ArticleAmerican journal of human genetics2018
Detecting Expansions of Tandem Repeats in Cohorts Sequenced with Short-Read Sequencing Data.
Article in American journal of human genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers, 2 of them syntheses that pooled it.
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79 citing papers in PubMed, 2 syntheses or guidelines pooled it, 149 citations in OpenAlex.
- Detection of repeat expansion variants using next generation sequencing: A points to consider statement of the American College of Medical Genetics and Genomics (ACMG).Genetics in medicine : official journal of the American College of Medical Genetics · 2026Guideline
- A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools.Nature protocols · 2026Guideline
- Large-scale genetic profiling of hereditary ataxias in China: implications for a stepwise molecular diagnostic strategy.Translational neurodegeneration · 2026Article
- TandemTwister: scalable genotyping and advanced visualization of tandem repeats.NAR genomics and bioinformatics · 2026Article
- Sequential sequencing reveals the architecture and complexity of genomic variants in patients with Alport syndrome.Nature communications · 2026Article
- MASTR-seq enables multiplexed analysis of short tandem repeats with sequencing.Cell reports methods · 2026Article
- Defining a tandem repeat catalog and variation clusters for genome-wide analyses.bioRxiv : the preprint server for biology · 2026Article
- A comprehensive tandem repeat catalog of the human genome.Nature communications · 2026Article
- Familial adult myoclonus epilepsy: A comprehensive diagnostic strategy for clinical practice.Epilepsia · 2025Review
- Additional Diagnostic Yield through the Analysis of Short Tandem Repeats Based on Exome Sequencing Data.The Journal of molecular diagnostics : JMD · 2025Article
- Long-read sequencing identifies ATXN3 repeat expansions, and transcriptomics reveals disease progression biomarkers and druggable targets for spinocerebellar ataxia type 3.BMC neurology · 2025Article
- STRaM: A genetic framework for improved cell product provenance for research and clinical translations.Communications biology · 2025Article
- Impact of the intronic RFC1 expansion size in CANVAS phenotype: an oculomotor study.Journal of neurology · 2025Article
- A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia.Genome research · 2025Article
- Optical genome mapping enables accurate testing of large repeat expansions.Genome research · 2025Article
- ScatTR: Estimating the Size of Long Tandem Repeat Expansions from Short-Reads.bioRxiv : the preprint server for biology · 2025Article
- Navigating triplet repeats sequencing: concepts, methodological challenges and perspective for Huntington's disease.Nucleic acids research · 2025Review
- Get ready for short tandem repeats analysis using long reads-the challenges and the state of the art.Frontiers in genetics · 2025Review
- The role of disease-associated short tandem repeats in amyotrophic lateral sclerosis.Brain communications · 2025Article
- Novel, complex configurations of theBrain communications · 2025Article
19 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Repeat expansions cause more than 30 inherited disorders, predominantly neurogenetic. These can present with overlapping clinical phenotypes, making molecular diagnosis challenging. Single-gene or small-panel PCR-based methods can help to identify the precise genetic cause, but they can be slow and costly and often yield no result. Researchers are increasingly performing genomic analysis via whole-exome and whole-genome sequencing (WES and WGS) to diagnose genetic disorders. However, until recently, analysis protocols could not identify repeat expansions in these datasets. We developed exSTRa (expanded short tandem repeat algorithm), a method that uses either WES or WGS to identify repeat expansions. Performance of exSTRa was assessed in a simulation study. In addition, four retrospective cohorts of individuals with eleven different known repeat-expansion disorders were analyzed with exSTRa. We assessed results by comparing the findings to known disease status. Performance was also compared to three other analysis methods (ExpansionHunter, STRetch, and TREDPARSE), which were developed specifically for WGS data. Expansions in the assessed STR loci were successfully identified in WES and WGS datasets by all four methods with high specificity and sensitivity. Overall, exSTRa demonstrated more robust and superior performance for WES data than did the other three methods. We demonstrate that exSTRa can be effectively utilized as a screening tool for detecting repeat expansions in WES and WGS data, although the best performance would be produced by consensus calling, wherein at least two out of the four currently available screening methods call an expansion.
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