Access the full text.
Sign up today, get DeepDyve free for 14 days.
R. Ben-Ami, A. Klochendler, M. Seidel, T. Sido, O. Gurel-Gurevich, M. Yassour, E. Meshorer, G. Benedek, I. Fogel, E. Oiknine-Djian, A. Gertler, Z. Rotstein, B. Lavi, Y. Dor, D. Wolf, M. Salton, Y. Drier (2020)
Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detectionClinical Microbiology and Infection, 26
( Bustin SA. AZ of Quantitative PCR. La Jolla, CA: International University Line; 2004.)
Bustin SA. AZ of Quantitative PCR. La Jolla, CA: International University Line; 2004.Bustin SA. AZ of Quantitative PCR. La Jolla, CA: International University Line; 2004., Bustin SA. AZ of Quantitative PCR. La Jolla, CA: International University Line; 2004.
Y. Daon, A. Huppert, U. Obolski (2020)
An accurate model for SARS-CoV-2 pooled RT-PCR test errorsRoyal Society Open Science, 8
A. Alexanderian, N. Petra, G. Stadler, O. Ghattas (2013)
A-Optimal Design of Experiments for Infinite-Dimensional Bayesian Linear Inverse Problems with Regularized ℓ0-SparsificationSIAM J. Sci. Comput., 36
( Ryan KJ. Estimating expected information gains for experimental designs with application to the random fatigue-limit model. J Comput Graph Stat2003; 12 (3): 585–603.)
Ryan KJ. Estimating expected information gains for experimental designs with application to the random fatigue-limit model. J Comput Graph Stat2003; 12 (3): 585–603.Ryan KJ. Estimating expected information gains for experimental designs with application to the random fatigue-limit model. J Comput Graph Stat2003; 12 (3): 585–603., Ryan KJ. Estimating expected information gains for experimental designs with application to the random fatigue-limit model. J Comput Graph Stat2003; 12 (3): 585–603.
( Barak N , Ben-AmiR, SidoT, et al; Hebrew University-Hadassah COVID-19 Diagnosis Team. Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests. Sci Transl Med2021; 13 (589): eabf2823.)
Barak N , Ben-AmiR, SidoT, et al; Hebrew University-Hadassah COVID-19 Diagnosis Team. Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests. Sci Transl Med2021; 13 (589): eabf2823.Barak N , Ben-AmiR, SidoT, et al; Hebrew University-Hadassah COVID-19 Diagnosis Team. Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests. Sci Transl Med2021; 13 (589): eabf2823., Barak N , Ben-AmiR, SidoT, et al; Hebrew University-Hadassah COVID-19 Diagnosis Team. Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests. Sci Transl Med2021; 13 (589): eabf2823.
Tao Liu, Wenjia Liang, Haojie Zhong, Jianfeng He, Zi-hui Chen, G. He, T. Song, Shaowei Chen, Ping Wang, Jialing Li, Y. Lan, M. Cheng, Jinxu Huang, Jiwei Niu, L. Xia, Jianpeng Xiao, Jianxiong Hu, Lifeng Lin, Qiong Huang, Z. Rong, A. Deng, W. Zeng, Jiansen Li, Xing Li, X. Tan, Min Kang, Lingchuan Guo, Zhihua Zhu, D. Gong, Guimin Chen, M. Dong, Wenjun Ma (2020)
Risk factors associated with COVID-19 infection: a retrospective cohort study based on contacts tracingEmerging Microbes & Infections, 9
Ana Christoff, G. Cruz, Aline Sereia, D. Boberg, D. Bastiani, Laís Yamanaka, G. Fongaro, P. Stoco, M. Bazzo, E. Grisard, C. Hernandes, L. Oliveira (2020)
Swab pooling for large-scale RT-qPCR screening of SARS-CoV-2SSRN Electronic Journal
N. Padhye (2020)
Reconstructed diagnostic sensitivity and specificity of the RT-PCR test for COVID-19medRxiv
(2020)
Interim guidance for antigen testing for SARS-CoV-2
( Lindley DV. On a measure of the information provided by an experiment. Ann Math Statist1956; 27 (4): 986–1005.)
Lindley DV. On a measure of the information provided by an experiment. Ann Math Statist1956; 27 (4): 986–1005.Lindley DV. On a measure of the information provided by an experiment. Ann Math Statist1956; 27 (4): 986–1005., Lindley DV. On a measure of the information provided by an experiment. Ann Math Statist1956; 27 (4): 986–1005.
( Wikramaratna PS , PatonRS, GhafariM, et alEstimating the false-negative test probability of SARS-CoV-2 by RT-PCR. Eurosurveillance2020; 25 (50): 2000568.)
Wikramaratna PS , PatonRS, GhafariM, et alEstimating the false-negative test probability of SARS-CoV-2 by RT-PCR. Eurosurveillance2020; 25 (50): 2000568.Wikramaratna PS , PatonRS, GhafariM, et alEstimating the false-negative test probability of SARS-CoV-2 by RT-PCR. Eurosurveillance2020; 25 (50): 2000568., Wikramaratna PS , PatonRS, GhafariM, et alEstimating the false-negative test probability of SARS-CoV-2 by RT-PCR. Eurosurveillance2020; 25 (50): 2000568.
( Mutesa L , NdishimyeP, ButeraY, et alA pooled testing strategy for identifying SARS-CoV-2 at low prevalence. Nature2021; 589 (7841): 276–80.33086375)
Mutesa L , NdishimyeP, ButeraY, et alA pooled testing strategy for identifying SARS-CoV-2 at low prevalence. Nature2021; 589 (7841): 276–80.33086375Mutesa L , NdishimyeP, ButeraY, et alA pooled testing strategy for identifying SARS-CoV-2 at low prevalence. Nature2021; 589 (7841): 276–80.33086375, Mutesa L , NdishimyeP, ButeraY, et alA pooled testing strategy for identifying SARS-CoV-2 at low prevalence. Nature2021; 589 (7841): 276–80.33086375
( Shental N , LevyS, WuvshetV, et alEfficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriers. Sci Adv2020; 6 (37): eabc5961.32917716)
Shental N , LevyS, WuvshetV, et alEfficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriers. Sci Adv2020; 6 (37): eabc5961.32917716Shental N , LevyS, WuvshetV, et alEfficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriers. Sci Adv2020; 6 (37): eabc5961.32917716, Shental N , LevyS, WuvshetV, et alEfficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriers. Sci Adv2020; 6 (37): eabc5961.32917716
( Sokal A. Monte Carlo methods in statistical mechanics: foundations and new algorithms In: Functional Integration. Springer; 1997: 131–92.)
Sokal A. Monte Carlo methods in statistical mechanics: foundations and new algorithms In: Functional Integration. Springer; 1997: 131–92.Sokal A. Monte Carlo methods in statistical mechanics: foundations and new algorithms In: Functional Integration. Springer; 1997: 131–92., Sokal A. Monte Carlo methods in statistical mechanics: foundations and new algorithms In: Functional Integration. Springer; 1997: 131–92.
( Yelin I , AharonyN, TamarES, et alEvaluation of COVID-19 RT-qPCR test in multi sample pools. Clin Infect Dis2020; 71 (16): 2073–8.32358960)
Yelin I , AharonyN, TamarES, et alEvaluation of COVID-19 RT-qPCR test in multi sample pools. Clin Infect Dis2020; 71 (16): 2073–8.32358960Yelin I , AharonyN, TamarES, et alEvaluation of COVID-19 RT-qPCR test in multi sample pools. Clin Infect Dis2020; 71 (16): 2073–8.32358960, Yelin I , AharonyN, TamarES, et alEvaluation of COVID-19 RT-qPCR test in multi sample pools. Clin Infect Dis2020; 71 (16): 2073–8.32358960
S. Lohse, T. Pfuhl, Barbara Berkó-Göttel, J. Rissland, Tobias Geißler, B. Gärtner, S. Becker, S. Schneitler, S. Smola (2020)
Pooling of samples for testing for SARS-CoV-2 in asymptomatic peopleThe Lancet. Infectious Diseases, 20
( Foster A , JankowiakM, BinghamE, et al Variational bayesian optimal experimental design. arXiv190305480, 2019, preprint: not peer reviewed.)
Foster A , JankowiakM, BinghamE, et al Variational bayesian optimal experimental design. arXiv190305480, 2019, preprint: not peer reviewed.Foster A , JankowiakM, BinghamE, et al Variational bayesian optimal experimental design. arXiv190305480, 2019, preprint: not peer reviewed., Foster A , JankowiakM, BinghamE, et al Variational bayesian optimal experimental design. arXiv190305480, 2019, preprint: not peer reviewed.
( Kim H-Y , HudgensMG, DreyfussJM, et alComparison of group testing algorithms for case identification in the presence of test error. Biometrics2007; 63 (4): 1152–63.17501946)
Kim H-Y , HudgensMG, DreyfussJM, et alComparison of group testing algorithms for case identification in the presence of test error. Biometrics2007; 63 (4): 1152–63.17501946Kim H-Y , HudgensMG, DreyfussJM, et alComparison of group testing algorithms for case identification in the presence of test error. Biometrics2007; 63 (4): 1152–63.17501946, Kim H-Y , HudgensMG, DreyfussJM, et alComparison of group testing algorithms for case identification in the presence of test error. Biometrics2007; 63 (4): 1152–63.17501946
( Dorfman R. The detection of defective members of large populations. Ann Math Statist1943; 14 (4): 436–40.)
Dorfman R. The detection of defective members of large populations. Ann Math Statist1943; 14 (4): 436–40.Dorfman R. The detection of defective members of large populations. Ann Math Statist1943; 14 (4): 436–40., Dorfman R. The detection of defective members of large populations. Ann Math Statist1943; 14 (4): 436–40.
N. Shental, S. Levy, Shosh Skorniakov, Vered Wuvshet, Y. Shemer-Avni, A. Porgador, T. Hertz (2020)
Efficient high throughput SARS-CoV-2 testing to detect asymptomatic carriersmedRxiv
( Huan X , MarzoukYM. Simulation-based optimal Bayesian experimental design for nonlinear systems. J Comput Phys2013; 232 (1): 288–317.)
Huan X , MarzoukYM. Simulation-based optimal Bayesian experimental design for nonlinear systems. J Comput Phys2013; 232 (1): 288–317.Huan X , MarzoukYM. Simulation-based optimal Bayesian experimental design for nonlinear systems. J Comput Phys2013; 232 (1): 288–317., Huan X , MarzoukYM. Simulation-based optimal Bayesian experimental design for nonlinear systems. J Comput Phys2013; 232 (1): 288–317.
J. Watson, P. Whiting, J. Brush (2020)
Interpreting a covid-19 test resultBMJ, 369
D. Foreman-Mackey, D. Hogg, D. Lang, J. Goodman (2012)
emcee: The MCMC HammerPublications of the Astronomical Society of the Pacific, 125
I. Yelin, N. Aharony, E. Tamar, Amir Argoetti, Esther Messer, Dina Berenbaum, Einat Shafran, Areen Kuzli, Nagham Gandali, Omer Shkedi, T. Hashimshony, Y. Mandel-Gutfreund, M. Halberthal, Y. Geffen, Moran Szwarcwort-Cohen, R. Kishony (2020)
Evaluation of COVID-19 RT-qPCR test in multi-sample poolsClinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
( van Kasteren PB , van Der VeerB, van den BrinkS, et alComparison of seven commercial RT-PCR diagnostic kits for COVID-19. J Clin Virol2020; 128: 104412.32416600)
van Kasteren PB , van Der VeerB, van den BrinkS, et alComparison of seven commercial RT-PCR diagnostic kits for COVID-19. J Clin Virol2020; 128: 104412.32416600van Kasteren PB , van Der VeerB, van den BrinkS, et alComparison of seven commercial RT-PCR diagnostic kits for COVID-19. J Clin Virol2020; 128: 104412.32416600, van Kasteren PB , van Der VeerB, van den BrinkS, et alComparison of seven commercial RT-PCR diagnostic kits for COVID-19. J Clin Virol2020; 128: 104412.32416600
Paul Wikramaratna, R. Paton, M. Ghafari, J. Lourenço (2020)
Estimating false-negative detection rate of SARS-CoV-2 by RT-PCRmedRxiv
( Aprahamian H , BishDR, BishEK. Optimal group testing: structural properties and robust solutions, with application to public health screening. INFORMS J Comput2020; 32: 895–911.)
Aprahamian H , BishDR, BishEK. Optimal group testing: structural properties and robust solutions, with application to public health screening. INFORMS J Comput2020; 32: 895–911.Aprahamian H , BishDR, BishEK. Optimal group testing: structural properties and robust solutions, with application to public health screening. INFORMS J Comput2020; 32: 895–911., Aprahamian H , BishDR, BishEK. Optimal group testing: structural properties and robust solutions, with application to public health screening. INFORMS J Comput2020; 32: 895–911.
A. Sterrett (1957)
On the Detection of Defective Members of Large PopulationsAnnals of Mathematical Statistics, 28
L. Mutesa, P. Ndishimye, Y. Butera, J. Souopgui, A. Uwineza, R. Rutayisire, Ella Ndoricimpaye, E. Musoni, N. Rujeni, Thierry Nyatanyi, E. Ntagwabira, M. Semakula, C. Musanabaganwa, D. Nyamwasa, Maurice Ndashimye, E. Ujeneza, I. Mwikarago, C. Muvunyi, J. Mazarati, S. Nsanzimana, N. Turok, W. Ndifon (2020)
A pooled testing strategy for identifying SARS-CoV-2 at low prevalenceNature, 589
Matthew Aldridge, O. Johnson, J. Scarlett (2019)
Group testing: an information theory perspectiveFound. Trends Commun. Inf. Theory, 15
W. Organization (2020)
Antigen-detection in the diagnosis of SARS-CoV-2 infection using rapid immunoassays
Paul Wikramaratna, R. Paton, M. Ghafari, J. Lourenço (2020)
Estimating the false-negative test probability of SARS-CoV-2 by RT-PCR.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 25 50
N. Shental, S. Levy, Vered Wuvshet, Shosh Skorniakov, B. Shalem, A. Ottolenghi, Yariv Greenshpan, R. Steinberg, Avishay Edri, Roni Gillis, M. Goldhirsh, Khen Moscovici, Sinai Sachren, Lilach Friedman, L. Nesher, Y. Shemer-Avni, A. Porgador, T. Hertz (2020)
Efficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriersScience Advances, 6
(2020)
Impact of false-positives and false-negatives in the UK's COVID-19 RT-PCR testing programme
( Eberhardt JN , BreuckmannNP, EberhardtCS. Multi-stage group testing improves efficiency of large-scale COVID-19 screening. J Clin Virol2020; 128: 104382.32388468)
Eberhardt JN , BreuckmannNP, EberhardtCS. Multi-stage group testing improves efficiency of large-scale COVID-19 screening. J Clin Virol2020; 128: 104382.32388468Eberhardt JN , BreuckmannNP, EberhardtCS. Multi-stage group testing improves efficiency of large-scale COVID-19 screening. J Clin Virol2020; 128: 104382.32388468, Eberhardt JN , BreuckmannNP, EberhardtCS. Multi-stage group testing improves efficiency of large-scale COVID-19 screening. J Clin Virol2020; 128: 104382.32388468
Alexander Pikovski, K. Bentele (2020)
Pooling of coronavirus tests under unknown prevalenceEpidemiology and Infection, 148
( Pikovski A , BenteleK. Pooling of coronavirus tests under unknown prevalence. Epidemiol Infect2020; 148: e183.)
Pikovski A , BenteleK. Pooling of coronavirus tests under unknown prevalence. Epidemiol Infect2020; 148: e183.Pikovski A , BenteleK. Pooling of coronavirus tests under unknown prevalence. Epidemiol Infect2020; 148: e183., Pikovski A , BenteleK. Pooling of coronavirus tests under unknown prevalence. Epidemiol Infect2020; 148: e183.
( Foreman-Mackey D , HoggDW, LangD, et alemcee: the MCMC hammer. Publ Astron Soc Pacific2013; 125 (925): 306–12.)
Foreman-Mackey D , HoggDW, LangD, et alemcee: the MCMC hammer. Publ Astron Soc Pacific2013; 125 (925): 306–12.Foreman-Mackey D , HoggDW, LangD, et alemcee: the MCMC hammer. Publ Astron Soc Pacific2013; 125 (925): 306–12., Foreman-Mackey D , HoggDW, LangD, et alemcee: the MCMC hammer. Publ Astron Soc Pacific2013; 125 (925): 306–12.
S. Bustin (2004)
A-Z of Quantitative PCR
S. Woloshin, Neeraj Patel, A. Kesselheim (2020)
False Negative Tests for SARS-CoV-2 Infection - Challenges and Implications.The New England journal of medicine
( Aldridge M , JohnsonO, ScarlettJ. Group testing: an information theory perspective. arXiv190206002, doi: 10.1561/0100000099, 2019, preprint: not peer reviewed.)
Aldridge M , JohnsonO, ScarlettJ. Group testing: an information theory perspective. arXiv190206002, doi: 10.1561/0100000099, 2019, preprint: not peer reviewed.Aldridge M , JohnsonO, ScarlettJ. Group testing: an information theory perspective. arXiv190206002, doi: 10.1561/0100000099, 2019, preprint: not peer reviewed., Aldridge M , JohnsonO, ScarlettJ. Group testing: an information theory perspective. arXiv190206002, doi: 10.1561/0100000099, 2019, preprint: not peer reviewed.
( Kwiatkowski TJ Jr , ZoghbiHY, LedbetterSA, et alRapid identification of yeast artificial chromosome clones by matrix pooling and crude lysate PCR. Nucleic Acids Res1990; 18 (23): 7191–2.2263507)
Kwiatkowski TJ Jr , ZoghbiHY, LedbetterSA, et alRapid identification of yeast artificial chromosome clones by matrix pooling and crude lysate PCR. Nucleic Acids Res1990; 18 (23): 7191–2.2263507Kwiatkowski TJ Jr , ZoghbiHY, LedbetterSA, et alRapid identification of yeast artificial chromosome clones by matrix pooling and crude lysate PCR. Nucleic Acids Res1990; 18 (23): 7191–2.2263507, Kwiatkowski TJ Jr , ZoghbiHY, LedbetterSA, et alRapid identification of yeast artificial chromosome clones by matrix pooling and crude lysate PCR. Nucleic Acids Res1990; 18 (23): 7191–2.2263507
( Kucirka LM , LauerSA, LaeyendeckerO, et alVariation in false-negative rate of reverse transcriptase polymerase chain reaction–based SARS-CoV-2 tests by time since exposure. Ann Intern Med2020; 173 (4): 262–7.32422057)
Kucirka LM , LauerSA, LaeyendeckerO, et alVariation in false-negative rate of reverse transcriptase polymerase chain reaction–based SARS-CoV-2 tests by time since exposure. Ann Intern Med2020; 173 (4): 262–7.32422057Kucirka LM , LauerSA, LaeyendeckerO, et alVariation in false-negative rate of reverse transcriptase polymerase chain reaction–based SARS-CoV-2 tests by time since exposure. Ann Intern Med2020; 173 (4): 262–7.32422057, Kucirka LM , LauerSA, LaeyendeckerO, et alVariation in false-negative rate of reverse transcriptase polymerase chain reaction–based SARS-CoV-2 tests by time since exposure. Ann Intern Med2020; 173 (4): 262–7.32422057
L. Basso, Vicente Salinas, Denis Sauré, Charles Thraves, N. Yankovic (2020)
The effect of correlation and false negatives in pool testing strategies for COVID-19Health Care Management Science, 25
L. Kucirka, S. Lauer, O. Laeyendecker, D. Boon, J. Lessler (2020)
Variation in False-Negative Rate of Reverse Transcriptase Polymerase Chain Reaction–Based SARS-CoV-2 Tests by Time Since ExposureAnnals of Internal Medicine
( Daon Y , HuppertA, ObolskiU. An accurate model for SARS-CoV-2 pooled RT-PCR test errors. medRxiv2021. 10.1101/2020.12.02.20242651)
Daon Y , HuppertA, ObolskiU. An accurate model for SARS-CoV-2 pooled RT-PCR test errors. medRxiv2021. 10.1101/2020.12.02.20242651Daon Y , HuppertA, ObolskiU. An accurate model for SARS-CoV-2 pooled RT-PCR test errors. medRxiv2021. 10.1101/2020.12.02.20242651, Daon Y , HuppertA, ObolskiU. An accurate model for SARS-CoV-2 pooled RT-PCR test errors. medRxiv2021. 10.1101/2020.12.02.20242651
( Mina MJ , AndersenKG. COVID-19 testing: one size does not fit all. Science2021; 371 (6525): 126–7.33414210)
Mina MJ , AndersenKG. COVID-19 testing: one size does not fit all. Science2021; 371 (6525): 126–7.33414210Mina MJ , AndersenKG. COVID-19 testing: one size does not fit all. Science2021; 371 (6525): 126–7.33414210, Mina MJ , AndersenKG. COVID-19 testing: one size does not fit all. Science2021; 371 (6525): 126–7.33414210
(Centers for Disease Control and Prevention. Interim guidance for antigen testing for SARS-CoV-2. 2020. https://www.cdc.gov/coronavirus/2019-ncov/lab/resources/antigen-tests-guidelines.html. Accessed August 24, 2021.)
Centers for Disease Control and Prevention. Interim guidance for antigen testing for SARS-CoV-2. 2020. https://www.cdc.gov/coronavirus/2019-ncov/lab/resources/antigen-tests-guidelines.html. Accessed August 24, 2021.Centers for Disease Control and Prevention. Interim guidance for antigen testing for SARS-CoV-2. 2020. https://www.cdc.gov/coronavirus/2019-ncov/lab/resources/antigen-tests-guidelines.html. Accessed August 24, 2021., Centers for Disease Control and Prevention. Interim guidance for antigen testing for SARS-CoV-2. 2020. https://www.cdc.gov/coronavirus/2019-ncov/lab/resources/antigen-tests-guidelines.html. Accessed August 24, 2021.
K. Chaloner, I. Verdinelli (1995)
Bayesian Experimental Design: A ReviewStatistical Science, 10
T. Cover, Joy Thomas (2005)
Elements of Information Theory
A. Cherif, N. Grobe, Xiaoling Wang, P. Kotanko (2020)
Simulation of Pool Testing to Identify Patients With Coronavirus Disease 2019 Under Conditions of Limited Test AvailabilityJAMA Network Open, 3
J. Eberhardt, N. Breuckmann, C. Eberhardt (2020)
Multi-Stage Group Testing Improves Efficiency of Large-Scale COVID-19 ScreeningJournal of Clinical Virology, 128
(World Health Organization. Antigen-detection in the diagnosis of SARS-CoV-2 infection using rapid immunoassays. 2020. https://www.who.int/publications/i/item/antigen-detection-in-the-diagnosis-of-sars-cov-2infection-using-rapid-immunoassays. Accessed August 24, 2021.)
World Health Organization. Antigen-detection in the diagnosis of SARS-CoV-2 infection using rapid immunoassays. 2020. https://www.who.int/publications/i/item/antigen-detection-in-the-diagnosis-of-sars-cov-2infection-using-rapid-immunoassays. Accessed August 24, 2021.World Health Organization. Antigen-detection in the diagnosis of SARS-CoV-2 infection using rapid immunoassays. 2020. https://www.who.int/publications/i/item/antigen-detection-in-the-diagnosis-of-sars-cov-2infection-using-rapid-immunoassays. Accessed August 24, 2021., World Health Organization. Antigen-detection in the diagnosis of SARS-CoV-2 infection using rapid immunoassays. 2020. https://www.who.int/publications/i/item/antigen-detection-in-the-diagnosis-of-sars-cov-2infection-using-rapid-immunoassays. Accessed August 24, 2021.
Q. Jing, Mingjin Liu, Zhoubing Zhang, L. Fang, Jun Yuan, Anran Zhang, N. Dean, L. Luo, M. Ma, I. Longini, E. Kenah, Ying Lu, Yu Ma, Neda Jalali, Zhicong Yang, Yang Yang (2020)
Household secondary attack rate of COVID-19 and associated determinants in Guangzhou, China: a retrospective cohort studyThe Lancet. Infectious Diseases, 20
Hrayer Aprahamian, D. Bish, E. Bish (2020)
Optimal Group Testing: Structural Properties and Robust Solutions, with Application to Public Health ScreeningINFORMS J. Comput., 32
( Alexanderian A , PetraN, StadlerG, et alA-optimal design of experiments for infinite-dimensional Bayesian linear inverse problems with regularized ℓ0-sparsification. SIAM J Sci Comput2014; 36 (5): A2122–A2148.)
Alexanderian A , PetraN, StadlerG, et alA-optimal design of experiments for infinite-dimensional Bayesian linear inverse problems with regularized ℓ0-sparsification. SIAM J Sci Comput2014; 36 (5): A2122–A2148.Alexanderian A , PetraN, StadlerG, et alA-optimal design of experiments for infinite-dimensional Bayesian linear inverse problems with regularized ℓ0-sparsification. SIAM J Sci Comput2014; 36 (5): A2122–A2148., Alexanderian A , PetraN, StadlerG, et alA-optimal design of experiments for infinite-dimensional Bayesian linear inverse problems with regularized ℓ0-sparsification. SIAM J Sci Comput2014; 36 (5): A2122–A2148.
B. Cleary, J. Hay, B. Blumenstiel, M. Harden, Michelle Cipicchio, Jon Bezney, Brooke Simonton, D. Hong, Madikay Senghore, A. Sesay, S. Gabriel, A. Regev, M. Mina (2020)
Using viral load and epidemic dynamics to optimize pooled testing in resource-constrained settingsScience Translational Medicine, 13
T. Kwiatkowski, H. Zoghbi, S. Ledbetter, K. Ellison, A. Chinault (1990)
Rapid identification of yeast artificial chromosome clones by matrix pooling and crude lysate PCR.Nucleic acids research, 18 23
( Ben-Ami R , KlochendlerA, SeidelM, et al; Hebrew University-Hadassah COVID-19 Diagnosis Team. Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection. Clin Microbiol Infect2020; 26 (9): 1248–53.32585353)
Ben-Ami R , KlochendlerA, SeidelM, et al; Hebrew University-Hadassah COVID-19 Diagnosis Team. Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection. Clin Microbiol Infect2020; 26 (9): 1248–53.32585353Ben-Ami R , KlochendlerA, SeidelM, et al; Hebrew University-Hadassah COVID-19 Diagnosis Team. Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection. Clin Microbiol Infect2020; 26 (9): 1248–53.32585353, Ben-Ami R , KlochendlerA, SeidelM, et al; Hebrew University-Hadassah COVID-19 Diagnosis Team. Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection. Clin Microbiol Infect2020; 26 (9): 1248–53.32585353
( Chaloner K , VerdinelliI. Bayesian experimental design: a review. Stat Sci1995; 10 (3): 273–304.)
Chaloner K , VerdinelliI. Bayesian experimental design: a review. Stat Sci1995; 10 (3): 273–304.Chaloner K , VerdinelliI. Bayesian experimental design: a review. Stat Sci1995; 10 (3): 273–304., Chaloner K , VerdinelliI. Bayesian experimental design: a review. Stat Sci1995; 10 (3): 273–304.
S. Lam, Antoine Pitrou, S. Seibert (2015)
Numba: a LLVM-based Python JIT compiler
M. Mina, R. Parker, D. Larremore (2020)
Rethinking Covid-19 Test Sensitivity - A Strategy for Containment.The New England journal of medicine
Hae-Young Kim, M. Hudgens, J. Dreyfuss, D. Westreich, C. Pilcher (2007)
Comparison of Group Testing Algorithms for Case Identification in the Presence of Test ErrorBiometrics, 63
K. Ryan (2003)
Estimating Expected Information Gains for Experimental Designs With Application to the Random Fatigue-Limit ModelJournal of Computational and Graphical Statistics, 12
A. Cohen, Bruce Kessel, M. Milgroom (2020)
False positives in reverse transcription PCR testing for SARS-CoV-2medRxiv
(2020)
Transmission of SARS-CoV-2 infections in households—Tennessee and Wisconsin, April-September 2020, MMWR
Puck Kasteren, B. Veer, Sharon Brink, Lisa Wijsman, J. Jonge, Anne-Marie Brandt, R. Molenkamp, C. Reusken, A. Meijer (2020)
Comparison of seven commercial RT-PCR diagnostic kits for COVID-19Journal of Clinical Virology, 128
( Cherif A , GrobeN, WangX, et alSimulation of pool testing to identify patients with coronavirus disease 2019 under conditions of limited test availability. JAMA Netw Open2020; 3 (6): e2013075.32573706)
Cherif A , GrobeN, WangX, et alSimulation of pool testing to identify patients with coronavirus disease 2019 under conditions of limited test availability. JAMA Netw Open2020; 3 (6): e2013075.32573706Cherif A , GrobeN, WangX, et alSimulation of pool testing to identify patients with coronavirus disease 2019 under conditions of limited test availability. JAMA Netw Open2020; 3 (6): e2013075.32573706, Cherif A , GrobeN, WangX, et alSimulation of pool testing to identify patients with coronavirus disease 2019 under conditions of limited test availability. JAMA Netw Open2020; 3 (6): e2013075.32573706
Charles Harris, K. Millman, S. Walt, R. Gommers, Pauli Virtanen, D. Cournapeau, Eric Wieser, Julian Taylor, Sebastian Berg, Nathaniel Smith, Robert Kern, Matti Picus, Stephan Hoyer, M. Kerkwijk, M. Brett, A. Haldane, Jaime R'io, Marcy Wiebe, Pearu Peterson, Pierre G'erard-Marchant, Kevin Sheppard, Tyler Reddy, Warren Weckesser, Hameer Abbasi, C. Gohlke, T. Oliphant (2020)
Array programming with NumPyNature, 585
( Basso LJ , SalinasV, SaureD, et al The effect of correlation and false negatives in pool testing strategies for COVID-19. Available SSRN 3732829 2020. 10.2139/ssrn.3732829)
Basso LJ , SalinasV, SaureD, et al The effect of correlation and false negatives in pool testing strategies for COVID-19. Available SSRN 3732829 2020. 10.2139/ssrn.3732829Basso LJ , SalinasV, SaureD, et al The effect of correlation and false negatives in pool testing strategies for COVID-19. Available SSRN 3732829 2020. 10.2139/ssrn.3732829, Basso LJ , SalinasV, SaureD, et al The effect of correlation and false negatives in pool testing strategies for COVID-19. Available SSRN 3732829 2020. 10.2139/ssrn.3732829
( Cover TM, Thomas, JA. Elements of Information Theory. New York, NY: John Wiley & Sons; 1999.)
Cover TM, Thomas, JA. Elements of Information Theory. New York, NY: John Wiley & Sons; 1999.Cover TM, Thomas, JA. Elements of Information Theory. New York, NY: John Wiley & Sons; 1999., Cover TM, Thomas, JA. Elements of Information Theory. New York, NY: John Wiley & Sons; 1999.
(2004)
CA: International University Line
D. Lindley (1956)
On a Measure of the Information Provided by an ExperimentAnnals of Mathematical Statistics, 27
Wei Li, Bo Zhang, Jian-hua Lu, Shihua Liu, Zhi-rong Chang, Peng Cao, Xinhua Liu, Peng Zhang, Yan Ling, K. Tao, Jianying Chen (2020)
The characteristics of household transmission of COVID-19Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
Adam Foster, M. Jankowiak, Eli Bingham, Paul Horsfall, Y. Teh, Tom Rainforth, Noah Goodman (2019)
Variational Bayesian Optimal Experimental Design
N. Barak, R. Ben-Ami, T. Sido, A. Perri, A. Shtoyer, M. Rivkin, T. Licht, A. Peretz, J. Magenheim, I. Fogel, A. Livneh, Y. Daitch, E. Oiknine-Djian, G. Benedek, Y. Dor, D. Wolf, M. Yassour (2020)
Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR testsScience Translational Medicine, 13
M. Mina, K. Andersen (2020)
COVID-19 testing: One size does not fit allScience, 371
S. Bustin, T. Nolan (2020)
RT-qPCR Testing of SARS-CoV-2: A PrimerInternational Journal of Molecular Sciences, 21
( Cohen AN , KesselB. False positives in reverse transcription PCR testing for SARS-CoV-2. MedRxiv2020. 10.1101/2020.04.26.20080911)
Cohen AN , KesselB. False positives in reverse transcription PCR testing for SARS-CoV-2. MedRxiv2020. 10.1101/2020.04.26.20080911Cohen AN , KesselB. False positives in reverse transcription PCR testing for SARS-CoV-2. MedRxiv2020. 10.1101/2020.04.26.20080911, Cohen AN , KesselB. False positives in reverse transcription PCR testing for SARS-CoV-2. MedRxiv2020. 10.1101/2020.04.26.20080911
X. Huan, Y. Marzouk (2011)
Simulation-based optimal Bayesian experimental design for nonlinear systemsJ. Comput. Phys., 232
(1997)
Monte Carlo methods in statistical mechanics: foundations and new algorithms In: Functional Integration
ObjectiveTesting individuals for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen causing the coronavirus disease 2019 (COVID-19), is crucial for curtailing transmission chains. Moreover, rapidly testing many potentially infected individuals is often a limiting factor in controlling COVID-19 outbreaks. Hence, pooling strategies, wherein individuals are grouped and tested simultaneously, are employed. Here, we present a novel pooling strategy that builds on the Bayesian D-optimal experimental design criterion.Materials and MethodsOur strategy, called DOPE (D-Optimal Pooling Experimental design), is built on a novel Bayesian formulation of pooling. DOPE defines optimal pooled tests as those maximizing the mutual information between data and infection states. We estimate said mutual information via Monte-Carlo sampling and employ a discrete optimization heuristic to maximize it.ResultsWe compare DOPE to other, commonly used pooling strategies, as well as to individual testing. DOPE dominates the other strategies as it yields lower error rates while utilizing fewer tests. We show that DOPE maintains this dominance for a variety of infection prevalence values.DiscussionDOPE has several additional advantages over common pooling strategies: it provides posterior distributions of the probability of infection rather than only binary classification outcomes; it naturally incorporates prior information of infection probabilities and test error rates; and finally, it can be easily extended to include other, newly discovered information regarding COVID-19.ConclusionDOPE can substantially improve accuracy and throughput over current pooling strategies. Hence, DOPE can facilitate rapid testing and aid the efforts of combating COVID-19 and other future pandemics.
Journal of the American Medical Informatics Association – Oxford University Press
Published: Oct 11, 2021
Keywords: Bayesian; Monte-Carlo; epidemiology; COVID-19; RT-PCR
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.