ArticleGenome research2024
Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR.
Article in Genome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Nanopore sequencing combined with adaptive sampling and NanoExpansion enables accurate characterization of repeat expansion disorders.NAR genomics and bioinformatics · 2026Article
- Toward the clinical application of long-read sequencing in repeat-expansion disorders.Nature genetics · 2026Review
- ECHO: a nanopore sequencing-based workflow for (epi)genetic profiling of the human repeatome.Bioinformatics (Oxford, England) · 2026Article
- Population-scale disease-associated tandem repeat analysis reveals locus and ancestry-specific insights.Nature communications · 2026Article
- A CT-dimer repeat expansion underlies a rare subtype of frontotemporal lobar degeneration.Nature genetics · 2026Article
- A repeat expansion in GOLGA8A is a major risk factor for atypical frontotemporal lobar degeneration with ubiquitin-positive inclusions.Nature genetics · 2026Article
- A comprehensive assessment of tandem repeat genotyping methods for Nanopore long-read genomes.bioRxiv : the preprint server for biology · 2026Article
- Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit.Genome research · 2026Article
- A comprehensive tandem repeat catalog of the human genome.Nature communications · 2026Article
- Computational tools for tandem repeat detection using long-read sequencing.Briefings in bioinformatics · 2026Review
- A Hitchhiker's Guide to long-read genomic analysis.Genome research · 2025Review
- STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci.Genome medicine · 2025Article
- ONT in Clinical Diagnostics of Repeat Expansion Disorders: Detection and Reporting Challenges.International journal of molecular sciences · 2025Article
- A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities.Genome research · 2024Article
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Authors and funding
7 authors.
Funding
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Abstract
The lack of population-scale databases hampers research and diagnostics for medically relevant tandem repeats and repeat expansions. We attempt to fill this gap using our pathSTR web tool, which leverages long-read sequencing of large cohorts to determine repeat length and sequence composition in a healthy population. The current version includes 1040 individuals of The 1000 Genomes Project cohort sequenced on the Oxford Nanopore Technologies PromethION. A comprehensive set of medically relevant tandem repeats has been genotyped using STRdust and LongTR to determine the tandem repeat length and sequence composition. PathSTR provides rich visualizations of this data set and the feature to upload one's data for comparison along the control cohort. We demonstrate the implementation of this application using data from targeted nanopore sequencing of a patient with myotonic dystrophy type 1. This resource will empower the genetics community to get a more complete overview of normal variation in tandem repeat length and sequence composition and, as such, enable a better assessment of rare tandem repeat alleles observed in patients.
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