NTP RESEARCH REPOrt ON NATIONAL TOXICOLOGY PROGRAM ApprOACH TO GENOMIC DOSE-RESPONSE MODELING NTP RR 5 APRIL 2018 NTP Research Report on National Toxicology Program Approach to Genomic Dose-Response Modeling Research Report 5 National Toxicology Program April 2018 National Toxicology Program Public Health Service U.S. Department of Health and Human Services ISSN: 2473-4756 National Toxicology Program Approach to Genomic Dose-Response Modeling Table of Contents About This Report.......................................................................................................................... iii Peer Review ................................................................................................................................... iv Publication Details ......................................................................................................................... vi Abstract ......................................................................................................................................... vii Introduction ......................................................................................................................................1 Overview of NTP’s Approach .........................................................................................................3 A Detailed Description of the Steps in the Genomic Dose-Response Analysis ..............................5 Determining Adequate Signal in the Data ..................................................................................5 Filtering of Measured Features ...................................................................................................5 Fitting Features to Dose-Response Models.................................................................................6 Determining Gene-Set Level Potencies ......................................................................................9 Addressing the Study Design ....................................................................................................10 Addressing Biological Interpretation ........................................................................................13 References ......................................................................................................................................15 Appendix A Comparison of BEPOD to Apical POD ................................................................. A-1 ii National Toxicology Program Approach to Genomic Dose-Response Modeling About This Report National Toxicology Program1 1Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA Collaborators Scott Auerbach, Frederick Parham, Mary Wolfe, John Bucher Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA Scientific and technical expertise to development of the NTP approach and modeling software, ensuring inclusion of appropriate mathematical methods Scott Auerbach, Ph.D. Frederick Parham, Ph.D. Oversight and implementation of activities related to the webinar series, external peer review, readability, and finalization of the NTP approach. Mary Wolfe, Ph.D. Scientific consultation, review, and support toward development of NTP’s approach to genomic dose-response modeling John Bucher, Ph.D. Contributors Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA Guidance on statistical and mathematical modeling methods Pierre Bushel, Ph.D. Keith Shockley, Ph.D. National Center for Computational Toxicology, Environmental Protection Agency, Research Triangle Park, North Carolina, USA Conceptual guidance methodology Russell Thomas, Ph.D. University of Pittsburgh, Graduate School of Public Health, Pittsburgh, Pennsylvania, USA Guidance on statistical and mathematical modeling methods Shyamal Pedadda, Ph.D. (formerly at NIEHS/DNTP) iii National Toxicology Program Approach to Genomic Dose-Response Modeling Peer Review NTP convened an expert panel on October 23–25, 2017, to peer review the NTP Research Report on National Toxicology Program Approach to Genomic Dose-Response Modeling. The panel members are listed below. These reviewers served as independent scientists, not as representatives of any institution, company, or governmental agency. In this capacity, the panel provided scientific input on NTP’s proposed approach at the public meeting. Prior to the expert panel meeting, NTP hosted four webinars that presented an overview of current approaches and best practices to genomic dose-response modeling and NTP’s proposed response. The expert panel considered the information presented in the webinars, as well as other technical factors, during its peer review of NTP’s proposed approach. Meeting materials, the peer review report, and webinar recordings can be found on the NTP website: https://ntp.niehs.nih.gov/about/org/sep/ntpexpertpanel/past/index.html. Peer Reviewers Carole Yauk, Ph.D. (Chair) Research Scientist, Environmental Health Science and Research Bureau Health Canada Ottawa, ON, Canada Lyle Burgoon, Ph.D. Leader, Bioinformatics and Computational Toxicology Group U.S. Army Engineer Research and Development Center Raleigh, NC Rebecca Clewell, Ph.D. Chief Scientific Officer ScitoVation Durham, NC Ruili Huang, Ph.D. Lead Informatics Scientist Division of Pre-Clinical Innovation National Center for Advancing Translational Sciences (NCATS) National Institutes of Health (NIH) Rockville, MD Kamin Johnson, Ph.D. Associate Toxicology Manager The Dow Chemical Company Midland, MI Jorge Naciff, Ph.D. Principal Scientist Global Product Stewardship Central Product Safety Division, Mason Business Center Procter & Gamble Mason, OH iv National Toxicology Program Approach to Genomic Dose-Response Modeling Setia Pramana, Ph.D. Associate Professor, Institute of Statistics Adjunct Faculty, Department of Medical Epidemiology and Biostatistics Karolinska Institutet Jakarta, Indonesia James Stevens, Ph.D. Distinguished Research Fellow Eli Lily and Company Indianapolis, IN Fred Wright, Ph.D. Professor, Director of the Bioinformatics Research Center North Carolina State University Raleigh, NC v National Toxicology Program Approach to Genomic Dose-Response Modeling Publication Details Publisher: National Toxicology Program Publishing Location: Research Triangle Park, NC ISSN: 2473-4756 DOI: http://dx.doi.org/10.22427/NTP-RR-5 Report Series: NTP Research Report Series Report Series Number: 5 Official citation: National Toxicology Program. 2018. NTP Research Report on National Toxicology Program Approach to Genomic Dose-Response Modeling. NTP RR 5. Research Triangle Park, NC. National Toxicology Program (5) 1-44. vi National Toxicology Program Approach to Genomic Dose-Response Modeling Abstract A major component of the National Toxicology Program’s effort to evolve the practice of toxicology from an observational science to one that is more mechanistic involves using functional omic technologies, such as transcriptomics. NTP’s approach to genomic dose- response modeling focuses on identifying biological potency of the test article. The approach reflects recommendations of experts in toxicology and toxicogenomics. The steps in the process include 1) developing a study design that includes a broad range of doses that sufficiently describe the shape of the dose-response and maximizes the accuracy of benchmark dose (BMD) values derived for all responsive genes; 2) incorporating a signal detection filter to ensure the modeled data contain adequate signal to lend confidence that any effect is treatment related; 3) conducting effect size and trend tests to identify those genes exhibiting a biologically plausible and reproducible response to test article treatment; 4) fitting of parametric dose- response models derived from the EPA BMD software to identify a biological potency estimate (i.e., a BMD) for each gene exhibiting a dose-related response to treatment; 5) grouping of genes into predefined Gene Ontologies (GO), identifying the GO gene sets responding to treatment, and then determining the composite potency of the gene set (i.e., a gene-set BMD); and 6) providing a biologically and mechanistically focused interpretation. NTP has developed a software package, BMDExpress 2.0, which enables users to implement the approach and perform extensive data visualization. The approach to genomic dose-response modeling is anticipated to lead to greater consistency in reporting of genomic dose-response data and to facilitate the use of genomic dose-response data in risk assessment. vii National Toxicology Program Approach to Genomic Dose-Response Modeling Introduction Changes in the approach to toxicological assessment1 and the advent of inexpensive, high- throughput transcriptomics data generation platforms have led to significant interest in the integration of genomic dose-response studies (GDRS) for determining test article biological potency. The focus on biological potency is related to observation that gene set-level potencies derived from GDRS generally provide a good approximation of toxicological potency (i.e., the most sensitive effects that are typically used as a point of departure for risk assessment) that have been determined using long-term, resource-intensive toxicity studies (e.g., carcinogenicity) in the same model organism (e.g., rat)2. Such an approximation of biological potency from short-term