Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line

Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1886-91. doi: 10.1073/pnas.0812945106. Epub 2009 Jan 30.


We have identified new genomic alterations in the breast cancer cell line HCC1954, using high-throughput transcriptome sequencing. With 120 Mb of cDNA sequences, we were able to identify genomic rearrangement events leading to fusions or truncations of genes including MRE11 and NSD1, genes already implicated in oncogenesis, and 7 rearrangements involving other additional genes. This approach demonstrates that high-throughput transcriptome sequencing is an effective strategy for the characterization of genomic rearrangements in cancers.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Breast Neoplasms / genetics*
  • Carrier Proteins / genetics
  • Cell Line, Tumor
  • DNA, Complementary
  • DNA-Binding Proteins / genetics
  • Female
  • Gene Expression Profiling / methods*
  • Gene Rearrangement*
  • Genome, Human / genetics*
  • Histone-Lysine N-Methyltransferase
  • Humans
  • MRE11 Homologue Protein
  • Neoplasm Proteins / genetics
  • Nuclear Proteins / genetics


  • Carrier Proteins
  • DNA, Complementary
  • DNA-Binding Proteins
  • MRE11 protein, human
  • Neoplasm Proteins
  • Nuclear Proteins
  • Histone-Lysine N-Methyltransferase
  • Nsd1 protein, mouse
  • MRE11 Homologue Protein