Division of Pharmacology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands.
Genome Med. 2024 Aug 15;16(1):101. doi: 10.1186/s13073-024-01354-z.
The Alpe-DPD study (NCT02324452) demonstrated that prospective genotyping and dose-individualization using four alleles in DPYD (DPYD*2A/rs3918290, c.1236G > A/rs75017182, c.2846A > T/rs67376798 and c.1679 T > G/rs56038477) can mitigate the risk of severe fluoropyrimidine toxicity. However, this could not prevent all toxicities. The goal of this study was to identify additional genetic variants, both inside and outside DPYD, that may contribute to fluoropyrimidine toxicity.
Biospecimens and data from the Alpe-DPD study were used. Exon sequencing was performed to identify risk variants inside DPYD. In silico and in vitro analyses were used to classify DPYD variants. A genome-wide association study (GWAS) with severe fluoropyrimidine-related toxicity was performed to identify variants outside DPYD. Association with severe toxicity was assessed using matched-pair analyses for the exon sequencing and logistic, Cox, and ordinal regression analyses for GWAS.
Twenty-four non-synonymous, frameshift, and splice site DPYD variants were detected in ten of 986 patients. Seven of these variants (c.1670C > T, c.1913 T > C, c.1925 T > C, c.506delC, c.731A > C, c.1740 + 1G > T, c.763 - 2A > G) were predicted to be deleterious. The carriers of either of these variants showed a trend towards a 2.14-fold (95% CI, 0.41-11.3, P = 0.388) increased risk of severe toxicity compared to matched controls (N = 30). After GWAS of 942 patients, no individual single nucleotide polymorphisms achieved genome-wide significance (P ≤ 5 × 10), however, five variants were suggestive of association (P < 5 × 10) with severe toxicity.
Results from DPYD exon sequencing and GWAS analysis did not identify additional genetic variants associated with severe toxicity, which suggests that testing for single markers at a population level currently has limited clinical value. Identifying additional variants on an individual level is still promising to explain fluoropyrimidine-related severe toxicity. In addition, studies with larger samples sizes, in more diverse cohorts are needed to identify potential clinically relevant genetic variants related to severe fluoropyrimidine toxicity.
Alpe-DPD 研究（NCT02324452）表明，前瞻性基因分型和剂量个体化使用 DPYD（DPYD*2A/rs3918290、c.1236G > A/rs75017182、c.2846A > T/rs67376798 和 c.1679 T > G/rs56038477）中的四个等位基因可以降低氟嘧啶毒性的严重风险。然而，这并不能预防所有的毒性。本研究的目的是确定 DPYD 内外可能导致氟嘧啶毒性的其他遗传变异。
使用 Alpe-DPD 研究的生物样本和数据。对 DPYD 内的风险变异进行外显子测序。使用计算机模拟和体外分析对 DPYD 变异进行分类。对严重氟嘧啶相关毒性进行全基因组关联研究（GWAS），以确定 DPYD 以外的变异。使用exon 测序的配对分析和 logistic、Cox 和 ordinal 回归分析评估与严重毒性的关联，用于 GWAS。
在 986 名患者中的 10 名中检测到 24 个非同义、移码和剪接位点的 DPYD 变异。其中 7 个变异（c.1670C > T、c.1913 T > C、c.1925 T > C、c.506delC、c.731A > C、c.1740 + 1G > T、c.763 - 2A > G）被预测为有害。与匹配对照（N = 30）相比，这些变异的携带者的严重毒性风险呈 2.14 倍（95%CI，0.41-11.3，P = 0.388）增加趋势。对 942 名患者进行 GWAS 后，没有单个单核苷酸多态性达到全基因组显著水平（P ≤ 5 × 10），然而，五个变异与严重毒性具有关联的趋势（P < 5 × 10）。
DPYD 外显子测序和 GWAS 分析的结果没有发现与严重毒性相关的其他遗传变异，这表明目前在人群水平上检测单个标记的检测具有有限的临床价值。在个体水平上识别其他变异仍然有希望解释氟嘧啶相关的严重毒性。此外，需要更大样本量、更多样化队列的研究来确定与严重氟嘧啶毒性相关的潜在临床相关遗传变异。
