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Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes.

Publication ,  Journal Article
Hillmer, AM; Yao, F; Inaki, K; Lee, WH; Ariyaratne, PN; Teo, ASM; Woo, XY; Zhang, Z; Zhao, H; Ukil, L; Chen, JP; Zhu, F; So, JBY; Poh, WT ...
Published in: Genome Res
May 2011

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 insert size allows the identification of breakpoints within repetitive or homology-containing regions of a few kilobases in size and results in a higher physical coverage compared with small insert libraries with the same sequencing effort. We have applied this approach to comprehensively characterize the SVs of 15 cancer and two noncancer genomes and used a filtering approach to strongly enrich for somatic SVs in the cancer genomes. Our analyses revealed that most inversions, deletions, and insertions are germ-line SVs, whereas tandem duplications, unpaired inversions, interchromosomal translocations, and complex rearrangements are over-represented among somatic rearrangements in cancer genomes. We demonstrate that the quantitative and connective nature of DNA-PET data is precise in delineating the genealogy of complex rearrangement events, we observe signatures that are compatible with breakage-fusion-bridge cycles, and we discover that large duplications are among the initial rearrangements that trigger genome instability for extensive amplification in epithelial cancers.

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Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

May 2011

Volume

21

Issue

5

Start / End Page

665 / 675

Location

United States

Related Subject Headings

  • Stomach Neoplasms
  • Sequence Analysis, DNA
  • Humans
  • Genomic Structural Variation
  • Genome, Human
  • Gene Rearrangement
  • Female
  • DNA
  • Computational Biology
  • Chromosome Mapping
 

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Hillmer, A. M., Yao, F., Inaki, K., Lee, W. H., Ariyaratne, P. N., Teo, A. S. M., … Ruan, Y. (2011). Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome Res, 21(5), 665–675. https://doi.org/10.1101/gr.113555.110
Hillmer, Axel M., Fei Yao, Koichiro Inaki, Wah Heng Lee, Pramila N. Ariyaratne, Audrey S. M. Teo, Xing Yi Woo, et al. “Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes.Genome Res 21, no. 5 (May 2011): 665–75. https://doi.org/10.1101/gr.113555.110.
Hillmer AM, Yao F, Inaki K, Lee WH, Ariyaratne PN, Teo ASM, et al. Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome Res. 2011 May;21(5):665–75.
Hillmer, Axel M., et al. “Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes.Genome Res, vol. 21, no. 5, May 2011, pp. 665–75. Pubmed, doi:10.1101/gr.113555.110.
Hillmer AM, Yao F, Inaki K, Lee WH, Ariyaratne PN, Teo ASM, Woo XY, Zhang Z, Zhao H, Ukil L, Chen JP, Zhu F, So JBY, Salto-Tellez M, Poh WT, Zawack KFB, Nagarajan N, Gao S, Li G, Kumar V, Lim HPJ, Sia YY, Chan CS, Leong ST, Neo SC, Choi PSD, Thoreau H, Tan PBO, Shahab A, Ruan X, Bergh J, Hall P, Cacheux-Rataboul V, Wei C-L, Yeoh KG, Sung W-K, Bourque G, Liu ET, Ruan Y. Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome Res. 2011 May;21(5):665–675.

Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

May 2011

Volume

21

Issue

5

Start / End Page

665 / 675

Location

United States

Related Subject Headings

  • Stomach Neoplasms
  • Sequence Analysis, DNA
  • Humans
  • Genomic Structural Variation
  • Genome, Human
  • Gene Rearrangement
  • Female
  • DNA
  • Computational Biology
  • Chromosome Mapping