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GrabBlur - a framework to facilitate the secure exchange of whole-exome and -genome SNV data using VCF files

BACKGROUND: Next Generation Sequencing (NGS) of whole exomes or genomes is increasingly being used in human genetic research and diagnostics. Sharing NGS data with third parties can help physicians and researchers to identify causative or predisposing mutations for a specific sample of interest more...

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Autores principales: Stade, Björn, Seelow, Dominik, Thomsen, Ingo, Krawczak, Michael, Franke, Andre
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083413/
https://www.ncbi.nlm.nih.gov/pubmed/25055742
http://dx.doi.org/10.1186/1471-2164-15-S4-S8
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author Stade, Björn
Seelow, Dominik
Thomsen, Ingo
Krawczak, Michael
Franke, Andre
author_facet Stade, Björn
Seelow, Dominik
Thomsen, Ingo
Krawczak, Michael
Franke, Andre
author_sort Stade, Björn
collection PubMed
description BACKGROUND: Next Generation Sequencing (NGS) of whole exomes or genomes is increasingly being used in human genetic research and diagnostics. Sharing NGS data with third parties can help physicians and researchers to identify causative or predisposing mutations for a specific sample of interest more efficiently. In many cases, however, the exchange of such data may collide with data privacy regulations. GrabBlur is a newly developed tool to aggregate and share NGS-derived single nucleotide variant (SNV) data in a public database, keeping individual samples unidentifiable. In contrast to other currently existing SNV databases, GrabBlur includes phenotypic information and contact details of the submitter of a given database entry. By means of GrabBlur human geneticists can securely and easily share SNV data from resequencing projects. GrabBlur can ease the interpretation of SNV data by offering basic annotations, genotype frequencies and in particular phenotypic information - given that this information was shared - for the SNV of interest. TOOL DESCRIPTION: GrabBlur facilitates the combination of phenotypic and NGS data (VCF files) via a local interface or command line operations. Data submissions may include HPO (Human Phenotype Ontology) terms, other trait descriptions, NGS technology information and the identity of the submitter. Most of this information is optional and its provision at the discretion of the submitter. Upon initial intake, GrabBlur merges and aggregates all sample-specific data. If a certain SNV is rare, the sample-specific information is replaced with the submitter identity. Generally, all data in GrabBlur are highly aggregated so that they can be shared with others while ensuring maximum privacy. Thus, it is impossible to reconstruct complete exomes or genomes from the database or to re-identify single individuals. After the individual information has been sufficiently "blurred", the data can be uploaded into a publicly accessible domain where aggregated genotypes are provided alongside phenotypic information. A web interface allows querying the database and the extraction of gene-wise SNV information. If an interesting SNV is found, the interrogator can get in contact with the submitter to exchange further information on the carrier and clarify, for example, whether the latter's phenotype matches with phenotype of their own patient.
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spelling pubmed-40834132014-07-18 GrabBlur - a framework to facilitate the secure exchange of whole-exome and -genome SNV data using VCF files Stade, Björn Seelow, Dominik Thomsen, Ingo Krawczak, Michael Franke, Andre BMC Genomics Research BACKGROUND: Next Generation Sequencing (NGS) of whole exomes or genomes is increasingly being used in human genetic research and diagnostics. Sharing NGS data with third parties can help physicians and researchers to identify causative or predisposing mutations for a specific sample of interest more efficiently. In many cases, however, the exchange of such data may collide with data privacy regulations. GrabBlur is a newly developed tool to aggregate and share NGS-derived single nucleotide variant (SNV) data in a public database, keeping individual samples unidentifiable. In contrast to other currently existing SNV databases, GrabBlur includes phenotypic information and contact details of the submitter of a given database entry. By means of GrabBlur human geneticists can securely and easily share SNV data from resequencing projects. GrabBlur can ease the interpretation of SNV data by offering basic annotations, genotype frequencies and in particular phenotypic information - given that this information was shared - for the SNV of interest. TOOL DESCRIPTION: GrabBlur facilitates the combination of phenotypic and NGS data (VCF files) via a local interface or command line operations. Data submissions may include HPO (Human Phenotype Ontology) terms, other trait descriptions, NGS technology information and the identity of the submitter. Most of this information is optional and its provision at the discretion of the submitter. Upon initial intake, GrabBlur merges and aggregates all sample-specific data. If a certain SNV is rare, the sample-specific information is replaced with the submitter identity. Generally, all data in GrabBlur are highly aggregated so that they can be shared with others while ensuring maximum privacy. Thus, it is impossible to reconstruct complete exomes or genomes from the database or to re-identify single individuals. After the individual information has been sufficiently "blurred", the data can be uploaded into a publicly accessible domain where aggregated genotypes are provided alongside phenotypic information. A web interface allows querying the database and the extraction of gene-wise SNV information. If an interesting SNV is found, the interrogator can get in contact with the submitter to exchange further information on the carrier and clarify, for example, whether the latter's phenotype matches with phenotype of their own patient. BioMed Central 2014-05-20 /pmc/articles/PMC4083413/ /pubmed/25055742 http://dx.doi.org/10.1186/1471-2164-15-S4-S8 Text en Copyright © 2014 Stade et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Stade, Björn
Seelow, Dominik
Thomsen, Ingo
Krawczak, Michael
Franke, Andre
GrabBlur - a framework to facilitate the secure exchange of whole-exome and -genome SNV data using VCF files
title GrabBlur - a framework to facilitate the secure exchange of whole-exome and -genome SNV data using VCF files
title_full GrabBlur - a framework to facilitate the secure exchange of whole-exome and -genome SNV data using VCF files
title_fullStr GrabBlur - a framework to facilitate the secure exchange of whole-exome and -genome SNV data using VCF files
title_full_unstemmed GrabBlur - a framework to facilitate the secure exchange of whole-exome and -genome SNV data using VCF files
title_short GrabBlur - a framework to facilitate the secure exchange of whole-exome and -genome SNV data using VCF files
title_sort grabblur - a framework to facilitate the secure exchange of whole-exome and -genome snv data using vcf files
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083413/
https://www.ncbi.nlm.nih.gov/pubmed/25055742
http://dx.doi.org/10.1186/1471-2164-15-S4-S8
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