The amplified oncogenes identified in metastatic tumor specimens included genes known to be frequently amplified in breast cancers such as PIK3CA and MYC. Pathway analysis of gene sets comprising amplifications showed significant enrichment for the Stem Cell Pluripotency pathway, highlighting our discovery of recurring significant amplification of SOX2, PIK3CA, NTRK1, GNAS, CTNNB1, and FGFR1 in the samples analyzed. Here, SOX2 is linked to breast carcinoma.