title: Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line.
abstract: 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.
authors.affiliation: J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
authors.forename: Qi
authors.initials: Q
authors.lastname: Zhao
authors.forename: Otavia L
authors.initials: OL
authors.lastname: Caballero
authors.forename: Samuel
authors.initials: S
authors.lastname: Levy
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Stevenson
authors.forename: Christian
authors.initials: C
authors.lastname: Iseli
authors.forename: Sandro J
authors.initials: SJ
authors.lastname: de Souza
authors.forename: Pedro A
authors.initials: PA
authors.lastname: Galante
authors.forename: Dana
authors.initials: D
authors.lastname: Busam
authors.forename: Margaret A
authors.initials: MA
authors.lastname: Leversha
authors.forename: Kalyani
authors.initials: K
authors.lastname: Chadalavada
authors.forename: Yu-Hui
authors.initials: YH
authors.lastname: Rogers
authors.forename: J Craig
authors.initials: JC
authors.lastname: Venter
authors.forename: Andrew J G
authors.initials: AJ
authors.lastname: Simpson
authors.forename: Robert L
authors.initials: RL
authors.lastname: Strausberg
mesh_terms: D001483:Base Sequence; D001943:Breast Neoplasms / Q000235:genetics*; D002352:Carrier Proteins / Q000235:genetics; D045744:Cell Line, Tumor; D018076:DNA, Complementary; D004268:DNA-Binding Proteins / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D015321:Gene Rearrangement; D015894:Genome, Human / Q000235:genetics*; D011495:Histone-Lysine N-Methyltransferase; D006801:Humans; D000076228:MRE11 Homologue Protein; D009363:Neoplasm Proteins / Q000235:genetics; D009687:Nuclear Proteins / Q000235:genetics
chemical_list: D002352:Carrier Proteins; D018076:DNA, Complementary; D004268:DNA-Binding Proteins; C121766:MRE11 protein, human; D009363:Neoplasm Proteins; D009687:Nuclear Proteins; D011495:Histone-Lysine N-Methyltransferase; C491867:Nsd1 protein, mouse; D000076228:MRE11 Homologue Protein