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Eur Urol. 2014 Dec;66(6):982-6. doi: 10.1016/j.eururo.2014.07.045. Epub 2014 Sep 6.

Next-generation RNA sequencing of archival formalin-fixed paraffin-embedded urothelial bladder cancer.

Author information

1
The Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
2
Department of Surgery, Division of Urology, University of Toronto, Mount Sinai Hospital and University Health Network, Toronto, Ontario, Canada.
3
The Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
4
Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada.
5
Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada; Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
6
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.
7
Department of Pathology, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada.
8
The Academic Urology Unit and Academic Unit of Molecular Oncology, University of Sheffield, Sheffield, UK.
9
The Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. Electronic address: wrana@lunenfeld.ca.

Abstract

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.

KEYWORDS:

Formalin-fixed paraffin-embedded; Grade; Personalised medicine; Protein–protein interaction; RNA sequencing; Transcriptome; Urinary bladder neoplasms

PMID:
25199720
DOI:
10.1016/j.eururo.2014.07.045
[Indexed for MEDLINE]

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