title: Genome-wide copy number variation pattern analysis and a classification signature for non-small cell lung cancer.
abstract: The accurate classification of non-small cell lung carcinoma (NSCLC) into lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) is essential for both clinical practice and lung cancer research. Although the standard WHO diagnosis of NSCLC on biopsy material is rapid and economic, more than 13% of NSCLC tumors in the USA are not further classified. The purpose of this study was to analyze the genome-wide pattern differences in copy number variations (CNVs) and to develop a CNV signature as an adjunct test for the routine histopathologic classification of NSCLCs. We investigated the genome-wide CNV differences between these two tumor types using three independent patient datasets. Approximately half of the genes examined exhibited significant differences between LUAD and LUSC tumors and the corresponding non-malignant tissues. A new classifier was developed to identify signature genes out of 20 000 genes. Thirty-three genes were identified as a CNV signature of NSCLC. Using only their CNV values, the classification model separated the LUADs from the LUSCs with an accuracy of 0.88 and 0.84, respectively, in the training and validation datasets. The same signature also classified NSCLC tumors from their corresponding non-malignant samples with an accuracy of 0.96 and 0.98, respectively. We also compared the CNV patterns of NSCLC tumors with those of histologically similar tumors arising at other sites, such as the breast, head, and neck, and four additional tumors. Of greater importance, the significant differences between these tumors may offer the possibility of identifying the origin of tumors whose origin is unknown.
authors.affiliation: School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China.
authors.forename: Zhe-Wei
authors.initials: ZW
authors.lastname: Qiu
authors.affiliation: School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China.
authors.forename: Jia-Hao
authors.initials: JH
authors.lastname: Bi
authors.affiliation: Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA.|Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA.
authors.forename: Adi F
authors.initials: AF
authors.lastname: Gazdar
authors.affiliation: School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China.|Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA.
authors.forename: Kai
authors.identifier: 0000-0001-9195-6160
authors.initials: K
authors.lastname: Song
mesh_terms: D002289:Carcinoma, Non-Small-Cell Lung / Q000145:classification / Q000175:diagnosis / Q000453:epidemiology* / Q000235:genetics*; D056915:DNA Copy Number Variations / Q000235:genetics*; D055106:Genome-Wide Association Study; D006801:Humans; D008175:Lung Neoplasms / Q000145:classification / Q000175:diagnosis / Q000453:epidemiology* / Q000235:genetics*; D009369:Neoplasms / Q000235:genetics