Abstract PD3-7: Plasma circulating tumor DNA as an alternative to metastatic biopsies for mutational analyses in breast cancer
Authors: Ignatiadis Michail , Rothe Françoise , Laes Jean-François , Lambrechts Diether , Smeets Dominiek , Vincent Delphine , Maetens Marion , Fumagalli Debora , Michiels Stefan , Drisis Stylianos , Moerman Carine , Detiffe Jean-Pol , Larsimont Denis , Awada Ahmad , Piccart Martine , Sotiriou Christos 
Published: May 2015

Abstract
Background: Molecular screening programs are using next-generation sequencing (NGS) for cancer gene panels in metastatic biopsies. We interrogated whether plasma can be used as an alternative to metastatic biopsies.
Patients and methods: The Ion AmpliSeqTM Cancer Hotspot Panel v2 (Ion Torrent), covering approximately 2,800 COSMIC mutations from 50 cancer genes was used to analyze 70 primary and/or metastases and 29 plasma samples from 17 metastatic breast cancer patients. The targeted coverage for tissue DNA was 1000x and for plasma circulating DNA 25000x. Whole blood normal DNA was used to exclude germline variants. The Illumina technology was used for independent validation.
Results: Twelve patients had estrogen receptor (ER)+/ human epidermal growth factor receptor 2 (HER2)-, 1 ER+/HER2+, 2 ER-/HER2+ and 2 ER-/HER2- tumors. Evaluable NGS results were obtained for 61 primary/metastases and 29 plasma samples from 17 patients. When primary/metastases were analyzed, 12 of 17 patients had at least 1 mutation (median 1 mutation per patient, range 0-2) in either p53, PIK3CA, PTEN, AKT1 or IDH2 gene. When plasma was analyzed, 11 of 17 patients had at least 1 mutation (median 1 mutation per patient, range 0-2) in either p53, PIK3CA, PTEN, AKT1, IDH2 and SMAD4. All primary/metastases/plasma mutations were independently validated using the illumina technology. When we focused on metastases and plasma samples collected at the same time point, we observed that in 4 patients, no mutation was identified in either metastases or plasma, in 9 patients the same mutations were identified in metastases and plasma, in 2 patients a mutation was identified in metastases but not in plasma and in 2 patients a mutation was identified in plasma but not in metastases (Table 1). Thus, in 13 of 17 (76%) patients, metastases and plasma analysis provided concordant results whereas in 4 of 17 (24%) demonstated discordant results providing complementary information (Table 1). Conclusion: Plasma can be tested as an alternative tissue source in molecular screening programs.
Table Mutational status of synchronous metastatic biopsies and plasma samples analysed using the Ion AmpliSeqTM Cancer Hotspot Panel v2Patient IDGeneMutationMetastasis (MAF)Plasma (MAF)3PTENp.Q171EYES (27.5%)YES (25.9%)3SMAD4p.E394*NOYES (10.9%)4NONO6PIK3CAp.H1047RYES (20.5-47.7%)YES (4.6%)7TP53p.V274AYES (35.6-56.1%)YES (20.7%)8IDH2p.R140RYES (28.2)YES (0.5%)10PIK3CAp.H1047RYES (19.7%)NO11PIK3CAp.E453KYES (4.6-17.8%)YES (2.8%)11PIK3CAp.E453KYES (13.1-23%)YES (3.4%)14PIK3CAp.H1047RYES (24.8%)NO14PIK3CAp.H1047RYES (0-13.8%)YES (0.5%)16TP53p.Y103*YES (59.8-86.3%)YES (49%)17NONO19NONO20PIK3CAp.E545KNOYES (14.3%)30TP53p.M237KYES (27.6-50%)YES (51.8%)37TP53p.H193LYES (61.6-82.9%)YES (55.5%)38AKT1p.E17KYES (26-68.2%)YES (10%)38TP53p.R248WYES (23.6-56.8%)YES (5.9%)39TP53p.R136HYES (7.5%)NO40NONOMAF: Mutant allele frequency; For patients with multiple metastases samples at the same time point, the MAF range is provided. Patients 11 & 14 had 2 timepoints with synchronous metastases/plasma samples.
Citation Format: Michail Ignatiadis, Françoise Rothe, Jean-François Laes, Diether Lambrechts, Dominiek Smeets, Delphine Vincent, Marion Maetens, Debora Fumagalli, Stefan Michiels, Stylianos Drisis, Carine Moerman, Jean-Pol Detiffe, Denis Larsimont, Ahmad Awada, Martine Piccart, Christos Sotiriou. Plasma circulating tumor DNA as an alternative to metastatic biopsies for mutational analyses in breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr PD3-7.