ArticleNucleic acids research2014
VNTRseek-a computational tool to detect tandem repeat variants in high-throughput sequencing data.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- TandemTwister: scalable genotyping and advanced visualization of tandem repeats.NAR genomics and bioinformatics · 2026Article
- Evolutionary Balancing of Genetic Consequence and Innovation in Mammals Through Variable Number Tandem Repeats.Genome biology and evolution · 2026Review
- STRaM: A genetic framework for improved cell product provenance for research and clinical translations.Communications biology · 2025Article
- Whole Genome Variable Number Tandem Repeat Analysis in Alzheimer Disease.Neurology. Genetics · 2025Article
- Navigating Genetic Testing in Nephrology: Options and Decision-Making Strategies.Kidney international reports · 2025Review
- Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT andGenome research · 2024Article
- DTDHM: detection of tandem duplications based on hybrid methods using next-generation sequencing data.PeerJ · 2024Article
- Rediscovering tandem repeat variation in schizophrenia: challenges and opportunities.Translational psychiatry · 2023Review
- Expanding horizons of tandem repeats in biology and medicine: Why 'genomic dark matter' matters.Emerging topics in life sciences · 2023Article
- A phenome-wide association study identifies effects of copy-number variation of VNTRs and multicopy genes on multiple human traits.American journal of human genetics · 2022Article
- The Concept of Immunogenetics.Advances in experimental medicine and biology · 2022Article
- The role of structural variations in Alzheimer's disease and other neurodegenerative diseases.Frontiers in aging neuroscience · 2022Review
- Analysis of Selected Variants ofGenes · 2021Article
- Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences.Nucleic acids research · 2021Article
- Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression.American journal of human genetics · 2021Article
- Variable number tandem repeats mediate the expression of proximal genes.Nature communications · 2021Article
- DINTD: Detection and Inference of Tandem Duplications From Short Sequencing Reads.Frontiers in genetics · 2020Article
- Targeted genotyping of variable number tandem repeats with adVNTR.Genome research · 2018Article
- Tandem repeats mediating genetic plasticity in health and disease.Nature reviews. Genetics · 2018Review
- A Census of Tandemly Repeated Polymorphic Loci in Genic Regions Through the Comparative Integration of Human Genome Assemblies.Frontiers in genetics · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA tandem repeats (TRs) are ubiquitous genomic features which consist of two or more adjacent copies of an underlying pattern sequence. The copies may be identical or approximate. Variable number of tandem repeats or VNTRs are polymorphic TR loci in which the number of pattern copies is variable. In this paper we describe VNTRseek, our software for discovery of minisatellite VNTRs (pattern size ≥ 7 nucleotides) using whole genome sequencing data. VNTRseek maps sequencing reads to a set of reference TRs and then identifies putative VNTRs based on a discrepancy between the copy number of a reference and its mapped reads. VNTRseek was used to analyze the Watson and Khoisan genomes (454 technology) and two 1000 Genomes family trios (Illumina). In the Watson genome, we identified 752 VNTRs with pattern sizes ranging from 7 to 84 nt. In the Khoisan genome, we identified 2572 VNTRs with pattern sizes ranging from 7 to 105 nt. In the trios, we identified between 2660 and 3822 VNTRs per individual and found nearly 100% consistency with Mendelian inheritance. VNTRseek is, to the best of our knowledge, the first software for genome-wide detection of minisatellite VNTRs. It is available at http://orca.bu.edu/vntrseek/.
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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 OpenQuestion graph.