Methodology for Good Machine Learning with Multi-Omics Data.

Journal: Clinical pharmacology and therapeutics
Published Date: Jan 31, 2024

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.

Authors

  • Thibaud Coroller
    Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
  • Berkman Sahiner
    Food and Drug Administration/CDRH, Silver Spring, USA.
  • Anup Amatya
    Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA.
  • Alexej Gossmann
    Division of Imaging, Diagnostics, and Software Reliability, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland, USA.
  • Konstantinos Karagiannis
    The Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA.
  • Conor Moloney
    Novartis Pharma AG, Rotkreuz, Switzerland.
  • Ravi K Samala
    Department of Radiology, University of Michigan, Ann Arbor, Michigan.
  • Luis Santana-Quintero
    The Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, 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
    Department of Gastroenterology, Sir Run Run Shaw Hospital of Zhejiang University, Hangzhou, China.
  • Kenny H Cha
    Department of Radiology, University of Michigan, Ann Arbor, Michigan.
  • 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
    People's Hospital of Deyang City, Deyang, 618000, Sichuan, China.
  • Ruihao Huang
    Department of Mathematical Sciences, Michigan Technological University, Houghton, MI, USA.
  • Jeffrey Kraft
    Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA.
  • Peter Krusche
    Novartis Pharma AG, Rotkreuz, Switzerland.
  • Yutong Li
    From CT Business Unit, Neusoft Medical System Company, Shenyang, China.
  • Zheng Li
    Department of Integrated Pulmonology, Fourth Clinical Medical College of Xinjiang Medical University, Urumqi, Xinjiang, China.
  • 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.
  • Susan Schnakenberg
    Novartis Pharmaceutical Company, East Hanover, New Jersey, USA.
  • Paolo Serra
    Novartis Pharmaceutical Company, East Hanover, New Jersey, USA.
  • Sean Smith
    The Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA.
  • Chi Song
    Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, USA. song.1188@osu.edu.
  • Fei Su
    School of Electrical and Information Engineering, Tianjin University, 300072, Tianjin, China. Electronic address: sufei@tju.edu.cn.
  • Mohit Tiwari
    Department of Computer Science and Engineering, Bharati Vidyapeeth's College of Engineering, Delhi, India.
  • Colin Vechery
    Novartis Pharmaceutical Company, East Hanover, New Jersey, USA.
  • Xin Xiong
    Department of Neurology, Chongqing Hospital of Traditional Chinese Medicine, Chongqing 400011, China.
  • Juan Pablo Zarate
    Novartis Pharmaceutical Company, East Hanover, New Jersey, USA.
  • Hao Zhu
    State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology Wuhan 430070 PR China chang@whut.edu.cn suntl@whut.edu.cn.
  • Arunava Chakravartty
    Novartis Pharmaceutical Company, East Hanover, New Jersey, USA.
  • Qi Liu
    National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China.
  • David Ohlssen
    Novartis Pharmaceutical Corporation, East Hanover, New Jersey, United States of America.
  • Nicholas Petrick
  • Julie A Schneider
    Oncology Center of Excellence, U.S. Food and Drug Administration, Silver Spring, Maryland, USA.
  • Mark Walderhaug
    Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States.
  • Emmanuel Zuber
    Novartis Pharma AG, Rotkreuz, Switzerland.

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