2a9d32c161c59ec9bd5d055843618ab15a703ce1 kate Mon Sep 7 20:02:37 2020 -0700 Finishing touches to COVID GWAS track. refs #26129 diff --git src/hg/makeDb/trackDb/human/covidHgiGwas.html src/hg/makeDb/trackDb/human/covidHgiGwas.html new file mode 100644 index 0000000..72158c3 --- /dev/null +++ src/hg/makeDb/trackDb/human/covidHgiGwas.html @@ -0,0 +1,97 @@ +<H2>Description</H2> +<p> +This track set shows <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 project bringing together the human genetics community 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 learn the genetic determinants of SARS-CoV-2 infection susceptibility, disease severity and +outcomes, and provides a platform to share the results from such activities, as well as +the individual-level data where possible. +</p> +<p> +The specific phenotypes studied by the COVID-19 HGI are those that benefit +from maximal sample size. The primary analysis focuses on disease severity. +Two meta-analyses are represented in this track: + +<ul> +<li><b>ANA_C2_V2</b>: covid vs. population (6696 cases from 18 studies)</li> +<li><b>ANA_B2_V2</b>: hospitalized covid vs. population (3199 cases from 8 studies)</li> +</ul> + +<H2>Display Conventions</H2> +<p> +Displayed items are colored by <b>GWAS effect</b>: red for positive, blue for negative. +The height of the item reflects the <b>effect size</b> (log OR scale). +The color saturation indicates <b>statistical significance</b>: greater than .05 pValue are +brightly colored (bright red +<span style='background-color: #ff0000;'> </span> +, bright blue +<span style='background-color: #0000ff;'> </span> +), +those with less significance are paler (light red +<span style='background-color: #ffa0a0;'> </span> +, light blue +<span style='background-color: #a0a0ff;'> </span> +). +</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 on log(OR) scale</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 on log(OR) scale, the -log10 p-value, and the number of studies. +Further information on each variant is displayed on the details page by a click onto any item. +</p> + +<H2>Methods</H2> +<p> +Data was generated from genome wide SNP array, exome and genome sequencing, leveraging the impact +of both common and rare variants. Statistical analysis takes into account differences between +sexes, ancestries, and date of sample collection. 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 3 (June 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>. +For automated analysis, the data may be queried from our <a target="_blank" +href="/goldenPath/help/api.html">REST API</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 and Juha Karjalainen 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> + + +