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| Status |
Public on Jan 07, 2014 |
| Title |
Concurrent Gene Signatures for Han Chinese Breast Cancers [Agilent] |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by array
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| Summary |
The interplay between copy number variation (CNV) and differential gene expression may be able to shed light on molecular process underlying breast cancer and lead to the discovery of cancer-related genes. In the current study, genes concurrently identified in array comparative genomic hybridization (CGH) and gene expression microarrays were used to derive gene signatures for Han Chinese breast cancers. We performed 23 array CGHs and 81 gene expression microarrays in breast cancer samples from Taiwanese women. Genes with coherent patterns of both CNV and differential gene expression were identified from the 21 samples assayed using both platforms. We used these genes to derive signatures associated with clinical ER and HER2 status and disease-free survival. Distributions of signature genes were strongly associated with chromosomal location: chromosome 16 for ER and 17 for HER2. A breast cancer risk predictive model was built based on the first supervised principal component from 16 genes (RCAN3, MCOLN2, DENND2D, RWDD3, ZMYM6, CAPZA1, GPR18, WARS2, TRIM45, SCRN1, CSNK1E, HBXIP, CSDE1, MRPL20, IKZF1, and COL20A1), and distinct survival patterns were observed between the high- and low-risk groups from the combined dataset of 408 microarrays. The risk score was significantly higher in breast cancer patients with recurrence, metastasis, or mortality than in relapse-free individuals (0.241 versus 0, P<0.001). The concurrent gene risk predictive model remained discriminative across distinct clinical ER and HER2 statuses in subgroup analysis. We conclude that parallel analysis of CGH and microarray data, in conjunction with known gene expression patterns, can be used to identify biomarkers with prognostic values in breast cancer.
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| Overall design |
We performed 23 array CGHs and 81 gene expression microarrays in breast cancer samples from Taiwanese women. Genes with coherent patterns of both CNV and differential gene expression were identified from the 21 samples assayed using both platforms. We used these genes to derive signatures associated with clinical ER and HER2 status and disease-free survival.
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| Contributor(s) |
Huang C, Tu S, Lien H, Jeng J, Huang C, Huang C, Lai L, Chuang EY |
| Citation(s) |
24098497, 34387660 |
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| Submission date |
Jun 26, 2013 |
| Last update date |
Sep 01, 2021 |
| Contact name |
Chi-Cheng Huang |
| E-mail(s) |
[email protected]
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| Organization name |
Cathay General Hospital SiJhih
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| Department |
Department of Medical Education and Research
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| Street address |
No.2, Lane 59, Jiancheng Rd. Xizhi Dist.
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| City |
New Taipei City |
| ZIP/Postal code |
22174 |
| Country |
Taiwan |
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| Platforms (1) |
| GPL9075 |
Agilent-014698 Human Genome CGH Microarray 105A (G4412A) [Probe Name version] |
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| Samples (23)
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| This SubSeries is part of SuperSeries: |
| GSE48391 |
Concurrent Gene Signatures for Han Chinese Breast Cancers |
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| Relations |
| BioProject |
PRJNA209984 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE48297.txt.gz |
12.3 Mb |
(ftp)(http) |
TXT |
| GSE48297_RAW.tar |
306.9 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data are available on Series record |
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