Minimizing the risk of reporting false positives in large-scale RNAi screens
A group of investigators from various institutions have written a Commentary in which they articulate their experience about caveats of large-scale RNAi screens. These authors propose that the use of standard controls should be adopted across the community of RNAi users to minimize the risk of reporting false positives among screen results.
Far from trying to dictate rules, this Commentary seeks to open a community-wide discussion leading to a consensus of best practices that can realistically be implemented across all experimental settings. Therefore, we welcome your reactions and hope for a constructive dialog for the benefit of all. Please post your comments below.
The urgent need for such debate has been highlighted in two recent papers by Ma et al. in Nature and Kulkarni et al. in Nature Methods. These two studies demonstrate that RNAi screens in the Drosophila melanogaster system—in which long dsRNAs are used as RNAi triggers—are affected by off-target effects to a much wider extent than previously thought.
As far as the use of RNAi in mammalian systems is concerned, off-target effects have been a constant preoccupation. Nature Methods’ recent focus, RNA interference – A user’s guide, contains practical discussion of issues revolving around the use of RNAi as a research tool in mammalian systems, and includes notably a Perspective by Yi Pei and Tom Tuschl on effective siRNA design and a Perspective by Bryan Cullen on experimental design to enhance and confirm specificity. The latter is, however, focused on experimental situations in which one aims at knocking down the expression of a single, specific gene of interest in mammalian cells.
For those involved in genome-wide screens in various model organisms, like the Commentary’s authors, the recommended controls may be technically difficult to implement—hence, the need for a discussion of appropriate measures to strike the right balance between practical feasibility and accuracy of published screen results.