Marsha Wheeler
Project Personnel, University of Washington
3 active projects
Demo - Assessment of pathogenic variants across the All of Us Research Program
Scientific Questions Being Studied
We will assess the relative frequency of positive findings across AoU samples and compare the aggregate findings with those from other cohorts - e.g. GnomAD. The frequencies of positive findings will be further broken down by the ancestry background of the participants to understand the impact of diverse backgrounds has on the rate of pathogenic findings.
Project Purpose(s)
- Other Purpose (Demonstrate the potential utility of Researcher Workbench data by describing the frequency of known pathogenic & pharmacogenomic variants in the current genomic dataset.)
Scientific Approaches
We will annotate genomic variants from AoU participants with variant curations that have been recorded by the HGSC-CL clinical annotation team in its ‘VIP’ database or in ClinVar. We will assess the frequency of these previously-known pathogenic mutations, and provide breakdowns by ancestry.
Anticipated Findings
These data will likely identify groups that are underrepresented and overrepresented by the current knowledge of pathogenic variants, and may provide important directions for prioritizing future research. Additionally, they may point to systematic differences between the AoU resource and other resources, such as GnomAD.
Demographic Categories of Interest
- Race / Ethnicity
Data Set Used
Controlled TierResearch Team
Owner:
- Eric Venner - Early Career Tenure-track Researcher, Baylor College of Medicine
- Marsha Wheeler - Project Personnel, University of Washington
- Jun Qian - Other, All of Us Program Operational Use
- Ashley Green - Project Personnel, All of Us Program Operational Use
Collaborators:
- Huyen Nguyen - Project Personnel, Baylor College of Medicine
- Philip Empey - Mid-career Tenured Researcher, University of Pittsburgh
- Karynne Patterson - Project Personnel, University of Washington
- Joshua Smith - Late Career Tenured Researcher, University of Washington
- Divya Kalra - Project Personnel, Baylor College of Medicine
- Andrew Haddad - Graduate Trainee, University of Pittsburgh
- Aniko Sabo - Other, Baylor College of Medicine
Duplicate of How to Get Started with Controlled Tier Data (v6)
Scientific Questions Being Studied
1. Socio-Economic Metrics: How to retrieve participants' socio-economic data from the CDR.
2. Observation Date: How to query and plot an observation date using survey completion date as example.
3. Demographics: Examples of how to query and plot participant demographic data.
4. Death Cause: How to retrieve and plot deceased participants' death causes.
Project Purpose(s)
- Educational
- Methods Development
- Other Purpose (This is an All of Us Featured Workspace: - teaches the users how to set up this notebook, install and import software packages, and select the correct version of the CDR. - gives an overview of the data types available in the current Controlled Tier Curated Data Repository (CDR) that are not available in the Registered Tier - shows how to retrieve and summarize this data.)
Scientific Approaches
We recommend that all researchers explore the notebooks in this workspace to learn the basics of All of Us Program Data. The tutorial Workspace contains two Jupyter Notebooks (one written in Python, the other in R). It contains helper functions for repeatedly, code readability and efficiency and repeatedly.
Anticipated Findings
By reading and running the notebooks in this Tutorial Workspace, you will understand the following: All of Us data are made available in two Curated Data Repository: the Registered Tier and Controlled Tier. The latter was subject to more relaxed privacy rules relative to the Registered Tier. As a result, you can expect to find more concept ids in certain data types such as EHR and Survey.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierDemo_Assessment_of_pathogenic_variants_in_AoURP_mw
Scientific Questions Being Studied
We will assess the relative frequency of positive findings across AoU samples and compare the aggregate findings with those from other cohorts - e.g. GnomAD. The frequencies of positive findings will be further broken down by the ancestry background of the participants to understand the impact of diverse backgrounds has on the rate of pathogenic findings.
Project Purpose(s)
- Other Purpose (Demonstrate the potential utility of Researcher Workbench data by describing the frequency of known pathogenic & pharmacogenomic variants in the current genomic dataset.)
Scientific Approaches
We will annotate genomic variants from AoU participants with variant curations that have been recorded by the HGSC-CL clinical annotation team in its ‘VIP’ database or in ClinVar. We will assess the frequency of these previously-known pathogenic mutations, and provide breakdowns by ancestry.
Anticipated Findings
These data will likely identify groups that are underrepresented and overrepresented by the current knowledge of pathogenic variants, and may provide important directions for prioritizing future research. Additionally, they may point to systematic differences between the AoU resource and other resources, such as GnomAD.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierResearch Team
Owner:
- Marsha Wheeler - Project Personnel, University of Washington
Collaborators:
- Laura Raffield - Other, University of North Carolina, Chapel Hill
- Quan Sun - Graduate Trainee, University of North Carolina, Chapel Hill
- Jia Wen - Research Fellow, University of North Carolina, Chapel Hill
- Bjoernar Tuftin - Project Personnel, University of North Carolina, Chapel Hill
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.
