title: Integrated Analysis of Genome-Wide Copy Number Alterations and Gene Expression Profiling of Lung Cancer in Xuanwei, China.
abstract: OBJECTIVE
  Lung cancer in Xuanwei (LCXW), China, is known throughout the world for its distinctive characteristics, but little is known about its pathogenesis. The purpose of this study was to screen potential novel "driver genes" in LCXW.
  
  
  METHODS
  Genome-wide DNA copy number alterations (CNAs) were detected by array-based comparative genomic hybridization and differentially expressed genes (DEGs) by gene expression microarrays in 8 paired LCXW and non-cancerous lung tissues. Candidate driver genes were screened by integrated analysis of CNAs and DEGs. The candidate genes were further validated by real-time quantitative polymerase chain reaction.
  
  
  RESULTS
  Large numbers of CNAs and DEGs were detected, respectively. Some of the most frequently occurring CNAs included gains at 5p15.33-p15.32, 5p15.1-p14.3, and 5p14.3-p14.2 and losses at 11q24.3, 21q21.1, 21q22.12-q22.13, and 21q22.2. Integrated analysis of CNAs and DEGs identified 24 candidate genes with frequent copy number gains and concordant upregulation, which were considered potential oncogenes, including CREB3L4, TRIP13, and CCNE2. In addition, the analysis identified 19 candidate genes with a negative association between copy number change and expression change, considered potential tumor suppressor genes, including AHRR, NKD2, and KLF10. One of the most studied oncogenes, MYC, may not play a carcinogenic role in LCXW.
  
  
  CONCLUSIONS
  This integrated analysis of CNAs and DEGs identified several potential novel LCXW-related genes, laying an important foundation for further research on the pathogenesis of LCXW and identification of novel biomarkers or therapeutic targets.
authors.affiliation: Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, the People's Republic of China.|Yunnan Institute of Laboratory Diagnosis, Kunming, Yunnan Province, the People's Republic of China.|Yunnan Key Laboratory of Laboratory Medicine, Kunming, Yunnan Province, the People's Republic of China.
authors.forename: Yanliang
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, the People's Republic of China.|Yunnan Institute of Laboratory Diagnosis, Kunming, Yunnan Province, the People's Republic of China.|Yunnan Key Laboratory of Laboratory Medicine, Kunming, Yunnan Province, the People's Republic of China.
authors.forename: Qiuyue
authors.initials: Q
authors.lastname: Xue
authors.affiliation: Department of Pathology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, the People's Republic of China.
authors.forename: Guoqing
authors.initials: G
authors.lastname: Pan
authors.affiliation: Department of Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America.
authors.forename: Qing H
authors.initials: QH
authors.lastname: Meng
authors.affiliation: Department of Pathology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, the People's Republic of China.
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Tuo
authors.affiliation: Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, the People's Republic of China.|Yunnan Institute of Laboratory Diagnosis, Kunming, Yunnan Province, the People's Republic of China.|Yunnan Key Laboratory of Laboratory Medicine, Kunming, Yunnan Province, the People's Republic of China.
authors.forename: Xuemei
authors.initials: X
authors.lastname: Cai
authors.affiliation: Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, the People's Republic of China.|Yunnan Institute of Laboratory Diagnosis, Kunming, Yunnan Province, the People's Republic of China.|Yunnan Key Laboratory of Laboratory Medicine, Kunming, Yunnan Province, the People's Republic of China.
authors.forename: Zhenghui
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, the People's Republic of China.|Yunnan Institute of Laboratory Diagnosis, Kunming, Yunnan Province, the People's Republic of China.|Yunnan Key Laboratory of Laboratory Medicine, Kunming, Yunnan Province, the People's Republic of China.
authors.forename: Ya
authors.initials: Y
authors.lastname: Li
authors.affiliation: Department of Thoracic Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, the People's Republic of China.
authors.forename: Tao
authors.initials: T
authors.lastname: Huang
authors.affiliation: Department of Biological Sciences, University of Wisconsin-Parkside, Somers, Wisconsin, United States of America.
authors.forename: Xincen
authors.initials: X
authors.lastname: Duan
authors.affiliation: Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, the People's Republic of China.|Yunnan Institute of Laboratory Diagnosis, Kunming, Yunnan Province, the People's Republic of China.|Yunnan Key Laboratory of Laboratory Medicine, Kunming, Yunnan Province, the People's Republic of China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Duan
mesh_terms: D002681:China; D055028:Comparative Genomic Hybridization / Q000379:methods*; D056915:DNA Copy Number Variations / Q000235:genetics*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D060888:Real-Time Polymerase Chain Reaction