Deyana Lewis
Research Fellow, National Institutes of Health (NIH)
9 active projects
Duplicate of PCa_test_V7_Hail
Scientific Questions Being Studied
To identify prostate cancer risk variants and genes in African American men. The reason for exploring this data is that prostate cancer develops more often in men of African ancestry than in men of other races. However, so far, prostate cancer genetic studies are based on the available data that mostly come from white men. This racial disparity has biased the discovery of genetic risk factors and therapeutic approaches, leading disparity in mortality rates
Project Purpose(s)
- Disease Focused Research (prostate carcinoma)
- Social / Behavioral
- Ancestry
Scientific Approaches
I will design a two matched case-control studies black and white men. Thereafter, conduct a GWAS to identify variants and genes with higher mutation frequency. Next, I will identify genes mutated with larger functional impact through functional annotation analyses. Will repeat analysis using rare variants which will include rare variant association tests
Anticipated Findings
I anticipate finding novel variants and confirming prostate cancer risk variants that are specific to men of African ancestry. Doing so will increase the representation of African American men in prostate cancer genomic studies and increase African American awareness of early detection screening protocols.
Demographic Categories of Interest
- Race / Ethnicity
Data Set Used
Controlled Tier
Duplicate of GWAS_EXAMPLE
Scientific Questions Being Studied
Hypertension is one of the most common diseases in the US. Here, we will be determining what genetic variants contribute to higher systolic blood pressure, diastolic blood pressure, and pulse pressure in participants of African ancestry.
Project Purpose(s)
- Disease Focused Research (hypertension)
- Ancestry
Scientific Approaches
I plan to use median measurement values to determine median SBP, DBP, and PP. Then I plan to use the genetic data available and a GWAS run with Plink to determine which associations exist. This GWAS will be using quantitative data and thus will use linear regression.
Anticipated Findings
We anticipate replicating previously reported hypertension GWAS findings. In addition, since most hypertension GWAS are done in European ancestry, we expect to identify new variants associated with participants of African ancestry
Demographic Categories of Interest
- Race / Ethnicity
Data Set Used
Controlled TierPCa_test_V7
Scientific Questions Being Studied
To identify prostate cancer risk variants and genes in African American men. The reason for exploring this data is that prostate cancer develops more often in men of African ancestry than in men of other races. However, so far, prostate cancer genetic studies are based on the available data that mostly come from white men. This racial disparity has biased the discovery of genetic risk factors and therapeutic approaches, leading disparity in mortality rates
Project Purpose(s)
- Disease Focused Research (prostate carcinoma)
- Social / Behavioral
- Ancestry
Scientific Approaches
I will design a two matched case-control studies black and white men. Thereafter, conduct a GWAS to identify variants and genes with higher mutation frequency. Next, I will identify genes mutated with larger functional impact through functional annotation analyses. Will repeat analysis using rare variants which will include rare variant association tests
Anticipated Findings
I anticipate finding novel variants and confirming prostate cancer risk variants that are specific to men of African ancestry. Doing so will increase the representation of African American men in prostate cancer genomic studies and increase African American awareness of early detection screening protocols.
Demographic Categories of Interest
- Race / Ethnicity
Data Set Used
Controlled TierPCa_v7
Scientific Questions Being Studied
Prostate Adenocarcinoma (PRAD) is associated with 1 in 25 African American men deaths, compared to 1 in 45 White American men deaths. Genetic and societal factors may contribute to this racial disparity and our project aims to shed light in both factors. Our goals are to find ethnic specific risk factors using survey-based features and genetic risk factors using the genetic variants data.
Project Purpose(s)
- Disease Focused Research (prostate cancer)
- Population Health
- Educational
- Methods Development
- Ancestry
Scientific Approaches
To achieve our goals we will use statistical tests and state-of-the-art tools to compare case and control genomes in order to identify variants that appear disproportionally in cases and genes with heavy variant load in cases. Such tools include the Evolutionary Action method and the software packages EMMAX and ACAT, amongst others.
Anticipated Findings
We anticipate obtaining lists of candidate genes and their variants that drive PRAD in African American men and in White American men, which we will contrast and compare with the current knowledge (e.g. BRCA1, BRCA2, and HOXB13 genes). This work may provide new genetic targets that affect the development and progression of PRAD, especially amongst the African American men and reduce the racial disparity in genetic risk diagnosis.
Demographic Categories of Interest
- Race / Ethnicity
Data Set Used
Controlled TierResearch Team
Owner:
- Victoria Mgbemena - Early Career Tenure-track Researcher, Baylor College of Medicine
- Sabur Badmos - Research Fellow, University of Texas at El Paso
- Lesley Chapman Hannah - Research Fellow, National Cancer Institute (NIH - NCI)
- Kimiko Krieger - Research Fellow, Baylor College of Medicine
- Panagiotis Katsonis - Other, Baylor College of Medicine
- Jose Nolazco - Research Fellow, Baylor College of Medicine
- Deyana Lewis - Research Fellow, National Institutes of Health (NIH)
Collaborators:
- Jun Qian - Other, All of Us Program Operational Use
Dream_Team
Scientific Questions Being Studied
Prostate Adenocarcinoma (PRAD) is associated with 1 in 25 African American men deaths, compared to 1 in 45 White American men deaths. Genetic and societal factors may contribute to this racial disparity and our project aims to shed light in both factors. Our goals are to find ethnic specific risk factors using survey-based features and genetic risk factors using the genetic variants data.
Project Purpose(s)
- Disease Focused Research (prostate cancer)
- Population Health
- Educational
- Methods Development
- Ancestry
Scientific Approaches
To achieve our goals we will use statistical tests and state-of-the-art tools to compare case and control genomes in order to identify variants that appear disproportionally in cases and genes with heavy variant load in cases. Such tools include the Evolutionary Action method and the software packages EMMAX and ACAT, amongst others.
Anticipated Findings
We anticipate obtaining lists of candidate genes and their variants that drive PRAD in African American men and in White American men, which we will contrast and compare with the current knowledge (e.g. BRCA1, BRCA2, and HOXB13 genes). This work may provide new genetic targets that affect the development and progression of PRAD, especially amongst the African American men and reduce the racial disparity in genetic risk diagnosis.
Demographic Categories of Interest
- Race / Ethnicity
Data Set Used
Controlled TierResearch Team
Owner:
- Victoria Mgbemena - Early Career Tenure-track Researcher, Baylor College of Medicine
- Sabur Badmos - Research Fellow, University of Texas at El Paso
- Lesley Chapman Hannah - Research Fellow, National Cancer Institute (NIH - NCI)
- Kimiko Krieger - Research Fellow, Baylor College of Medicine
- Panagiotis Katsonis - Other, Baylor College of Medicine
- Jose Nolazco - Research Fellow, Baylor College of Medicine
- Deyana Lewis - Research Fellow, National Institutes of Health (NIH)
Collaborators:
- Jun Qian - Other, All of Us Program Operational Use
Duplicate of Introductory example of GWAS with type 2 diabetes phenotype
Scientific Questions Being Studied
Not applicable - this workspace is intended to be an introductory example of how to do a genome-wide association study on the All of Us genomic data that individuals can easily click through and understand.
Project Purpose(s)
- Educational
Scientific Approaches
Not applicable - this workspace is intended to be an introductory example of how to do a genome-wide association study on the All of Us genomic data that individuals can easily click through and understand.
Anticipated Findings
Not applicable - this workspace is intended to be an introductory example of how to do a genome-wide association study on the All of Us genomic data that individuals can easily click through and understand.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierDuplicate of How to Work with All of Us Genomic Data (Hail - Plink)(v6)
Scientific Questions Being Studied
Not applicable - these notebooks demonstrate example analysis how to use Hail and PLINK to perform genome-wide association studies using the All of Us genomic data and phenotypic data.
Project Purpose(s)
- Other Purpose (Demonstrate to the All of Us Researcher Workbench users how to get started with the All of Us genomic data and tools. It includes an overview of all the All of Us genomic data and shows some simple examples on how to use these data.)
Scientific Approaches
Not applicable - these notebooks demonstrate example analysis how to use Hail and PLINK to perform genome-wide association studies using the All of Us genomic data and phenotypic data.
Anticipated Findings
Not applicable - these notebooks demonstrate example analysis how to use Hail and PLINK to perform genome-wide association studies using the All of Us genomic data and phenotypic data.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierExploring Hypertension Data Types
Scientific Questions Being Studied
Not applicable-this Workspace is intended for educational purposes at the 2022 UBR Faculty Summit to learn how to use the Researcher Workbench by analyzing a data type for hypertension.
Project Purpose(s)
- Educational
Scientific Approaches
Not applicable-this Workspace is intended for educational purposes at the 2022 UBR Faculty Summit to learn how to use the Researcher Workbench by analyzing a data type for hypertension.
Anticipated Findings
Not applicable-this Workspace is intended for educational purposes at the 2022 UBR Faculty Summit to learn how to use the Researcher Workbench by analyzing a data type for hypertension.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Registered TierDuplicate of Introductory example of GWAS with type 2 diabetes phenotype
Scientific Questions Being Studied
Not applicable - this workspace is intended to be an introductory example of how to do a genome-wide association study on the All of Us genomic data that individuals can easily click through and understand.
Project Purpose(s)
- Educational
Scientific Approaches
Not applicable - this workspace is intended to be an introductory example of how to do a genome-wide association study on the All of Us genomic data that individuals can easily click through and understand.
Anticipated Findings
Not applicable - this workspace is intended to be an introductory example of how to do a genome-wide association study on the All of Us genomic data that individuals can easily click through and understand.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled 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.
