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Bernier A, Knoppers BM, Bermudez P, Beauvais MJS, Thorogood A. Open Data governance at the Canadian Open Neuroscience Platform (CONP): From the Walled Garden to the Arboretum. Gigascience 2024; 13:giad114. [PMID: 38217404 PMCID: PMC10787360 DOI: 10.1093/gigascience/giad114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/14/2023] [Accepted: 12/10/2023] [Indexed: 01/15/2024] Open
Abstract
Scientific research communities pursue dual imperatives in implementing strategies to share their data. These communities attempt to maximize the accessibility of biomedical data for downstream research use, in furtherance of open science objectives. Simultaneously, such communities safeguard the interests of research participants through data stewardship measures and the integration of suitable risk disclosures to the informed consent process. The Canadian Open Neuroscience Platform (CONP) convened an Ethics and Governance Committee composed of experts in bioethics, neuroethics, and law to develop holistic policy tools, organizational approaches, and technological supports to align the open governance of data with ethical and legal norms. The CONP has adopted novel platform governance methods that favor full data openness, legitimated through the use of robust deidentification processes and informed consent practices. The experience of the CONP is articulated as a potential template for other open science efforts to further build upon. This experience highlights informed consent guidance, deidentification practices, ethicolegal metadata, platform-level norms, and commercialization and publication policies as the principal pillars of a practicable approach to the governance of open data. The governance approach adopted by the CONP stands as a viable model for the broader neuroscience and open science communities to adopt for sharing data in full open access.
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Affiliation(s)
- Alexander Bernier
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, 740, Dr Penfield Ave, suite 5200, Montréal, Québec H3A 0G1, Canada
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, 740, Dr Penfield Ave, suite 5200, Montréal, Québec H3A 0G1, Canada
| | - Patrick Bermudez
- McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Michael J S Beauvais
- Faculty of Law, University of Toronto, Falconer Hall, 84 Queens Park, Toronto, Ontario M5S 2C5, Canada
| | - Adrian Thorogood
- The Terry Fox Research Institute, 110 Pine Ave W, Montreal, Quebec H2W IR7, Canada
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2
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Flores M, Ly C, Ho E, Ceberio N, Felix K, Thorner HM, Guardado M, Paunovich M, Godek C, Kalaydjian C, Rohlfs R. Decreased accuracy of forensic DNA mixture analysis for groups with lower genetic diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554311. [PMID: 37745566 PMCID: PMC10515773 DOI: 10.1101/2023.08.25.554311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Forensic investigation of DNA samples from multiple contributors has become commonplace. These complex analyses use statistical frameworks accounting for multiple levels of uncertainty in allelic contributions from different individuals, particularly for samples containing few molecules of DNA. These methods have been thoroughly tested along some axes of variation, but less attention has been paid to accuracy across human genetic variation. Here, we quantify the accuracy of DNA mixture analysis over 244 human groups. We find higher false inclusion rates for mixtures with more contributors, and for groups with lower genetic diversity. Even for two-contributor mixtures where one contributor is known and the reference group is correctly specified, false inclusion rates are 1e-5 or higher for 56 out of 244 groups. This means that, depending on multiple testing, some false inclusions may be expected. These false positives could be lessened with more selective and conservative use of DNA mixture analysis.
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Affiliation(s)
- Maria Flores
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
- University of California, Los Angeles; Department of Molecular, Cell and Developmental Biology; Los Angeles, CA, 90095, USA
| | - Cara Ly
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
| | - Evan Ho
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
| | - Niquo Ceberio
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
| | - Kamillah Felix
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
| | - Hannah Mariko Thorner
- George Washington University; Department of Forensic Sciences - Forensic Molecular Biology; Washington, DC, 20007, USA
| | - Miguel Guardado
- University of California, San Francisco; Biological and Medical Informatics Graduate Program; San Francisco CA, 94143, USA
| | - Matt Paunovich
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
| | - Chris Godek
- San Francisco State University; Department of Mathematics; San Francisco, CA, 94132, USA
| | - Carina Kalaydjian
- San Francisco State University; Department of Mathematics; San Francisco, CA, 94132, USA
| | - Rori Rohlfs
- San Francisco State University; Department of Biology; San Francisco, CA, 94132, USA
- University of Oregon; Department of Data Science; Eugene, OR, 97403, USA
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Knoppers BM, Bernier A, Bowers S, Kirby E. Open Data in the Era of the GDPR: Lessons from the Human Cell Atlas. Annu Rev Genomics Hum Genet 2023; 24:369-391. [PMID: 36791787 DOI: 10.1146/annurev-genom-101322-113255] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The Human Cell Atlas (HCA) is striving to build an open community that is inclusive of all researchers adhering to its principles and as open as possible with respect to data access and use. However, open data sharing can pose certain challenges. For instance, being a global initiative, the HCA must contend with a patchwork of local and regional privacy rules. A notable example is the implementation of the European Union General Data Protection Regulation (GDPR), which caused some concern in the biomedical and genomic data-sharing community. We examine how the HCA's large, international group of researchers is investing tremendous efforts into ensuring appropriate sharing of data. We describe the HCA's objectives and governance, how it defines open data sharing, and ethico-legal challenges encountered early in its development; in particular, we describe the challenges prompted by the GDPR. Finally, we broaden the discussion to address tools and strategies that can be used to address ethical data governance.
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Affiliation(s)
- Bartha Maria Knoppers
- Centre of Genomics and Policy, School of Biomedical Sciences, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada; , ,
| | - Alexander Bernier
- Centre of Genomics and Policy, School of Biomedical Sciences, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada; , ,
| | | | - Emily Kirby
- Centre of Genomics and Policy, School of Biomedical Sciences, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada; , ,
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Harding RJ, Bermudez P, Bernier A, Beauvais M, Bellec P, Hill S, Karakuzu A, Knoppers BM, Pavlidis P, Poline JB, Roskams J, Stikov N, Stone J, Strother S, Evans AC. The Canadian Open Neuroscience Platform-An open science framework for the neuroscience community. PLoS Comput Biol 2023; 19:e1011230. [PMID: 37498959 PMCID: PMC10374086 DOI: 10.1371/journal.pcbi.1011230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Abstract
The Canadian Open Neuroscience Platform (CONP) takes a multifaceted approach to enabling open neuroscience, aiming to make research, data, and tools accessible to everyone, with the ultimate objective of accelerating discovery. Its core infrastructure is the CONP Portal, a repository with a decentralized design, where datasets and analysis tools across disparate platforms can be browsed, searched, accessed, and shared in accordance with FAIR principles. Another key piece of CONP infrastructure is NeuroLibre, a preprint server capable of creating and hosting executable and fully reproducible scientific publications that embed text, figures, and code. As part of its holistic approach, the CONP has also constructed frameworks and guidance for ethics and data governance, provided support and developed resources to help train the next generation of neuroscientists, and has fostered and grown an engaged community through outreach and communications. In this manuscript, we provide a high-level overview of this multipronged platform and its vision of lowering the barriers to the practice of open neuroscience and yielding the associated benefits for both individual researchers and the wider community.
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Affiliation(s)
- Rachel J Harding
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Patrick Bermudez
- McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, McGill University, Montréal, Québec, Canada
| | - Alexander Bernier
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Michael Beauvais
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Pierre Bellec
- Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Montréal, Québec, Canada
- Department of Psychology, Université de Montréal, Montréal, Québec, Canada
| | - Sean Hill
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Agâh Karakuzu
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montréal, Montréal, Québec, Canada
- Montréal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montréal, Québec, Canada
- Canada Research Chair in Law and Medicine, Montréal, Québec, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
- Djavad Mowafaghian Center for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jean-Baptiste Poline
- ORIGAMI Neuro Data Science Laboratory, Montreal Neurological Institute, McGill University, Montréal, Québec, Canada
| | - Jane Roskams
- Djavad Mowafaghian Center for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
- Neurosurgery University of Washington, Seattle, Washington, United States of America
| | - Nikola Stikov
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montréal, Montréal, Québec, Canada
- Montréal Heart Institute, Université de Montréal, Montréal, Québec, Canada
- Center for Advanced Interdisciplinary Research, Ss. Cyril and Methodius University, Skopje, North Macedonia
| | - Jessica Stone
- McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, McGill University, Montréal, Québec, Canada
| | - Stephen Strother
- Rotman Research Institute, Baycrest, and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Alan C Evans
- McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, McGill University, Montréal, Québec, Canada
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Patrinos D, Knoppers BM, Kleiderman E, Rahbari N, Laplante DP, Wazana A. Re-contact Following Withdrawal of Minors from Research. CANADIAN JOURNAL OF BIOETHICS 2022. [DOI: 10.7202/1087202ar] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Chen F, Wendl MC, Wyczalkowski MA, Bailey MH, Li Y, Ding L. Moving pan-cancer studies from basic research toward the clinic. NATURE CANCER 2021; 2:879-890. [PMID: 35121865 DOI: 10.1038/s43018-021-00250-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 07/21/2021] [Indexed: 06/14/2023]
Abstract
Although all cancers share common hallmarks, we have long realized that there is no silver-bullet treatment for the disease. Many clinical oncologists specialize in a single cancer type, based predominantly on the tissue of origin. With advances brought by genetics and cancer genomic research, we now know that cancers are profoundly different, both in origins and in genetic alterations. At the same time, commonalities such as key driver mutations, altered pathways, mutational, immune and microbial signatures and other areas (many revealed by pan-cancer studies) point to the intriguing possibility of targeting common traits across diverse cancer types with the same therapeutic strategies. Studies designed to delineate differences and similarities across cancer types are thus critical in discerning the basic dynamics of oncogenesis, as well as informing diagnoses, prognoses and therapies. We anticipate growing emphases on the development and application of therapies targeting underlying commonalities of different cancer types, while tailoring to the unique tissue environment and intrinsic molecular fingerprints of each cancer type and subtype. Here we summarize the facets of pan-cancer research and how they are pushing progress toward personalized medicine.
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Affiliation(s)
- Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael C Wendl
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
- Department of Mathematics, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Matthew H Bailey
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA.
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA.
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Bernier A, Knoppers BM. Longitudinal Health Studies: Secondary Uses Serving the Future. Biopreserv Biobank 2021; 19:404-413. [PMID: 34171963 DOI: 10.1089/bio.2020.0171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Our research compares the ethical and institutional conditions that govern the sharing and secondary use of longitudinal population health data from multiple cohorts. The data use and data sharing conditions applicable to 27 population health cohorts were assessed. This assessment was performed in consulting the informed consent materials and institutional policies applicable to the use of data. Descriptions drawn from the research ethics consent materials were refined through dialog with the institutional staff responsible for overseeing access to data, where possible. Our results demonstrate that data of longitudinal population health cohorts assessed can generally be shared and used for secondary purposes. However, the purposes of secondary use and the preconditions applicable thereto are highly variable. Heterogeneous use conditions can also impede the storage of legacy research data and the pooling thereof for the purpose of common reuse.
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Affiliation(s)
- Alexander Bernier
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Bartha Maria Knoppers
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
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Abstract
The Canadian Genomics Partnership for Rare Diseases, spearheaded by Genome Canada, will integrate genome-wide sequencing to rare disease clinical care in Canada. Centralized and tiered models of data stewardship are proposed to ensure that the data generated can be shared for secondary clinical, research, and quality assurance purposes in compliance with ethics and law. The principal ethico-legal obligations of clinicians, researchers, and institutions are synthesized. Governance infrastructures such as registered access platforms, data access compliance offices, and Beacon systems are proposed as potential organizational and technical foundations of responsible rare disease data sharing. The appropriate delegation of responsibilities, the transparent communication of rights and duties, and the integration of data privacy safeguards into infrastructure design are proposed as the cornerstones of rare disease data stewardship.
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Affiliation(s)
- Alexander Bernier
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, QC H3A 0G1, Canada
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