Genetic Biomarkers for Fluorouracil Toxicity Prediction: The Long Road to Clinical Utility
Authors: Adam M. Lee, Robert B. Diasio
Journal: Journal of Clinical Oncology (2014)

In Journal of Clinical Oncology, Rosmarin et al examine the utility of various genetic markers as predictors of fluoropyrimidine toxicity in patients being treated for colorectal cancer. In their study using 927 white stage II/III colorectal cancer patients from QUASAR (Quick and Simple and Reliable) 2, the authors conducted an association analysis between 21 gene variants in seven different candidate genes and grade 3 toxicities in patients who received adjuvant capecitabine with or without bevacizumab. Their analysis identified significant associations between three variants and global grade 3 toxicities in the population: TYMS 5 VNTR 2R/3R (rs45445694), TYMS 3 UTR 6bp ins-del (rs16430/rs151264360), and DPYD c.2846 TA (rs67376798). Both TYMS variants showed strong linkage disequilibrium and resulted in a significant association with global grade 3 toxicity when genotypes for each variant were combined according to their individual effect on resultant thymidylate synthase levels. Of interest, the most well-known DPYD variant, DPYD*2A (c.1905 1 GA, also designated IVS14 1 GA; rs3918290), was not significantly associated with global grade 3 toxicity in the study population, presumably as a result of relatively low frequency in this population that included fewer than 1,000 patients. Previous gene function studies have demonstrated the deleterious effect of DPYD*2A on DPD enzyme activity. In addition, an association of both DPYD*2A and DPYD c.2846 TA with fluorouracil (FU) -related toxicities has been shown. Therefore, Rosmarin et al elected to group both DPYD*2A and DPYD c.2846 TA together as dysfunctional DPYD alleles, and were able to observe a statistically significant association with global toxicity in the QUASAR 2 study. Lastly, it should be noted that in deciding which DPYD variant to examine, several of the variants chosen for inclusion in QUASAR 2 (DPYD *4, *6 and *9) have long been recognized as being without deleterious effect on DPD activity, with no or limited associations with fluoropyrimidine toxicity; thus, the absence of individual association of these variants with toxicity in Rosmarin et al is not unexpected. Subsequently, Rosmarin et al attempt to expand their study population by conducting a meta-analysis of 16 previously published studies (summarized in Data Supplement item 6) that investigated potential toxicity-related genetic markers with fluoropyrimidine-based therapies to further validate the observations from QUASAR2. Although the TYMS and DPYD variants remained statistically significant in three different meta-analyses performed in capecitabine and FU infusional and bolus monotherapy cohorts, no associations were detected between these markers and toxicity in FU combination chemotherapy regimens. Furthermore, 16 of the 21 potential genetic biomarkers were unable to be assessed by the current meta-analysis in the combination chemotherapy cohort because these genetic variants were unavailable within the combined studies. Indeed, review of the Rosmarin et al Data Supplement (item 16) demonstrates that only five variants could be examined by meta-analysis in patients who received FUbased combination chemotherapy regimens (TYMS 5 VNTR 2R/3R, TYMS 5 VNTR G/C, TYMS 3 UTR6bp in/del, MTHFR c.677 CT, and MTHFR c.1298 AC). Of particular concern, the known deleterious DPYD variants DPYD*2A and DPYD c.2846 TA could not be included in this meta-analysis. Numerous significant differences between individual association studies greatly limit the usefulness of a meta-analytic approach: for example, genes (and the specific variants) chosen, types and stages of cancer, toxicity assessment, treatment regimens, and pertinent clinical data (eg, whether dose reductions were used). Such limitations need to be addressed in future studies by a more complete assessment of potential genetic biomarkers in larger populations of patients receiving comparable treatment regimens with uniform clinical data. As an example, we recently reported initial genotypic data from a much larger adjuvant trial of 2,886 treated with stage III colon cancer treated with either infusional fluorouracil, leucovorin, and oxaliplatin (FOLFOX) or fluorouracil, leucovorin, and irinotecan (FOLFIRI) plus cetuximab (N0147). In this protocol, whether patients were treated with either mFOLFOX6 or FOLFIRI, all received FU essentially by a similar administration regimen (ie, an infusion of FU over 46 hours together with an intravenous bolus of FU). In this study, we were able to assess DPYD*2A and DPYD c.2846 TA variants individually. These studies identified significant associations between grade 3 adverse events and DPYD*2A (odds ratio 11.9; 95% CI, 4.0 to 32.7, P .0001) and DPYD c.2846 TA (odds ratio 5.5; 95% CI, 2.5 to 12.1, P .0001), confirming their potential utility in the prediction of toxicity in patients who receive FU-based combination therapies. In developing a logic-based design for selecting genes and their specific variants in the future, the opportunity to be able to select variants on the basis of the functional consequence of changes in gene structure would be highly desirable. Genomic research has seen substantial technological advancements, leading to the identification of more than 40 million variants in the human genome. Although it has become relatively inexpensive to sequence a patient’s entire genome, the ability to understand and comprehend the functional consequences of structural change remains a challenge. Using DPYD as an JOURNAL OF CLINICAL ONCOLOGY E D I T O R I A L VOLUME 32 NUMBER 10 APRIL 1 2014