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Method: Estimation of rearrangement phylogeny for cancer genomes
- Chris D. Greenman,
- Erin D. Pleasance,
- Scott Newman,
- Fengtang Yang,
- Beiyuan Fu,
- Serena Nik-Zainal,
- David Jones,
- King Wai Lau,
- Nigel Carter,
- Paul A.W. Edwards,
- P. Andrew Futreal,
- Michael R. Stratton,
- and Peter J. Campbell
Genome Res. February 2012 22: 346-361; Published in Advance October 12, 2011, doi:10.1101/gr.118414.110
...rearrangements resulting in complex patterns of genomic architecture and copy number changes (Bignell et al. 2007, 2010; Pleasance et al. 2010a,b). Unlocking the temporal dynamics of these complex genomic structures may provide important insights into the mechanisms of cancer development. Although recent methods...
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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 somatic genomic rearrangement in human cancer amplicons at sequence-level resolution . Genome Res. 17 : 1296 – 1303 . ↵ Campbell, P.J. , Stephens, P.J. , Pleasance, E.D. , O'Meara, S. , Li, H. , Santarius, T. , Stebbings, L.A. , Leroy, C. , Edkins, S. , Hardy, C. , et al. ( 2008 ) Identification...
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Method: nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing
- Andrew McPherson,
- Chunxiao Wu,
- Alexander W. Wyatt,
- Sohrab Shah,
- Colin Collins,
- and S. Cenk Sahinalp
Genome Res. November 2012 22: 2250-2261; Published in Advance June 28, 2012, doi:10.1101/gr.136572.111
...distance between breakpoints. Tables shows counts for each group. Complex genomic rearrangements in cancer Genome Research 2255 www..org rangements in tumor amplicons and identified 59 unique breakpoints in HCC1954. Zhao et al. (2009) used long transcriptome reads to nominate fusion transcripts...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...of various mutational processes (Carvalho and Lupski 2016) that could be specific to cancer types or environmental exposures (Alexandrov et al. 2020). In addition to gradually accumulating somatic mutations, cancer s are often characterized by genomic instability (Drews et al. 2022) and rearranged s (Li et...
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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
...contributed equally to this work. Abstract Somatic genome rearrangements are thought to play important roles in cancer development. We optimized a long-span paired-end-tag (PET) sequencing approach using 10-Kb genomic DNA inserts to study human genome structural variations (SVs). The use of a 10-Kb...
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Research: RAF gene fusion breakpoints in pediatric brain tumors are characterized by significant enrichment of sequence microhomology
- Andrew R.J. Lawson,
- Guy F.L. Hindley,
- Tim Forshew,
- Ruth G. Tatevossian,
- Gabriel A. Jamie,
- Gavin P. Kelly,
- Geoffrey A. Neale,
- Jing Ma,
- Tania A. Jones,
- David W. Ellison,
- and Denise Sheer
Genome Res. April 2011 21: 505-514; Published in Advance March 10, 2011, doi:10.1101/gr.115782.110
...in human cancer amplicons at sequence-level resolution. Genome Res 17: 1296–1303. Campbell PJ, Stephens PJ, Pleasance ED, O’Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S, Hardy C, et al. 2008. Identification of somatically acquired rearrangements in cancer using -wide massively parallel...
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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
...Tumor genomes are generally thought to evolve through a gradual accumulation of mutations, but the observation that extraordinarily complex rearrangements can arise through single mutational events suggests that evolution may be accelerated by punctuated changes in genome architecture. To assess...
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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
...the best candidate region to mediate NAHR, resulting in the deletion found in CH03-29. There were no somatic cell hybrids available for this patient, thus we used long-range PCR to directly amplify the junction fragment in CH03-29 using total genomic DNA. We designed PCR primers to amplify a rearranged...
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Perspective: Translating cancer ‘omics’ to improved outcomes
- Emily A. Vucic,
- Kelsie L. Thu,
- Keith Robison,
- Leszek A. Rybaczyk,
- Raj Chari,
- Carlos E. Alvarez,
- and Wan L. Lam
Genome Res. February 2012 22: 188-195; doi:10.1101/gr.124354.111
...amplicons at sequence-level resolution. Genome Res 17: 1296–1303. Boca SM, Kinzler KW, Velculescu VE, Vogelstein B, Parmigiani G. 2010. Patient-oriented gene set analysis for cancer mutation data. Genome Biol 11: R112. doi: 10.1186/gb-2010-11-11-r112. Boyko AR, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD...
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Research: Gene amplification as double minutes or homogeneously staining regions in solid tumors: Origin and structure
- Clelia Tiziana Storlazzi,
- Angelo Lonoce,
- Maria C. Guastadisegni,
- Domenico Trombetta,
- Pietro D'Addabbo,
- Giulia Daniele,
- Alberto L'Abbate,
- Gemma Macchia,
- Cecilia Surace,
- Klaas Kok,
- Reinhard Ullmann,
- Stefania Purgato,
- Orazio Palumbo,
- Massimo Carella,
- Peter F. Ambros,
- and Mariano Rocchi
Genome Res. September 2010 20: 1198-1206; Published in Advance July 14, 2010, doi:10.1101/gr.106252.110
...rearrangement in human cancer amplicons at sequence-level resolution. Genome Res 17: 1296–1303. Campbell PJ, Stephens PJ, Pleasance ED, O’Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S, Hardy C, et al. 2008. Identification of somatically acquired rearrangements in cancer using wide massively...

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