Estimating the False-Positive Rate of Highly Automated SARS-CoV-2 Nucleic Acid Amplification Testing
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SciScore for 10.1101/2021.04.25.21254890: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Description of cohort and testing: This study was approved by the University of Washington Institutional Review Board.
Field Sample Permit: Specimens were processed and run within 72 hours of collection if refrigerated or frozen within 72 hours of collection.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication Authentication: Testing was performed according to the manufacturer’s instructions for use (IFU) as detailed in each respective assay’s emergency use authorization (EUA) through the United States Food and Drug Administration (FDA) and as validated for use in the University of Washington Clinical … SciScore for 10.1101/2021.04.25.21254890: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Description of cohort and testing: This study was approved by the University of Washington Institutional Review Board.
Field Sample Permit: Specimens were processed and run within 72 hours of collection if refrigerated or frozen within 72 hours of collection.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication Authentication: Testing was performed according to the manufacturer’s instructions for use (IFU) as detailed in each respective assay’s emergency use authorization (EUA) through the United States Food and Drug Administration (FDA) and as validated for use in the University of Washington Clinical Virology Lab. Table 2: Resources
Software and Algorithms Sentences Resources Data analysis was performed using RStudio (Version 1.2.1335) and Microsoft Excel. RStudiosuggested: (RStudio, RRID:SCR_000432)Microsoft Excelsuggested: (Microsoft Excel, RRID:SCR_016137)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:There are several limitations to the work presented here. This study was performed at a single site and our measured false positivity rate is likely dependent on our own testing processes. This analysis only covers high-throughput automated platforms. Other PCR methods that use a 96 well plate format which involve sample transfers and manipulation likely will experience a higher false positivity rate. The individuals tested here were not uniformly sampled in time after a positive result. Also, the specimen type, nasal swab, may have influenced the positive rate. Nasopharyngeal swabs are considered the gold standard, with a higher rate of positivity compared to other, less invasive sample types. (15) Specimens which resulted as negative after a prior positive were not repeated on an orthogonal platform, thus raising the specter of false negatives. It is unclear how generalizable these numbers are to other laboratories or platforms. More work is required to understand the inherent false positivity rate associated with the automated platforms in use within our laboratory.
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.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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