Identification of Cancer Genes Based on De Novo Transposon Insertion Site Analysis Using RNA and DNA Sequencing

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Forward genetic insertional mutagenesis screens are used by many labs to identify candidate cancer genes. We and others have used the Sleeping Beauty DNA transposon to generate random mutations within the murine genome that cause cancer. Identification of the insertion sites, either via RNA sequencing or DNA sequencing, is required for cancer gene discovery. Multiple sequencing-based approaches have been utilized to identify locations of transposon insertions within a genome including linker-mediated PCR, RNA-Seq, and Seq capture. Here, a bioinformatics pipeline is presented applicable to both the identification of transposon-generated fusions in RNA-Seq data and the direct identification of transposon insertion sites in DNA sequencing data. We are currently utilizing this method to identify transposon insertions generated by Sleeping Beauty transposase-mediated mobilization of the T2/Onc transposon within the murine genome. With slight modification, this approach is amenable to the identification of any mobile genetic element within any genome.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages73-79
Number of pages7
DOIs
StatePublished - Jan 1 2019

Publication series

NameMethods in Molecular Biology
Volume1907
ISSN (Print)1064-3745

Fingerprint

RNA Sequence Analysis
Neoplasm Genes
DNA Sequence Analysis
Genome
Beauty
RNA
Interspersed Repetitive Sequences
Transposases
DNA Transposable Elements
Insertional Mutagenesis
Genetic Association Studies
Computational Biology
Polymerase Chain Reaction
Mutation
Neoplasms

Keywords

  • Fusion
  • Insertion site
  • RNA-Seq
  • Seq-capture
  • Sequencing
  • Transposon

Cite this

Sarver, A. L. (2019). Identification of Cancer Genes Based on De Novo Transposon Insertion Site Analysis Using RNA and DNA Sequencing. In Methods in Molecular Biology (pp. 73-79). (Methods in Molecular Biology; Vol. 1907). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-8967-6_5

Identification of Cancer Genes Based on De Novo Transposon Insertion Site Analysis Using RNA and DNA Sequencing. / Sarver, Aaron L.

Methods in Molecular Biology. Humana Press Inc., 2019. p. 73-79 (Methods in Molecular Biology; Vol. 1907).

Research output: Chapter in Book/Report/Conference proceedingChapter

Sarver, AL 2019, Identification of Cancer Genes Based on De Novo Transposon Insertion Site Analysis Using RNA and DNA Sequencing. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1907, Humana Press Inc., pp. 73-79. https://doi.org/10.1007/978-1-4939-8967-6_5
Sarver, Aaron L. / Identification of Cancer Genes Based on De Novo Transposon Insertion Site Analysis Using RNA and DNA Sequencing. Methods in Molecular Biology. Humana Press Inc., 2019. pp. 73-79 (Methods in Molecular Biology).
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