8caadf44150cd873343bb6af062f064cf039ce33 jnavarr5 Fri Apr 10 16:04:39 2026 -0700 Announing the STR superTrack and the gnomAD STR track, refs #36652 and #35420 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 84dc1b69b22..0b9c316c753 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,105 @@

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. 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: +

WebSTR – + 1,710,833 STR loci from the + EnsembleTR panel with + allele frequency distributions for five continental populations from the + 1000 Genomes Project + (3,550 individuals). The EnsembleTR panel represents consensus calls from four STR + genotyping methods (HipSTR, GangSTR, ExpansionHunter, and AdVNTR). +
STRchive – + 75 disease-associated tandem repeat expansion loci curated from published literature by the + STRchive project. Each locus includes + the pathogenic repeat motif, minimum pathogenic repeat count, mode of inheritance, and + associated disease. Items are colored by inheritance mode. +
TRExplorer V2 + – 5,599,658 tandem repeat loci (STRs and VNTRs) from the + TRExplorer catalog at + the Broad Institute, compiled from 17 sources including perfect repeats in the reference, + polymorphic TRs from T2T assemblies, and curated disease-associated loci. Includes + population allele frequency histograms from TenK10K and HPRC256 cohorts. +
ToMMo 61K STR + – 174,300 STR loci with allele count distributions from 61,000 Japanese individuals + from the Tohoku Medical + Megabank Organization (ToMMo), genotyped with Expansion Hunter. +
1KG Vienna ONT + VNTR – 361,362 VNTR loci with allele statistics from 1,019 samples of the + 1000 Genomes + ONT Vienna project, genotyped with VAMOS from Oxford Nanopore long-read sequencing. + Unlike the other tracks which use short-read data, this track can span longer repeat regions. +

+Additionally, a new +gnomAD STR +track has been added under the gnomAD Variants collection. This track displays genotype data +for 87 disease-associated STR loci from +gnomAD v3.1.3, including +loci associated with Huntington disease, fragile X syndrome, Friedreich ataxia, and various +spinocerebellar ataxias. The data were generated using +ExpansionHunter v5 +on 18,511 whole-genome sequenced samples across 10 populations. Each locus shows the +distribution of repeat allele sizes, providing a reference for normal and expanded allele +ranges. +

+We would like to thank Melissa Gymrek (UC San Diego) and the +WebSTR team for providing the +WebSTR data, Harriet Dashnow (University of Colorado) and the +STRchive team for their curated +disease-associated loci, Ben Weisburd, Egor Dolzhenko, and the +TRExplorer team at the +Broad Institute for their tandem repeat catalog, the +Tohoku Medical Megabank +Organization for the ToMMo STR data, the 1000 Genomes ONT Vienna consortium and the +Marschall Lab at Heinrich Heine University Düsseldorf for the VNTR data, and the +gnomAD production +team for making the STR genotype data available. We would also like to thank +Max Haeussler and Jairo Navarro Gonzalez for the creation and release of these +tracks. +

Apr. 3, 2026 New heatmap display mode for bigBed tracks

We are pleased to announce a new heatmap display mode for the Genome Browser.

Heatmaps replace the standard block-and-line gene display with a color-coded grid: each block position along the item (e.g., an exon) becomes a column, each row represents a sample or condition, and cells are colored by score using a customizable gradient. This makes it easy to spot patterns in multi-sample quantitative data—such as variant effects, gene expression, or methylation levels—directly in their genomic context.