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Research: Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion syndrome
- Lisanne Vervoort,
- Nicolas Dierckxsens,
- Marta Sousa Santos,
- Senne Meynants,
- Erika Souche,
- Ruben Cools,
- Tracy Heung,
- Koen Devriendt,
- Hilde Peeters,
- Donna M. McDonald-McGinn,
- Ann Swillen,
- Jeroen Breckpot,
- Beverly S. Emanuel,
- Hilde Van Esch,
- Anne S. Bassett,
- and Joris R. Vermeesch
Genome Res. April 2025 35: 786-797; Published in Advance November 13, 2024, doi:10.1101/gr.279331.124
...). They are defined as DNA segments with a length of at least 1 kb that share >90% of sequence identity (Bailey et al. 2001, 2002). Their high sequence homology is known to be a driver of nonallelic homologous recombination (NAHR), caused by meiotic misalignment of homologous chromosomes or sister chromatids...
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Research: Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis
- Brooke Weckselblatt,
- Karen E. Hermetz,
- and M. Katharine Rudd
Genome Res. July 2015 25: 937-947; Published in Advance June 12, 2015, doi:10.1101/gr.191247.115
...a parent who carries the balanced form of the rearrangement or may arise de novo. Recurrent translocations may be mediated by nonallelic homologous recombination (NAHR) between segmental duplications (Giglioet al. 2002;Ouet al. 2011)orparalogous interspersed repeats (Luo et al. 2011; Hermetz et al. 2012...
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Research: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
- Scott Ferguson,
- Ashley Jones,
- Kevin Murray,
- Rose Andrew,
- Benjamin Schwessinger,
- and Justin Borevitz
Genome Res. April 2024 34: 606-619; Published in Advance April 8, 2024, doi:10.1101/gr.277999.123
...as lineage-specific mutations erode sequence homology. Rearrangements, likely because of their recombination effects and subsequent fixation/reduction of alleles (Faria and Navarro 2010), are lost more rapidly than are syntenic regions. Translocations and duplications were the major disruptors of synteny...
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Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
- Tianfu Zeng,
- Haotian Liao,
- Lin Xia,
- Siyao You,
- Yanqun Huang,
- Jiaxun Zhang,
- Yahui Liu,
- Xuyan Liu,
- and Dan Xie
Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
.... Notably, hepatitis B virus (HBV) DNA integration frequently results in the generation of somatic SVs, particularly inducing interchromosomal translocations (TRAs). Although HBV DNA integration into the liver occurs randomly, multisite shared HBV-induced SVs are early driving events in the pathogenesis...
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Research: Causes and consequences of a complex recombinational landscape in the ant Cardiocondyla obscurior
- Mohammed Errbii,
- Jürgen Gadau,
- Kerstin Becker,
- Lukas Schrader,
- and Jan Oettler
Genome Res. June 2024 34: 863-876; Published in Advance June 5, 2024, doi:10.1101/gr.278392.123
...patterns persist when using recombination rates estimated for a population of the Old World lineage.Recombination is associated with small and large rearrangementsEctopic recombination (i.e., crossovers between nonallelic homologous loci), particularly in repeat-rich regions, has been shown to produce...
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Research: Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells
- Nick Riddiford,
- Katarzyna Siudeja,
- Marius van den Beek,
- Benjamin Boumard,
- and Allison J. Bardin
Genome Res. August 2021 31: 1419-1432; Published in Advance June 24, 2021, doi:10.1101/gr.268441.120
...hypothesize that the TE sequence was integrated during DNA repair. (D) In class II events, two germline TE sequences were found at breakpoint junctions. We hypothesize that these sequences underwent nonallelic homologous recombination, deleting the central region. (E,F) Class III events had evidence...
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Research: Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
- David Thybert,
- Maša Roller,
- Fábio C.P. Navarro,
- Ian Fiddes,
- Ian Streeter,
- Christine Feig,
- David Martin-Galvez,
- Mikhail Kolmogorov,
- Václav Janoušek,
- Wasiu Akanni,
- Bronwen Aken,
- Sarah Aldridge,
- Varshith Chakrapani,
- William Chow,
- Laura Clarke,
- Carla Cummins,
- Anthony Doran,
- Matthew Dunn,
- Leo Goodstadt,
- Kerstin Howe,
- Matthew Howell,
- Ambre-Aurore Josselin,
- Robert C. Karn,
- Christina M. Laukaitis,
- Lilue Jingtao,
- Fergal Martin,
- Matthieu Muffato,
- Stefanie Nachtweide,
- Michael A. Quail,
- Cristina Sisu,
- Mario Stanke,
- Klara Stefflova,
- Cock Van Oosterhout,
- Frederic Veyrunes,
- Ben Ward,
- Fengtang Yang,
- Golbahar Yazdanifar,
- Amonida Zadissa,
- David J. Adams,
- Alvis Brazma,
- Mark Gerstein,
- Benedict Paten,
- Son Pham,
- Thomas M. Keane,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. April 2018 28: 448-459; Published in Advance March 21, 2018, doi:10.1101/gr.234096.117
...in the vicinity of chromosomal breakpoints (Bailey et al. 2004; The Bovine Genome Sequencing and Analysis Consortium 2009; Carbone et al. 2014). It is not clear whether these transposable elements directly cause chromosomal rearrangement by triggering nonallelic homologous recombination (NAHR) (Janoušek et al...
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