Overview of fusion detection strategies using next-generation sequencing

Jan Schröder, Amit Kumar, Stephen Q. Wong

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Otherpeer-review

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.

Original languageEnglish
Title of host publicationTumor Profiling
Subtitle of host publicationMethods and Protocols
EditorsSarah S. Murray
Place of PublicationNew York, NY
PublisherHumana Press
Chapter9
Pages125-138
Number of pages14
ISBN (Electronic)9781493990047
ISBN (Print)9781493990023
DOIs
Publication statusPublished - 2019
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume1908
ISSN (Print)1064-3745

Keywords

  • Chimeric transcripts
  • Chromosome rearrangement
  • Fusion detection
  • Gene fusions
  • RNA-seq
  • Structural chromosome abnormalities
  • Whole-genome sequencing

Cite this

Schröder, J., Kumar, A., & Wong, S. Q. (2019). Overview of fusion detection strategies using next-generation sequencing. In S. S. Murray (Ed.), Tumor Profiling: Methods and Protocols (pp. 125-138). (Methods in Molecular Biology; Vol. 1908). New York, NY: Humana Press. https://doi.org/10.1007/978-1-4939-9004-7_9
Schröder, Jan ; Kumar, Amit ; Wong, Stephen Q. / Overview of fusion detection strategies using next-generation sequencing. Tumor Profiling: Methods and Protocols. editor / Sarah S. Murray. New York, NY : Humana Press, 2019. pp. 125-138 (Methods in Molecular Biology).
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Schröder, J, Kumar, A & Wong, SQ 2019, Overview of fusion detection strategies using next-generation sequencing. in SS Murray (ed.), Tumor Profiling: Methods and Protocols. Methods in Molecular Biology, vol. 1908, Humana Press, New York, NY, pp. 125-138. https://doi.org/10.1007/978-1-4939-9004-7_9

Overview of fusion detection strategies using next-generation sequencing. / Schröder, Jan; Kumar, Amit; Wong, Stephen Q.

Tumor Profiling: Methods and Protocols. ed. / Sarah S. Murray. New York, NY : Humana Press, 2019. p. 125-138 (Methods in Molecular Biology; Vol. 1908).

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Otherpeer-review

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Schröder J, Kumar A, Wong SQ. Overview of fusion detection strategies using next-generation sequencing. In Murray SS, editor, Tumor Profiling: Methods and Protocols. New York, NY: Humana Press. 2019. p. 125-138. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-9004-7_9