A Case Study of Precision Medicine: Next Generation Sequencing Compared with Oncoscan in a Patient with Breast Cancer in Kentucky

Purpose: Precision medicine of tumors is designed to tailor treatment combinations to individual patients, targeting specific genotypes with corresponding inhibitors. The purpose of this study was to determine whether genotype predicted target gene expression-a critical parameter for treatment-and to test whether alternate modes of gene amplification could affect gene expression. Patients and methods: The cohort consisted of patients in Kentucky with recurrent breast cancer who were analyzed by nextgeneration sequencing. Tumors with amplifications in CCND1, AURKA, and MYC were then stained by immunohistochemistry. We subsequently selected a patient with triple-negative breast cancer for analysis by FISH, immunohistochemistry and OncoScan genome-wide copy number array. Results: The extent of CCND1 staining was highly variable between tumors. In one patient with heterogeneous CCND1 staining, the CCND1 gene was maintained as an extra-chromosomal DNA (ecDNA), which changed with both DNA copy number (increased) and expression (decreased) during metastatic progression. The tumor DNA was then analyzed by OncoScan array, which confirmed an increased CCND1 copy number with treatment and mapped the ecDNA size. Elsewhere in the genome, VAV3 (encoding a RhoA and RhoG guanidine exchange factor) increased in copy number and expression during metastasis. In addition, several actionable genes were detected by OncoScan that were not reported by nextgeneration sequencing. Conclusion: NGS reported numerous tumors with CCND1 gene amplification, but the proportion of cells with CCND1 expression was highly variable. Genetic factors, such as mode of amplification, may contribute to expression patterns in tumors.