E-GEOD-52513 - Gene signature predictive of response to chemotherapy in mCRC [RT-PCR]

Status
Released on 20 November 2013, last updated on 11 June 2014
Organism
Homo sapiens
Samples (119)
Array (1)
Protocols (5)
Description
The objective is to generate a robust and validated predictor profile for chemotherapy response in patients with mCRC using microarray gene expression profiles of primary colorectal cancer tissue. To define a gene signature of response to chemotherapy in metastatic colorectal cancer, samples were obtained from 40 patients from Marques de Valdecilla Hospital who underwent primary surgery. Gene expression was detected and quantified using the Human Whole Genome U133 Plus 2.0 array (Affymetrix), containing 54675 human gene probes. The validation set consisted of 119 samples from Hospital Virgen del Rocio, Seville, Spain; Hospital Virgen de la Victoria, Malaga, Spain; Hospital de la Merced, Osuna, Spain and Hospital Marqués de Valdecilla, Santander, Spain, and included 86 tumor samples (40 coming from the training set and 46 from newly treated CRC patients) and 33 normal tissue samples of CRC patients used as controls. Custom-designed TaqMan® Low Density Arrays (TLDA) 7900 HT Micro Fluidic Cards including the 161 genes selected for validation were run and analyzed by the ABI PRISM® 7900HT Sequence Detection System (SDS 2.2, Applied Biosystems) according to manufacturer's protocol (Applied Biosystems). Expression of target miRNAs was normalized in relation to the expression of GAPDH. Cycle threshold (Ct) values were calculated using the SDS software v.4.2 using automatic baseline settings and a threshold of 0.2. Relative quantification of gene expression was calculated by the 2−ΔCt method (Applied Biosystems user bulletin no. 2 (P/N 4303859)). This submission represents the RT-PCR component of the study only
Experiment type
transcription profiling by RT-PCR 
Contacts
Amancio Carnero, Fernando Rivero, Javier Gomez, Luis Paz-Ares, Maria D Pastor, Marta Benavent-Viñuales, Purificacion Estevez-Garcia, Rocio Garcia-Carbonero, Sonia Molina-Pinelo
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-52513.idf.txt
Sample and data relationshipE-GEOD-52513.sdrf.txt
Raw data (1)E-GEOD-52513.raw.1.zip
Processed data (1)E-GEOD-52513.processed.1.zip
Array designA-GEOD-17954.adf.txt
Links