Using Whole-Exome Sequencing to Identify Genetic Markers for Carboplatin and Gemcitabine-Induced Toxicities

Henrik Gréen, Johanna Hasmats, Ilya Kupershmidt, Daniel Edsgärd, Luigi de Petris, Rolf Lewensohn, Fiona Blackhall, Svante Vikingsson, Benjamin Besse, Andrea Lindgren, Eva Brandén, Hirsh Koyi, Curt Peterson, Joakim Lundeberg

Chemotherapies are associated with significant inter-individual variability in therapeutic effect and adverse drug reactions. In lung cancer, the use of gemcitabine and carboplatin induces grade 3 or 4 myelosuppression in about a quarter of the patients, while an equal fraction of patients are basically unaffected in terms of myelosuppressive side effects. We therefore set out to identify genetic markers for gemcitabine/carboplatin-induced myelosuppression. We exome sequenced 32 patients that suffered extremely high neutropenia and thrombocytopenia (grade 3-4 after first chemotherapy cycle) or were virtually unaffected (grade 0-1). The genetic differences/polymorphism between the groups were compared using six different bioinformatics strategies: 1) whole-exome non-synonymous single nucleotide variants association analysis, 2) deviation from Hardy-Weinberg equilibrium, 3) analysis of genes selected by a priori biological knowledge, 4) analysis of genes selected from gene expression meta-analysis of toxicity datasets, 5) Ingenuity-Pathway Analysis, and 6) FunCoup network enrichment analysis. A total of 53 genetic variants that differed among these groups were validated in an additional 291 patients and were correlated to the patients' myelosuppression. In the validation, we identified rs1453542 in OR4D6 (p=0.0008, OR = 5.2, 95%CI=1.8-18) as a marker for gemcitabine/carboplatin-induced neutropenia and rs5925720 in DDX53 (p=0.0015, OR=0.36,95%CI=0.17-0.71) as a marker for thrombocytopenia. Patients homozygous for the minor allele of rs1453542 had a higher risk of neutropenia, and for rs5925720 the minor allele was associated with a lower risk for thrombocytopenia. We have identified two new genetic markers with the potential to predict myelosuppression induced by gemcitabine/carboplatin chemotherapy.