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Resource: Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
- Flavia Angela Maria Maggiolini,
- Ashley D. Sanders,
- Colin James Shew,
- Arvis Sulovari,
- Yafei Mao,
- Marta Puig,
- Claudia Rita Catacchio,
- Maria Dellino,
- Donato Palmisano,
- Ludovica Mercuri,
- Miriana Bitonto,
- David Porubský,
- Mario Cáceres,
- Evan E. Eichler,
- Mario Ventura,
- Megan Y. Dennis,
- Jan O. Korbel,
- and Francesca Antonacci
Genome Res. November 2020 30: 1680-1693; Published in Advance October 22, 2020, doi:10.1101/gr.265322.120
...Single-cell strand sequencing of a macaque reveals multiple nested inversions and breakpoint reuse during primate evolution Flavia Angela Maria Maggiolini1, Ashley D. Sanders2, Colin James Shew3, Arvis Sulovari4, Yafei Mao4, Marta Puig5, Claudia Rita Catacchio1, Maria Dellino1, Donato Palmisano1...
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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
...into the human . Additionally, a substantial proportion of chimeric reads contained HBV sequences at only one terminus (designated “single-end chimeric reads”), and breakpoints in these single-end reads coincided with those in translocation/duplication-bridging chimeric reads (Supplemental Fig. S2...
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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
...of bioinformatic pipelines to create haplotype-resolved LCR22 assemblies (Vollger et al. 2019). Several attempts to map the rearrangements have provided anecdotal results: using long-range PCR and sequencing of two distal 22q11.2 deletions, the breakpoint cluster region (BCR) module was suggested to be the NAHR...
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Research: Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers
- David E. Symer,
- Keiko Akagi,
- Heather M. Geiger,
- Yang Song,
- Gaiyun Li,
- Anne-Katrin Emde,
- Weihong Xiao,
- Bo Jiang,
- André Corvelo,
- Nora C. Toussaint,
- Jingfeng Li,
- Amit Agrawal,
- Enver Ozer,
- Adel K. El-Naggar,
- Zoe Du,
- Jitesh B. Shewale,
- Birgit Stache-Crain,
- Mark Zucker,
- Nicolas Robine,
- Kevin R. Coombes,
- and Maura L. Gillison
Genome Res. January 2022 32: 55-70; Published in Advance December 13, 2021, doi:10.1101/gr.275911.121
...loci harboring one or more breakpoints, a majority contain “simple” integrants identified by two or fewer breakpoints, rather than clusters (Fig. 1E).Integration hotspots target genes involved in epithelial stem cell maintenance and immune evasionTo account for the lack of independence of virus...
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LETTER: Chromosomal instability mediated by non-B DNA: Cruciform conformation and not DNA sequence is responsible for recurrent translocation in humans
- Hidehito Inagaki,
- Tamae Ohye,
- Hiroshi Kogo,
- Takema Kato,
- Hasbaira Bolor,
- Mariko Taniguchi,
- Tamim H. Shaikh,
- Beverly S. Emanuel,
- and Hiroki Kurahashi
Genome Res. February 2009 19: 191-198; Published in Advance November 7, 2008, doi:10.1101/gr.079244.108
.... , Hosoba, E. , Kato, T. , Ohye, T. , Kogo, H. , Emanuel, B.S. ( 2007 ) Molecular cloning of a translocation breakpoint hotspot in 22q11 . Genome Res. 17 : 461 – 469 . ↵ Leach, D.R.F. ( 1994 ) Long DNA palindromes, cruciform structures, genetic instability and secondary structure repair . Bioessays 16 : 893...
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Method: Large-scale detection and characterization of inter-chromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets
- Jeanlin Jourdain,
- Harmonie Barasc,
- Thomas Faraut,
- Anne Calgaro,
- Nathalie Bonnet,
- Camille Marcuzzo,
- Amandine Suin,
- Anne Barbat,
- Chris Hozé,
- Florian Besnard,
- Sébastien Taussat,
- Cécile Grohs,
- Claire Kuchly,
- Carole Iampietro,
- Cécile Donnadieu,
- Alain Pinton,
- Didier Boichard,
- and Aurélien Capitan
Genome Res. July 6, 2023 ; Published in Advance July 6, 2023, doi:10.1101/gr.277787.123
...Fig. S10J). At the end of the cytogenetic analysis, we confirmed 12 IRs, consisting of one Robertsonian translocation, one insertional translocation, and 10 reciprocal translocations, including one with derivative loss. By analyzing the location of the breakpoints in more detail, we found...
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LETTER: Low copy repeats mediate distal chromosome 22q11.2 deletions: Sequence analysis predicts breakpoint mechanisms
- Tamim H. Shaikh,
- Ronald J. O’Connor,
- Mary Ella Pierpont,
- James McGrath,
- April M. Hacker,
- Manjunath Nimmakayalu,
- Elizabeth Geiger,
- Beverly S. Emanuel,
- and Sulagna C. Saitta
Genome Res. April 2007 17: 482-491; Published in Advance March 9, 2007, doi:10.1101/gr.5986507
...localized to a 3 Mb region containing four large LCRs. Immediately distal to this region, there are another four related but smaller LCRs that have not been characterized extensively. We used paralog-specific primers and long-range PCR to clone, sequence, and examine the distal deletion breakpoints from two...
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LETTER: Unexpected complexity at breakpoint junctions in phenotypically normal individuals and mechanisms involved in generating balanced translocations t(1;22)(p36;q13)
- Marzena Gajecka,
- Andrew J. Gentles,
- Albert Tsai,
- David Chitayat,
- Katherine L. Mackay,
- Caron D. Glotzbach,
- Michael R. Lieber,
- and Lisa G. Shaffer
Genome Res. November 2008 18: 1733-1742; Published in Advance September 2, 2008, doi:10.1101/gr.077453.108
.... , Kato, T. , Ohye, T. , Kogo, H. , Emanuel, B.S. ( 2007 ) Molecular cloning of a translocation breakpoint hotspot in 22q11 . Genome Res. 17 : 461 – 469 . ↵ Liang, F. , Han, M. , Romanienko, P.J. , Jasin, M. ( 1998 ) Homology-directed repair is a major double-strand break repair pathway in mammalian cells...
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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
...breakpoint insertion.In human cancer s, structural variant breakpoints are distributed nonuniformly and are commonly found to be located in regions of the that are inherently prone to double-strand break (DSB) damage (Glodzik et al. 2017). To establish whether hotspot regions existed in the Notch locus, we...
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Research: Large duplications at reciprocal translocation breakpoints that might be the counterpart of large deletions and could arise from stalled replication bubbles
- Karen D. Howarth,
- Jessica C.M. Pole,
- Juliet C. Beavis,
- Elizabeth M. Batty,
- Scott Newman,
- Graham R. Bignell,
- and Paul A.W. Edwards
Genome Res. April 2011 21: 525-534; Published in Advance January 20, 2011, doi:10.1101/gr.114116.110
...Large duplications at reciprocal translocation breakpoints that might be the counterpart of large deletions and could arise from stalled replication bubbles Karen D. Howarth 1 , 4 , Jessica C.M. Pole 1 , 3 , Juliet C. Beavis 1 , Elizabeth M. Batty 1...

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