A compendium of genetic regulatory effects across pig tissues.
A compendium of genetic regulatory effects across pig tissues.
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跨猪组织的遗传调控效应纲要。
DOI：
10.1038/s41588-023-01585-7
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发表时间：
2024-01
期刊：
影响因子：
30.8
通讯作者：
Fang, Lingzhao
中科院分区：
文献类型：
--
作者：
Teng, Jinyan;Gao, Yahui;Yin, Hongwei;Bai, Zhonghao;Liu, Shuli;Zeng, Haonan;Bai, Lijing;Cai, Zexi;Zhao, Bingru;Li, Xiujin;Xu, Zhiting;Lin, Qing;Pan, Zhangyuan;Yang, Wenjing;Yu, Xiaoshan;Guan, Dailu;Hou, Yali;Keel, Brittney N.;Rohrer, Gary A.;Lindholm-Perry, Amanda K.;Oliver, William T.;Ballester, Maria;Crespo-Piazuelo, Daniel;Quintanilla, Raquel;Canela-Xandri, Oriol;Rawlik, Konrad;Xia, Charley;Yao, Yuelin;Zhao, Qianyi;Yao, Wenye;Yang, Liu;Li, Houcheng;Zhang, Huicong;Liao, Wang;Chen, Tianshuo;Karlskov-Mortensen, Peter;Fredholm, Merete;Amills, Marcel;Clop, Alex;Giuffra, Elisabetta;Wu, Jun;Cai, Xiaodian;Diao, Shuqi;Pan, Xiangchun;Wei, Chen;Li, Jinghui;Cheng, Hao;Wang, Sheng;Su, Guosheng;Sahana, Goutam;Lund, Mogens Sando;Dekkers, Jack C. M.;Kramer, Luke;Tuggle, Christopher K.;Corbett, Ryan;Groenen, Martien A. M.;Madsen, Ole;Godia, Marta;Rocha, Dominique;Charles, Mathieu;Li, Cong-jun;Pausch, Hubert;Hu, Xiaoxiang;Frantz, Laurent;Luo, Yonglun;Lin, Lin;Zhou, Zhongyin;Zhang, Zhe;Chen, Zitao;Cui, Leilei;Xiang, Ruidong;Shen, Xia;Li, Pinghua;Huang, Ruihua;Tang, Guoqing;Li, Mingzhou;Zhao, Yunxiang;Yi, Guoqiang;Tang, Zhonglin;Jiang, Jicai;Zhao, Fuping;Yuan, Xiaolong;Liu, Xiaohong;Chen, Yaosheng;Xu, Xuewen;Zhao, Shuhong;Zhao, Pengju;Haley, Chris;Zhou, Huaijun;Wang, Qishan;Pan, Yuchun;Ding, Xiangdong;Ma, Li;Li, Jiaqi;Navarro, Pau;Zhang, Qin;Li, Bingjie;Tenesa, Albert;Li, Kui;Liu, George E.;Zhang, Zhe;Fang, Lingzhao
农场动物基因型-组织表达（FarmGTEx）项目已经建立，以开发家畜遗传调控变体的公共资源，这对于将遗传多态性与表型变异联系起来至关重要，有助于动物育种和人类生物医学的基础生物发现和开发。在这里，我们展示了PigGTEx中试阶段的结果，通过处理来自猪的5，457份RNA测序和1，602份全基因组测序样本，通过了质量控制。我们建立了一个猪基因型插补面板，并将数百万个遗传变异与34个组织中的5种转录组表型相关联。我们评估组织特异性的调节作用，并阐明其作用的分子机制，使用多组学数据。利用这一资源，我们破译了207个猪复杂表型背后的调控机制，并证明了猪在基因表达方面与人类的相似性以及复杂表型背后的遗传调控，支持了猪作为人类生物医学模型的重要性。PigGTEx的试验阶段，重新分析了5，457个已发表的RNA-seq样本，提出了一个分子数量性状基因座的泛组织目录。跨物种比较可以识别人类共有的遗传调控特征。
The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model. The pilot phase of PigGTEx, re-analyzing 5,457 published RNA-seq samples, presents a pan-tissue catalog of molecular quantitative trait loci. Cross-species comparisons identify traits with shared genetic regulation in humans.
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影响因子：
64.8
作者：
Bycroft C;Freeman C;Petkova D;Band G;Elliott LT;Sharp K;Motyer A;Vukcevic D;Delaneau O;O'Connell J;Cortes A;Welsh S;Young A;Effingham M;McVean G;Leslie S;Allen N;Donnelly P;Marchini J
通讯作者：
Marchini J
影响因子：
30.8
作者：
Kerimov N;Hayhurst JD;Peikova K;Manning JR;Walter P;Kolberg L;Samoviča M;Sakthivel MP;Kuzmin I;Trevanion SJ;Burdett T;Jupp S;Parkinson H;Papatheodorou I;Yates AD;Zerbino DR;Alasoo K
通讯作者：
Alasoo K
影响因子：
30.8
作者：
Bulik-Sullivan, Brendan K.;Loh, Po-Ru;Finucane, Hilary K.;Ripke, Stephan;Yang, Jian;Patterson, Nick;Daly, Mark J.;Price, Alkes L.;Neale, Benjamin M.
通讯作者：
Neale, Benjamin M.
DOI：
10.1038/s43586-022-00188-6
发表时间：
2023-01-25
期刊：
NATURE REVIEWS METHODS PRIMERS
影响因子：
--
作者：
Aguet, Francois;Alasoo, Kaur;Lappalainen, Tuuli
通讯作者：
Lappalainen, Tuuli
影响因子：
30.8
作者：
Freimer, Jacob W.;Shaked, Oren;Naqvi, Sahin;Sinnott-Armstrong, Nasa;Kathiria, Arwa;Chen, Amy F.;Cortez, Jessica T.;Greenleaf, William J.;Pritchard, Jonathan K.;Marson, Alexander;Garrido, Christian M.
通讯作者：
Garrido, Christian M.