PharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation

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...

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Autores principales:	Jittima Piriyapongsa, Chanathip Sukritha, Pavita Kaewprommal, Chalermpong Intarat, Kwankom Triparn, Krittin Phornsiricharoenphant, Chadapohn Chaosrikul, Philip J. Shaw, Wasun Chantratita, Surakameth Mahasirimongkol, Sissades Tongsima
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	pharmacogenomics variant analysis web-based-tool next-generation sequencing allele prediction CPIC dosing recommendation Medicine R
Acceso en línea:	https://doaj.org/article/12229e615c8b45a3a02129a35f5ed467
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spelling	oai:doaj.org-article:12229e615c8b45a3a02129a35f5ed4672021-11-25T18:08:11ZPharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation10.3390/jpm111112302075-4426https://doaj.org/article/12229e615c8b45a3a02129a35f5ed4672021-11-01T00:00:00Zhttps://www.mdpi.com/2075-4426/11/11/1230https://doaj.org/toc/2075-4426The 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.Jittima PiriyapongsaChanathip SukrithaPavita KaewprommalChalermpong IntaratKwankom TriparnKrittin PhornsiricharoenphantChadapohn ChaosrikulPhilip J. ShawWasun ChantratitaSurakameth MahasirimongkolSissades TongsimaMDPI AGarticlepharmacogenomicsvariant analysisweb-based-toolnext-generation sequencingallele predictionCPIC dosing recommendationMedicineRENJournal of Personalized Medicine, Vol 11, Iss 1230, p 1230 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	pharmacogenomics variant analysis web-based-tool next-generation sequencing allele prediction CPIC dosing recommendation Medicine R
spellingShingle	pharmacogenomics variant analysis web-based-tool next-generation sequencing allele prediction CPIC dosing recommendation Medicine R Jittima Piriyapongsa Chanathip Sukritha Pavita Kaewprommal Chalermpong Intarat Kwankom Triparn Krittin Phornsiricharoenphant Chadapohn Chaosrikul Philip J. Shaw Wasun Chantratita Surakameth Mahasirimongkol Sissades Tongsima PharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation
description	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.
format	article
author	Jittima Piriyapongsa Chanathip Sukritha Pavita Kaewprommal Chalermpong Intarat Kwankom Triparn Krittin Phornsiricharoenphant Chadapohn Chaosrikul Philip J. Shaw Wasun Chantratita Surakameth Mahasirimongkol Sissades Tongsima
author_facet	Jittima Piriyapongsa Chanathip Sukritha Pavita Kaewprommal Chalermpong Intarat Kwankom Triparn Krittin Phornsiricharoenphant Chadapohn Chaosrikul Philip J. Shaw Wasun Chantratita Surakameth Mahasirimongkol Sissades Tongsima
author_sort	Jittima Piriyapongsa
title	PharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation
title_short	PharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation
title_full	PharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation
title_fullStr	PharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation
title_full_unstemmed	PharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation
title_sort	pharmvip: a web-based tool for pharmacogenomic variant analysis and interpretation
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/12229e615c8b45a3a02129a35f5ed467
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PharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation

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