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The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system

PURPOSE: Clinicians and researchers must contextualize a patient’s genetic variants against population-based references with detailed phenotyping. We sought to establish globally scalable technology, policy, and procedures for sharing biosamples and associated genomic and phenotypic data on broadly...

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Autores principales: Mandl, Kenneth D., Glauser, Tracy, Krantz, Ian D., Avillach, Paul, Bartels, Anna, Beggs, Alan H., Biswas, Sawona, Bourgeois, Florence T., Corsmo, Jeremy, Dauber, Andrew, Devkota, Batsal, Fleisher, Gary R., Heath, Allison P., Helbig, Ingo, Hirschhorn, Joel N., Kilbourn, Judson, Kong, Sek Won, Kornetsky, Susan, Majzoub, Joseph A., Marsolo, Keith, Martin, Lisa J., Nix, Jeremy, Schwarzhoff, Amy, Stedman, Jason, Strauss, Arnold, Sund, Kristen L., Taylor, Deanne M., White, Peter S., Marsh, Eric, Grimberg, Adda, Hawkes, Colin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group US 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7000325/
https://www.ncbi.nlm.nih.gov/pubmed/31481752
http://dx.doi.org/10.1038/s41436-019-0646-3
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author Mandl, Kenneth D.
Glauser, Tracy
Krantz, Ian D.
Avillach, Paul
Bartels, Anna
Beggs, Alan H.
Biswas, Sawona
Bourgeois, Florence T.
Corsmo, Jeremy
Dauber, Andrew
Devkota, Batsal
Fleisher, Gary R.
Heath, Allison P.
Helbig, Ingo
Hirschhorn, Joel N.
Kilbourn, Judson
Kong, Sek Won
Kornetsky, Susan
Majzoub, Joseph A.
Marsolo, Keith
Martin, Lisa J.
Nix, Jeremy
Schwarzhoff, Amy
Stedman, Jason
Strauss, Arnold
Sund, Kristen L.
Taylor, Deanne M.
White, Peter S.
Marsh, Eric
Grimberg, Adda
Hawkes, Colin
author_facet Mandl, Kenneth D.
Glauser, Tracy
Krantz, Ian D.
Avillach, Paul
Bartels, Anna
Beggs, Alan H.
Biswas, Sawona
Bourgeois, Florence T.
Corsmo, Jeremy
Dauber, Andrew
Devkota, Batsal
Fleisher, Gary R.
Heath, Allison P.
Helbig, Ingo
Hirschhorn, Joel N.
Kilbourn, Judson
Kong, Sek Won
Kornetsky, Susan
Majzoub, Joseph A.
Marsolo, Keith
Martin, Lisa J.
Nix, Jeremy
Schwarzhoff, Amy
Stedman, Jason
Strauss, Arnold
Sund, Kristen L.
Taylor, Deanne M.
White, Peter S.
Marsh, Eric
Grimberg, Adda
Hawkes, Colin
author_sort Mandl, Kenneth D.
collection PubMed
description PURPOSE: Clinicians and researchers must contextualize a patient’s genetic variants against population-based references with detailed phenotyping. We sought to establish globally scalable technology, policy, and procedures for sharing biosamples and associated genomic and phenotypic data on broadly consented cohorts, across sites of care. METHODS: Three of the nation’s leading children’s hospitals launched the Genomic Research and Innovation Network (GRIN), with federated information technology infrastructure, harmonized biobanking protocols, and material transfer agreements. Pilot studies in epilepsy and short stature were completed to design and test the collaboration model. RESULTS: Harmonized, broadly consented institutional review board (IRB) protocols were approved and used for biobank enrollment, creating ever-expanding, compatible biobanks. An open source federated query infrastructure was established over genotype–phenotype databases at the three hospitals. Investigators securely access the GRIN platform for prep to research queries, receiving aggregate counts of patients with particular phenotypes or genotypes in each biobank. With proper approvals, de-identified data is exported to a shared analytic workspace. Investigators at all sites enthusiastically collaborated on the pilot studies, resulting in multiple publications. Investigators have also begun to successfully utilize the infrastructure for grant applications. CONCLUSIONS: The GRIN collaboration establishes the technology, policy, and procedures for a scalable genomic research network.
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spelling pubmed-70003252020-02-06 The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system Mandl, Kenneth D. Glauser, Tracy Krantz, Ian D. Avillach, Paul Bartels, Anna Beggs, Alan H. Biswas, Sawona Bourgeois, Florence T. Corsmo, Jeremy Dauber, Andrew Devkota, Batsal Fleisher, Gary R. Heath, Allison P. Helbig, Ingo Hirschhorn, Joel N. Kilbourn, Judson Kong, Sek Won Kornetsky, Susan Majzoub, Joseph A. Marsolo, Keith Martin, Lisa J. Nix, Jeremy Schwarzhoff, Amy Stedman, Jason Strauss, Arnold Sund, Kristen L. Taylor, Deanne M. White, Peter S. Marsh, Eric Grimberg, Adda Hawkes, Colin Genet Med Article PURPOSE: Clinicians and researchers must contextualize a patient’s genetic variants against population-based references with detailed phenotyping. We sought to establish globally scalable technology, policy, and procedures for sharing biosamples and associated genomic and phenotypic data on broadly consented cohorts, across sites of care. METHODS: Three of the nation’s leading children’s hospitals launched the Genomic Research and Innovation Network (GRIN), with federated information technology infrastructure, harmonized biobanking protocols, and material transfer agreements. Pilot studies in epilepsy and short stature were completed to design and test the collaboration model. RESULTS: Harmonized, broadly consented institutional review board (IRB) protocols were approved and used for biobank enrollment, creating ever-expanding, compatible biobanks. An open source federated query infrastructure was established over genotype–phenotype databases at the three hospitals. Investigators securely access the GRIN platform for prep to research queries, receiving aggregate counts of patients with particular phenotypes or genotypes in each biobank. With proper approvals, de-identified data is exported to a shared analytic workspace. Investigators at all sites enthusiastically collaborated on the pilot studies, resulting in multiple publications. Investigators have also begun to successfully utilize the infrastructure for grant applications. CONCLUSIONS: The GRIN collaboration establishes the technology, policy, and procedures for a scalable genomic research network. Nature Publishing Group US 2019-09-04 2020 /pmc/articles/PMC7000325/ /pubmed/31481752 http://dx.doi.org/10.1038/s41436-019-0646-3 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, and provide a link to the Creative Commons license. You do not have permission under this license to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
spellingShingle Article
Mandl, Kenneth D.
Glauser, Tracy
Krantz, Ian D.
Avillach, Paul
Bartels, Anna
Beggs, Alan H.
Biswas, Sawona
Bourgeois, Florence T.
Corsmo, Jeremy
Dauber, Andrew
Devkota, Batsal
Fleisher, Gary R.
Heath, Allison P.
Helbig, Ingo
Hirschhorn, Joel N.
Kilbourn, Judson
Kong, Sek Won
Kornetsky, Susan
Majzoub, Joseph A.
Marsolo, Keith
Martin, Lisa J.
Nix, Jeremy
Schwarzhoff, Amy
Stedman, Jason
Strauss, Arnold
Sund, Kristen L.
Taylor, Deanne M.
White, Peter S.
Marsh, Eric
Grimberg, Adda
Hawkes, Colin
The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system
title The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system
title_full The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system
title_fullStr The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system
title_full_unstemmed The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system
title_short The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system
title_sort genomics research and innovation network: creating an interoperable, federated, genomics learning system
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7000325/
https://www.ncbi.nlm.nih.gov/pubmed/31481752
http://dx.doi.org/10.1038/s41436-019-0646-3
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