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Integrated Genomic and Bioinformatics Approaches to Identify Molecular Links between Endocrine Disruptors and Adverse Outcomes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19010574. [PMID: 35010832 PMCID: PMC8744944 DOI: 10.3390/ijerph19010574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/13/2021] [Accepted: 12/21/2021] [Indexed: 12/04/2022]
Abstract
Exposure to Endocrine Disrupting Chemicals (EDC) has been linked with several adverse outcomes. In this review, we examine EDCs that are pervasive in the environment and are of concern in the context of human, animal, and environmental health. We explore the consequences of EDC exposure on aquatic life, terrestrial animals, and humans. We focus on the exploitation of genomics technologies and in particular whole transcriptome sequencing. Genome-wide analyses using RNAseq provides snap shots of cellular, tissue and whole organism transcriptomes under normal physiological and EDC perturbed conditions. A global view of gene expression provides highly valuable information as it uncovers gene families or more specifically, pathways that are affected by EDC exposures, but also reveals those that are unaffected. Hypotheses about genes with unknown functions can also be formed by comparison of their expression levels with genes of known function. Risk assessment strategies leveraging genomic technologies and the development of toxicology databases are explored. Finally, we review how the Adverse Outcome Pathway (AOP) has exploited this high throughput data to provide a framework for toxicology studies.
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Rehm HL, Page AJ, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJ, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SO, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Guidry Auvil JM, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CW, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJ, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen R, Li S, Lin MF, Linden M, Liu X, Liyanage IU, Lopez J, Lucassen AM, Lukowski M, Mann AL, Marshall J, Mattioni M, Metke-Jimenez A, Middleton A, Milne RJ, Molnár-Gábor F, Mulder N, Munoz-Torres MC, Nag R, Nakagawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyrönen TH, O’Connor BD, Oesterle S, Ogishima S, Ota Wang V, Paglione LA, Palumbo E, Parkinson HE, Philippakis AA, Pizarro AD, Prlic A, Rambla J, Rendon A, Rider RA, Robinson PN, Rodarmer KW, Rodriguez LL, Rubin AF, Rueda M, Rushton GA, Ryan RS, Saunders GI, Schuilenburg H, Schwede T, Scollen S, Senf A, Sheffield NC, Skantharajah N, Smith AV, Sofia HJ, Spalding D, Spurdle AB, Stark Z, Stein LD, Suematsu M, Tan P, Tedds JA, Thomson AA, Thorogood A, Tickle TL, Tokunaga K, Törnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Vamathevan J, Varma S, Vears DF, Viner C, Voisin C, Wagner AH, Wallace SE, Walsh BP, Williams MS, Winkler EC, Wold BJ, Wood GM, Woolley JP, Yamasaki C, Yates AD, Yung CK, Zass LJ, Zaytseva K, Zhang J, Goodhand P, North K, Birney E. GA4GH: International policies and standards for data sharing across genomic research and healthcare. CELL GENOMICS 2021; 1:100029. [PMID: 35072136 PMCID: PMC8774288 DOI: 10.1016/j.xgen.2021.100029] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
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Affiliation(s)
- Heidi L. Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Angela J.H. Page
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - Lindsay Smith
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jeremy B. Adams
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gil Alterovitz
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | - Michael Baudis
- University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michael J.S. Beauvais
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | - Tim Beck
- University of Leicester, Leicester, UK
| | | | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - David Bernick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Tiffany F. Boughtwood
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Guillaume Bourque
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
| | | | | | - Michael Brudno
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | - David Bujold
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | - Daniel L. Cameron
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | | | | | | | - Bimal P. Chaudhari
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | - Shu Hui Chen
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Justina Chung
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Melissa Cline
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | | | - Mélanie Courtot
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | | | | | | | - L. Jonathan Dursi
- University Health Network, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | | | | | | | - Susan Fairley
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Khalid A. Fakhro
- Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Helen V. Firth
- Wellcome Sanger Institute, Hinxton, UK
- Addenbrooke’s Hospital, Cambridge, UK
| | | | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ian M. Fore
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mallory A. Freeberg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Lauren A. Fromont
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Clara L. Gaff
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Weiniu Gan
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elena M. Ghanaim
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Glazer
- Verily Life Sciences, South San Francisco, CA, USA
| | - Robert C. Green
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Malachi Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Obi L. Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | | | | | - Roderic Guigó
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Dipayan Gupta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Ada Hamosh
- Johns Hopkins University, Baltimore, MD, USA
| | - David P. Hansen
- Australian Genomics, Parkville, VIC, Australia
- The Australian e-Health Research Centre, CSIRO, Herston, QLD, Australia
| | - Reece K. Hart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Invitae, San Francisco, CA, USA
- MyOme, Inc, San Bruno, CA, USA
| | | | - David Haussler
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | - Michael M. Hoffman
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - Oliver M. Hofmann
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Petr Holub
- BBMRI-ERIC, Graz, Austria
- Masaryk University, Brno, Czech Republic
| | | | | | - Sarah E. Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ammar Husami
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | | | - Saumya S. Jamuar
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Republic of Singapore
| | - Elizabeth L. Janes
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- University of Waterloo, Waterloo, ON, Canada
| | | | - Aina Jené
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Amber L. Johns
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Yann Joly
- McGill University, Montreal, QC, Canada
| | - Steven J.M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Alexander Kanitz
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Thomas M. Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- University of Nottingham, Nottingham, UK
| | - Kristina Kekesi-Lafrance
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | | | - Giselle Kerry
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Seik-Soon Khor
- National Center for Global Health and Medicine Hospital, Tokyo, Japan
- University of Tokyo, Tokyo, Japan
| | | | | | | | | | | | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Stephanie Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | | | - Mikael Linden
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Isuru Udara Liyanage
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Alice L. Mann
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Wellcome Sanger Institute, Hinxton, UK
| | | | | | | | - Anna Middleton
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | - Richard J. Milne
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | | | - Nicola Mulder
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | | | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Hidewaki Nakagawa
- Japan Agency for Medical Research & Development (AMED), Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Arcadi Navarro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
| | | | - Ania Niewielska
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Amy Nisselle
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
| | - Jeffrey Niu
- University Health Network, Toronto, ON, Canada
| | - Tommi H. Nyrönen
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Sabine Oesterle
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Vivian Ota Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Emilio Palumbo
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Helen E. Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Jordi Rambla
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Renee A. Rider
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter N. Robinson
- The Jackson Laboratory, Farmington, CT, USA
- University of Connecticut, Farmington, CT, USA
| | - Kurt W. Rodarmer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Alan F. Rubin
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Manuel Rueda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | | | | | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Torsten Schwede
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | | | | | - Neerjah Skantharajah
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Heidi J. Sofia
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dylan Spalding
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Zornitza Stark
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Lincoln D. Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | | | - Patrick Tan
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- Precision Health Research Singapore, Singapore, Republic of Singapore
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | | | - Alastair A. Thomson
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adrian Thorogood
- McGill University, Montreal, QC, Canada
- University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Katsushi Tokunaga
- University of Tokyo, Tokyo, Japan
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Juha Törnroos
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | - David Torrents
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Sean Upchurch
- California Institute of Technology, Pasadena, CA, USA
| | - Alfonso Valencia
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Jessica Vamathevan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Susheel Varma
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- Health Data Research UK, London, UK
| | - Danya F. Vears
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
- Melbourne Law School, University of Melbourne, Parkville, VIC, Australia
| | - Coby Viner
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
| | | | - Alex H. Wagner
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | | | | | | | - Eva C. Winkler
- Section of Translational Medical Ethics, University Hospital Heidelberg, Heidelberg, Germany
| | | | | | | | | | - Andrew D. Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Christina K. Yung
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Indoc Research, Toronto, ON, Canada
| | - Lyndon J. Zass
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | - Ksenia Zaytseva
- McGill University, Montreal, QC, Canada
- Canadian Centre for Computational Genomics, Montreal, QC, Canada
| | - Junjun Zhang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Peter Goodhand
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Kathryn North
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- European Molecular Biology Laboratory, Heidelberg, Germany
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Albalwy F, Brass A, Davies A. A Blockchain-Based Dynamic Consent Architecture to Support Clinical Genomic Data Sharing (ConsentChain): Proof-of-Concept Study. JMIR Med Inform 2021; 9:e27816. [PMID: 34730538 PMCID: PMC8600428 DOI: 10.2196/27816] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/15/2021] [Accepted: 07/25/2021] [Indexed: 11/30/2022] Open
Abstract
Background In clinical genomics, sharing of rare genetic disease information between genetic databases and laboratories is essential to determine the pathogenic significance of variants to enable the diagnosis of rare genetic diseases. Significant concerns regarding data governance and security have reduced this sharing in practice. Blockchain could provide a secure method for sharing genomic data between involved parties and thus help overcome some of these issues. Objective This study aims to contribute to the growing knowledge of the potential role of blockchain technology in supporting the sharing of clinical genomic data by describing blockchain-based dynamic consent architecture to support clinical genomic data sharing and provide a proof-of-concept implementation, called ConsentChain, for the architecture to explore its performance. Methods The ConsentChain requirements were captured from a patient forum to identify security and consent concerns. The ConsentChain was developed on the Ethereum platform, in which smart contracts were used to model the actions of patients, who may provide or withdraw consent to share their data; the data creator, who collects and stores patient data; and the data requester, who needs to query and access the patient data. A detailed analysis was undertaken of the ConsentChain performance as a function of the number of transactions processed by the system. Results We describe ConsentChain, a blockchain-based system that provides a web portal interface to support clinical genomic sharing. ConsentChain allows patients to grant or withdraw data requester access and allows data requesters to query and submit access to data stored in a secure off-chain database. We also developed an ontology model to represent patient consent elements into machine-readable codes to automate the consent and data access processes. Conclusions Blockchains and smart contracts can provide an efficient and scalable mechanism to support dynamic consent functionality and address some of the barriers that inhibit genomic data sharing. However, they are not a complete answer, and a number of issues still need to be addressed before such systems can be deployed in practice, particularly in relation to verifying user credentials.
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Affiliation(s)
- Faisal Albalwy
- Department of Computer Science, University of Manchester, Manchester, United Kingdom.,Department of Computer Science, College of Computer Science and Engineering, Taibah University, Madinah, Saudi Arabia.,Division of Informatics, Imaging and Data Sciences, University of Manchester, Manchester, United Kingdom
| | - Andrew Brass
- Department of Computer Science, University of Manchester, Manchester, United Kingdom.,Division of Informatics, Imaging and Data Sciences, University of Manchester, Manchester, United Kingdom
| | - Angela Davies
- Division of Informatics, Imaging and Data Sciences, University of Manchester, Manchester, United Kingdom
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Huang Q, Carrio-Cordo P, Gao B, Paloots R, Baudis M. The Progenetix oncogenomic resource in 2021. Database (Oxford) 2021; 2021:baab043. [PMID: 34272855 PMCID: PMC8285936 DOI: 10.1093/database/baab043] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/16/2021] [Accepted: 06/30/2021] [Indexed: 12/02/2022]
Abstract
In cancer, copy number aberrations (CNAs) represent a type of nearly ubiquitous and frequently extensive structural genome variations. To disentangle the molecular mechanisms underlying tumorigenesis as well as identify and characterize molecular subtypes, the comparative and meta-analysis of large genomic variant collections can be of immense importance. Over the last decades, cancer genomic profiling projects have resulted in a large amount of somatic genome variation profiles, however segregated in a multitude of individual studies and datasets. The Progenetix project, initiated in 2001, curates individual cancer CNA profiles and associated metadata from published oncogenomic studies and data repositories with the aim to empower integrative analyses spanning all different cancer biologies. During the last few years, the fields of genomics and cancer research have seen significant advancement in terms of molecular genetics technology, disease concepts, data standard harmonization as well as data availability, in an increasingly structured and systematic manner. For the Progenetix resource, continuous data integration, curation and maintenance have resulted in the most comprehensive representation of cancer genome CNA profiling data with 138 663 (including 115 357 tumor) copy number variation (CNV) profiles. In this article, we report a 4.5-fold increase in sample number since 2013, improvements in data quality, ontology representation with a CNV landscape summary over 51 distinctive National Cancer Institute Thesaurus cancer terms as well as updates in database schemas, and data access including new web front-end and programmatic data access. Database URL: progenetix.org.
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Affiliation(s)
- Qingyao Huang
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
- Swiss Institute of Bioinformatics, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Paula Carrio-Cordo
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
- Swiss Institute of Bioinformatics, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Bo Gao
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
- Swiss Institute of Bioinformatics, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Rahel Paloots
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
- Swiss Institute of Bioinformatics, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Michael Baudis
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
- Swiss Institute of Bioinformatics, Winterthurerstrasse 190, Zurich 8057, Switzerland
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5
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Wang Y, Lakoma A, Zogopoulos G. Building towards Precision Oncology for Pancreatic Cancer: Real-World Challenges and Opportunities. Genes (Basel) 2020; 11:E1098. [PMID: 32967105 PMCID: PMC7563487 DOI: 10.3390/genes11091098] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 02/06/2023] Open
Abstract
The advent of next-generation sequencing (NGS) has provided unprecedented insight into the molecular complexity of pancreatic ductal adenocarcinoma (PDAC). This has led to the emergence of biomarker-driven treatment paradigms that challenge empiric treatment approaches. However, the growth of sequencing technologies is outpacing the development of the infrastructure required to implement precision oncology as routine clinical practice. Addressing these logistical barriers is imperative to maximize the clinical impact of molecular profiling initiatives. In this review, we examine the evolution of precision oncology in PDAC, spanning from germline testing for cancer susceptibility genes to multi-omic tumor profiling. Furthermore, we highlight real-world challenges to delivering precision oncology for PDAC, and propose strategies to improve the generation, interpretation, and clinical translation of molecular profiling data.
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Affiliation(s)
- Yifan Wang
- Department of Surgery, McGill University, Montreal, QC H4A 3J1, Canada; (Y.W.); (A.L.)
- Research Institute of the McGill University Health Centre, McGill University, Montreal, QC H4A 3J1, Canada
- The Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
| | - Anna Lakoma
- Department of Surgery, McGill University, Montreal, QC H4A 3J1, Canada; (Y.W.); (A.L.)
- Research Institute of the McGill University Health Centre, McGill University, Montreal, QC H4A 3J1, Canada
- The Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
| | - George Zogopoulos
- Department of Surgery, McGill University, Montreal, QC H4A 3J1, Canada; (Y.W.); (A.L.)
- Research Institute of the McGill University Health Centre, McGill University, Montreal, QC H4A 3J1, Canada
- The Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
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6
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Bonomi L, Huang Y, Ohno-Machado L. Privacy challenges and research opportunities for genomic data sharing. Nat Genet 2020; 52:646-654. [PMID: 32601475 PMCID: PMC7761157 DOI: 10.1038/s41588-020-0651-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/22/2020] [Indexed: 12/17/2022]
Abstract
The sharing of genomic data holds great promise in advancing precision medicine and providing personalized treatments and other types of interventions. However, these opportunities come with privacy concerns, and data misuse could potentially lead to privacy infringement for individuals and their blood relatives. With the rapid growth and increased availability of genomic datasets, understanding the current genome privacy landscape and identifying the challenges in developing effective privacy-protecting solutions are imperative. In this work, we provide an overview of major privacy threats identified by the research community and examine the privacy challenges in the context of emerging direct-to-consumer genetic-testing applications. We additionally present general privacy-protection techniques for genomic data sharing and their potential applications in direct-to-consumer genomic testing and forensic analyses. Finally, we discuss limitations in current privacy-protection methods, highlight possible mitigation strategies and suggest future research opportunities for advancing genomic data sharing.
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Affiliation(s)
- Luca Bonomi
- UCSD Health Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, USA.
| | - Yingxiang Huang
- UCSD Health Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, USA
| | - Lucila Ohno-Machado
- UCSD Health Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, USA
- Division of Health Services Research & Development, VA San Diego Healthcare System, San Diego, La Jolla, CA, USA
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7
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Jain NM, Culley A, Knoop T, Micheel C, Osterman T, Levy M. Conceptual Framework to Support Clinical Trial Optimization and End-to-End Enrollment Workflow. JCO Clin Cancer Inform 2020; 3:1-10. [PMID: 31225983 PMCID: PMC6873934 DOI: 10.1200/cci.19.00033] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In this work, we present a conceptual framework to support clinical trial optimization and enrollment workflows and review the current state, limitations, and future trends in this space. This framework includes knowledge representation of clinical trials, clinical trial optimization, clinical trial design, enrollment workflows for prospective clinical trial matching, waitlist management, and, finally, evaluation strategies for assessing improvement.
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Affiliation(s)
- Neha M Jain
- Vanderbilt University Medical Center, Nashville, TN
| | | | - Teresa Knoop
- Vanderbilt University Medical Center, Nashville, TN
| | | | | | - Mia Levy
- Vanderbilt University Medical Center, Nashville, TN.,Rush University Medical Center, Chicago, IL
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8
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Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu-Pons J, Duren RP, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Pitel BA, Sezerman OU, Ellrott K, Warner JL, Rieke DT, Aittokallio T, Cerami E, Ritter DI, Schriml LM, Freimuth RR, Haendel M, Raca G, Madhavan S, Baudis M, Beckmann JS, Dienstmann R, Chakravarty D, Li XS, Mockus S, Elemento O, Schultz N, Lopez-Bigas N, Lawler M, Goecks J, Griffith M, Griffith OL, Margolin AA. A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Nat Genet 2020; 52:448-457. [PMID: 32246132 PMCID: PMC7127986 DOI: 10.1038/s41588-020-0603-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 02/26/2020] [Indexed: 12/19/2022]
Abstract
Precision oncology relies on accurate discovery and interpretation of genomic variants, enabling individualized diagnosis, prognosis and therapy selection. We found that six prominent somatic cancer variant knowledgebases were highly disparate in content, structure and supporting primary literature, impeding consensus when evaluating variants and their relevance in a clinical setting. We developed a framework for harmonizing variant interpretations to produce a meta-knowledgebase of 12,856 aggregate interpretations. We demonstrated large gains in overlap between resources across variants, diseases and drugs as a result of this harmonization. We subsequently demonstrated improved matching between a patient cohort and harmonized interpretations of potential clinical significance, observing an increase from an average of 33% per individual knowledgebase to 57% in aggregate. Our analyses illuminate the need for open, interoperable sharing of variant interpretation data. We also provide a freely available web interface (search.cancervariants.org) for exploring the harmonized interpretations from these six knowledgebases.
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Affiliation(s)
- Alex H Wagner
- Washington University School of Medicine, St. Louis, MO, USA
| | - Brian Walsh
- Oregon Health and Science University, Portland, OR, USA
| | | | - David Tamborero
- Pompeu Fabra University, Barcelona, Spain
- Karolinska Institute, Solna, Sweden
| | | | | | - Jordi Deu-Pons
- Institute for Research in Biomedicine, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | | | - Jianjiong Gao
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julie McMurry
- Oregon Health and Science University, Portland, OR, USA
| | - Sara Patterson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | | | - Kyle Ellrott
- Oregon Health and Science University, Portland, OR, USA
| | | | | | - Tero Aittokallio
- Institute for Molecular Medicine Finland, Helsinki, Finland
- University of Turku, Turku, Finland
| | | | - Deborah I Ritter
- Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Lynn M Schriml
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Melissa Haendel
- Oregon Health and Science University, Portland, OR, USA
- Linus Pauling Institute at Oregon State University, Corvallis, OR, USA
| | - Gordana Raca
- Children's Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Subha Madhavan
- Georgetown University Medical Center, Washington, DC, USA
| | | | | | | | | | | | - Susan Mockus
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | - Nuria Lopez-Bigas
- Pompeu Fabra University, Barcelona, Spain
- Institute for Research in Biomedicine, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | | | - Jeremy Goecks
- Oregon Health and Science University, Portland, OR, USA
| | | | - Obi L Griffith
- Washington University School of Medicine, St. Louis, MO, USA.
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9
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Pishvaian MJ, Blais EM, Bender RJ, Rao S, Boca SM, Chung V, Hendifar AE, Mikhail S, Sohal DPS, Pohlmann PR, Moore KN, He K, Monk BJ, Coleman RL, Herzog TJ, Halverson DD, DeArbeloa P, Petricoin EF, Madhavan S. A virtual molecular tumor board to improve efficiency and scalability of delivering precision oncology to physicians and their patients. JAMIA Open 2019; 2:505-515. [PMID: 32025647 PMCID: PMC6994017 DOI: 10.1093/jamiaopen/ooz045] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/28/2019] [Accepted: 09/04/2019] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES Scalable informatics solutions that provide molecularly tailored treatment recommendations to clinicians are needed to streamline precision oncology in care settings. MATERIALS AND METHODS We developed a cloud-based virtual molecular tumor board (VMTB) platform that included a knowledgebase, scoring model, rules engine, an asynchronous virtual chat room and a reporting tool that generated a treatment plan for each of the 1725 patients based on their molecular profile, previous treatment history, structured trial eligibility criteria, clinically relevant cancer gene-variant assertions, biomarker-treatment associations, and current treatment guidelines. The VMTB systematically allows clinician users to combine expert-curated data and structured data from clinical charts along with molecular testing data to develop consensus on treatments, especially those that require off-label and clinical trial considerations. RESULTS The VMTB was used as part of the cancer care process for a focused subset of 1725 patients referred by advocacy organizations wherein resultant personalized reports were successfully delivered to treating oncologists. Median turnaround time from data receipt to report delivery decreased from 14 days to 4 days over 4 years while the volume of cases increased nearly 2-fold each year. Using a novel scoring model for ranking therapy options, oncologists chose to implement the VMTB-derived therapies over others, except when pursuing immunotherapy options without molecular support. DISCUSSION VMTBs will play an increasingly critical role in precision oncology as the compendium of biomarkers and associated therapy options available to a patient continues to expand. CONCLUSION Further development of such clinical augmentation tools that systematically combine patient-derived molecular data, real-world evidence from electronic health records and expert curated knowledgebases on biomarkers with computational tools for ranking best treatments can support care pathways at point of care.
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Affiliation(s)
- Michael J Pishvaian
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
- Perthera, Inc, McLean, Virginia, USA
| | | | | | - Shruti Rao
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington DC, USA
| | - Simina M Boca
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington DC, USA
| | | | | | - Sam Mikhail
- Mark H. Zangmeister Cancer Center, Columbus, Ohio, USA
| | - Davendra P S Sohal
- Case Comprehensive Cancer Center, University Hospitals Seidman Cancer Center, Cleveland Clinic Taussig Cancer Institute, Cleveland, Ohio, USA
| | - Paula R Pohlmann
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Kathleen N Moore
- Stephenson Oklahoma Cancer Center, University of Oklahoma, Oklahoma City, Oklahoma, USA
| | - Kai He
- Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Bradley J Monk
- Arizona Oncology, University of Arizona College of Medicine, Phoenix, Arizona, USA
| | - Robert L Coleman
- University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Thomas J Herzog
- University of Cincinnati Cancer Institute, University of Cincinnati, Cincinnati, Ohio, USA
| | | | | | - Emanuel F Petricoin
- Perthera, Inc, McLean, Virginia, USA
- George Mason University, Fairfax, Virginia, USA
| | - Subha Madhavan
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington DC, USA
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10
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Conway JR, Warner JL, Rubinstein WS, Miller RS. Next-Generation Sequencing and the Clinical Oncology Workflow: Data Challenges, Proposed Solutions, and a Call to Action. JCO Precis Oncol 2019; 3:PO.19.00232. [PMID: 32923847 PMCID: PMC7446333 DOI: 10.1200/po.19.00232] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2019] [Indexed: 02/04/2023] Open
Abstract
PURPOSE Next-generation sequencing (NGS) of tumor and germline DNA is foundational for precision oncology, with rapidly expanding diagnostic, prognostic, and therapeutic implications. Although few question the importance of NGS in modern oncology care, the process of gathering primary molecular data, integrating it into electronic health records, and optimally using it as part of a clinical workflow remains far from seamless. Numerous challenges persist around data standards and interoperability, and clinicians frequently face difficulties in managing the growing amount of genomic knowledge required to care for patients and keep up to date. METHODS This review provides a descriptive analysis of genomic data workflows for NGS data in clinical oncology and issues that arise from the inconsistent use of standards for sharing data across systems. Potential solutions are described. RESULTS NGS technology, especially for somatic genomics, is well established and widely used in routine patient care, quality measurement, and research. Available genomic knowledge bases play an evolving role in patient management but lack harmonization with one another. Questions about their provenance and timeliness of updating remain. Potentially useful standards for sharing genomic data, such as HL7 FHIR and mCODE, remain primarily in the research and/or development stage. Nonetheless, their impact will likely be seen as uptake increases across care settings and laboratories. The specific use case of ASCO CancerLinQ, as a clinicogenomic database, is discussed. CONCLUSION Because the electronic health records of today seem ill suited for managing genomic data, other solutions are required, including universal data standards and applications that use application programming interfaces, along with a commitment on the part of sequencing laboratories to consistently provide structured genomic data for clinical use.
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Affiliation(s)
- Jake R. Conway
- Harvard Medical School, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
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11
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Abstract
One of the recommendations of the Cancer Moonshot Blue Ribbon Panel report from 2016 was the creation of a national cancer data ecosystem. We review some of the approaches for building cancer data ecosystems and some of the progress that has been made. A data commons is the colocation of data with cloud computing infrastructure and commonly used software services, tools, and applications for managing, integrating, analyzing, and sharing data to create an interoperable resource for the research community. We discuss data commons and their potential role in cancer data ecosystems and, in particular, how multiple data commons can interoperate to form part of the foundation for a cancer data ecosystem.
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12
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Enabling precision medicine via standard communication of HTS provenance, analysis, and results. PLoS Biol 2018; 16:e3000099. [PMID: 30596645 PMCID: PMC6338479 DOI: 10.1371/journal.pbio.3000099] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/18/2019] [Indexed: 11/30/2022] Open
Abstract
A personalized approach based on a patient's or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet-lab procedures to computational methods. The BioCompute framework (https://w3id.org/biocompute/1.3.0) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated if needed, and compared by scientists, regulators, test developers, and clinicians. Easing the burden of performing the aforementioned tasks greatly extends the range of practical application. Large clinical trials, precision medicine, and regulatory submissions require a set of agreed upon standards that ensures efficient communication and documentation of genomic analyses. The BioCompute paradigm and the resulting BioCompute Objects (BCOs) offer that standard and are freely accessible as a GitHub organization (https://github.com/biocompute-objects) following the “Open-Stand.org principles for collaborative open standards development.” With high-throughput sequencing (HTS) studies communicated using a BCO, regulatory agencies (e.g., Food and Drug Administration [FDA]), diagnostic test developers, researchers, and clinicians can expand collaboration to drive innovation in precision medicine, potentially decreasing the time and cost associated with next-generation sequencing workflow exchange, reporting, and regulatory reviews. This Community Page article presents a communication standard for the provenance of high-throughput sequencing data; a BioCompute Object (BCO) can serve as a history of what was computed, be used as part of a validation process, or provide clarity and transparency of an experimental process to collaborators.
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13
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Danos AM, Ritter DI, Wagner AH, Krysiak K, Sonkin D, Micheel C, McCoy M, Rao S, Raca G, Boca SM, Roy A, Barnell EK, McMichael JF, Kiwala S, Coffman AC, Kujan L, Kulkarni S, Griffith M, Madhavan S, Griffith OL. Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards. Hum Mutat 2018; 39:1721-1732. [PMID: 30311370 PMCID: PMC6282863 DOI: 10.1002/humu.23651] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/02/2018] [Accepted: 08/28/2018] [Indexed: 12/19/2022]
Abstract
Harmonization of cancer variant representation, efficient communication, and free distribution of clinical variant-associated knowledge are central problems that arise with increased usage of clinical next-generation sequencing. The Clinical Genome Resource (ClinGen) Somatic Working Group (WG) developed a minimal variant level data (MVLD) representation of cancer variants, and has an ongoing collaboration with Clinical Interpretations of Variants in Cancer (CIViC), an open-source platform supporting crowdsourced and expert-moderated cancer variant curation. Harmonization between MVLD and CIViC variant formats was assessed by formal field-by-field analysis. Adjustments to the CIViC format were made to harmonize with MVLD and support ClinGen Somatic WG curation activities, including four new features in CIViC: (1) introduction of an assertions feature for clinical variant assessment following the Association of Molecular Pathologists (AMP) guidelines, (2) group-level curation tracking for organizations, enabling member transparency, and curation effort summaries, (3) introduction of ClinGen Allele Registry IDs to CIViC, and (4) mapping of CIViC assertions into ClinVar submission with automated submissions. A generalizable workflow utilizing MVLD and new CIViC features is outlined for use by ClinGen Somatic WG task teams for curation and submission to ClinVar, and provides a model for promoting harmonization of cancer variant representation and efficient distribution of this information.
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Affiliation(s)
- Arpad M. Danos
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | | | - Alex H. Wagner
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Kilannin Krysiak
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Dmitriy Sonkin
- Biometric Research Program, Division of Cancer Treatment and DiagnosisNational Cancer InstituteRockvilleMaryland
| | | | - Matthew McCoy
- Georgetown Lombardi Comprehensive Cancer CenterWashingtonDistrict of Columbia
| | - Shruti Rao
- Georgetown Lombardi Comprehensive Cancer CenterWashingtonDistrict of Columbia
| | - Gordana Raca
- Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCalifornia
| | - Simina M. Boca
- Georgetown Lombardi Comprehensive Cancer CenterWashingtonDistrict of Columbia
| | | | - Erica K. Barnell
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Joshua F. McMichael
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Susanna Kiwala
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Adam C. Coffman
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Lynzey Kujan
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Shashikant Kulkarni
- Baylor College of MedicineHoustonTexas
- Baylor GeneticsHoustonTexas
- Dan L. Duncan Cancer CenterHoustonTexas
| | - Malachi Griffith
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Subha Madhavan
- Georgetown Lombardi Comprehensive Cancer CenterWashingtonDistrict of Columbia
| | - Obi L. Griffith
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
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14
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Challenges of Identifying Clinically Actionable Genetic Variants for Precision Medicine. JOURNAL OF HEALTHCARE ENGINEERING 2018; 2016:3617572. [PMID: 27195526 PMCID: PMC4955563 DOI: 10.1155/2016/3617572] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 03/17/2016] [Indexed: 12/30/2022]
Abstract
Advances in genomic medicine have the potential to change the way we treat human disease, but translating these advances into reality for improving healthcare outcomes depends essentially on our ability to discover disease- and/or drug-associated clinically actionable genetic mutations. Integration and manipulation of diverse genomic data and comprehensive electronic health records (EHRs) on a big data infrastructure can provide an efficient and effective way to identify clinically actionable genetic variants for personalized treatments and reduce healthcare costs. We review bioinformatics processing of next-generation sequencing (NGS) data, bioinformatics infrastructures for implementing precision medicine, and bioinformatics approaches for identifying clinically actionable genetic variants using high-throughput NGS data and EHRs.
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15
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Agarwala V, Khozin S, Singal G, O’Connell C, Kuk D, Li G, Gossai A, Miller V, Abernethy AP. Real-World Evidence In Support Of Precision Medicine: Clinico-Genomic Cancer Data As A Case Study. Health Aff (Millwood) 2018; 37:765-772. [DOI: 10.1377/hlthaff.2017.1579] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Vineeta Agarwala
- Vineeta Agarwala is a resident in the Department of Medicine, Stanford University, in California, and director of product management at Flatiron Health, in New York City
| | - Sean Khozin
- Sean Khozin is associate director (acting) of the Oncology Center of Excellence, Food and Drug Administration, in Silver Spring, Maryland
| | - Gaurav Singal
- Gaurav Singal is vice president for data strategy and product development, Foundation Medicine, in Cambridge, and a physician in the Department of Medicine, Brigham and Women's Hospital, in Boston, both in Massachusetts
| | | | - Deborah Kuk
- Deborah Kuk is a quantitative scientist at Flatiron Health
| | - Gerald Li
- Gerald Li is a data scientist at Foundation Medicine
| | - Anala Gossai
- Anala Gossai is a quantitative scientist at Flatiron Health
| | - Vincent Miller
- Vincent Miller is chief medical officer at Foundation Medicine
| | - Amy P. Abernethy
- Amy P. Abernethy is chief medical officer and chief scientific officer at Flatiron Health
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16
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High-depth whole genome sequencing of an Ashkenazi Jewish reference panel: enhancing sensitivity, accuracy, and imputation. Hum Genet 2018; 137:343-355. [PMID: 29705978 DOI: 10.1007/s00439-018-1886-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 04/21/2018] [Indexed: 12/31/2022]
Abstract
While increasingly large reference panels for genome-wide imputation have been recently made available, the degree to which imputation accuracy can be enhanced by population-specific reference panels remains an open question. Here, we sequenced at full-depth (≥ 30×), across two platforms (Illumina X Ten and Complete Genomics, Inc.), a moderately large (n = 738) cohort of samples drawn from the Ashkenazi Jewish population. We developed a series of quality control steps to optimize sensitivity, specificity, and comprehensiveness of variant calls in the reference panel, and then tested the accuracy of imputation against target cohorts drawn from the same population. Quality control (QC) thresholds for the Illumina X Ten platform were identified that permitted highly accurate calling of single nucleotide variants across 94% of the genome. QC procedures also identified numerous regions that are poorly mapped using current reference or alternate assemblies. After stringent QC, the population-specific reference panel produced more accurate and comprehensive imputation results relative to publicly available, large cosmopolitan reference panels, especially in the range of rare variants that may be most critical to further progress in mapping of complex phenotypes. The population-specific reference panel also permitted enhanced filtering of clinically irrelevant variants from personal genomes.
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17
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Vassilakopoulou P, Skorve E, Aanestad M. Enabling openness of valuable information resources: Curbing data subtractability and exclusion. INFORMATION SYSTEMS JOURNAL 2018. [DOI: 10.1111/isj.12191] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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18
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Lawler M, Maughan T. From Rosalind Franklin to Barack Obama: Data Sharing Challenges and Solutions in Genomics and Personalised Medicine. New Bioeth 2018; 23:64-73. [PMID: 28517986 PMCID: PMC5448399 DOI: 10.1080/20502877.2017.1314883] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The collection, storage and use of genomic and clinical data from patients and healthy individuals is a key component of personalised medicine enterprises such as the Precision Medicine Initiative, the Cancer Moonshot and the 100,000 Genomes Project. In order to maximise the value of this data, it is important to embed a culture within the scientific, medical and patient communities that supports the appropriate sharing of genomic and clinical information. However, this aspiration raises a number of ethical, legal and regulatory challenges that need to be addressed. The Global Alliance for Genomics and Health, a worldwide coalition of researchers, healthcare professionals, patients and industry partners, is developing innovative solutions to support the responsible and effective sharing of genomic and clinical data. This article identifies the challenges that a data sharing culture poses and highlights a series of practical solutions that will benefit patients, researchers and society.
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Affiliation(s)
- Mark Lawler
- a Centre for Cancer Research , Queen's University Belfast , Belfast , UK.,b Clinical Working Group , Global Alliance for Genomics and Health , Boston , USA
| | - Tim Maughan
- c CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford , Oxford , UK
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19
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Broes S, Lacombe D, Verlinden M, Huys I. Toward a Tiered Model to Share Clinical Trial Data and Samples in Precision Oncology. Front Med (Lausanne) 2018; 5:6. [PMID: 29435448 PMCID: PMC5797296 DOI: 10.3389/fmed.2018.00006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/11/2018] [Indexed: 02/05/2023] Open
Abstract
The recent revolution in science and technology applied to medical research has left in its wake a trial of biomedical data and human samples; however, its opportunities remain largely unfulfilled due to a number of legal, ethical, financial, strategic, and technical barriers. Precision oncology has been at the vanguard to leverage this potential of "Big data" and samples into meaningful solutions for patients, considering the need for new drug development approaches in this area (due to high costs, late-stage failures, and the molecular diversity of cancer). To harness the potential of the vast quantities of data and samples currently fragmented across databases and biobanks, it is critical to engage all stakeholders and share data and samples across research institutes. Here, we identified two general types of sharing strategies. First, open access models, characterized by the absence of any review panel or decision maker, and second controlled access model where some form of control is exercised by either the donor (i.e., patient), the data provider (i.e., initial organization), or an independent party. Further, we theoretically describe and provide examples of nine different strategies focused on greater sharing of patient data and material. These models provide varying levels of control, access to various data and/or samples, and different types of relationship between the donor, data provider, and data requester. We propose a tiered model to share clinical data and samples that takes into account privacy issues and respects sponsors' legitimate interests. Its implementation would contribute to maximize the value of existing datasets, enabling unraveling the complexity of tumor biology, identify novel biomarkers, and re-direct treatment strategies better, ultimately to help patients with cancer.
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Affiliation(s)
- Stefanie Broes
- European Organisation for Research and Treatment of Cancer, Brussels, Belgium
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Denis Lacombe
- European Organisation for Research and Treatment of Cancer, Brussels, Belgium
| | - Michiel Verlinden
- European Organisation for Research and Treatment of Cancer, Brussels, Belgium
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Isabelle Huys
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
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20
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Lacombe D, Liu L, Meunier F, Golfinopoulos V. Precision Medicine: From "Omics" to Economics towards Data-Driven Healthcare - Time for European Transformation. Biomed Hub 2017; 2:212-221. [PMID: 31988951 PMCID: PMC6945945 DOI: 10.1159/000480117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/09/2017] [Indexed: 12/20/2022] Open
Abstract
There is room for improvement for optimally bringing the latest science to the patient while taking into account patient priorities such as quality of life. Too often, regulatory agencies, governments, and funding agencies do not stimulate the integration of research into care and vice versa. Re-engineering the drug development process is a priority, and healthcare systems are long due for transformation. On one hand, patients need efficient access to treatments, but despite precision oncology approaches, efficiently shared screening platforms for sorting patients based on the biology of their tumour for trial access are lacking and, on the other hand, the true value of cancer care is poorly addressed as central questions such as dose, scheduling, duration, and combination are not or sub-optimally addressed by registration trials. Solid evidence on those parameters could potentially lead to a rational and wiser use of anti-cancer treatments. Together, optimally targeting patient population and robust comparative effectiveness data could lead to more affordable and economically sound approaches. The drug development process and healthcare models need to be interconnected through redesigned systems taking into account the full math from drug development into affordable care.
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Affiliation(s)
- Denis Lacombe
- European Organisation for Research and Treatment of Cancer, Brussels, Belgium
| | - Lifang Liu
- European Organisation for Research and Treatment of Cancer, Brussels, Belgium
| | - Françoise Meunier
- European Organisation for Research and Treatment of Cancer, Brussels, Belgium
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21
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Amin AD, Peters TL, Li L, Rajan SS, Choudhari R, Puvvada SD, Schatz JH. Diffuse large B-cell lymphoma: can genomics improve treatment options for a curable cancer? Cold Spring Harb Mol Case Stud 2017; 3:a001719. [PMID: 28487884 PMCID: PMC5411687 DOI: 10.1101/mcs.a001719] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Gene-expression profiling and next-generation sequencing have defined diffuse large B-cell lymphoma (DLBCL), the most common lymphoma diagnosis, as a heterogeneous group of subentities. Despite ongoing explosions of data illuminating disparate pathogenic mechanisms, however, the five-drug chemoimmunotherapy combination R-CHOP remains the frontline standard treatment. This has not changed in 15 years, since the anti-CD20 monoclonal antibody rituximab was added to the CHOP backbone, which first entered use in the 1970s. At least a third of patients are not cured by R-CHOP, and relapsed or refractory DLBCL is fatal in ∼90%. Targeted small-molecule inhibitors against distinct molecular pathways activated in different subgroups of DLBCL have so far translated poorly into the clinic, justifying the ongoing reliance on R-CHOP and other long-established chemotherapy-driven combinations. New drugs and improved identification of biomarkers in real time, however, show potential to change the situation eventually, despite some recent setbacks. Here, we review established and putative molecular drivers of DLBCL identified through large-scale genomics, highlighting among other things the care that must be taken when differentiating drivers from passengers, which is influenced by the promiscuity of activation-induced cytidine deaminase. Furthermore, we discuss why, despite having so much genomic data available, it has been difficult to move toward personalized medicine for this umbrella disorder and some steps that may be taken to hasten the process.
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Affiliation(s)
- Amit Dipak Amin
- Department of Medicine, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Tara L Peters
- Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Lingxiao Li
- Department of Medicine, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Soumya Sundara Rajan
- Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Ramesh Choudhari
- Department of Medicine, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Soham D Puvvada
- Department of Medicine, Division of Hematology-Oncology, University of Arizona Comprehensive Cancer Center, Tucson, Arizona 85719, USA
| | - Jonathan H Schatz
- Department of Medicine, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
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22
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Johnson T, Liebner D, Chen JL. Opportunities for Patient Matching Algorithms to Improve Patient Care in Oncology. JCO Clin Cancer Inform 2017; 1:1-8. [PMID: 30657369 DOI: 10.1200/cci.16.00042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
| | - David Liebner
- All authors: The Ohio State University, Columbus, OH
| | - James L Chen
- All authors: The Ohio State University, Columbus, OH
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23
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Cook-Deegan R, Ankeny RA, Maxson Jones K. Sharing Data to Build a Medical Information Commons: From Bermuda to the Global Alliance. Annu Rev Genomics Hum Genet 2017; 18:389-415. [PMID: 28415857 PMCID: PMC5634517 DOI: 10.1146/annurev-genom-083115-022515] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Human Genome Project modeled its open science ethos on nematode biology, most famously through daily release of DNA sequence data based on the 1996 Bermuda Principles. That open science philosophy persists, but daily, unfettered release of data has had to adapt to constraints occasioned by the use of data from individual people, broader use of data not only by scientists but also by clinicians and individuals, the global reach of genomic applications and diverse national privacy and research ethics laws, and the rising prominence of a diverse commercial genomics sector. The Global Alliance for Genomics and Health was established to enable the data sharing that is essential for making meaning of genomic variation. Data-sharing policies and practices will continue to evolve as researchers, health professionals, and individuals strive to construct a global medical and scientific information commons.
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Affiliation(s)
- Robert Cook-Deegan
- School for the Future of Innovation in Society, Arizona State University, Washington, DC 20009;
| | - Rachel A Ankeny
- School of Humanities, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Kathryn Maxson Jones
- Program in History of Science, Department of History, Princeton University, Princeton, New Jersey 08544
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24
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Rowhani-Farid A, Allen M, Barnett AG. What incentives increase data sharing in health and medical research? A systematic review. Res Integr Peer Rev 2017; 2:4. [PMID: 29451561 PMCID: PMC5803640 DOI: 10.1186/s41073-017-0028-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/13/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The foundation of health and medical research is data. Data sharing facilitates the progress of research and strengthens science. Data sharing in research is widely discussed in the literature; however, there are seemingly no evidence-based incentives that promote data sharing. METHODS A systematic review (registration: 10.17605/OSF.IO/6PZ5E) of the health and medical research literature was used to uncover any evidence-based incentives, with pre- and post-empirical data that examined data sharing rates. We were also interested in quantifying and classifying the number of opinion pieces on the importance of incentives, the number observational studies that analysed data sharing rates and practices, and strategies aimed at increasing data sharing rates. RESULTS Only one incentive (using open data badges) has been tested in health and medical research that examined data sharing rates. The number of opinion pieces (n = 85) out-weighed the number of article-testing strategies (n = 76), and the number of observational studies exceeded them both (n = 106). CONCLUSIONS Given that data is the foundation of evidence-based health and medical research, it is paradoxical that there is only one evidence-based incentive to promote data sharing. More well-designed studies are needed in order to increase the currently low rates of data sharing.
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Affiliation(s)
- Anisa Rowhani-Farid
- Australian Centre for Health Services Innovation, Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, 4059 Australia
| | - Michelle Allen
- Australian Centre for Health Services Innovation, Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, 4059 Australia
| | - Adrian G. Barnett
- Australian Centre for Health Services Innovation, Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, 4059 Australia
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25
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Prawira A, Pugh T, Stockley T, Siu L. Data resources for the identification and interpretation of actionable mutations by clinicians. Ann Oncol 2017; 28:946-957. [DOI: 10.1093/annonc/mdx023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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26
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Vis DJ, Lewin J, Liao RG, Mao M, Andre F, Ward RL, Calvo F, Teh BT, Camargo AA, Knoppers BM, Sawyers CL, Wessels LFA, Lawler M, Siu LL, Voest E. Towards a global cancer knowledge network: dissecting the current international cancer genomic sequencing landscape. Ann Oncol 2017; 28:1145-1151. [PMID: 28453708 PMCID: PMC5406763 DOI: 10.1093/annonc/mdx037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND While next generation sequencing has enhanced our understanding of the biological basis of malignancy, current knowledge on global practices for sequencing cancer samples is limited. To address this deficiency, we developed a survey to provide a snapshot of current sequencing activities globally, identify barriers to data sharing and use this information to develop sustainable solutions for the cancer research community. METHODS A multi-item survey was conducted assessing demographics, clinical data collection, genomic platforms, privacy/ethics concerns, funding sources and data sharing barriers for sequencing initiatives globally. Additionally, respondents were asked as to provide the primary intent of their initiative (clinical diagnostic, research or combination). RESULTS Of 107 initiatives invited to participate, 59 responded (response rate = 55%). Whole exome sequencing (P = 0.03) and whole genome sequencing (P = 0.01) were utilized less frequently in clinical diagnostic than in research initiatives. Procedures to identify cancer-specific variants were heterogeneous, with bioinformatics pipelines employing different mutation calling/variant annotation algorithms. Measurement of treatment efficacy varied amongst initiatives, with time on treatment (57%) and RECIST (53%) being the most common; however, other parameters were also employed. Whilst 72% of initiatives indicated data sharing, its scope varied, with a number of restrictions in place (e.g. transfer of raw data). The largest perceived barriers to data harmonization were the lack of financial support (P < 0.01) and bioinformatics concerns (e.g. lack of interoperability) (P = 0.02). Capturing clinical data was more likely to be perceived as a barrier to data sharing by larger initiatives than by smaller initiatives (P = 0.01). CONCLUSIONS These results identify the main barriers, as perceived by the cancer sequencing community, to effective sharing of cancer genomic and clinical data. They highlight the need for greater harmonization of technical, ethical and data capture processes in cancer sample sequencing worldwide, in order to support effective and responsible data sharing for the benefit of patients.
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Affiliation(s)
- D. J. Vis
- Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - J. Lewin
- Princess Margaret Cancer Centre, Toronto, Canada
| | - R. G. Liao
- Global Alliance for Genomics and Health, Broad Institute, Cambridge, USA
| | - M. Mao
- Yonsei Cancer Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - F. Andre
- INSERM U981, Université Paris Sud, Institut Gustave Roussy, Villejuif, France
| | - R. L. Ward
- Research, University of Queensland, Brisbane, Australia
| | - F. Calvo
- Cancer Core Europe, Gustave Roussy, Villejuif, France
| | | | | | - B. M. Knoppers
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - C. L. Sawyers
- Memorial Sloan Kettering Cancer Centre, New York, USA
| | - L. F. A. Wessels
- Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Bioinformatics & Statistics, Delft University of Technology, Delft, The Netherlands
| | - M. Lawler
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, UK
| | - L. L. Siu
- Princess Margaret Cancer Centre, Toronto, Canada
| | - E. Voest
- Netherlands Cancer Institute, Amsterdam, The Netherlands
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Affiliation(s)
- Susanne B Haga
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, 304 Research Drive, Box 90141, Durham, NC 27708, USA
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28
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Davis-Turak J, Courtney SM, Hazard ES, Glen WB, da Silveira WA, Wesselman T, Harbin LP, Wolf BJ, Chung D, Hardiman G. Genomics pipelines and data integration: challenges and opportunities in the research setting. Expert Rev Mol Diagn 2017; 17:225-237. [PMID: 28092471 DOI: 10.1080/14737159.2017.1282822] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
INTRODUCTION The emergence and mass utilization of high-throughput (HT) technologies, including sequencing technologies (genomics) and mass spectrometry (proteomics, metabolomics, lipids), has allowed geneticists, biologists, and biostatisticians to bridge the gap between genotype and phenotype on a massive scale. These new technologies have brought rapid advances in our understanding of cell biology, evolutionary history, microbial environments, and are increasingly providing new insights and applications towards clinical care and personalized medicine. Areas covered: The very success of this industry also translates into daunting big data challenges for researchers and institutions that extend beyond the traditional academic focus of algorithms and tools. The main obstacles revolve around analysis provenance, data management of massive datasets, ease of use of software, interpretability and reproducibility of results. Expert commentary: The authors review the challenges associated with implementing bioinformatics best practices in a large-scale setting, and highlight the opportunity for establishing bioinformatics pipelines that incorporate data tracking and auditing, enabling greater consistency and reproducibility for basic research, translational or clinical settings.
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Affiliation(s)
| | - Sean M Courtney
- b MUSC Bioinformatics , Center for Genomics Medicine, Medical University of South Carolina (MUSC) , Charleston , SC.,c Department of Pathology and Laboratory Medicine , MUSC , Charleston , USA
| | - E Starr Hazard
- b MUSC Bioinformatics , Center for Genomics Medicine, Medical University of South Carolina (MUSC) , Charleston , SC.,d Library Science and Informatics , MUSC , Charleston , USA
| | - W Bailey Glen
- b MUSC Bioinformatics , Center for Genomics Medicine, Medical University of South Carolina (MUSC) , Charleston , SC.,c Department of Pathology and Laboratory Medicine , MUSC , Charleston , USA
| | - Willian A da Silveira
- b MUSC Bioinformatics , Center for Genomics Medicine, Medical University of South Carolina (MUSC) , Charleston , SC.,c Department of Pathology and Laboratory Medicine , MUSC , Charleston , USA
| | | | - Larry P Harbin
- e Department of Public Health Sciences , MUSC , Charleston , USA
| | - Bethany J Wolf
- e Department of Public Health Sciences , MUSC , Charleston , USA
| | - Dongjun Chung
- e Department of Public Health Sciences , MUSC , Charleston , USA
| | - Gary Hardiman
- b MUSC Bioinformatics , Center for Genomics Medicine, Medical University of South Carolina (MUSC) , Charleston , SC.,e Department of Public Health Sciences , MUSC , Charleston , USA.,f Department of Medicine , MUSC , Charleston , USA
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O'Connor BD, Yuen D, Chung V, Duncan AG, Liu XK, Patricia J, Paten B, Stein L, Ferretti V. The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows. F1000Res 2017; 6:52. [PMID: 28344774 PMCID: PMC5333608 DOI: 10.12688/f1000research.10137.1] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/11/2017] [Indexed: 11/20/2022] Open
Abstract
As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing. If run locally, an operation at this scale would have monopolized a typical academic data centre for many months, and would have presented major challenges for data storage and distribution. However, this scale is increasingly typical for genomics projects and necessitates a rethink of how analytical tools are packaged and moved to the data. For PCAWG, we embraced the use of highly portable Docker images for encapsulating and sharing complex alignment and variant calling workflows across highly variable environments. While successful, this endeavor revealed a limitation in Docker containers, namely the lack of a standardized way to describe and execute the tools encapsulated inside the container. As a result, we created the Dockstore ( https://dockstore.org), a project that brings together Docker images with standardized, machine-readable ways of describing and running the tools contained within. This service greatly improves the sharing and reuse of genomics tools and promotes interoperability with similar projects through emerging web service standards developed by the Global Alliance for Genomics and Health (GA4GH).
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Affiliation(s)
- Brian D O'Connor
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Denis Yuen
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, Canada
| | - Vincent Chung
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, Canada
| | - Andrew G Duncan
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, Canada
| | - Xiang Kun Liu
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, Canada
| | - Janice Patricia
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, Canada
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Lincoln Stein
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, Canada
| | - Vincent Ferretti
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, Canada
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30
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Brouwer A, De Laere B, Peeters D, Peeters M, Salgado R, Dirix L, Van Laere S. Evaluation and consequences of heterogeneity in the circulating tumor cell compartment. Oncotarget 2016; 7:48625-48643. [PMID: 26980749 PMCID: PMC5217044 DOI: 10.18632/oncotarget.8015] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 02/18/2016] [Indexed: 02/06/2023] Open
Abstract
A growing understanding of the molecular biology of cancer and the identification of specific aberrations driving cancer evolution have led to the development of various targeted agents. Therapeutic decisions concerning these drugs are often guided by single biopsies of the primary tumor. Yet, it is well known that tumors can exhibit significant heterogeneity and change over time as a result of selective pressure. Circulating tumor cells (CTCs) are shed from various tumor sites and are thought to represent the molecular landscape of a patient's overall tumor burden. Moreover, a minimal-invasive liquid biopsy facilitates monitoring of clonal evolution during therapy pressure and disease progression in real-time. While more information becomes available regarding heterogeneity among CTCs, comparison between these studies is needed. In this review, we focus on the genomic and transcriptional heterogeneity found in the CTC compartment, and its significance for clinical decision making.
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Affiliation(s)
- Anja Brouwer
- Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium
- Department of Oncology, Antwerp University Hospital, Antwerp, Belgium
| | - Bram De Laere
- Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium
| | - Dieter Peeters
- Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium
- Department of Pathology, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Marc Peeters
- Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium
- Department of Oncology, Antwerp University Hospital, Antwerp, Belgium
| | - Roberto Salgado
- Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium
- Department of Pathology, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
- Breast Cancer Translational Research Laboratory, Jules Bordet Institute, Brussels, Belgium
| | - Luc Dirix
- Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium
- Department of Oncology, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Steven Van Laere
- Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium
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Abstract
As with other complex diseases, unbiased association studies followed by physiological and experimental characterization have for years formed a paradigm for identifying genes or processes of relevance to type 2 diabetes mellitus (T2D). Recent large-scale common and rare variant genome-wide association studies (GWAS) suggest that substantially larger association studies are needed to identify most T2D loci in the population. To hasten clinical translation of genetic discoveries, new paradigms are also required to aid specialized investigation of nascent hypotheses. We argue for an integrated T2D knowledgebase, designed for a worldwide community to access aggregated large-scale genetic data sets, as one paradigm to catalyse convergence of these efforts.
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Dunne PD, O'Reilly PG, Coleman HG, Gray RT, Longley DB, Johnston PG, Salto-Tellez M, Lawler M, McArt DG. Stratified analysis reveals chemokine-like factor (CKLF) as a potential prognostic marker in the MSI-immune consensus molecular subtype CMS1 of colorectal cancer. Oncotarget 2016; 7:36632-36644. [PMID: 27153559 PMCID: PMC5095027 DOI: 10.18632/oncotarget.9126] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/16/2016] [Indexed: 11/25/2022] Open
Abstract
The Colorectal Cancer (CRC) Subtyping Consortium (CRCSC) recently published four consensus molecular subtypes (CMS's) representing the underlying biology in CRC. The Microsatellite Instable (MSI) immune group, CMS1, has a favorable prognosis in early stage disease, but paradoxically has the worst prognosis following relapse, suggesting the presence of factors enabling neoplastic cells to circumvent this immune response. To identify the genes influencing subsequent poor prognosis in CMS1, we analyzed this subtype, centered on risk of relapse. In a cohort of early stage colon cancer (n=460), we examined, in silico, changes in gene expression within the CMS1 subtype and demonstrated for the first time the favorable prognostic value of chemokine-like factor (CKLF) gene expression in the adjuvant disease setting [HR=0.18, CI=0.04-0.89]. In addition, using transcription profiles originating from cell sorted CRC tumors, we delineated the source of CKLF transcription within the colorectal tumor microenvironment to the leukocyte component of these tumors. Further to this, we confirmed that CKLF gene expression is confined to distinct immune subsets in whole blood samples and primary cell lines, highlighting CKLF as a potential immune cell-derived factor promoting tumor immune-surveillance of nascent neoplastic cells, particularly in CMS1 tumors. Building on the recently reported CRCSC data, we provide compelling evidence that leukocyte-infiltrate derived CKLF expression is a candidate biomarker of favorable prognosis, specifically in MSI-immune stage II/III disease.
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Affiliation(s)
- Philip D. Dunne
- Centre for Cancer Research and Cell Biology, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, UK
| | - Paul G. O'Reilly
- Centre for Cancer Research and Cell Biology, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, UK
| | - Helen G. Coleman
- Centre for Public Health, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, UK
| | - Ronan T. Gray
- Centre for Public Health, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, UK
| | - Daniel B. Longley
- Centre for Cancer Research and Cell Biology, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, UK
| | - Patrick G. Johnston
- Centre for Cancer Research and Cell Biology, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, UK
| | - Manuel Salto-Tellez
- Centre for Cancer Research and Cell Biology, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, UK
| | - Mark Lawler
- Centre for Cancer Research and Cell Biology, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, UK
| | - Darragh G. McArt
- Centre for Cancer Research and Cell Biology, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, UK
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Siu LL, Lawler M, Haussler D, Knoppers BM, Lewin J, Vis DJ, Liao RG, Andre F, Banks I, Barrett JC, Caldas C, Camargo AA, Fitzgerald RC, Mao M, Mattison JE, Pao W, Sellers WR, Sullivan P, Teh BT, Ward R, ZenKlusen JC, Sawyers CL, Voest EE. Facilitating a culture of responsible and effective sharing of cancer genome data. Nat Med 2016; 22:464-71. [PMID: 27149219 PMCID: PMC4995884 DOI: 10.1038/nm.4089] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 03/21/2016] [Indexed: 12/17/2022]
Abstract
Rapid and affordable tumor molecular profiling has led to an explosion of clinical and genomic data poised to enhance the diagnosis, prognostication and treatment of cancer. A critical point has now been reached at which the analysis and storage of annotated clinical and genomic information in unconnected silos will stall the advancement of precision cancer care. Information systems must be harmonized to overcome the multiple technical and logistical barriers to data sharing. Against this backdrop, the Global Alliance for Genomic Health (GA4GH) was established in 2013 to create a common framework that enables responsible, voluntary and secure sharing of clinical and genomic data. This Perspective from the GA4GH Clinical Working Group Cancer Task Team highlights the data-aggregation challenges faced by the field, suggests potential collaborative solutions and describes how GA4GH can catalyze a harmonized data-sharing culture.
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Affiliation(s)
- Lillian L. Siu
- Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
| | - Mark Lawler
- Centre for Cancer Research and Cell Biology, Queen’s University, Belfast, UK
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | - Jeremy Lewin
- Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
| | - Daniel J. Vis
- The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Rachel G. Liao
- The Global Alliance for Genomics and Health, Toronto, Canada and the Broad Institute, Cambridge, MA, USA
| | - Fabrice Andre
- Gustave Roussy and Université Paris Sud, Villejuif, France
| | - Ian Banks
- Patient’s Advocacy Committee, European Cancer Organization, Brussels, Belgium
| | - J. Carl Barrett
- Translational Sciences, Oncology iMED, AstraZeneca, Waltham, MA, USA
| | | | | | | | - Mao Mao
- Yonsei Cancer Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | | | - William Pao
- Roche Innovation Center Basel, Pharma Research and Early Development, Roche, Basel, Switzerland
| | | | - Patrick Sullivan
- Advocacy for Canadian Children Oncology Network, Vancouver, Canada
| | | | - Robyn Ward
- University of Queensland, St. Lucia, Australia
| | - Jean Claude ZenKlusen
- The Cancer Genome Atlas, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Emile E. Voest
- The Netherlands Cancer Institute, Amsterdam, the Netherlands
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Nair P, Bizzari S, Rajah N, Assaf N, Al-Ali MT, Hamzeh AR. Genetics of multifactorial disorders: proceedings of the 6th Pan Arab Human Genetics Conference. J Transl Med 2016; 14:96. [PMID: 27095177 PMCID: PMC4837509 DOI: 10.1186/s12967-016-0854-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 04/06/2016] [Indexed: 11/10/2022] Open
Abstract
The 6th Pan Arab Human Genetics Conference (PAHGC), "Genetics of Multifactorial Disorders" was organized by the Center for Arab Genomic Studies (http://www.cags.org.ae) in Dubai, United Arab Emirates from 21 to 23 January, 2016. The PAHGCs are held biennially to provide a common platform to bring together regional and international geneticists to share their knowledge and to discuss common issues. Over 800 delegates attended the first 2 days of the conference and these came from various medical and scientific backgrounds. They consisted of geneticists, molecular biologists, medical practitioners, postdoctoral researchers, technical staff (e.g., nurses and lab technicians) and medical students from 35 countries around the world. On the 3rd day, a one-day workshop on "Genetic Counseling" was delivered to 26 participants. The conference focused on four major topics, namely, diabetes, genetics of neurodevelopmental disorders, congenital anomalies and cancer genetics. Personalized medicine was a recurrent theme in most of the research presented at the conference, as was the application of novel molecular findings in clinical settings. This report discusses a summary of the presentations from the meeting.
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Affiliation(s)
- Pratibha Nair
- Centre for Arab Genomic Studies, P.O. Box 22252, Dubai, UAE
| | - Sami Bizzari
- Centre for Arab Genomic Studies, P.O. Box 22252, Dubai, UAE
| | - Nirmal Rajah
- Centre for Arab Genomic Studies, P.O. Box 22252, Dubai, UAE
| | - Nada Assaf
- Centre for Arab Genomic Studies, P.O. Box 22252, Dubai, UAE
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Horgan D, Lawler M, Brand A. Getting Personal: Accelerating Personalised and Precision Medicine Integration into Clinical Cancer Research and Care in Clinical Trials. Public Health Genomics 2015; 18:325-8. [DOI: 10.1159/000441554] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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