NGS-based <i>DPYD</i> diplotype analysis beyond conventional targeted variant testing in an ethnically diverse cancer patient cohort.

Abstract

e15131 Background: Germline variants in the highly polymorphic DPYD gene are the main cause of dihydropyrimidine dehydrogenase (DPD) deficiency and are strongly associated with fluoropyrimidine-related toxicity. PCR-based assays test limited predefined variants and may miss clinically relevant alleles, particularly in ethnically diverse populations. Next-generation sequencing (NGS) allows broader and comprehensive assessment of DPYD variation. Methods: This retrospective study included 4,380 diagnosed cancer patients of Caucasian and non-Caucasian ancestry undergoing routine DPYD testing using NGS-based profiling with the Shield assay at Datar Cancer Genetics. Identified variants were translated into diplotypes and assigned activity scores according to CPIC and DPWG guidelines, classifying patients as normal, intermediate, or poor metabolizers. Results: Clinically relevant DPYD variants associated with reduced or absent DPD activity were identified in 4.8% (211/4380) of patients, comprising 4.7% (n = 209) intermediate and 0.1% (n = 2) poor metabolizers. Reduced-function and no-function alleles detected in the cohort included *2A, HapB3, and c.557A&gt;G, either in heterozygous or compound diplotype configurations. Intermediate metabolizer status was driven by diplotypes such as *9A/HapB3 and c.557A&gt;G–containing combinations, reflecting the impact of a single reduced-function allele when paired with an otherwise normal allele. Poor metabolizer phenotypes were exclusively associated with biallelic or compound heterozygous diplotypes involving known no-function or severely reduced-function alleles, including *2A/*2A and HapB3/*2A. Notably, several clinically actionable diplotypes would not have been detected by assays limited to a small set of predefined variants, emphasizing the importance of comprehensive NGS-based DPYD profiling and diplotype-level interpretation for accurate phenotype assignment. Conclusions: Nearly 5% of patients were classified as intermediate or poor metabolizers, placing them at increased risk for severe fluoropyrimidine toxicity. Comprehensive NGS-based DPYD testing enables detection of both common and rare reduced-function variants, supports more accurate phenotype assignment, and provides a practical approach to safer fluoropyrimidine dosing in ethnically diverse clinical populations. Clinically actionable DPYD alleles identified by NGS. Allele Frequency Function HapB3 3.04% Reduced function allele *2A 0.91% Absent DPYD activity allele c.2846A&gt;T 0.50% Reduced function allele c.2279C&gt;T 0.23% Reduced function allele c.557A&gt;G 0.11% Reduced function allele *4 3.45% Absent DPYD activity allele *13 0.07% Absent DPYD activity allele *3 0.02% Absent DPYD activity allele *8 0.02% Absent DPYD activity allele