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Series GSE18626 Query DataSets for GSE18626
Status Public on Feb 01, 2011
Title Comparative genomic hybridization of BRCAX breast tumors
Organism Homo sapiens
Experiment type Genome variation profiling by array
Summary Only about 25% of familial breast cancer is explained by mutations in BRCA1 and BRCA2, fewer by moderate penetrance genes like P53, PTEN, CHEK2, ATM and PALB2 and an unknown fraction by common variants of genes with low penetrance. Evidence suggests that additional dominant breast cancer genes exist and these are referred to as BRCAX.
Clinical presentation of families with highly increased incidence of breast cancer that are non-BRCA1/BRCA2, suggests dominant inheritance of such high penetrance breast cancer genes. Because cancer genes often confer a specific clinical presentation (e.g. age of onset, sex-ratio, tissue spectrum) it seems useful to initiate their discovery by such clinical criteria. An earlier linkage study of BRCAX / non-BRCA1/2 breast cancer families aimed to enrich for a common genetic defect by setting stringent inclusion criteria, failed to identify new breast cancer susceptibility loci.
Motivated by results of BRCA1 and BRCA2 breast tumors that have characteristic genomic signatures (array-CGH 'phenotypes'), we present the largest dataset to date showing the genomic profiles of 58 BRCAX primary breast tumors by array-CGH and show by unsupervised hierarchical clustering that they form a heterogeneous group with 4 distinct subtypes that are different from (n = 48) sporadic controls.
This provides a possible explanation for the lack of high LOD scores in linkage studies. The presence of more than one BRCAX sub-type suggests the existence of more than one BRCAX gene. We propose approaches that can be employed to stratify BRCAX families based on array-CGH data.
 
Overall design 58 primary breast carcinomas from non-BRCA1/2 hereditary breast cancer families (HBC) compared to 48 sporadic tumors
 
Contributor(s) van Beers EH, Joosse SA, Oldenburg RA, Verhoef S, Devilee P, Nederlof PM
Citation(s) 21286804
Submission date Oct 19, 2009
Last update date Mar 21, 2012
Contact name Petra Nederlof
E-mail(s) [email protected]
Phone +31 205122757
Fax +31 205122759
URL http://www.nki.nl
Organization name The Netherlands Cancer Institute
Department Pathology
Lab Molecular Pathology
Street address Plesmanlaan 121
City Amsterdam
ZIP/Postal code 1066CX
Country Netherlands
 
Platforms (1)
GPL4560 Netherlands Cancer Institute human 3.5k BAC array
Samples (106)
GSM462909 non-BRCA1/2 hereditary breast tumor (BRCAx)_BX403_HB376-13
GSM462910 non-BRCA1/2 hereditary breast tumor (BRCAx)_BX405_HB375-19
GSM462911 non-BRCA1/2 hereditary breast tumor (BRCAx)_BX406_HB376-20
Relations
BioProject PRJNA121465

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
GSE18626_RAW.tar 255.3 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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