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Series GSE118527 Query DataSets for GSE118527
Status Public on Mar 09, 2019
Title Affymetrix SNP array data (Oncoscan CNV) for Fudan University Shanghai Cancer Center Triple Negative Breast Cancer (FUSCCTNBC) project
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary We comprehensively analyzed clinical, genomic and transcriptomic data of a cohort of 465 primary triple-negative breast cancer (TNBC). PIK3CA mutations and copy number gains of chromosome 22q11 were more frequent in our Chinese cohort than in The Cancer Genome Atlas. We classified TNBCs into four transcriptome-based subtypes: 1) luminal androgen receptor (LAR), 2) immunomodulatory (IM), 3) basal-like immune-suppressed (BLIS), and 4) mesenchymal (MES). Putative therapeutic targets or biomarkers were identified among each subtype. Importantly, the LAR subtype showed more ERBB2 somatic mutations, infrequent mutational signature 3 and frequent CDKN2A loss. The comprehensive profile of TNBCs provided here will serve as a reference to further advance the understanding and precision treatment of TNBC.
 
Overall design Copy number analysis of Affymetrix Oncoscan (Oncoscan CNV) SNP arrays was performed for samples from 401 primary triple negative breast cancer patients treated at Fudan University Shanghai Cancer Center. There are also 23 randomly selected white blood cell samples from the mentioned patients, which were used as references for eliminating potential recurrent germline CNV and/or recurrent false positive calls.
 
Contributor(s) Shao Z, Jiang Y, Ma D
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BioProject PRJNA486023
Submission date Aug 14, 2018
Last update date Mar 11, 2019
Contact name Zhi-Ming Shao
E-mail 09301010134@fudan.edu.cn
Organization name Fudan University Shanghai Cancer Center
Street address 270 Dong An Road, Build 7, RM304
City Shanghai
ZIP/Postal code 200032
Country China
 
Platforms (1)
GPL21558 [OncoScan_CNV] Affymetrix OncoScan CNV FFPE Assay
Samples (424)
GSM3331599 FUSCCTNBC001_FrozenPrimaryTumorTissue
GSM3331600 FUSCCTNBC002_FrozenPrimaryTumorTissue
GSM3331601 FUSCCTNBC004_FrozenPrimaryTumorTissue

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
GSE118527_RAW.tar 6.0 Gb (http)(custom) TAR (of CEL, TXT)
Raw data provided as supplementary file
Processed data provided as supplementary file

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