Table5_Characterization of ADME Gene Variation in Colombian Population by Exome Sequencing.xlsx

In genes related to drug pharmacokinetics, molecular variations determine interindividual variability in the therapeutic efficacy and adverse drug reactions. The assessment of single-nucleotide variants (SNVs) is used with growing frequency in pharmacogenetic practice, and recently, high-throughput genomic analyses obtained through next-generation sequencing (NGS) have been recognized as powerful tools to identify common, rare and novel variants. These genetic profiles remain underexplored in Latin-American populations, including Colombia. In this study, we investigated the variability of 35 genes included in the ADME core panel (absorption, distribution, metabolism, and excretion) by whole-exome sequencing (WES) of 509 unrelated Colombian individuals with no previous reports of adverse drug reactions. Rare variants were filtered according to the minor allele frequencies (MAF) <1% and potential deleterious consequences. The functional impact of novel and rare missense variants was assessed using an optimized framework for pharmacogenetic variants. Bioinformatic analyses included the identification of clinically validated variants described in PharmGKB and ClinVar databases. Ancestry from WES data was inferred using the R package EthSEQ v2.1.4. Allelic frequencies were compared to other populations reported in the public gnomAD database. Our analysis revealed that rare missense pharmacogenetic variants were 2.1 times more frequent than common variants with 121 variants predicted as potentially deleterious. Rare loss of function (LoF) variants were identified in 65.7% of evaluated genes. Regarding variants with clinical pharmacogenetic effect, our study revealed 89 sequence variations in 28 genes represented by missense (62%), synonymous (22.5%), splice site (11.2%), and indels (3.4%). In this group, ABCB1, ABCC2, CY2B6, CYP2D6, DPYD, NAT2, SLC22A1, and UGTB2B7, are the most polymorphic genes. NAT2, CYP2B6 and DPYD metabolizer phenotypes demonstrated the highest variability. Ancestry analysis indicated admixture in 73% of the population. Allelic frequencies exhibit significant differences with other Latin-American populations, highlighting the importance of pharmacogenomic studies in populations of different ethnicities. Altogether, our data revealed that rare variants are an important source of variability in pharmacogenes involved in the pharmacokinetics of drugs and likely account for the unexplained interindividual variability in drug response. These findings provide evidence of the utility of WES for pharmacogenomic testing and into clinical practice.

与药物药代动力学相关的基因中，分子变异决定了个体间治疗疗效与药物不良反应的差异。单核苷酸变异（single-nucleotide variants, SNVs）的检测在药物基因组学临床实践中的应用愈发频繁；近年来，通过下一代测序（next-generation sequencing, NGS）获得的高通量基因组分析技术，已成为识别常见、罕见及新型变异的有力工具。包括哥伦比亚在内的拉美人群中，此类遗传特征的研究仍有待深入。本研究针对ADME核心基因组合（涵盖吸收、分布、代谢与排泄过程）中的35个基因，对509名无药物不良反应既往史的无亲缘关系哥伦比亚个体开展全外显子组测序（whole-exome sequencing, WES），以此分析其遗传变异特征。研究按照次要等位基因频率（minor allele frequencies, MAF）<1%的标准及潜在有害性对罕见变异进行筛选。针对新型及罕见错义变异，采用优化的药物基因组学变异分析框架评估其功能影响。生物信息学分析环节包括对PharmGKB与ClinVar数据库中已临床验证的变异进行识别。研究借助R软件包EthSEQ v2.1.4，基于全外显子组测序数据推断研究对象的祖先血统信息。将本研究得到的等位基因频率与公共数据库gnomAD中收录的其他人群数据进行对比。分析结果显示，罕见错义型药物基因组学变异的出现频率是常见变异的2.1倍，共预测得到121个潜在有害变异。在65.7%的被评估基因中，均检出罕见功能丧失（loss of function, LoF）变异。针对具有临床药物基因组学效应的变异，本研究在28个基因中共检出89处序列变异，其中错义变异占比62%、同义变异占比22.5%、剪接位点变异占比11.2%、插入缺失变异占比3.4%。该组中多态性最高的基因为ABCB1、ABCC2、CY2B6、CYP2D6、DPYD、NAT2、SLC22A1及UGTB2B7。NAT2、CYP2B6及DPYD的代谢型表型展现出最高的变异程度。血统分析结果显示，73%的研究对象呈现混合血统特征。本研究人群的等位基因频率与其他拉美人群存在显著差异，这凸显了针对不同族裔人群开展药物基因组学研究的重要性。综合来看，本研究数据表明，罕见变异是参与药物药代动力学的药物基因组基因变异的重要来源，或可解释尚未明确的药物反应个体间差异。本研究结果证实，全外显子组测序可用于药物基因组学检测并有望应用于临床实践。