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Genome-wide profiling of heritable and de novo STR variations

https://doi.org/10.1038/nmeth.4267
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates
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Expandable DNA repeats and human disease
inferredcites →https://doi.org/10.1038/nature11396openalex-snapshot
Rate of de novo mutations and the importance of father’s age to disease risk
inferredcites →https://doi.org/10.1038/nature15393openalex-snapshot
A global reference for human genetic variation
inferredcites →https://doi.org/10.1038/nature18964openalex-snapshot
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
inferredcites →https://doi.org/10.1038/nbt.2835openalex-snapshot
Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
inferredcites →https://doi.org/10.1038/ng.3036openalex-snapshot
Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications
inferredcites →https://doi.org/10.1038/ng.3121openalex-snapshot
Comprehensive variation discovery in single human genomes
inferredcites →https://doi.org/10.1038/ng.3292openalex-snapshot
Genome-wide patterns and properties of de novo mutations in humans
inferredcites →https://doi.org/10.1038/ng.3461openalex-snapshot
Abundant contribution of short tandem repeats to gene expression variation in humans
inferredcites →https://doi.org/10.1038/ng.806openalex-snapshot
A framework for variation discovery and genotyping using next-generation DNA sequencing data
inferredcites →https://doi.org/10.1038/ng836openalex-snapshot
A polymorphic microsatellite that mediates induction of PIG3 by p53
inferredcites →https://doi.org/10.1046/j.1365-294x.2002.01576.xopenalex-snapshot
Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis
inferredcites →https://doi.org/10.1073/pnas.0400182101openalex-snapshot
A variable dinucleotide repeat in the CFTR gene contributes to phenotype diversity by forming RNA secondary structures that alter splicing
inferredcites →https://doi.org/10.1086/521987openalex-snapshot
Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btv440openalex-snapshot
FermiKit: assembly-based variant calling for Illumina resequencing data
inferredcites →https://doi.org/10.1093/nar/27.2.573openalex-snapshot
Tandem repeats finder: a program to analyze DNA sequences
inferredcites →https://doi.org/10.1093/nar/gkj144openalex-snapshot
The UCSC Genome Browser Database: update 2006
inferredcites →https://doi.org/10.1093/nar/gks981openalex-snapshot
Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles
inferredcites →https://doi.org/10.1101/gr.112326.110openalex-snapshot
Dindel: Accurate indel calls from short-read data
inferredcites →https://doi.org/10.1101/gr.129684.111openalex-snapshot
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
inferredcites →https://doi.org/10.1101/gr.135780.111openalex-snapshot
lobSTR: A short tandem repeat profiler for personal genomes
inferredcites →https://doi.org/10.1101/gr.177774.114openalex-snapshot
The landscape of human STR variation
inferredcites →https://doi.org/10.1101/gr.185892.114openalex-snapshot
Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
inferredcites →https://doi.org/10.1101/gr.210500.116openalex-snapshot
A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree
inferredcites →https://doi.org/10.1111/j.2517-6161.1977.tb01600.xopenalex-snapshot
Maximum Likelihood from Incomplete Data Via the EM Algorithm
inferredcites →https://doi.org/10.1371/journal.pgen.0010070openalex-snapshot
Clines, Clusters, and the Effect of Study Design on the Inference of Human Population Structure
inferredcites →https://doi.org/10.48550/arxiv.1207.3907openalex-snapshot
Haplotype-based variant detection from short-read sequencing
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Optimized Cas9‐Enriched Nanopore Sequencing and Analysis Workflow for Clinical Diagnosis of Repeat Expansion Disorders
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Adaptive Long‐Read Sequencing Reveals GGC Repeat Expansion in ZFHX3 Associated with Spinocerebellar Ataxia Type 4
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pSTRminer: integrated bioinformatic software for genome-wide identification and population-scale evaluation of polymorphic short tandem repeats
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Pan-SSR architecture in Acrossocheilus fasciatus links cross-assembly repeat conservation, repeat-unit count variation, and genomic context
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A High-Throughput Genotyping Workflow and an Optimized SSR Panel for High-Accuracy Parentage Analysis in Largemouth Black Bass
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Genome-wide discovery of polymorphic simple sequence repeat (SSR) markers through comparative analysis of closely related hami melon cultivars
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Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in brown trout (Salmo trutta)
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HMOX1 Genetic Polymorphisms Display Ancestral Diversity and May Be Linked to Hypertensive Disorders in Pregnancy
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Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries
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Analysis and comparison of the STR genotypes called with HipSTR, STRait Razor and toaSTR by using next generation sequencing data in a Brazilian population sample
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HipSTR-UI: A cross-platform graphical interface for accessible str genotyping from next-generation sequencing data
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Assessing sequence variation and genetic diversity of currently untapped Y-STR loci
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A genomic view of short tandem repeats
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Genome-wide identification of microsatellites for mapping, genetic diversity and cross-transferability in wheat (Triticum spp)
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Microsatellites used in forensics are in regions enriched for trait-associated variants
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The kringle IV type 2 domain variant 4925G>A causes the elusive association signal of the LPA pentanucleotide repeat
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WebSTR: A Population-wide Database of Short Tandem Repeat Variation in Humans
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Advancing molecular diagnostics of myotonic dystrophy type 1 using short-read whole genome sequencing
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Genetic architecture of autism spectrum disorder: Lessons from large-scale genomic studies
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Reconstructing the Lineage Histories and Differentiation Trajectories of Individual Cancer Cells in Myeloproliferative Neoplasms
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SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains
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Polymorphic short tandem repeats make widespread contributions to blood and serum traits
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Long-read genome sequencing improves detection and functional interpretation of structural and repeat variants in autism
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Genotyping TOMM40′523 poly-T polymorphisms using whole-genome sequencing
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Systematic analysis of short tandem repeats in 38,095 exomes provides an additional diagnostic yield
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A reference haplotype panel for genome-wide imputation of short tandem repeats
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Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software
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Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes
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Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats
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Properties of structural variants and short tandem repeats associated with gene expression and complex traits
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Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
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Phenome-wide association study of loci harboring de novo tandem repeat mutations in UK Biobank exomes
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A deep population reference panel of tandem repeat variation
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The pan-tandem repeat map highlights multiallelic variants underlying gene expression and agronomic traits in rice
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A phenome-wide association study of tandem repeat variation in 168,554 individuals from the UK Biobank
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Direct measurement of the male germline mutation rate in individuals using sequential sperm samples
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Variant calling and benchmarking in an era of complete human genome sequences
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Sequencing and characterizing short tandem repeats in the human genome
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Molecular mechanisms underlying nucleotide repeat expansion disorders
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Patterns of de novo tandem repeat mutations and their role in autism
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Characterization and visualization of tandem repeats at genome scale
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Analysis and benchmarking of small and large genomic variants across tandem repeats
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The impact of short tandem repeat variation on gene expression
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Epigenetic variation impacts individual differences in the transcriptional response to influenza infection
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A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 associated with intellectual disability
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Multi-omic quantitative trait loci link tandem repeat size variation to gene regulation in human brain
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DNA repair processes are critical mediators of p53-dependent tumor suppression
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Autism risk in offspring can be assessed through quantification of male sperm mosaicism
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A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools
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Large scale in silico characterization of repeat expansion variation in human genomes
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Genetic structure and polymorphisms of Gelao ethnicity residing in southwest china revealed by X-chromosomal genetic markers
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A Computational Method to Quantify the Effects of Slipped Strand Mispairing on Bacterial Tetranucleotide Repeats
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Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions
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Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes
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Multi-marker GWAS and variant-specific genomic prediction for growth traits in Pacific white shrimp
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Genome-wide discovery of short sequence repeat markers useful for genetic diversity studies in Lima bean (Phaseolus lunatus L.)
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STRaM: A genetic framework for improved cell product provenance for research and clinical translations
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Genotyping short tandem repeats across copy number alterations, aneuploidies, and polyploid organisms
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The role of tandem repeat expansions in brain disorders
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Advances in the discovery and analyses of human tandem repeats
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Expanding horizons of tandem repeats in biology and medicine: Why ‘genomic dark matter’ matters
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Deep Intronic FGF14 GAA Repeat Expansion in Late-Onset Cerebellar Ataxia
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Associations between forensic loci and expression levels of neighboring genes may compromise medical privacy
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An ancient founder mutation located between ROBO1 and ROBO2 is responsible for increased microtia risk in Amerindigenous populations
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Environmental radiation exposure at Chornobyl has not systematically affected the genomes or chemical mutagen tolerance phenotypes of local worms
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Dinucleotide (CA)n tandem repeats on the human X-chromosome and the history of the Mediterranean populations
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Paternal genetic structure of an endogamous Saraiki population from Pakistan inferred from rapidly mutating Y-STRs
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Phenotypic Associations With the HMOX1 GT(n) Repeat in European Populations
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STRsensor: a computationally efficient method for STR allele-typing from massively parallel sequencing data
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Computational tools for tandem repeat detection using long-read sequencing
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MuRaL-indel: a deep learning framework for building insertion and deletion mutation rate maps
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TRTools: a toolkit for genome-wide analysis of tandem repeats
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ProDerAl: reference position dependent alignment
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Assessing and assuring interoperability of a genomics file format
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WarpSTR: determining tandem repeat lengths using raw nanopore signals
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Genome-wide detection of somatic mosaicism at short tandem repeats
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TriosCompass: a snakemake workflow for integrated detection of SNVs, indels, STRs, and structural de novo variants in parent–child trios
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Dot2dot : accurate whole-genome tandem repeats discovery
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popSTR2 enables clinical and population-scale genotyping of microsatellites
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Genome-wide contribution of common short-tandem repeats to Parkinson’s disease genetic risk
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Functional genomics provide key insights to improve the diagnostic yield of hereditary ataxia
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Nosocomial Malaria Transmissions Resolved by Genomic Analyses—A Retrospective Case Report Study in France: 2007–2021
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Detection of tandem repeats in the Capsicum annuum genome
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Divergent evolution of hepatocellular carcinoma genomes in chimpanzees and humans
inferred← citeshttps://doi.org/10.1093/g3journal/jkac330openalex-snapshot
The rate of spontaneous mutations in yeast deficient for MutSβ function
inferred← citeshttps://doi.org/10.1093/g3journal/jkae213openalex-snapshot
Y and mitochondrial chromosomes in the heterogeneous stock rat population
inferred← citeshttps://doi.org/10.1093/gbe/evaf162openalex-snapshot
Single Nucleotide Polymorphisms, Structural Variants, and Short Tandem Repeats Capture Distinct Signals of Adaptive Divergence in the Atlantic Puffin
inferred← citeshttps://doi.org/10.1093/gbe/evag018openalex-snapshot
Genomics of Sable ( Martes zibellina) × Pine Marten ( Martes martes ) Hybridization
inferred← citeshttps://doi.org/10.1093/gbe/evz140openalex-snapshot
Mode and Tempo of Microsatellite Length Change in a Malaria Parasite Mutation Accumulation Experiment
inferred← citeshttps://doi.org/10.1093/genetics/iyad161openalex-snapshot
Structural variants and short tandem repeats impact gene expression and splicing in bovine testis tissue
inferred← citeshttps://doi.org/10.1093/genetics/iyag080openalex-snapshot
The selective dynamics of interruptions at short tandem repeats
inferred← citeshttps://doi.org/10.1093/gigascience/giy025openalex-snapshot
Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola
inferred← citeshttps://doi.org/10.1093/molbev/msad067openalex-snapshot
Interplay Between Polymorphic Short Tandem Repeats and Gene Expression Variation inCaenorhabditis elegans
inferred← citeshttps://doi.org/10.1093/nar/gkab224openalex-snapshot
Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences
inferred← citeshttps://doi.org/10.1093/nar/gkac723openalex-snapshot
Accurate measurement of microsatellite length by disrupting its tandem repeat structure
inferred← citeshttps://doi.org/10.1093/nar/gkad187openalex-snapshot
Short tandem repeats are important contributors to silencer elements in T cells
inferred← citeshttps://doi.org/10.1093/nar/gkae1155openalex-snapshot
Navigating triplet repeats sequencing: concepts, methodological challenges and perspective for Huntington’s disease
inferred← citeshttps://doi.org/10.1093/nar/gkaf866openalex-snapshot
Accurate detection of tandem repeats exposes ubiquitous reuse of biological sequences
inferred← citeshttps://doi.org/10.1093/nar/gky1318openalex-snapshot
Short tandem repeat stutter model inferred from direct measurement ofin vitrostutter noise
inferred← citeshttps://doi.org/10.1093/nar/gkz501openalex-snapshot
Profiling the genome-wide landscape of tandem repeat expansions
inferred← citeshttps://doi.org/10.1093/plcell/koab107openalex-snapshot
Length variation in short tandem repeats affects gene expression in natural populations of Arabidopsis thaliana
inferred← citeshttps://doi.org/10.1101/145128openalex-snapshot
Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana
inferred← citeshttps://doi.org/10.1101/164574openalex-snapshot
Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangered Solenodon paradoxus from the island of Hispaniola
inferred← citeshttps://doi.org/10.1101/191213openalex-snapshot
Genetic drivers of repeat expansion disorders localize to 3-D chromatin domain boundaries
inferred← citeshttps://doi.org/10.1101/191296openalex-snapshot
Retrospective cell lineage reconstruction in Humans using short tandem repeats
inferred← citeshttps://doi.org/10.1101/2020.03.04.974170openalex-snapshot
Genome-wide patterns of de novo tandem repeat mutations and their contribution to autism spectrum disorders
inferred← citeshttps://doi.org/10.1101/2020.07.10.195636openalex-snapshot
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
inferred← citeshttps://doi.org/10.1101/2020.08.20.259168openalex-snapshot
Global prevalence of potentially pathogenic short-tandem repeats in an epilepsy cohort
inferred← citeshttps://doi.org/10.1101/2021.02.22.432191openalex-snapshot
bMSI-CAST: a systematic method for next generation sequencing-based microsatellite instability detection in plasma cell-free DNA
inferred← citeshttps://doi.org/10.1101/2021.04.05.438449openalex-snapshot
Ultrafast, alignment-free detection of repeat expansions in next-generation DNA and RNA sequencing data
inferred← citeshttps://doi.org/10.1101/2021.09.06.459168openalex-snapshot
Open-Access STRS Database Of Populations From The 1000 Genomes Project Using High Coverage Phase 3 Data
inferred← citeshttps://doi.org/10.1101/2022.04.21.489063openalex-snapshot
Deep sequencing of a large family of isogenic mice enables complex variants discovery and accurate phenotype mapping
inferred← citeshttps://doi.org/10.1101/2022.04.28.22274424openalex-snapshot
Phenotypic associations with the HMOX1 GT(n) promoter repeat in European populations
inferred← citeshttps://doi.org/10.1101/2022.05.10.491413openalex-snapshot
Epigenetic variation impacts ancestry-associated differences in the transcriptional response to influenza infection
inferred← citeshttps://doi.org/10.1101/2022.09.27.509703openalex-snapshot
Genome-wide regulatory effects of STRs stabilized by elevated expression of antioxidant genes in C. elegans
inferred← citeshttps://doi.org/10.1101/2023.02.15.528687openalex-snapshot
Precise and ultrafast tandem repeat variant detection in massively parallel sequencing reads
inferred← citeshttps://doi.org/10.1101/2023.02.27.23286496openalex-snapshot
The impact of Short Tandem Repeats on grey matter brain imaging derived phenotypes in UK Biobank
inferred← citeshttps://doi.org/10.1101/2023.03.07.531629openalex-snapshot
Microsatellites used in forensics are located in regions unusually rich in trait-associated variants
inferred← citeshttps://doi.org/10.1101/2023.05.03.23289461openalex-snapshot
A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 as a significant cause of intellectual disability
inferred← citeshttps://doi.org/10.1101/2023.05.05.539588openalex-snapshot
Insights from a genome-wide truth set of tandem repeat variation
inferred← citeshttps://doi.org/10.1101/2023.05.12.540470openalex-snapshot
Resolving the unsolved: Comprehensive assessment of tandem repeats at scale
inferred← citeshttps://doi.org/10.1101/2023.10.29.564632openalex-snapshot
Benchmarking of small and large variants across tandem repeats
inferred← citeshttps://doi.org/10.1101/2023.12.11.23299818openalex-snapshot
Exome-wide tandem repeats confer large effects on subcortical volumes in UK Biobank participants
inferred← citeshttps://doi.org/10.1101/2024.01.20.576266openalex-snapshot
Genome-wide profiling of genetic variation at tandem repeat from long reads
inferred← citeshttps://doi.org/10.1101/2024.02.24.581865openalex-snapshot
Multi-ancestry tandem repeat association study of hair colour using exome-wide sequencing
inferred← citeshttps://doi.org/10.1101/2024.04.19.590273openalex-snapshot
Optical genome mapping enables accurate repeat expansion testing
inferred← citeshttps://doi.org/10.1101/2024.06.12.598682openalex-snapshot
Large-scale genotyping and meta-analysis of PIEZO1 short tandem repeat alleles suggest a modest association with malaria susceptibility
inferred← citeshttps://doi.org/10.1101/2024.10.04.615514openalex-snapshot
Defining a tandem repeat catalog and variation clusters for genome-wide analyses
inferred← citeshttps://doi.org/10.1101/2024.11.02.621562openalex-snapshot
Tandem repeat variation shapes immune cell type-specific gene expression
inferred← citeshttps://doi.org/10.1101/2024.12.13.628141openalex-snapshot
Genotyping Short Tandem Repeats Across Copy Number Alterations, Aneuploidies, and Polyploid Organisms
inferred← citeshttps://doi.org/10.1101/2025.01.22.634325openalex-snapshot
StrPhaser constructs tandem repeat alleles from VCF data
inferred← citeshttps://doi.org/10.1101/2025.01.24.634728openalex-snapshot
High short tandem repeat mutation recurrence in heat-stressed Arabidopsis thaliana lines
inferred← citeshttps://doi.org/10.1101/2025.05.06.25327057openalex-snapshot
Identification of (ultra-)rare functional promoter mutations in cancer using sequence-based deep learning models
inferred← citeshttps://doi.org/10.1101/2025.05.13.653434openalex-snapshot
ATaRVa: Analysis of Tandem Repeat Variation from Long-Read Sequencing data
inferred← citeshttps://doi.org/10.1101/2025.09.14.676153openalex-snapshot
Systematic evaluation of the impact of promoter proximal short tandem repeats on expression
inferred← citeshttps://doi.org/10.1101/2025.11.18.689146openalex-snapshot
A deep learning framework for building INDEL mutation rate maps
inferred← citeshttps://doi.org/10.1101/2025.11.24.690106openalex-snapshot
Cas9-enriched nanopore sequencing enables comprehensive and multiplexed detection of repeat expansions
inferred← citeshttps://doi.org/10.1101/2025.11.25.690584openalex-snapshot
Efficient Identification of Short Tandem Repeats via Context-Aware Motif Discovery and Ultra-Fast Sequence Alignment
inferred← citeshttps://doi.org/10.1101/221754openalex-snapshot
Targeted Genotyping of Variable Number Tandem Repeats with adVNTR
inferred← citeshttps://doi.org/10.1101/310045openalex-snapshot
Adaptive protein evolution through length variation in short tandem repeats
inferred← citeshttps://doi.org/10.1101/495226openalex-snapshot
Multi-tissue analysis reveals short tandem repeats as ubiquitous regulators of gene expression and complex traits
inferred← citeshttps://doi.org/10.1101/517839openalex-snapshot
Cancer Classification from Healthy DNA
inferred← citeshttps://doi.org/10.1101/605642openalex-snapshot
BreakCA, a method to discover indels using ChIP-seq and ATAC-seq reads, finds recurrent indels in regulatory regions of neuroblastoma genomes
inferred← citeshttps://doi.org/10.1101/713198openalex-snapshot
Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats
inferred← citeshttps://doi.org/10.1101/714477openalex-snapshot
Genomic properties of structural variants and short tandem repeats that impact gene expression and complex traits in humans
inferred← citeshttps://doi.org/10.1101/729467openalex-snapshot
Absence of pathogenic Short Tandem Repeat expansions in Systemic Lupus Erythematosus disease-associated genes
inferred← citeshttps://doi.org/10.1101/gr.231753.117openalex-snapshot
Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana
inferred← citeshttps://doi.org/10.1101/gr.235119.118openalex-snapshot
Targeted genotyping of variable number tandem repeats with adVNTR
inferred← citeshttps://doi.org/10.1101/gr.235820.118openalex-snapshot
HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay
inferred← citeshttps://doi.org/10.1101/gr.247965.118openalex-snapshot
Pedigree-based estimation of human mobile element retrotransposition rates
inferred← citeshttps://doi.org/10.1101/gr.255851.119openalex-snapshot
RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells
inferred← citeshttps://doi.org/10.1101/gr.277057.122openalex-snapshot
Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
inferred← citeshttps://doi.org/10.1101/gr.277067.122openalex-snapshot
Natural variation in C. elegans short tandem repeats
inferred← citeshttps://doi.org/10.1101/gr.277576.122openalex-snapshot
A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
inferred← citeshttps://doi.org/10.1101/gr.278785.123openalex-snapshot
High-fidelity, large-scale targeted profiling of microsatellites
inferred← citeshttps://doi.org/10.1101/gr.279491.124openalex-snapshot
Optical genome mapping enables accurate testing of large repeat expansions
inferred← citeshttps://doi.org/10.1101/gr.280563.125openalex-snapshot
Estimating the size of long tandem repeat expansions from short reads with ScatTR
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