Journal Article

Determination of sample size in genome-scale RNAi screens

Xiaohua Douglas Zhang and Joseph F. Heyse

in Bioinformatics

Volume 25, issue 7, pages 841-844
Published in print April 2009 | ISSN: 1367-4803
Published online February 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp082
Determination of sample size in genome-scale RNAi screens

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Motivation: 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.

Contact: Xiaohua_zhang@merck.com

Journal Article.  3401 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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