Idle thoughts of a ‘well‐calibrated’ Bayesian in clinical drug development

The use of Bayesian approaches in the regulated world of pharmaceutical drug development has not been without its difficulties or its critics. The recent Food and Drug Administration regulatory guidance on the use of Bayesian approaches in device submissions has mandated an investigation into the operating characteristics of Bayesian approaches and has suggested how to make adjustments in order that the proposed approaches are in a sense calibrated. In this paper, I present examples of frequentist calibration of Bayesian procedures and argue that we need not necessarily aim for perfect calibration but should be allowed to use procedures, which are well-calibrated, a position supported by the guidance.

[1]  David Draper,et al.  Assessment and Propagation of Model Uncertainty , 2011 .

[2]  L. Pericchi,et al.  Changing the paradigm of fixed significance levels: Testing Hypothesis by Minimizing Sum of Errors Type I and Type II , 2013, 1310.0039.

[3]  S. Oliver,et al.  Enhancing transparency in reporting the synthesis of qualitative research: ENTREQ , 2012, BMC Medical Research Methodology.

[4]  Roderick Little,et al.  Calibrated Bayes, for Statistics in General, and Missing Data in Particular , 2011, 1108.1917.

[5]  P. Thall,et al.  Practical Bayesian adaptive randomisation in clinical trials. , 2007, European journal of cancer.

[6]  Whole Grain Label Statements Guidance for Industry and FDA Staff , 2006 .

[7]  C. Liebermeister,et al.  Ueber Wahrscheinlichkeitsrechnung in Anwendung auf therapeutische Statistik , 2022 .

[8]  David J. Spiegelhalter,et al.  Consensus and controversy in pharmaceutical statistics - Discussion , 2000 .

[9]  B. Neuenschwander,et al.  Collection, synthesis, and interpretation of evidence: a proof‐of‐concept study in COPD , 2013, Statistics in medicine.

[10]  J. Cornfield Sequential Trials, Sequential Analysis and the Likelihood Principle , 1966 .

[11]  P M Fayers,et al.  Tutorial in biostatistics Bayesian data monitoring in clinical trials. , 1997, Statistics in medicine.

[12]  William G. Hunter,et al.  A Bayesian Analysis of the Linear Calibration Problem , 1981 .

[13]  Gene Pennello,et al.  Experience with Reviewing Bayesian Medical Device Trials , 2007, Journal of biopharmaceutical statistics.

[14]  W. R. Thompson On the Theory of Apportionment , 1935 .

[15]  Theodore R. Holford,et al.  Sequential Medical Trials, 2nd Edition , 1977, The Yale Journal of Biology and Medicine.

[16]  J. Kyle Wathen,et al.  Some caveats for outcome adaptive randomization in clinical trials , 2015 .

[17]  J. Lüroth,et al.  Vergleichung von zwei Werthen des wahrscheinlichen Fehlers , 2022 .

[18]  I. Bross Sequential clinical trials. , 1958, Journal of chronic diseases.

[19]  Testing Equivalence Simultaneously for Location and Dispersion of two Normally Distributed Populations , 1994 .

[20]  Heinz Schmidli,et al.  A practical guide to Bayesian group sequential designs , 2014, Pharmaceutical statistics.

[21]  T. Bayes An essay towards solving a problem in the doctrine of chances , 2003 .

[22]  Walter Bartky,et al.  Multiple Sampling with Constant Probability , 1943 .

[23]  D. Ashby Bayesian statistics in medicine: a 25 year review , 2006, Statistics in medicine.

[24]  D L DeMets,et al.  Computations for group sequential boundaries using the Lan-DeMets spending function method. , 2000, Controlled clinical trials.

[25]  D J Spiegelhalter,et al.  Comparison of Bayesian with group sequential methods for monitoring clinical trials. , 1989, Controlled clinical trials.

[26]  D. Spiegelhalter,et al.  Summarizing historical information on controls in clinical trials , 2010, Clinical trials.

[27]  A P Grieve,et al.  Extending a Bayesian analysis of the two-period crossover to allow for baseline measurements. , 1994, Statistics in medicine.

[28]  D. Rubin Bayesianly Justifiable and Relevant Frequency Calculations for the Applied Statistician , 1984 .

[29]  D J Spiegelhalter,et al.  The what, why and how of Bayesian clinical trials monitoring. , 1994, Statistics in medicine.

[30]  Andrew P Grieve,et al.  How to test hypotheses if you must , 2015, Pharmaceutical statistics.

[31]  R. Daniel Meyer,et al.  An Analysis for Unreplicated Fractional Factorials , 1986 .

[32]  Donald A. Berry,et al.  Group sequential clinical trials: a classical evaluation of Bayesian decision-theoretic designs , 1994 .

[33]  D. Rennie,et al.  SPIRIT 2013 statement: defining standard protocol items for clinical trials. , 2013, Annals of internal medicine.

[34]  P. Thall,et al.  Randomized phase II study of gemcitabine and docetaxel compared with gemcitabine alone in patients with metastatic soft tissue sarcomas: results of sarcoma alliance for research through collaboration study 002 [corrected]. , 2007, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[35]  D A Berry,et al.  A case for Bayesianism in clinical trials. , 1993, Statistics in medicine.

[36]  P. Armitage,et al.  Sequential tests in prophylactic and therapeutic trials. , 1954, The Quarterly journal of medicine.

[37]  Frank Bretz,et al.  Type I error rate control in adaptive designs for confirmatory clinical trials with treatment selection at interim , 2011, Pharmaceutical statistics.

[38]  Roderick J. A. Little,et al.  Calibrated Bayes, an alternative inferential paradigm for official statistics , 2012 .

[39]  Mkb Parmar,et al.  Bayesian data monitoring in clinical trials , 1997 .

[40]  David J. Spiegelhalter,et al.  Bayesian Approaches to Randomized Trials , 1994, Bayesian Biostatistics.

[41]  Curtis L. Meinert,et al.  A proposal for structured reporting of randomized controlled trials. The Standards of Reporting Trials Group. , 1994, JAMA.

[42]  Clifford Hildrethi BAYESIAN STATISTICIANS AND REMOTE CLIENTS , 1963 .

[43]  S J Pocock,et al.  Interim analyses for randomized clinical trials: the group sequential approach. , 1982, Biometrics.

[44]  K A Cronin,et al.  Bayesian monitoring of phase II trials in cancer chemoprevention. , 1999, Journal of clinical epidemiology.

[45]  D J Spiegelhalter,et al.  A unified method for monitoring and analysing controlled trials. , 1994, Statistics in medicine.

[46]  P. M. E. Altham,et al.  Exact Bayesian Analysis of a 2 Times 2 Contingency Table, and Fisher's “Exact” Significance Test , 1969 .

[47]  J. Andel Sequential Analysis , 2022, The SAGE Encyclopedia of Research Design.

[48]  A O'Hagan,et al.  Bayesian Assessment of Sample Size for Clinical Trials of Cost-Effectiveness , 2001, Medical decision making : an international journal of the Society for Medical Decision Making.

[49]  David Moher,et al.  Consolidated Health Economic Evaluation Reporting Standards (CHEERS) statement , 2013, International Journal of Technology Assessment in Health Care.

[50]  Greg Ogrinc,et al.  Publication guidelines for improvement studies in health care: evolution of the SQUIRE Project. , 2008, Annals of internal medicine.

[51]  Jill Hayden,et al.  Seven items were identified for inclusion when reporting a Bayesian analysis of a clinical study. , 2005, Journal of clinical epidemiology.

[52]  Harold P. Lehmann,et al.  Model Formulation: Bayesian Communication: A Clinically Significant Paradigm for Electronic Publication , 2000, J. Am. Medical Informatics Assoc..

[53]  J. Eric Bickel,et al.  Comparing NWS POP Forecasts to Third-Party Providers , 2011 .

[54]  Frank Bretz,et al.  From Adaptive Design to Modern Protocol Design for Drug Development: Part I. Editorial and Summary of Adaptive Designs Session at the Third FDA/DIA Statistics Forum , 2010 .

[55]  Eugene Seneta,et al.  Carl Liebermeister's hypergeometric tails , 1994 .

[56]  Call for Comments on a Proposal To Improve Reporting of Clinical Trials in the Biomedical Literature , 1994, Annals of Internal Medicine.

[57]  David Moher,et al.  The STARD Statement for Reporting Studies of Diagnostic Accuracy: Explanation and Elaboration , 2003, Annals of Internal Medicine [serial online].

[58]  N. D’Esopo,et al.  STREPTOMYCIN TREATMENT OF PULMONARY TUBERCULOSIS , 1998, The Journal of clinical investigation.

[59]  P. Armitage,et al.  Repeated Significance Tests on Accumulating Data , 1969 .

[60]  J. Ioannidis,et al.  Strengthening the reporting of genetic association studies (STREGA): an extension of the STROBE statement , 2009, European Journal of Epidemiology.

[61]  D. Spiegelhalter,et al.  Monitoring of large randomised clinical trials: a new approach with Bayesian methods , 2001, The Lancet.

[62]  J. Hammersley,et al.  A new Monte Carlo technique: antithetic variates , 1956, Mathematical Proceedings of the Cambridge Philosophical Society.

[63]  D. Berry,et al.  Interim analyses in clinical trials: classical vs. Bayesian approaches. , 1985, Statistics in medicine.

[64]  K. Pearson,et al.  Mathematical Contributions to the Theory of Evolution. IV. On the Probable Errors of Frequency Constants and on the Influence of Random Selection on Variation and Correlation , .

[65]  I. Bross,et al.  Sequential Medical Plans. , 1952 .

[66]  A. Hall The Method of Least Squares , 1872, Nature.

[67]  D. Moher,et al.  Preferred reporting items for systematic reviews and meta-analyses: the PRISMA statement. , 2010, International journal of surgery.

[68]  P. Sainsbury,et al.  Consolidated criteria for reporting qualitative research (COREQ): a 32-item checklist for interviews and focus groups. , 2007, International journal for quality in health care : journal of the International Society for Quality in Health Care.

[69]  A. Grieve Joint equivalence of means and variances of two populations. , 1998, Journal of biopharmaceutical statistics.

[70]  C. Daniel Use of Half-Normal Plots in Interpreting Factorial Two-Level Experiments , 1959 .

[71]  E. Seneta,et al.  Carl Liebermeister (1833–1901): A Pioneer of the Investigation and Treatment of Fever and the Developer of a Statistical Test , 2004, Journal of medical biography.

[72]  P. O'Brien,et al.  A multiple testing procedure for clinical trials. , 1979, Biometrics.

[73]  B. Freidlin,et al.  Outcome--adaptive randomization: is it useful? , 2011, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[74]  S. Goodman Stopping at Nothing? Some Dilemmas of Data Monitoring in Clinical Trials , 2007, Annals of Internal Medicine.

[75]  A P Grieve,et al.  A Bayesian analysis of the two-period crossover design for clinical trials. , 1985, Biometrics.

[76]  R. Lenth Quick and easy analysis of unreplicated factorials , 1989 .

[77]  Andrew P Grieve,et al.  ASTIN: a Bayesian adaptive dose–response trial in acute stroke , 2005, Clinical trials.

[78]  I. Olkin,et al.  Improving the quality of reporting of randomized controlled trials. The CONSORT statement. , 1996, JAMA.

[79]  Daniel L Gillen,et al.  Bayesian evaluation of group sequential clinical trial designs , 2007, Statistics in medicine.

[80]  R. Ineichen Der “Vierfeldertest” von Carl Liebermeister (Bemerkungen zur Entwicklung der medizinischen Statistik im 19. Jahrhundert) , 1994 .

[81]  K. K. Lan,et al.  Discrete sequential boundaries for clinical trials , 1983 .

[82]  F. Y. Edgeworth L. The method of least squares , 1883 .

[83]  P. Armitage,et al.  Sequential methods in clinical trials. , 1958, American journal of public health and the nation's health.

[84]  Joseph F. Mudge,et al.  Setting an Optimal α That Minimizes Errors in Null Hypothesis Significance Tests , 2012, PloS one.

[85]  J. Haybittle,et al.  Repeated assessment of results in clinical trials of cancer treatment. , 1971, The British journal of radiology.

[86]  W. R. Thompson ON THE LIKELIHOOD THAT ONE UNKNOWN PROBABILITY EXCEEDS ANOTHER IN VIEW OF THE EVIDENCE OF TWO SAMPLES , 1933 .

[87]  S. Pocock Group sequential methods in the design and analysis of clinical trials , 1977 .

[88]  Alessandra Giovagnoli,et al.  Simulation of Clinical Trias: A Review with Emphasis on the Design Issues , 2012 .

[89]  D. Berry Adaptive clinical trials: the promise and the caution. , 2011, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[90]  H. F. Dodge,et al.  A method of sampling inspection , 1929 .

[91]  P. Armitage,et al.  Design and analysis of randomized clinical trials requiring prolonged observation of each patient. I. Introduction and design. , 1976, British Journal of Cancer.

[92]  Andrew P Grieve,et al.  25 years of Bayesian methods in the pharmaceutical industry: a personal, statistical bummel , 2007, Pharmaceutical statistics.

[93]  S. Pocock,et al.  Strengthening the Reporting of Observational Studies in Epidemiology (STROBE): Explanation and Elaboration , 2007, PLoS medicine.

[94]  Helmert Die Genauigkeit der Formel von Peters zur Berechnung des wahrscheinlichen Beobachtungsfehlers directer Beobachtungen gleicher Genauigkeit , 1876 .

[95]  David R. Jones,et al.  Bayesian methods in health technology assessment: a review. , 2000, Health technology assessment.

[96]  Fang Chen,et al.  Use of historical control data for assessing treatment effects in clinical trials , 2014, Pharmaceutical statistics.

[97]  J. Lee,et al.  Calibrating the prior distribution for a normal model with conjugate prior , 2015, Journal of statistical computation and simulation.

[98]  Student Probable Error of a Correlation Coefficient , 1908 .

[99]  Say-Beng Tan,et al.  Where's the utility in Bayesian data-monitoring of clinical trials? , 2005, Clinical trials.

[100]  Donald A. Berry,et al.  Interim analysis in clinical trials; the role of the likelihood principle , 1987 .

[101]  I. Olkin,et al.  Improving the quality of reporting of randomized controlled trials. The CONSORT statement. , 1996, JAMA.

[102]  D. Berry,et al.  Adaptive randomized study of idarubicin and cytarabine versus troxacitabine and cytarabine versus troxacitabine and idarubicin in untreated patients 50 years or older with adverse karyotype acute myeloid leukemia. , 2003, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[103]  J. Cornfield A BAYESIAN TEST OF SOME CLASSICAL HYPOTHESES- WITH APPLICATIONS TO SEQUENTIAL CLINICAL TRIALS , 1966 .