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Method: Estimating the size of long tandem repeat expansions from short reads with ScatTR
- Rashid Al-Abri and
- Gamze Gürsoy
Genome Res. December 2025 35: 2701-2713; Published in Advance August 21, 2025, doi:10.1101/gr.280563.125
....gursoy@columbia.eduAbstractTandem repeats (TRs) are sequences of DNA in which ≥2 bp are repeated back-to-back at specific locations in the . TR expansions, in which the number of repeat units exceeds the normal range, have been implicated in more than 50 conditions. However, accurately measuring the copy number of TRs is challenging...
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Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
...). By looking at the mutations through -wide “breadth”, the limited number of equivalents becomes less restrictive, enabling the identification of tumor fractions (TFs) ∼100 times lower compared to targeted “depth” in SNV analysis (Zviran et al. 2020). Genome-wide cfDNA can also reveal tumor-specific copy...
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Method: Highly accurate assembly polishing with DeepPolisher
- Mira Mastoras,
- Mobin Asri,
- Lucas Brambrink,
- Prajna Hebbar,
- Alexey Kolesnikov,
- Daniel E. Cook,
- Maria Nattestad,
- Julian Lucas,
- Taylor S. Won,
- Pi-Chuan Chang,
- Andrew Carroll,
- Benedict Paten,
- Kishwar Shafin,
- and and the Human Pangenome Reference Consortium
Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
...technologies contain errors that are not completely random but are influenced by biases toward different genomic features. Even using a consensus approach, recurrent errors in the reads can propagate into the assembly. Low complexity regions like homopolymers and tandem repeats are particularly challenging...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...and genomic features of gars, (2) assess the conservation of gars in comparison with other vertebrates, (3) examine the rates of chromosome rearrangement and repeat evolution in gars relative to other vertebrates, and (4) determine whether there has been ancient gene flow among gar species based...
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Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
- Mikhail O. Maksimov,
- Cynthia Wu,
- David G. Ashbrook,
- Flavia Villani,
- Vincenza Colonna,
- Nima Mousavi,
- Nichole Ma,
- Lu Lu,
- Jonathan K. Pritchard,
- Alon Goren,
- Robert W. Williams,
- Abraham A. Palmer,
- and Melissa Gymrek
Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
...A novel quantitative trait locus implicates Msh3 in the propensity for -wide short tandem repeat expansions in mice Mikhail O. Maksimov1,2,12, Cynthia Wu3,12, David G. Ashbrook4, Flavia Villani4, Vincenza Colonna4,5, Nima Mousavi6, Nichole Ma1, Lu Lu4, Jonathan K. Pritchard7,8, Alon Goren1...
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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
...for repeat units within a specified range. Finally, improved heuristics for identifying cycles that combine both weights and optimal positional coverage would enable the weighted graph to represent complex repeat patterns more accurately. We plan to explore these strategies to enhance EquiRep's accuracy...
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Method: Accurate allocation of multimapped reads enables regulatory element analysis at repeats
- Alexis Morrissey,
- Jeffrey Shi,
- Daniela Q. James,
- and Shaun Mahony
Genome Res. June 2024 34: 937-951; Published in Advance July 10, 2024, doi:10.1101/gr.278638.123
...genomics analysis pipelines discard “multimapped” reads that align equally well to multiple genomic locations. Because multimapped reads arise predominantly from repeats, current analysis pipelines fail to detect a substantial portion of regulatory events that occur in repetitive regions. To address...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...results demonstrate the advantage of the proposed ILP/IQP approaches for accurate inference, especially with low-coverage data (coverage, 0.1×–1×). Thus, our algorithm can facilitate affordable genotyping and association studies of complex and repeat-rich regions of the .Although our approach is currently...
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Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
- Nora Zidane,
- Carla Rodrigues,
- Valérie Bouchez,
- Martin Rethoret-Pasty,
- Virginie Passet,
- Sylvain Brisse,
- and Chiara Crestani
Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
....9.0 allows for accurate genomic typing of the three pathogensWe analyzed the number of cgMLST mismatches after allele calling compared with Illumina assembly calls used as reference. In most cases, the average number of mismatches per isolate did not differ significantly between data basecalled with the HAC...
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Resource: Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser
- Jiawei Shen,
- Siyuan Cheng,
- Deepak Purushotham,
- Xiaoyu Zhuo,
- Alan Y Du,
- Wenjin Zhang,
- Daofeng Li,
- and Ting Wang
Genome Res. February 21, 2025 gr.279764.124; Published in Advance February 21, 2025, doi:10.1101/gr.279764.124
...Exploring the epi profiles of repetitive elements with the WashU Repeat Browser Jiawei Shen1, 2, Siyuan Cheng1, Deepak Purushotham1, Xiaoyu Zhuo1, Alan Y. Du1, Wenjin Zhang1, Daofeng Li1, *, Ting Wang1, 2, 3, * Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology...
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