Prioritisation of Structural Variant Calls in Cancer Genomes

Overview

Journal PeerJ

Specialties Biology
Environmental Health
General Medicine

Date 2017 Apr 11

PMID 28392986

Citations 9

Authors

Miika J Ahdesmaki

Brad A Chapman

Pablo Cingolani

Oliver Hofmann

Aleksandr Sidoruk

Zhongwu Lai

Gennadii Zakharov

Mikhail Rodichenko

Mikhail Alperovich

David Jenkins

T Hedley Carr

Daniel Stetson

Brian Dougherty

J Carl Barrett

Justin H Johnson

Affiliations

Soon will be listed here.

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.

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