Table 1.

Systems for Cancer Functional Genomics.

Mutagenesis System	Advantages	Disadvantages
CRISPR/Cas9	Genome wide Useful in loss and gain of function studies Bias can be eliminated by careful guide RNA library design	Difficult to employ in primary cells, useful in only established cell lines Difficult to employ in vivo Difficult to select for phenotypes requiring multiple cooperating genetic alterations
Transposon	Genome wide Useful in loss and gain of function studies Allows screens to be done in cell lines or primary cells in vivo Useful for selection of traits requiring multiple cooperating mutations Non-coding or regulatory regions of the genome can be identified	Bias for or against parts of the genome due to local hopping and insertion site preference Some genes are unlikely to be activated by transposon insertion if first ATG is in exon 1 Some genes are unlikely to be inactivated due to their small size (e.g., microRNAs) Does not induce the full spectrum of mutations found in human cancers (e.g., point mutations and translocations) Transposon mutagenesis can create mutations not tagged by the transposon due to re-mobilization
Retroviruses	Many have been isolated with various tissue tropisms Can activate endogenous promoters by enhancement mechanisms Do not require generation of new transgenic lines of mice	Tend to not induce loss of function mutations, relatively few tumor suppressor genes identified in screens Systems generally found and not created, meaning there are no retroviruses useful for modeling many important types of cancer Tissue tropisms limit usefulness and types of cancer that can be modeled Generally, cells must be dividing for infection Many retroviruses have severe strain-specific effects and limitations