title: Liquid biopsy - Performance of the PAXgene® Blood ccfDNA Tubes for the isolation and characterization of cell-free plasma DNA from tumor patients.
abstract: BACKGROUND
  In most research laboratories the use of EDTA tubes for the isolation of plasma DNA from tumor patients is standard. Unfortunately these tubes do not allow for an extended storage of samples before processing and prevent EDTA tubes from being shipped at ambient temperature. The aim of our study was to compare the quantity and quality of plasma DNA isolated from EDTA and PAXgene® Blood ccfDNA Tubes in different downstream applications.
  
  
  METHODS
  We enrolled 29 patients in our study. Blood samples were drawn into EDTA and PAXgene® Blood ccfDNA Tubes and were processed on day 0 and day 7 after storage at ambient temperature. The plasma DNA from 10 patients was isolated manually. For the DNA isolation from the plasma of 19 additional patients we used the automated QIAsymphony system. The total amount DNA from all samples was measured with a quantitative real-time PCR assay. In addition the amount of methylated mSHOX2 plasma DNA was determined.
  
  
  RESULTS
  While the 7day storage lead to an increased amount of total DNA in almost all EDTA tubes, this effect was only seen in very few PAXgene® Blood ccfDNA Tubes. The stabilization solution which prevents the lysis of blood cells had no effect on the method for quantification of methylated sequences in these samples.
  
  
  CONCLUSIONS
  The quantity and quality of plasma DNA from both types of blood draw tubes are comparable. DNA from PAXgene® Blood ccfDNA was successfully used for PCR-based quantification of total amount of cell-free DNA and for methylation analysis as well.
authors.affiliation: DRK Kliniken Berlin/Mitte, Klinik für Innere Medizin - Schwerpunkt Pneumologie und Schlafmedizin, Drontheimer Straße 39-40, 13359 Berlin, Germany.
authors.forename: Bernd
authors.initials: B
authors.lastname: Schmidt
authors.affiliation: Universitätsklinikum Halle/Saale, Klinik f. Innere Medizin, Abtlg. Pneumologie, Ernst Grube Str. 40, 06120 Halle/Saale, Germany.
authors.forename: Dana
authors.initials: D
authors.lastname: Reinicke
authors.affiliation: Universitätsklinikum Halle/Saale, Klinik f. Innere Medizin, Abtlg. Pneumologie, Ernst Grube Str. 40, 06120 Halle/Saale, Germany.
authors.forename: Iris
authors.initials: I
authors.lastname: Reindl
authors.affiliation: Universitätsklinikum Halle/Saale, Klinik f. Innere Medizin, Abtlg. Pneumologie, Ernst Grube Str. 40, 06120 Halle/Saale, Germany.
authors.forename: Ines
authors.initials: I
authors.lastname: Bork
authors.affiliation: Universitätsklinikum Halle/Saale, Klinik f. Innere Medizin, Abtlg. Pneumologie, Ernst Grube Str. 40, 06120 Halle/Saale, Germany.
authors.forename: Bettina
authors.initials: B
authors.lastname: Wollschläger
authors.affiliation: Universitätsklinikum Halle/Saale, Klinik f. Innere Medizin, Abtlg. Pneumologie, Ernst Grube Str. 40, 06120 Halle/Saale, Germany.
authors.forename: Nina
authors.initials: N
authors.lastname: Lambrecht
authors.affiliation: Universitätsklinikum Halle/Saale, Klinik f. Innere Medizin, Abtlg. Pneumologie, Ernst Grube Str. 40, 06120 Halle/Saale, Germany. Electronic address: michael.fleischhacker@uk-halle.de.
authors.forename: Michael
authors.initials: M
authors.lastname: Fleischhacker
mesh_terms: D001800:Blood Specimen Collection / Q000379:methods*; D000074141:Circulating Tumor DNA / Q000097:blood* / Q000302:isolation & purification*; D006801:Humans; D000073890:Liquid Biopsy / Q000379:methods*; D008175:Lung Neoplasms / Q000097:blood*
chemical_list: D000074141:Circulating Tumor DNA
keywords: Blood drawing; Cell-free DNA; Liquid biopsy; Methylation; Quantitative real-time PCR; Standardization