Storing and analyzing a genome on a blockchain

There are major efforts underway to make genome sequencing a routine part of clinical practice. A critical barrier to these is achieving practical solutions for data ownership and integrity. Blockchain provides solutions to these challenges in other realms, such as finance. However, its use in genom...

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Autores principales: Gürsoy, Gamze, Brannon, Charlotte M., Ni, Eric, Wagner, Sarah, Khanna, Amol, Gerstein, Mark
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9241283/
https://www.ncbi.nlm.nih.gov/pubmed/35765079
http://dx.doi.org/10.1186/s13059-022-02699-7
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author Gürsoy, Gamze
Brannon, Charlotte M.
Ni, Eric
Wagner, Sarah
Khanna, Amol
Gerstein, Mark
author_facet Gürsoy, Gamze
Brannon, Charlotte M.
Ni, Eric
Wagner, Sarah
Khanna, Amol
Gerstein, Mark
author_sort Gürsoy, Gamze
collection PubMed
description There are major efforts underway to make genome sequencing a routine part of clinical practice. A critical barrier to these is achieving practical solutions for data ownership and integrity. Blockchain provides solutions to these challenges in other realms, such as finance. However, its use in genomics is stymied due to the difficulty in storing large-scale data on-chain, slow transaction speeds, and limitations on querying. To overcome these roadblocks, we developed a private blockchain network to store genomic variants and reference-aligned reads on-chain. It uses nested database indexing with an accompanying tool suite to rapidly access and analyze the data. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02699-7.
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spelling pubmed-92412832022-06-30 Storing and analyzing a genome on a blockchain Gürsoy, Gamze Brannon, Charlotte M. Ni, Eric Wagner, Sarah Khanna, Amol Gerstein, Mark Genome Biol Software There are major efforts underway to make genome sequencing a routine part of clinical practice. A critical barrier to these is achieving practical solutions for data ownership and integrity. Blockchain provides solutions to these challenges in other realms, such as finance. However, its use in genomics is stymied due to the difficulty in storing large-scale data on-chain, slow transaction speeds, and limitations on querying. To overcome these roadblocks, we developed a private blockchain network to store genomic variants and reference-aligned reads on-chain. It uses nested database indexing with an accompanying tool suite to rapidly access and analyze the data. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02699-7. BioMed Central 2022-06-29 /pmc/articles/PMC9241283/ /pubmed/35765079 http://dx.doi.org/10.1186/s13059-022-02699-7 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Gürsoy, Gamze
Brannon, Charlotte M.
Ni, Eric
Wagner, Sarah
Khanna, Amol
Gerstein, Mark
Storing and analyzing a genome on a blockchain
title Storing and analyzing a genome on a blockchain
title_full Storing and analyzing a genome on a blockchain
title_fullStr Storing and analyzing a genome on a blockchain
title_full_unstemmed Storing and analyzing a genome on a blockchain
title_short Storing and analyzing a genome on a blockchain
title_sort storing and analyzing a genome on a blockchain
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9241283/
https://www.ncbi.nlm.nih.gov/pubmed/35765079
http://dx.doi.org/10.1186/s13059-022-02699-7
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