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Zhou I, Plana D, Palmer AC. Tumor-Specific Activity of Precision Medicines in the NCI-MATCH Trial. Clin Cancer Res 2024; 30:786-792. [PMID: 38109210 PMCID: PMC10922532 DOI: 10.1158/1078-0432.ccr-23-0983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 09/07/2023] [Accepted: 12/13/2023] [Indexed: 12/20/2023]
Abstract
PURPOSE National Cancer Institute Molecular Analysis for Therapy Choice (NCI-MATCH) is a precision medicine basket trial designed to test the effectiveness of treating cancers based on specific genetic changes in patients' tumors, regardless of cancer type. Multiple subprotocols have each tested different targeted therapies matched to specific genetic aberrations. Most subprotocols exhibited low rates of tumor shrinkage as evaluated across all tumor types enrolled. We hypothesized that these results may arise because these precision cancer therapies have tumor type-specific efficacy, as is common among other cancer therapies. EXPERIMENTAL DESIGN To test the hypothesis that certain tumor types are more sensitive to specific therapies than other tumor types, we applied permutation testing to tumor volume change and progression-free survival data from 10 published NCI-MATCH subprotocols (together n = 435 patients). FDR was controlled by the Benjamini-Hochberg procedure. RESULTS Six of ten subprotocols exhibited statistically significant evidence of tumor-specific drug sensitivity, four of which were previously considered negative based on response rate across all tumors. This signal-finding analysis highlights potential uses of FGFR tyrosine kinase inhibition in urothelial carcinomas with actionable FGFR aberrations and MEK inhibition in lung cancers with BRAF non-V600E mutations. In addition, it identifies low-grade serious ovarian carcinoma with BRAF v600E mutation as especially sensitive to BRAF and MEK co-inhibition (dabrafenib plus trametinib), a treatment that received accelerated FDA approval for advanced solid tumors with BRAF v600E mutation. CONCLUSIONS These findings support the value of basket trials because even when precision medicines do not have tumor-agnostic activity, basket trials can identify tumor-specific activity for future study.
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Affiliation(s)
- Ivvone Zhou
- Department of Pharmacology, Computational Medicine Program, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Deborah Plana
- Laboratory of Systems Pharmacology, and the Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, 02139, USA
| | - Adam C. Palmer
- Department of Pharmacology, Computational Medicine Program, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
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Kasim A, Bean N, Hendriksen SJ, Chen TT, Zhou H, Psioda MA. Basket trials in oncology: a systematic review of practices and methods, comparative analysis of innovative methods, and an appraisal of a missed opportunity. Front Oncol 2023; 13:1266286. [PMID: 38033501 PMCID: PMC10684308 DOI: 10.3389/fonc.2023.1266286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023] Open
Abstract
Background Basket trials are increasingly used in oncology drug development for early signal detection, accelerated tumor-agnostic approvals, and prioritization of promising tumor types in selected patients with the same mutation or biomarker. Participants are grouped into so-called baskets according to tumor type, allowing investigators to identify tumors with promising responses to treatment for further study. However, it remains a question as to whether and how much the adoption of basket trial designs in oncology have translated into patient benefits, increased pace and scale of clinical development, and de-risking of downstream confirmatory trials. Methods Innovation in basket trial design and analysis includes methods that borrow information across tumor types to increase the quality of statistical inference within each tumor type. We build on the existing systematic reviews of basket trials in oncology to discuss the current practices and landscape. We conceptually illustrate recent innovative methods for basket trials, with application to actual data from recently completed basket trials. We explore and discuss the extent to which innovative basket trials can be used to de-risk future trials through their ability to aid prioritization of promising tumor types for subsequent clinical development. Results We found increasing adoption of basket trial design in oncology, but largely in the design of single-arm phase II trials with a very low adoption of innovative statistical methods. Furthermore, the current practice of basket trial design, which does not consider its impact on the clinical development plan, may lead to a missed opportunity in improving the probability of success of a future trial. Gating phase II with a phase Ib basket trial reduced the size of phase II trials, and losses in the probability of success as a result of not using innovative methods may not be recoverable by running a larger phase II trial. Conclusion Innovative basket trial methods can reduce the size of early phase clinical trials, with sustained improvement in the probability of success of the clinical development plan. We need to do more as a community to improve the adoption of these methods.
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Affiliation(s)
- Adetayo Kasim
- Disease Area Strategy, Oncology Biostatistics, GlaxoSmithKline, Brentford, United Kingdom
| | - Nathan Bean
- Statistics and Data Science – Innovation Hub, GlaxoSmithKline, Philadelphia, PA, United States
| | - Sarah Jo Hendriksen
- Medical and Market Access, Oncology Biostatistics, GlaxoSmithKline, Stevenage, United Kingdom
| | - Tai-Tsang Chen
- Disease Area Strategy, Oncology Biostatistics, GlaxoSmithKline, Philadelphia, PA, United States
| | - Helen Zhou
- Disease Area Strategy, Oncology Biostatistics, GlaxoSmithKline, Philadelphia, PA, United States
| | - Matthew A. Psioda
- Statistics and Data Science – Innovation Hub, GlaxoSmithKline, Philadelphia, PA, United States
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Schiller J, Eckhardt H, Schmitter S, Alber VA, Rombey T. Challenges and Solutions for the Benefit Assessment of Tumor-Agnostic Therapies in Germany. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2023; 26:854-864. [PMID: 36709043 DOI: 10.1016/j.jval.2023.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/11/2022] [Accepted: 01/09/2023] [Indexed: 06/04/2023]
Abstract
OBJECTIVES Precision medicine is increasingly important in cancer treatment. Tumor-agnostic therapies are used regardless of tumor entity because they target specific biomarkers in tumors. In Germany, the benefit assessment of oncological pharmaceuticals has traditionally been entity specific. Thus, the assessment of tumor-agnostic therapies leaves stakeholders with various challenges. Our aim was to systematically identify challenges and possible solutions for the benefit assessment of therapies in tumor-agnostic indications using a 2-step sequential qualitative approach. METHODS To identify relevant challenges, we conducted qualitative interviews with different stakeholders who were involved in previous benefit assessments of tumor-agnostic therapies in Germany. To identify possible solutions for these challenges, we systematically searched MEDLINE, Embase, and the websites of European health technology assessment bodies for relevant literature. RESULTS We identified 9 categories of challenges of which the following were deemed particularly relevant: the absence of direct comparative studies, challenges regarding the use of basket studies and indirect comparisons, challenges in determining the appropriate comparative therapy in a tumor-agnostic indication, and challenges on the system side. Seven categories of solutions were identified, including an increased use of real-world evidence, making conditional decisions in the context of systematic reassessments, splitting the field of application, and finding (new) ways to design and analyze basket studies. CONCLUSION A range of possible solutions, which can help to meet the identified challenges in Germany, have been found. Future research should investigate the acceptance and feasibility of these solutions.
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Affiliation(s)
- Juliane Schiller
- Department of Health Care Management, Technische Universität Berlin, Berlin, Germany; Pfizer Pharma GmbH, Berlin, Germany.
| | - Helene Eckhardt
- Department of Health Care Management, Technische Universität Berlin, Berlin, Germany
| | | | - Valerie A Alber
- Department of Health Care Management, Technische Universität Berlin, Berlin, Germany
| | - Tanja Rombey
- Department of Health Care Management, Technische Universität Berlin, Berlin, Germany
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Zhou I, Plana D, Palmer AC. Tumor-specific activity of precision medicines in the NCI-MATCH trial. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.30.23287951. [PMID: 37034644 PMCID: PMC10081392 DOI: 10.1101/2023.03.30.23287951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Background NCI-MATCH is a precision medicine basket trial designed to test the effectiveness of treating cancers based on specific genetic changes in patients' tumors, regardless of cancer type. Multiple subprotocols have each tested different targeted therapies matched to specific genetic aberrations. Most subprotocols exhibited low rates of tumor shrinkage as evaluated across all tumor types enrolled. We hypothesized that these results may arise because these precision cancer therapies have tumor type-specific efficacy, as is common among other cancer therapies. Methods To test the hypothesis that certain tumor types are more sensitive to specific therapies than other tumor types, we applied permutation testing to tumor volume change and progression-free survival data from ten published NCI-MATCH subprotocols (together n=435 patients). False discovery rate was controlled by the Benjamini-Hochberg procedure. Results Six of ten subprotocols exhibited statistically significant evidence of tumor-specific drug sensitivity, four of which were previously considered negative based on response rate across all tumors. This signal-finding analysis highlights potential uses of FGFR tyrosine kinase inhibition in urothelial carcinomas with actionable FGFR aberrations, MEK inhibition in lung cancers with BRAF non-V600E mutations, and MEK inhibition in cholangiocarcinomas with NRAS mutations. Conclusions These findings support the value of basket trials because even when precision medicines do not have tumor-agnostic activity, basket trials can identify tumor-specific activity for future study.
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Affiliation(s)
- Ivvone Zhou
- Department of Pharmacology, Computational Medicine Program, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Deborah Plana
- Laboratory of Systems Pharmacology, and the Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, 02139, USA
| | - Adam C. Palmer
- Department of Pharmacology, Computational Medicine Program, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
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Plana D, Fell G, Alexander BM, Palmer AC, Sorger PK. Cancer patient survival can be parametrized to improve trial precision and reveal time-dependent therapeutic effects. Nat Commun 2022; 13:873. [PMID: 35169116 PMCID: PMC8847344 DOI: 10.1038/s41467-022-28410-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 01/06/2022] [Indexed: 12/16/2022] Open
Abstract
Individual participant data (IPD) from oncology clinical trials is invaluable for identifying factors that influence trial success and failure, improving trial design and interpretation, and comparing pre-clinical studies to clinical outcomes. However, the IPD used to generate published survival curves are not generally publicly available. We impute survival IPD from ~500 arms of Phase 3 oncology trials (representing ~220,000 events) and find that they are well fit by a two-parameter Weibull distribution. Use of Weibull functions with overall survival significantly increases the precision of small arms typical of early phase trials: analysis of a 50-patient trial arm using parametric forms is as precise as traditional, non-parametric analysis of a 90-patient arm. We also show that frequent deviations from the Cox proportional hazards assumption, particularly in trials of immune checkpoint inhibitors, arise from time-dependent therapeutic effects. Trial duration therefore has an underappreciated impact on the likelihood of success. Analysis of more than 150 Phase 3 oncology clinical trials supports parametric statistical analysis, significantly increasing the precision of small early-phase trials and relating deviations from the Cox proportional hazards model to trial duration.
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Affiliation(s)
- Deborah Plana
- Laboratory of Systems Pharmacology and the Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School and MIT, Cambridge, MA, USA
| | | | - Brian M Alexander
- Dana-Farber Cancer Institute, Boston, MA, USA.,Foundation Medicine Inc., Cambridge, MA, USA
| | - Adam C Palmer
- Department of Pharmacology, Computational Medicine Program, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Peter K Sorger
- Laboratory of Systems Pharmacology and the Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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