Loss of heterozygosity at the CYP2D6 locus in breast cancer: implications for germline pharmacogenetic studies.

Abstract

BACKGROUND:

Controversy exists regarding the impact of CYP2D6 genotype on tamoxifen responsiveness. We examined loss of heterozygosity (LOH) at the CYP2D6 locus and determined its impact on genotyping error when tumor tissue is used as a DNA source.

METHODS:

Genomic tumor data from the adjuvant and metastatic settings (The Cancer Genome Atlas [TCGA] and Foundation Medicine [FM]) were analyzed to characterize the impact of CYP2D6 copy number alterations (CNAs) and LOH on Hardy Weinberg equilibrium (HWE). Additionally, we analyzed CYP2D6 *4 genotype from formalin-fixed paraffin-embedded (FFPE) tumor blocks containing nonmalignant tissue and buccal (germline) samples from patients on the North Central Cancer Treatment Group (NCCTG) 89-30-52 tamoxifen trial. All statistical tests were two-sided.

RESULTS:

In TCGA samples (n =627), the CYP2D6 LOH rate was similar in estrogen receptor (ER)-positive (41.2%) and ER-negative (35.2%) but lower in HER2-positive tumors (15.1%) (P < .001). In FM ER+ samples (n = 290), similar LOH rates were observed (40.8%). In 190 NCCTG samples, the agreement between CYP2D6 genotypes derived from FFPE tumors and FFPE tumors containing nonmalignant tissue was moderate (weighted Kappa = 0.74; 95% CI = 0.63 to 0.84). Comparing CYP2D6 genotypes derived from buccal cells to FFPE tumor DNA, CYP2D6*4 genotype was discordant in six of 31(19.4%). In contrast, there was no disagreement between CYP2D6 genotypes derived from buccal cells with FFPE tumors containing nonmalignant tissue.

CONCLUSIONS:

LOH at the CYP2D6 locus is common in breast cancer, resulting in potential misclassification of germline CYP2D6 genotypes. Tumor DNA should not be used to determine germline CYP2D6 genotype without sensitive techniques to detect low frequency alleles and quality control procedures appropriate for somatic DNA.

• Authors: Matthew P Goetz, James X Sun, Vera J Suman, Grace O Silva, Charles M Perou, Yusuke Nakamura, Nancy J Cox, Philip J Stephens, Vincent A Miller, Jeffrey S Ross, David Chen, Stephanie L Safgren, Mary J Kuffel, Matthew M Ames, Krishna R Kalari, Henry L Gomez, Ana M Gonzalez-Angulo, Octavio Burgues, Hiltrud B Brauch, James N Ingle, Mark J Ratain, Roman Yelensky
• Journal: Journal of the National Cancer Institute (J Natl Cancer Inst) Vol. 107 Issue 2 (Dec 08 2014) ISSN: 1460-2105 [Electronic] United States
• PMID: 25490892 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't)
• Copyright: © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: [email protected].

Chemical References

• Antineoplastic Agents, Hormonal
• Biomarkers, Tumor
• DNA, Neoplasm
• Receptors, Estrogen
• Tamoxifen
• Formaldehyde
• Cytochrome P-450 CYP2D6
• ERBB2 protein, human
• Receptor, ErbB-2

Topics

• Adult
• Aged
• Antineoplastic Agents, Hormonal (pharmacology, therapeutic use)
• Biomarkers, Tumor (analysis)
• Breast Neoplasms (chemistry, drug therapy, genetics)
• Cytochrome P-450 CYP2D6 (genetics)
• DNA, Neoplasm (analysis)
• Disease-Free Survival
• Female
• Formaldehyde
• Genotype
• Humans
• Loss of Heterozygosity
• Middle Aged
• Mouth Mucosa
• Paraffin Embedding
• Receptor, ErbB-2 (analysis)
• Receptors, Estrogen (analysis)
• Survival Analysis
• Tamoxifen (pharmacology, therapeutic use)
• Tissue Fixation