be4311c07e14feb728abc6425ee606ffaa611a58 markd Fri Jan 22 06:46:58 2021 -0800 merge with master diff --git src/hg/makeDb/trackDb/human/covidHgiGwasR4.html src/hg/makeDb/trackDb/human/covidHgiGwasR4.html new file mode 100644 index 0000000..4e03962 --- /dev/null +++ src/hg/makeDb/trackDb/human/covidHgiGwasR4.html @@ -0,0 +1,131 @@ +<H2>Description</H2> +<p> +This track set shows the results of the +<a target=_blank href="https://www.covid19hg.org/blog/2020-11-24-covid-19-hgi-results-for-data-freeze-4-october-2020/"<b>Data Release 4 (October 2020)</b></a> +of <b>GWAS meta-analyses</b> from the +<a target=_blank href="https://www.covid19hg.org/"> +<b>COVID-19 Host Genetics Initiative (HGI)</b></a>: +a collaborative effort to facilitate +the generation, analysis and sharing of COVID-19 host genetics research. +The COVID-19 HGI organizes meta-analyses across multiple studies contributed by +<a target="_blank" href="https://www.covid19hg.org/partners/">partners world-wide</a> +to identify the genetic determinants of SARS-CoV-2 infection susceptibility and disease severity +and outcomes. Moreover, 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 where +possible. +At the time of this release, a total of 137 studies were registered with this effort. +</p> + +<p> +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 increased sample size resulted in strong evidence of +seven genomic regions associated with severe COVID-19, on chromosomes 3, 6, 9, 12, 19, and 21; and +one additional signal on chromosome 3 associated with COVID-19 partial-susceptibility. +The four tracks here are based on data from HGI meta-analyses A2, B2, C1, and C2, described here: +</p> + +<ul> +<li>Severe COVID GWAS (<b>A2</b>): Very severe respiratory confirmed covid vs. population (4933 cases from 14 studies)</li> +<li>Hosp COVID GWAS (<b>B2</b>): Hospitalized covid vs. population (8638 cases from 23 studies)</li> +<li>Tested COVID GWAS (<b>C1</b>): Covid vs. lab/self-reported negative (8638 cases from 23 studies)</li> +<li>COVID GWAS (<b>C2</b>): Covid vs. population (30937 cases from 36 studies)</li> +</ul> + +Due to privacy concerns, these browser tracks exclude some of the data in the full analysis +results (specifically, data provided by 23andMe contributed studies). The actual study and case +and control counts for the individual browser tracks are listed in the track labels (shown +in the 'List subtracks' section above). + + +<H2>Display Conventions</H2> +<p> +Displayed items are colored by <b>GWAS effect</b>: red for positive (harmful) effect, +blue for negative (protective) effect. +The height ('lollipop stem') of the item is based on statistical significance (<b>pvalue</b>) +or effect size (<b>beta coefficient</b>). +For better visualization of the data, only SNPs with p-values smaller than 1e-3 are +displayed by default.</p> +<p> +For tracks based on effect size, the +color saturation indicates statistical significance: p-values smaller than 1e-5 +are brightly colored (bright red +<span style='background-color: #ff0000;'> </span> +, bright blue +<span style='background-color: #0000ff;'> </span> +), +those with less significance (p >= 1e-5) are paler (light red +<span style='background-color: #ffa0a0;'> </span> +, light blue +<span style='background-color: #a0a0ff;'> </span> +). +For track based on pvalue, the color brightness reflects the effect size.</p> +<p> +Each track has separate display controls and data can be filtered according to the +<b>number of studies</b>, <b>minimum -log10 p-value</b>, and the +<b>effect size (beta coefficient)</b>, using the track <b>Configure</b> options.</p> +<p> +<b>Mouseover</b> 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. </p> + +<H2>Methods</H2> +<p> +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 <a target=_blank href="https://www.covid19hg.org/results/">COVID-19 phenotype definitions</a>.</p> +<p> +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 <b>SAIGE GWAS</b> 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 +<b>INFO > 0.6</b> and <b>MAF > 0.0001</b> prior to meta-analyzing the entirety of the data. +</p> +The meta-analysis was performed using fixed effects inverse variance weighting. +The meta-analysis software and workflow are available <a target=_blank +href="https://github.com/covid19-hg/META_ANALYSIS">here</a>. More information about the +prospective studies, processing pipeline, results and data sharing can be found +<a target=_blank href="https://www.covid19hg.org/about/">here</a>. +</p> + +<H2>Data Access</H2> +<p> +The data underlying these tracks and summary statistics results are publicly available in <a target=_blank href="https://www.covid19hg.org/results">COVID19-hg Release 4 (October 2020)</a>. +The raw data can be explored interactively with the <a target="_blank" href="../cgi-bin/hgTables"> +Table Browser</a>, or the <a target="_blank" href="../cgi-bin/hgIntegrator">Data Integrator</a>. +Please refer to +our <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome" +target="_blank">mailing list archives</a> for questions, or our <a target="_blank" +href="../FAQ/FAQdownloads.html#download36">Data Access FAQ</a> for more information. +</p> + +<H2>Credits</H2> +<p> +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. +</p> + +<H2>References</H2> + +<p> +COVID-19 Host Genetics Initiative. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/32404885" target="_blank"> +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</a>. +<em>Eur J Hum Genet</em>. 2020 Jun;28(6):715-718. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32404885" target="_blank">32404885</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7220587/" target="_blank">PMC7220587</a> +</p> + + +