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Sample pooling methods for efficient pathogen screening: Practical implications

Due to the large number of negative tests, individually screening large populations for rare pathogens can be wasteful and expensive. Sample pooling methods improve the efficiency of large-scale pathogen screening campaigns by reducing the number of tests and reagents required to accurately categori...

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Autores principales: Furstenau, Tara N., Cocking, Jill H., Hepp, Crystal M., Fofanov, Viacheslav Y.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7657563/
https://www.ncbi.nlm.nih.gov/pubmed/33175841
http://dx.doi.org/10.1371/journal.pone.0236849
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author Furstenau, Tara N.
Cocking, Jill H.
Hepp, Crystal M.
Fofanov, Viacheslav Y.
author_facet Furstenau, Tara N.
Cocking, Jill H.
Hepp, Crystal M.
Fofanov, Viacheslav Y.
author_sort Furstenau, Tara N.
collection PubMed
description Due to the large number of negative tests, individually screening large populations for rare pathogens can be wasteful and expensive. Sample pooling methods improve the efficiency of large-scale pathogen screening campaigns by reducing the number of tests and reagents required to accurately categorize positive and negative individuals. Such methods rely on group testing theory which mainly focuses on minimizing the total number of tests; however, many other practical concerns and tradeoffs must be considered when choosing an appropriate method for a given set of circumstances. Here we use computational simulations to determine how several theoretical approaches compare in terms of (a) the number of tests, to minimize costs and save reagents, (b) the number of sequential steps, to reduce the time it takes to complete the assay, (c) the number of samples per pool, to avoid the limits of detection, (d) simplicity, to reduce the risk of human error, and (e) robustness, to poor estimates of the number of positive samples. We found that established methods often perform very well in one area but very poorly in others. Therefore, we introduce and validate a new method which performs fairly well across each of the above criteria making it a good general use approach.
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spelling pubmed-76575632020-11-18 Sample pooling methods for efficient pathogen screening: Practical implications Furstenau, Tara N. Cocking, Jill H. Hepp, Crystal M. Fofanov, Viacheslav Y. PLoS One Research Article Due to the large number of negative tests, individually screening large populations for rare pathogens can be wasteful and expensive. Sample pooling methods improve the efficiency of large-scale pathogen screening campaigns by reducing the number of tests and reagents required to accurately categorize positive and negative individuals. Such methods rely on group testing theory which mainly focuses on minimizing the total number of tests; however, many other practical concerns and tradeoffs must be considered when choosing an appropriate method for a given set of circumstances. Here we use computational simulations to determine how several theoretical approaches compare in terms of (a) the number of tests, to minimize costs and save reagents, (b) the number of sequential steps, to reduce the time it takes to complete the assay, (c) the number of samples per pool, to avoid the limits of detection, (d) simplicity, to reduce the risk of human error, and (e) robustness, to poor estimates of the number of positive samples. We found that established methods often perform very well in one area but very poorly in others. Therefore, we introduce and validate a new method which performs fairly well across each of the above criteria making it a good general use approach. Public Library of Science 2020-11-11 /pmc/articles/PMC7657563/ /pubmed/33175841 http://dx.doi.org/10.1371/journal.pone.0236849 Text en © 2020 Furstenau et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://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
Furstenau, Tara N.
Cocking, Jill H.
Hepp, Crystal M.
Fofanov, Viacheslav Y.
Sample pooling methods for efficient pathogen screening: Practical implications
title Sample pooling methods for efficient pathogen screening: Practical implications
title_full Sample pooling methods for efficient pathogen screening: Practical implications
title_fullStr Sample pooling methods for efficient pathogen screening: Practical implications
title_full_unstemmed Sample pooling methods for efficient pathogen screening: Practical implications
title_short Sample pooling methods for efficient pathogen screening: Practical implications
title_sort sample pooling methods for efficient pathogen screening: practical implications
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7657563/
https://www.ncbi.nlm.nih.gov/pubmed/33175841
http://dx.doi.org/10.1371/journal.pone.0236849
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