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

Linda S Powers; Jason L Weirather; Joseph Zabner; Pegah Tootoonchi Afshar; Tyson A Clark; Elizabeth Tseng; Jason G Underwood; Jonas Korlach; Wing Hung Wong; Kin Fai Au

doi:10.1093/nar/gkv562

Back

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

Journal article

Open access

Peer reviewed

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

Linda S Powers, Jason L Weirather, Joseph Zabner, Pegah Tootoonchi Afshar, Tyson A Clark, Elizabeth Tseng, Jason G Underwood, Jonas Korlach, Wing Hung Wong and Kin Fai Au

Nucleic acids research, Vol.43(18), pp.e116-e116

10/15/2015

DOI: 10.1093/nar/gkv562

PMCID: PMC4605286

PMID: 26040699

Files and links (1)

url

https://doi.org/10.1093/nar/gkv562View

Published (Version of record) Open Access

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.

Sequence Alignment

Breast Neoplasms - genetics

Protein Isoforms - metabolism

MCF-7 Cells

Humans

Carcinogenesis - genetics

Female

Gene Fusion

Gene Expression Profiling

High-Throughput Nucleotide Sequencing - methods

Breast Neoplasms - metabolism

Protein Isoforms - genetics

Details

Title: Subtitle: Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing
Creators: Linda S Powers - Department of Internal Medicine, University of Iowa, 200 Hawkins Dr, Iowa City, IA 52242, USA
Jason L Weirather - Department of Internal Medicine, University of Iowa, 200 Hawkins Dr, Iowa City, IA 52242, USA
Joseph Zabner - Department of Internal Medicine, University of Iowa, 200 Hawkins Dr, Iowa City, IA 52242, USA
Pegah Tootoonchi Afshar - Department of Electrical Engineering, School of Engineering, Stanford University, Stanford, CA 94305, USA
Tyson A Clark - Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
Elizabeth Tseng - Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
Jason G Underwood - Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle WA 98195-5065, USA
Jonas Korlach - Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
Wing Hung Wong - Department of Statistics and Department of Health Research & Policy, 390 Serra Mall, Stanford University, Stanford, CA 94305, USA
Kin Fai Au - Department of Internal Medicine, University of Iowa, 200 Hawkins Dr, Iowa City, IA 52242, USA kinfai-au@uiowa.edu
Resource Type: Journal article
Publication Details: Nucleic acids research, Vol.43(18), pp.e116-e116
DOI: 10.1093/nar/gkv562
PMID: 26040699
PMCID: PMC4605286
NLM abbreviation: Nucleic Acids Res
ISSN: 0305-1048
eISSN: 1362-4962
Grant note: R01HG007834 / NHGRI NIH HHS R01 GM109836 / NIGMS NIH HHS R01 HG007834 / NHGRI NIH HHS R01GM109836 / NIGMS NIH HHS
Language: English
Date published: 10/15/2015
Academic Unit: Pulmonary, Critical Care, and Occupational Medicine; Internal Medicine
Record Identifier: 9984094539702771

Metrics

17 Record Views

84 Times Cited - Web of Science