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Research: Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
- Aaron R. Quinlan,
- Royden A. Clark,
- Svetlana Sokolova,
- Mitchell L. Leibowitz,
- Yujun Zhang,
- Matthew E. Hurles,
- Joshua C. Mell,
- and Ira M. Hall
Genome Res. May 2010 20: 623-635; Published in Advance March 22, 2010, doi:10.1101/gr.102970.109
...Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome Aaron R. Quinlan 1 , Royden A. Clark 1 , Svetlana Sokolova 1 , Mitchell L. Leibowitz 1 , Yujun Zhang 2 , Matthew E. Hurles 2 , Joshua C...
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LETTER: Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution
- Graham R. Bignell,
- Thomas Santarius,
- Jessica C.M. Pole,
- Adam P. Butler,
- Janet Perry,
- Erin Pleasance,
- Chris Greenman,
- Andrew Menzies,
- Sheila Taylor,
- Sarah Edkins,
- Peter Campbell,
- Michael Quail,
- Bob Plumb,
- Lucy Matthews,
- Kirsten McLay,
- Paul A.W. Edwards,
- Jane Rogers,
- Richard Wooster,
- P. Andrew Futreal,
- and Michael R. Stratton
Genome Res. September 2007 17: 1296-1303; Published in Advance August 3, 2007, doi:10.1101/gr.6522707
...to identify those with potential rearrangements, and subsequent shotgun sequencing of rearranged clones. In an analysis of the breast cancer cell line, MCF7, end sequencing revealed many rearranged bacterial artificial chromosomes (BACs) connecting multiple amplified genomic regions ( Volik et al. 2003 , 2006...
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Research: Transcriptional consequences of genomic structural aberrations in breast cancer
- Koichiro Inaki,
- Axel M. Hillmer,
- Leena Ukil,
- Fei Yao,
- Xing Yi Woo,
- Leah A. Vardy,
- Kelson Folkvard Braaten Zawack,
- Charlie Wah Heng Lee,
- Pramila Nuwantha Ariyaratne,
- Yang Sun Chan,
- Kartiki Vasant Desai,
- Jonas Bergh,
- Per Hall,
- Thomas Choudary Putti,
- Wai Loon Ong,
- Atif Shahab,
- Valere Cacheux-Rataboul,
- Radha Krishna Murthy Karuturi,
- Wing-Kin Sung,
- Xiaoan Ruan,
- Guillaume Bourque,
- Yijun Ruan,
- and Edison T. Liu
Genome Res. May 2011 21: 676-687; Published in Advance April 5, 2011, doi:10.1101/gr.113225.110
...; ISSN 1088-9051/11; www..org explore the transcriptional consequences of these structural aberrations on a genomic scale, focusing on the results from three breast cancer cell lines and five primary tissues. Using a breast cancer cell line, MCF-7, as a testing platform, we found that gene expression...
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Methods: Decoding the fine-scale structure of a breast cancer genome and transcriptome
- Stanislav Volik,
- Benjamin J. Raphael,
- Guiqing Huang,
- Michael R. Stratton,
- Graham Bignel,
- John Murnane,
- John H. Brebner,
- Krystyna Bajsarowicz,
- Pamela L. Paris,
- Quanzhou Tao,
- David Kowbel,
- Anna Lapuk,
- Dmitri A. Shagin,
- Irina A. Shagina,
- Joe W. Gray,
- Jan-Fang Cheng,
- Pieter J. de Jong,
- Pavel Pevzner,
- and Colin Collins
Genome Res. March 2006 16: 394-404; Published in Advance February 3, 2006, doi:10.1101/gr.4247306
...in cancer. Incidentally, one of the aforementioned 13 breakpoints identified in the normal human library was also identified by Tuzun et. al. ( 2005 ) and another is located within 80 kb of a structural polymorphism reported in their study. Mapping the ends of 19,831 MCF-7 BAC clones yielded 13,303 mapped...
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Research: Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms
- Ankit Malhotra,
- Michael Lindberg,
- Gregory G. Faust,
- Mitchell L. Leibowitz,
- Royden A. Clark,
- Ryan M. Layer,
- Aaron R. Quinlan,
- and Ira M. Hall
Genome Res. May 2013 23: 762-776; Published in Advance February 14, 2013, doi:10.1101/gr.143677.112
...to profile rearrangement breakpoints at single-base resolution, and compare mutational signatures and intra-tumor allele frequencies at both simple and complex mutational events. Results Breakpoint mapping This study includes 64 tumors from The Cancer Genome Atlas (TCGA) including 12 basal-like breast...
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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
...between chromosomes 9 and 22 (Groffen et al. 1984; Daley et al. 1990; Heisterkamp et al. 1990) and the previously reported BCAS3– BCAS4 fusion between chromosomes 17 and 20 in MCF-7 (Ruan et al. 2007). Characteristics of SVs in cancer s The structural maps of the 17 s should include both germline...
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Method: Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations
- Anand Patel,
- Richard Schwab,
- Yu-Tsueng Liu,
- and Vineet Bafna
Genome Res. February 2014 24: 318-328; Published in Advance December 4, 2013, doi:10.1101/gr.161497.113
...,828,685–21,996,997 168,887 164,123 575–4189 Detroit562 Pharynx carcinoma 21,970,804–21,985,229 14,425 MCF7 Breast carcinoma 21,834,611–21,989,073 21,819,532–21,989,621 154,462 170,089 15,079–548 T98G Glioblastoma 21,868,909–21,991,923 21,865,639–21,992,514 123,014 126,875 3270–591 Estimated breakpoints are according...
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Letter: Copy number abnormalities in sporadic canine colorectal cancers
- Jie Tang,
- Shoshona Le,
- Liang Sun,
- Xiuzhen Yan,
- Mucheng Zhang,
- Jennifer MacLeod,
- Bruce LeRoy,
- Nicole Northrup,
- Angela Ellis,
- Timothy J. Yeatman,
- Yanchun Liang,
- Michael E. Zwick,
- and Shaying Zhao
Genome Res. March 2010 20: 341-350; Published in Advance January 19, 2010, doi:10.1101/gr.092726.109
...www..org effort reported that, in the of the breast cancer cell line MCF7, dispersed rearrangement breakpoint regions are significantly enriched with SDs (5.23), whereas clustered breakpoint regions are not (Hampton et al. 2009). It would be interesting to know if clustered breakpoint regions...
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Resource: Circos: An information aesthetic for comparative genomics
- Martin Krzywinski,
- Jacqueline Schein,
- İnanç Birol,
- Joseph Connors,
- Randy Gascoyne,
- Doug Horsman,
- Steven J. Jones,
- and Marco A. Marra
Genome Res. September 2009 19: 1639-1645; Published in Advance June 18, 2009, doi:10.1101/gr.092759.109
...of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer .Genome Res 19: 167–177. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, et al. 2007. The grapevine sequence suggests ancestral hexaploidization...

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