Mutational profiles in triple-negative breast cancer defined by ultradeep multigene sequencing show high rates of PI3K pathway alterations and clinically relevant entity subgroup specific differences

// Mark Kriegsmann 1 , Volker Endris 1,2 , Thomas Wolf 1 , Nicole Pfarr 1 , Albrecht Stenzinger 1 , Sibylle Loibl 3 , Carsten Denkert 4,6 , Andreas Schneeweiss 5,6 , Jan Budczies 4,6 , Peter Sinn 1 and Wilko Weichert 1,5,6 1 Institute of Pathology, University of Heidelberg, Germany 2 German Cancer Research Center, Heidelberg, Germany 3 German Breast Group, Neu-Isenburg, Germany 4 Institute of Pathology, University Hospital Charité Berlin, Germany 5 National Center for Tumor Diseases, Heidelberg, Germany 6 German Cancer Consortium (DKTK), Germany Correspondence: Mark Kriegsmann, email: // Keywords : triple-negative breast cancer, next generation sequencing, immunohistochemistry, mutation profiling Received : July 09, 2014 Accepted : September 15, 2014 Published : September 16, 2014 Abstract Mutational profiling of triple-negative breast cancer (TNBC) by whole exome sequencing (WES) yielded a landscape of genomic alterations in this tumor entity. However, the clinical significance of these findings remains enigmatic. Further, integration of WES in routine diagnostics using formalin-fixed paraffin-embedded (FFPE) material is currently not feasible. Therefore, we designed and validated a breast cancer specific gene panel for semiconductor-based sequencing comprising 137 amplicons covering mutational hotspots in 44 genes and applied this panel on a cohort of 104 well-characterized FFPE TNBC with complete clinical follow-up. TP53 mutations were present in more than 80% of cases. PI3K pathway alterations (29.8%) comprising mainly PIK3CA mutations (22.1%) but also mutations and/or amplifications/deletions in other PI3K-associated genes (7.7%) were far more frequently observed, when compared to WES data. Alterations in MAPK signaling genes (8.7%) and cell-cycle regulators (14.4%) were also frequent. Mutational profiles were linked to TNBC subgroups defined by morphology and immunohistochemistry. Alterations in cell-cycle pathway regulators were linked with better overall (p=0.053) but not disease free survival. Taken together, we could demonstrate that breast cancer targeted hotspot sequencing is feasible in a routine setting and yields reliable and clinically meaningful results. Mutational spectra were linked to clinical and immunohistochemically defined parameters.