Open AccessIdentification of mutant genes with high‐frequency, high‐risk, and high‐expression in lung adenocarcinoma
Author(s) -
Li Guiyuan,
Yi Shengming,
Yang Fan,
Zhou Yongxin,
Ji Qiang,
Cai Jianzhi,
Mei Yunqing
Publication year - 2014
Publication title -
thoracic cancer
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.823
H-Index - 28
eISSN - 1759-7714
pISSN - 1759-7706
DOI - 10.1111/1759-7714.12080
Subject(s) - gene , biology , mutant , genetics , mutation frequency , germline mutation , exon , microbiology and biotechnology , mutation , cancer research
Background To identify mutant genes with high‐frequency‐risk‐expression between lung adenocarcinoma and normal samples. Methods The ribonucleic acid RNA ‐ S eq data GSE 34914 and GSE 37765 were downloaded from the G ene E xpression O mnibus database, including 12 lung adenocarcinoma samples and six controls. All RNA ‐ S eq 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. G ene O ntology ( GO) functional analysis was performed. The reported cancer genes were searched in tumor suppressor genes, C ancer G enes, 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 ( STAT 2) was the only transcription factor ( TF ) with high‐risk mutation and its expression was detected. Conclusion For the mutant genes with high‐frequency‐risk‐expression, CTNND 1, DUSP 6, MDH 1 and RBM 5 were identified. TRIP 12 might be a potential cancer‐related gene, and expression of TF STAT 2 with high‐risk was detected. These mutant gene candidates might promote the development of lung adenocarcinoma and provide new diagnostic potential targets for treatment.