Springer Proceedings in Mathematics & Statistics Ray Liu Yi Tsong Editors Pharmaceutical Statistics MBSW 39, Muncie, Indiana, USA, May 16–18, 2016 Springer Proceedings in Mathematics & Statistics Volume 218 Springer Proceedings in Mathematics & Statistics This book series features volumes composed of selected contributions from workshops and conferences in all areas of current research in mathematics and statistics, including operation research and optimization. In addition to an overall evaluation of the interest, scientific quality, and timeliness of each proposal at the hands of the publisher, individual contributions are all refereed to the high quality standards of leading journals in the field. Thus, this series provides the research community with well-edited, authoritative reports on developments in the most exciting areas of mathematical and statistical research today. More information about this series at http://www.springer.com/series/10533 Ray Liu Yi Tsong (cid:129) Editors Pharmaceutical Statistics MBSW 39, Muncie, Indiana, USA, – May 16 18, 2016 123 Editors RayLiu YiTsong Statistical Innovation Division of Biometrics VI, CDER andConsultation Group U.S. FoodandDrugAdministration Takeda Pharmaceuticals Silver Spring, MD,USA Cambridge, MA, USA ISSN 2194-1009 ISSN 2194-1017 (electronic) SpringerProceedings in Mathematics& Statistics ISBN978-3-319-67385-1 ISBN978-3-319-67386-8 (eBook) https://doi.org/10.1007/978-3-319-67386-8 LibraryofCongressControlNumber:2019933200 MathematicsSubjectClassification(2010): 62-06,62-07,62-09,62H12,62H15,62H20,65C20,65C60, 92-08,97M60 ©SpringerNatureSwitzerlandAG2019 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpart of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission orinformationstorageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilar methodologynowknownorhereafterdeveloped. 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ThisSpringerimprintispublishedbytheregisteredcompanySpringerNatureSwitzerlandAG Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland Contents Part I Specification and Sampling Acceptance Tests Statistical Considerations in Setting Quality Specification Limits Using Quality Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Yi Tsong, Tianhua Wang and Xin Hu Counting Test and Parametric Two One-Sided Tolerance Interval Test for Content Uniformity Using Large Sample Sizes. . . . . . . . . . . . . 13 Meiyu Shen, Yi Tsong and Richard Lostritto Part II Analytical Biosimilar and Process Validation Sample Size Consideration for Equivalent Test of Tier-1 Quality Attributes for Analytical Biosimilarity Assessment. . . . . . . . . . . . . . . . . 27 Tianhua Wang, Yi Tsong and Meiyu Shen A Probability Based Equivalence Test of NIR Versus HPLC Analytical Methods in a Continuous Manufacturing Process Validation Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 Areti Manola, Steven Novick, Jyh-Ming Shoung and Stan Altan A Further Look at the Current Equivalence Test for Analytical Similarity Assessment. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 Neal Thomas and Aili Cheng Shiny Tools for Sample Size Calculation in Process Performance Qualification of Large Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 Qianqiu Li and Bill Pikounis Part III Continuous Process Risk Evaluation of Registered Specifications and Internal Release Limits Using a Bayesian Approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 Yijie Dong and Tianhua Wang v vi Contents Development of Statistical Computational Tools Through Pharmaceutical Drug Development and Manufacturing Life Cycle . . . . 101 Fasheng Li and Ke Wang Application of Advanced Statistical Tools to Achieve Continuous Analytical Verification: A Risk Assessment Case of the Impact of Analytical Method Performance on Process Performance Using a Bayesian Approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113 Iris Yan and Yijie Dong Part IV Clinical Trial Design and Analysis Exact Inference for Adaptive Group Sequential Designs . . . . . . . . . . . . 131 Cyrus Mehta, Lingyun Liu, Pranab Ghosh and Ping Gao A Novel Framework for Bayesian Response-Adaptive Randomization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141 Jian Zhu, Ina Jazić and Yi Liu Sample Size Determination Under Non-proportional Hazards . . . . . . . . 157 Miao Yang, Zhaowei Hua and Saran Vardhanabhuti Adaptive Three-Stage Clinical Trial Design for a Binary Endpoint in the Rare Disease Setting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167 Lingrui Gan and Zhaowei Hua Part V Biomarker-Driven Trial Design Clinical Trial Designs to Evaluate Predictive Biomarkers: What’s Being Estimated?. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183 Gene Pennello and Jingjing Ye Biomarker Enrichment Design Considerations in Oncology Single Arm Studies. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203 Hong Tian and Kevin Liu Challenges of Bridging Studies in Biomarker Driven Clinical Trials: The Impact of Companion Diagnostic Device Performance on Clinical Efficacy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215 Szu-Yu Tang and Bonnie LaFleur Part VI Application of Novel Data Modality Parallel-Tempered Feature Allocation for Large-Scale Tumor Heterogeneity with Deep Sequencing Data. . . . . . . . . . . . . . . . . . . . . . . 233 Yang Ni, Peter Müller, Max Shpak and Yuan Ji Contents vii Analysis of T-Cell Immune Responses as Measured by Intracellular Cytokine Staining with Application to Vaccine Clinical Trials. . . . . . . . 249 Yunzhi Lin and Cong Han Project Data Sphere and the Applications of Historical Patient Level Clinical Trial Data in Oncology Drug Development. . . . . . . . . . . . . . . . 263 Greg Hather and Ray Liu NovelTestfortheEqualityofContinuousCurveswithHomoscedastic or Heteroscedastic Measurement Errors . . . . . . . . . . . . . . . . . . . . . . . . 273 Zhongfa Zhang, Yarong Yang and Jiayang Sun Quality Control Metrics for Extraction-Free Targeted RNA-Seq Under a Compositional Framework. . . . . . . . . . . . . . . . . . . . . . . . . . . . 299 Dominic LaRoche, Dean Billheimer, Kurt Michels and Bonnie LaFleur Part VII Omics Data Analysis Leveraging Omics Biomarker Data in Drug Development: With a GWAS Case Study. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 317 Weidong Zhang ASimulationStudyComparingSNPBasedPredictionModelsofDrug Response . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327 Wencan Zhang, Pingye Zhang, Feng Gao, Yonghong Zhu and Ray Liu Contributors Stan Altan Janssen Pharmaceutical R&D, Raritan, NJ, USA Dean Billheimer Department of Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA Aili Cheng Pfizer, Pharmaceutical Sciences and Manufacturing Statistics, Andover, MA, USA Yijie Dong Global Statistics, Bristol-Myers Squibb Co., New Brunswick, NJ, USA Lingrui Gan Department of Statistics, University of Illinois at Urbana- Champaign, Champaign, IL, USA Feng Gao Biogen, Cambridge, MA, USA Ping Gao Brightech-International, Somerset, NJ, USA Pranab Ghosh Cytel Corporation, Cambridge, MA, USA Cong Han Takeda Pharmaceutical Company Limited, Cambridge, MA, USA Greg Hather Takeda Pharmaceuticals Inc., Cambridge, MA, USA Xin Hu The George Washington University, Washington, USA; ORISE, Oak Ridge, USA Zhaowei Hua Alnylam Pharmaceuticals, Inc., Cambridge, MA, USA Ina Jazić Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Cambridge, MA, USA Yuan Ji Program of Computational Genomics & Medicine, NorthShore University HealthSystem, Evanston, IL, USA; Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA ix x Contributors Bonnie LaFleur HTG Molecular Diagnostics, Inc., Tucson, AZ, USA Dominic LaRoche HTG Molecular Diagnostics, Inc., Tucson, AZ, USA Fasheng Li Pharmaceutical Science and Manufacturing Statistics, Pfizer Inc., Groton, CT, USA Qianqiu Li Janssen Research & Development LLC, Spring House, PA, USA Yunzhi Lin Takeda Pharmaceutical Company Limited, Cambridge, MA, USA Kevin Liu Janssen Research & Development, Raritan, NJ, USA Lingyun Liu Cytel Corporation, Cambridge, MA, USA Ray Liu Takeda Pharmaceuticals Inc., Cambridge, MA, USA Yi Liu Takeda Pharmaceuticals, Cambridge, MA, USA Richard Lostritto Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, USA Areti Manola Janssen Pharmaceutical R&D, Raritan, NJ, USA Cyrus Mehta Cytel Corporation, Cambridge, MA, USA; Harvard School of Public Health, Boston, MA, USA Kurt Michels HTG Molecular Diagnostics, Inc., Tucson, AZ, USA Peter Müller Department of Mathematics, The University of Texas at Austin, Austin, TX, USA Yang Ni Department of Statistics and Data Sciences, The University of Texas at Austin, Austin, TX, USA Steven Novick Medimmune, Gaithersburg, MD, USA Gene Pennello Division of Biostatistics, Office of Surveillance and Biometrics, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, MD, USA Bill Pikounis Janssen Research & Development LLC, Spring House, PA, USA Meiyu Shen Division Biometrics VI, Office of Biostatistics, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA Jyh-Ming Shoung Janssen Pharmaceutical R&D, Raritan, NJ, USA Max Shpak Sarah Cannon Research Institute, Nashville, TN, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA; Fresh Pond Research Institute, Cambridge, MA, USA