Copy number profiling of synchronous primary and metastasis of invasive breast cancer

We sought to define the repertoire of genetic alterations in synchronous primary and metastasis of invasive breast cancer In this study, we subjected up to two anatomically distinct diagnostic biopsies of primary breast cancers and up to two anatomically distinct diagnostic biopsies of their synchronous metastatic deposits from patients who presented with de novo metastatic disease and who had not received any local or systemic therapy to gene copy number analysis and high-depth whole exome sequencing. DNA from the second diagnostic biopsy of the primary breast cancer and the second diagnostic biopsy of the metastatic deposit for the cases for which samples were available was hybridized on the molecular inverse probe assay using the OncoScan® FFPE Express custom service (Affymetrix, Santa Clara, CA).