title: The dynamic range of circulating tumor DNA in metastatic breast cancer.
abstract: BACKGROUND
  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.
authors.forename: Maryam
authors.initials: M
authors.lastname: Heidary
authors.forename: Martina
authors.initials: M
authors.lastname: Auer
authors.forename: Peter
authors.initials: P
authors.lastname: Ulz
authors.forename: Ellen
authors.initials: E
authors.lastname: Heitzer
authors.forename: Edgar
authors.initials: E
authors.lastname: Petru
authors.forename: Christin
authors.initials: C
authors.lastname: Gasch
authors.forename: Sabine
authors.initials: S
authors.lastname: Riethdorf
authors.forename: Oliver
authors.initials: O
authors.lastname: Mauermann
authors.forename: Ingrid
authors.initials: I
authors.lastname: Lafer
authors.forename: Gunda
authors.initials: G
authors.lastname: Pristauz
authors.forename: Sigurd
authors.initials: S
authors.lastname: Lax
authors.forename: Klaus
authors.initials: K
authors.lastname: Pantel
authors.forename: Jochen B
authors.initials: JB
authors.lastname: Geigl
authors.forename: Michael R
authors.initials: MR
authors.lastname: Speicher
mesh_terms: D014408:Biomarkers, Tumor; D001943:Breast Neoplasms / Q000097:blood* / Q000235:genetics / Q000473:pathology*; D016000:Cluster Analysis; D019295:Computational Biology; D056915:DNA Copy Number Variations; D004273:DNA, Neoplasm / Q000097:blood* / Q000235:genetics; D059472:Exome; D005260:Female; D005787:Gene Frequency; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009154:Mutation; D009362:Neoplasm Metastasis; D009360:Neoplastic Cells, Circulating; D012016:Reference Values
chemical_list: D014408:Biomarkers, Tumor; D004273:DNA, Neoplasm
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