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Clinical implications of routine genomic mutation sequencing in PIK3CA/AKT1 and KRAS/NRAS/BRAF in metastatic breast cancer



There is increasing interest in the molecular profiling of tumour tissues in order to investigate alternative breast cancer (BC) therapies. However, the impact of genomic screening for druggable mutations with targeted gene panel sequencing (TGPS) in routine practice remains controversial.


This is a retrospective analysis of data from a genomic screening programme at our institution, in which we performed simplified TGPS for mutations in PIK3CA, AKT1, KRAS, NRAS, and BRAF in order to select patients for targeted therapy clinical trials. The genomes of archived samples of primary (PT) and/or metastatic (MT) tumours from advanced BC patients were analysed with MassARRAY technology (Sequenom MassARRAY, OncoCarta v1.0). The level of PTEN expression was assessed by immunohistochemistry. The primary endpoint was to identify the proportion of BC patients with PI3 K and MAPK alterations who were included in clinical trials using targeted therapies against these pathways.


Two hundred and fifteen metastatic BC patients (65 PT and 168 MT) were included. Fifty-two patients (24.19 %) were enrolled in tailored clinical trials, of whom 29 (55.77, 13.49 % of all patients screened) harboured mutations targeted by the study drug. Moreover, 12 wild-type patients out of the 215 (5.58 %) were included in the clinical trials for which mutation analysis was an inclusion criteria. All the patients received drugs targeting the PI3K-AKT pathway and only two were given combinations directed against the PI3K and MAPK pathways. PI3KCA mutations were present in 33.7 % (61/181) of the patients, 45.83 % in PTs and 29.32 % in MTs. AKT1 mutations were detected in 5.48 % (8/146) of patients and PTEN loss in 34.67 % (52/150). KRAS, NRAS, and BRAF mutations were present in 12.06, 5.67, and 3.18 % of patients, respectively.


Genomic screening with a simplified TGPS is feasible, and was used to identify 13.49 % of patients who were included in clinical trials using targeted therapy against the mutations they harboured; PI3KCA mutations were the most frequent aberration in our series.

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Fig. 1
Fig. 2



Breast cancer,


Targeted gene panel sequencing,


Primary tumour,


Metastatic tumour,




Oestrogen receptor


Human epidermal growth factor receptor 2


Next generation sequencing


Phosphoinositide 3-kinase


Mitogen-activated protein kinase


Triple-negative breast cancer


Luminal breast cancer


Formalin-fixed paraffin-embedded


Fluorescence in situ hybridisation


Epidermal growth factor receptor


Haematoxylin and eosin


Progesterone receptor


Shrimp alkaline phosphatase


Cancer genome ATLAS network


Fibroblast growth factor receptor


V-akt murine thymoma viral oncogene homolog 1


Kirsten rat sarcoma viral oncogene homolog


Neuroblastoma ras viral (V-ras) oncogene homolog


B-raf proto-oncogene, serine/threonine kinase


Phosphatase and tensin homolog


Phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha


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This study was supported by grants from the Generalitat Valenciana (Prometeo 2015/005), the Ministerio de Salud Carlos III (PI12/02,767 and PI13/00606), and European FEDER Funds. MTM was funded by the Ministerio de Salud Carlos III on a Rio Hortega contract (CM12/00264). GR and MI-V were funded by the Ministerio de Salud Carlos III on a Miquel Servet II (CPII14-00013) and Sara Borell contract (CD15/00153), respectively. We would like to thank the expert personnel at the Genotyping and Epigenetics Laboratory at the Central Biomedical Research Unit (Unidad Central de Investigación de Medicina; UCIM) at the University of Valencia.

Author contributions

Study conception and design: ALL, AC, JAPF, and JMC. Data acquisition: OB, GR, and MI-V. Data analysis and interpretation: all authors. All the authors were also involved in drafting or critically revising the article for important intellectual content, and they approved the final version of the manuscript.

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Corresponding authors

Correspondence to Juan Miguel Cejalvo or Ana Lluch.

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Conflict of interest

The authors state that they have no potential conflict of interest.

Ethics approval

This research was performed in accordance with the Declaration of Helsinki and was approved by the ethics committee at the Hospital Clinico Universitario, Valencia.

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Cejalvo, J.M., Pérez-Fidalgo, J.A., Ribas, G. et al. Clinical implications of routine genomic mutation sequencing in PIK3CA/AKT1 and KRAS/NRAS/BRAF in metastatic breast cancer. Breast Cancer Res Treat 160, 69–77 (2016).

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  • Breast cancer
  • Genomic mutation sequencing
  • Clinical trials
  • PI3K pathway