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© Research
Publication : Bioinformatics

GDSCTools for Mining Pharmacogenomic Interactions in Cancer.

Team: Bioinformatics and Biostatistics HUB
Member: Thomas Cokelaer
Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Bioinformatics - 24 Nov 2017

Cokelaer T, Chen E, Iorio F, Menden MP, Lightfoot H, Saez-Rodriguez J, Garnett MJ

Link to Pubmed [PMID] – 29186349

Bioinformatics. 2017 Nov 24. doi: 10.1093/bioinformatics/btx744.

Large pharmacogenomic screenings integrate heterogeneous cancer genomic data sets as well as anti-cancer drug responses on thousand human cancer cell lines. Mining this data to identify new therapies for cancer sub-populations would benefit from common data structures, modular computational biology tools and user-friendly interfaces.
Results:

We have developed GDSCTools: a software aimed at the identification of clinically relevant genomic markers of drug response. The Genomics of Drug Sensitivity in Cancer (GDSC) database (www.cancerRxgene.org) integrates heterogeneous cancer genomic data sets as well as anti-cancer drug responses on a thousand cancer cell lines. Including statistical tools (ANOVA) and predictive methods (Elastic Net), as well as common data structures, GDSCTools allows users to reproduce published results from GDSC and to implement new analytical methods. In addition, non-GDSC data resources can also be analysed since drug responses and genomic features can be encoded as CSV files.