b03430ed0a650b5d4f644ed65b0a9e7fac1aeaf4 jnavarr5 Wed Jul 23 15:32:36 2025 -0700 Announcing the Bionano track for hg38 and hg19, refs #36033 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 3ba92df22ce..313840f1806 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,54 @@ <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> <!-- ============= 2025 archived news ============= --> <a name="2025"></a> +<a name="072325"></a> +<h2>July 23, 2025 Bionano DLE-1 CTTAAG sites for human, hg38 and hg19</h2> +<p> +We are happy to annouce the release the Bionano DLE-1 track for human assemblies +<a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=genotypeArrays" target="_blank">hg38</a> and +<a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=genotypeArrays" target="_blank">hg19</a>. +These tracks shows the CTTAAG sites used by the +<a href="https://www.bionano.com/" target="_blank">Bionano Optical Genome Mapping system</a>, an +assay to detect structural variants. +</p> +<p> +OGM (Optical Genome Mapping) begins with the isolation of ultra-high molecular weight (UHMW) DNA +from blood, bone marrow aspirates, cultured cells (including chorionic villi and amniocytes), +tissue, or tumor biopsies. A single enzymatic reaction places fluorescent labels all throughout +the genome at a specific sequence motif. The labeled DNA molecules are linearized in nanochannel +arrays on the chip. Changes in the patterning or spacing of the labels are identified by software +solutions to accurately detect all classes of structural variants. The OGM data generated can be +analyzed alone, or in combination with sequencing or array data.</p> +<p> +We would like to thank Bionano Laboratories for providing the BED files for the OGM data. We would +also like to thank Max Haeussler and Jairo Navarro for the creation and release of the UCSC Genome +Browser tracks. +</p> + <a name="071525"></a> <h2>July 15, 2025 New pathogenicity prediction scores for human: MutScore and M-CAP</h2> <p> We have two new pathogenicity prediction score tracks available in our <a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=predictionScoresSuper" target="_blank">Deleteriousness Predictions</a> super track.</p> <ul> <li><a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=mutScore" target="_blank">MutScore</a> (hg19/hg38) - MutScore is a pathogenicity predictor that integrates unsupervised features of single DNA variants with information derived from such clusters. The predictive model for MutScore was trained with a random forest approach on medically-relevant mutations and subsequently tested against various genomic databases for both hereditary conditions and cancer (ClinVar, HGMD, and DoCM) to achieve high performance.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=mcap" target="_blank">M-CAP</a> (hg19) - M-CAP is a pathogenicity classifier for