Deyana Lewis

Project Personnel, Morehouse School of Medicine

9 active projects

Duplicate of Introductory example of GWAS with type 2 diabetes phenotype

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.

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 Tier

Research Team

Owner:

  • Deyana Lewis - Project Personnel, Morehouse School of Medicine

Duplicate of Evaluation of genetic risk in a diverse PCa patients

Prostate cancer accounts for roughly 9% of all cancers in men, and disproportionately affects men of African descent more than any other racial group. Studies are needed to improve early detection of cancer risk in diverse groups of patients. Identifying…

Scientific Questions Being Studied

Prostate cancer accounts for roughly 9% of all cancers in men, and disproportionately affects men of African descent more than any other racial group. Studies are needed to improve early detection of cancer risk in diverse groups of patients. Identifying factors, such as novel cancer risk variants, could lead to more accurate screening and early detection in diverse groups. Studies have shown that variants within DNA repair pathway genes are found at higher rates in aggressive forms of prostate cancer compared to non-aggressive forms of the disease. We hope to identify general trends in germline variants within DNA repair pathway genes across diverse groups of prostate cancer patients. Specifically, our goal is to identify germline variants associated with prostate cancer patients from medically underserved racial and ethnic groups. The initial stage of our analysis will be exploratory, our goal is to use these initial characterizations to inform future studies.

Project Purpose(s)

  • Disease Focused Research (prostate cancer)
  • Ancestry

Scientific Approaches

Our analysis will involve three steps: (1) variant annotation, (2) variant selection, and (3) identification of groups of variants associated with cancer risk. (1) Germline variant annotation will be annotated in order to identify common and rare variants within our dataset. Variants will also be annotated to describe potential biological function and pathogenicity by adding on annotations from large databases. The distribution of these select variants will be characterized in cases versus controls. (2) Variants will be selected for modeling and analysis based on biological function and pathogenicity. (3) To identify variants associated with cancer risk, we will use variants selected in step (2) above to train basic linear models - logistic regression models - to identify putative risk variants. Our analysis will include all 4210 prostate cancer cases from the All of Us Workbench as well as 4210 non-cancer controls.

Anticipated Findings

The goal of our study is to identify novel variants associated with disease risk in a racially diverse groups of prostate cancer patients. We expect to find novel groups of putative risk variants within each racial group. By evaluating germline variants within DNA repair pathway genes, we hope to better understand genetic susceptibility to prostate cancer. Identifying novel risk variants could lead to improved disease risk prediction, and could help improve early detection and screening for prostate cancer. Specifically, the putative risk variants identified within this study could be used to inform and improve screening approaches for individuals from diverse racial backgrounds, which could inform approaches for early intervention strategies.

Demographic Categories of Interest

  • Race / Ethnicity
  • Age

Data Set Used

Controlled Tier

Research Team

Owner:

  • Deyana Lewis - Project Personnel, Morehouse School of Medicine

PCa_test_V7

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…

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

Research Team

Owner:

  • Deyana Lewis - Project Personnel, Morehouse School of Medicine

Duplicate of GWAS_EXAMPLE

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.

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 Tier

Research Team

Owner:

  • Deyana Lewis - Project Personnel, Morehouse School of Medicine

Duplicate of Introductory example of GWAS with type 2 diabetes phenotype

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.

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 Tier

Research Team

Owner:

  • Deyana Lewis - Project Personnel, Morehouse School of Medicine

Duplicate of PCa_test_V7_Hail

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…

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

Research Team

Owner:

  • Deyana Lewis - Project Personnel, Morehouse School of Medicine

Duplicate of Introductory example of GWAS with type 2 diabetes phenotype

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.

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 Tier

Research Team

Owner:

  • Deyana Lewis - Project Personnel, Morehouse School of Medicine

Duplicate of How to Work with All of Us Genomic Data (Hail - Plink)(v6)

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.

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 Tier

Research Team

Owner:

  • Deyana Lewis - Project Personnel, Morehouse School of Medicine

Exploring Hypertension Data Types

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.

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 Tier

Research Team

Owner:

  • Deyana Lewis - Project Personnel, Morehouse School of Medicine
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