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Youssef A, Ng MY, Long J, Hernandez-Boussard T, Shah N, Miner A, Larson D, Langlotz CP. Organizational Factors in Clinical Data Sharing for Artificial Intelligence in Health Care. JAMA Netw Open 2023; 6:e2348422. [PMID: 38113040 PMCID: PMC10731479 DOI: 10.1001/jamanetworkopen.2023.48422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/03/2023] [Indexed: 12/21/2023] Open
Abstract
Importance Limited sharing of data sets that accurately represent disease and patient diversity limits the generalizability of artificial intelligence (AI) algorithms in health care. Objective To explore the factors associated with organizational motivation to share health data for AI development. Design, Setting, and Participants This qualitative study investigated organizational readiness for sharing health data across the academic, governmental, nonprofit, and private sectors. Using a multiple case studies approach, 27 semistructured interviews were conducted with leaders in data-sharing roles from August 29, 2022, to January 9, 2023. The interviews were conducted in the English language using a video conferencing platform. Using a purposive and nonprobabilistic sampling strategy, 78 individuals across 52 unique organizations were identified. Of these, 35 participants were enrolled. Participant recruitment concluded after 27 interviews, as theoretical saturation was reached and no additional themes emerged. Main Outcome and Measure Concepts defining organizational readiness for data sharing and the association between data-sharing factors and organizational behavior were mapped through iterative qualitative analysis to establish a framework defining organizational readiness for sharing clinical data for AI development. Results Interviews included 27 leaders from 18 organizations (academia: 10, government: 7, nonprofit: 8, and private: 2). Organizational readiness for data sharing centered around 2 main constructs: motivation and capabilities. Motivation related to the alignment of an organization's values with data-sharing priorities and was associated with its engagement in data-sharing efforts. However, organizational motivation could be modulated by extrinsic incentives for financial or reputational gains. Organizational capabilities comprised infrastructure, people, expertise, and access to data. Cross-sector collaboration was a key strategy to mitigate barriers to access health data. Conclusions and Relevance This qualitative study identified sector-specific factors that may affect the data-sharing behaviors of health organizations. External incentives may bolster cross-sector collaborations by helping overcome barriers to accessing health data for AI development. The findings suggest that tailored incentives may boost organizational motivation and facilitate sustainable flow of health data for AI development.
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Affiliation(s)
- Alaa Youssef
- Department of Radiology, Stanford University School of Medicine, Stanford, California
- Department of Medicine, Biomedical Informatics Research, Stanford University School of Medicine, California
| | - Madelena Y. Ng
- Department of Medicine, Biomedical Informatics Research, Stanford University School of Medicine, California
| | - Jin Long
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Tina Hernandez-Boussard
- Department of Medicine, Biomedical Informatics Research, Stanford University School of Medicine, California
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California
| | - Nigam Shah
- Department of Medicine, Biomedical Informatics Research, Stanford University School of Medicine, California
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California
| | - Adam Miner
- Department of Psychiatry, Stanford University School of Medicine, Stanford, California
| | - David Larson
- Department of Radiology, Stanford University School of Medicine, Stanford, California
| | - Curtis P. Langlotz
- Department of Radiology, Stanford University School of Medicine, Stanford, California
- Department of Medicine, Biomedical Informatics Research, Stanford University School of Medicine, California
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California
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2
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Ohnmacht AJ, Rajamani A, Avar G, Kutkaite G, Gonçalves E, Saur D, Menden MP. The pharmacoepigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity. Commun Biol 2023; 6:825. [PMID: 37558831 PMCID: PMC10412573 DOI: 10.1038/s42003-023-05198-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 08/01/2023] [Indexed: 08/11/2023] Open
Abstract
Aberrant DNA methylation accompanies genetic alterations during oncogenesis and tumour homeostasis and contributes to the transcriptional deregulation of key signalling pathways in cancer. Despite increasing efforts in DNA methylation profiling of cancer patients, there is still a lack of epigenetic biomarkers to predict treatment efficacy. To address this, we analyse 721 cancer cell lines across 22 cancer types treated with 453 anti-cancer compounds. We systematically detect the predictive component of DNA methylation in the context of transcriptional and mutational patterns, i.e., in total 19 DNA methylation biomarkers across 17 drugs and five cancer types. DNA methylation constitutes drug sensitivity biomarkers by mediating the expression of proximal genes, thereby enhancing biological signals across multi-omics data modalities. Our method reproduces anticipated associations, and in addition, we find that the NEK9 promoter hypermethylation may confer sensitivity to the NEDD8-activating enzyme (NAE) inhibitor pevonedistat in melanoma through downregulation of NEK9. In summary, we envision that epigenomics will refine existing patient stratification, thus empowering the next generation of precision oncology.
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Affiliation(s)
- Alexander Joschua Ohnmacht
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany
| | - Anantharamanan Rajamani
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Ismaninger Str. 22, 81675, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Göksu Avar
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany
| | - Ginte Kutkaite
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany
| | - Emanuel Gonçalves
- Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001, Lisbon, Portugal
- INESC-ID, 1000-029, Lisbon, Portugal
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Ismaninger Str. 22, 81675, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Michael Patrick Menden
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany.
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany.
- Department of Biochemistry and Pharmacology, University of Melbourne, Victoria, VIC, 3010, Australia.
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3
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Sora V, Tiberti M, Beltrame L, Dogan D, Robbani SM, Rubin J, Papaleo E. PyInteraph2 and PyInKnife2 to Analyze Networks in Protein Structural Ensembles. J Chem Inf Model 2023; 63:4237-4245. [PMID: 37437128 DOI: 10.1021/acs.jcim.3c00574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Due to the complex nature of noncovalent interactions and their long-range effects, analyzing protein conformations using network theory can be enlightening. Protein Structure Networks (PSNs) provide a convenient formalism to study protein structures in relation to essential properties such as key residues for structural stability, allosteric communication, and the effects of modifications of the protein. PSNs can be defined according to very different principles, and the available tools have limitations in input formats, supported models, and version control. Other outstanding problems are related to the definition of network cutoffs and the assessment of the stability of the network properties. The protein science community could benefit from a common framework to carry out these analyses and make them easier to reproduce, reuse, and evaluate. We here provide two open-source software packages, PyInteraph2 and PyInKnife2, to implement and analyze PSNs in a reproducible and documented manner. PyInteraph2 interfaces with multiple formats for protein ensembles and incorporates different network models with the possibility of integrating them into a macronetwork and performing various downstream analyses, including hubs, connected components, and several other centrality measures, and visualizes the networks or further analyzes them thanks to compatibility with Cytoscape.PyInKnife2 that supports the network models implemented in PyInteraph2. It employs a jackknife resampling approach to estimate the convergence of network properties and streamline the selection of distance cutoffs. We foresee that the modular structure of the code and the supported version control system will promote the transition to a community-driven effort, boost reproducibility, and establish common protocols in the PSN field. As developers, we will guarantee the introduction of new functionalities and maintenance, assistance, and training of new contributors.
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Affiliation(s)
- Valentina Sora
- Cancer Structural Biology, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark
- Cancer Systems Biology, Section of Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Ludovica Beltrame
- Cancer Systems Biology, Section of Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Deniz Dogan
- Cancer Structural Biology, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Shahriyar Mahdi Robbani
- Cancer Structural Biology, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Joshua Rubin
- Cancer Structural Biology, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark
- Cancer Systems Biology, Section of Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
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4
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A patient-driven clinicogenomic partnership for metastatic prostate cancer. CELL GENOMICS 2022; 2. [PMID: 36177448 PMCID: PMC9518748 DOI: 10.1016/j.xgen.2022.100169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular profiling studies have enabled discoveries for metastatic prostate cancer (MPC) but have predominantly occurred in academic medical institutions and involved non-representative patient populations. We established the Metastatic Prostate Cancer Project (MPCproject, mpcproject.org), a patient-partnered initiative to involve patients with MPC living anywhere in the US and Canada in molecular research. Here, we present results from our partnership with the first 706 MPCproject participants. While 41% of patient partners live in rural, physician-shortage, or medically underserved areas, the MPCproject has not yet achieved racial diversity, a disparity that demands new initiatives detailed herein. Among molecular data from 333 patient partners (572 samples), exome sequencing of 63 tumor and 19 cell-free DNA (cfDNA) samples recapitulated known findings in MPC, while inexpensive ultra-low-coverage sequencing of 318 cfDNA samples revealed clinically relevant AR amplifications. This study illustrates the power of a growing, longitudinal partnership with patients to generate a more representative understanding of MPC. Crowdis et al. describe the MPCproject (mpcproject.org), a decentralized initiative to partner with patients with metastatic prostate cancer in the US and Canada to accelerate molecular research. The authors describe clinicogenomic results from the first 706 geographically diverse patient partners and lay the foundation for sustained and inclusive partnership in this disease.
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Identification and Assessment of Risks in Biobanking: The Case of the Cancer Institute of Bari. Cancers (Basel) 2022; 14:cancers14143460. [PMID: 35884521 PMCID: PMC9319616 DOI: 10.3390/cancers14143460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Risk assessment is one of the requirements for all activities involving the management of human biological samples within the framework of the new ISO 20387:2018. Although some theoretical approaches are available for preparing risk assessments in general, there is no evidence in the literature of examples of listed insurable risks for cancer biobanks. To fill this gap and to provide an overview of the survey performed in our cancer Biobank, we have assessed potential exposures to insurable risks. After an analysis of the Biobank structure and focusing on natural catastrophe risks, we produced a summary map of risk scenarios. In addition to implementing security awareness, this also lays the foundation for transferring the residual risk arising from Biobank activities to the insurance market. Abstract Although research biobanks are among the most promising tools to fight disease and improve public health, there are a range of risks biobanks may face that mainly need to be assessed in an attempt to be relieved. We conducted a strategic insurance review of an institutional cancer biobank with the aim of both identifying the insurable risks of our own Biobank and gathering useful evidence of primary exposure to insurable risks. In this practical scenario, risks have been outlined and categorized into inherent and residual risks, along with their possible impact on biobank maintenance. Results at the Biobank of the Cancer Institute of Bari showed evidence of potentially significant and intrinsic risk due to highly relevant threats, along with already implemented improvements that significantly reduce risks to a range of relative acceptability.
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Mateo J, Steuten L, Aftimos P, André F, Davies M, Garralda E, Geissler J, Husereau D, Martinez-Lopez I, Normanno N, Reis-Filho JS, Stefani S, Thomas DM, Westphalen CB, Voest E. Delivering precision oncology to patients with cancer. Nat Med 2022; 28:658-665. [PMID: 35440717 DOI: 10.1038/s41591-022-01717-2] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/26/2022] [Indexed: 12/15/2022]
Abstract
With the increasing use of genomic profiling for diagnosis and therapy guidance in many tumor types, precision oncology is rapidly reshaping cancer care. However, the current trajectory of drug development in oncology results in a paradox: if patients cannot access advanced diagnostics, we may be developing drugs that will reach few patients. In this Perspective, we outline the major challenges to the implementation of precision oncology and discuss critical steps toward resolving these, including facilitation of equal access to genomics tests, ensuring that clinical studies provide robust evidence for new drugs and technologies, enabling physicians to interpret genomics data, and empowering patients toward shared decision-making. A multi-stakeholder approach to evidence generation, value assessment, and healthcare delivery is necessary to translate advances in precision oncology into benefits for patients with cancer globally.
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Affiliation(s)
- Joaquin Mateo
- Vall d'Hebron Institute of Oncology (VHIO) and Vall d'Hebron University Hospital, Barcelona, Spain
| | - Lotte Steuten
- Office of Health Economics, London, UK
- City University of London, London, UK
| | - Philippe Aftimos
- Institut Jules Bordet - Université Libre de Bruxelles, Brussels, Belgium
| | - Fabrice André
- Institut Gustave Roussy, INSERM U981, Université Paris Saclay, Villejuif, France
| | | | - Elena Garralda
- Vall d'Hebron Institute of Oncology (VHIO) and Vall d'Hebron University Hospital, Barcelona, Spain
| | | | | | - Iciar Martinez-Lopez
- Unit of Genetics and Genomics of the Balearic Islands, Son Espases University Hospital, Illes, Balears, Spain
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS 'Fondazione G. Pascale', Naples, Italy
| | | | | | - David M Thomas
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - C Benedikt Westphalen
- Comprehensive Cancer Center Munich & Department of Medicine III, Ludwig Maximilian University of Munich, Munich, Germany
- German Cancer Consortium (DKTK partner site Munich), Heidelberg, Germany
| | - Emile Voest
- Netherlands Cancer Institute, Amsterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
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7
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Casaletto J, Parsons M, Markello C, Iwasaki Y, Momozawa Y, Spurdle AB, Cline M. Federated analysis of BRCA1 and BRCA2 variation in a Japanese cohort. CELL GENOMICS 2022; 2:100109. [PMID: 35373174 PMCID: PMC8975122 DOI: 10.1016/j.xgen.2022.100109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
More than 40% of the germline variants in ClinVar today are variants of uncertain significance (VUSs). These variants remain unclassified in part because the patient-level data needed for their interpretation is siloed. Federated analysis can overcome this problem by "bringing the code to the data": analyzing the sensitive patient-level data computationally within its secure home institution and providing researchers with valuable insights from data that would not otherwise be accessible. We tested this principle with a federated analysis of breast cancer clinical data at RIKEN, derived from the BioBank Japan repository. We were able to analyze these data within RIKEN's secure computational framework without the need to transfer the data, gathering evidence for the interpretation of several variants. This exercise represents an approach to help realize the core charter of the Global Alliance for Genomics and Health (GA4GH): to responsibly share genomic data for the benefit of human health.
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Affiliation(s)
- James Casaletto
- UC Santa Cruz Genomics Institute, Mail Stop: Genomics, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
- Corresponding author
| | - Michael Parsons
- QIMR Berghofer Medical Research Institute, 300 Herston Rd., Herston, QLD 4006, Australia
| | - Charles Markello
- UC Santa Cruz Genomics Institute, Mail Stop: Genomics, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Yusuke Iwasaki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
| | - Amanda B. Spurdle
- QIMR Berghofer Medical Research Institute, 300 Herston Rd., Herston, QLD 4006, Australia
| | - Melissa Cline
- UC Santa Cruz Genomics Institute, Mail Stop: Genomics, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
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8
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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: 6] [Impact Index Per Article: 2.0] [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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Plana A, Furner B, Palese M, Dussault N, Birz S, Graglia L, Kush M, Nicholson J, Hecker-Nolting S, Gaspar N, Rasche M, Bisogno G, Reinhardt D, Zwaan CM, Koscielniak E, Frazier AL, Janeway K, S Hawkins D, Kolb EA, Cohn SL, Pearson ADJ, Volchenboum SL. Pediatric Cancer Data Commons: Federating and Democratizing Data for Childhood Cancer Research. JCO Clin Cancer Inform 2021; 5:1034-1043. [PMID: 34662145 DOI: 10.1200/cci.21.00075] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The international pediatric oncology community has a long history of research collaboration. In the United States, the 2019 launch of the Children's Cancer Data Initiative puts the focus on developing a rich and robust data ecosystem for pediatric oncology. In this spirit, we present here our experience in constructing the Pediatric Cancer Data Commons (PCDC) to highlight the significance of this effort in fighting pediatric cancer and improving outcomes and to provide essential information to those creating resources in other disease areas. The University of Chicago's PCDC team has worked with the international research community since 2015 to build data commons for children's cancers. We identified six critical features of successful data commons design and implementation: (1) establish the need for a data commons, (2) develop and deploy the technical infrastructure, (3) establish and implement governance, (4) make the data commons platform easy and intuitive for researchers, (5) socialize the data commons and create working knowledge and expertise in the research community, and (6) plan for longevity and sustainability. Data commons are critical to conducting research on large patient cohorts that will ultimately lead to improved outcomes for children with cancer. There is value in connecting high-quality clinical and phenotype data to external sources of data such as genomic, proteomics, and imaging data. Next steps for the PCDC include creating an informed and invested data-sharing culture, developing sustainable methods of data collection and sharing, standardizing genetic biomarker reporting, incorporating radiologic and molecular analysis data, and building models for electronic patient consent. The methods and processes described here can be extended to any clinical area and provide a blueprint for others wishing to develop similar resources.
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Affiliation(s)
- Alejandro Plana
- Department of Pediatrics, University of Chicago, Chicago, IL
| | - Brian Furner
- Center for Research Informatics, University of Chicago, Chicago, IL
| | - Monica Palese
- Department of Pediatrics, University of Chicago, Chicago, IL
| | - Nicole Dussault
- Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - Suzi Birz
- Department of Pediatrics, University of Chicago, Chicago, IL
| | - Luca Graglia
- Department of Pediatrics, University of Chicago, Chicago, IL
| | - Maura Kush
- Department of Pediatrics, University of Chicago, Chicago, IL
| | - James Nicholson
- Department of Paediatric Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Stefanie Hecker-Nolting
- Klinikum Stuttgart-Olgahospital, Zentrum für Kinder-, Jugend- und Frauenmedizin; Pädiatrie 5 (Onkologie, Hämatologie, Immunologie), Stuttgart Cancer Center, Stuttgart, Germany
| | - Nathalie Gaspar
- Département of Oncology for Child and Adolescent, Gustave Roussy, Villejuif, France
| | - Mareike Rasche
- Department of Pediatric Hematology-Oncology, Pediatrics III, University Hospital of Essen, Essen, Germany
| | - Gianni Bisogno
- Maternal and Child Health Department, Padua University Hospital, Padua, Italy
| | - Dirk Reinhardt
- Department of Pediatric Hematology-Oncology, Pediatrics III, University Hospital of Essen, Essen, Germany
| | - C Michel Zwaan
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Ewa Koscielniak
- Klinikum Stuttgart-Olgahospital, Zentrum für Kinder-, Jugend- und Frauenmedizin; Pädiatrie 5 (Onkologie, Hämatologie, Immunologie), Stuttgart Cancer Center, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - A Lindsay Frazier
- Department of Pediatrics, Harvard University, Dana Farber Cancer Institute, Boston, MA
| | - Katherine Janeway
- Department of Pediatrics, Harvard University, Dana Farber Cancer Institute, Boston, MA
| | | | - E Anders Kolb
- Nemours Center for Cancer and Blood Disorders, Alfred I. duPont Hospital for Children, Wilmington, DE
| | - Susan L Cohn
- Department of Pediatrics, University of Chicago, Chicago, IL
| | - Andrew D J Pearson
- Division of Clinical Studies, Institute of Cancer Research, Royal Marsden Hospital, Sutton, United Kingdom.,retired
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10
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Vesteghem C, Brøndum RF, Sønderkær M, Sommer M, Schmitz A, Bødker JS, Dybkær K, El-Galaly TC, Bøgsted M. Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives. Brief Bioinform 2021; 21:936-945. [PMID: 31263868 PMCID: PMC7299292 DOI: 10.1093/bib/bbz044] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/13/2019] [Accepted: 03/21/2019] [Indexed: 12/26/2022] Open
Abstract
Compelling research has recently shown that cancer is so heterogeneous that single research centres cannot produce enough data to fit prognostic and predictive models of sufficient accuracy. Data sharing in precision oncology is therefore of utmost importance. The Findable, Accessible, Interoperable and Reusable (FAIR) Data Principles have been developed to define good practices in data sharing. Motivated by the ambition of applying the FAIR Data Principles to our own clinical precision oncology implementations and research, we have performed a systematic literature review of potentially relevant initiatives. For clinical data, we suggest using the Genomic Data Commons model as a reference as it provides a field-tested and well-documented solution. Regarding classification of diagnosis, morphology and topography and drugs, we chose to follow the World Health Organization standards, i.e. ICD10, ICD-O-3 and Anatomical Therapeutic Chemical classifications, respectively. For the bioinformatics pipeline, the Genome Analysis ToolKit Best Practices using Docker containers offer a coherent solution and have therefore been selected. Regarding the naming of variants, we follow the Human Genome Variation Society's standard. For the IT infrastructure, we have built a centralized solution to participate in data sharing through federated solutions such as the Beacon Networks.
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Affiliation(s)
- Charles Vesteghem
- Department of Clinical Medicine, Aalborg University, Denmark.,Department of Haematology, Aalborg University Hospital, Denmark
| | | | - Mads Sønderkær
- Department of Haematology, Aalborg University Hospital, Denmark
| | - Mia Sommer
- Department of Clinical Medicine, Aalborg University, Denmark.,Department of Haematology, Aalborg University Hospital, Denmark
| | | | | | - Karen Dybkær
- Department of Clinical Medicine, Aalborg University, Denmark.,Department of Haematology, Aalborg University Hospital, Denmark.,Clinical Cancer Research Center, Aalborg University Hospital, Denmark
| | - Tarec Christoffer El-Galaly
- Department of Clinical Medicine, Aalborg University, Denmark.,Department of Haematology, Aalborg University Hospital, Denmark.,Clinical Cancer Research Center, Aalborg University Hospital, Denmark
| | - Martin Bøgsted
- Department of Clinical Medicine, Aalborg University, Denmark.,Department of Haematology, Aalborg University Hospital, Denmark.,Clinical Cancer Research Center, Aalborg University Hospital, Denmark
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Krentel F, Singer F, Rosano-Gonzalez ML, Gibb EA, Liu Y, Davicioni E, Keller N, Stekhoven DJ, Kruithof-de Julio M, Seiler R. A showcase study on personalized in silico drug response prediction based on the genetic landscape of muscle invasive bladder cancer. Sci Rep 2021; 11:5849. [PMID: 33712636 PMCID: PMC7955125 DOI: 10.1038/s41598-021-85151-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/24/2021] [Indexed: 01/31/2023] Open
Abstract
Improved and cheaper molecular diagnostics allow the shift from "one size fits all" therapies to personalised treatments targeting the individual tumor. However, the wealth of potential targets based on comprehensive sequencing remains a yet unsolved challenge that prevents its routine use in clinical practice. Thus, we designed a workflow that selects the most promising treatment targets based on multi-omics sequencing and in silico drug prediction. In this study we demonstrate the workflow with focus on bladder cancer (BLCA), as there are, to date, no reliable diagnostics available to predict the potential benefit of a therapeutic approach. Within the TCGA-BLCA cohort, our workflow identified a panel of 21 genes and 72 drugs that suggested personalized treatment for 95% of patients-including five genes not yet reported as prognostic markers for clinical testing in BLCA. The automated predictions were complemented by manually curated data, thus allowing for accurate sensitivity- or resistance-directed drug response predictions. We discuss potential improvements of drug-gene interaction databases on the basis of pitfalls that were identified during manual curation.
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Affiliation(s)
| | - Franziska Singer
- NEXUS Personalized Health Technologies, ETH Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - María Lourdes Rosano-Gonzalez
- NEXUS Personalized Health Technologies, ETH Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Yang Liu
- GenomeDx Biosciences, Vancouver, Canada
| | | | | | - Daniel J Stekhoven
- NEXUS Personalized Health Technologies, ETH Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marianna Kruithof-de Julio
- Department of Urology, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, Urology Research Laboratory, University of Bern, Bern, Switzerland
- Translational Organoid Research, Department for BioMedical Research, University of Bern, Bern, Switzerland
- Bern Center for Precision Medicine, University of Bern, Bern University Hospital, Bern, Switzerland
| | - Roland Seiler
- Department of Urology, University of Bern, 3010, Bern, Switzerland.
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12
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How wide is the application of genetic big data in biomedicine. Biomed Pharmacother 2020; 133:111074. [PMID: 33378973 DOI: 10.1016/j.biopha.2020.111074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/16/2020] [Accepted: 11/27/2020] [Indexed: 12/17/2022] Open
Abstract
In the era of big data, massive genetic data, as a new industry, has quickly swept almost all industries, especially the pharmaceutical industry. As countries around the world start to build their own gene banks, scientists study the data to explore the origins and migration of humans. Moreover, big data encourage the development of cancer therapy and bring good news to cancer patients. Big datum has been involved in the study of many diseases, and it has been found that analyzing diseases at the gene level can lead to more beneficial treatment options than ordinary treatments. This review will introduce the development of extensive data in medical research from the perspective of big data and tumor, neurological and psychiatric diseases, cardiovascular diseases, other applications and the development direction of big data in medicine.
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13
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Seoighe C, Bracken AP, Buckley P, Doran P, Green R, Healy S, Kavanagh D, Kenny E, Lawler M, Lowery M, Morris D, Morrissey D, O'Byrne JJ, Shields D, Smith O, Steward CA, Sweeney B, Kolch W. The future of genomics in Ireland - focus on genomics for health. HRB Open Res 2020; 3:89. [PMID: 33855271 PMCID: PMC7993626 DOI: 10.12688/hrbopenres.13187.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2020] [Indexed: 12/15/2022] Open
Abstract
Genomics is revolutionizing biomedical research, medicine and healthcare globally in academic, public and industry sectors alike. Concrete examples around the world show that huge benefits for patients, society and economy can be accrued through effective and responsible genomic research and clinical applications. Unfortunately, Ireland has fallen behind and needs to act now in order to catch up. Here, we identify key issues that have resulted in Ireland lagging behind, describe how genomics can benefit Ireland and its people and outline the measures needed to make genomics work for Ireland and Irish patients. There is now an urgent need for a national genomics strategy that enables an effective, collaborative, responsible, well-regulated, and patient centred environment where genome research and clinical genomics can thrive. We present eight recommendations that could be the pillars of a national genomics health strategy.
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Affiliation(s)
- Cathal Seoighe
- National University of Ireland Galway, Galway, H91 TK33, Ireland
| | | | | | - Peter Doran
- University College Dublin, Dublin, 4, Ireland
- Mater Misericordiae University Hospital, Dublin, 7, Ireland
| | - Robert Green
- Brigham Health, Broad Institute, Ariadne Labs, Harvard Medical School, Boston, MA, 02115, USA
| | - Sandra Healy
- National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - David Kavanagh
- Genuity Science (Ireland) Ltd., Dublin, D18 K7W4, Ireland
| | - Elaine Kenny
- Trinity College Dublin, Dublin, 2, Ireland
- ELDA Biotech, Trinity Translational Medicine Institute, St James's Hospital, Dublin, D08 W9RT, Ireland
| | - Mark Lawler
- Queen's University Belfast, Belfast, Northern Ireland, BT7 1NN, Ireland
| | - Maeve Lowery
- Trinity College Dublin, Dublin, 2, Ireland
- Saint James' Hospital, Dublin, D08 NHY1, Ireland
| | - Derek Morris
- National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - Darrin Morrissey
- National Institute for Bioprocessing Research and Training, Blackrock, A94 X099, Ireland
| | | | | | - Owen Smith
- University College Dublin, Dublin, 4, Ireland
- Children’s Health Ireland, Crumlin, Dublin, D12 N512, Ireland
| | | | | | - Walter Kolch
- National University of Ireland Galway, Galway, H91 TK33, Ireland
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14
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Zhu Q, Nguyen DT, Alyea G, Hanson K, Sid E, Pariser A. Phenotypically Similar Rare Disease Identification from an Integrative Knowledge Graph for Data Harmonization: Preliminary Study. JMIR Med Inform 2020; 8:e18395. [PMID: 33006565 PMCID: PMC7568218 DOI: 10.2196/18395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 08/02/2020] [Accepted: 08/19/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Although many efforts have been made to develop comprehensive disease resources that capture rare disease information for the purpose of clinical decision making and education, there is no standardized protocol for defining and harmonizing rare diseases across multiple resources. This introduces data redundancy and inconsistency that may ultimately increase confusion and difficulty for the wide use of these resources. To overcome such encumbrances, we report our preliminary study to identify phenotypical similarity among genetic and rare diseases (GARD) that are presenting similar clinical manifestations, and support further data harmonization. OBJECTIVE To support rare disease data harmonization, we aim to systematically identify phenotypically similar GARD diseases from a disease-oriented integrative knowledge graph and determine their similarity types. METHODS We identified phenotypically similar GARD diseases programmatically with 2 methods: (1) We measured disease similarity by comparing disease mappings between GARD and other rare disease resources, incorporating manual assessment; 2) we derived clinical manifestations presenting among sibling diseases from disease classifications and prioritized the identified similar diseases based on their phenotypes and genotypes. RESULTS For disease similarity comparison, approximately 87% (341/392) identified, phenotypically similar disease pairs were validated; 80% (271/392) of these disease pairs were accurately identified as phenotypically similar based on similarity score. The evaluation result shows a high precision (94%) and a satisfactory quality (86% F measure). By deriving phenotypical similarity from Monarch Disease Ontology (MONDO) and Orphanet disease classification trees, we identified a total of 360 disease pairs with at least 1 shared clinical phenotype and gene, which were applied for prioritizing clinical relevance. A total of 662 phenotypically similar disease pairs were identified and will be applied for GARD data harmonization. CONCLUSIONS We successfully identified phenotypically similar rare diseases among the GARD diseases via 2 approaches, disease mapping comparison and phenotypical similarity derivation from disease classification systems. The results will not only direct GARD data harmonization in expanding translational science research but will also accelerate data transparency and consistency across different disease resources and terminologies, helping to build a robust and up-to-date knowledge resource on rare diseases.
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Affiliation(s)
- Qian Zhu
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Dac-Trung Nguyen
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | | | - Karen Hanson
- ICF International Inc, Rockville, MD, United States
| | - Eric Sid
- Office of Rare Diseases Research (ORDR), National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Anne Pariser
- Office of Rare Diseases Research (ORDR), National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD, United States
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15
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Dass G, Vu MT, Xu P, Audain E, Hitz MP, Grüning B, Hermjakob H, Perez-Riverol Y. The omics discovery REST interface. Nucleic Acids Res 2020; 48:W380-W384. [PMID: 32374843 PMCID: PMC7319562 DOI: 10.1093/nar/gkaa326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/11/2020] [Accepted: 04/21/2020] [Indexed: 01/22/2023] Open
Abstract
The Omics Discovery Index is an open source platform that can be used to access, discover and disseminate omics datasets. OmicsDI integrates proteomics, genomics, metabolomics, models and transcriptomics datasets. Using an efficient indexing system, OmicsDI integrates different biological entities including genes, transcripts, proteins, metabolites and the corresponding publications from PubMed. In addition, it implements a group of pipelines to estimate the impact of each dataset by tracing the number of citations, reanalysis and biological entities reported by each dataset. Here, we present the OmicsDI REST interface (www.omicsdi.org/ws/) to enable programmatic access to any dataset in OmicsDI or all the datasets for a specific provider (database). Clients can perform queries on the API using different metadata information such as sample details (species, tissues, etc), instrumentation (mass spectrometer, sequencer), keywords and other provided annotations. In addition, we present two different libraries in R and Python to facilitate the development of tools that can programmatically interact with the OmicsDI REST interface.
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Affiliation(s)
- Gaurhari Dass
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK
| | - Manh-Tu Vu
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK
| | - Pan Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, 102206 Beijing, China
| | - Enrique Audain
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Marc-Phillip Hitz
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Björn A Grüning
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, 102206 Beijing, China
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK
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16
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Jones SF, McKenzie AJ. Molecular Profiling in Drug Development: Paving a Way Forward. Am Soc Clin Oncol Educ Book 2020; 40:309-318. [PMID: 32463698 DOI: 10.1200/edbk_100024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
As researchers learn more about tumor biology and the molecular mechanisms involved in tumorigenesis, metastasis, and tumor evolution, clinical trials are growing more complex and patient selection for clinical trials is becoming more specific. Rather than exploit certain phenotypic characteristics of tumor cells (e.g., rapid cell division and uncontrolled cell growth), pharmaceuticals targeting the genotypic causes of tumorigenesis are emerging. The sequencing of the human genome, advances in chemical techniques, and increased efficiency in drug target identification have changed the way drugs are developed. Now, more precise drugs targeting specific mutations within individual genes are being used to treat narrow patient populations harboring these specific driver mutations, often with greater efficacy and lower toxicity than traditional chemotherapeutic agents. This precision in drug development relies not only on the ability to design exquisitely specific pharmaceuticals but also to identify (with the same level of precision) the patients who are most likely to respond to those therapies. Robust screening techniques and adequate molecular oncology education are required to match the appropriate patient to precision therapies, and these same screening techniques provide the data necessary to advance to the next generation of drug development.
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17
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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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18
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Terkelsen T, Krogh A, Papaleo E. CAncer bioMarker Prediction Pipeline (CAMPP)-A standardized framework for the analysis of quantitative biological data. PLoS Comput Biol 2020; 16:e1007665. [PMID: 32176694 PMCID: PMC7108742 DOI: 10.1371/journal.pcbi.1007665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 03/31/2020] [Accepted: 01/18/2020] [Indexed: 01/21/2023] Open
Abstract
With the improvement of -omics and next-generation sequencing (NGS) methodologies, along with the lowered cost of generating these types of data, the analysis of high-throughput biological data has become standard both for forming and testing biomedical hypotheses. Our knowledge of how to normalize datasets to remove latent undesirable variances has grown extensively, making for standardized data that are easily compared between studies. Here we present the CAncer bioMarker Prediction Pipeline (CAMPP), an open-source R-based wrapper (https://github.com/ELELAB/CAncer-bioMarker-Prediction-Pipeline -CAMPP) intended to aid bioinformatic software-users with data analyses. CAMPP is called from a terminal command line and is supported by a user-friendly manual. The pipeline may be run on a local computer and requires little or no knowledge of programming. To avoid issues relating to R-package updates, a renv .lock file is provided to ensure R-package stability. Data-management includes missing value imputation, data normalization, and distributional checks. CAMPP performs (I) k-means clustering, (II) differential expression/abundance analysis, (III) elastic-net regression, (IV) correlation and co-expression network analyses, (V) survival analysis, and (VI) protein-protein/miRNA-gene interaction networks. The pipeline returns tabular files and graphical representations of the results. We hope that CAMPP will assist in streamlining bioinformatic analysis of quantitative biological data, whilst ensuring an appropriate bio-statistical framework.
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Affiliation(s)
- Thilde Terkelsen
- Computational Biology Laboratory, Danish Cancer Society Research Center and Center for Autophagy, Recycling and Disease, Copenhagen, Denmark
| | - Anders Krogh
- Unit of Computational and RNA biology, Department of Biology, University of Copenhagen, Copenhagen Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center and Center for Autophagy, Recycling and Disease, Copenhagen, Denmark
- Translational Disease System Biology, Faculty of Health and Medical Science, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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19
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Development of a Precision Medicine Workflow in Hematological Cancers, Aalborg University Hospital, Denmark. Cancers (Basel) 2020; 12:cancers12020312. [PMID: 32013121 PMCID: PMC7073219 DOI: 10.3390/cancers12020312] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/10/2020] [Accepted: 01/27/2020] [Indexed: 12/17/2022] Open
Abstract
Within recent years, many precision cancer medicine initiatives have been developed. Most of these have focused on solid cancers, while the potential of precision medicine for patients with hematological malignancies, especially in the relapse situation, are less elucidated. Here, we present a demographic unbiased and observational prospective study at Aalborg University Hospital Denmark, referral site for 10% of the Danish population. We developed a hematological precision medicine workflow based on sequencing analysis of whole exome tumor DNA and RNA. All steps involved are outlined in detail, illustrating how the developed workflow can provide relevant molecular information to multidisciplinary teams. A group of 174 hematological patients with progressive disease or relapse was included in a non-interventional and population-based study, of which 92 patient samples were sequenced. Based on analysis of small nucleotide variants, copy number variants, and fusion transcripts, we found variants with potential and strong clinical relevance in 62% and 9.5% of the patients, respectively. The most frequently mutated genes in individual disease entities were in concordance with previous studies. We did not find tumor mutational burden or micro satellite instability to be informative in our hematologic patient cohort.
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20
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Factors influencing harmonized health data collection, sharing and linkage in Denmark and Switzerland: A systematic review. PLoS One 2019; 14:e0226015. [PMID: 31830124 PMCID: PMC6907832 DOI: 10.1371/journal.pone.0226015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 11/18/2019] [Indexed: 02/06/2023] Open
Abstract
Introduction The digitalization of medicine has led to a considerable growth of heterogeneous health datasets, which could improve healthcare research if integrated into the clinical life cycle. This process requires, amongst other things, the harmonization of these datasets, which is a prerequisite to improve their quality, re-usability and interoperability. However, there is a wide range of factors that either hinder or favor the harmonized collection, sharing and linkage of health data. Objective This systematic review aims to identify barriers and facilitators to health data harmonization—including data sharing and linkage—by a comparative analysis of studies from Denmark and Switzerland. Methods Publications from PubMed, Web of Science, EMBASE and CINAHL involving cross-institutional or cross-border collection, sharing or linkage of health data from Denmark or Switzerland were searched to identify the reported barriers and facilitators to data harmonization. Results Of the 345 projects included, 240 were single-country and 105 were multinational studies. Regarding national projects, a Swiss study reported on average more barriers and facilitators than a Danish study. Barriers and facilitators of a technical nature were most frequently reported. Conclusion This systematic review gathered evidence from Denmark and Switzerland on barriers and facilitators concerning data harmonization, sharing and linkage. Barriers and facilitators were strictly interrelated with the national context where projects were carried out. Structural changes, such as legislation implemented at the national level, were mirrored in the projects. This underlines the impact of national strategies in the field of health data. Our findings also suggest that more openness and clarity in the reporting of both barriers and facilitators to data harmonization constitute a key element to promote the successful management of new projects using health data and the implementation of proper policies in this field. Our study findings are thus meaningful beyond these two countries.
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21
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Horgan D, Bernini C, Thomas PPM, Morre SA. Cooperating on Data: The Missing Element in Bringing Real Innovation to Europe's Healthcare Systems. Public Health Genomics 2019; 22:77-101. [PMID: 31634895 PMCID: PMC6943808 DOI: 10.1159/000503296] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/03/2019] [Indexed: 12/25/2022] Open
Abstract
Europe's growing awareness of gaps in its healthcare provision is not being matched by an increase in remedial action - despite the rich transformative potential of new approaches to data. The new availability of data offers policymakers tools that would allow Europe's huge investments in health to be far better spent, by being properly targeted. The result would be far better health for far more Europeans. But that requires a step that most European policymakers have not been ready to take. They need to cooperate so that the data can be shared and its full value realised. This paper explores the potential and the challenges that stand in the way of mobilising health data for wider health benefits. This paper goes on to summarise the results of a survey on how different components of the healthcare sector perceive the opportunities from mobilising data effectively, and the barriers to doing so. The responses demonstrated a widespread genuine will to promote research and innovation, and its take-up, for the betterment of healthcare. There was strong appreciation of the merits of data sharing and readiness - under the right circumstances - to share personal health data for research purposes and to undergo genetic sequencing. This paper also suggests the strategic direction that should influence policy formation. The solution can be found without changing the EU treaties, which already provide an adequate base for cooperation. Properly handled, the problems facing European healthcare can be turned into major assets for Europe and make it easier for citizens to have equal access to high-quality care through the meaningful use of digital innovations.
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Affiliation(s)
- Denis Horgan
- European Alliance for Personalised Medicine, Brussels, Belgium,
- Institute for Public Health Genomics, Department of Genetics and Cell Biology, Research Institute GROW, Faculty of Health, Medicine and Life Sciences, University of Maastricht, Maastricht, The Netherlands,
| | - Chiara Bernini
- European Alliance for Personalised Medicine, Brussels, Belgium
| | - Pierre P M Thomas
- Institute for Public Health Genomics, Department of Genetics and Cell Biology, Research Institute GROW, Faculty of Health, Medicine and Life Sciences, University of Maastricht, Maastricht, The Netherlands
| | - Servaas A Morre
- Institute for Public Health Genomics, Department of Genetics and Cell Biology, Research Institute GROW, Faculty of Health, Medicine and Life Sciences, University of Maastricht, Maastricht, The Netherlands
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
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22
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Costigan DC, Dong F. The extended spectrum of RAS-MAPK pathway mutations in colorectal cancer. Genes Chromosomes Cancer 2019; 59:152-159. [PMID: 31589789 DOI: 10.1002/gcc.22813] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 01/07/2023] Open
Abstract
Current clinical guidelines recommend mutation analysis for select codons in KRAS and NRAS exons 2, 3, and 4 and BRAF V600E to guide therapy selection and prognostic stratification in advanced colorectal cancer. This study evaluates the impact of extended molecular testing on the detection of RAS-MAPK pathway mutations. Panel next-generation sequencing results of colorectal cancer specimens from 5795 individuals from the American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange (AACR Project GENIE) were included. Mutations in RAS-MAPK pathway genes were analyzed and functionally annotated. Colorectal cancers had recurrent pathogenic pathway activating mutations in KRAS (44%), NRAS (4%), HRAS (<1%), BRAF (10%), MAP2K1 (1%), RAF1 (<1%), and PTPN11 (<1%). The proportion of colorectal cancers with pathogenic RAS pathway mutations was 37% when only KRAS codon 12 and 13 mutations were considered, 46% when also including select KRAS and NRAS exons 2, 3, and 4 mutations, 53% when including BRAF V600E mutations, and 56% when including all pathogenic mutations. Panel next-generation sequencing testing identifies additional RAS-MAPK pathway driver mutations beyond current guideline recommendations. These mutations have potential implications in treatment selection for patients with advanced colorectal cancer.
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Affiliation(s)
- Danielle C Costigan
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Fei Dong
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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23
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Milne R, Morley KI, Howard H, Niemiec E, Nicol D, Critchley C, Prainsack B, Vears D, Smith J, Steed C, Bevan P, Atutornu J, Farley L, Goodhand P, Thorogood A, Kleiderman E, Middleton A. Trust in genomic data sharing among members of the general public in the UK, USA, Canada and Australia. Hum Genet 2019; 138:1237-1246. [PMID: 31531740 PMCID: PMC6874520 DOI: 10.1007/s00439-019-02062-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/09/2019] [Indexed: 01/08/2023]
Abstract
Trust may be important in shaping public attitudes to genetics and intentions to participate in genomics research and big data initiatives. As such, we examined trust in data sharing among the general public. A cross-sectional online survey collected responses from representative publics in the USA, Canada, UK and Australia (n = 8967). Participants were most likely to trust their medical doctor and less likely to trust other entities named. Company researchers were least likely to be trusted. Low, Variable and High Trust classes were defined using latent class analysis. Members of the High Trust class were more likely to be under 50 years, male, with children, hold religious beliefs, have personal experience of genetics and be from the USA. They were most likely to be willing to donate their genomic and health data for clinical and research uses. The Low Trust class were less reassured than other respondents by laws preventing exploitation of donated information. Variation in trust, its relation to areas of concern about the use of genomic data and potential of legislation are considered. These findings have relevance for efforts to expand genomic medicine and data sharing beyond those with personal experience of genetics or research participants.
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Affiliation(s)
- Richard Milne
- Society and Ethics Research, Connecting Science, Wellcome Genome Campus, Cambridge, UK
- Institute of Public Health, University of Cambridge, Cambridge, UK
| | - Katherine I Morley
- RAND Europe, Cambridge, UK
- National Addiction Centre, King's College London Institute of Psychiatry, Psychology and Neuroscience, London, UK
- Centre for Epidemiology and Biostatistics, Melbourne School of Global and Population Health, The University of Melbourne, Melbourne, Australia
| | - Heidi Howard
- Centre for Research Ethics and Bioethics, Uppsala University, Uppsala, Sweden
| | - Emilia Niemiec
- Centre for Research Ethics and Bioethics, Uppsala University, Uppsala, Sweden
| | - Dianne Nicol
- Centre for Law and Genetics, University of Tasmania, Hobart, Australia
| | - Christine Critchley
- Centre for Law and Genetics, University of Tasmania, Hobart, Australia
- Department of Statistics and Epidemiology, Swinburne University of Technology, Melbourne, Australia
| | - Barbara Prainsack
- Department of Political Science, University of Vienna, Vienna, Austria
- Department of Global Health and Social Medicine, King's College, London, UK
| | - Danya Vears
- Melbourne Law School, University of Melbourne, Parkville, VIC, Australia
- Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Public Health and Primary Care, Centre for Biomedical Ethics and Law, KU Leuven, Leuven, Belgium
- Leuven Institute for Human Genomics and Society (LIGAS), KU Leuven, Leuven, Belgium
| | - James Smith
- Web Team, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Claire Steed
- Web Team, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Paul Bevan
- Web Team, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jerome Atutornu
- Society and Ethics Research, Connecting Science, Wellcome Genome Campus, Cambridge, UK
- School of Health Sciences, University of Suffolk, Ipswich, UK
| | - Lauren Farley
- Society and Ethics Research, Connecting Science, Wellcome Genome Campus, Cambridge, UK
| | - Peter Goodhand
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada
| | - Adrian Thorogood
- Centre of Genomics and Policy, McGill University, Montreal, QC, Canada
| | - Erika Kleiderman
- Centre of Genomics and Policy, McGill University, Montreal, QC, Canada
| | - Anna Middleton
- Society and Ethics Research, Connecting Science, Wellcome Genome Campus, Cambridge, UK.
- Faculty of Education, University of Cambridge, Cambridge, UK.
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24
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Kieler M, Unseld M, Bianconi D, Waneck F, Mader R, Wrba F, Fuereder T, Marosi C, Raderer M, Staber P, Berger W, Sibilia M, Polterauer S, Müllauer L, Preusser M, Zielinski CC, Prager GW. Interim analysis of a real-world precision medicine platform for molecular profiling of metastatic or advanced cancers: MONDTI. ESMO Open 2019; 4:e000538. [PMID: 31423337 PMCID: PMC6677998 DOI: 10.1136/esmoopen-2019-000538] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/09/2019] [Accepted: 06/14/2019] [Indexed: 12/25/2022] Open
Abstract
Background High-throughput genomic profiling of tumour specimens facilitates the identification of individual actionable mutations which could be used for individualised targeted therapy. This approach is becoming increasingly more common in the clinic; however, the interpretation of results from molecular profiling tests and efficient guiding of molecular therapies to patients with advanced cancer offer a significant challenge to the oncology community. Experimental design MONDTI is a precision medicine platform for molecular characterisation of metastatic solid tumours to identify actionable genomic alterations. From 2013 to 2016, comprehensive molecular profiles derived from real-time biopsy specimens and archived tumour tissue samples of 295 patients were performed. Results and treatment suggestions were discussed within multidisciplinary tumour board meetings. Results The mutational profile was obtained from 293 (99%) patients and a complete immunohistochemical (IHC) and cytogenetic profile was obtained in 181 (61%) and 188 (64%) patients. The most frequent cancer types were colorectal cancer (12%), non-Hodgkin's lymphomas (9.8%) and head and neck cancers (7.8%). The most commonly detected mutations were TP53 (39%), KRAS (19%) and PIK3CA (9.5%), whereas ≥1 mutation were identified in 217 (74%) samples. Regarding the results for IHC testing, samples were positive for phospho-mammalian target of rapamycin (phospho-mTOR) (71%), epidermal growth factor receptor (EGFR) (68%), mesenchymal epithelial transition (MET) (56%) and/or platelet-derived growth factor alpha (PDGFRα)-expression (48%). Of the 288 tumour samples with one or more genetic alteration detected, 160 (55.6%) targeted therapy recommendations through 67 multidisciplinary tumour board meetings were made; in 69 (24%) cases, an individual treatment concept was initiated. Conclusions The results reveal that the open concept for all solid tumours characterised for molecular profile and immunotherapy could not only match individualised treatment concepts at a high rate but also underscores the challenges encountered when offering molecularly matched therapies to a patient population with an advanced stage cancer.
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Affiliation(s)
- Markus Kieler
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Wien, Austria
| | - Matthias Unseld
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Wien, Austria
| | - Daniela Bianconi
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Wien, Austria
| | - Fredrik Waneck
- Department of Biomedical Imaging and Image-guided Therapy, Division of Cardiovascular and Interventional Radiology, Medical University of Vienna, Wien, Austria
| | - Robert Mader
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Wien, Austria
| | - Fritz Wrba
- Department of Pathology, Medical University of Vienna, Wien, Austria
| | - Thorsten Fuereder
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Wien, Austria
| | - Christine Marosi
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Wien, Austria
| | - Markus Raderer
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Wien, Austria
| | - Philipp Staber
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Wien, Austria
| | - Walter Berger
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Wien, Austria
| | - Maria Sibilia
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Wien, Austria
| | - Stephan Polterauer
- Department of Obstetrics and Gynecology, Division of General Gynecology and Gynecologic Oncology, Medical University of Vienna, Wien, Austria
| | - Leonhard Müllauer
- Department of Pathology, Medical University of Vienna, Wien, Austria
| | - Matthias Preusser
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Wien, Austria
| | - Christoph C Zielinski
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Wien, Austria
| | - Gerald W Prager
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Wien, Austria
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25
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Abstract
The complexity of human cancer underlies its devastating clinical consequences. Drugs designed to target the genetic alterations that drive cancer have improved the outcome for many patients, but not the majority of them. Here, we review the genomic landscape of cancer, how genomic data can provide much more than a sum of its parts, and the approaches developed to identify and validate genomic alterations with potential therapeutic value. We highlight notable successes and pitfalls in predicting the value of potential therapeutic targets and discuss the use of multi-omic data to better understand cancer dependencies and drug sensitivity. We discuss how integrated approaches to collecting, curating, and sharing these large data sets might improve the identification and prioritization of cancer vulnerabilities as well as patient stratification within clinical trials. Finally, we outline how future approaches might improve the efficiency and speed of translating genomic data into clinically effective therapies and how the use of unbiased genome-wide information can identify novel predictive biomarkers that can be either simple or complex.
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Affiliation(s)
- Gary J Doherty
- Department of Oncology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge CB2 0QQ, United Kingdom; ,
| | - Michele Petruzzelli
- Department of Oncology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge CB2 0QQ, United Kingdom; ,
- Medical Research Council (MRC) Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, United Kingdom
| | - Emma Beddowes
- Department of Oncology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge CB2 0QQ, United Kingdom; ,
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Saif S Ahmad
- Department of Oncology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge CB2 0QQ, United Kingdom; ,
- Medical Research Council (MRC) Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, United Kingdom
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Carlos Caldas
- Department of Oncology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge CB2 0QQ, United Kingdom; ,
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Richard J Gilbertson
- Department of Oncology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge CB2 0QQ, United Kingdom; ,
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
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26
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Krumm N, Shirts BH. Technical, Biological, and Systems Barriers for Molecular Clinical Decision Support. Clin Lab Med 2019; 39:281-294. [PMID: 31036281 DOI: 10.1016/j.cll.2019.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genome-enabled or molecular clinical decision support (CDS) systems provide unique advantages for the clinical use of genomic data; however, their implementation is complicated by technical, biological, and systemic barriers. This article reviews the substantial technical progress that has been made in the past decade and finds that the underlying biological limitations of genomics as well as systemic barriers to adoption of molecular CDS have been comparatively underestimated. A hybrid consultative CDS system, which integrates a genomics consultant into an active CDS system, may provide an interim path forward.
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Affiliation(s)
- Niklas Krumm
- Department of Laboratory Medicine, University of Washington, Box 357110, 1959 Northeast Pacific Street, NW120, Seattle, WA 98195-7110, USA.
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Box 357110, 1959 Northeast Pacific Street, NW120, Seattle, WA 98195-7110, USA
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27
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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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28
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New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx. PLoS Comput Biol 2019; 15:e1006701. [PMID: 30835723 PMCID: PMC6420023 DOI: 10.1371/journal.pcbi.1006701] [Citation(s) in RCA: 255] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 03/15/2019] [Accepted: 12/10/2018] [Indexed: 02/07/2023] Open
Abstract
The advent of Next-Generation Sequencing (NGS) technologies has opened new perspectives in deciphering the genetic mechanisms underlying complex diseases. Nowadays, the amount of genomic data is massive and substantial efforts and new tools are required to unveil the information hidden in the data. The Genomic Data Commons (GDC) Data Portal is a platform that contains different genomic studies including the ones from The Cancer Genome Atlas (TCGA) and the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiatives, accounting for more than 40 tumor types originating from nearly 30000 patients. Such platforms, although very attractive, must make sure the stored data are easily accessible and adequately harmonized. Moreover, they have the primary focus on the data storage in a unique place, and they do not provide a comprehensive toolkit for analyses and interpretation of the data. To fulfill this urgent need, comprehensive but easily accessible computational methods for integrative analyses of genomic data that do not renounce a robust statistical and theoretical framework are required. In this context, the R/Bioconductor package TCGAbiolinks was developed, offering a variety of bioinformatics functionalities. Here we introduce new features and enhancements of TCGAbiolinks in terms of i) more accurate and flexible pipelines for differential expression analyses, ii) different methods for tumor purity estimation and filtering, iii) integration of normal samples from other platforms iv) support for other genomics datasets, exemplified here by the TARGET data. Evidence has shown that accounting for tumor purity is essential in the study of tumorigenesis, as these factors promote confounding behavior regarding differential expression analysis. With this in mind, we implemented these filtering procedures in TCGAbiolinks. Moreover, a limitation of some of the TCGA datasets is the unavailability or paucity of corresponding normal samples. We thus integrated into TCGAbiolinks the possibility to use normal samples from the Genotype-Tissue Expression (GTEx) project, which is another large-scale repository cataloging gene expression from healthy individuals. The new functionalities are available in the TCGAbiolinks version 2.8 and higher released in Bioconductor version 3.7. The advent of Next-Generation Sequencing (NGS) technologies has been generating a massive amount of data which require continuous efforts in developing and maintain computational tool for data analyses. The Genomic Data Commons (GDC) Data Portal is a platform that contains different cancer genomic studies. Such platforms have often the primary focus on the data storage and they do not provide a comprehensive toolkit for analyses. To fulfil this urgent need, comprehensive but accessible computational protocols that do not renounce a robust statistical framework are thus required. In this context, we here present the new functions of the R/Bioconductor package TCGAbiolinks to improve the discovery of differentially expressed genes in cancer and tumor (sub)types, include the estimate of tumor purity and tumor infiltrations, use normal samples from other platforms and support more broadly other genomics datasets.
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29
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Selby P, Popescu R, Lawler M, Butcher H, Costa A. The Value and Future Developments of Multidisciplinary Team Cancer Care. Am Soc Clin Oncol Educ Book 2019; 39:332-340. [PMID: 31099640 DOI: 10.1200/edbk_236857] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Multidisciplinary teams (MDTs) have been recommended as a key part of best cancer care for 25 years. Here, we set out the functions and approaches of MDTs and review their impact. Although the literature is patchy in quality, MDTs contribute to improving cancer care and outcomes. They must be well organized, efficient, and well led; work with sound and timely information; and communicate well within the team and with their patients. Patients need carefully prepared information to help them share in the decision-making process. MDTs will be improved by a series of ongoing innovative developments. Increasing information from molecular pathology will increase the precision of their decisions, although the technologies remain expensive and may not be accessible in all countries for some time. New point-of-care testing technologies will improve the quality and timeliness of testing. Good informatics is essential to deliver the information to patients and the MDT. MDTs should be research active, delivering clinical trials, and this should improve outcomes for all of their patients. Patient engagement and empowerment in MDTs should improve patient satisfaction and outcomes. Patient-reported outcome measures will improve MDTs' insights into their patients' problems and symptoms and can improve patient outcomes.
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Affiliation(s)
- Peter Selby
- 1 Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | | | - Mark Lawler
- 3 Centre for Cancer Research and Cell Biology, Queen's University, Belfast, United Kingdom
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30
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Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WWH, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV. Best practice data life cycle approaches for the life sciences. F1000Res 2018; 6:1618. [PMID: 30109017 DOI: 10.12688/f1000research.12344.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/17/2017] [Indexed: 11/20/2022] Open
Abstract
Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a 'life cycle' view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain. Here we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on 'omics' datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices.
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Affiliation(s)
- Philippa C Griffin
- EMBL Australia Bioinformatics Resource, The University of Melbourne, Parkville, VIC, 3010, Australia.,Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jyoti Khadake
- NIHR BioResource, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust Hills Road, Cambridge , CB2 0QQ, UK
| | - Kate S LeMay
- Australian National Data Service, Monash University, Malvern East , VIC, 3145, Australia
| | - Suzanna E Lewis
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, 94720, USA
| | - Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK
| | - Andrew Pask
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Bernard Pope
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ute Roessner
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Keith Russell
- Australian National Data Service, Monash University, Malvern East , VIC, 3145, Australia
| | - Torsten Seemann
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Andrew Treloar
- Australian National Data Service, Monash University, Malvern East , VIC, 3145, Australia
| | - Sonika Tyagi
- Australian Genome Research Facility Ltd, Parkville, VIC, 3052, Australia.,Monash Bioinformatics Platform, Monash University, Clayton, VIC, 3800, Australia
| | - Jeffrey H Christiansen
- Queensland Cyber Infrastructure Foundation and the University of Queensland Research Computing Centre, St Lucia, QLD, 4072, Australia
| | - Saravanan Dayalan
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Simon Gladman
- EMBL Australia Bioinformatics Resource, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Sandra B Hangartner
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Helen L Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Bundoora, VIC, 3083, Australia
| | - William W H Ho
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Gabriel Keeble-Gagnère
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia.,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Bundoora, VIC, 3083, Australia
| | - Pasi K Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Peter Neish
- The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Priscilla R Prestes
- Faculty of Science and Engineering, Federation University Australia, Mt Helen , VIC, 3350, Australia
| | - Mark F Richardson
- Bioinformatics Core Research Group & Centre for Integrative Ecology, Deakin University, Geelong, VIC, 3220, Australia
| | - Nathan S Watson-Haigh
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Kelly L Wyres
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Neil D Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Maria Victoria Schneider
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia.,The University of Melbourne, Parkville, VIC, 3010, Australia
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31
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Lai-Kwon J, Siva S, Lewin J. Assessing the Clinical Utility of Computed Tomography-Based Radiomics. Oncologist 2018; 23:747-749. [PMID: 29728471 PMCID: PMC6058332 DOI: 10.1634/theoncologist.2018-0193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 04/03/2018] [Indexed: 01/27/2023] Open
Abstract
This commentary provides an overview of the evolving field of radiomics, which aims to noninvasively augment clinical prognostic nomograms, correlate imaging phenotypes, and support clinical decision‐making.
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Affiliation(s)
- Julia Lai-Kwon
- Department of Cancer Medicine, Peter MacCallum Cancer Centre, Parkville, Australia
| | - Shankar Siva
- Department of Radiation Oncology, Peter MacCallum Cancer Centre, Parkville, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Jeremy Lewin
- Department of Cancer Medicine, Peter MacCallum Cancer Centre, Parkville, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
- ONTrac at Peter Mac Victorian Adolescent & Young Adult Cancer Service, Peter MacCallum Cancer Centre, Parkville, Australia
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32
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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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33
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Minari J, Brothers KB, Morrison M. Tensions in ethics and policy created by National Precision Medicine Programs. Hum Genomics 2018; 12:22. [PMID: 29665847 PMCID: PMC5904987 DOI: 10.1186/s40246-018-0151-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/29/2018] [Indexed: 12/01/2022] Open
Abstract
Precision medicine promises to use genomics and other data-intensive approaches to improve diagnosis and develop new treatments for major diseases, but also raises a range of ethical and governance challenges. Implementation of precision medicine in “real world” healthcare systems blurs the boundary between research and care. This has implications for the meaning and validity of consent, and increased potential for discrimination, among other challenges. Increased sharing of personal information raises concerns about privacy, commercialization, and public trust. This paper considers national precision medicine schemes from the USA, the UK, and Japan, comparing how these challenges manifest in each national context and examining the range of approaches deployed to mitigate the potential undesirable social consequences. There is rarely a “one size” fits all solution to these complex problems, but the most viable approaches are those which take account of cultural preferences and attitudes, available resources, and the wider political landscape in which national healthcare systems are embedded.
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Affiliation(s)
- Jusaku Minari
- Uehiro Research Division for iPS Cell Ethics, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Kyle B Brothers
- Kosair Charities Pediatric Clinical Research Unit, University of Louisville School of Medicine, Louisville, KY, USA.
| | - Michael Morrison
- Centre for Health, Law and Emerging Technologies (HeLEX), Nuffield Department of Population Health, University of Oxford, Ewert House, Ewert Place, Banbury Road, Oxford, OX2 7DD, UK.
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34
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Personalising Prostate Radiotherapy in the Era of Precision Medicine: A Review. J Med Imaging Radiat Sci 2018; 49:376-382. [PMID: 30514554 DOI: 10.1016/j.jmir.2018.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 12/27/2017] [Accepted: 01/18/2018] [Indexed: 12/14/2022]
Abstract
Prostate cancer continues to be the most commonly diagnosed cancer among Canadian men. The introduction of routine screening and advanced treatment options have allowed for a decrease in prostate cancer-related mortality, but outcomes following treatment continue to vary widely. In addition, the overtreatment of indolent prostate cancers causes unnecessary treatment toxicities and burdens health care systems. Accurate identification of patients who should undergo aggressive treatment, and those which should be managed more conservatively, needs to be implemented. More tumour and patient information is needed to stratify patients into low-, intermediate-, and high-risk groups to guide treatment options. This paper reviews the current literature on personalised prostate cancer management, including targeting tumour hypoxia, genomic and radiomic prognosticators, and radiobiological tumour targeting. A review of the current applications and future directions for the use of big data in radiation therapy is also presented. Prostate cancer management has a lot to gain from the implementation of personalised medicine into practice. Using specific tumour and patient characteristics to personalise prostate radiotherapy in the era of precision medicine will improve survival, decrease unnecessary toxicities, and minimise the heterogeneity of outcomes following treatment.
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35
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Bryce AH, Egan JB, Borad MJ, Stewart AK, Nowakowski GS, Chanan-Khan A, Patnaik MM, Ansell SM, Banck MS, Robinson SI, Mansfield AS, Klee EW, Oliver GR, McCormick JB, Huneke NE, Tagtow CM, Jenkins RB, Rumilla KM, Kerr SE, Kocher JPA, Beck SA, Fernandez-Zapico ME, Farrugia G, Lazaridis KN, McWilliams RR. Experience with precision genomics and tumor board, indicates frequent target identification, but barriers to delivery. Oncotarget 2018; 8:27145-27154. [PMID: 28423702 PMCID: PMC5432324 DOI: 10.18632/oncotarget.16057] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/15/2017] [Indexed: 01/16/2023] Open
Abstract
Background The ability to analyze the genomics of malignancies has opened up new possibilities for off-label targeted therapy in cancers that are refractory to standard therapy. At Mayo Clinic these efforts are organized through the Center for Individualized Medicine (CIM). Results Prior to GTB, datasets were analyzed and integrated by a team of bioinformaticians and cancer biologists. Therapeutically actionable mutations were identified in 65% (92/141) of the patients tested with 32% (29/92) receiving genomically targeted therapy with FDA approved drugs or in an independent clinical trial with 45% (13/29) responding. Standard of care (SOC) options were continued by 15% (14/92) of patients tested before exhausting SOC options, with 71% (10/14) responding to treatment. Over 35% (34/92) of patients with actionable targets were not treated with 65% (22/34) choosing comfort measures or passing away. Materials and Methods Patients (N = 165) were referred to the CIM Clinic between October 2012 and December 2015. All patients received clinical genomic panel testing with selected subsets receiving array comparative genomic hybridization and clinical whole exome sequencing to complement and validate panel findings. A genomic tumor board (GTB) reviewed results and, when possible, developed treatment recommendations. Conclusions Treatment decisions driven by tumor genomic analysis can lead to significant clinical benefit in a minority of patients. The success of genomically driven therapy depends both on access to drugs and robustness of bioinformatics analysis. While novel clinical trial designs are increasing the utility of genomic testing, robust data sharing of outcomes is needed to optimize clinical benefit for all patients.
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Affiliation(s)
- Alan H Bryce
- Hematology/Oncology, Mayo Clinic, Phoenix, AZ, U.S.A.,Mayo Clinic Cancer Center, Phoenix, AZ, U.S.A.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - Jan B Egan
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - Mitesh J Borad
- Hematology/Oncology, Mayo Clinic, Phoenix, AZ, U.S.A.,Mayo Clinic Cancer Center, Phoenix, AZ, U.S.A.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - A Keith Stewart
- Hematology/Oncology, Mayo Clinic, Phoenix, AZ, U.S.A.,Mayo Clinic Cancer Center, Phoenix, AZ, U.S.A.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - Grzegorz S Nowakowski
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Hematology, Mayo Clinic, Rochester, MN, U.S.A
| | - Asher Chanan-Khan
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Hematology/Oncology, Mayo Clinic, Jacksonville, FL, U.S.A
| | - Mrinal M Patnaik
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Hematology, Mayo Clinic, Rochester, MN, U.S.A
| | - Stephen M Ansell
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Hematology, Mayo Clinic, Rochester, MN, U.S.A
| | - Michaela S Banck
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Medical Oncology, Mayo Clinic, Rochester, MN, U.S.A
| | - Steven I Robinson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Medical Oncology, Mayo Clinic, Rochester, MN, U.S.A
| | - Aaron S Mansfield
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Medical Oncology, Mayo Clinic, Rochester, MN, U.S.A
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Health Sciences Research, Mayo Clinic, Rochester, MN, U.S.A
| | - Gavin R Oliver
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Health Sciences Research, Mayo Clinic, Rochester, MN, U.S.A
| | | | - Norine E Huneke
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - Colleen M Tagtow
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - Robert B Jenkins
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, U.S.A
| | | | - Sarah E Kerr
- Anatomic Pathology, Mayo Clinic, Rochester, MN, U.S.A
| | - Jean-Pierre A Kocher
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Health Sciences Research, Mayo Clinic, Rochester, MN, U.S.A
| | - Scott A Beck
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - Martin E Fernandez-Zapico
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Medical Oncology, Mayo Clinic, Rochester, MN, U.S.A
| | - Gianrico Farrugia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Gastroenterology, Mayo Clinic, Rochester, MN, U.S.A
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Gastroenterology, Mayo Clinic, Rochester, MN, U.S.A
| | - Robert R McWilliams
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Medical Oncology, Mayo Clinic, Rochester, MN, U.S.A.,Mayo Clinic Cancer Center, Rochester, MN, U.S.A
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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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Lawler M, Alsina D, Adams RA, Anderson AS, Brown G, Fearnhead NS, Fenwick SW, Halloran SP, Hochhauser D, Hull MA, Koelzer VH, McNair AGK, Monahan KJ, Näthke I, Norton C, Novelli MR, Steele RJC, Thomas AL, Wilde LM, Wilson RH, Tomlinson I. Critical research gaps and recommendations to inform research prioritisation for more effective prevention and improved outcomes in colorectal cancer. Gut 2018; 67:179-193. [PMID: 29233930 PMCID: PMC5754857 DOI: 10.1136/gutjnl-2017-315333] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 10/24/2017] [Accepted: 10/25/2017] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Colorectal cancer (CRC) leads to significant morbidity/mortality worldwide. Defining critical research gaps (RG), their prioritisation and resolution, could improve patient outcomes. DESIGN RG analysis was conducted by a multidisciplinary panel of patients, clinicians and researchers (n=71). Eight working groups (WG) were constituted: discovery science; risk; prevention; early diagnosis and screening; pathology; curative treatment; stage IV disease; and living with and beyond CRC. A series of discussions led to development of draft papers by each WG, which were evaluated by a 20-strong patient panel. A final list of RGs and research recommendations (RR) was endorsed by all participants. RESULTS Fifteen critical RGs are summarised below: RG1: Lack of realistic models that recapitulate tumour/tumour micro/macroenvironment; RG2: Insufficient evidence on precise contributions of genetic/environmental/lifestyle factors to CRC risk; RG3: Pressing need for prevention trials; RG4: Lack of integration of different prevention approaches; RG5: Lack of optimal strategies for CRC screening; RG6: Lack of effective triage systems for invasive investigations; RG7: Imprecise pathological assessment of CRC; RG8: Lack of qualified personnel in genomics, data sciences and digital pathology; RG9: Inadequate assessment/communication of risk, benefit and uncertainty of treatment choices; RG10: Need for novel technologies/interventions to improve curative outcomes; RG11: Lack of approaches that recognise molecular interplay between metastasising tumours and their microenvironment; RG12: Lack of reliable biomarkers to guide stage IV treatment; RG13: Need to increase understanding of health related quality of life (HRQOL) and promote residual symptom resolution; RG14: Lack of coordination of CRC research/funding; RG15: Lack of effective communication between relevant stakeholders. CONCLUSION Prioritising research activity and funding could have a significant impact on reducing CRC disease burden over the next 5 years.
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Affiliation(s)
- Mark Lawler
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, UK
| | | | | | - Annie S Anderson
- Research into Cancer Prevention and Screening, University of Dundee, Dundee, UK
| | - Gina Brown
- Department of Radiology, Royal Marsden Hospital, Sutton, UK
| | | | - Stephen W Fenwick
- Hepatobiliary Surgery Unit, Aintree University Hospital, Liverpool, UK
| | - Stephen P Halloran
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Daniel Hochhauser
- Department of Oncology, University College London Cancer Institute, London, UK
| | - Mark A Hull
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, UK
| | - Viktor H Koelzer
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK
| | - Angus G K McNair
- Centre for Surgical Research, University of Bristol, Bristol, UK
| | - Kevin J Monahan
- Family History of Bowel Cancer Clinic, Imperial College London, London, UK
| | - Inke Näthke
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Christine Norton
- Florence Nightingale Faculty of Nursing and Midwifery, King’s College London, London, UK
| | - Marco R Novelli
- Research Department of Pathology, University College London Medical School, London, UK
| | - Robert J C Steele
- Research into Cancer Prevention and Screening, University of Dundee, Dundee, UK
| | - Anne L Thomas
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Lisa M Wilde
- Bowel Cancer UK, London, UK
- Atticus Consultants Ltd, Croydon, UK
| | - Richard H Wilson
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, UK
| | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
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Horgan D. Keeping the Person in Personalised Healthcare. Biomed Hub 2017; 2:63-71. [PMID: 31988936 PMCID: PMC6945942 DOI: 10.1159/000481683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 11/19/2022] Open
Abstract
Proponents of personalised medicine believe that the involvement of the patients, including in "risk-sharing agreements," will result in cost savings, the use of the genetic makeup of an individual patient as the starting point will save resources and, indirectly, there will be great potential for startups and new business in many areas. But how can Europe ensure that the "person" is central stage and allow us to focus on the development of personalised medicine for his or her ultimate benefit? The EU has a clear role to play, argues the author. One way for this to happen is for the EU to focus investment in guidelines for governance. This will go a long way to ensuring that the citizen is the principal factor when it comes to utilising the new wealth of innovation in health. The citizen must always come first when innovation is harnessed.
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Affiliation(s)
- Denis Horgan
- European Alliance for Personalised Medicine, Brussels, Belgium
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39
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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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40
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Papaleo E, Gromova I, Gromov P. Gaining insights into cancer biology through exploration of the cancer secretome using proteomic and bioinformatic tools. Expert Rev Proteomics 2017; 14:1021-1035. [PMID: 28967788 DOI: 10.1080/14789450.2017.1387053] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Tumor-associated proteins released by cancer cells and by tumor stroma cells, referred as 'cancer secretome', represent a valuable resource for discovery of potential cancer biomarkers. The last decade was marked by a great increase in number of studies focused on various aspects of cancer secretome including, composition and identification of components externalized by malignant cells and by the components of tumor microenvironment. Areas covered: Here, we provide an overview of achievements in the proteomic analysis of the cancer secretome, elicited through the tumor-associated interstitial fluid recovered from malignant tissues ex vivo or the protein component of conditioned media obtained from cultured cancer cells in vitro. We summarize various bioinformatic tools and approaches and critically appraise their outcomes, focusing on problems and challenges that arise when applied for the analysis of cancer secretomic databases. Expert commentary: Recent achievements in the omics- analysis of structural and metabolic aspects of altered cancer secretome contribute greatly to the various hallmarks of cancer including the identification of clinically significant biomarkers and potential targets for therapeutic intervention.
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Affiliation(s)
- Elena Papaleo
- a Danish Cancer Society Research Center, Computational Biology Laboratory , Copenhagen , Denmark
| | - Irina Gromova
- b Danish Cancer Society Research Center, Genome Integrity Unit, Breast Cancer Biology Group , Copenhagen , Denmark
| | - Pavel Gromov
- b Danish Cancer Society Research Center, Genome Integrity Unit, Breast Cancer Biology Group , Copenhagen , Denmark
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Reporting Data Quality Assessment Results: Identifying Individual and Organizational Barriers and Solutions. EGEMS 2017; 5:16. [PMID: 29881736 PMCID: PMC5982990 DOI: 10.5334/egems.214] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Introduction: Electronic health record (EHR) data are known to have significant data quality issues, yet the practice and frequency of assessing EHR data is unknown. We sought to understand current practices and attitudes towards reporting data quality assessment (DQA) results by data professionals. Methods: The project was conducted in four Phases: (1) examined current DQA practices among informatics/CER stakeholders via engagement meeting (07/2014); (2) characterized organizations conducting DQA by interviewing key personnel and data management professionals (07-08/2014); (3) developed and administered an anonymous survey to data professionals (03-06/2015); and (4) validated survey results during a follow-up informatics/CER stakeholder engagement meeting (06/2016). Results: The first engagement meeting identified the theme of unintended consequences as a primary barrier to DQA. Interviewees were predominantly medical groups serving distributed networks with formalized DQAs. Consistent with the interviews, most survey (N=111) respondents utilized DQA processes/programs. A lack of resources and clear definitions of how to judge the quality of a dataset were the most commonly cited individual barriers. Vague quality action plans/expectations and data owners not trained in problem identification and problem-solving skills were the most commonly cited organizational barriers. Solutions included allocating resources for DQA, establishing standards and guidelines, and changing organizational culture. Discussion: Several barriers affecting DQA and reporting were identified. Community alignment towards systematic DQA and reporting is needed to overcome these barriers. Conclusion: Understanding barriers and solutions to DQA reporting is vital for establishing trust in the secondary use of EHR data for quality improvement and the pursuit of personalized medicine.
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Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WWH, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV. Best practice data life cycle approaches for the life sciences. F1000Res 2017; 6:1618. [PMID: 30109017 PMCID: PMC6069748 DOI: 10.12688/f1000research.12344.2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/29/2018] [Indexed: 11/20/2022] Open
Abstract
Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a 'life cycle' view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain. Here we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on 'omics' datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices.
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Affiliation(s)
- Philippa C Griffin
- EMBL Australia Bioinformatics Resource, The University of Melbourne, Parkville, VIC, 3010, Australia.,Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jyoti Khadake
- NIHR BioResource, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust Hills Road, Cambridge , CB2 0QQ, UK
| | - Kate S LeMay
- Australian National Data Service, Monash University, Malvern East , VIC, 3145, Australia
| | - Suzanna E Lewis
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, 94720, USA
| | - Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK
| | - Andrew Pask
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Bernard Pope
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ute Roessner
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Keith Russell
- Australian National Data Service, Monash University, Malvern East , VIC, 3145, Australia
| | - Torsten Seemann
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Andrew Treloar
- Australian National Data Service, Monash University, Malvern East , VIC, 3145, Australia
| | - Sonika Tyagi
- Australian Genome Research Facility Ltd, Parkville, VIC, 3052, Australia.,Monash Bioinformatics Platform, Monash University, Clayton, VIC, 3800, Australia
| | - Jeffrey H Christiansen
- Queensland Cyber Infrastructure Foundation and the University of Queensland Research Computing Centre, St Lucia, QLD, 4072, Australia
| | - Saravanan Dayalan
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Simon Gladman
- EMBL Australia Bioinformatics Resource, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Sandra B Hangartner
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Helen L Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Bundoora, VIC, 3083, Australia
| | - William W H Ho
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Gabriel Keeble-Gagnère
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia.,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Bundoora, VIC, 3083, Australia
| | - Pasi K Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Peter Neish
- The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Priscilla R Prestes
- Faculty of Science and Engineering, Federation University Australia, Mt Helen , VIC, 3350, Australia
| | - Mark F Richardson
- Bioinformatics Core Research Group & Centre for Integrative Ecology, Deakin University, Geelong, VIC, 3220, Australia
| | - Nathan S Watson-Haigh
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Kelly L Wyres
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Neil D Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Maria Victoria Schneider
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia.,The University of Melbourne, Parkville, VIC, 3010, Australia
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Jagadeesh KA, Wu DJ, Birgmeier JA, Boneh D, Bejerano G. Deriving genomic diagnoses without revealing patient genomes. Science 2017; 357:692-695. [DOI: 10.1126/science.aam9710] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 07/18/2017] [Indexed: 11/02/2022]
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AACR Project GENIE: Powering Precision Medicine through an International Consortium. Cancer Discov 2017; 7:818-831. [PMID: 28572459 PMCID: PMC5611790 DOI: 10.1158/2159-8290.cd-17-0151] [Citation(s) in RCA: 1218] [Impact Index Per Article: 174.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/31/2017] [Accepted: 05/18/2017] [Indexed: 01/18/2023]
Abstract
The AACR Project GENIE is an international data-sharing consortium focused on generating an evidence base for precision cancer medicine by integrating clinical-grade cancer genomic data with clinical outcome data for tens of thousands of cancer patients treated at multiple institutions worldwide. In conjunction with the first public data release from approximately 19,000 samples, we describe the goals, structure, and data standards of the consortium and report conclusions from high-level analysis of the initial phase of genomic data. We also provide examples of the clinical utility of GENIE data, such as an estimate of clinical actionability across multiple cancer types (>30%) and prediction of accrual rates to the NCI-MATCH trial that accurately reflect recently reported actual match rates. The GENIE database is expected to grow to >100,000 samples within 5 years and should serve as a powerful tool for precision cancer medicine.Significance: The AACR Project GENIE aims to catalyze sharing of integrated genomic and clinical datasets across multiple institutions worldwide, and thereby enable precision cancer medicine research, including the identification of novel therapeutic targets, design of biomarker-driven clinical trials, and identification of genomic determinants of response to therapy. Cancer Discov; 7(8); 818-31. ©2017 AACR.See related commentary by Litchfield et al., p. 796This article is highlighted in the In This Issue feature, p. 783.
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Flowers M, Birkey Reffey S, Mertz SA, Hurlbert M. Obstacles, Opportunities and Priorities for Advancing Metastatic Breast Cancer Research. Cancer Res 2017; 77:3386-3390. [DOI: 10.1158/0008-5472.can-17-0232] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/28/2017] [Accepted: 04/20/2017] [Indexed: 11/16/2022]
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46
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The NCI Genomic Data Commons as an engine for precision medicine. Blood 2017; 130:453-459. [PMID: 28600341 DOI: 10.1182/blood-2017-03-735654] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/08/2017] [Indexed: 12/19/2022] Open
Abstract
The National Cancer Institute Genomic Data Commons (GDC) is an information system for storing, analyzing, and sharing genomic and clinical data from patients with cancer. The recent high-throughput sequencing of cancer genomes and transcriptomes has produced a big data problem that precludes many cancer biologists and oncologists from gleaning knowledge from these data regarding the nature of malignant processes and the relationship between tumor genomic profiles and treatment response. The GDC aims to democratize access to cancer genomic data and to foster the sharing of these data to promote precision medicine approaches to the diagnosis and treatment of cancer.
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Dalton WB, Forde PM, Kang H, Connolly RM, Stearns V, Gocke CD, Eshleman JR, Axilbund J, Petry D, Geoghegan C, Wolff AC, Loeb DM, Pratilas CA, Meyer CF, Christenson ES, Slater SA, Ensminger J, Parsons HA, Park BH, Lauring J. Personalized Medicine in the Oncology Clinic: Implementation and Outcomes of the Johns Hopkins Molecular Tumor Board. JCO Precis Oncol 2017; 2017. [PMID: 30003184 DOI: 10.1200/po.16.00046] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Purpose Tumor genomic profiling for personalized oncology therapy is being widely applied in clinical practice even as it is being evaluated more formally in clinical trials. Given the complexities of genomic data and its application to clinical use, molecular tumor boards with diverse expertise can provide guidance to oncologists and patients seeking to implement personalized genetically targeted therapy in practice. Methods A multidisciplinary molecular tumor board reviewed tumor molecular profiling reports from consecutive referrals at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins over a 3-year period. The tumor board weighed evidence for actionability of genomic alterations identified by molecular profiling and provided recommendations including US Food and Drug Administration-approved drug therapy, clinical trials of matched targeted therapy, off-label use of such therapy, and additional tumor or germline genetic testing. Results One hundred fifty-five patients were reviewed. Actionable genomic alterations were identified in 132 patients (85%). Off-label therapies were recommended in 37 patients (24%). Eleven patients were treated off-label, and 13 patients were enrolled onto clinical trials of matched targeted therapies. Median progression-free survival of patients treated with matched therapies was 5 months (95% CI, 2.9 months to not reached), and the progression-free survival probability at 6 months was 43%(95% CI, 26% to 71%). Lack of locally available clinical trials was the major limitation on clinical actionability of tumor profiling reports. Conclusion The molecular tumor board recommended off-label targeted therapies for a quarter of all patients reviewed. Outcomes were heterogeneous, although 43% of patients receiving genomically matched therapy derived clinical benefit lasting at least 6 months. Until more data become available from precision oncology trials, molecular tumor boards can help guide appropriate use of tumor molecular testing to direct therapy.
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Affiliation(s)
- W Brian Dalton
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Patrick M Forde
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Hyunseok Kang
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Roisin M Connolly
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Vered Stearns
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Christopher D Gocke
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - James R Eshleman
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | | | - Dana Petry
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | | | - Antonio C Wolff
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - David M Loeb
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | | | - Christian F Meyer
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Eric S Christenson
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Shannon A Slater
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Jennifer Ensminger
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Heather A Parsons
- Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Ben H Park
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Josh Lauring
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
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Hyman DM, Taylor BS, Baselga J. Implementing Genome-Driven Oncology. Cell 2017; 168:584-599. [PMID: 28187282 DOI: 10.1016/j.cell.2016.12.015] [Citation(s) in RCA: 310] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 12/18/2022]
Abstract
Early successes in identifying and targeting individual oncogenic drivers, together with the increasing feasibility of sequencing tumor genomes, have brought forth the promise of genome-driven oncology care. As we expand the breadth and depth of genomic analyses, the biological and clinical complexity of its implementation will be unparalleled. Challenges include target credentialing and validation, implementing drug combinations, clinical trial designs, targeting tumor heterogeneity, and deploying technologies beyond DNA sequencing, among others. We review how contemporary approaches are tackling these challenges and will ultimately serve as an engine for biological discovery and increase our insight into cancer and its treatment.
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Affiliation(s)
- David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - José Baselga
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA.
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Kloosterman WP, Coebergh van den Braak RR, Pieterse M, van Roosmalen MJ, Sieuwerts AM, Stangl C, Brunekreef R, Lalmahomed ZS, Ooft S, van Galen A, Smid M, Lefebvre A, Zwartkruis F, Martens JW, Foekens JA, Biermann K, Koudijs MJ, Ijzermans JN, Voest EE. A Systematic Analysis of Oncogenic Gene Fusions in Primary Colon Cancer. Cancer Res 2017; 77:3814-3822. [DOI: 10.1158/0008-5472.can-16-3563] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/08/2017] [Accepted: 05/12/2017] [Indexed: 11/16/2022]
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Dheensa S, Carrieri D, Kelly S, Clarke A, Doheny S, Turnpenny P, Lucassen A. A 'joint venture' model of recontacting in clinical genomics: challenges for responsible implementation. Eur J Med Genet 2017; 60:403-409. [PMID: 28501562 DOI: 10.1016/j.ejmg.2017.05.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/21/2017] [Accepted: 05/09/2017] [Indexed: 10/19/2022]
Abstract
Advances in genomics often lead healthcare professionals (HCPs) to learn new information, e.g., about reinterpreted variants that could have clinical significance for patients seen previously. A question arises of whether HCPs should recontact these former patients. We present some findings interrogating the views of patients (or parents of patients) with a rare or undiagnosed condition about how such recontacting might be organised ethically and practically. Forty-one interviews were analysed thematically. Participants suggested a 'joint venture' model in which efforts to recontact are shared with HCPs. Some proposed an ICT-approach involving an electronic health record that automatically alerts them to potentially relevant updates. The need for rigorous privacy controls and transparency about who could access their data was emphasised. Importantly, these findings highlight that the lack of clarity about recontacting is a symptom of a wider problem: the lack of necessary infrastructure to pool genomic data responsibly, to aggregate it with other health data, and to enable patients/parents to receive updates. We hope that our findings will instigate a debate about the way responsibilities for recontacting under any joint venture model could be allocated, as well as the limitations and normative implications of using ICT as a solution to this intractable problem. As a first step to delineating responsibilities in the clinical setting, we suggest HCPs should routinely discuss recontacting with patients/parents, including the new information that should trigger a HCP to initiate recontact, as part of the consent process for genetic testing.
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Affiliation(s)
- Sandi Dheensa
- Clinical Ethics and Law, Faculty of Medicine, University of Southampton, UK; ELSI Group, Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| | | | | | - Angus Clarke
- Division of Cancer & Genetics, School of Medicine, Cardiff University, UK
| | - Shane Doheny
- Division of Cancer & Genetics, School of Medicine, Cardiff University, UK
| | - Peter Turnpenny
- Egenis, University of Exeter, UK; Peninsular Genetics Service, Royal, Devon and Exeter Hospital, UK
| | - Anneke Lucassen
- Clinical Ethics and Law, Faculty of Medicine, University of Southampton, UK; ELSI Group, Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, UK
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