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/covidGwas.html src/hg/makeDb/trackDb/human/covidGwas.html index a38c9cc..72158c3 100644 --- src/hg/makeDb/trackDb/human/covidGwas.html +++ src/hg/makeDb/trackDb/human/covidGwas.html @@ -1,97 +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 (COVID-19 HGI)</b></a>, +<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 <i>COVID-19 HGI</i> organizes meta-analyses across multiple studies contributed by +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 <i>COVID-19 HGI</i> are those that benefit +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>