title: Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing.
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.
authors.affiliation: Department of Internal Medicine, University of Iowa, 200 Hawkins Dr, Iowa City, IA 52242, USA.
authors.forename: Jason L
authors.initials: JL
authors.lastname: Weirather
authors.affiliation: Department of Electrical Engineering, School of Engineering, Stanford University, Stanford, CA 94305, USA.
authors.forename: Pegah Tootoonchi
authors.initials: PT
authors.lastname: Afshar
authors.affiliation: Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA.
authors.forename: Tyson A
authors.initials: TA
authors.lastname: Clark
authors.affiliation: Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Tseng
authors.affiliation: Department of Internal Medicine, University of Iowa, 200 Hawkins Dr, Iowa City, IA 52242, USA.
authors.forename: Linda S
authors.initials: LS
authors.lastname: Powers
authors.affiliation: Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle WA 98195-5065, USA.
authors.forename: Jason G
authors.initials: JG
authors.lastname: Underwood
authors.affiliation: Department of Internal Medicine, University of Iowa, 200 Hawkins Dr, Iowa City, IA 52242, USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Zabner
authors.affiliation: Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA.
authors.forename: Jonas
authors.initials: J
authors.lastname: Korlach
authors.affiliation: Department of Statistics and Department of Health Research & Policy, 390 Serra Mall, Stanford University, Stanford, CA 94305, USA.
authors.forename: Wing Hung
authors.initials: WH
authors.lastname: Wong
authors.affiliation: Department of Internal Medicine, University of Iowa, 200 Hawkins Dr, Iowa City, IA 52242, USA kinfai-au@uiowa.edu.
authors.forename: Kin Fai
authors.initials: KF
authors.lastname: Au
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism; D063646:Carcinogenesis / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling; D050939:Gene Fusion; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D061986:MCF-7 Cells; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D020033:Protein Isoforms