Lack of Association Between Genetic Variants at ACE2 and TMPRSS2 Genes Involved in SARS-CoV-2 Infection and Human Quantitative Phenotypes
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SciScore for 10.1101/2020.04.22.20074963: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: It was approved by the medical ethics committee of the University Medical Center Groningen and conducted in accordance with Helsinki Declaration Guidelines.
Consent: All participants signed an informed consent form prior to enrollmentRandomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable The genotyping dataset was then imputed using the Haplotype Reference Consortium (HRC) panel v1.1 at the Sanger imputation server (see URLs) (Consortium 2015), and variants with an imputation quality score higher than 0.4 for variants with a MAF>0.01 and higher than 0.8 for rare variants (MAF<0.01) were retained. 58.40% of the … SciScore for 10.1101/2020.04.22.20074963: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: It was approved by the medical ethics committee of the University Medical Center Groningen and conducted in accordance with Helsinki Declaration Guidelines.
Consent: All participants signed an informed consent form prior to enrollmentRandomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable The genotyping dataset was then imputed using the Haplotype Reference Consortium (HRC) panel v1.1 at the Sanger imputation server (see URLs) (Consortium 2015), and variants with an imputation quality score higher than 0.4 for variants with a MAF>0.01 and higher than 0.8 for rare variants (MAF<0.01) were retained. 58.40% of the 21,241 individuals whose genotype passed quality control were female, and the average age at phenotype collection was 39.9 years (±16.3 years). Table 2: Resources
Software and Algorithms Sentences Resources After conversion to anatomical therapeutic chemical classification (ATC) codes, the first four letters (level 3) were used to define drug categories for association analyses. ATCsuggested: NoneThese were analysed using PLINK v2.00a3LM. PLINKsuggested: (PLINK, RRID:SCR_001757)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:Our study has the following limitations. First, only age and sex were used as covariates in our analyses, which may not be sufficient to correct for confounders for all traits, such as drug usage or diseases, although the effect of these confounders should be mitigated by our large sample size. Secondly, our analyses on medication use are underpowered given the limited number of individuals in the general population who use the medications that we tested, and thus none of the associations found here met the multiple-testing adjusted significance. Third, our results for medication use did not include low frequency and none of the analysis include rare variants (MAF<0.005) which could still be relevant. Fourth, while we can speculate about potential connections of our results with current knowledge of COVID-19, longitudinal and well-characterized data on patients is needed to further explore our hypothesis. In conclusion we carried out an extensive screening of potential genetic associations at common and low frequency variants in the ACE2 and TMPRSS2 genes, and found a lack of substantial effect in human quantitative phenotype variation in the general population. Genetic analyses in more phenotypes are needed to evaluate their functional role in other physiological processes. Finally, since genetic variation in other genes, for example those involved in regulating the immune system, could also be important in determining SARS-CoV-2 susceptibility and disease severity, large sc...
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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SciScore for 10.1101/2020.04.22.20074963: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement It was approved by the medical ethics committee of the University Medical Center Groningen and conducted in accordance with Helsinki Declaration Guidelines. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable their association between males and females to explore potential gender differences that could modulate SARSCoV-2 infection. Table 2: Resources
Software and Algorithms Sentences Resources After conversion to anatomical therapeutic chemical classification ( ATC ) codes , the first four letters ( level 3 ) were used to define drug categories for association analyses . ATC…SciScore for 10.1101/2020.04.22.20074963: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement It was approved by the medical ethics committee of the University Medical Center Groningen and conducted in accordance with Helsinki Declaration Guidelines. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable their association between males and females to explore potential gender differences that could modulate SARSCoV-2 infection. Table 2: Resources
Software and Algorithms Sentences Resources After conversion to anatomical therapeutic chemical classification ( ATC ) codes , the first four letters ( level 3 ) were used to define drug categories for association analyses . ATCsuggested: NoneThese were analysed using PLINK v2.00a3LM. PLINKsuggested: (PLINK, SCR_001757)Results from OddPub: Thank you for sharing your data.
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