Javan Carter
Research Associate, All of Us Researcher Academy/RTI International
6 active projects
RTI Type I Diabetes PRS Validation Analysis
Scientific Questions Being Studied
Based on the research done from the Sharp et. al. 2019 paper and the Qu et. al. paper, Polygenic Risk Scores (PRS's) were developed for European and African biological and ancestral groups. We would like to go and validate the PRS's against and independent cohort of individuals associated with Type I Diabetes to recalculate the PRS threshold using the all of us database. Additionally, we want to further validate the PRS's against other biological ancestral races such as East Asian and Hispanic.
Project Purpose(s)
- Disease Focused Research (type 1 diabetes mellitus)
- Methods Development
- Control Set
- Ancestry
Scientific Approaches
Create cohorts representing individuals with Type I Diabetes from various backgrounds and races based off of PTA ancestral predictions and run a customized PRS calculation script on the candidate PRS markers described in Qu et. al., 2022.
Anticipated Findings
The anticipated findings for the study could either be confirming that all 72 PRS candidate markers are sufficient across multiple ancestral populations, or that confoundment plays a role in the overall effect size of the PRS markers for given or specific ancestral populations, thus requiring new thresholds to be established for different ancestral populations, other than European.
Demographic Categories of Interest
- Race / Ethnicity
Data Set Used
Controlled TierResearch Team
Owner:
- Kristin Glaze - Project Personnel, All of Us Researcher Academy/RTI International
- Javan Carter - Research Associate, All of Us Researcher Academy/RTI International
RTI OUD GWAS analysis
Scientific Questions Being Studied
The purpose of this workspace is to further explore the GWS significant loci identified in GWAS analyses of OUD using a more diverse and bigger sample.
Project Purpose(s)
- Ancestry
Scientific Approaches
The datasets will include cohorts of different combinations of parameters from All of Us, including their genomic data. The methods and tools will include QC and model selection for analyses using the notebooks.
Anticipated Findings
The anticipated findings from this study include further identification of novel loci associated with OUD given a more diverse dataset and confirmation of previous findings.
Demographic Categories of Interest
- Sex at Birth
- Gender Identity
- Sexual Orientation
Data Set Used
Controlled TierResearch Team
Owner:
- Javan Carter - Research Associate, All of Us Researcher Academy/RTI International
Collaborators:
- Amy Moore - Research Associate, Research Triangle Institute
GWAS on OUD
Scientific Questions Being Studied
The purpose of this workspace is to further explore the GWS significant loci identified in GWAS analyses of OUD using a more diverse and bigger sample.
Project Purpose(s)
- Ancestry
Scientific Approaches
The datasets will include cohorts of different combinations of parameters from All of Us, including their genomic data. The methods and tools will include QC and model selection for analyses using the notebooks.
Anticipated Findings
The anticipated findings from this study include further identification of novel loci associated with OUD given a more diverse dataset and confirmation of previous findings.
Demographic Categories of Interest
- Sex at Birth
- Gender Identity
- Sexual Orientation
Data Set Used
Controlled TierResearch Team
Owner:
- Rahma Jamac - Other, All of Us Researcher Academy/RTI International
- Javan Carter - Research Associate, All of Us Researcher Academy/RTI International
- Wendy Deng - Project Personnel, All of Us Researcher Academy/RTI International
- Caryn Willis - Research Associate, All of Us Researcher Academy/RTI International
P50 Opioid Meta Analysis
Scientific Questions Being Studied
This study intends to investigate the association between calcium and muscular weakness in an attempt to identify the role of calcium in muscle contraction.
Project Purpose(s)
- Educational
Scientific Approaches
This study will investigate actionable biological drives of opioid use disorder through completing a GWAS study.
Anticipated Findings
This is integral in contributing in the knowledge base regarding the biology underlying opioid use disorder.
Demographic Categories of Interest
- Race / Ethnicity
Data Set Used
Controlled TierResearch Team
Owner:
- Rahma Jamac - Other, All of Us Researcher Academy/RTI International
- Javan Carter - Research Associate, All of Us Researcher Academy/RTI International
- Wendy Deng - Project Personnel, All of Us Researcher Academy/RTI International
- Caryn Willis - Research Associate, All of Us Researcher Academy/RTI International
RTI Research Academy R workshop (sickle cell project) with v.8
Scientific Questions Being Studied
This workbench is designed to be used as an educational tool for the RTI Research academy. Therefore, there isn't a scientific question that will be explored. The pseudo- question is associated with Sickle cell and how to identify it using GWAS. The target audience are students, graduate students, post-docs, and PIs from HBCUs (Historically Black Community Colleges/ Universities). The goal is the reduce the gap of knowledge between HBCUs and PWI and give HBCUs the tools and confidence to use the AoU workbench.
Project Purpose(s)
- Educational
Scientific Approaches
We will be creating a cohort of individuals with the sickle cell disease and those who do not (control). This cohort will be converted into a dataset and processed in the R notebook. We will be using PLINK as a genotyping and GWAS tool. The overall goal is "education without intimidation". We want to introduce these topics to our students in the most parsimonious way with high accuracy and correctness to remove the fluff and allow the student to feel comfortable with the knowledge presented.
Anticipated Findings
There are no anticipated findings because of the nature of the project. This study will ultimately contribute to the scientific knowledge by advancing the knowledge of the individuals who take the course and eventually start their own amazing research study.
Demographic Categories of Interest
- Race / Ethnicity
Data Set Used
Controlled TierResearch Team
Owner:
- Javan Carter - Research Associate, All of Us Researcher Academy/RTI International
Collaborators:
- Kristin Glaze - Project Personnel, All of Us Researcher Academy/RTI International
RTI Research Academy R workshop (sickle cell project)
Scientific Questions Being Studied
This workbench is designed to be used as an educational tool for the RTI Research academy. Therefore, there isn't a scientific question that will be explored. The pseudo- question is associated with Sickle cell and how to identify it using GWAS. The target audience are students, graduate students, post-docs, and PIs from HBCUs (Historically Black Community Colleges/ Universities). The goal is the reduce the gap of knowledge between HBCUs and PWI and give HBCUs the tools and confidence to use the AoU workbench.
Project Purpose(s)
- Educational
Scientific Approaches
We will be creating a cohort of individuals with the sickle cell disease and those who do not (control). This cohort will be converted into a dataset and processed in the R notebook. We will be using PLINK as a genotyping and GWAS tool. The overall goal is "education without intimidation". We want to introduce these topics to our students in the most parsimonious way with high accuracy and correctness to remove the fluff and allow the student to feel comfortable with the knowledge presented.
Anticipated Findings
There are no anticipated findings because of the nature of the project. This study will ultimately contribute to the scientific knowledge by advancing the knowledge of the individuals who take the course and eventually start their own amazing research study.
Demographic Categories of Interest
- Race / Ethnicity
Data Set Used
Controlled TierResearch Team
Owner:
- Javan Carter - Research Associate, All of Us Researcher Academy/RTI International
Collaborators:
- Trey-Rashad Hawkins - Project Personnel, All of Us Researcher Academy/RTI International
- Danielle Johnson - Project Personnel, All of Us Researcher Academy/RTI International
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