be4311c07e14feb728abc6425ee606ffaa611a58 markd Fri Jan 22 06:46:58 2021 -0800 merge with master diff --git src/hg/makeDb/trackDb/human/covidMuts.html src/hg/makeDb/trackDb/human/covidMuts.html index d47d628..f92b7e5 100644 --- src/hg/makeDb/trackDb/human/covidMuts.html +++ src/hg/makeDb/trackDb/human/covidMuts.html @@ -1,133 +1,136 @@ <h2>Description</h2> <p> This track shows rare variants associated with monogenic congenital defects of immunity to the <b>SARS-CoV-2</b> virus identified by the <a target=_blank href="https://www.covidhge.com/">COVID Human Genetic Effort</a>. This international consortium aims to discover truly causative variations: those underlying severe forms of COVID-19 in previously healthy individuals, and those that make certain individuals resistant to infection by the SARS-CoV2 virus despite repeated exposure. </p> <p> The major feature of the small set of variants in this track is that they are functionally tested to be <b>deleterious</b> and genetically tested to be <b>disease-causing</b>. Specifically, rare variants were predicted to be loss-of-function at human loci known to govern interferon (IFN) immunity to influenza virus in patients with life-threatening COVID-19 pneumonia, relative to subjects with asymptomatic or benign infection. These genetic defects display incomplete penetrance for influenza respiratory distress and only appear clinically upon infection with the more virulent SARS-CoV-2. </p> <h2>Display Conventions</h2> <p> -Only eight genes and few variants are contained in this track. Use the links in the table to -browse the gene of interest: +Only eight genes with 23 variants are contained in this track. +Use the links below to navigate to the gene of interest or view +all eight genes together using the following sessions for +<a href="http://genome.ucsc.edu/s/dschmelt/CovidRareHarmfulVars">hg38</a> or +<a href="http://genome.ucsc.edu/s/dschmelt/hg19RareCovidAssocMuts">hg19</a>. </p> <table class="stdTbl"> <tr> <th>Gene Name</th> <th>Human GRCh37/hg19 Assembly</th> <th>Human GRCh38/hg38 Assembly</th> </tr> <tr> <td>TLR3</td> <td><a href="../cgi-bin/hgTracks?db=hg19&covidMuts=pack&position=chr4:186990309-187006252"> chr4:186990309-187006252</a></td> <td><a href="../cgi-bin/hgTracks?db=hg38&covidMuts=pack&position=chr4:186069152-186088069"> chr4:186069152-186088069</a></td> </tr> <tr> <td>IRF7</td> <td><a href="../cgi-bin/hgTracks?db=hg19&covidMuts=pack&position=chr11:612555-615999"> chr11:612555-615999</a></td> <td><a href="../cgi-bin/hgTracks?db=hg38&covidMuts=pack&position=chr11:612591-615970"> chr11:612591-615970</a></td> </tr> <tr> <td>UNC93B1</td> <td><a href="../cgi-bin/hgTracks?db=hg19&covidMuts=pack&position=chr11:67758575-67771593"> chr11:67758575-67771593</a></td> <td><a href="../cgi-bin/hgTracks?db=hg38&covidMuts=pack&position=chr11:67991100-68004097"> chr11:67991100-68004097</a></td> </tr> <tr> <td>TBK1</td> <td><a href="../cgi-bin/hgTracks?db=hg19&covidMuts=pack&position=chr12:64845840-64895899"> chr12:64845840-64895899</a></td> <td><a href="../cgi-bin/hgTracks?db=hg38&covidMuts=pack&position=chr12:64452120-64502114"> chr12:64452120-64502114</a></td> </tr> <tr> <td>TICAM1</td> <td><a href="../cgi-bin/hgTracks?db=hg19&covidMuts=pack&position=chr19:4815936-4831754"> chr19:4815936-4831754</a></td> <td><a href="../cgi-bin/hgTracks?db=hg38&covidMuts=pack&position=chr19:4815932-4831704"> chr19:4815932-4831704</a></td> </tr> <tr> <td>IRF3</td> <td><a href="../cgi-bin/hgTracks?db=hg19&covidMuts=pack&position=chr19:50162826-50169132"> chr19:50162826-50169132</a></td> <td><a href="../cgi-bin/hgTracks?db=hg38&covidMuts=pack&position=chr19:49659570-49665875"> chr19:49659570-49665875</a></td> </tr> <tr> <td>IFNAR1</td> <td><a href="../cgi-bin/hgTracks?db=hg19&covidMuts=pack&position=chr21:34697214-34732128"> chr21:34697214-34732128</a></td> <td><a href="../cgi-bin/hgTracks?db=hg38&covidMuts=pack&position=chr21:33324970-33359864"> chr21:33324970-33359864</a></td> </tr> <tr> <td>IFNAR2</td> <td><a href="../cgi-bin/hgTracks?db=hg19&covidMuts=pack&position=chr21:34602231-34636820"> chr21:34602231-34636820</a></td> <td><a href="../cgi-bin/hgTracks?db=hg38&covidMuts=pack&position=chr21:33229974-33264525"> chr21:33229974-33264525</a></td> </tr> </table> <h2>Methods</h2> <p> This track uses variant calls in autosomal IFN-related genes from whole exome and genome data with a MAF lower than 0.001 (gnomAD v2.1.1) and experimental demonstration of loss-of-function. The patient population studied consisted of 659 patients with life-threatening COVID-19 pneumonia relative to 534 subjects with asymptomatic or benign infection of varying ethnicities. Variants underlying autosomal-recessive or autosomal-dominant deficiencies were identified in 23 patients (3.5%) 17 to 77 years of age. The proportion of individuals carrying at least one variant was compared between severe cases and control cases by means of logistic regression with the likelihood ratio test. Principal Component Analysis (PCA) was conducted with Plink v1.9 software on whole exome and genome sequencing data with the 1000 Genomes (1kG) Project phase 3 public database as reference. Analysis of enrichment in rare synonymous variants of the genes was performed to check the calibration of the burden test. The odds ratio was also estimated by logistic regression and adjusted for ethnic heterogeneity. </p> <h2>Data Access</h2> <p> 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 Human Genetic Effort contributors for making these data available, and in particular to Qian Zhang at the Rockefeller University for review and input during browser track development. </p> <h2>References</h2> <p> Zhang Q, Bastard P, Liu Z, Le Pen J, Moncada-Velez M, Chen J, Ogishi M, Sabli IKD, Hodeib S, Korol C <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/32972995" target="_blank"> Inborn errors of type I IFN immunity in patients with life-threatening COVID-19</a>. <em>Science</em>. 2020 Sep 24;. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32972995" target="_blank">32972995</a> </p>