Table 2 Comparison of different methods used to map genetic interactions

Loss-of-function

shRNA, RNAi or CRISPRi

Allows investigation of essential genes Phenotype is reversible

Phenotype is gene-dosage dependent

Essential genes that are specific to a particular cell type are of interest

CRISPR-Cas9

Allows investigation of complete functional shutdown

Ploidy in cancer cells may make the complete knockout of the gene difficult

Combinatorial or multiplexed knockouts enable investigation of the phenotypic effects of disrupting multiple genes at once

Chemical inhibition

Allows direct investigation of therapeutic relevance

Dynamic range is dependent on drug dosage and treatment duration

Chemical-inhibition-based screens provide information on the mechanisms of action of the drugs

Gain-of-function

CRISPRa

Allows investigation of gain-of-function mutations

Feasibility beyond the K562 cell line is not clear

Combinations of CRISPRa and CRISPRi screens provide information on directionality of GIs

Screening approaches

Targeted or arrayed GI screening

Gene-editing efficiency can be analyzed by Sanger sequencing

Enables straightforward exploration of multiple cell lines and conditions

Amenable to the incorporation of more mechanistically informative phenotypes (e.g. using single-cell RNA-seq or imaging technologies)

Requires information on the genes and pathways of focus

Milder phenotypes may inform rational combinatory therapy designs

Genome-wide GI screening

Allows determination of functional relations between previously unexplored gene pairs

Gene-editing efficiency is analyzed by next generation sequencing

Requires increased computational bandwidth

Clustering analysis may enable identification of novel multi-molecular modules