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Sample size calculation for phylogenetic case linkage

Sample size calculations are an essential component of the design and evaluation of scientific studies. However, there is a lack of clear guidance for determining the sample size needed for phylogenetic studies, which are becoming an essential part of studying pathogen transmission. We introduce a s...

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Detalles Bibliográficos
Autores principales: Wohl, Shirlee, Giles, John R., Lessler, Justin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8284614/
https://www.ncbi.nlm.nih.gov/pubmed/34228722
http://dx.doi.org/10.1371/journal.pcbi.1009182
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author Wohl, Shirlee
Giles, John R.
Lessler, Justin
author_facet Wohl, Shirlee
Giles, John R.
Lessler, Justin
author_sort Wohl, Shirlee
collection PubMed
description Sample size calculations are an essential component of the design and evaluation of scientific studies. However, there is a lack of clear guidance for determining the sample size needed for phylogenetic studies, which are becoming an essential part of studying pathogen transmission. We introduce a statistical framework for determining the number of true infector-infectee transmission pairs identified by a phylogenetic study, given the size and population coverage of that study. We then show how characteristics of the criteria used to determine linkage and aspects of the study design can influence our ability to correctly identify transmission links, in sometimes counterintuitive ways. We test the overall approach using outbreak simulations and provide guidance for calculating the sensitivity and specificity of the linkage criteria, the key inputs to our approach. The framework is freely available as the R package phylosamp, and is broadly applicable to designing and evaluating a wide array of pathogen phylogenetic studies.
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spelling pubmed-82846142021-07-28 Sample size calculation for phylogenetic case linkage Wohl, Shirlee Giles, John R. Lessler, Justin PLoS Comput Biol Research Article Sample size calculations are an essential component of the design and evaluation of scientific studies. However, there is a lack of clear guidance for determining the sample size needed for phylogenetic studies, which are becoming an essential part of studying pathogen transmission. We introduce a statistical framework for determining the number of true infector-infectee transmission pairs identified by a phylogenetic study, given the size and population coverage of that study. We then show how characteristics of the criteria used to determine linkage and aspects of the study design can influence our ability to correctly identify transmission links, in sometimes counterintuitive ways. We test the overall approach using outbreak simulations and provide guidance for calculating the sensitivity and specificity of the linkage criteria, the key inputs to our approach. The framework is freely available as the R package phylosamp, and is broadly applicable to designing and evaluating a wide array of pathogen phylogenetic studies. Public Library of Science 2021-07-06 /pmc/articles/PMC8284614/ /pubmed/34228722 http://dx.doi.org/10.1371/journal.pcbi.1009182 Text en © 2021 Wohl et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Wohl, Shirlee
Giles, John R.
Lessler, Justin
Sample size calculation for phylogenetic case linkage
title Sample size calculation for phylogenetic case linkage
title_full Sample size calculation for phylogenetic case linkage
title_fullStr Sample size calculation for phylogenetic case linkage
title_full_unstemmed Sample size calculation for phylogenetic case linkage
title_short Sample size calculation for phylogenetic case linkage
title_sort sample size calculation for phylogenetic case linkage
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8284614/
https://www.ncbi.nlm.nih.gov/pubmed/34228722
http://dx.doi.org/10.1371/journal.pcbi.1009182
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