Functional prediction and comparative population analysis of variants in genes for proteases and innate immunity related to SARS-CoV-2 infection
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SciScore for 10.1101/2020.05.13.093690: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Written informed consent was obtained from all participants.
IRB: The study was conducted in accordance with the Helsinki Declaration and approved by the Ethic Committee of Institute of Molecular Genetics and Genetic Engineering, University of Belgrade.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable Total of 143 unrelated Serbian individuals (84 males and 59 females) were previously analyzed by NGS approach using the Illumina Clinical Exome Sequencing TruSight One Gene Panel (Illumina, San Diego, CA, USA), as previoustly described [23]. Table 2: Resources
Software and Algorithms Sentences Resources Total … SciScore for 10.1101/2020.05.13.093690: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Written informed consent was obtained from all participants.
IRB: The study was conducted in accordance with the Helsinki Declaration and approved by the Ethic Committee of Institute of Molecular Genetics and Genetic Engineering, University of Belgrade.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable Total of 143 unrelated Serbian individuals (84 males and 59 females) were previously analyzed by NGS approach using the Illumina Clinical Exome Sequencing TruSight One Gene Panel (Illumina, San Diego, CA, USA), as previoustly described [23]. Table 2: Resources
Software and Algorithms Sentences Resources Total of 143 unrelated Serbian individuals (84 males and 59 females) were previously analyzed by NGS approach using the Illumina Clinical Exome Sequencing TruSight One Gene Panel (Illumina, San Diego, CA, USA), as previoustly described [23]. NGSsuggested: (PM4NGS, RRID:SCR_019164)Genotype data were extracted from the VCF files of Phase 3 variant calls of the 1000 Genomes Project (1kGP) sample collection (https://www.internationalgenome.org/) via Ensembl Data Slicer Tool. 1000 Genomes Projectsuggested: (1000 Genomes Project and AWS, RRID:SCR_008801)To predict the effect of nonsynonymous amino acid substitutions, we used in silico prediction algorithms: PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2), SIFT/PROVEAN (http://provean.jcvi.org/index.php) and MutPred2 (http://mutpred.mutdb.org/). PolyPhen-2suggested: NoneMutPred2suggested: Nonehttp://mutpred.mutdb.org/suggested: (MutPred, RRID:SCR_010778)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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