6dcb8be23e6ca3c41fd73fa5d1fc16db3e3e644d abenetpa Fri Sep 11 06:48:03 2020 -0700 corrected smaller instead for greater in html refs #2619 diff --git src/hg/makeDb/trackDb/human/covidHgiGwas.html src/hg/makeDb/trackDb/human/covidHgiGwas.html index e0c4343..c44752f 100644 --- src/hg/makeDb/trackDb/human/covidHgiGwas.html +++ src/hg/makeDb/trackDb/human/covidHgiGwas.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 (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: </p> <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 +The color saturation indicates <b>statistical significance</b>: smaller 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. Additional information on each variant can be found on the details page by clicking on the item. </p> <H2>Methods</H2> <p> Data were generated from genome wide SNP arrays, exome and genome sequencing, leveraging the impact of both common and rare variants. Statistical analysis takes into account differences between sex, ancestry, 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>. 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>