Computational protocol: Diagnostic and prognostic value of long noncoding RNAs as biomarkers in urothelial carcinoma

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Protocol publication

[…] The set of tissue samples (set 1) used for quantitative real time RT-PCR analysis (RT-qPCR) consisted of 106 tumour tissues and 10 benign tissues. The majority of the patients was diagnosed with muscle-invasive and high-grade bladder cancer (13 pTa, 13 pT1, 15 pT2, 44 pT3, 19 pT4; 39 low-grade, 67 high-grade). This tissue set was collected according to the principles expressed in the Declaration of Helsinki and with written patient informed consent as approved by the ethics committee of the medical faculty of the University Duisburg-Essen, Study Number 07–3537. A further amendment was approved by the committee allowing the extensive characterization of such tissues including the analysis of tissue-RNA by RT-PCR. Median follow up time for the complete cohort was 22.7 months (range 0.2–198).Sample preparation and expression analyses were performed and described in accordance with the MIQE guidelines (minimum information for publication of quantitative real time PCR experiments) as detailed in the supplementary methods section () and supplementary – Tables.Expression data provided for lncRNAs by the TANRIC database is based on the TCGA bladder urothelial carcinoma (BLCA) dataset (set 2) consisting of 252 tumour tissue samples and 19 benign tissue samples, which were with only few exceptions obtained from muscle-invasive tumours (one pT1, 72 pT2, 118 pT3, 38 pT4, 23 without information about staging). Median follow-up time for this cohort was 15.9 months (0.49–163).Analyses of molecular subtype gene expression signatures were performed by means of the cBioPortal tool based on the provisional TCGA bladder urothelial carcinoma set (“extended” data set: 413 tumors in total; 408 tumor samples with RNA Sequencing mRNA expression (3 pTa, 121 pT2, 195 pT3 and 59 pT4) and Genesis 1.0 software. [...] The TANRIC database provides easy access to publicly available RNA-Seq data for various tumour entities, especially for lncRNA expression. In the TANRIC database lncRNA expression was analyzed for the TCGA bladder urothelial carcinoma (BLCA) dataset and queried in the “My lnRNA”-tool by either lncRNA annotation or, for linc-UBC1 [chr1:205404014–205425214] and [chr17:74553846–74561430] for ncRAN, in hg19 genomic coordinates. LncRNA expression values were obtained as log2 RPMK (reads per kilo base per million mapped reads) from the TANRIC database as indicated in the “My lncRNA”-tool and median expression was calculated for benign and tumour samples and visualized in boxplots using R. Additional boxplots and Kaplan-Meier curves for each lncRNA were obtained from the database tool.The cBioPortal database tools (Oncoprint, download of mRNA Expression z-Scores (RNA Seq V2 RSEM)) were employed to explore correlations between expression of lncRNA and marker genes defining molecular subtypes of UC. […]

Pipeline specifications

Software tools TANRIC, cBioPortal, RSEM
Databases TCGA Data Portal
Application RNA-seq analysis
Organisms Homo sapiens
Diseases Carcinoma, Neoplasms