Development of a Rapid and Sensitive CasRx-Based Diagnostic Assay for SARS-CoV-2
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SciScore for 10.1101/2020.10.14.20212795: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Patient samples ethics statement: Human samples from patients were collected under University of California San Diego’s Human Research Protection Program protocol number 200470 for negatives (PI: Lauge Farnaes), and under a waiver of consent from clinical samples from San Diego County for positives (PI: Kristian Andersen), as part of the SEARCH Alliance activities. 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 Bioinformatic scripts can be found in File S1. Bioinformaticsuggested: (QFAB Bioinformatics, RRID:SCR_012513)The … SciScore for 10.1101/2020.10.14.20212795: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Patient samples ethics statement: Human samples from patients were collected under University of California San Diego’s Human Research Protection Program protocol number 200470 for negatives (PI: Lauge Farnaes), and under a waiver of consent from clinical samples from San Diego County for positives (PI: Kristian Andersen), as part of the SEARCH Alliance activities. 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 Bioinformatic scripts can be found in File S1. Bioinformaticsuggested: (QFAB Bioinformatics, RRID:SCR_012513)The synthetic targets were chosen based on sequence homology identified using NCBI BLAST searches against gRNA-T and gRNA-Z. BLASTsuggested: (BLASTX, RRID:SCR_001653)We synthesized both the synthetic vRNA and gRNAs through in vitro transcription (IVT) using MEGAscript™ T7 Transcription Kit (Invitrogen™ #AM1334), followed by DNaseI digestion and purification using the MEGAclear™ Transcription Clean-Up Kit (Invitrogen™ #AM1908). MEGAscript™suggested: NoneTo check for possible cross-reactivity with human transcripts, the probes were mapped to the human transcriptome (GRCh38, ENSEMBL release 99, ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/) comprising both coding and non-coding RNAs using bowtie 1.2.3 allowing up to two mismatches (-v 2). bowtiesuggested: (Bowtie, RRID:SCR_005476)Viral genes that are affected by each probe were identified using the intersect function of bedtools (Table S3). bedtoolssuggested: (BEDTools, RRID:SCR_006646)Patient samples ethics statement: Human samples from patients were collected under University of California San Diego’s Human Research Protection Program protocol number 200470 for negatives (PI: Lauge Farnaes), and under a waiver of consent from clinical samples from San Diego County for positives (PI: Kristian Andersen), as part of the SEARCH Alliance activities. Human Research Protection Programsuggested: NoneResults 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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
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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