1. SciScore for 10.1101/2021.07.21.21260624: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsIRB: 5 Recruiting Centers and Ethics Committee Approval IDs: The project protocol involved the rapid recruitment of patient-participants and no additional project-related procedures (we primarily used material from clinically indicated venipunctures) and afforded anonymity, owing to the minimal dataset collected.
    Consent: Differences in recruitment and consent procedures among the centers arose because some centers integrated the project into larger COVID-19 biobanking efforts, whereas other centers did not, and because there were differences in how local ethics committees provided guidance on the handling of anonymization or deidentification of data as well as consent procedures.
    Sex as a biological variableAnalysis of the Y-chromosome haplotypes: First, we produced high quality Y-chromosome genotypes by manually calling and visually inspecting Y-chromosome SNPs in the male fraction of the cohorts only.
    Randomizationnot detected.
    Blindingnot detected.
    Power AnalysisSub-analyses in age groups of 20-40, 41-60, 61-80 and > 80 years were carried out, with the highest sample numbers and statistical power in the age groups of 41-60 and 61-80 years, such that only these are reported (Supplementary Table 1e).

    Table 2: Resources

    Experimental Models: Organisms/Strains
    SentencesResources
    Blood types A and AB were also analyzed combined as “A and AB”.
    AB
    suggested: RRID:BDSC_203)
    Software and Algorithms
    SentencesResources
    Association analysis of the 17q21.31 inversion: 17q21.31 inversion genotypes were imputed using IMPUTE v2.3.245, 46 from quality controlled SNP data (first and second analysis) based on experimentally-validated inversion genotypes from 109 individuals from the 1000 Genomes Project or from P-values (COVID-19 HGI A2/B2 release 5 data) using Fast and accurate P-value Imputation for genome-wide association study (FAPI) (Supplementary Methods).
    1000 Genomes Project
    suggested: (1000 Genomes Project and AWS, RRID:SCR_008801)
    22 Candidate coding genes were selected based on their inclusion in the GWAS credible sets and/or if any of the variants had been identified as lead eQTL or sQTL.
    sQTL
    suggested: (SQTL, RRID:SCR_000827)
    The analysis was carried out using hurdle modeling, implemented in the R package MAST.52 Finally, to check the effect of the 17q21.31 inversion on monocytes stimulated by infection-like conditions we also performed a differential expression analysis in the RNA-seq data from Quach et al.53 by imputing the inversion genotypes with IMPUTE v2.3.225 and quantifying gene and transcript expression differences with Kallisto v0.46.020 and QTLtools v1.154.
    IMPUTE
    suggested: (IMPUTE, RRID:SCR_009245)
    Kallisto
    suggested: (kallisto, RRID:SCR_016582)
    QTLtools
    suggested: None

    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.
    • Thank you for including a protocol registration statement.

    Results from scite Reference Check: We found no unreliable references.


    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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