A direct look at RNAi screens

Mol Syst Biol. 8: 580Over the last decade, cell‐based RNAi screens have emerged as a powerful research tool. High‐content RNAi screening in particular has been successfully used to systematically determine genes that contribute to a wide variety of cellular processes, identify new disease genes, and gain insights into the architecture of signalling networks (Mohr et al , 2010). As with the development of any new technology, RNAi screening has encountered growing pains, but technical improvements have been implemented to reduce false‐positive rates due to factors such as off‐target effects (Bakal and Perrimon, 2010). However, recent studies have revealed inconsistencies between the phenotypes generated by different siRNAs targeting the same gene (from either the same or different libraries; Collinet et al , 2010) and poor reproducibility of similar screens performed by different laboratories. A striking example is the low overlap (<7%) of hits identified between three published screens that identified host factors required for HIV infection (Bushman et al , 2009). Through a novel experimental and computational analysis, Lucas Pelkmans and colleagues now show that the reproducibility of RNAi screens can be improved when the population heterogeneity of cell lines is considered (Snijder et al , 2012).It is now clear that genetically identical cells, such as those frequently used in RNAi screens, display heterogeneity in their cellular …