Characterization of DPYD variants across ancestries in a large real-world cohort of cancer patients.

Abstract

814 Background: Dihydropyrimidine dehydrogenase (DPD), encoded by the DPYD gene, metabolizes 5-fluorouracil (5FU). DPD deficiency due to DPYD variants can cause severe drug-related toxicities. Most genomic studies focus on populations of European (EUR) genetic ancestry, underscoring the need for broader ancestral representation. Methods: Using Natera’s Real-World Database, we analyzed clinicogenomic data from 228,239 solid tumor patients who underwent Signatera ctDNA testing (2019–2025). Whole-exome sequencing and ancestry inference (EthSeq) grouped patients into EUR, African (AFR), East Asian (EAS), and South Asian (SAS) cohorts. DPYD variants were annotated using VEP (v1.1.4, GRCh37) and classified as Tier 1/2 per AMP guidelines. Results: After excluding cancer types not treated with 5FU (lung, N=8,711; melanoma, N=7,600), the most common cancer types were CRC (N=106,839; 47.3%), breast (N=54,410; 24.1%), and bladder (N=8,154; 3.6%). The cohort was predominantly EUR (183,842; 81.3%), followed by AFR (24,117; 10.7%), EAS (10,882; 4.8%), and SAS (3,285; 1.5%). A total of 1,789 DPYD variants (1,603 loci) were detected. Fourteen unique Tier 1/2 variants (13 loci) were detected in 5.0% of patients (99.3% heterozygous). Combined Tier 1/2 frequencies were similar for EUR (5.2%) and AFR (5.4%), but markedly lower in EAS (0.7%), with individual variants displaying strong divergence between ancestry groups (top variants listed in the table). Conclusions: This study, which includes a substantial number of patients from ancestries often underrepresented in genomic research (>3,000 SAS, >10,000 EAS, and >24,000 AFR), reveals marked differences in the prevalence of clinically relevant DPYD variants across populations. The higher frequency of certain individual variants in AFR patients underscores the limitations of current pharmacogenetic testing panels optimized largely based on EUR cohorts. These findings support broader ancestry-informed pharmacogenetic screening to reduce 5FU toxicity risk across diverse populations. Prevalence of top tier 1/2 variants across ancestry groups. Variant ID Tier All EUR AFR EAS rs56038477 1 2.97% 3.42% 0.70% 0.15% rs67376798 1 0.89% 1.04% 0.26% 0.09% rs3918290 1 0.47% 0.54% 0.09% 0.02% rs115232898 1 0.46% 0.06% 3.79% 0.03% rs55886062 1 0.10% 0.11% 0.03% 0.00% rs146356975 1 0.06% 0.01% 0.54% 0.01% rs72549309 2 0.03% 0.03% 0.01% 0.00% rs59086055 2 0.02% 0.01% 0.01% 0.26%