ArticleNature biotechnology2024
Characterization and visualization of tandem repeats at genome scale.
Article in Nature biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers, 1 of them a synthesis that pooled it.
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Who cites it
90 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools.Nature protocols · 2026Guideline
- Haplotype analysis of spinocerebellar ataxia type 36 suggests a shared permissive core haplotype across populations.Journal of human genetics · 2026Article
- Article
- Somatic mosaicism in the brain: linking development, ageing and neurodegeneration.Nature reviews. Neurology · 2026Review
- Cost-efficient long-read trio-barcoded adaptive sequencing improves rare disease diagnosis.Nature communications · 2026Article
- TandemTwister: scalable genotyping and advanced visualization of tandem repeats.NAR genomics and bioinformatics · 2026Article
- Frequency of ZFHX3-Mediated Spinocerebellar Ataxia 4 in a US Undiagnosed Ataxia Cohort.Movement disorders : official journal of the Movement Disorder Society · 2026Article
- Toward the clinical application of long-read sequencing in repeat-expansion disorders.Nature genetics · 2026Review
- Performance Evaluation of PacBio PureTarget for Multiple Short Tandem Repeat Expansion Detection.Annals of laboratory medicine · 2026Article
- 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
- Benchmarking long-read variant sensitivity across ONT and PacBio platforms using known clinically reported variants in a cohort of critically ill newborns.medRxiv : the preprint server for health sciences · 2026Article
- Near-perfect genome sequencing in medical genetics.Nature genetics · 2026Review
- Structural variant discovery and diagnostic impact in rare diseases from short-read and long-read sequencing.medRxiv : the preprint server for health sciences · 2026Article
- Aardvark: sifting through differences in a mound of variants.Genome biology · 2026Article
- Tandem repeat variation within and between species reveals signatures of selection in humans and chimpanzees.bioRxiv : the preprint server for biology · 2026Article
- A family portrait of the genomic factors shaping tandem repeat mutagenesis.bioRxiv : the preprint server for biology · 2026Article
- Quantification of disease-associated RNA tandem repeats by nanopore sensing.Nature communications · 2026Article
- Genome-wide detection and clinical prioritization of tandem repeat outliers using long-read sequencing.medRxiv : the preprint server for health sciences · 2026Article
- Somatic mosaicism in ALS and FTD identifies focal mutations associated with widespread degeneration.Nature genetics · 2026Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
23 authors.
Funding
Abstract
Tandem repeat (TR) variation is associated with gene expression changes and numerous rare monogenic diseases. Although long-read sequencing provides accurate full-length sequences and methylation of TRs, there is still a need for computational methods to profile TRs across the genome. Here we introduce the Tandem Repeat Genotyping Tool (TRGT) and an accompanying TR database. TRGT determines the consensus sequences and methylation levels of specified TRs from PacBio HiFi sequencing data. It also reports reads that support each repeat allele. These reads can be subsequently visualized with a companion TR visualization tool. Assessing 937,122 TRs, TRGT showed a Mendelian concordance of 98.38%, allowing a single repeat unit difference. In six samples with known repeat expansions, TRGT detected all expansions while also identifying methylation signals and mosaicism and providing finer repeat length resolution than existing methods. Additionally, we released a database with allele sequences and methylation levels for 937,122 TRs across 100 genomes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.