Nicole Deflaux
All of Us Program Operational Use
2 active projects
Duplicate of Demo - Siloed Analysis of All of Us and UK Biobank Genomic Data
Scientific Questions Being Studied
Historically, researchers responded to limitations in genomic data sharing policy and practice by conducting meta analysis on summary outputs from isolated genomic datasets. Recent work has demonstrated the increased power of individual-level genetic analysis on pooled datasets. In addition, advancements in data access and sharing policies coupled with technological advancements in cloud-based environments for data access and analysis have opened up new possibilities for pooled analysis of large-scale genomic datasets. The NIH All of Us Research Program and UK Biobank are two leading examples of large, population scale studies which combine genomic data with deep phenotypic health data. There is a grand opportunity to demonstrate how the world’s largest research-ready biomedical datasets can create more value together and advance discovery in genome science.
Project Purpose(s)
- Educational
- Other Purpose (This is a demonstration project meant to support research with All of Us genomic data. Please see https://www.biorxiv.org/content/10.1101/2022.11.29.518423)
Scientific Approaches
The primary goal of this project is to demonstrate the potential of the All of Us Researcher Workbench for pooled analyses of All of Us and UK Biobank data. Specifically, we aim to: 1. Develop and describe an approved, secure path for connecting UK Biobank data to the All of Us Researcher Workbench. 2. Conduct a genome-wide association study of blood lipids on the pooled dataset aimed at demonstrating that biomedical researchers can be more productive when permitted to analyze the union of the cohorts, as opposed to computing aggregate results in separate data silos for each cohort and then combining those aggregates.
Anticipated Findings
The secondary goal of this project is to demonstrate and measure the experience when the same analyses are repeated in a siloed manner. Specifically we aim to: 3. Repeat the previously described genome-wide association study on the All of Us Researcher Workbench when working with the All of Us data and on UK Biobank’s DNAnexus when working with the UK Biobank data. 4. Conduct a meta analysis on the aggregate results for each cohort (in accordance with each program’s data use policies) and compare the result of combining those aggregates to the results from the pooled analysis. Evaluate not only differences in results, but also differences in analysis cost and analyst productivity.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierResearch Team
Owner:
- Roshan Paudel - Early Career Tenure-track Researcher, Morgan State University
- Kelsey Mayo - Other, All of Us Program Operational Use
- Nicole Deflaux - Other, All of Us Program Operational Use
- CH Albach - Other, All of Us Program Operational Use
Collaborators:
- Margaret Sunitha Selvaraj - Research Fellow, Broad Institute
- Melissa Patrick - Project Personnel, All of Us Program Operational Use
- Jennifer Zhang - Project Personnel, All of Us Program Operational Use
- Gage Rion - Project Personnel, All of Us Program Operational Use
- David Glazer - Other, All of Us Program Operational Use
- Christopher Lord - Project Personnel, All of Us Program Operational Use
- Aymone Kouame - Other, All of Us Program Operational Use
- Alexander Bick - Early Career Tenure-track Researcher, Vanderbilt University Medical Center
Duplicate of Demo - Siloed Analysis of All of Us and UK Biobank Genomic Data
Scientific Questions Being Studied
Historically, researchers responded to limitations in genomic data sharing policy and practice by conducting meta analysis on summary outputs from isolated genomic datasets. Recent work has demonstrated the increased power of individual-level genetic analysis on pooled datasets. In addition, advancements in data access and sharing policies coupled with technological advancements in cloud-based environments for data access and analysis have opened up new possibilities for pooled analysis of large-scale genomic datasets. The NIH All of Us Research Program and UK Biobank are two leading examples of large, population scale studies which combine genomic data with deep phenotypic health data. There is a grand opportunity to demonstrate how the world’s largest research-ready biomedical datasets can create more value together and advance discovery in genome science.
Project Purpose(s)
- Other Purpose (This is a demonstration project meant to support research with All of Us genomic data. Please see https://www.biorxiv.org/content/10.1101/2022.11.29.518423)
Scientific Approaches
The primary goal of this project is to demonstrate the potential of the All of Us Researcher Workbench for pooled analyses of All of Us and UK Biobank data. Specifically, we aim to: 1. Develop and describe an approved, secure path for connecting UK Biobank data to the All of Us Researcher Workbench. 2. Conduct a genome-wide association study of blood lipids on the pooled dataset aimed at demonstrating that biomedical researchers can be more productive when permitted to analyze the union of the cohorts, as opposed to computing aggregate results in separate data silos for each cohort and then combining those aggregates.
Anticipated Findings
The secondary goal of this project is to demonstrate and measure the experience when the same analyses are repeated in a siloed manner. Specifically we aim to: 3. Repeat the previously described genome-wide association study on the All of Us Researcher Workbench when working with the All of Us data and on UK Biobank’s DNAnexus when working with the UK Biobank data. 4. Conduct a meta analysis on the aggregate results for each cohort (in accordance with each program’s data use policies) and compare the result of combining those aggregates to the results from the pooled analysis. Evaluate not only differences in results, but also differences in analysis cost and analyst productivity.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierResearch Team
Owner:
- Kelsey Mayo - Other, All of Us Program Operational Use
- Jessica Hamblin - Graduate Trainee, Pennsylvania State University
- Nicole Deflaux - Other, All of Us Program Operational Use
- CH Albach - Other, All of Us Program Operational Use
Collaborators:
- Margaret Sunitha Selvaraj - Research Fellow, Broad Institute
- Melissa Patrick - Project Personnel, All of Us Program Operational Use
- Jennifer Zhang - Project Personnel, All of Us Program Operational Use
- Gage Rion - Project Personnel, All of Us Program Operational Use
- David Glazer - Other, All of Us Program Operational Use
- Christopher Lord - Project Personnel, All of Us Program Operational Use
- Aymone Kouame - Other, All of Us Program Operational Use
- Alexander Bick - Early Career Tenure-track Researcher, Vanderbilt University Medical Center
Request 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.
