Journal
GENOME BIOLOGY
Volume 15, Issue 12, Pages -Publisher
BMC
DOI: 10.1186/s13059-014-0554-4
Keywords
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Funding
- NIH [R01 GM099409]
- Claudia Adams Barr Award in Innovative Basic Cancer Research from the Dana-Farber Cancer Institute
- NATIONAL CANCER INSTITUTE [T32CA009337] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM099409] Funding Source: NIH RePORTER
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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 the KBM7 cells bearing a BCR-ABL fusion, and IGF1R in the HL-60 cells, which depends on the insulin signaling pathway for proliferation.
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