1. Challenges of Bridging Studies in Biomarker Driven Clinical Trials May 19, 2015. MBSW Conference. Muncie, IN. Szu-Yu Tang, Chang Xu, Bonnie LaFleur May 19, 2015. MBSW Conference. Muncie, IN. 1

2.  Bridging Studies in diagnostic device: Bridge the “efficacy” in the subpopulation tested from the clinical trial assay (CTA or old assay) to the subpopulation tested by a companion in vitro diagnostic device (CDx or new assay) 2 Clinical bridging studies : A bridging study is defined as a study performed in the new region to provide pharmacodynamic or clinical data on efficacy, safety, dosage and dose regimen in the new region that will allow extrapolation of the foreign clinical data to the population in the new region (ICH E5 guideline).

3. Outline Bridging study examples The impact of diagnostic accuracy to treatment efficacy in enrichment trail Single assay Old assay to new assay Conclusion 3

4. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Companion Diagnostic Test (CDx) DISCOVERY PRECLINICAL Phase 1 Phase 2 Phase 3 CUT-OFF DETERMINATION ANALYTICAL VALIDATION CLINICAL VALIDATION EARLY RESEARCH PROTOTYPE & DEVELOPMENT EARLY PHASE ALGORITHM DEVELOPMENT VALIDATION STUDIES 4 Companion diagnostic test (CDx): the use of a diagnostic assay as a test, assay, or test system to screen, or select patients who may be candidates for a specific drug therapy.

5. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Bridging Study Examples No CDx available in clinical trial A laboratory-development test (LDT) is used in the clinical trial instead of CDx Note: The FDA defines a Laboratory Developed Test (LDT) as an in vitro diagnostic test that is manufactured by and used within a single laboratory (i.e. a laboratory with a single CLIA certificate). LDTs are also sometimes called in-house developed tests, or “home brew” tests. Multiple CDx products Multiple (competing) CDx products can be driven by improved efficiency, cost, novel/new technologies, or updated techniques over time. 5

6. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Bridging Study Challenges Verification Bias: Lack of specimen material or lack of consent for re-testing from patients Lack of efficacy outcome for negative group from old assay in enrichment trial Old Assay +- New Assay +ac -bd 6 No clinical Outcome!!

7. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Impact of diagnostic accuracy on treatment efficacy (single assay) Goal: establish quantitative relationship between response rate and components of CDx accuracy in an enrichment trial. All screened patients + - Stratified by marker Marker (+) T NT Enrichment Trial Randomize Response No Response 7 Marker (-)

8. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Analytical versus clinical accuracy Analytical accuracy is sensitivity/ specificity but clinical accuracy needs to link the assay performance to treatment efficacy. Method comparison studies Method comparison studies are used to compare the new assay with the one currently in use to see whether their measurements are indeed comparable. Issues with method comparison studies: Reference standard, non-identifiability, conditional independent assumptions (CIA)…etc Impact of diagnostic accuracy on treatment efficacy (single assay) 8

9. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. The impact of diagnostic accuracy on treatment efficacy (single assay) 9

10. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Simulation Results 10

11. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. The impact of diagnostic accuracy on treatment efficacy (single assay) What we seeWhat it means Dotted curves have steeper slope than solid curves when sensitivity or specificity is large Specificity improves response rate faster than sensitivity 11

12. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Method comparison studies Old Assay +- New Assay +ac -bd Old Assay +- New Assay +a´ c´c´ -b´d´ True Biomarker Positive True Biomarker Negative 12 (Ref [2]) Lu Y, Dendukuri N, Schiller I, Joseph L: A Bayesian approach to simultaneously adjusting for verification and reference standard bias in diagnostic test studies.Stat Med 2010, 29(24):2532-2543.

13. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Link of assay performance to efficacy 13

14. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Assumptions Old Assay +- New Assay + 6480 - 100 True Positive (Ref [3]) Zhou XH, Obuchowski N, McLish D. Statistical Methods in Diagnostic Medicine, 2 nd ed. Hoboken, New Jersey: John Wiley and Sons; 2011. 14

15. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Assay performance affect on efficacy 15 (Ref [2]) Lu Y, Dendukuri N, Schiller I, Joseph L: A Bayesian approach to simultaneously adjusting for verification and reference standard bias in diagnostic test studies.Stat Med 2010, 29(24):2532-2543.

16. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Simulation parameters 16

17. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Simulation results CIA only 17

18. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Summary of results CIA only What we seeWhat it means 18

19. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Simulation results CIA only 19

20. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. What we seeWhat it means Simulation results CIA only 20

21. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Simulation results dependency of 80% compared to CIA 21

22. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. What we seeWhat it means Compared to CIA, high dependency between two assays enhances efficacy when old assay’s sensitivity or specificity is low except when the new assay has high sensitivity. Compared to CIA, high dependency between two assays reduces efficacy when old assay’s sensitivity or specificity is high except for the scenario of low sensitivity in new assay and high specificity in old assay. Simulation results dependency of 80% compared to CIA 22

23. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Simulation results dependency of 80% compared to CIA 23

24. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Simulation results dependency of 80% compared to CIA What we seeWhat it means Compared to CIA, high dependency between two assays enhances efficacy when old assay’s sensitivity or specificity is low except when both assays have low sensitivity. Compared to CIA, high dependency between two assays reduces efficacy when old assay’s sensitivity or specificity is high except for the scenario of high sensitivity in new assay and high specificity in old assay. 24

25. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Conclusion We established a statistical framework that describes how assay accuracy affects clinical efficacy in biomarker driven clinical trials Inaccurate CDx diminishes treatment efficacy but specificity is the driving factor to improve response rate. We describe the processes for methods comparison studies between two assays under the following conditions Conditional independence assumption is satisfied: Depending on positive or negative result of old assay, sensitivity or specificity of old assay has opposite effect on new assay’s efficacy. However, high specificity of new assay improves efficacy no matter what test result of old assay is. Dependency is about 80%, compared with CIA: In general, when old assay’s sensitivity or specificity is low, high dependency enhances new assay’s efficacy. On the contrary, high dependency reduces the efficacy when old assay’s sensitivity or specificity is high.

26. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. Future Work Generalize the simulation to cover the range of sensitivity/ specificity, marker prevalence and dependency. Use measurement error models to incorporate impact of assay methods comparison to efficacy evaluation Evaluate and compare impact of clinical study design on assay bridging studies (e.g., all-comers versus enrichment studies) 26

27. Confidential and proprietary to Ventana Medical Systems, Inc. For internal use only. Do not copy. Do not distribute. References [1] Maitournam A, Simon R: On the efficiency of targeted clinical trials. Statistics in Medicine 2005; 24:329–339. [2] Lu Y, Dendukuri N, Schiller I, Joseph L: A Bayesian approach to simultaneously adjusting for verification and reference standard bias in diagnostic test studies.Stat Med 2010, 29(24):2532-2543. [3] Zhou XH, Obuchowski N, McLish D. Statistical Methods in Diagnostic Medicine, 2 nd ed. Hoboken, New Jersey: John Wiley and Sons; 2011. 27

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