Outcomes of SARS-CoV-2 Infection in Patients With Chronic Liver Disease and Cirrhosis: A National COVID Cohort Collaborative Study

  1. Jin Ge
  2. Mark J. Pletcher
  3. Jennifer C. Lai
  4. Jeremy R. Harper
  5. Christopher G. Chute
  6. Melissa A. Haendel

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Abstract

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  1. Version published to 10.1053/j.gastro.2021.07.010
  2. ScreenIT

    SciScore for 10.1101/2021.06.03.21258312: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: 29 Institutional Review Board Oversight: Submission of data from individual centers to N3C are governed by a central institutional review board (IRB) protocol #IRB00249128 hosted at Johns Hopkins University School of Medicine via the SMART IRB40 Master Common Reciprocal reliance agreement.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    17 Vocabulary classification and mapping of various ontologies to the OMOP standard vocabulary is maintained by OHDSI and publicly available on ATHENA (http://athena.ohdsi.org/), which is a web-based vocabulary repository.
    ATHENA
    suggested: (Athena, RRID:SCR_008110)
    Data queries, extractions, and transformations of OMOP data elements and concepts in the N3C Data Enclave were conducted using the Palantir Foundry implementations of Spark-Python, version 3.6, and Spark-SQL, version 3.0.
    Spark-Python
    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: We detected the following sentences addressing limitations in the study:
    We acknowledge the following limitations. First, as data were aggregated from many sites, there is systematic missingness of certain variables. In our study, this is most apparent in that we were only able to calculate the MELD-Na scores for 17,460 patients. We accounted for this by conducting sensitivity analyses that showed our main finding of SARS-CoV-2 infection in patients with cirrhosis was associated with two-fold hazard in mortality did not change. In addition, our sensitivity analyses revealed that certain geographic and CLD etiology associations with mortality were eliminated once adjustments for MELD-Na and serum albumin were made in Cirrhosis/Positive patients. This most likely reflected that data missingness in N3C occurs not at random and is associated with certain sites. Second, although N3C has standardized protocols for data curation and harmonization, there likely remains variations in terminology and ontology between various sites. The use of the OMOP common data model, however, decreases such differences and enforces a degree of standardization.15,16,30 Third, due to date-shifting employed in the process of de-identification in the N3C Data Enclave and differences in data harmonization times between data partner sites, there may be a delay in ascertainment of outcomes. This means that there may have been misclassification of outcomes if the date of SARS-CoV-2 testing was close to the latest known date of records (“maximum data date”) for that data partner ...

    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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    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.

  3. Version published to 10.1101/2021.06.03.21258312v1 on medRxiv