False negative rates in Drosophila cell-based RNAi screens: a case study

BMC Genomics

Research Article

Young Kwon¹  Ian Flockhart¹  Anastasia A Samsonova¹  Stephanie E Mohr¹  Matthew Booker²  Norbert Perrimon³ 

[1] Department of Genetics, Harvard Medical School, (77 Avenue Louis Pasteur), (02115), Boston, Massachusetts, USA;Department of Genetics, Harvard Medical School, (77 Avenue Louis Pasteur), (02115), Boston, Massachusetts, USA;Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, (185 Meeting Street), (02192), Providence, Rhode Island, USA;Department of Genetics, Harvard Medical School, (77 Avenue Louis Pasteur), (02115), Boston, Massachusetts, USA;Howard Hughes Medical Institute, (77 Avenue Louis Pasteur), (02115), Boston, Massachusetts, USA;

关键词: False Negative Result;    False Negative Rate;    RNAi Screen;    Focus RNAi;    Proteasome Complex;   

DOI  :  10.1186/1471-2164-12-50

 received in 2010-10-08, accepted in 2011-01-20,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundHigh-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.ResultsWe 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.ConclusionsRNAi 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.

【 授权许可】

Unknown   
© Booker et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.