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Bornkamp B, Zaoli S, Azzarito M, Martin R, Müller CP, Moloney C, Capestro G, Ohlssen D, Baillie M. Predicting subgroup treatment effects for a new study: Motivations, results and learnings from running a data challenge in a pharmaceutical corporation. Pharm Stat 2024; 23:495-510. [PMID: 38326967 DOI: 10.1002/pst.2368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 12/01/2023] [Accepted: 01/21/2024] [Indexed: 02/09/2024]
Abstract
We present the motivation, experience, and learnings from a data challenge conducted at a large pharmaceutical corporation on the topic of subgroup identification. The data challenge aimed at exploring approaches to subgroup identification for future clinical trials. To mimic a realistic setting, participants had access to 4 Phase III clinical trials to derive a subgroup and predict its treatment effect on a future study not accessible to challenge participants. A total of 30 teams registered for the challenge with around 100 participants, primarily from Biostatistics organization. We outline the motivation for running the challenge, the challenge rules, and logistics. Finally, we present the results of the challenge, the participant feedback as well as the learnings. We also present our view on the implications of the results on exploratory analyses related to treatment effect heterogeneity.
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Affiliation(s)
- Björn Bornkamp
- Global Drug Development, Novartis Pharma AG, Basel, Switzerland
| | - Silvia Zaoli
- Global Drug Development, Novartis Pharma AG, Basel, Switzerland
| | | | - Ruvie Martin
- Global Drug Development, Novartis Pharmaceuticals Corporation, East Hanover, New Jersey, USA
| | | | - Conor Moloney
- Global Drug Development, Novartis Pharma AG, Dublin, Ireland
| | - Giulia Capestro
- Global Drug Development, Novartis Pharma AG, Basel, Switzerland
| | - David Ohlssen
- Global Drug Development, Novartis Pharmaceuticals Corporation, East Hanover, New Jersey, USA
| | - Mark Baillie
- Global Drug Development, Novartis Pharma AG, Basel, Switzerland
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Coroller T, Sahiner B, Amatya A, Gossmann A, Karagiannis K, Moloney C, Samala RK, Santana-Quintero L, Solovieff N, Wang C, Amiri-Kordestani L, Cao Q, Cha KH, Charlab R, Cross FH, Hu T, Huang R, Kraft J, Krusche P, Li Y, Li Z, Mazo I, Paul R, Schnakenberg S, Serra P, Smith S, Song C, Su F, Tiwari M, Vechery C, Xiong X, Zarate JP, Zhu H, Chakravartty A, Liu Q, Ohlssen D, Petrick N, Schneider JA, Walderhaug M, Zuber E. Methodology for Good Machine Learning with Multi-Omics Data. Clin Pharmacol Ther 2024; 115:745-757. [PMID: 37965805 DOI: 10.1002/cpt.3105] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/20/2023] [Indexed: 11/16/2023]
Abstract
In 2020, Novartis Pharmaceuticals Corporation and the U.S. Food and Drug Administration (FDA) started a 4-year scientific collaboration to approach complex new data modalities and advanced analytics. The scientific question was to find novel radio-genomics-based prognostic and predictive factors for HR+/HER- metastatic breast cancer under a Research Collaboration Agreement. This collaboration has been providing valuable insights to help successfully implement future scientific projects, particularly using artificial intelligence and machine learning. This tutorial aims to provide tangible guidelines for a multi-omics project that includes multidisciplinary expert teams, spanning across different institutions. We cover key ideas, such as "maintaining effective communication" and "following good data science practices," followed by the four steps of exploratory projects, namely (1) plan, (2) design, (3) develop, and (4) disseminate. We break each step into smaller concepts with strategies for implementation and provide illustrations from our collaboration to further give the readers actionable guidance.
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Affiliation(s)
| | - Berkman Sahiner
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Anup Amatya
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Alexej Gossmann
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Konstantinos Karagiannis
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | | | - Ravi K Samala
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Luis Santana-Quintero
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Nadia Solovieff
- Novartis Pharmaceutical Company, East Hanover, New Jersey, USA
| | - Craig Wang
- Novartis Pharma AG, Rotkreuz, Switzerland
| | - Laleh Amiri-Kordestani
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Qian Cao
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Kenny H Cha
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Rosane Charlab
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Frank H Cross
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Tingting Hu
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Ruihao Huang
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Jeffrey Kraft
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | | | - Yutong Li
- Novartis Pharmaceutical Company, East Hanover, New Jersey, USA
| | - Zheng Li
- Novartis Pharmaceutical Company, East Hanover, New Jersey, USA
| | - Ilya Mazo
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Rahul Paul
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | | | - Paolo Serra
- Novartis Pharmaceutical Company, East Hanover, New Jersey, USA
| | - Sean Smith
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Chi Song
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Fei Su
- Novartis Pharmaceutical Company, East Hanover, New Jersey, USA
| | - Mohit Tiwari
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Colin Vechery
- Novartis Pharmaceutical Company, East Hanover, New Jersey, USA
| | - Xin Xiong
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | | | - Hao Zhu
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | | | - Qi Liu
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - David Ohlssen
- Novartis Pharmaceutical Company, East Hanover, New Jersey, USA
| | - Nicholas Petrick
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Julie A Schneider
- Oncology Center of Excellence, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Mark Walderhaug
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
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Baillie M, Moloney C, Mueller CP, Dorn J, Branson J, Ohlssen D. Good Data Science Practice: Moving toward a Code of Practice for Drug Development (Rejoinder). Stat Biopharm Res 2023. [DOI: 10.1080/19466315.2022.2128402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- Mark Baillie
- Clinical Development & Analytics, Novartis Pharma AG, Basel, Switzerland
| | - Conor Moloney
- Clinical Development & Analytics, Novartis Pharma AG, Dublin, Ireland
| | | | - Jonas Dorn
- Roche Pharma Research and Early Development, pRED Informatics, Roche Innovation Center, Basel, Switzerland
| | - Janice Branson
- Clinical Development & Analytics, Novartis Pharma AG, Basel, Switzerland
| | - David Ohlssen
- Clinical Development & Analytics, Novartis Pharma AG, East Hannover, NJ
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