1
|
Huang CS, Tsai ML, Lu TP, Tu CC, Liu CY, Huang CJ, Ho YS, Tu SH, Chuang EY, Tseng LM, Huang CC. The extended concurrent genes signature for disease-free survival in breast cancer. J Formos Med Assoc 2022; 121:1945-1955. [PMID: 35181201 DOI: 10.1016/j.jfma.2022.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/11/2021] [Accepted: 01/18/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND/PURPOSE Previously we had identified concurrent genes, which highlighted the interplay between copy number variation (CNV) and differential gene expression (GE) for Han Chinese breast cancers. The merit of the approach is to discovery biomarkers not identifiable by conventional GE only data, for which phenotype-correlation or gene variability is the criteria of gene selection. MATERIALS AND METHODS Thirty-one comparative genomic hybridization (CGH) and 83 GE microarrays were performed, with 29 breast cancers assayed from both platforms. Potential targets were revealed by Genomic Identification of Significant Targets in Cancer (GISTIC) from CGH arrays. Concurrent genes and genes with significant GISTIC scores were used to derive the extended concurrent genes signature, which was consensus from leading edge analysis across all studies and a supervised partial least square (PLS) regression predictive model of disease-free survival was constructed. RESULTS There were 1584 concurrent genes from 29 samples with both CGH and GE microarrays. Enriched concurrent genes sets for disease-free survival were identified independently from 83 GE arrays and another one with Han Chinese origin as well as three studies of Western origin. For five studies with disease-free survival follow up, prognostic discrepancy was observed between predicted high-risk and low-risk group patients. CONCLUSION We concluded that through parallel analyses of CGH and GE microarrays, the proposed extended concurrent gene expression signature can identify biomarkers with prognostic values.
Collapse
Affiliation(s)
- Ching-Shui Huang
- Division of General Surgery, Department of Surgery, Cathay General Hospital, Taipei, Taiwan; School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ming-Lin Tsai
- Division of General Surgery, Department of Surgery, Cathay General Hospital, Taipei, Taiwan
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Chao-Chiang Tu
- Department of Surgery, Fu-Jen Catholic University Hospital, New Taipei, Taiwan; School of Medicine, College of Medicine, Fu-Jen Catholic University, New Taipei, Taiwan
| | - Chih-Yi Liu
- Division of Pathology, Cathay General Hospital Sijhih, New Taipei, Taiwan
| | - Chi-Jung Huang
- Department of Medical Research, Cathay General Hospital, Taipei, Taiwan; Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan
| | - Yuan-Soon Ho
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan; Taipei Cancer Center, Taipei Medical University, Taipei, Taiwan; Department of Medical Laboratory, Taipei Medical University Hospital, Taipei, Taiwan; School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Shih-Hsin Tu
- School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Taipei Cancer Center, Taipei Medical University, Taipei, Taiwan; Division of Breast Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei, Taiwan
| | - Eric Y Chuang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Ling-Ming Tseng
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan.
| | - Chi-Cheng Huang
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan; Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan.
| |
Collapse
|