%0 Journal Article %J Nat Methods %D 2006 %T Evidence of off-target effects associated with long dsRNAs in Drosophila melanogaster cell-based assays. %A Kulkarni, Meghana M %A Booker, Matthew %A Silver, Serena J %A Friedman, Adam %A Hong, Pengyu %A Perrimon, Norbert %A Mathey-Prevot, Bernard %K Animals %K drosophila melanogaster %K False Positive Reactions %K Gene Library %K Genetic Testing %K RNA Interference %K RNA, Double-Stranded %K Sensitivity and Specificity %X

To evaluate the specificity of long dsRNAs used in high-throughput RNA interference (RNAi) screens performed at the Drosophila RNAi Screening Center (DRSC), we performed a global analysis of their activity in 30 genome-wide screens completed at our facility. Notably, our analysis predicts that dsRNAs containing > or = 19-nucleotide perfect matches identified in silico to unintended targets may contribute to a significant false positive error rate arising from off-target effects. We confirmed experimentally that such sequences in dsRNAs lead to false positives and to efficient knockdown of a cross-hybridizing transcript, raising a cautionary note about interpreting results based on the use of a single dsRNA per gene. Although a full appreciation of all causes of false positive errors remains to be determined, we suggest simple guidelines to help ensure high-quality information from RNAi high-throughput screens.

%B Nat Methods %V 3 %P 833-8 %8 2006 Oct %G eng %N 10 %1 http://www.ncbi.nlm.nih.gov/pubmed/16964256?dopt=Abstract %R 10.1038/nmeth935