Resolving CYP2D6 Structural Complexity with Long‐Read Sequencing: Implications for Tamoxifen Precision Dosing in Thai Breast Cancer Patients

Cytochrome P450 2D6 (CYP2D6)-mediated bioactivation of tamoxifen to endoxifen is a key determinant of therapeutic efficacy in estrogen receptor-positive breast cancer. In Asian populations, the high prevalence of structurally complex CYP2D6 alleles complicates conventional genotyping, limiting accurate genotype-phenotype correlation. To address these gaps, long-read Oxford Nanopore sequencing was applied to resolve CYP2D6 structural complexity and evaluate its impact on endoxifen metabolism. The study cohort included 492 Thai breast cancer patients, with multivariable analysis performed on 361 individuals receiving standard-dose tamoxifen to determine the association between CYP2D6 activity scores and plasma endoxifen concentrations. Long-read sequencing identified 82 distinct diplotypes and successfully resolved complex structural variations, including the prevalent CYP2D6*36 + *10 non-identical duplication. Overall, 46.55% of patients were classified as having decreased enzyme function, primarily intermediate metabolizers (45.53%). CYP2D6 activity score emerged as the strongest determinant of endoxifen exposure (P < 0.001). Decreased-function genotypes were significantly associated with lower endoxifen levels (using an exploratory benchmark of ≤5.97 ng/mL), independent of parent drug concentration. These findings demonstrate that long-read sequencing enables the precise resolution of CYP2D6 structural complexity. By accurately capturing rare and complex CYP2D6 alleles, the results indicate that standard genotyping may misclassify certain patients, potentially placing a large portion of the studied population at an unrecognized risk of low tamoxifen exposure.