MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens

Wei Li, Han Xu, Tengfei Xiao, Le Cong, Michael I. Love, Feng Zhang, Rafael A. Irizarry, Jun S. Liu, Myles Brown, X. Shirley Liu

Research output: Contribution to journalArticle

Abstract

We propose the Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) method for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens. MAGeCK demonstrates better performance compared with existing methods, identifies both positively and negatively selected genes simultaneously, and reports robust results across different experimental conditions. Using public datasets, MAGeCK identified novel essential genes and pathways, including EGFR in vemurafenib-treated A375 cells harboring a BRAF mutation. MAGeCK also detected cell type-specific essential genes, including BCR and ABL1, in KBM7 cells bearing a BCR-ABL fusion, and IGF1R in HL-60 cells, which depends on the insulin signaling pathway for proliferation.

Original languageEnglish (US)
Pages (from-to)554
Number of pages1
JournalGenome Biology
Volume15
Issue number12
StatePublished - 2014
Externally publishedYes

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Clustered Regularly Interspaced Short Palindromic Repeats
Essential Genes
genome
Genome
gene
Guide RNA
cells
HL-60 Cells
Genes
RNA
mutation
insulin
genes
analysis
essential genes
Insulin
Mutation
methodology

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Cite this

Li, W., Xu, H., Xiao, T., Cong, L., Love, M. I., Zhang, F., ... Liu, X. S. (2014). MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biology, 15(12), 554.

MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. / Li, Wei; Xu, Han; Xiao, Tengfei; Cong, Le; Love, Michael I.; Zhang, Feng; Irizarry, Rafael A.; Liu, Jun S.; Brown, Myles; Liu, X. Shirley.

In: Genome Biology, Vol. 15, No. 12, 2014, p. 554.

Research output: Contribution to journalArticle

Li, W, Xu, H, Xiao, T, Cong, L, Love, MI, Zhang, F, Irizarry, RA, Liu, JS, Brown, M & Liu, XS 2014, 'MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens', Genome Biology, vol. 15, no. 12, pp. 554.
Li, Wei ; Xu, Han ; Xiao, Tengfei ; Cong, Le ; Love, Michael I. ; Zhang, Feng ; Irizarry, Rafael A. ; Liu, Jun S. ; Brown, Myles ; Liu, X. Shirley. / MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. In: Genome Biology. 2014 ; Vol. 15, No. 12. pp. 554.
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