|
| 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)
|
|
| Relations |
| BioProject |
PRJNA282584 |
Less...
More...