UMCU colon cancer - Biopsies Of Surgical Specimens (BOSS)

Validation of the RT-qPCR test by comparison with the 4-gene microarray test and the original random forest-based CMS (consensus molecular subtypes) classifier For validation of the RT-qPCR test and assessment of intratumor heterogeneity, 20 colon cancer resection specimens were collected from routine surgery. Immediately after resection, five biopsy samples from randomly selected non-adjacent tumor areas were obtained with endoscopic biopsy forceps to simulate the clinical diagnostic setting. 29 samples from 7/20 specimens, representative of the encountered intra-tumoral variation in RT-qPCR-based predicted chances of CMS4 in the entire series, were selected for full Affymetrix gene expression profiling. This allowed direct comparison of the RT-qPCR test with the 4-gene microarray test and the original CMS classifier. Please note that [1] CMS classification for each sample was performed by combining various datasets, including the one uploaded here. If other datasets are combined, or if solely this dataset is analyzed, CMS classification could vary slightly, due to required post-processing steps. Therefore the classification information was not included as a sample characteristic. Users that wish to review the data can classify the samples as described in the CMS paper (Guinney et al. Nat Med 2015). [2] From each tumor multiple biopsies were obtained from different regions; BOSS+number represent specimen ID, the roman numeral represents the biopsy number