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 @@
You can sign-up to get these announcements via our
Genome-announce
email list. We send around one short announcement email every two weeks.
Smaller software changes are not announced here. A summary of the three-weekly release changes can be
found here.
For the full list of our daily code changes head to our GitHub page. Lastly, see our
credits page for acknowledgments of the data we host.
+
+Apr. 22, 2026 New NMD Escape tracks on hg38
+
+We are pleased to announce a new
+NMD Escape
+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.
+
+
+The container track includes:
+
+
+ - NMD escape ruleset tracks for
+ GENCODE V49 and
+ NCBI RefSeq
+ 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).
+ - NMDetective machine-learning prediction tracks from
+ Lindeboom et al. 2016,
+ providing continuous NMD efficiency scores for every possible PTC position.
+
+
+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.
+
+
Apr. 10, 2026 New Short Tandem Repeat (STR) tracks on hg38
We are pleased to announce several new Short Tandem Repeat (STR) tracks on the
human genome assembly (GRCh38/hg38).
A new Tandem Repeat
Variation track collection brings together population-level tandem repeat variation
data from multiple sources: