Sharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange

Abstract Genetic variants causing underlying pharmacogenetic and disease phenotypes have been used as the basis for clinical decision-making. However, due to the lack of standards for next-generation sequencing (NGS) pipelines, reproducing genetic variants among institutions is still difficult. The...

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Autores principales:	Jeong Hoon Lee, Solbi Kweon, Yu Rang Park
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b026acb47b924d8a853c52553e34ffb5
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spelling	oai:doaj.org-article:b026acb47b924d8a853c52553e34ffb52021-12-02T14:16:58ZSharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange10.1038/s41598-021-82006-92045-2322https://doaj.org/article/b026acb47b924d8a853c52553e34ffb52021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-82006-9https://doaj.org/toc/2045-2322Abstract Genetic variants causing underlying pharmacogenetic and disease phenotypes have been used as the basis for clinical decision-making. However, due to the lack of standards for next-generation sequencing (NGS) pipelines, reproducing genetic variants among institutions is still difficult. The aim of this study is to show how many important variants for clinical decisions can be individually detected using different pipelines. Genetic variants were derived from 105 breast cancer patient target DNA sequences via three different variant-calling pipelines. HaplotypeCaller, Mutect2 tumor-only mode in the Genome Analysis ToolKit (GATK), and VarScan were used in variant calling from the sequence read data processed by the same NGS preprocessing tools using Variant Effect Predictor. GATK HaplotypeCaller, VarScan, and MuTect2 found 25,130, 16,972, and 4232 variants, comprising 1491, 1400, and 321 annotated variants with ClinVar significance, respectively. The average number of ClinVar significant variants in the patients was 769.43, 16.50% of the variants were detected by only one variant caller. Despite variants with significant impact on clinical decision-making, the detected variants are different for each algorithm. To utilize genetic variants in the clinical field, a strict standard for NGS pipelines is essential.Jeong Hoon LeeSolbi KweonYu Rang ParkNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-7 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jeong Hoon Lee Solbi Kweon Yu Rang Park Sharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange
description	Abstract Genetic variants causing underlying pharmacogenetic and disease phenotypes have been used as the basis for clinical decision-making. However, due to the lack of standards for next-generation sequencing (NGS) pipelines, reproducing genetic variants among institutions is still difficult. The aim of this study is to show how many important variants for clinical decisions can be individually detected using different pipelines. Genetic variants were derived from 105 breast cancer patient target DNA sequences via three different variant-calling pipelines. HaplotypeCaller, Mutect2 tumor-only mode in the Genome Analysis ToolKit (GATK), and VarScan were used in variant calling from the sequence read data processed by the same NGS preprocessing tools using Variant Effect Predictor. GATK HaplotypeCaller, VarScan, and MuTect2 found 25,130, 16,972, and 4232 variants, comprising 1491, 1400, and 321 annotated variants with ClinVar significance, respectively. The average number of ClinVar significant variants in the patients was 769.43, 16.50% of the variants were detected by only one variant caller. Despite variants with significant impact on clinical decision-making, the detected variants are different for each algorithm. To utilize genetic variants in the clinical field, a strict standard for NGS pipelines is essential.
format	article
author	Jeong Hoon Lee Solbi Kweon Yu Rang Park
author_facet	Jeong Hoon Lee Solbi Kweon Yu Rang Park
author_sort	Jeong Hoon Lee
title	Sharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange
title_short	Sharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange
title_full	Sharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange
title_fullStr	Sharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange
title_full_unstemmed	Sharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange
title_sort	sharing genetic variants with the ngs pipeline is essential for effective genomic data sharing and reproducibility in health information exchange
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/b026acb47b924d8a853c52553e34ffb5
work_keys_str_mv	AT jeonghoonlee sharinggeneticvariantswiththengspipelineisessentialforeffectivegenomicdatasharingandreproducibilityinhealthinformationexchange AT solbikweon sharinggeneticvariantswiththengspipelineisessentialforeffectivegenomicdatasharingandreproducibilityinhealthinformationexchange AT yurangpark sharinggeneticvariantswiththengspipelineisessentialforeffectivegenomicdatasharingandreproducibilityinhealthinformationexchange
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Sharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange

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