Sarah Reed

Graduate Trainee, Vanderbilt University

3 active projects

Duplicate of Clonal Hematopoiesis of Indeterminate Potential and Solid Tumors

The specific questions I intend to study is how clonal hematopoiesis of indeterminate potential (CHIP) mutations can impact the development of malignancies. I will specifically be examining how the molecular processes involved in CHIP influence the formation of solid tumors…

Scientific Questions Being Studied

The specific questions I intend to study is how clonal hematopoiesis of indeterminate potential (CHIP) mutations can impact the development of malignancies. I will specifically be examining how the molecular processes involved in CHIP influence the formation of solid tumors and the relationship between the tumor microenvironment and CHIP. I will be studying co-variants as well, like smoking, sex, or environmental factors, and seeing how those relate to CHIP and solid tumors. This is relevant in order to further research into the predisposition for malignant diseases and tumors by having CHIP, and to delve into the complex morphology between the tumor microenvironment and CHIP.

Project Purpose(s)

  • Disease Focused Research (Clonal Hematopoiesis of Indeterminate Potential, Solid Tumors)
  • Educational
  • Ancestry

Scientific Approaches

I plan on using Jupyter notebooks in the R programming language to analyze data relating to my scientific questions. I plan on building a cohort with certain CHIP mutations, filtering for certain factors (like smoking, sex, and environmental or lifestyle factors), seeing how many develop a malignant disease (solid tumors), and then synthesizing this data with the genomic features of the controlled tier, as it relates to CHIP mutations and its molecular processes, to examine the relationship between CHIP, the tumor microenvironment, and certain factors mentioned previously.

Anticipated Findings

The anticipated findings from this study are unknown, as this is an exploratory study, but my findings should contribute to the growing field of CHIP and how this impacts malignant disease. This should also shed light on the relationship between CHIP and solid tumors and their microenvironment, as not much research has been done that deals with this. Furthermore, it should explain how certain factors, mentioned previously can influence all of the above, including the prognosis of these malignant diseases.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Sarah Reed - Graduate Trainee, Vanderbilt University

Duplicate of Kidney disease workspace – controlled tier V6

We seek to identify genetic or environmental factors that modify kidney disease risk in individuals with APOL1 mutations. In the United States, African American patients who are of West-African descent have a fourfold increase in the risk of end stage…

Scientific Questions Being Studied

We seek to identify genetic or environmental factors that modify kidney disease risk in individuals with APOL1 mutations.

In the United States, African American patients who are of West-African descent have a fourfold increase in the risk of end stage kidney disease (ESKD) compared to patients of other ancestry background. Although some of this difference can be attributed to socioeconomic and clinical risk, previous studies have also identified genetic mutations in apolipoprotein L1 (APOL1) that significantly increase risk of kidney disease. The two APOL1 high-risk mutations (G1 & G2) are common as they confer resistance to lethal Trypanosoma brucei infections, which is a pathogen endemic to West Africa. While just one copy of APOL1 G1 or G2 confers protection against T. brucei rhodesiense, two copies confer increased risk of kidney disease. Although ~13% of individuals of African Americans carry two APOL1 high-risk mutations; the majority do not develop kidney disease.

Project Purpose(s)

  • Disease Focused Research (kidney disease)
  • Ancestry

Scientific Approaches

Population: Subset of AoU Data set with available genetic data that is of West African Ancestry as determined by ancestry informative genetic markers
Outcome: Kidney disease phenotypes including chronic kidney disease (CKD), end stage renal disease (ESRD) or other kidney diseases or kidney disease markers as defined in the electronic health record or other AoU datasets.
Analysis plan: We will begin by identifying which individuals have APOL1 high-risk variants G1 (rs73885319 p.S342G; rs60910145 p.I384M) and G2 (rs71785313, a 6–base pair deletion that removes amino acids N388 and Y389). We will then determine whether carrying two of these high risk variants are associated with kidney disease (recessive genetic model). We will identify whether additional genetic mutations or environmental factors modify the association between APOL1 genetic risk variants and kidney disease using multivariate logistic regression.

Anticipated Findings

The identification of genetic or environmental factors that modify kidney disease risk, might guide lifestyle modification strategies or therapeutic development for individuals with APOL1 high risk mutations.

Demographic Categories of Interest

  • Race / Ethnicity

Data Set Used

Controlled Tier

Research Team

Owner:

  • Sarah Reed - Graduate Trainee, Vanderbilt University

Duplicate of How to Work with All of Us Survey Data (v6)

We recommend that all researchers explore the notebooks in this workspace to learn the basics of All of Us Program Data. What should you expect? By running the notebooks in this workspace, you should get familiar with how to query…

Scientific Questions Being Studied

We recommend that all researchers explore the notebooks in this workspace to learn the basics of All of Us Program Data.

What should you expect?
By running the notebooks in this workspace, you should get familiar with how to query PPI questions/surveys, what the frequencies of answers for each question in each PPI module are.

Project Purpose(s)

  • Educational
  • Methods Development
  • Other Purpose (This is an All of Us Tutorial Workspace created by the Researcher Workbench Support team. It is meant to provide instruction for key Researcher Workbench components and All of Us data representation.)

Scientific Approaches

By running the notebooks in this workspace, you should get familiar with how to query PPI questions/surveys, what the frequencies of answers for each question in each PPI module are.

Anticipated Findings

By reading and running the notebooks in this Tutorial Workspace, researchers will learn the following:
- how to query the survey data,
- how to summarize PPI modules, and questions.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Registered Tier

Research Team

Owner:

  • Sarah Reed - Graduate Trainee, Vanderbilt University
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