ArticleAmerican journal of human genetics2017
Profiling of Short-Tandem-Repeat Disease Alleles in 12,632 Human Whole Genomes.
Article in American journal of human genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 102 papers, 1 of them a synthesis that pooled it.
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Who cites it
102 citing papers in PubMed, 1 synthesis or guideline pooled it, 212 citations in OpenAlex.
- Genome-wide contribution of common short-tandem repeats to Parkinson's disease genetic risk.Brain : a journal of neurology · 2023Pooled it
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- Augmenting cost-effectiveness in clinical diagnosis using extended whole-exome sequencing: SNVs, SVs, and beyond.Journal of human genetics · 2026Article
- Identification of a large off-ladder allele of the D21S2055 locus during population genetics analysis.International journal of legal medicine · 2026Article
- Detection of short tandem repeat expansions on a targeted neurological gene panel using STRipy improves the diagnostic rate for ataxias.Brain communications · 2026Article
- Article
- Estimating the Genetic Risk of First-Degree Relatives for Chronic Diseases Using the Short Tandem Repeat Score as Model of Polygenic Inheritance.Biochemical genetics · 2025Article
- Additional Diagnostic Yield through the Analysis of Short Tandem Repeats Based on Exome Sequencing Data.The Journal of molecular diagnostics : JMD · 2025Article
- STRaM: A genetic framework for improved cell product provenance for research and clinical translations.Communications biology · 2025Article
- Reanalysis of Next-Generation Sequencing Data to Detect Tandem Repeat Expansions in 1,106 Czech Probands With Neurologic Disease.Neurology. Genetics · 2025Article
- Optical genome mapping enables accurate testing of large repeat expansions.Genome research · 2025Article
- Multisample motif discovery and visualization for tandem repeats.Genome research · 2025Article
- STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci.Genome medicine · 2025Article
- A detailed analysis of second and third-generation sequencing approaches for accurate length determination of short tandem repeats and homopolymers.Nucleic acids 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
- The role of disease-associated short tandem repeats in amyotrophic lateral sclerosis.Brain communications · 2025Article
- Short tandem repeat variants are possibly associated with RNA secondary structure and gene expression.PloS one · 2025Article
- The human SMAD9 (GCC) repeat links to natural selection and late-onset neurocognitive disorders.Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology · 2024Article
- A Hypermutable Region in the DISP2 Gene Links to Natural Selection and Late-Onset Neurocognitive Disorders in Humans.Molecular neurobiology · 2024Article
42 more citing papers are in PubMed but not listed here.
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Authors and funding
16 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Short tandem repeats (STRs) are hyper-mutable sequences in the human genome. They are often used in forensics and population genetics and are also the underlying cause of many genetic diseases. There are challenges associated with accurately determining the length polymorphism of STR loci in the genome by next-generation sequencing (NGS). In particular, accurate detection of pathological STR expansion is limited by the sequence read length during whole-genome analysis. We developed TREDPARSE, a software package that incorporates various cues from read alignment and paired-end distance distribution, as well as a sequence stutter model, in a probabilistic framework to infer repeat sizes for genetic loci, and we used this software to infer repeat sizes for 30 known disease loci. Using simulated data, we show that TREDPARSE outperforms other available software. We sampled the full genome sequences of 12,632 individuals to an average read depth of approximately 30× to 40× with Illumina HiSeq X. We identified 138 individuals with risk alleles at 15 STR disease loci. We validated a representative subset of the samples (n = 19) by Sanger and by Oxford Nanopore sequencing. Additionally, we validated the STR calls against known allele sizes in a set of GeT-RM reference cell-line materials (n = 6). Several STR loci that are entirely guanine or cytosines (G or C) have insufficient read evidence for inference and therefore could not be assayed precisely by TREDPARSE. TREDPARSE extends the limit of STR size detection beyond the physical sequence read length. This extension is critical because many of the disease risk cutoffs are close to or beyond the short sequence read length of 100 to 150 bases.
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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.