Salma Bargal
Graduate Trainee, University of Maryland, Baltimore
2 active projects
SGLT2i
Scientific Questions Being Studied
We intend to investigate the use of All of Us data by developing an algorithm to find responses to SGLT2i. We aim to define an algorithm that best maximizes usage of All of Us data while maintaining a representative dataset of responses to SGLT2i from a diverse population. Working on defining the phenotype of SGLT2i responses from All of Us data includes looking into average SGLT2i lowering of HbA1c. This can be obtained by comparing HbA1c level before and after SGLT2i in diabetic patients taking into consideration confounding factors. This is important to help us understand the inter-individual variability in efficacy measures.
Project Purpose(s)
- Drug Development
- Ancestry
Scientific Approaches
We plan to extract data from diabetic patients treated with SGLT2i. We will evaluate baseline HbA1c before starting an SGLT2i and follow-up HbA1c measurement following maintenance on an SGLT2i for a defined period of time without other changes to diabetes treatment. In addition, attention to confounding factors, such as renal function and changes to other medications would need to be considered.
Anticipated Findings
We anticipate we will have defined a phenotype for SGLT2i responses that can be used for our future study on genetic predictors of SGLT2i response, as well as other genetic studies.
Demographic Categories of Interest
- Race / Ethnicity
- Age
Data Set Used
Controlled Tier
Duplicate of PGRN 2024 Scientific Meeting All of Us Genomics workshop[SAB]
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: extracting phenotypic data for Hail GWAS (notebook)
Exercise 2: running Hail GWAS (notebook)
Exercise 3: extracting phenotypic data for Plink GWAS (notebook)
Exercise 4: running GWAS using Plink(notebook)
Exercise 5: running GWAS using Plink via dsub (notebook)
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 PGRN 2024 Scientific Meeting All of Us Genomics workshop. In this workshop, participants will get hands-on experience using the genomics data running a genome-wide association study (GWAS) using Hail/plink. )
Scientific Approaches
We are using the All of Us dataset in order to run a genome-wide association study (GWAS) using Hail/Plink. 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/Plink, we will visualize the results.
Anticipated Findings
This study is running a genome-wide association study (GWAS) using Hail/Plink, using QT-interval corrected 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 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.
