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Chang SK, Liu D, Mitchem J, Papageorgiou C, Kaifi J, Shyu CR. Understanding common key indicators of successful and unsuccessful cancer drug trials using a contrast mining framework on ClinicalTrials.gov. J Biomed Inform 2023; 139:104321. [PMID: 36806327 DOI: 10.1016/j.jbi.2023.104321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 02/04/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023]
Abstract
Clinical trials are essential to the process of new drug development. As clinical trials involve significant investments of time and money, it is crucial for trial designers to carefully investigate trial settings prior to designing a trial. Utilizing trial documents from ClinicalTrials.gov, we aim to understand the common characteristics of successful and unsuccessful cancer drug trials to provide insights about what to learn and what to avoid. In this research, we first computationally classified cancer drug trials into successful and unsuccessful cases and then utilized natural language processing to extract eligibility criteria information from the trial documents. To provide explainable and potentially modifiable recommendations for new trial design, contrast mining was applied to discoverhighly contrasted patterns with a significant difference in prevalence between successful (completion with advancement to the next phase) and unsuccessful (suspended, withdrawn, or terminated) groups. Our method identified contrast patterns consisting of combinations of drug categories, eligibility criteria, study organization, and study design for nine major cancers. In addition to a literature review for the qualitative validation of mined contrast patterns, we found that contrast-pattern-based classifiers using the top 200 contrast patterns as feature representations can achieve approximately 80% F1 score for eight out of ten cancer types in our experiments. In summary, aligning with the modernization efforts of ClinicalTrials.gov, our study demonstrates that understanding the contrast characteristics of successful and unsuccessful cancer trials may provide insights into the decision-making process for trial investigators and therefore facilitate improved cancer drug trial design.
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Affiliation(s)
- Shu-Kai Chang
- Institute for Data Science & Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Danlu Liu
- Electrical Engineering and Computer Science Department, University of Missouri, Columbia, MO 65211, USA
| | - Jonathan Mitchem
- Institute for Data Science & Informatics, University of Missouri, Columbia, MO 65211, USA; Department of Surgery, School of Medicine, University of Missouri, Columbia, MO 65212, USA; Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA
| | - Christos Papageorgiou
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Jussuf Kaifi
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO 65212, USA; Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA
| | - Chi-Ren Shyu
- Institute for Data Science & Informatics, University of Missouri, Columbia, MO 65211, USA; Electrical Engineering and Computer Science Department, University of Missouri, Columbia, MO 65211, USA; Department of Medicine, School of Medicine, University of Missouri, Columbia, MO 65212, USA.
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2
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Ammitzbøll G, Levinsen AKG, Kjær TK, Ebbestad FE, Horsbøl TA, Saltbæk L, Badre-Esfahani SK, Joensen A, Kjeldsted E, Halgren Olsen M, Dalton SO. Socioeconomic inequality in cancer in the Nordic countries. A systematic review. Acta Oncol 2022; 61:1317-1331. [DOI: 10.1080/0284186x.2022.2143278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Gunn Ammitzbøll
- Survivorship and Inequality in Cancer, Danish Cancer Society Research Center, Copenhagen, Denmark
- Danish Research Center for Equality in Cancer (COMPAS), Department of Clinical Oncology & Palliative Care, Zealand University Hospital, Næstved, Denmark
| | | | - Trille Kristina Kjær
- Survivorship and Inequality in Cancer, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Freja Ejlebæk Ebbestad
- Survivorship and Inequality in Cancer, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Trine Allerslev Horsbøl
- Survivorship and Inequality in Cancer, Danish Cancer Society Research Center, Copenhagen, Denmark
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Lena Saltbæk
- Survivorship and Inequality in Cancer, Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Clinical Oncology and Palliative Care, Zealand University Hospital, Næstved, Denmark
| | - Sara Koed Badre-Esfahani
- Department of Gynecology and Obstetrics, Aarhus University Hospital, Aarhus, Denmark
- Department of Public Health Programmes, Randers Regional Hospital, Randers, Denmark
| | - Andrea Joensen
- Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eva Kjeldsted
- Danish Research Center for Equality in Cancer (COMPAS), Department of Clinical Oncology & Palliative Care, Zealand University Hospital, Næstved, Denmark
| | - Maja Halgren Olsen
- Survivorship and Inequality in Cancer, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Susanne Oksbjerg Dalton
- Survivorship and Inequality in Cancer, Danish Cancer Society Research Center, Copenhagen, Denmark
- Danish Research Center for Equality in Cancer (COMPAS), Department of Clinical Oncology & Palliative Care, Zealand University Hospital, Næstved, Denmark
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3
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Husby S, Favero F, Rodriguez-Gonzalez FG, Sutton LA, Haastrup EK, Ørskov AD, Hansen JW, Arboe B, Aslan D, Clasen-Linde E, Rahbek Gjerdrum LM, Gørlev JS, Brown P, Fischer-Nielsen A, Rosenquist R, Weischenfeldt J, Grønbæk K. Mutations known from B-cell lymphoid malignancies are not found in CD34 + stem cells from patients with lymphoma. Leuk Lymphoma 2021; 62:2808-2811. [PMID: 34151700 DOI: 10.1080/10428194.2021.1933473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Simon Husby
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.,Faculty of Health Sciences, Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, University of Copenhagen, Copenhagen, Denmark
| | - Francesco Favero
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.,Finsen Laboratory, Rigshospitalet, Copenhagen, Denmark
| | - Francisco G Rodriguez-Gonzalez
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.,Finsen Laboratory, Rigshospitalet, Copenhagen, Denmark
| | - Lesley A Sutton
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Eva K Haastrup
- Department of Clinical Immunology, Rigshospitalet, Copenhagen, Denmark
| | - Andreas Due Ørskov
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Jakob W Hansen
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.,Faculty of Health Sciences, Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, University of Copenhagen, Copenhagen, Denmark
| | - Bente Arboe
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Derya Aslan
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Peter Brown
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
| | | | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Joachim Weischenfeldt
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.,Finsen Laboratory, Rigshospitalet, Copenhagen, Denmark
| | - Kirsten Grønbæk
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.,Faculty of Health Sciences, Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, University of Copenhagen, Copenhagen, Denmark
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4
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Magnuson A, Bruinooge SS, Singh H, Wilner KD, Jalal S, Lichtman SM, Kluetz PG, Lyman GH, Klepin HD, Fleury ME, Hirsch B, Melemed A, Arnaldez FI, Basu Roy U, Schenkel C, Sherwood S, Garrett-Mayer E. Modernizing Clinical Trial Eligibility Criteria: Recommendations of the ASCO-Friends of Cancer Research Performance Status Work Group. Clin Cancer Res 2021; 27:2424-2429. [PMID: 33563633 PMCID: PMC8102305 DOI: 10.1158/1078-0432.ccr-20-3868] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Performance status (PS) is one of the most common eligibility criteria. Many trials are limited to patients with high-functioning PS, resulting in important differences between trial participants and patient populations with the disease. In addition, existing PS measures are subjective and susceptible to investigator bias. EXPERIMENTAL DESIGN A multidisciplinary working group of the American Society of Clinical Oncology and Friends of Cancer Research evaluated how PS eligibility criteria could be more inclusive. The working group recommendations are based on a literature search, review of trials, simulation study, and multistakeholder consensus. The working group prioritized inclusiveness and access to investigational therapies, while balancing patient safety and study integrity. RESULTS Broadening PS eligibility criteria may increase the number of potentially eligible patients for a given clinical trial, thus shortening accrual time. It may also result in greater participant diversity, potentially reduce trial participant and patient disparities, and enable clinicians to more readily translate trial results to patients with low-functioning PS. Potential impact on outcomes was explored through a simulation trial demonstrating that when the number of Eastern Cooperative Oncology Group PS2 participants was relatively small, the effect on the estimated HR and power was modest, even when PS2 patients did not derive a treatment benefit. CONCLUSIONS Expanding PS eligibility criteria to be more inclusive may be justified in many cases and could result in faster accrual rates and more representative trial populations.See related commentary by Giantonio, p. 2369.
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Affiliation(s)
| | | | | | | | - Shadia Jalal
- Indiana University School of Medicine, Indianapolis, Indiana
| | | | | | - Gary H Lyman
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Heidi D Klepin
- Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
| | - Mark E Fleury
- American Cancer Society Cancer Action Network, Washington, D.C
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High-dose therapy and autologous stem cell transplantation for relapsed or high-risk diffuse large B-cell lymphoma: a nationwide survey. Int J Hematol 2019; 111:256-266. [PMID: 31732878 DOI: 10.1007/s12185-019-02772-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 12/21/2022]
Abstract
To investigate the use of high-dose therapy and autologous stem cell transplantation (ASCT) for relapsed or high-risk diffuse large B-cell lymphoma (DLBCL) between 1990 and 2007, we conducted a nationwide survey using the registry database of the Japan Society for Hematopoietic Cell Transplantation. Of the 1222 patients in the database, 576 (47%) received ASCT in first complete remission (CR1), 140 (12%) in first partial remission, 281 (23%) in sensitive relapse, 150 (12%) in resistant or sensitivity-unknown relapse, and 75 (6%) in primary refractory status. With a median follow-up of 22 months, the 2-year overall survival (OS) and progression-free survival rates were 71% and 68%, respectively. The cumulative incidences of 2-year non-relapse mortality and relapse/progression were 6% and 26%, respectively. Relapse/progression after ASCT in the rituximab era (2002-2007) was significantly lower than that in the pre-rituximab era (1990-2001; P < 0.001). Older age, male gender, poor performance status at ASCT, non-CR1 at ASCT, ASCT performed in 1990-2001, and LEED or MCEC regimen were adverse predictors of OS. Because ASCT for newly diagnosed high-risk DLBCL has not been performed recently, a registry database study to assess the impact of ASCT for relapsed or refractory DLBCL in the rituximab era is warranted.
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