1. Using Predictive Classifiers in the Design of Phase III Clinical Trials Richard Simon, D.Sc. Chief, Biometric Research Branch National Cancer Institute http://linus.nci.nih.gov/brb

2. “Biomarkers” Predictive classifiers –A measurement made before treatment to select good patient candidates for the treatment Biomarker of disease activity –A measurement made before and after treatment to determine an effect of treatment Surrogate endpoints –Biomarker of disease activity used as surrogate for clinical benefit

3. Surrogate Endpoints It is very difficult to properly validate a biomarker as a surrogate for clinical benefit. It requires a series of randomized trials with both the candidate biomarker and clinical outcome measured –Must demonstrate that treatment vs control differences for the candidate surrogate are concordant with the treatment vs control differences for clinical outcome –It is not sufficient to demonstrate that the biomarker responders survive longer than the biomarker non- responders

4. A biomarker of disease activity used as endpoint in phase I or II studies need not be a validated surrogate of clinical benefit Unvalidated biomarkers can also be used for early “futility analyses” in phase III trials

5. Medicine Needs Predictive Markers not Prognostic Factors Most prognostic factors are not used because they are not therapeutically relevant Most prognostic factor studies are not focused on a clear objective – they use a convenience sample of patients for whom tissue is available –often the patients are too heterogeneous to support therapeutically relevant conclusions

6. In new drug development –The focus should be on evaluating the new drug in a population defined by a predictive classifier, not on “validating” the classifier

7. New Drug Developmental Strategy (I) Develop a diagnostic classifier that identifies the patients likely to benefit from the new drug Develop a reproducible assay for the classifier Use the diagnostic to restrict eligibility to a prospectively planned evaluation of the new drug Demonstrate that the new drug is effective in the prospectively defined set of patients determined by the diagnostic

8. Using phase II data, develop predictor of response to new drug Develop Predictor of Response to New Drug Patient Predicted Responsive New Drug Control Patient Predicted Non-Responsive Off Study

9. Evaluating the Efficiency of Strategy (I) Simon R and Maitnourim A. Evaluating the efficiency of targeted designs for randomized clinical trials. Clinical Cancer Research 10:6759-63, 2004; Correction 12:3229,2006 Maitnourim A and Simon R. On the efficiency of targeted clinical trials. Statistics in Medicine 24:329-339, 2005.

10. Two Clinical Trial Designs Compared Un-targeted design –Randomized comparison of T to C without classifier screening Targeted design –Randomize only classifier positive patients

11. Parameters that Determine Efficiency of Targeted Clinical Trials  1 = treatment effect for Assay + patients  0 = treatment effect for Assay – patients Proportion of patients classifier positive

12. Randomized Ratio n conventional /n targeted Proportion classifier positive  0 =0  0 =  1 /2 0.751.781.31 0.541.78 0.25162.56

13. Screened Ratio Proportion classifier positive  0 =0  0 =  1 /2 0.751.330.98 0.520.89 0.2540.64

14. Trastuzumab Metastatic breast cancer 234 randomized patients per arm 90% power for 13.5% improvement in 1-year survival over 67% baseline at 2-sided.05 level If benefit were limited to the 25% assay + patients, overall improvement in survival would have been 3.375% –4025 patients/arm would have been required If assay – patients benefited half as much, 627 patients per arm would have been required

15. Gefitinib Two negative untargeted randomized trials first line advanced NSCLC –2130 patients 10% have EGFR mutations If only mutation + patients benefit by 20% increase of 1-year survival, then 12,806 patients/arm are needed For trial targeted to patients with mutations, 138 are needed

16. Web Based Software for Comparing Sample Size Requirements http://linus.nci.nih.gov/brb/

21. Developmental Strategy (II) Develop Predictor of Response to New Rx Predicted Non- responsive to New Rx Predicted Responsive To New Rx Control New RXControl New RX

22. Developmental Strategy (II) Do not use the diagnostic to restrict eligibility, but to structure a prospective analysis plan. Compare the new drug to the control overall for all patients ignoring the classifier. –If p overall  0.04 claim effectiveness for the eligible population as a whole Otherwise perform a single subset analysis evaluating the new drug in the classifier + patients –If p subset  0.01 claim effectiveness for the classifier + patients.

23. This analysis strategy is designed to not penalize sponsors for having developed a classifier It provides sponsors with an incentive to develop genomic classifiers

24. Predictive Medicine not Correlative Science The purpose of the RCT is to evaluate the new treatment overall and for the pre-defined subset The purpose is not to re-evaluate the components of the classifier, or to modify or refine the classifier The purpose is not to demonstrate that repeating the classifier development process on independent data results in the same classifier

25. The Roadmap 1.Develop a completely specified genomic classifier of the patients likely to benefit from a new drug 2.Establish reproducibility of measurement of the classifier 3.Use the completely specified classifier to design and analyze a new clinical trial to evaluate effectiveness of the new treatment with a pre-defined analysis plan.

26. Guiding Principle The data used to develop the classifier must be distinct from the data used to test hypotheses about treatment effect in subsets determined by the classifier –Developmental studies are exploratory And not closely regulated by FDA –Studies on which treatment effectiveness claims are to be based should be definitive studies that test a treatment hypothesis in a patient population completely pre-specified by the classifier

27. Development of Genomic Classifiers Single gene or protein based on knowledge of therapeutic target Empirically determined based on evaluation of a set of candidate genes –e.g. EGFR assays Empirically determined based on genome- wide correlating gene expression or genotype to patient outcome after treatment

28. Development of Genomic Classifiers During phase II development or After failed phase III trial using archived specimens. Adaptively during early portion of phase III trial.

29. Use of Archived Samples From a non-targeted “negative” clinical trial to develop a binary classifier of a subset thought to benefit from treatment Test that subset hypothesis in a separate clinical trial –Prospective targeted type I trial –Using archived specimens from a second previously conducted clinical trial

31. Biomarker Adaptive Threshold Design Have identified a predictive biomarker B thought to be predictive of patients likely to benefit from E relative to C No threshold for biomarker determined –Biomarker value scaled to range (0,1) Randomized phase III trial comparing new treatment E to control C –Eligibility not restricted by biomarker –Survival or DFS endpoint

32. Test E vs C restricted to patients with biomarker B > b –For all b values b=0, 0.1, 0.2, …, 1 –S(b)=log likelihood ratio statistic for treatment effect T=max{S(b)} Compute null distribution of T by permuting treatment labels If the data value of T is significant at 0.05 level, then reject null hypothesis that E is ineffective Compute point and interval estimates of the threshold b

33. Estimated Power of Broad Eligibility Design (n=386 events) vs Adaptive Design A (n=412 events) 80% power for 30% hazard reduction ModelBroad Eligibility Design Biomarker Adaptive Design A 40% reduction in 50% of patients (22% overall reduction).70.78 60% reduction in 25% of patients (20% overall reduction).65.91 79% reduction in 10% of patients (14% overall reduction).35.93

37. Adaptive Signature Design End of Trial Analysis Compare E to C for all patients at significance level 0.04 –If overall H 0 is rejected, then claim effectiveness of E for eligible patients –Otherwise

38. Otherwise: –Using only the first half of patients accrued during the trial, develop a binary classifier that predicts the subset of patients most likely to benefit from the new treatment E compared to control C –Compare E to C for patients accrued in second stage who are predicted responsive to E based on classifier Perform test at significance level 0.01 If H 0 is rejected, claim effectiveness of E for subset defined by classifier

39. Treatment effect restricted to subset. 10% of patients sensitive, 10 sensitivity genes, 10,000 genes, 400 patients. TestPower Overall.05 level test46.7 Overall.04 level test43.1 Sensitive subset.01 level test (performed only when overall.04 level test is negative) 42.2 Overall adaptive signature design85.3

40. Conclusions Many cancer treatments benefit only a small proportion of the patients to which they are administered Targeting treatment to the right patients can greatly improve the therapeutic ratio of benefit to adverse effects –Treated patients benefit –Treatment more cost-effective for society Effectively translating genomic technology and advances in tumor biology to enhance the effectiveness of therapeutics development requires –Improved appreciation of the relationship of biomarkers and clinical development pathways and the differences between correlative science and predictive medicine –Re-focus of emphasis and resources from validating surrogate endpoints to development and utilization of predictive classifiers –new paradigms of collaboration among industry, regulators and clinical trial organizations Without changes, it is likely that the use of predictive classifiers will slow clinical development as a result of conservatism of regulators and lack of utilization of innovative designs by clinical investigators

41. Collaborators Boris Freidlin Wenyu Jiang Aboubakar Maitournam Yingdong Zhao