Multiomic analysis reveals cell-type-specific molecular determinants of COVID-19 severity

Article activity feed

1. Version published to 10.1016/j.cels.2022.05.007

   Aug 1, 2022
2. 

   ScreenIT

   Jul 1, 2021

   SciScore for 10.1101/2021.06.15.21258703: (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
   Here, since we have no access to the individual-level data, we used EUR samples from the 1000 Genomes Project (Phase 3) to estimate Σk, yielding the out-sample LD matrix.	1000 Genomes Project suggested: (1000 Genomes Project and AWS, RRID:SCR_008801)
   WGS data processing in the MVP was performed via the functional equivalence GATK variant calling pipeline96, which was developed by the Broad Institute and plugged into our data and task management system Trellis.	WGS suggested: None
   We used BWA-MEM (v0.7.15) to align reads, Picard 2.15.0 to mark PCR duplicates, and GATK 4.1.0.0 for BQSR and …

   SciScore for 10.1101/2021.06.15.21258703: (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
   Here, since we have no access to the individual-level data, we used EUR samples from the 1000 Genomes Project (Phase 3) to estimate Σk, yielding the out-sample LD matrix.	1000 Genomes Project suggested: (1000 Genomes Project and AWS, RRID:SCR_008801)
   WGS data processing in the MVP was performed via the functional equivalence GATK variant calling pipeline96, which was developed by the Broad Institute and plugged into our data and task management system Trellis.	WGS suggested: None
   We used BWA-MEM (v0.7.15) to align reads, Picard 2.15.0 to mark PCR duplicates, and GATK 4.1.0.0 for BQSR and variant calling via the haplotypeCaller function.	BWA-MEM suggested: (Sniffles, RRID:SCR_017619) Picard suggested: (Picard, RRID:SCR_006525) GATK suggested: (GATK, RRID:SCR_001876)
   We also used FASTQC (v0.11.4), SAMTools flagstat (v0.1.19), and RTG Tools vcfstats (v3.7.1) to assess the qualities of the FASTQ, BAM, and gVCF files, respectively.	FASTQC suggested: (FastQC, RRID:SCR_014583) SAMTools suggested: (SAMTOOLS, RRID:SCR_002105)
   Genomic positions resided in low complexity regions or ENCODE blacklisted regions were first removed.	ENCODE suggested: (Encode, RRID:SCR_015482)
   Regeneron’s burden testing results were obtained from the Regeneron results browser (https://rgc-covid19.regeneron.com/results), where only semi-significant genes (P<1e-03, REGENIE103) were available.	Regeneron results browser suggested: None
   The PULSE model: Feature engineering: Given the variant annotations from ANNOVAR, we calculated gene-level mutation profiles for each individual.	ANNOVAR suggested: (ANNOVAR, RRID:SCR_012821)
   Network analysis: We first downloaded the human PPIs from STRING v11, including 19,567 proteins and 11,759,455 protein interactions.	STRING suggested: (STRING, RRID:SCR_005223)

   ---

   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: 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.

   ---

   Read the original source
3. 

   Version published to 10.1101/2021.06.15.21258703v1 on medRxiv

   Jun 21, 2021