d04f55a6ff0fd8cbead80ada3a91dc9c5726cc93 kate Thu Oct 22 15:05:41 2020 -0700 Add template for table of gene regions with data. refs #26351 diff --git src/hg/makeDb/trackDb/human/covidHgeMuts.html src/hg/makeDb/trackDb/human/covidHgeMuts.html index 44e66ca..87bea61 100644 --- src/hg/makeDb/trackDb/human/covidHgeMuts.html +++ src/hg/makeDb/trackDb/human/covidHgeMuts.html @@ -7,32 +7,37 @@ in previously healthy individuals, as well as rare or common monogenic variations that make certain individuals resistant to the infection by SARS-CoV2 itself 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> +Gene Position Size +<br> +IRF7 +<a target="_blank" href="../cgi-bin/hgTracks?position=IRF7&singleSearch=knownCanonical"> +chr11</a> 3 kbp +</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. 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 war 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>