Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors
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...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-12-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S266616672200689X |
| _version_ | 1798006853893881856 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Rosalyn W. Sayaman |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T13:02:18Z |
| format | Article |
| id | doaj.art-0ca429312e1c4a1f8fe9a9562396dc10 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-11T13:02:18Z |
| publishDate | 2022-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-0ca429312e1c4a1f8fe9a9562396dc102022-12-22T04:22:53ZengElsevierSTAR Protocols2666-16672022-12-0134101809Analytic pipelines to assess the relationship between immune response and germline genetics in human tumorsRosalyn W. Sayaman0Mohamad Saad1Carolina Heimann2Donglei Hu3Khalid Kunji4Jessica Roelands5Denise M. Wolf6Scott Huntsman7Michele Ceccarelli8Vésteinn Thorsson9Elad Ziv10Davide Bedognetti11Department 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 authorQatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar; Neuroscience Research Center, Faculty of Medical Sciences, Lebanese University, Beirut, LebanonInstitute for Systems Biology, Seattle, WA 98109, USADepartment of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USAQatar Computing Research Institute, Hamad Bin Khalifa University, Doha, QatarHuman Immunology Department, Cancer Program, Research Branch, Sidra Medicine, PO Box 26999, Doha, Qatar; Department of Pathology, Leiden University Medical Center, Leiden, the NetherlandsDepartment of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USADepartment of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USADepartment of Electrical Engineering and Information Technology, University of Naples ''Federico II'', 80128 Naples, Italy; BIOGEM Institute of Molecular Biology and Genetics, 83031 Ariano Irpino, ItalyInstitute for Systems Biology, Seattle, WA 98109, USADepartment of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Corresponding authorHuman 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 authorSummary: 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.http://www.sciencedirect.com/science/article/pii/S266616672200689XBioinformaticsCancerGeneticsGenomicsImmunologyGene expression |
| spellingShingle | 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 Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors STAR Protocols Bioinformatics Cancer Genetics Genomics Immunology Gene expression |
| title | Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors |
| title_full | Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors |
| title_fullStr | Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors |
| title_full_unstemmed | Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors |
| title_short | Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors |
| title_sort | analytic pipelines to assess the relationship between immune response and germline genetics in human tumors |
| topic | Bioinformatics Cancer Genetics Genomics Immunology Gene expression |
| url | http://www.sciencedirect.com/science/article/pii/S266616672200689X |
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