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/covidMuts.html src/hg/makeDb/trackDb/human/covidMuts.html
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+<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 &lt 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 &gt0.01 and a call rate &gt0.99. 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> 
+
+