Allelic Variants of the DPYD Gene in Russian Patients with Cancer: The Results of Exome Sequencing

Abstract

Background/Objectives: Pharmacogenetic testing of the dihydropyrimidine dehydrogenase gene (DPYD) is increasingly incorporated into clinical practice to identify patients at increased risk of fluoropyrimidine-related toxicity. However, most routine assays target a limited number of well-established variants, whereas the DPYD gene demonstrates substantial population variability and may harbor rare potentially functional alleles that are not detected by conventional targeted testing. Data describing coding and splice-region DPYD variants detectable by whole-exome sequencing in Russian oncology populations remain limited. This study aimed to characterize the frequency and distribution of common, clinically relevant, and rare DPYD variants in a Russian cohort of patients receiving fluoropyrimidine-containing chemotherapy and to compare the observed allele frequencies with European and East Asian reference populations. Methods: Descriptive pharmacogenetic analysis was performed in 339 patients with malignant tumors treated with fluorouracil, leucovorin, oxaliplatin, and docetaxel (FLOT), folinic acid, fluorouracil, and oxaliplatin (FOLFOX), or folinic acid, fluorouracil, irinotecan, and oxaliplatin (FOLFIRINOX) regimens. Whole-exome sequencing was performed using Illumina technology with exome enrichment by KAPA HyperExome and a sequencing depth of at least 100×. Sequence reads were aligned to the Genome Reference Consortium Human Build 38 (GRCh38) reference genome, germline variants were called using Genome Analysis Toolkit (GATK), HaplotypeCaller, and functional annotation was performed with Ensembl Variant Effect Predictor. DPYD variants were classified according to their population frequency, predicted functional effect, ClinVar annotations, and current pharmacogenetic recommendations. Allele and genotype frequencies were calculated and descriptively compared with Genome Aggregation Database (gnomAD) v4.1.1 Non-Finnish European and East Asian populations. Results: Seventeen DPYD variants were identified. The most frequent alternative alleles were rs1801265 (24.93%), rs1801159 (17.70%), rs2297595 (11.06%), rs1801160 (7.08%), and rs17376848 (5.16%). Their distribution was generally closer to that observed in the Non-Finnish European population than in East Asian populations. The established reduced-function variant rs67376798 (c.2846A>T, p.Asp949Val) was detected in one heterozygous patient, corresponding to a carrier frequency of 0.29% and an allele frequency of 0.15%. The HapB3 proxy variant rs56038477 (c.1236G>A) was identified in 13 heterozygous patients, with a carrier frequency of 3.83% and an allele frequency of 1.92%; confirmation of the functional intronic variant rs75017182 would be required for definitive HapB3 assignment. Overall, rs67376798 or rs56038477 was detected in 14 patients (4.13%). In addition, rare variants with a cohort allele frequency below 1% were identified in 11 patients (3.24%). Among these, p.Thr65Ala, p.Thr65Met, p.Asn151Asp, and p.Val691Leu represented potentially relevant findings requiring further functional validation. Conclusions: Whole-exome analysis revealed a heterogeneous spectrum of DPYD variants in the studied Russian oncology cohort, including both established pharmacogenetic markers and rare variants that would not be captured by limited targeted panels. The overall allele-frequency pattern was predominantly similar to that of European reference populations, although several rare variants demonstrated distinct distributions. These findings support the value of population-specific characterization of DPYD and suggest that expanded sequencing approaches may complement conventional pharmacogenetic testing by identifying rare potentially functional alleles.