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Pan J, Ma B, Hou X, Li C, Xiong T, Gong Y, Song F. The construction of transcriptional risk scores for breast cancer based on lightGBM and multiple omics data. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:12353-12370. [PMID: 36654001 DOI: 10.3934/mbe.2022576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
BACKGROUND Polygenic risk score (PRS) can evaluate the individual-level genetic risk of breast cancer. However, standalone single nucleotide polymorphisms (SNP) data used for PRS may not provide satisfactory prediction accuracy. Additionally, current PRS models based on linear regression have insufficient power to leverage non-linear effects from thousands of associated SNPs. Here, we proposed a transcriptional risk score (TRS) based on multiple omics data to estimate the risk of breast cancer. METHODS The multiple omics data and clinical data of breast invasive carcinoma (BRCA) were collected from the cancer genome atlas (TCGA) and the gene expression omnibus (GEO). First, we developed a novel TRS model for BRCA utilizing single omic data and LightGBM algorithm. Subsequently, we built a combination model of TRS derived from each omic data to further improve the prediction accuracy. Finally, we performed association analysis and prognosis prediction to evaluate the utility of the TRS generated by our method. RESULTS The proposed TRS model achieved better predictive performance than the linear models and other ML methods in single omic dataset. An independent validation dataset also verified the effectiveness of our model. Moreover, the combination of the TRS can efficiently strengthen prediction accuracy. The analysis of prevalence and the associations of the TRS with phenotypes including case-control and cancer stage indicated that the risk of breast cancer increases with the increases of TRS. The survival analysis also suggested that TRS for the cancer stage is an effective prognostic metric of breast cancer patients. CONCLUSIONS Our proposed TRS model expanded the current definition of PRS from standalone SNP data to multiple omics data and outperformed the linear models, which may provide a powerful tool for diagnostic and prognostic prediction of breast cancer.
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Affiliation(s)
- Jianqiao Pan
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Baoshan Ma
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Xiaoyu Hou
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Chongyang Li
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Tong Xiong
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Yi Gong
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Fengju Song
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
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Ma B, Yan G, Chai B, Hou X. XGBLC: an improved survival prediction model based on XGBoost. Bioinformatics 2022; 38:410-418. [PMID: 34586380 DOI: 10.1093/bioinformatics/btab675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/06/2021] [Accepted: 09/23/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Survival analysis using gene expression profiles plays a crucial role in the interpretation of clinical research and assessment of disease therapy programs. Several prediction models have been developed to explore the relationship between patients' covariates and survival. However, the high-dimensional genomic features limit the prediction performance of the survival model. Thus, an accurate and reliable prediction model is necessary for survival analysis using high-dimensional genomic data. RESULTS In this study, we proposed an improved survival prediction model based on XGBoost framework called XGBLC, which used Lasso-Cox to enhance the ability to analyze high-dimensional genomic data. The novel first- and second-order gradient statistics of Lasso-Cox were defined to construct the loss function of XGBLC. We extensively tested our XGBLC algorithm on both simulated and real-world datasets, and estimated the performance of models with 5-fold cross-validation. Based on 20 cancer datasets from The Cancer Genome Atlas (TCGA), XGBLC outperforms five state-of-the-art survival methods in terms of C-index, Brier score and AUC. The results show that XGBLC still keeps good accuracy and robustness by comparing the performance on the simulated datasets with different scales. The developed prediction model would be beneficial for physicians to understand the effects of patient's genomic characteristics on survival and make personalized treatment decisions. AVAILABILITY AND IMPLEMENTATION The implementation of XGBLC algorithm based on R language is available at: https://github.com/lab319/XGBLC. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Baoshan Ma
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Ge Yan
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Bingjie Chai
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Xiaoyu Hou
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
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3
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Kim YM, Hong S. Controversial roles of cold‑inducible RNA‑binding protein in human cancer (Review). Int J Oncol 2021; 59:91. [PMID: 34558638 DOI: 10.3892/ijo.2021.5271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/06/2021] [Indexed: 11/05/2022] Open
Abstract
Cold‑inducible RNA‑binding protein (CIRBP) is a cold‑shock protein comprised of an RNA‑binding motif that is induced by several stressors, such as cold shock, UV radiation, nutrient deprivation, reactive oxygen species and hypoxia. CIRBP can modulate post‑transcriptional regulation of target mRNA, which is required to control DNA repair, circadian rhythms, cell growth, telomere integrity and cardiac physiology. In addition, the crucial function of CIRBP in various human diseases, including cancers and inflammatory disease, has been reported. Although CIRBP is primarily considered to be an oncogene, it may also serve a role in tumor suppression. In the present study, the controversial roles of CIRBP in various human cancers is summarized, with a focus on the interconnectivity between CIRBP and its target mRNAs involved in tumorigenesis. CIRBP may represent an important prognostic marker and therapeutic target for cancer therapy.
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Affiliation(s)
- Young-Mi Kim
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology, Gachon University, Incheon 21999, Republic of Korea
| | - Suntaek Hong
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology, Gachon University, Incheon 21999, Republic of Korea
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Su K, Yu Q, Shen R, Sun SY, Moreno CS, Li X, Qin ZS. Pan-cancer analysis of pathway-based gene expression pattern at the individual level reveals biomarkers of clinical prognosis. CELL REPORTS METHODS 2021; 1:100050. [PMID: 34671755 PMCID: PMC8525796 DOI: 10.1016/j.crmeth.2021.100050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/07/2021] [Accepted: 06/16/2021] [Indexed: 02/08/2023]
Abstract
Identifying biomarkers to predict the clinical outcomes of individual patients is a fundamental problem in clinical oncology. Multiple single-gene biomarkers have already been identified and used in clinics. However, multiple oncogenes or tumor-suppressor genes are involved during the process of tumorigenesis. Additionally, the efficacy of single-gene biomarkers is limited by the extensively variable expression levels measured by high-throughput assays. In this study, we hypothesize that in individual tumor samples, the disruption of transcription homeostasis in key pathways or gene sets plays an important role in tumorigenesis and has profound implications for the patient's clinical outcome. We devised a computational method named iPath to identify, at the individual-sample level, which pathways or gene sets significantly deviate from their norms. We conducted a pan-cancer analysis and demonstrated that iPath is capable of identifying highly predictive biomarkers for clinical outcomes, including overall survival, tumor subtypes, and tumor-stage classifications.
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Affiliation(s)
- Kenong Su
- Department of Computer Science, Emory University, Atlanta, GA 30322, USA
| | - Qi Yu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Ronglai Shen
- Department of Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10017, USA
| | - Shi-Yong Sun
- Department of Hematology & Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Carlos S. Moreno
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xiaoxian Li
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Zhaohui S. Qin
- Department of Computer Science, Emory University, Atlanta, GA 30322, USA
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA 30322, USA
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Brown AL, Jeong J, Wahab RA, Zhang B, Mahoney MC. Diagnostic accuracy of MRI textural analysis in the classification of breast tumors. Clin Imaging 2021; 77:86-91. [PMID: 33652269 DOI: 10.1016/j.clinimag.2021.02.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/31/2021] [Accepted: 02/21/2021] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To investigate whether textural analysis (TA) of MRI heterogeneity may play a role in the clinical assessment and classification of breast tumors. MATERIALS AND METHODS For this retrospective study, patients with breast masses ≥1 cm on contrast-enhanced MRI were obtained in 69 women (mean age: 51 years; range 21-78 years) with 77 masses (38 benign, 39 malignant) from 2006 to 2018. The selected single slice sagittal peak post-contrast T1-weighted image was analyzed with commercially available TA software [TexRAD Ltd., UK]. Eight histogram TA parameters were evaluated at various spatial scaling factors (SSF) including mean pixel intensity, standard deviation of the pixel histogram (SD), entropy, mean of the positive pixels (MPP), skewness, kurtosis, sigma, and Tx_sigma. Additional statistical tests were used to determine their predictiveness. RESULTS Entropy showed a significant difference between benign and malignant tumors at all textural scales (p < 0.0001) and kurtosis was significant at SSF = 0-5 (p = 0.0026-0.0241). The single best predictor was entropy at SSF = 4 with AUC = 0.80, giving a sensitivity of 95% and specificity of 53%. An AUC of 0.91 was found using a model combining entropy with sigma, which yielded better performance with a sensitivity of 92% and specificity of 79%. CONCLUSION TA of breast masses has the potential to assist radiologists in categorizing tumors as benign or malignant on MRI. Measurements of entropy, kurtosis, and entropy combined with sigma may provide the best predictability.
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Affiliation(s)
- Ann L Brown
- Department of Radiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States of America. https://twitter.com/AnnBrownMD
| | - Joanna Jeong
- Department of Radiology, Confluence Health, Wenatchee, WA, United States of America
| | - Rifat A Wahab
- Department of Radiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States of America. https://twitter.com/RifatWahab
| | - Bin Zhang
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States of America
| | - Mary C Mahoney
- Department of Radiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States of America. https://twitter.com/MaryMahoneyMD
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Huang R, Guo J, Yan P, Zhai S, Hu P, Zhu X, Zhang J, Qiao Y, Zhang Y, Liu H, Huang L, Zhang J, Yang D, Huang Z. The Construction of Bone Metastasis-Specific Prognostic Model and Co-expressed Network of Alternative Splicing in Breast Cancer. Front Cell Dev Biol 2020; 8:790. [PMID: 32984314 PMCID: PMC7477087 DOI: 10.3389/fcell.2020.00790] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/28/2020] [Indexed: 01/17/2023] Open
Abstract
Background Breast cancer (BRCA) ranks among the top most common female malignancies and was regarded as incurable when combined with bone and distant metastasis. Alternative splicing events (ASEs) together with splicing factors (SFs) were considered responsible for the development and progression of tumors. Methods Datasets including RNA sequencing and ASEs of BRCA samples were achieved from TCGA and TCGASpliceSeq databases. Then, a survival model was built including 15 overall-survival-associated splicing events (OS-SEs) by Cox regression and Lasso regression. The co-expressed SFs of each bone-and-distant-metastasis-related OS-SE were discovered by Pearson correlation analysis. Additionally, Gene Set Variation Analysis (GSVA) was performed to identify the downstream mechanisms of the key OS-SEs. Finally, the results were validated in different online platforms. Results A reliable survival model was established (the area under ROC = 0.856), and CIRBP was found co-expressed with FAM110B (R = 0.320, P < 0.001) associated with the fatty acid metabolism pathway. Conclusion Aberrant SF, CIRBP, regulated a specific ASE, exon skip (ES) of FAM110B, during which the fatty acid metabolism pathway played an essential part in tumorigenesis and prognosis of BRCA.
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Affiliation(s)
- Runzhi Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Division of Spine, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Juanru Guo
- Tongji University School of Mathematical Sciences, Tongji University, Shanghai, China
| | - Penghui Yan
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Suna Zhai
- Department of Radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Peng Hu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaolong Zhu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiayao Zhang
- Tongji University School of Mathematical Sciences, Tongji University, Shanghai, China
| | - Yannan Qiao
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Zhang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hui Liu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ling Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Zhang
- Tongji University School of Medicine, Shanghai, China
| | - Daoke Yang
- Department of Radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zongqiang Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Tong D, Tian Y, Zhou T, Ye Q, Li J, Ding K, Li J. Improving prediction performance of colon cancer prognosis based on the integration of clinical and multi-omics data. BMC Med Inform Decis Mak 2020; 20:22. [PMID: 32033604 PMCID: PMC7006213 DOI: 10.1186/s12911-020-1043-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 01/31/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Colon cancer is common worldwide and is the leading cause of cancer-related death. Multiple levels of omics data are available due to the development of sequencing technologies. In this study, we proposed an integrative prognostic model for colon cancer based on the integration of clinical and multi-omics data. METHODS In total, 344 patients were included in this study. Clinical, gene expression, DNA methylation and miRNA expression data were retrieved from The Cancer Genome Atlas (TCGA). To accommodate the high dimensionality of omics data, unsupervised clustering was used as dimension reduction method. The bias-corrected Harrell's concordance index was used to verify which clustering result provided the best prognostic performance. Finally, we proposed a prognostic prediction model based on the integration of clinical data and multi-omics data. Uno's concordance index with cross-validation was used to compare the discriminative performance of the prognostic model constructed with different covariates. RESULTS Combinations of clinical and multi-omics data can improve prognostic performance, as shown by the increase of the bias-corrected Harrell's concordance of the prognostic model from 0.7424 (clinical features only) to 0.7604 (clinical features and three types of omics features). Additionally, 2-year, 3-year and 5-year Uno's concordance statistics increased from 0.7329, 0.7043, and 0.7002 (clinical features only) to 0.7639, 0.7474 and 0.7597 (clinical features and three types of omics features), respectively. CONCLUSION In conclusion, this study successfully combined clinical and multi-omics data for better prediction of colon cancer prognosis.
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Affiliation(s)
- Danyang Tong
- Engineering Research Center of EMR and Intelligent Expert System, Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, No. 38 Zheda Road, Hangzhou, 310027, Zhejiang Province, China
| | - Yu Tian
- Engineering Research Center of EMR and Intelligent Expert System, Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, No. 38 Zheda Road, Hangzhou, 310027, Zhejiang Province, China
| | - Tianshu Zhou
- Engineering Research Center of EMR and Intelligent Expert System, Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, No. 38 Zheda Road, Hangzhou, 310027, Zhejiang Province, China
| | - Qiancheng Ye
- Engineering Research Center of EMR and Intelligent Expert System, Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, No. 38 Zheda Road, Hangzhou, 310027, Zhejiang Province, China
| | - Jun Li
- Department of Surgical Oncology, Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 31009, Zhejiang Province, China
| | - Kefeng Ding
- Department of Surgical Oncology, Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 31009, Zhejiang Province, China
| | - Jingsong Li
- Engineering Research Center of EMR and Intelligent Expert System, Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, No. 38 Zheda Road, Hangzhou, 310027, Zhejiang Province, China.
- Research Center for Healthcare Data Science, Zhejiang Lab, Hangzhou, China.
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Fararjeh AFS, Tu SH, Chen LC, Liu YR, Lin YK, Chang HL, Chang HW, Wu CH, Hwang-Verslues WW, Ho YS. The impact of the effectiveness of GATA3 as a prognostic factor in breast cancer. Hum Pathol 2018; 80:219-230. [PMID: 29902578 DOI: 10.1016/j.humpath.2018.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/24/2018] [Accepted: 06/01/2018] [Indexed: 01/21/2023]
Abstract
The transcription factor GATA3 plays a significant role in mammary gland development and differentiation. We analyzed expression of GATA3 in breast cancer (BC) cell lines and clinical specimens from BC patients in Taiwan. Semiquantitative reverse-transcription polymerase chain reaction (RT-PCR), quantitative real-time PCR were carried out to determine the mRNA level of GATA3 from 241 pairs of matched tumor and adjacent normal tissues from anonymous female donors. GATA3 immunohistochemistry (IHC) staining and H-score were performed (n = 25). Inducing and silencing of GATA3 were done by exposure MCF-7 cell line to nicotine or curcumin, respectively. GATA3 expression was detected in most of the estrogen receptor-positive (ER+) tumor specimens (176/241, 73%) compared with paired normal tissues (65/241, 27%) (P < .001). The GATA3 level was highest in Luminal A, and independent t-tests revealed higher GATA3 was associated with ER+ (P = .018) and BC stages (stage II, and stage IV). Nuclear protein expression of GATA3 was detected in tumor tissues (P < .001) with higher H-score in Luminal A patients (P = .012). Kaplan-Meier survival analyses showed that ER+/progesterone receptor (PgR)+ and lower grade BC patients with relatively high GATA3 had better clinical overall survival (OS). GATA3 regulates ERα and BCL-2 as BC luminal subtype markers. Cox univariate and multivariate analyses demonstrated that the expression of GATA3 was an effective predictor of the risk of death. We demonstrated a correlation between GATA3 expression and only ER+ and suggest that a higher GATA3 expression is a good prognostic factor for OS for ER+ BC patients.
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Affiliation(s)
- Abdul-Fattah Salah Fararjeh
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, 110 Taipei, Taiwan
| | - Shih-Hsin Tu
- Breast Medical Center, Taipei Medical University Hospital, Taipei, Taiwan; Taipei Cancer Center, Taipei Medical University Hospital, Taipei, Taiwan; Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Li-Ching Chen
- Breast Medical Center, Taipei Medical University Hospital, Taipei, Taiwan; Taipei Cancer Center, Taipei Medical University Hospital, Taipei, Taiwan; TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yun-Ru Liu
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, Taiwan
| | - Yen-Kuang Lin
- Research Center of Biostatistics, Taipei Medical University, Taipei, Taiwan
| | - Hang-Lung Chang
- Department of General Surgery, EnChun Kong Hospital, New Taipei City, Taiwan
| | - Hui-Wen Chang
- Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei, Taiwan
| | - Chih-Hsiung Wu
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Department of General Surgery, EnChun Kong Hospital, New Taipei City, Taiwan
| | | | - Yuan-Soon Ho
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan; Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei, Taiwan; Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan; School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
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