A Panel-Based Method for the Reproduction of Distinct Molecular Subtype Classifications of Muscle-Invasive Urothelial Bladder Cancer

Abstract

Transcriptome-based molecular subtype classification of muscle-invasive urothelial bladder cancer was shown to have prognostic and therapy-predictive relevance and thus may help to inform therapeutic decision-making. However, current classification systems rely on whole transcriptome analysis, which is expensive, requires higher amounts of tissue samples, and therefore is not compatible with the daily clinical routine. Therefore, we developed a simple and robust gene panel-based classifier method to reproduce various relevant molecular classification systems (TCGA, MDA, GSC, LundTax, and Consensus). This approach was then tested on institutional cohorts of frozen and formalin-fixed and paraffin-embedded tissue samples using reverse transcription quantitative PCR and NanoString analyses. Here, we provide a step-by-step description of our panel-based subtype classifier method.

Keywords: Consensus classification; Gene expression analysis; LundTax classification; Molecular subtype classification; Rule set; Signature scores; TCGA.