Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors.
Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors.
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DOI：
10.1016/j.xpro.2022.101809
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发表时间：
2022-12-16
期刊：
影响因子：
--
通讯作者：
Bedognetti, Davide
中科院分区：
文献类型：
--
作者：
Sayaman, Rosalyn W.;Saad, Mohamad;Heimann, Carolina;Hu, Donglei;Kunji, Khalid;Roelands, Jessica;Wolf, Denise M.;Huntsman, Scott;Ceccarelli, Michele;Thorsson, Vesteinn;Ziv, Elad;Bedognetti, Davide
生殖系遗传变异调节人类免疫反应。我们使用来自癌症基因组图谱（TCGA）中9，000多名患者的协调数据，提出了用于评估宿主遗传背景对实体瘤免疫景观的贡献的分析管道。这些包括遗传性，全基因组关联研究（GWAS），共定位和罕见变异分析的协议。这些工作流程是围绕TCGA的结构开发的，但可以适应于探索其他知识库或癌症免疫治疗的背景。有关本方案使用和执行的完整详细信息，请参阅。评估生殖系遗传学对肿瘤免疫结构贡献的管道数据下载、处理、组装、管理和注释的工作流程遗传性、GWAS、共定位和罕见变异分析的协议iAtlas和PheWeb探索结果的可视化工具出版商说明：进行任何实验方案都需要遵守当地机构的实验室安全和伦理指南。生殖系遗传变异调节人类免疫反应。我们使用来自癌症基因组图谱（TCGA）中9，000多名患者的协调数据，提出了用于评估宿主遗传背景对实体瘤免疫景观的贡献的分析管道。这些包括遗传性，全基因组关联研究（GWAS），共定位和罕见变异分析的协议。这些工作流程是围绕TCGA的结构开发的，但可以适应于探索其他知识库或癌症免疫治疗的背景。
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. Pipelines for assessing the contribution of germline genetics on tumor immune contexture Workflow for data download, processing, assembly, curation, and annotation Protocols for heritability, GWAS, colocalization, and rare variant analysis Visualization tools for exploration of the results by iAtlas and PheWeb Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. 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 variants analysis. These workflows are developed around the structure of TCGA but can be adapted to explore other repositories or in the context of cancer immunotherapy.
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影响因子：
48
作者：
Huber W;Carey VJ;Gentleman R;Anders S;Carlson M;Carvalho BS;Bravo HC;Davis S;Gatto L;Girke T;Gottardo R;Hahne F;Hansen KD;Irizarry RA;Lawrence M;Love MI;MacDonald J;Obenchain V;Oleś AK;Pagès H;Reyes A;Shannon P;Smyth GK;Tenenbaum D;Waldron L;Morgan M
通讯作者：
Morgan M
影响因子：
50.3
作者：
Carrot-Zhang, Jian;Chambwe, Nyasha;Beroukhim, Rameen
通讯作者：
Beroukhim, Rameen
影响因子：
4.6
作者：
Bonneville R;Krook MA;Kautto EA;Miya J;Wing MR;Chen HZ;Reeser JW;Yu L;Roychowdhury S
通讯作者：
Roychowdhury S
影响因子：
9.2
作者：
Chang CC;Chow CC;Tellier LC;Vattikuti S;Purcell SM;Lee JJ
通讯作者：
Lee JJ
影响因子：
3.8
作者：
Amara, Dominic;Wolf, Denise M.;Yau, Christina
通讯作者：
Yau, Christina