Lesley Chapman Hannah

Research Fellow, National Cancer Institute (NIH - NCI)

16 active projects

Prostate_Cancer_Risk_Variant_Analysis_2024_v2_test_notebook

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…

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 Tier

Research Team

Owner:

Prostate_Cancer_Risk_Variant_Analysis_2024_cnv

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…

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 Tier

Research Team

Owner:

Prostate_Cancer_Risk_Variant_Analysis_2024_v1_snv_chr9_10

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…

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 Tier

Research Team

Owner:

Prostate_Cancer_Risk_Variant_Analysis_2024_v1_snv_chr10_11

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…

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 Tier

Research Team

Owner:

Prostate_Cancer_Risk_Variant_Analysis_2024_v1_snv_chr7_8

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…

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 Tier

Research Team

Owner:

Prostate_Cancer_Risk_Variant_Analysis_2024_v1_snv_v2

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…

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 Tier

Research Team

Owner:

Prostate_Cancer_Risk_Variant_Analysis_2024_v1_snv

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…

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 Tier

Research Team

Owner:

Duplicate of Prostate_Cancer_Risk_Variant_Analysis_2024_v2

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…

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 Tier

Research Team

Owner:

Duplicate of Prostate_Cancer_Risk_Variant_Analysis_2024_v2

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…

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 Tier

Research Team

Owner:

Evaluation of Risk Variants in Adult Cancer

Scientific Question: identify sets of germline SNPs that are significantly associated with cancer survival predictions in adults with eye cancer Purpose: This research question is a part of my overall master's in statistics research question which aims to identify variants…

Scientific Questions Being Studied

Scientific Question: identify sets of germline SNPs that are significantly associated with cancer survival predictions in adults with eye cancer

Purpose: This research question is a part of my overall master's in statistics research question which aims to identify variants associated with cancer risk in a set of pediatric cancers including retinoblastomas (RBL). I am training models with data from a set of 200 RBL patients to identify variants associated with cancer risk. Once these variants are identified, I will look for the distribution of these variants in patients within the All of Us Cohort that have eye cancer.

Project Purpose(s)

  • Educational

Scientific Approaches

Datasets: DNA variant data from eye cancer patients and age matched non-cancer controls
Research methods and tools: I plan to use ggplot and other R based software packages to plot the distribution of variants within cases and non-cancer controls. I also plan to look at survival rates between the two groups and will generate survival plots to compare rates of survival between patients that carry putative risk variants identified from our study versus non-cancer controls. The R survival package will be used for this comparison; reference: https://cran.r-project.org/web/packages/survival/index.html

Anticipated Findings

I expect to find a distribution of risk variants uniquely found in cases and not found in controls. The purpose of this analysis is to provide further evidence of risk variants identified within a cohort of retinoblastoma patients. The goal of the overall project is to identify unique variants associated with cancer risk.

Demographic Categories of Interest

  • Age

Data Set Used

Controlled Tier

Research Team

Owner:

Duplicate of Test_Control_Population

Prostate cancer is the most common non-cutaneous cancer among males accounting for 27% of all cancers and the second cause of cancer-related deaths (1). African Americans (AA) are disproportionately affected by higher prostate cancer incidence rates, earlier onset of disease,…

Scientific Questions Being Studied

Prostate cancer is the most common non-cutaneous cancer among males accounting for 27% of all cancers and the second cause of cancer-related deaths (1). African Americans (AA) are disproportionately affected by higher prostate cancer incidence rates, earlier onset of disease, higher mortality rates, and poorer outcomes than European Americans (EA) (2- 7).
The goal of this study is to identify a group of non-cancer controls that can be used to help identify novel germline risk variants.

Project Purpose(s)

  • Educational

Scientific Approaches

Research Plan. Our research plan consists of two aims: Aim 1 follows a data science approach to discover genetic risk factors for prostate cancer, and Aim 2 involves wet lab experiments to validate known and new prostate cancer risk variants in DNA repair genes identified in Aim 1.

Anticipated Findings

We will implement the activities described in this proposal according to the management plan and timeline. We will recruit students at our respective institutions to work on the outlined activities beginning in 2023. We will submit manuscripts into peer-reviewed academic journals in 2024. We will present our findings at the following conferences in 2024: the American Urological Association Annual Meeting, the American Association for Cancer Research (AACR) Annual Meeting, and the AACR Special Conference on Advances in Prostate Cancer Research. Undergraduates will present their work at conferences in 2023, such as Leadership Alliance National Symposium (LANS) and Annual Biomedical Research Conference for Minoritized Students (ABRCMS).

Demographic Categories of Interest

  • Race / Ethnicity

Data Set Used

Controlled Tier

Research Team

Owner:

Evaluation of genetic risk in a diverse group of prostate cancer 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:

Collaborators:

  • Victoria Mgbemena - Early Career Tenure-track Researcher, Baylor College of Medicine
  • Sabur Badmos - Research Fellow, University of Texas at El Paso
  • 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 - Project Personnel, Morehouse School of Medicine

Evaluation of Risk Variants in Adult Uveal Melanoma

Scientific Question: identify sets of germline SNPs that are significantly associated with cancer survival predictions in adults with eye cancer Purpose: This research question is a part of my overall master's in statistics research question which aims to identify variants…

Scientific Questions Being Studied

Scientific Question: identify sets of germline SNPs that are significantly associated with cancer survival predictions in adults with eye cancer

Purpose: This research question is a part of my overall master's in statistics research question which aims to identify variants associated with cancer risk in a set of pediatric cancers including retinoblastomas (RBL). I am training models with data from a set of 200 RBL patients to identify variants associated with cancer risk. Once these variants are identified, I will look for the distribution of these variants in patients within the All of Us Cohort that have eye cancer.

Project Purpose(s)

  • Educational

Scientific Approaches

Datasets: DNA variant data from eye cancer patients and age matched non-cancer controls
Research methods and tools: I plan to use ggplot and other R based software packages to plot the distribution of variants within cases and non-cancer controls. I also plan to look at survival rates between the two groups and will generate survival plots to compare rates of survival between patients that carry putative risk variants identified from our study versus non-cancer controls. The R survival package will be used for this comparison; reference: https://cran.r-project.org/web/packages/survival/index.html

Anticipated Findings

I expect to find a distribution of risk variants uniquely found in cases and not found in controls. The purpose of this analysis is to provide further evidence of risk variants identified within a cohort of retinoblastoma patients. The goal of the overall project is to identify unique variants associated with cancer risk.

Demographic Categories of Interest

  • Age

Data Set Used

Controlled Tier

Research Team

Owner:

Duplicate of Duplicate of Quick Demo of Plots and Analyses

Not applicable - this workspace is intended to be an introductory example of how to easily click-through analyses for new users to the All of Us Researcher Workbench with whom this Notebook will be shared. This workspace is adapted from…

Scientific Questions Being Studied

Not applicable - this workspace is intended to be an introductory example of how to easily click-through analyses for new users to the All of Us Researcher Workbench with whom this Notebook will be shared. This workspace is adapted from the demo workspace "How to Get Started with the Registered Tier Data"

Project Purpose(s)

  • Educational
  • Methods Development

Scientific Approaches

Not applicable - this workspace is intended to be an introductory example of how to easily click-through analyses for new users to the All of Us Researcher Workbench with whom this Notebook will be shared. This workspace is adapted from the demo workspace "How to Get Started with the Registered Tier Data"

Anticipated Findings

Not applicable - this workspace is intended to be an introductory example of how to easily click-through analyses for new users to the All of Us Researcher Workbench with whom this Notebook will be shared. This workspace is adapted from the demo workspace "How to Get Started with the Registered Tier Data"

Demographic Categories of Interest

  • Race / Ethnicity
  • Access to Care
  • Education Level
  • Income Level

Data Set Used

Registered Tier

Research Team

Owner:

Hypertension

The purpose of this analysis is to complete a tutorial for the All of Us Evenings in Genetics Workshop on May 20 2022.

Scientific Questions Being Studied

The purpose of this analysis is to complete a tutorial for the All of Us Evenings in Genetics Workshop on May 20 2022.

Project Purpose(s)

  • Educational

Scientific Approaches

For this section I will learn how to generate SQL queries to select patients based on phenotypes of interest, and will later analyze data from selected patients.

Anticipated Findings

I anticipate that I will select a diverse cohort of patients that will be used for later analysis.

Demographic Categories of Interest

  • Race / Ethnicity
  • Age

Data Set Used

Registered Tier

Research Team

Owner:

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

  • Race / Ethnicity

Data Set Used

Controlled Tier

Research Team

Owner:

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