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Authors: F. Abate 1 ; G. Paciello 1 ; A. Acquaviva 1 ; E. Ficarra 1 ; A. Ferrarini 2 ; M. Delledonne 2 and E. Macii 1

Affiliations: 1 Politecnico di Torino, Italy ; 2 Università di Verona, Italy

ISBN: 978-989-8425-90-4

Keyword(s): Next generation sequencing, RNA-Seq data, Chimeric transcript detection, Gene fusions, Alternative splicing, Deep sequencing analysis, Paired-end reads.

Related Ontology Subjects/Areas/Topics: Bioinformatics ; Biomedical Engineering ; Next Generation Sequencing ; Sequence Analysis

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 several formats:
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

@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},
}

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

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