Alex Winters

Research Associate, Geisinger Clinic

8 active projects

Duplicate of How to use Nextflow in the Researcher Workbench

Demonstrate using Nextflow in the Researcher Workbench

Scientific Questions Being Studied

Demonstrate using Nextflow in the Researcher Workbench

Project Purpose(s)

  • Educational

Scientific Approaches

Demonstrate using Nextflow in the Researcher Workbench with a validate VCF nextflow process

Anticipated Findings

N/A

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Duplicate of How to run WDLs using Cromwell in the Researcher Workbench

The purpose of this workspace is to demonstrate how to use Cromwell within the Researcher Workbench. This workspace will demonstrate writing a WDL script to validate VCF files.

Scientific Questions Being Studied

The purpose of this workspace is to demonstrate how to use Cromwell within the Researcher Workbench. This workspace will demonstrate writing a WDL script to validate VCF files.

Project Purpose(s)

  • Educational

Scientific Approaches

The purpose of this workspace is to demonstrate how to use Cromwell within the researcher workbench. This workspace will demonstrate writing a WDL script to validate VCF files.

Anticipated Findings

N/A

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Duplicate of FH & ASCVD Risk

Familial hypercholesterolemia (FH) is an inherited disorder characterized by lifelong elevated low density lipoprotein cholesterol (LDL-C) and dramatically increased risk for premature atherosclerotic cardiovascular disease (ASCVD). Genetic studies now suggest that familial hypercholesterolemia (FH) encompasses five discrete subtypes based on…

Scientific Questions Being Studied

Familial hypercholesterolemia (FH) is an inherited disorder characterized by lifelong elevated low density lipoprotein cholesterol (LDL-C) and dramatically increased risk for premature atherosclerotic cardiovascular disease (ASCVD). Genetic studies now suggest that familial hypercholesterolemia (FH) encompasses five discrete subtypes based on LDL-c levels, 1) a monogenic FH variant, 2) a high low density lipoprotein cholesterol (LDL-c) polygenic score, 3) elevated lipoprotein(a), 4) elevated LDL-c polygenic score with elevated lipoprotein(a), and 5) a positive family history without an identifiable genetic cause, or true “phenotypic FH.” The primary question of this project is: Are there differences in treatment, comorbidities, and ASCVD outcomes between FH subtypes?

Project Purpose(s)

  • Disease Focused Research (familial hypercholesterolemia)
  • Ancestry

Scientific Approaches

We plan to screen all individuals with whole genome sequences available for monogenic variants in an FH gene. We will calculate an LDL cholesterol polygenic risk score from each participant’s whole genome sequence. Using labs and measurements, we will identify individuals with an FH subtype. Additionally, we will stratify the cohort into statin treated and untreated individuals using medication data. Finally, we will use EH data to determine comorbidities and ASCVD outcomes. We will primarily use regression analyses to compare ASCVD risk in those with each FH subtype to individuals without FH.

Anticipated Findings

We expect ASCVD risk to vary among FH subtypes and to be more pronounced in each of the subtypes, relative to those without FH. We also anticipate ASCVD risk and comorbidities to vary between individuals using lipid-lowering medication and those not using medication. Our findings may demonstrate the importance of considering subtypes in ASCVD risk assessment for patients with the FH phenotype.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Pilot Association of recurrent CNVs with NPDs

This is a pilot project to look at the feasibility of calling copy number variants (CNVS) in All of Us. The goal of this project is to look for an association in All of Us between recurrent CNVs and neuropsychiatric…

Scientific Questions Being Studied

This is a pilot project to look at the feasibility of calling copy number variants (CNVS) in All of Us. The goal of this project is to look for an association in All of Us between recurrent CNVs and neuropsychiatric disorders (NPDs), such as autism and schizophrenia and others.

Project Purpose(s)

  • Ancestry

Scientific Approaches

This study will used an open source CNV caller (PennCNV) to call copy number variants from the single sample vcfs provided by All of Us and use both EHR and self-report data from All of Us participants to assess whether recurrent CNVs are associated with increased likelihood of NPDs.

Anticipated Findings

Other studies have seen an association between recurrent CNVs and NPDs, however most of those cohorts were medical or disease-based cohorts, so this project will evaluate the association in All of Us, which is a more population based cohort. All of Us all has increased representation from underrepresented groups not available in other cohorts. Finally, All of Us has self-report data on NPDs which can provide a useful extension from the typically available EHR data.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Copy of How to Work with All of Us Genomic Data(v6)

Not applicable - these notebooks demonstrate example analysis how to use Hail and PLINK to perform genome-wide association studies using the All of Us genomic data and phenotypic data.

Scientific Questions Being Studied

Not applicable - these notebooks demonstrate example analysis how to use Hail and PLINK to perform genome-wide association studies using the All of Us genomic data and phenotypic data.

Project Purpose(s)

  • Other Purpose (Demonstrate to the All of Us Researcher Workbench users how to get started with the All of Us genomic data and tools. It includes an overview of all the All of Us genomic data and shows some simple examples on how to use these data.)

Scientific Approaches

Not applicable - these notebooks demonstrate example analysis how to use Hail and PLINK to perform genome-wide association studies using the All of Us genomic data and phenotypic data.

Anticipated Findings

Not applicable - these notebooks demonstrate example analysis how to use Hail and PLINK to perform genome-wide association studies using the All of Us genomic data and phenotypic data.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Investigation of desmosome gene variant carriers by ancestry group

Determine the prevalence of pathogenic and likely pathogenic genetic variants in four desmosome genes (DSG2, DSC2, PKP2, and DSP) by race/ancestry group and their association with Arrhythmogenic Cardiomyopathy (ARVC) and ARVC-related cardiac traits. ARVC often presents with sudden death frequently…

Scientific Questions Being Studied

Determine the prevalence of pathogenic and likely pathogenic genetic variants in four desmosome genes (DSG2, DSC2, PKP2, and DSP) by race/ancestry group and their association with Arrhythmogenic Cardiomyopathy (ARVC) and ARVC-related cardiac traits. ARVC often presents with sudden death frequently with no prior symptoms. It is unclear how race modifies the association between variants in the four genes of interest and the disease phenotype.

Project Purpose(s)

  • Disease Focused Research (Arrhythmogenic Cardiomyopathy )
  • Control Set
  • Ancestry

Scientific Approaches

This study will use the All of Us data to enrich our number of individuals of non-European ancestry individuals by comparing allele frequencies for the four genes of interest in All of Us participants to those in our Geisinger data, which is of majority European ancestry. Additionally, this study will assess the race-specific impact of these variants on the ARVC-related traits available in All of Us, and we plan to assess associations with endurance exercise from the Fitbit data available.

Anticipated Findings

It is important to know the prevalence of these variants in different ancestry groups to better understand the penetrance and phenotypic effects of these variants (i.e. who is at risk of sudden death) and whether those effects are modified by race, exercise history, or other factors.

Demographic Categories of Interest

  • Race / Ethnicity

Data Set Used

Controlled Tier

Research Team

Owner:

Collaborators:

  • Matthew Oetjens - Senior Researcher, Geisinger Clinic
  • Nuha Mohammed - Research Assistant, Geisinger Clinic
  • John Seibert - Project Personnel, Geisinger Clinic
  • Alexander Berry - Research Associate, Geisinger Clinic

ARVC by race

Determine the race-specific prevalence of pathogenic and likely pathogenic ARVC genetic variants in four desmosome genes (DSG2, DSC2, PKP2, and DSP)

Scientific Questions Being Studied

Determine the race-specific prevalence of pathogenic and likely pathogenic ARVC genetic variants in four desmosome genes (DSG2, DSC2, PKP2, and DSP)

Project Purpose(s)

  • Disease Focused Research (ARVC)
  • Ancestry

Scientific Approaches

Will use the All of Us data to enrich data on genetic variation in non-European ancestry individuals by comparing allele frequencies in All of Us participants to those in our Geisinger data which is of majority European ancestry. Also will assess the race-specific impact of these variants on the ECG traits available in All of Us.

Anticipated Findings

It is important to know the prevalence of these variants in different ancestry groups to better understand the penetrance and phenotypic effects of these variants and whether those effects are modified by race.

Demographic Categories of Interest

  • Race / Ethnicity

Data Set Used

Registered Tier

Research Team

Owner:

Duplicate of How to Work with All of Us Genomic Data (Hail - Plink)

Not applicable - these notebooks demonstrate example analysis how to use Hail and PLINK to perform genome-wide association studies using the All of Us genomic data and phenotypic data.

Scientific Questions Being Studied

Not applicable - these notebooks demonstrate example analysis how to use Hail and PLINK to perform genome-wide association studies using the All of Us genomic data and phenotypic data.

Project Purpose(s)

  • Other Purpose (Demonstrate to the All of Us Researcher Workbench users how to get started with the All of Us genomic data and tools. It includes an overview of all the All of Us genomic data and shows some simple examples on how to use these data.)

Scientific Approaches

Not applicable - these notebooks demonstrate example analysis how to use Hail and PLINK to perform genome-wide association studies using the All of Us genomic data and phenotypic data.

Anticipated Findings

Not applicable - these notebooks demonstrate example analysis how to use Hail and PLINK to perform genome-wide association studies using the All of Us genomic data and phenotypic data.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

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.