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Literature DB >> 29186130

Correcting CRISPR for copy number.

Abstract

The CRISPR-Cas9 system enables global screens of gene function with high sensitivity and specificity, but off-target effects have been reported for CRISPR guide RNAs targeting genes that are amplified at high copy number. A new study describes a computational approach to correct for this copy number effect, increasing the specificity of CRIPSR screens to identify essential genes.

Mesh：

Substances：
RNA, Guide

Year: 2017 PMID： 29186130 DOI： 10.1038/ng.3994

Source DB: PubMed Journal: Nat Genet ISSN： 1061-4036 Impact factor: 38.330

12 in total

1. Identification and characterization of essential genes in the human genome.

Authors: Tim Wang; Kıvanç Birsoy; Nicholas W Hughes; Kevin M Krupczak; Yorick Post; Jenny J Wei; Eric S Lander; David M Sabatini
Journal: Science Date: 2015-10-15 Impact factor: 47.728

2. Defining a Cancer Dependency Map.

Authors: Aviad Tsherniak; Francisca Vazquez; Phil G Montgomery; Barbara A Weir; Gregory Kryukov; Glenn S Cowley; Stanley Gill; William F Harrington; Sasha Pantel; John M Krill-Burger; Robin M Meyers; Levi Ali; Amy Goodale; Yenarae Lee; Guozhi Jiang; Jessica Hsiao; William F J Gerath; Sara Howell; Erin Merkel; Mahmoud Ghandi; Levi A Garraway; David E Root; Todd R Golub; Jesse S Boehm; William C Hahn
Journal: Cell Date: 2017-07-27 Impact factor: 41.582

Review 3. Cornerstones of CRISPR-Cas in drug discovery and therapy.

Authors: Christof Fellmann; Benjamin G Gowen; Pei-Chun Lin; Jennifer A Doudna; Jacob E Corn
Journal: Nat Rev Drug Discov Date: 2016-12-23 Impact factor: 84.694

4. High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities.

Authors: Traver Hart; Megha Chandrashekhar; Michael Aregger; Zachary Steinhart; Kevin R Brown; Graham MacLeod; Monika Mis; Michal Zimmermann; Amelie Fradet-Turcotte; Song Sun; Patricia Mero; Peter Dirks; Sachdev Sidhu; Frederick P Roth; Olivia S Rissland; Daniel Durocher; Stephane Angers; Jason Moffat
Journal: Cell Date: 2015-11-25 Impact factor: 41.582

5. Gene Essentiality Profiling Reveals Gene Networks and Synthetic Lethal Interactions with Oncogenic Ras.

Authors: Tim Wang; Haiyan Yu; Nicholas W Hughes; Bingxu Liu; Arek Kendirli; Klara Klein; Walter W Chen; Eric S Lander; David M Sabatini
Journal: Cell Date: 2017-02-02 Impact factor: 41.582

6. CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for Highly Amplified Genomic Regions.

Authors: Diana M Munoz; Pamela J Cassiani; Li Li; Eric Billy; Joshua M Korn; Michael D Jones; Javad Golji; David A Ruddy; Kristine Yu; Gregory McAllister; Antoine DeWeck; Dorothee Abramowski; Jessica Wan; Matthew D Shirley; Sarah Y Neshat; Daniel Rakiec; Rosalie de Beaumont; Odile Weber; Audrey Kauffmann; E Robert McDonald; Nicholas Keen; Francesco Hofmann; William R Sellers; Tobias Schmelzle; Frank Stegmeier; Michael R Schlabach
Journal: Cancer Discov Date: 2016-06-03 Impact factor: 39.397

7. Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting.

Authors: Andrew J Aguirre; Robin M Meyers; Barbara A Weir; Francisca Vazquez; Cheng-Zhong Zhang; Uri Ben-David; April Cook; Gavin Ha; William F Harrington; Mihir B Doshi; Maria Kost-Alimova; Stanley Gill; Han Xu; Levi D Ali; Guozhi Jiang; Sasha Pantel; Yenarae Lee; Amy Goodale; Andrew D Cherniack; Coyin Oh; Gregory Kryukov; Glenn S Cowley; Levi A Garraway; Kimberly Stegmaier; Charles W Roberts; Todd R Golub; Matthew Meyerson; David E Root; Aviad Tsherniak; William C Hahn
Journal: Cancer Discov Date: 2016-06-03 Impact factor: 39.397

8. Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains.

Authors: Junwei Shi; Eric Wang; Joseph P Milazzo; Zihua Wang; Justin B Kinney; Christopher R Vakoc
Journal: Nat Biotechnol Date: 2015-05-11 Impact factor: 54.908

9. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions.

Authors: John Paul Shen; Dongxin Zhao; Roman Sasik; Jens Luebeck; Amanda Birmingham; Ana Bojorquez-Gomez; Katherine Licon; Kristin Klepper; Daniel Pekin; Alex N Beckett; Kyle Salinas Sanchez; Alex Thomas; Chih-Chung Kuo; Dan Du; Assen Roguev; Nathan E Lewis; Aaron N Chang; Jason F Kreisberg; Nevan Krogan; Lei Qi; Trey Ideker; Prashant Mali
Journal: Nat Methods Date: 2017-03-20 Impact factor: 28.547

Correcting CRISPR for copy number.

1. Identification and characterization of essential genes in the human genome.

2. Defining a Cancer Dependency Map.

Review 3. Cornerstones of CRISPR-Cas in drug discovery and therapy.

4. High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities.

5. Gene Essentiality Profiling Reveals Gene Networks and Synthetic Lethal Interactions with Oncogenic Ras.

6. CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for Highly Amplified Genomic Regions.

7. Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting.

8. Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains.

9. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions.

10. Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach.

Review 1. CRISPR-based genome editing through the lens of DNA repair.

Review 2. Common computational tools for analyzing CRISPR screens.

3. Programmable Single and Multiplex Base-Editing in Bombyx mori Using RNA-Guided Cytidine Deaminases.

4. Efficient Generation of P53 Biallelic Mutations in Diannan Miniature Pigs Using RNA-Guided Base Editing.