title: The characterization of four gene expression analysis in circulating tumor cells made by Multiplex-PCR from the AdnaTest kit on the lab-on-a-chip Agilent DNA 1000 platform.
abstract: BACKGROUND
  Nowadays, on-a-chip capillary electrophoresis is a routine method for the detection of PCR fragments. The Agilent 2100 Bioanalyzer was one of the first commercial devices in this field. Our project was designed to study the characteristics of Agilent DNA 1000 kit in PCR fragment analysis as a part of circulating tumour cell (CTC) detection technique. Despite the common use of this kit a complex analysis of the results from a long-term project is still missing.
  
  
  METHODS
  A commercially available Agilent DNA 1000 kit was used as a final step in the CTC detection (AdnaTest) for the determination of the presence of PCR fragments generated by Multiplex PCR. Data from 30 prostate cancer patients obtained during two years of research were analyzed to determine the trueness and precision of the PCR fragment size determination. Additional experiments were performed to demonstrate the precision (repeatability, reproducibility) and robustness of PCR fragment concentration determination.
  
  
  RESULTS
  The trueness and precision of the size determination was below 3% and 2% respectively. The repeatability of the concentration determination was below 15%. The difference in concentration determination increases when Multiplex-PCR/storage step is added between the two measurements of one sample.
  
  
  CONCLUSIONS
  The characteristics established in our study are in concordance with the manufacturer's specifications established for a ladder as a sample. However, the concentration determination may vary depending on chip preparation, sample storage and concentration. The 15% variation of concentration determination repeatability was shown to be partly proportional and can be suppressed by proper normalization.
authors.affiliation: Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Czech Republic.
authors.forename: Markéta
authors.initials: M
authors.lastname: Škereňová
authors.affiliation: Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Czech Republic.
authors.forename: Veronika
authors.initials: V
authors.lastname: Mikulová
authors.affiliation: Department of Urology, General University Hospital and First Faculty of Medicine, Charles University in Prague, Czech Republic.
authors.forename: Otakar
authors.initials: O
authors.lastname: Čapoun
authors.affiliation: Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Czech Republic.
authors.forename: Tomáš
authors.initials: T
authors.lastname: Zima
mesh_terms: D000199:Actins / Q000235:genetics; D000954:Antigens, Surface / Q000235:genetics; D014408:Biomarkers, Tumor / Q000235:genetics*; D004273:DNA, Neoplasm / Q000235:genetics*; D066246:ErbB Receptors / Q000235:genetics; D015972:Gene Expression Regulation, Neoplastic; D043425:Glutamate Carboxypeptidase II / Q000235:genetics; D006801:Humans; D056656:Lab-On-A-Chip Devices; D008297:Male; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods*; D009360:Neoplastic Cells, Circulating / Q000378:metabolism*; D017430:Prostate-Specific Antigen / Q000235:genetics; D064129:Prostatic Neoplasms, Castration-Resistant / Q000097:blood / Q000235:genetics; D011933:Reagent Kits, Diagnostic; D015203:Reproducibility of Results
chemical_list: D000199:Actins; D000954:Antigens, Surface; D014408:Biomarkers, Tumor; D004273:DNA, Neoplasm; D011933:Reagent Kits, Diagnostic; D066246:ErbB Receptors; C473848:FOLH1 protein, human; D043425:Glutamate Carboxypeptidase II; D017430:Prostate-Specific Antigen
keywords: Agilent DNA 1000 kit; capillary electrophoresis; circulating tumour cells; lab-on-a-chip devices; multiplex PCR