PharmacoGx: an R package for analysis of large pharmacogenomic datasets

被引：179

作者：

Smirnov, Petr ^{[1
]}

Safikhani, Zhaleh ^{[1
,2
]}

El-Hachem, Nehme ^{[3
]}

Wang, Dong ^{[1
]}

She, Adrian ^{[1
]}

Olsen, Catharina ^{[1
,4
,5
]}

Freeman, Mark ^{[1
]}

Selby, Heather ^{[6
,7
]}

Gendoo, Deena M. A. ^{[1
,2
]}

Grossmann, Patrick ^{[6
]}

Beck, Andrew H. ^{[8
]}

Aerts, Hugo J. W. L. ^{[6
]}

Lupien, Mathieu ^{[1
,2
,9
]}

Goldenberg, Anna ^{[10
,11
]}

Haibe-Kains, Benjamin ^{[1
,2
]}

机构：

[1] Univ Hlth Network, Princess Margaret Canc Ctr, Toronto, ON, Canada

[2] Univ Toronto, Dept Med Biophys, Toronto, ON, Canada

[3] Inst Rech Clin Montreal, Montreal, PQ H2W 1R7, Canada

[4] Interuniv Inst Bioinformat Brussels IB 2, Brussels, Belgium

[5] Univ Libre Bruxelles, Dept Informat, MLG, Brussels, Belgium

[6] Harvard Univ, Sch Med, Dana Farber Canc Inst, 44 Binney St, Boston, MA 02115 USA

[7] Boston Univ, Dept Bioinformat, Boston, MA 02215 USA

[8] Beth Israel Deaconess Med Ctr, Boston, MA 02215 USA

[9] Ontario Inst Canc Res, Toronto, ON, Canada

[10] Hosp Sick Children, 555 Univ Ave, Toronto, ON M5G 1X8, Canada

[11] Univ Toronto, Dept Comp Sci, Toronto, ON, Canada

来源：

BIOINFORMATICS | 2016年 / 32卷 / 08期

关键词：

D O I：

10.1093/bioinformatics/btv723

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Pharmacogenomics holds great promise for the development of biomarkers of drug response and the design of new therapeutic options, which are key challenges in precision medicine. However, such data are scattered and lack standards for efficient access and analysis, consequently preventing the realization of the full potential of pharmacogenonnics. To address these issues, we implemented PharmacoGx, an easy-to-use, open source package for integrative analysis of multiple pharnnacogenomic datasets. We demonstrate the utility of our package in comparing large drug sensitivity datasets, such as the Genomics of Drug Sensitivity in Cancer and the Cancer Cell Line Encyclopedia. Moreover, we show how to use our package to easily perform Connectivity Map analysis. With increasing availability of drug -related data, our package will open new avenues of research for meta-analysis of pharmacogenomic data.

引用

页码：1244 / 1246

页数：3

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