Kaitlyn Ford
Undergraduate Student, Salve Regina University
3 active projects
Duplicate of Genomics-Workshop-July2023
Scientific Questions Being Studied
This workspace is meant to help researchers get familiar with the All of Us Researcher Workbench. There are five hands-on exercises during the workshop, each with a specific notebook.
Exercise 1: Duplicate the workspace & start the cloud environment
Exercise 2: Looking at the genomic data (notebook)
Exercise 3: GWAS - extracting phenotypic data (notebook)
Exercise 4: GWAS - running Hail GWAS (notebook)
Exercise 5: Advanced GWAS (2 notebooks)
By running the exercises in this workspace, researchers will become more familiar with the genomic data, know how to access the genomic data, see how the genomic data and tools can be used in the Researcher Workbench, and be able to start their own genomic data project.
Project Purpose(s)
- Other Purpose (This workspace is meant for use during the Introduction to Analyzing All of Us Genomic Data workshop. In this workshop, participants will get hands-on experience using the genomics data running a genome-wide association study (GWAS) using Hail. )
Scientific Approaches
We are using the All of Us dataset in order to run a genome-wide association study (GWAS) using Hail. In the workshop, we will give an introduction to the All of Us Researcher Workbench and demonstrate how to use the Cohort Builder and Jupyter Notebooks to set up a research project. Using Jupyter notebooks, we will create a dataset linking the All of Us phenotypic data to the short read whole genome sequencing (srWGS) data. After running the GWAS steps using Hail, we will visualize the results.
Anticipated Findings
This study is running a genome-wide association study (GWAS) using Hail, using height as the selected phenotypic data. We do not anticipate findings from this example workspace but we expect that workshop participants will be able to apply similar methods to their future research.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled Tier
StarD6 SNPs in relation to Alzheimer's Disease
Scientific Questions Being Studied
Previous studies have shown a link between the StarD6 SNP rs10164112 and Alzheimer's Disease. These studies have concluded that this risk is especially increased if the individual is also an APOe4 carrier. These studies have been conducted on 3 different Asian populations and only have a few hundred individuals, the question that is driving my research is if these factors remain true in the United States population. By using the All of Us database I will not only be able to test the question of population but also have many more individuals to study.
Project Purpose(s)
- Disease Focused Research (Alzheimer's Disease)
- Ancestry
Scientific Approaches
I plan to make two cohorts to study the data. One cohort will consist of individuals who don't have any MCI diagnoses and the other will be individuals who have Alzheimer's Disease. Once we have these individuals picked I will separate each cohort into two, one that doesn't take age into consideration, and the other that only looks at individuals with the previous criteria who are either 65 years of age or older. When looking at these two cohorts of individuals I will look at the SNP rs10164112 and analyze the Thymine and Cytosine frequencies in this sequence. Once I identify these groups of individuals I will search for the presence of APOe2, APOe3, and APOe4 in those with and without Alzheimer's Disease to see if this gene is related to AD risk as stated in previous studies.
Anticipated Findings
I anticipate finding that the Thymine levels in the rs 10164112 SNP are higher in people who don't have any MCIs, and in contrast, I anticipate finding increased Cytosine levels in the rs 10164112 SNP in people who do have Alzheimer's Disease. These findings would create further evidence that the StarD6 protein is linked to AD progression and would give me and other scientists a new target area of focus when researching this disease.
Demographic Categories of Interest
- Race / Ethnicity
- Age
- Disability Status
Data Set Used
Controlled TierDuplicate of Skills Assessment Training Notebooks For Users (v7)
Scientific Questions Being Studied
This workspace contains multiple notebooks that assess users' understanding of the workbench and OMOP. These notebooks are meant to help users check their knowledge not only on Python, R, and SQL, but also on the general data structure and data model used by the All of Us program.
Project Purpose(s)
- Educational
Scientific Approaches
There are no scientific approach used in this workspace because it is meant for educational purposes only. We will cover all aspects of OMOP, and hence will use most datasets available in the workbench.
Anticipated Findings
We do not anticipate to have any findings. Instead, we are educating people on the use of the workbench and the common data model OMOP used by the program.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Registered 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.
