VPMBench: a test bench for variant prioritization methods

Abstract Background Clinical diagnostics of whole-exome and whole-genome sequencing data requires geneticists to consider thousands of genetic variants for each patient. Various variant prioritization methods have been developed over the last years to aid clinicians in identifying variants that are...

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Autores principales:	Andreas Ruscheinski, Anna Lena Reimler, Roland Ewald, Adelinde M. Uhrmacher
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Bioinformatics Software Test bench Variant prioritization Evaluation Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/5dce2ef8cf3d43689c1b771f49ae7724
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spelling	oai:doaj.org-article:5dce2ef8cf3d43689c1b771f49ae77242021-11-14T12:13:08ZVPMBench: a test bench for variant prioritization methods10.1186/s12859-021-04458-01471-2105https://doaj.org/article/5dce2ef8cf3d43689c1b771f49ae77242021-11-01T00:00:00Zhttps://doi.org/10.1186/s12859-021-04458-0https://doaj.org/toc/1471-2105Abstract Background Clinical diagnostics of whole-exome and whole-genome sequencing data requires geneticists to consider thousands of genetic variants for each patient. Various variant prioritization methods have been developed over the last years to aid clinicians in identifying variants that are likely disease-causing. Each time a new method is developed, its effectiveness must be evaluated and compared to other approaches based on the most recently available evaluation data. Doing so in an unbiased, systematic, and replicable manner requires significant effort. Results The open-source test bench “VPMBench” automates the evaluation of variant prioritization methods. VPMBench introduces a standardized interface for prioritization methods and provides a plugin system that makes it easy to evaluate new methods. It supports different input data formats and custom output data preparation. VPMBench exploits declaratively specified information about the methods, e.g., the variants supported by the methods. Plugins may also be provided in a technology-agnostic manner via containerization. Conclusions VPMBench significantly simplifies the evaluation of both custom and published variant prioritization methods. As we expect variant prioritization methods to become ever more critical with the advent of whole-genome sequencing in clinical diagnostics, such tool support is crucial to facilitate methodological research.Andreas RuscheinskiAnna Lena ReimlerRoland EwaldAdelinde M. UhrmacherBMCarticleBioinformaticsSoftwareTest benchVariant prioritizationEvaluationComputer applications to medicine. Medical informaticsR858-859.7Biology (General)QH301-705.5ENBMC Bioinformatics, Vol 22, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Bioinformatics Software Test bench Variant prioritization Evaluation Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5
spellingShingle	Bioinformatics Software Test bench Variant prioritization Evaluation Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5 Andreas Ruscheinski Anna Lena Reimler Roland Ewald Adelinde M. Uhrmacher VPMBench: a test bench for variant prioritization methods
description	Abstract Background Clinical diagnostics of whole-exome and whole-genome sequencing data requires geneticists to consider thousands of genetic variants for each patient. Various variant prioritization methods have been developed over the last years to aid clinicians in identifying variants that are likely disease-causing. Each time a new method is developed, its effectiveness must be evaluated and compared to other approaches based on the most recently available evaluation data. Doing so in an unbiased, systematic, and replicable manner requires significant effort. Results The open-source test bench “VPMBench” automates the evaluation of variant prioritization methods. VPMBench introduces a standardized interface for prioritization methods and provides a plugin system that makes it easy to evaluate new methods. It supports different input data formats and custom output data preparation. VPMBench exploits declaratively specified information about the methods, e.g., the variants supported by the methods. Plugins may also be provided in a technology-agnostic manner via containerization. Conclusions VPMBench significantly simplifies the evaluation of both custom and published variant prioritization methods. As we expect variant prioritization methods to become ever more critical with the advent of whole-genome sequencing in clinical diagnostics, such tool support is crucial to facilitate methodological research.
format	article
author	Andreas Ruscheinski Anna Lena Reimler Roland Ewald Adelinde M. Uhrmacher
author_facet	Andreas Ruscheinski Anna Lena Reimler Roland Ewald Adelinde M. Uhrmacher
author_sort	Andreas Ruscheinski
title	VPMBench: a test bench for variant prioritization methods
title_short	VPMBench: a test bench for variant prioritization methods
title_full	VPMBench: a test bench for variant prioritization methods
title_fullStr	VPMBench: a test bench for variant prioritization methods
title_full_unstemmed	VPMBench: a test bench for variant prioritization methods
title_sort	vpmbench: a test bench for variant prioritization methods
publisher	BMC
publishDate	2021
url	https://doaj.org/article/5dce2ef8cf3d43689c1b771f49ae7724
work_keys_str_mv	AT andreasruscheinski vpmbenchatestbenchforvariantprioritizationmethods AT annalenareimler vpmbenchatestbenchforvariantprioritizationmethods AT rolandewald vpmbenchatestbenchforvariantprioritizationmethods AT adelindemuhrmacher vpmbenchatestbenchforvariantprioritizationmethods
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VPMBench: a test bench for variant prioritization methods

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