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Series GSE25307 Query DataSets for GSE25307
Status Public on Jun 27, 2012
Title The retinoblastoma gene is targeted for rearrangements in BRCA1-deficient basal-like breast cancer.
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Breast tumors from BRCA1 germ line mutation carriers typically exhibit features of the basal-like molecular subtype. However, the specific genes recurrently mutated as a consequence of BRCA1 dysfunction have not been fully elucidated. In this study, we utilized gene expression profiling to molecularly subtype 577 breast tumors, including 73 breast tumors from BRCA1/2 mutation carriers. Focusing on the RB1 locus, we analyzed 33 BRCA1-mutated, 36 BRCA2-mutated and 48 non-BRCA1/2-mutated breast tumors using a custom-designed high-density oligomicroarray covering the RB1 gene. We found a strong association between the basal-like subtype and BRCA1-mutated breast tumors and the luminal B subtype and BRCA2-mutated breast tumors. RB1 was identified as a major target for genomic disruption in tumors arising in BRCA1 mutation carriers and in sporadic tumors with BRCA1 promoter-methylation, but rarely in other breast cancers. Homozygous deletions, intragenic breaks, or microdeletions were found in 33% of BRCA1-mutant tumors, 36% of BRCA1 promoter-methylated basal-like tumors, 13% of non-BRCA1 deficient basal-like tumors, and 3% of BRCA2-mutated tumors. In addition, RB1 was frequently inactivated by gross gene disruption in BRCA1-related hereditary breast cancer and BRCA1-methylated sporadic basal-like breast cancer, but rarely in BRCA2-hereditary breast cancer and non-BRCA1-deficient sporadic breast cancers. Together, our findings demonstrate the existence of genetic heterogeneity within the basal-like breast cancer subtype that is based upon BRCA1-status.
 
Overall design Gene expression profiling of breast tumors. Dual color common reference gene expression study using 55K oligonucleotide microarrays.
 
Contributor(s) Jönsson GB, Staaf J, Vallon-Christersson J, Ringner M, Gruvberger-Saal S, Saal LH, Holm K, Hegardt C, Arason A, Fagerholm R, Persson C, Grabau D, Johnsson E, Lövgren K, Magnusson L, Heikkilä P, Agnarsson BA, Johannsson OT, Malmström P, Fernö M, Olsson H, Loman N, Nevanlinna H, Barkardottir RB, Borg A
Citation(s) 22706203
Submission date Nov 12, 2010
Last update date Jun 28, 2012
Contact name Johan Staaf
Organization name SCIBLU - Swegene Centre for Integrative Biology at Lund University
Street address Medicon Village
City Lund
ZIP/Postal code SE-223 81
Country Sweden
 
Platforms (1)
GPL5345 SWEGENE H_v2.1.1 55K
Samples (577)
GSM551608 TAX577147
GSM551609 TAX577192
GSM551610 TAX577067
Relations
BioProject PRJNA134797

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE25307_RAW.tar 2.6 Gb (http)(custom) TAR (of GPR)
GSE25307_SupplementaryProbeAnnotations.txt.gz 287.1 Kb (ftp)(http) TXT
GSE25307_readme.txt.gz 452 b (ftp)(http) TXT
GSE25307_sample_annotations.txt.gz 5.1 Kb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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