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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
...the prevalence and origins of complex genomic rearrangements (CGRs), we mapped 6179 somatic structural variation breakpoints in 64 cancer genomes from seven tumor types and screened for clusters of three or more interconnected breakpoints. We find that complex breakpoint clusters are extremely common: 154...
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Method: Discovery of recurrent structural variants in nasopharyngeal carcinoma
- Anton Valouev,
- Ziming Weng,
- Robert T. Sweeney,
- Sushama Varma,
- Quynh-Thu Le,
- Christina Kong,
- Arend Sidow,
- and Robert B. West
Genome Res. February 2014 24: 300-309; Published in Advance November 8, 2013, doi:10.1101/gr.156224.113
.... 2011. Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer s. Genome Res 21: 665–675. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human . Nature 409: 860–921. International Human...
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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
...have described the precise identification of structural abnormalities in cancer cells using a long-span, paired-end-tag sequencing approach called DNA-PET (Hillmer et al. 2011). We now These authors contributed equally to this work. 11Corresponding author. E-mail liue@gis.a-star.edu.sg; fax 65...
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Research: Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability
- Keiko Akagi,
- Jingfeng Li,
- Tatevik R. Broutian,
- Hesed Padilla-Nash,
- Weihong Xiao,
- Bo Jiang,
- James W. Rocco,
- Theodoros N. Teknos,
- Bhavna Kumar,
- Danny Wangsa,
- Dandan He,
- Thomas Ried,
- David E. Symer,
- and Maura L. Gillison
Genome Res. February 2014 24: 185-199; Published in Advance November 7, 2013, doi:10.1101/gr.164806.113
...genomic structural variation in human cancer cell lines and primary tumors. Whole-genome sequencing revealed HPV integrants flanking and bridging extensive host genomic amplifications and rearrangements, including deletions, inversions, and chromosomal translocations. We present a model of “looping...
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Research: Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line
- Maria Nattestad,
- Sara Goodwin,
- Karen Ng,
- Timour Baslan,
- Fritz J. Sedlazeck,
- Philipp Rescheneder,
- Tyler Garvin,
- Han Fang,
- James Gurtowski,
- Elizabeth Hutton,
- Elizabeth Tseng,
- Chen-Shan Chin,
- Timothy Beck,
- Yogi Sundaravadanam,
- Melissa Kramer,
- Eric Antoniou,
- John D. McPherson,
- James Hicks,
- W. Richard McCombie,
- and Michael C. Schatz
Genome Res. August 2018 28: 1126-1135; Published in Advance June 28, 2018, doi:10.1101/gr.231100.117
..., Inaki K, Lee WH, Ariyaratne PN, Teo ASM, Woo XY, Zhang Z, Zhao H, Ukil L, et al. 2011. Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer s. Genome Res 21: 665–675. ↵Huddleston J, Chaisson MJP, Steinberg KM, Warren W, Hoekzema K...
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Research: Systems consequences of amplicon formation in human breast cancer
- Koichiro Inaki,
- Francesca Menghi,
- Xing Yi Woo,
- Joel P. Wagner,
- Pierre-Étienne Jacques,
- Yi Fang Lee,
- Phung Trang Shreckengast,
- Wendy WeiJia Soon,
- Ankit Malhotra,
- Audrey S.M. Teo,
- Axel M. Hillmer,
- Alexis Jiaying Khng,
- Xiaoan Ruan,
- Swee Hoe Ong,
- Denis Bertrand,
- Niranjan Nagarajan,
- R. Krishna Murthy Karuturi,
- Alfredo Hidalgo Miranda,
- and Edison T. Liu
Genome Res. October 2014 24: 1559-1571; Published in Advance September 3, 2014, doi:10.1101/gr.164871.113
...patterns of copy number alterations, we focused on the functional genomic consequences of structural variations, which are likely to initiate massive copy number changes. Because the mate-pair sequencing method is able to detect all forms of structural variations quantitatively andwithhigh sensitivity...
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Research: An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells
- Zhizhuo Zhang,
- Kern Rei Chng,
- Shreyas Lingadahalli,
- Zikai Chen,
- Mei Hui Liu,
- Huy Hoang Do,
- Shaojiang Cai,
- Nicola Rinaldi,
- Huay Mei Poh,
- Guoliang Li,
- Ying Ying Sung,
- Charlie L. Heng,
- Leighton J. Core,
- Si Kee Tan,
- Xiaoan Ruan,
- John T. Lis,
- Manolis Kellis,
- Yijun Ruan,
- Wing-Kin Sung,
- and Edwin Cheung
Genome Res. February 2019 29: 223-235; Published in Advance January 3, 2019, doi:10.1101/gr.230243.117
...of genomic structural alterations.In this study, utilizing our previously developed genomic technology (Fullwood et al. 2009), chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing, we comprehensively mapped AR- and ERG-associated chromatin loops and characterized in detail their interaction...

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