IBCN 2018: MIBC Genomics in and Beyond TCGA and the PanCancerAtlas
Two goals were to integrate into clinical practice and also stimulate the research community into global integration of research initiatives. Dr. Gordon described how TCGA MIBC project came to fruition and the 2017 publication from the perspective of the BC Cancer Agency’s Genome Sciences Centre, where he generated miRNA-seq data for over 11 thousand tumour and tissue normal samples across 33 cancer types. He was responsible for integrated marker papers for each project limited to 3000 words with 5+ platforms focused on genome and expression features.
Specifically for the MIBC project, he screened RNA and DNA sequence data for bacteria, fungi and viruses, and used de novo transcriptome assembly to assess viral genomic integration. Because lncRNAs can be specific to biological state, he used lncRNA expression profiles calculated from mRNA-seq data for subtyping analysis. Furthermore, he calculated regulon activity profiles for a subset of 23 bladder cancer-associated regulators, and used this RNA-based functional readout to characterize differences between subtypes. A multivariate survival analysis integrated diverse clinical and molecular covariates including FGFR3 mutations, luminal and basal and neuronal subtypes.
Finally, from his ongoing work on bladder cancer genomics, he discussed results generated in TCGA PanCancerAtlas projects, and results from extended regulon analyses.
In summary, Dr. Gordon and the team’s efforts have helped propel our understanding RNA differences in MIBC via TCGA but importantly has stimulated collaborations via experts in each field to enable future projects.
Presented by: Gordon Robertson, Canada’s Michael Smith Genome Sciences Centre British Columbia Cancer Agency, Vancouver, Canada.
Written by: Stephen B. Williams, M.D., Associate Professor, Division of Urology, The University of Texas Medical Branch, Galveston, TX. and Ashish M. Kamat, M.D. Professor, Department of Urology, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX at the 16th Annual Meeting of the International Bladder Cancer Network (IBCN) October 11-13, 2018 - the Inntel Hotels Rotterdam Centre, Rotterdam, The Netherlands