CUP-AI-Dx: A tool for inferring cancer tissue of origin and molecular subtype using RNA gene-expression data and artificial intelligence.

Journal: EBioMedicine
PMID: 33039710

Abstract

BACKGROUND: Cancer of unknown primary (CUP), representing approximately 3-5% of all malignancies, is defined as metastatic cancer where a primary site of origin cannot be found despite a standard diagnostic workup. Because knowledge of a patient's primary cancer remains fundamental to their treatment, CUP patients are significantly disadvantaged and most have a poor survival outcome. Developing robust and accessible diagnostic methods for resolving cancer tissue of origin, therefore, has significant value for CUP patients.

Authors

  • Yue Zhao
    The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China.
  • Ziwei Pan
    The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA; Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA.
  • Sandeep Namburi
    The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA.
  • Andrew Pattison
    Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Parkville, Melbourne, Australia.
  • Atara Posner
    Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Parkville, Melbourne, Australia.
  • Shiva Balachander
    Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Parkville, Melbourne, Australia.
  • Carolyn A Paisie
    The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA.
  • Honey V Reddi
    The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA; The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA.
  • Jens Rueter
    The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA.
  • Anthony J Gill
    Royal North Shore Hospital, Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Sydney, Australia.
  • Stephen Fox
    Peter MacCallum Cancer Centre, Department of Pathology, University of Melbourne, Victoria, Australia.
  • Kanwal P S Raghav
    Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • William F Flynn
    The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA.
  • Richard W Tothill
    Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Parkville, Melbourne, Australia; Peter MacCallum Cancer Centre, Parkville, Melbourne, Australia. Electronic address: rtothill@unimelb.edu.au.
  • Sheng Li
    School of Data Science, University of Virginia, Charlottesville, VA, United States.
  • R Krishna Murthy Karuturi
    The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA; The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA; Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA. Electronic address: krishna.karuturi@jax.org.
  • Joshy George
    The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA; The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA. Electronic address: joshy.george@jax.org.

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