c248c85dafaa2167b3ad8e0ad76be7d4a9a05385 max Fri Oct 30 09:02:47 2020 -0700 lifting covid rare mutations to hg38 and polishing up the track a bit more, refs #26351 diff --git src/hg/makeDb/trackDb/human/covidHgeMuts.html src/hg/makeDb/trackDb/human/covidHgeMuts.html deleted file mode 100644 index 303b490..0000000 --- src/hg/makeDb/trackDb/human/covidHgeMuts.html +++ /dev/null @@ -1,82 +0,0 @@ -<h2>Description</h2> -<p> -This track shows variants associated with monogenic congenital defects of immunity to <b>SARS-CoV-2</b>, -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. -</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> -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> -Only eight genes and few variants are contained in this track. Use the links below to browse the -the gene of interest: - -<dl> - <dd>Gene 1 chr:</dd> - <dd>Gene 2 chr:</dd> -</dl> -</p> - -<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> - -