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The dynamic range of circulating tumor DNA in metastatic breast cancer
INTRODUCTION: The management of metastatic breast cancer needs improvement. As clinical evaluation is not very accurate in determining the progression of disease, the analysis of circulating tumor DNA (ctDNA) has evolved to a promising noninvasive marker of disease evolution. Indeed, ctDNA was repor...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4303230/ https://www.ncbi.nlm.nih.gov/pubmed/25107527 http://dx.doi.org/10.1186/s13058-014-0421-y |
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author | Heidary, Maryam Auer, Martina Ulz, Peter Heitzer, Ellen Petru, Edgar Gasch, Christin Riethdorf, Sabine Mauermann, Oliver Lafer, Ingrid Pristauz, Gunda Lax, Sigurd Pantel, Klaus Geigl, Jochen B Speicher, Michael R |
author_facet | Heidary, Maryam Auer, Martina Ulz, Peter Heitzer, Ellen Petru, Edgar Gasch, Christin Riethdorf, Sabine Mauermann, Oliver Lafer, Ingrid Pristauz, Gunda Lax, Sigurd Pantel, Klaus Geigl, Jochen B Speicher, Michael R |
author_sort | Heidary, Maryam |
collection | PubMed |
description | INTRODUCTION: The management of metastatic breast cancer needs improvement. As clinical evaluation is not very accurate in determining the progression of disease, the analysis of circulating tumor DNA (ctDNA) has evolved to a promising noninvasive marker of disease evolution. Indeed, ctDNA was reported to represent a highly sensitive biomarker of metastatic cancer disease directly reflecting tumor burden and dynamics. However, at present little is known about the dynamic range of ctDNA in patients with metastatic breast cancer. METHODS: In this study, 74 plasma DNA samples from 58 patients with metastasized breast cancer were analyzed with a microfluidic device to determine the plasma DNA size distribution and copy number changes in the plasma were identified by whole-genome sequencing (plasma-Seq). Furthermore, in an index patient we conducted whole-genome, exome, or targeted deep sequencing of the primary tumor, metastases, and circulating tumor cells (CTCs). Deep sequencing was done to accurately determine the allele fraction (AFs) of mutated DNA fragments. RESULTS: Although all patients had metastatic disease, plasma analyses demonstrated highly variable AFs of mutant fragments. We analyzed an index patient with more than 100,000 CTCs in detail. We first conducted whole-genome, exome, or targeted deep sequencing of four different regions from the primary tumor and three metastatic lymph node regions, which enabled us to establish the phylogenetic relationships of these lesions, which were consistent with a genetically homogeneous cancer. Subsequent analyses of 551 CTCs confirmed the genetically homogeneous cancer in three serial blood analyses. However, the AFs of ctDNA were only 2% to 3% in each analysis, neither reflecting the tumor burden nor the dynamics of this progressive disease. These results together with high-resolution plasma DNA fragment sizing suggested that differences in phagocytosis and DNA degradation mechanisms likely explain the variable occurrence of mutated DNA fragments in the blood of patients with cancer. CONCLUSIONS: The dynamic range of ctDNA varies substantially in patients with metastatic breast cancer. This has important implications for the use of ctDNA as a predictive and prognostic biomarker. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13058-014-0421-y) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4303230 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-43032302015-01-23 The dynamic range of circulating tumor DNA in metastatic breast cancer Heidary, Maryam Auer, Martina Ulz, Peter Heitzer, Ellen Petru, Edgar Gasch, Christin Riethdorf, Sabine Mauermann, Oliver Lafer, Ingrid Pristauz, Gunda Lax, Sigurd Pantel, Klaus Geigl, Jochen B Speicher, Michael R Breast Cancer Res Research Article INTRODUCTION: The management of metastatic breast cancer needs improvement. As clinical evaluation is not very accurate in determining the progression of disease, the analysis of circulating tumor DNA (ctDNA) has evolved to a promising noninvasive marker of disease evolution. Indeed, ctDNA was reported to represent a highly sensitive biomarker of metastatic cancer disease directly reflecting tumor burden and dynamics. However, at present little is known about the dynamic range of ctDNA in patients with metastatic breast cancer. METHODS: In this study, 74 plasma DNA samples from 58 patients with metastasized breast cancer were analyzed with a microfluidic device to determine the plasma DNA size distribution and copy number changes in the plasma were identified by whole-genome sequencing (plasma-Seq). Furthermore, in an index patient we conducted whole-genome, exome, or targeted deep sequencing of the primary tumor, metastases, and circulating tumor cells (CTCs). Deep sequencing was done to accurately determine the allele fraction (AFs) of mutated DNA fragments. RESULTS: Although all patients had metastatic disease, plasma analyses demonstrated highly variable AFs of mutant fragments. We analyzed an index patient with more than 100,000 CTCs in detail. We first conducted whole-genome, exome, or targeted deep sequencing of four different regions from the primary tumor and three metastatic lymph node regions, which enabled us to establish the phylogenetic relationships of these lesions, which were consistent with a genetically homogeneous cancer. Subsequent analyses of 551 CTCs confirmed the genetically homogeneous cancer in three serial blood analyses. However, the AFs of ctDNA were only 2% to 3% in each analysis, neither reflecting the tumor burden nor the dynamics of this progressive disease. These results together with high-resolution plasma DNA fragment sizing suggested that differences in phagocytosis and DNA degradation mechanisms likely explain the variable occurrence of mutated DNA fragments in the blood of patients with cancer. CONCLUSIONS: The dynamic range of ctDNA varies substantially in patients with metastatic breast cancer. This has important implications for the use of ctDNA as a predictive and prognostic biomarker. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13058-014-0421-y) contains supplementary material, which is available to authorized users. BioMed Central 2014-08-09 2014 /pmc/articles/PMC4303230/ /pubmed/25107527 http://dx.doi.org/10.1186/s13058-014-0421-y Text en © Heidary et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Heidary, Maryam Auer, Martina Ulz, Peter Heitzer, Ellen Petru, Edgar Gasch, Christin Riethdorf, Sabine Mauermann, Oliver Lafer, Ingrid Pristauz, Gunda Lax, Sigurd Pantel, Klaus Geigl, Jochen B Speicher, Michael R The dynamic range of circulating tumor DNA in metastatic breast cancer |
title | The dynamic range of circulating tumor DNA in metastatic breast cancer |
title_full | The dynamic range of circulating tumor DNA in metastatic breast cancer |
title_fullStr | The dynamic range of circulating tumor DNA in metastatic breast cancer |
title_full_unstemmed | The dynamic range of circulating tumor DNA in metastatic breast cancer |
title_short | The dynamic range of circulating tumor DNA in metastatic breast cancer |
title_sort | dynamic range of circulating tumor dna in metastatic breast cancer |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4303230/ https://www.ncbi.nlm.nih.gov/pubmed/25107527 http://dx.doi.org/10.1186/s13058-014-0421-y |
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