3972ba54c468ace338d4a5578de1d20bf6c1f9ec lrnassar Mon Apr 20 15:39:26 2026 -0700 Adding Rule 4 (long-exon rule, Lindeboom 2016) to NMD Escape tracks and releasing on Apr. 22, 2026. refs #33737 Script: added a fourth rule to genePredNmdEsc. Coding exons longer than 400 bp (excluding the last coding exon, which is already covered by the 50 bp rule) are flagged as NMD-escape regions. Rebuilt the Gencode and NCBI RefSeq bigBed files. trackDb: - nmd.ra: appended "/400nt" to the nmdEsc longLabels, set nmdEscGencode default visibility to dense so the track is visible in cart-reset views, changed all four NMDetective subtracks from "visibility full" to "visibility hide", updated pennantIcon to the Apr. 22, 2026 release date and anchor. - nmd.html: mention long internal exons in the overview description, update the rule count from three to four. - nmdEscTranscripts.html: add the long-exon rule to the rule list and color legend (gold, #FFD700), expand the Background section with mechanisms for the intronless, start-proximal, and long-exon rules, correct the 50 bp rule description to include the entire last coding exon, fix Lindeboom 2016 author initials (RG -> RGH). News: - newsarch.html: add the 2026-04-22 NMD Escape news entry covering all four rules, with acknowledgements to Guido Neidhardt and Andreas Lahner for suggesting the track and the Decipher Genome Browser team for inspiring the visualization. - indexNews.html: add the front-page news link. makedoc: - nmd.txt: dated note for the Rule 4 rebuild. diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 6ff2fdbe1bf..b3e19653e23 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,65 @@ <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> <!-- ============= 2026 archived news ============= --> <a name="2026"></a> +<a name="042226"></a> +<h2>Apr. 22, 2026 New NMD Escape tracks on hg38</h2> +<p> +We are pleased to announce a new +<a href="/cgi-bin/hgTrackUi?db=hg38&g=nmd" target="_blank"><b>NMD Escape</b></a> +track on the human genome assembly (GRCh38/hg38). This track collection displays +regions where premature termination codons (PTCs) are predicted to escape +nonsense-mediated mRNA decay (NMD), a cellular quality control mechanism that normally +degrades transcripts with premature stop codons. Identifying NMD escape regions is +important for interpreting the clinical significance of truncating variants under the +ACMG/AMP PVS1 criterion. +</p> +<p> +The container track includes: +</p> +<ul> + <li><b>NMD escape ruleset</b> tracks for + <a href="/cgi-bin/hgTrackUi?db=hg38&g=nmdEscGencode" target="_blank">GENCODE V49</a> and + <a href="/cgi-bin/hgTrackUi?db=hg38&g=nmdEscNcbiRefSeq" target="_blank">NCBI RefSeq</a> + transcripts, applying four rules derived from Nagy & Maquat 1998 and Lindeboom + et al. 2016: the 50 bp last-junction rule, the intronless transcript rule, the + start-proximal 100 bp rule, and the long-exon rule (PTCs in coding exons + longer than 400 bp, which show reduced NMD efficiency due to the large + distance between the stalled ribosome and the downstream EJC).</li> + <li><b>NMDetective</b> machine-learning prediction tracks from + <a href="https://www.ncbi.nlm.nih.gov/pubmed/27618451" target="_blank">Lindeboom et al. 2016</a>, + providing continuous NMD efficiency scores for every possible PTC position.</li> +</ul> +<p> +We would like to thank Guido Neidhardt and Andreas Lahner for suggesting this track +and providing feedback throughout its development, and the Decipher +Genome Browser team for inspiring this type of visualization. We also would like to thank Max +Haeussler and Lou Nassar for the creation and release of the UCSC Genome Browser tracks. +</p> + <a name="041026"></a> <h2>Apr. 10, 2026 New Short Tandem Repeat (STR) tracks on hg38</h2> <p> We are pleased to announce several new Short Tandem Repeat (STR) tracks on the human genome assembly (GRCh38/hg38). </p> <p> A new <a href="/cgi-bin/hgTrackUi?db=hg38&g=strVar" target="_blank"><b>Tandem Repeat Variation</b></a> track collection brings together population-level tandem repeat variation data from multiple sources: </p> <ul> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=webstr" target="_blank"><b>WebSTR</b></a> – 1,710,833 STR loci from the <a href="https://github.com/gymrek-lab/EnsembleTR" target="_blank">EnsembleTR</a> panel with