Abstract
BackgroundCancer is a heterogeneous disease with many genetic variations. Lines of evidence have shown copy number variations (CNVs) of certain genes are involved in development and progression of many cancers through the alterations of their gene expression levels on individual or several cancer types. However, it is not quite clear whether the correlation will be a general phenomenon across multiple cancer types.MethodsIn this study we applied a bioinformatics approach integrating CNV and differential gene expression mathematically across 1025 cell lines and 9159 patient samples to detect their potential relationship.ResultsOur results showed there is a close correlation between CNV and differential gene expression and the copy number displayed a positive linear influence on gene expression for the majority of genes, indicating that genetic variation generated a direct effect on gene transcriptional level. Another independent dataset is utilized to revalidate the relationship between copy number and expression level. Further analysis show genes with general positive linear influence on gene expression are clustered in certain disease-related pathways, which suggests the involvement of CNV in pathophysiology of diseases.ConclusionsThis study shows the close correlation between CNV and differential gene expression revealing the qualitative relationship between genetic variation and its downstream effect, especially for oncogenes and tumor suppressor genes. It is of a critical importance to elucidate the relationship between copy number variation and gene expression for prevention, diagnosis and treatment of cancer.
Highlights
Cancer is a heterogeneous disease with many genetic variations
Differential gene expression is highly associated with copy number variation (CNV) across multiple cancer types and cancer cell lines It is known that CNV is related to alteration on gene expression
Integrated analysis of CNV and differential gene expression was performed across 31 cancer types and 2 cancer cell lines resources (Additional file 2: Table S1)
Summary
Lines of evidence have shown copy number variations (CNVs) of certain genes are involved in development and progression of many cancers through the alterations of their gene expression levels on individual or several cancer types. It is not quite clear whether the correlation will be a general phenomenon across multiple cancer types. Genetic structural variation in the human genome can be present in many forms, ranging from single nucleotide polymorphisms (SNPs) to large chromosome aberrance [1]. Dong et al [16] analyzed the copy number alterations and differentially transcribed genes in esophageal cancer and observed a
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