False negative rates in Drosophila cell-based RNAi screens: a case study.
False negative rates in Drosophila cell-based RNAi screens: a case study.
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DOI：
10.1186/1471-2164-12-50
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发表时间：
2011-01-20
期刊：
影响因子：
4.4
通讯作者：
Perrimon N
中科院分区：
文献类型：
--
作者：
Booker M;Samsonova AA;Kwon Y;Flockhart I;Mohr SE;Perrimon N
使用RNAi的高通量筛选是一种强大的基因发现方法，但经常被假阳性和假阴性结果所复杂化。尽管与RNAi试剂相关的假阳性结果已经是广泛研究的问题，但假阴性的问题受到的关注较少。我们对几种全基因组、基于细胞的果蝇RNAi筛选以及更集中的RNAi筛选进行了荟萃分析，并得出结论，假阴性结果率至少为8%。此外，我们展示了细胞转录组的知识如何用于解决模糊的结果，以及如何通过使用多个独立测试的RNAi试剂来减少假阴性结果的数量。由于假阳性和弱或无效的试剂，靶向相同基因的RNAi试剂并不总是产生一致的结果。假阳性结果可以通过用转录组数据过滤来部分地最小化。当仔细消除不一致的结果时，每个基因具有多个试剂的RNAi文库也减少了假阳性和假阴性结果。
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. 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. 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.
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