Article open access publication

Decoding complex patterns of genomic rearrangement in hepatocellular carcinoma

Genomics, Elsevier, ISSN 0888-7543

Volume 103, 2-3, 2014

DOI:10.1016/j.ygeno.2014.01.003, Dimensions: pub.1033643494, PMID: 24462510,

Affiliations

Organisations

  1. (1) Pfizer Oncology, San Diego, CA, USA
  2. (2) University of Hong Kong, grid.194645.b
  3. (3) Beijing Genomics Institute, grid.21155.32
  4. (4) University of Copenhagen, grid.5254.6, KU
  5. (5) Genome Institute of Singapore, grid.418377.e
  6. (6) National University of Singapore, grid.4280.e
  7. (7) Asian Cancer Research Group, Inc., Wilmington, DE, USA

Countries

China

Singapore

Denmark

Continents

Asia

Europe

Description

Elucidating the molecular basis of hepatocellular carcinoma (HCC) is crucial to developing targeted diagnostics and therapies for this deadly disease. The landscape of somatic genomic rearrangements (GRs), which can lead to oncogenic gene fusions, remains poorly characterized in HCC. We have predicted 4314 GRs including large-scale insertions, deletions, inversions and translocations based on the whole-genome sequencing data for 88 primary HCC tumor/non-tumor tissues. We identified chromothripsis in 5 HCC genomes (5.7%) recurrently affecting chromosomal arms 1q and 8q. Albumin (ALB) was found to harbor GRs, deactivating mutations and deletions in 10% of cohort. Integrative analysis identified a pattern of paired intra-chromosomal translocations flanking focal amplifications and asymmetrical patterns of copy number variation flanking breakpoints of translocations. Furthermore, we predicted 260 gene fusions which frequently result in aberrant over-expression of the 3' genes in tumors and validated 18 gene fusions, including recurrent fusion (2/88) of ABCB11 and LRP2.

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University of Copenhagen

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2014: Unused

Research area: Science & Technology

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Times Cited: 33

Field Citation Ratio (FCR): 3.76

Relative Citation ratio (RCR): 1.1

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