title: Identification and validation of the methylation biomarkers of non-small cell lung cancer (NSCLC).
abstract: BACKGROUND
  DNA methylation was suggested as the promising biomarker for lung cancer diagnosis. However, it is a great challenge to search for the optimal combination of methylation biomarkers to obtain maximum diagnostic performance.
  
  
  RESULTS
  In this study, we developed a panel of DNA methylation biomarkers and validated their diagnostic efficiency for non-small cell lung cancer (NSCLC) in a large Chinese Han NSCLC retrospective cohort. Three high-throughput DNA methylation microarray datasets (458 samples) were collected in the discovery stage. After normalization, batch effect elimination and integration, significantly differentially methylated genes and the best combination of the biomarkers were determined by the leave-one-out SVM (support vector machine) feature selection procedure. Then, candidate promoters were examined by the methylation status determined single nucleotide primer extension technique (MSD-SNuPET) in an independent set of 150 pairwise NSCLC/normal tissues. Four statistical models with fivefold cross-validation were used to evaluate the performance of the discriminatory algorithms. The sensitivity, specificity and accuracy were 86.3%, 95.7% and 91%, respectively, in Bayes tree model. The logistic regression model incorporated five gene methylation signatures at AGTR1, GALR1, SLC5A8, ZMYND10 and NTSR1, adjusted for age, sex and smoking, showed robust performances in which the sensitivity, specificity, accuracy, and area under the curve (AUC) were 78%, 97%, 87%, and 0.91, respectively.
  
  
  CONCLUSIONS
  In summary, a high-throughput DNA methylation microarray dataset followed by batch effect elimination can be a good strategy to discover optimal DNA methylation diagnostic panels. Methylation profiles of AGTR1, GALR1, SLC5A8, ZMYND10 and NTSR1, could be an effective methylation-based assay for NSCLC diagnosis.
authors: State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University Jiangwan Campus, 2005 Songhu Road, Shanghai, 200438 China ; Fudan-Taizhou Institute of Health Sciences, 1 Yaocheng Road, Taizhou, Jiangsu 225300 China.
authors: Shicheng
authors: S
authors: Guo
authors: State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University Jiangwan Campus, 2005 Songhu Road, Shanghai, 200438 China.
authors: Fengyang
authors: F
authors: Yan
authors: Department of Cardiothoracic Surgery, Changzheng Hospital of Shanghai, Fengyang Road 415, Shanghai, 200000 China.
authors: Jibin
authors: J
authors: Xu
authors: Yangzhou No.1 People's Hospital, 368 Hanjiang Road, Yangzhou, 225001 China.
authors: Yang
authors: Y
authors: Bao
authors: Department of Cardiothoracic Surgery, Changhai Hospital of Shanghai, Changhai Road 168, Shanghai, 200433 China.
authors: Ji
authors: J
authors: Zhu
authors: State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University Jiangwan Campus, 2005 Songhu Road, Shanghai, 200438 China.
authors: Xiaotian
authors: X
authors: Wang
authors: State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University Jiangwan Campus, 2005 Songhu Road, Shanghai, 200438 China ; Department of Pneumology, Changhai Hospital of Shanghai, Changhai Road 168, Shanghai, 200433 China.
authors: Junjie
authors: J
authors: Wu
authors: State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University Jiangwan Campus, 2005 Songhu Road, Shanghai, 200438 China.
authors: Yi
authors: Y
authors: Li
authors: State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University Jiangwan Campus, 2005 Songhu Road, Shanghai, 200438 China.
authors: Weilin
authors: W
authors: Pu
authors: Center for Genetic & Genomic Analysis, Genesky Biotechnologies Inc., 787 Kangqiao Road, Shanghai, 201203 China.
authors: Yan
authors: Y
authors: Liu
authors: Center for Genetic & Genomic Analysis, Genesky Biotechnologies Inc., 787 Kangqiao Road, Shanghai, 201203 China.
authors: Zhengwen
authors: Z
authors: Jiang
authors: State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University Jiangwan Campus, 2005 Songhu Road, Shanghai, 200438 China.
authors: Yanyun
authors: Y
authors: Ma
authors: Department of Cardiothoracic Surgery, Huashan Hospital, Fudan University, 12 Wulumuqi Road, Shanghai, 200040 China.
authors: Xiaofeng
authors: X
authors: Chen
authors: Human Genetics Center, The University of Texas School of Public Health, 1200 Herman Pressler, Houston, Texas 77030 USA.
authors: Momiao
authors: M
authors: Xiong
authors: State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University Jiangwan Campus, 2005 Songhu Road, Shanghai, 200438 China ; Fudan-Taizhou Institute of Health Sciences, 1 Yaocheng Road, Taizhou, Jiangsu 225300 China.
authors: Li
authors: L
authors: Jin
authors: State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University Jiangwan Campus, 2005 Songhu Road, Shanghai, 200438 China ; Fudan-Taizhou Institute of Health Sciences, 1 Yaocheng Road, Taizhou, Jiangsu 225300 China.
authors: Jiucun
authors: J
authors: Wang
keywords: Batch effect elimination; Biomarker; DNA methylation; Diagnosis; Non-small cell lung cancer
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