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Designing and interpreting limiting dilution assays: general principles and applications to the latent reservoir for HIV-1

View ORCID ProfileDaniel I. S. Rosenbloom, View ORCID ProfileOliver Elliott, View ORCID ProfileAlison L. Hill, View ORCID ProfileTimothy J. Henrich, View ORCID ProfileJanet M. Siliciano, View ORCID ProfileRobert F. Siliciano
doi: https://doi.org/10.1101/018911
Daniel I. S. Rosenbloom
1Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, USA
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Oliver Elliott
1Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, USA
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Alison L. Hill
2Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts, USA
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Timothy J. Henrich
3Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
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Janet M. Siliciano
4Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Robert F. Siliciano
4Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
5Howard Hughes Medical Institute, Baltimore, Maryland, USA
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Abstract

Limiting dilution assays are commonly used to measure the extent of infection, and in the context of HIV they represent an essential tool for studying latency and potential curative strategies. To assist investigators using dilution assays, we illustrate the major statistical method for estimating the frequency of infected cells (or other infectious units) from assay results, and we offer an online tool for computing this estimate. We then recommend a procedure for optimizing assay design to achieve any desired set of sensitivity and precision goals, subject to experimental constraints. We discuss challenges involved in interpreting experiments in which no viral growth is observed and explain how using alternative measures for viral outgrowth may make measurement of HIV latency more efficient. Finally, we discuss how biological complications – such as probabilistic growth of a small infection in culture – alter interpretations of experimental results.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 03, 2015.
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Designing and interpreting limiting dilution assays: general principles and applications to the latent reservoir for HIV-1
Daniel I. S. Rosenbloom, Oliver Elliott, Alison L. Hill, Timothy J. Henrich, Janet M. Siliciano, Robert F. Siliciano
bioRxiv 018911; doi: https://doi.org/10.1101/018911
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Designing and interpreting limiting dilution assays: general principles and applications to the latent reservoir for HIV-1
Daniel I. S. Rosenbloom, Oliver Elliott, Alison L. Hill, Timothy J. Henrich, Janet M. Siliciano, Robert F. Siliciano
bioRxiv 018911; doi: https://doi.org/10.1101/018911

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