Alex Petty

Project Personnel, Vanderbilt University Medical Center

4 active projects

Duplicate of How to use Nextflow in the Researcher Workbench

Learn how to use Nextflow in the Researcher Workbench to manage bigger jobs.

Scientific Questions Being Studied

Learn how to use Nextflow in the Researcher Workbench to manage bigger jobs.

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:

  • Alex Petty - Project Personnel, Vanderbilt University Medical Center

AOU x COMPADRE

We (the Below Lab in the Division of Genetic Medicine at VUMC) are interested in applying our recently-improved genetic relatedness estimation and reconstruction software tools to the diverse genomic cohort present in the All of Us cloud data repository. At…

Scientific Questions Being Studied

We (the Below Lab in the Division of Genetic Medicine at VUMC) are interested in applying our recently-improved genetic relatedness estimation and reconstruction software tools to the diverse genomic cohort present in the All of Us cloud data repository. At this stage in our research, we are interested in conducting a broad relatedness characterization of as much of the cohort as possible to not just formalize a phenotype-specific inquiry in the future, but also as a proof-of-concept application of our cloud-optimized software in restricted online data repositories so that other researchers can apply the same tools to conduct a wide variety of relatedness-anchored analyses.

Project Purpose(s)

  • Methods Development

Scientific Approaches

We plan to utilize a development build of a new software suite, COMPADRE that harmonizes three separate relatedness estimation and pedigree reconstruction tools - PRIMUS (Pedigree Reconstruction and Identification of the Maximum Unrelated Set), ERSA (Estimation of Recent Shared Ancestry), and PADRE (Pedigree Aware Distant Relatedness Estimation). We will be using this software to analyze the PLINK-binary data and potentially the VCF data available for both the whole-genome sequencing and microarray data types available from AOU; specifically, estimating pedigree structure present in the entire dataset from the raw genomic data available.

Anticipated Findings

At this stage in the inquiry, we’re not totally certain as to what to expect to identify in the data, other than a variety of data artifacts such as admixture and other sources of heterogeneity that might impact traditional software’s ability to infer relatedness from a large data input. However, we are hoping that in conjunction with phenotype data per individual we might be able to identify patterns unique to the way that our software bridges genetic data and pedigree data. We’re confident in this because the All of Us data available now through the Researcher Workbench poses a unique opportunity to identify patterns of relatedness relative to other disease indicators, as it is one of few biorepositories constructed out of voluntarily-enrolled individuals (compared to UK Biobank, BioVU, etc).

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Alex Petty - Project Personnel, Vanderbilt University Medical Center
  • Grahame Evans - Graduate Trainee, Vanderbilt University

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

I am testing working with genetic data inside of the all of us platform. I am hoping to learn enough to be able to educate the rest of my lab about how to use the all of us platform.

Scientific Questions Being Studied

I am testing working with genetic data inside of the all of us platform. I am hoping to learn enough to be able to educate the rest of my lab about how to use the all of us platform.

Project Purpose(s)

  • Educational

Scientific Approaches

I plan to use the plink files and the hail matrix tables to follow the example data flow. I hope to test data transfers via several methods, and multiple types of cmputing.

Anticipated Findings

I do not anticipate any actionable results. I do hope to gain knowledge and familiarity with the all of us workbench platform, which will enable future analyses.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Alex Petty - Project Personnel, Vanderbilt University Medical Center

Learning to work with All of Us Physical Measurements

I am using this workspace to familiarize myself with the All of Us researcher workbench, following the tutorial workbooks. I will be investigating the data and cohort builders, querying and working with data in a notebook, and evaluating which of…

Scientific Questions Being Studied

I am using this workspace to familiarize myself with the All of Us researcher workbench, following the tutorial workbooks. I will be investigating the data and cohort builders, querying and working with data in a notebook, and evaluating which of our existing analysis tools can easily work inside of the all of us environment with All of Us Data.

Project Purpose(s)

  • Educational
  • Methods Development

Scientific Approaches

I am hoping to validate that the tools that the Below Lab uses for genomics quality control and analysis within our on-premises environment can be made to work effectively in the All of Us cloud environment. We use a wide variety of tools implemented in a range of programming languages, including Python, Perl, Java, and R. I'm expecting to install those tools via the shell, and run them there. For python tools, I may potentially use the notebook interface to run them.

In order to validate this, I expect to access a small subset of the available VCFs and other genetic data available.

Anticipated Findings

At this time, our only intent for this workspace is to validate that our tooling will work in this environment. In the near future, we hope to use the all-of-us dataset to investigate the genetics of stuttering.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Registered Tier

Research Team

Owner:

  • Alex Petty - Project Personnel, Vanderbilt University Medical Center
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