GWAS analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis.
GWAS analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis.
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DOI：
10.1093/bioinformatics/btp714
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发表时间：
2010-02-15
期刊：
影响因子：
--
通讯作者：
Brittnacher M
中科院分区：
文献类型：
--
作者：
Fong C;Ko DC;Wasnick M;Radey M;Miller SI;Brittnacher M
动机：全基因组关联研究开始阐明我们的遗传差异如何影响疾病的易感性和严重性。虽然以前已经开发了计算工具来支持全基因组关联研究的各个方面，但目前需要促进来自多个来源的数据整合的信息学解决方案。结果如下：在这里，我们提出了GWAS分析仪，一个数据库驱动的基于网络的工具，整合基因型和表型数据，关联分析结果和基因组注释从多个公共资源。GWAS分析器包含浏览这些相关数据、按家族或基因型探索表型值以及基于多个标准过滤关联结果的功能。该工具的实用性已通过人类体外细菌感染易感性的全基因组关联研究得到证实。GWAS分析仪有助于管理大量的表型和基因型数据，分析表型变异和遗传力，最重要的是，生成一组精确的候选单核苷酸多态性（SNP）。该工具揭示了一个SNP，该SNP经实验验证与沙门氏菌感染的HapMap细胞系中细胞死亡增加相关。可用性：http://www.nwrce.org/gwas-analyzer联系：mbrittna@u.washington.edu补充信息：补充数据可在生物信息学在线。
Motivation: Genome-wide association studies are beginning to elucidate how our genetic differences contribute to susceptibility and severity of disease. While computational tools have previously been developed to support various aspects of genome-wide association studies, there is currently a need for informatics solutions that facilitate the integration of data from multiple sources. Results: Here we present GWAS Analyzer, a database driven web-based tool that integrates genotype and phenotype data, association analysis results and genomic annotations from multiple public resources. GWAS Analyzer contains features for browsing these interrelated data, exploring phenotypic values by family or genotype, and filtering association results based on multiple criteria. The utility of the tool has been demonstrated by a genome-wide association study of human in vitro susceptibility to bacterial infection. GWAS Analyzer facilitated management of large sets of phenotype and genotype data, analysis of phenotypic variation and heritability, and most importantly, generation of a refined set of candidate single nucleotide polymorphisms (SNPs). The tool revealed a SNP that was experimentally validated to be associated with increased cell death among Salmonella infected HapMap cell lines. Availability: http://www.nwrce.org/gwas-analyzer Contact: mbrittna@u.washington.edu Supplementary Information: Supplementary data are available at Bioinformatics online.
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影响因子：
64.8
作者：
Frazer, Kelly A.;Ballinger, Dennis G.;Cox, David R.;Hinds, David A.;Stuve, Laura L.;Gibbs, Richard A.;Belmont, John W.;Boudreau, Andrew;Hardenbol, Paul;Leal, Suzanne M.;Pasternak, Shiran;Wheeler, David A.;Willis, Thomas D.;Yu, Fuli;Yang, Huanming;Zeng, Changqing;Gao, Yang;Hu, Haoran;Hu, Weitao;Li, Chaohua;Lin, Wei;Liu, Siqi;Pan, Hao;Tang, Xiaoli;Wang, Jian;Wang, Wei;Yu, Jun;Zhang, Bo;Zhang, Qingrun;Zhao, Hongbin;Zhao, Hui;Zhou, Jun;Gabriel, Stacey B.;Barry, Rachel;Blumenstiel, Brendan;Camargo, Amy;Defelice, Matthew;Faggart, Maura;Goyette, Mary;Gupta, Supriya;Moore, Jamie;Nguyen, Huy;Onofrio, Robert C.;Parkin, Melissa;Roy, Jessica;Stahl, Erich;Winchester, Ellen;Ziaugra, Liuda;Altshuler, David;Shen, Yan;Yao, Zhijian;Huang, Wei;Chu, Xun;He, Yungang;Jin, Li;Liu, Yangfan;Shen, Yayun;Sun, Weiwei;Wang, Haifeng;Wang, Yi;Wang, Ying;Xiong, Xiaoyan;Xu, Liang;Waye, Mary M. Y.;Tsui, Stephen K. W.;Wong, J. Tze-Fei;Galver, Luana M.;Fan, Jian-Bing;Gunderson, Kevin;Murray, Sarah S.;Oliphant, Arnold R.;Chee, Mark S.;Montpetit, Alexandre;Chagnon, Fanny;Ferretti, Vincent;Leboeuf, Martin;Olivier, Jean-Franccois;Phillips, Michael S.;Roumy, Stephanie;Sallee, Clementine;Verner, Andrei;Hudson, Thomas J.;Kwok, Pui-Yan;Cai, Dongmei;Koboldt, Daniel C.;Miller, Raymond D.;Pawlikowska, Ludmila;Taillon-Miller, Patricia;Xiao, Ming;Tsui, Lap-Chee;Mak, William;Song, You Qiang;Tam, Paul K. H.;Nakamura, Yusuke;Kawaguchi, Takahisa;Kitamoto, Takuya;Morizono, Takashi;Nagashima, Atsushi;Ohnishi, Yozo;Sekine, Akihiro;Tanaka, Toshihiro;Tsunoda, Tatsuhiko;Deloukas, Panos;Bird, Christine P.;Delgado, Marcos;Dermitzakis, Emmanouil T.;Gwilliam, Rhian;Hunt, Sarah;Morrison, Jonathan;Powell, Don;Stranger, Barbara E.;Whittaker, Pamela;Bentley, David R.;Daly, Mark J.;de Bakker, Paul I. W.;Barrett, Jeff;Chretien, Yves R.;Maller, Julian;McCarroll, Steve;Patterson, Nick;Pe'er, Itsik;Price, Alkes;Purcell, Shaun;Richter, Daniel J.;Sabeti, Pardis;Saxena, Richa;Schaffner, Stephen F.;Sham, Pak C.;Varilly, Patrick;Altshuler, David;Stein, Lincoln D.;Krishnan, Lalitha;Smith, Albert Vernon;Tello-Ruiz, Marcela K.;Thorisson, Gudmundur A.;Chakravarti, Aravinda;Chen, Peter E.;Cutler, David J.;Kashuk, Carl S.;Lin, Shin;Abecasis, Goncalo R.;Guan, Weihua;Li, Yun;Munro, Heather M.;Qin, Zhaohui Steve;Thomas, Daryl J.;McVean, Gilean;Auton, Adam;Bottolo, Leonardo;Cardin, Niall;Eyheramendy, Susana;Freeman, Colin;Marchini, Jonathan;Myers, Simon;Spencer, Chris;Stephens, Matthew;Donnelly, Peter;Cardon, Lon R.;Clarke, Geraldine;Evans, David M.;Morris, Andrew P.;Weir, Bruce S.;Tsunoda, Tatsuhiko;Johnson, Todd A.;Mullikin, James C.;Sherry, Stephen T.;Feolo, Michael;Skol, Andrew
通讯作者：
Skol, Andrew
影响因子：
30.8
作者：
Hampe, Jochen;Franke, Andre;Schreiber, Stefan
通讯作者：
Schreiber, Stefan
影响因子：
7
作者：
Li, JL;Deng, HY;Deng, HW
通讯作者：
Deng, HW
影响因子：
3
作者：
Monnier, S;Cox, DG;Canzian, F
通讯作者：
Canzian, F
影响因子：
4.4
作者：
Yeung, J. M. Y.;Sham, P. C.;Cherny, S. S.
通讯作者：
Cherny, S. S.