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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
...regions using STRkit running in two modes: one mode incorporating SNV data to help call and locally phase alleles, and one mode without SNVs or other haplotype tag data.Our benchmark STR regions are derived from an approximately 1.7 million tandem repeat benchmark variant set developed for HG002 (English...
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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
...(CANVAS), expansions of the repeat in replication factor C subunit 1 (RFC1) gene are composed primarily of AAGGG or GACAG, variations from the more common AAAAG motif found in nonexpanded alleles (Cortese et al. 2019; Scriba et al. 2020).Furthermore, TRs can provide insight into (the evolution of...
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Research: Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples
- Kohei Hagiwara,
- Andrew Thrasher,
- Nadezhda V. Terekhanova,
- and Jinghui Zhang
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
...demonstrates their utility in RNA-based mutation calling. [Supplemental material is available for this article.] In a diploid , allele-specific expression (ASE) refers to a phenomenon of preferential expression of one allele over the other in a cell, which can unveil cis-acting regulatory mechanisms...
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Research: Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes
- Suleyman Gulsuner,
- Amal AbuRayyan,
- Jessica B. Mandell,
- Ming K. Lee,
- Greta V. Bernier,
- Barbara M. Norquist,
- Sarah B. Pierce,
- Mary-Claire King,
- and Tom Walsh
Genome Res. November 2024 34: 1825-1831; Published in Advance September 13, 2024, doi:10.1101/gr.279158.124
...applied to evaluation of pathogenicity of an exonic duplication of BRCA1 (Filser et al. 2023). Genome-wide, long-read cDNA sequencing revealed 70,000 novel transcripts in GTEx tissues and cell lines and demonstrated the feasibility of assessing allele-specific expression mediated by rare cis...
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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
...circular RNAs from rolling-circular long-read sequencing data, using both simulated and raw sequencing data sets. Our results show that EquiRep consistently outperforms or matches state-of-the-art methods, demonstrating robustness to sequencing errors and superior performance on long repeat units and low...
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Method: RAmbler resolves complex repeats in human Chromosomes 8, 19, and X
- Sakshar Chakravarty,
- Glennis Logsdon,
- and Stefano Lonardi
Genome Res. April 2025 35: 863-876; Published in Advance March 4, 2025, doi:10.1101/gr.279308.124
...on human data sets. The first two experiments were aimed at demonstrating RAmbler's ability to resolve repeats without manual curation. For these two experiments, we used as inputs (1) the T2T assembly with CHM13 HiFi reads and (2) the MAT002 assembly with HG002 HiFi reads. The other three experiments...
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Method: Enabling efficient and robust analysis of tandem repeats in genomic data using wavefront-based string decomposer
- Junhai Qi,
- Zhidong Yang,
- Ting Yu,
- and Guojun Li
Genome Res. April 8, 2026 gr.281346.125; Published in Advance April 8, 2026, doi:10.1101/gr.281346.125
...University5 of Science and Technology, Hong Kong S.A.R., China, 9990776 ∗Correspondence to: tingy@sdu.edu.cn and gjli@sdu.edu.cn7 Abstract8 Tandem repeats (TRs) analysis is crucial for understanding structure and variation. However, string de-9 composition, a key challenge in TRs analysis, remains...
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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
...community to get a more complete overview of normal variation in tandem repeat length and sequence composition and, as such, enable a better assessment of rare tandem repeat alleles observed in patients.Tandem repeats are head-to-tail direct repetitions of a DNA motif, which can be repeated exactly...
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Research: Variation in histone configurations correlates with gene expression across nine inbred strains of mice
- Anna L Tyler,
- Catrina Spruce,
- Romy Kursawe,
- Annat Haber,
- Robyn L Ball,
- Wendy A Pitman,
- Alexander D Fine,
- Narayanan Raghupathy,
- Michael Walker,
- Vivek M Philip,
- Christopher L Baker,
- J. Matthew Mahoney,
- Gary A. Churchill,
- Jennifer J Trowbridge,
- Michael L Stitzel,
- Kenneth Paigen,
- Petko M Petkov,
- and Gregory W Carter
Genome Res. May 22, 2023 gr.277467.122; Published in Advance May 22, 2023, doi:10.1101/gr.277467.122
...to all DO/CC founders, we undertook a strain survey63 of epigenetic variation in hepatocytes across the eight founders of the DO/CC mice, as well as64 DBA/2J, which, along with C57BL/6J, is one of the founders of the widely used BxD recombinant65 inbred panel of mice (Ashbrook et al., 2019).66 We assayed...
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Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
- Kohei Hamanaka,
- Daisuke Yamauchi,
- Eriko Koshimizu,
- Kei Watase,
- Kaoru Mogushi,
- Kinya Ishikawa,
- Hidehiro Mizusawa,
- Naomi Tsuchida,
- Yuri Uchiyama,
- Atsushi Fujita,
- Kazuharu Misawa,
- Takeshi Mizuguchi,
- Satoko Miyatake,
- and Naomichi Matsumoto
Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
...; Polysciences, Inc.) in accordance with the manufacturer's protocol. Cells were harvested 24 h after transfection, and total RNA was extracted using RNeasy Mini Kit (Qiagen). Two micrograms of total RNA was subjected to reverse transcription (RT) using random hexamer primers (PrimeScript 1st strand cDNA...

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