从临床下一代测序中计算药物基因型提取
Tyler Shugg1, Reynold C Ly2, Wilberforce Osei1
1Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.
Frontiers in oncology
|July 20, 2023
概括
阿尔迪计算方法从临床全基因组测序 (WGS) 和全外因组测序 (WES) 数据中准确地提取药物基因组 (PGx) 基因型. 这支持将NGS数据重新用于个性化医学和临床PGx应用.
科学领域:
- 基因组医学是基因组医学.
- 计算生物学 计算生物学
- 临床药理学 临床药理学
背景情况:
- 下一代测序 (NGS) 越来越多地用于临床护理.
- 为临床药物基因组学 (PGx) 重用NGS数据需要验证的计算方法.
- 目前从NGS数据获得PGx的计算方法缺乏广泛的临床验证.
研究的目的:
- 评估Aldy计算方法从临床WGS和WES数据中提取PGx基因型的准确性.
- 根据CLIA认证的PGx基因型鉴定参考标准验证Aldy的性能.
- 确定Aldy在从NGS数据中识别临床可操作的PGx变异中的实用性.
主要方法:
- 分析了264名患者的生殖系DNA,使用基于小组的基因型和临床WGS/WES.
- Aldy 3.3 和 4.4 版本用于从 NGS 数据中提取 PGx 基因型.
- 将阿尔迪衍生的基因型与一个参考标准进行比较,该标准包括14个主要药物基因中的45个明星等位基因定义变异.
主要成果:
- 艾尔迪v3.3与WGS数据的基因型识别达到了>99%的一致性,确定了额外的可操作的等位基因.
- 阿尔迪v4.4显示WGS和WES数据的一致性>99%,即使有CYP2D6拷贝数等变异,也具有很高的准确性.
- WGS和WES数据的平均读取深度超过了30倍,确保了可靠的基因型调用.
结论:
- 阿尔迪v3.3和v4.4从临床WGS和WES数据中准确地调用药物基因双型,准确度>99%.
- 这些发现验证了Aldy重新利用临床NGS数据以告知临床PGx决策的能力.
- 该研究支持将Aldy集成到临床工作流程中,以提高个性化医疗.
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