Screening of lung cancer related SNPs and CNVs with SNP microarrays

The objective of this study was to analyze the lung cancer related SNPs (Single Nucleotide Polymorphisms) and CNVs (copy number variations) with SNP microarrays, as well as to identify the CNV related genes and functions.

The GSE29172 SNP array data were downloaded from Gene Expression Omnibus, including 100%, 30%, 50%, 70% cancer samples, and the mixture is matched blood. The PennCNV software was applied to analyze SNP arrays, and then the related SNPs and CNVs in different degrees of cancer samples were identified. Furthermore, according to the CNVs related chromosome loci, their corresponding genes were selected from University of California Santa genome browser database. Finally, the corresponding genes were performed Gene Ontology and pathway enrichment analysis using DAVID.

The numbers of SNPs in four different degrees of cancer samples were 4299, 1108, 483 and 417, respectively. Meanwhile, most of these SNPs distributed on chromosome 1, 3, 7, 11, 15, 17 and 21. Compared with the known SNPs, all the SNPs identified in our research were novel SNPs associated with lung cancer. The CNVs related genes, ABCG8 and ABCG5 were identified in clusters; meanwhile, the KO05223 pathway and Forkhead gene were screened out in pathway enrichment analysis.

The lung cancer related SNPs and CNVs were analyzed and their corresponding genes were identified. Furthermore, by analyzing the functions of these genes, the researchers may explore the relationship between genetic mutation and the initiation and development of lung cancer.