Vivian S. Gainer
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View article: Evaluation of T2DM Phenotyping Using Optimized Retrieval-Augmented Generation (RAG) and the Impact of Embedding Model, Context, and Prompt
Evaluation of T2DM Phenotyping Using Optimized Retrieval-Augmented Generation (RAG) and the Impact of Embedding Model, Context, and Prompt Open
Objective Identification of patient cohorts from EHRs is challenging because ICD codes primarily serve billing and may misrepresent disease status, while key information is buried in unstructured notes. Existing computed phenotyping method…
View article: Current Limitations of Electronic Health Record Systems in Supporting Pragmatic Clinical Trials: Insights from the eMERGE Consortium
Current Limitations of Electronic Health Record Systems in Supporting Pragmatic Clinical Trials: Insights from the eMERGE Consortium Open
Pragmatic clinical trials (PCTs) evaluate interventions in real-world settings, often using electronic health records (EHRs) for efficient data collection. We report on the challenges in performing EHR analysis of health-care provider orde…
View article: LATTE: Label-efficient Incident Phenotyping from Longitudinal Electronic Health Records
LATTE: Label-efficient Incident Phenotyping from Longitudinal Electronic Health Records Open
Electronic health record (EHR) data are increasingly used to support real-world evidence (RWE) studies. Yet its ability to generate reliable RWE is limited by the lack of readily available precise information on the timing of clinical even…
View article: The Evolution of a Large Biobank at Mass General Brigham
The Evolution of a Large Biobank at Mass General Brigham Open
The Mass General Brigham Biobank (formerly Partners HealthCare Biobank) is a large repository of biospecimens and data linked to extensive electronic health record data and survey data. Its objective is to support and enable translational …
View article: Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations
Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations Open
Background Type 2 diabetes (T2D) is a worldwide scourge caused by both genetic and environmental risk factors that disproportionately afflicts communities of color. Leveraging existing large-scale genome-wide association studies (GWAS), po…
View article: Under-specification as the source of ambiguity and vagueness in narrative phenotype algorithm definitions
Under-specification as the source of ambiguity and vagueness in narrative phenotype algorithm definitions Open
Introduction Currently, one of the commonly used methods for disseminating electronic health record (EHR)-based phenotype algorithms is providing a narrative description of the algorithm logic, often accompanied by flowcharts. A challenge …
View article: Additional file 2 of Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations
Additional file 2 of Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations Open
Additional File 2: Supplementary Tables S1-S7.
View article: The Mass General Brigham Biobank Portal: an i2b2-based data repository linking disparate and high-dimensional patient data to support multimodal analytics
The Mass General Brigham Biobank Portal: an i2b2-based data repository linking disparate and high-dimensional patient data to support multimodal analytics Open
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 …
View article: Validation of a Trans-Ancestry Polygenic Risk Score for Type 2 Diabetes in Diverse Populations
Validation of a Trans-Ancestry Polygenic Risk Score for Type 2 Diabetes in Diverse Populations Open
Type 2 diabetes (T2D) is a worldwide scourge caused by both genetic and environmental risk factors that disproportionately afflicts communities of color. Leveraging existing large-scale genome-wide association studies (GWAS), polygenic ris…
View article: Under-specification as the Source of Ambiguity and Vagueness in Narrative Phenotype Algorithm Definitions
Under-specification as the Source of Ambiguity and Vagueness in Narrative Phenotype Algorithm Definitions Open
Introduction Currently, one of the commonly used methods for disseminating electronic health record (EHR)-based phenotype algorithms is providing a narrative description of the algorithm logic, often accompanied by flowcharts. A challenge …
View article: The Digital Analytic Patient Reviewer (DAPR) for COVID-19 Data Mart Validation
The Digital Analytic Patient Reviewer (DAPR) for COVID-19 Data Mart Validation Open
Objective To provide high-quality data for COVID-19 research, we validated COVID-19 clinical indicators and 22 associated computed phenotypes, which were derived by machine learning algorithms, in the Mass General Brigham (MGB) COVID-19 Da…
View article: Development of a Coronavirus Disease 2019 (COVID-19) Application Ontology for the Accrual to Clinical Trials (ACT) network
Development of a Coronavirus Disease 2019 (COVID-19) Application Ontology for the Accrual to Clinical Trials (ACT) network Open
Clinical data networks that leverage large volumes of data in electronic health records (EHRs) are significant resources for research on coronavirus disease 2019 (COVID-19). Data harmonization is a key challenge in seamless use of multisit…
View article: Development of a COVID-19 Application Ontology for the ACT Network
Development of a COVID-19 Application Ontology for the ACT Network Open
Clinical data networks that leverage large volumes of data in electronic health records (EHRs) are significant resources for research on coronavirus disease 2019 (COVID-19). Data harmonization is a key challenge in seamless use of multisit…
View article: Morphological variables associated with ruptured basilar tip aneurysms
Morphological variables associated with ruptured basilar tip aneurysms Open
Morphological factors of intracranial aneurysms and the surrounding vasculature could affect aneurysm rupture risk in a location specific manner. Our goal was to identify image-based morphological parameters that correlated with ruptured b…
View article: Surrounding vascular geometry associated with basilar tip aneurysm formation
Surrounding vascular geometry associated with basilar tip aneurysm formation Open
Hemodynamic stress is thought to play an important role in the formation of intracranial aneurysms, which is conditioned by the geometry of the surrounding vasculature. Our goal was to identify image-based morphological parameters that wer…
View article: Age and morphology of posterior communicating artery aneurysms
Age and morphology of posterior communicating artery aneurysms Open
Risk of intracranial aneurysm rupture could be affected by geometric features of intracranial aneurysms and the surrounding vasculature in a location specific manner. Our goal is to investigate the morphological characteristics associated …
View article: sureLDA: A multidisease automated phenotyping method for the electronic health record
sureLDA: A multidisease automated phenotyping method for the electronic health record Open
Objective A major bottleneck hindering utilization of electronic health record data for translational research is the lack of precise phenotype labels. Chart review as well as rule-based and supervised phenotyping approaches require labori…
View article: sureLDA: A Multi-Disease Automated Phenotyping Method for the Electronic Health Record
sureLDA: A Multi-Disease Automated Phenotyping Method for the Electronic Health Record Open
Objective A major bottleneck hindering utilization of electronic health record (EHR) data for translational research is the lack of precise phenotype labels. Chart review as well as rule-based and supervised phenotyping approaches require …