PT  - JOURNAL ARTICLE
AU  - Pieter-Jan Volders
AU  - Jo Vandesompele
AU  - Steve Lefever
AU  - Shalina Baute
AU  - Justine Nuytens
AU  - Katrien Vanderheyden
AU  - Björn Menten
AU  - Pieter Mestdagh
TI  - Targeted genomic screen reveals focal long non-coding RNA copy number alterations in cancer
AID  - 10.1101/113316
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 113316
4099  - http://biorxiv.org/content/early/2017/03/03/113316.short
4100  - http://biorxiv.org/content/early/2017/03/03/113316.full
AB  - The landscape of somatic copy-number alterations (SCNAs) affecting long non-coding RNAs (lncRNAs) in human cancer remains largely unexplored. While the majority of lncRNAs remains to be functionally characterized, several have been implicated in cancer development and metastasis. Considering the plethora of lncRNAs genes that is currently reported, it is conceivable that several lncRNAs might function as oncogenes or tumor suppressor genes.We devised a strategy to detect focal lncRNA SCNAs using a custom DNA microarray platform probing 20 418 lncRNA genes. By screening a panel of 80 cancer cell lines, we detected numerous focal aberrations targeting one or multiple lncRNAs without affecting neighboring protein-coding genes. These focal aberrations are highly suggestive for a tumor suppressive or oncogenic role of the targeted lncRNA gene. Although functional validation remains an essential step in the further characterization of the involved candidate cancer lncRNAs, our results provide a direct way of prioritizing candidate lncRNAs involved in cancer pathogenesis.