A NOVEL ANALYSIS FLOW FOR FUSED TRANSCRIPTS DISCOVERY FROM PAIRED-END RNA-SEQ DATA

F. Abate, G. Paciello, A. Acquaviva, E. Ficarra, A. Ferrarini, M. Delledonne, E. Macii

Abstract

Chimeric phenomena have been recently recognized to play a significant role in the investigation and understanding of the fundamental mechanisms behind highly diffused pathologies such as tumors. In this paper we present a new methodology for the detection of fusion transcript from Next Generation Sequencing (NGS) data. The methodology exploits short paired-end reads coming from RNA-Seq experiments to determine a list of fused genes and to exactly identify the fusion boundaries, so that the exact chimeric sequence can be analysed. Both known and unknown transcripts are considered, enabling the detection of fusions involving unannotated genes. An automated toolflow that reports a set of candidate fused genes and the associated junctions has been implemented and applied to a publicly available data set of melanoma.

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Paper Citation


in Harvard Style

Abate F., Paciello G., Acquaviva A., Ficarra E., Ferrarini A., Delledonne M. and Macii E. (2012). A NOVEL ANALYSIS FLOW FOR FUSED TRANSCRIPTS DISCOVERY FROM PAIRED-END RNA-SEQ DATA . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012) ISBN 978-989-8425-90-4, pages 331-334. DOI: 10.5220/0003789003310334


in Bibtex Style

@conference{bioinformatics12,
author={F. Abate and G. Paciello and A. Acquaviva and E. Ficarra and A. Ferrarini and M. Delledonne and E. Macii},
title={A NOVEL ANALYSIS FLOW FOR FUSED TRANSCRIPTS DISCOVERY FROM PAIRED-END RNA-SEQ DATA},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)},
year={2012},
pages={331-334},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003789003310334},
isbn={978-989-8425-90-4},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)
TI - A NOVEL ANALYSIS FLOW FOR FUSED TRANSCRIPTS DISCOVERY FROM PAIRED-END RNA-SEQ DATA
SN - 978-989-8425-90-4
AU - Abate F.
AU - Paciello G.
AU - Acquaviva A.
AU - Ficarra E.
AU - Ferrarini A.
AU - Delledonne M.
AU - Macii E.
PY - 2012
SP - 331
EP - 334
DO - 10.5220/0003789003310334