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LETTER: A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications
- Xinwei She,
- Ge Liu,
- Mario Ventura,
- Shaying Zhao,
- Doriana Misceo,
- Roberta Roberto,
- Maria Francesca Cardone,
- Mariano Rocchi,
- NISC Comparative Sequencing Program,
- Eric D. Green,
- Nicoletta Archidiacano,
- and Evan E. Eichler
Genome Res. May 2006 16: 576-583; Published in Advance April 10, 2006, doi:10.1101/gr.4949406
....G. , Repping S. , Pyntikova T. , Ali J. , Bieri T. , et al. ( 2003 ) The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 433 : 825 – 837 . ↵ Stankiewicz P. , Shaw C.J. , Withers M. , Inoue K. , Lupski J.R. ( 2004 ) Serial segmental duplications during primate...
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Resource: The genomic architecture of segmental duplications and associated copy number variants in dogs
- Thomas J. Nicholas,
- Ze Cheng,
- Mario Ventura,
- Katrina Mealey,
- Evan E. Eichler,
- and Joshua M. Akey
Genome Res. March 2009 19: 491-499; Published in Advance January 7, 2009, doi:10.1101/gr.084715.108
...of genomic DNA. Amplification was done under the following conditions: one cycle at 50°C for 2 min, one cycle at 95°C for 10 min, 40 cycles at 95°C for 15 sec, and 60°C for 1 min. Serial dilutions were performed for each assay to estimate the PCR efficiency (E). Using the ΔCT method, relative copy number...
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LETTER: Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions
- Eva Darai-Ramqvist,
- Agneta Sandlund,
- Stefan Müller,
- George Klein,
- Stefan Imreh,
- and Maria Kost-Alimova
Genome Res. March 2008 18: 370-379; Published in Advance January 29, 2008, doi:10.1101/gr.7010208
...be found in human tumors, and if the answer is affirmative, do these break-prone regions have any structural characteristics? Recently, it was shown that ∼5% of the human is composed of duplicated genomic segments, which emerged mostly during the past 35 million years of primate evolution. These segmental...
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LETTER: Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions
- Stefan Kirsch,
- Claudia Münch,
- Zhaoshi Jiang,
- Ze Cheng,
- Lin Chen,
- Christiane Batz,
- Evan E. Eichler,
- and Werner Schempp
Genome Res. July 2008 18: 1030-1042; Published in Advance April 29, 2008, doi:10.1101/gr.076711.108
...-chromosomal segmental duplications. A multi-step process is depicted leading to the current distribution pattern of duplicated sequences on the Y chromosomes of the great and lesser apes. Serial intrachromosomal duplicative transpositions and chromosomal rearrangements generated a mosaic pattern on all great ape Y...
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ARTICLE: Traffic of genetic information between segmental duplications flanking the typical 22q11.2 deletion in velo-cardio-facial syndrome/DiGeorge syndrome
- Adam Pavlicek,
- Reniqua House,
- Andrew J. Gentles,
- Jerzy Jurka,
- and Bernice E. Morrow
Genome Res. November 2005 15: 1487-1495; doi:10.1101/gr.4281205
...: 312 –329. ↵ Stankiewicz, P. and Lupski, J.R. 2002b . Genome architecture, rearrangements and genomic disorders. Trends Genet. 18 : 74 –82. ↵ Stankiewicz, P., Shaw, C.J., Withers, M., Inoue, K., and Lupski, J.R. 2004 . Serial segmental duplications during primate evolution result in complex human...
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Method: Short template switch events explain mutation clusters in the human genome
- Ari Löytynoja and
- Nick Goldman
Genome Res. June 2017 27: 1039-1049; Published in Advance April 6, 2017, doi:10.1101/gr.214973.116
..., it is available under a Creative Commons License (AttributionNonCommercial 4.0 International), as described at http://creativecommons. org/licenses/by-nc/4.0/. Method 27:1039–1049 Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/17; www..org Genome Research 1039 www..org serial replication...
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LETTER: Punctuated duplication seeding events during the evolution of human chromosome 2p11
- Julie E. Horvath,
- Cassandra L. Gulden,
- Rhea U. Vallente,
- Marla Y. Eichler,
- Mario Ventura,
- John D. McPherson,
- Tina A. Graves,
- Richard K. Wilson,
- Stuart Schwartz,
- Mariano Rocchi,
- and Evan E. Eichler
Genome Res. July 2005 15: 914-927; Published in Advance June 17, 2005, doi:10.1101/gr.3916405
..., H.F. 2004 . Analysis of the centromeric regions of the human assembly. Trends Genet. 20 : 529 -533. ↵ Samonte, R.V. and Eichler, E.E. 2002 . Segmental duplications and the evolution of the primate . Nat. Rev. Genet. 3 : 65 -72. ↵ Saupe, S., Roizes, G., Peter, M., Boyle, S., Gardiner, K., and De...
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LETTER: A genome-wide survey of structural variation between human and chimpanzee
- Tera L. Newman,
- Eray Tuzun,
- V. Anne Morrison,
- Karen E. Hayden,
- Mario Ventura,
- Sean D. McGrath,
- Mariano Rocchi,
- and Evan E. Eichler
Genome Res. October 2005 15: 1344-1356; Published in Advance September 16, 2005, doi:10.1101/gr.4338005
...). We validated a subset (19/23) of insertion and deletions using PCR and Southern blot assays, confirming the accuracy of our method. The events are distributed throughout the genome on all chromosomes but are highly correlated with sites of segmental duplication in human and chimpanzee...
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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
...threatened or historical breeds is also urgently needed to prioritize and support conservation efforts.The discovery of structural variation (SV) revolutionized the understanding of the genomic landscape in many species (Eichler et al. 2007). This form of variation involves larger segments of the than...
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ARTICLE: Evolutionary mechanisms shaping the genomic structure of the Williams-Beuren syndrome chromosomal region at human 7q11.23
- Anna Antonell,
- Oscar de Luis,
- Xavier Domingo-Roura,
- and Luis Alberto Pérez-Jurado
Genome Res. September 2005 15: 1179-1188; doi:10.1101/gr.3944605
...and accelerate the evolution in specific regions of the of primates. Inversions, selection, and evolution The generation of small paracentric inversions appear to be a common evolutionary event associated with regions rich in segmental duplications. As genomic inversions have a clear effect of suppressing...

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