be4311c07e14feb728abc6425ee606ffaa611a58 markd Fri Jan 22 06:46:58 2021 -0800 merge with master diff --git src/hg/makeDb/trackDb/human/covidHgiGwasR4Pval.html src/hg/makeDb/trackDb/human/covidHgiGwasR4Pval.html new file mode 100644 index 0000000..975c1e2 --- /dev/null +++ src/hg/makeDb/trackDb/human/covidHgiGwasR4Pval.html @@ -0,0 +1,224 @@ +<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>GWAS Data Release 4 (October 2020)</b></a> +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 of meta-analysis across multiple studies contributed by +<a target="_blank" href="https://www.covid19hg.org/partners/">partners world-wide</a> +to identify the genetic determinants of <b>SARS-CoV-2</b> infection susceptibility, disease severity +and outcomes. 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 of COVID-19 +host genetics research. 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. +</p> + +<p> +The four tracks here are based on data from HGI meta-analyses A2, B2, C1, and C2, described here: +</p> + +<ul> +<li><b>Severe COVID vars (A2):</b> Cases with very severe respiratory failure confirmed + for COVID-19 vs. population (i.e. everybody that is not a case). + The increased sample size resulted in strong evidence of + seven genomic regions associated with severe COVID-19 and one additional signal associated with + COVID-19 partial-susceptibility. Many of these regions were identified by the + <a target="_blank" href="https://genomicc.org/">Genetics of Mortality in Critical Care (GenOMICC)</a> + study and are shown below (table adapted from + <a target="_blank" href="https://www.nature.com/articles/s41586-020-03065-y">Pairo-Castineira <em>et. al.</em></a>). +</li> +<p></p> + +<table class="stdTbl"> + <tr> + <th>SNP</th> + <th>Human GRCh37/hg19 Assembly</th> + <th>Human GRCh38/hg38 Assembly</th> + <th>Risk Allele</th> + <th>Alternative</th> + <th>Gene nearest to SNP</th> + </tr> + <tr> + <td>rs73064425</td> + <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgiGwasR4Pval=pack&position=chr3:45901089-45901089">chr3:45901089-45901089</a></td> + <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgiGwasR4Pval=pack&position=chr3:45859597-45859597">chr3:45859597-45859597</a></td> + <td>T</td> + <td>C</td> + <td>LZTFL1</td> + </tr> + <tr> + <td>rs9380142</td> + <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgiGwasR4Pval=pack&position=chr6:29798794-29798794">chr6:29798794-29798794</a></td> + <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgiGwasR4Pval=pack&position=chr6:29831017-29831017">chr6:29831017-29831017</a></td> + <td>A</td> + <td>G</td> + <td>HLA-G</td> + </tr> + <tr> + <td>rs143334143</td> + <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgiGwasR4Pval=pack&position=chr6:31121426-31121426">chr6:31121426-31121426</a></td> + <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgiGwasR4Pval=pack&position=chr6:31153649-31153649">chr6:31153649-31153649</a></td> + <td>A</td> + <td>G</td> + <td>CCHCR1</td> + </tr> + <tr> + <td>rs10735079</td> + <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgiGwasR4Pval=pack&position=chr12:113380008-113380008">chr12:113380008-113380008</a></td> + <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgiGwasR4Pval=pack&position=chr12:112942203-112942203">chr12:112942203-112942203</a></td> + <td>A</td> + <td>G</td> + <td>OAS3</td> + </tr> + <tr> + <td>rs74956615</td> + <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgiGwasR4Pval=pack&position=chr19:10427721-10427721">chr19:10427721-10427721</a></td> + <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgiGwasR4Pval=pack&position=chr19:10317045-10317045">chr19:10317045-10317045</a></td> + <td>A</td> + <td>T</td> + <td>ICAM5/TYK2</td> + </tr> + <tr> + <td>rs2109069</td> + <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgiGwasR4Pval=pack&position=chr19:4719443-4719443">chr19:4719443-4719443</a></td> + <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgiGwasR4Pval=pack&position=chr19:4719431-4719431">chr19:4719431-4719431</a></td> + <td>A</td> + <td>G</td> + <td>DPP9</td> + </tr> + <tr> + <td>rs2236757</td> + <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgiGwasR4Pval=pack&position=chr21:34624917-34624917">chr21:34624917-34624917</a></td> + <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgiGwasR4Pval=pack&position=chr21:33252612-33252612">chr21:33252612-33252612</a></td> + <td>A</td> + <td>G</td> + <td>IFNAR2</td> + </tr> +</table> +</p> +<p> +<li><b>Hosp COVID vars (B2):</b> Cases hospitalized and confirmed for COVID-19 vs. +population (i.e. everybody that is not a case)</li> +</p> +<p> +<li><b>Tested COVID vars (C1):</b> Cases with laboratory confirmed SARS-CoV-2 infection, or +health record/physician-confirmed COVID-19, or self-reported COVID-19 via questionare vs. laboratory +/self-reported negative cases</li> +</p> +<p> +<li><b>All COVID vars (C2):</b> Cases with laboratory confirmed SARS-CoV-2 infection, or +health record/physician-confirmed COVID-19, or self-reported COVID-19 vs. population (i.e. everybody +that is not a case)</li> +</p> +</ul> + +Due to privacy concerns, these browser tracks exclude data provided by 23andMe contributed +studies in the full analysis results. The actual study and case +and control counts for the individual browser tracks are listed in the track labels. Details on +all studies can be found <a target="=blank" href="https://www.covid19hg.org/results/">here</a>. + +<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>p-value</b>). +For better visualization of the data, only SNPs with p-values smaller than 1e-3 are +displayed by default.</p> +<p> +The color saturation indicates effect size (beta coefficient): values over the median of effect +size are brightly colored (bright red +<span style='background-color: #ff0000;'> </span> +, bright blue +<span style='background-color: #0000ff;'> </span> +), +those below the median 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 (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> + +<p> +Pairo-Castineira E, Clohisey S, Klaric L, Bretherick AD, Rawlik K, Pasko D, Walker S, Parkinson N, +Fourman MH, Russell CD <em>et al</em>. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/33307546" target="_blank"> +Genetic mechanisms of critical illness in Covid-19</a>. +<em>Nature</em>. 2020 Dec 11;. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33307546" target="_blank">33307546</a> +</p> + +