Functional prediction and comparative population analysis of variants in genes for proteases and innate immunity related to SARS-CoV-2 infection

  1. Kristel Klaassen
  2. Biljana Stankovic
  3. Branka Zukic
  4. Nikola Kotur
  5. Vladimir Gasic
  6. Sonja Pavlovic
  7. Maja Stojiljkovic

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Abstract

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  1. Version published to 10.1016/j.meegid.2020.104498
  2. ScreenIT

    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 StatementConsent: 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.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variableTotal 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
    SentencesResources
    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].
    NGS
    suggested: (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 Project
    suggested: (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-2
    suggested: None
    MutPred2
    suggested: None
    http://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.

    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.

  3. Version published to 10.1101/2020.05.13.093690v1 on bioRxiv