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Ginsburg GS, Picard RW, Friend SH. Key Issues as Wearable Digital Health Technologies Enter Clinical Care. N Engl J Med 2024; 390:1118-1127. [PMID: 38507754 DOI: 10.1056/nejmra2307160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Affiliation(s)
- Geoffrey S Ginsburg
- From the All of Us Research Program, National Institutes of Health, Bethesda, MD (G.S.G.); the MIT Media Lab, Cambridge, and Empatica, Boston - both in Massachusetts (R.W.P.); the Department of Psychiatry, University of Oxford, Oxford, United Kingdom (S.H.F.), and 4YouandMe, Seattle (S.H.F.)
| | - Rosalind W Picard
- From the All of Us Research Program, National Institutes of Health, Bethesda, MD (G.S.G.); the MIT Media Lab, Cambridge, and Empatica, Boston - both in Massachusetts (R.W.P.); the Department of Psychiatry, University of Oxford, Oxford, United Kingdom (S.H.F.), and 4YouandMe, Seattle (S.H.F.)
| | - Stephen H Friend
- From the All of Us Research Program, National Institutes of Health, Bethesda, MD (G.S.G.); the MIT Media Lab, Cambridge, and Empatica, Boston - both in Massachusetts (R.W.P.); the Department of Psychiatry, University of Oxford, Oxford, United Kingdom (S.H.F.), and 4YouandMe, Seattle (S.H.F.)
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2
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Affiliation(s)
- Stephen H Friend
- From the Department of Psychiatry, University of Oxford, Oxford, United Kingdom (S.H.F.); 4YouandMe, Seattle (S.H.F.); All of Us Research Program, National Institutes of Health, Bethesda, MD (G.S.G.); and the MIT Media Lab, Massachusetts Institute of Technology, Cambridge (R.W.P.)
| | - Geoffrey S Ginsburg
- From the Department of Psychiatry, University of Oxford, Oxford, United Kingdom (S.H.F.); 4YouandMe, Seattle (S.H.F.); All of Us Research Program, National Institutes of Health, Bethesda, MD (G.S.G.); and the MIT Media Lab, Massachusetts Institute of Technology, Cambridge (R.W.P.)
| | - Rosalind W Picard
- From the Department of Psychiatry, University of Oxford, Oxford, United Kingdom (S.H.F.); 4YouandMe, Seattle (S.H.F.); All of Us Research Program, National Institutes of Health, Bethesda, MD (G.S.G.); and the MIT Media Lab, Massachusetts Institute of Technology, Cambridge (R.W.P.)
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3
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Goodday SM, Karlin DR, Friend SH. The digital redesign of mental health: leveraging connected digital technologies for agency-driven patient-focused care. Br J Psychiatry 2023; 222:51-53. [PMID: 36408682 PMCID: PMC10895509 DOI: 10.1192/bjp.2022.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/29/2022] [Accepted: 10/07/2022] [Indexed: 11/22/2022]
Abstract
Digital psychiatry could empower individuals to navigate their context-specific experiences outside healthcare visits. This editorial discusses how leveraging digital health technologies could dramatically transform how we conceptualise mental health and the mental health professional's day-day practice, and how patients could be enabled to navigate their mental health with greater agency.
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Affiliation(s)
- Sarah M. Goodday
- 4YouandMe, Seattle, WA, USA; and Department of Psychiatry, University of Oxford, UK
| | - Daniel R. Karlin
- 4YouandMe, Seattle, WA, USA; MindMed, Inc., New York, NY, USA; and Tufts University School of Medicine, Boston, MA, USA
| | - Stephen H. Friend
- 4YouandMe, Seattle, WA, USA; and Department of Psychiatry, University of Oxford, UK
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4
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Dwibedi C, Mellergård E, Gyllensten AC, Nilsson K, Axelsson AS, Bäckman M, Sahlgren M, Friend SH, Persson S, Franzén S, Abrahamsson B, Carlsson KS, Rosengren AH. Effect of self-managed lifestyle treatment on glycemic control in patients with type 2 diabetes. NPJ Digit Med 2022; 5:60. [PMID: 35545657 PMCID: PMC9095642 DOI: 10.1038/s41746-022-00606-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 04/18/2022] [Indexed: 12/22/2022] Open
Abstract
The lack of effective, scalable solutions for lifestyle treatment is a global clinical problem, causing severe morbidity and mortality. We developed a method for lifestyle treatment that promotes self-reflection and iterative behavioral change, provided as a digital tool, and evaluated its effect in 370 patients with type 2 diabetes (ClinicalTrials.gov identifier: NCT04691973). Users of the tool had reduced blood glucose, both compared with randomized and matched controls (involving 158 and 204 users, respectively), as well as improved systolic blood pressure, body weight and insulin resistance. The improvement was sustained during the entire follow-up (average 730 days). A pathophysiological subgroup of obese insulin-resistant individuals had a pronounced glycemic response, enabling identification of those who would benefit in particular from lifestyle treatment. Natural language processing showed that the metabolic improvement was coupled with the self-reflective element of the tool. The treatment is cost-saving because of improved risk factor control for cardiovascular complications. The findings open an avenue for self-managed lifestyle treatment with long-term metabolic efficacy that is cost-saving and can reach large numbers of people.
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Affiliation(s)
- Chinmay Dwibedi
- Department of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | | | | | | | - Annika S Axelsson
- Department of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | | | | | - Stephen H Friend
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Sofie Persson
- Swedish Institute for Health Economics, Lund, Sweden
| | - Stefan Franzén
- RegisterCentrum Västra Götaland, Göteborg, Sweden.,Health Metrics, Department of Public Health and Community Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Birgitta Abrahamsson
- Department of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | | | - Anders H Rosengren
- Department of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden. .,Faculty of Medicine, Lund University, Lund, Sweden.
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5
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Goodday SM, Travis S, Walsh A, Friend SH. Stress-related consequences of the coronavirus disease 2019 pandemic on symptoms of Crohn's disease. Eur J Gastroenterol Hepatol 2021; 33:1511-1516. [PMID: 33512845 PMCID: PMC8555884 DOI: 10.1097/meg.0000000000002081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/03/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES A link between stress and Crohn's disease activity suggests an association, but results have been conflicting. The purpose of this study was to assess whether the stress related to the coronavirus disease 2019 (COVID-19) pandemic affected disease activity in patients with Crohn's disease. BASIC METHODS An anonymous survey was distributed to patients through gastroenterology clinics and networks. Patients were asked to report their Crohn's disease symptoms in the months prior to the COVID-19 pandemic and again during the early stages of the COVID-19 pandemic using the Manitoba inflammatory bowel disease index in addition to questions about stress, perception of reasons for symptom change and personal impact. MAIN RESULTS Out of 243 individuals with a confirmed diagnosis of Crohn's disease, there was a 24% relative increase in active symptoms between the pre-COVID-19 period to the during-COVID-19 period (P < 0.0001) reflecting an absolute change from 45 to 56%, respectively. The most frequent reported reason for a change in symptoms was 'Increased stress/and or feeling overwhelmed' (118/236), and personal impact of the pandemic was, 'I'm worrying a lot about the future' (113/236), both reported by approximately half of respondents. PRINCIPAL CONCLUSIONS This study serves as a 'proof of concept' demonstrating the impact of a significant and uniquely uniform stressor as a natural experiment on Crohn's disease activity. The severity of symptoms of Crohn's disease increased during the COVID-19 pandemic. The primary reported reason for symptom change was an increase in stress, not a change in diet, exercise or other lifestyle behaviours, corroborating the hypothesis that stress affects Crohn's disease activity.
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Affiliation(s)
- Sarah M. Goodday
- 4YouandMe, Seattle, Washington, USA
- Department of Psychiatry, University of Oxford
| | - Simon Travis
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Alissa Walsh
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Stephen H. Friend
- 4YouandMe, Seattle, Washington, USA
- Department of Psychiatry, University of Oxford
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6
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Goodday SM, Geddes JR, Friend SH. Disrupting the power balance between doctors and patients in the digital era. Lancet Digit Health 2021; 3:e142-e143. [PMID: 33516653 DOI: 10.1016/s2589-7500(21)00004-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/16/2020] [Accepted: 01/06/2021] [Indexed: 01/26/2023]
Affiliation(s)
- Sarah M Goodday
- 4YouandMe, Seattle, WA 98121, USA; Department of Psychiatry, University of Oxford, Oxford, UK.
| | - John R Geddes
- Department of Psychiatry, University of Oxford, Oxford, UK; Oxford Health NHS Foundation Trust, Oxford, UK
| | - Stephen H Friend
- 4YouandMe, Seattle, WA 98121, USA; Department of Psychiatry, University of Oxford, Oxford, UK
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7
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Chaibub Neto E, Pratap A, Perumal TM, Tummalacherla M, Snyder P, Bot BM, Trister AD, Friend SH, Mangravite L, Omberg L. Detecting the impact of subject characteristics on machine learning-based diagnostic applications. NPJ Digit Med 2019; 2:99. [PMID: 31633058 PMCID: PMC6789029 DOI: 10.1038/s41746-019-0178-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/12/2019] [Indexed: 12/25/2022] Open
Abstract
Collection of high-dimensional, longitudinal digital health data has the potential to support a wide-variety of research and clinical applications including diagnostics and longitudinal health tracking. Algorithms that process these data and inform digital diagnostics are typically developed using training and test sets generated from multiple repeated measures collected across a set of individuals. However, the inclusion of repeated measurements is not always appropriately taken into account in the analytical evaluations of predictive performance. The assignment of repeated measurements from each individual to both the training and the test sets ("record-wise" data split) is a common practice and can lead to massive underestimation of the prediction error due to the presence of "identity confounding." In essence, these models learn to identify subjects, in addition to diagnostic signal. Here, we present a method that can be used to effectively calculate the amount of identity confounding learned by classifiers developed using a record-wise data split. By applying this method to several real datasets, we demonstrate that identity confounding is a serious issue in digital health studies and that record-wise data splits for machine learning- based applications need to be avoided.
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Affiliation(s)
| | - Abhishek Pratap
- Sage Bionetworks, Seattle, USA
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, USA
| | | | | | | | | | | | - Stephen H. Friend
- Sage Bionetworks, Seattle, USA
- 4YouandMe, Seattle, USA
- Visiting Professor of Connected Medicine, Department of Psychiatry, Oxford University, Oxford, UK
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8
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Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN, Kellen MR, Chen K, Norman TC, Friend SH, Guinney J, Stolovitzky G, Haussler D, Margolin AA, Stuart JM, Boutros PC. Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection. Genome Biol 2018; 19:188. [PMID: 30400818 PMCID: PMC6219177 DOI: 10.1186/s13059-018-1539-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/12/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The phenotypes of cancer cells are driven in part by somatic structural variants. Structural variants can initiate tumors, enhance their aggressiveness, and provide unique therapeutic opportunities. Whole-genome sequencing of tumors can allow exhaustive identification of the specific structural variants present in an individual cancer, facilitating both clinical diagnostics and the discovery of novel mutagenic mechanisms. A plethora of somatic structural variant detection algorithms have been created to enable these discoveries; however, there are no systematic benchmarks of them. Rigorous performance evaluation of somatic structural variant detection methods has been challenged by the lack of gold standards, extensive resource requirements, and difficulties arising from the need to share personal genomic information. RESULTS To facilitate structural variant detection algorithm evaluations, we create a robust simulation framework for somatic structural variants by extending the BAMSurgeon algorithm. We then organize and enable a crowdsourced benchmarking within the ICGC-TCGA DREAM Somatic Mutation Calling Challenge (SMC-DNA). We report here the results of structural variant benchmarking on three different tumors, comprising 204 submissions from 15 teams. In addition to ranking methods, we identify characteristic error profiles of individual algorithms and general trends across them. Surprisingly, we find that ensembles of analysis pipelines do not always outperform the best individual method, indicating a need for new ways to aggregate somatic structural variant detection approaches. CONCLUSIONS The synthetic tumors and somatic structural variant detection leaderboards remain available as a community benchmarking resource, and BAMSurgeon is available at https://github.com/adamewing/bamsurgeon .
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Affiliation(s)
- Anna Y Lee
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Adam D Ewing
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.,Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia
| | - Kyle Ellrott
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.,Computational Biology Program, Oregon Health & Science University, Portland, OR, USA
| | - Yin Hu
- Sage Bionetworks, Seattle, WA, USA
| | | | | | | | - Vincent Huang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Zechen Chong
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.,Informatics Institute, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | | | | | - Ken Chen
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | - Gustavo Stolovitzky
- IBM Computational Biology Center, T.J.Watson Research Center, Yorktown Heights, NY, USA
| | - David Haussler
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Adam A Margolin
- Computational Biology Program, Oregon Health & Science University, Portland, OR, USA. .,Sage Bionetworks, Seattle, WA, USA.
| | - Joshua M Stuart
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
| | - Paul C Boutros
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. .,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.
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9
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Axelsson AS, Tubbs E, Mecham B, Chacko S, Nenonen HA, Tang Y, Fahey JW, Derry JMJ, Wollheim CB, Wierup N, Haymond MW, Friend SH, Mulder H, Rosengren AH. Sulforaphane reduces hepatic glucose production and improves glucose control in patients with type 2 diabetes. Sci Transl Med 2017; 9:9/394/eaah4477. [DOI: 10.1126/scitranslmed.aah4477] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 02/23/2017] [Accepted: 05/05/2017] [Indexed: 12/13/2022]
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10
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Abstract
Because of their growing popularity and functionality, smartphones are increasingly valuable potential tools for health and medical research. Using ResearchKit, Apple's open-source platform to build applications ("apps") for smartphone research, collaborators have developed apps for researching asthma, breast cancer, cardiovascular disease, type 2 diabetes, and Parkinson disease. These research apps enhance widespread participation by removing geographical barriers to participation, provide novel ways to motivate healthy behaviors, facilitate high-frequency assessments, and enable more objective data collection. Although the studies have great potential, they also have notable limitations. These include selection bias, identity uncertainty, design limitations, retention, and privacy. As smartphone technology becomes increasingly available, researchers must recognize these factors to ensure that medical research is conducted appropriately. Despite these limitations, the future of smartphones in health research is bright. Their convenience grants unprecedented geographic freedom to researchers and participants alike and transforms the way clinical research can be conducted.
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Affiliation(s)
- E Ray Dorsey
- E.R. Dorsey is professor, Department of Neurology, and director, Center for Human Experimental Technologies (CHET), University of Rochester Medical Center, Rochester, New York. Y.F. Chan is assistant professor, Department of Genetics and Genomic Sciences and Department of Emergency Medicine, and director of digital health, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York. M.V. McConnell is professor, Department of Medicine, and director of cardiovascular health innovation, Stanford University School of Medicine, Stanford, California. S.Y. Shaw is assistant professor, Department of Medicine, and cofounder and codirector, Center for Assessment Technology and Continuous Health (CATCH), Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts. A.D. Trister is senior physician, Sage Bionetworks, Seattle, Washington. S.H. Friend is president, cofounder, and director, Sage Bionetworks, Seattle, Washington
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11
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Dang K, Perumal TM, Allen M, Funk C, Wang M, Xu J, Logsdon B, Yu L, Schuyler S, Friend SH, Bennett DA, Zhang B, Schadt E, Jager P, Price ND, Ertekin-Taner N, Mangravite LM. P4‐027: Combing Evidence Across Multiple Cohorts for Systems‐Based Target Discovery: the AMP‐AD Knowledge Portal. Alzheimers Dement 2016. [DOI: 10.1016/j.jalz.2016.06.2116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | | | | | | | - Minghui Wang
- Icahn School of Medicine at Mount SinaiNew YorkNY USA
| | | | | | - Lei Yu
- Rush University Medical CenterChicagoIL USA
| | | | | | | | - Bin Zhang
- Icahn School of Medicine at Mount SinaiNew YorkNY USA
| | - Eric Schadt
- Icahn School of Medicine at Mount SinaiNew YorkNY USA
| | - Philip Jager
- Broad InstituteCambridgeMA USA
- Harvard Medical SchoolBostonMA USA
- Brigham and Women’s HospitalBostonMA USA
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12
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Affiliation(s)
- David Malkin
- Division of Hematology/Oncology, Hospital for Sick Children and Department of Pediatrics, University of Toronto, Toronto, Ontario M5G 1X8, Canada
| | - Judy E. Garber
- Division of Population Sciences, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Louise C. Strong
- Department of Genetics, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
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13
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Affiliation(s)
- Stephen H Friend
- Stephen H. Friend is the president of Sage Bionetworks, Seattle, WA 98109, USA. E-mail:
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14
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Allen GI, Amoroso N, Anghel C, Balagurusamy V, Bare CJ, Beaton D, Bellotti R, Bennett DA, Boehme KL, Boutros PC, Caberlotto L, Caloian C, Campbell F, Chaibub Neto E, Chang YC, Chen B, Chen CY, Chien TY, Clark T, Das S, Davatzikos C, Deng J, Dillenberger D, Dobson RJB, Dong Q, Doshi J, Duma D, Errico R, Erus G, Everett E, Fardo DW, Friend SH, Fröhlich H, Gan J, St George-Hyslop P, Ghosh SS, Glaab E, Green RC, Guan Y, Hong MY, Huang C, Hwang J, Ibrahim J, Inglese P, Iyappan A, Jiang Q, Katsumata Y, Kauwe JSK, Klein A, Kong D, Krause R, Lalonde E, Lauria M, Lee E, Lin X, Liu Z, Livingstone J, Logsdon BA, Lovestone S, Ma TW, Malhotra A, Mangravite LM, Maxwell TJ, Merrill E, Nagorski J, Namasivayam A, Narayan M, Naz M, Newhouse SJ, Norman TC, Nurtdinov RN, Oyang YJ, Pawitan Y, Peng S, Peters MA, Piccolo SR, Praveen P, Priami C, Sabelnykova VY, Senger P, Shen X, Simmons A, Sotiras A, Stolovitzky G, Tangaro S, Tateo A, Tung YA, Tustison NJ, Varol E, Vradenburg G, Weiner MW, Xiao G, Xie L, Xie Y, Xu J, Yang H, Zhan X, Zhou Y, Zhu F, Zhu H, Zhu S. Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease. Alzheimers Dement 2016; 12:645-53. [PMID: 27079753 DOI: 10.1016/j.jalz.2016.02.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/15/2016] [Accepted: 02/18/2016] [Indexed: 10/22/2022]
Abstract
Identifying accurate biomarkers of cognitive decline is essential for advancing early diagnosis and prevention therapies in Alzheimer's disease. The Alzheimer's disease DREAM Challenge was designed as a computational crowdsourced project to benchmark the current state-of-the-art in predicting cognitive outcomes in Alzheimer's disease based on high dimensional, publicly available genetic and structural imaging data. This meta-analysis failed to identify a meaningful predictor developed from either data modality, suggesting that alternate approaches should be considered for prediction of cognitive performance.
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Affiliation(s)
- Genevera I Allen
- Department of Statistics and Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Nicola Amoroso
- Dipartimento di Fisica "M. Merlin", Università degli studi di Bari "A. Moro", Bari, Italy; Sezione di Bari, Istituto Nazionale di Fisica Nucleare, Bari, Italy
| | - Catalina Anghel
- Ontario Institute for Cancer Research, Informatics and Bio-computing Program, MaRS Centre, Toronto, ON, Canada
| | | | | | - Derek Beaton
- School of Behavioral and Brain Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Roberto Bellotti
- Dipartimento di Fisica "M. Merlin", Università degli studi di Bari "A. Moro", Bari, Italy; Sezione di Bari, Istituto Nazionale di Fisica Nucleare, Bari, Italy
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Kevin L Boehme
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Paul C Boutros
- Ontario Institute for Cancer Research, Informatics and Bio-computing Program, MaRS Centre, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Canada; Department of Pharmacology & Toxicology, University of Toronto, Toronto, Canada
| | - Laura Caberlotto
- The Microsoft Research, University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | - Cristian Caloian
- Ontario Institute for Cancer Research, Informatics and Bio-computing Program, MaRS Centre, Toronto, ON, Canada
| | - Frederick Campbell
- Department of Statistics and Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | | | - Yu-Chuan Chang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Beibei Chen
- Quantitative Biomedical Research Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chien-Yu Chen
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, Taiwan
| | - Ting-Ying Chien
- Innovation Center for Big Data and Digital Convergence, Yuan Ze University, Taoyuan, Taiwan
| | - Tim Clark
- Department of Neurology, Massachusetts General Hospital, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Sudeshna Das
- Department of Neurology, Massachusetts General Hospital, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Christos Davatzikos
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA, USA
| | - Jieyao Deng
- School of Computer Science, Fudan University, Shanghai, Shanghai, China; Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, Shanghai, China
| | | | - Richard J B Dobson
- NIHR Biomedical Research Centre for Mental Health, Kings College London, London, UK; Institute of Psychiatry, Psychology and Neuroscience, MRC Social, Genetic and Developmental Psychiatry Centre, Kings College London, London, UK; Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London WC1E 6BT, UK
| | - Qilin Dong
- School of Computer Science, Fudan University, Shanghai, Shanghai, China; Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, Shanghai, China
| | - Jimit Doshi
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA, USA
| | - Denise Duma
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA
| | | | - Guray Erus
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA, USA
| | - Evan Everett
- Department of Statistics and Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - David W Fardo
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA; Department of Biostatistics, University of Kentucky, Lexington, KY, USA
| | | | - Holger Fröhlich
- Bonn-Aachen International Center for IT, University of Bonn, Bonn, Germany
| | - Jessica Gan
- Department of Statistics and Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Peter St George-Hyslop
- Cambridge Institute for Medical Research, University of Cambridge and University of Toronto, Cambridge, CB2, UK
| | - Satrajit S Ghosh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Otology and Laryngology, Harvard Medical School, Boston, MA, USA
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Broad Institute and Harvard Medical School, Boston, MA, USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Ming-Yi Hong
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, Taiwan
| | - Chao Huang
- Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jinseub Hwang
- Department of Computer science and Statistics, Daegu University, Gyeongsan-si, Gyeongsangbuk-do, Republic of Korea
| | - Joseph Ibrahim
- Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paolo Inglese
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Anandhi Iyappan
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Department for Bioinformatics, Schloss Birlinghoven, Sankt Augustin, Germany; Bonn-Aachen International Center for IT, University of Bonn, Bonn, Germany
| | - Qijia Jiang
- Department of Statistics and Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Yuriko Katsumata
- Department of Biostatistics, University of Kentucky, Lexington, KY, USA
| | - John S K Kauwe
- Department of Biology, Brigham Young University, Provo, UT, USA.
| | | | - Dehan Kong
- Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Roland Krause
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Emilie Lalonde
- Ontario Institute for Cancer Research, Informatics and Bio-computing Program, MaRS Centre, Toronto, ON, Canada
| | - Mario Lauria
- The Microsoft Research, University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | - Eunjee Lee
- Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xihui Lin
- Ontario Institute for Cancer Research, Informatics and Bio-computing Program, MaRS Centre, Toronto, ON, Canada
| | - Zhandong Liu
- Department of Statistics and Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Julie Livingstone
- Ontario Institute for Cancer Research, Informatics and Bio-computing Program, MaRS Centre, Toronto, ON, Canada
| | | | - Simon Lovestone
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, UK
| | - Tsung-Wei Ma
- Quantitative Biomedical Research Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ashutosh Malhotra
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Department for Bioinformatics, Schloss Birlinghoven, Sankt Augustin, Germany; Bonn-Aachen International Center for IT, University of Bonn, Bonn, Germany
| | | | - Taylor J Maxwell
- Computational Biology Institute, The George Washington University, Ashburn, VA, USA
| | - Emily Merrill
- Department of Neurology, Massachusetts General Hospital, Cambridge, MA, USA
| | - John Nagorski
- Department of Statistics and Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Aishwarya Namasivayam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Manjari Narayan
- Department of Statistics and Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Mufassra Naz
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Department for Bioinformatics, Schloss Birlinghoven, Sankt Augustin, Germany; Bonn-Aachen International Center for IT, University of Bonn, Bonn, Germany
| | - Stephen J Newhouse
- NIHR Biomedical Research Centre for Mental Health, Kings College London, London, UK; Department of Biostatistics, Kings College London, London, UK
| | | | - Ramil N Nurtdinov
- Department of Neuroimmunology, Foundation Institut de Recerca, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Yen-Jen Oyang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Shengwen Peng
- School of Computer Science, Fudan University, Shanghai, Shanghai, China; Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, Shanghai, China
| | | | | | - Paurush Praveen
- The Microsoft Research, University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy; Bonn-Aachen International Center for IT, University of Bonn, Bonn, Germany
| | - Corrado Priami
- The Microsoft Research, University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | - Veronica Y Sabelnykova
- Ontario Institute for Cancer Research, Informatics and Bio-computing Program, MaRS Centre, Toronto, ON, Canada
| | - Philipp Senger
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Department for Bioinformatics, Schloss Birlinghoven, Sankt Augustin, Germany
| | - Xia Shen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK; MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew Simmons
- NIHR Biomedical Research Centre for Mental Health, Kings College London, London, UK
| | - Aristeidis Sotiras
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA, USA
| | - Gustavo Stolovitzky
- Genetics and Genomics Sciences Department, Icahn School of Medicine at Mount Sinai, New York, NY, USA; IBM Computational Biology Center, IBM Research, NY, USA
| | - Sabina Tangaro
- Sezione di Bari, Istituto Nazionale di Fisica Nucleare, Bari, Italy
| | - Andrea Tateo
- Dipartimento di Fisica "M. Merlin", Università degli studi di Bari "A. Moro", Bari, Italy
| | - Yi-An Tung
- Genome and systems biology degree program, National Taiwan University, Taipei, Taiwan
| | - Nicholas J Tustison
- Department of Radiology and Medical Imaging, The University of Virginia, Charlottesville, VA, USA
| | - Erdem Varol
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Michael W Weiner
- Radiology, Medicine, Psychiatry, and Neurology, UCSF, SFVAMC, San Francisco, CA, USA
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lei Xie
- Department of Computer Science, Hunter College, The City University of New York, New York, NY, USA
| | - Yang Xie
- Quantitative Biomedical Research Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jia Xu
- Quantitative Biomedical Research Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hojin Yang
- Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xiaowei Zhan
- Quantitative Biomedical Research Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yunyun Zhou
- Quantitative Biomedical Research Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Fan Zhu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Hongtu Zhu
- Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shanfeng Zhu
- School of Computer Science, Fudan University, Shanghai, Shanghai, China; Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, Shanghai, China; Centre for Computational Systems Biology, Fudan University, Shanghai, China
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15
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Chen R, Shi L, Hakenberg J, Naughton B, Sklar P, Zhang J, Zhou H, Tian L, Prakash O, Lemire M, Sleiman P, Cheng WY, Chen W, Shah H, Shen Y, Fromer M, Omberg L, Deardorff MA, Zackai E, Bobe JR, Levin E, Hudson TJ, Groop L, Wang J, Hakonarson H, Wojcicki A, Diaz GA, Edelmann L, Schadt EE, Friend SH. Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases. Nat Biotechnol 2016; 34:531-8. [PMID: 27065010 DOI: 10.1038/nbt.3514] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 02/12/2016] [Indexed: 12/21/2022]
Abstract
Genetic studies of human disease have traditionally focused on the detection of disease-causing mutations in afflicted individuals. Here we describe a complementary approach that seeks to identify healthy individuals resilient to highly penetrant forms of genetic childhood disorders. A comprehensive screen of 874 genes in 589,306 genomes led to the identification of 13 adults harboring mutations for 8 severe Mendelian conditions, with no reported clinical manifestation of the indicated disease. Our findings demonstrate the promise of broadening genetic studies to systematically search for well individuals who are buffering the effects of rare, highly penetrant, deleterious mutations. They also indicate that incomplete penetrance for Mendelian diseases is likely more common than previously believed. The identification of resilient individuals may provide a first step toward uncovering protective genetic variants that could help elucidate the mechanisms of Mendelian diseases and new therapeutic strategies.
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Affiliation(s)
- Rong Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lisong Shi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jörg Hakenberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Pamela Sklar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | - Lifeng Tian
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Om Prakash
- Department of Clinical Sciences, Diabetes &Endocrinology, Lund University Diabetes Center, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Patrick Sleiman
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Wei-Yi Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Menachem Fromer
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Matthew A Deardorff
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Elaine Zackai
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jason R Bobe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Elissa Levin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Leif Groop
- Department of Clinical Sciences, Diabetes &Endocrinology, Lund University Diabetes Center, Skåne University Hospital, Lund University, Malmö, Sweden
| | | | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - George A Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stephen H Friend
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sage Bionetworks, Seattle, Washington, USA
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16
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Bot BM, Suver C, Neto EC, Kellen M, Klein A, Bare C, Doerr M, Pratap A, Wilbanks J, Dorsey ER, Friend SH, Trister AD. The mPower study, Parkinson disease mobile data collected using ResearchKit. Sci Data 2016; 3:160011. [PMID: 26938265 PMCID: PMC4776701 DOI: 10.1038/sdata.2016.11] [Citation(s) in RCA: 276] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/02/2016] [Indexed: 01/12/2023] Open
Abstract
Current measures of health and disease are often insensitive, episodic, and subjective. Further, these measures generally are not designed to provide meaningful feedback to individuals. The impact of high-resolution activity data collected from mobile phones is only beginning to be explored. Here we present data from mPower, a clinical observational study about Parkinson disease conducted purely through an iPhone app interface. The study interrogated aspects of this movement disorder through surveys and frequent sensor-based recordings from participants with and without Parkinson disease. Benefitting from large enrollment and repeated measurements on many individuals, these data may help establish baseline variability of real-world activity measurement collected via mobile phones, and ultimately may lead to quantification of the ebbs-and-flows of Parkinson symptoms. App source code for these data collection modules are available through an open source license for use in studies of other conditions. We hope that releasing data contributed by engaged research participants will seed a new community of analysts working collaboratively on understanding mobile health data to advance human health.
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Affiliation(s)
- Brian M Bot
- Sage Bionetworks, Seattle, Washington 98109, USA
| | | | | | | | - Arno Klein
- Sage Bionetworks, Seattle, Washington 98109, USA
| | | | - Megan Doerr
- Sage Bionetworks, Seattle, Washington 98109, USA
| | | | | | - E Ray Dorsey
- Center for Human Experimental Therapeutics, University of Rochester Medical Center, Rochester, New York 14642, USA
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17
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Chaibub Neto E, Bot BM, Perumal T, Omberg L, Guinney J, Kellen M, Klein A, Friend SH, Trister AD. PERSONALIZED HYPOTHESIS TESTS FOR DETECTING MEDICATION RESPONSE IN PARKINSON DISEASE PATIENTS USING iPHONE SENSOR DATA. Pac Symp Biocomput 2016; 21:273-284. [PMID: 26776193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We propose hypothesis tests for detecting dopaminergic medication response in Parkinson disease patients, using longitudinal sensor data collected by smartphones. The processed data is composed of multiple features extracted from active tapping tasks performed by the participant on a daily basis, before and after medication, over several months. Each extracted feature corresponds to a time series of measurements annotated according to whether the measurement was taken before or after the patient has taken his/her medication. Even though the data is longitudinal in nature, we show that simple hypothesis tests for detecting medication response, which ignore the serial correlation structure of the data, are still statistically valid, showing type I error rates at the nominal level. We propose two distinct personalized testing approaches. In the first, we combine multiple feature-specific tests into a single union-intersection test. In the second, we construct personalized classifiers of the before/after medication labels using all the extracted features of a given participant, and test the null hypothesis that the area under the receiver operating characteristic curve of the classifier is equal to 1/2. We compare the statistical power of the personalized classifier tests and personalized union-intersection tests in a simulation study, and illustrate the performance of the proposed tests using data from mPower Parkinsons disease study, recently launched as part of Apples ResearchKit mobile platform. Our results suggest that the personalized tests, which ignore the longitudinal aspect of the data, can perform well in real data analyses, suggesting they might be used as a sound baseline approach, to which more sophisticated methods can be compared to.
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Affiliation(s)
- Elias Chaibub Neto
- Sage Bionetworks, 1100 Fairview Avenue North, Seattle, Washington 98109, USA*Corresponding author.,
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18
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Guinney J, Dienstmann R, Wang X, de Reyniès A, Schlicker A, Soneson C, Marisa L, Roepman P, Nyamundanda G, Angelino P, Bot BM, Morris JS, Simon IM, Gerster S, Fessler E, De Sousa E Melo F, Missiaglia E, Ramay H, Barras D, Homicsko K, Maru D, Manyam GC, Broom B, Boige V, Perez-Villamil B, Laderas T, Salazar R, Gray JW, Hanahan D, Tabernero J, Bernards R, Friend SH, Laurent-Puig P, Medema JP, Sadanandam A, Wessels L, Delorenzi M, Kopetz S, Vermeulen L, Tejpar S. The consensus molecular subtypes of colorectal cancer. Nat Med 2015; 21:1350-6. [PMID: 26457759 PMCID: PMC4636487 DOI: 10.1038/nm.3967] [Citation(s) in RCA: 3045] [Impact Index Per Article: 338.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 09/06/2015] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) is a frequently lethal disease with heterogeneous outcomes and drug responses. To resolve inconsistencies among the reported gene expression-based CRC classifications and facilitate clinical translation, we formed an international consortium dedicated to large-scale data sharing and analytics across expert groups. We show marked interconnectivity between six independent classification systems coalescing into four consensus molecular subtypes (CMSs) with distinguishing features: CMS1 (microsatellite instability immune, 14%), hypermutated, microsatellite unstable and strong immune activation; CMS2 (canonical, 37%), epithelial, marked WNT and MYC signaling activation; CMS3 (metabolic, 13%), epithelial and evident metabolic dysregulation; and CMS4 (mesenchymal, 23%), prominent transforming growth factor-β activation, stromal invasion and angiogenesis. Samples with mixed features (13%) possibly represent a transition phenotype or intratumoral heterogeneity. We consider the CMS groups the most robust classification system currently available for CRC-with clear biological interpretability-and the basis for future clinical stratification and subtype-based targeted interventions.
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Affiliation(s)
| | - Rodrigo Dienstmann
- Sage Bionetworks, Seattle, Washington, USA
- Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xin Wang
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong
| | | | | | | | | | | | | | - Paolo Angelino
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | | | - Jeffrey S Morris
- The University of Texas, M.D. Anderson Cancer Center, Houston, Texas, USA
| | | | - Sarah Gerster
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Evelyn Fessler
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Felipe De Sousa E Melo
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | | | - Hena Ramay
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - David Barras
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | | | - Dipen Maru
- The University of Texas, M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Ganiraju C Manyam
- The University of Texas, M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Bradley Broom
- The University of Texas, M.D. Anderson Cancer Center, Houston, Texas, USA
| | | | - Beatriz Perez-Villamil
- Laboratorio de Genomica y Microarrays, Instituto de Investigación Sanitaria San Carlos, Hospital Clinico San Carlos, Madrid, Spain
| | | | - Ramon Salazar
- Institut Catala d'Oncologia, L'Institut d'Investigació Biomèdica de Bellvitge, Barcelona, Spain
| | - Joe W Gray
- Biomedical Engineering, Oregon Health Sciences University, Portland, Oregon, USA
| | - Douglas Hanahan
- École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Josep Tabernero
- Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rene Bernards
- Netherlands Cancer Institute (NKI), Amsterdam, the Netherlands
| | | | - Pierre Laurent-Puig
- Université Paris Descartes, Paris, France
- Department of Biology, Hôpital Européen Georges-Pompidou, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Jan Paul Medema
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | | | - Lodewyk Wessels
- Netherlands Cancer Institute (NKI), Amsterdam, the Netherlands
| | - Mauro Delorenzi
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | - Scott Kopetz
- The University of Texas, M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
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19
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Commo F, Ferté C, Soria JC, Friend SH, André F, Guinney J. Impact of centralization on aCGH-based genomic profiles for precision medicine in oncology. Ann Oncol 2014; 26:582-8. [PMID: 25538175 DOI: 10.1093/annonc/mdu582] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Comparative genomic hybridization (CGH) arrays are increasingly used in personalized medicine programs to identify gene copy number aberrations (CNAs) that may be used to guide clinical decisions made during molecular tumor boards. However, analytical processes such as the centralization step may profoundly affect CGH array results and therefore may adversely affect outcomes in the precision medicine context. PATIENTS AND METHODS The effect of three different centralization methods: median, maximum peak, alternative peak, were evaluated on three datasets: (i) the NCI60 cell lines panel, (ii) the Cancer Cell Line Encyclopedia (CCLE) panel, and (iii) the patients enrolled in prospective molecular screening trials (SAFIR-01 n = 283, MOSCATO-01 n = 309), and compared with karyotyping, drug sensitivity, and patient-drug matching, respectively. RESULTS Using the NCI60 cell lines panel, the profiles generated by the alternative peak method were significantly closer to the cell karyotypes than those generated by the other centralization strategies (P < 0.05). Using the CCLE dataset, selected genes (ERBB2, EGFR) were better or equally correlated to the IC50 of their companion drug (lapatinib, erlotinib), when applying the alternative centralization. Finally, focusing on 24 actionable genes, we observed as many as 7.1% (SAFIR-01) and 6.8% (MOSCATO-01) of patients originally not oriented to a specific treatment, but who could have been proposed a treatment based on the alternative peak centralization method. CONCLUSION The centralization method substantially affects the call detection of CGH profiles and may thus impact precision medicine approaches. Among the three methods described, the alternative peak method addresses limitations associated with existing approaches.
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Affiliation(s)
- F Commo
- Sage Bionetworks, Seattle, USA INSERM U981, Gustave Roussy, University Paris XI, Villejuif
| | - C Ferté
- Sage Bionetworks, Seattle, USA INSERM U981, Gustave Roussy, University Paris XI, Villejuif Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - J C Soria
- INSERM U981, Gustave Roussy, University Paris XI, Villejuif Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | | | - F André
- INSERM U981, Gustave Roussy, University Paris XI, Villejuif Department of Medical Oncology, Gustave Roussy, Villejuif, France
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20
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Trister AD, Rostomily R, Friend SH. Abstract 359: An age-related 99-gene signature from glioblastoma implicates differences in survival related to RAS activation. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Glioblastoma (GBM) is the most common primary brain tumor with universally poor prognosis despite treatment with surgery, radiation and chemotherapy. One of the most significant prognostic factors is the patient's age at onset of disease, with younger patients demonstrating longer survival despite similar therapies. The aim of this work is to examine genomic differences that are tied to the age of onset that could explain the differences in outcomes.
Methods: We used the gene expression profiles from 559 GBM patients (pts) included in the Cancer Genome Atlas (TCGA) to build a gene expression model of the expression of 12185 genes to predict patient age using elasticnet with 500 bootstraps. This model was used to predict the age of patients in a testing set of 419 pts with gliomas included in Repository for Brain Neoplasia Data (REMBRANDT) (99 grade II, 71 grade III and 125 grade IV and 124 with no grade). Receiver-operating characteristic (ROC) and survival analysis were performed to measure the performance of the model in predicting age, gene-set enrichment analysis (GSEA) was used to reveal network topology perturbations, Cox proportional hazards were used to predict survival of the different predicted classes.
Results: Using a FDR cutoff of p=0.005, the bootstrapped elasticnet discovered 99 genes that were highly correlated with age in GBM patients that predicts age in the testing set of patients with gliomas with an area under the ROC curve of 0.97. GSEA motifs within these genes related to RAS activation in multiple cell lines, as well as genes related to immune modulation and increased CpG methylation. Survival analysis of the REMBRANDT pts showed that the cohort with an “older” gene signature had worse survival (median 27 months versus 15 months, log-rank p<0.00005). When applied to pts in REMBRANDT for whom age was not recorded (n=36), the model predicted classes also had significantly different survival (median 6 versus 10 months, log-rank p=0.001).
Conclusions: We have developed a gene expression model related to age of onset of GBM, to investigate the differences inherent in the biology that may lead to better prognosis in younger patients. Of the 99 genes that are strongly predictive of age in an external validation set, many were related to RAS activation in cell lines, immune modulation and CpG methylation. RAS perturbations have been previously shown to induce gliomas in mice, and this study shows a relationship between RAS gene network activation and age that may play a role in the different survival outcomes between different ages. Future work will include the use of RAS targeted agents to elucidate their role in the management of gliomas for select pts.
Citation Format: Andrew D. Trister, Robert Rostomily, Stephen H. Friend. An age-related 99-gene signature from glioblastoma implicates differences in survival related to RAS activation. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 359. doi:10.1158/1538-7445.AM2014-359
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21
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Affiliation(s)
- Stephen H Friend
- Sage Bionetworks, Seattle, WA, 98109 USA Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences and the Icahn Institute for Genomics and Multiscale Biology, New York, NY 10029, USA.
| | - Eric E Schadt
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences and the Icahn Institute for Genomics and Multiscale Biology, New York, NY 10029, USA.
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22
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Boutros PC, Ewing AD, Ellrott K, Norman TC, Dang KK, Hu Y, Kellen MR, Suver C, Bare JC, Stein LD, Spellman PT, Stolovitzky G, Friend SH, Margolin AA, Stuart JM. Global optimization of somatic variant identification in cancer genomes with a global community challenge. Nat Genet 2014; 46:318-319. [PMID: 24675517 DOI: 10.1038/ng.2932] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Paul C Boutros
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Adam D Ewing
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, USA
| | - Kyle Ellrott
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, USA
| | | | | | - Yin Hu
- Sage Bionetworks, Seattle, Washington, USA
| | | | | | | | - Lincoln D Stein
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Paul T Spellman
- Department of Molecular and Medical Genetics, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Gustavo Stolovitzky
- IBM Computational Biology Center, T.J. Watson Research Center, Yorktown Heights, New York, USA
| | | | | | - Joshua M Stuart
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, USA
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Neto EC, Jang IS, Friend SH, Margolin AA. The Stream algorithm: computationally efficient ridge-regression via Bayesian model averaging, and applications to pharmacogenomic prediction of cancer cell line sensitivity. Pac Symp Biocomput 2014:27-38. [PMID: 24297531 PMCID: PMC3911888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Computational efficiency is important for learning algorithms operating in the "large p, small n" setting. In computational biology, the analysis of data sets containing tens of thousands of features ("large p"), but only a few hundred samples ("small n"), is nowadays routine, and regularized regression approaches such as ridge-regression, lasso, and elastic-net are popular choices. In this paper we propose a novel and highly efficient Bayesian inference method for fitting ridge-regression. Our method is fully analytical, and bypasses the need for expensive tuning parameter optimization, via cross-validation, by employing Bayesian model averaging over the grid of tuning parameters. Additional computational efficiency is achieved by adopting the singular value decomposition reparametrization of the ridge-regression model, replacing computationally expensive inversions of large p × p matrices by efficient inversions of small and diagonal n × n matrices. We show in simulation studies and in the analysis of two large cancer cell line data panels that our algorithm achieves slightly better predictive performance than cross-validated ridge-regression while requiring only a fraction of the computation time. Furthermore, in comparisons based on the cell line data sets, our algorithm systematically out-performs the lasso in both predictive performance and computation time, and shows equivalent predictive performance, but considerably smaller computation time, than the elastic-net.
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24
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Jang IS, Neto EC, Guinney J, Friend SH, Margolin AA. Systematic assessment of analytical methods for drug sensitivity prediction from cancer cell line data. Pac Symp Biocomput 2014:63-74. [PMID: 24297534 PMCID: PMC3995541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Large-scale pharmacogenomic screens of cancer cell lines have emerged as an attractive pre-clinical system for identifying tumor genetic subtypes with selective sensitivity to targeted therapeutic strategies. Application of modern machine learning approaches to pharmacogenomic datasets have demonstrated the ability to infer genomic predictors of compound sensitivity. Such modeling approaches entail many analytical design choices; however, a systematic study evaluating the relative performance attributable to each design choice is not yet available. In this work, we evaluated over 110,000 different models, based on a multifactorial experimental design testing systematic combinations of modeling factors within several categories of modeling choices, including: type of algorithm, type of molecular feature data, compound being predicted, method of summarizing compound sensitivity values, and whether predictions are based on discretized or continuous response values. Our results suggest that model input data (type of molecular features and choice of compound) are the primary factors explaining model performance, followed by choice of algorithm. Our results also provide a statistically principled set of recommended modeling guidelines, including: using elastic net or ridge regression with input features from all genomic profiling platforms, most importantly, gene expression features, to predict continuous-valued sensitivity scores summarized using the area under the dose response curve, with pathway targeted compounds most likely to yield the most accurate predictors. In addition, our study provides a publicly available resource of all modeling results, an open source code base, and experimental design for researchers throughout the community to build on our results and assess novel methodologies or applications in related predictive modeling problems.
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Affiliation(s)
- In Sock Jang
- Sage Bionetworks, 1100 Fairview Ave. N Seattle, WA 98109, USA
| | | | - Justin Guinney
- Sage Bionetworks, 1100 Fairview Ave. N Seattle, WA 98109, USA
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25
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Affiliation(s)
- Sebastian M B Nijman
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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26
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Omberg L, Ellrott K, Yuan Y, Kandoth C, Wong C, Kellen MR, Friend SH, Stuart J, Liang H, Margolin AA. Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas. Nat Genet 2013; 45:1121-6. [PMID: 24071850 PMCID: PMC3950337 DOI: 10.1038/ng.2761] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Cancer Genome Atlas Pan-Cancer Analysis Working Group collaborated on the Synapse software platform to share and evolve data, results and methodologies while performing integrative analysis of molecular profiling data from 12 tumor types. The group's work serves as a pilot case study that provides (i) a template for future large collaborative studies; (ii) a system to support collaborative projects; and (iii) a public resource of highly curated data, results and automated systems for the evaluation of community-developed models.
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27
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Ferté C, Trister AD, Huang E, Bot BM, Guinney J, Commo F, Sieberts S, André F, Besse B, Soria JC, Friend SH. Impact of bioinformatic procedures in the development and translation of high-throughput molecular classifiers in oncology. Clin Cancer Res 2013; 19:4315-25. [PMID: 23780890 DOI: 10.1158/1078-0432.ccr-12-3937] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The progressive introduction of high-throughput molecular techniques in the clinic allows for the extensive and systematic exploration of multiple biologic layers of tumors. Molecular profiles and classifiers generated from these assays represent the foundation of what the National Academy describes as the future of "precision medicine". However, the analysis of such complex data requires the implementation of sophisticated bioinformatic and statistical procedures. It is critical that oncology practitioners be aware of the advantages and limitations of the methods used to generate classifiers to usher them into the clinic. This article uses publicly available expression data from patients with non-small cell lung cancer to first illustrate the challenges of experimental design and preprocessing of data before clinical application and highlights the challenges of high-dimensional statistical analysis. It provides a roadmap for the translation of such classifiers to clinical practice and makes key recommendations for good practice.
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Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA. Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Comput Biol 2013; 9:e1003047. [PMID: 23671412 PMCID: PMC3649990 DOI: 10.1371/journal.pcbi.1003047] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 03/18/2013] [Indexed: 01/09/2023] Open
Abstract
Breast cancer is the most common malignancy in women and is responsible for hundreds of thousands of deaths annually. As with most cancers, it is a heterogeneous disease and different breast cancer subtypes are treated differently. Understanding the difference in prognosis for breast cancer based on its molecular and phenotypic features is one avenue for improving treatment by matching the proper treatment with molecular subtypes of the disease. In this work, we employed a competition-based approach to modeling breast cancer prognosis using large datasets containing genomic and clinical information and an online real-time leaderboard program used to speed feedback to the modeling team and to encourage each modeler to work towards achieving a higher ranked submission. We find that machine learning methods combined with molecular features selected based on expert prior knowledge can improve survival predictions compared to current best-in-class methodologies and that ensemble models trained across multiple user submissions systematically outperform individual models within the ensemble. We also find that model scores are highly consistent across multiple independent evaluations. This study serves as the pilot phase of a much larger competition open to the whole research community, with the goal of understanding general strategies for model optimization using clinical and molecular profiling data and providing an objective, transparent system for assessing prognostic models.
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Affiliation(s)
- Erhan Bilal
- IBM TJ Watson Research, Yorktown Heights, New York, United States of America
| | - Janusz Dutkowski
- Departments of Medicine and Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Justin Guinney
- Sage Bionetworks, Seattle, Washington, United States of America
| | - In Sock Jang
- Sage Bionetworks, Seattle, Washington, United States of America
| | - Benjamin A. Logsdon
- Sage Bionetworks, Seattle, Washington, United States of America
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Gaurav Pandey
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | | | - Yishai Shimoni
- Columbia Initiative in Systems Biology, Columbia University, New York, New York, United States of America
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America
| | - Hans Kristian Moen Vollan
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- The K. G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Cambridge Research Institute, Cancer Research UK, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Oslo, Norway
| | | | - Oscar M. Rueda
- Cambridge Research Institute, Cancer Research UK, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Jorg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA, Institut de Génomique, Evry, France
| | - Christina Curtis
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Mariano J. Alvarez
- Columbia Initiative in Systems Biology, Columbia University, New York, New York, United States of America
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America
| | - Vessela N. Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- The K. G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Biology, Division of Medicine, Akershus University Hospital, Ahus, Norway
| | - Samuel Aparicio
- Department of Pathology and Laboratory Medicine, University of British Colombia, Vancouver, British Colombia, Canada
- Molecular Oncology, British Colombia Cancer Research Center, Vancouver, British Colombia, Canada
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- The K. G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Carlos Caldas
- Cambridge Research Institute, Cancer Research UK, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Experimental Cancer Medicine Centre, Cambridge, United Kingdom
- Cambridge Breast Unit, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Andrea Califano
- Columbia Initiative in Systems Biology, Columbia University, New York, New York, United States of America
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America
- Department of Biomedical Informatics, Columbia University, New York, New York, United States of America
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
- Institute for Cancer Genetics, Columbia University, Columbia University, New York, New York, United States of America
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, United States of America
| | | | - Trey Ideker
- Departments of Medicine and Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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Plenge RM, Greenberg JD, Mangravite LM, Derry JMJ, Stahl EA, Coenen MJH, Barton A, Padyukov L, Klareskog L, Gregersen PK, Mariette X, Moreland LW, Bridges SL, de Vries N, Huizinga TWJ, Guchelaar HJ, Friend SH, Stolovitzky G. Crowdsourcing genetic prediction of clinical utility in the Rheumatoid Arthritis Responder Challenge. Nat Genet 2013; 45:468-9. [PMID: 23619782 PMCID: PMC4084858 DOI: 10.1038/ng.2623] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Robert M. Plenge
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Jeffrey D. Greenberg
- Division of Rheumatology, New York University School of Medicine, New York, New York, USA
| | | | | | - Eli A. Stahl
- Division of Psychiatric Genomics and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mt. Sinai, New York, New York, USA
| | - Marieke J. H. Coenen
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Anne Barton
- Arthritis Research UK Epidemiology Unit, Musculoskeletal Research Group, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lars Klareskog
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Peter K. Gregersen
- The Feinstein Institute for Medical Research, North Shore–Long Island Jewish Health System, Manhasset, New York, USA
| | - Xavier Mariette
- Université Paris-Sud, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Paris-Sud, Institut National de la Santé et de la Recherche Médicale (INSERM) U1012, Rheumatology, le Kremlin-Bicêtre, France
| | - Larry W. Moreland
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - S Louis Bridges
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Niek de Vries
- Department of Clinical Immunology and Rheumatology, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Tom W. J. Huizinga
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Stephen H. Friend
- Sage Bionetworks, Seattle, Washington, USA
- Sage/DREAM Project, Sage Bionetworks, Seattle, Washington, USA
| | - Gustavo Stolovitzky
- Sage/DREAM Project, Sage Bionetworks, Seattle, Washington, USA
- IBM Computational Biology Center, T.J. Watson Research Center, Yorktown Heights, New York, USA
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30
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Margolin AA, Bilal E, Huang E, Norman TC, Ottestad L, Mecham BH, Sauerwine B, Kellen MR, Mangravite LM, Furia MD, Vollan HKM, Rueda OM, Guinney J, Deflaux NA, Hoff B, Schildwachter X, Russnes HG, Park D, Vang VO, Pirtle T, Youseff L, Citro C, Curtis C, Kristensen VN, Hellerstein J, Friend SH, Stolovitzky G, Aparicio S, Caldas C, Børresen-Dale AL. Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer. Sci Transl Med 2013; 5:181re1. [PMID: 23596205 PMCID: PMC3897241 DOI: 10.1126/scitranslmed.3006112] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Although molecular prognostics in breast cancer are among the most successful examples of translating genomic analysis to clinical applications, optimal approaches to breast cancer clinical risk prediction remain controversial. The Sage Bionetworks-DREAM Breast Cancer Prognosis Challenge (BCC) is a crowdsourced research study for breast cancer prognostic modeling using genome-scale data. The BCC provided a community of data analysts with a common platform for data access and blinded evaluation of model accuracy in predicting breast cancer survival on the basis of gene expression data, copy number data, and clinical covariates. This approach offered the opportunity to assess whether a crowdsourced community Challenge would generate models of breast cancer prognosis commensurate with or exceeding current best-in-class approaches. The BCC comprised multiple rounds of blinded evaluations on held-out portions of data on 1981 patients, resulting in more than 1400 models submitted as open source code. Participants then retrained their models on the full data set of 1981 samples and submitted up to five models for validation in a newly generated data set of 184 breast cancer patients. Analysis of the BCC results suggests that the best-performing modeling strategy outperformed previously reported methods in blinded evaluations; model performance was consistent across several independent evaluations; and aggregating community-developed models achieved performance on par with the best-performing individual models.
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Affiliation(s)
- Adam A. Margolin
- Sage Bionetworks, 1100 Fairview Avenue North, MS: M1-C108, Seattle, WA 98109, USA
| | - Erhan Bilal
- Functional Genomics and Systems Biology, IBM Computational Biology Center, P. O. Box 218, Yorktown Heights, NY 10598, USA
| | - Erich Huang
- Sage Bionetworks, 1100 Fairview Avenue North, MS: M1-C108, Seattle, WA 98109, USA
- Institute for Genome Sciences & Policy, Duke University, Durham, NC 27708, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Thea C. Norman
- Sage Bionetworks, 1100 Fairview Avenue North, MS: M1-C108, Seattle, WA 98109, USA
| | - Lars Ottestad
- Department of Oncology, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, 0450 Oslo, Norway
| | - Brigham H. Mecham
- Sage Bionetworks, 1100 Fairview Avenue North, MS: M1-C108, Seattle, WA 98109, USA
- Trialomics, LLC, Seattle, WA 98103, USA
| | - Ben Sauerwine
- Google Inc., 651 North 34th Street, Seattle, WA 98103, USA
| | - Michael R. Kellen
- Sage Bionetworks, 1100 Fairview Avenue North, MS: M1-C108, Seattle, WA 98109, USA
| | - Lara M. Mangravite
- Sage Bionetworks, 1100 Fairview Avenue North, MS: M1-C108, Seattle, WA 98109, USA
| | - Matthew D. Furia
- Sage Bionetworks, 1100 Fairview Avenue North, MS: M1-C108, Seattle, WA 98109, USA
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Hans Kristian Moen Vollan
- Department of Oncology, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, 0450 Oslo, Norway
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Oscar M. Rueda
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Justin Guinney
- Sage Bionetworks, 1100 Fairview Avenue North, MS: M1-C108, Seattle, WA 98109, USA
| | - Nicole A. Deflaux
- Sage Bionetworks, 1100 Fairview Avenue North, MS: M1-C108, Seattle, WA 98109, USA
| | - Bruce Hoff
- Sage Bionetworks, 1100 Fairview Avenue North, MS: M1-C108, Seattle, WA 98109, USA
| | - Xavier Schildwachter
- Sage Bionetworks, 1100 Fairview Avenue North, MS: M1-C108, Seattle, WA 98109, USA
| | - Hege G. Russnes
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway
- Department of Pathology, Oslo University Hospital, 0450 Oslo, Norway
| | - Daehoon Park
- Department of Pathology, Drammen Hospital, Vestre Viken HF, 3004 Drammen, Norway
| | - Veronica O. Vang
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway
| | - Tyler Pirtle
- Google Inc., 651 North 34th Street, Seattle, WA 98103, USA
| | - Lamia Youseff
- Google Inc., 651 North 34th Street, Seattle, WA 98103, USA
| | - Craig Citro
- Google Inc., 651 North 34th Street, Seattle, WA 98103, USA
| | - Christina Curtis
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Vessela N. Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway
- Department of Clinical Molecular Oncology, Division of Medicine, Akershus University Hospital, 1478 Ahus, Norway
| | | | - Stephen H. Friend
- Sage Bionetworks, 1100 Fairview Avenue North, MS: M1-C108, Seattle, WA 98109, USA
| | - Gustavo Stolovitzky
- Functional Genomics and Systems Biology, IBM Computational Biology Center, P. O. Box 218, Yorktown Heights, NY 10598, USA
| | - Samuel Aparicio
- Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Carlos Caldas
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK
- Cambridge Experimental Cancer Medicine Centre, Cambridge CB2 0RE, UK
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway
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Trister AD, Mikheev AM, Rockhill JK, Friend SH, Rostomily RC. Abstract 1210: Periostin expression in glioma correlates with genes related to mesenchymal transition and survival. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-1210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Gliomas are the most common primary brain tumors and their prognosis is related to WHO histopathological grade. Glioblastoma (grade IV astrocytoma or GBM) is characterized by microscopic invasion into surrounding brain and universally poor prognosis despite treatment with surgery, radiation and chemotherapy . Recently, the matricellular protein periostin (POSTN) has been shown to be associated with increased parenchymal invasion (measured by edema on MRI) and poor prognosis in GBM. The specific aim of the present analysis was to determine the mechanistic impact of POSTN on glioma outcome.
Methods: We used the gene expression of POSTN from 559 GBM patients (pts) included in the Cancer Genome Atlas (TCGA) to build a gene expression model of the expression of 12184 genes to predict POSTN expression using elastic net. This model was used to predict the POSTN expression in a testing set of 419 pts with gliomas included in Repository for Brain Neoplasia Data (REMBRANDT) (99 grade II, 71 grade III and 125 grade IV and 124 with no grade). Receiver-operating characteristic (ROC) and survival analysis were performed to measure the performance of the model, and gene-set enrichment analysis (GSEA) was used to reveal network topology perturbations.
Results: The gene expression model discovered 721 genes highly correlated to POSTN expression that predict POSTN in the testing set with an area under the curve (AUC) of 0.96 on ROC curve. GSEA reveals genes involved in “mesenchymal transition,” transition of invasive ductal carcinoma (IDC) from ductal carcinoma in situ (DCIS) in breast cancer and stem cell signatures. Survival analysis of the TCGA GBM pts showed that the cohort with “high POSTN” had worse survival (median 12 months versus 15 months, log-rank p=0.0002). When applied to all pts in REMBRANDT, the model predicted classes also had significantly different survival (median 13.4 versus 38 months, log-rank p<0.0001). Interestingly, this classification of survival persists in the subset of pts with grade III (n=71, median survival 17.7 versus 42.4 months, p=0.0125) and grade II (n=99, median survival 17.9 versus 50.8, p=0.02) gliomas.
Conclusions: We have developed a gene expression model related to POSTN, a gene linked to poor prognosis in GBM, to investigate the role correlated genes may play in the aggressive phenotype. Some of the genes found to be highly correlated to POSTN are related to mesenchymal transition, invasive behavior in breast cancer and stemness. We verify that high POSTN expression is a strong prognostic indicator for poor outcome in GBM, and reveal for the first time that pts with grade II and III glioma with a “high” POSTN signature have significantly worse survival. Given that low grade glioma pts often have less aggressive treatment at time of diagnosis, we propose studying the role of early chemoradiation in the subset of pts with poor POSTN signature to potentially improve their outcome.
Citation Format: Andrew D. Trister, Andrei M. Mikheev, Jason K. Rockhill, Stephen H. Friend, Robert C. Rostomily. Periostin expression in glioma correlates with genes related to mesenchymal transition and survival. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1210. doi:10.1158/1538-7445.AM2013-1210
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Derry JMJ, Mangravite LM, Suver C, Furia MD, Henderson D, Schildwachter X, Bot B, Izant J, Sieberts SK, Kellen MR, Friend SH. Developing predictive molecular maps of human disease through community-based modeling. Nat Genet 2012; 44:127-30. [PMID: 22281773 DOI: 10.1038/ng.1089] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Abstract
Medicine will move from a reactive to a proactive discipline over the next decade--a discipline that is predictive, personalized, preventive and participatory (P4). P4 medicine will be fueled by systems approaches to disease, emerging technologies and analytical tools. There will be two major challenges to achieving P4 medicine--technical and societal barriers--and the societal barriers will prove the most challenging. How do we bring patients, physicians and members of the health-care community into alignment with the enormous opportunities of P4 medicine? In part, this will be done by the creation of new types of strategic partnerships--between patients, large clinical centers, consortia of clinical centers and patient-advocate groups. For some clinical trials it will necessary to recruit very large numbers of patients--and one powerful approach to this challenge is the crowd-sourced recruitment of patients by bringing large clinical centers together with patient-advocate groups.
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Affiliation(s)
- Leroy Hood
- Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA.
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Abstract
The possibility that experimental data from diverse cell biology experiments might shed light on other experiments has been generally outside the realm of cancer biologists. Recent experiments suggest that core RNA expression profiles distilled from experiments using a set of known members with related attributes may be used as query tools to probe expression profiles from other unrelated experiments. The potential benefit arises from the possibility to share findings without fully reconstructing the exact initial conditions. The limitations will be framed by the robustness of the hypotheses so generated.
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Affiliation(s)
- Stephen H Friend
- Merck Research Laboratories, Merck & Co, Inc., Upper Gwynedd, Pennsylvania 19454, USA.
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38
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Bartz SR, Zhang Z, Burchard J, Imakura M, Martin M, Palmieri A, Needham R, Guo J, Gordon M, Chung N, Warrener P, Jackson AL, Carleton M, Oatley M, Locco L, Santini F, Smith T, Kunapuli P, Ferrer M, Strulovici B, Friend SH, Linsley PS. Small interfering RNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 disruptions. Mol Cell Biol 2006; 26:9377-86. [PMID: 17000754 PMCID: PMC1698535 DOI: 10.1128/mcb.01229-06] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
RNA interference technology allows the systematic genetic analysis of the molecular alterations in cancer cells and how these alterations affect response to therapies. Here we used small interfering RNA (siRNA) screens to identify genes that enhance the cytotoxicity (enhancers) of established anticancer chemotherapeutics. Hits identified in drug enhancer screens of cisplatin, gemcitabine, and paclitaxel were largely unique to the drug being tested and could be linked to the drug's mechanism of action. Hits identified by screening of a genome-scale siRNA library for cisplatin enhancers in TP53-deficient HeLa cells were significantly enriched for genes with annotated functions in DNA damage repair as well as poorly characterized genes likely having novel functions in this process. We followed up on a subset of the hits from the cisplatin enhancer screen and validated a number of enhancers whose products interact with BRCA1 and/or BRCA2. TP53(+/-) matched-pair cell lines were used to determine if knockdown of BRCA1, BRCA2, or validated hits that associate with BRCA1 and BRCA2 selectively enhances cisplatin cytotoxicity in TP53-deficient cells. Silencing of BRCA1, BRCA2, or BRCA1/2-associated genes enhanced cisplatin cytotoxicity approximately 4- to 7-fold more in TP53-deficient cells than in matched TP53 wild-type cells. Thus, tumor cells having disruptions in BRCA1/2 network genes and TP53 together are more sensitive to cisplatin than cells with either disruption alone.
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39
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Abstract
The purpose of this paper is to provide some perspectives on whether we are at a tipping point in understanding oncology and oncology drug discovery. It describes how model organisms have prepared us for more efficient drug discovery, lessons that are in use today. It provides examples of the emerging integration of biomarkers in patient care. It also details how over the next several years the processes of carrying out target identification and identifying responders to drugs will become more and more similar. In conclusion, a discussion is provided about who can do what to link the various components of this information-rich drug discovery process together.
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Affiliation(s)
- S H Friend
- Merck Research Laboratories, West Point, Pennsylvania 19486, USA
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Abstract
The allure of the emerging genomic technologies in cancer is their ability to generate new biomarkers that predict how individual cancer patients will respond to various treatments. However, productive implementation of cancer biomarkers into patient care will require fundamental changes in how we consider approvals for cancer indications and how we track patient responses. Here we briefly describe ongoing efforts to identify and to validate cancer biomarkers, discuss the technological hurdles that lie ahead, and then focus on the more pressing political and cultural issues that, if left unheeded, could derail many of the anticipated benefits of biomarker research.
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Affiliation(s)
- William S Dalton
- H. Lee Moffitt Cancer Center, University of South Florida, Tampa, FL 33613, USA.
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41
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Abstract
Information from genomic, proteomic and metabolomic measurements has already benefited target discovery and validation, assessment of efficacy and toxicity of compounds, identification of disease subgroups and the prediction of responses of individual patients. Greater benefits can be expected from the application of these technologies on a significantly larger scale; by simultaneously collecting diverse measurements from the same subjects or cell cultures; by exploiting the steadily improving quantitative accuracy of the technologies; and by interpreting the emerging data in the context of underlying biological models of increasing sophistication. The benefits of applying molecular profiling to drug discovery and development will include much lower failure rates at all stages of the drug development pipeline, faster progression from discovery through to clinical trials and more successful therapies for patient subgroups. Upheavals in existing organizational structures in the current 'conveyor belt' models of drug discovery might be required to take full advantage of these methods.
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Affiliation(s)
- Roland B Stoughton
- GHC Technologies, Inc., 505 Coast Boulevard South, Suite 309, La Jolla, California 92037, USA.
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Lampe JW, Stepaniants SB, Mao M, Radich JP, Dai H, Linsley PS, Friend SH, Potter JD. Signatures of Environmental Exposures Using Peripheral Leukocyte Gene Expression: Tobacco Smoke. Cancer Epidemiol Biomarkers Prev 2004. [DOI: 10.1158/1055-9965.445.13.3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Functional biological markers of environmental exposures are important in epidemiological studies of disease risk. Such markers not only provide a measure of the exposure, they also reflect the degree of physiological and biochemical response to the exposure. In an observational study, using DNA microarrays, we show that it is possible to distinguish between 85 individuals exposed and unexposed to tobacco smoke on the basis of mRNA expression in peripheral leukocytes. Furthermore, we show that active exposure to tobacco smoke is associated with a biologically relevant mRNA expression signature. These findings suggest that expression patterns can be used to identify a complex environmental exposure in humans.
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Affiliation(s)
| | | | - Mao Mao
- 2Rosetta Inpharmatics, LLC, Merck Research Laboratories, Kirkland, WA
| | | | - Hongyue Dai
- 2Rosetta Inpharmatics, LLC, Merck Research Laboratories, Kirkland, WA
| | - Peter S. Linsley
- 2Rosetta Inpharmatics, LLC, Merck Research Laboratories, Kirkland, WA
| | - Stephen H. Friend
- 2Rosetta Inpharmatics, LLC, Merck Research Laboratories, Kirkland, WA
| | - John D. Potter
- 1Fred Hutchinson Cancer Research Center, Seattle, WA and
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Lampe JW, Stepaniants SB, Mao M, Radich JP, Dai H, Linsley PS, Friend SH, Potter JD. Signatures of environmental exposures using peripheral leukocyte gene expression: tobacco smoke. Cancer Epidemiol Biomarkers Prev 2004; 13:445-53. [PMID: 15006922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
Functional biological markers of environmental exposures are important in epidemiological studies of disease risk. Such markers not only provide a measure of the exposure, they also reflect the degree of physiological and biochemical response to the exposure. In an observational study, using DNA microarrays, we show that it is possible to distinguish between 85 individuals exposed and unexposed to tobacco smoke on the basis of mRNA expression in peripheral leukocytes. Furthermore, we show that active exposure to tobacco smoke is associated with a biologically relevant mRNA expression signature. These findings suggest that expression patterns can be used to identify a complex environmental exposure in humans.
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44
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Affiliation(s)
- Stephen H Friend
- Merck Research Laboratories, Merck & Company, West Point, Pennsylvania, USA.
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Schadt EE, Monks SA, Friend SH. A new paradigm for drug discovery: integrating clinical, genetic, genomic and molecular phenotype data to identify drug targets. Biochem Soc Trans 2003; 31:437-43. [PMID: 12653656 DOI: 10.1042/bst0310437] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Application of statistical genetics approaches to variations in mRNA transcript abundances in segregating populations can be used to identify genes and pathways associated with common human diseases. The combination of this genetic information with gene expression and clinical trait data can also be used to identify subtypes of a disease and the genetic loci specific to each subtype. Here we highlight results from some of our recent work in this area and further explore the many possibilities that exist in employing a more comprehensive genetics and functional genomics approach to the functional annotation of genomes, and in applying such methods to the validation of targets for complex traits in the drug discovery process.
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Affiliation(s)
- E E Schadt
- Rosetta Inpharmatics LLC, 12040 115th Avenue N.E., Kirkland, WA 98034, U.S.A.
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46
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Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G, Linsley PS, Mao M, Stoughton RB, Friend SH. Genetics of gene expression surveyed in maize, mouse and man. Nature 2003; 422:297-302. [PMID: 12646919 DOI: 10.1038/nature01434] [Citation(s) in RCA: 1028] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2002] [Accepted: 01/10/2003] [Indexed: 11/09/2022]
Abstract
Treating messenger RNA transcript abundances as quantitative traits and mapping gene expression quantitative trait loci for these traits has been pursued in gene-specific ways. Transcript abundances often serve as a surrogate for classical quantitative traits in that the levels of expression are significantly correlated with the classical traits across members of a segregating population. The correlation structure between transcript abundances and classical traits has been used to identify susceptibility loci for complex diseases such as diabetes and allergic asthma. One study recently completed the first comprehensive dissection of transcriptional regulation in budding yeast, giving a detailed glimpse of a genome-wide survey of the genetics of gene expression. Unlike classical quantitative traits, which often represent gross clinical measurements that may be far removed from the biological processes giving rise to them, the genetic linkages associated with transcript abundance affords a closer look at cellular biochemical processes. Here we describe comprehensive genetic screens of mouse, plant and human transcriptomes by considering gene expression values as quantitative traits. We identify a gene expression pattern strongly associated with obesity in a murine cross, and observe two distinct obesity subtypes. Furthermore, we find that these obesity subtypes are under the control of different loci.
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MESH Headings
- Animals
- Chromosome Mapping
- Chromosomes, Human, Pair 20/genetics
- Chromosomes, Mammalian/genetics
- Crosses, Genetic
- Female
- Genomics/methods
- Humans
- Lod Score
- Male
- Mice/genetics
- Mice, Inbred C57BL
- Mice, Inbred DBA
- Obesity/genetics
- Oligonucleotide Array Sequence Analysis
- Pedigree
- Polymorphism, Genetic/genetics
- Quantitative Trait Loci/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Transcription, Genetic/genetics
- Tumor Cells, Cultured
- Zea mays/genetics
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Affiliation(s)
- Eric E Schadt
- Rosetta Inpharmatics, LLC, 12040 115th Avenue N.E., Kirkland, Washington 98034, USA.
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Affiliation(s)
- Laura J van 't Veer
- Division of Diagnostic Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Center for Biomedical Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- A wholly-owned subsidiary of Merck & Co., Inc
| | - Hongyue Dai
- Rosetta Inpharmatics, Inc.,* Kirkland, Washington, USA
| | - Marc J van de Vijver
- Division of Diagnostic Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Yudong D He
- Rosetta Inpharmatics, Inc.,* Kirkland, Washington, USA
| | - Augustinus AM Hart
- Division of Radiotherapy, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - René Bernards
- Center for Biomedical Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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48
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van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AAM, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, Parrish M, Atsma D, Witteveen A, Glas A, Delahaye L, van der Velde T, Bartelink H, Rodenhuis S, Rutgers ET, Friend SH, Bernards R. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002; 347:1999-2009. [PMID: 12490681 DOI: 10.1056/nejmoa021967] [Citation(s) in RCA: 4354] [Impact Index Per Article: 197.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND A more accurate means of prognostication in breast cancer will improve the selection of patients for adjuvant systemic therapy. METHODS Using microarray analysis to evaluate our previously established 70-gene prognosis profile, we classified a series of 295 consecutive patients with primary breast carcinomas as having a gene-expression signature associated with either a poor prognosis or a good prognosis. All patients had stage I or II breast cancer and were younger than 53 years old; 151 had lymph-node-negative disease, and 144 had lymph-node-positive disease. We evaluated the predictive power of the prognosis profile using univariable and multivariable statistical analyses. RESULTS Among the 295 patients, 180 had a poor-prognosis signature and 115 had a good-prognosis signature, and the mean (+/-SE) overall 10-year survival rates were 54.6+/-4.4 percent and 94.5+/-2.6 percent, respectively. At 10 years, the probability of remaining free of distant metastases was 50.6+/-4.5 percent in the group with a poor-prognosis signature and 85.2+/-4.3 percent in the group with a good-prognosis signature. The estimated hazard ratio for distant metastases in the group with a poor-prognosis signature, as compared with the group with the good-prognosis signature, was 5.1 (95 percent confidence interval, 2.9 to 9.0; P<0.001). This ratio remained significant when the groups were analyzed according to lymph-node status. Multivariable Cox regression analysis showed that the prognosis profile was a strong independent factor in predicting disease outcome. CONCLUSIONS The gene-expression profile we studied is a more powerful predictor of the outcome of disease in young patients with breast cancer than standard systems based on clinical and histologic criteria.
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Affiliation(s)
- Marc J van de Vijver
- Division of Diagnostic Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
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50
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van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AAM, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002; 415:530-6. [PMID: 11823860 DOI: 10.1038/415530a] [Citation(s) in RCA: 6230] [Impact Index Per Article: 283.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Breast cancer patients with the same stage of disease can have markedly different treatment responses and overall outcome. The strongest predictors for metastases (for example, lymph node status and histological grade) fail to classify accurately breast tumours according to their clinical behaviour. Chemotherapy or hormonal therapy reduces the risk of distant metastases by approximately one-third; however, 70-80% of patients receiving this treatment would have survived without it. None of the signatures of breast cancer gene expression reported to date allow for patient-tailored therapy strategies. Here we used DNA microarray analysis on primary breast tumours of 117 young patients, and applied supervised classification to identify a gene expression signature strongly predictive of a short interval to distant metastases ('poor prognosis' signature) in patients without tumour cells in local lymph nodes at diagnosis (lymph node negative). In addition, we established a signature that identifies tumours of BRCA1 carriers. The poor prognosis signature consists of genes regulating cell cycle, invasion, metastasis and angiogenesis. This gene expression profile will outperform all currently used clinical parameters in predicting disease outcome. Our findings provide a strategy to select patients who would benefit from adjuvant therapy.
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Affiliation(s)
- Laura J van 't Veer
- Division of Diagnostic Oncology, The Netherlands Cancer Institute, 121 Plesmanlaan, 1066 CX Amsterdam, The Netherlands
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