Appendix A
Table of Papers About Biomarker Qualification



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Appendix A Table of Papers About Biomarker Qualification 

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 EVALUATION OF BIOMARKERS AND SURROGATE ENDPOINTS TABLE A-1 Historical Review of the Biomarker–Surrogate Endpoint Literature with Special Reference to the Nomenclature, Initial Reports, Systems of Classification, and Statistical Methods Developed for Their Evaluation Year Author Focus Field/Summary and Commentary 1963 Mainland Nomenclature: Statistics and Medicine Substituted In his Elementary Medical Statistics, variables he discusses substituting variables that are easy to observe for ones that are difficult to observe. 1966 Rushing Nomenclature: Psychology, Ethics, Social Science, First report of Law surrogate used The role of the hospital nurse in any context as a mother surrogate. (Many publications followed in the 1960s and 1970s where surrogate was used in this context of a person’s role in the fields of psychology, ethics, social science, and law.) 1973 Rho et al. Nomenclature: Biology First report of A search for porphyrin biomarker biomarkers in nonesuch shale and extraterrestrial samples. Biomarker here represents biological marker—origins of biological life. 1976 Schlenger Nomenclature: Epidemiology First report of Mortality and morbidity rates as surrogate AND surrogates for “health.” outcome 1977 Karpetsky et al. Nomenclature: Oncology Second report of Serum RNase level was found to biomarker be an indicator of renal function, and was not a biomarker either for the presence or extent of the plasma cell tumor. (Forty of 46 biomarker reports from 1977 to 1985 were in oncology.) 1978 Baker Nomenclature: Oncology Third report of Preoperative assessment of the biomarker patient with breast cancer. 1980 Regelson Nomenclature: General Medicine First report Biomarkers in aging: A beginning of biomarker for a therapeutic approach in outside cancer Transactions of the Association of in medicine Life Insurance Medical Directors of America.

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 APPENDIX A TABLE A-1 Continued Year Author Focus Field/Summary and Commentary Webb and Lin Nomenclature: Oncology First report Urinary fibronectin: Potential as a of biomarker biomarker in prostatic cancer. in title of publication 1982 Waalkes et al. Biomarkers Oncology for clinical Feasibility study in the application development of 17 biological markers for ovarian cancer. 1983 Wood Nomenclature: Rheumatology First report Nature of surrogate endpoints. of surrogate Relationships considered at two AND endpoint, levels: (1) ability of the attribute second report of to act as a surrogate in detection surrogate AND of the underlying state (at a outcome particular point in time); (2) potential of the surrogate to reveal changes in the underlying state as its course unfolds. 1986 Bigger Second Cardiology surrogate and Electrophysiological testing to endpoint, third select patients with ventricular surrogate and arrhythmias for drug trials and outcome to determine anti-arrhythmic drug efficacy. (By the end of the decade, the use of biomarkers as surrogates in cardiology had a number of high-profile failures.) Buccheri et al. First report Oncology of biomarker Clinical value of a multiple as measure of biomarker assay (CEA, TPA, tumor burden b-HCG, LDH) in patients with and predict bronchogenic carcinoma. outcome 1987 Kalish et al. Third surrogate Oncology and endpoint Surrogates as endpoints in bladder cancer trials. Data show that superficial disease endpoints do not predict surrogates for invasive disease endpoints. Schulof et al. Surrogates HIV markers Phase I/II trial of thymosin first used as fraction 5 and thymosin alpha one response to in HTLV-III–seropositive subjects. therapy continued

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 EVALUATION OF BIOMARKERS AND SURROGATE ENDPOINTS TABLE A-1 Continued Year Author Focus Field/Summary and Commentary Rosin et al. Intermediate Oncology endpoints Promise of intermediate endpoints in quantitating the response of precancerous lesions to chemopreventive agents. 1989 The Cardiac First example Cardiology Arrhythmia of study to CAST showed that successful Suppression test surrogate; suppression of the ventricular Trial (CAST) treatment of arrhythmia biomarker with Investigators; a biomarker antiarrhythmic therapy was Ruskin successful, but associated with increased rather patient outcome than decreased patient mortality. worse Herson First substantive Methodology discussion An introduction to four invited on surrogate papers on surrogate endpoints in endpoints in clinical trials. These were pivotal clinical trials papers. Trigger was an FDA criticism of new drug applications in cardiology and oncology because they used surrogate endpoints. Ellenberg and All key issues Methodology Hamilton discussed using Advantages and disadvantages of examples from surrogate endpoints. Key points: oncology Used when endpoints of interest are too difficult and/or expensive to measure; must be sufficiently well correlated with the endpoints of interest to justify substitution; initial choice often based on biologic rationale as primary endpoints are more acceptable in early drug development than later pivotal studies. Wittes et al. Many key issues Methodology discussed using Key points: “True” endpoint is examples from one with clinical importance to cardiology the patient, such as mortality or a major clinical outcome; surrogate is one biologically closer to the process of disease; surrogate is useful if easily measured and highly correlated with the true endpoint; surrogates can dramatically reduce sample size and trial duration.

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 APPENDIX A TABLE A-1 Continued Year Author Focus Field/Summary and Commentary Prentice First report Statistics addressing the Prentice defines a surrogate key statistical endpoint to be a “response barrier to variable for which a test of the the use of null hypothesis of no relationship surrogates to the treatment groups under comparison is also a valid test of the corresponding null hypothesis based on the true endpoint.” Beaudry and First report Cardiology Spence of surrogate Atherosclerosis severity index outcome based on noninvasive ultrasound assessment to replace angiographic measurement of atherosclerosis (costly and invasive), which in turn replaced clinical endpoints (latter most expensive). (Example of developing a surrogate to replace another surrogate.) Buchwald et al. Empirical Cardiology surrogate RCT to demonstrate a reduction endpoint in overall mortality by lipid validation modification and to validate coronary arteriographic change as a surrogate for change in coronary heart disease risk. 1990 Machado et al. Testing validity HIV Medicine of surrogate Pros for surrogate endpoints: therapeutics Ethical/practical reasons for hastening decision making about the efficacy of new treatments for HIV infection. Cons: Serious overestimates of clinical benefit if treatment had delayed toxicity or only transient beneficial effects; serious underestimates of clinical benefit when the treatment had no effect on the transition from healthy to the marker state. continued

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 EVALUATION OF BIOMARKERS AND SURROGATE ENDPOINTS TABLE A-1 Continued Year Author Focus Field/Summary and Commentary Schatzkin et al. Statistical Oncology validation The intermediate endpoint is strategy a valid cancer surrogate if the attributable proportion is near 1.0, but not if it is near 0 (usually the attributable proportion is neither 1.0 nor 0); in this case in an established exposure-cancer relationship, the exposure effect would vanish if adjusted for the intermediate endpoint. Woosley Further Cardiology commentary on High-profile study that illustrated CAST results the dangers of surrogate and implications therapeutics. (Further failures for drug followed in other cardiology development studies. Within a few years, surrogates rarely used in cardiology and large outcome trials with patient endpoints were the norm. Other fields in medicine did not have resources to conduct large, long studies and continued to argue for the use of surrogates in drug development.) Lippman et al. Schema Oncology Proposed three classes of biomarkers: genomic, proliferation, and differentiation markers. Biomarker validation studies should follow an evolutionary process. This leads to first generation (short-term trials in high-risk patients), second generation (dose and schedule trials), and third generation trials (long-term phase III trials to validate first generation candidate biomarkers). 1992 New drug, FDA General antibiotic, “accelerated Accelerate approval of new drugs and biological approval” and biological products for serious drug product regulation or life-threatening illnesses, with regulations; provisions for any necessary accelerated continued study of the drugs’ approval—FDA. clinical benefits after approval. Final Rulea

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 APPENDIX A TABLE A-1 Continued Year Author Focus Field/Summary and Commentary Freedman et al. Statistical Statistics validation Statistical validation of intermediate endpoints requires exposure or intervention effect, adjusted for the intermediate endpoint, to be reduced to zero. The estimating statistic—PTE—is explained by the intermediate/ surrogate endpoint and its 95% confidence limits are determined. Boissel et al. Schema Methodology Three provisos for surrogate outcome evaluation. Proviso 1, the surrogate endpoint, should occur more frequently than corresponding clinical endpoint. Proviso 2, that relationship between the surrogate and clinical endpoint, is well established through relevant epidemiological studies. Proviso 3, that the estimate of the expected clinical benefit should be derivable from the estimate of the reduction on the surrogate endpoint, which can be obtained from randomized clinical trials data. Freedman et al. Schema Methodology A new validation criterion based on an analysis of the three-way relationship of exposure (E), marker (M), and disease (D). Provides the level of evidence required for using intermediate markers as endpoints for Phase II and Phase III trials. (These criteria were conceptual and qualitative only.) Freedman and Sample-size Methodology Schatzkin issues Different sample-size requirements for questions on surrogate endpoint validity: Does the intervention affect the intermediate endpoint? Is the intermediate endpoint associated with the main outcome? Is the intervention effect on the main outcome mediated by the intermediate endpoint? continued

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0 EVALUATION OF BIOMARKERS AND SURROGATE ENDPOINTS TABLE A-1 Continued Year Author Focus Field/Summary and Commentary 1993 The Targeting Cardiology Hypertension biomarker Dose–response relationship Optimal between surrogate target and Treatment Study clinical outcome. (the HOT Study) Lin et al. Application of AIDS Prentice CD4-lymphocyte count captures part of the relationship between zidovudine and time to a first critical event, but does not fulfill the Prentice criterion. 1994 Aickin Surrogate Oncology endpoint If there is gold in the labeling biomarker index hills, are we digging in the right place? (Tool for cancer chemoprevention studies.) 1995 Temple Schema Methodology “Feels function or survives” definition for surrogate endpoint. Lee et al. Review Methodology Surrogate biochemical markers: Precise measurement for strategic drug and biologics development. Hughes et al. Review Statistics/HIV Evaluating surrogate markers. Scientific Consensus HIV Medicine Advisory Consensus statement. Scientific Committee advisory committee on surrogate on Surrogate markers of HIV. Markers of HIV

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 APPENDIX A TABLE A-1 Continued Year Author Focus Field/Summary and Commentary 1996 Fleming and Review Methodology DeMets Surrogate endpoints in clinical trials. Are we being misled? Argues for use of surrogate endpoints in Phase II, but not Phase III pivotal trials. Failure of surrogate endpoints because: (1) surrogate is not in the causal pathway of the disease process; (2) of several causal pathways of the disease, the intervention affects only the pathway mediated through the surrogate; (3) surrogate is not in the pathway of the intervention’s effect or is insensitive to its effect; and (4) intervention has mechanisms of action independent of disease process. Schatzkin et al. Review Methodology Surrogate endpoints in cancer research: a critique. 1997 De Gruttola Schema Methodology et al. Validating surrogate markers: Are we being naïve? The variety of proposed metrics for evaluating the degree to which this criterion is met are subject to misinterpretation because of the multiplicity of mechanisms by which drugs operate. Without detailed understanding of these mechanisms, metrics of “surrogacy” are not directly interpretable. Even when all of the mechanisms are understood, these metrics are associated with a high degree of uncertainty unless either treatment effects are large in moderate-sized studies or sample sizes are large in studies of moderately effective treatments. Lin et al. Statistics Statistics Estimating the proportion of a treatment effect explained by surrogate marker. continued

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 EVALUATION OF BIOMARKERS AND SURROGATE ENDPOINTS TABLE A-1 Continued Year Author Focus Field/Summary and Commentary Mildvan et al. Schema Methodology An approach to the validation of markers for use in AIDS clinical trials. Rolan Schema Methodology The contribution of clinical pharmacology surrogates and models to drug development. Proposes five dimensional properties of surrogates. These are validation (statistical), innovation, proximity to clinical outcome, specificity for an intervention, and practicality. Topol et al. Review Methodology Need clinical endpoints to establish safety and efficacy. Daniels and Schema Statistical Method/HIV Hughes Meta-analysis for the evaluation of potential surrogate markers. Boissel et al. Schema Methodology Clinical evaluation: From intermediate to surrogate criteria (French). Colburn Schema Methodology Selecting and validating biologic markers for drug development. 1998 Albert et al. Review– Methodology/HIV consensus Statistical issues for HIV surrogate endpoints: Point/counterpoint. Buyse and Statistics Statistics Molenberghs Introduction of the relative effect (RE) and adjusted association (AA) for single-unit studies. FDA and NIH Review and Methodology abstracts Biomarkers and surrogate endpoints: Advancing clinical research and applications. (Abstracts.)

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 APPENDIX A TABLE A-1 Continued Year Author Focus Field/Summary and Commentary Hayes Schema Methodology Tumor Marker Utility Grading System (TMUGS) proposed to evaluate the clinical utility of tumor markers and to establish an investigational agenda for evaluation of new tumor markers for risk assessment, screening, differential diagnosis, prognosis, monitoring clinical course, and use in clinical trials. Includes a TMUGS Worksheet that clarifies the precise characteristics of the marker in question and evaluates its clinical utility on a six-point scale (ranging from 0 to +++). 1999 Bucher et al. Schema Methodology How to use and article measuring the effects of an intervention on surrogate endpoints. 2000 Buyse et al. Statistics Statistics Validation of surrogate endpoints in meta-analysis of randomized experiments. Buyse et al. Statistics Statistics Statistical validation of surrogate endpoints. Colburn Schema Methodology Optimizing the use of biomarkers, surrogate endpoints, and clinical endpoints for efficient drug development. continued

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 EVALUATION OF BIOMARKERS AND SURROGATE ENDPOINTS TABLE A-1 Continued Year Author Focus Field/Summary and Commentary Johnson et al. Statistics Oncology Prediction bands used in a meta- analysis of RCTs to determine the surrogate threshold for response- rate and time to progression endpoints as predictors of mortality in metastatic colorectal cancer and non-small-cell lung cancer. FDA Regulatory Update on Critical Path Initiative. initiatives 2007 Lassere et al., Schema Methodology 2007b Definitions and validation criteria for biomarkers and surrogate endpoints: Development and testing of quantitative hierarchical levels of evidence schema. Lassere et al., Statistics Review 2007a Simulation studies of surrogate endpoint validation using single trial and multitrial statistical approaches. Wagner et al. Schema Methodology Biomarker qualification, a graded, “fit-for-purpose” qualitative evidentiary process linking a biomarker with biology and clinical endpoints. NOTES: a 57 Federal Register 239 (1992) pp. 58942–58960. AA = adjusted association; AIDS = acquired immune deficiency syndrome; b-HCG = beta-human chorionic gonadotropin; CAST = The Cardiac Arrhythmia Suppression Trial; CEA = carcinoembryonic antigen; FDA = Food and Drug Administration; HIV = human immunodeficiency virus; HOT = The Hypertension Optimal Treatment Study; HTLV-III = human T-lymphotropic virus type III; LDH = lactate dehydrogenase; NIH = National Institutes of Health; PTE = proportion of treatment effect; RCT = randomized controlled trial; RE = relative effect; TPA = tissue plasminogen activator. SOURCE: Lassere (2008). Reprinted with permission from SAGE publications, Copyright 2009 by SAGE Publications.

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 APPENDIX A TABLE A-2 Continuation of Table A-1 for 2007-2009 Year Author Focus Field/Summary and Commentary 2007 Alonso and Statistics Methodology Molenberghs An information-based validation method for surrogate endpoints. Pryseley et al. Statistics Methodology The authors test and review a meta- analytic approach to biomarker qualification and support use of a recently proposed, more computationally efficient process in some circumstances. Rasnake et al. Regulatory Nutrition Discussion of emerging surrogate endpoints and the use of surrogate endpoints in the review of health claims at the FDA. 2008 Alonso and Statistics Methodology/Oncology Molenberghs Evaluation of time to cancer recurrence as a surrogate endpoint for survival, as evaluated using a meta-analytic framework. Altar et al. Schema Methodology Provides an “evidence map” for grading available evidence and a process for biomarker qualification. Burzykowski Comment Methodology A concise summary of the topic of surrogate endpoint qualification. Chakravarty Regulatory Oncology/Regulatory Issues and Sridhara Discussion of use of progression- free survival as a trial endpoint. Green et al. Statistics Methodology Use of multiple methods, both statistical and clinically relevant qualitative methods, is proposed. Joy and Hegele Comment Methodology Discussion of the failure of the torcetrapib trials and the implications for CETP inhibition as a treatment target. Krumholz and Comment Methodology Lee Recent failures of surrogate endpoints in cardiology and endocrinology. continued

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0 EVALUATION OF BIOMARKERS AND SURROGATE ENDPOINTS TABLE A-2 Continued Year Author Focus Field/Summary and Commentary Lassere Review, schema Methodology Systematic review of biomarker and surrogate endpoint validation criteria from 1950 to 2007; also provides criteria for ranking surrogate validity. Osborne Comment Alzheimer’s/Regulatory Comment on shifts in use of surrogate endpoints for Alzheimer’s disease drug development. Psaty and Comment Cardiology Lumley Further discussion of recent surrogate endpoint failures in lipid- altering drug clinical trials. Wagner Schema Methodology Comprehensive discussion of fit- for-purpose biomarker qualification for all stages of drug development. 2009 Hlatky et al. Schema Methodology/Cardiology Title: Criteria for evaluation of novel markers of cardiovascular risk: A scientific statement from the American Heart Association. Lathia et al. Schema Methodology Successes and failures in use of surrogate endpoints for drug development; discussion of necessary criteria for surrogate endpoint qualification and use. Prentice Statistics Methodology Title: Surrogate and mediating endpoints: Current status and future directions. Rigatto and Review Methodology Barrett Statement of definitions, advantages, and disadvantages to biomarker and surrogate endpoint use for clinical trials.

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