Disease Bundling or Specimen Bundling? Cost- and Capacity-Efficient Strategies for Multidisease Testing with Genetic Assays

Published Online:https://doi.org/10.1287/msom.2022.0296

References

  • Al Ghounaim M, Xiao Y, Caya C, Papenburg J (2017) Diagnostic yield and clinical impact of routine cell culture for respiratory viruses among children with a negative multiplex RT-PCR result. J. Clinical Virology 94:107–109.CrossrefGoogle Scholar
  • American Red Cross (2022) Infectious disease, HLA and ABO donor qualification testing. Accessed June 1, 2022, https://www.redcrossblood.org/biomedical-services/blood-diagnostic-testing/blood-testing.html.Google Scholar
  • Anily S, Federgruen A (1991) Structured partitioning problems. Oper. Res. 39(1):130–149.LinkGoogle Scholar
  • Aprahamian H, Bish DR, Bish EK (2020) Optimal group testing: Structural properties and robust solutions, with application to public health screening. INFORMS J. Comput. 32(4):895–911.AbstractGoogle Scholar
  • Balakrishnan G, Landeen C, Dy-Boarman EA, Wall GC (2016) Outcomes with multplex PCR respiratory sample testing on hospital inpatients: Outcomes and cost associated with a multiplex PCR system on nasopharyngeal swab specimens (FilmArray Respiratory Panel) in a large tertiary inpatient hospital population. J. Acad. Hospital Medicine 8(3):1–4.Google Scholar
  • Balas E, Padberg MW (1976) Set partitioning: A survey. SIAM Rev. 18(4):710–760.CrossrefGoogle Scholar
  • Barahona F, Anbil R (2002) On some difficult linear programs coming from set partitioning. Discrete Appl. Math. 118(1–2):3–11.CrossrefGoogle Scholar
  • BCL-APH (2022) Discussion with Mark Ellis of the Bureau of Clinical Laboratories—Alabama Public Health. Working paper.Google Scholar
  • Beckmann C, Hirsch HH (2016) Comparing Luminex NxTAG-Respiratory Pathogen Panel and RespiFinder-22 for multiplex detection of respiratory pathogens. J. Medical Virology 88(8):1319–1324.CrossrefGoogle Scholar
  • Biomérieux (2022) FILMARRAYTM Respiratory Panel. Accessed June 1, 2022, https://www.biomerieux-nordic.com/product/filmarray-respiratory-panel.Google Scholar
  • Bish DR, Bish EK, El Hajj H, Aprahamian H (2021) A robust pooled testing approach to expand COVID-19 screening capacity. PLoS One 16(2):e0246285.CrossrefGoogle Scholar
  • Borges CM, Pathela P, Pirillo R, Blank S (2015) Targeting the use of pooled HIV RNA screening to reduce cost in health department STD clinics: New York City, 2009–2011. Public Health Rep. 130(1):81–86.CrossrefGoogle Scholar
  • Boschetti MA, Mingozzi A, Ricciardelli S (2008) A dual ascent procedure for the set partitioning problem. Discrete Optim. 5(4):735–747.CrossrefGoogle Scholar
  • Centers for Disease Control and Prevention (2021a) Interim guidance for use of pooling procedures in sars-cov-2 diagnostic and screening testing. Accessed June 1, 2022, https://www.cdc.gov/coronavirus/2019-ncov/lab/pooling-procedures.html.Google Scholar
  • Centers for Disease Control and Prevention (2021b) Nucleic acid amplification tests (NAATs). Accessed June 1, 2022, https://www.cdc.gov/coronavirus/2019-ncov/lab/naats.html.Google Scholar
  • Centers for Disease Control and Prevention (2021c) Past weekly surveillance reports. Accessed June 1, 2022, https://www.cdc.gov/coronavirus/2019-ncov/covid-data/covidview/index.html.Google Scholar
  • Centers for Disease Control and Prevention (2022a) Similarities and differences between flu and COVID-19. Accessed June 1, 2022, https://www.cdc.gov/flu/symptoms/flu-vs-covid19.htm.Google Scholar
  • Centers for Disease Control and Prevention (2022b) The National Respiratory and Enteric Virus Surveillance System (NREVSS). Accessed June 1, 2022, https://www.cdc.gov/surveillance/nrevss/.Google Scholar
  • Centers for Disease Control and Prevention Influenza Division (2022) FluView—Weekly U.S. Influenza Surveillance Report. Accessed June 1, 2022, https://www.cdc.gov/flu/weekly/#ClinicalLaboratories.Google Scholar
  • Chakravarty AK, Orlin JB, Rothblum UG (1982) A partitioning problem with additive objective with an application to optimal inventory groupings for joint replenishment. Oper. Res. 30(5):1018–1022.LinkGoogle Scholar
  • Chan M, Koo SH, Jiang B, Lim PQ, Tan TY (2018) Comparison of the Biofire Film Array Respiratory Panel, Seegene AnyplexII RV16, and Argene for the detection of respiratory viruses. J. Clinical Virology 106:13–17.CrossrefGoogle Scholar
  • Chan TJ, Yano CA (1992) A multiplier adjustment approach for the set partitioning problem. Oper. Res. 40(1 suppl 1):S40–S47.LinkGoogle Scholar
  • Chen H, Weng H, Lin M, He P, Li Y, Xie Q, Ke C, Jiao X (2017) The clinical significance of FilmArray Respiratory Panel in diagnosing community-acquired pneumonia. BioMed Res. Internat. 2017:7320859.CrossrefGoogle Scholar
  • Corless RM, Gonnet GH, Hare DE, Jeffrey DJ, Knuth DE (1996) On the LambertW function. Adv. Comput. Math. 5(1):329–359.CrossrefGoogle Scholar
  • Cormen TH, Leiserson CE, Rivest RL, Stein C (2009) Introduction to Algorithms (MIT Press, Cambridge, MA).Google Scholar
  • Dai B, Ding S, Wahba G (2013) Multivariate Bernoulli distribution. Bernoulli 19(4):1465–1483.CrossrefGoogle Scholar
  • Das S, Dunbar S, Tang Y-W (2018) Laboratory diagnosis of respiratory tract infections in children—The state of the art. Frontiers Microbiology 9:2478.CrossrefGoogle Scholar
  • Dorfman R (1943) The detection of defective members of large populations. Ann. Math. Statist. 14(4):436–440.CrossrefGoogle Scholar
  • El Amine H, Bish EK, Bish DR (2017) Robust post-donation blood screening under prevalence rate uncertainty. Oper. Res. 66(1):1–17.LinkGoogle Scholar
  • El Hajj H, Bish DR, Bish EK (2022a) Optimal genetic screening for cystic fibrosis. Oper. Res. 70(1):265–287.LinkGoogle Scholar
  • El Hajj H, Bish DR, Bish EK, Aprahamian H (2022b) Screening multi-dimensional heterogeneous populations for infectious diseases under scarce testing resources, with application to COVID-19. Naval Res. Logist. 69(1):3–20.CrossrefGoogle Scholar
  • El Hajj H, Bish DR, Bish EK, Kay D (2022c) Novel pooling strategies for genetic testing, with application to newborn screening. Management Sci. 68(11):7994–8014.LinkGoogle Scholar
  • Elmachtoub AN, Levi R (2016) Supply chain management with online customer selection. Oper. Res. 64(2):458–473.LinkGoogle Scholar
  • Emrich L, Piedmonte M (1991) A method for generating high-dimensional multivariate binary variates. Amer. Statist. 45(4):302–303.Google Scholar
  • Fisher ML, Kedia P (1990) Optimal solution of set covering/partitioning problems using dual heuristics. Management Sci. 36(6):674–688.LinkGoogle Scholar
  • Fleming-Dutra KE, Hersh AL, Shapiro DJ, Bartoces M, Enns EA, File TM, Finkelstein JA, et al. (2016) Prevalence of inappropriate antibiotic prescriptions among US ambulatory care visits, 2010–2011. JAMA 315(17):1864–1873.CrossrefGoogle Scholar
  • Food and Drug Administration (2020) Pooled sample testing and screening testing for COVID-19. Accessed June 1, 2022, https://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/pooled-sample-testing-and-screening-testing-covid-19.Google Scholar
  • Food and Drug Administration (2021) Nucleic acid based tests. Accessed June 1, 2022, https://www.fda.gov/medical-devices/in-vitro-diagnostics/nucleic-acid-based-tests.Google Scholar
  • Gharabaghi F, Hawan A, Drews SJ, Richardson SE (2011) Evaluation of multiple commercial molecular and conventional diagnostic assays for the detection of respiratory viruses in children. Clinical Microbiology Infect. 17(12):1900–1906.CrossrefGoogle Scholar
  • Ginocchio CC, McAdam AJ (2011) Current best practices for respiratory virus testing. J. Clinical Microbiology 49:S44–S48.CrossrefGoogle Scholar
  • Golrezaei N, Nazerzadeh H, Rusmevichientong P (2014) Real-time optimization of personalized assortments. Management Sci. 60(6):1532–1551.LinkGoogle Scholar
  • Gonsalves S, Mahony J, Rao A, Dunbar S, Juretschko S (2019) Multiplexed detection and identification of respiratory pathogens using the NxTAG® respiratory pathogen panel. Methods 158:61–68.CrossrefGoogle Scholar
  • Hou P, Tebbs JM, Bilder CR, McMahan CS (2017) Hierarchical group testing for multiple infections. Biometrics 73(2):656–665.CrossrefGoogle Scholar
  • Hou P, Tebbs JM, Wang D, McMahan CS, Bilder CR (2020) Array testing for multiplex assays. Biostatistics 21(3):417–431.CrossrefGoogle Scholar
  • Hwang FK (1981) Optimal partitions. J. Optim. Theory Appl. 34(1):1–10.CrossrefGoogle Scholar
  • Hwang FK, Sun J, Yao EY (1985) Optimal set partitioning. SIAM J. Algebraic Discrete Methods 6(1):163–170.CrossrefGoogle Scholar
  • Johns Hopkins University (2022) Coronavirus Resource Center. Accessed June 1, 2022, https://coronavirus.jhu.edu/region/united-states.Google Scholar
  • Johnson M (2021) PCR machines. Materials Methods 3:193.Google Scholar
  • Kenmoe S, Tcharnenwa C, Monamele GC, Kengne CN, Ripa MN, Whitaker B, Alroy KA, et al. (2019) Comparison of FTD® respiratory pathogens 33 and a singleplex CDC assay for the detection of respiratory viruses: A study from Cameroon. Diagnostic Microbiology Infectious Disease 94(3):236–242.CrossrefGoogle Scholar
  • Keyvanshokooh E, Shi C, Van Oyen MP (2021) Online advance scheduling with overtime: A primal-dual approach. Manufacturing Service Oper. Management 23(1):246–266.LinkGoogle Scholar
  • Kim H-Y, 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
  • Leland DS, Ginocchio CC (2007) Role of cell culture for virus detection in the age of technology. Clinical Microbiology Rev. 20(1):49–78.CrossrefGoogle Scholar
  • Levine D (1996) A Parallel Genetic Algorithm for the Set Partitioning Problem (Springer, Boston), 23–35.CrossrefGoogle Scholar
  • Lewis M, Kochenberger G, Alidaee B (2008) A new modeling and solution approach for the set-partitioning problem. Comput. Oper. Res. 35(3):807–813.CrossrefGoogle Scholar
  • Lindan C, Mathur M, Kumta S, Jerajani H, Gogate A, Schachter J, Moncada J (2005) Utility of pooled urine specimens for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in men attending public sexually transmitted infection clinics in Mumbai, India, by PCR. J. Clinical Microbiology 43(4):1674–1677.CrossrefGoogle Scholar
  • Llor C, Bjerrum L (2014) Antimicrobial resistance: Risk associated with antibiotic overuse and initiatives to reduce the problem. Therapeutic Adv. Drug Safety 5(6):229–241.CrossrefGoogle Scholar
  • Mahony JB, Blackhouse G, Babwah J, Smieja M, Buracond S, Chong S, Ciccotelli W, et al. (2009) Cost analysis of multiplex PCR testing for diagnosing respiratory virus infections. J. Clinical Microbiology 47(9):2812–2817.CrossrefGoogle Scholar
  • Manne F, Sorevik T (1995) Optimal partitioning of sequences. J. Algorithms 19(2):235–249.CrossrefGoogle Scholar
  • Mastrantonio P, Stefanelli P, Giuliano M, Herrera Rojas Y, Ciofi degli Atti M, Anemona A, Tozzi AE (1998) Bordetella parapertussis infection in children: Epidemiology, clinical symptoms, and molecular characteristics of isolates. J. Clinical Microbiology 36(4):999–1002.CrossrefGoogle Scholar
  • May S, Gamst A, Haubrich R, Benson C, Smith DM (2010) Pooled nucleic acid testing to identify antiretroviral treatment failure during HIV infection. J. Acquired Immune Deficiency Syndromes 53(2):194–201.CrossrefGoogle Scholar
  • Newcombe RG (1998) Two-sided confidence intervals for the single proportion: Comparison of seven methods. Statist. Medicine 17(8):857–872.CrossrefGoogle Scholar
  • Nguyen NT, Bish EK, Bish DR (2021) Optimal pooled testing design for prevalence estimation under resource constraints. Omega 105:102504.CrossrefGoogle Scholar
  • Nguyen NT, Aprahamian H, Bish EK, Bish DR (2019) A methodology for deriving the sensitivity of pooled testing, based on viral load progression and pooling dilution. J. Translational Medicine 17(1):1–10.CrossrefGoogle Scholar
  • Ogilvie M (2001) Molecular techniques should not now replace cell culture in diagnostic virology laboratories. Rev. Medical Virology 11(6):351–354.CrossrefGoogle Scholar
  • Olstad B, Manne F (1995) Efficient partitioning of sequences. IEEE Trans. Comput. 44(11):1322–1326.CrossrefGoogle Scholar
  • Oved K, Cohen A, Boico O, Navon R, Friedman T, Etshtein L, Kriger O, et al. (2015) A novel host-proteome signature for distinguishing between acute bacterial and viral infections. PLoS One 10(3):e0120012.CrossrefGoogle Scholar
  • Perakis G, Roels G (2008) Regret in the newsvendor model with partial information. Oper. Res. 56(1):188–203.LinkGoogle Scholar
  • Pinsky B, Hayden R (2019) Cost-effective respiratory virus testing. J. Clinical Microbiology 57(9):e00373-19.CrossrefGoogle Scholar
  • Rachlin J, Ding C, Cantor C, Kasif S (2005) MuPlex: Multi-objective multiplex PCR assay design. Nucleic Acids Res. 33(suppl 2):W544–W547.CrossrefGoogle Scholar
  • Ramanan P, Bryson AL, Binnicker MJ, Pritt BS, Patel R (2018) Syndromic panel-based testing in clinical microbiology. Clinical Microbiology Rev. 31(1):e00024-17.CrossrefGoogle Scholar
  • Rogers BB, Shankar P, Jerris RC, Kotzbauer D, Anderson EJ, Watson JR, O’Brien LA, Uwindatwa F, McNamara K, Bost JE (2015) Impact of a rapid respiratory panel test on patient outcomes. Arch. Pathology Laboratory Medicine 139(5):636–641.CrossrefGoogle Scholar
  • Schreckenberger PC, McAdam AJ (2015) Point-counterpoint: Large multiplex PCR panels should be first-line tests for detection of respiratory and intestinal pathogens. J. Clinical Microbiology 53(10):3110–3115.CrossrefGoogle Scholar
  • Subramony A, Zachariah P, Krones A, Whittier S, Saiman L (2016) Impact of multiplex polymerase chain reaction testing for respiratory pathogens on healthcare resource utilization for pediatric inpatients. J. Pediatrics 173:196–201.CrossrefGoogle Scholar
  • Taylor SM, Juliano JJ, Trottman PA, Griffin JB, Landis SH, Kitsa P, Tshefu AK, Meshnick SR (2010) High-throughput pooling and real-time PCR-based strategy for malaria detection. J. Clinical Microbiology 48(2):512–519.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
  • Templeton KE (2007) Why diagnose respiratory viral infection? J. Clinical Virology 40:S2–S4.CrossrefGoogle Scholar
  • Vallières E, Renaud C (2013) Clinical and economical impact of multiplex respiratory virus assays. Diagnostic Microbiology Infectious Disease 76(3):255–261.CrossrefGoogle Scholar
  • Van TT, Miller J, Warshauer DM, Reisdorf E, Jernigan D, Humes R, Shult PA (2012) Pooling nasopharyngeal/throat swab specimens to increase testing capacity for influenza viruses by PCR. J. Clinical Microbiology 50(3):891–896.CrossrefGoogle Scholar
  • Van Hulst M, Hubben GA, Sagoe KW, Promwong C, Permpikul P, Fongsatitkul L, Glynn DM, Smit Sibinga CT, Postma MJ (2009) Web interface-supported transmission risk assessment and cost-effectiveness analysis of postdonation screening: A global model applied to Ghana, Thailand, and the Netherlands. Transfusion 49(12):2729–2742.CrossrefGoogle Scholar
  • van Zyl G, Preiser W, Potschka S, Lundershausen A, Haubrich R, Smith D (2011) Pooling strategies to reduce the cost of HIV-1 RNA load monitoring in a resource-limited setting. Clinical Infectious Diseases 52(2):264–270.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.CrossrefGoogle Scholar
  • Yuan J, Yi J, Zhan M, Xie Q, Zhen TT, Zhou J, Li Z, Li Z (2021) The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: Up to 100-plex multiplicity. BMC Genomics 22(1):835.CrossrefGoogle Scholar
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