False negative rates in Drosophila cell-based RNAi screens: a case study.
BACKGROUND
High-throughput screening using RNAi is a powerful gene discovery method but is often complicated by false positive and false negative results. Whereas false positive results associated with RNAi reagents has been a matter of extensive study, the issue of false negatives has received less attention.


RESULTS
We performed a meta-analysis of several genome-wide, cell-based Drosophila RNAi screens, together with a more focused RNAi screen, and conclude that the rate of false negative results is at least 8%. Further, we demonstrate how knowledge of the cell transcriptome can be used to resolve ambiguous results and how the number of false negative results can be reduced by using multiple, independently-tested RNAi reagents per gene.


CONCLUSIONS
RNAi reagents that target the same gene do not always yield consistent results due to false positives and weak or ineffective reagents. False positive results can be partially minimized by filtering with transcriptome data. RNAi libraries with multiple reagents per gene also reduce false positive and false negative outcomes when inconsistent results are disambiguated carefully.
Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
Matthew
M
Booker
Anastasia A
AA
Samsonova
Young
Y
Kwon
Ian
I
Flockhart
Stephanie E
SE
Mohr
Norbert
N
Perrimon
D000818:Animals; D016000:Cluster Analysis; D004330:Drosophila / Q000235:genetics*; D020869:Gene Expression Profiling; D046988:Proteasome Endopeptidase Complex / Q000235:genetics; D034622:RNA Interference / Q000502:physiology*; D012330:RNA, Double-Stranded / Q000235:genetics; D012270:Ribosomes / Q000235:genetics
D012330:RNA, Double-Stranded; D046988:Proteasome Endopeptidase Complex
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