Targeted next-generation sequencing detects a high frequency of potentially actionable mutations in metastatic breast cancers

Exp Mol Pathol. 2016 Jun;100(3):421-5. doi: 10.1016/j.yexmp.2016.04.002. Epub 2016 Apr 16.


Background: Metastatic breast cancer is a genetically heterogeneous disease and effective therapies for advanced stage disease are limited.

Methods: In this study, distant metastases of 22 formalin-fixed, paraffin-embedded (FFPE) breast cancer samples were sequenced using the Ion Torrent PGM and the 50 gene AmpliSeq Cancer Hotspot Panel v2 from 10ng of extracted DNA using 318 chips. Data analysis was performed with the Ion Torrent Variant Caller Plugin (hg19) and Golden Helix's SVS software for annotation and prediction of the significance of the variants.

Results: All patients were female with a median age of 61years (range 37-85years). Metastatic sites included liver (n=6, 27%), skin (n=5, 23%), brain (n=4, 18%), lymph node (n=3, 14%), lung (n=2, 9%), retroperitoneum (n=1, 4.5%), and colon (n=1, 4.5%). Overall, 28 variants in 11 genes were observed. Five (23%) samples showed no alterations and 17 (77%) showed at least one potentially biologically significant variant (BSV) defined as having FDA-approved drugs or clinical trials evaluating their significance. BSVs included mutations in the following genes: TP53 (n=8), APC (n=4), PIK3CA (n=5), MET (n=2), ERBB2 (n=2), AKT1 (n=1), CDKN2A (n=1), KRAS (n=1), and FGFR3 (n=1).

Conclusions: Potentially actionable mutations were identified in the majority of breast cancer metastases. Evaluating metastatic breast tumors using a NGS approach provides a better understanding of the mechanisms behind tumor progression and evolution and also identifies additional potentially beneficial therapeutic targets for patient management or eligibility for clinical trials.

Keywords: Breast cancer; Metastatic cancer; Next-generation sequencing; Somatic mutations; Targeted therapy.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenomatous Polyposis Coli Protein / genetics
  • Adult
  • Aged
  • Aged, 80 and over
  • Breast Neoplasms / genetics*
  • Breast Neoplasms / pathology
  • Class I Phosphatidylinositol 3-Kinases
  • Female
  • Genetic Predisposition to Disease / genetics*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Middle Aged
  • Mutation*
  • Neoplasm Metastasis
  • Phosphatidylinositol 3-Kinases / genetics
  • Proto-Oncogene Proteins c-met / genetics
  • Receptor, ErbB-2 / genetics
  • Tumor Suppressor Protein p53 / genetics


  • APC protein, human
  • Adenomatous Polyposis Coli Protein
  • TP53 protein, human
  • Tumor Suppressor Protein p53
  • Phosphatidylinositol 3-Kinases
  • Class I Phosphatidylinositol 3-Kinases
  • PIK3CA protein, human
  • ERBB2 protein, human
  • MET protein, human
  • Proto-Oncogene Proteins c-met
  • Receptor, ErbB-2