Abstract P6-09-02: Analysis of the International tamoxifen pharmacogenomics consortium (ITPC) dataset shows that genotyping DNA derived from tumor does not introduce CYP2D6 genotyping error or mask an association with tamoxifen efficacy
Authors: Kidwell KM , Hertz DL , Leyland-Jones B , Regan MM , Dowsett M , Rae JM 
Published: May 2016

Abstract
Background: The anti-estrogen tamoxifen is metabolized into the more potent anti-estrogen, endoxifen, primarily by polymorphic CYP2D6. An association between CYP2D6 genotype and tamoxifen efficacy was assessed in a meta-analysis of 4,973 breast cancer patients by the ITPC. A subgroup analysis in 1,996 estrogen receptor (ER)-positive postmenopausal patients receiving 20[thinsp]mg/day tamoxifen for 5 years (criterion 1) found CYP2D6 poor metabolizer genotype was associated with worse invasive disease free survival (IDFS; hazard ratio (HR) 1.25, 95% confidence interval (CI) 1.06-1.47, P=0.009). This meta-analysis did not include data from two prospective trials (Anastrozole, Tamoxifen, Alone or In Combination (ATAC) and Breast Intergroup (BIG) 1-98) both of which meet the patient criteria but failed to replicate the ITPC findings. Some ITPC investigators criticized ATAC and BIG 1-98 for genotyping CYP2D6 from tumor-derived DNA, positing this leads to genotyping errors detected by Hardy-Weinberg Equilibrium (HWE). However, ITPC analyses did not exclude tumor-derived CYP2D6 genotypes or report HWE. Therefore, we re-analyzed the ITPC data to investigate claims that tumor-derived genotyping causes HWE departure and masks the association between CYP2D6 genotype and tamoxifen efficacy.
Methods: The ITPC dataset was filtered to patients fulfilling criterion 1. HWE for CYP2D6*4 was analyzed in Caucasian patients (n=1,619) by study, by DNA source (tumor or blood), and in the entire subgroup. The ITPC meta-analysis was rerun stratified by DNA source using the same specifications (patients, phenotype, genotype, statistical model, etc.) as in ITPC.
Results: Significant HWE deviation for CYP2D6*4, the most common variant (MAF =0.2), was not observed in any study genotyped from tumor but was observed in one study genotyped from blood. Combining studies led to significant HWE deviations in studies genotyped from both blood and tumor, and for the entire subcohort (Table 1). Associations between CYP2D6 genotype and IDFS stratified by DNA source yielded similar, non-statistically significant, results (blood: n=933, HR=1.19, 95% CI 0.91-1.57, P=0.21; tumor: n=997, HR=1.19, 95% CI 0.99-1.44, P=0.07).
Conclusions: HWE deviations for CYP2D6*4 are not uniformly or exclusively found in studies using tumor DNA, but can occur as a statistical consequence of combining genotypes from heterogeneous populations like in the multi-institution BIG 1-98 and ATAC studies. Re-analysis of the ITPC dataset stratified by DNA source refutes the hypothesis that genotyping tumor DNA masks a pharmacogenetic association. These findings reaffirm the validity of the BIG 1-98 and ATAC analyses and support inclusion of these studies in the ITPC meta-analysis to rigorously assess the association between CYP2D6 genotype and tamoxifen efficacy.
CYP2D6*4 HWE Test in Caucasian Patients from Each ITPC Study, by DNA Source, and CombinedDNA SourceStudy NumberNHWEBlood2700.68 4530.03 6130.28 84640.12 930.56 102220.0002 Total8250.0004Tumor51970.41 62170.04 83800.04 Total7940.0037CombinedTotal16190.000006
Citation Format: Kidwell KM, Hertz DL, Leyland-Jones B, Regan MM, Dowsett M, Rae JM. Analysis of the International tamoxifen pharmacogenomics consortium (ITPC) dataset shows that genotyping DNA derived from tumor does not introduce CYP2D6 genotyping error or mask an association with tamoxifen efficacy. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-09-02.