Incomplete linkage disequilibrium between DPYD HapB3 variants: implications for pharmacogenetic phenotype assignment
Abstract
BackgroundReduced dihydropyrimidine dehydrogenase (DPD) activity is a major determinant of severe fluoropyrimidine-associated toxicity. The DPYD HapB3 haplotype is commonly identified through the synonymous variant c.1236G>A (rs56038477), which has traditionally been used as a proxy for the functional intronic variant c.1129–5923C>G (rs75017182). However, emerging evidence suggests that the linkage between these variants may not be absolute, potentially leading to inaccurate haplotype assignment. This study aimed to determine the frequency of clinically relevant DPYD variants in our population and to assess concordance between c.1236G>A and c.1129–5923C>G.MethodsWe conducted a retrospective observational study including 3276 individuals who underwent routine pharmacogenetic testing. Genotyping was performed using the OpenArray™ platform. Allele and genotype frequencies of clinically relevant DPYD variants were calculated, and concordance between c.1236G>A and c.1129–5923C>G was evaluated. Samples showing discordant or atypical HapB3-associated genotypes were subjected to confirmatory analysis by next-generation sequencing (NGS).ResultsAllele frequencies were consistent with those reported in European and Spanish populations. One biologically discordant genotype configuration was identified among 3276 individuals, in which c.1236G>A was detected in the absence of c.1129–5923C>G; this finding was confirmed by NGS. A second apparently discordant case, initially classified as homozygous for c.1129–5923C>G but heterozygous for c.1236G>A, was attributed to automated genotype misclassification by the Thermo Fisher Connect Platform. NGS analysis subsequently demonstrated homozygosity for both variants, whereas review of the cluster plot revealed atypical fluorescence patterns likely responsible for the erroneous automated genotype call. These findings indicate that, in our population, incomplete linkage disequilibrium between these variants, as well as technical limitations of genotyping platforms, may compromise accurate HapB3 characterization.ConclusionConcordance between the HapB3-associated variants c.1236G>A and c.1129–5923C>G is extremely high but not absolute. Apparent HapB3 discordance may result from either rare biological dissociation or technical genotype misclassification, both of which can affect DPYD phenotype assignment. These findings support direct genotyping of c.1129–5923C>G whenever feasible and orthogonal confirmation of atypical or discordant genotyping results.
Related
- Genetic Insights Into Cardiomyopathy With Restrictive Phenotype: Implications for Diagnosis and Personalized Care.
- Diverse PAX6 variants in three Chinese families with congenital aniridia: genotype–phenotype correlations and diagnostic implications
- Development and Preliminary Evaluation of a Pharmacogenetic Panel for Risk Stratification of Liver Injury in Polypharmacy
- Pharmacogenetic testing to improve care in the emergency department
- Pharmacogenetic Evidence in Opioid-Related Toxicity and Death with an Appraisal of Emerging Multi-Omics Studies: A Systematic Review
BibTeX
@article{alvarezmontero2026incomplete,
title = {{Incomplete linkage disequilibrium between DPYD HapB3 variants: implications for pharmacogenetic phenotype assignment}},
author = {Miguel Álvarez-Montero and Fiorela C. Dueñas-López and Ramón Pardo-Puras and Tania S. Rubio-Lepe and Elena Diago-Sempere and Pedro Arias and Belén Ferrer-Martínez and Ismael Ghanem and Lucía de Dios-Blázquez and Carlos Rodríguez-Antolín and Irene García-García and Rocío Rosas-Alonso and Alberto M. Borobia},
journal = {Frontiers in Pharmacology},
year = {2026},
month = nov,
doi = {10.3389/fphar.2026.1954600},
url = {https://www.frontiersin.org/articles/10.3389/fphar.2026.1954600},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Incomplete linkage disequilibrium between DPYD HapB3 variants: implications for pharmacogenetic phenotype assignment
AU - Miguel Álvarez-Montero
AU - Fiorela C. Dueñas-López
AU - Ramón Pardo-Puras
AU - Tania S. Rubio-Lepe
AU - Elena Diago-Sempere
AU - Pedro Arias
AU - Belén Ferrer-Martínez
AU - Ismael Ghanem
AU - Lucía de Dios-Blázquez
AU - Carlos Rodríguez-Antolín
AU - Irene García-García
AU - Rocío Rosas-Alonso
AU - Alberto M. Borobia
PY - 2026
DA - 2026/11/06
JO - Frontiers in Pharmacology
DO - 10.3389/fphar.2026.1954600
UR - https://www.frontiersin.org/articles/10.3389/fphar.2026.1954600
AB - BackgroundReduced dihydropyrimidine dehydrogenase (DPD) activity is a major determinant of severe fluoropyrimidine-associated toxicity. The DPYD HapB3 haplotype is commonly identified through the synonymous variant c.1236G>A (rs56038477), which has traditionally been used as a proxy for the functional intronic variant c.1129–5923C>G (rs75017182). However, emerging evidence suggests that the linkage between these variants may not be absolute, potentially leading to inaccurate haplotype assignment. This study aimed to determine the frequency of clinically relevant DPYD variants in our population and to assess concordance between c.1236G>A and c.1129–5923C>G.MethodsWe conducted a retrospective observational study including 3276 individuals who underwent routine pharmacogenetic testing. Genotyping was performed using the OpenArray™ platform. Allele and genotype frequencies of clinically relevant DPYD variants were calculated, and concordance between c.1236G>A and c.1129–5923C>G was evaluated. Samples showing discordant or atypical HapB3-associated genotypes were subjected to confirmatory analysis by next-generation sequencing (NGS).ResultsAllele frequencies were consistent with those reported in European and Spanish populations. One biologically discordant genotype configuration was identified among 3276 individuals, in which c.1236G>A was detected in the absence of c.1129–5923C>G; this finding was confirmed by NGS. A second apparently discordant case, initially classified as homozygous for c.1129–5923C>G but heterozygous for c.1236G>A, was attributed to automated genotype misclassification by the Thermo Fisher Connect Platform. NGS analysis subsequently demonstrated homozygosity for both variants, whereas review of the cluster plot revealed atypical fluorescence patterns likely responsible for the erroneous automated genotype call. These findings indicate that, in our population, incomplete linkage disequilibrium between these variants, as well as technical limitations of genotyping platforms, may compromise accurate HapB3 characterization.ConclusionConcordance between the HapB3-associated variants c.1236G>A and c.1129–5923C>G is extremely high but not absolute. Apparent HapB3 discordance may result from either rare biological dissociation or technical genotype misclassification, both of which can affect DPYD phenotype assignment. These findings support direct genotyping of c.1129–5923C>G whenever feasible and orthogonal confirmation of atypical or discordant genotyping results.
SN - 1663-9812
ER -