Interferon pathway lupus risk alleles modulate risk of death from acute COVID-19
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SciScore for 10.1101/2021.11.01.21265766: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: All subjects provided informed consent and the study was approved by the NYU Institutional Review Board.
IRB: All subjects provided informed consent and the study was approved by the NYU Institutional Review Board.Sex as a biological variable The mean (standard deviation) age and body mass index (BMI) for the cohort were 67.72 (17.86) years and 34.96 (15.7) respectively. 46.9% of the subjects were female. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources After quality control, low coverage data were used to impute all common (minor allele frequency >1%) human polymorphism genotypes for each sample, … SciScore for 10.1101/2021.11.01.21265766: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: All subjects provided informed consent and the study was approved by the NYU Institutional Review Board.
IRB: All subjects provided informed consent and the study was approved by the NYU Institutional Review Board.Sex as a biological variable The mean (standard deviation) age and body mass index (BMI) for the cohort were 67.72 (17.86) years and 34.96 (15.7) respectively. 46.9% of the subjects were female. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources After quality control, low coverage data were used to impute all common (minor allele frequency >1%) human polymorphism genotypes for each sample, using reference populations from the 1000 Genomes data sets. 1000 Genomessuggested: (1000 Genomes Project and AWS, RRID:SCR_008801)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 limitations, as the large COVID-19 wave in New York City in 2020 occurred, many subjects were recruited but we have not been able to assemble a large replication cohort as case numbers in New York City have remained low after the severe first wave. A replication cohort would be ideal, and we will await with interest future studies of these loci from data sets at other centers. This is a candidate gene study, which allows us to benefit from prior knowledge and rationale, and we maintain an appropriate type I error correction. Despite this, replication in future studies will be important. In summary, we document a number of IFN pathway lupus risk alleles that significantly impact mortality following COVID-19 infection, and these alleles provide some clues about key points in our viral defense against COVID-19. The study also supports the idea that type I IFN pathway risk alleles for autoimmune disease may persist in high frequency in modern human populations due to a benefit in our defense against viral infections.
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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