DNA copy number variant is a DNA segment in which copy-number differences have been found by comparison of reference genomes. DNA copy number variants have been studied for prognostic/diagnostic biomarkers, tumor classifications, tumor progression markers, and so on. However, there was no paper to classify tumors using combined analysis of DNA copy number variants and gene expression data based on pathway analysis. We introduced new features which have classification power from DNA copy number variants based on pathway analysis. Also, we confirmed that human breast cancer samples have specific DNA copy number pattern related with gene ER. From this result, we found that combined analysis of DNA copy number variants and gene expression profiles improved the accuracy of human breast cancer classification.