Molecular profiling of individual cancers is key to personalised medicine. While sequencing technologies have required stringent sample collection and handling, recent technical advances offer sequencing from tissues collected in routine practice and tissues already stored in archives.
In this paper, researchers from the Mount Sinai Hospital, Toronto establish methods for whole-transcriptome RNA sequencing (RNA-seq) from formalin-fixed paraffin-embedded tissues. They obtain average RNA-seq reads of >100 million per sample using the Illumina HiSeq2000 platform. They find high concordance with results from matching fresh frozen samples (>0.8 Spearman correlation). For validation, the researchers compared low- and high-grade bladder cancer transcriptomes in 49 tumour samples after transurethral resection of bladder tumour. They found 947 differentially expressed protein-coding genes. While high-grade lesions exhibited distinct intertumour transcriptome heterogeneity, the transcriptome of low-grade tumours was homogeneous.