ArticleNucleic acids research2014
Inferring short tandem repeat variation from paired-end short reads.
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 29 papers.
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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
29 citing papers in PubMed.
- STRaM: A genetic framework for improved cell product provenance for research and clinical translations.Communications biology · 2025Article
- Mutations of short tandem repeats explain abundant trait heritability in Arabidopsis.Genome biology · 2025Article
- Get ready for short tandem repeats analysis using long reads-the challenges and the state of the art.Frontiers in genetics · 2025Review
- LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants.BMC genomics · 2024Article
- nPoRe: n-polymer realigner for improved pileup-based variant calling.BMC bioinformatics · 2023Article
- Detection of repeat expansions in large next generation DNA and RNA sequencing data without alignment.Scientific reports · 2022Article
- DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing.Genome biology · 2022Article
- The Concept of Immunogenetics.Advances in experimental medicine and biology · 2022Article
- Genome-wide detection of short tandem repeat expansions by long-read sequencing.BMC bioinformatics · 2020Article
- Article
- Accuracy of short tandem repeats genotyping tools in whole exome sequencing data.F1000Research · 2020Article
- Detecting Expansions of Tandem Repeats in Cohorts Sequenced with Short-Read Sequencing Data.American journal of human genetics · 2018Article
- HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay.Genome research · 2018Article
- STRetch: detecting and discovering pathogenic short tandem repeat expansions.Genome biology · 2018Article
- GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing.BMC bioinformatics · 2018Article
- Tandem repeats mediating genetic plasticity in health and disease.Nature reviews. Genetics · 2018Review
- Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants.Molecules (Basel, Switzerland) · 2018Review
- Characterization of Duck (Frontiers in genetics · 2018Article
- A microsatellite repeat in PCA3 long non-coding RNA is associated with prostate cancer risk and aggressiveness.Scientific reports · 2017Article
- Profiling of Short-Tandem-Repeat Disease Alleles in 12,632 Human Whole Genomes.American journal of human genetics · 2017Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The advances of high-throughput sequencing offer an unprecedented opportunity to study genetic variation. This is challenged by the difficulty of resolving variant calls in repetitive DNA regions. We present a Bayesian method to estimate repeat-length variation from paired-end sequence read data. The method makes variant calls based on deviations in sequence fragment sizes, allowing the analysis of repeats at lengths of relevance to a range of phenotypes. We demonstrate the method's ability to detect and quantify changes in repeat lengths from short read genomic sequence data across genotypes. We use the method to estimate repeat variation among 12 strains of Arabidopsis thaliana and demonstrate experimentally that our method compares favourably against existing methods. Using this method, we have identified all repeats across the genome, which are likely to be polymorphic. In addition, our predicted polymorphic repeats also included the only known repeat expansion in A. thaliana, suggesting an ability to discover potential unstable repeats.
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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.