Piriyapongsa Jittima, Sukritha Chanathip, Kaewprommal Pavita, Intarat Chalermpong, Triparn Kwankom, Phornsiricharoenphant Krittin, Chaosrikul Chadapohn, Shaw Philip J, Chantratita Wasun, Mahasirimongkol Surakameth, Tongsima Sissades
National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand.
National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand.
J Pers Med. 2021 Nov 19;11(11):1230. doi: 10.3390/jpm11111230.
The increasing availability of next generation sequencing (NGS) for personal genomics could promote pharmacogenomics (PGx) discovery and application. However, current tools for analysis and interpretation of pharmacogenomic variants from NGS data are inadequate, as none offer comprehensive analytic functions in a simple, web-based platform. In addition, no tools exist to analyze human leukocyte antigen (HLA) genes for determining potential risks of immune-mediated adverse drug reaction (IM-ADR). We describe PharmVIP, a web-based PGx tool, for one-stop comprehensive analysis and interpretation of genome-wide variants obtained from NGS platforms. PharmVIP comprises three main interpretation modules covering analyses of pharmacogenes involved in pharmacokinetics, pharmacodynamics and IM-ADR. The Guideline module provides Clinical Pharmacogenetics Implementation Consortium (CPIC) drug guideline recommendations based on the translation of genotypic data in genes having guidelines. The HLA module reports HLA genotypes, potential adverse drug reactions, and the relevant drug guidelines. The Pharmacogenes module is employed for prioritizing variants according to variant effect on gene function. Detailed, customizable reports are provided as exportable files and as an interactive web version. PharmVIP is a new integrated NGS workflow for the PGx community to facilitate discovery and clinical application.
用于个人基因组学的下一代测序（NGS）技术日益普及，这可能会推动药物基因组学（PGx）的发现与应用。然而，目前用于分析和解读NGS数据中的药物基因组变异的工具并不完善，因为没有一个工具能在简单的基于网络的平台上提供全面的分析功能。此外，也没有工具可用于分析人类白细胞抗原（HLA）基因，以确定免疫介导的药物不良反应（IM-ADR）的潜在风险。我们介绍了PharmVIP，这是一个基于网络的PGx工具，用于对从NGS平台获得的全基因组变异进行一站式综合分析和解读。PharmVIP包含三个主要的解读模块，涵盖对涉及药代动力学、药效学和IM-ADR的药物基因的分析。指南模块根据有指南的基因中的基因型数据转换，提供临床药物遗传学实施联盟（CPIC）的药物指南建议。HLA模块报告HLA基因型、潜在的药物不良反应以及相关的药物指南。药物基因模块用于根据变异对基因功能的影响对变异进行优先级排序。详细的、可定制的报告以可导出文件和交互式网络版本的形式提供。PharmVIP是一种新的集成式NGS工作流程，供PGx领域使用，以促进发现和临床应用。
