d23d0116ff17b126a498c8d02bdef578d0ab1b53 lrnassar Wed Apr 22 12:51:20 2026 -0700 Update NMD Escape newsarch entry to match shipped Rule 2 definition. refs #33737 Rule 2 is no longer the 'intronless transcript rule' after the round 4 gate refinement (single coding exon AND no 3'UTR intron). Updated the newsarch entry to match. diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index b3e19653e23..1e6d0beaeed 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -72,31 +72,32 @@ 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 + et al. 2016: the 50 bp last-junction rule, the no-downstream-EJC rule + (transcripts with a single coding exon and no 3′UTR intron), 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.