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sfkit: a web-based toolkit for secure and federated genomic analysis

Advances in genomics are increasingly depending upon the ability to analyze large and diverse genomic data collections, which are often difficult to amass due to privacy concerns. Recent works have shown that it is possible to jointly analyze datasets held by multiple parties, while provably preserv...

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Autores principales: Mendelsohn, Simon, Froelicher, David, Loginov, Denis, Bernick, David, Berger, Bonnie, Cho, Hyunghoon
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320181/
https://www.ncbi.nlm.nih.gov/pubmed/37246709
http://dx.doi.org/10.1093/nar/gkad464
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author Mendelsohn, Simon
Froelicher, David
Loginov, Denis
Bernick, David
Berger, Bonnie
Cho, Hyunghoon
author_facet Mendelsohn, Simon
Froelicher, David
Loginov, Denis
Bernick, David
Berger, Bonnie
Cho, Hyunghoon
author_sort Mendelsohn, Simon
collection PubMed
description Advances in genomics are increasingly depending upon the ability to analyze large and diverse genomic data collections, which are often difficult to amass due to privacy concerns. Recent works have shown that it is possible to jointly analyze datasets held by multiple parties, while provably preserving the privacy of each party’s dataset using cryptographic techniques. However, these tools have been challenging to use in practice due to the complexities of the required setup and coordination among the parties. We present sfkit, a secure and federated toolkit for collaborative genomic studies, to allow groups of collaborators to easily perform joint analyses of their datasets without compromising privacy. sfkit consists of a web server and a command-line interface, which together support a range of use cases including both auto-configured and user-supplied computational environments. sfkit provides collaborative workflows for the essential tasks of genome-wide association study (GWAS) and principal component analysis (PCA). We envision sfkit becoming a one-stop server for secure collaborative tools for a broad range of genomic analyses. sfkit is open-source and available at: https://sfkit.org.
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spelling pubmed-103201812023-07-06 sfkit: a web-based toolkit for secure and federated genomic analysis Mendelsohn, Simon Froelicher, David Loginov, Denis Bernick, David Berger, Bonnie Cho, Hyunghoon Nucleic Acids Res Web Server Issue Advances in genomics are increasingly depending upon the ability to analyze large and diverse genomic data collections, which are often difficult to amass due to privacy concerns. Recent works have shown that it is possible to jointly analyze datasets held by multiple parties, while provably preserving the privacy of each party’s dataset using cryptographic techniques. However, these tools have been challenging to use in practice due to the complexities of the required setup and coordination among the parties. We present sfkit, a secure and federated toolkit for collaborative genomic studies, to allow groups of collaborators to easily perform joint analyses of their datasets without compromising privacy. sfkit consists of a web server and a command-line interface, which together support a range of use cases including both auto-configured and user-supplied computational environments. sfkit provides collaborative workflows for the essential tasks of genome-wide association study (GWAS) and principal component analysis (PCA). We envision sfkit becoming a one-stop server for secure collaborative tools for a broad range of genomic analyses. sfkit is open-source and available at: https://sfkit.org. Oxford University Press 2023-05-29 /pmc/articles/PMC10320181/ /pubmed/37246709 http://dx.doi.org/10.1093/nar/gkad464 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Web Server Issue
Mendelsohn, Simon
Froelicher, David
Loginov, Denis
Bernick, David
Berger, Bonnie
Cho, Hyunghoon
sfkit: a web-based toolkit for secure and federated genomic analysis
title sfkit: a web-based toolkit for secure and federated genomic analysis
title_full sfkit: a web-based toolkit for secure and federated genomic analysis
title_fullStr sfkit: a web-based toolkit for secure and federated genomic analysis
title_full_unstemmed sfkit: a web-based toolkit for secure and federated genomic analysis
title_short sfkit: a web-based toolkit for secure and federated genomic analysis
title_sort sfkit: a web-based toolkit for secure and federated genomic analysis
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320181/
https://www.ncbi.nlm.nih.gov/pubmed/37246709
http://dx.doi.org/10.1093/nar/gkad464
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