CRISPER/cas9

CRISPR/Cas is undoubtedly a game changer in the field of functional genomics. In the space of less than 5 years, it has enabled laboratories of all sizes and capabilities to edit genomes at will. Although the initial indications are that the technology is less plagued by off-target effects than siRNA or shRNA, direct comparisons of the three technologies are still required. However, there are some encouraging findings. For example, several common hits that mediate resistance to the BRAF inhibitor, PLX-4720, were identified in CRISPR and shRNA loss-of-function screens.9,107 Furthermore, there are overlapping hits between a CRISPR transcriptional activation screen conducted by Zhang and colleagues11 and a cDNA overexpression screen carried out by the Garraway lab.108 Specifically, each group identified genes that, when overexpressed, conferred resistance to inhibitors of the RAS/RAF/MAPK pathway. Theoretically, CRISPR/Cas loss-of-function screens could reveal hits that were not found in shRNA screens. This is because shRNA-mediated knockdown acts at the level of RNA, rather than by deleting the coding sequence; thus, partial mRNA knockdown may lead to false-negatives in shRNA screens. Of course, CRISPR/Cas9 screens will also have a certain false-nega- tive rate because of variations in sgRNA targeting efficiency, Cas9 activity, and the efficacy of NHEJ in each cellular background. Future benchmarking studies should be prospective, rather than rely on reanalysis of existing data sets. The availability of relatively inexpensive methods to analyze genome-wide modifications, combined with the wealth of computational expertise in genomic data analysis, will also allow the field to rapidly optimize targeting strate- gies and reagents. In the interests of rapid and continual scientific progress, it is hoped that such information is shared with, and remains in, the larger academic community