Allyson Motter
Research Assistant, National Human Genome Research Institute (NIH-NHGRI)
4 active projects
Duplicate of Data Wrangling in All of Us Program (v7)
Scientific Questions Being Studied
For Educational purpose to show best practices when using jupyter notebooks for data access, storage, data manipulations - transformations, conversions, cleaning, optimization and other research support related issues that is useful for multiple AoU researchers.
Project Purpose(s)
- Educational
- Other Purpose (For use with Office hours. notebooks for adding code snippets useful for researchers. This is a placeholder for creating notebooks for best practices among other things)
Scientific Approaches
For Educational purpose to show best practices when using jupyter notebooks for data access, storage, data manipulations - transformations, conversions, cleaning, optimization and other research support related issues that is useful for multiple AoU researchers.
Anticipated Findings
For Educational purpose to show best practices when using jupyter notebooks for data access, storage, data manipulations - transformations, conversions, cleaning, optimization and other research support related issues that is useful for multiple AoU researchers.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Registered TierResearch Team
Owner:
- Allyson Motter - Research Assistant, National Human Genome Research Institute (NIH-NHGRI)
Alloimmunization test cohort
Scientific Questions Being Studied
This project investigates anti-red blood cell alloimmunization, a phenomenon disproportionally exhibited by patients with Sickle Cell Disease (SCD). We published a novel association between development of alloantibodies and a genetic variant of African ancestry at chromosome 5q33, using a multi-cohort GWAS study of adult transfusion recipients with SCD. Identifying a biomarker predictive of alloimmunization susceptibility will allow for identification of a subset of SCD patients at greatest risk of alloimmunization prior to beginning transfusions. Prospectively identifying individuals at highest risk of becoming responders and understanding the mechanism of alloantibody development will allow for improved patient management, equitable resource allocation, and novel avenues for therapeutic development.
Project Purpose(s)
- Disease Focused Research (Sickle cell disease)
- Methods Development
- Ancestry
Scientific Approaches
We hope to identify a cohort of individuals with sickle cell disease who have a history of receiving blood transfusions. Among these individuals, we will stratify them into those who have a record of alloantibody development post transfusion (responders) and those who do not (non-responders). We also hope to utilize the controlled tier dataset to identify carriers of our variant of interest and develop a clinical profile/phenotype of these individuals.
Anticipated Findings
We hope to find a higher frequency of transfusion responders among individuals with our variant of interest in order to validate its causal role in the alloimmune response. We also hope to have a better understanding of the risk factors, comorbidities, and phenotypic and/or demographic characteristics of risk variant carriers and transfusion responders that exist in the All of Us database.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierResearch Team
Owner:
- Allyson Motter - Research Assistant, National Human Genome Research Institute (NIH-NHGRI)
Duplicate of Beginner Intro to AoU Data and the Workbench (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 TierResearch Team
Owner:
- Allyson Motter - Research Assistant, National Human Genome Research Institute (NIH-NHGRI)
Duplicate of How to Work with Genomics Data (CRAM_Processing and IGV)_v7HC
Scientific Questions Being Studied
This workspace and its notebooks neither ask nor answer any scientific questions. The purpose of this workspace is to serve as a tutorial which shows how to localize the All of Us (AoU) CRAM files individually or in groups via the CRAM manifest in addition to showing how to render the Integrated Genome Viewer (IGV) on the AoU workbench to explore the CRAM files.
Project Purpose(s)
- Methods Development
Scientific Approaches
This workspace conducts no study and applies no scientific approaches. This workspace and its notebooks are tutorials for localizing AoU CRAM files with R commands and using IGV to explore their contents. The methods and tools employed include R system commands for localizing individual CRAM files, an R for loop for localizing multiple CRAM files by referencing the manifest, and the commands for importing and rendering IGV to view the localized CRAM files.
Anticipated Findings
There will be no findings or contribution to scientific knowledge as there is no study being conducted nor questions asked. Informal 'findings' include the usability of the aforementioned tools and AoU CRAM files on the All of Us workbench.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierResearch Team
Owner:
- Allyson Motter - Research Assistant, National Human Genome Research Institute (NIH-NHGRI)
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