Whole genome sequence analysis reveals intratumoral heterogeneity in dissemination of breast cancer to lymph nodes

Background: Intratumoral heterogeneity may help drive resistance to targeted therapies in cancer. In breast cancer, the presence of nodal metastases is a key indicator of poorer overall survival. The aim of this study was to identify somatic genetic alterations in early dissemination of breast cancer by whole genome next generation sequencing (NGS) of a primary breast tumor, matched locally-involved axillary lymph node and healthy normal DNA from blood. Methods: Whole genome NGS was performed on 12µg (range 11.1-13.3µg) of DNA isolated from fresh-frozen primary breast tumor, axillary lymph node and peripheral blood following the DNA nanoball sequencing protocol. Single nucleotide variants, insertions, deletions, and substitutions were identified through a bioinformatic pipeline and compared to CIN25, a key set of genes associated with tumor metastasis. Results: Whole genome sequencing revealed overlapping variants between the tumor and node, but also variants that were unique to each. Novel mutations unique to the node included two CIN25 targets, TGIF2 and CCNB2, related to transcription cyclin activity and chromosomal stability, and a frameshift in PDS5B, which is required for accurate sister chromatid segregation during cell division. Conclusion: These data provide evidence that primary tumor and early nodal metastasis have largely overlapping somatic genetic alterations. There were very few mutations unique to the involved node, but results suggest that clonal evolution is an early event in the development of metastatic spread and that multiple clones can persist in early dissemination to the node.