Abstract：
UNLABELLED: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, we establish methods for whole-transcriptome RNA sequencing (RNA-seq) from formalin-fixed paraffin-embedded tissues. We obtain average RNA-seq reads of >100 million per sample using the Illumina HiSeq2000 platform. We find high concordance with results from matching fresh frozen samples (>0.8 Spearman correlation). For validation, we compared low- and high-grade bladder cancer transcriptomes in 49 tumour samples after transurethral resection of bladder tumour. We found 947 differentially expressed protein-coding genes. While high-grade lesions exhibited distinct intertumour transcriptome heterogeneity, the transcriptome of low-grade tumours was homogeneous. PATIENT SUMMARY:In this report, we show that it is now possible to use universally available bladder cancer samples that have been fixed in formalin to perform high-quality transcriptome analysis. This ability will facilitate the development of transcriptome-wide tests based on gene expression correlated with clinical outcome.
journal_name
Eur Uroljournal_title
European urologyauthors
Liu Y,Noon AP,Aguiar Cabeza E,Shen J,Kuk C,Ilczynski C,Ni R,Sukhu B,Chan K,Barbosa-Morais NL,Hermanns T,Blencowe BJ,Azad A,van der Kwast TH,Catto JW,Zlotta AR,Wrana JLdoi
10.1016/j.eururo.2014.07.045subject
Has Abstractpub_date
2014-12-01 00:00:00pages
982-6issue
6eissn
0302-2838issn
1873-7560pii
S0302-2838(14)00735-0journal_volume
66pub_type
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