BiNGS!SL-seq: A bioinformatics pipeline for the analysis and interpretation of deep sequencing genome-wide synthetic lethal screen

Jihye Kim, Aik Choon Tan

Research output: Chapter in Book/Report/Conference proceedingChapter

23 Citations (Scopus)

Abstract

While targeted therapies have shown clinical promise, these therapies are rarely curative for advanced cancers. The discovery of pathways for drug compounds can help to reveal novel therapeutic targets as rational combination therapy in cancer treatment. With a genome-wide shRNA screen using high-throughput genomic sequencing technology, we have identified gene products whose inhibition synergizes with their target drug to eliminate lung cancer cells. In this chapter, we described BiNGS!SL-seq, an efficient bioinformatics workflow to manage, analyze, and interpret the massive synthetic lethal screen data for finding statistically significant gene products. With our pipeline, we identified a number of druggable gene products and potential pathways for the screen in an example of lung cancer cells.

Original languageEnglish
Title of host publicationNext Generation Microarray Bioinformatics
Subtitle of host publicationMethods and Protocols
EditorsJunbai Wang, Tianhai Tian, Aik Choon Tan
Pages389-398
Number of pages10
DOIs
Publication statusPublished - 2012 Jan 2

Publication series

NameMethods in Molecular Biology
Volume802
ISSN (Print)1064-3745

Keywords

  • Next generation sequencing
  • Synthetic lethal screen
  • shRNA

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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  • Cite this

    Kim, J., & Tan, A. C. (2012). BiNGS!SL-seq: A bioinformatics pipeline for the analysis and interpretation of deep sequencing genome-wide synthetic lethal screen. In J. Wang, T. Tian, & A. C. Tan (Eds.), Next Generation Microarray Bioinformatics: Methods and Protocols (pp. 389-398). (Methods in Molecular Biology; Vol. 802). https://doi.org/10.1007/978-1-61779-400-1_26