ArticleNature communications2021
Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
45 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
- Genetics of type 2 diabetes: Beyond single nucleotide variant studies.Molecular metabolism · 2026Review
- dicast: a machine learning method for accurate structural variant detection from short-read sequencing data.Genome biology · 2026Article
- Pan-SSR architecture in Acrossocheilus fasciatus links cross-assembly repeat conservation, repeat-unit count variation, and genomic context.Molecular genetics and genomics : MGG · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Complex structural variation, phylogeny, and disease associations of the mucin pangenome.medRxiv : the preprint server for health sciences · 2026Article
- Pangenome-based human genome analysis improves trait association and genomic prediction.bioRxiv : the preprint server for biology · 2026Article
- MORC3 represses a tandem repeat enhancer to regulate interferon.The EMBO journal · 2026Article
- High-quality mouse reference genomes reveal the structural complexity of the murine protein-coding landscape.Cell genomics · 2026Article
- A comprehensive tandem repeat catalog of the human genome.Nature communications · 2026Article
- Short tandem repeats in populations of the Qinghai-Tibet Plateau and adjacent regions provide insights into high-altitude adaptation.Science advances · 2025Article
- Structure of a polymorphic repeat at theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Diverse short tandem repeat sequences influence gene regulation in human populations.Genome biology · 2025Article
- Structure of a polymorphic repeat at themedRxiv : the preprint server for health sciences · 2025Article
- Advancing fungal phylogenetics: integrating modern sequencing, dark taxa discovery, and machine learning.Archives of microbiology · 2025Review
- Multisample motif discovery and visualization for tandem repeats.Genome research · 2025Article
- Analysis of targeted and whole genome sequencing of PacBio HiFi reads for a comprehensive genotyping of gene-proximal and phenotype-associated Variable Number Tandem Repeats.PLoS computational biology · 2025Article
- Complexity welcome: Pangenome graphs for comprehensive population genomics.Quantitative plant biology · 2025Review
- Genome-wide investigation of VNTR motif polymorphisms in 8,222 genomes: Implications for biological regulation and human traits.Cell genomics · 2024Article
- Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning.Plants (Basel, Switzerland) · 2024Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Variable number tandem repeats (VNTRs) are composed of consecutive repetitive DNA with hypervariable repeat count and composition. They include protein coding sequences and associations with clinical disorders. It has been difficult to incorporate VNTR analysis in disease studies that use short-read sequencing because the traditional approach of mapping to the human reference is less effective for repetitive and divergent sequences. In this work, we solve VNTR mapping for short reads with a repeat-pangenome graph (RPGG), a data structure that encodes both the population diversity and repeat structure of VNTR loci from multiple haplotype-resolved assemblies. We develop software to build a RPGG, and use the RPGG to estimate VNTR composition with short reads. We use this to discover VNTRs with length stratified by continental population, and expression quantitative trait loci, indicating that RPGG analysis of VNTRs will be critical for future studies of diversity and disease.
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Registered trials
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 OpenQuestion graph.