1
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Riba M, Sala C, Culhane AC, Flobak Å, Patocs A, Boye K, Plevova K, Pospíšilová Š, Gandolfi G, Morelli MJ, Bucci G, Edsjö A, Lassen U, Al-Shahrour F, Lopez-Bigas N, Hovland R, Cuppen E, Valencia A, Poirel HA, Rosenquist R, Scollen S, Arenas Marquez J, Belien J, De Nicolo A, De Maria R, Torrents D, Tonon G. The 1+Million Genomes Minimal Dataset for Cancer. Nat Genet 2024:10.1038/s41588-024-01721-x. [PMID: 38702538 DOI: 10.1038/s41588-024-01721-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2024]
Affiliation(s)
- Michela Riba
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Cinzia Sala
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Aedin C Culhane
- Limerick Digital Cancer Research Centre, Health Research Institute, School of Medicine, University of Limerick, Limerick, Ireland
| | - Åsmund Flobak
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- The Cancer Clinic, St. Olav's University Hospital, Trondheim, Norway
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Attila Patocs
- Department of Molecular Genetics and the National Tumour Biology Laboratory, National Institute of Oncology, Budapest, Hungary
- Department of Oncology Biobank, National Institute of Oncology, Budapest, Hungary
- Hereditary Tumours Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
| | - Kjetil Boye
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Karla Plevova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, Masaryk University and University Hospital, Brno, Czech Republic
- Department of Medical Genetics and Genomics, University Hospital and Faculty of Medicine, Brno, Czech Republic
| | - Šárka Pospíšilová
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, Masaryk University and University Hospital, Brno, Czech Republic
- Department of Medical Genetics and Genomics, University Hospital and Faculty of Medicine, Brno, Czech Republic
| | - Giorgia Gandolfi
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marco J Morelli
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Gabriele Bucci
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Anders Edsjö
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Ulrik Lassen
- Department of Oncology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Fátima Al-Shahrour
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Nuria Lopez-Bigas
- Institución Catalana de Investigación y Estudios Avanzados (ICREA), Barcelona, Spain
| | - Randi Hovland
- Section of Cancer Genomics Haukeland University Hospital, Bergen, Norway
| | - Edwin Cuppen
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, the Netherlands
- Hartwig Medical Foundation, Amsterdam, the Netherlands
| | - Alfonso Valencia
- Institución Catalana de Investigación y Estudios Avanzados (ICREA), Barcelona, Spain
| | | | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Serena Scollen
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Jeroen Belien
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Arcangela De Nicolo
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ruggero De Maria
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
- Fondazione Policlinico Universitario 'A. Gemelli' - Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - David Torrents
- Institución Catalana de Investigación y Estudios Avanzados (ICREA), Barcelona, Spain
| | - Giovanni Tonon
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Vita-Salute San Raffaele University, Milan, Italy.
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Pastorino R, Pezzullo AM, Osti T, Adany R, Borry P, Barnhoorn F, Fadil E, Kroese M, Metspalu A, Perez-Gomez B, Perola M, Quaggia D, Scollen S, Shabani M, Swartling Peterson S, van El C, Vicente A, Boccia S. The PROPHET project paves the way for personalized prevention in the future healthcare. Eur J Cancer Prev 2024:00008469-990000000-00127. [PMID: 38598497 DOI: 10.1097/cej.0000000000000873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Affiliation(s)
- Roberta Pastorino
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Angelo Maria Pezzullo
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Tommaso Osti
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Roza Adany
- ELKH DE Public Health Research Group, Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Pascal Borry
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Floris Barnhoorn
- European Public Health Association (EUPHA), Utrecht, Netherlands
| | - Eva Fadil
- G.A.C., Innovation Department., G.A.C. Group, Issy-les-Moulineaux, France
| | - Mark Kroese
- PHG Foundation, University of Cambridge, Cambridge, UK
| | | | - Beatriz Perez-Gomez
- Consortium for Biomedical Research in Epidemiology and Public Health
- Department of Epidemiology of Chronic Diseases, National Centre for Epidemiology, Carlos III Institute of Health, Madrid, Spain
| | - Markus Perola
- Genomics and Biomarkers Unit, Department of Health, National Institute for Health and Welfare (THL), Helsinki, Finland
| | | | | | - Mahsa Shabani
- Department of Criminology, Criminal Law and Social Law, University of Gent, Gent, Belgium
| | | | - Carla van El
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Clinical Genetics, Section Community Genetics, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Astrid Vicente
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal
| | - Stefania Boccia
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Woman and Child Health and Public Health-Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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3
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Nikolski M, Hovig E, Al-Shahrour F, Blomberg N, Scollen S, Valencia A, Saunders G. Roadmap for a European cancer data management and precision medicine infrastructure. Nat Cancer 2024; 5:367-372. [PMID: 38321342 DOI: 10.1038/s43018-023-00717-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Affiliation(s)
- Macha Nikolski
- University of Bordeaux, CNRS-IBGC, UMR 5095, Bordeaux, France.
- University of Bordeaux, Bordeaux Bioinformatics Center CBiB, Bordeaux, France.
| | - Eivind Hovig
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Fatima Al-Shahrour
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Serena Scollen
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alfonso Valencia
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Gary Saunders
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
- EATRIS-ERIC, Amsterdam, the Netherlands
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Rocca-Serra P, Gu W, Ioannidis V, Abbassi-Daloii T, Capella-Gutierrez S, Chandramouliswaran I, Splendiani A, Burdett T, Giessmann RT, Henderson D, Batista D, Emam I, Gadiya Y, Giovanni L, Willighagen E, Evelo C, Gray AJG, Gribbon P, Juty N, Welter D, Quast K, Peeters P, Plasterer T, Wood C, van der Horst E, Reilly D, van Vlijmen H, Scollen S, Lister A, Thurston M, Granell R, Sansone SA. The FAIR Cookbook - the essential resource for and by FAIR doers. Sci Data 2023; 10:292. [PMID: 37208467 PMCID: PMC10198982 DOI: 10.1038/s41597-023-02166-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/19/2023] [Indexed: 05/21/2023] Open
Abstract
The notion that data should be Findable, Accessible, Interoperable and Reusable, according to the FAIR Principles, has become a global norm for good data stewardship and a prerequisite for reproducibility. Nowadays, FAIR guides data policy actions and professional practices in the public and private sectors. Despite such global endorsements, however, the FAIR Principles are aspirational, remaining elusive at best, and intimidating at worst. To address the lack of practical guidance, and help with capability gaps, we developed the FAIR Cookbook, an open, online resource of hands-on recipes for "FAIR doers" in the Life Sciences. Created by researchers and data managers professionals in academia, (bio)pharmaceutical companies and information service industries, the FAIR Cookbook covers the key steps in a FAIRification journey, the levels and indicators of FAIRness, the maturity model, the technologies, the tools and the standards available, as well as the skills required, and the challenges to achieve and improve data FAIRness. Part of the ELIXIR ecosystem, and recommended by funders, the FAIR Cookbook is open to contributions of new recipes.
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Affiliation(s)
- Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX13QG, Oxford, UK.
- AstraZeneca, Data Office, Data Science & AI unit R&D, 136 Hills Rd, Cambridge, UK.
| | - Wei Gu
- Luxembourg Centre for Systems Biomedicine, ELIXIR Luxembourg, University of Luxembourg, L-4367, Belval, Luxembourg
- Luxembourg National Data Service, 6 Avenue des Hauts-Fourneaux, Esch-sur-Alzette, Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
| | - Vassilios Ioannidis
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Tooba Abbassi-Daloii
- Department of Bioinformatics (BiGCaT), NUTRIM, FHML, Maastricht University, Maastricht, the Netherlands
| | | | - Ishwar Chandramouliswaran
- Office of Data Science Strategy, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland, 20892, USA
| | | | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK
| | - Robert T Giessmann
- Bayer AG, Business Development & Licensing & OI, Pharmaceuticals, 13342, Berlin, Germany
- Institute for Globally Distributed Open Research and Education (IGDORE), Berlin, Germany
| | - David Henderson
- Bayer AG, Business Development & Licensing & OI, Pharmaceuticals, 13342, Berlin, Germany
| | - Dominique Batista
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX13QG, Oxford, UK
| | - Ibrahim Emam
- Data Science Institute, Imperial College London, William Penney Laboratory, South Kensington Campus, London, SW7 2AZ, UK
| | - Yojana Gadiya
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590, Frankfurt, Germany
| | - Lucas Giovanni
- Department of Bioinformatics (BiGCaT), NUTRIM, FHML, Maastricht University, Maastricht, the Netherlands
| | - Egon Willighagen
- Department of Bioinformatics (BiGCaT), NUTRIM, FHML, Maastricht University, Maastricht, the Netherlands
| | - Chris Evelo
- Department of Bioinformatics (BiGCaT), NUTRIM, FHML, Maastricht University, Maastricht, the Netherlands
| | - Alasdair J G Gray
- Department of Computer Science, Heriot-Watt University, Edinburgh, EH14 4AS, Scotland, UK
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590, Frankfurt, Germany
| | - Nick Juty
- The University of Manchester, Department of Computer Science, The University of Manchester, Manchester, M13 9PL, UK
| | - Danielle Welter
- Luxembourg Centre for Systems Biomedicine, ELIXIR Luxembourg, University of Luxembourg, L-4367, Belval, Luxembourg
- Luxembourg National Data Service, 6 Avenue des Hauts-Fourneaux, Esch-sur-Alzette, Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
| | - Karsten Quast
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach an der Riss, Germany
| | - Paul Peeters
- Janssen, Turnhoutseweg 30, B-2340, Beerse, Belgium
| | - Tom Plasterer
- AstraZeneca Pharmaceuticals, 36 Gatehouse Drive, Waltham, MA, 02451, USA
| | - Colin Wood
- AstraZeneca, da Vinci Building, Melbourn Science Park, Cambridge Road, Royston, SG8 6HM, UK
| | - Eelke van der Horst
- The Hyve BV, Arthur van Schendelstraat 650, 3511 MJ, Utrecht, The Netherlands
| | - Dorothy Reilly
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | | | - Serena Scollen
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Allyson Lister
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX13QG, Oxford, UK
| | - Milo Thurston
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX13QG, Oxford, UK
| | - Ramon Granell
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX13QG, Oxford, UK
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX13QG, Oxford, UK.
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Costa A, Merchant A, Lopes MF, Konopko M, Cardoso ML, Sitjà X, Bourbon M, Scollen S, Vicente A. Key issues for implementation of Genomics in Healthcare: a Policy Brief. Eur J Public Health 2022. [DOI: 10.1093/eurpub/ckac131.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Issue/problem
Healthcare (HC) can significantly benefit from genomic information for earlier, accurate diagnosis, effective personalized treatment with less adverse events, and accurate profiling of individuals for disease prevention. However, European countries are currently at variable maturity stages regarding the implementation of genomic medicine (GM) in healthcare, hindering the equitable delivery of personalized medicine to citizens across borders.
Description of the problem
The European 1+Million Genomes Initiative (1+MG) aims to provide cross-border access to quality genomic information and related clinical data, to advance data-driven research and HC solutions to benefit citizens. This initiative is encouraging countries to develop national GM strategies, but guidance for successful implementation is needed. In this context, the Beyond 1 Million Genomes, a supporting action to the 1+MG initiative, organized three Country Exchange Visits (CEV) to discuss critical issues, share experiences and best practices, for the implementation of sustainable GM strategies in healthcare.
Results
The United Kingdom, Estonia and Finland, which have advanced GM programs, hosted CEV describing progress and lessons learnt. Representatives of 1+MG signatory countries participated in these events and were able to present country level progress. The resulting Policy Brief (PB) captures key issues discussed at the CEVs, with real-life examples, and proposes policy recommendations for the successful implementation of GM in European healthcare systems.
Lessons
Sustainable GM implementation in HC systems requires: 1) Patient and citizens trust and engagement; 2) Sustainable infrastructure and data regulation, with solid ethical and legal frameworks; 3) Capacity building of healthcare professionals; 4) A strong ecosystem involving all stakeholders, and encouraging synergies between healthcare, research and industry to promote continuous innovation.
Key messages
• The implementation of GM in healthcare will take countries further towards making personalized medicine a reality, with remarkable health and socioeconomic benefits for patients and healthcare systems.
• Promoting cooperation, capacity building and sharing of best practices is crucial to reduce asymmetries between countries, which constrains effective and equitable cross-border personalized medicine.
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Affiliation(s)
- A Costa
- Department of Health Promotion and NCD Prevention, National Institute of Health Doutor Ricardo Jorge , Lisbon, Portugal
- Institute of Social and Political Sciences, University of Lisbon , Lisbon, Portugal
| | - A Merchant
- ELIXIR Hub, Wellcome Genome Campus , Cambridge, UK
| | - MF Lopes
- Department of Health Promotion and NCD Prevention, National Institute of Health Doutor Ricardo Jorge , Lisbon, Portugal
| | - M Konopko
- ELIXIR Hub, Wellcome Genome Campus , Cambridge, UK
| | - ML Cardoso
- Department of Health Promotion and NCD Prevention, National Institute of Health Doutor Ricardo Jorge , Lisbon, Portugal
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon , Lisbon, Portugal
| | - X Sitjà
- ELIXIR Hub, Wellcome Genome Campus , Cambridge, UK
| | - M Bourbon
- Department of Health Promotion and NCD Prevention, National Institute of Health Doutor Ricardo Jorge , Lisbon, Portugal
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon , Lisbon, Portugal
| | - S Scollen
- ELIXIR Hub, Wellcome Genome Campus , Cambridge, UK
| | - A Vicente
- Department of Health Promotion and NCD Prevention, National Institute of Health Doutor Ricardo Jorge , Lisbon, Portugal
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon , Lisbon, Portugal
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Oldoni E, Saunders G, Bietrix F, Garcia Bermejo ML, Niehues A, ’t Hoen PAC, Nordlund J, Hajduch M, Scherer A, Kivinen K, Pitkänen E, Mäkela TP, Gut I, Scollen S, Kozera Ł, Esteller M, Shi L, Ussi A, Andreu AL, van Gool AJ. Tackling the translational challenges of multi-omics research in the realm of European personalised medicine: A workshop report. Front Mol Biosci 2022; 9:974799. [PMID: 36310597 PMCID: PMC9608444 DOI: 10.3389/fmolb.2022.974799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Personalised medicine (PM) presents a great opportunity to improve the future of individualised healthcare. Recent advances in -omics technologies have led to unprecedented efforts characterising the biology and molecular mechanisms that underlie the development and progression of a wide array of complex human diseases, supporting further development of PM. This article reflects the outcome of the 2021 EATRIS-Plus Multi-omics Stakeholder Group workshop organised to 1) outline a global overview of common promises and challenges that key European stakeholders are facing in the field of multi-omics research, 2) assess the potential of new technologies, such as artificial intelligence (AI), and 3) establish an initial dialogue between key initiatives in this space. Our focus is on the alignment of agendas of European initiatives in multi-omics research and the centrality of patients in designing solutions that have the potential to advance PM in long-term healthcare strategies.
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Affiliation(s)
- Emanuela Oldoni
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
- *Correspondence: Gary Saunders, ; Emanuela Oldoni,
| | - Gary Saunders
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
- *Correspondence: Gary Saunders, ; Emanuela Oldoni,
| | - Florence Bietrix
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
| | - Maria Laura Garcia Bermejo
- Biomarkers and Therapeutic Targets Group, Ramon and Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Anna Niehues
- Translational Metabolomic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Peter A. C. ’t Hoen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Precision Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Olomouc, Czechia
| | - Andreas Scherer
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Katja Kivinen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Esa Pitkänen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Tomi Pekka Mäkela
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | - Łukasz Kozera
- Biobanking and BioMolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC), Graz, Austria
| | - Manel Esteller
- Josep Carreras Leukemia Research Institute (IJC), Badalona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Anton Ussi
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
| | - Antonio L. Andreu
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
| | - Alain J. van Gool
- Translational Metabolomic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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7
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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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8
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Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, Heringa J, Holub P, Hooyberghs J, Juty N, Keane TM, Korbel JO, Lappalainen I, Leskosek B, Matthijs G, Mayrhofer MT, Metspalu A, Navarro A, Newhouse S, Nyrönen T, Page A, Persson B, Palotie A, Parkinson H, Rambla J, Salgado D, Steinfelder E, Swertz MA, Valencia A, Varma S, Blomberg N, Scollen S. Leveraging European infrastructures to access 1 million human genomes by 2022. Nat Rev Genet 2019; 20:693-701. [PMID: 31455890 PMCID: PMC7115898 DOI: 10.1038/s41576-019-0156-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [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] [Accepted: 07/03/2019] [Indexed: 01/22/2023]
Abstract
Human genomics is undergoing a step change from being a predominantly research-driven activity to one driven through health care as many countries in Europe now have nascent precision medicine programmes. To maximize the value of the genomic data generated, these data will need to be shared between institutions and across countries. In recognition of this challenge, 21 European countries recently signed a declaration to transnationally share data on at least 1 million human genomes by 2022. In this Roadmap, we identify the challenges of data sharing across borders and demonstrate that European research infrastructures are well-positioned to support the rapid implementation of widespread genomic data access.
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Affiliation(s)
- Gary Saunders
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Regina Becker
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, Luxembourg
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Christophe Béroud
- Aix Marseille Univ, INSERM, MMG, Marseille, France
- Département de Génétique Médicale et de Biologie Cellulaire, APHM, Hôpital d'Enfants de la Timone, Marseille, France
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Cath Brooksbank
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Søren Brunak
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Peter Goodhand
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jaap Heringa
- Department of Computer Science, Vrije Universiteit, Amsterdam, Netherlands
| | | | - Jef Hooyberghs
- Flemish Institute for Technological Research, VITO, Mol, Belgium
| | - Nick Juty
- School of Computer Science, The University of Manchester, Manchester, UK
| | - Thomas M Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | | | - Brane Leskosek
- IBMI, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | | | | | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Steven Newhouse
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Angela Page
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bengt Persson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala, Sweden
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jordi Rambla
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | | | - Morris A Swertz
- BBMRI-NL/University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Alfonso Valencia
- Barcelona Supercomputing Centre (BSC), Barcelona, Spain
- ICREA, Pg., Barcelona, Spain
| | - Susheel Varma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Serena Scollen
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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9
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Fiume M, Cupak M, Keenan S, Rambla J, de la Torre S, Dyke SOM, Brookes AJ, Carey K, Lloyd D, Goodhand P, Haeussler M, Baudis M, Stockinger H, Dolman L, Lappalainen I, Törnroos J, Linden M, Spalding JD, Ur-Rehman S, Page A, Flicek P, Sherry S, Haussler D, Varma S, Saunders G, Scollen S. Publisher Correction: Federated discovery and sharing of genomic data using Beacons. Nat Biotechnol 2019; 37:480. [PMID: 30894680 PMCID: PMC7608460 DOI: 10.1038/s41587-019-0094-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Stephen Keenan
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | | | - Stephanie O M Dyke
- Centre of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | | | - David Lloyd
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Peter Goodhand
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Michael Baudis
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Lena Dolman
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Ilkka Lappalainen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,CSC - IT Center for Science Ltd, Espoo, Finland
| | | | | | - J Dylan Spalding
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Saif Ur-Rehman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Angela Page
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Stephen Sherry
- National Center for Biotechnology Information, US National Library of Medicine, Bethesda, MD, USA
| | - David Haussler
- Genomics Institute, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Susheel Varma
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Gary Saunders
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Serena Scollen
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
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10
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Dyke SOM, Linden M, Lappalainen I, De Argila JR, Carey K, Lloyd D, Spalding JD, Cabili MN, Kerry G, Foreman J, Cutts T, Shabani M, Rodriguez LL, Haeussler M, Walsh B, Jiang X, Wang S, Perrett D, Boughtwood T, Matern A, Brookes AJ, Cupak M, Fiume M, Pandya R, Tulchinsky I, Scollen S, Törnroos J, Das S, Evans AC, Malin BA, Beck S, Brenner SE, Nyrönen T, Blomberg N, Firth HV, Hurles M, Philippakis AA, Rätsch G, Brudno M, Boycott KM, Rehm HL, Baudis M, Sherry ST, Kato K, Knoppers BM, Baker D, Flicek P. Registered access: authorizing data access. Eur J Hum Genet 2018; 26:1721-1731. [PMID: 30069064 PMCID: PMC6244209 DOI: 10.1038/s41431-018-0219-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 02/26/2018] [Revised: 05/08/2018] [Accepted: 06/20/2018] [Indexed: 12/14/2022] Open
Abstract
The Global Alliance for Genomics and Health (GA4GH) proposes a data access policy model-"registered access"-to increase and improve access to data requiring an agreement to basic terms and conditions, such as the use of DNA sequence and health data in research. A registered access policy would enable a range of categories of users to gain access, starting with researchers and clinical care professionals. It would also facilitate general use and reuse of data but within the bounds of consent restrictions and other ethical obligations. In piloting registered access with the Scientific Demonstration data sharing projects of GA4GH, we provide additional ethics, policy and technical guidance to facilitate the implementation of this access model in an international setting.
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Affiliation(s)
- Stephanie O M Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, QC, Canada.
- Montreal Neurological Institute, Faculty of Medicine, McGill University, Montreal, QC, Canada.
| | - Mikael Linden
- CSC - IT Center for Science, Espoo, Finland
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ilkka Lappalainen
- CSC - IT Center for Science, Espoo, Finland
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Jordi Rambla De Argila
- Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | | | - David Lloyd
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
- The Global Alliance for Genomics and Health, MaRS Centre, West Tower, 661 University Avenue, Suite 510, Toronto, M5G 0A3, ON, Canada
| | - J Dylan Spalding
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | | | - Giselle Kerry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Julia Foreman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tim Cutts
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mahsa Shabani
- Center for Biomedical Ethics and Law, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
| | | | | | | | - Xiaoqian Jiang
- Department of Biomedical Informatics, UC San Diego, La Jolla, CA, USA
| | - Shuang Wang
- Department of Biomedical Informatics, UC San Diego, La Jolla, CA, USA
| | - Daniel Perrett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tiffany Boughtwood
- Australian Genomics Health Alliance, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | | | - Anthony J Brookes
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | | | | | | | - Serena Scollen
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Samir Das
- McGill Centre for Integrative Neurosciences, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Alan C Evans
- McGill Centre for Integrative Neurosciences, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | | | - Stephan Beck
- UCL Cancer Institute, University College London, London, UK
| | - Steven E Brenner
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, USA
| | - Tommi Nyrönen
- CSC - IT Center for Science, Espoo, Finland
- ELIXIR Compute Platform, ELIXIR, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Matthew Hurles
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Gunnar Rätsch
- Department of Computer Science, Biomedical Informatics, ETH Zurich, Zurich, Switzerland
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Brigham & Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Michael Baudis
- University of Zurich & Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Stephen T Sherry
- National Centre for Biotechnology Information, US National Library of Medicine, Bethesda, MD, USA
| | - Kazuto Kato
- Department of Biomedical Ethics and Public Policy, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Dixie Baker
- Martin, Blanck & Associates, Alexandria, VA, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
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11
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Scollen S, Page A, Wilson J. From the Data on Many, Precision Medicine for "One": The Case for Widespread Genomic Data Sharing. Biomed Hub 2017; 2:104-110. [PMID: 31988941 PMCID: PMC6945905 DOI: 10.1159/000481682] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 11/26/2022] Open
Abstract
Within the decade, genome sequencing promises to become a routine part of healthcare around the globe. Many millions of genomes linked to health records will soon be available for researchers and clinicians to make use of to advance precision medicine. To realise the full impact of genomic medicine, genomic and clinical data must be interoperable across traditional geographic, jurisdictional, sectoral, and domain boundaries. Extremely large and diverse data sets are needed to provide a context for interpretation of genetic sequences. No single country or institution can achieve the necessary scale and diversity alone. Data must be shared within an internationally federated, learning health system.
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Affiliation(s)
- Serena Scollen
- ELIXIR Hub, Cambridge, UK.,Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - Angela Page
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - Julia Wilson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Global Alliance for Genomics and Health, Toronto, ON, Canada
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12
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Zhang C, Bijlard J, Staiger C, Scollen S, van Enckevort D, Hoogstrate Y, Senf A, Hiltemann S, Repo S, Pipping W, Bierkens M, Payralbe S, Stringer B, Heringa J, Stubbs A, Bonino Da Silva Santos LO, Belien J, Weistra W, Azevedo R, van Bochove K, Meijer G, Boiten JW, Rambla J, Fijneman R, Spalding JD, Abeln S. Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data. F1000Res 2017; 6. [PMID: 29123641 PMCID: PMC5657030 DOI: 10.12688/f1000research.12168.1] [Citation(s) in RCA: 7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/14/2017] [Indexed: 01/11/2023] Open
Abstract
The availability of high-throughput molecular profiling techniques has provided more accurate and informative data for regular clinical studies. Nevertheless, complex computational workflows are required to interpret these data. Over the past years, the data volume has been growing explosively, requiring robust human data management to organise and integrate the data efficiently. For this reason, we set up an ELIXIR implementation study, together with the Translational research IT (TraIT) programme, to design a data ecosystem that is able to link raw and interpreted data. In this project, the data from the TraIT Cell Line Use Case (TraIT-CLUC) are used as a test case for this system. Within this ecosystem, we use the European Genome-phenome Archive (EGA) to store raw molecular profiling data; tranSMART to collect interpreted molecular profiling data and clinical data for corresponding samples; and Galaxy to store, run and manage the computational workflows. We can integrate these data by linking their repositories systematically. To showcase our design, we have structured the TraIT-CLUC data, which contain a variety of molecular profiling data types, for storage in both tranSMART and EGA. The metadata provided allows referencing between tranSMART and EGA, fulfilling the cycle of data submission and discovery; we have also designed a data flow from EGA to Galaxy, enabling reanalysis of the raw data in Galaxy. In this way, users can select patient cohorts in tranSMART, trace them back to the raw data and perform (re)analysis in Galaxy. Our conclusion is that the majority of metadata does not necessarily need to be stored (redundantly) in both databases, but that instead FAIR persistent identifiers should be available for well-defined data ontology levels: study, data access committee, physical sample, data sample and raw data file. This approach will pave the way for the stable linkage and reuse of data.
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Affiliation(s)
- Chao Zhang
- Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, Netherlands
| | - Jochem Bijlard
- Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, Netherlands.,The Hyve, Utrecht, 3511 MJ, Netherlands
| | | | | | - David van Enckevort
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, 9712 CP, Netherlands
| | - Youri Hoogstrate
- Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, 3015 CE, Netherlands
| | | | - Saskia Hiltemann
- Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, 3015 CE, Netherlands
| | | | | | | | | | - Bas Stringer
- Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, Netherlands
| | - Jaap Heringa
- Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, Netherlands
| | - Andrew Stubbs
- Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, 3015 CE, Netherlands
| | | | - Jeroen Belien
- Department of Pathology, VU University Medical Center Amsterdam, Amsterdam, 1081 HV, Netherlands
| | | | | | | | - Gerrit Meijer
- Netherlands Cancer Institute, Amsterdam, 1066 CX, Netherlands
| | | | - Jordi Rambla
- Centre for Genomic Regulation (CRG), Barcelona, 08003, Spain
| | - Remond Fijneman
- Netherlands Cancer Institute, Amsterdam, 1066 CX, Netherlands
| | | | - Sanne Abeln
- Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, Netherlands
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13
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Jones AV, Tilley M, Gutteridge A, Hyde C, Nagle M, Ziemek D, Gorman D, Fauman EB, Chen X, Miller MR, Tian C, Hu Y, Hinds DA, Cox P, Scollen S. GWAS of self-reported mosquito bite size, itch intensity and attractiveness to mosquitoes implicates immune-related predisposition loci. Hum Mol Genet 2017; 26:1391-1406. [PMID: 28199695 PMCID: PMC5390679 DOI: 10.1093/hmg/ddx036] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/23/2017] [Indexed: 12/31/2022] Open
Abstract
Understanding the interaction between humans and mosquitoes is a critical area of study due to the phenomenal burdens on public health from mosquito-transmitted diseases. In this study, we conducted the first genome-wide association studies (GWAS) of self-reported mosquito bite reaction size (n = 84,724), itchiness caused by bites (n = 69,057), and perceived attractiveness to mosquitoes (n = 16,576). In total, 15 independent significant (P < 5×10−8) associations were identified. These loci were enriched for immunity-related genes that are involved in multiple cytokine signalling pathways. We also detected suggestive enrichment of these loci in enhancer regions that are active in stimulated T-cells, as well as within loci previously identified as controlling central memory T-cell levels. Egger regression analysis between the traits suggests that perception of itchiness and attractiveness to mosquitoes is driven, at least in part, by the genetic determinants of bite reaction size. Our findings illustrate the complex genetic and immunological landscapes underpinning human interactions with mosquitoes.
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Affiliation(s)
- Amy V. Jones
- Pfizer WRD, Human Genetics and Computational Biomedicine, The Portway Building, Granta Park, Cambridge CB21 6GS, UK
| | - Mera Tilley
- Pfizer WRD, Pharmatherapeutics Clinical R&D, Precision Medicine, 300 Technology Square Fl #3, Cambridge, MA 02139, USA
| | - Alex Gutteridge
- Pfizer WRD, Computational Sciences CoE, The Portway Building, Granta Park, Cambridge CB21 6GS, UK
| | - Craig Hyde
- Pfizer WRD, Research Statistics, 558 Eastern Point Rd, Groton, CT 06340, USA
| | - Michael Nagle
- Pfizer WRD, Human Genetics and Computational Biomedicine, 610 Main Street S, Cambridge, MA 02139, USA
| | - Daniel Ziemek
- Pfizer WRD, Computational Sciences CoE, Linkstraße 10, 10785 Berlin, Germany
| | - Donal Gorman
- Pfizer WRD, Research Statistics, The Portway Building, Granta Park, Cambridge CB21 6GS, UK
| | - Eric B. Fauman
- Pfizer WRD, Computational Sciences CoE, 610 Main Street S, Cambridge, MA 02139, USA
| | - Xing Chen
- Pfizer WRD, Research Statistics, 558 Eastern Point Rd, Groton, CT 06340, USA
| | - Melissa R. Miller
- Pfizer WRD, Human Genetics and Computational Biomedicine, 610 Main Street S, Cambridge, MA 02139, USA
| | - Chao Tian
- 23andMe, Inc, 899 W Evelyn Avenue, Mountain View, California, CA 94043, USA
| | - Youna Hu
- 23andMe, Inc, 899 W Evelyn Avenue, Mountain View, California, CA 94043, USA
| | - David A. Hinds
- 23andMe, Inc, 899 W Evelyn Avenue, Mountain View, California, CA 94043, USA
| | - Peter Cox
- Pfizer Ltd, Neuroscience and Pain Research Unit, The Portway Building, Granta Park, Cambridge CB21 6GS, UK
| | - Serena Scollen
- Pfizer WRD, Human Genetics and Computational Biomedicine, The Portway Building, Granta Park, Cambridge CB21 6GS, UK
- To whom correspondence should be addressed at: ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Tel: +44 1223494322; Fax: +44 (0)1223 484696;
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14
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McIntosh AM, Hall LS, Zeng Y, Adams MJ, Gibson J, Wigmore E, Hagenaars SP, Davies G, Fernandez-Pujals AM, Campbell AI, Clarke TK, Hayward C, Haley CS, Porteous DJ, Deary IJ, Smith DJ, Nicholl BI, Hinds DA, Jones AV, Scollen S, Meng W, Smith BH, Hocking LJ. Genetic and Environmental Risk for Chronic Pain and the Contribution of Risk Variants for Major Depressive Disorder: A Family-Based Mixed-Model Analysis. PLoS Med 2016; 13:e1002090. [PMID: 27529168 PMCID: PMC4987025 DOI: 10.1371/journal.pmed.1002090] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 06/13/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Chronic pain is highly prevalent and a significant source of disability, yet its genetic and environmental risk factors are poorly understood. Its relationship with major depressive disorder (MDD) is of particular importance. We sought to test the contribution of genetic factors and shared and unique environment to risk of chronic pain and its correlation with MDD in Generation Scotland: Scottish Family Health Study (GS:SFHS). We then sought to replicate any significant findings in the United Kingdom Biobank study. METHODS AND FINDINGS Using family-based mixed-model analyses, we examined the contribution of genetics and shared family environment to chronic pain by spouse, sibling, and household relationships. These analyses were conducted in GS:SFHS (n = 23,960), a family- and population-based study of individuals recruited from the Scottish population through their general practitioners. We then examined and partitioned the correlation between chronic pain and MDD and estimated the contribution of genetic factors and shared environment in GS:SFHS. Finally, we used data from two independent genome-wide association studies to test whether chronic pain has a polygenic architecture and examine whether genomic risk of psychiatric disorder predicted chronic pain and whether genomic risk of chronic pain predicted MDD. These analyses were conducted in GS:SFHS and repeated in UK Biobank, a study of 500,000 from the UK population, of whom 112,151 had genotyping and phenotypic data. Chronic pain is a moderately heritable trait (heritability = 38.4%, 95% CI 33.6% to 43.9%) that is significantly concordant in spouses (variance explained 18.7%, 95% CI 9.5% to 25.1%). Chronic pain is positively correlated with depression (ρ = 0.13, 95% CI 0.11 to 0.15, p = 2.72x10-68) and shows a tendency to cluster within families for genetic reasons (genetic correlation = 0.51, 95%CI 0.40 to 0.62, p = 8.24x10-19). Polygenic risk profiles for pain, generated using independent GWAS data, were associated with chronic pain in both GS:SFHS (maximum β = 6.18x10-2, 95% CI 2.84 x10-2 to 9.35 x10-2, p = 4.3x10-4) and UK Biobank (maximum β = 5.68 x 10-2, 95% CI 4.70x10-2 to 6.65x10-2, p < 3x10-4). Genomic risk of MDD is also significantly associated with chronic pain in both GS:SFHS (maximum β = 6.62x10-2, 95% CI 2.82 x10-2 to 9.76 x10-2, p = 4.3x10-4) and UK Biobank (maximum β = 2.56x10-2, 95% CI 1.62x10-2 to 3.63x10-2, p < 3x10-4). Limitations of the current study include the possibility that spouse effects may be due to assortative mating and the relatively small polygenic risk score effect sizes. CONCLUSIONS Genetic factors, as well as chronic pain in a partner or spouse, contribute substantially to the risk of chronic pain for an individual. Chronic pain is genetically correlated with MDD, has a polygenic architecture, and is associated with polygenic risk of MDD.
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Affiliation(s)
- Andrew M. McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, United Kingdom
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| | - Lynsey S. Hall
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, United Kingdom
| | - Yanni Zeng
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, United Kingdom
| | - Mark J. Adams
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, United Kingdom
| | - Jude Gibson
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, United Kingdom
| | - Eleanor Wigmore
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, United Kingdom
| | - Saskia P. Hagenaars
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Archie I. Campbell
- Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Toni-Kim Clarke
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, United Kingdom
| | - Caroline Hayward
- Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Chris S. Haley
- Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - David J. Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel J. Smith
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, United Kingdom
| | - Barbara I. Nicholl
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, United Kingdom
| | - David A. Hinds
- 23andMe Inc., Mountain View, California, United States of America
| | - Amy V. Jones
- Pfizer WRD, Human Genetics and Computational Biomedicine, Granta Park, Cambridge, United Kingdom
| | - Serena Scollen
- Pfizer WRD, Human Genetics and Computational Biomedicine, Granta Park, Cambridge, United Kingdom
| | - Weihua Meng
- Division of Population Health Sciences, University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - Blair H. Smith
- Division of Population Health Sciences, University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - Lynne J. Hocking
- The Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
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15
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Oei L, Hsu YH, Styrkarsdottir U, Eussen BH, de Klein A, Peters MJ, Halldorsson B, Liu CT, Alonso N, Kaptoge SK, Thorleifsson G, Hallmans G, Hocking LJ, Husted LB, Jameson KA, Kruk M, Lewis JR, Patel MS, Scollen S, Svensson O, Trompet S, van Schoor NM, Zhu K, Buckley BM, Cooper C, Ford I, Goltzman D, González-Macías J, Langdahl BL, Leslie WD, Lips P, Lorenc RS, Olmos JM, Pettersson-Kymmer U, Reid DM, Riancho JA, Slagboom PE, Garcia-Ibarbia C, Ingvarsson T, Johannsdottir H, Luben R, Medina-Gómez C, Arp P, Nandakumar K, Palsson ST, Sigurdsson G, van Meurs JBJ, Zhou Y, Hofman A, Jukema JW, Pols HAP, Prince RL, Cupples LA, Marshall CR, Pinto D, Sato D, Scherer SW, Reeve J, Thorsteinsdottir U, Karasik D, Richards JB, Stefansson K, Uitterlinden AG, Ralston SH, Ioannidis JPA, Kiel DP, Rivadeneira F, Estrada K. A genome-wide copy number association study of osteoporotic fractures points to the 6p25.1 locus. J Med Genet 2014; 51:122-31. [PMID: 24343915 DOI: 10.1136/jmedgenet-2013-102064] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [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: 12/15/2022]
Abstract
BACKGROUND Osteoporosis is a systemic skeletal disease characterised by reduced bone mineral density and increased susceptibility to fracture; these traits are highly heritable. Both common and rare copy number variants (CNVs) potentially affect the function of genes and may influence disease risk. AIM To identify CNVs associated with osteoporotic bone fracture risk. METHOD We performed a genome-wide CNV association study in 5178 individuals from a prospective cohort in the Netherlands, including 809 osteoporotic fracture cases, and performed in silico lookups and de novo genotyping to replicate in several independent studies. RESULTS A rare (population prevalence 0.14%, 95% CI 0.03% to 0.24%) 210 kb deletion located on chromosome 6p25.1 was associated with the risk of fracture (OR 32.58, 95% CI 3.95 to 1488.89; p = 8.69 × 10(-5)). We performed an in silico meta-analysis in four studies with CNV microarray data and the association with fracture risk was replicated (OR 3.11, 95% CI 1.01 to 8.22; p = 0.02). The prevalence of this deletion showed geographic diversity, being absent in additional samples from Australia, Canada, Poland, Iceland, Denmark, and Sweden, but present in the Netherlands (0.34%), Spain (0.33%), USA (0.23%), England (0.15%), Scotland (0.10%), and Ireland (0.06%), with insufficient evidence for association with fracture risk. CONCLUSIONS These results suggest that deletions in the 6p25.1 locus may predispose to higher risk of fracture in a subset of populations of European origin; larger and geographically restricted studies will be needed to confirm this regional association. This is a first step towards the evaluation of the role of rare CNVs in osteoporosis.
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Affiliation(s)
- Ling Oei
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
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Fleischmann R, van Vollenhoven RF, Smolen J, Emery P, Florentinus S, Rathmann S, Kupper H, Kavanaugh A, Taylor P, Genovese M, Keystone EC, Drescher E, Berclaz PY, Lee C, Fidelus-Gort R, Schlichting D, Beattie S, Luchi M, Macias W, Kavanaugh A, Emery P, van Vollenhoven RF, Dikranian AH, Alten R, Klearman M, Musselman D, Agarwal S, Green J, Gabay C, Weinblatt ME, Schiff MH, Fleischmann R, Valente R, van der Heijde D, Citera G, Zhao C, Maldonado MA, Rakieh C, Nam JL, Hunt L, Villeneuve E, Bissell LA, Das S, Conaghan P, McGonagle D, Wakefield RJ, Emery P, Wright HL, Thomas HB, Moots R, Edwards SW, Hamann P, Heward J, McHugh N, Lindsay MA, Haroon M, Giles JT, Winchester R, FitzGerald O, Karaderi T, Cohen CJ, Keidel S, Appleton LH, Macfarlane GJ, Siebert S, Evans D, Paul Wordsworth B, Plant D, Bowes J, Orozco G, Morgan AW, Wilson AG, Isaacs J, Barton A, Williams FM, Livshits G, Spector T, MacGregor A, Williams FM, Scollen S, Cao D, Memari Y, Hyde CL, Zhang B, Sidders B, Ziemek D, Shi Y, Harris J, Harrow I, Dougherty B, Malarstig A, McEwen R, Stephens JL, Patel K, Shin SY, Surdulescu G, He W, Jin X, McMahon SB, Soranzo N, John S, Wang J, Spector TD, Baker J, Litherland GJ, Rowan AD, Kite KA, Bayley R, Yang P, Smith JP, Williams J, Harper L, Kitas GD, Buckley C, Young SP, Fitzpatrick MA, Young SP, McGettrick HM, Filer A, Raza K, Nash G, Buckley C, Muthana M, Davies H, Khetan S, Adeleke G, Hawtree S, Tazzyman S, Morrow F, Ciani B, Wilson G, Quirke AM, Lugli E, Wegner N, Charles P, Hamilton B, Chowdhury M, Ytterberg J, Potempa J, Fisher B, Thiele G, Mikuls T, Venables P, Adebajo AO, Kavanaugh A, Mease P, Gomez-Reino JJ, Wollenhaupt J, Hu C, Stevens R, Sieper J, van der Heijde D, Dougados M, Van den Bosch F, Goupille P, Rathmann SS, Pangan AL, van der Heijde D, Sieper J, Maksymowych WP, Brown MA, Rathmann S, Pangan AL, Sieper J, van der Heijde D, Elewaut D, Pangan AL, Anderson J, Haroon M, Ramasamy P, O'Rourke M, Murphy C, Fitzgerald O, Jani M, Moore S, Mirjafari H, Macphie E, Chinoy H, Rao C, McLoughlin Y, Preeti S. Oral Abstracts 7: RA Clinical * O37. Long-Term Outcomes of Early RA Patients Initiated with Adalimumab Plus Methotrexate Compared with Methotrexate Alone Following a Targeted Treatment Approach. Rheumatology (Oxford) 2013. [DOI: 10.1093/rheumatology/ket198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Southgate L, Scollen S, He W, Moss A, Simpson MA, Zhang B, Xi L, Schlitt T, Weale ME, Hyde CL, Stephens JC, Sjöstrand C, Russell MB, Leone M, John SL, Trembath RC. Elucidating the molecular genetic basis of cluster headache: delineation of the genetic architecture by exome sequencing. J Headache Pain 2013. [PMCID: PMC3620257 DOI: 10.1186/1129-2377-14-s1-p34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Southgate L, Scollen S, He W, Moss A, Simpson MA, Zhang B, Xi L, Schlitt T, Weale ME, Hyde CL, Stephens JC, Sjöstrand C, Russell MB, Leone M, John SL, Trembath RC. Elucidating the molecular genetic basis of cluster headache: delineation of the genetic architecture by exome sequencing. J Headache Pain 2013. [DOI: 10.1186/1129-2377-1-s1-p34] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Williams FMK, Scollen S, Cao D, Memari Y, Hyde CL, Zhang B, Sidders B, Ziemek D, Shi Y, Harris J, Harrow I, Dougherty B, Malarstig A, McEwen R, Stephens JC, Patel K, Menni C, Shin SY, Hodgkiss D, Surdulescu G, He W, Jin X, McMahon SB, Soranzo N, John S, Wang J, Spector TD. Genes contributing to pain sensitivity in the normal population: an exome sequencing study. PLoS Genet 2012; 8:e1003095. [PMID: 23284290 PMCID: PMC3527205 DOI: 10.1371/journal.pgen.1003095] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [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: 05/28/2012] [Accepted: 10/01/2012] [Indexed: 12/02/2022] Open
Abstract
Sensitivity to pain varies considerably between individuals and is known to be heritable. Increased sensitivity to experimental pain is a risk factor for developing chronic pain, a common and debilitating but poorly understood symptom. To understand mechanisms underlying pain sensitivity and to search for rare gene variants (MAF<5%) influencing pain sensitivity, we explored the genetic variation in individuals' responses to experimental pain. Quantitative sensory testing to heat pain was performed in 2,500 volunteers from TwinsUK (TUK): exome sequencing to a depth of 70× was carried out on DNA from singletons at the high and low ends of the heat pain sensitivity distribution in two separate subsamples. Thus in TUK1, 101 pain-sensitive and 102 pain-insensitive were examined, while in TUK2 there were 114 and 96 individuals respectively. A combination of methods was used to test the association between rare variants and pain sensitivity, and the function of the genes identified was explored using network analysis. Using causal reasoning analysis on the genes with different patterns of SNVs by pain sensitivity status, we observed a significant enrichment of variants in genes of the angiotensin pathway (Bonferroni corrected p = 3.8×10−4). This pathway is already implicated in animal models and human studies of pain, supporting the notion that it may provide fruitful new targets in pain management. The approach of sequencing extreme exome variation in normal individuals has provided important insights into gene networks mediating pain sensitivity in humans and will be applicable to other common complex traits. Chronic widespread pain is a complex clinical problem. Identification of underlying genetic factors would shed light on the biology of pain and offer targets for novel therapies. We aimed to identify rare genetic variants in the normal population associated with pain sensation by performing exome sequencing on individuals who were more or less sensitive to heat pain. While we did not identify any single variants having large effect, we did observe major group differences between the sensitive and insensitive individuals. Network analysis suggested a role for the angiotensin pathway, which previous work in animal models has suggested is important in pain mediation. Our results cast light on the genetic factors underlying normal pain sensation in humans and the utility of exome analyses. It suggests that further exploration of the angiotensin pathway may reveal novel targets for the treatment of pain.
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Affiliation(s)
- Frances M. K. Williams
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Serena Scollen
- Pfizer Limited, Neusentis, Granta Park, Cambridge, United Kingdom
| | | | - Yasin Memari
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Craig L. Hyde
- Pfizer Research Laboratories, Groton, Connecticut, United States of America
| | - Baohong Zhang
- Pfizer Research Laboratories, Groton, Connecticut, United States of America
| | - Benjamin Sidders
- Pfizer Limited, Neusentis, Granta Park, Cambridge, United Kingdom
| | - Daniel Ziemek
- Worldwide R&D, Pfizer, Cambridge, Massachusetts, United States of America
| | | | - Juliette Harris
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Ian Harrow
- Pfizer Global Research and Development, Sandwich, United Kingdom
| | - Brian Dougherty
- Pfizer Research Laboratories, Groton, Connecticut, United States of America
| | - Anders Malarstig
- Pfizer Limited, Neusentis, Granta Park, Cambridge, United Kingdom
| | - Robert McEwen
- Pfizer Global Research and Development, Sandwich, United Kingdom
| | - Joel C. Stephens
- Pfizer Research Laboratories, Groton, Connecticut, United States of America
| | - Ketan Patel
- Pfizer Global Research and Development, Sandwich, United Kingdom
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - So-Youn Shin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Dylan Hodgkiss
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Gabriela Surdulescu
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Wen He
- Pfizer Research Laboratories, Groton, Connecticut, United States of America
| | - Xin Jin
- BGI–Shenzhen, Shenzhen, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, China
| | | | - Nicole Soranzo
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Sally John
- Pfizer Research Laboratories, Groton, Connecticut, United States of America
| | - Jun Wang
- BGI–Shenzhen, Shenzhen, China
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (JW); (TDS)
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
- * E-mail: (JW); (TDS)
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Scollen S, Luccarini C, Baynes C, Driver K, Humphreys MK, Garcia-Closas M, Figueroa J, Lissowska J, Pharoah PD, Easton DF, Hesketh R, Metcalfe JC, Dunning AM. TGF-β signaling pathway and breast cancer susceptibility. Cancer Epidemiol Biomarkers Prev 2011; 20:1112-9. [PMID: 21527583 PMCID: PMC3112459 DOI: 10.1158/1055-9965.epi-11-0062] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [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: 12/23/2022] Open
Abstract
BACKGROUND TGF-β acts as a suppressor of primary tumor initiation but has been implicated as a promoter of the later malignant stages. Here associations with risk of invasive breast cancer are assessed for single-nucleotide polymorphisms (SNP) tagging 17 genes in the canonical TGF-β ALK5/SMADs 2&3 and ALK1/SMADs 1&5 signaling pathways: LTBP1, LTBP2, LTBP4, TGFB1, TGFB2, TGFB3, TGFBR1(ALK5), ALK1, TGFBR2, Endoglin, SMAD1, SMAD2, SMAD3, SMAD4, SMAD5, SMAD6, and SMAD7 [Approved Human Gene Nomenclature Committee gene names: ACVRL1 (for ALK1) and ENG (for Endoglin)]. METHODS Three-hundred-fifty-four tag SNPs (minor allele frequency > 0.05) were selected for genotyping in a staged study design using 6,703 cases and 6,840 controls from the Studies of Epidemiology and Risk Factors in Cancer Heredity (SEARCH) study. Significant associations were meta-analyzed with data from the NCI Polish Breast Cancer Study (PBCS; 1,966 cases and 2,347 controls) and published data from the Breast Cancer Association Consortium (BCAC). RESULTS Associations of three SNPs, tagging TGFB1 (rs1982073), TGFBR1 (rs10512263), and TGFBR2 (rs4522809), were detected in SEARCH; however, associations became weaker in meta-analyses including data from PBCS and BCAC. Tumor subtype analyses indicated that the TGFB1 rs1982073 association may be confined to increased risk of developing progesterone receptor negative (PR(-)) tumors [1.18 (95% CI: 1.09-1.28), 4.1 × 10(-5) (P value for heterogeneity of ORs by PR status = 2.3 × 10(-4))]. There was no evidence for breast cancer risk associations with SNPs in the endothelial-specific pathway utilizing ALK1/SMADs 1&5 that promotes angiogenesis. CONCLUSION Common variation in the TGF-β ALK5/SMADs 2&3 signaling pathway, which initiates signaling at the cell surface to inhibit cell proliferation, might be related to risk of specific tumor subtypes. IMPACT The subtype specific associations require very large studies to be confirmed.
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Affiliation(s)
- Serena Scollen
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge, United Kingdom.
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Dunning AM, Healey CS, Baynes C, Maia AT, Scollen S, Vega A, Rodríguez R, Barbosa-Morais NL, Ponder BAJ, Low YL, Bingham S, Haiman CA, Le Marchand L, Broeks A, Schmidt MK, Hopper J, Southey M, Beckmann MW, Fasching PA, Peto J, Johnson N, Bojesen SE, Nordestgaard B, Milne RL, Benitez J, Hamann U, Ko Y, Schmutzler RK, Burwinkel B, Schürmann P, Dörk T, Heikkinen T, Nevanlinna H, Lindblom A, Margolin S, Mannermaa A, Kosma VM, Chen X, Spurdle A, Change-Claude J, Flesch-Janys D, Couch FJ, Olson JE, Severi G, Baglietto L, Børresen-Dale AL, Kristensen V, Hunter DJ, Hankinson SE, Devilee P, Vreeswijk M, Lissowska J, Brinton L, Liu J, Hall P, Kang D, Yoo KY, Shen CY, Yu JC, Anton-Culver H, Ziogoas A, Sigurdson A, Struewing J, Easton DF, Garcia-Closas M, Humphreys MK, Morrison J, Pharoah PDP, Pooley KA, Chenevix-Trench G. Association of ESR1 gene tagging SNPs with breast cancer risk. Hum Mol Genet 2009; 18:1131-9. [PMID: 19126777 PMCID: PMC2722230 DOI: 10.1093/hmg/ddn429] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [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] [Indexed: 11/14/2022] Open
Abstract
We have conducted a three-stage, comprehensive single nucleotide polymorphism (SNP)-tagging association study of ESR1 gene variants (SNPs) in more than 55,000 breast cancer cases and controls from studies within the Breast Cancer Association Consortium (BCAC). No large risks or highly significant associations were revealed. SNP rs3020314, tagging a region of ESR1 intron 4, is associated with an increase in breast cancer susceptibility with a dominant mode of action in European populations. Carriers of the c-allele have an odds ratio (OR) of 1.05 [95% Confidence Intervals (CI) 1.02-1.09] relative to t-allele homozygotes, P = 0.004. There is significant heterogeneity between studies, P = 0.002. The increased risk appears largely confined to oestrogen receptor-positive tumour risk. The region tagged by SNP rs3020314 contains sequence that is more highly conserved across mammalian species than the rest of intron 4, and it may subtly alter the ratio of two mRNA splice forms.
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Scollen S, Dunning AM, Bradshaw AC, Hesketh R, Metcalfe JC. Association of gene variants in the TGF-beta signalling pathways with invasive breast cancer risk. Breast Cancer Res 2008. [PMCID: PMC3300751 DOI: 10.1186/bcr1932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Langdahl BL, Uitterlinden AG, Ralston SH, Trikalinos TA, Balcells S, Brandi ML, Scollen S, Lips P, Lorenc R, Obermayer-Pietsch B, Reid DM, Armas JB, Arp PP, Bassiti A, Bustamante M, Husted LB, Carey AH, Pérez Cano R, Dobnig H, Dunning AM, Fahrleitner-Pammer A, Falchetti A, Karczmarewicz E, Kruk M, van Leeuwen JPTM, Masi L, van Meurs JBJ, Mangion J, McGuigan FEA, Mellibovsky L, Mosekilde L, Nogués X, Pols HAP, Reeve J, Renner W, Rivadeneira F, van Schoor NM, Ioannidis JPA. Large-scale analysis of association between polymorphisms in the transforming growth factor beta 1 gene (TGFB1) and osteoporosis: the GENOMOS study. Bone 2008; 42:969-81. [PMID: 18284942 DOI: 10.1016/j.bone.2007.11.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [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] [Received: 06/27/2007] [Revised: 11/05/2007] [Accepted: 11/12/2007] [Indexed: 10/22/2022]
Abstract
INTRODUCTION The TGFB1 gene which encodes transforming growth factor beta 1, is a strong candidate for susceptibility to osteoporosis and several studies have reported associations between bone mineral density (BMD), osteoporotic fractures and polymorphisms of TGFB1, although these studies have yielded conflicting results. METHODS We investigated associations between TGFB1 polymorphisms and BMD and fracture in the GENOMOS study: a prospective multicenter study involving 10 European research studies including a total of 28,924 participants. Genotyping was conducted for known TGFB1 polymorphisms at the following sites: G-1639-A (G-800-A, rs1800468), C-1348-T (C-509-T, rs1800469), T29-C (Leu10Pro, rs1982073), G74-C (Arg25Pro, rs1800471) and C788-T (Thr263Ile, rs1800472). These polymorphisms were genotyped prospectively and methodology was standardized across research centers. Genotypes and haplotypes were related to BMD at the lumbar sine and femoral neck and fractures. RESULTS There were no significant differences in either women or men at either skeletal site for any of the examined polymorphisms with the possible exception of a weak association with reduced BMD (-12 mg/cm2) in men with the T-1348 allele (p<0.05). None of the haplotypes was associated with BMD and none of the polymorphisms or haplotypes significantly affected overall risk of fractures, however, the odds ratio for incident vertebral fracture in carriers of the rare T788 allele was 1.64 (95% CI: 1.09-2.64), p<0.05. CONCLUSIONS This study indicates that polymorphic variation in the TGFB1 gene does not play a major role in regulating BMD or susceptibility to fractures. The weak associations we observed between the C-1348-T and lumbar spine BMD in men and between C788-T and risk of incident vertebral fractures are of interest but could be chance findings and will need replication in future studies.
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Affiliation(s)
- Bente L Langdahl
- Department of Endocrinology, Aarhus University Hospital, Aarhus, Denmark.
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Ahmed S, Maranian M, Gregory CS, Udler M, Field HI, Tyrer J, Hesketh R, Metcalfe JC, Scollen S, Stuewing JP, Ponder BAJ, Pharoah PDP, Easton DF, Dunning AM. From association to cause: fine mapping of the TNRC9gene region, a novel susceptibility locus identified in the first genome-wide association study for breast cancer. Breast Cancer Res 2008. [PMCID: PMC3300752 DOI: 10.1186/bcr1933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
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van Meurs JBJ, Trikalinos TA, Ralston SH, Balcells S, Brandi ML, Brixen K, Kiel DP, Langdahl BL, Lips P, Ljunggren O, Lorenc R, Obermayer-Pietsch B, Ohlsson C, Pettersson U, Reid DM, Rousseau F, Scollen S, Van Hul W, Agueda L, Akesson K, Benevolenskaya LI, Ferrari SL, Hallmans G, Hofman A, Husted LB, Kruk M, Kaptoge S, Karasik D, Karlsson MK, Lorentzon M, Masi L, McGuigan FEA, Mellström D, Mosekilde L, Nogues X, Pols HAP, Reeve J, Renner W, Rivadeneira F, van Schoor NM, Weber K, Ioannidis JPA, Uitterlinden AG. Large-scale analysis of association between LRP5 and LRP6 variants and osteoporosis. JAMA 2008; 299:1277-90. [PMID: 18349089 PMCID: PMC3282142 DOI: 10.1001/jama.299.11.1277] [Citation(s) in RCA: 210] [Impact Index Per Article: 13.1] [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: 11/14/2022]
Abstract
CONTEXT Mutations in the low-density lipoprotein receptor-related protein 5 (LRP5) gene cause rare syndromes characterized by altered bone mineral density (BMD). More common LRP5 variants may affect osteoporosis risk in the general population. OBJECTIVE To generate large-scale evidence on whether 2 common variants of LRP5 (Val667Met, Ala1330Val) and 1 variant of LRP6 (Ile1062Val) are associated with BMD and fracture risk. DESIGN AND SETTING Prospective, multicenter, collaborative study of individual-level data on 37,534 individuals from 18 participating teams in Europe and North America. Data were collected between September 2004 and January 2007; analysis of the collected data was performed between February and May 2007. Bone mineral density was assessed by dual-energy x-ray absorptiometry. Fractures were identified via questionnaire, medical records, or radiographic documentation; incident fracture data were available for some cohorts, ascertained via routine surveillance methods, including radiographic examination for vertebral fractures. MAIN OUTCOME MEASURES Bone mineral density of the lumbar spine and femoral neck; prevalence of all fractures and vertebral fractures. RESULTS The Met667 allele of LRP5 was associated with reduced lumbar spine BMD (n = 25,052 [number of participants with available data]; 20-mg/cm2 lower BMD per Met667 allele copy; P = 3.3 x 10(-8)), as was the Val1330 allele (n = 24,812; 14-mg/cm2 lower BMD per Val1330 copy; P = 2.6 x 10(-9)). Similar effects were observed for femoral neck BMD, with a decrease of 11 mg/cm2 (P = 3.8 x 10(-5)) and 8 mg/cm2 (P = 5.0 x 10(-6)) for the Met667 and Val1330 alleles, respectively (n = 25 193). Findings were consistent across studies for both LRP5 alleles. Both alleles were associated with vertebral fractures (odds ratio [OR], 1.26; 95% confidence interval [CI], 1.08-1.47 for Met667 [2001 fractures among 20 488 individuals] and OR, 1.12; 95% CI, 1.01-1.24 for Val1330 [1988 fractures among 20,096 individuals]). Risk of all fractures was also increased with Met667 (OR, 1.14; 95% CI, 1.05-1.24 per allele [7876 fractures among 31,435 individuals)]) and Val1330 (OR, 1.06; 95% CI, 1.01-1.12 per allele [7802 fractures among 31 199 individuals]). Effects were similar when adjustments were made for age, weight, height, menopausal status, and use of hormone therapy. Fracture risks were partly attenuated by adjustment for BMD. Haplotype analysis indicated that Met667 and Val1330 variants both independently affected BMD. The LRP6 Ile1062Val polymorphism was not associated with any osteoporosis phenotype. All aforementioned associations except that between Val1330 and all fractures and vertebral fractures remained significant after multiple-comparison adjustments. CONCLUSIONS Common LRP5 variants are consistently associated with BMD and fracture risk across different white populations. The magnitude of the effect is modest. LRP5 may be the first gene to reach a genome-wide significance level (a conservative level of significance [herein, unadjusted P < 10(-7)] that accounts for the many possible comparisons in the human genome) for a phenotype related to osteoporosis.
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Baynes C, Healey CS, Pooley KA, Scollen S, Luben RN, Thompson DJ, Pharoah PDP, Easton DF, Ponder BAJ, Dunning AM. Common variants in the ATM, BRCA1, BRCA2, CHEK2 and TP53 cancer susceptibility genes are unlikely to increase breast cancer risk. Breast Cancer Res 2007; 9:R27. [PMID: 17428325 PMCID: PMC1868915 DOI: 10.1186/bcr1669] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [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: 01/29/2007] [Revised: 03/27/2007] [Accepted: 04/11/2007] [Indexed: 12/29/2022] Open
Abstract
INTRODUCTION Certain rare, familial mutations in the ATM, BRCA1, BRCA2, CHEK2 or TP53 genes increase susceptibility to breast cancer but it has not, until now, been clear whether common polymorphic variants in the same genes also increase risk. METHODS We have attempted a comprehensive, single nucleotide polymorphism (SNP)- and haplotype-tagging association study on each of these five genes in up to 4,474 breast cancer cases from the British, East Anglian SEARCH study and 4,560 controls from the EPIC-Norfolk study, using a two-stage study design. Nine tag SNPs were genotyped in ATM, together with five in BRCA1, sixteen in BRCA2, ten in CHEK2 and five in TP53, with the aim of tagging all other known, common variants. SNPs generating the common amino acid substitutions were specifically forced into the tagging set for each gene. RESULTS No significant breast cancer associations were detected with any individual or combination of tag SNPs. CONCLUSION It is unlikely that there are any other common variants in these genes conferring measurably increased risks of breast cancer in our study population.
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Affiliation(s)
- Caroline Baynes
- Cancer Research-UK Dept of Oncology, Cancer Research-UK Genetic Epidemiology Unit and EPIC, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Catherine S Healey
- Cancer Research-UK Dept of Oncology, Cancer Research-UK Genetic Epidemiology Unit and EPIC, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Karen A Pooley
- Cancer Research-UK Dept of Oncology, Cancer Research-UK Genetic Epidemiology Unit and EPIC, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Serena Scollen
- Cancer Research-UK Dept of Oncology, Cancer Research-UK Genetic Epidemiology Unit and EPIC, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Robert N Luben
- Cancer Research-UK Dept of Oncology, Cancer Research-UK Genetic Epidemiology Unit and EPIC, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Deborah J Thompson
- Cancer Research-UK Dept of Oncology, Cancer Research-UK Genetic Epidemiology Unit and EPIC, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Paul DP Pharoah
- Cancer Research-UK Dept of Oncology, Cancer Research-UK Genetic Epidemiology Unit and EPIC, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Douglas F Easton
- Cancer Research-UK Dept of Oncology, Cancer Research-UK Genetic Epidemiology Unit and EPIC, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Bruce AJ Ponder
- Cancer Research-UK Dept of Oncology, Cancer Research-UK Genetic Epidemiology Unit and EPIC, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Alison M Dunning
- Cancer Research-UK Dept of Oncology, Cancer Research-UK Genetic Epidemiology Unit and EPIC, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - the SEARCH breast cancer study
- Cancer Research-UK Dept of Oncology, Cancer Research-UK Genetic Epidemiology Unit and EPIC, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
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Cox A, Dunning AM, Garcia-Closas M, Balasubramanian S, Reed MWR, Pooley KA, Scollen S, Baynes C, Ponder BAJ, Chanock S, Lissowska J, Brinton L, Peplonska B, Southey MC, Hopper JL, McCredie MRE, Giles GG, Fletcher O, Johnson N, dos Santos Silva I, Gibson L, Bojesen SE, Nordestgaard BG, Axelsson CK, Torres D, Hamann U, Justenhoven C, Brauch H, Chang-Claude J, Kropp S, Risch A, Wang-Gohrke S, Schürmann P, Bogdanova N, Dörk T, Fagerholm R, Aaltonen K, Blomqvist C, Nevanlinna H, Seal S, Renwick A, Stratton MR, Rahman N, Sangrajrang S, Hughes D, Odefrey F, Brennan P, Spurdle AB, Chenevix-Trench G, Beesley J, Mannermaa A, Hartikainen J, Kataja V, Kosma VM, Couch FJ, Olson JE, Goode EL, Broeks A, Schmidt MK, Hogervorst FBL, Van't Veer LJ, Kang D, Yoo KY, Noh DY, Ahn SH, Wedrén S, Hall P, Low YL, Liu J, Milne RL, Ribas G, Gonzalez-Neira A, Benitez J, Sigurdson AJ, Stredrick DL, Alexander BH, Struewing JP, Pharoah PDP, Easton DF. A common coding variant in CASP8 is associated with breast cancer risk. Nat Genet 2007; 39:352-8. [PMID: 17293864 DOI: 10.1038/ng1981] [Citation(s) in RCA: 392] [Impact Index Per Article: 23.1] [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: 08/18/2006] [Accepted: 01/17/2007] [Indexed: 01/30/2023]
Abstract
The Breast Cancer Association Consortium (BCAC) has been established to conduct combined case-control analyses with augmented statistical power to try to confirm putative genetic associations with breast cancer. We genotyped nine SNPs for which there was some prior evidence of an association with breast cancer: CASP8 D302H (rs1045485), IGFBP3 -202 C --> A (rs2854744), SOD2 V16A (rs1799725), TGFB1 L10P (rs1982073), ATM S49C (rs1800054), ADH1B 3' UTR A --> G (rs1042026), CDKN1A S31R (rs1801270), ICAM5 V301I (rs1056538) and NUMA1 A794G (rs3750913). We included data from 9-15 studies, comprising 11,391-18,290 cases and 14,753-22,670 controls. We found evidence of an association with breast cancer for CASP8 D302H (with odds ratios (OR) of 0.89 (95% confidence interval (c.i.): 0.85-0.94) and 0.74 (95% c.i.: 0.62-0.87) for heterozygotes and rare homozygotes, respectively, compared with common homozygotes; P(trend) = 1.1 x 10(-7)) and weaker evidence for TGFB1 L10P (OR = 1.07 (95% c.i.: 1.02-1.13) and 1.16 (95% c.i.: 1.08-1.25), respectively; P(trend) = 2.8 x 10(-5)). These results demonstrate that common breast cancer susceptibility alleles with small effects on risk can be identified, given sufficiently powerful studies.
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Affiliation(s)
- Angela Cox
- Sheffield University Medical School, Sheffield S10 2RX, UK
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Scollen S, Dunning AM, Hesketh R, Metcalfe JC. Association of gene variants in the transforming growth factor beta signalling pathways with invasive breast cancer risk. Breast Cancer Res 2006. [PMCID: PMC3300275 DOI: 10.1186/bcr1583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Low YL, Taylor JI, Grace PB, Mulligan AA, Welch AA, Scollen S, Dunning AM, Luben RN, Khaw KT, Day NE, Wareham NJ, Bingham SA. Phytoestrogen Exposure, Polymorphisms in COMT, CYP19, ESR1, and SHBG Genes, and Their Associations With Prostate Cancer Risk. Nutr Cancer 2006; 56:31-9. [PMID: 17176215 DOI: 10.1207/s15327914nc5601_5] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [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] [Indexed: 10/31/2022]
Abstract
Prospective phytoestrogen exposure was assessed using both biomarkers and estimates of intake in 89 British men recruited into the Norfolk arm of the European Prospective Investigation into Cancer and Nutrition study, men who subsequently developed prostate cancer. Results were compared with those from 178 healthy men matched by age and date of recruitment. Levels of seven phytoestrogens (daidzein, genistein, glycitein, O-desmethylangolensin, equol, enterodiol, and enterolactone) were measured in spot urine and serum samples. Five single-nucleotide polymorphisms in COMT, CYP19, ESR1, and SHBG genes were genotyped. Urinary levels of all phytoestrogens correlated strongly with serum levels. Correlation coefficients ranged from 0.63 (glycitein) to 0.88 (daidzein) (P < 0.001). Urinary and serum levels correlated significantly with isoflavone intake assessed from food diaries (R = 0.15-0.20; P < 0.05) but not with that from a food-frequency questionnaire. Odds ratios for phytoestrogen exposure, as assessed using the four methods, were not significantly associated with prostate cancer risk (P = 0.15-0.94). Men with the CC genotype for the ESRI PvuII polymorphism had significantly higher risk for prostate cancer compared with men with the TT genotype [adjusted odds ratio = 4.65 (1.60-13.49); P = 0.005]. Our results utilizing a combined prospective exposure provide no evidence that phytoestrogens alter prostate cancer risk in British men, whereas the C allele for the PvuII polymorphism may be associated with increased risk.
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Affiliation(s)
- Yen-Ling Low
- MRC Dunn Human Nutrition Unit, Cambridge CB2 2XY, UK
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Uitterlinden AG, Ralston SH, Brandi ML, Carey AH, Grinberg D, Langdahl BL, Lips P, Lorenc R, Obermayer-Pietsch B, Reeve J, Reid DM, Amedei A, Amidei A, Bassiti A, Bustamante M, Husted LB, Diez-Perez A, Dobnig H, Dunning AM, Enjuanes A, Fahrleitner-Pammer A, Fang Y, Karczmarewicz E, Kruk M, van Leeuwen JPTM, Mavilia C, van Meurs JBJ, Mangion J, McGuigan FEA, Pols HAP, Renner W, Rivadeneira F, van Schoor NM, Scollen S, Sherlock RE, Ioannidis JPA. The association between common vitamin D receptor gene variations and osteoporosis: a participant-level meta-analysis. Ann Intern Med 2006; 145:255-64. [PMID: 16908916 DOI: 10.7326/0003-4819-145-4-200608150-00005] [Citation(s) in RCA: 184] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Polymorphisms of the vitamin D receptor (VDR) gene have been implicated in the genetic regulation of bone mineral density (BMD). However, the clinical impact of these variants remains unclear. OBJECTIVE To evaluate the relation between VDR polymorphisms, BMD, and fractures. DESIGN Prospective multicenter large-scale association study. SETTING The Genetic Markers for Osteoporosis consortium, involving 9 European research teams. PARTICIPANTS 26,242 participants (18,405 women). MEASUREMENTS Cdx2 promoter, FokI, BsmI, ApaI, and TaqI polymorphisms; BMD at the femoral neck and the lumbar spine by dual x-ray absorptiometry; and fractures. RESULTS Comparisons of BMD at the lumbar spine and femoral neck showed nonsignificant differences less than 0.011 g/cm2 for any genotype with or without adjustments. A total of 6067 participants reported a history of fracture, and 2088 had vertebral fractures. For all VDR alleles, odds ratios for fractures were very close to 1.00 (range, 0.98 to 1.02) and collectively the 95% CIs ranged from 0.94 (lowest) to 1.07 (highest). For vertebral fractures, we observed a 9% (95% CI, 0% to 18%; P = 0.039) risk reduction for the Cdx2 A-allele (13% risk reduction in a dominant model). LIMITATIONS The authors analyzed only selected VDR polymorphisms. Heterogeneity was detected in some analyses and may reflect some differences in collection of fracture data across cohorts. Not all fractures were related to osteoporosis. CONCLUSIONS The FokI, BsmI, ApaI, and TaqI VDR polymorphisms are not associated with BMD or with fractures, but the Cdx2 polymorphism may be associated with risk for vertebral fractures.
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Ralston SH, Uitterlinden AG, Brandi ML, Balcells S, Langdahl BL, Lips P, Lorenc R, Obermayer-Pietsch B, Scollen S, Bustamante M, Husted LB, Carey AH, Diez-Perez A, Dunning AM, Falchetti A, Karczmarewicz E, Kruk M, van Leeuwen JPTM, van Meurs JBJ, Mangion J, McGuigan FEA, Mellibovsky L, del Monte F, Pols HAP, Reeve J, Reid DM, Renner W, Rivadeneira F, van Schoor NM, Sherlock RE, Ioannidis JPA. Large-scale evidence for the effect of the COLIA1 Sp1 polymorphism on osteoporosis outcomes: the GENOMOS study. PLoS Med 2006; 3:e90. [PMID: 16475872 PMCID: PMC1370920 DOI: 10.1371/journal.pmed.0030090] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.1] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Accepted: 12/12/2005] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Osteoporosis and fracture risk are considered to be under genetic control. Extensive work is being performed to identify the exact genetic variants that determine this risk. Previous work has suggested that a G/T polymorphism affecting an Sp1 binding site in the COLIA1 gene is a genetic marker for low bone mineral density (BMD) and osteoporotic fracture, but there have been no very-large-scale studies of COLIA1 alleles in relation to these phenotypes. METHODS AND FINDINGS Here we evaluated the role of COLIA1 Sp1 alleles as a predictor of BMD and fracture in a multicenter study involving 20,786 individuals from several European countries. At the femoral neck, the average (95% confidence interval [CI]) BMD values were 25 mg/cm2 (CI, 16 to 34 mg/cm2) lower in TT homozygotes than the other genotype groups (p < 0.001), and a similar difference was observed at the lumbar spine; 21 mg/cm2 (CI, 1 to 42 mg/cm2), (p = 0.039). These associations were unaltered after adjustment for potential confounding factors. There was no association with fracture overall (odds ratio [OR] = 1.01 [CI, 0.95 to 1.08]) in either unadjusted or adjusted analyses, but there was a non-significant trend for association with vertebral fracture and a nominally significant association with incident vertebral fractures in females (OR = 1.33 [CI, 1.00 to 1.77]) that was independent of BMD, and unaltered in adjusted analyses. CONCLUSIONS Allowing for the inevitable heterogeneity between participating teams, this study-which to our knowledge is the largest ever performed in the field of osteoporosis genetics for a single gene-demonstrates that the COLIA1 Sp1 polymorphism is associated with reduced BMD and could predispose to incident vertebral fractures in women, independent of BMD. The associations we observed were modest however, demonstrating the importance of conducting studies that are adequately powered to detect and quantify the effects of common genetic variants on complex diseases.
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Affiliation(s)
- Stuart H Ralston
- Rheumatic Diseases Unit, University of Edinburgh, Western General Hospital Edinburgh, Edinburgh, United Kingdom
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Low YL, Taylor JI, Grace PB, Dowsett M, Folkerd E, Doody D, Dunning AM, Scollen S, Mulligan AA, Welch AA, Luben RN, Khaw KT, Day NE, Wareham NJ, Bingham SA. Polymorphisms in the CYP19 gene may affect the positive correlations between serum and urine phytoestrogen metabolites and plasma androgen concentrations in men. J Nutr 2005; 135:2680-6. [PMID: 16251630 DOI: 10.1093/jn/135.11.2680] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Phytoestrogens have been hypothesized to protect against prostate cancer via modulation of circulating androgen concentrations. We conducted a cross-sectional study of 267 men in the Norfolk arm of the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort with 2 aims: first, to investigate the association between phytoestrogen exposure (measured from diet, urine, and serum) and plasma concentrations of sex hormone-binding globulin (SHBG), androstanediol glucuronide, testosterone and Free Androgen Index (FAI); and second, whether the association may be modified by polymorphisms in CYP19 and SHBG genes. Dietary daidzein and genistein intakes were obtained from food diaries and computed using an in-house food composition database. Urinary and serum concentrations of 3 isoflavones (daidzein, genistein, glycitein), 2 daidzein metabolites O-desmethylangolensin (O-DMA) and 2 lignan metabolites (enterodiol and enterolactone) were measured using mass spectrometry. There was no association between dietary, urinary, and serum phytoestrogens and plasma SHBG concentrations. Enterolactone was positively associated with plasma androstanediol glucuronide concentrations (urinary enterolactone: r = 0.127, P = 0.043; serum enterolactone: r = 0.172, P = 0.006) and FAI (urinary enterolactone: r = 0.115, P = 0.067; serum enterolactone: r = 0.158, P = 0.011). Both urinary and serum equol were associated with plasma testosterone (urinary equol: r = 0.332, P = 0.013; serum equol: r = 0.318, P = 0.018) and FAI (urinary equol: r = 0.297, P = 0.027; serum equol: r = 0.380, P = 0.004) among men with the TT genotype but not the CC or CT genotypes (r = -0.029 to -0.134, P = 0.091-0.717) for the CYP19 3'untranslated region (UTR) T-C polymorphism. Urinary and serum enterolactone showed similar genotype-dependent associations with testosterone but not with FAI. In this first study on phytoestrogen-gene associations in men, we conclude that enterolactone and equol are positively associated with plasma androgen concentrations, and interactions with CYP19 gene may be involved.
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Low YL, Taylor JI, Grace PB, Dowsett M, Scollen S, Dunning AM, Mulligan AA, Welch AA, Luben RN, Khaw KT, Day NE, Wareham NJ, Bingham SA. Phytoestrogen Exposure Correlation with Plasma Estradiol in Postmenopausal Women in European Prospective Investigation of Cancer and Nutrition-Norfolk May Involve Diet-Gene Interactions. Cancer Epidemiol Biomarkers Prev 2005. [DOI: 10.1158/1055-9965.213.14.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [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] Open
Abstract
Abstract
Cross-sectional studies investigating the relationship between phytoestrogens in diet, urine, or blood with plasma estradiol and sex hormone binding globulin (SHBG) have been inconclusive. We investigated the relationship among phytoestrogen exposure, polymorphisms in the ESR1, COMT, CYP19, and SHBG genes, and plasma estradiol and SHBG levels in 125 free-living postmenopausal women taking part in a cohort study (European Prospective Investigation of Cancer and Nutrition-Norfolk) using three different markers: dietary, urinary, and serum phytoestrogens. Phytoestrogen levels (daidzein, genistein, glycitein, O-desmethylangolensin, equol, enterodiol, and enterolactone) in spot urine and serum were analyzed by gas chromatography/mass spectrometry and liquid chromatography/tandem mass spectrometry, respectively. Plasma estradiol and SHBG were measured by immunoassays. Adjusting for age and body mass index, urinary daidzein, genistein, glycitein, and serum daidzein and glycitein were negatively correlated with plasma estradiol (R = −0.199 to −0.277, P <0.03), with particularly strong associations found in the 18 women with CC genotype for ESR1 PvuII polymorphism (R = −0.597 to −0.834, P < 0.03). The negative correlations observed between isoflavones and estradiol in women as a whole became no longer significant when we excluded women with ESR1 PvuII CC genotype, indicating that the correlations observed were due mainly to this group of women. There was no relationship between dietary isoflavones and plasma estradiol and no association was found between any of the dietary, urinary, and serum phytoestrogen and plasma SHBG or between these factors and polymorphisms in CYP19, SHBG, and COMT. We conclude that higher isoflavone exposure is associated with lower plasma estradiol in postmenopausal women and that this preliminary study is suggestive of the involvement of diet-gene interactions.
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Affiliation(s)
- Yen-Ling Low
- 1Medical Research Council Dunn Human Nutrition Unit
| | | | | | - Mitch Dowsett
- 2Institute of Cancer Research, London, United Kingdom and
| | - Serena Scollen
- 3Cancer Research UK, Department of Oncology, Strangeways Research Laboratory and European Prospective Investigation of Cancer and Nutrition, Institute of Public Health and Strangeways Research Laboratory, Cambridge, United Kingdom
| | | | - Angela A. Mulligan
- 3Cancer Research UK, Department of Oncology, Strangeways Research Laboratory and European Prospective Investigation of Cancer and Nutrition, Institute of Public Health and Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Ailsa A. Welch
- 3Cancer Research UK, Department of Oncology, Strangeways Research Laboratory and European Prospective Investigation of Cancer and Nutrition, Institute of Public Health and Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Robert N. Luben
- 3Cancer Research UK, Department of Oncology, Strangeways Research Laboratory and European Prospective Investigation of Cancer and Nutrition, Institute of Public Health and Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Kay-Tee Khaw
- 3Cancer Research UK, Department of Oncology, Strangeways Research Laboratory and European Prospective Investigation of Cancer and Nutrition, Institute of Public Health and Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Nick E. Day
- 3Cancer Research UK, Department of Oncology, Strangeways Research Laboratory and European Prospective Investigation of Cancer and Nutrition, Institute of Public Health and Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Nick J. Wareham
- 3Cancer Research UK, Department of Oncology, Strangeways Research Laboratory and European Prospective Investigation of Cancer and Nutrition, Institute of Public Health and Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Sheila A. Bingham
- 1Medical Research Council Dunn Human Nutrition Unit
- 3Cancer Research UK, Department of Oncology, Strangeways Research Laboratory and European Prospective Investigation of Cancer and Nutrition, Institute of Public Health and Strangeways Research Laboratory, Cambridge, United Kingdom
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Low YL, Taylor JI, Grace PB, Dowsett M, Scollen S, Dunning AM, Mulligan AA, Welch AA, Luben RN, Khaw KT, Day NE, Wareham NJ, Bingham SA. Phytoestrogen exposure correlation with plasma estradiol in postmenopausal women in European Prospective Investigation of Cancer and Nutrition-Norfolk may involve diet-gene interactions. Cancer Epidemiol Biomarkers Prev 2005; 14:213-20. [PMID: 15668497] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
Cross-sectional studies investigating the relationship between phytoestrogens in diet, urine, or blood with plasma estradiol and sex hormone binding globulin (SHBG) have been inconclusive. We investigated the relationship among phytoestrogen exposure, polymorphisms in the ESR1, COMT, CYP19, and SHBG genes, and plasma estradiol and SHBG levels in 125 free-living postmenopausal women taking part in a cohort study (European Prospective Investigation of Cancer and Nutrition-Norfolk) using three different markers: dietary, urinary, and serum phytoestrogens. Phytoestrogen levels (daidzein, genistein, glycitein, O-desmethylangolensin, equol, enterodiol, and enterolactone) in spot urine and serum were analyzed by gas chromatography/mass spectrometry and liquid chromatography/tandem mass spectrometry, respectively. Plasma estradiol and SHBG were measured by immunoassays. Adjusting for age and body mass index, urinary daidzein, genistein, glycitein, and serum daidzein and glycitein were negatively correlated with plasma estradiol (R = -0.199 to -0.277, P <0.03), with particularly strong associations found in the 18 women with CC genotype for ESR1 PvuII polymorphism (R = -0.597 to -0.834, P < 0.03). The negative correlations observed between isoflavones and estradiol in women as a whole became no longer significant when we excluded women with ESR1 PvuII CC genotype, indicating that the correlations observed were due mainly to this group of women. There was no relationship between dietary isoflavones and plasma estradiol and no association was found between any of the dietary, urinary, and serum phytoestrogen and plasma SHBG or between these factors and polymorphisms in CYP19, SHBG, and COMT. We conclude that higher isoflavone exposure is associated with lower plasma estradiol in postmenopausal women and that this preliminary study is suggestive of the involvement of diet-gene interactions.
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Affiliation(s)
- Yen-Ling Low
- Medical Research Council Dunn Human Nutrition Unit, Wellcome Trust/Medical Research Council Building, Hills Road, Cambridge CB2 2XY, United Kingdom.
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Ioannidis JPA, Ralston SH, Bennett ST, Brandi ML, Grinberg D, Karassa FB, Langdahl B, van Meurs JBJ, Mosekilde L, Scollen S, Albagha OME, Bustamante M, Carey AH, Dunning AM, Enjuanes A, van Leeuwen JPTM, Mavilia C, Masi L, McGuigan FEA, Nogues X, Pols HAP, Reid DM, Schuit SCE, Sherlock RE, Uitterlinden AG. Differential genetic effects of ESR1 gene polymorphisms on osteoporosis outcomes. JAMA 2004; 292:2105-14. [PMID: 15523071 DOI: 10.1001/jama.292.17.2105] [Citation(s) in RCA: 203] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
CONTEXT Both bone mineral density (BMD) and fracture risk have a strong genetic component. Estrogen receptor alpha (ESR1) is a candidate gene for osteoporosis, but previous studies of ESR1 polymorphisms in this field were hampered by small sample size, lack of standardization, and inconclusive results. OBJECTIVE To generate large-scale evidence on whether 3 common ESR1 polymorphisms (intron 1 polymorphisms XbaI [dbSNP: rs9340799] and PvuII [dbSNP: rs2234693] and promoter TA repeats microsatellite) and haplotypes thereof are associated with BMD and fractures. DESIGN AND SETTING Meta-analysis of individual-level data involving standardized genotyping of 18 917 individuals in 8 European centers. MAIN OUTCOME MEASURES BMD of femoral neck and lumbar spine; all fractures and vertebral fractures by genotype. RESULTS No between-center heterogeneity was observed for any outcome in any genetic contrast. None of the 3 polymorphisms or haplotypes had any statistically significant effect on BMD in adjusted or unadjusted analyses, and estimated differences between genetic contrasts were 0.01 g/cm2 or less. Conversely, we found significant reductions in fracture risk. In women homozygous for the absence of an XbaI recognition site, the adjusted odds of all fractures were reduced by 19% (odds ratio, 0.81 [95% CI, 0.71-0.93]; P = .002) and vertebral fractures by 35% (odds ratio, 0.65 [95% CI, 0.49-0.87]; P = .003). Effects on fractures were independent of BMD and unaltered in adjusted analyses. No significant effects on fracture risk were seen for PvuII and TA repeats. CONCLUSIONS ESR1 is a susceptibility gene for fractures, and XbaI determines fracture risk by mechanisms independent of BMD. Our study demonstrates the value of adequately powered studies with standardized genotyping and clinical outcomes in defining effects of common genetic variants on complex diseases.
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Affiliation(s)
- John P A Ioannidis
- Clinical and Molecular Epidemiology Unit, Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece.
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Atkinson C, Oosthuizen W, Scollen S, Loktionov A, Day NE, Bingham SA. Modest protective effects of isoflavones from a red clover-derived dietary supplement on cardiovascular disease risk factors in perimenopausal women, and evidence of an interaction with ApoE genotype in 49-65 year-old women. J Nutr 2004; 134:1759-64. [PMID: 15226466 DOI: 10.1093/jn/134.7.1759] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Data suggest that soy protein, a source of isoflavones, may have favorable effects on cardiovascular risk factors. Women (n = 205), ages 49-65 y, were randomized into this double blind, placebo-controlled trial of 43.5 mg red clover-derived isoflavones/d. A total of 177 women completed the trial. There were no differences between treatments for changes from baseline to 12 mo in total cholesterol, LDL cholesterol, triglycerides, HDL cholesterol, systolic and diastolic blood pressures, fibrinogen, and plasminogen activator inhibitor type 1 (PAI-1) (P >/= 0.1). Interactions between treatment and menopausal status were significant for changes in triglycerides and PAI-1 (P = 0.02 and P = 0.01), and changes were significant among perimenopausal women. In the isoflavone and placebo groups, changes in triglycerides were -0.2 +/- 0.6 and 0.4 +/- 0.6 mmol/L, P = 0.02, and changes in PAI-1 were -3.06 +/- 5.88 and 4.95 +/- 6.25 IU/L, P = 0.004, respectively. Interactions between apolipoprotein E (apoE) genotype and treatment tended to be significant for changes in total and LDL cholesterol (P = 0.06 and P = 0.05), and differences between treatments were significant in E2/E3 women. In the isoflavone and placebo groups, changes in total cholesterol were -0.61 +/- 0.79 and 0.18 +/- 0.79 mmol/L, P = 0.03, and changes in LDL cholesterol were -0.84 +/- 0.79 and -0.04 +/- 0.69 mmol/L, P = 0.02, respectively. Although there were potentially beneficial changes in triglycerides and PAI-1 among perimenopausal women consuming isoflavones, this study suggests that isoflavones alone are not responsible for the well-documented effects of soy protein on blood lipids. A larger study is required to confirm the effect modification by apoE genotype.
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Affiliation(s)
- Charlotte Atkinson
- MRC Biostatistics Unit, Institute of Public Health, Cambridge, CB2 2SR, UK
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Loktionov A, Scollen S, McKeown N, Bingham SA. Gene-nutrient interactions: dietary behaviour associated with high coronary heart disease risk particularly affects serum LDL cholesterol in apolipoprotein E epsilon4-carrying free-living individuals. Br J Nutr 2000; 84:885-90. [PMID: 11177205] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Apolipoprotein E (ApoE) genotype influence on the relationship between dietary risk factors for cardiovascular disease and blood serum lipid levels was investigated in 132 free-living individuals participating in the European Prospective Investigation of Cancer (EPIC) study. All subjects (age 40-69) were clinically healthy and provided information on their usual diet. ApoE genotype and serum lipid concentrations were determined in all subjects. Relationships of intake of dietary constituents with serum lipid levels were compared in different genotype groups. There was a significant correlation between total serum cholesterol and intake of energy derived from total fat (r 0.195; P 0.025) and saturated fat (r 0.174; P 0.046) in the cohort as a whole. However, individuals with the ApoE epsilon3/epsilon4 genotype displayed a much stronger positive correlation between LDL cholesterol level and the percentage of energy derived from intake of saturated fat (r 0.436; P 0.043). There were no significant associations in the groups with epsilon3/epsilon3 or epsilon2/epsilon2 & epsilon2/epsilon3 genotype. A significant positive correlation between alcohol consumption and HDL cholesterol level was present in individuals bearing ApoE epsilon2 allele. These findings support current public health recommendations that saturated fat consumption should be reduced in order to reduce coronary heart disease risk. Total cholesterol concentrations were positively related to saturated fat intake in the cohort as a whole, but elevated LDL cholesterol levels associated with high saturated fat intake can be expected particularly in those individuals who combine a 'risky' dietary behaviour with the presence of the epsilon4 variant of ApoE.
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Affiliation(s)
- A Loktionov
- Dunn Human Nutrition Unit, Wellcome Trust/ MRC, Cambridge,
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