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Resource: Analysis of copy number variations among diverse cattle breeds
- George E. Liu,
- Yali Hou,
- Bin Zhu,
- Maria Francesca Cardone,
- Lu Jiang,
- Angelo Cellamare,
- Apratim Mitra,
- Leeson J. Alexander,
- Luiz L. Coutinho,
- Maria Elena Dell'Aquila,
- Lou C. Gasbarre,
- Gianni Lacalandra,
- Robert W. Li,
- Lakshmi K. Matukumalli,
- Dan Nonneman,
- Luciana C. de A. Regitano,
- Tim P.L. Smith,
- Jiuzhou Song,
- Tad S. Sonstegard,
- Curt P. Van Tassell,
- Mario Ventura,
- Evan E. Eichler,
- Tara G. McDaneld,
- and John W. Keele
Genome Res. May 2010 20: 693-703; Published in Advance March 8, 2010, doi:10.1101/gr.105403.110
...CNV/. Liu et al . 696 Genome Research www..org with nonvariable regions is unknown. We note, however, that the animals for the three cell lines used in the FISH experiments were different from the animals used for array CGH, and structural polymorphism, as well as limitations of BAC-FISH to detect...
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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
...transcription factors. We designed high-density tiling arrays spanning all predicted segmental duplications and performed aCGH in a panel of 17 breeds and a gray wolf. In total, we identified 3583 CNVs, ∼68% of which were found in two or more samples that map to 678 unique regions. CNVs span 429 genes...
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Research: Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
- Axel M. Hillmer,
- Fei Yao,
- Koichiro Inaki,
- Wah Heng Lee,
- Pramila N. Ariyaratne,
- Audrey S.M. Teo,
- Xing Yi Woo,
- Zhenshui Zhang,
- Hao Zhao,
- Leena Ukil,
- Jieqi P. Chen,
- Feng Zhu,
- Jimmy B.Y. So,
- Manuel Salto-Tellez,
- Wan Ting Poh,
- Kelson F.B. Zawack,
- Niranjan Nagarajan,
- Song Gao,
- Guoliang Li,
- Vikrant Kumar,
- Hui Ping J. Lim,
- Yee Yen Sia,
- Chee Seng Chan,
- See Ting Leong,
- Say Chuan Neo,
- Poh Sum D. Choi,
- Hervé Thoreau,
- Patrick B.O. Tan,
- Atif Shahab,
- Xiaoan Ruan,
- Jonas Bergh,
- Per Hall,
- Valère Cacheux-Rataboul,
- Chia-Lin Wei,
- Khay Guan Yeoh,
- Wing-Kin Sung,
- Guillaume Bourque,
- Edison T. Liu,
- and Yijun Ruan
Genome Res. May 2011 21: 665-675; Published in Advance April 5, 2011, doi:10.1101/gr.113555.110
...), fluorescence in situ hybridization (FISH), and array comparative genomic hybridization (aCGH), are valuable tools for the analysis of (cancer) structural alterations. Although each of the methods bears individual advantages, they all have specific limitations regarding resolution, throughput, and the ability...
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LETTER: A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome
- Oliver A. Hampton,
- Petra Den Hollander,
- Christopher A. Miller,
- David A. Delgado,
- Jian Li,
- Cristian Coarfa,
- Ronald A. Harris,
- Stephen Richards,
- Steven E. Scherer,
- Donna M. Muzny,
- Richard A. Gibbs,
- Adrian V. Lee,
- and Aleksandar Milosavljevic
Genome Res. February 2009 19: 167-177; Published in Advance December 3, 2008, doi:10.1101/gr.080259.108
...of recurrent copy number changes in 157 somatic breakpoint loci Copy number variation in the 157 somatic breakpoint loci identified in this study was examined. In order to identify recurrent copy number changes in breakpoint loci, array CGH data from 201 breast cancer cell lines and tumors ( Chin et al. 2006...
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Resource: Copy number variation of individual cattle genomes using next-generation sequencing
- Derek M. Bickhart,
- Yali Hou,
- Steven G. Schroeder,
- Can Alkan,
- Maria Francesca Cardone,
- Lakshmi K. Matukumalli,
- Jiuzhou Song,
- Robert D. Schnabel,
- Mario Ventura,
- Jeremy F. Taylor,
- Jose Fernando Garcia,
- Curtis P. Van Tassell,
- Tad S. Sonstegard,
- Evan E. Eichler,
- and George E. Liu
Genome Res. April 2012 22: 778-790; Published in Advance February 2, 2012, doi:10.1101/gr.133967.111
...chromosomal sequence, we identified 1265 CNV regions comprising ∼55.6-Mbp sequence—476 of which (∼38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH...
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LETTER: Genomic copy number and expression variation within the C57BL/6J inbred mouse strain
- Dawn E. Watkins-Chow and
- William J. Pavan
Genome Res. January 2008 18: 60-66; Published in Advance November 21, 2007, doi:10.1101/gr.6927808
...with chromosome substitution strains of mice . Science 304 : 445 – 448 . ↵ Snijders, A.M. , Nowak, N.J. , Huey, B. , Fridlyand, J. , Law, S. , Conroy, J. , Tokuyasu, T. , Demir, K. , Chiu, R. , Mao, J.H. , et al. ( 2005 ) Mapping segmental and sequence variations among laboratory mice using BAC array CGH . Genome...
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Research: Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution
- Martin Völker,
- Niclas Backström,
- Benjamin M. Skinner,
- Elizabeth J. Langley,
- Sydney K. Bunzey,
- Hans Ellegren,
- and Darren K. Griffin
Genome Res. April 2010 20: 503-511; Published in Advance March 31, 2010, doi:10.1101/gr.103663.109
...on apparent relative copynumber losses (but not gains) may be confounded by sequence divergence, we nonetheless contend that array CGH is a robust means of obtaining a reasonably accurate map of interspecific copy number variation. In addition to the observed association of structural variation...
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Research: Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor
- Ruth A. Swanson-Wagner,
- Steven R. Eichten,
- Sunita Kumari,
- Peter Tiffin,
- Joshua C. Stein,
- Doreen Ware,
- and Nathan M. Springer
Genome Res. December 2010 20: 1689-1699; Published in Advance October 29, 2010, doi:10.1101/gr.109165.110
...Dooner (2006) documented that only 25%–84% of bases within a ;100-kb region were shared among eight haplotypes. The frequency of CNV and PAV between the reference (B73) and a second genotype (Mo17) has been assayed using BAC libraries (Morgante et al. 2005) and comparative genomic hybridization (CGH) (Springer...
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ARTICLE: Copy number variation and evolution in humans and chimpanzees
- George H. Perry,
- Fengtang Yang,
- Tomas Marques-Bonet,
- Carly Murphy,
- Tomas Fitzgerald,
- Arthur S. Lee,
- Courtney Hyland,
- Anne C. Stone,
- Matthew E. Hurles,
- Chris Tyler-Smith,
- Evan E. Eichler,
- Nigel P. Carter,
- Charles Lee,
- and Richard Redon
Genome Res. November 2008 18: 1698-1710; Published in Advance September 4, 2008, doi:10.1101/gr.082016.108
.... 2006 ; Dumas et al. 2007 ) together under an evolutionary framework. In this study, we have used array-based comparative genomic hybridization (aCGH) on a human whole- tile-path (WGTP) platform comprised of 28,708 large-insert DNA clones to identify CNVs among the s of 30 unrelated chimpanzees ( Pan...
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LETTER: Significant gene content variation characterizes the genomes of inbred mouse strains
- Gene Cutler,
- Lisa A. Marshall,
- Ni Chin,
- Helene Baribault,
- and Paul D. Kassner
Genome Res. December 2007 17: 1743-1754; Published in Advance November 7, 2007, doi:10.1101/gr.6754607
.... Reproduction 121 : 529 – 539 . ↵ Snijders, A.M. , Nowak, N.J. , Huey, B. , Fridlyand, J. , Law, S. , Conroy, J. , Tokuyasu, T. , Demir, K. , Chiu, R. , Mao, J.H. , et al. ( 2005 ) Mapping segmental and sequence variations among laboratory mice using BAC array CGH . Genome Res. 15 : 302 – 311 . ↵ Svenson, K...

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