkau B, Palmer CNA, Lyssenko V, Tuomi T, Isomaa B, Hunter DJ, Qi L, Shuldiner AR, Roden M, Barroso I, Wilsgaard T, Beilby J, Hovingh K, Price JF, Wilson JF, Rauramaa R, Lakka TA, Lind L, Dedoussis G, Njølstad I, Pedersen NL, Khaw KT, Wareham NJ, Keinanen-Kiukaanniemi SM, Saaristo TE, Korpi-Hyövälti E, Saltevo J, Laakso M, Kuusisto J, Metspalu A, Collins FS, Mohlke KL, Bergman RN, Tuomilehto J, Boehm BO, Gieger C, Hveem K, Cauchi S, Froguel P, Baldassarre D, Tremoli E, Humphries SE, Saleheen D, Danesh J, Ingelsson E, Ripatti S, Salomaa V, Erbel R, Jöckel KH, Moebus S, Peters A, Illig T, de Faire U, Hamsten A, Morris AD, Donnelly PJ, Frayling TM, Hattersley AT, Boerwinkle E, Melander O, Kathiresan S, Nilsson PM, Deloukas P, Thorsteinsdottir U, Groop LC, Stefansson K, Hu F, Pankow JS, Dupuis J, Meigs JB, Altshuler D, Boehnke M, McCarthy MI. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat Genet 2012; 44:981-90. [PMID: 22885922 PMCID: PMC3442244 DOI: 10.1038/ng.2383] [Citation(s) in RCA: 1413] [Impact Index Per Article: 117.8] [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: 01/23/2012] [Accepted: 07/11/2012] [Indexed: 11/09/2022]
Abstract
To extend understanding of the genetic architecture and molecular basis of type 2 diabetes (T2D), we conducted a meta-analysis of genetic variants on the Metabochip, including 34,840 cases and 114,981 controls, overwhelmingly of European descent. We identified ten previously unreported T2D susceptibility loci, including two showing sex-differentiated association. Genome-wide analyses of these data are consistent with a long tail of additional common variant loci explaining much of the variation in susceptibility to T2D. Exploration of the enlarged set of susceptibility loci implicates several processes, including CREBBP-related transcription, adipocytokine signaling and cell cycle regulation, in diabetes pathogenesis.
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Affiliation(s)
- Andrew P Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, UK.
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Evans DM, Spencer CCA, Pointon JJ, Su Z, Harvey D, Kochan G, Oppermann U, Opperman U, Dilthey A, Pirinen M, Stone MA, Appleton L, Moutsianas L, Moutsianis L, Leslie S, Wordsworth T, Kenna TJ, Karaderi T, Thomas GP, Ward MM, Weisman MH, Farrar C, Bradbury LA, Danoy P, Inman RD, Maksymowych W, Gladman D, Rahman P, Morgan A, Marzo-Ortega H, Bowness P, Gaffney K, Gaston JSH, Smith M, Bruges-Armas J, Couto AR, Sorrentino R, Paladini F, Ferreira MA, Xu H, Liu Y, Jiang L, Lopez-Larrea C, Díaz-Peña R, López-Vázquez A, Zayats T, Band G, Bellenguez C, Blackburn H, Blackwell JM, Bramon E, Bumpstead SJ, Casas JP, Corvin A, Craddock N, Deloukas P, Dronov S, Duncanson A, Edkins S, Freeman C, Gillman M, Gray E, Gwilliam R, Hammond N, Hunt SE, Jankowski J, Jayakumar A, Langford C, Liddle J, Markus HS, Mathew CG, McCann OT, McCarthy MI, Palmer CNA, Peltonen L, Plomin R, Potter SC, Rautanen A, Ravindrarajah R, Ricketts M, Samani N, Sawcer SJ, Strange A, Trembath RC, Viswanathan AC, Waller M, Weston P, Whittaker P, Widaa S, Wood NW, McVean G, Reveille JD, Wordsworth BP, Brown MA, Donnelly P. Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility. Nat Genet 2011; 43:761-7. [PMID: 21743469 PMCID: PMC3640413 DOI: 10.1038/ng.873] [Citation(s) in RCA: 648] [Impact Index Per Article: 49.8] [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: 12/21/2011] [Accepted: 06/03/2011] [Indexed: 02/07/2023]
Abstract
Ankylosing spondylitis is a common form of inflammatory arthritis predominantly affecting the spine and pelvis that occurs in approximately 5 out of 1,000 adults of European descent. Here we report the identification of three variants in the RUNX3, LTBR-TNFRSF1A and IL12B regions convincingly associated with ankylosing spondylitis (P < 5 × 10(-8) in the combined discovery and replication datasets) and a further four loci at PTGER4, TBKBP1, ANTXR2 and CARD9 that show strong association across all our datasets (P < 5 × 10(-6) overall, with support in each of the three datasets studied). We also show that polymorphisms of ERAP1, which encodes an endoplasmic reticulum aminopeptidase involved in peptide trimming before HLA class I presentation, only affect ankylosing spondylitis risk in HLA-B27-positive individuals. These findings provide strong evidence that HLA-B27 operates in ankylosing spondylitis through a mechanism involving aberrant processing of antigenic peptides.
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Affiliation(s)
- David M Evans
- Medical Research Council (MRC) Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol, UK
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Frank RAW, McRae AF, Pocklington AJ, van de Lagemaat LN, Navarro P, Croning MDR, Komiyama NH, Bradley SJ, Challiss RAJ, Armstrong JD, Finn RD, Malloy MP, MacLean AW, Harris SE, Starr JM, Bhaskar SS, Howard EK, Hunt SE, Coffey AJ, Ranganath V, Deloukas P, Rogers J, Muir WJ, Deary IJ, Blackwood DH, Visscher PM, Grant SGN. Clustered coding variants in the glutamate receptor complexes of individuals with schizophrenia and bipolar disorder. PLoS One 2011; 6:e19011. [PMID: 21559497 PMCID: PMC3084736 DOI: 10.1371/journal.pone.0019011] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [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: 10/15/2010] [Accepted: 03/21/2011] [Indexed: 01/03/2023] Open
Abstract
Current models of schizophrenia and bipolar disorder implicate multiple genes, however their biological relationships remain elusive. To test the genetic role of glutamate receptors and their interacting scaffold proteins, the exons of ten glutamatergic 'hub' genes in 1304 individuals were re-sequenced in case and control samples. No significant difference in the overall number of non-synonymous single nucleotide polymorphisms (nsSNPs) was observed between cases and controls. However, cluster analysis of nsSNPs identified two exons encoding the cysteine-rich domain and first transmembrane helix of GRM1 as a risk locus with five mutations highly enriched within these domains. A new splice variant lacking the transmembrane GPCR domain of GRM1 was discovered in the human brain and the GRM1 mutation cluster could perturb the regulation of this variant. The predicted effect on individuals harbouring multiple mutations distributed in their ten hub genes was also examined. Diseased individuals possessed an increased load of deleteriousness from multiple concurrent rare and common coding variants. Together, these data suggest a disease model in which the interplay of compound genetic coding variants, distributed among glutamate receptors and their interacting proteins, contribute to the pathogenesis of schizophrenia and bipolar disorders.
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Affiliation(s)
- René A. W. Frank
- Wellcome Trust Sanger Institute, Genome
Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Allan F. McRae
- Queensland Institute of Medical Research,
Royal Brisbane Hospital, Brisbane, Australia
| | | | | | - Pau Navarro
- MRC Human Genetics, Institute of Genetics and
Molecular Medicine, Western General Hospital, Edinburgh, United
Kingdom
| | - Mike D. R. Croning
- Wellcome Trust Sanger Institute, Genome
Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Noboru H. Komiyama
- Wellcome Trust Sanger Institute, Genome
Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Sophie J. Bradley
- Department of Cell Physiology and
Pharmacology, University of Leicester, Leicester, United Kingdom
| | - R. A. John Challiss
- Department of Cell Physiology and
Pharmacology, University of Leicester, Leicester, United Kingdom
| | | | - Robert D. Finn
- Wellcome Trust Sanger Institute, Genome
Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Mary P. Malloy
- Division of Psychiatry, University of
Edinburgh, Royal Edinburgh Hospital, Edinburgh, United Kingdom
| | - Alan W. MacLean
- Division of Psychiatry, University of
Edinburgh, Royal Edinburgh Hospital, Edinburgh, United Kingdom
| | - Sarah E. Harris
- Department of Psychology, Centre for Cognitive
Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United
Kingdom
| | - John M. Starr
- Department of Psychology, Centre for Cognitive
Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United
Kingdom
| | - Sanjeev S. Bhaskar
- Wellcome Trust Sanger Institute, Genome
Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Eleanor K. Howard
- Wellcome Trust Sanger Institute, Genome
Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Sarah E. Hunt
- Wellcome Trust Sanger Institute, Genome
Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Alison J. Coffey
- Wellcome Trust Sanger Institute, Genome
Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Venkatesh Ranganath
- Wellcome Trust Sanger Institute, Genome
Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Genome
Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Jane Rogers
- Wellcome Trust Sanger Institute, Genome
Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Walter J. Muir
- Division of Psychiatry, University of
Edinburgh, Royal Edinburgh Hospital, Edinburgh, United Kingdom
| | - Ian J. Deary
- Department of Psychology, Centre for Cognitive
Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United
Kingdom
| | - Douglas H. Blackwood
- Division of Psychiatry, University of
Edinburgh, Royal Edinburgh Hospital, Edinburgh, United Kingdom
| | - Peter M. Visscher
- Queensland Institute of Medical Research,
Royal Brisbane Hospital, Brisbane, Australia
| | - Seth G. N. Grant
- Wellcome Trust Sanger Institute, Genome
Campus, Hinxton, Cambridgeshire, United Kingdom
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Panoutsopoulou K, Southam L, Elliott KS, Wrayner N, Zhai G, Beazley C, Thorleifsson G, Arden NK, Carr A, Chapman K, Deloukas P, Doherty M, McCaskie A, Ollier WER, Ralston SH, Spector TD, Valdes AM, Wallis GA, Wilkinson JM, Arden E, Battley K, Blackburn H, Blanco FJ, Bumpstead S, Cupples LA, Day-Williams AG, Dixon K, Doherty SA, Esko T, Evangelou E, Felson D, Gomez-Reino JJ, Gonzalez A, Gordon A, Gwilliam R, Halldorsson BV, Hauksson VB, Hofman A, Hunt SE, Ioannidis JPA, Ingvarsson T, Jonsdottir I, Jonsson H, Keen R, Kerkhof HJM, Kloppenburg MG, Koller N, Lakenberg N, Lane NE, Lee AT, Metspalu A, Meulenbelt I, Nevitt MC, O'Neill F, Parimi N, Potter SC, Rego-Perez I, Riancho JA, Sherburn K, Slagboom PE, Stefansson K, Styrkarsdottir U, Sumillera M, Swift D, Thorsteinsdottir U, Tsezou A, Uitterlinden AG, van Meurs JBJ, Watkins B, Wheeler M, Mitchell S, Zhu Y, Zmuda JM, Zeggini E, Loughlin J. Insights into the genetic architecture of osteoarthritis from stage 1 of the arcOGEN study. Ann Rheum Dis 2010; 70:864-7. [PMID: 21177295 PMCID: PMC3070286 DOI: 10.1136/ard.2010.141473] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [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] [Indexed: 12/21/2022]
Abstract
Objectives The genetic aetiology of osteoarthritis has not yet been elucidated. To enable a well-powered genome-wide association study (GWAS) for osteoarthritis, the authors have formed the arcOGEN Consortium, a UK-wide collaborative effort aiming to scan genome-wide over 7500 osteoarthritis cases in a two-stage genome-wide association scan. Here the authors report the findings of the stage 1 interim analysis. Methods The authors have performed a genome-wide association scan for knee and hip osteoarthritis in 3177 cases and 4894 population-based controls from the UK. Replication of promising signals was carried out in silico in five further scans (44 449 individuals), and de novo in 14 534 independent samples, all of European descent. Results None of the association signals the authors identified reach genome-wide levels of statistical significance, therefore stressing the need for corroboration in sample sets of a larger size. Application of analytical approaches to examine the allelic architecture of disease to the stage 1 genome-wide association scan data suggests that osteoarthritis is a highly polygenic disease with multiple risk variants conferring small effects. Conclusions Identifying loci conferring susceptibility to osteoarthritis will require large-scale sample sizes and well-defined phenotypes to minimise heterogeneity.
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Saleheen D, Soranzo N, Rasheed A, Scharnagl H, Gwilliam R, Alexander M, Inouye M, Zaidi M, Potter S, Haycock P, Bumpstead S, Kaptoge S, Di Angelantonio E, Sarwar N, Hunt SE, Sheikh N, Shah N, Samuel M, Haider SR, Murtaza M, Thompson A, Gobin R, Butterworth A, Ahmad U, Hakeem A, Zaman KS, Kundi A, Yaqoob Z, Cheema LA, Qamar N, Faruqui A, Mallick NH, Azhar M, Samad A, Ishaq M, Rasheed SZ, Jooma R, Niazi JH, Gardezi AR, Memon NA, Ghaffar A, Rehman FU, Hoffmann MM, Renner W, Kleber ME, Grammer TB, Stephens J, Attwood A, Koch K, Hussain M, Kumar K, Saleem A, Kumar K, Daood MS, Gul AA, Abbas S, Zafar J, Shahid F, Bhatti SM, Ali SS, Muhammad F, Sagoo G, Bray S, McGinnis R, Dudbridge F, Winkelmann BR, Böehm B, Thompson S, Ouwehand W, März W, Frossard P, Danesh J, Deloukas P. Genetic Determinants of Major Blood Lipids in Pakistanis Compared With Europeans. ACTA ACUST UNITED AC 2010; 3:348-57. [DOI: 10.1161/circgenetics.109.906180] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background—
Evidence is sparse about the genetic determinants of major lipids in Pakistanis.
Methods and Results—
Variants (n=45 000) across 2000 genes were assessed in 3200 Pakistanis and compared with 2450 Germans using the same gene array and similar lipid assays. We also did a meta-analysis of selected lipid-related variants in Europeans. Pakistani genetic architecture was distinct from that of several ethnic groups represented in international reference samples. Forty-one variants at 14 loci were significantly associated with levels of HDL-C, triglyceride, or LDL-C. The most significant lipid-related variants identified among Pakistanis corresponded to genes previously shown to be relevant to Europeans, such as
CETP
associated with HDL-C levels (rs711752;
P
<10
−13
),
APOA5/ZNF259
(rs651821;
P
<10
−13
) and
GCKR
(rs1260326;
P
<10
−13
) with triglyceride levels; and
CELSR2
variants with LDL-C levels (rs646776;
P
<10
−9
). For Pakistanis, these 41 variants explained 6.2%, 7.1%, and 0.9% of the variation in HDL-C, triglyceride, and LDL-C, respectively. Compared with Europeans, the allele frequency of rs662799 in
APOA5
among Pakistanis was higher and its impact on triglyceride concentration was greater (
P
-value for difference <10
−4
).
Conclusions—
Several lipid-related genetic variants are common to Pakistanis and Europeans, though they explain only a modest proportion of population variation in lipid concentration. Allelic frequencies and effect sizes of lipid-related variants can differ between Pakistanis and Europeans.
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Affiliation(s)
- Danish Saleheen
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Nicole Soranzo
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Asif Rasheed
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Hubert Scharnagl
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Rhian Gwilliam
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Myriam Alexander
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Michael Inouye
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Moazzam Zaidi
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Simon Potter
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Philip Haycock
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Suzanna Bumpstead
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Stephen Kaptoge
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Emanuele Di Angelantonio
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Nadeem Sarwar
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Sarah E. Hunt
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Nasir Sheikh
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Nabi Shah
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Maria Samuel
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Shajjia Razi Haider
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Muhammed Murtaza
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Alexander Thompson
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Reeta Gobin
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Adam Butterworth
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Usman Ahmad
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Abdul Hakeem
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Khan Shah Zaman
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Assadullah Kundi
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Zia Yaqoob
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Liaquat Ali Cheema
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Nadeem Qamar
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Azhar Faruqui
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Nadeem Hayat Mallick
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Muhammad Azhar
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Abdus Samad
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Muhammad Ishaq
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Syed Zahed Rasheed
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Rashid Jooma
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Jawaid Hassan Niazi
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Ali Raza Gardezi
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Nazir Ahmed Memon
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Abdul Ghaffar
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Fazal-ur Rehman
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Michael Marcus Hoffmann
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Wilfried Renner
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Marcus E. Kleber
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Tanja B. Grammer
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Jonathon Stephens
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Anthony Attwood
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Kerstin Koch
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Mustafa Hussain
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Kishore Kumar
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Asim Saleem
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Kishwar Kumar
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Muhammad Salman Daood
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Aftab Alam Gul
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Shahid Abbas
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Junaid Zafar
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Faisal Shahid
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Shahzad Majeed Bhatti
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Syed Saadat Ali
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Fahim Muhammad
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Gurdeep Sagoo
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Sarah Bray
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Ralph McGinnis
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Frank Dudbridge
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Bernhard R. Winkelmann
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Bernhard Böehm
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Simon Thompson
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Willem Ouwehand
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Winfried März
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Philippe Frossard
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - John Danesh
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
| | - Panos Deloukas
- From the Center for Non-Communicable Diseases (D.S., A.F., M.Z., N.Shah, M.S., S.R.H., M.M., U.A., K.Kumar, A.H., M.H., A.S., Kishore Kumar, Kishwar Kumar, M.S.D., A.A.G., S.S., J.Z., F.S., S.M.B., S.S.A., S.M.B., S.S.Ali, M.F., P.F.) Karachi, Pakistan; Department of Public Health and Primary Care (D.S., M.A., P.H., S.K., E.D.A., N.Sarwar, N.Sheikh, A.T., R.G., A.B., J.D.), University of Cambridge, United Kingdom; Wellcome Trust Sanger Institute (N.S., R.G., M.I., S.P., S.B., P.D., S.E.H., R.G.),
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Abstract
Exercise is commonly recommended to counteract aging-related muscle weakness. While numerous exercise intervention studies on the elderly have been performed, few have included elite senior athletes, such as those who participate in the National Senior Games. The extent to which participation in highly competitive exercise affects muscle strength is unknown, as well as the extent to which such participation mitigates any aging-related strength losses. The purpose of this study was to examine isometric thigh muscle strength in selected athletes of the National Senior Games and healthy noncompetitive controls of similar age, as well as to investigate strength changes with aging in both groups. In all, 95 athletes of the Games and 72 healthy controls participated. Of the senior athletes, 43 were runners, 12 cyclists, and 40 swimmers. Three trials of isometric knee flexion and extension strength were collected using a load cell affixed to a custom-designed chair. Strength data were normalized to dual-energy x-ray absorptiometry-obtained lean mass of the leg. A 3-factor multivariate analysis of variance (group x gender x age group) was performed, which included both the extension and flexion variables (alpha = 0.05). Athletes exhibited 38% more extension strength and 66% more flexion strength than the controls (p < 0.001). Strength did not decrease with advancing age in either the athletes or the controls (p = 0.345). In conclusion, senior athletes who participate in highly competitive exercise have greater strength than healthy aged-matched individuals who do not. Neither group displayed the expected strength losses with aging. Our subject cohorts, however, were not typical of those over age 65 years because individuals with existing health conditions were excluded from the study.
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Affiliation(s)
- Jean L McCrory
- Department of Health and Physical Activity, School of Education, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
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Robertson RJ, Goss FL, Aaron DJ, Nagle EF, Gallagher M, Kane IR, Tessmer KA, Schafer MA, Hunt SE. Concurrent muscle hurt and perceived exertion of children during resistance exercise. Med Sci Sports Exerc 2009; 41:1146-54. [PMID: 19346971 DOI: 10.1249/mss.0b013e3181930321] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
PURPOSE Rating of muscle hurt (RMH) and RPE were concurrently measured for 10- to 14-yr-old females (n = 50) and males (n = 50) performing unilateral biceps curl (BC) and knee extension (KE) isotonic exercise. METHODS BC and KE exercises were counterbalanced within subjects. Three counterbalanced, 10 repetition sets (30%, 50%, and 70% one repetition maximum (1-RM)) were performed for both exercises. RMH and RPE were obtained for active muscles using the Children's OMNI-Hurt Scale and the Children's OMNI-Resistance Exercise Scale of Perceived Exertion, respectively. RESULTS For both females and males, RMH ranged across sets from 1.5 to 6.0 during BC and 3.2 to 6.7 during KE. RPE ranged from 3.4 to 8.3 during BC and 5.0 to 8.9 during KE. Ratings expressed as percent scores were lower (P < 0.01) for RMH than for RPE at the 30%, 50%, and 70% 1-RM during BC and KE for females and males. Regression coefficients for weight lifted as a function of RMH ranged from r = 0.67 to r = 0.87 (P < 0.01) for BC and KE. Correlations between RMH and RPE ranged from r = 0.19 to r = 0.82 across sets for both genders. CONCLUSIONS Female and male children can concurrently and differentially rate their perceived intensity of muscle hurt and exertion during upper and lower body resistance exercise using numerical category metrics (i.e., OMNI scales) having construct-specific pictorial and verbal descriptors.
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Affiliation(s)
- Robert J Robertson
- Center for Exercise and Health-Fitness Research, Department of Health and Physical Activity, University of Pittsburgh, Pittsburgh, PA 15261, USA.
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Hunt SE, Goss F, Robertson R, Greenspan SL, McCrory JL. The Relations Between Regional Bone Mineral Density And Body Composition In Older Athletes And Controls. Med Sci Sports Exerc 2009. [DOI: 10.1249/01.mss.0000353504.01600.0b] [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: 11/21/2022]
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Loos RJF, Lindgren CM, Li S, Wheeler E, Zhao JH, Prokopenko I, Inouye M, Freathy RM, Attwood AP, Beckmann JS, Berndt SI, Jacobs KB, Chanock SJ, Hayes RB, Bergmann S, Bennett AJ, Bingham SA, Bochud M, Brown M, Cauchi S, Connell JM, Cooper C, Smith GD, Day I, Dina C, De S, Dermitzakis ET, Doney ASF, Elliott KS, Elliott P, Evans DM, Sadaf Farooqi I, Froguel P, Ghori J, Groves CJ, Gwilliam R, Hadley D, Hall AS, Hattersley AT, Hebebrand J, Heid IM, Lamina C, Gieger C, Illig T, Meitinger T, Wichmann HE, Herrera B, Hinney A, Hunt SE, Jarvelin MR, Johnson T, Jolley JDM, Karpe F, Keniry A, Khaw KT, Luben RN, Mangino M, Marchini J, McArdle WL, McGinnis R, Meyre D, Munroe PB, Morris AD, Ness AR, Neville MJ, Nica AC, Ong KK, O'Rahilly S, Owen KR, Palmer CNA, Papadakis K, Potter S, Pouta A, Qi L, Randall JC, Rayner NW, Ring SM, Sandhu MS, Scherag A, Sims MA, Song K, Soranzo N, Speliotes EK, Syddall HE, Teichmann SA, Timpson NJ, Tobias JH, Uda M, Vogel CIG, Wallace C, Waterworth DM, Weedon MN, Willer CJ, Wraight, Yuan X, Zeggini E, Hirschhorn JN, Strachan DP, Ouwehand WH, Caulfield MJ, Samani NJ, Frayling TM, Vollenweider P, Waeber G, Mooser V, Deloukas P, McCarthy MI, Wareham NJ, Barroso I, Jacobs KB, Chanock SJ, Hayes RB, Lamina C, Gieger C, Illig T, Meitinger T, Wichmann HE, Kraft P, Hankinson SE, Hunter DJ, Hu FB, Lyon HN, Voight BF, Ridderstrale M, Groop L, Scheet P, Sanna S, Abecasis GR, Albai G, Nagaraja R, Schlessinger D, Jackson AU, Tuomilehto J, Collins FS, Boehnke M, Mohlke KL. Common variants near MC4R are associated with fat mass, weight and risk of obesity. Nat Genet 2008; 40:768-75. [PMID: 18454148 DOI: 10.1038/ng.140] [Citation(s) in RCA: 927] [Impact Index Per Article: 57.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Accepted: 02/19/2008] [Indexed: 01/15/2023]
Abstract
To identify common variants influencing body mass index (BMI), we analyzed genome-wide association data from 16,876 individuals of European descent. After previously reported variants in FTO, the strongest association signal (rs17782313, P = 2.9 x 10(-6)) mapped 188 kb downstream of MC4R (melanocortin-4 receptor), mutations of which are the leading cause of monogenic severe childhood-onset obesity. We confirmed the BMI association in 60,352 adults (per-allele effect = 0.05 Z-score units; P = 2.8 x 10(-15)) and 5,988 children aged 7-11 (0.13 Z-score units; P = 1.5 x 10(-8)). In case-control analyses (n = 10,583), the odds for severe childhood obesity reached 1.30 (P = 8.0 x 10(-11)). Furthermore, we observed overtransmission of the risk allele to obese offspring in 660 families (P (pedigree disequilibrium test average; PDT-avg) = 2.4 x 10(-4)). The SNP location and patterns of phenotypic associations are consistent with effects mediated through altered MC4R function. Our findings establish that common variants near MC4R influence fat mass, weight and obesity risk at the population level and reinforce the need for large-scale data integration to identify variants influencing continuous biomedical traits.
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Affiliation(s)
- Ruth J F Loos
- MRC Epidemiology Unit, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
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McCrory JL, Salacinski AJ, Hunt SE, Greenspan SL. Relationship Between Thigh Muscle Strength, Competitive Exercise, and BMD in Elderly Athletes and Controls. Med Sci Sports Exerc 2008. [DOI: 10.1249/01.mss.0000321564.34672.10] [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: 11/21/2022]
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Hunt SE. Age Related Differences in Regional Body Composition in Elite Competitive Older Athletes and Healthy Controls. Med Sci Sports Exerc 2008. [DOI: 10.1249/01.mss.0000321449.03936.f1] [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: 11/21/2022]
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McCrory JL, Salacinski AJ, Hunt SE, Greenspan SL. Isometric Thigh Muscle Strength in Elite Senior Athletes. Med Sci Sports Exerc 2007. [DOI: 10.1249/01.mss.0000273095.87200.47] [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: 11/21/2022]
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Hunt SE, DiAlesandro A, Lambright G, Williams D, Aaron D, Goss F, Robertson R. Predicted and Actual Leg Pain and Perceived Exertion During Cycle Exercise in Young Women. Med Sci Sports Exerc 2007. [DOI: 10.1249/01.mss.0000274926.75195.a1] [Citation(s) in RCA: 2] [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] [Indexed: 11/21/2022]
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Zeggini E, Damcott CM, Hanson RL, Karim MA, Rayner NW, Groves CJ, Baier LJ, Hale TC, Hattersley AT, Hitman GA, Hunt SE, Knowler WC, Mitchell BD, Ng MCY, O'Connell JR, Pollin TI, Vaxillaire M, Walker M, Wang X, Whittaker P, Xiang K, Kunsun X, Jia W, Chan JCN, Froguel P, Deloukas P, Shuldiner AR, Elbein SC, McCarthy MI. Variation within the gene encoding the upstream stimulatory factor 1 does not influence susceptibility to type 2 diabetes in samples from populations with replicated evidence of linkage to chromosome 1q. Diabetes 2006; 55:2541-8. [PMID: 16936202 DOI: 10.2337/db06-0088] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The gene encoding the transcription factor upstream stimulatory factor (USF)1 influences susceptibility to familial combined hyperlipidemia (FCHL) and triglyceride levels. Phenotypic overlap between FCHL and type 2 diabetes makes USF1 a compelling positional candidate for the widely replicated type 2 diabetes linkage signal on chromosome 1q. We typed 22 variants in the F11R/USF1 region (1 per 3 kb), including those previously implicated in FCHL-susceptibility (or proxies thereof) in 3,726 samples preferentially enriched for 1q linkage. We also examined glucose- and lipid-related continuous traits in an overlapping set of 1,215 subjects of European descent. There was no convincing evidence for association with type 2 diabetes in any of seven case-control comparisons, individually or combined. Family-based association analyses in 832 Pima subjects were similarly negative. At rs3737787 (the variant most strongly associated with FCHL), the combined odds ratio, per copy of the rarer A-allele, was 1.10 (95% CI 0.97-1.24, P = 0.13). In 124 Utah subjects, rs3737787 was significantly associated (P = 0.002) with triglyceride levels, but direction of this association was opposite to previous reports, and there was no corroboration in three other samples. These data exclude USF1 as a major contributor to type 2 diabetes susceptibility and the basis for the chromosome 1q linkage. They reveal only limited evidence for replication of USF1 effects on continuous metabolic traits.
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Affiliation(s)
- Eleftheria Zeggini
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LJ, UK
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