PT  - JOURNAL ARTICLE
AU  - Matthew H. Ung
AU  - Evelien Schaafsma
AU  - Daniel E. Mattox
AU  - George L. Wang
AU  - Chao Cheng
TI  - Pan-cancer systematic identification of lncRNAs associated with cancer prognosis
AID  - 10.1101/353334
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 353334
4099  - http://biorxiv.org/content/early/2018/06/21/353334.short
4100  - http://biorxiv.org/content/early/2018/06/21/353334.full
AB  - The “dark matter” of the genome harbors several non-coding RNA species including IncRNAs, which have been implicated in neoplasias but remain understudied. RNA-seq has provided deep insights into the nature of lncRNAs in cancer but current RNA-seq data are rarely accompanied by longitudinal patient survival information. In contrast, a plethora of microarray studies have collected these clinical metadata that can be leveraged to identify novel associations between gene expression and clinical phenotypes. In this study, we developed an analysis framework that computationally integrates RNA-seq and microarray data to systematically screen 9,463 lncRNAs for association with mortality risk across 20 cancer types. In total, we identified a comprehensive list of associations between lncRNAs and patient survival and demonstrate that these prognostic lncRNAs are under selective pressure and may be functional. Our results provide valuable insights that facilitate further exploration of lncRNAs and their potential as cancer biomarkers and drug targets.