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The Power Decoder simulator for the evaluation of pooled shRNA screen performance
Poster Title: The Power Decoder simulator for the evaluation of pooled shRNA screen performance
Submitted on 06 Apr 2015
Author(s): Jesse Stombaugh, Abel Licon, Žaklina Strezoska, Joshua Stahl, Sarah Bael Anderson, Michael Banos, Anja van Brabant Smith, Amanda Birmingham, Annaleen Vermeulen
Affiliations: GE Healthcare Dharmacon, Inc.
Poster Views: 2,248
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Poster Information
Abstract: RNA interference (RNAi) screening using pooled, short hairpin (sh)RNA is a powerful, high-throughput tool for determining the biological relevance of genes for a phenotype. Assessing an shRNA pooled screen’s performance is difficult in practice; one can estimate the performance only by using reproducibility as a proxy for power or by employing a large number of validated positive and negative controls. Here, we develop an open-source software tool, the Power Decoder simulator, for generating shRNA pooled screening experiments in silico that can be used to estimate a screen’s statistical power. Using the negative binomial distribution, it models both the relative abundance of multiple shRNAs within a single screening replicate and the biological noise between replicates for each individual shRNA. We demonstrate that this simulator can successfully model the data from an actual laboratory experiment. We then use it to evaluate the effects of biological replicates and sequencing counts on the performance of a pooled screen, without the necessity of gathering additional data. The Power Decoder simulator is written in R and Python, and is available for download under the GNU General Public License v3.0.Summary: Power Decoder (written in R and Python) simulates shRNA pooled screening experiments in silico to allow for the estimation of a screen’s statistical power. Populations of shRNAs were engineered in such a way that the magnitude of depletion and enrichment was known, then using the negative binomial distribution, an in silico model was developed to successfully resemble data from an actual laboratory experiment.References: These investigations demonstrate how the Power Decoder simulator can help scientists plan future screens and easily investigate the likely effects of various experimental factors in silico, saving both time and money. Data from existing screens can also be analyzed retrospectively to evaluate their power and thus estimate the completeness of their resulting hit lists. Additionally, the Power Decoder simulator can be used to streamline optimization of novel pooled screening technologies such as gene knockout screens employing the new CRISPR (clustered regularly interspaced short palindrome repeats)-associated nuclease Cas9. The ability to do fast, easy, accurate power analyses before screening will enable researchers to perform adequately powered experiments, thereby delivering reliable answers to crucial biological questions.Report abuse »
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