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Series GSE68379 Query DataSets for GSE68379
Status Public on Jul 05, 2016
Title The landscape of pharmacogenomic interactions in human cancer
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Systematic studies of the cancer genome are providing unprecedented insights into the molecular nature of human cancer. Using this information to guide the development and application of therapies in the clinic remains challenging. Here we report how cancer driving alterations detected in 11,215 tumors and 29 different tissues (integrating multiple omics) correlate with response to 265 compounds profiled in 1,001 cancer cell lines. We find that cell lines faithfully resemble tumours on the domain of these alterations, and numerous examples of altered genes and pathways conferring drug sensitivity and resistance. Significantly, logic-based modeling improves our ability to identify drug sensitive sub-types and machine-learning methods enable us to investigate the predictive ability of the different data-omics. We provide a comprehensive analysis of how somatic alterations identified from the large-scale analysis of primary tumors impact on drug response. This represents a rich resource to help identify therapeutic options for selected cancer populations.
 
Overall design DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacturer's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intensities of the images are extracted using GenomeStudio (2011.2) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value.
The cell lines are not treated with any drug or coumpound.
 
Contributor(s) Moran S, Heyn H, Esteller M
Citation(s) 27397505
Submission date Apr 28, 2015
Last update date Mar 22, 2019
Contact name Sebastian Moran
Organization name IDIBELL
Department PEBC
Street address Av. Gran Via de l'Hospitalet, 199-203
City L'Hospitalet del Llobregat
State/province Barcelona
ZIP/Postal code 08908
Country Spain
 
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (1028)
GSM1669562 CellLine_697
GSM1669563 CellLine_5637
GSM1669564 CellLine_201T
Relations
BioProject PRJNA282584

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE68379_Matrix.Signal.Intensities.txt.gz 7.7 Gb (ftp)(http) TXT
GSE68379_Matrix.processed.txt.gz 3.8 Gb (ftp)(http) TXT
GSE68379_RAW.tar 8.4 Gb (http)(custom) TAR (of IDAT)
Raw data is available on Series record
Processed data is available on Series record
Raw data provided as supplementary file

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