Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line.
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.
Zhao
Qi
Q
J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
Caballero
Otavia L
OL
Levy
Samuel
S
Stevenson
Brian J
BJ
Iseli
Christian
C
de Souza
Sandro J
SJ
Galante
Pedro A
PA
Busam
Dana
D
Leversha
Margaret A
MA
Chadalavada
Kalyani
K
Rogers
Yu-Hui
YH
Venter
J Craig
JC
Simpson
Andrew J G
AJ
Strausberg
Robert L
RL
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
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