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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...is accompanied by the formation of de novo enhancer contacts and activation of MYC, illustrating how structural genomic variants can alter the 3D during oncogenesis. In summary, our findings provide evidence for the loss of organization at multiple scales during breast cancer progression, revealing novel...
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Research: Gaps and complex structurally variant loci in phased genome assemblies
- David Porubsky,
- Mitchell R. Vollger,
- William T. Harvey,
- Allison N. Rozanski,
- Peter Ebert,
- Glenn Hickey,
- Patrick Hasenfeld,
- Ashley D. Sanders,
- Catherine Stober,
- Human Pangenome Reference Consortium,
- Jan O. Korbel,
- Benedict Paten,
- Tobias Marschall,
- and Evan E. Eichler
Genome Res. April 2023 33: 496-510; Published in Advance May 10, 2023, doi:10.1101/gr.277334.122
...Gaps and complex structurally variant loci in phased assemblies David Porubsky1, Mitchell R. Vollger1, William T. Harvey1, Allison N. Rozanski1, Peter Ebert2,3, Glenn Hickey4, Patrick Hasenfeld5, Ashley D. Sanders6,7,8, Catherine Stober5, Human Pan Reference Consortium11, Jan O. Korbel5,9, Benedict...
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Method: SvABA: genome-wide detection of structural variants and indels by local assembly
- Jeremiah A. Wala,
- Pratiti Bandopadhayay,
- Noah F. Greenwald,
- Ryan O'Rourke,
- Ted Sharpe,
- Chip Stewart,
- Steve Schumacher,
- Yilong Li,
- Joachim Weischenfeldt,
- Xiaotong Yao,
- Chad Nusbaum,
- Peter Campbell,
- Gad Getz,
- Matthew Meyerson,
- Cheng-Zhong Zhang,
- Marcin Imielinski,
- and Rameen Beroukhim
Genome Res. April 2018 28: 581-591; Published in Advance March 13, 2018, doi:10.1101/gr.221028.117
...-sequence insertions occur in ∼4% of all somatic rearrangements. Finally, we demonstrate that SvABA can identify sites of viral integration and cancer driver alterations containing medium-sized (50–300 bp) SVs.Structural variants (SVs) are a broad class of genomic alterations that includes deletions, duplications...
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Research: Somatic structural variant formation is guided by and influences genome architecture
- Nikos Sidiropoulos,
- Balca R. Mardin,
- F. Germán Rodríguez-González,
- Ivan D. Bochkov,
- Shilpa Garg,
- Adrian M. Stütz,
- Jan O. Korbel,
- Erez Lieberman Aiden,
- and Joachim Weischenfeldt
Genome Res. April 2022 32: 643-655; Published in Advance February 17, 2022, doi:10.1101/gr.275790.121
..., Germany ↵9 These authors contributed equally to this work. Corresponding author: joachim.weischenfeldt@bric.ku.dkAbstractThe occurrence and formation of genomic structural variants (SVs) is known to be influenced by the 3D chromatin architecture, but the extent and magnitude have been challenging to study...
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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
...conducted using Canu, quality control was conducted with BUSCO and Quast, and a visual comparison was conducted with MUMmer (see Supplemental Methods; Kurtz et al. 2004; Simão et al. 2015; Koren et al. 2017; Mikheenko et al. 2018; Manni et al. 2021).Genome-wide structural variant and transposable element...
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Research: AGAP duplicons associate with structural diversity at Chromosome 10q11.22
- Stefania Fornezza,
- Vincenza Simona Delvecchio,
- William T. Harvey,
- Philip C. Dishuck,
- Evan E. Eichler,
- and Giuliana Giannuzzi
Genome Res. October 2024 34: 1487-1499; Published in Advance September 25, 2024, doi:10.1101/gr.279454.124
....Refinement of structural variation breakpointsTo gain insights into the mechanism originating 10q11.22 structural diversity, we sought to (1) identify the location of the variant breakpoints; (2) narrow down as much as possible the interval; (3) assess sequence features at the refined locations. We considered...
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Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...sequence difference, with 0.1%–0.25% pairwise divergence between Lake Malawi species. These were based on aligning short reads to a single linear reference and ignored the contribution of larger-scale structural variants (SVs). We constructed a pan graph that integrates six new and two existing long...
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Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
- Tanner D. Jensen,
- Bohan Ni,
- Chloe M. Reuter,
- John E. Gorzynski,
- Sarah Fazal,
- Devon Bonner,
- Rachel A. Ungar,
- Pagé C. Goddard,
- Archana Raja,
- Euan A. Ashley,
- Jonathan A. Bernstein,
- Stephan Zuchner,
- Undiagnosed Diseases Network,
- Michael D. Greicius,
- Stephen B. Montgomery,
- Michael C. Schatz,
- Matthew T. Wheeler,
- and Alexis Battle
Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
.... Corresponding authors: smontgom@stanford.edu, mschatz@cs.jhu.edu, wheelerm@stanford.edu, ajbattle@jhu.eduAbstractRare structural variants (SVs)—insertions, deletions, and complex rearrangements—can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed...
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Research: Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate
- Wilfried M. Guiblet,
- Marzia A. Cremona,
- Monika Cechova,
- Robert S. Harris,
- Iva Kejnovská,
- Eduard Kejnovsky,
- Kristin Eckert,
- Francesca Chiaromonte,
- and Kateryna D. Makova
Genome Res. December 2018 28: 1767-1778; Published in Advance November 6, 2018, doi:10.1101/gr.241257.118
...al. 2010). Genome-wide, (CGG)n repeats showed a strong periodic decrease in polymerization speed (elevated IPDs) on the annotated strand (up to ninefold IPD increase at the 95th quantile) (Fig. 2C), consistent with their ability to form G4-like structures and hairpins (Nadel et al. 1995). The pattern...
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Method: Genome-wide TOP2A DNA cleavage is biased toward translocated and highly transcribed loci
- Xiang Yu,
- James W. Davenport,
- Karen A. Urtishak,
- Marie L. Carillo,
- Sager J. Gosai,
- Christos P. Kolaris,
- Jo Ann W. Byl,
- Eric F. Rappaport,
- Neil Osheroff,
- Brian D. Gregory,
- and Carolyn A. Felix
Genome Res. July 2017 27: 1238-1249; Published in Advance April 6, 2017, doi:10.1101/gr.211615.116
...in a leukemia cell line 3′ in the KMT2A breakpoint cluster region (bcr) (Cowell et al. 2012). In KMT2A-rearranged (KMT2A-R) leukemia in infants, maternal-fetal exposures to dietary TOP2 interacting substances (Spector et al. 2005) and an inactivating variant in NQO1, which detoxifies the TOP2 poison p...

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