Predicting Dihydropyrimidine Dehydrogenase Deficiency and Related 5-Fluorouracil Toxicity: Opportunities and Challenges of DPYD Exon Sequencing and the Role of Phenotyping Assays

Abstract

Deficiency of dihydropyrimidine dehydrogenase (DPD), encoded by the DPYD gene, is associated with severe toxicity induced by the anti-cancer drug 5-Fluorouracil (5-FU). DPYD genotyping of four recommended polymorphisms is widely used to predict toxicity, yet their prediction power is limited. Increasing availability of next generation sequencing (NGS) will allow us to screen rare variants, predicting a larger fraction of DPD deficiencies. Genotype–phenotype correlations were investigated by performing DPYD exon sequencing in 94 patients assessed for DPD deficiency by the 5-FU degradation rate (5-FUDR) assay. Association of common variants with 5-FUDR was analyzed with the SNPStats software. Functional interpretation of rare variants was performed by in-silico analysis (using the HSF system and PredictSNP) and literature review. A total of 23 rare variants and 8 common variants were detected. Among common variants, a significant association was found between homozygosity for the rs72728438 (c.1974+75A>G) and decreased 5-FUDR. Haplotype analysis did not detect significant associations with 5-FUDR. Overall, in our sample cohort, NGS exon sequencing allowed us to explain 42.5% of the total DPD deficiencies. NGS sharply improves prediction of DPD deficiencies, yet a broader collection of genotype–phenotype association data is needed to enable the clinical use of sequencing data.

Complete DPYD genotyping combined with dihydropyrimidine dehydrogenase phenotyping to prevent fluoropyrimidine toxicity: A retrospective study

“…Finally, in the combined DPD screening group, we found that approximately 8% of patients were at high risk of PF toxicity. Our findings also confirm the low concordance between phenotyping and genotyping approaches, consistent with previous studies 9,16 …”

“…Our findings also confirm the low concordance between phenotyping and genotyping approaches, consistent with previous studies. 9 , 16 …”

Implementing pharmacogenetic testing in fluoropyrimidine-treated cancer patients: DPYD genotyping to guide chemotherapy dosing in Greece

“…It is known that additional, albeit rare variants, exist that may significantly increase FP-induced toxicity risk. Rare DPYD variants could contribute in predicting a larger fraction of DPD deficiencies and partially address the missing heritability and improve prediction of FP-induced toxicity ( De Luca et al, 2022 ; De Mattia et al, 2022 ; Lešnjaković et al, 2023 ). It is expected, however, that even if additional rare variants are incorporated into DPYD dosing guidelines, sensitivity will remain low.…”

Implementation of upfront DPYD genotyping with a low-cost and high-throughput assay to guide fluoropyrimidine treatment in cancer patients

“…The sensitivity of a genetic test depends on the number of tested variants, and a genetic analysis based on a selected panel of variants may exclude rare genetic variants, for which information on DPD activity would be scarce. Although at the moment sequencing the whole DPYD gene by next-generation sequencing does not seem to increase the performance of the genetic test, at least in European populations, some studies show that the screening of the complete DYPD coding sequence could improve the identification of patients with rare variants associated with an increased risk of developing fluoropyrimidine toxicity [32,39,40]. Fluoropyrimidine toxicity can also be due to genetic variants in other genes related to the fluoropyrimidine metabolic pathways.…”