Abstract 5493: Genome-wide study of carboplatin and paclitaxel disposition in ovarian cancer patients
Authors: Gao Bo , Lu Yi , Nieuweboer Annemieke J.M. , Xu Hongmei , Beesley Jonathan , Boere Ingrid , de Graan Anne-Joy M. , de Bruijn Peter , Gurney Howard , Kennedy Catherine , Chiew Yoke-Eng , Johnatty Sharon E. , Beale Philip , Harrison Michelle , Luccarini Craig , Dunning Alison M. , Mathijssen Ron H.J. , Harnett Paul , Balleine Rosemary L. , Chenevix-Trench Georgia , MacGregor Stuart , deFazio Anna 
Published: August 2015

Germline genetic variation can affect chemotherapeutic drug disposition, toxicity and efficacy. Identifying single nucleotide polymorphisms (SNPs) that influence chemotherapy disposition may help to personalize individual treatment. Compared to the traditional candidate gene approach, a genome-wide association study (GWAS) is unbiased but usually requires a large sample size. Since most cytotoxics have a short half-life and are given cyclically, multiple blood samples are therefore required to adequately define drug disposition and systemic exposure. This limits patient sample sizes in pharmacokinetic studies. The aim of this study was to identify SNPs that are associated with carboplatin and paclitaxel pharmacokinetic parameters using a GWAS approach in two small patient cohorts. Methods: Two independent pharmacokinetic cohorts were recruited in Australia (N = 61, both carboplatin and paclitaxel) and the Netherlands (N = 35, paclitaxel only). A total of 719,665 SNPs were genotyped using Illumina Human OmniExpress arrays. Linear regression was used to test the association between each SNP and the trait of interest, both unadjusted and adjusted for corresponding covariates using PLINK. We performed separate analysis within each population and then ran meta-analysis combining results from different populations weighted by sample sizes using METAL. Results: Carboplatin and paclitaxel disposition is a relative stable phenotype. The genomic control parameters in the test statistics for the adjusted carboplatin and paclitaxel analysis were 1.03 and 1.02 respectively, suggesting that there was little concern for population substructure or other artefacts. We identified highly significant SNPs in ABCC2 associated with carboplatin clearance (asymptotic p = 5.2 × 10−6, empirical p = 1.4 × 10−5 from 107 permutations) which are highly plausible pharmacogenomic markers given the known role of ABCC2 in carboplatin efflux. We also identified a novel SNP associated with paclitaxel disposition with genome wide significance in chromosome 1 (rs17130142, asymptotic p = 2.0 × 10−9, empirical p = 1.3× 10−7), in an intergenic region, neighboring PKN2. Conclusion: Although these findings requires a validation in a larger study, our work demonstrated that GWAS of chemotherapeutic drug disposition can be effective even when performed in a relative small sample number and can be adopted in drug development and treatment programs.

Citation Format: Bo Gao, Yi Lu, Annemieke J.M. Nieuweboer, Hongmei Xu, Jonathan Beesley, Ingrid Boere, Anne-Joy M. de Graan, Peter de Bruijn, Howard Gurney, Catherine Kennedy, Yoke-Eng Chiew, Sharon E. Johnatty, Philip Beale, Michelle Harrison, Craig Luccarini, Alison M. Dunning, Ron H.J. Mathijssen, Paul Harnett, Rosemary L. Balleine, Georgia Chenevix-Trench, Stuart MacGregor, Anna deFazio. Genome-wide study of carboplatin and paclitaxel disposition in ovarian cancer patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5493. doi:10.1158/1538-7445.AM2015-5493