title: Prioritisation of structural variant calls in cancer genomes.
abstract: Sensitivity of short read DNA-sequencing for gene fusion detection is improving, but is hampered by the significant amount of noise composed of uninteresting or false positive hits in the data. In this paper we describe a tiered prioritisation approach to extract high impact gene fusion events from existing structural variant calls. Using cell line and patient DNA sequence data we improve the annotation and interpretation of structural variant calls to best highlight likely cancer driving fusions. We also considerably improve on the automated visualisation of the high impact structural variants to highlight the effects of the variants on the resulting transcripts. The resulting framework greatly improves on readily detecting clinically actionable structural variants.
authors.affiliation: Innovative Medicines and Early Development, Oncology, AstraZeneca , Cambridge , United Kingdom.
authors.forename: Miika J
authors.initials: MJ
authors.lastname: Ahdesmäki
authors.affiliation: Harvard T.H. Chan School of Public Health, Harvard University , Boston , MA , United States.
authors.forename: Brad A
authors.initials: BA
authors.lastname: Chapman
authors.affiliation: Kew Inc. , Cambridge , MA , United States.
authors.forename: Pablo
authors.initials: P
authors.lastname: Cingolani
authors.affiliation: Centre for Cancer Research, University of Melbourne , Melbourne , Australia.
authors.forename: Oliver
authors.initials: O
authors.lastname: Hofmann
authors.affiliation: EPAM Systems Inc., Newtown, PA, United States; Department of software engineering, St. Petersburg State University, St. Petersburg, Russia.
authors.forename: Aleksandr
authors.initials: A
authors.lastname: Sidoruk
authors.affiliation: Innovative Medicines and Early Development, Oncology, AstraZeneca , Waltham , MA , United States.
authors.forename: Zhongwu
authors.initials: Z
authors.lastname: Lai
authors.affiliation: EPAM Systems Inc., Newtown, PA, United States; Pavlov Institute of Physiology, Russian Academy of Sciences, St. Petersburg, Russia.
authors.forename: Gennadii
authors.initials: G
authors.lastname: Zakharov
authors.affiliation: EPAM Systems Inc. , Newtown , PA , United States.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Rodichenko
authors.affiliation: EPAM Systems Inc. , Newtown , PA , United States.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Alperovich
authors.affiliation: Boston University , Boston , MA , United States.
authors.forename: David
authors.initials: D
authors.lastname: Jenkins
authors.affiliation: Innovative Medicines and Early Development, Oncology, AstraZeneca , Cambridge , United Kingdom.
authors.forename: T Hedley
authors.initials: TH
authors.lastname: Carr
authors.affiliation: Innovative Medicines and Early Development, Oncology, AstraZeneca , Waltham , MA , United States.
authors.forename: Daniel
authors.initials: D
authors.lastname: Stetson
authors.affiliation: Innovative Medicines and Early Development, Oncology, AstraZeneca , Waltham , MA , United States.
authors.forename: Brian
authors.initials: B
authors.lastname: Dougherty
authors.affiliation: Innovative Medicines and Early Development, Oncology, AstraZeneca , Waltham , MA , United States.
authors.forename: J Carl
authors.initials: JC
authors.lastname: Barrett
authors.affiliation: Innovative Medicines and Early Development, Oncology, AstraZeneca , Waltham , MA , United States.
authors.forename: Justin H
authors.initials: JH
authors.lastname: Johnson
keywords: Annotation; Gene fusion; Oncology; Prioritisation; Structural variation; Visualisation