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Santi I, Vellekoop H, M Versteegh M, A Huygens S, Dinjens WNM, Mölken MRV. Estimating the Prognostic Value of the NTRK Fusion Biomarker for Comparative Effectiveness Research in The Netherlands. Mol Diagn Ther 2024; 28:319-328. [PMID: 38616205 PMCID: PMC11068666 DOI: 10.1007/s40291-024-00704-2] [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] [Accepted: 03/10/2024] [Indexed: 04/16/2024]
Abstract
OBJECTIVES We evaluated the prognostic value of the neurotrophic tyrosine receptor kinase (NTRK) gene fusions by comparing the survival of patients with NTRK+ tumours with patients without NTRK+ tumours. METHODS We used genomic and clinical registry data from the Center for Personalized Cancer Treatment (CPCT-02) study containing a cohort of cancer patients who were treated in Dutch clinical practice between 2012 and 2020. We performed a propensity score matching analysis, where NTRK+ patients were matched to NTRK- patients in a 1:4 ratio. We subsequently analysed the survival of the matched sample of NTRK+ and NTRK- patients using the Kaplan-Meier method and Cox regression, and performed an analysis of credibility to evaluate the plausibility of our result. RESULTS Among 3556 patients from the CPCT-02 study with known tumour location, 24 NTRK+ patients were identified. NTRK+ patients were distributed across nine different tumour types: bone/soft tissue, breast, colorectal, head and neck, lung, pancreas, prostate, skin and urinary tract. NTRK fusions involving the NTRK3 gene (46%) and NTRK1 gene (33%) were most common. The survival analysis rendered a hazard ratio (HR) of 1.44 (95% CI 0.81-2.55) for NTRK+ patients. Using the point estimates of three prior studies on the prognostic value of NTRK fusions, our finding that the HR is > 1 was deemed plausible. CONCLUSIONS NTRK+ patients may have an increased risk of death compared with NTRK- patients. When using historic control data to assess the comparative effectiveness of TRK inhibitors, the prognostic value of the NTRK fusion biomarker should therefore be accounted for.
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Affiliation(s)
- Irene Santi
- Institute for Medical Technology Assessment, Erasmus University Rotterdam, Burgemeester Oudlaan 50, 3062 PA, Rotterdam, The Netherlands.
| | - Heleen Vellekoop
- Institute for Medical Technology Assessment, Erasmus University Rotterdam, Burgemeester Oudlaan 50, 3062 PA, Rotterdam, The Netherlands
| | - Matthijs M Versteegh
- Institute for Medical Technology Assessment, Erasmus University Rotterdam, Burgemeester Oudlaan 50, 3062 PA, Rotterdam, The Netherlands
| | - Simone A Huygens
- Institute for Medical Technology Assessment, Erasmus University Rotterdam, Burgemeester Oudlaan 50, 3062 PA, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Maureen Rutten-van Mölken
- Institute for Medical Technology Assessment, Erasmus University Rotterdam, Burgemeester Oudlaan 50, 3062 PA, Rotterdam, The Netherlands
- School of Health Policy and Management, Erasmus University Rotterdam, Rotterdam, The Netherlands
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Kelter R. Reducing the false discovery rate of preclinical animal research with Bayesian statistical decision criteria. Stat Methods Med Res 2023; 32:1880-1901. [PMID: 37519294 PMCID: PMC10563376 DOI: 10.1177/09622802231184636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
The success of preclinical research hinges on exploratory and confirmatory animal studies. Traditional null hypothesis significance testing is a common approach to eliminate the chaff from a collection of drugs, so that only the most promising treatments are funneled through to clinical research phases. Balancing the number of false discoveries and false omissions is an important aspect to consider during this process. In this paper, we compare several preclinical research pipelines, either based on null hypothesis significance testing or based on Bayesian statistical decision criteria. We build on a recently published large-scale meta-analysis of reported effect sizes in preclinical animal research and elicit a non-informative prior distribution under which both approaches are compared. After correcting for publication bias and shrinkage of effect sizes in replication studies, simulations show that (i) a shift towards statistical approaches which explicitly incorporate the minimum clinically important difference reduces the false discovery rate of frequentist approaches and (ii) a shift towards Bayesian statistical decision criteria can improve the reliability of preclinical animal research by reducing the number of false-positive findings. It is shown that these benefits hold while keeping the number of experimental units low which are required for a confirmatory follow-up study. Results show that Bayesian statistical decision criteria can help in improving the reliability of preclinical animal research and should be considered more frequently in practice.
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Affiliation(s)
- Riko Kelter
- Department of Mathematics, University of Siegen, Germany
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van Ravenzwaaij D, Bakker M, Heesen R, Romero F, van Dongen N, Crüwell S, Field SM, Held L, Munafò MR, Pittelkow MM, Tiokhin L, Traag VA, van den Akker OR, van ‘t Veer AE, Wagenmakers EJ. Perspectives on scientific error. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230448. [PMID: 37476516 PMCID: PMC10354464 DOI: 10.1098/rsos.230448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/27/2023] [Indexed: 07/22/2023]
Abstract
Theoretical arguments and empirical investigations indicate that a high proportion of published findings do not replicate and are likely false. The current position paper provides a broad perspective on scientific error, which may lead to replication failures. This broad perspective focuses on reform history and on opportunities for future reform. We organize our perspective along four main themes: institutional reform, methodological reform, statistical reform and publishing reform. For each theme, we illustrate potential errors by narrating the story of a fictional researcher during the research cycle. We discuss future opportunities for reform. The resulting agenda provides a resource to usher in an era that is marked by a research culture that is less error-prone and a scientific publication landscape with fewer spurious findings.
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Affiliation(s)
- D. van Ravenzwaaij
- Department of Psychology, University of Groningen, Grote Kruisstraat 2/1, Heymans Building, room 239, 9712 TS Groningen, The Netherlands
| | - M. Bakker
- Tilburg University, 5037 AB Tilburg, The Netherlands
| | - R. Heesen
- University of Western Australia, Perth, Western Australia 6009, Australia
- London School of Economics and Political Science, London WC2A 2AE, UK
| | - F. Romero
- Department of Psychology, University of Groningen, Grote Kruisstraat 2/1, Heymans Building, room 239, 9712 TS Groningen, The Netherlands
| | - N. van Dongen
- University of Amsterdam, 1012 WP Amsterdam, The Netherlands
| | - S. Crüwell
- Department of History and Philosophy of Science, University of Cambridge, Cambridge CB2 1TN, UK
| | - S. M. Field
- Centre for Science and Technology Studies (CWTS), Leiden University, 2311 EZ Leiden, The Netherlands
| | - L. Held
- University of Zurich, 8006 Zürich, Switzerland
| | - M. R. Munafò
- School of Psychological Science, University of Bristol, Bristol BS8 1QU, UK
| | - M. M. Pittelkow
- Department of Psychology, University of Groningen, Grote Kruisstraat 2/1, Heymans Building, room 239, 9712 TS Groningen, The Netherlands
- QUEST Center for Transforming Biomedical Research, Berlin Institute of Health, Charité—Universitätsmedizin, 10178 Berlin, Germany
| | - L. Tiokhin
- IG&H Consulting, 3528 AC Utrecht, The Netherlands
| | - V. A. Traag
- Centre for Science and Technology Studies (CWTS), Leiden University, 2311 EZ Leiden, The Netherlands
| | - O. R. van den Akker
- Tilburg University, 5037 AB Tilburg, The Netherlands
- QUEST Center for Transforming Biomedical Research, Berlin Institute of Health, Charité—Universitätsmedizin, 10178 Berlin, Germany
| | - A. E. van ‘t Veer
- Methodology and Statistics Unit, Institute of Psychology, Leiden University, 2333 AK Leiden, The Netherlands
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Deemer SE, Owora AH, Allison DB. Taking a Hard Look at the Empirical Evidence for Popular Community-Based Interventions in Obesity. JAMA Pediatr 2022; 176:639-641. [PMID: 35532910 DOI: 10.1001/jamapediatrics.2022.1150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Comment on "Bayesian additional evidence for decision making under small sample uncertainty". BMC Med Res Methodol 2022; 22:149. [PMID: 35614410 PMCID: PMC9134648 DOI: 10.1186/s12874-022-01635-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/12/2022] [Indexed: 11/12/2022] Open
Abstract
We examine the concept of Bayesian Additional Evidence (BAE) recently proposed by Sondhi et al. We derive simple closed-form expressions for BAE and compare its properties with other methods for assessing findings in the light of new evidence. We find that while BAE is easy to apply, it lacks both a compelling rationale and clarity of use needed for reliable decision-making.
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Pawel S, Held L. The sceptical Bayes factor for the assessment of replication success. J R Stat Soc Series B Stat Methodol 2022. [DOI: 10.1111/rssb.12491] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samuel Pawel
- Epidemiology, Biostatistics and Prevention InstituteCenter for Reproducible ScienceUniversity of Zurich ZurichSwitzerland
| | - Leonhard Held
- Epidemiology, Biostatistics and Prevention InstituteCenter for Reproducible ScienceUniversity of Zurich ZurichSwitzerland
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