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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Sample size calculation for phylogenetic case linkage.

Shirlee Wohl1, John R Giles1, Justin Lessler1

  • 1Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, Maryland, United States of America.

Plos Computational Biology
|July 6, 2021
PubMed
Summary
This summary is machine-generated.

Calculating sample size for pathogen transmission studies is crucial. This research provides a statistical framework and R package (phylosamp) to determine the necessary sample size for accurate phylogenetic analysis of infection links.

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Area of Science:

  • Epidemiology
  • Genomics
  • Biostatistics

Background:

  • Sample size calculations are vital for scientific study design and evaluation.
  • Phylogenetic studies are increasingly important for understanding pathogen transmission.
  • Clear guidance for sample size determination in phylogenetic studies is lacking.

Purpose of the Study:

  • To introduce a statistical framework for determining sample size in phylogenetic studies.
  • To assess how study design and linkage criteria influence the identification of true infector-infectee transmission pairs.
  • To provide a tool for designing and evaluating pathogen phylogenetic studies.

Main Methods:

  • Developed a statistical framework to calculate the number of true infector-infectee pairs based on study size and population coverage.
  • Investigated the impact of linkage criteria and study design on identifying transmission links.
  • Utilized outbreak simulations to test the framework and provide guidance on calculating sensitivity and specificity of linkage criteria.

Main Results:

  • The study presents a method to determine the number of true transmission pairs identifiable by phylogenetic studies.
  • Demonstrated how study design elements can counterintuitively affect the accuracy of identifying transmission links.
  • Offered guidance for calculating sensitivity and specificity of linkage criteria, essential inputs for the framework.

Conclusions:

  • The developed statistical framework aids in determining appropriate sample sizes for phylogenetic studies of pathogen transmission.
  • The R package 'phylosamp' is available for practical application in study design and evaluation.
  • This approach is broadly applicable to various pathogen phylogenetic studies, enhancing their rigor and accuracy.