Literature DB >> 27485003

Genomic Amplifications Cause False Positives in CRISPR Screens.

Ankur Sheel1, Wen Xue2.   

Abstract

In CRISPR-based screens for essential genes, Munoz and colleagues and Aguirre and colleagues show that gene-independent targeting of genomic amplifications in human cancer cell lines reduces proliferation or survival. The correlation between CRISPR target site copy number and lethality demonstrates the need for scrutiny and complementary approaches to rule out off-target effects and false positives in CRISPR screens. Cancer Discov; 6(8); 824-6. ©2016 AACR.See related article by Munoz et al., p. 900See related article by Aguirre et al., p. 914. ©2016 American Association for Cancer Research.

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Year:  2016        PMID: 27485003      PMCID: PMC4975541          DOI: 10.1158/2159-8290.CD-16-0665

Source DB:  PubMed          Journal:  Cancer Discov        ISSN: 2159-8274            Impact factor:   39.397


  10 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

Review 2.  Genome editing. The new frontier of genome engineering with CRISPR-Cas9.

Authors:  Jennifer A Doudna; Emmanuelle Charpentier
Journal:  Science       Date:  2014-11-28       Impact factor: 47.728

3.  Comparing CRISPR and RNAi-based screening technologies.

Authors:  Benjamin E Housden; Norbert Perrimon
Journal:  Nat Biotechnol       Date:  2016-06-09       Impact factor: 54.908

Review 4.  High-throughput functional genomics using CRISPR-Cas9.

Authors:  Ophir Shalem; Neville E Sanjana; Feng Zhang
Journal:  Nat Rev Genet       Date:  2015-04-09       Impact factor: 53.242

Review 5.  Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases.

Authors:  Shengdar Q Tsai; J Keith Joung
Journal:  Nat Rev Genet       Date:  2016-05       Impact factor: 53.242

6.  Genetic compensation induced by deleterious mutations but not gene knockdowns.

Authors:  Andrea Rossi; Zacharias Kontarakis; Claudia Gerri; Hendrik Nolte; Soraya Hölper; Marcus Krüger; Didier Y R Stainier
Journal:  Nature       Date:  2015-07-13       Impact factor: 49.962

7.  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

8.  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

9.  The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.

Authors:  Jordi Barretina; Giordano Caponigro; Nicolas Stransky; Kavitha Venkatesan; Adam A Margolin; Sungjoon Kim; Christopher J Wilson; Joseph Lehár; Gregory V Kryukov; Dmitriy Sonkin; Anupama Reddy; Manway Liu; Lauren Murray; Michael F Berger; John E Monahan; Paula Morais; Jodi Meltzer; Adam Korejwa; Judit Jané-Valbuena; Felipa A Mapa; Joseph Thibault; Eva Bric-Furlong; Pichai Raman; Aaron Shipway; Ingo H Engels; Jill Cheng; Guoying K Yu; Jianjun Yu; Peter Aspesi; Melanie de Silva; Kalpana Jagtap; Michael D Jones; Li Wang; Charles Hatton; Emanuele Palescandolo; Supriya Gupta; Scott Mahan; Carrie Sougnez; Robert C Onofrio; Ted Liefeld; Laura MacConaill; Wendy Winckler; Michael Reich; Nanxin Li; Jill P Mesirov; Stacey B Gabriel; Gad Getz; Kristin Ardlie; Vivien Chan; Vic E Myer; Barbara L Weber; Jeff Porter; Markus Warmuth; Peter Finan; Jennifer L Harris; Matthew Meyerson; Todd R Golub; Michael P Morrissey; William R Sellers; Robert Schlegel; Levi A Garraway
Journal:  Nature       Date:  2012-03-28       Impact factor: 49.962

10.  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

  10 in total
  3 in total

1.  Correction of copy number induced false positives in CRISPR screens.

Authors:  Antoine de Weck; Javad Golji; Michael D Jones; Joshua M Korn; Eric Billy; E Robert McDonald; Tobias Schmelzle; Hans Bitter; Audrey Kauffmann
Journal:  PLoS Comput Biol       Date:  2018-07-19       Impact factor: 4.475

Review 2.  Utilization of CRISPR-Mediated Tools for Studying Functional Genomics in Hematological Malignancies: An Overview on the Current Perspectives, Challenges, and Clinical Implications.

Authors:  Maheswaran Solayappan; Adam Azlan; Kang Zi Khor; Mot Yee Yik; Matiullah Khan; Narazah Mohd Yusoff; Emmanuel Jairaj Moses
Journal:  Front Genet       Date:  2022-01-28       Impact factor: 4.599

3.  Complementary CRISPR genome-wide genetic screens in PARP10-knockout and overexpressing cells identify synthetic interactions for PARP10-mediated cellular survival.

Authors:  Jude B Khatib; Emily M Schleicher; Lindsey M Jackson; Ashna Dhoonmoon; George-Lucian Moldovan; Claudia M Nicolae
Journal:  Oncotarget       Date:  2022-09-28
  3 in total

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