Updated DPYD HapB3 haplotype structure and implications for pharmacogenomic testing

Abstract

The DPYD gene encodes dihydropyrimidine dehydrogenase, the rate-limiting enzyme for the metabolism of fluoropyrimidines 5-fluorouracil and capecitabine. Genetic variants in DPYD have been associated with altered enzyme activity, therefore accurate detection and interpretation is critical to predict metabolizer status for individualized fluoropyrimidine therapy. The most commonly observed deleterious variation is the causal variant linked to the previously described HapB3 haplotype, c.1129-5923C>G (rs75017182) in intron 10, which introduces a cryptic splice site. A benign synonymous variant in exon 11, c.1236G>A (rs56038477) is also linked to HapB3 and is commonly used for testing. Previously, these single-nucleotide polymorphisms (SNPs) have been reported to be in perfect linkage disequilibrium (LD); therefore, c.1236G>A is often utilized as a proxy for the function-altering intronic variant. Clinical genotyping of DPYD identified a patient who had c.1236G>A, but not c.1129-5923C>G, suggesting that these two SNPs may not be in perfect LD, as previously assumed. Additional individuals with c.1236G>A, but not c.1129-5923C>G, were identified in the Children's Mercy Data Warehouse and the All of Us Research Program version 7 cohort substantiating incomplete SNP linkage. Consequently, testing only c.1236G>A can generate false-positive results in some cases and lead to suboptimal dosing that may negatively impact patient therapy and prospect of survival. Our data show that DPYD genotyping should include the functional variant c.1129-5923C>G, and not the c.1236G>A proxy, to accurately predict DPD activity.

FIGURE 1

Pedigree of a trio demonstrating that c.1236G>A can occur by itself and is not in complete linkage with the causal variant, c.1129‐5923C>G. As shown, the father does not have any variants while the mother is homozygous for c.1236G>A and heterozygous for c.1129‐5923C>G; the child revealed only one variant, c.1236G>A, which was inherited from the mother. Inheritance also revealed that, in this case, c.85T>C (p.Cys29Arg) is in cis with c.1129‐5923C>G and c.1236G>A. The common c.85T>C variant (gnomAD global frequency of ~28%) is classified as “normal function” by the Clinical Pharmacogenetics Implementation Consortium.