Integrated epigenomic exposure signature discovery.

Journal: Epigenomics
PMID: 39225561

Abstract

The epigenome influences gene regulation and phenotypes in response to exposures. Epigenome assessment can determine exposure history aiding in diagnosis. Here we developed and implemented a machine learning algorithm, the exposure signature discovery algorithm (ESDA), to identify the most important features present in multiple epigenomic and transcriptomic datasets to produce an integrated exposure signature (ES). Signatures were developed for seven exposures including , human immunodeficiency virus, SARS-CoV-2, influenza A (H3N2) virus and vaccinations. ESs differed in the assays and features selected and predictive value. Integrated ESs can potentially be utilized for diagnosis or forensic attribution. The ESDA identifies the most distinguishing features enabling diagnostic panel development for future precision health deployment.

Authors

  • Jared Schuetter
    Health Business Unit, Battelle Memorial Institute, Columbus, OH 43201, USA.
  • Angela Minard-Smith
    Health Business Unit, Battelle Memorial Institute, Columbus, OH 43201, USA.
  • Brandon Hill
    Nationwide Insurance, Columbus, OH 43215, USA.
  • Jennifer L Beare
    Health Business Unit, Battelle Memorial Institute, Columbus, OH 43201, USA.
  • Alexandria Vornholt
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Thomas W Burke
    Division of Infectious Diseases, Duke University, Durham, NC 27710, USA.
  • Vel Murugan
    Center for Personalized Diagnostics, Biodesign Institute at Arizona State University, Tempe, AZ 85281, 85281USA.
  • Anthony K Smith
    Health Business Unit, Battelle Memorial Institute, Columbus, OH 43201, USA.
  • Thiruppavai Chandrasekaran
    Center for Personalized Diagnostics, Biodesign Institute at Arizona State University, Tempe, AZ 85281, 85281USA.
  • Hiba J Shamma
    Health Business Unit, Battelle Memorial Institute, Columbus, OH 43201, USA.
  • Sarah C Kahaian
    Health Business Unit, Battelle Memorial Institute, Columbus, OH 43201, USA.
  • Keegan L Fillinger
    Health Business Unit, Battelle Memorial Institute, Columbus, OH 43201, USA.
  • Mary Anne S Amper
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Wan-Sze Cheng
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Yongchao Ge
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Mary Catherine George
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Kristy Guevara
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Nora Lovette-Okwara
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Avinash Mahajan
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Nada Marjanovic
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Natalia Mendelev
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Vance G Fowler
    Division of Infectious Diseases, Duke University, Durham, NC 27710, USA.
  • Micah T McClain
    Division of Infectious Diseases, Duke University, Durham, NC 27710, USA.
  • Clare M Miller
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Sagie Mofsowitz
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Venugopalan D Nair
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • German Nudelman
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Thomas G Evans
    Barinthus Biotherapeutics, Harwell, Oxfordshire, UK.
  • Flora Castellino
    Biomedical Advanced Research & Development Authority-Administration for Strategic Preparedness & Response,Washington, DC 20201, USA.
  • Irene Ramos
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Stas Rirak
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Frederique Ruf-Zamojski
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Nitish Seenarine
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Alessandra Soares-Shanoski
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Sindhu Vangeti
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Mital Vasoya
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Xuechen Yu
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Elena Zaslavsky
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Lishomwa C Ndhlovu
    Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
  • Michael J Corley
    Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
  • Scott Bowler
    Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
  • Steven G Deeks
    University of California San Francisco, San Francisco, CA 94143, 94143USA.
  • Andrew G Letizia
    Naval Medical Research Unit INDO PACIFIC, Singapore.
  • Stuart C Sealfon
    Icahn School of Medicine at Mount Sinai, New York City, NY 10029, 10029USA.
  • Christopher W Woods
    Division of Infectious Diseases, Duke University, Durham, NC 27710, USA.
  • Rachel R Spurbeck
    Health Business Unit, Battelle Memorial Institute, Columbus, OH 43201, USA.

Keywords

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