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Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors.
Sayaman, Rosalyn W; Saad, Mohamad; Heimann, Carolina; Hu, Donglei; Kunji, Khalid; Roelands, Jessica; Wolf, Denise M; Huntsman, Scott; Ceccarelli, Michele; Thorsson, Vésteinn; Ziv, Elad; Bedognetti, Davide.
Afiliação
  • Sayaman RW; 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 Scienc
  • Saad M; Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar; Neuroscience Research Center, Faculty of Medical Sciences, Lebanese University, Beirut, Lebanon.
  • Heimann C; Institute for Systems Biology, Seattle, WA 98109, USA.
  • Hu D; Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
  • Kunji K; Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar.
  • Roelands J; Human Immunology Department, Cancer Program, Research Branch, Sidra Medicine, PO Box 26999, Doha, Qatar; Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands.
  • Wolf DM; Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
  • Huntsman S; Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
  • Ceccarelli M; 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.
  • Thorsson V; Institute for Systems Biology, Seattle, WA 98109, USA.
  • Ziv E; Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address: elad.ziv@ucsf.edu.
  • Bedognetti D; 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. Electro
STAR Protoc ; 3(4): 101809, 2022 12 16.
Article em En | MEDLINE | ID: mdl-36595917
ABSTRACT
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).
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Estudo de Associação Genômica Ampla / Neoplasias Idioma: En Ano de publicação: 2022 Tipo de documento: Article
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Estudo de Associação Genômica Ampla / Neoplasias Idioma: En Ano de publicação: 2022 Tipo de documento: Article