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Das S, Abou-Haidar R, Rabalais H, Sun SDLW, Rosli Z, Chatpar K, Boivin MN, Tabatabaei M, Rogers C, Legault M, Lo D, Degroot C, Dagher A, Dyke SOM, Durcan TM, Seyller A, Doyon J, Poupon V, Fon EA, Genge A, Rouleau GA, Karamchandani J, Evans AC. The C-BIG Repository: an Institution-Level Open Science Platform. Neuroinformatics 2022; 20:139-153. [PMID: 34003431 PMCID: PMC9537233 DOI: 10.1007/s12021-021-09516-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2021] [Indexed: 01/07/2023]
Abstract
In January 2016, the Montreal Neurological Institute-Hospital (The Neuro) declared itself an Open Science organization. This vision extends beyond efforts by individual scientists seeking to release individual datasets, software tools, or building platforms that provide for the free dissemination of such information. It involves multiple stakeholders and an infrastructure that considers governance, ethics, computational resourcing, physical design, workflows, training, education, and intra-institutional reporting structures. The C-BIG repository was built in response as The Neuro's institutional biospecimen and clinical data repository, and collects biospecimens as well as clinical, imaging, and genetic data from patients with neurological disease and healthy controls. It is aimed at helping scientific investigators, in both academia and industry, advance our understanding of neurological diseases and accelerate the development of treatments. As many neurological diseases are quite rare, they present several challenges to researchers due to their small patient populations. Overcoming these challenges required the aggregation of datasets from various projects and locations. The C-BIG repository achieves this goal and stands as a scalable working model for institutions to collect, track, curate, archive, and disseminate multimodal data from patients. In November 2020, a Registered Access layer was made available to the wider research community at https://cbigr-open.loris.ca , and in May 2021 fully open data will be released to complement the Registered Access data. This article outlines many of the aspects of The Neuro's transition to Open Science by describing the data to be released, C-BIG's full capabilities, and the design aspects that were implemented for effective data sharing.
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Affiliation(s)
- Samir Das
- grid.14709.3b0000 0004 1936 8649McGill Centre for Integrative Neuroscience, McGill University, Montréal, Québec, Canada ,grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada ,grid.416102.00000 0004 0646 3639McConnell Brain Imaging Centre, Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Rida Abou-Haidar
- grid.14709.3b0000 0004 1936 8649McGill Centre for Integrative Neuroscience, McGill University, Montréal, Québec, Canada ,grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Henri Rabalais
- grid.14709.3b0000 0004 1936 8649McGill Centre for Integrative Neuroscience, McGill University, Montréal, Québec, Canada ,grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Sonia Denise Lai Wing Sun
- grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada ,grid.14709.3b0000 0004 1936 8649Clinical Research Unit, McGill University, Montreal, Quebec, Canada
| | - Zaliqa Rosli
- grid.14709.3b0000 0004 1936 8649McGill Centre for Integrative Neuroscience, McGill University, Montréal, Québec, Canada ,grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Krishna Chatpar
- grid.14709.3b0000 0004 1936 8649McGill Centre for Integrative Neuroscience, McGill University, Montréal, Québec, Canada ,grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Marie-Noëlle Boivin
- grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Mahdieh Tabatabaei
- grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Christine Rogers
- grid.14709.3b0000 0004 1936 8649McGill Centre for Integrative Neuroscience, McGill University, Montréal, Québec, Canada ,grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Melanie Legault
- grid.14709.3b0000 0004 1936 8649McGill Centre for Integrative Neuroscience, McGill University, Montréal, Québec, Canada ,grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Derek Lo
- grid.14709.3b0000 0004 1936 8649McGill Centre for Integrative Neuroscience, McGill University, Montréal, Québec, Canada ,grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Clotilde Degroot
- grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Alain Dagher
- grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada ,grid.416102.00000 0004 0646 3639McConnell Brain Imaging Centre, Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Stephanie O. M. Dyke
- grid.14709.3b0000 0004 1936 8649McGill Centre for Integrative Neuroscience, McGill University, Montréal, Québec, Canada ,grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada ,grid.14709.3b0000 0004 1936 8649Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Thomas M. Durcan
- grid.14709.3b0000 0004 1936 8649Clinical Research Unit, McGill University, Montreal, Quebec, Canada ,grid.416102.00000 0004 0646 3639Early Drug Discovery Unit (EDDU), Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Annabel Seyller
- grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Julien Doyon
- grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada ,grid.416102.00000 0004 0646 3639McConnell Brain Imaging Centre, Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Viviane Poupon
- grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Edward A. Fon
- grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada ,grid.14709.3b0000 0004 1936 8649Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Angela Genge
- grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada ,grid.14709.3b0000 0004 1936 8649Clinical Research Unit, McGill University, Montreal, Quebec, Canada
| | - Guy A. Rouleau
- grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Jason Karamchandani
- grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada ,grid.14709.3b0000 0004 1936 8649Clinical Research Unit, McGill University, Montreal, Quebec, Canada
| | - Alan C. Evans
- grid.14709.3b0000 0004 1936 8649McGill Centre for Integrative Neuroscience, McGill University, Montréal, Québec, Canada ,grid.416102.00000 0004 0646 3639Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada ,grid.416102.00000 0004 0646 3639McConnell Brain Imaging Centre, Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
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Tremblay-Mercier J, Madjar C, Das S, Pichet Binette A, Dyke SOM, Étienne P, Lafaille-Magnan ME, Remz J, Bellec P, Louis Collins D, Natasha Rajah M, Bohbot V, Leoutsakos JM, Iturria-Medina Y, Kat J, Hoge RD, Gauthier S, Tardif CL, Mallar Chakravarty M, Poline JB, Rosa-Neto P, Evans AC, Villeneuve S, Poirier J, Breitner JCS. Open science datasets from PREVENT-AD, a longitudinal cohort of pre-symptomatic Alzheimer's disease. Neuroimage Clin 2021; 31:102733. [PMID: 34192666 PMCID: PMC8254111 DOI: 10.1016/j.nicl.2021.102733] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 02/07/2023]
Abstract
To move Alzheimer Disease (AD) research forward it is essential to collect data from large cohorts, but also make such data available to the global research community. We describe the creation of an open science dataset from the PREVENT-AD (PResymptomatic EValuation of Experimental or Novel Treatments for AD) cohort, composed of cognitively unimpaired older individuals with a parental or multiple-sibling history of AD. From 2011 to 2017, 386 participants were enrolled (mean age 63 years old ± 5) for sustained investigation among whom 349 have retrospectively agreed to share their data openly. Repositories are findable through the unified interface of the Canadian Open Neuroscience Platform and contain up to five years of longitudinal imaging data, cerebral fluid biochemistry, neurosensory capacities, cognitive, genetic, and medical information. Imaging data can be accessed openly at https://openpreventad.loris.ca while most of the other information, sensitive by nature, is accessible by qualified researchers at https://registeredpreventad.loris.ca. In addition to being a living resource for continued data acquisition, PREVENT-AD offers opportunities to facilitate understanding of AD pathogenesis.
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Affiliation(s)
| | - Cécile Madjar
- StoP-AD Centre, Douglas Mental Health Institute Research Centre, Montréal, QC, Canada; McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, McGill University, Montréal, QC, Canada.
| | - Samir Das
- McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, McGill University, Montréal, QC, Canada.
| | - Alexa Pichet Binette
- StoP-AD Centre, Douglas Mental Health Institute Research Centre, Montréal, QC, Canada; McGill University, Montréal, QC, Canada.
| | - Stephanie O M Dyke
- McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, McGill University, Montréal, QC, Canada; McGill University, Montréal, QC, Canada; McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University, Montréal, QC, Canada.
| | - Pierre Étienne
- StoP-AD Centre, Douglas Mental Health Institute Research Centre, Montréal, QC, Canada; McGill University, Montréal, QC, Canada.
| | - Marie-Elyse Lafaille-Magnan
- StoP-AD Centre, Douglas Mental Health Institute Research Centre, Montréal, QC, Canada; McGill University, Montréal, QC, Canada; Centre for Child Development and Mental Health, Jewish General Hospital. Montréal, QC, Canada.
| | - Jordana Remz
- StoP-AD Centre, Douglas Mental Health Institute Research Centre, Montréal, QC, Canada.
| | - Pierre Bellec
- CRIUGM - Université de Montréal, Montréal, QC, Canada; Université de Montréal, Montréal, QC, Canada.
| | - D Louis Collins
- McGill University, Montréal, QC, Canada; McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University, Montréal, QC, Canada.
| | - M Natasha Rajah
- StoP-AD Centre, Douglas Mental Health Institute Research Centre, Montréal, QC, Canada; McGill University, Montréal, QC, Canada.
| | - Veronique Bohbot
- StoP-AD Centre, Douglas Mental Health Institute Research Centre, Montréal, QC, Canada; McGill University, Montréal, QC, Canada.
| | | | - Yasser Iturria-Medina
- McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, McGill University, Montréal, QC, Canada; McGill University, Montréal, QC, Canada; McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University, Montréal, QC, Canada.
| | - Justin Kat
- StoP-AD Centre, Douglas Mental Health Institute Research Centre, Montréal, QC, Canada; McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, McGill University, Montréal, QC, Canada.
| | - Richard D Hoge
- McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, McGill University, Montréal, QC, Canada; McGill University, Montréal, QC, Canada; McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University, Montréal, QC, Canada; Université de Montréal, Montréal, QC, Canada.
| | - Serge Gauthier
- StoP-AD Centre, Douglas Mental Health Institute Research Centre, Montréal, QC, Canada; McGill University, Montréal, QC, Canada; McGill University Research Centre for Studies in Aging, McGill University, Montréal, QC, Canada.
| | - Christine L Tardif
- McGill University, Montréal, QC, Canada; McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University, Montréal, QC, Canada.
| | - M Mallar Chakravarty
- StoP-AD Centre, Douglas Mental Health Institute Research Centre, Montréal, QC, Canada; McGill University, Montréal, QC, Canada.
| | - Jean-Baptiste Poline
- McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, McGill University, Montréal, QC, Canada; McGill University, Montréal, QC, Canada; McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University, Montréal, QC, Canada.
| | - Pedro Rosa-Neto
- StoP-AD Centre, Douglas Mental Health Institute Research Centre, Montréal, QC, Canada; McGill University, Montréal, QC, Canada; McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University, Montréal, QC, Canada; McGill University Research Centre for Studies in Aging, McGill University, Montréal, QC, Canada.
| | - Alan C Evans
- StoP-AD Centre, Douglas Mental Health Institute Research Centre, Montréal, QC, Canada; McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, McGill University, Montréal, QC, Canada; McGill University, Montréal, QC, Canada; McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University, Montréal, QC, Canada.
| | - Sylvia Villeneuve
- StoP-AD Centre, Douglas Mental Health Institute Research Centre, Montréal, QC, Canada; McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, McGill University, Montréal, QC, Canada; McGill University, Montréal, QC, Canada; McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University, Montréal, QC, Canada.
| | - Judes Poirier
- StoP-AD Centre, Douglas Mental Health Institute Research Centre, Montréal, QC, Canada; McGill University, Montréal, QC, Canada.
| | - John C S Breitner
- StoP-AD Centre, Douglas Mental Health Institute Research Centre, Montréal, QC, Canada; McGill University, Montréal, QC, Canada.
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Dyke SOM, Ennis CA, Joly Y, Walter J, Siebert R, Pastinen T. Communicating science: epigenetics in the spotlight. Environ Epigenet 2020; 6:dvaa015. [PMID: 33240528 PMCID: PMC7673471 DOI: 10.1093/eep/dvaa015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/06/2020] [Accepted: 07/09/2020] [Indexed: 05/13/2023]
Abstract
Given the public interest in epigenetic science, this study aimed to better understand media representations of epigenetics in national newspaper coverage in various regions in North America, Europe, and Asia. Content analysis was used to study media messages about epigenetics, their policy focus, and the balance of the reporting. We identified several recurring themes in the news reports, including policy messages relating to individual and societal responsibilities. We also found shortcomings in the media's portrayal of epigenetic science, and sought to identify potential causes by considering the underlying scientific evidence that the media reported on. A case study analysis showed that the results of epigenetic studies were often overstated in academic research publications due to common experimental limitations. We suggest that defining standardized criteria with which to evaluate epigenetic studies could help to overcome some of the challenges inherent in translating complex epigenetic research findings for non-technical audiences, and present a Press Kit template that researchers can adapt and use to aid in the development of accurate and balanced press releases.
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Affiliation(s)
- Stephanie O M Dyke
- Faculty of Medicine, Centre of Genomics and Policy, McGill University, Montreal (Quebec), H3A 0G1, Canada
- Faculty of Medicine, Montreal Neurological Institute, McGill Centre for Integrative Neuroscience, McGill University, Montréal, Quebec, H3A 2B4, Canada
- Correspondence address. E-mail:
| | - Catherine A Ennis
- Human Early Learning Partnership, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
- Amphoraxe Life Sciences, Inc., Vancouver, BC, V6L 3C9, Canada
| | - Yann Joly
- Faculty of Medicine, Centre of Genomics and Policy, McGill University, Montreal (Quebec), H3A 0G1, Canada
| | - Jörn Walter
- Saarland University, 66123, Saarbrücken, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University Medical Center, Ulm University, Albert-Einstein-Allee 29, D-89081, Ulm, Germany
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal (Quebec), H3A 0G1, Canada
- Center for Pediatric Genomic Medicine, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
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4
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Dyke SOM, Saulnier KM, Dupras C, Webster AP, Maschke K, Rothstein M, Siebert R, Walter J, Beck S, Pastinen T, Joly Y. Points-to-consider on the return of results in epigenetic research. Genome Med 2019; 11:31. [PMID: 31122281 PMCID: PMC6533659 DOI: 10.1186/s13073-019-0646-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
As epigenetic studies become more common and lead to new insights into health and disease, the return of individual epigenetic results to research participants, in particular in large-scale epigenomic studies, will be of growing importance. Members of the International Human Epigenome Consortium (IHEC) Bioethics Workgroup considered the potential ethical, legal, and social issues (ELSI) involved in returning epigenetic research results and incidental findings in order to produce a set of 'Points-to-consider' (P-t-C) for the epigenetics research community. These P-t-C draw on existing guidance on the return of genetic research results, while also integrating the IHEC Bioethics Workgroup's ELSI research on and discussion of the issues associated with epigenetic data as well as the experience of a return of results pilot study by the Personal Genome Project UK (PGP-UK). Major challenges include how to determine the clinical validity and actionability of epigenetic results, and considerations related to environmental exposures and epigenetic marks, including circumstances warranting the sharing of results with family members and third parties. Interdisciplinary collaboration and good public communication regarding epigenetic risk will be important to advance the return of results framework for epigenetic science.
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Affiliation(s)
- Stephanie O M Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, H3A 0G1, Canada.
- Montreal Neurological Institute, Faculty of Medicine, McGill University, Montreal, Quebec, H3A 2B4, Canada.
| | - Katie M Saulnier
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Charles Dupras
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Amy P Webster
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | | | - Mark Rothstein
- Institute for Bioethics, Health Policy and Law, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University Medical Center, 89091, Ulm, Germany
| | - Jörn Walter
- Saarland University, 66123, Saarbrücken, Germany
| | - Stephan Beck
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, H3A 0G1, Canada
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Yann Joly
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, H3A 0G1, Canada
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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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Cline MS, Liao RG, Parsons MT, Paten B, Alquaddoomi F, Antoniou A, Baxter S, Brody L, Cook-Deegan R, Coffin A, Couch FJ, Craft B, Currie R, Dlott CC, Dolman L, den Dunnen JT, Dyke SOM, Domchek SM, Easton D, Fischmann Z, Foulkes WD, Garber J, Goldgar D, Goldman MJ, Goodhand P, Harrison S, Haussler D, Kato K, Knoppers B, Markello C, Nussbaum R, Offit K, Plon SE, Rashbass J, Rehm HL, Robson M, Rubinstein WS, Stoppa-Lyonnet D, Tavtigian S, Thorogood A, Zhang C, Zimmermann M, Burn J, Chanock S, Rätsch G, Spurdle AB. BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2. PLoS Genet 2018; 14:e1007752. [PMID: 30586411 PMCID: PMC6324924 DOI: 10.1371/journal.pgen.1007752] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/08/2019] [Indexed: 12/20/2022] Open
Abstract
The BRCA Challenge is a long-term data-sharing project initiated within the Global Alliance for Genomics and Health (GA4GH) to aggregate BRCA1 and BRCA2 data to support highly collaborative research activities. Its goal is to generate an informed and current understanding of the impact of genetic variation on cancer risk across the iconic cancer predisposition genes, BRCA1 and BRCA2. Initially, reported variants in BRCA1 and BRCA2 available from public databases were integrated into a single, newly created site, www.brcaexchange.org. The purpose of the BRCA Exchange is to provide the community with a reliable and easily accessible record of variants interpreted for a high-penetrance phenotype. More than 20,000 variants have been aggregated, three times the number found in the next-largest public database at the project’s outset, of which approximately 7,250 have expert classifications. The data set is based on shared information from existing clinical databases—Breast Cancer Information Core (BIC), ClinVar, and the Leiden Open Variation Database (LOVD)—as well as population databases, all linked to a single point of access. The BRCA Challenge has brought together the existing international Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium expert panel, along with expert clinicians, diagnosticians, researchers, and database providers, all with a common goal of advancing our understanding of BRCA1 and BRCA2 variation. Ongoing work includes direct contact with national centers with access to BRCA1 and BRCA2 diagnostic data to encourage data sharing, development of methods suitable for extraction of genetic variation at the level of individual laboratory reports, and engagement with participant communities to enable a more comprehensive understanding of the clinical significance of genetic variation in BRCA1 and BRCA2. The goal of this study and paper has been to develop an international resource to generate an informed and current understanding of the impact of genetic variation on cancer risk across the cancer predisposition genes, BRCA1 and BRCA2. Reported variants in BRCA1 and BRCA2 available from public databases were integrated into a single, newly created site, www.brcaexchange.org, to provide a reliable and easily accessible record of variants interpreted for a high-penetrance phenotype.
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Affiliation(s)
- Melissa S. Cline
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Rachel G. Liao
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Michael T. Parsons
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Benedict Paten
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Faisal Alquaddoomi
- Department of Computer Science, Biomedical Informatics Group Universitätsstrasse, Zürich, Switzerland
- Biomedical Informatics, University Hospital Zurich, Zurich, Switzerland
- Biocybernetics Laboratory, Computer Science Department, University of California, Los Angeles, California, United States of America
| | - Antonis Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Samantha Baxter
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Larry Brody
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Robert Cook-Deegan
- School for the Future of Innovation in Society, and Consortium for Science, Policy & Outcomes, Arizona State University, Tempe, Arizona, United States of America
| | - Amy Coffin
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Fergus J. Couch
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Brian Craft
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Robert Currie
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Chloe C. Dlott
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Lena Dolman
- The Global Alliance for Genomics and Health, Toronto, Ontario, Canada
| | - Johan T. den Dunnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Stephanie O. M. Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Susan M. Domchek
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Zachary Fischmann
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - William D. Foulkes
- Program in Cancer Genetics, Department of Oncology and Human Genetics, McGill University, Montréal, Quebec, Canada
| | - Judy Garber
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David Goldgar
- Huntsman Cancer Institute and Department of Dermatology, University of Utah, Salt Lake City, Utah, United States of America
| | - Mary J. Goldman
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Peter Goodhand
- The Global Alliance for Genomics and Health, Toronto, Ontario, Canada
| | - Steven Harrison
- Partners HealthCare Laboratory for Molecular Medicine and Harvard Medical School, Boston, Massachusetts, United States of America
| | - David Haussler
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Kazuto Kato
- Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Bartha Knoppers
- Centre of Genomics and Policy, Faculty of Medicine, Human Genetics, McGill University, Montreal, Québec, Canada
| | - Charles Markello
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- Center for Biomolecular Science & Engineering, University of California, Santa Cruz, California, United States of America
| | - Robert Nussbaum
- Invitae, San Francisco, California, United States of America
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Sharon E. Plon
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jem Rashbass
- National Disease Registration, National Cancer Registration and Analysis Service, Public Health England, London, United Kingdom
| | - Heidi L. Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, United States of America
- Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mark Robson
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Wendy S. Rubinstein
- CancerLinQ at American Society of Clinical Oncology (ASCO), Alexandria, Virginia, United States of America
| | | | - Sean Tavtigian
- Partners HealthCare Laboratory for Molecular Medicine and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Oncological Sciences, The University of Utah, Salt Lake City, Utah, United States of America
| | - Adrian Thorogood
- The Global Alliance for Genomics and Health, Toronto, Ontario, Canada
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - Can Zhang
- Department of Computer Science, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Marc Zimmermann
- Department of Computer Science, Biomedical Informatics Group Universitätsstrasse, Zürich, Switzerland
- Biomedical Informatics, University Hospital Zurich, Zurich, Switzerland
| | | | - John Burn
- Institute of Genetic Medicine, Newcastle University, Centre for Life, Newcastle upon Tyne, United Kingdom
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Gunnar Rätsch
- Department of Computer Science, Biomedical Informatics Group Universitätsstrasse, Zürich, Switzerland
- Biomedical Informatics, University Hospital Zurich, Zurich, Switzerland
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Swiss Institute for Bioinformatics, Lausanne, Switzerland
- * E-mail: (GR); (ABS)
| | - Amanda B. Spurdle
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
- * E-mail: (GR); (ABS)
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7
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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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8
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Shabani M, Dyke SOM, Marelli L, Borry P. Variant data sharing by clinical laboratories through public databases: consent, privacy and further contact for research policies. Genet Med 2018; 21:1031-1037. [PMID: 30293992 DOI: 10.1038/s41436-018-0316-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/10/2018] [Indexed: 11/09/2022] Open
Abstract
Access to detailed variant data is key to inform and verify the interpretation of genomic data. Clinical laboratories can play a significant role in sharing patients' data through public variant databases. To facilitate data sharing, various public databases, such as ClinVar and DECIPHER have been established, which accept data submission from laboratories, clinicians, researchers, and patients. Despite clear benefits to sharing, questions may arise about the adequate form of consent to be obtained from patients when sharing data from their clinical tests through public databases. In this paper, we provide an overview and critical analysis of the relevant consent policies of the major public databases, and of the consent forms of clinical laboratories that share variant data via ClinVar.
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Affiliation(s)
- Mahsa Shabani
- Center for Biomedical Ethics and Law, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium.
| | | | - Luca Marelli
- Life Sciences and Society Lab, Centre for Sociological Research, University of Leuven, Leuven, Belgium
| | - Pascal Borry
- Center for Biomedical Ethics and Law, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
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9
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Woolley JP, Kirby E, Leslie J, Jeanson F, Cabili MN, Rushton G, Hazard JG, Ladas V, Veal CD, Gibson SJ, Tassé AM, Dyke SOM, Gaff C, Thorogood A, Knoppers BM, Wilbanks J, Brookes AJ. Responsible sharing of biomedical data and biospecimens via the "Automatable Discovery and Access Matrix" (ADA-M). NPJ Genom Med 2018; 3:17. [PMID: 30062047 PMCID: PMC6056554 DOI: 10.1038/s41525-018-0057-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 05/31/2018] [Accepted: 06/08/2018] [Indexed: 11/15/2022] Open
Abstract
Given the data-rich nature of modern biomedical research, there is a pressing need for a systematic, structured, computer-readable way to capture, communicate, and manage sharing rules that apply to biomedical resources. This is essential for responsible recording, versioning, communication, querying, and actioning of resource sharing plans. However, lack of a common “information model” for rules and conditions that govern the sharing of materials, methods, software, data, and knowledge creates a fundamental barrier. Without this, it can be virtually impossible for Research Ethics Committees (RECs), Institutional Review Boards (IRBs), Data Access Committees (DACs), biobanks, and end users to confidently track, manage, and interpret applicable legal and ethical requirements. This raises costs and burdens of data stewardship and decreases efficient and responsible access to data, biospecimens, and other resources. To address this, the GA4GH and IRDiRC organizations sponsored the creation of the Automatable Discovery and Access Matrix (ADA-M, read simply as “Adam”). ADA-M is a comprehensive information model that provides the basis for producing structured metadata “Profiles” of regulatory conditions, thereby enabling efficient application of those conditions across regulatory spheres. Widespread use of ADA-M will aid researchers in globally searching and prescreening potential data and/or biospecimen resources for compatibility with their research plans in a responsible and efficient manner, increasing likelihood of timely DAC approvals while also significantly reducing time and effort DACs, RECs, and IRBs spend evaluating resource requests and research proposals. Extensive online documentation, software support, video guides, and an Application Programming Interface (API) for ADA-M have been made available.
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Affiliation(s)
- J Patrick Woolley
- 1Harris Manchester College, University of Oxford, Mansfield Road, Oxford, OX1 3TD UK
| | - Emily Kirby
- 2Public Population Project in Genomics and Society (P3G), McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Suite 5104, Montreal, QC H3A 0G1 Canada
| | - Josh Leslie
- Stewardly, Centre for Social Innovation, Suite 400, 215 Spadina Ave., Toronto, ON M5T 2C7 Canada
| | | | - Moran N Cabili
- 5Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Gregory Rushton
- 5Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | | | - Vagelis Ladas
- 7Department of Genetics and Genome Biology, University of Leicester, Adrian Building, University Road, Leicester, LE1 7RH UK
| | - Colin D Veal
- 7Department of Genetics and Genome Biology, University of Leicester, Adrian Building, University Road, Leicester, LE1 7RH UK
| | - Spencer J Gibson
- 7Department of Genetics and Genome Biology, University of Leicester, Adrian Building, University Road, Leicester, LE1 7RH UK
| | - Anne-Marie Tassé
- 2Public Population Project in Genomics and Society (P3G), McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Suite 5104, Montreal, QC H3A 0G1 Canada
| | - Stephanie O M Dyke
- 8Centre of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, suite 5200, Montreal, QC H3A 0G1 Canada
| | - Clara Gaff
- 9Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, VIC 3052 Australia.,10The University of Melbourne, Melbourne, VIC 3010 Australia
| | - Adrian Thorogood
- 8Centre of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, suite 5200, Montreal, QC H3A 0G1 Canada
| | - Bartha Maria Knoppers
- 8Centre of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, suite 5200, Montreal, QC H3A 0G1 Canada
| | - John Wilbanks
- 11Sage Bionetworks, 1100 Fairview Ave. N., Mailstop M1-C108, Seattle, WA 98109 USA
| | - Anthony J Brookes
- 7Department of Genetics and Genome Biology, University of Leicester, Adrian Building, University Road, Leicester, LE1 7RH UK
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10
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Dyke SOM, Knoppers BM, Hamosh A, Firth HV, Hurles M, Brudno M, Boycott KM, Philippakis AA, Rehm HL. "Matching" consent to purpose: The example of the Matchmaker Exchange. Hum Mutat 2017; 38:1281-1285. [PMID: 28699299 DOI: 10.1002/humu.23278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 06/05/2017] [Accepted: 06/07/2017] [Indexed: 01/11/2023]
Abstract
The Matchmaker Exchange (MME) connects rare disease clinicians and researchers to facilitate the sharing of data from undiagnosed patients for the purpose of novel gene discovery. Such sharing raises the odds that two or more similar patients with candidate genes in common may be found, thereby allowing their condition to be more readily studied and understood. Consent considerations for data sharing in MME included both the ethical and legal differences between clinical and research settings and the level of privacy risk involved in sharing varying amounts of rare disease patient data to enable patient matches. In this commentary, we discuss these consent considerations and the resulting MME Consent Policy as they may be relevant to other international data sharing initiatives.
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Affiliation(s)
- Stephanie O M Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - 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
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ontario, Canada
| | | | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts
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11
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Boycott KM, Rath A, Chong JX, Hartley T, Alkuraya FS, Baynam G, Brookes AJ, Brudno M, Carracedo A, den Dunnen JT, Dyke SOM, Estivill X, Goldblatt J, Gonthier C, Groft SC, Gut I, Hamosh A, Hieter P, Höhn S, Hurles ME, Kaufmann P, Knoppers BM, Krischer JP, Macek M, Matthijs G, Olry A, Parker S, Paschall J, Philippakis AA, Rehm HL, Robinson PN, Sham PC, Stefanov R, Taruscio D, Unni D, Vanstone MR, Zhang F, Brunner H, Bamshad MJ, Lochmüller H. International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases. Am J Hum Genet 2017; 100:695-705. [PMID: 28475856 PMCID: PMC5420351 DOI: 10.1016/j.ajhg.2017.04.003] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Provision of a molecularly confirmed diagnosis in a timely manner for children and adults with rare genetic diseases shortens their "diagnostic odyssey," improves disease management, and fosters genetic counseling with respect to recurrence risks while assuring reproductive choices. In a general clinical genetics setting, the current diagnostic rate is approximately 50%, but for those who do not receive a molecular diagnosis after the initial genetics evaluation, that rate is much lower. Diagnostic success for these more challenging affected individuals depends to a large extent on progress in the discovery of genes associated with, and mechanisms underlying, rare diseases. Thus, continued research is required for moving toward a more complete catalog of disease-related genes and variants. The International Rare Diseases Research Consortium (IRDiRC) was established in 2011 to bring together researchers and organizations invested in rare disease research to develop a means of achieving molecular diagnosis for all rare diseases. Here, we review the current and future bottlenecks to gene discovery and suggest strategies for enabling progress in this regard. Each successful discovery will define potential diagnostic, preventive, and therapeutic opportunities for the corresponding rare disease, enabling precision medicine for this patient population.
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Affiliation(s)
- Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada.
| | - Ana Rath
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Research Center, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Gareth Baynam
- Genetic Services of Western Australia, Perth, WA 6008, Australia
| | - Anthony J Brookes
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto M5S 1A1, Canada
| | - Angel Carracedo
- Genomic Medicine Group, Galician Foundation of Genomic Medicine and University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Johan T den Dunnen
- Departments of Human Genetics and Clinical Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Stephanie O M Dyke
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC H3A 1A4, Canada
| | - Xavier Estivill
- Experimental Division, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar; Genetics Unit, Dexeus Woman's Health, 08028 Barcelona, Spain
| | - Jack Goldblatt
- Genetic Services of Western Australia, Perth, WA 6008, Australia
| | - Catherine Gonthier
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Stephen C Groft
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-4874, USA
| | - Ivo Gut
- Centre Nacional d'Anàlisi Genòmica, Center for Genomic Regulation, Barcelona Institute of Science and Technology, Universitat Pompeu Fabra, 08028 Barcelona, Spain
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21286, USA
| | - Philip Hieter
- Michael Smith Laboratories, Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sophie Höhn
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Petra Kaufmann
- Office of Rare Diseases Research, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-4874, USA
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC H3A 1A4, Canada
| | - Jeffrey P Krischer
- University of South Florida Health Informatics Institute, Tampa, FL 33620, USA
| | - Milan Macek
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, 150 06 Prague 5, Czech Republic
| | - Gert Matthijs
- Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Annie Olry
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | | | - Justin Paschall
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | | | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peter N Robinson
- Institut für Medizinische Genetik und Humangenetik, Charité Universitätsmdizin Berlin, 13353 Berlin, Germany; Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Pak-Chung Sham
- Centre for Genomic Sciences, University of Hong Kong, Hong Kong, China
| | - Rumen Stefanov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv 4002, Bulgaria
| | - Domenica Taruscio
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome 299-00161, Italy
| | - Divya Unni
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Megan R Vanstone
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Feng Zhang
- WuXi AppTec, Waigaoqiao Free Trade Zone, Shanghai 200131, China; WuXi NextCODE, Cambridge, MA 02142, USA
| | - Han Brunner
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Maastricht University Medical Center, Department of Clinical Genetics, 6229 GT Maastricht, the Netherlands
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
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12
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Abstract
We review emerging strategies to protect the privacy of research participants in international epigenome research: open consent, genome donation, registered access, automated procedures, and privacy-enhancing technologies.
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Affiliation(s)
- Yann Joly
- Centre of Genomics and Policy, McGill University, Montreal, QC H3A 0G1, Canada.
| | - Stephanie O M Dyke
- Centre of Genomics and Policy, McGill University, Montreal, QC H3A 0G1, Canada
| | - Bartha M Knoppers
- Centre of Genomics and Policy, McGill University, Montreal, QC H3A 0G1, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
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13
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Abstract
In setting up a data access policy to share controlled access data from the McGill Epigenomics Mapping Centre (EMC), an International Human Epigenome Consortium (IHEC) partner project, we encountered ethical and legal challenges that are likely to be relevant to other researchers sharing data, especially from Canadian projects. We discuss our solutions to the following data-sharing challenges, based on comparative legal and policy analysis: (1) providing access to data to a growing number of researchers; (2) maintaining Canadian privacy standards while sharing controlled access data internationally; (3) freedom of information requests; and (4) providing more incentives for researchers to share pre-publication data.
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Affiliation(s)
- Stephanie O M Dyke
- Department of Human Genetics, Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, QC H3A 0G1, Canada
| | - Katie M Saulnier
- Department of Human Genetics, Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, QC H3A 0G1, Canada
| | - Tomi Pastinen
- Department of Human Genetics, Epigenomics Mapping Centre, Faculty of Medicine, McGill University, Montreal, QC H3A 0G1, Canada
| | - Guillaume Bourque
- Department of Human Genetics, Epigenomics Mapping Centre, Faculty of Medicine, McGill University, Montreal, QC H3A 0G1, Canada
| | - Yann Joly
- Department of Human Genetics, Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, QC H3A 0G1, Canada
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14
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Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SOM, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL. The Matchmaker Exchange: a platform for rare disease gene discovery. Hum Mutat 2016; 36:915-21. [PMID: 26295439 DOI: 10.1002/humu.22858] [Citation(s) in RCA: 340] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/21/2015] [Indexed: 12/21/2022]
Abstract
There are few better examples of the need for data sharing than in the rare disease community, where patients, physicians, and researchers must search for "the needle in a haystack" to uncover rare, novel causes of disease within the genome. Impeding the pace of discovery has been the existence of many small siloed datasets within individual research or clinical laboratory databases and/or disease-specific organizations, hoping for serendipitous occasions when two distant investigators happen to learn they have a rare phenotype in common and can "match" these cases to build evidence for causality. However, serendipity has never proven to be a reliable or scalable approach in science. As such, the Matchmaker Exchange (MME) was launched to provide a robust and systematic approach to rare disease gene discovery through the creation of a federated network connecting databases of genotypes and rare phenotypes using a common application programming interface (API). The core building blocks of the MME have been defined and assembled. Three MME services have now been connected through the API and are available for community use. Additional databases that support internal matching are anticipated to join the MME network as it continues to grow.
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Affiliation(s)
- Anthony A Philippakis
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Cardiology, Brigham & Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Danielle R Azzariti
- Laboratory for Molecular Medicine, Partners Personalized Medicine, Boston, Massachusetts
| | - Sergi Beltran
- Centro Nacional de Análisis Genómico, Barcelona, Spain
| | | | - Catherine A Brownstein
- Harvard Medical School, Boston, Massachusetts.,Division of Genetics and Genomics and the Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Han G Brunner
- Radboud University Medical Center, Department of Human Genetics, Nijmegen 6500 HB, The Netherlands.,Maastricht University Medical Center, Department of Clinical Genetics, Maastricht 6202AZ, The Netherlands
| | - Orion J Buske
- Department of Computer Science, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | | | | | - Sergiu Dumitriu
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Stephanie O M Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Quebec, Canada
| | - Johan T den Dunnen
- Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Helen V Firth
- East Anglian Medical Genetics Service, Box 134, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030
| | - Marta Girdea
- Department of Computer Science, University of Toronto, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | | | - Melissa A Haendel
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Ingrid A Holm
- Harvard Medical School, Boston, Massachusetts.,Division of Genetics and Genomics and the Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts
| | - Lijia Huang
- The Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Ben Hutton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Joel B Krier
- Harvard Medical School, Boston, Massachusetts.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, 02115
| | - Andriy Misyura
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | | | - Justin Paschall
- European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, Santa Cruz, California
| | - Peter N Robinson
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin 13353, Germany.,Max Planck Institute for Molecular Genetics, Berlin 14195, Germany.,Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin 14195, Germany.,Berlin Brandenburg Center for Regenerative Therapies, Berlin 13353, Germany
| | | | - Nara L Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Ganesh J Swaminathan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Peter E Taschner
- Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Generade Center of Expertise Genomics, University of Applied Sciences Leiden, Leiden, The Netherlands
| | | | | | - Stephan Züchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Heidi L Rehm
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Laboratory for Molecular Medicine, Partners Personalized Medicine, Boston, Massachusetts.,Department of Pathology, Brigham & Women's Hospital, Boston, Massachusetts
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15
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Rahimzadeh V, Dyke SOM, Knoppers BM. An International Framework for Data Sharing: Moving Forward with the Global Alliance for Genomics and Health. Biopreserv Biobank 2016; 14:256-9. [PMID: 27082668 DOI: 10.1089/bio.2016.0005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Global Alliance for Genomics and Health is marshaling expertise in biomedical research and data sharing policy to propel bench-to-bedside translation of genomics in parallel with many of the BioSHaRE-EU initiatives described at length in this Issue. Worldwide representation of institutions, funders, researchers, and patient advocacy groups at the Global Alliance is testament to a shared ideal that sees maximizing the public good as a chief priority of genomic innovation in health. The Global Alliance has made a critical stride in this regard with the development of its Framework for Responsible Sharing of Genomic and Health-related Data.(1) This article first discusses the human rights pillars that underlie the Framework and mission of the Global Alliance. Second, it outlines the Global Alliance's use of data governance policies through a number of demonstration projects. Finally, the authors describe how the Global Alliance envisions international data sharing moving forward in the postgenomic era.
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16
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Dyke SOM, Philippakis AA, Rambla De Argila J, Paltoo DN, Luetkemeier ES, Knoppers BM, Brookes AJ, Spalding JD, Thompson M, Roos M, Boycott KM, Brudno M, Hurles M, Rehm HL, Matern A, Fiume M, Sherry ST. Consent Codes: Upholding Standard Data Use Conditions. PLoS Genet 2016; 12:e1005772. [PMID: 26796797 PMCID: PMC4721915 DOI: 10.1371/journal.pgen.1005772] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A systematic way of recording data use conditions that are based on consent permissions as found in the datasets of the main public genome archives (NCBI dbGaP and EMBL-EBI/CRG EGA).
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Affiliation(s)
- Stephanie O. M. Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- * E-mail:
| | | | - Jordi Rambla De Argila
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Dina N. Paltoo
- Office of Science Policy, Office of the Director, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Erin S. Luetkemeier
- Office of Science Policy, Office of the Director, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Bartha M. Knoppers
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Anthony J. Brookes
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - J. Dylan Spalding
- European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL—EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Mark Thompson
- Human Genetics Department, Leiden University Medical Center, Leiden, The Netherlands
| | - Marco Roos
- Human Genetics Department, Leiden University Medical Center, Leiden, The Netherlands
| | - Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Brudno
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Matthew Hurles
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Heidi L. Rehm
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Andreas Matern
- Bioreference Laboratories, Inc., Elmwood Park, New Jersey, United States of America
| | | | - Stephen T. Sherry
- National Centre for Biotechnology Information, US National Library of Medicine, Bethesda, Maryland, United States of America
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Abstract
In parallel with massive genomic data production, data sharing practices have rapidly expanded over the last decade. To ensure authorized access to data, access review by data access committees (DACs) has been utilized as one potential solution. Here we discuss core elements to be integrated into the fabric of access review by both established and emerging DACs in order to foster fair, efficient, and responsible access to datasets. We particularly highlight the fact that the access review process could be adversely influenced by the potential conflicts of interest of data producers, particularly when they are directly involved in DACs management. Therefore, in structuring DACs and access procedures, possible data withholding by data producers should receive thorough attention.
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Affiliation(s)
- Mahsa Shabani
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
- * E-mail:
| | - Stephanie O. M. Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Yann Joly
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Pascal Borry
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
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18
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Dyke SOM, Cheung WA, Joly Y, Ammerpohl O, Lutsik P, Rothstein MA, Caron M, Busche S, Bourque G, Rönnblom L, Flicek P, Beck S, Hirst M, Stunnenberg H, Siebert R, Walter J, Pastinen T. Epigenome data release: a participant-centered approach to privacy protection. Genome Biol 2015; 16:142. [PMID: 26185018 PMCID: PMC4504083 DOI: 10.1186/s13059-015-0723-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [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] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 07/09/2015] [Indexed: 11/10/2022] Open
Abstract
Large-scale epigenome mapping by the NIH Roadmap Epigenomics Project, the ENCODE Consortium and the International Human Epigenome Consortium (IHEC) produces genome-wide DNA methylation data at one base-pair resolution. We examine how such data can be made open-access while balancing appropriate interpretation and genomic privacy. We propose guidelines for data release that both reduce ambiguity in the interpretation of open-access data and limit immediate access to genetic variation data that are made available through controlled access.
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Affiliation(s)
- Stephanie O M Dyke
- Centre of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, QC, H3A 0G1, Canada.
| | - Warren A Cheung
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, H3A 0G1, Canada
| | - Yann Joly
- Centre of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, QC, H3A 0G1, Canada
| | - Ole Ammerpohl
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel & Christian-Albrechts-University Kiel, 24105, Kiel, Germany
| | - Pavlo Lutsik
- Saarland University, 66123, Saarbrücken, Germany
| | - Mark A Rothstein
- Institute for Bioethics, Health Policy and Law, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Maxime Caron
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, H3A 0G1, Canada
| | - Stephan Busche
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, H3A 0G1, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, H3A 0G1, Canada
| | - Lars Rönnblom
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stephan Beck
- Medical Genomics, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Martin Hirst
- Centre for High-Throughput Biology, University of British Columbia and Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Henk Stunnenberg
- Department of Molecular Biology, RIMLS, Faculty of Science, Radboud University, 6500 HB, Nijmegen, The Netherlands
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel & Christian-Albrechts-University Kiel, 24105, Kiel, Germany
| | - Jörn Walter
- Saarland University, 66123, Saarbrücken, Germany
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, H3A 0G1, Canada.
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19
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Abstract
The roles played by host-derived nitric oxide (NO) in the growth and subsequent immune rejection of a immunogenic murine lymphoma were investigated by growing the tumor in mice in which the gene for either inducible NO synthase (iNOS) or endothelial NOS (eNOS) had been ablated. This showed that NO from tumor-infiltrating host cells had no significant effect on either tumor growth or immune rejection, although measurements of tumor nitrite levels and protein nitration showed that there had been significant NO production in the rejected tumors, in both the eNOS and iNOS knockout mice. Inhibition of both tumor and host NOS activities, with an iNOS-selective inhibitor (1400W), a nonselective NOS inhibitor [Nomega-nitro-L-arginine methyl ester (L-NAME)], or scavenging NO with a ruthenium-based scavenger, significantly delayed tumor rejection, while having no appreciable effect on tumor growth. Incubation of tumor cells with medium taken from cultured splenocytes, that had been isolated from immunized animals and activated by incubating them with irradiated tumor cells, resulted in an increase in tumor cell NOS activity and an increase in tumor cell apoptosis, which could be inhibited using L-NAME. We propose that, during the immune rejection of this tumor model, there is induction of tumor NOS activity by cytokines secreted by activated lymphocytes within the tumor and that this results in increased levels of tumor NO that induce tumor cell apoptosis and facilitate immune rejection of the tumor.
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Affiliation(s)
- De-En Hu
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
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