0506b5e5664de6618ba073285e0f9bc561c5e959 abenetpa Tue Sep 15 01:57:52 2020 -0700 improved desc page after covid19 HGI folks feedback refs #26129 diff --git src/hg/makeDb/trackDb/human/covidHgiGwas.html src/hg/makeDb/trackDb/human/covidHgiGwas.html index c44752f..88d2789 100644 --- src/hg/makeDb/trackDb/human/covidHgiGwas.html +++ src/hg/makeDb/trackDb/human/covidHgiGwas.html @@ -1,96 +1,98 @@ <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 +<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 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. +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. </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: +The specific phenotypes studied by the COVID-19 HGI are those that benefit from maximal sample +size: primary analysis 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>: smaller than .05 pValue are -brightly colored (bright red +The height of the item reflects the <b>effect size</b> (beta coefficient). +The color saturation indicates <b>statistical significance</b>: <em>P</em> values smaller than .05 +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 +those with less significance (<em>P</em> >= .05) are paler (light red <span style='background-color: #ffa0a0;'> </span> , light blue <span style='background-color: #a0a0ff;'> </span> -). +). For better visualization of the data, only SNPs with <em>P</em> values smaller than .03 are +displayed by default. </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. +<b>number of studies</b>, <b>minimum -log10 <em>P</em> 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 on log(OR) scale, the -log10 p-value, and the number of studies. +and effect alleles, the effect size (beta coefficient), the <em>P</em> 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 +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. 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. +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>