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Open Forum Infect Dis. 2015 Aug 26;2(4):ofv123. doi: 10.1093/ofid/ofv123. eCollection 2015 Dec.

Designing and Interpreting Limiting Dilution Assays: General Principles and Applications to the Latent Reservoir for Human Immunodeficiency Virus-1.

Author information

1
Department of Biomedical Informatics , Columbia University Medical Center , New York, New York.
2
Program for Evolutionary Dynamics , Harvard University , Cambridge.
3
Division of Infectious Diseases , Brigham and Women's Hospital , Boston, Massachusetts.
4
Department of Medicine , Johns Hopkins University School of Medicine.
5
Department of Medicine , Johns Hopkins University School of Medicine ; Howard Hughes Medical Institute , Baltimore, Maryland.

Abstract

Limiting dilution assays are widely used in infectious disease research. These assays are crucial for current human immunodeficiency virus (HIV)-1 cure research in particular. In this study, we offer new tools to help investigators design and analyze dilution assays based on their specific research needs. 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. Yet standard assay designs may not discern whether an intervention reduces an already miniscule latent infection. This review addresses challenges arising in this setting and in the general use of dilution assays. We illustrate the major statistical method for estimating frequency of infectious units from assay results, and we offer an online tool for computing this estimate. We recommend a procedure for customizing assay design to achieve desired sensitivity and precision goals, subject to experimental constraints. We consider experiments in which no viral outgrowth is observed and explain how using alternatives to viral outgrowth may make measurement of HIV latency more efficient. Finally, we discuss how biological complications, such as probabilistic growth of small infections, alter interpretations of experimental results.

KEYWORDS:

HIV; dilution assay; latent reservoir; maximum-likelihood statistics; viral outgrowth

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