LamPORE: rapid, accurate and highly scalable molecular screening for SARS-CoV-2 infection, based on nanopore sequencing
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Abstract
LamPORE™ is a rapid way of testing/screening large numbers of samples for the presence or absence of SARS-CoV-2, the virus causing COVID-19. It combines barcoded multi-target amplification, 15-minute barcoded library preparation and real-time nanopore sequencing. Starting with extracted RNA, results can be obtained from 12 samples in approximately an hour and from 96 samples in under 2 hours. High scalability is achieved by combinatorial barcoding. Performance characteristics are currently being established and regulatory clearance to market is underway.
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SciScore for 10.1101/2020.08.07.20161737: (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
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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar …
SciScore for 10.1101/2020.08.07.20161737: (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
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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.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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SciScore for 10.1101/2020.08.07.20161737: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Ethics declaration Patient consent was not required as these were routinely collected samples and stored as per normal protocols used for clinical practice. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources More than one forward and reverse primer is used in each LAMP reaction at each target region, so the repeating units are not of a uniform length (Fig. iv) FIP barcode optimisation Verification of the FIP barcodes for each target was carried out using a dilution series of the Twist Synthetic … SciScore for 10.1101/2020.08.07.20161737: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Ethics declaration Patient consent was not required as these were routinely collected samples and stored as per normal protocols used for clinical practice. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources More than one forward and reverse primer is used in each LAMP reaction at each target region, so the repeating units are not of a uniform length (Fig. iv) FIP barcode optimisation Verification of the FIP barcodes for each target was carried out using a dilution series of the Twist Synthetic RNA Control 2 (Twist Biosciences) for the SARS-CoV-2 loci and total human RNA extracted from GM12878 (Coriell) for the actin control. GM12878suggested: Coriell Cat# GM12878, RRID:CVCL_7526)Software and Algorithms Sentences Resources This requires the accurate identification of i) the barcode added during library preparation by the Rapid Barcoding Kit (RBK), ii) the barcode added as part of the FIP oligo during the LAMP reaction and iii) the sequence of the LAMP product associated with each target region. LAMPsuggested: (LAMP, RRID:SCR_001740)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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
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.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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