title: Whole genome sequencing analysis of lung adenocarcinoma in Xuanwei, China.
abstract: The lung cancer mortality rate in Xuanwei city is among the highest in China and adenocarcinoma is the major histological type. Lung cancer has been associated with exposure to indoor smoky coal emissions that contain high levels of polycyclic aromatic hydrocarbons; however, the pathogenesis of lung cancer has not yet been fully elucidated.
  
  
  
  We performed whole genome sequencing with lung adenocarcinoma and corresponding non-tumor tissue to explore the genomic features of Xuanwei lung cancer. We used the Molecule Annotation System to determine and plot alterations in genes and signaling pathways.
  
  
  
  A total of 3 428 060 and 3 416 989 single nucleotide variants were detected in tumor and normal genomes, respectively. After comparison of these two genomes, 977 high-confidence somatic single nucleotide variants were identified. We observed a remarkably high proportion of C·G-A·T transversions. HECTD4, RCBTB2, KLF15, and CACNA1C may be cancer-related genes. Nine copy number variations increased in chromosome 5 and one in chromosome 7. The novel junctions were detected via clustered discordant paired ends and 1955 structural variants were discovered. Among these, we found 44 novel chromosome structural variations. In addition, EGFR and CACNA1C in the mitogen-activated protein kinase signaling pathway were mutated or amplified in lung adenocarcinoma tumor tissue.
  
  
  
  We obtained a comprehensive view of somatic alterations of Xuanwei lung adenocarcinoma. These findings provide insight into the genomic landscape in order to further learn about the progress and development of Xuanwei lung adenocarcinoma.
authors.affiliation: Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China.|Yunnan Institute of Diagnosis, Kunming, China.|Yunnan Key Laboratory of Laboratory Medicine, Kunming, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Wang
authors.affiliation: Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China.|Yunnan Institute of Diagnosis, Kunming, China.|Yunnan Key Laboratory of Laboratory Medicine, Kunming, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China.|Yunnan Institute of Diagnosis, Kunming, China.|Yunnan Key Laboratory of Laboratory Medicine, Kunming, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Duan
authors.affiliation: Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China.|Yunnan Institute of Diagnosis, Kunming, China.|Yunnan Key Laboratory of Laboratory Medicine, Kunming, China.
authors.forename: Huifei
authors.initials: H
authors.lastname: Wu
authors.affiliation: Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China.|Yunnan Institute of Diagnosis, Kunming, China.|Yunnan Key Laboratory of Laboratory Medicine, Kunming, China.
authors.forename: Qiuyue
authors.initials: Q
authors.lastname: Xu
authors.affiliation: Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China.|Yunnan Institute of Diagnosis, Kunming, China.|Yunnan Key Laboratory of Laboratory Medicine, Kunming, China.
authors.forename: Yanliang
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D000230:Adenocarcinoma / Q000139:chemically induced / Q000235:genetics*; D000077192:Adenocarcinoma of Lung; D000328:Adult; D002681:China; D003032:Coal Mining; D059472:Exome; D053263:Gene Regulatory Networks; D020022:Genetic Predisposition to Disease; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008175:Lung Neoplasms / Q000139:chemically induced / Q000235:genetics*; D008297:Male; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*
keywords: 
  Lung adenocarcinoma; single nucleotide variants; somatic mutations; whole genome sequencing