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Noncoding RNA. 2018 Sep 13;4(3). pii: E21. doi: 10.3390/ncrna4030021.

Targeted Genomic Screen Reveals Focal Long Non-Coding RNA Copy Number Alterations in Cancer Cell Lines.

Author information

1
Center for Medical Genetics (CMGG), Ghent University, 9000 Ghent, Belgium. pieterjan.volders@ugent.be.
2
Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium. pieterjan.volders@ugent.be.
3
Bioinformatics Institute Ghent N2N (BIG N2N), 9000 Ghent, Belgium. pieterjan.volders@ugent.be.
4
Center for Medical Genetics (CMGG), Ghent University, 9000 Ghent, Belgium. Steve.Lefever@UGent.be.
5
Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium. Steve.Lefever@UGent.be.
6
Bioinformatics Institute Ghent N2N (BIG N2N), 9000 Ghent, Belgium. Steve.Lefever@UGent.be.
7
Center for Medical Genetics (CMGG), Ghent University, 9000 Ghent, Belgium. shalina.baute@ugent.be.
8
Center for Medical Genetics (CMGG), Ghent University, 9000 Ghent, Belgium. Justine.Nuytens@UGent.be.
9
Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium. Justine.Nuytens@UGent.be.
10
Center for Medical Genetics (CMGG), Ghent University, 9000 Ghent, Belgium. Katrien.Vanderheyden@UGent.be.
11
Center for Medical Genetics (CMGG), Ghent University, 9000 Ghent, Belgium. Bjorn.Menten@UGent.be.
12
Bioinformatics Institute Ghent N2N (BIG N2N), 9000 Ghent, Belgium. Bjorn.Menten@UGent.be.
13
Center for Medical Genetics (CMGG), Ghent University, 9000 Ghent, Belgium. Pieter.Mestdagh@UGent.be.
14
Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium. Pieter.Mestdagh@UGent.be.
15
Bioinformatics Institute Ghent N2N (BIG N2N), 9000 Ghent, Belgium. Pieter.Mestdagh@UGent.be.
16
Center for Medical Genetics (CMGG), Ghent University, 9000 Ghent, Belgium. Jo.Vandesompele@UGent.be.
17
Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium. Jo.Vandesompele@UGent.be.
18
Bioinformatics Institute Ghent N2N (BIG N2N), 9000 Ghent, Belgium. Jo.Vandesompele@UGent.be.

Abstract

The landscape of somatic copy-number alterations (SCNAs) affecting long non-coding RNAs (lncRNAs) in human cancers remains largely unexplored. While the majority of lncRNAs remain to be functionally characterized, several have been implicated in cancer development and metastasis. Considering the plethora of lncRNAs genes that have been currently reported, it is conceivable that many more 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 10,519 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 that are involved in cancer pathogenesis.

KEYWORDS:

array CGH; lncRNA; long non-coding RNA; somatic copy-number alterations

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