Determination of sample size in genome-scale RNAi screens.
BACKGROUND
For genome-scale RNAi research, it is critical to investigate sample size required for the achievement of reasonably low false negative rate (FNR) and false positive rate.


RESULTS
The analysis in this article reveals that current design of sample size contributes to the occurrence of low signal-to-noise ratio in genome-scale RNAi projects. The analysis suggests that (i) an arrangement of 16 wells per plate is acceptable and an arrangement of 20-24 wells per plate is preferable for a negative control to be used for hit selection in a primary screen without replicates; (ii) in a confirmatory screen or a primary screen with replicates, a sample size of 3 is not large enough, and there is a large reduction in FNRs when sample size increases from 3 to 4. To search a tradeoff between benefit and cost, any sample size between 4 and 11 is a reasonable choice. If the main focus is the selection of siRNAs with strong effects, a sample size of 4 or 5 is a good choice. If we want to have enough power to detect siRNAs with moderate effects, sample size needs to be 8, 9, 10 or 11. These discoveries about sample size bring insight to the design of a genome-scale RNAi screen experiment.
Zhang
Xiaohua Douglas
XD
Biometrics Research and BARDS, Merck Research Laboratories, West Point, PA 19486, USA. Xiaohua_zhang@merck.com
Heyse
Joseph F
JF
D000818:Animals; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D016678:Genome; D006801:Humans; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000235:genetics; D018401:Sample Size
D034741:RNA, Small Interfering