title: Fraction of neoplastic cells in breast cancer samples. Correction for the oncogene amplification test.
abstract: OBJECTIVE
  To develop the necessary correction for the polymerase chain reaction-based oncogene amplification test applied to paraffin-embedded tissue sections.
  
  
  METHODS
  The theoretical basis for making the correction in test results and for determining the neoplastic cell fraction was clarified, and a method for microscopic sampling was developed. The cell count bias was corrected by applying an equation by Ebbeson and Tang and using two adjacent tissue sections of different thickness, cut from the block from which DNA was isolated.
  
  
  RESULTS
  There was no need to determine the absolute thicknesses of the sections. Section thickness, as a relevant feature, was cancelled out in developing the formula for estimating the cell fraction. The correction was applied in practice, and when tested on 10 breast cancer samples, the correlation between amplification estimates from two observers was good (r = .96).
  
  
  CONCLUSIONS
  This method is valuable for interpreting the test results based on paraffin sections and for developing simpler quantitating methods for special test applications. The study also showed that amplifications may be more common than expected on the basis of the crude results of this type of test.
authors.affiliation: Department of Pathology, University of Turku, Finland.
authors.forename: Y
authors.initials: Y
authors.lastname: Collan
authors.forename: J
authors.initials: J
authors.lastname: Haikonen
authors.forename: C
authors.initials: C
authors.lastname: Sundfors
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D002452:Cell Count; D017931:DNA Primers / Q000737:chemistry; D004273:DNA, Neoplasm / Q000032:analysis*; D005260:Female; D005784:Gene Amplification; D016259:Genes, myc / Q000235:genetics*; D006801:Humans; D019044:Image Cytometry / Q000379:methods; D008954:Models, Biological; D016612:Paraffin Embedding; D016133:Polymerase Chain Reaction / Q000379:methods*
chemical_list: D017931:DNA Primers; D004273:DNA, Neoplasm