a9883c85708472dcd0be71920acdd2b0c2cd31c7 jnavarr5 Tue Sep 10 15:00:35 2024 -0700 Announcing the ENIGMA and BRCA Exchange hubs, refs #34352 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index de96913..a04f36c 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -54,30 +54,110 @@ <p>You can sign-up to get these announcements via our <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a> email list. We send around one short announcement email every two weeks.</p> <p>Smaller software changes are not announced here. A summary of the three-weekly release changes can be found <a target=_blank href="https://genecats.gi.ucsc.edu/builds/versions.html">here</a>. For the full list of our daily code changes head to our <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>GitHub page</a>. Lastly, see our <a href="credits.html" target="_blank"> credits page</a> for acknowledgments of the data we host.</p> <!-- ============= 2024 archived news ============= --> <a name="2024"></a> +<a name="083024"></a> +<h2>Aug. 30, 2024 Two new public hubs: ENIGMA VCEP and BRCAExchange</h2> +<p> +We are excited to announce the addition of two new hubs to the +<a href="/cgi-bin/hgHubConnect?#publicHubs" target="_blank">Public Hubs</a> page. +</p> +<p> +The <a href="/cgi-bin/hgTracks?genome=hg38&position=default&hubUrl=https://brcaexchange.org/trackhubs/hub.txt" +target="blank"><b>BRCAExchange</b></a> track hub presents the variants from +<a href ="https://brcaexchange.org/" target="_blank">BRCA Exchange</a> in the +context of the human genome, offering further details on each variant in the variant details pages. +This set of variants is obtained by integrating data from +genomic variation repositories including ClinVar, LOVD and gnomAD, and annotating these variants +according to methods selected and developed in close collaboration with the ENIGMA Consortium, the +international expert consortium on research on HBOC variants. +<ul> + Data on BRCA variants is available for the hg19 and hg38 genomes assemblies and the tracks + available are: + <ul> + <li><b>BRCA Variants</b> - <br> + Shows single nucleotide variants (SNVs) and small insertion/deletion + variants of < 50 nucleotides (indels)</li> + <li><b>BRCA Structural Variants</b> - <br> + Shows variants <= 50 nucleotides</li> + <li><b>ACMG Popfreq Variants</b> - <br> + Shows the provisionally-assigned ACMG evidence code for the + Population Frequency group, for variants of < 50 nucleotides</li> + <li><b>ACMG Popfreq SVs</b> - <br> + Shows the provisionally-assigned ACMG evidence code for the Population + Frequency group, for variants of <= 50 nucleotides</li> + </ul> +</ul> + +<p> +The <a href="/cgi-bin/hgTracks?genome=hg38&position=default&hubUrl=https://hgdownload.soe.ucsc.edu/hubs/enigma/hub.txt" +target="blank"><b>ENIGMA BRCA1/BRCA2 specs 1.1.0</b></a> track hub contains data from the +<a href="https://enigmaconsortium.org/" target="_blank">ClinGen ENIGMA BRCA1 and BRCA2 Expert Panel +Specifications</a> to the ACMG/AMP Variant Interpretation +Guidelines for BRCA1/BRCA1 Version 1.1.0. The ENIGMA VCEP has adapted the ACMG-AMP codes for the +BRCA1 and BRCA2 genes. Before using the data, always verify that the ClinGen Criteria Specification +(CSpec) version numbers here match the latest version on the +<a target="_blank" href="https://cspec.genome.network/cspec/ui/svi/affiliation/50087"> +CSpec Registry</a>. +</p> +<ul> + Data is available for the hg19 and hg38 genomes assemblies and the tracks + available are: + <ul> + <li><b>BRCA1/BRCA2 protein domains 1.1.0</b> -<br> + Shows the (potentially) clinically important functional domains for + the genes BRCA1 and BRCA2 as defined by ENIGMA. + </li> + <li><b>BRCA1/BRCA2 exon weights 1.1.0</b> - <br> + This track shows exon-specific weights for PM5_PTC ACMG code with evidence strong used + for application of this code for novel protein termination codon (PTC) + variants in an exon where a different proven pathogenic PTC variant + has been seen before. + </li> + <li><b>BRCA1/BRCA2 functional assays 1.1.0</b> - <br> + Summary of BRCA1 and BRCA2 functional assay results reviewed for + application of PS3 and BS3 ACMG codes. + </li> + <li><b>BRCA1/BRCA2 splicing 1.1.0</b> - <br> + Summary of ACMG codes applicable for variants considered against + the BRCA1 and BRCA2 PVS1 decision trees. Includes PVS1 and PM5 + codes recommended for initiation, nonsense/frameshift, deletion, + duplication, and splice site (donor/acceptor ±1,2) variant— + organized by exon. + </li> + <li><b>BRCA1/BRCA2 likelihood for PP4 and BP5</b> - <br> + Summary of BRCA1 and BRCA2 multifactorial likelihood analysis + scores (displayed as Combined LR score) for ACMG codes PP4 and BP5. + </li> + </ul> +</ul> +<p> +We would like to give thanks to Melissa Cline for the creation of the BRCA Exchange hub. +We would also like to thank Ana Benet Pages and Andreas Laner for making the ENIGMA VCEP hub +available.</p> + <a name="082924"></a> <h2>Aug. 29, 2024 Download track data in view</h2> <p> We are pleased to announce a new feature that allows users to download all visible data in the current region directly from our tracks display. This facilitates reproducibility when writing reports or publications as data can update and change over time.</p> <p> This feature can be found in the blue bar menu by going to <b>Downloads</b> > <b>Download Current Track Data</b>. The resulting pop-up dialogue box can configure the exact tracks to download from all visible tracks, as well as the file name and the output format (JSON, csv, tsv). While most track types are supported, please <a href="../contacts.html">contact us</a> if you encounter an unsupported format you would like to export.</p>