title: Concordance of metabolic enzyme genotypes assayed from paraffin-embedded, formalin-fixed breast tumors and normal lymphatic tissue.
abstract: OBJECTIVE
  Translational epidemiology studies often use archived tumor specimens to evaluate genetic hypotheses involving cancer outcomes. When the exposure of interest is a germline polymorphism, a key concern is whether the genotype assayed from tumor-derived DNA is representative of the germline. We evaluated the concordance between breast tumor-derived and normal lymph node-derived genotypes for three polymorphic tamoxifen-metabolizing enzymes.
  
  
  METHODS
  We assayed paired DNA samples extracted from archived tumor and normal lymph node tissues from 106 breast cancer patients. We used TaqMan assays to determine the genotypes of three enzyme variants hypothesized to modify tamoxifen effectiveness, ie, CYP2D6*4, UGT2B15*2, and UGT1A8*2. We assessed genotype agreement between the two DNA sources by calculating the percent agreement and the weighted kappa statistic.
  
  
  RESULTS
  We successfully obtained genotypes for CYP2D6*4, UGT2B15*2, and UGT1A8*2 in 99%, 100%, and 84% of the paired samples, respectively. Genotype concordance was perfect for the CYP2D6*4 and UGT1A8*2 variants (weighted kappa for both = 1.00; 95% confidence interval [CI] 1.00, 1.00). For UGT2B15*2, one pair out of 106 gave a discordant result that persisted over several assay repeats.
  
  
  CONCLUSIONS
  We observed strong agreement between DNA from breast tumors and normal lymphatic tissue in the genotyping of polymorphisms in three tamoxifen-metabolizing enzymes. Genotyping DNA extracted from tumor tissue avoids the time-consuming practice of microdissecting adjacent normal tissue when other normal tissue sources are not available. Therefore, the demonstrated reliability of tumor-derived DNA allows resources to be spent instead on increasing sample size or the number of polymorphisms examined.
authors.affiliation: Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts;
authors.forename: Thomas P
authors.initials: TP
authors.lastname: Ahern
authors.forename: Mariann
authors.initials: M
authors.lastname: Christensen
authors.forename: Deirdre P
authors.initials: DP
authors.lastname: Cronin-Fenton
authors.forename: Kathryn L
authors.initials: KL
authors.lastname: Lunetta
authors.forename: Carol L
authors.initials: CL
authors.lastname: Rosenberg
authors.forename: Henrik Toft
authors.initials: HT
authors.lastname: Sørensen
authors.forename: Timothy L
authors.initials: TL
authors.lastname: Lash
authors.forename: Stephen
authors.initials: S
authors.lastname: Hamilton-Dutoit