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Series GSE19177 Query DataSets for GSE19177
Status Public on Dec 16, 2009
Title Subtypes of familial breast tumors revealed by expression and copy number profiling
Organism Homo sapiens
Experiment type Expression profiling by array
Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary We analysed a cohort of 75 BRCA1, BRCA2 and non-BRCA1/2 breast tumors by gene expression profiling and found that 74% BRCA1 tumors were basal-like, 73% of BRCA2 tumors were luminal A or B, and 52% non-BRCA1/2 tumors were luminal A. Thirty-four tumors were also analysed by single nucleotide polymorphism-comparative genomic hybridization (SNP-CGH) arrays. Copy number data could predict whether a tumor was basal-like or luminal with high accuracy, but could not predict its mutation class. Basal-like BRCA1 and basal-like non-BRCA1 tumors were very similar, and contained the highest number of chromosome aberrations. We identified regions of frequent gain containing potential driver genes in the basal (8q and 12p) and luminal A tumors (1q and 17q). Regions of homozygous loss associated with decreased expression of potential tumor suppressor genes were also detected, including in basal tumors (5q and 9p), and basal and luminal tumors (10q). This study highlights the heterogeneity of familial tumors and the clinical consequences for treatment and prognosis.
Overall design RNA was extracted from 75 Familial breast tumours, which were more than 50% tumour cells, comprising BRCA1 (19), BRCA2 (30), non-BRCA1/2 (25) and one familial tumour of unknown mutation status. DNA was also extracted from 34 of these samples which were more than 75% tumour.
Contributor(s) Waddell N
Citation(s) 19960244, 22537934
Submission date Nov 25, 2009
Last update date Sep 10, 2014
Contact name Nic Waddell
Organization name Queensland Centre for Medical Genomics
Street address St Lucia
City Brisbane
ZIP/Postal code 4072
Country Australia
Platforms (2)
GPL6106 Sentrix Human-6 v2 Expression BeadChip
GPL6986 Illumina HumanCNV370-Duov1 DNA Analysis BeadChip (HumanCNV370v1)
Samples (109)
GSM475354 BRCA2 Breast tumor 20447 RNA
GSM475355 BRCA1 Breast tumor 80607 RNA
GSM475356 non-BRCA1/2 Breast tumor 50567 RNA
BioProject PRJNA120595

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
GSE19177_CNV_GEO_14samples_Matrix_signal_intensities.txt.gz 67.4 Mb (ftp)(http) TXT
GSE19177_CNV_GEO_14samples_Matrixprocessed.txt.gz 97.1 Mb (ftp)(http) TXT
GSE19177_CNV_GEO_20samples_Matrix_signal_intensities.txt.gz 98.2 Mb (ftp)(http) TXT
GSE19177_CNV_GEO_20samples_Matrixprocessed.txt.gz 134.6 Mb (ftp)(http) TXT
GSE19177_RAW.tar 38.9 Mb (http)(custom) TAR
GSE19177_non-normalized_data.txt.gz 15.6 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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