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Updated: May 4, 2026

Testing Targeted Therapies in Cancer using Structural DNA Alteration Analysis and Patient-Derived Xenografts
Published on: July 25, 2020
Drug-diagnostics co-development in oncology
1Biometric Research Branch, National Cancer Institute , Bethesda, MD , USA.
Abstract:
Developments in genomics are providing a biological basis for the heterogeneity of clinical course and response to treatment that have long been apparent to clinicians. The ability to molecularly characterize human diseases presents new opportunities to develop more effective treatments and new challenges for the design and analysis of clinical trials. In oncology, treatment of broad populations with regimens that benefit a minority of patients is less economically sustainable with expensive molecularly targeted therapeutics. The established molecular heterogeneity of human diseases requires the development of new paradigms for the design and analysis of randomized clinical trials as a reliable basis for predictive medicine. We review prospective designs for the development of new therapeutics and predictive biomarkers to inform their use. We cover designs for a wide range of settings. At one extreme is the development of a new drug with a single candidate biomarker and strong biological evidence that marker negative patients are unlikely to benefit from the new drug. At the other extreme are phase III clinical trials involving both genome-wide discovery of a predictive classifier and internal validation of that classifier. We have outlined a prediction based approach to the analysis of randomized clinical trials that both preserves the type I error and provides a reliable internally validated basis for predicting which patients are most likely or unlikely to benefit from a new regimen.
Insights
Genomic insights reveal disease heterogeneity, necessitating new clinical trial designs. These predictive approaches ensure new treatments benefit the right patients, improving personalized medicine.
Area of Science:
- Genomic Medicine
- Clinical Trial Design
- Biostatistics
Background:
- Clinical observations of diverse disease progression and treatment responses are now supported by genomic data.
- Molecular characterization of diseases offers new therapeutic avenues but complicates clinical trial design and analysis.
- In oncology, broad patient treatment with targeted therapies is unsustainable if only a few benefit.
Purpose of the Study:
- To review prospective designs for developing novel therapeutics and predictive biomarkers.
- To address the need for new paradigms in randomized clinical trial (RCT) design and analysis for predictive medicine.
- To present a prediction-based analysis approach for RCTs that maintains statistical integrity.
Main Methods:
- Review of prospective clinical trial designs, ranging from single-biomarker development to genome-wide classifier discovery and validation.
- Outline of a prediction-based analysis framework for RCTs.
- Focus on designs that integrate biomarker development with therapeutic evaluation.
Main Results:
- The proposed prediction-based analysis preserves the type I error rate.
- The approach provides a reliable, internally validated method for identifying patient subgroups likely to benefit from new treatments.
- Designs accommodate various scenarios, from single biomarker-drug pairs to complex genome-wide predictive models.
Conclusions:
- Genomic heterogeneity demands innovative clinical trial designs and analysis methods.
- Predictive medicine requires robust statistical frameworks to ensure targeted therapies are effectively evaluated and applied.
- The outlined approach supports the development of personalized medicine by accurately predicting treatment response.
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