Jan 15, 2016

The prognostic potential of alternative transcript isoforms across human tumors

BioRxiv : the Preprint Server for Biology
Juan L. TrincadoEduardo Eyras

Abstract

Phenotypic changes during cancer progression are associated to alterations in gene expression, which can be exploited to build molecular signatures for tumor stage identification and prognosis. However, it is not yet known whether the relative abundance of transcript isoforms may be informative for clinical stage and survival. Using information theory and machine learning methods, we integrated RNA sequencing and clinical data from The Cancer Genome Atlas project to perform the first systematic analysis of the prognostic potential of transcript isoforms in 12 solid tumors to build new predictive signatures for stage and prognosis. This study was also performed in breast tumors according to estrogen receptor status and melanoma tumors with proliferative and invasive phenotypes. Transcript isoform signatures accurately separate early from late stage and metastatic from non-metastatic tumors, and are predictive of the survival of patients with undetermined lymph node invasion or metastatic status. These signatures show similar, and sometimes better, accuracies compared with known gene expression signatures, and are largely independent of gene expression changes. Furthermore, we show frequent transcript isoform changes in breast tu...Continue Reading

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Mentioned in this Paper

Study
Genome
Estrogen receptor alpha, human
Sequence Determinations, RNA
Neoplasms
Cancer Progression
Gene Expression
Lymph Node Tissue
Lymph Nodes
Melanoma vaccine

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