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Concurrent Gene Signatures for Han Chinese Breast Cancers

Author

Listed:
  • Chi-Cheng Huang
  • Shih-Hsin Tu
  • Heng-Hui Lien
  • Jaan-Yeh Jeng
  • Ching-Shui Huang
  • Chi-Jung Huang
  • Liang-Chuan Lai
  • Eric Y Chuang

Abstract

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

Suggested Citation

  • Chi-Cheng Huang & Shih-Hsin Tu & Heng-Hui Lien & Jaan-Yeh Jeng & Ching-Shui Huang & Chi-Jung Huang & Liang-Chuan Lai & Eric Y Chuang, 2013. "Concurrent Gene Signatures for Han Chinese Breast Cancers," PLOS ONE, Public Library of Science, vol. 8(10), pages 1-1, October.
    • Handle: RePEc:plo:pone00:0076421
    DOI: 10.1371/journal.pone.0076421
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    1. Charles M. Perou & Therese Sørlie & Michael B. Eisen & Matt van de Rijn & Stefanie S. Jeffrey & Christian A. Rees & Jonathan R. Pollack & Douglas T. Ross & Hilde Johnsen & Lars A. Akslen & Øystein Flu, 2000. "Molecular portraits of human breast tumours," Nature, Nature, vol. 406(6797), pages 747-752, August.
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