Introduction
Despite growing appreciation of the importance of long noncoding RNAs (lncRNAs) in normal physiology and disease, our knowledge of cancer-related lncRNAs remains limited. By repurposing microarray probes, we constructed expression profiles of 10,207 lncRNA genes in approximately 1,300 tumors over four different cancer types. Through integrative analysis of the lncRNA expression profiles with clinical outcome and somatic copy-number alterations, we identified lncRNAs that are associated with cancer subtypes and clinical prognosis and predicted those that are potential drivers of cancer progression. We validated our predictions by experimentally confirming prostate cancer cell growth dependence on two newly identified lncRNAs. Our analysis provides a resource of clinically relevant lncRNAs for the development of lncRNA biomarkers and the identification of lncRNA therapeutic targets. It also demonstrates the power of integrating publically available genomic data sets and clinical information for discovering disease-associated lncRNAs.
How to cite our work
Zhou Du, Teng Fei, Roel G W Verhaak, Zhen Su, Yong Zhang, Myles Brown*, Yiwen Chen* & X Shirley Liu*. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nature Structural & Molecular Biology. [Full Paper]
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*The exon array probe ID was generated based on annotation in probe sequence file. For example, for the probe in sequence file
>probe:HG_U95Av2:1138_at:395:301; Interrogation_Position=2631; Antisense;
I generated a ID "395_301" using a segment of this line (395:301).
