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

doi:10.1016/j.xpro.2022.101809

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^*

^*Corresponding author for this work

Qatar Computing Research Institute

University of California at San Francisco
City of Hope National Med Center
Lawrence Berkeley National Laboratory
Lebanese University
Institute for Systems Biology
Sidra Medical and Research Center
Leiden University
University of Naples Federico II
Biogem S.c.a.r.l.
Hamad bin Khalifa University
University of Genoa

Research output: Contribution to journal › Article › peer-review

3 Citations (Scopus)

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).

Original language	English
Article number	101809
Journal	STAR Protocols
Volume	3
Issue number	4
DOIs	https://doi.org/10.1016/j.xpro.2022.101809
Publication status	Published - 16 Dec 2022

Keywords

Bioinformatics
Cancer
Gene expression
Genetics
Genomics
Immunology

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10.1016/j.xpro.2022.101809

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title = "Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors",

abstract = "Germline genetic variants modulate human immune response. We present analytical pipelines for assessing the contribution of hosts{\textquoteright} 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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doi = "10.1016/j.xpro.2022.101809",

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AU - Sayaman, Rosalyn W.

AU - Saad, Mohamad

AU - Heimann, Carolina

AU - Hu, Donglei

AU - Kunji, Khalid

AU - Roelands, Jessica

AU - Wolf, Denise M.

AU - Huntsman, Scott

AU - Ceccarelli, Michele

AU - Thorsson, Vésteinn

AU - Ziv, Elad

AU - Bedognetti, Davide

PY - 2022/12/16

Y1 - 2022/12/16

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AB - 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).

KW - Bioinformatics

KW - Cancer

KW - Gene expression

KW - Genetics

KW - Genomics

KW - Immunology

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DO - 10.1016/j.xpro.2022.101809

M3 - Article

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

Abstract

Keywords

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