The Mass General Brigham Biobank Portal: an i2b2-based data repository linking disparate and high-dimensional patient data to support multimodal analytics

Abstract

Objective Integrating and harmonizing disparate patient data sources into one consolidated data portal enables researchers to conduct analysis efficiently and effectively. Materials and Methods We describe an implementation of Informatics for Integrating Biology and the Bedside (i2b2) to create the Mass General Brigham (MGB) Biobank Portal data repository. The repository integrates data from primary and curated data sources and is updated weekly. The data are made readily available to investigators in a data portal where they can easily construct and export customized datasets for analysis. Results As of July 2021, there are 125 645 consented patients enrolled in the MGB Biobank. 88 527 (70.5%) have a biospecimen, 55 121 (43.9%) have completed the health information survey, 43 552 (34.7%) have genomic data and 124 760 (99.3%) have EHR data. Twenty machine learning computed phenotypes are calculated on a weekly basis. There are currently 1220 active investigators who have run 58 793 patient queries and exported 10 257 analysis files. Discussion The Biobank Portal allows noninformatics researchers to conduct study feasibility by querying across many data sources and then extract data that are most useful to them for clinical studies. While institutions require substantial informatics resources to establish and maintain integrated data repositories, they yield significant research value to a wide range of investigators. Conclusion The Biobank Portal and other patient data portals that integrate complex and simple datasets enable diverse research use cases. i2b2 tools to implement these registries and make the data interoperable are open source and freely available.

Impact of Selection Bias on Polygenic Risk Score Estimates in Healthcare Settings

“…The primary data source was the MGB RPDR, an EHR data warehouse covering 4.6 million patients across the MGB HealthCare hospital system (formerly Partners HealthCare) including Brigham & Women’s Hospital, Massachusetts General Hospital, and other affiliated hospitals in the greater Boston area. To assemble the cohort for this study, we queried the MGB RPDR for 1,546,440 patients who self-identified as non-Hispanic White (that is, 74% of the overall MGB patient population) having at least three visits after 2005, more than 30 days apart between the first and last visits, and at least one visit greater than age 10 and less than age 90, as of February 2020 (22,23) (see Figure 1 ). The race and ethnicity restriction was applied here because the subsequent PRS were based on samples of European ancestry.…”

“…Each consented participant was asked to provide blood samples (e.g., plasma, serum, DNA), which are then linked to their clinical data in the EHRs as well as survey data on lifestyle, behavioral and environmental factors, and family history. Leveraging in-person and electronic recruitment methods, the MGB Biobank has currently enrolled more than 130,000 participants, collected 82,092 DNA samples, and generated genotyping microarray data for more than 56,923 participants (4,920 using the Illumina MEGA, 5,334 using the Illumina MEGA EX, 26,144 using the Illumina MEG, and 24,789 using the Illumina GSA) (23). This research was conducted as part of the PsycheMERGE Consortium (24), under approval from the MGB Institutional Review Board.…”

“…Leveraging in-person and electronic recruitment methods, the MGB Biobank has currently enrolled more than 130,000 participants, collected 82,092 DNA samples, and generated genotyping microarray data for more than 56,923 participants (4,920 using the Illumina MEGA, 5,334 using the Illumina MEGA EX, 26,144 using the Illumina MEG, and 24,789 using the Illumina GSA) (23). This research was conducted as part of the PsycheMERGE Consortium (24), under approval from the MGB Institutional Review Board.…”

I2b2-etl: Python application for importing electronic health data into the informatics for integrating biology and the bedside platform

“…The platform has been used for a wide spectrum of use cases including clinical-trial enrollment ( Bucalo et al , 2021 ), population management ( Wagholikar et al , 2019 ), biobanking ( Castro et al , 2021 ; Mate et al , 2017 ; Segagni et al , 2011 ), clinical decision support and epidemiological analysis ( Klann and Murphy, 2013 ; Murchison et al , 2021 ; Pfiffner et al , 2016 ; Segagni et al , 2011 ; Wagholikar et al , 2017a , b ). However, despite its impact and open-source availability, the deployment of the platform is largely limited to large academic medical centers.…”

Levels of CC motif chemokine 22 (CCL22) and IL-13, but not levels of IL-5, predict response to mepolizumab in asthma

“…Data source was the Mass General Brigham (MGB) Electronic Health Records (EHR) and Biobank which stores blood samples from patients at MGB who have consented to provide samples for research purposes. 3 We identified 15 patients who received mepolizumab for the treatment of asthma and who had samples in the biobank, of whom 5 were determined to be responders to mepolizumab, and 10 were non-responders. We compared the pre-treatment serum level of each cytokine at mepolizumab initiation between responders and non-responders using moderated t-test to select top cytokines with highest differential expression between responders and nonresponders.…”