UROMOL 2020 - RNA-seq data

The molecular landscape in non-muscle-invasive bladder cancer (NMIBC) is characterized by large biological heterogeneity with variable clinical outcomes. Here, we performed a large integrative multi-omics analysis of patients diagnosed with NMIBC (n=834). Transcriptomic analysis identifies four classes (1, 2a, 2b and 3) reflecting tumor biology and disease aggressiveness. Both transcriptome-based subtyping and the level of chromosomal instability provide independent prognostic value beyond established prognostic clinicopathological parameters.

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

1 Dataset 3 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
EGAD00001006656	For this project about non-muscle invasive bladder cancer (NMIBC), we analysed total RNA-seq data from 535 patients. Sequencing of total RNA was performed using ScriptSeq-v2 RNA-Seq Library Preparation Kit (Illumina) and KAPA RNA HyperPrep Kit with RiboErase HMR (Roche). RNA input was 500 ng for both kits. The dataset is composed of 1,596 fastq files.	Illumina HiSeq 2000 Illumina MiSeq Illumina NovaSeq 6000 NextSeq 550	535

Publications	Citations
An integrated multi-omics analysis identifies prognostic molecular subtypes of non-muscle-invasive bladder cancer. Lindskrog SV, Prip F, Lamy P, Taber A, Groeneveld CS, Birkenkamp-Demtröder K, Jensen JB, Strandgaard T, Nordentoft I, Christensen E, Sokac M, Birkbak NJ, Maretty L, Hermann GG, Petersen AC, Weyerer V, Grimm MO, Horstmann M, Sjödahl G, Höglund M, Steiniche T, Mogensen K, de Reyniès A, Nawroth R, Jordan B, Lin X, Dragicevic D, Ward DG, Goel A, Hurst CD, Raman JD, Warrick JI, Segersten U, Sikic D, van Kessel KEM, Maurer T, Meeks JJ, DeGraff DJ, Bryan RT, Knowles MA, Simic T, Hartmann A, Zwarthoff EC, Malmström PU, Malats N, Real FX, Dyrskjøt L. Nat Commun 12: 2021 2301	91
A transcriptional network of cell cycle dysregulation in noninvasive papillary urothelial carcinoma. Warrick JI, Knowles MA, Hurst CD, Shuman L, Raman JD, Walter V, Putt J, Dyrskjøt L, Groeneveld C, Castro MAA, Robertson AG, DeGraff DJ. Sci Rep 12: 2022 16538	2
Spatial transformation of multi-omics data unlocks novel insights into cancer biology. Sokač M, Kjær A, Dyrskjøt L, Haibe-Kains B, Jwl Aerts H, Birkbak NJ. Elife 12: 2023 RP87133	1