Research Projects Directory

Research Projects Directory

17,903 active projects

This information was updated 5/9/2025

The Research Projects Directory includes information about all projects that currently exist in the Researcher Workbench to help provide transparency about how the Workbench is being used. Each project specifies whether Registered Tier or Controlled Tier data are used.

Note: Researcher Workbench users provide information about their research projects independently. Views expressed in the Research Projects Directory belong to the relevant users and do not necessarily represent those of the All of Us Research Program. Information in the Research Projects Directory is also cross-posted on AllofUs.nih.gov in compliance with the 21st Century Cures Act.

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[MJ] Duplicate of 2024 ASHG workshop: Type 2 diabetes genomic analyses

This workspace is intended for educational purposes for a 2024 ASHG workshop training on getting started with biomedical and genomic data in the All of Us Researcher Workbench. This workspace demonstrates preparing a phenotype file and running a genome-wide association…

Scientific Questions Being Studied

This workspace is intended for educational purposes for a 2024 ASHG workshop training on getting started with biomedical and genomic data in the All of Us Researcher Workbench. This workspace demonstrates preparing a phenotype file and running a genome-wide association study (GWAS) with Hail for type 2 diabetes as well as querying the All by All tables. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Project Purpose(s)

  • Educational

Scientific Approaches

In the Cohort Builder Tool and Dataset Builder Tool, we will create a cohort for type 2 diabetes (cases) and use this cohort to create a dataset. In the Cohort Builder Tool and Dataset Builder Tool, we will also create a cohort for having short read whole-genome sequencing (srWGS) data (cases and controls) and use this cohort to create a dataset that includes demographic concepts. In the first Jupyter Notebook, we will form the two datasets created into one dataset of phenotypic data in the proper format for GWAS analysis with Hail. In the second Jupyter Notebook, we will retrieve desired genomic datasets as a Hail MatrixTable (MT), downsample the genomic data for preliminary runs before a final GWAS, annotate the phenotypic data onto the genomic data, perform quality control (QC), view allele frequencies (AFs), run GWAS, and query All by All tables.

Anticipated Findings

There are not any anticipated findings as these notebooks are for demonstration purposes to educate others on the Researcher Workbench.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Minjung Kho - Other, Seoul National University, Graduate School of Data Science

Collaborators:

  • Seokho Jeong - Graduate Trainee, Seoul National University, Graduate School of Data Science
Request a Review of this Research Project

Duplicate of BCM All of Us EwG - V8 Demo of GWAS with type 2 diabetes

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query…

Scientific Questions Being Studied

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Project Purpose(s)

  • Educational

Scientific Approaches

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Anticipated Findings

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Request a Review of this Research Project

NRM Duplicate of BCM All of Us EwG - V8 Demo of GWAS with type 2 diabetes

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query…

Scientific Questions Being Studied

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Project Purpose(s)

  • Educational

Scientific Approaches

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Anticipated Findings

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Request a Review of this Research Project

Duplicate of BCM All of Us EwG - V8 Demo of GWAS with type 2 diabetes

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query…

Scientific Questions Being Studied

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Project Purpose(s)

  • Educational

Scientific Approaches

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Anticipated Findings

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Saeid Parvandeh - Teacher/Instructor/Professor, Baylor College of Medicine
Request a Review of this Research Project

LWZ Duplicate of BCM All of Us EwG - V8 Demo of GWAS with type 2 diabetes

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query…

Scientific Questions Being Studied

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Project Purpose(s)

  • Educational

Scientific Approaches

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Anticipated Findings

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Request a Review of this Research Project

The Relationship Between Sleep Duration and Conditions (Hypertension & Diabetes)

This study will research the degree of correlation between sleep duration and these chronic diseases, specifically Hypertension and Diabetes. All of Us includes EHR, surveys (e.g., sleep habits), and physical measurements.

Scientific Questions Being Studied

This study will research the degree of correlation between sleep duration and these chronic diseases, specifically Hypertension and Diabetes. All of Us includes EHR, surveys (e.g., sleep habits), and physical measurements.

Project Purpose(s)

  • Educational

Scientific Approaches

The study will analyze:

Average sleep duration across demographics.
Does short/long sleep associate with higher odds of hypertension/diabetes?
Differences by age, gender, or race/ethnicity.
The findings of study will further inform our knowledge on the connection between sleep habits and risk of chronic diseases.

Anticipated Findings

The findings of this study will provide insight into the degree of correlation between sleep habits and chronic conditions like hypertension and diabetes.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Registered Tier

Research Team

Owner:

Request a Review of this Research Project

Duplicate of BCM All of Us EwG - V8 Demo of GWAS with type 2 diabetes

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query…

Scientific Questions Being Studied

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Project Purpose(s)

  • Educational

Scientific Approaches

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Anticipated Findings

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Request a Review of this Research Project

OmicsPredDiabetes

We want to identify genetically-controlled molecular features associated to the risk of Type 1 Diabetes, Type 2 Diabetes and their comorbidities. This can improve our understanding of disease biology and unveil druggable targets.

Scientific Questions Being Studied

We want to identify genetically-controlled molecular features associated to the risk of Type 1 Diabetes, Type 2 Diabetes and their comorbidities. This can improve our understanding of disease biology and unveil druggable targets.

Project Purpose(s)

  • Disease Focused Research (Type 1 Diabetes, Type 2 Diabetes and their Comorbidities )
  • Ancestry

Scientific Approaches

We will use Omiscpred (https://www.omicspred.org/) variant/weight files to predict protein, transcript or metabolite levels for All of Us participants with whole genome sequencing data. T1D and T2D cases and their comorbidities will be extracted from electronic health records. We will evaluate the association of these imputed features to the risk of T1D, T2D and their comorbidities using Logistic Regression and/or Cox Regression. The analysis will be performed across genetic ancestries. Parallel analyses will be performed on external cohorts (such as the UK Biobank) and the results will be aggregated using common effect meta analysis to obtain a robust ser of associations to disease risk. The most promising targets might be validated experimentally in animal models.

Anticipated Findings

Our findings will improve the understanding of diabetes biology, how it is conditioned by genetic and unveil potentially druggable targets against disease.

Demographic Categories of Interest

  • Race / Ethnicity

Data Set Used

Controlled Tier

Research Team

Owner:

Request a Review of this Research Project

Diabetes medication initiation by English proficiency

In the context of type 2 diabetes, early treatment to meet glycemic goals confers long-term health benefits. These benefits are sometimes called "the legacy effect," which refers to the long-term benefits of early and intensive blood glucose management on future…

Scientific Questions Being Studied

In the context of type 2 diabetes, early treatment to meet glycemic goals confers long-term health benefits. These benefits are sometimes called "the legacy effect," which refers to the long-term benefits of early and intensive blood glucose management on future complications. However, multiple factors may contribute to delays in initial treatment of type 2 diabetes among those who are newly diagnosed with type 2 diabetes. These factors may stem from the provider (e.g., therapeutic inertia) or the patient (e.g., resistance to medications). One potential barrier to initial treatment in type 2 diabetes is limited English proficiency. The purpose of this exploratory study is to examine whether limited English proficiency is associated with delays in initial treatment for type 2 diabetes among those newly diagnosed with type 2 diabetes.

Project Purpose(s)

  • Disease Focused Research (type 2 diabetes)
  • Population Health
  • Social / Behavioral

Scientific Approaches

We will use the All of Use dataset. We will use a serial cross-sectional design to examine the likelihood of being prescribed a glucose-lowering medication at the time of diagnosis, and at 3, 6, and 12 months, by English proficiency.

Anticipated Findings

We anticipate that limited English proficiency will be associated with delays in treatment initiation relative to those with English proficiency.

Demographic Categories of Interest

  • Others

Data Set Used

Registered Tier

Research Team

Owner:

  • Loretta Hsueh - Early Career Tenure-track Researcher, University of Illinois at Chicago
Request a Review of this Research Project

depression in diabetes population

Traditionally, depression is considered as one of the risk factor that associated with overall healthy outcomes for people diagnosis with diabetes. It is not clear, however, depressed people is also associated with higher risk of developing diabetes compared to its…

Scientific Questions Being Studied

Traditionally, depression is considered as one of the risk factor that associated with overall healthy outcomes for people diagnosis with diabetes. It is not clear, however, depressed people is also associated with higher risk of developing diabetes compared to its counterpart. Identifying the disease progression direction is a crucial step to guide the clinical treatment or prevention in people with higher risk of developing diabetes.

Project Purpose(s)

  • Disease Focused Research (diabetes)

Scientific Approaches

We will explore the whole survey questions within the up-to-date all-of-us dataset to construct the study cohort. We will use multivariable logistic regression method to explore the relationship between the exposure (depression) and outcome (diabetes) with the adjusted sociodemographic variables that collected from survey questions. All the statistical analysis will be conducted within the R software.

Anticipated Findings

We expected people who suffering the long time depression will associated with higher risk of developing diabetes. Time of being depressed is the key variable to determined the odds ratio of developing diabetes for all-of-us participants. This finding would give a clear focus on guiding the mental health screening intervention for people at higher risk of developing diabetes.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Registered Tier

Research Team

Owner:

  • Hugh Lu - Research Fellow, Tulane University
Request a Review of this Research Project

Exploring All of Us data for Type 2 Diabetes and other phenotypes

Not applicable - this workspace is intended for educational purposes at the BR Faculty Summit and after. We are practicing how to use the Researcher Workbench by analyzing data for Type 2 Diabetes and other phenotypes.

Scientific Questions Being Studied

Not applicable - this workspace is intended for educational purposes at the BR Faculty Summit and after. We are practicing how to use the Researcher Workbench by analyzing data for Type 2 Diabetes and other phenotypes.

Project Purpose(s)

  • Educational

Scientific Approaches

Not applicable - this workspace is intended for educational purposes at the BR Faculty Summit and after. We are practicing how to use the Researcher Workbench by analyzing data for Type 2 Diabetes and other phenotypes.

Anticipated Findings

Not applicable - this workspace is intended for educational purposes at the BR Faculty Summit and after. We are practicing how to use the Researcher Workbench by analyzing data for Type 2 Diabetes and other phenotypes.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Kyu Won Lee - Graduate Trainee, Baylor College of Medicine
Request a Review of this Research Project

ST_Duplicate of BCM All of Us EwG - V8 Demo of GWAS with type 2 diabetes

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query…

Scientific Questions Being Studied

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Project Purpose(s)

  • Educational

Scientific Approaches

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Anticipated Findings

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Request a Review of this Research Project

Duplicate of BCM All of Us EwG - V8 Demo of GWAS with type 2 diabetes

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query…

Scientific Questions Being Studied

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Project Purpose(s)

  • Educational

Scientific Approaches

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Anticipated Findings

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Zian Liao - Graduate Trainee, Baylor College of Medicine
Request a Review of this Research Project

XH Duplicate of BCM All of Us EwG - V8 Demo of GWAS with type 2 diabetes

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query…

Scientific Questions Being Studied

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Project Purpose(s)

  • Educational

Scientific Approaches

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Anticipated Findings

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Xiaowei Hu - Early Career Tenure-track Researcher, University of Virginia
Request a Review of this Research Project

MMC, Duplicate of BCM All of Us EwG - V8 Demo of GWAS with type 2 diabetes

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query…

Scientific Questions Being Studied

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Project Purpose(s)

  • Educational

Scientific Approaches

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Anticipated Findings

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • May Cheung - Early Career Tenure-track Researcher, City University of New York (CUNY)
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ML Diabetes Health Disparities (MC)

We are looking at investigating the social | economic | genetic | and geographic causes of health disparities, with an exploratory study using diabetes. This part of the research taking place in the Jordan Lab at Georgia Tech will also…

Scientific Questions Being Studied

We are looking at investigating the social | economic | genetic | and geographic causes of health disparities, with an exploratory study using diabetes. This part of the research taking place in the Jordan Lab at Georgia Tech will also be used to introduce masters students to advanced data analysis techniques.

Project Purpose(s)

  • Disease Focused Research (type 2 diabetes mellitus)
  • Population Health
  • Educational
  • Ancestry

Scientific Approaches

We intend to use new metrics that combine geographic and socioeconomic data with a genetic basis for ancestry to stratify the occurence of diabetes in populations, then use advanced machine learning techniques to determine the relative occurence of diabetes within those populations.

Anticipated Findings

This research is as much a validation study of the metrics proposed by others in the lab group as it is an exploratory study. We will first seek to see if the conclusions rendered from UK biobank are matched.

Demographic Categories of Interest

  • Race / Ethnicity
  • Geography
  • Education Level
  • Income Level

Data Set Used

Controlled Tier

Research Team

Owner:

  • Shivam Sharma - Graduate Trainee, Georgia Institute of Technology
  • Rick Lee - Undergraduate Student, Georgia Institute of Technology
  • Onyinye Chukka - Graduate Trainee, Georgia Institute of Technology
  • Manoj Kambara - Other, National Institute on Minority Health and Health Disparities (NIH-NIMHD)

Collaborators:

  • Ganesh Arvapalli - Other, The MITRE Corporation
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YS - BCM All of Us EwG - V8 Demo of GWAS with type 2 diabetes

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query…

Scientific Questions Being Studied

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Project Purpose(s)

  • Educational

Scientific Approaches

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Anticipated Findings

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Request a Review of this Research Project

Duplicate of BCM All of Us EwG - V8 Demo of GWAS with type 2 diabetes

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query…

Scientific Questions Being Studied

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Project Purpose(s)

  • Educational

Scientific Approaches

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Anticipated Findings

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Jingyue Wu - Graduate Trainee, Baylor College of Medicine
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Duplicate of BCM All of Us EwG - V8 Demo of GWAS with type 2 diabetes

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query…

Scientific Questions Being Studied

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Project Purpose(s)

  • Educational

Scientific Approaches

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Anticipated Findings

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Request a Review of this Research Project

Duplicate of BCM All of Us EwG - V8 Demo of GWAS with type 2 diabetes

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query…

Scientific Questions Being Studied

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Project Purpose(s)

  • Educational

Scientific Approaches

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Anticipated Findings

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Xinyu Wang - Graduate Trainee, Baylor College of Medicine
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Duplicate of BCM All of Us EwG - V8 Demo of GWAS with type 2 diabetes

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query…

Scientific Questions Being Studied

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Project Purpose(s)

  • Educational

Scientific Approaches

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Anticipated Findings

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Holly Quang - Graduate Trainee, Baylor College of Medicine
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Duplicate of BCM All of Us EwG - V8 Demo of GWAS with type 2 diabetes

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query…

Scientific Questions Being Studied

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Project Purpose(s)

  • Educational

Scientific Approaches

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Anticipated Findings

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Request a Review of this Research Project

Duplicate of BCM All of Us EwG - V8 Demo of GWAS with type 2 diabetes SK

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query…

Scientific Questions Being Studied

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Project Purpose(s)

  • Educational

Scientific Approaches

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Anticipated Findings

This workspace is intended to be an introductory example of how to do a genome-wide association study (GWAS) and other genomic analyses. It includes additional notebooks on how to curate the phenotype file for a GWAS and how to query the All by All tables.. This workspace is for demonstration and educational purposes only, including presentation at the All of Us Evenings with Genetic's 2025 Biomedical Researcher Faculty Summit. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

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AD and diabetes

Recently, GWAS and proteomics data have been used to examine the association between genotypes and protein abundance that has promoted the emergence of data analyses, which facilitate the combination of multidimensional data and integrate protein expression data with GWAS findings…

Scientific Questions Being Studied

Recently, GWAS and proteomics data have been used to examine the association between genotypes and protein abundance that has promoted the emergence of data analyses, which facilitate the combination of multidimensional data and integrate protein expression data with GWAS findings in Alzheimer's disease (AD) and diabetic pathogenesis.

Project Purpose(s)

  • Disease Focused Research (dementia and diabetes)
  • Population Health
  • Social / Behavioral
  • Control Set
  • Ancestry

Scientific Approaches

The data from GWAS will be analyzed by following steps:
1. Performing GWAS using data from the All of Us research program to identify potential genes related to AD and diabetes.
2. Conducting protein quantitative trait locus (QTL) analysis of 191,440 proteins in serum or plasma to detect associations between AD-associated genotypes and protein abundance.

Anticipated Findings

Overall, this grant proposal seeks to advance our understanding of the genetic basis and protein biomarkers of AD and diabetes and identify novel therapeutic targets for the disease.

Demographic Categories of Interest

  • Race / Ethnicity
  • Age

Data Set Used

Controlled Tier

Research Team

Owner:

  • Chun (Cathy) Xu - Mid-career Tenured Researcher, University of Texas, Rio Grande Valley

Collaborators:

  • Kesheng Wang - Teacher/Instructor/Professor, University of South Carolina
  • Belinda Alvarado - Graduate Trainee, University of Texas, Rio Grande Valley
  • Bassent Abdelbary - Other, University of Texas, Rio Grande Valley
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Duplicate of 2024 ASHG workshop: Type 2 diabetes genomic analyses

This workspace is intended for educational purposes for a 2024 ASHG workshop training on getting started with biomedical and genomic data in the All of Us Researcher Workbench. This workspace demonstrates preparing a phenotype file and running a genome-wide association…

Scientific Questions Being Studied

This workspace is intended for educational purposes for a 2024 ASHG workshop training on getting started with biomedical and genomic data in the All of Us Researcher Workbench. This workspace demonstrates preparing a phenotype file and running a genome-wide association study (GWAS) with Hail for type 2 diabetes as well as querying the All by All tables. This workspace and its workshop are developed by Baylor College of Medicine’s All of Us Evenings with Genetics Research Program (https://bcm.edu/allofuseveningswithgenetics). Any questions about the workspace can be directed to Julie Coleman (julie.coleman@bcm.edu).

Project Purpose(s)

  • Educational

Scientific Approaches

In the Cohort Builder Tool and Dataset Builder Tool, we will create a cohort for type 2 diabetes (cases) and use this cohort to create a dataset. In the Cohort Builder Tool and Dataset Builder Tool, we will also create a cohort for having short read whole-genome sequencing (srWGS) data (cases and controls) and use this cohort to create a dataset that includes demographic concepts. In the first Jupyter Notebook, we will form the two datasets created into one dataset of phenotypic data in the proper format for GWAS analysis with Hail. In the second Jupyter Notebook, we will retrieve desired genomic datasets as a Hail MatrixTable (MT), downsample the genomic data for preliminary runs before a final GWAS, annotate the phenotypic data onto the genomic data, perform quality control (QC), view allele frequencies (AFs), run GWAS, and query All by All tables.

Anticipated Findings

There are not any anticipated findings as these notebooks are for demonstration purposes to educate others on the Researcher Workbench.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Joanne Berghout - Research Associate, National Institute of Allergy and Infectious Diseases (NIH - NIAID)
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