Comparison of Genomic Copy Number Variations Among Breast Cancer Subtypes

Objective To compare genomic copy number variations (CNVs) among different subtypes of breast cancer and analyze specific CNVs in each subtype.

Methods AIMS software was used for genotype breast cancer (BasL, Her2, LumA and LumB), and GISTIC2.0 software was used to analyze genome-wide CNVs in tumor tissues from TCGA. We collected and analyzed the information and samples of 324 cases of invasive breast cancer admitted to Jiangmen Central Hospital(JMCH). Fluorescence quantitative PCR was used to detect the CNV of ERBB2, TFDP1, MIR148B, CCND1, MDM2 and MIR139 genes in the tumor tissues, to verify TCGA analysis.

Results 13q34 was specifically amplified and 12q13.13 was specifically deleted in BasL-type breast cancer. The 17q12 was specifically amplified in Her2 type. The 12q15 was specifically amplified and 11q13.4 was specifically deleted in LumB type, but LumA type had no specific amplification or deletion of chromosome region. The proportion of TFDP1 amplification or MIR148B deletion in BasL type were 57.8% (TCGA) and 71.4% (JMCH), which were significantly higher than other subtypes (P < 0.001). The proportion of ERBB2 amplification of Her2 type were 55.2% (TCGA) and 86.7% (JMCH), which were significantly higher than other subtypes (P < 0.001). The proportion of LumB type with CCND1 or MDM2 amplification or MIR139 deletion were 47.6% (TCGA) and 61.8% (JMCH), which were significantly higher than other subtypes (P < 0.05).

Conclusion At the CNV level of breast cancer, Her2 type is characterized by the amplification of ERBB2, BasL type is characterized by the amplification of TFDP1 or the deletion of MIR148B, LumB type is characterized by the amplification of CCND1 or MDM2 or the deletion of MIR139, but LumA type lacks specific CNV characteristics.