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Group testing via hypergraph factorization applied to COVID-19

Author

Listed:
  • David Hong

    (University of Pennsylvania)

  • Rounak Dey

    (Harvard T.H. Chan School of Public Health)

  • Xihong Lin

    (Harvard T.H. Chan School of Public Health
    Harvard University
    Broad Institute of MIT and Harvard)

  • Brian Cleary

    (Broad Institute of MIT and Harvard)

  • Edgar Dobriban

    (University of Pennsylvania)

Abstract

Large scale screening is a critical tool in the life sciences, but is often limited by reagents, samples, or cost. An important recent example is the challenge of achieving widespread COVID-19 testing in the face of substantial resource constraints. To tackle this challenge, screening methods must efficiently use testing resources. However, given the global nature of the pandemic, they must also be simple (to aid implementation) and flexible (to be tailored for each setting). Here we propose HYPER, a group testing method based on hypergraph factorization. We provide theoretical characterizations under a general statistical model, and carefully evaluate HYPER with alternatives proposed for COVID-19 under realistic simulations of epidemic spread and viral kinetics. We find that HYPER matches or outperforms the alternatives across a broad range of testing-constrained environments, while also being simpler and more flexible. We provide an online tool to aid lab implementation: http://hyper.covid19-analysis.org .

Suggested Citation

  • David Hong & Rounak Dey & Xihong Lin & Brian Cleary & Edgar Dobriban, 2022. "Group testing via hypergraph factorization applied to COVID-19," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-29389-z
    DOI: 10.1038/s41467-022-29389-z
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    References listed on IDEAS

    as
    1. Leon Mutesa & Pacifique Ndishimye & Yvan Butera & Jacob Souopgui & Annette Uwineza & Robert Rutayisire & Ella Larissa Ndoricimpaye & Emile Musoni & Nadine Rujeni & Thierry Nyatanyi & Edouard Ntagwabir, 2021. "A pooled testing strategy for identifying SARS-CoV-2 at low prevalence," Nature, Nature, vol. 589(7841), pages 276-280, January.
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    3. Christopher S. McMahan & Joshua M. Tebbs & Christopher R. Bilder, 2012. "Informative Dorfman Screening," Biometrics, The International Biometric Society, vol. 68(1), pages 287-296, March.
    4. Hae-Young Kim & Michael G. Hudgens, 2009. "Three-Dimensional Array-Based Group Testing Algorithms," Biometrics, The International Biometric Society, vol. 65(3), pages 903-910, September.
    5. H. M. Finucan, 1964. "The Blood Testing Problem," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 13(1), pages 43-50, March.
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