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Nucleic Acids Res. 2015 Oct 15;43(18):e116. doi: 10.1093/nar/gkv562. Epub 2015 Jun 3.

Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing.

Author information

1
Department of Internal Medicine, University of Iowa, 200 Hawkins Dr, Iowa City, IA 52242, USA.
2
Department of Electrical Engineering, School of Engineering, Stanford University, Stanford, CA 94305, USA.
3
Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA.
4
Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle WA 98195-5065, USA.
5
Department of Statistics and Department of Health Research & Policy, 390 Serra Mall, Stanford University, Stanford, CA 94305, USA.
6
Department of Internal Medicine, University of Iowa, 200 Hawkins Dr, Iowa City, IA 52242, USA kinfai-au@uiowa.edu.

Abstract

We developed an innovative hybrid sequencing approach, IDP-fusion, to detect fusion genes, determine fusion sites and identify and quantify fusion isoforms. IDP-fusion is the first method to study gene fusion events by integrating Third Generation Sequencing long reads and Second Generation Sequencing short reads. We applied IDP-fusion to PacBio data and Illumina data from the MCF-7 breast cancer cells. Compared with the existing tools, IDP-fusion detects fusion genes at higher precision and a very low false positive rate. The results show that IDP-fusion will be useful for unraveling the complexity of multiple fusion splices and fusion isoforms within tumorigenesis-relevant fusion genes.

PMID:
26040699
PMCID:
PMC4605286
DOI:
10.1093/nar/gkv562
[Indexed for MEDLINE]
Free PMC Article

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