Digital CRISPR-based method for the rapid detection and absolute quantification of nucleic acids
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SciScore for 10.1101/2020.11.03.20223602: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources UGENE software was used to analyze and align viral genomes (MUSCLE or Kalign). MUSCLEsuggested: (MUSCLE, RRID:SCR_011812)After incubation, a Clarity™ Reader was used to read the fluorescent signal in the partitions, and Clarity™ software was used to calculate input DNA copy numbers. Clarity™suggested: (Clarity resources, RRID:SCR_001387)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 …
SciScore for 10.1101/2020.11.03.20223602: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources UGENE software was used to analyze and align viral genomes (MUSCLE or Kalign). MUSCLEsuggested: (MUSCLE, RRID:SCR_011812)After incubation, a Clarity™ Reader was used to read the fluorescent signal in the partitions, and Clarity™ software was used to calculate input DNA copy numbers. Clarity™suggested: (Clarity resources, RRID:SCR_001387)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:This limitation may potentially complicate CRISPR-based virus detection since mutations in the viral PAM sequence may disable recognition by the Cas protein as the virus evolves. In contrast, our simpler digital CRISPR crRNA design is independent of the PAM sequence because it targets single-stranded DNA generated after amplification24. RADICA reported here uses commercially available chips and devices that can potentially be adapted to other devices already in use at some hospitals and service laboratories. These are QuantStudio 3D Digital PCR System (Thermo Fisher), QIAcuity Digital PCR System (QIAGEN), and Droplet Digital PCR System (Bio-Rad). We therefore envisage greater ease of adoption of our technology at these facilities. Furthermore, RADICA offers a potentially customizable solution that is amenable to other DNA isothermal amplification platforms such as loop-mediated isothermal amplification, rolling circle amplification, and strand displacement amplification technologies, as well as the use of other Cas proteins, such as Cas13a, Cas12b, Cas14 for multiplex detection. We have established and characterized RADICA, which combines the speed and sensitivity of isothermal amplification, the specificity of CRISPR-based detection, and the ability to obtain absolute quantification by sample partitioning. Our RADICA detects a concentration of viral DNA as low as 0.897 copy/µL and enables rapid, absolute quantification with a dynamic range of 0.6 to 2027 copies/µL within one...
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.
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