| Literature DB >> 31481752 |
Kenneth D Mandl1,2,3, Tracy Glauser4,5, Ian D Krantz6,7, Paul Avillach8,9, Anna Bartels10, Alan H Beggs11,12,13, Sawona Biswas6, Florence T Bourgeois8,11,13, Jeremy Corsmo5,14, Andrew Dauber5,15, Batsal Devkota16, Gary R Fleisher11,13, Allison P Heath16, Ingo Helbig7,17,18, Joel N Hirschhorn11,19,20, Judson Kilbourn8, Sek Won Kong8,11, Susan Kornetsky21, Joseph A Majzoub11,13,19, Keith Marsolo22, Lisa J Martin5,23, Jeremy Nix24, Amy Schwarzhoff25, Jason Stedman9, Arnold Strauss5,26, Kristen L Sund23, Deanne M Taylor7,17, Peter S White5,24,27, Eric Marsh28, Adda Grimberg29, Colin Hawkes29.
Abstract
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.Entities:
Keywords: biobanking; electronic health records; federated networks; genomic medicine; information technology
Mesh:
Year: 2019 PMID: 31481752 PMCID: PMC7000325 DOI: 10.1038/s41436-019-0646-3
Source DB: PubMed Journal: Genet Med ISSN: 1098-3600 Impact factor: 8.822
Fig. 1Collaboration structure for the Genomics Research and Innovation Network.
Fig. 2The PIC-SURE application programming interface (API) is used to access genotype and phenotype data from databases at each site of care. Currently the databases are i2b2/TranSMART instances, but the API is agnostic. Authorized investigators from the three institutions can log in with their standard hospital credentials at the Genomics Research and Innovation Network (GRIN) Central Access Portal. Investigators can interrogate data all three hospitals using the discover portal, which returns aggregate counts by institution. With proper institutional review board (IRB) authorization, they can access line-level de-identified data for exploratory analyses using i2b2/TranSMART, or export line-level data to the analysis portal, an Amazon Web Services (AWS)–hosted environment shared across the three institutions.
Fig. 3The discovery user interface (UI) finding patients across the hospital with a diagnosis of epilepsy and recurrent seizures. The figure illustrates not only the power of distributed query, but also the nature of a modular, scalable federated network, in that the three hospitals are at different stages of data contribution. The Cincinnati Children’s Hospital Medical Center has made its full corpus of electronic health record (EHR) data available for query. The Children’s Hospital of Philadelphia and Boston Children’s Hospital have only made data available for consented biobank cohorts. Note—both of the latter hospitals are committed to making the full EHR cohort available during 2019.
Fig. 4The discovery user interface (UI) finding three patients with a specific variant at one of the hospitals. With proper approvals, samples, sequence, electronic health record data, or recontact can be requested by any investigator at the hospitals.