Protocol for obtaining cancer type and subtype predictions using subSCOPE

Jasleen K Grewal; A Gordon Robertson; Kyle Ellrott; Christopher K Wong; Jordan A Lee; Christina Yau; Bahar Tercan; Mauro A A Castro; Christopher C Benz; Cancer Genome Atlas Analysis Network; Jean C Zenklusen; Andrew D Cherniack; Peter W Laird; Steven J M Jones

doi:10.1016/j.xpro.2025.103705

Protocol for obtaining cancer type and subtype predictions using subSCOPE

STAR Protoc. 2025 Jun 20;6(2):103705. doi: 10.1016/j.xpro.2025.103705. Epub 2025 Apr 10.

Collaborators

Cancer Genome Atlas Analysis Network:
Theo A Knijnenburg, Mauro A A Castro, Vinicius S Chagas, Victor H Apolonio, Verena Friedl, Joshua M Stuart, Vladislav Uzunangelov, Christopher K Wong, Jesper B Andersen, Andrew D Cherniack, Galen F Gao, Gad Getz, Stephanie H Hoyt, Whijae Roh, Lindsay Westlake, Christopher C Benz, Jasleen K Grewal, Steven J M Jones, A Gordon Robertson, Samantha J Caesar-Johnson, John A Demchok, Ina Felau, Anab Kemal, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C Zenklusen, Rehan Akbani, Bradley M Broom, Zhenlin Ju, Andre Schultz, Akinyemi I Ojesina, Katherine A Hoadley, Avantika Lal, Daniele Ramazzotti, Chen Wang, Alexander J Lazar, Lewis R Roberts, Taek-Kyun Kim, Ilya Shmulevich, Bahar Tercan, Paulos Charonyktakis, Vincenzo Lagani, Ioannis Tsamardinos, Esther Drill, Ronglai Shen, Martin L Ferguson, Kami E Chiotti, Kyle Ellrott, Brian J Karlberg, Jordan A Lee, Eve Lowenstein, Adam Struck, Paul T Spellman, Christina Yau, Toshinori Hinoue, Peter W Laird

Affiliations

¹ Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada. Electronic address: jgrewal@nvidia.com.
² Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada.
³ Oregon Health and Science University, Portland, OR 97239, USA.
⁴ UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, Santa Cruz, CA 95060, USA.
⁵ University of California, San Francisco, Department of Surgery, San Francisco, CA 94158, USA; Buck Institute for Research on Aging, Novato, CA 94945, USA.
⁶ Institute of Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA.
⁷ Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, Paraná 81520-260, Brazil.
⁸ Buck Institute for Research on Aging, Novato, CA 94945, USA.
⁹ Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA.
¹⁰ The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA. Electronic address: achernia@broadinstitute.org.
¹¹ Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA. Electronic address: peter.laird@vai.org.
¹² Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada. Electronic address: sjones@bcgsc.ca.

Abstract

We present a protocol for obtaining cancer type and subtype predictions using a machine learning method (subSCOPE). We describe steps for data preparation, subSCOPE setup, and running subSCOPE inference on prepared data. The protocol supports five -omics data types as input (DNA methylation, gene expression, microRNA [miRNA] expression, point mutations, and copy-number variants) and allows individual cancer type and data type selection. For non-The Cancer Genome Atlas (TCGA) cancer samples, it provides subtype-level classification across 26 different TCGA cancer cohorts and 106 subtypes. For complete details on the use and execution of this protocol, please refer to Ellrott et al.¹.

Keywords: Bioinformatics; Cancer; Computer sciences; Genomics.

MeSH terms

Computational Biology* / methods
DNA Copy Number Variations / genetics
DNA Methylation / genetics
Humans
Machine Learning*
MicroRNAs / genetics
Neoplasms* / classification
Neoplasms* / diagnosis
Neoplasms* / genetics

Substances

MicroRNAs