Chenchal Subraveti
Project Personnel, All of Us Program Operational Use
5 active projects
Cancer and the Environment - Paper 1
Scientific Questions Being Studied
The purpose of this workspace is to have a look at any environmental health variables included at the Controlled Tier. Our group hopes to be able to conduct an analysis of the relationship between PM2.5 and cardiometabolic outcomes in the AoU dataset, and we will create a new workspace with our research plan once we have a better idea of whether the dataset has the necessary variables to support this project.
Project Purpose(s)
- Other Purpose (The purpose of this workspace is to have a look at any environmental health variables included at the Controlled Tier. Our group hopes to be able to conduct an analysis of PM2.5 and cardiometabolic outcomes, and we will create a new workspace with our research plan once we have a better idea of whether the dataset has the necessary variables to support this project. )
Scientific Approaches
Regression analysis and other methods to be determined by the data.
The purpose of this workspace is to have a look at any environmental health variables included at the Controlled Tier. Our group hopes to be able to conduct an analysis of the relationship between PM2.5 and cardiometabolic outcomes in the AoU dataset, and we will create a new workspace with our research plan once we have a better idea of whether the dataset has the necessary variables to support this project.
Anticipated Findings
We hope to gain a better understanding of any associations between environmental PM 2.5 and cardiometabolic outcomes among the All of Us cohort. Such an analysis with a sample of this size would be a novel addition to the environmental health literature.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierResearch Team
Owner:
- Maia Griffith - Project Personnel, University of Chicago
- Chenchal Subraveti - Project Personnel, All of Us Program Operational Use
- Andrew Craver - Project Personnel, University of Chicago
AOU_Recover_Long_Covid_v6
Scientific Questions Being Studied
The purpose of this workspace was to implement the published XGBoost machine learning (ML) model, which was developed using the National COVID Cohort Collaborative’s (N3C) EHR repository to identify potential patients with PASC/Long COVID in All of Us Research Program. N3C, All of Us, PCORnet and RECOVER teams collaborated to execute this purpose to enhance the overall PASC/Long COVID efforts.
Project Purpose(s)
- Disease Focused Research (Long COVID)
Scientific Approaches
To achieve this objective, data science workflows were used to apply ML algorithms on the Researcher Workbench. This effort allowed an expansion in the number of participants used to evaluate the ML models used to identify risk of PASC/Long COVID and also serve to validate the efforts of one team and providing insight to other teams. These models were implemented within the All of Us Controlled Tier data (C2022Q2R2), which was last refreshed on June 22, 2022. We intend to provide a step-by-step guide for the implementation of N3C's ML Model for identification of PASC/Long COVID Phenotype in the All of Us dataset. It also evaluated demographic characteristics for participants who were identified as possibly having PASC/Long COVID, and provides additional details on model performance, such as areas under the receiver operator characteristic curve and confusion matrix.
Anticipated Findings
We intend to provide a step-by-step guide for the implementation of N3C's ML Model for identification of PASC/Long COVID Phenotype in the All of Us dataset. The findings and code use to generate the demographic characteristics for participants who were identified as possibly having PASC/Long COVID, and provides additional details on model performance, such as areas under the receiver operator characteristic curve and confusion matrix.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierResearch Team
Owner:
- WeiQi Wei - Other, All of Us Program Operational Use
- Vern Kerchberger - Early Career Tenure-track Researcher, Vanderbilt University Medical Center
- Srushti Gangireddy - Project Personnel, Vanderbilt University Medical Center
- Mark Weiner - Mid-career Tenured Researcher, Cornell University
- Hiral Master - Project Personnel, All of Us Program Operational Use
- Gabriel Anaya - Administrator, National Heart, Lung, and Blood Institute (NIH - NHLBI)
- David Mohs - Other, All of Us Program Operational Use
- Christopher Lord - Project Personnel, All of Us Program Operational Use
- Chenchal Subraveti - Project Personnel, All of Us Program Operational Use
Collaborators:
- Jun Qian - Other, All of Us Program Operational Use
- Chris Lunt - Other, All of Us Program Operational Use
Duplicate of Skills Assessment Training Notebooks For Users
Scientific Questions Being Studied
This workspace contains multiple notebooks that assess users' understanding of the workbench and OMOP. These notebooks are meant to help users check their knowledge not only on Python, R, and SQL, but also on the general data structure and data model used by the All of Us program.
Project Purpose(s)
- Educational
Scientific Approaches
There are no scientific approach used in this workspace because it is meant for educational purposes only. We will cover all aspects of OMOP, and hence will use most datasets available in the workbench.
Anticipated Findings
We do not anticipate to have any findings. Instead, we are educating people on the use of the workbench and the common data model OMOP used by the program.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Registered TierResearch Team
Owner:
- Kammarauche Aneni - Other, Yale University
- Hiral Master - Project Personnel, All of Us Program Operational Use
- Chenchal Subraveti - Project Personnel, All of Us Program Operational Use
- Aymone Kouame - Other, All of Us Program Operational Use
Collaborators:
- Michael Lyons - Project Personnel, All of Us Program Operational Use
- Hunter Hollis - Project Personnel, All of Us Program Operational Use
- Christopher Lord - Project Personnel, All of Us Program Operational Use
Wearables and The Human Phenome (Published Work)
Scientific Questions Being Studied
Our primary goal is to understand the relation between activity levels with the development and progression of human disease. Higher physical activity is associated with lower prevalence and better outcomes in virtually every human disease. These analyses will generate hypotheses guiding clinical and research interventions focused on activity to reduce morbidity and mortality in patients seeking care.
This workspace is replication workspace for Wearables and The Human Phenome project. We replicated the workspace to provide a clean and reduced version of code that was used to generate the findings, which were published in Nature Medicine (https://www.nature.com/articles/s41591-022-02012-w).
Project Purpose(s)
- Population Health
- Social / Behavioral
Scientific Approaches
We will examine the relationship between daily activity (steps, activity intensity) over time and the prevalence and progression of coded human diseases. We will use the Fitbit data, EHR-curated diagnoses, laboratory values, and survey results.
Anticipated Findings
We expect to find that lower levels of activity are associated with a higher prevalence and more rapid progression of chronic diseases. These data will provide the rationale to link wearables data with electronic health records nationwide as a window into behavioral activity choice as a modifiable risk factor for chronic diseases. We may find substantial variation in activity and disease prevalence/severity by socioeconomic status, which would motivate studies/interventions to reduce these health disparities.
Demographic Categories of Interest
- Race / Ethnicity
- Geography
- Access to Care
- Education Level
- Income Level
Data Set Used
Registered TierResearch Team
Owner:
- Hiral Master - Project Personnel, All of Us Program Operational Use
- Christopher Lord - Project Personnel, All of Us Program Operational Use
- Chenchal Subraveti - Project Personnel, All of Us Program Operational Use
- Jeffrey Annis - Other, Vanderbilt University Medical Center
Collaborators:
- Jun Qian - Other, All of Us Program Operational Use
Cs-Test
Scientific Questions Being Studied
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Project Purpose(s)
- Other Purpose (For testing cohort - age groupings For testing cohort - age groupings For testing cohort - age groupings For testing cohort - age groupings For testing cohort - age groupings For testing cohort - age groupings)
Scientific Approaches
For testing cohort - age groupingsFor testing cohort - age groupingsFor testing cohort - age groupingsFor testing cohort - age groupings
Anticipated Findings
For testing cohort - age groupingsFor testing cohort - age groupingsFor testing cohort - age groupingsFor testing cohort - age groupings
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Registered TierRequest a Review of this Research Project
You can request that the All of Us Resource Access Board (RAB) review a research purpose description if you have concerns that this research project may stigmatize All of Us participants or violate the Data User Code of Conduct in some other way. To request a review, you must fill in a form, which you can access by selecting ‘request a review’ below.
