c8294a0f61de291ccf0eb848363768c1d502a2f6 Merge parents 1880602 a8a28f7 abenetpa Fri Nov 6 05:09:43 2020 -0800 tables added to desc page #26351 diff --cc src/hg/makeDb/trackDb/human/covidMuts.html index 0000000,ce57e1f..22cb9a3 mode 000000,100644..100644 --- src/hg/makeDb/trackDb/human/covidMuts.html +++ src/hg/makeDb/trackDb/human/covidMuts.html @@@ -1,0 -1,134 +1,119 @@@ -<h2>Description</h2> ++<h2>Display Conventions</h2> + <p> -This track shows variants associated with monogenic congenital defects of immunity to <b>SARS-CoV-2</b>, -virus with incomplete or complete penetrance from the <a target=_blank -href="https://www.covidhge.com/">COVID Human Genetic Effort</a>. This international consortium aims -to detect rare or common monogenic inborn immunity errors (IEI) underlying severe forms of COVID-19 -in previously healthy individuals, as well as rare or common monogenic variations that make certain -individuals resistant to infection by SARS-CoV2 virus despite repeated exposure. ++Unlike a regular genome browser track, the <b>COVID-19 Immunity Variants</b> track displays all ++affected genes in <a href="https://genome.ucsc.edu/goldenPath/help/multiRegionHelp.html">multi-region view</a>, ++showing the variants within the coordinates of the gene, but hiding all the intergenic bases. To ++return to the default Genome Browser view, click on the "-" button next to the "region" box. + </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 (LOF) at 13 human loci known to govern -TLR3- and IRF7-dependent type I 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 -manifested 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: + </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&covidHgeMuts=pack&position=chr4:186990309-187006252"> + chr4:186990309-187006252</a></td> + <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgeMuts=pack&position=chr4:186069152-186088069"> + chr4:186069152-186088069</a></td> + </tr> + <tr> + <td>IRF7</td> + <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgeMuts=pack&position=chr11:612555-615999"> + chr11:612555-615999</a></td> + <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgeMuts=pack&position=chr11:612591-615970"> + chr11:612591-615970</a></td> + </tr> + <tr> + <td>UNC93B1</td> + <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgeMuts=pack&position=chr11:67758575-67771593"> + chr11:67758575-67771593</a></td> + <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgeMuts=pack&position=chr11:67991100-68004097"> + chr11:67991100-68004097</a></td> + </tr> + <tr> + <td>TBK1</td> + <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgeMuts=pack&position=chr12:64845840-64895899"> + chr12:64845840-64895899</a></td> + <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgeMuts=pack&position=chr12:64452120-64502114"> + chr12:64452120-64502114</a></td> + </tr> + <tr> + <td>TICAM1</td> + <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgeMuts=pack&position=chr19:4815936-4831754"> + chr19:4815936-4831754</a></td> + <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgeMuts=pack&position=chr19:4815932-4831704"> + chr19:4815932-4831704</a></td> + </tr> + <tr> + <td>IRF3</td> + <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgeMuts=pack&position=chr19:50162826-50169132"> + chr19:50162826-50169132</a></td> + <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgeMuts=pack&position=chr19:49659570-49665875"> + chr19:49659570-49665875</a></td> + </tr> + <tr> + <td>IFNAR1</td> + <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgeMuts=pack&position=chr21:34697214-34732128"> + chr21:34697214-34732128</a></td> + <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgeMuts=pack&position=chr21:33324970-33359864"> + chr21:33324970-33359864</a></td> + </tr> + <tr> + <td>IFNAR2</td> + <td><a href="../cgi-bin/hgTracks?db=hg19&covidHgeMuts=pack&position=chr21:34602231-34636820"> + chr21:34602231-34636820</a></td> + <td><a href="../cgi-bin/hgTracks?db=hg38&covidHgeMuts=pack&position=chr21:33229974-33264525"> + chr21:33229974-33264525</a></td> + </tr> + </table> + + <h2>Methods</h2> + <p> + Variant calls in 12 autosomal IFN-related genes from whole exome or genome data with a MAF lower + than 0.001 (gnomAD v2.1.1) and experimental demonstration of loss-of-function (LOF) were considered + for statistical analysis. The proportion of individuals carrying at least one pLOF variant was + compared between cases and controls by means of logistic regression with the likelihood ratio test. + The first three principal components of the PCA were included in the logistic regression model + to account for ethnic heterogeneity of the cohorts. + Analysis of enrichment in rare (MAF < 0.001) synonymous + variants of the 12 genes was performed to check the calibration of the burden test. PCA was + conducted with Plink v1.9 software on whole exome and genome sequencing data and 1000 Genomes (1kG) + Project phase 3 public database as reference, using 27,480 exonic variants with a minor allele + frequency >0.01 and a call rate >0.99. 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> +