Levinson, G. & Gutman, G. A. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4, 203–221 (1987).

CAS  PubMed  Google Scholar 

Fan, H. & Chu, J.-Y. A brief review of short tandem repeat mutation. Genom. Proteom. Bioinform. 5, 7–14 (2007).

Article  CAS  Google Scholar 

Shriver, M. D., Jin, L., Chakraborty, R. & Boerwinkle, E. VNTR allele frequency distributions under the stepwise mutation model: a computer simulation approach. Genetics 134, 983–993 (1993).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wright, J. M. Mutation at VNTRs: are minisatellites the evolutionary progeny of microsatellites? Genome 37, 345–347 (1994).

Article  CAS  PubMed  Google Scholar 

Willems, T. et al. The landscape of human STR variation. Genome Res. 24, 1894–1904 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ren, J., Gu, B. & Chaisson, M. J. P. vamos: variable-number tandem repeats annotation using efficient motif sets. Genome Biol. 24, 175 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Noyes, M. D. et al. Familial long-read sequencing increases yield of de novo mutations. Am. J. Hum. Genet. 109, 631–646 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

DeJesus-Hernandez, M. et al. Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron 72, 245–256 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Depienne, C. & Mandel, J.-L. 30 years of repeat expansion disorders: what have we learned and what are the remaining challenges? Am. J. Hum. Genet. 108, 764–785 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mirceta, M., Shum, N., Schmidt, M. H. M. & Pearson, C. E. Fragile sites, chromosomal lesions, tandem repeats, and disease. Front. Genet. 13, 985975 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hannan, A. J. Repeat DNA expands our understanding of autism spectrum disorder. Nature 589, 200–202 (2021).

Article  CAS  PubMed  Google Scholar 

Hannan, A. J. Tandem repeats mediating genetic plasticity in health and disease. Nat. Rev. Genet. 19, 286–298 (2018).

Article  CAS  PubMed  Google Scholar 

Stanley, U. et al. Forensic DNA profiling: autosomal short tandem repeat as a prominent marker in crime investigation. Malays. J. Med. Sci. 27, 22–35 (2020).

Google Scholar 

Hall, C. L. et al. Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device. Forensic Sci. Int. Genet. 56, 102629 (2022).

Article  CAS  PubMed  Google Scholar 

Warner, J. P. et al. A general method for the detection of large CAG repeat expansions by fluorescent PCR. J. Med. Genet. 33, 1022–1026 (1996).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jeffreys, A. J., Wilson, V. & Thein, S. L. Hypervariable ‘minisatellite’ regions in human DNA. Nature 314, 67–73 (1985).

Article  CAS  PubMed  Google Scholar 

Dolzhenko, E. et al. ExpansionHunter: a sequence-graph based tool to analyze variation in short tandem repeat regions. Bioinformatics 35, 4754–4756 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Willems, T. et al. Genome-wide profiling of heritable and de novo STR variations. Nat. Methods 14, 590–592 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mousavi, N., Shleizer-Burko, S., Yanicky, R. & Gymrek, M. Profiling the genome-wide landscape of tandem repeat expansions. Nucleic Acids Res. 47, e90 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dolzhenko, E. et al. Characterization and visualization of tandem repeats at genome scale. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-02057-3 (2024).

Article  PubMed  Google Scholar 

Chiu, R., Rajan-Babu, I.-S., Friedman, J. M. & Birol, I. Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences. Genome Biol. 22, 224 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nurk, S. et al. The complete sequence of a human genome. Science 376, 44–53 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Aganezov, S. et al. A complete reference genome improves analysis of human genetic variation. Science 376, eabl3533 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rhie, A. et al. The complete sequence of a human Y chromosome. Nature 621, 344–354 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Olson, N. D. et al. Variant calling and benchmarking in an era of complete human genome sequences. Nat. Rev. Genet. 24, 464–483 (2023).

Article  CAS  PubMed  Google Scholar 

Majidian, S., Agustinho, D. P., Chin, C.-S., Sedlazeck, F. J. & Mahmoud, M. Genomic variant benchmark: if you cannot measure it, you cannot improve it. Genome Biol. 24, 221 (2023).

Article  PubMed  PubMed Central  Google Scholar 

Wagner, J. et al. Benchmarking challenging small variants with linked and long reads. Cell Genom. 2, 100128 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zook, J. M. et al. A robust benchmark for detection of germline large deletions and insertions. Nat. Biotechnol. 38, 1347–1355 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wagner, J. et al. Curated variation benchmarks for challenging medically relevant autosomal genes. Nat. Biotechnol. 40, 672–680 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

English, A. C., Menon, V. K., Gibbs, R. A., Metcalf, G. A. & Sedlazeck, F. J. Truvari: refined structural variant comparison preserves allelic diversity. Genome Biol. 23, 271 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yang, J. & Chaisson, M. J. P. TT-Mars: structural variants assessment based on haplotype-resolved assemblies. Genome Biol. 23, 110 (2022).

Article  PubMed  PubMed Central  Google Scholar 

Audano, P. A. & Beck, C. R. Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement. Genome Res. 34, 7–19 (2024).

Article  PubMed  PubMed Central  Google Scholar 

Fu, Y., Mahmoud, M., Muraliraman, V. V., Sedlazeck, F. J. & Treangen, T. J. Vulcan: improved long-read mapping and structural variant calling via dual-mode alignment. GigaScience 10, giab063 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Gelfand, Y., Rodriguez, A. & Benson, G. TRDB—the Tandem Repeats Database. Nucleic Acids Res. 35, D80–D87 (2007).

Article  CAS  PubMed  Google Scholar 

Halman, A., Dolzhenko, E. & Oshlack, A. STRipy: a graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data. Hum. Mutat. 43, 859–868 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kent, W. J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Saini, S., Mitra, I., Mousavi, N., Fotsing, S. F. & Gymrek, M. A reference haplotype panel for genome-wide imputation of short tandem repeats. Nat. Commun. 9, 4397 (2018).

Article