Impact of natural selection on global patterns of genetic variation and association with clinical phenotypes at genes involved in SARS-CoV-2 infection

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1. Version published to 10.1073/pnas.2123000119

   May 17, 2022
2. 

   Version published to 10.1101/2021.06.28.21259529v2 on medRxiv

   Aug 9, 2021
3. 

   ScreenIT

   Jul 4, 2021

   SciScore for 10.1101/2021.06.28.21259529: (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
   Genomic data: The genomic data used in this study were from three sources: the Africa 6K project (referred to as the the “African Diversity” dataset) which is part of the TopMed consortium25, the 1000 Genomes project (1KG)26, and the Penn Medicine BioBank (PMBB).	TopMed suggested: None
   Whole genome sequencing (WGS) was performed to a median depth of 30X using DNA isolated from blood, PCR-free library construction and Illumina HiSeq X technology, as described elsewhere25.	WGS suggested: None
   The 1000 Genomes datasets with super population ancestry labels (EUR, AFR, EAS, SAS, Other) were used …

   SciScore for 10.1101/2021.06.28.21259529: (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
   Genomic data: The genomic data used in this study were from three sources: the Africa 6K project (referred to as the the “African Diversity” dataset) which is part of the TopMed consortium25, the 1000 Genomes project (1KG)26, and the Penn Medicine BioBank (PMBB).	TopMed suggested: None
   Whole genome sequencing (WGS) was performed to a median depth of 30X using DNA isolated from blood, PCR-free library construction and Illumina HiSeq X technology, as described elsewhere25.	WGS suggested: None
   The 1000 Genomes datasets with super population ancestry labels (EUR, AFR, EAS, SAS, Other) were used as QDA training datasets to determine the genetic ancestry labels for the PMBB population.	1000 Genomes suggested: (1000 Genomes Project and AWS, RRID:SCR_008801)
   Variant annotations: We used Ensembl Variant Effect Predictor (VEP) for variant annotations27.	Ensembl Variant Effect Predictor suggested: None Variant suggested: (VARIANT, RRID:SCR_005194)
   For pathogenicity predictions, we used CADD28, SIFT29, PolyPhen30, Condel31, and REVEL scores in Ensembl.	Ensembl suggested: (Ensembl, RRID:SCR_002344)
   We visualized the location of these regulatory and eQTL variants using the UCSC genome browser and highlighted the variants using Adobe Illustrator.	Adobe Illustrator suggested: (Adobe Illustrator, RRID:SCR_010279)
   Association Testing: We used the R SKAT package for conducting a gene-based dispersion test and Biobin37; 38 for gene burden analysis.	SKAT suggested: (SKAT, RRID:SCR_009396)
   The chimpanzee sequence (Clint_PTRv2/panTro6) used in the analysis was obtained from the UCSC genome browser.	UCSC genome browser suggested: (UCSC Genome Browser, RRID:SCR_005780)
   The overlapped SNPs were uploaded to the UCSC browser for visualization.	UCSC browser suggested: None
   The ChIP-seq density dataset was obtained from http://remap.univ-amu.fr/ 33. DNase-seq and ChIP-seq clusters, layered H3K4Me3 (often found near Promoters), H3K4Me1 and H3K27Ac (often found near Regulatory Elements) data are from ENCODE32.	ChIP-seq suggested: (ChIP-seq, RRID:SCR_001237)

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   Results from OddPub: Thank you for sharing your data.

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   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.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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

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4. 

   Version published to 10.1101/2021.06.28.21259529v1 on medRxiv

   Jul 1, 2021