Integrative modeling identifies genetic ancestry-associated molecular correlates in human cancer

A. Gordon Robertson; Christina Yau; Jian Carrot-Zhang; Jeffrey S. Damrauer; Theo A. Knijnenburg; Nyasha Chambwe; Katherine A. Hoadley; Anab Kemal; Jean C. Zenklusen; Andrew D. Cherniack; Rameen Beroukhim; Wanding Zhou

STAR Protocols (Jun 2021)

Integrative modeling identifies genetic ancestry-associated molecular correlates in human cancer

A. Gordon Robertson,
Christina Yau,
Jian Carrot-Zhang,
Jeffrey S. Damrauer,
Theo A. Knijnenburg,
Nyasha Chambwe,
Katherine A. Hoadley,
Anab Kemal,
Jean C. Zenklusen,
Andrew D. Cherniack,
Rameen Beroukhim,
Wanding Zhou

Affiliations

A. Gordon Robertson: Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
Christina Yau: Buck Institute for Research on Aging, Novato, CA 94945, USA; Department of Surgery, University of California, San Francisco, San Francisco, CA 94115, USA
Jian Carrot-Zhang: 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
Jeffrey S. Damrauer: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
Theo A. Knijnenburg: Institute for Systems Biology, Seattle, WA 98109, USA
Nyasha Chambwe: Institute for Systems Biology, Seattle, WA 98109, USA
Katherine A. Hoadley: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
Anab Kemal: National Cancer Institute, Bethesda, MD 20892, USA
Jean C. Zenklusen: National Cancer Institute, Bethesda, MD 20892, USA
Andrew D. Cherniack: 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; Corresponding author
Rameen Beroukhim: 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; Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Corresponding author
Wanding Zhou: Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Corresponding author

Journal volume & issue: Vol. 2, no. 2
p. 100483

Abstract

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Summary: Cellular and molecular aberrations contribute to the disparity of human cancer incidence and etiology between ancestry groups. Multiomics profiling in The Cancer Genome Atlas (TCGA) allows for querying of the molecular underpinnings of ancestry-specific discrepancies in human cancer. Here, we provide a protocol for integrative associative analysis of ancestry with molecular correlates, including somatic mutations, DNA methylation, mRNA transcription, miRNA transcription, and pathway activity, using TCGA data. This protocol can be generalized to analyze other cancer cohorts and human diseases.For complete details on the use and execution of this protocol, please refer to Carrot-Zhang et al. (2020).

Published in STAR Protocols

ISSN: 2666-1667 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Science (General)
Website: https://star-protocols.cell.com/

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