0871110b9e07cfb8001e6de9d156e7e7f74f8c25 max Fri Sep 4 17:00:53 2026 -0700 STRchive track now updates itself, and is on hg19 and hs1 as well as hg38 STRchive builds a Genome Browser bigBed with every release now and publishes it on their GitHub releases page, so there is nothing left for us to convert. A new otto job checks weekly for a new release, downloads the file into its own releases/<tag> directory, sanity-checks the locus count, and repoints the /gbdb symlinks at it. Silent when there is no new release. See STRchive issue 333 for the correspondence that set this up. Their releases carry hg19, hg38 and T2T-chm13 (= hs1) files and we take all three, so the new strVar stanza lives in human/strVarNew.ra rather than under hg38. The bigDataUrls use $D, and hgTrackDb -strict drops any member whose file is missing, so each assembly gets only the tracks that were built for it: STRchive on all three, the other four on hg38 only. The description page is rewritten for the new evidence-level coloring, gains an evidence filter, and now says that the track updates itself and that older versions are on GitHub rather than here. All of that is alpha only. Nothing copies /gbdb/*/strVar/ out to the RR yet, so releasing this trackDb would have it promise data the RR does not have. The old hg38-only version stays as human/hg38/strVar.ra, tagged beta,public, until the sysadmins install the strchiveAutoPush cron drafted alongside the otto job. The header of strVarNew.ra lists what to delete and rename then. refs #38268 diff --git src/hg/makeDb/trackDb/human/strchiveNew.html src/hg/makeDb/trackDb/human/strchiveNew.html new file mode 100644 index 00000000000..a9d91caa79d --- /dev/null +++ src/hg/makeDb/trackDb/human/strchiveNew.html @@ -0,0 +1,128 @@ +<h2>Description</h2> +<p> +The <b>STRchive</b> track displays the disease-associated short tandem repeat (STR) loci +curated by the <a href="https://strchive.org" target="_blank">STRchive</a> project. +STRchive is a dynamic, community-driven resource that compiles population-level and +locus-specific data for tandem repeat loci implicated in human genetic diseases.</p> + +<p> +Tandem repeat expansion disorders are caused by the expansion of short repetitive DNA +sequences beyond a pathogenic threshold. These expansions can cause a wide range of +neurological, neuromuscular, and developmental disorders, including Huntington disease, +fragile X syndrome, Friedreich ataxia, and many forms of spinocerebellar ataxia.</p> + +<p> +This track shows the genomic positions of disease-associated STR loci from the STRchive +catalog, along with the reference and pathogenic repeat motifs, minimum pathogenic repeat +count thresholds, mode of inheritance, and associated diseases. STRchive publishes +coordinates for GRCh38/hg38, GRCh37/hg19 and T2T-CHM13/hs1, so the track carries the +same set of loci on all three assemblies.</p> + +<h2>Display Conventions</h2> +<p> +Items are colored by how strong the evidence is for the locus-disease association. +A few loci are in the catalog for historical reasons and have since been disputed or +refuted in the literature, and the coloring is meant to make those stand out:</p> +<ul> +<li><span style="color: #008000;">Green</span> – Definitive</li> +<li><span style="color: #40A000;">Light green</span> – Strong</li> +<li><span style="color: #0000C8;">Blue</span> – Moderate</li> +<li><span style="color: #E69100;">Orange</span> – Limited</li> +<li><span style="color: #808080;">Gray</span> – Provisional (newly reported)</li> +<li><span style="color: #C80000;">Red</span> – Disputed</li> +<li><span style="color: #800000;">Dark red</span> – Refuted</li> +</ul> + +<p> +The track configuration page has a filter on the same evidence categories, so +disputed and refuted loci can be hidden from the display.</p> + +<p> +Each item is labeled by its STRchive locus ID, which combines the disease abbreviation +and gene symbol (e.g., "HD_HTT" for Huntington disease at the <em>HTT</em> +gene). Hovering over an item shows the repeat motif, gene, pathogenic threshold, +inheritance mode, and evidence level. Clicking an item links to the corresponding +<a href="https://strchive.org" target="_blank">STRchive</a> locus page with detailed +clinical and population-level information.</p> + +<h2>Methods</h2> +<p> +The catalog is manually curated by the STRchive team from published literature and +contains loci where tandem repeat expansions have been reported to cause or be +associated with human disease. STRchive builds a Genome Browser file for every one of +its releases and publishes it on their +<a href="https://github.com/dashnowlab/STRchive/releases" target="_blank">GitHub +releases page</a> (file +<code>STRchive-disease-loci-<version>.<assembly>.ucsc.bb</code>). +We display that file as it is published, with no changes on our side, so the track +always shows exactly what STRchive released.</p> + +<p> +<b>This track updates itself.</b> Once a week we check whether STRchive has cut a new +release, and if so the track switches to it. STRchive releases one to two times a +month, so in practice the track is at most a few weeks behind the STRchive catalog. +The version number and release date of the data currently shown are at the top of +this page.</p> + +<p> +We only keep the current release. Earlier versions of the data are not archived here, +but every past release, including the Genome Browser files, stays available on the +<a href="https://github.com/dashnowlab/STRchive/releases" target="_blank">STRchive +releases page</a>. A file from there can be loaded into the Browser as a +<a href="/goldenPath/help/customTrack.html" target="_blank">custom track</a> to +compare an older version against the current one.</p> + +<p> +For each locus, the catalog provides:</p> +<ul> +<li><b>Reference motif</b> – the repeat unit found in the reference genome</li> +<li><b>Pathogenic motif</b> – the repeat unit associated with disease (may differ +from the reference motif, as in some familial adult myoclonic epilepsies where +TTTCA insertions into TTTTA repeats are pathogenic)</li> +<li><b>Pathogenic minimum</b> – the minimum number of repeat copies reported to +cause disease</li> +<li><b>Inheritance</b> – the mode of inheritance (AD, AR, XR, XD)</li> +<li><b>Disease</b> – the associated disease name(s)</li> +<li><b>Evidence</b> – the strength of the evidence for the locus-disease +association, from Definitive down to Refuted</li> +</ul> + +<h2>Data Access</h2> +<p> +The raw data can be explored interactively with the +<a href="hgTables" target="_blank">Table Browser</a> or the +<a href="hgIntegrator" target="_blank">Data Integrator</a>. For automated +analysis, the data may be queried from our +<a href="/goldenPath/help/api.html" target="_blank">REST API</a>. The underlying bigBed +file can be downloaded from our +<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/strVar/" target="_blank">download +server</a>.</p> + +<p> +The complete STRchive dataset, including additional annotations not shown in this track, +is available from <a href="https://strchive.org" target="_blank">strchive.org</a> and +the <a href="https://github.com/dashnowlab/STRchive" target="_blank">STRchive GitHub +repository</a>. The data are released under a +<a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">CC BY 4.0</a> +license.</p> + +<h2>Credits</h2> +<p> +Thanks to Harriet Dashnow (University of Colorado), Laurel Hiatt (University of Utah), +Ben Weisburd (Broad Institute), and the STRchive team for creating and maintaining this +resource.</p> + +<h2>References</h2> +<p> +Hiatt L, Weisburd B, Dolzhenko E, Rubinetti V, Avvaru AK, +VanNoy GE, Kurtas NE, Rehm HL, Quinlan AR, Dashnow H. +<a href="https://doi.org/10.1186/s13073-025-01454-4" +target="_blank"> +STRchive: a dynamic resource detailing population-level and +locus-specific insights at tandem repeat disease loci</a>. +<em>Genome Med</em>. 2025 Mar 26;17(1):29. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/40140942" +target="_blank">40140942</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11938676/" +target="_blank">PMC11938676</a> +</p>