title: Identification of mutant genes with high-frequency, high-risk, and high-expression in lung adenocarcinoma.
abstract: BACKGROUND
  To identify mutant genes with high-frequency-risk-expression between lung adenocarcinoma and normal samples.
  
  
  METHODS
  The ribonucleic acid RNA-Seq data GSE34914 and GSE37765 were downloaded from the Gene Expression Omnibus database, including 12 lung adenocarcinoma samples and six controls. All RNA-Seq reads were processed and the gene-expression level was calculated. Single nucleotide variation (SNV) was analyzed and the locations of mutant sites were recorded. In addition, the frequency and risk-level of mutant genes were calculated. Gene Ontology (GO) functional analysis was performed. The reported cancer genes were searched in tumor suppressor genes, Cancer Genes, and the Catalogue of Somatic Mutations in Cancer (COSMIC) database.
  
  
  RESULTS
  The SNV annotations of somatic mutation sites showed that 70% of mutation sites in the exon region occurred in the coding sequence (CDS). Thyroid hormone receptor interactor (TRIP)12 was identified with the highest frequency. A total of 118 mutant genes with high frequency and high-risk were selected and significantly enriched into several GO terms. No base mutation of cyclin C (CCNC) or RAB11A was recorded. At fragments per kilobase per million reads (FPKM) ≥ 56.5, reported tumor suppressor genes catenin (cadherin-associated protein), delta (CTNND)1, dual specificity phosphatase (DUSP)6, malate dehydrogenase (MDH)1 and RNA binding motif protein (RBM)5, were identified. Notably, signal transducer and activator of transcription 2 (STAT2) was the only transcription factor (TF) with high-risk mutation and its expression was detected.
  
  
  CONCLUSIONS
  For the mutant genes with high-frequency-risk-expression, CTNND1, DUSP6, MDH1 and RBM5 were identified. TRIP12 might be a potential cancer-related gene, and expression of TF STAT2 with high-risk was detected. These mutant gene candidates might promote the development of lung adenocarcinoma and provide new diagnostic potential targets for treatment.
authors.affiliation: Department of Oncology, Tongji Hospital, Tongji University School of Medicine Shanghai, China.
authors.forename: Guiyuan
authors.initials: G
authors.lastname: Li
authors.affiliation: Department of Oncology, Tongji Hospital, Tongji University School of Medicine Shanghai, China.
authors.forename: Shengming
authors.initials: S
authors.lastname: Yi
authors.affiliation: Department of Clinical Laboratory Medicine, Tongji Hospital, Tongji University School of Medicine Shanghai, China.
authors.forename: Fan
authors.initials: F
authors.lastname: Yang
authors.affiliation: Department of Thoracic Cardiovascular Surgery, Tongji Hospital, Tongji University School of Medicine Shanghai, China.
authors.forename: Yongxin
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Department of Thoracic Cardiovascular Surgery, Tongji Hospital, Tongji University School of Medicine Shanghai, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Ji
authors.affiliation: Department of Thoracic Cardiovascular Surgery, Tongji Hospital, Tongji University School of Medicine Shanghai, China.
authors.forename: Jianzhi
authors.initials: J
authors.lastname: Cai
authors.affiliation: Department of Thoracic Cardiovascular Surgery, Tongji Hospital, Tongji University School of Medicine Shanghai, China.
authors.forename: Yunqing
authors.initials: Y
authors.lastname: Mei
keywords: High expression; RNA-Seq; high frequency; high-risk; lung adenocarcinoma; mutant gene