Genome-wide discovery of genetic variants affecting tamoxifen sensitivity and their clinical and functional validation

L. Weng, D. Ziliak, H. K. Im, E. R. Gamazon, S. Philips, A. T. Nguyen, Z. Desta, T. C. Skaar, D. A. Flockhart, R. S. Huang

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


Background: Beyond estrogen receptor (ER), there are no validated predictors for tamoxifen (TAM) efficacy and toxicity. We utilized a genome-wide cell-based model to comprehensively evaluate genetic variants for their contribution to cellular sensitivity to TAM. Design: Our discovery model incorporates multidimensional datasets, including genome-wide genotype, gene expression, and endoxifen-induced cellular growth inhibition in the International HapMap lymphoblastoid cell lines (LCLs). Genome-wide findings were further evaluated in NCI60 cancer cell lines. Gene knock-down experiments were performed in four breast cancer cell lines. Genetic variants identified in the cell-based model were examined in 245 Caucasian breast cancer patients who underwent TAM treatment. Results: We identified seven novel single-nucleotide polymorphisms (SNPs) associated with endoxifen sensitivity through the expression of 10 genes using the genome-wide integrative analysis. All 10 genes identified in LCLs were associated with TAM sensitivity in NCI60 cancer cell lines, including USP7. USP7 knock-down resulted in increasing resistance to TAM in four breast cancer cell lines tested, which is consistent with the finding in LCLs and in the NCI60 cells. Furthermore, we identified SNPs that were associated with TAM-induced toxicities in breast cancer patients, after adjusting for other clinical factors. Conclusion: Our work demonstrates the utility of a cell-based model in genome-wide identification of pharmacogenomic markers.

Original languageEnglish (US)
Pages (from-to)1867-1873
Number of pages7
JournalAnnals of Oncology
Issue number7
StatePublished - Jul 2013

Bibliographical note

Funding Information:
This study was supported by the University of Chicago Cancer Center support grant (#P30 CA14599) and National Institutes of Health/National Institute of General Medical Science (Pharmacogenomics of Anticancer Agents grant U01GM61393). Patient data were collected by the Consortium on Breast Cancer Pharmacogenomics (COBRA) investigators. RSH also received support from National Institute of General Medical Science K08 (GM089941), the National Cancer Institute R21 (CA139278), the University of Chicago Breast Cancer SPORE Career Development Award (CA125183), and the National Center for Advancing Translational Sciences of the National Institutes of Health (UL1RR024999).


  • Gene expression
  • Genome-wide association study
  • HapMap
  • SNP
  • Tamoxifen


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