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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...). Hepatocellular carcinoma (HCC) is the most common PLC, accounting for >80% of cases (Llovet et al. 2021). China is among the areas associated with the highest risk of developing HCC, accounting for 42.5% of the global incidence of liver cancer (Bray et al. 2024; Miao et al. 2024). Notably, ∼90% of HCC cases...
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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
..., including an aneuploid (Aneu), inverse triplications characteristic of origin-dependent inverted repeat amplification (ODIRA; Trip1, Trip2), a supernumerary chromosome (Sup), and more complex structures probably resulting from multiple mutational events (ComTrip, ComQuad, ComSup). The diversity in GAP1 CNVs...
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Resource: An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
- Chong Li,
- Marc Jan Bonder,
- Sabriya Syed,
- Matthew Jensen,
- Human Genome Structural Variation Consortium (HGSVC),
- HGSVC Functional Analysis Working Group,
- Mark B. Gerstein,
- Michael C. Zody,
- Mark J.P. Chaisson,
- Michael E. Talkowski,
- Tobias Marschall,
- Jan O. Korbel,
- Evan E. Eichler,
- Charles Lee,
- and Xinghua Shi
Genome Res. December 2024 34: 2304-2318; Published in Advance December 5, 2024, doi:10.1101/gr.279419.124
...the impact of other types of SVs (e.g., duplications and inversions) and ancestral alleles on human-specific chromatin structure and gene regulation. Furthermore, the primary focus of our current pipeline centers around TAD calling, given the scope of the current study. It has been shown that chromatin loops...
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Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
- Yang Zhou,
- Lv Yang,
- Xiaotao Han,
- Jiazheng Han,
- Yan Hu,
- Fan Li,
- Han Xia,
- Lingwei Peng,
- Clarissa Boschiero,
- Benjamin D. Rosen,
- Derek M. Bickhart,
- Shujun Zhang,
- Aizhen Guo,
- Curtis P. Van Tassell,
- Timothy P.L. Smith,
- Liguo Yang,
- and George E. Liu
Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
...the previously recognized microsatellite, single-nucleotide polymorphism (SNP), and short insertion/deletion (indel) variants. SVs can take the form of deletions, insertions, and duplications (commonly grouped under the term copy number variation [CNV]), as well as inversions and translocations, which have been...
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Research: Primate segmental duplication creates novel promoters for the LRRC37 gene family within the 17q21.31 inversion polymorphism region
- Cemalettin Bekpen,
- Ibrahim Tastekin,
- Priscillia Siswara,
- Cezmi A. Akdis,
- and Evan E. Eichler
Genome Res. June 2012 22: 1050-1058; Published in Advance March 14, 2012, doi:10.1101/gr.134098.111
...Primate segmental duplication creates novel promoters for the LRRC37 gene family within the 17q21.31 inversion polymorphism region Cemalettin Bekpen 1 , 2 , 5 , Ibrahim Tastekin 2 , Priscillia Siswara 3 , Cezmi A. Akdis 1 and Evan E...
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Method: Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR
- Marta Puig,
- Jon Lerga-Jaso,
- Carla Giner-Delgado,
- Sarai Pacheco,
- David Izquierdo,
- Alejandra Delprat,
- Magdalena Gayà-Vidal,
- Jack F. Regan,
- George Karlin-Neumann,
- and Mario Cáceres
Genome Res. May 2020 30: 724-735; Published in Advance May 18, 2020, doi:10.1101/gr.255273.119
...the opportunity to easily study these inversions in parents of patients and determine their role in the generation of pathological variants, contributing to a more complete picture of the genomic impact of inversions.View larger version: In this window In a new window Figure 5. Polymorphic inversions...
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Research: Shifts in the intensity of purifying selection: An analysis of genome-wide polymorphism data from two closely related yeast species
- Eyal Elyashiv,
- Kevin Bullaughey,
- Shmuel Sattath,
- Yosef Rinott,
- Molly Przeworski,
- and Guy Sella
Genome Res. November 2010 20: 1558-1573; Published in Advance September 4, 2010, doi:10.1101/gr.108993.110
...Shifts in the intensity of purifying selection: An analysis of genome-wide polymorphism data from two closely related yeast species Eyal Elyashiv 1 , Kevin Bullaughey 2 , Shmuel Sattath 1 , Yosef Rinott 3 , Molly Przeworski 2 , 4 , 5...
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Methods: High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis
- Marilyn A.L. West,
- Hans van Leeuwen,
- Alexander Kozik,
- Daniel J. Kliebenstein,
- R.W. Doerge,
- Dina A. St. Clair,
- and Richard W. Michelmore
Genome Res. June 2006 16: 787-795; Published in Advance May 15, 2006, doi:10.1101/gr.5011206
...High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis High-density haplotyping with microarrays Marilyn A.L. West 1 , 4 , Hans van Leeuwen 1 , Alexander Kozik 2 , Daniel J. Kliebenstein 1...
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LETTER: Many or most genes in Arabidopsis transposed after the origin of the order Brassicales
- Michael Freeling,
- Eric Lyons,
- Brent Pedersen,
- Maqsudul Alam,
- Ray Ming,
- and Damon Lisch
Genome Res. December 2008 18: 1924-1937; Published in Advance October 3, 2008, doi:10.1101/gr.081026.108
...Many or most genes in Arabidopsis transposed after the origin of the order Brassicales Michael Freeling 1 , 4 , Eric Lyons 1 , Brent Pedersen 1 , Maqsudul Alam 2 , Ray Ming 3 , and Damon Lisch 1 1 Department...
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Methods: Recovering the geographic origin of early modern humans by realistic and spatially explicit simulations
- Nicolas Ray,
- Mathias Currat,
- Pierre Berthier,
- and Laurent Excoffier
Genome Res. August 2005 15: 1161-1167; doi:10.1101/gr.3708505
...markers tested in 22 populations points toward a unique but surprising North African origin of modern humans. We show that this result could be due to ascertainment bias in favor of markers selected to be polymorphic in Europeans. A new estimation modeling this bias explicitly reveals that East Africa...

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