BAGEL: A computational framework for identifying essential genes from pooled library screens

BMC Bioinformatics

Volumn 17, Issue 1, 2016, Pages

  Hart, Traver ^a   Moffat, Jason ^b,c  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^b UNIVERSITY OF TORONTO   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

Cancer; CRISPR; Essential genes; Functional genomics; Genetic screens

Indexed keywords

CELL CULTURE; MAMMALS;

CANCER; CRISPR; ESSENTIAL GENE; FUNCTIONAL GENOMICS; GENETIC SCREENS;

GENES;

BAYES THEOREM; CELL LINE; DIAGNOSTIC TEST ACCURACY STUDY; ESSENTIAL GENE; GENE DISRUPTION; GOLD STANDARD; HUMAN; HUMAN CELL; KNOCKOUT GENE; LEARNING; LIBRARY; SENSITIVITY AND SPECIFICITY; BIOLOGICAL MODEL; BIOLOGY; EPITHELIUM CELL; GENE INACTIVATION; GENE LIBRARY; GENETICS; GLIOBLASTOMA; HCT 116 CELL LINE; HELA CELL LINE; MACHINE LEARNING; METABOLISM; PROCEDURES; REPRODUCTIVE FITNESS; RNA INTERFERENCE; TUMOR CELL LINE;

CELL LINE, TUMOR; COMPUTATIONAL BIOLOGY; EPITHELIAL CELLS; GENE KNOCKOUT TECHNIQUES; GENE LIBRARY; GENES, ESSENTIAL; GENETIC FITNESS; GLIOBLASTOMA; HCT116 CELLS; HELA CELLS; HUMANS; MACHINE LEARNING; MODELS, GENETIC; RNA INTERFERENCE; SENSITIVITY AND SPECIFICITY;

EID: 84963595182     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-016-1015-8     Document Type: Article

References (17)

1. Carette JE, Guimaraes CP, Wuethrich I, Blomen VA, Varadarajan M, Sun C, Bell G, Yuan B, Muellner MK, Nijman SM, et al. Global gene disruption in human cells to assign genes to phenotypes by deep sequencing. Nat Biotechnol. 2011;29(6):542-6.
2. Echeverri CJ, Beachy PA, Baum B, Boutros M, Buchholz F, Chanda SK, Downward J, Ellenberg J, Fraser AG, Hacohen N, et al. Minimizing the risk of reporting false positives in large-scale RNAi screens. Nat Methods. 2006;3(10):777-9.
3. Hart T, Brown KR, Sircoulomb F, Rottapel R, Moffat J. Measuring error rates in genomic perturbation screens: gold standards for human functional genomics. Mol Syst Biol. 2014;10:733.
4. Kaelin Jr WG. Molecular biology. Use and abuse of RNAi to study mammalian gene function. Science. 2012;337(6093):421-2.
5. Chen S, Sanjana NE, Zheng K, Shalem O, Lee K, Shi X, Scott DA, Song J, Pan JQ, Weissleder R, et al. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell. 2015;160(6):1246-60.
6. Koike-Yusa H, Li Y, Tan EP, Velasco-Herrera Mdel C, Yusa K. Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nat Biotechnol. 2014;32(3):267-73.
7. Parnas O JM, Eisenhaure TM, Herbst RH, Dixit A YC, Przybylski D, Platt RJ, Tirosh I, Sanjana NE SO, Satija R, Raychowdhury, R MP, Carr SA, Zhang F, Hacohen N, A R. A genome-wide CRISPR screen in primary immune cells to dissect regulatory networks. Cell. 2015;162(3):675-86.
8. Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelson T, Heckl D, Ebert BL, Root DE, Doench JG et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2013;343(6166):84-7.
9. Wang T, Wei JJ, Sabatini DM, Lander ES. Genetic screens in human cells using the CRISPR/Cas9 system. Science. 2013.
10. Konig R, Chiang CY, Tu BP, Yan SF, DeJesus PD, Romero A, Bergauer T, Orth A, Krueger U, Zhou Y, et al. A probability-based approach for the analysis of large-scale RNAi screens. Nat Methods. 2007;4(10):847-9.
11. Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, Irizarry RA, Liu JS, Brown M, Liu XS. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol. 2014;15(12):554.
12. Luo B, Cheung HW, Subramanian A, Sharifnia T, Okamoto M, Yang X, Hinkle G, Boehm JS, Beroukhim R, Weir BA, et al. Highly parallel identification of essential genes in cancer cells. Proc Natl Acad Sci U S A. 2008;105(51):20380-5.
13. Marcotte R, Brown KR, Suarez F, Sayad A, Karamboulas K, Krzyzanowski PM, Sircoulomb F, Medrano M, Fedyshyn Y, Koh JL, et al. Essential gene profiles in breast, pancreatic, and ovarian cancer cells. Cancer Discov. 2012;2(2):172-89.
14. Yu J, Silva J, Califano A. ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling. Bioinformatics. 2015;32(2):260-7.
15. Hart T, Chandrashekhar M, Aregger M, Steinhart Z, Brown KR, MacLeod G, Mis M, Zimmerman M, Fradet-Turcotte A, Sun S et al. High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. Cell. 2015; doi: 10.1016/j.cell.2015.11.015.
16. Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics. 2009;10:48.
17. Wang T, Birsoy K, Hughes NW, Krupczak KM, Post Y, Wei JJ, Lander ES, Sabatini DM. Identification and characterization of essential genes in the human genome. Science. 2015;350(6264):1096-101.