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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...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
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.
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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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