STAR Protocols (Sep 2022)
Analysis of germline-driven ancestry-associated gene expression in cancers
- Nyasha Chambwe,
- Rosalyn W. Sayaman,
- Donglei Hu,
- Scott Huntsman,
- Anab Kemal,
- Samantha Caesar-Johnson,
- Jean C. Zenklusen,
- Elad Ziv,
- Rameen Beroukhim,
- Andrew D. Cherniack,
- Jian Carrot-Zhang,
- Ashton C. Berger,
- Seunghun Han,
- Matthew Meyerson,
- Jeffrey S. Damrauer,
- Katherine A. Hoadley,
- Ina Felau,
- John A. Demchok,
- Michael K.A. Mensah,
- Roy Tarnuzzer,
- Zhining Wang,
- Liming Yang,
- Theo A. Knijnenburg,
- A. Gordon Robertson,
- Christina Yau,
- Christopher Benz,
- Kuan-lin Huang,
- Justin Y. Newberg,
- Garrett M. Frampton,
- R. Jay Mashl,
- Li Ding,
- Alessandro Romanel,
- Francesca Demichelis,
- Wanding Zhou,
- Peter W. Laird,
- Hui Shen,
- Christopher K. Wong,
- Joshua M. Stuart,
- Alexander J. Lazar,
- Xiuning Le,
- Ninad Oak
Affiliations
- Nyasha Chambwe
- Institute for Systems Biology, Seattle, WA 98109, USA
- Rosalyn W. Sayaman
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; Biological Sciences and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Corresponding author
- Donglei Hu
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
- Scott Huntsman
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
- Anab Kemal
- National Cancer Institute, Bethesda, MD 20892, USA
- Samantha Caesar-Johnson
- National Cancer Institute, Bethesda, MD 20892, USA
- Jean C. Zenklusen
- National Cancer Institute, Bethesda, MD 20892, USA
- Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
- 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
- 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
- Jian Carrot-Zhang
- Ashton C. Berger
- Seunghun Han
- Matthew Meyerson
- Jeffrey S. Damrauer
- Katherine A. Hoadley
- Ina Felau
- John A. Demchok
- Michael K.A. Mensah
- Roy Tarnuzzer
- Zhining Wang
- Liming Yang
- Theo A. Knijnenburg
- A. Gordon Robertson
- Christina Yau
- Christopher Benz
- Kuan-lin Huang
- Justin Y. Newberg
- Garrett M. Frampton
- R. Jay Mashl
- Li Ding
- Alessandro Romanel
- Francesca Demichelis
- Wanding Zhou
- Peter W. Laird
- Hui Shen
- Christopher K. Wong
- Joshua M. Stuart
- Alexander J. Lazar
- Xiuning Le
- Ninad Oak
- Journal volume & issue
-
Vol. 3,
no. 3
p. 101586
Abstract
Summary: Differential mRNA expression between ancestry groups can be explained by both genetic and environmental factors. We outline a computational workflow to determine the extent to which germline genetic variation explains cancer-specific molecular differences across ancestry groups. Using multi-omics datasets from The Cancer Genome Atlas (TCGA), we enumerate ancestry-informative markers colocalized with cancer-type-specific expression quantitative trait loci (e-QTLs) at ancestry-associated genes. This approach is generalizable to other settings with paired germline genotyping and mRNA expression data for a multi-ethnic cohort.For complete details on the use and execution of this protocol, please refer to Carrot-Zhang et al. (2020), Robertson et al. (2021), and Sayaman et al. (2021). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
