title: Plasma circulating tumor DNA as an alternative to metastatic biopsies for mutational analysis in breast cancer.
abstract: BACKGROUND
  Molecular screening programs use next-generation sequencing (NGS) of cancer gene panels to analyze metastatic biopsies. We interrogated whether plasma could be used as an alternative to metastatic biopsies.
  
  
  METHODS
  The Ion AmpliSeq™ Cancer Hotspot Panel v2 (Ion Torrent), covering 2800 COSMIC mutations from 50 cancer genes was used to analyze 69 tumor (primary/metastases) and 31 plasma samples from 17 metastatic breast cancer patients. The targeted coverage for tumor DNA was ×1000 and for plasma cell-free DNA ×25 000. Whole blood normal DNA was used to exclude germline variants. The Illumina technology was used to confirm observed mutations.
  
  
  RESULTS
  Evaluable NGS results were obtained for 60 tumor and 31 plasma samples from 17 patients. When tumor samples were analyzed, 12 of 17 (71%, 95% confidence interval (CI) 44% to 90%) patients had ≥1 mutation (median 1 mutation per patient, range 0-2 mutations) in either p53, PIK3CA, PTEN, AKT1 or IDH2 gene. When plasma samples were analyzed, 12 of 17 (71%, 95% CI: 44-90%) patients had ≥1 mutation (median 1 mutation per patient, range 0-2 mutations) in either p53, PIK3CA, PTEN, AKT1, IDH2 and SMAD4. All mutations were confirmed. When we focused on tumor and plasma samples collected at the same time-point, we observed that, in four patients, no mutation was identified in either tumor or plasma; in nine patients, the same mutations was identified in tumor and plasma; in two patients, a mutation was identified in tumor but not in plasma; in two patients, a mutation was identified in plasma but not in tumor. Thus, in 13 of 17 (76%, 95% CI 50% to 93%) patients, tumor and plasma provided concordant results whereas in 4 of 17 (24%, 95% CI 7% to 50%) patients, the results were discordant, providing complementary information.
  
  
  CONCLUSIONS
  Plasma can be prospectively tested as an alternative to metastatic biopsies in molecular screening programs.
authors.affiliation: Breast Cancer Translational Research Laboratory J.C. Heuson, Université Libre de Bruxelles, Institut Jules Bordet, Brussels.
authors.forename: F
authors.initials: F
authors.lastname: Rothé
authors.affiliation: OncoDNA, Gosselies, KU Leuven, Leuven.
authors.forename: J-F
authors.initials: JF
authors.lastname: Laes
authors.affiliation: Laboratory of Translational Genetics, KU Leuven, Leuven; Vesalius Research Center, VIB, Leuven, Belgium.
authors.forename: D
authors.initials: D
authors.lastname: Lambrechts
authors.affiliation: Laboratory of Translational Genetics, KU Leuven, Leuven; Vesalius Research Center, VIB, Leuven, Belgium.
authors.forename: D
authors.initials: D
authors.lastname: Smeets
authors.affiliation: Breast Cancer Translational Research Laboratory J.C. Heuson, Université Libre de Bruxelles, Institut Jules Bordet, Brussels.
authors.forename: D
authors.initials: D
authors.lastname: Vincent
authors.affiliation: Breast Cancer Translational Research Laboratory J.C. Heuson, Université Libre de Bruxelles, Institut Jules Bordet, Brussels.
authors.forename: M
authors.initials: M
authors.lastname: Maetens
authors.affiliation: Breast Cancer Translational Research Laboratory J.C. Heuson, Université Libre de Bruxelles, Institut Jules Bordet, Brussels.
authors.forename: D
authors.initials: D
authors.lastname: Fumagalli
authors.affiliation: Department of Biostatistic and Epidemiology, Gustave Roussy, Univ. Paris-Sud, Villejuif, France.
authors.forename: S
authors.initials: S
authors.lastname: Michiels
authors.affiliation: Department of Radiology, Université Libre de Bruxelles, Institut Jules Bordet, Brussels.
authors.forename: S
authors.initials: S
authors.lastname: Drisis
authors.affiliation: Department of Radiology, Université Libre de Bruxelles, Institut Jules Bordet, Brussels.
authors.forename: C
authors.initials: C
authors.lastname: Moerman
authors.affiliation: OncoDNA, Gosselies, KU Leuven, Leuven.
authors.forename: J-P
authors.initials: JP
authors.lastname: Detiffe
authors.affiliation: Department of Pathology, Université Libre de Bruxelles, Institut Jules Bordet, Brussels.
authors.forename: D
authors.initials: D
authors.lastname: Larsimont
authors.affiliation: Department of Medical Oncology, Université Libre de Bruxelles, Institut Jules Bordet, Brussels.
authors.forename: A
authors.initials: A
authors.lastname: Awada
authors.affiliation: Department of Medical Oncology, Université Libre de Bruxelles, Institut Jules Bordet, Brussels.
authors.forename: M
authors.initials: M
authors.lastname: Piccart
authors.affiliation: Breast Cancer Translational Research Laboratory J.C. Heuson, Université Libre de Bruxelles, Institut Jules Bordet, Brussels; Department of Medical Oncology, Université Libre de Bruxelles, Institut Jules Bordet, Brussels. Electronic address: michail.ignatiadis@bordet.be.
authors.forename: C
authors.initials: C
authors.lastname: Sotiriou
authors.affiliation: Breast Cancer Translational Research Laboratory J.C. Heuson, Université Libre de Bruxelles, Institut Jules Bordet, Brussels; Department of Medical Oncology, Université Libre de Bruxelles, Institut Jules Bordet, Brussels.
authors.forename: M
authors.initials: M
authors.lastname: Ignatiadis
mesh_terms: D000328:Adult; D001706:Biopsy; D001943:Breast Neoplasms / Q000097:blood* / Q000235:genetics*; D058534:Class I Phosphatidylinositol 3-Kinases; D004252:DNA Mutational Analysis; D004273:DNA, Neoplasm / Q000097:blood* / Q000302:isolation & purification; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007521:Isocitrate Dehydrogenase / Q000235:genetics; D008875:Middle Aged; D009362:Neoplasm Metastasis; D009360:Neoplastic Cells, Circulating; D051059:PTEN Phosphohydrolase / Q000235:genetics; D019869:Phosphatidylinositol 3-Kinases / Q000235:genetics; D051057:Proto-Oncogene Proteins c-akt / Q000235:genetics; D016159:Tumor Suppressor Protein p53 / Q000235:genetics
chemical_list: D058534:Class I Phosphatidylinositol 3-Kinases; D004273:DNA, Neoplasm; D007521:Isocitrate Dehydrogenase; D051059:PTEN Phosphohydrolase; D019869:Phosphatidylinositol 3-Kinases; D051057:Proto-Oncogene Proteins c-akt; D016159:Tumor Suppressor Protein p53; C495901:TP53 protein, human; C538784:IDH2 protein, human; C484760:PIK3CA protein, human; C494918:AKT1 protein, human; C494929:PTEN protein, human
keywords: breast cancer; circulating tumor DNA; liquid biopsy; targeted gene sequencing