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

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

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 negativel...

Full description

Bibliographic Details
Main Authors: Li, Wei, Xu, Han, Xiao, Tengfei, Cong, Le, Love, Michael I., Zhang, Feng, Irizarry, Rafael A., Liu, Jun S., Brown, Myles, Liu, X. Shirley
Other Authors: Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences
Format: Article
Language:English
Published: BioMed Central Ltd 2015
Online Access:http://hdl.handle.net/1721.1/92852
https://orcid.org/0000-0003-2782-2509
Description
Summary: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.

Similar Items