Platinum Sensitivity–Related Germline Polymorphism Discovered via a Cell-Based Approach and Analysis of Its Association with Outcome in Ovarian Cancer Patients

Abstract

Purpose Utilizing cell-based approaches to identify genetic markers predictive of patients’ risk for poor response prior to chemotherapy. Experimental Design We performed genome-wide association studies (GWASs) to identify SNPs associated with cellular sensitivity to carboplatin through their effects on mRNA expression using International HapMap lymphoblastoid cell lines (LCLs) and replicated them in additional LCLs. SNPs passing both stages of the cell-based study were tested for association with progression free survival (PFS) in patients. Phase-1 validation was based on 377 ovarian cancer patients receiving at least 4-cycle of carboplatin and paclitaxel from the Australian Ovarian Cancer Study (AOCS). Positive associations were then assessed in the phase-2 validation analysis of 1,326 patients from the Ovarian Cancer Association Consortium and The Cancer Genome Atlas. Results In the initial GWAS, 342 SNPs were associated with carboplatin-induced cytotoxicity, of which 18 unique SNPs were retained after assessing their association with gene expression. One SNP (rs1649942) was replicated in an independent LCL set (p-valueBonferroni adjusted=9×10−3). It was found to be significantly associated with decreased PFS in phase-1 AOCS patients (Pper-allele=2×10−2), with a stronger effect in the subset of women with optimally debulked tumours (Pper-allele=4×10−3). rs1649942 was also associated with poorer overall survival in women with optimally debulked tumours (Pper-allele=9×10−3). However, this SNP was not significant in the phase-2 validation with patients from numerous cohorts. Conclusion This study demonstrates the potential of cell-based, genome-wide approaches to identify germ-line predictors of treatment outcome and highlights the need for extensive validation in patients to assess their clinical effect.

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