ArticleGenome research2023
The motif composition of variable number tandem repeats impacts gene expression.
Article in Genome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 59 citations in OpenAlex.
- MORC3 represses a tandem repeat enhancer to regulate interferon.The EMBO journal · 2026Article
- Linked origins but distinct roles for extreme length and sequence variation at a tandem repeat inbioRxiv : the preprint server for biology · 2026Article
- A comprehensive tandem repeat catalog of the human genome.Nature communications · 2026Article
- Evolutionary Balancing of Genetic Consequence and Innovation in Mammals Through Variable Number Tandem Repeats.Genome biology and evolution · 2026Review
- Structure of a polymorphic repeat at theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- TRsv: simultaneous detection of tandem repeat variations, structural variations, and short indels using long read sequencing data.Genome biology · 2025Article
- Structure of a polymorphic repeat at themedRxiv : the preprint server for health sciences · 2025Article
- Pytrf: a python package for finding tandem repeats from genomic sequences.BMC bioinformatics · 2025Article
- Long and Accurate: How HiFi Sequencing is Transforming Genomics.Genomics, proteomics & bioinformatics · 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
- Enhanced detection and genotyping of disease-associated tandem repeats using HMMSTR and targeted long-read sequencing.Nucleic acids research · 2025Article
- Challenges in structural variant calling in low-complexity regions.GigaScience · 2025Article
- Genome-wide investigation of VNTR motif polymorphisms in 8,222 genomes: Implications for biological regulation and human traits.Cell genomics · 2024Article
- Structural and genetic diversity in the secreted mucins MUC5AC and MUC5B.American journal of human genetics · 2024Article
- Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References.Annual review of genomics and human genetics · 2024Review
- Rhesus Macaques: VNTR Polymorphism of the FCGRT Gene.Bulletin of experimental biology and medicine · 2024Article
- Discovering mechanisms of human genetic variation and controlling cell states at scale.Trends in genetics : TIG · 2024Review
- Resolving intra-repeat variation in medically relevant VNTRs from short-read sequencing data using the cardiovascular risk gene LPA as a model.Genome biology · 2024Article
- Structural and genetic diversity in the secreted mucins,bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Understanding the impact of DNA variation on human traits is a fundamental question in human genetics. Variable number tandem repeats (VNTRs) make up ∼3% of the human genome but are often excluded from association analysis owing to poor read mappability or divergent repeat content. Although methods exist to estimate VNTR length from short-read data, it is known that VNTRs vary in both length and repeat (motif) composition. Here, we use a repeat-pangenome graph (RPGG) constructed on 35 haplotype-resolved assemblies to detect variation in both VNTR length and repeat composition. We align population-scale data from the Genotype-Tissue Expression (GTEx) Consortium to examine how variations in sequence composition may be linked to expression, including cases independent of overall VNTR length. We find that 9422 out of 39,125 VNTRs are associated with nearby gene expression through motif variations, of which only 23.4% are accessible from length. Fine-mapping identifies 174 genes to be likely driven by variation in certain VNTR motifs and not overall length. We highlight two genes,
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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.