ArticleGenome research2015
Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
60 citing papers in PubMed, 109 citations in OpenAlex.
- DNA polymerase characteristics influence noise levels in sequencing of short tandem repeats.BMC genomics · 2026Article
- The contribution of short tandem repeats to splicing variation in the human cortex.bioRxiv : the preprint server for biology · 2026Article
- Detection of short tandem repeats in the cattle genome: a comparison of bioinformatic tools.BMC genomics · 2026Article
- MASTR-seq enables multiplexed analysis of short tandem repeats with sequencing.Cell reports methods · 2026Article
- Mammalian mitochondrial DNA accumulates insertions and deletions with age in energetically demanding tissues.Molecular biology and evolution · 2026Article
- The repertoire of short tandem repeats across the tree of life.Genome biology · 2025Article
- STRaM: A genetic framework for improved cell product provenance for research and clinical translations.Communications biology · 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
- Tracking Somatic Mutations for Lineage Reconstruction.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Microsatellites explorer: A database of short tandem repeats across genomes.Computational and structural biotechnology journal · 2024Article
- High-fidelity, large-scale targeted profiling of microsatellites.Genome research · 2024Article
- Heterodisomy in theFrontiers in endocrinology · 2024Article
- Accurate sequencing of DNA motifs able to form alternative (non-B) structures.Genome research · 2023Article
- The Autosomal Short Tandem Repeat Polymorphisms Are Potentially Associated with Cardiovascular Disease Predisposition in the Latin American Population: A Mini Review.BioMed research international · 2023Review
- The mutational dynamics of short tandem repeats in large, multigenerational families.Genome biology · 2022Article
- Article
- Accurate measurement of microsatellite length by disrupting its tandem repeat structure.Nucleic acids research · 2022Article
- Orthologous microsatellites, transposable elements, and DNA deletions correlate with generation time and body mass in neoavian birds.Science advances · 2022Article
- An efficient five-lncRNA signature for lung adenocarcinoma prognosis, with AL606489.1 showing sexual dimorphism.Frontiers in genetics · 2022Article
- Review
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
Abstract
Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCR-free protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution.
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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.