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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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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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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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Mamzer MF, Duchange N, Darquy S, Marvanne P, Rambaud C, Marsico G, Cerisey C, Scotté F, Burgun A, Badoual C, Laurent-Puig P, Hervé C. Partnering with patients in translational oncology research: ethical approach. J Transl Med 2017; 15:74. [PMID: 28390420 PMCID: PMC5385033 DOI: 10.1186/s12967-017-1177-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/01/2017] [Indexed: 11/10/2022] Open
Abstract
Background The research program CARPEM (cancer research and personalized medicine) brings together the expertise of researchers and hospital-based oncologists to develop translational research in the context of personalized or “precision” medicine for cancer. There is recognition that patient involvement can help to take into account their needs and priorities in the development of this emerging practice but there is currently no consensus about how this can be achieved. In this study, we developed an empirical ethical research action aiming to improve patient representatives’ involvement in the development of the translational research program together with health professionals. The aim is to promote common understanding and sharing of knowledge between all parties and to establish a long-term partnership integrating patient’s expectations. Methods Two distinct committees were settled in CARPEM: an “Expert Committee”, gathering healthcare and research professionals, and a “Patient Committee”, gathering patients and patient representatives. A multidisciplinary team trained in medical ethics research ensured communication between the two committees as well as analysis of discussions, minutes and outputs from all stakeholders. Results The results highlight the efficiency of the transfer of knowledge between interested parties. Patient representatives and professionals were able to identify new ethical challenges and co-elaborate new procedures to gather information and consent forms for adapting to practices and recommendations developed during the process. Moreover, included patient representatives became full partners and participated in the transfer of knowledge to the public via conferences and publications. Conclusions Empirical ethical research based on a patient-centered approach could help in establishing a fair model for coordination and support actions during cancer research, striking a balance between the regulatory framework, researcher needs and patient expectations. Our approach addresses the concept of translational ethics as a way to handle the main remaining gap between combining care and research activities in the medical pathway and the existing framework.
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Affiliation(s)
- Marie-France Mamzer
- Laboratoire d'Ethique Médicale et Médecine Légale EA4569, Faculté de Médecine, Université Paris Descartes, 45 rue des Saints-Pères, 75006, Paris, France. .,Unité fonctionnelle d'éthique et médecine légale, Hôpital Necker-Enfants malades, Assistance publique-Hôpitaux de Paris, 75015, Paris, France.
| | - Nathalie Duchange
- Laboratoire d'Ethique Médicale et Médecine Légale EA4569, Faculté de Médecine, Université Paris Descartes, 45 rue des Saints-Pères, 75006, Paris, France
| | - Sylviane Darquy
- Laboratoire d'Ethique Médicale et Médecine Légale EA4569, Faculté de Médecine, Université Paris Descartes, 45 rue des Saints-Pères, 75006, Paris, France
| | | | - Claude Rambaud
- Collectif Interassociatif Sur la Santé (CISS), 75007, Paris, France
| | | | | | - Florian Scotté
- Laboratoire d'Ethique Médicale et Médecine Légale EA4569, Faculté de Médecine, Université Paris Descartes, 45 rue des Saints-Pères, 75006, Paris, France.,Soins de support, Service de cancérologie, Hôpital Européen Georges Pompidou, Assistance publique-Hôpitaux de Paris, 75015, Paris, France
| | - Anita Burgun
- Département d'informatique médicale, de biostatistique et de santé publique, Hôpital Européen Georges Pompidou, Assistance publique-Hôpitaux de Paris, 75015, Paris, France.,UMR-S 1138, Centre de recherche des Cordeliers, 75006, Paris, France.,Faculté de médecine Paris Descartes, Sorbonne universités, Paris, France
| | - Cécile Badoual
- Centre de Ressources biologiques, Service d'anatomo-pathologie, Hôpital Européen Georges Pompidou, Assistance publique-Hôpitaux de Paris, 75015, Paris, France
| | - Pierre Laurent-Puig
- Inserm UMR-S 1147, Université Paris Descartes, 75006, Paris, France.,Service de Biochimie Pharmacogénétique et Oncologie Moléculaire, Hôpital Européen Georges Pompidou, Assistance publique-Hôpitaux de Paris, 75015, Paris, France
| | - Christian Hervé
- Laboratoire d'Ethique Médicale et Médecine Légale EA4569, Faculté de Médecine, Université Paris Descartes, 45 rue des Saints-Pères, 75006, Paris, France
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Predicting clinical benefit from everolimus in patients with advanced solid tumors, the CPCT-03 study. Oncotarget 2017; 8:55582-55592. [PMID: 28903445 PMCID: PMC5589684 DOI: 10.18632/oncotarget.16029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 02/07/2017] [Indexed: 01/18/2023] Open
Abstract
Background In this study, our aim was to identify molecular aberrations predictive for response to everolimus, an mTOR inhibitor, regardless of tumor type. Methods To generate hypotheses about potential markers for sensitivity to mTOR inhibition, drug sensitivity and genomic profiles of 835 cell lines were analyzed. Subsequently, a multicenter study was conducted. Patients with advanced solid tumors lacking standard of care treatment options were included and underwent a pre-treatment tumor biopsy to enable DNA sequencing of 1,977 genes, derive copy number profiles and determine activation status of pS6 and pERK. Treatment benefit was determined according to TTP ratio and RECIST. We tested for associations between treatment benefit and single molecular aberrations, clusters of aberrations and pathway perturbation. Results Cell line screens indicated several genes, such as PTEN (P = 0.016; Wald test), to be associated with sensitivity to mTOR inhibition. Subsequently 73 patients were included, of which 59 started treatment with everolimus. Response and molecular data were available from 43 patients. PTEN aberrations, i.e. copy number loss or mutation, were associated with treatment benefit (P = 0.046; Fisher's exact test). Conclusion Loss-of-function aberrations in PTEN potentially represent a tumor type agnostic biomarker for benefit from everolimus and warrants further confirmation in subsequent studies.
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Abstract
In this Perspective, David Hyman and coauthors discuss clinical research on the application of genomic information in oncology.
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Affiliation(s)
- Alison M. Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Michael F. Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Weill Cornell Medical College, New York, New York, United States of America
| | - David M. Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Weill Cornell Medical College, New York, New York, United States of America
- * E-mail:
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A cloud-based workflow to quantify transcript-expression levels in public cancer compendia. Sci Rep 2016; 6:39259. [PMID: 27982081 PMCID: PMC5159871 DOI: 10.1038/srep39259] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/22/2016] [Indexed: 01/08/2023] Open
Abstract
Public compendia of sequencing data are now measured in petabytes. Accordingly, it is infeasible for researchers to transfer these data to local computers. Recently, the National Cancer Institute began exploring opportunities to work with molecular data in cloud-computing environments. With this approach, it becomes possible for scientists to take their tools to the data and thereby avoid large data transfers. It also becomes feasible to scale computing resources to the needs of a given analysis. We quantified transcript-expression levels for 12,307 RNA-Sequencing samples from the Cancer Cell Line Encyclopedia and The Cancer Genome Atlas. We used two cloud-based configurations and examined the performance and cost profiles of each configuration. Using preemptible virtual machines, we processed the samples for as little as $0.09 (USD) per sample. As the samples were processed, we collected performance metrics, which helped us track the duration of each processing step and quantified computational resources used at different stages of sample processing. Although the computational demands of reference alignment and expression quantification have decreased considerably, there remains a critical need for researchers to optimize preprocessing steps. We have stored the software, scripts, and processed data in a publicly accessible repository (https://osf.io/gqrz9).
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Rasmussen LV, Overby CL, Connolly J, Chute CG, Denny JC, Freimuth R, Hartzler AL, Holm IA, Manzi S, Pathak J, Peissig PL, Smith M, Williams MS, Shirts BH, Stoffel EM, Tarczy-Hornoch P, Rohrer Vitek CR, Wolf WA, Starren J. Practical considerations for implementing genomic information resources. Experiences from eMERGE and CSER. Appl Clin Inform 2016; 7:870-82. [PMID: 27652374 DOI: 10.4338/aci-2016-04-ra-0060] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 08/12/2016] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES To understand opinions and perceptions on the state of information resources specifically targeted to genomics, and approaches to delivery in clinical practice. METHODS We conducted a survey of genomic content use and its clinical delivery from representatives across eight institutions in the electronic Medical Records and Genomics (eMERGE) network and two institutions in the Clinical Sequencing Exploratory Research (CSER) consortium in 2014. RESULTS Eleven responses representing distinct projects across ten sites showed heterogeneity in how content is being delivered, with provider-facing content primarily delivered via the electronic health record (EHR) (n=10), and paper/pamphlets as the leading mode for patient-facing content (n=9). There was general agreement (91%) that new content is needed for patients and providers specific to genomics, and that while aspects of this content could be shared across institutions there remain site-specific needs (73% in agreement). CONCLUSION This work identifies a need for the improved access to and expansion of information resources to support genomic medicine, and opportunities for content developers and EHR vendors to partner with institutions to develop needed resources, and streamline their use - such as a central content site in multiple modalities while implementing approaches to allow for site-specific customization.
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Affiliation(s)
- Luke V Rasmussen
- Luke Rasmussen, Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 750 North Lake Shore Drive, 11th Floor, Rubloff Building, Chicago, IL 60611, Phone: 312-503-2823
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Jordan B. [Does a cancer moonshot make sense?]. Med Sci (Paris) 2016; 32:784-6. [PMID: 27615190 DOI: 10.1051/medsci/20163208030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The recently announced "Cancer moonshot" may be greeted with scepticism: the previous "War on cancer" (1971) was not very successful. However the current plan seems well targeted, with emphasis not only on research investment but also on a strong effort to "break down silos" and ensure wide dissemination and use of clinical and molecular data. One big uncertainty, however, is what will happen to the programme after the 2016 presidential election… ‡.
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Affiliation(s)
- Bertrand Jordan
- UMR 7268 ADÉS, Aix-Marseille, Université/EFS/CNRS, Espace éthique méditerranéen, hôpital d'adultes la Timone, 264, rue Saint-Pierre, 13385 Marseille Cedex 05, France
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Perales Palacios I, García Campos F, Michaus Oquiñena L, Blanco Guzmán S, Lantero Benedito M. [Isolation of Plesiomonas shigelloides in a case of gastroenteritis]. Rev Clin Esp 1984; 15:353-365. [PMID: 6658089 DOI: 10.1038/s41571-018-0002-6] [Citation(s) in RCA: 308] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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