title: MAGeCK enables robust identification of essential  genes from genome-scale CRISPR/Cas9 knockout  screens.
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.
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Han
authors.initials: H
authors.lastname: Xu
authors.forename: Tengfei
authors.initials: T
authors.lastname: Xiao
authors.forename: Le
authors.initials: L
authors.lastname: Cong
authors.forename: Michael I
authors.initials: MI
authors.lastname: Love
authors.forename: Feng
authors.initials: F
authors.lastname: Zhang
authors.forename: Rafael A
authors.initials: RA
authors.lastname: Irizarry
authors.forename: Jun S
authors.initials: JS
authors.lastname: Liu
authors.forename: Myles
authors.initials: M
authors.lastname: Brown
authors.forename: X Shirley
authors.initials: XS
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D064130:CRISPR-Associated Proteins / Q000235:genetics*; D064113:CRISPR-Cas Systems; D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D055786:Gene Knockout Techniques; D020043:Genes, Essential; D020022:Genetic Predisposition to Disease; D018922:HL-60 Cells; D006801:Humans; D009369:Neoplasms / Q000235:genetics*
chemical_list: D064130:CRISPR-Associated Proteins