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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...Institute, Kansas City, Missouri 64108, USA; 4Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec H3A 0G1, Canada Corresponding authors: david.lougheed@mail.mcgill.ca, guil.bourque@mcgill.caAbstractVariation in short tandem repeats (STRs) is implicated in Mendelian...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...dataWe then tested all methods on reconstructing repeat units for satellite DNA in human Chromosome 5 (Paar et al. 2007). This known satellite DNA consists of 13 units (i.e., 13 monomers), each of which is ∼171 bp in size. To construct the input sequence for methods to predict, we concatenated the 13...
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Method: CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing
- Kaiyuan Zhu,
- Matthew G. Jones,
- Jens Luebeck,
- Xinxin Bu,
- Hyerim Yi,
- King L. Hung,
- Ivy Tsz-Lo Wong,
- Shu Zhang,
- Paul S. Mischel,
- Howard Y. Chang,
- and Vineet Bafna
Genome Res. September 2024 34: 1344-1354; Published in Advance July 9, 2024, doi:10.1101/gr.279131.124
...CoRAL accurately resolves extrachromosomal DNA structures with long-read sequencing Kaiyuan Zhu1,10, Matthew G. Jones2,10, Jens Luebeck1, Xinxin Bu3, Hyerim Yi2,4, King L. Hung2, Ivy Tsz-Lo Wong5,6, Shu Zhang2,5,7, Paul S. Mischel5,6, Howard Y. Chang2,4,8 and Vineet Bafna1,9 1Department of Computer...
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Research: Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths
- Fangyuan Yang,
- Li-Jun Cao,
- Petr Nguyen,
- Zhong-Zheng Ma,
- Jin-Cui Chen,
- Wei Song,
- and Shu-Jun Wei
Genome Res. January 2025 35: 66-77; Published in Advance January 6, 2025, doi:10.1101/gr.279569.124
...(Charlesworth et al. 1987, 2018). Second, fusions could be selected if they tighten the linkage between adaptive alleles (Guerrero and Kirkpatrick 2014; Liu et al. 2022) or resolve sexual conflict via sex linkage (Kitano et al. 2009). Third, the evolution of SCDC on young sex chromosomes could facilitate...
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Method: Multisample motif discovery and visualization for tandem repeats
- Yaran Zhang,
- Marc Hulsman,
- Alex Salazar,
- Niccolò Tesi,
- Lydian Knoop,
- Sven van der Lee,
- Sanduni Wijesekera,
- Jana Krizova,
- Erik-Jan Kamsteeg,
- and Henne Holstege
Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
...Nijmegen, The Netherlands; 5Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, 1081HV Amsterdam, The Netherlands Corresponding author: h.holstege@amsterdamumc.nlAbstractTandem repeats (TRs) occupy a significant portion of the human and are a source...
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Method: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
- Sergey Koren,
- Zhigui Bao,
- Andrea Guarracino,
- Shujun Ou,
- Sara Goodwin,
- Katharine M. Jenike,
- Julian Lucas,
- Brandy McNulty,
- Jimin Park,
- Mikko Rautiainen,
- Arang Rhie,
- Dick Roelofs,
- Harrie Schneiders,
- Ilse Vrijenhoek,
- Koen Nijbroek,
- Olle Nordesjo,
- Sergey Nurk,
- Mike Vella,
- Katherine R. Lawrence,
- Doreen Ware,
- Michael C. Schatz,
- Erik Garrison,
- Sanwen Huang,
- William Richard McCombie,
- Karen H. Miga,
- Alexander H.J. Wittenberg,
- and Adam M. Phillippy
Genome Res. November 2024 34: 1919-1930; Published in Advance November 6, 2024, doi:10.1101/gr.279334.124
..., Chromosome 2 harbored a complex unresolved repeat, corresponding to the 45S rDNA array, which has been estimated at 2300 (Ganal et al. 1988) copies or over 20 Mbp in size (Fig. 4). Chromosomes 11 and 12 shared high similarity in a peri-telomeric region that could not be resolved, and Chromosome 3 had a gap...
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Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
..., Germany Corresponding authors: pnavarro@pasteur.fr, job.dekker@umassmed.eduAbstractMitotic chromosomes are considered to be universally folded as loop arrays across species and cell types. However, some studies suggest that features of mitotic chromosomes might be cell type– or species-specific. We...
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Resource: Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR
- Wouter De Coster,
- Ida Höijer,
- Inge Bruggeman,
- Svenn D'Hert,
- Malin Melin,
- Adam Ameur,
- and Rosa Rademakers
Genome Res. November 2024 34: 2074-2080; Published in Advance August 15, 2024, doi:10.1101/gr.279265.124
...for an individual, except for genotypes on Chr X for individuals with one copy of the X Chromosome.View larger version: In this window In a new window Figure 1. pathSTR visualization of the repeat length. (A) Scatter plot length visualization of the RFC1 repeat, comparing, per individual, the longer allele against...
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Research: Natural variation in C. elegans short tandem repeats
- Gaotian Zhang,
- Ye Wang,
- and Erik C. Andersen
Genome Res. October 2022 32: 1852-1861; Published in Advance October 4, 2022, doi:10.1101/gr.277067.122
...and a minimum repeat number of 11, 6, 5, 3.75, 3.4, and 3, respectively, for each ascending motif length. The reference STRs were unevenly distributed across the (Supplemental Fig. S1A) with higher density on chromosome arms and tips than centers, suggesting that higher recombination is associated...
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Research: The motif composition of variable number tandem repeats impacts gene expression
- Tsung-Yu Lu,
- Paulina N. Smaruj,
- Geoffrey Fudenberg,
- Nicholas Mancuso,
- and Mark J.P. Chaisson
Genome Res. April 2023 33: 511-524; Published in Advance April 10, 2023, doi:10.1101/gr.276768.122
...from short-read data, it is known that VNTRs vary in both length and repeat (motif) composition. Here, we use a repeat-pan graph (RPGG) constructed on 35 haplotype-resolved assemblies to detect variation in both VNTR length and repeat composition. We align population-scale data from the Genotype...
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