Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors

Rosalyn W. Sayaman; Mohamad Saad; Carolina Heimann; Donglei Hu; Khalid Kunji; Jessica Roelands; Denise M. Wolf; Scott Huntsman; Michele Ceccarelli; Vésteinn Thorsson; Elad Ziv; Davide Bedognetti

STAR Protocols (Dec 2022)

Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors

Rosalyn W. Sayaman,
Mohamad Saad,
Carolina Heimann,
Donglei Hu,
Khalid Kunji,
Jessica Roelands,
Denise M. Wolf,
Scott Huntsman,
Michele Ceccarelli,
Vésteinn Thorsson,
Elad Ziv,
Davide Bedognetti

Affiliations

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 Comprehensive Cancer Center, Duarte, CA 91010, USA; Biological Sciences and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Corresponding author
Mohamad Saad: Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar; Neuroscience Research Center, Faculty of Medical Sciences, Lebanese University, Beirut, Lebanon
Carolina Heimann: Institute for Systems Biology, Seattle, WA 98109, USA
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
Khalid Kunji: Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar
Jessica Roelands: Human Immunology Department, Cancer Program, Research Branch, Sidra Medicine, PO Box 26999, Doha, Qatar; Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
Denise M. Wolf: Department of Laboratory Medicine, 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
Michele Ceccarelli: Department of Electrical Engineering and Information Technology, University of Naples ''Federico II'', 80128 Naples, Italy; BIOGEM Institute of Molecular Biology and Genetics, 83031 Ariano Irpino, Italy
Vésteinn Thorsson: Institute for Systems Biology, Seattle, WA 98109, 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; Corresponding author
Davide Bedognetti: Human Immunology Department, Cancer Program, Research Branch, Sidra Medicine, PO Box 26999, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar; Department of Internal Medicine and Medical Specialties (Di.M.I.), University of Genoa, 16132 Genoa, Italy; Corresponding author

Journal volume & issue: Vol. 3, no. 4
p. 101809

Abstract

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Summary: Germline genetic variants modulate human immune response. We present analytical pipelines for assessing the contribution of hosts’ genetic background to the immune landscape of solid tumors using harmonized data from more than 9,000 patients in The Cancer Genome Atlas (TCGA). These include protocols for heritability, genome-wide association studies (GWAS), colocalization, and rare variant analyses. These workflows are developed around the structure of TCGA but can be adapted to explore other repositories or in the context of cancer immunotherapy.For complete details on the use and execution of this protocol, please refer to Sayaman et al. (2021). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

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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