Updated DPYDHapB3 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 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 v7 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 shows that DPYD genotyping should include the functional variant c.1129‐5923C>G, and not the c.1236G>A proxy, to accurately predict DPD activity.

DPYD genotyping panels: Impact of population diversity

“…The updated analysis of DPYD HapB3 haplotype structure by Turner et al. 1 identified individuals who had c.1236G>A (rs56038477), but not c.1129‐5923C>G (rs75017182), suggesting that the two SNPs may not be in complete linkage disequilibrium (LD), as previously assumed. Accordingly, LD in the All‐of‐Us cohort ( n = 245,394) was reported at 0.9985: 13 individuals of European ancestry and one of “Other” ancestry, out of 6265 carriers of c.1236G>A, lacked c.1129‐5923C>G, while LD was perfect in African/African American, Admixed American/Latino, East Asian, Middle Eastern, and South Asian cohorts.…”

“…Importantly, the proportion of carriers of rs115232898 among Admixed Americans (range 0.2%–0.4%) and African/African Americans (>4%) in the gnomAD and 1KG cohorts is similar to, and nearly 20‐fold greater, respectively, than the proportion of individual who had c.1236G>A without c.1129‐5923C>G in the overall All‐of‐Us cohort (0.223%). 1 Thus, exclusion of rs115232898 from DPYD genotyping panels impacts the inference of DPD function in Admixed Americans to a similar, and in African/African Americans to a considerably greater extent as the reported lack of LD between c.1236G>A and c.1129‐5923C>G, which prompted the update of the CPIC guideline for fluoropyrimidines. Of note, all but one individual who had c.1236G>A but not c.1129‐5923C>G had European ancestry.…”

Response to “DPYD genotyping panels: Impact of population diversity”

“…We thank Dr. Suarez-Kurtz for his Letter to the Editor on our publication "DPYD HapB3 haplotype structure and implications for pharmacogenomic testing". 1 In response to our findings, the Clinical Pharmacogenetics Implementation Consortium (CPIC) posted an update to their online guideline for fluoropyrimidines and DPYD 2 to promote awareness that the c.1236G>A variant may not always be linked to the causal, deep intronic c.1129-5923C>G variant. Based on our "All of US" data, false-positive calls due to the presence of c.1236G>A, while c.1129-5923C>G is absent, are most likely presenting in patients of European ancestry (13 cases had European ancestry and one was "Other").…”