Abstract P4-01-14: Whole exome sequencing of circulating and disseminated tumour cells in patients with metastatic breast cancer
Authors: Peeters Dieter JE , Op De Beeck Ken , Brouwer Anja , Vandeweyer Geert , Pauwels Patrick , Peeters Marc , Vermeulen Peter B , van Dam Peter A , Van Laere Steven J , Van Camp Guy , Dirix Luc Y 
Published: May 2015

Abstract
Introduction:
Circulating tumour cells (CTC) found in the blood of patients with cancer offer the potential to provide a repeatedly accessible source of tumour cells for the real-time assessment of tumour characteristics in patients with metastatic breast cancer (MBC). Questions remain to what extent CTC are truly representative of the actually present tumour mass in a patient at a specific moment in time and the molecular heterogeneity within the CTC population is only now being explored. Here, we report on the first results of an ongoing comparative study of mutation profiles of CTC and synchronously isolated disseminated tumour cells (DTC) from metastatic effusions or biopsies of solid metastases of patients with clinically progressive MBC.
Materials and methods:
For this project CTC are isolated from 7.5 ml blood samples of patients with MBC using the CellSearch system. CellSearch enriched CTC samples are subsequently further purified and sorted into several batches of 1-125 CTC per patient using the DEPArray system. DNA is isolated and amplified using the Ampli1 whole genome amplification (WGA) kit and subjected to whole exome paired-end sequencing (WES). DTC from metastatic effusions, fresh frozen tissue from solid metastases or the primary tumour, or - in patients with extremely high CTC counts (&gt;10.000/7.5 ml) - pooled CTC from the CellSearch Profile sample, are sequenced as a comparator for mutation profiles. DNA from the buffy coat of white blood cells are sequenced to enable somatic mutation analysis.
Results:
Eight samples of 1-125 CTC and a CellSearch Profile sample of one patient with MBC who had ca. 30.000 CTC/7.5 ml of blood (patient 1) and 4 CTC samples of 5-10 CTC, 2 temporally matched DTC samples of 10 and 20 DTC from a pleural effusion and a fresh frozen tissue sample of the primary tumour of a second patient (patient 2) have been sequenced so far. Average base coverages were 13.6x (patient 1) and 11.8x (patient 2) for CTC/DTC samples and 175x and 120x for the CellSearch profile sample (patient 1) and the primary tumour sample (patient 2) respectively. Between 29.64% and 53.57% of the exomes of amplification products of CTC/DTC DNA were uncovered, probably due to technical limitations of the WGA procedure. Overall, if adequately covered, good concordances were observed for variants identified with MuTect in 28 frequently mutated genes in breast cancer between samples of amplification products of 1-125 CTC and the CellSearch Profile sample of patient 1. In patient 2, the same H1047R PIK3CA mutation was identified in the primary tumour and all CTC and DTC samples. In-depth analyses of the full exome data are being conducted.
Discussion:
Our data provide insight into clinically relevant questions to what extent CTC reflect mutational profiles in temporally matched metastatic tumour cells, and – by analysing multiple CTC samples of the same patient – genetic heterogeneity between CTC in patients with MBC. Sample accrual and analysis is being expanded and updated results will be presented at the conference.
Citation Format: Dieter JE Peeters, Ken Op De Beeck, Anja Brouwer, Geert Vandeweyer, Patrick Pauwels, Marc Peeters, Peter B Vermeulen, Peter A van Dam, Steven J Van Laere, Guy Van Camp, Luc Y Dirix. Whole exome sequencing of circulating and disseminated tumour cells in patients with metastatic 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 P4-01-14.