Integrating Experimental and Analytic Approaches to Improve Data Quality in Genome-wide RNAi Screens

@article{Zhang2008IntegratingEA,
  title={Integrating Experimental and Analytic Approaches to Improve Data Quality in Genome-wide RNAi Screens},
  author={Xiaohua Douglas Zhang and Amy S. Espeseth and Eric N. Johnson and Jayne Chin and Adam T. Gates and Lyndon J. Mitnaul and Shane D. Marine and Jenny Tian and Erica M. Stec and Priya Kunapuli and Daniel J. Holder and Joseph F. Heyse and Berta Strulovici and Marc Ferrer},
  journal={Journal of Biomolecular Screening},
  year={2008},
  volume={13},
  pages={378 - 389}
}
RNA interference (RNAi) not only plays an important role in drug discovery but can also be developed directly into drugs. RNAi high-throughput screening (HTS) biotechnology allows us to conduct genome-wide RNAi research. A central challenge in genome-wide RNAi research is to integrate both experimental and computational approaches to obtain high quality RNAi HTS assays. Based on our daily practice in RNAi HTS experiments, we propose the implementation of 3 experimental and analytic processes to… 
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References

SHOWING 1-10 OF 39 REFERENCES
A pair of new statistical parameters for quality control in RNA interference high-throughput screening assays.
TLDR
A pair of new parameters are proposed, strictly standardized mean difference (SSMD) and coefficient of variability in difference (CVD), as QC metrics in RNAi HTS assays, compared to S/B and S/N, which capture the variabilities in both compared populations.
Median Absolute Deviation to Improve Hit Selection for Genome-Scale RNAi Screens
TLDR
The authors demonstrate that the MAD-based hit selection method rescued physiologically relevant false negatives that would have been missed in the SD-based method, and they believe it to be the desirable 1st-choice hitselection method for RNAi screen results.
Novel Analytic Criteria and Effective Plate Designs for Quality Control in Genome-Scale RNAi Screens
TLDR
Novel QC criteria are constructed for evaluating data quality in genome-wide RNAi screens based on a recently proposed parameter, strictly standardized mean difference (SSMD), and these QC criteria obtain consistent QC results for multiple positive controls with different effect sizes.
Increasing the robustness and validity of RNAi screens.
  • S. Haney
  • Medicine, Biology
    Pharmacogenomics
  • 2007
TLDR
This review will discuss how approaches can improve RNAi screening data at the community level and for an individual researcher trying to manage an RNAi screen.
Robust statistical methods for hit selection in RNA interference high-throughput screening experiments.
TLDR
This investigation suggested that platewise analysis (determining effective siRNAs on a plate-by-plate basis) can adjust for systematic errors in different plates, while an experimentwise analysis, in which effectiveSiRNAs are identified in an analysis of the entire experiment, cannot.
High-throughput screening of effective siRNAs from RNAi libraries delivered via bacterial invasion
TLDR
It is demonstrated that functional short hairpin RNAs (shRNAs) could be synthesized in Escherichia coli and delivered directly via bacterial invasion to the near entirety of a mammalian cell population to trigger RNAi.
The Use of Strictly Standardized Mean Difference for Hit Selection in Primary RNA Interference High-Throughput Screening Experiments
TLDR
The applications presented in this article demonstrate that the SSMD method addresses scientific questions and fills scientific needs better than both percentage inhibition and the commonly used z-score method for hit selection.
Translating RNA interference into therapies for human disease.
TLDR
The process of selecting an RNAi-based drug candidate may simply involve the synthesis and testing of a relatively small number of short double strands of RNA, incorporating chemical modifications that confer stability and direct these RNA duplexes to the appropriate tissues and cells, and/or formulating these RNA Duplexes with appropriate delivery agents to achieve the same goals.
High-Throughput Screening by RNA Interference: Control of Two Distinct Types of Variance
TLDR
Basic guidelines for screen development are outlined that will help the researcher to control these forms of variance and maximize the utility of genome-wide RNAi screening.
Design and implementation of high-throughput RNAi screens in cultured Drosophila cells
TLDR
This protocol offers a set of suggestions and considerations for screen optimization and a step-by-step description of the procedures successfully used at the Drosophila RNAi Screening Center for screen implementation, data collection and analysis to identify potential hits.
...
1
2
3
4
...