Description

The STRchive track displays the disease-associated short tandem repeat (STR) loci curated by the STRchive 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.

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.

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.

Display Conventions

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:

• Green – Definitive
• Light green – Strong
• Blue – Moderate
• Orange – Limited
• Gray – Provisional (newly reported)
• Red – Disputed
• Dark red – Refuted

The track configuration page has a filter on the same evidence categories, so disputed and refuted loci can be hidden from the display.

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 HTT gene). Hovering over an item shows the repeat motif, gene, pathogenic threshold, inheritance mode, and evidence level. Clicking an item links to the corresponding STRchive locus page with detailed clinical and population-level information.

Methods

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 GitHub releases page (file STRchive-disease-loci-<version>.<assembly>.ucsc.bb). We display that file as it is published, with no changes on our side, so the track always shows exactly what STRchive released.

This track updates itself. 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.

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 STRchive releases page. A file from there can be loaded into the Browser as a custom track to compare an older version against the current one.

For each locus, the catalog provides:

• Reference motif – the repeat unit found in the reference genome
• Pathogenic motif – 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)
• Pathogenic minimum – the minimum number of repeat copies reported to cause disease
• Inheritance – the mode of inheritance (AD, AR, XR, XD)
• Disease – the associated disease name(s)
• Evidence – the strength of the evidence for the locus-disease association, from Definitive down to Refuted

Data Access

The raw data can be explored interactively with the Table Browser or the Data Integrator. For automated analysis, the data may be queried from our REST API. The underlying bigBed file can be downloaded from our download server.

The complete STRchive dataset, including additional annotations not shown in this track, is available from strchive.org and the STRchive GitHub repository. The data are released under a CC BY 4.0 license.

Credits

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.

References

Hiatt L, Weisburd B, Dolzhenko E, Rubinetti V, Avvaru AK, VanNoy GE, Kurtas NE, Rehm HL, Quinlan AR, Dashnow H. STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci. Genome Med. 2025 Mar 26;17(1):29. PMID: 40140942; PMC: PMC11938676