Description

The STRchive track displays 75 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. The data are based on the GRCh38/hg38 reference assembly.

Display Conventions

Items are colored by mode of inheritance:

• Blue – autosomal dominant (AD)
• Red – autosomal recessive (AR)
• Orange – both AD and AR
• Purple – X-linked recessive (XR)
• Magenta – X-linked dominant (XD)
• Gray – unknown

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, and inheritance mode. Clicking an item links to the corresponding STRchive locus page with detailed clinical and population-level information.

Methods

The STRchive disease locus catalog was downloaded from the STRchive GitHub repository (file STRchive-disease-loci.hg38.general.bed). 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.

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)

The BED file was converted to bigBed format for display in the Genome Browser. Coordinates were used as provided (0-based half-open BED format).

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