Correlation Improves Group Testing: Modeling Concentration-Dependent Test Errors

Published Online:https://doi.org/10.1287/mnsc.2021.04217

References

  • Aprahamian H, Bish DR, Bish EK (2019) Optimal risk-based group testing. Management Sci. 65(9):4365–4384.LinkGoogle Scholar
  • Augenblick N, Kolstad JT, Obermeyer Z, Wang A (2020) Group testing in a pandemic: The role of frequent testing, correlated risk, and machine learning. Technical report, National Bureau of Economic Research, Cambridge, MA.Google Scholar
  • Barak N, Ben-Ami R, Sido T, Perri A, Shtoyer A, Rivkin M, Licht T, et al. (2021) Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests. Sci. Translational Medicine 13(589):eabf2823.CrossrefGoogle Scholar
  • Basso LJ, Salinas V, Sauré D, Thraves C, Yankovic N (2021) The effect of correlation and false negatives in pool testing strategies for COVID-19. Health Care Management Sci. 25(1):146–165. Google Scholar
  • Basu AS (2017) Digital assays part I: Partitioning statistics and digital PCR. SLAS Tech. Translating Life Sci. Innovation 22(4):369–386.CrossrefGoogle Scholar
  • Bateman AC, Mueller S, Guenther K, Shult P (2020) Assessing the dilution effect of specimen pooling on the sensitivity of SARS-CoV-2 PCR tests. J. Medical Virology 93(3):1568–1572.CrossrefGoogle Scholar
  • Bharti AR, Letendre SL, Patra KP, Vinetz JM, Smith DM (2009) Malaria diagnosis by a polymerase chain reaction–based assay using a pooling strategy. Amer. J. Tropical Medicine Hygiene 81(5):754.CrossrefGoogle Scholar
  • Bilder CR, Tebbs JM (2012) Pooled-testing procedures for screening high volume clinical specimens in heterogeneous populations. Statist. Medicine 31(27):3261–3268.CrossrefGoogle Scholar
  • Bilder CR, Tebbs JM, Chen P (2010) Informative retesting. J. Amer. Statist. Assoc. 105(491):942–955.CrossrefGoogle Scholar
  • Brault V, Mallein B, Rupprecht JF (2021) Group testing as a strategy for COVID-19 epidemiological monitoring and community surveillance. PLoS Comput. Biology 17(3):e1008726.CrossrefGoogle Scholar
  • Carcione D, Giele C, Goggin L, Kwan KS, Smith D, Dowse G, Mak D, et al. (2011) Secondary attack rate of pandemic influenza A (H1N1) 2009 in Western Australian households, 29 May–7 August 2009. Eurosurveillance 16(3):19765.CrossrefGoogle Scholar
  • Chang L, Zhao J, Guo F, Ji H, Zhang L, Jiang X, Wang L, et al. (2020) Comparative evaluation and measure of accuracy of ELISAs, CLIAs, and ECLIAs for the detection of HIV infection among blood donors in China. Canadian J. Infectious Diseases Medical Microbiology 2020(1):2164685.CrossrefGoogle Scholar
  • Chatterjee S, Aprahamian H (2022) Capturing the dilution effect of risk-based grouping with application to covid-19 screening. Naval Res. Logist. 72(1):24–44.CrossrefGoogle Scholar
  • Chatterjee K, Agarwal N, Coshic P, Borgohain M, Chakroborty S (2014) Sensitivity of individual and mini-pool nucleic acid testing assessed by dilution of hepatitis B nucleic acid testing yield samples. Asian J. Transfusion Sci. 8(1):26–28.CrossrefGoogle Scholar
  • Cheraghchi M, Karbasi A, Mohajer S, Saligrama V (2012) Graph-constrained group testing. IEEE Trans. Inform. Theory 58(1):248–262.CrossrefGoogle Scholar
  • Cleary B, Hay JA, Blumenstiel B, Harden M, Cipicchio M, Bezney J, Simonton B, et al. (2021) Using viral load and epidemic dynamics to optimize pooled testing in resource-constrained settings. Sci. Translational Medicine 13(589):eabf1568.CrossrefGoogle Scholar
  • Comess S, Wang H, Holmes S, Donnat C (2022) Statistical modeling for practical pooled testing during the COVID-19 pandemic. Statist. Sci. 37(2):229–250.Google Scholar
  • Deckert A, Bärnighausen T, Kyei NN (2020) Simulation of pooled-sample analysis strategies for COVID-19 mass testing. Bull. World Health Organ. 98(9):590.CrossrefGoogle Scholar
  • Denny TN (2020) Implementation of a pooled surveillance testing program for asymptomatic SARS-CoV-2 infections on a college campus—Duke university, Durham, North Carolina, August 2–October 11, 2020. Morbidity Mortality Weekly Rep 69(45):1743–1747.Google Scholar
  • Dorfman R (1943) The detection of defective members of large populations. Ann. Math. Statist. 14(4):436–440.CrossrefGoogle Scholar
  • Eberhardt JN, Breuckmann NP, Eberhardt CS (2020) Multi-stage group testing improves efficiency of large-scale COVID-19 screening. J. Clinical Virology 128:104382.CrossrefGoogle Scholar
  • Fan W (2020) Wuhan tests nine million people for coronavirus in 10 days. Accessed May 18, 2021, https://www.wsj.com/articles/wuhan-tests-nine-million-people-for-coronavirus-in-10-days-11590408910.Google Scholar
  • Ganesan A, Jaggi S, Saligrama V (2017) Learning immune-defectives graph through group tests. IEEE Trans. Inform. Theory 63(5):3010–3028.Google Scholar
  • Ghaffari A, Meurant R, Ardakani A (2020) COVID-19 serological tests: How well do they actually perform? Diagnostics 10(7):453.CrossrefGoogle Scholar
  • Glynn JR, Bower H, Johnson S, Turay C, Sesay D, Mansaray SH, Kamara O, et al. (2018) Variability in intrahousehold transmission of Ebola virus, and estimation of the household secondary attack rate. J. Infectious Dis. 217(2):232–237.CrossrefGoogle Scholar
  • Graff LE, Roeloffs R (1972) Group testing in the presence of test error; an extension of the Dorfman procedure. Technometrics 14(1):113–122.CrossrefGoogle Scholar
  • Han X, Li J, Chen Y, Li Y, Xu Y, Ying B, Shang H (2022) SARS-CoV-2 nucleic acid testing is China’s key pillar of COVID-19 containment. Lancet 399(10336):1690–1691.CrossrefGoogle Scholar
  • Hsiang MS, Lin M, Dokomajilar C, Kemere J, Pilcher CD, Dorsey G, Greenhouse B (2010) PCR-based pooling of dried blood spots for detection of malaria parasites: Optimization and application to a cohort of Ugandan children. J. Clinical Microbiology 48(10):3539–3543.CrossrefGoogle Scholar
  • Hu H, Nigmatulina K, Eckhoff P (2013) The scaling of contact rates with population density for the infectious disease models. Math. Biosciences 244(2):125–134. CrossrefGoogle Scholar
  • Hung M, Swallow WH (1999) Robustness of group testing in the estimation of proportions. Biometrics 55(1):231–237.CrossrefGoogle Scholar
  • Hwang FK (1976) Group testing with a dilution effect. Biometrika 63(3):671–680.CrossrefGoogle Scholar
  • Jones C (2021) Wuhan tests nine million people for coronavirus in 10 days. Accessed March 18, 2024, https://edsource.org/2021/pool-testing-to-combat-covid-on-campus-grows-popular-in-california-schools/661144.Google Scholar
  • Kemper M, Witt D, Madsen T, Kuramoto K, Holland P (1998) The effects of dilution on the outcome of pooled plasma testing with HIV type 1 (HIV-1) RNA genome amplification as compared to the outcome of individual-unit testing with other HIV-1 markers. Transfusion 38(5):469–472.CrossrefGoogle Scholar
  • Kermack WO, McKendrick AG (1927) A contribution to the mathematical theory of epidemics. Proc. Roy. Soc. London. Ser. A 115(772):700–721.CrossrefGoogle Scholar
  • Kim HY, Hudgens MG, Dreyfuss JM, Westreich DJ, Pilcher CD (2007) Comparison of group testing algorithms for case identification in the presence of test error. Biometrics 63(4):1152–1163.CrossrefGoogle Scholar
  • Lan FY, Wei CF, Hsu YT, Christiani DC, Kales SN (2020) Work-related COVID-19 transmission in six Asian countries/areas: A follow-up study. PLoS One 15(5):e0233588.CrossrefGoogle Scholar
  • Larremore DB, Wilder B, Lester E, Shehata S, Burke JM, Hay JA, Tambe M, et al. (2021) Test sensitivity is secondary to frequency and turnaround time for COVID-19 screening. Sci. Advances 7(1):eabd5393.CrossrefGoogle Scholar
  • Laverack M, Tallmadge RL, Venugopalan R, Sheehan D, Ross S, Rustamov R, Frederici C, et al. (2023) The Cornell COVID-19 testing laboratory: A model to high-capacity testing hubs for infectious disease emergency response and preparedness. Viruses 15(7):1555.CrossrefGoogle Scholar
  • Lefkowitz M (2020) Robots, know-how drive COVID lab’s massive testing effort. Accessed June 23, 2021, https://news.cornell.edu/stories/2020/08/robots-know-how-drive-covid-labs-massive-testing-effort.Google Scholar
  • Lendle SD, Hudgens MG, Qaqish BF (2012) Group testing for case identification with correlated responses. Biometrics 68(2):532–540.CrossrefGoogle Scholar
  • Lin YJ, Yu CH, Liu TH, Chang CS, Chen WT (2021) Positively correlated samples save pooled testing costs. IEEE Trans. Network Sci. Engrg. 8(3):2170–2182.Google Scholar
  • Liu Y, Yan LM, Wan L, Xiang TX, Le A, Liu JM, Peiris M, et al. (2020) Viral dynamics in mild and severe cases of COVID-19. Lancet Infectious Dis. 20(6):656–657.CrossrefGoogle Scholar
  • Lohse S, Pfuhl T, Berkó-Göttel B, Rissland J, Geiβler T, Gärtner B, Becker SL, et al. (2020) Pooling of samples for testing for SARS-CoV-2 in asymptomatic people. Lancet Infectious Dis. 20(11):1231–1232.CrossrefGoogle Scholar
  • Madewell ZJ, Yang Y, Longini IM Jr, Halloran ME, Dean NE (2020) Household transmission of SARS-CoV-2: A systematic review and meta-analysis of secondary attack rate. JAMA Network Open 3(12):e2031756.Google Scholar
  • Mahase E (2020) COVID-19: Universities roll out pooled testing of students in bid to keep campuses open. British Medical J. 370:m3789.Google Scholar
  • McGee RS (2021) SEIRS+ model framework. Accessed June 1, 2023, https://github.com/ryansmcgee/seirsplus.Google Scholar
  • McMahan CS, Tebbs JM, Bilder CR (2012a) Informative dorfman screening. Biometrics 68(1):287–296.CrossrefGoogle Scholar
  • McMahan CS, Tebbs JM, Bilder CR (2012b) Two-dimensional informative array testing. Biometrics 68(3):793–804.CrossrefGoogle Scholar
  • Mendoza RP, Bi C, Cheng HT, Gabutan E, Pagaspas GJ, Khan N, Hoxie H, et al. (2021) Implementation of a pooled surveillance testing program for asymptomatic SARS-CoV-2 infections in K-12 schools and universities. EClinicalMedicine 38:101028.CrossrefGoogle Scholar
  • Meningococcal Disease Surveillance Group (1976) Meningococcal disease. Secondary attack rate and chemoprophylaxis in the united states, 1974. J. Amer. Medical Assoc. 235(3):261–265.CrossrefGoogle Scholar
  • Mercer TR, Salit M (2021) Testing at scale during the COVID-19 pandemic. Nature Rev. Genetics 22(7):415–426.CrossrefGoogle Scholar
  • Mutesa L, Ndishimye P, Butera Y, Souopgui J, Uwineza A, Rutayisire R, Musoni E, et al. (2021) A pooled testing strategy for identifying SARS-CoV-2 at low prevalence. Nature 589(7481):276–280.Google Scholar
  • Odaira F, Takahashi H, Toyokawa T, Tsuchihashi Y, Kodama T, Yahata Y, Sunagawa T, et al. (2009) Assessment of secondary attack rate and effectiveness of antiviral prophylaxis among household contacts in an influenza A(H1N1)v outbreak in Kobe, Japan, May–June 2009. Eurosurveillance 14(35):19320.CrossrefGoogle Scholar
  • Pilcher CD, Westreich D, Hudgens MG (2020) Group testing for SARS-Cov-2 to enable rapid scale-up of testing and real-time surveillance of incidence. J. Infectious Dis. 222(6):903–909.CrossrefGoogle Scholar
  • Public Health Ontario (2020) COVID-19 laboratory testing Q&As. Accessed July 9, 2021, https://www.publichealthontario.ca/-/media/documents/lab/covid-19-lab-testing-faq.pdf?la=en.Google Scholar
  • Rader B, Scarpino SV, Nande A, Hill AL, Adlam B, Reiner RC, Pigott DM, et al. (2020) Crowding and the shape of COVID-19 epidemics. Nature Medicine 26(12):1829–1834.CrossrefGoogle Scholar
  • Stanford Medicine (2020) The vera cloud testing platform, protecting our communities by enabling testing at scale. Accessed May 18, 2021, https://med.stanford.edu/vera.html.Google Scholar
  • Suo T, Liu X, Feng J, Guo M, Hu W, Guo D, Ullah H, et al. (2020) ddPCR: A more accurate tool for SARS-CoV-2 detection in low viral load specimens. Emerging Microbes Infections 9(1):1259–1268.CrossrefGoogle Scholar
  • Tebbs JM, McMahan CS, Bilder CR (2013) Two-stage hierarchical group testing for multiple infections with application to the infertility prevention project. Biometrics 69(4):1064–1073.CrossrefGoogle Scholar
  • van Kasteren PB, van Der Veer B, van Den Brink S, Wijsman L, de Jonge J, van Den Brandt A, Molenkamp R, et al. (2020) Comparison of seven commercial RT-PCR diagnostic kits for COVID-19. J. Clinical Virology 128:104412.CrossrefGoogle Scholar
  • Vang KE, Krow-Lucal ER, James AE, Cima MJ, Kothari A, Zohoori N, Porter A, et al. (2021) Participation in fraternity and sorority activities and the spread of COVID-19 among residential university communities—Arkansas, August 21–September 5, 2020. Morbidity Mortality Weekly Rep. 70(1):20.CrossrefGoogle Scholar
  • Wein LM, Zenios SA (1996) Pooled testing for HIV screening: Capturing the dilution effect. Oper. Res. 44(4):543–569.LinkGoogle Scholar
  • Westreich DJ, Hudgens MG, Fiscus SA, Pilcher CD (2008) Optimizing screening for acute human immunodeficiency virus infection with pooled nucleic acid amplification tests. J. Clinical Microbiology 46(5):1785–1792.CrossrefGoogle Scholar
  • Whalen CC, Zalwango S, Chiunda A, Malone L, Eisenach K, Joloba M, Boom WH, et al. (2011) Secondary attack rate of tuberculosis in urban households in Kampala, Uganda. PLoS One 6(2):e16137.CrossrefGoogle Scholar
  • World Health Organization (2020) Modes of transmission of virus causing COVID-19: Implications for IPC precaution recommendations: Scientific brief, 29 March 2020. Technical report, World Health Organization, Geneva.Google Scholar
  • Wyllie AL, Fournier J, Casanovas-Massana A, Campbell M, Tokuyama M, Vijayakumar P, Geng B, et al. (2020) Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs. New England J. Medicine 383(13):1283–1286.Google Scholar
  • Xing Y, Wong GW, Ni W, Hu X, Xing Q (2020) Rapid response to an outbreak in Qingdao, China. New England J. Medicine 383(23):e129.CrossrefGoogle Scholar
  • Xu T, Chen C, Zhu Z, Cui M, Chen C, Dai H, Xue Y (2020) Clinical features and dynamics of viral load in imported and non-imported patients with COVID-19. Internat. J. Infectious Diseases 94:68–71.CrossrefGoogle Scholar
  • Yelin I, Aharony N, Tamar ES, Argoetti A, Messer E, Berenbaum D, Shafran E, et al. (2020) Evaluation of COVID-19 RT-qPCR Test in multi sample pools. Clinical Infectious Diseases 71(16):2073–2078.Google Scholar
  • Zenios SA, Wein LM (1998) Pooled testing for HIV prevalence estimation: Exploiting the dilution effect. Statist. Medicine 17(13):1447–1467.CrossrefGoogle Scholar
INFORMS site uses cookies to store information on your computer. Some are essential to make our site work; Others help us improve the user experience. By using this site, you consent to the placement of these cookies. Please read our Privacy Statement to learn more.