+This track set shows the results of the +GWAS Data Release 4 (October 2020) +from the + +COVID-19 Host Genetics Initiative (HGI): +a collaborative effort to facilitate +the generation of meta-analysis across multiple studies contributed by +partners world-wide +to identify the genetic determinants of SARS-CoV-2 infection susceptibility, disease severity +and outcomes. The COVID-19 HGI also aims to provide a platform for study partners to +share analytical results in the form of summary statistics and/or individual level data of COVID-19 +host genetics research. At the time of this release, a total of 137 studies were registered with +this effort. +
+ ++The specific phenotypes studied by the COVID-19 HGI are those that benefit from maximal sample +size: primary analysis on disease severity. For the Data Release 4 the number of cases have +increased by nearly ten-fold (over 30,000 COVID-19 cases and 1.47 million controls) by combining +data from 34 studies across 16 countries. +
+ ++The four tracks here are based on data from HGI meta-analyses A2, B2, C1, and C2, described here: +
+ +| SNP | +Human GRCh37/hg19 Assembly | +Human GRCh38/hg38 Assembly | +Risk Allele | +Alternative | +Gene nearest to SNP | +
|---|---|---|---|---|---|
| rs73064425 | +chr3:45901089-45901089 | +chr3:45859597-45859597 | +T | +C | +LZTFL1 | +
| rs9380142 | +chr6:29798794-29798794 | +chr6:29831017-29831017 | +A | +G | +HLA-G | +
| rs143334143 | +chr6:31121426-31121426 | +chr6:31153649-31153649 | +A | +G | +CCHCR1 | +
| rs10735079 | +chr12:113380008-113380008 | +chr12:112942203-112942203 | +A | +G | +OAS3 | +
| rs74956615 | +chr19:10427721-10427721 | +chr19:10317045-10317045 | +A | +T | +ICAM5/TYK2 | +
| rs2109069 | +chr19:4719443-4719443 | +chr19:4719431-4719431 | +A | +G | +DPP9 | +
| rs2236757 | +chr21:34624917-34624917 | +chr21:33252612-33252612 | +A | +G | +IFNAR2 | +
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+Displayed items are colored by GWAS effect: red for positive (harmful) effect, +blue for negative (protective) effect. +The height ('lollipop stem') of the item is based on statistical significance (p-value). +For better visualization of the data, only SNPs with p-values smaller than 1e-3 are +displayed by default.
++The color saturation indicates effect size (beta coefficient): values over the median of effect +size are brightly colored (bright red + +, bright blue + +), +those below the median are paler (light red + +, light blue + +). +
++Each track has separate display controls and data can be filtered according to the +number of studies, minimum -log10 p-value, and the +effect size (beta coefficient), using the track Configure options.
++Mouseover on items shows the rs ID (or chrom:pos if none assigned), both the non-effect +and effect alleles, the effect size (beta coefficient), the p-value, and the number of +studies. +Additional information on each variant can be found on the details page by clicking on +the item.
+ ++COVID-19 Host Genetics Initiative (HGI) GWAS meta-analysis round 4 (October 2020) results were +used in this study. +Each participating study partner submitted GWAS summary statistics for up to four +of the COVID-19 phenotype definitions.
++Data were generated from genome-wide SNP array and whole exome and genome +sequencing, leveraging the impact of both common and rare variants. The statistical analysis +performed takes into account differences between sex, ancestry, and date of sample collection. +Alleles were harmonized across studies and reported allele frequencies are based on gnomAD +version 3.0 reference data. Most study partners used the SAIGE GWAS pipeline in order +to generate summary statistics used for the COVID-19 HGI meta-analysis. The summary statistics +of individual studies were manually examined for inflation, +deflation, and excessive number of false positives. +Qualifying summary statistics were filtered for +INFO > 0.6 and MAF > 0.0001 prior to meta-analyzing the entirety of the data. +
+The meta-analysis was performed using fixed effects inverse variance weighting. +The meta-analysis software and workflow are available here. More information about the +prospective studies, processing pipeline, results and data sharing can be found +here. + + ++The data underlying these tracks and summary statistics results are publicly available in COVID19-hg Release 4 (October 2020). +The raw data can be explored interactively with the +Table Browser, or the Data Integrator. +Please refer to +our mailing list archives for questions, or our Data Access FAQ for more information. +
+ ++Thanks to the COVID-19 Host Genetics Initiative contributors and project leads for making these +data available, and in particular to Rachel Liao, Juha Karjalainen, and Kumar Veerapen at the +Broad Institute for their review and input during browser track development. +
+ ++COVID-19 Host Genetics Initiative. + +The COVID-19 Host Genetics Initiative, a global initiative to elucidate the role of host genetic +factors in susceptibility and severity of the SARS-CoV-2 virus pandemic. +Eur J Hum Genet. 2020 Jun;28(6):715-718. +PMID: 32404885; PMC: PMC7220587 +
+ ++Pairo-Castineira E, Clohisey S, Klaric L, Bretherick AD, Rawlik K, Pasko D, Walker S, Parkinson N, +Fourman MH, Russell CD et al. + +Genetic mechanisms of critical illness in Covid-19. +Nature. 2020 Dec 11;. +PMID: 33307546 +
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