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Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput Sequencing

  • Andrew McPherson
  • Chunxiao Wu
  • Alexander Wyatt
  • Sohrab Shah
  • Colin Collins
  • S. Cenk Sahinalp
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7262)

Motivation

High-throughput sequencing now allows researchers to identify patterns of rearrangement in tumour genomes, and has led to the discovery of Complex Genomic Rearrangements (CGRs) as a new cytogenetic feature of some cancers. Closed chain breakage and rejoining (CCBR), a generalization of reciprocal translocation, was recently identified in prostate cancer [4]. CCBRs involve the balanced rearrangement of some n loci, and thus have the potential to fuse or interrupt up to n genes. In addition, dispersed throughout some breast cancer genomes are ‘genomic shards’, small fragments of DNA originating from elsewhere in the genome and inserted at the breakpoints of larger scale rearrangements.

References

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    Bignell, G.R., et al.: Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome. Res. 17, 1296–1303 (2007)CrossRefGoogle Scholar
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    Stephens, P.J., et al.: Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 462, 1005–1010 (2009)CrossRefGoogle Scholar
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    Galante, P., et al.: Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same indiv. Nucl. Acids Res. 39, 6056–6068 (2011)CrossRefGoogle Scholar
  4. 4.
    Berger, M.F., et al.: The genomic complexity of primary human prostate cancer. Nature 470, 214–220 (2011)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Andrew McPherson
    • 1
  • Chunxiao Wu
    • 2
  • Alexander Wyatt
    • 2
  • Sohrab Shah
    • 3
  • Colin Collins
    • 2
  • S. Cenk Sahinalp
    • 1
  1. 1.School of Computer ScienceSimon Fraser UniversityCanada
  2. 2.Vancouver Prostate CentreCanada
  3. 3.Department of Molecular OncologyBC Cancer Research CentreCanada

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