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...

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Vydáno v:	Genome biology Ročník 15; číslo 12; s. 554
Hlavní autoři:	Li, Wei, Xu, Han, Xiao, Tengfei, Cong, Le, Love, Michael I, Zhang, Feng, Irizarry, Rafael A, Liu, Jun S, Brown, Myles, Liu, X Shirley
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	London BioMed Central 05.12.2014
Témata:	Algorithms Animal Genetics and Genomics Bioinformatics Biomedical and Life Sciences Cell Line, Tumor Computational Biology - methods CRISPR-Associated Proteins - genetics CRISPR-Cas Systems data collection essential genes Evolutionary Biology Gene Expression Regulation, Neoplastic Gene Knockout Techniques Genes, Essential Genetic Predisposition to Disease HL-60 Cells Human Genetics Humans insulin Life Sciences Method Microbial Genetics and Genomics mutation Neoplasms - genetics Plant Genetics and Genomics RNA signal transduction False Discovery Rate Sequencing Depth Read Count Essential Gene Negative Binomial Distribution
ISSN:	1474-760X, 1465-6906, 1474-760X, 1465-6914
On-line přístup:	Získat plný text
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Popis
Shrnutí:	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.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1474-760X 1465-6906 1474-760X 1465-6914
DOI:	10.1186/s13059-014-0554-4