Henry Condon

Project Personnel, Vanderbilt University Medical Center

7 active projects

AoU_A3_LDL_GWAS_Hail_CT

The main questions this workspace is attempting to address is whether a scalable GWAS can be created on the AoU platform and whether (and how) that GWAS can be optimized for run cost and time. These questions are important for…

Scientific Questions Being Studied

The main questions this workspace is attempting to address is whether a scalable GWAS can be created on the AoU platform and whether (and how) that GWAS can be optimized for run cost and time. These questions are important for making the AoU platform—and a common genomics analysis like a GWAS—as accessible and understandable as possible for researchers of all experience levels; by attempting to address the scalability of this GWAS it will hopefully be more future-proof and allow researchers to quickly analyze future AoU data releases, and performing this GWAS multiple times and tracking cluster metrics will unveil optimized configurations to better inform future researches seeking to recreate this GWAS or perform other analyses of similar computational intensity.

Project Purpose(s)

  • Methods Development
  • Other Purpose (The purpose of this workspace is to recreate an efficient and scalable Genome Wide Association Study (GWAS) across whole genome sequenced data on an LDL Cholesterol phenotype.)

Scientific Approaches

This workspace is intended to provide a functional and scalable GWAS on AoU data. The GWAS will apply the methodologies of the hail.is GWAS tutorial, the featured workspace GWAS, Nicole DeFlaux's and Margret Sunitha's phenotype generation and PC analysis, as well as Seung Hoan Choi and Xin Wang's QC methodologies used in their GWAS demonstration project.

Anticipated Findings

The research conducted in this study is not novel and there are no anticipated findings from this study other than a successful recreation of prior GWAS performances. This study will not contribute to the body of scientific knowledge in this field in any meaningful way other than illuminating the capabilities of the AoU platform and account for the associated time and cost constraints necessary to perform the GWAS correctly and efficiently.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Henry Condon - Project Personnel, Vanderbilt University Medical Center

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:

  • Henry Condon - Project Personnel, Vanderbilt University Medical Center

FW-TutorialWorkspace: 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:

  • Henry Condon - Project Personnel, Vanderbilt University Medical Center

FW-TutorialWorkspace: How to Work with All of Us Physical Measurements Data

How to navigate around physical measurements?

Scientific Questions Being Studied

How to navigate around physical measurements?

Project Purpose(s)

  • Educational
  • Methods Development

Scientific Approaches

N/A

Anticipated Findings

N/A

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Registered Tier

Research Team

Owner:

  • Henry Condon - Project Personnel, Vanderbilt University Medical Center

AoU_A3_LDL_GWAS_Hail

The main questions this workspace is attempting to address is whether a scalable GWAS can be created on the AoU platform and whether (and how) that GWAS can be optimized for run cost and time. These questions are important for…

Scientific Questions Being Studied

The main questions this workspace is attempting to address is whether a scalable GWAS can be created on the AoU platform and whether (and how) that GWAS can be optimized for run cost and time. These questions are important for making the AoU platform—and a common genomics analysis like a GWAS—as accessible and understandable as possible for researchers of all experience levels; by attempting to address the scalability of this GWAS it will hopefully be more future-proof and allow researchers to quickly analyze future AoU data releases, and performing this GWAS multiple times and tracking cluster metrics will unveil optimized configurations to better inform future researches seeking to recreate this GWAS or perform other analyses of similar computational intensity.

Project Purpose(s)

  • Methods Development
  • Other Purpose (The purpose of this workspace is to recreate an efficient and scalable Genome Wide Association Study (GWAS) across whole genome sequenced data on an LDL Cholesterol phenotype. )

Scientific Approaches

This workspace is intended to provide a functional and scalable GWAS on AoU data. The GWAS will apply the methodologies of the hail.is GWAS tutorial, the featured workspace GWAS, Nicole DeFlaux's and Margret Sunitha's phenotype generation and PC analysis, as well as Seung Hoan Choi and Xin Wang's QC methodologies used in their GWAS demonstration project.

Anticipated Findings

The research conducted in this study is not novel and there are no anticipated findings from this study other than a successful recreation of prior GWAS performances. This study will not contribute to the body of scientific knowledge in this field in any meaningful way other than illuminating the capabilities of the AoU platform and account for the associated time and cost constraints necessary to perform the GWAS correctly and efficiently.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Registered Tier

Research Team

Owner:

  • Henry Condon - Project Personnel, Vanderbilt University Medical Center

Duplicate of How to Work with All of Us Survey Data (tier 5)

We recommend that all researchers explore the notebooks in this workspace to learn the basics of All of Us Program Data. What should you expect? By running the notebooks in this workspace, you should get familiar with how to query…

Scientific Questions Being Studied

We recommend that all researchers explore the notebooks in this workspace to learn the basics of All of Us Program Data.

What should you expect?
By running the notebooks in this workspace, you should get familiar with how to query PPI questions/surveys, what the frequencies of answers for each question in each PPI module are.

Project Purpose(s)

  • Educational
  • Methods Development
  • Other Purpose (This is an All of Us Tutorial Workspace created by the Researcher Workbench Support team. It is meant to provide instruction for key Researcher Workbench components and All of Us data representation.)

Scientific Approaches

This is a duplication of this workspace and the analyses therein and will reproduce the approaches and tools applied by the original.

Anticipated Findings

By reading and running the notebooks in this Tutorial Workspace, researchers will learn the following:
- how to query the survey data,
- how to summarize PPI modules, and questions.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Registered Tier

Research Team

Owner:

  • Henry Condon - Project Personnel, Vanderbilt University Medical Center

Collaborators:

  • Jun Qian - Other, All of Us Program Operational Use
  • Jennifer Zhang - Project Personnel, All of Us Program Operational Use
  • Chenchal Subraveti - Project Personnel, All of Us Program Operational Use
  • Aymone Kouame - Other, All of Us Program Operational Use

HCTestWorkspace

This workspace is to test and solve problems encountered by users and flagged by the help desk. There should be no science occurring in this work space other than the science of engineering involved with finding solutions.

Scientific Questions Being Studied

This workspace is to test and solve problems encountered by users and flagged by the help desk. There should be no science occurring in this work space other than the science of engineering involved with finding solutions.

Project Purpose(s)

  • Other Purpose (To test and solve problems encountered by users and flagged by the help desk. )

Scientific Approaches

This workspace is to test and solve problems encountered by users and flagged by the help desk. The datasets, research methods, and tools used will depend on the particular problem a user is encountering.

Anticipated Findings

This workspace is to test and solve problems encountered by users and flagged by the help desk. The only anticipated findings are those that would solve the particular issues a user is encountering, and as such it only contributes to the larger body of scientific knowledge by allowing the respective researcher to continue doing so in their own field.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Henry Condon - Project Personnel, Vanderbilt University Medical Center
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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.