Use of compressed sensing to expedite high-throughput diagnostic testing for COVID-19 and beyond
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
The rapid spread of SARS-CoV-2 has placed a significant burden on public health systems to provide swift and accurate diagnostic testing highlighting the critical need for innovative testing approaches for future pandemics. In this study, we present a novel sample pooling procedure based on compressed sensing theory to accurately identify virally infected patients at high prevalence rates utilizing an innovative viral RNA extraction process to minimize sample dilution. At prevalence rates ranging from 0–14.3%, the number of tests required to identify the infection status of all patients was reduced by 69.26% as compared to conventional testing in primary human SARS-CoV-2 nasopharyngeal swabs and a coronavirus model system. Our method provided quantification of individual sample viral load within a pool as well as a binary positive-negative result. Additionally, our modified pooling and RNA extraction process minimized sample dilution which remained constant as pool sizes increased. Compressed sensing can be adapted to a wide variety of diagnostic testing applications to increase throughput for routine laboratory testing as well as a means to increase testing capacity to combat future pandemics.
Article activity feed
-
-
SciScore for 10.1101/2021.08.09.21261669: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Additionally, one major caveat of pooled testing is sample dilution and the increase of false negatives. To eliminate the pooling dilution effect, we utilized a modified RNA extraction protocol which differs from current clinical diagnostic lab procedures …
SciScore for 10.1101/2021.08.09.21261669: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Additionally, one major caveat of pooled testing is sample dilution and the increase of false negatives. To eliminate the pooling dilution effect, we utilized a modified RNA extraction protocol which differs from current clinical diagnostic lab procedures by simply concentrating the RNA to a set volume regardless of the patient input number (Fig. 2A). This standardizes the dilution to an expected and reproducible ΔCt from the ground truth value that does not change if the number of patients within a pool increases (Fig. 2B). This protocol alone removes the risk of samples with low levels of virus being diluted in a pool and being read as a false negative. Our approach demonstrates an effective process to combat testing bottlenecks for future pandemics. Many clinical testing labs currently utilize automated RNA extraction systems in which parameters can be changed to fit our new protocols. Additionally, we have created a beta decoding software in which qPCR data can be entered and the program will decode the data, identify positive patients, and generate additional pools for further testing, if needed, all automatically (software code available upon request). Most importantly, the application of our testing method is broad and can be applied to many testing applications within medicine and beyond such as serum antibody testing, drug screening, avian influenza surveillance, water contamination testing, etc. Our application of compressed sensing is perfectly positioned for testi...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a protocol registration statement.
Results from scite Reference Check: We found no unreliable references.
-
