Discordant molecular subtype classification of muscle-invasive bladder cancer and matched lymph-node metastases occurs preferentially in the Basal/Squamous-like subtype.

By combining molecular pathology, mRNA profiling, and exome-sequencing we describe muscle-invasive bladder tumors and matched lymph-node metastases. Data from 307 FFPE embedded bladder cancers (availabe in GSE83586) and 28 lymph node metastasis were generated using the GeneChip Human Gene 1.0 ST Arrays (Affymetrix). Total RNA was extracted using the High Pure FFPET RNA isolation kit (Roche), assessed for quality using Nanodrop ND-1000, and labeled using SensationPlus FFPE Amplification and WT labeling kit. The full dataset of 335 CEL files were normalized using RMA by labeling batches. Batches were combined and RMA normalized. The data was filtered for probes with signal intensity less than the median of negative control probes for >80% of the values. Gene symbols and EntrezID were appended using Bioconductor (hugene10stprobeset.db Version 8.3.1). Probes not mapping to a gene symbol were removed. The probes were median merged by gene symbol and log-transformed. Batch correction was performed using ComBat. The 28 lymph node samples and the 28 matched tumors (available in GSE83586) were used in this cohort. These 56 samples were median centered and used for subtype classification and pair-wise t tests.