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Series GSE54193 Query DataSets for GSE54193
Status Public on Jan 17, 2017
Title Proper genomic profiling of (BRCA1-mutated) basal-like breast carcinomas requires prior removal of tumor infiltrating lymphocytes
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary To find BRCA1-associated copy number abberations, the copy number profiles of Familial Basal-like BRCA1-mutated breast carcinomas were compared to Familial Basal-like carcinomas with no pathgogenic BRCA1/2 mutation. This led to the observation of unanticipated heterogeneity of the BRCA1 associated copy number profiles. Gene expression analysis on the same samples identified tumor infiltrating lymphocytes to be responsible for this observation. High number of infiltrating lymphocytes proved to be detrimental for copy number profiling efforts. After optimal sample selection, BRCA1-associated copy number abberations could be detected.
 
Overall design Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from fresh frozen primary breast tumors
Copy number analysis of Affymetrix 500K SNP arrays was performed for 120 famlial primary breast tumors. 90 Female HAPMAP samples (http://hapmap.ncbi.nlm.nih.gov/) with CEU ancestry were used as baseline.
 
Contributor(s) Massink MP, Waisfisz Q, Meijers-Heijboer H
Citation(s) 25616998, 21614566, 26553136
Submission date Jan 17, 2014
Last update date May 17, 2017
Contact name Marcel Smid
Organization name Erasmus MC
Department Medical Oncology
Street address Dr. Molewaterplein 50
City Rotterdam
ZIP/Postal code PO Box 2040, 3000CA
Country Netherlands
 
Platforms (2)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
Samples (240)
GSM1309541 Primary Breast Cancer255-250knsp
GSM1309542 Primary Breast Cancer461-250knsp
GSM1309543 Primary Breast Cancer804-250knsp
This SubSeries is part of SuperSeries:
GSE54219 Molecular genomic and transcriptomic profiling of familial breast cancer.
Relations
BioProject PRJNA235956

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
GSE54193_RAW.tar 5.9 Gb (http)(custom) TAR (of CEL)
Processed data included within Sample table
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