Micah Hysong

Graduate Trainee, University of North Carolina, Chapel Hill

8 active projects

WorkbenchBackChannel

This workspace is to be used for researchers to share scripts with each other. We will copy over notebooks of interest for each other to use.

Scientific Questions Being Studied

This workspace is to be used for researchers to share scripts with each other. We will copy over notebooks of interest for each other to use.

Project Purpose(s)

  • Ancestry

Scientific Approaches

This workspace is to be used for researchers to share scripts with each other. We will copy over notebooks of interest for each other to use.

Anticipated Findings

This team-science approach will advance research by harmonizing methods and avoiding redundancy in script writing.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Micah Hysong - Graduate Trainee, University of North Carolina, Chapel Hill

Collaborators:

  • Laura Raffield - Other, University of North Carolina, Chapel Hill
  • Bjoernar Tuftin - Project Personnel, University of North Carolina, Chapel Hill

PheWAS

HbA1c is a clinical measure used to assess glycemic control over time. However some genetic variants may interfere with the accuracy of HbA1c as a measure of glycemic control. This could have negative implications for management of patients with diabetes/prediabetes…

Scientific Questions Being Studied

HbA1c is a clinical measure used to assess glycemic control over time. However some genetic variants may interfere with the accuracy of HbA1c as a measure of glycemic control. This could have negative implications for management of patients with diabetes/prediabetes and lead to an increased risk of complications. This is particularly an issue for individuals with ancestry from malaria endemic regions, whose genomes may contain high impact variants in genes such as G6PD and HBB (i.e. sickle cell trait) that have been under selective pressure from malaria in the past and may now be interfering with accurate clinical use of the HbA1c measure. Our goal for this study is to characterize whether variants in G6PD and HBB impact the rate of diabetes related complications, likely due to impacts on HbA1c measurement accuracy.

Project Purpose(s)

  • Disease Focused Research (Diabetes)
  • Ancestry

Scientific Approaches

- Datasets: those with type 1 or 2 diabetes and WGS
- Sickle Cell status rs334(A;T) - yes or no
- G6PD variants – where males are multiplied by two

Hypothesis 1: Individuals with diabetes and with known G6PD coding variants, particularly hemizygous males or homozygous females, will have a higher rate of diabetic retinopathy.
Cox proportional hazards models:
1. outcome~age+ sex + G6PD variant count+ sickle cell trait status + 10 principal components of genetic ancestry
2. + BMI

Hypothesis 2: In individuals with diabetes, HbA1c will be more predictive of retinopathy when adjusted for G6PD coding variant status. All models should be stratified by diabetes status (any diabetes, including either type 1 or type 2) at beginning of follow-up.
Cox proportional hazards models:
1. outcome~HbA1c+age+ sex + G6PD variant count+ sickle cell trait status + 10 principal components of genetic ancestry
2. +BMI

Anticipated Findings

We anticipate that coding variants in G6PD and HBB will lead to increased diabetic retinopathy. Understanding how variants from diverse populations impact our clinical measures and outcomes is imperative for reducing racial health disparities.

Demographic Categories of Interest

  • Race / Ethnicity

Data Set Used

Controlled Tier

Research Team

Owner:

  • Micah Hysong - Graduate Trainee, University of North Carolina, Chapel Hill

Collaborators:

  • Jun Qian - Other, All of Us Program Operational Use
  • Emily Drzymalla - Other, University of North Carolina, Chapel Hill

BCT PTRS (V7)

PRS have been demonstrated to have low portability between ancestry groups (Duncan et al., 2019). This is largely due to the fact that 78% of GWAS has been performed in individuals of European ancestry (Gurdasani et al., 2019). Generous participants…

Scientific Questions Being Studied

PRS have been demonstrated to have low portability between ancestry groups (Duncan et al., 2019). This is largely due to the fact that 78% of GWAS has been performed in individuals of European ancestry (Gurdasani et al., 2019). Generous participants in the All of Us research program are from diverse genetic ancestry backgrounds, allowing for the statistical power necessary to test methods to improve PRS performance in individuals of non-European ancestry. Specifically, I will be exploring the ability of Polygenic Transcriptomic Risk Scores (PTRS) to improve performance of the PRS for a variety of test quantitative traits, including blood Increasing PRS performance in different ancestry groups is imperative to equitable implementation of PRS to improve health outcomes.

Project Purpose(s)

  • Methods Development
  • Ancestry

Scientific Approaches

Datasets: Cohort: Whole Genome Sequencing Derive PTRS that includes all ancestry groups and then individual PTRS for each ancestry group. Generate a generalized linear model that includes age, sex at birth, and PRS as covariates.

Anticipated Findings

We expect that PRS scores trained in European ancestry will have lower accuracy for predicting blood cell indices in cohorts with non-European ancestry. We also predict that training a new PTRS in more diverse populations will make a PTRS that is more accurate across all ancestries. Overall, these findings would contribute to the growing body of literature supporting the need for including more diverse ancestry groups in genomic studies. Importantly, this will improve health-outcomes in minoritized groups.

Demographic Categories of Interest

  • Race / Ethnicity

Data Set Used

Controlled Tier

Research Team

Owner:

  • Micah Hysong - Graduate Trainee, University of North Carolina, Chapel Hill

Collaborators:

  • Bjoernar Tuftin - Project Personnel, University of North Carolina, Chapel Hill
  • Reagan Ballard - Undergraduate Student, University of North Carolina, Chapel Hill
  • Emily Drzymalla - Other, University of North Carolina, Chapel Hill

Duffy

Do variants at the Duffy locus lead to any diseases or disorders? Duffy null status (2 copies rs2814778) is common in ancestry groups from malaria endemic regions and has been associated with unnecessary bone marrow biopsies; therefore, understanding the role…

Scientific Questions Being Studied

Do variants at the Duffy locus lead to any diseases or disorders? Duffy null status (2 copies rs2814778) is common in ancestry groups from malaria endemic regions and has been associated with unnecessary bone marrow biopsies; therefore, understanding the role of this variant in various disease etiologies is of upmost importance.

Project Purpose(s)

  • Ancestry

Scientific Approaches

I will identify ancestry groups with high rs2814778 allele frequencies and conduct a PheWas in them to identify if this SNP leads to any increased liklihood of disease.

Anticipated Findings

This variant has been associated with changes in neutrophil counts but has not yet actually been associated with any diseases. If this holds up, it will add evidence to the case for controlling for certain variants in blood cell ranges.

Demographic Categories of Interest

  • Race / Ethnicity

Data Set Used

Controlled Tier

Research Team

Owner:

  • Micah Hysong - Graduate Trainee, University of North Carolina, Chapel Hill

Collaborators:

  • Bjoernar Tuftin - Project Personnel, University of North Carolina, Chapel Hill
  • Emily Drzymalla - Other, University of North Carolina, Chapel Hill

Elena_lit_review

Demographics of those with Multiple Sclerosis, COPD, Ischaemic Stroke, Atopic Dermatitis, Asthma, Rheumatoid Arthritis, Venuous Thromboembolism, ALS, Major Depressive Disorder, Schizophrenia, Platelet Count, Alzheimers in v7

Scientific Questions Being Studied

Demographics of those with Multiple Sclerosis, COPD, Ischaemic Stroke, Atopic Dermatitis, Asthma, Rheumatoid Arthritis, Venuous Thromboembolism, ALS, Major Depressive Disorder, Schizophrenia, Platelet Count, Alzheimers in v7

Project Purpose(s)

  • Ancestry

Scientific Approaches

Want to test blood cell traits for associations with these diseases, but first need to assess if AllofUs has enough individuals with these diseases.

Anticipated Findings

I will obtain the age, sex, and ancestry of indivduals with these diseases. This will determine if there is enough data to look for associations

Demographic Categories of Interest

  • Race / Ethnicity

Data Set Used

Controlled Tier

Research Team

Owner:

  • Micah Hysong - Graduate Trainee, University of North Carolina, Chapel Hill

BCX PRS (V7)

PRS have been demonstrated to have low portability between ancestry groups (Duncan et al., 2019). This is largely due to the fact that 78% of GWAS has been performed in individuals of European ancestry (Gurdasani et al., 2019). Generous participants…

Scientific Questions Being Studied

PRS have been demonstrated to have low portability between ancestry groups (Duncan et al., 2019). This is largely due to the fact that 78% of GWAS has been performed in individuals of European ancestry (Gurdasani et al., 2019). Generous participants in the All of Us research program are from diverse genetic ancestry backgrounds, allowing for the statistical power necessary to test methods to improve PRS performance in individuals of non-European ancestry. Specifically, I will be exploring the performance of the PRS for a variety of test quantitative traits, including blood cell indices. Moreover, I will use the All of Us data to test/train new PRS in non-European ancestry groups and assess if this leads to higher performance. Increasing PRS performance in different ancestry groups is imperative to equitable implementation of PRS to improve health outcomes.

Project Purpose(s)

  • Ancestry

Scientific Approaches

Datasets: Cohort: Whole Genome Sequencing Derive PRS that includes all ancestry groups and then individual PRS for each ancestry group. Generate a generalized linear model that includes age, sex at birth, and PRS as covariates.

Anticipated Findings

We expect that PRS scores trained in European ancestry will have lower accuracy for predicting blood cell indices in cohorts with non-European ancestry. We also predict that training a new PRS in more diverse populations will make a PRS that is more accurate across all ancestries. Overall, these findings would contribute to the growing body of literature supporting the need for including more diverse ancestry groups in genomic studies. Importantly, this will improve health-outcomes in minoritized groups.

Demographic Categories of Interest

  • Race / Ethnicity
  • Age

Data Set Used

Controlled Tier

Research Team

Owner:

  • Micah Hysong - Graduate Trainee, University of North Carolina, Chapel Hill

Collaborators:

  • Jun Qian - Other, All of Us Program Operational Use

Duplicate of Demo - PheWAS Smoking

As a demonstration project, this study will present the results of Phenome-Wide Association Studies (PheWAS) to show how the various sources of data contained within All of Us research dataset can be used to inform scientific discovery. We will perform…

Scientific Questions Being Studied

As a demonstration project, this study will present the results of Phenome-Wide Association Studies (PheWAS) to show how the various sources of data contained within All of Us research dataset can be used to inform scientific discovery. We will perform separate PheWAS studies with smoking status as the independent variable. Specific questions include:

1. How can one implement a PheWAS within the All of Us Researcher Workbench?
2. How can one use heterogeneous data sources within the All of Us dataset to explore disease associations using self-reported exposures (Participant Provided Information, or “PPI”) and exposures captured in the electronic medical record (EHR).

Project Purpose(s)

  • Methods Development
  • Other Purpose (This work is a result of an All of Us Research Program Demonstration Project. The projects are efforts by the Program designed to meet the program's goal of ensuring the quality and utility of the Research Hub as a resource for accelerating discovery in science and medicine. This work was reviewed and overseen by the All of Us Research Program Science Committee and the Data and Research Center to ensure compliance with program policy, including policies for acceptable data access and use.)

Scientific Approaches

As a method for assessing the health burden of smoking on potential observed phenotypes, we implement a Phenome-Wide Association study. A Phenome-wide association study consists of an array of association tests over an indexed representation of the human phenome. In this analysis, we will conduct PheWAS for EHR derived smoking and PPI derived smoking exposures included in the All of Us research dataset. We will be representing "Smoking Exposure” in three ways:
EHR Smoking ICD Billing Codes
Participant Provided Information (PPI) Smoking lifetime 100 cigarettes yes/no
Participant Provided Information (PPI) Smoking lifetime smoking everyday
To perform PheWAS, we will map ICD representations of disease to a common vocabulary of PheCodes. We then use Jupyter Notebooks to create reusable functions to perform PheWAS and generate Manhattan Plots to summarize associations.

Anticipated Findings

For this study, we anticipate that we will be able to replicate known disease associations with smoking exposure. This will serve to demonstrate the quality, utility, and diversity of the All of Us data and tools and the power of gathering multiple data sources for a single phenotype, providing researchers options for study design and validation. Importantly the entire pheWAS package is made available for reuse by researchers in the Workbench, for new hypothesis generation.

Demographic Categories of Interest

  • Race / Ethnicity

Data Set Used

Registered Tier

Research Team

Owner:

  • Micah Hysong - Graduate Trainee, University of North Carolina, Chapel Hill

PRS for Blood Cell Traits

PRS have been demonstrated to have low portability between ancestry groups (Duncan et al., 2019). This is largely due to the fact that 78% of GWAS has been performed in individuals of European ancestry (Gurdasani et al., 2019). Generous participants…

Scientific Questions Being Studied

PRS have been demonstrated to have low portability between ancestry groups (Duncan et al., 2019). This is largely due to the fact that 78% of GWAS has been performed in individuals of European ancestry (Gurdasani et al., 2019). Generous participants in the All of Us research program are from diverse genetic ancestry backgrounds, allowing for the statistical power necessary to test methods to improve PRS performance in individuals of non-European ancestry. Specifically, I will be exploring the performance of the PRS for a variety of test quantitative traits, including blood cell indices. Moreover, I will use the All of Us data to test/train new PRS in non-European ancestry groups and assess if this leads to higher performance. Increasing PRS performance in different ancestry groups is imperative to equitable implementation of PRS to improve health outcomes.

Project Purpose(s)

  • Ancestry

Scientific Approaches

Datasets: Cohort: Whole Genome Sequencing Derive PRS that includes all ancestry groups and then individual PRS for each ancestry group. Generate a generalized linear model that includes age, sex at birth, and PRS as covariates.

Anticipated Findings

We expect that PRS scores trained in European ancestry will have lower accuracy for predicting blood cell indices in cohorts with non-European ancestry. We also predict that training a new PRS in more diverse populations will make a PRS that is more accurate across all ancestries. Overall, these findings would contribute to the growing body of literature supporting the need for including more diverse ancestry groups in genomic studies. Importantly, this will improve health-outcomes in minoritized groups.

Demographic Categories of Interest

  • Race / Ethnicity
  • Age

Data Set Used

Controlled Tier

Research Team

Owner:

  • Micah Hysong - Graduate Trainee, University of North Carolina, Chapel Hill
1 - 8 of 8
<
>
Request 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.