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Overview of Fusion Detection Strategies Using Next-Generation Sequencing

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Tumor Profiling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1908))

Abstract

Structural gene fusion rearrangements leading to aberrant signaling are frequently detected in many cancer types. Gene fusions have significant prognostic and predictive value and are screened as part of molecular pathology testing for patient management. Many bioinformatic approaches have been developed to detect fusion mutations including whole-genome sequencing, targeted-based hybridization capture, and transcriptome-based approaches. Here we describe the most commonly used experimental methods to sequence and identify gene fusions using either DNA or RNA. We contrast experimental approaches both in the research and diagnostic setting and describe typical bioinformatic pipelines and software packages used to identify fusions.

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Authors and Affiliations

  1. Peter MacCallum Cancer Center, Melbourne, VIC, Australia

    Jan Schröder, Amit Kumar & Stephen Q. Wong

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  1. Jan Schröder
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  2. Amit Kumar
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  3. Stephen Q. Wong
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Corresponding author

Correspondence to Stephen Q. Wong .

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Editors and Affiliations

  1. Department of Pathology, University of California San Diego, La Jolla, CA, USA

    Sarah S. Murray

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Schröder, J., Kumar, A., Wong, S.Q. (2019). Overview of Fusion Detection Strategies Using Next-Generation Sequencing. In: Murray, S. (eds) Tumor Profiling. Methods in Molecular Biology, vol 1908. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9004-7_9

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  • DOI: https://doi.org/10.1007/978-1-4939-9004-7_9

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  • Publisher Name: Humana Press, New York, NY

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