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An improvement of current hypercube pooling PCR tests for SARS-CoV-2 detection
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic can be effectively controlled by rapid and accurate identification of SARS-CoV-2-infected cases through large-scale screening. Hypercube pooling polymerase chain reaction (PCR) is frequently used as a pooling technique because...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9627488/ https://www.ncbi.nlm.nih.gov/pubmed/36339215 http://dx.doi.org/10.3389/fpubh.2022.994712 |
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author | Wu, Tai-Yin Liao, Yu-Ciao Fuh, Chiou-Shann Weng, Pei-Wei Wang, Jr-Yi Chen, Chih-Yu Huang, Yu-Min Chen, Chung-Pei Chu, Yo-Lun Chen, Cheng-Kuang Yeh, Kuei-Lin Yu, Ching-Hsiao Wu, Hung-Kang Lin, Wei-Peng Liou, Tsan-Hon Wu, Mai-Szu Liaw, Chen-Kun |
author_facet | Wu, Tai-Yin Liao, Yu-Ciao Fuh, Chiou-Shann Weng, Pei-Wei Wang, Jr-Yi Chen, Chih-Yu Huang, Yu-Min Chen, Chung-Pei Chu, Yo-Lun Chen, Cheng-Kuang Yeh, Kuei-Lin Yu, Ching-Hsiao Wu, Hung-Kang Lin, Wei-Peng Liou, Tsan-Hon Wu, Mai-Szu Liaw, Chen-Kun |
author_sort | Wu, Tai-Yin |
collection | PubMed |
description | The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic can be effectively controlled by rapid and accurate identification of SARS-CoV-2-infected cases through large-scale screening. Hypercube pooling polymerase chain reaction (PCR) is frequently used as a pooling technique because of its high speed and efficiency. We attempted to implement the hypercube pooling strategy and found it had a large quantization effect. This raised two questions: is hypercube pooling with edge = 3 actually the optimal strategy? If not, what is the best edge and dimension? We used a C++ program to calculate the expected number of PCR tests per patient for different values of prevalence, edge, and dimension. The results showed that every edge had a best performance range. Then, using C++ again, we created a program to calculate the optimal edge and dimension required for pooling samples when entering prevalence into our program. Our program will be provided as freeware in the hope that it can help governments fight the SARS-CoV-2 pandemic. |
format | Online Article Text |
id | pubmed-9627488 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-96274882022-11-03 An improvement of current hypercube pooling PCR tests for SARS-CoV-2 detection Wu, Tai-Yin Liao, Yu-Ciao Fuh, Chiou-Shann Weng, Pei-Wei Wang, Jr-Yi Chen, Chih-Yu Huang, Yu-Min Chen, Chung-Pei Chu, Yo-Lun Chen, Cheng-Kuang Yeh, Kuei-Lin Yu, Ching-Hsiao Wu, Hung-Kang Lin, Wei-Peng Liou, Tsan-Hon Wu, Mai-Szu Liaw, Chen-Kun Front Public Health Public Health The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic can be effectively controlled by rapid and accurate identification of SARS-CoV-2-infected cases through large-scale screening. Hypercube pooling polymerase chain reaction (PCR) is frequently used as a pooling technique because of its high speed and efficiency. We attempted to implement the hypercube pooling strategy and found it had a large quantization effect. This raised two questions: is hypercube pooling with edge = 3 actually the optimal strategy? If not, what is the best edge and dimension? We used a C++ program to calculate the expected number of PCR tests per patient for different values of prevalence, edge, and dimension. The results showed that every edge had a best performance range. Then, using C++ again, we created a program to calculate the optimal edge and dimension required for pooling samples when entering prevalence into our program. Our program will be provided as freeware in the hope that it can help governments fight the SARS-CoV-2 pandemic. Frontiers Media S.A. 2022-10-19 /pmc/articles/PMC9627488/ /pubmed/36339215 http://dx.doi.org/10.3389/fpubh.2022.994712 Text en Copyright © 2022 Wu, Liao, Fuh, Weng, Wang, Chen, Huang, Chen, Chu, Chen, Yeh, Yu, Wu, Lin, Liou, Wu and Liaw. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Public Health Wu, Tai-Yin Liao, Yu-Ciao Fuh, Chiou-Shann Weng, Pei-Wei Wang, Jr-Yi Chen, Chih-Yu Huang, Yu-Min Chen, Chung-Pei Chu, Yo-Lun Chen, Cheng-Kuang Yeh, Kuei-Lin Yu, Ching-Hsiao Wu, Hung-Kang Lin, Wei-Peng Liou, Tsan-Hon Wu, Mai-Szu Liaw, Chen-Kun An improvement of current hypercube pooling PCR tests for SARS-CoV-2 detection |
title | An improvement of current hypercube pooling PCR tests for SARS-CoV-2 detection |
title_full | An improvement of current hypercube pooling PCR tests for SARS-CoV-2 detection |
title_fullStr | An improvement of current hypercube pooling PCR tests for SARS-CoV-2 detection |
title_full_unstemmed | An improvement of current hypercube pooling PCR tests for SARS-CoV-2 detection |
title_short | An improvement of current hypercube pooling PCR tests for SARS-CoV-2 detection |
title_sort | improvement of current hypercube pooling pcr tests for sars-cov-2 detection |
topic | Public Health |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9627488/ https://www.ncbi.nlm.nih.gov/pubmed/36339215 http://dx.doi.org/10.3389/fpubh.2022.994712 |
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