MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens
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Author(s)
Li, Wei
Xu, Han
Xiao, Tengfei
Cong, Le
Love, Michael I.
Zhang, Feng
Irizarry, Rafael A.
Liu, Jun S.
Brown, Myles
Liu, X. Shirley
Date Issued
December 2014
Journal
Genome Biology
Publisher
BioMed Central Ltd
Citation
Li, Wei, Han Xu, Tengfei Xiao, Le Cong, Michael I Love, Feng Zhang, Rafael A Irizarry, Jun S Liu, Myles Brown, and X Shirley Liu. “MAGeCK Enables Robust Identification of Essential Genes from Genome-Scale CRISPR/Cas9 Knockout Screens.” Genome Biology 15, no. 12 (December 2014).
Version
Final published version
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.
MIT Department
Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences
McGovern Institute for Brain Research at MIT
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DOI of Published Version
https://doi.org/10.1186/s13059-014-0554-4
