Next Article in Journal
Detection of Colorectal Cancer and Advanced Adenoma by Liquid Biopsy (Decalib Study): The ddPCR Challenge
Next Article in Special Issue
Circulating miR-16-5p, miR-92a-3p, and miR-451a in Plasma from Lung Cancer Patients: Potential Application in Early Detection and a Regulatory Role in Tumorigenesis Pathways
Previous Article in Journal
Oncogenic Properties of the EBV ZEBRA Protein
Previous Article in Special Issue
Novel Gene Fusions in Glioblastoma Tumor Tissue and Matched Patient Plasma
Open AccessArticle

Shallow Whole-Genome Sequencing from Plasma Identifies FGFR1 Amplified Breast Cancers and Predicts Overall Survival

1
Division of Biotechnology, Servier Research Institute, 125, Chemin de ronde, 78290 Croissy Sur-seine, France
2
Department of Medical Oncology, Institut Curie, 26 rue d’Ulm, 75005 Paris, France
3
Circulating Tumor Biomarkers Laboratory, Institut Curie, PSL Research University, INSERM CIC 1428, 26 rue d’Ulm, 75005 Paris, France
4
Université de Paris, 75005 Paris, France
5
Division of Methodology and Valorisation of Data, Servier Research and Development Institute, 50 rue carnot, 92150 Suresnes, France
6
Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
7
BioTechMed-Graz, 8010 Graz, Austria
8
Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, 8010 Graz, Austria
*
Author to whom correspondence should be addressed.
The first two authors have contributed equally to this work.
Current address: Cancer Research UK Cambridge Centre, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Cancers 2020, 12(6), 1481; https://doi.org/10.3390/cancers12061481
Received: 14 April 2020 / Revised: 26 May 2020 / Accepted: 4 June 2020 / Published: 6 June 2020
(This article belongs to the Special Issue Liquid Biopsy in Cancer)
Background: Focal amplification of fibroblast growth factor receptor 1 (FGFR1) defines a subgroup of breast cancers with poor prognosis and high risk of recurrence. We sought to demonstrate the potential of circulating cell-free DNA (cfDNA) analysis to evaluate FGFR1 copy numbers from a cohort of 100 metastatic breast cancer (mBC) patients. Methods: Formalin-fixed paraffin-embedded (FFPE) tissue samples were screened for FGFR1 amplification by FISH, and positive cases were confirmed with a microarray platform (OncoscanTM). Subsequently, cfDNA was evaluated by two approaches, i.e., mFAST-SeqS and shallow whole-genome sequencing (sWGS), to estimate the circulating tumor DNA (ctDNA) allele fraction (AF) and to evaluate the FGFR1 status. Results: Tissue-based analyses identified FGFR1 amplifications in 20/100 tumors. All cases with a ctDNA AF above 3% (n = 12) showed concordance for FGFR1 status between tissue and cfDNA. In one case, we were able to detect a high-level FGFR1 amplification, although the ctDNA AF was below 1%. Furthermore, high levels of ctDNA indicated an association with unfavorable prognosis based on overall survival. Conclusions: Screening for FGFR1 amplification in ctDNA might represent a viable strategy to identify patients eligible for treatment by FGFR inhibition, and mBC ctDNA levels might be used for the evaluation of prognosis in clinical drug trials. View Full-Text
Keywords: clinical trials; FGFR1; liquid biopsy; breast Cancer; sWGS; ctDNA clinical trials; FGFR1; liquid biopsy; breast Cancer; sWGS; ctDNA
Show Figures

Figure 1

MDPI and ACS Style

Bourrier, C.; Pierga, J.-Y.; Xuereb, L.; Salaun, H.; Proudhon, C.; Speicher, M.R.; Belic, J.; Heitzer, E.; Lockhart, B.P.; Guigal-Stephan, N. Shallow Whole-Genome Sequencing from Plasma Identifies FGFR1 Amplified Breast Cancers and Predicts Overall Survival. Cancers 2020, 12, 1481.

AMA Style

Bourrier C, Pierga J-Y, Xuereb L, Salaun H, Proudhon C, Speicher MR, Belic J, Heitzer E, Lockhart BP, Guigal-Stephan N. Shallow Whole-Genome Sequencing from Plasma Identifies FGFR1 Amplified Breast Cancers and Predicts Overall Survival. Cancers. 2020; 12(6):1481.

Chicago/Turabian Style

Bourrier, Chantal; Pierga, Jean-Yves; Xuereb, Laura; Salaun, Hélène; Proudhon, Charlotte; Speicher, Michael R.; Belic, Jelena; Heitzer, Ellen; Lockhart, Brian P.; Guigal-Stephan, Nolwen. 2020. "Shallow Whole-Genome Sequencing from Plasma Identifies FGFR1 Amplified Breast Cancers and Predicts Overall Survival" Cancers 12, no. 6: 1481.

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Search more from Scilit
 
Search
Back to TopTop