Oncogenic gene fusions in primary colon cancers

This study represents RNA-sequencing data from 278 primary colon cancers obtained from fresh-frozen tumor sections. The project goal was to identify novel oncogenic gene fusions in these data. In addition, we studied the detected gene fusions at the molecular level and defined their effects on downstream pathways.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 4 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001003291	This dataset represents RNA-sequencing data from 278 primary colon cancers obtained from fresh-frozen tumor sections. RNA-sequencing was performed using TruSeq library preparation and samples were sequenced on Illumina NextSeq and HiSeq. The data are available as Illumina NextSeq and HiSeq fastq files (_R1.fastq and _R2.fastq for each tumor sample, 556 files in total).	Illumina HiSeq 2500 NextSeq 500	278

Publications	Citations
Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons. Smid M, Coebergh van den Braak RRJ, van de Werken HJG, van Riet J, van Galen A, de Weerd V, van der Vlugt-Daane M, Bril SI, Lalmahomed ZS, Kloosterman WP, Wilting SM, Foekens JA, IJzermans JNM, MATCH study group, Martens JWM, Sieuwerts AM. BMC Bioinformatics 19: 2018 236	83
Interconnectivity between molecular subtypes and tumor stage in colorectal cancer. Coebergh van den Braak RRJ, Ten Hoorn S, Sieuwerts AM, Tuynman JB, Smid M, Wilting SM, Martens JWM, Punt CJA, Foekens JA, Medema JP, IJzermans JNM, Vermeulen L. BMC Cancer 20: 2020 850	17
A panel of DNA methylation markers for the classification of consensus molecular subtypes 2 and 3 in patients with colorectal cancer. van den Berg I, Smid M, Coebergh van den Braak RRJ, van de Wiel MA, van Deurzen CHM, de Weerd V, Martens JWM, IJzermans JNM, Wilting SM. Mol Oncol 15: 2021 3348-3362	5
Molecular characterization of colorectal cancer related peritoneal metastatic disease. Lenos KJ, Bach S, Ferreira Moreno L, Ten Hoorn S, Sluiter NR, Bootsma S, Vieira Braga FA, Nijman LE, van den Bosch T, Miedema DM, van Dijk E, Ylstra B, Kulicke R, Davis FP, Stransky N, Smolen GA, Coebergh van den Braak RRJ, IJzermans JNM, Martens JWM, Hallam S, Beggs AD, Kops GJPL, Lansu N, Bastiaenen VP, Klaver CEL, Lecca MC, El Makrini K, Elbers CC, Dings MPG, van Noesel CJM, Kranenburg O, Medema JP, Koster J, Koens L, Punt CJA, Tanis PJ, de Hingh IH, Bijlsma MF, Tuynman JB, Vermeulen L. Nat Commun 13: 2022 4443	38