Clinical Characteristics of Patients with Coronavirus Disease (COVID-19): Preliminary Baseline Report of Japan COVID-19 Task Force, a Nationwide Consortium to Investigate Host Genetics of COVID-19
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SciScore for 10.1101/2021.05.17.21256513: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources We applied stringent QC filters to the samples (sample call rate < 0.97, excess heterozygosity of genotypes > mean + 3SD, related samples with PI_HAT > 0.175, or outlier samples from East Asian clusters in principal component analysis with 1000 Genomes Project samples), and variants (variant call rate < 0.99, significant call rate differences between cases and controls with P < 5.0 × 10-8, deviation from Hardy-Weinberg equilibrium with P < 1.0 × 10-6, or minor allele count < 5), as described elsewhere48. 1000 Genomes Projectsuggested: (1000 Genomes Project and AWS, RRID:SCR_008801)We … SciScore for 10.1101/2021.05.17.21256513: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources We applied stringent QC filters to the samples (sample call rate < 0.97, excess heterozygosity of genotypes > mean + 3SD, related samples with PI_HAT > 0.175, or outlier samples from East Asian clusters in principal component analysis with 1000 Genomes Project samples), and variants (variant call rate < 0.99, significant call rate differences between cases and controls with P < 5.0 × 10-8, deviation from Hardy-Weinberg equilibrium with P < 1.0 × 10-6, or minor allele count < 5), as described elsewhere48. 1000 Genomes Projectsuggested: (1000 Genomes Project and AWS, RRID:SCR_008801)We assessed accuracy by comparing the imputed dosages with WGS data for the part of the controls (n = 236), and confirmed high concordance rate of 97.5%. WGSsuggested: NoneWe extracted the independent lead variants with genome-wide significance (or the proxy variants in linkage disequilibrium r2 ≥ 0.8 in the EAS or EUR subjects of the 1000 Genomes Project Phase3v5 databases) from the GWAS results of the exposure phenotypes. 1000 Genomes Project Phase3v5suggested: 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 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.
Results from scite Reference Check: We found no unreliable references.
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