Brian Sharber

Project Personnel, Vanderbilt University Medical Center

14 active projects

UNIFIER

The purpose of this workspace is to demonstrate how to develop a quality control pipeline for All of Us data in the measurement table.

Scientific Questions Being Studied

The purpose of this workspace is to demonstrate how to develop a quality control pipeline for All of Us data in the measurement table.

Project Purpose(s)

  • Methods Development

Scientific Approaches

The purpose of the workspace is to demonstrate an end-to-end quality control pipeline within the Researcher Workbench. This workspace will demonstrate the process and generate a reproducible workflow for other researchers to emulate in their data generation process.

Anticipated Findings

New methods to harmonize data units to make use of measurement table data seamless for researchers.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Brian Sharber - Project Personnel, Vanderbilt University Medical Center
  • James Brogan - Research Fellow, Vanderbilt University Medical Center
  • Alexander Bick - Early Career Tenure-track Researcher, Vanderbilt University Medical Center

Collaborators:

  • Robert Corty - Research Fellow, Vanderbilt University Medical Center
  • Ashwin Kishtagari - Research Fellow, Vanderbilt University Medical Center

Clonal Hematopoiesis in All of Us Genomes

With age, our blood stem cells acquire mutations. Most of these mutations are inconsequential, but some cause the blood stem cells to expand, a process known as clonal hematopoiesis. In this study, we seek to identify clonal hematopoiesis in the…

Scientific Questions Being Studied

With age, our blood stem cells acquire mutations. Most of these mutations are inconsequential, but some cause the blood stem cells to expand, a process known as clonal hematopoiesis. In this study, we seek to identify clonal hematopoiesis in the All of Us Research participant partners to understand the spectrum of clonal hematopoiesis, its causes and consequences.

Project Purpose(s)

  • Ancestry

Scientific Approaches

We plan to identify clonal hematopoiesis from all of us genomic data. This will be done using Mutect2 somatic mutation caller applied to the genome sequencing data and other algorithms applied to the array genotyping data.

Anticipated Findings

We expect that this will expand our understanding of the spectrum of mutations in clonal hematopoiesis in diverse populations.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Taralynn Mack - Graduate Trainee, Vanderbilt University
  • Henry Condon - Project Personnel, All of Us Program Operational Use
  • Caitlyn Vlasschaert - Graduate Trainee, Vanderbilt University Medical Center
  • Brian Sharber - Project Personnel, Vanderbilt University Medical Center
  • Alexander Bick - Early Career Tenure-track Researcher, Vanderbilt University Medical Center

Collaborators:

  • Yash Pershad - Graduate Trainee, Vanderbilt University Medical Center
  • Jun Qian - Other, All of Us Program Operational Use
  • Christopher Lord - Project Personnel, All of Us Program Operational Use
  • Brandy Mapes - Other, All of Us Program Operational Use
  • Varun Gupta - Project Personnel, Albert Einstein College of Medicine
  • Quanhu Sheng - Early Career Tenure-track Researcher, Vanderbilt University Medical Center
  • LaShaunta Glover - Teacher/Instructor/Professor, Duke University
  • Brice Laurent - Undergraduate Student, Harvard Medical School
  • Brian Johnson - Graduate Trainee, University of California, San Diego
  • Alex Silver - Graduate Trainee, Vanderbilt University Medical Center

Somatic Mutations and Auto-Immunity

We are using the All Of Us Research Program data to investigate the causes of inflammatory diseases such as VEXAS, adult onset Still's disease, and others. In general, inflammation can be a good thing. When we get an infection, our…

Scientific Questions Being Studied

We are using the All Of Us Research Program data to investigate the causes of inflammatory diseases such as VEXAS, adult onset Still's disease, and others. In general, inflammation can be a good thing. When we get an infection, our bodies use inflammation to fight it off. But some people get inflammation without any known attack, which is called auto-immunity. Auto-immune diseases can hamper people's lives and cause pain and disability. More research is needed into the causes and inner workings of these diseases.

Project Purpose(s)

  • Disease Focused Research (VEXAS, adult onset Stills disease, and others)
  • Ancestry

Scientific Approaches

We will examine genetic sequencing data, diagnosis codes, and laboratory values to test whether any genetic variants that arise during adulthood may contribute to auto-immune or auto-inflammatory diseases as described above.

Anticipated Findings

We anticipate that we may discover some new genetic variants that can arise in adulthood and cause inflammation, either in one part of the body or throughout the whole body.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Robert Corty - Research Fellow, Vanderbilt University Medical Center
  • Brian Sharber - Project Personnel, Vanderbilt University Medical Center
  • Alexander Bick - Early Career Tenure-track Researcher, Vanderbilt University Medical Center

Collaborators:

  • Suebin Choi - Undergraduate Student, Vanderbilt University
  • James Brogan - Research Fellow, Vanderbilt University Medical Center

CHIP in All of Us Genomes with Mutect2 v7

The purpose of this workspace is to demonstrate how to use dsub within the Researcher Workbench to perform clonal hematopoiesis analysis. This workspace will demonstrate writing dsub jobs.

Scientific Questions Being Studied

The purpose of this workspace is to demonstrate how to use dsub within the Researcher Workbench to perform clonal hematopoiesis analysis. This workspace will demonstrate writing dsub jobs.

Project Purpose(s)

  • Educational

Scientific Approaches

The purpose of this workspace is to demonstrate how to use dsub within the Researcher Workbench. This workspace will demonstrate writing dsub jobs.

Anticipated Findings

N/A

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Brian Sharber - Project Personnel, Vanderbilt University Medical Center
  • Alexander Bick - Early Career Tenure-track Researcher, Vanderbilt University Medical Center

Collaborators:

  • Suebin Choi - Undergraduate Student, Vanderbilt University
  • Robert Corty - Research Fellow, Vanderbilt University Medical Center
  • Yash Pershad - Graduate Trainee, Vanderbilt University Medical Center
  • Nicholas Parrish - Research Fellow, Vanderbilt University Medical Center
  • Moira Dillon - Other, All of Us Program Operational Use
  • Md Mesbah Uddin - Research Fellow, Broad Institute
  • Taralynn Mack - Graduate Trainee, Vanderbilt University
  • Shohei Kojima - Research Fellow, Vanderbilt University Medical Center
  • Ashwin Kishtagari - Research Fellow, Vanderbilt University Medical Center
  • Hannah Poisner - Graduate Trainee, Vanderbilt University
  • Caitlyn Vlasschaert - Graduate Trainee, Vanderbilt University Medical Center
  • James Brogan - Research Fellow, Vanderbilt University Medical Center
  • Uma Arora - Research Fellow, Broad Institute
  • Alex Silver - Graduate Trainee, Vanderbilt University Medical Center
  • Xiaolong Ma - Project Personnel, Medical College of Wisconsin
  • Paul Auer - Mid-career Tenured Researcher, Medical College of Wisconsin
  • Md Manzur Rahman Farazi - Early Career Tenure-track Researcher, Medical College of Wisconsin
  • kali quade - Undergraduate Student, Medical College of Wisconsin
  • Henry Condon - Project Personnel, All of Us Program Operational Use
  • KELLY BOLTON - Early Career Tenure-track Researcher, Washington University in St. Louis

Identifying CHIP in All of Us Genomes with Mutect2

In the context of genomic analysis, the task of identifying CHIP (Clonal Hematopoiesis of Indeterminate Potential) variants within the All of Us genomes involves employing dsub and Mutect2, a somatic variant caller, to extract specific genomic variations from the All…

Scientific Questions Being Studied

In the context of genomic analysis, the task of identifying CHIP (Clonal Hematopoiesis of Indeterminate Potential) variants within the All of Us genomes involves employing dsub and Mutect2, a somatic variant caller, to extract specific genomic variations from the All of Us CRAM files. CHIP refers to the presence of certain genetic mutations in hematopoietic stem cells that can lead to the clonal expansion of mutated cells, potentially predisposing individuals to various blood-related disorders and even certain cancers.

The workflow aims to leverage Mutect2's capabilities to pinpoint somatic mutations, which are alterations present in a subset of cells rather than the entire organism. By analyzing the CRAM files provided by the All of Us initiative, researchers aim to identify these somatic variants indicative of CHIP, contributing valuable insights into the genetic landscapes of diverse populations.

Project Purpose(s)

  • Educational

Scientific Approaches

The process involves meticulous analysis and interpretation of genomic data, utilizing Mutect2 to discern relevant mutations and their potential implications. Through this endeavor, researchers seek to enhance our understanding of CHIP prevalence, associated genetic patterns, and their potential clinical ramifications within the All of Us participant cohort. Ultimately, this work advances genomic research efforts aimed at elucidating the complexities of human health and disease susceptibility on a broader scale.

Anticipated Findings

N/A

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Brian Sharber - Project Personnel, Vanderbilt University Medical Center

Collaborators:

  • Shimon Rura - Project Personnel, All of Us Program Operational Use
  • Sarah Reed - Graduate Trainee, Vanderbilt University
  • Robert Corty - Research Fellow, Vanderbilt University Medical Center
  • Yash Pershad - Graduate Trainee, Vanderbilt University Medical Center
  • Moira Dillon - Other, All of Us Program Operational Use
  • Md Mesbah Uddin - Research Fellow, Broad Institute
  • Taralynn Mack - Graduate Trainee, Vanderbilt University
  • Shohei Kojima - Research Fellow, Vanderbilt University Medical Center
  • Kelly von Beck - Graduate Trainee, Vanderbilt University Medical Center
  • Hannah Poisner - Graduate Trainee, Vanderbilt University
  • Henry Condon - Project Personnel, All of Us Program Operational Use
  • Lide Han - Project Personnel, Vanderbilt University Medical Center
  • Emma Bunch - Other, Vanderbilt University Medical Center
  • Caitlyn Vlasschaert - Graduate Trainee, Vanderbilt University Medical Center
  • Uma Arora - Research Fellow, Broad Institute
  • Alexander Bick - Early Career Tenure-track Researcher, Vanderbilt University Medical Center
  • Alex Silver - Graduate Trainee, Vanderbilt University Medical Center

Somatic Mutations and Inflammation

We are using the All Of Us Research Program data to investigate the causes of inflammatory diseases such as VEXAS, adult onset Still's disease, and others. In general, inflammation can be a good thing. When we get an infection, our…

Scientific Questions Being Studied

We are using the All Of Us Research Program data to investigate the causes of inflammatory diseases such as VEXAS, adult onset Still's disease, and others. In general, inflammation can be a good thing. When we get an infection, our bodies use inflammation to fight it off. But some people get inflammation without any known attack, which is called auto-immunity. Auto-immune diseases can hamper people's lives and cause pain and disability. More research is needed into the causes and inner workings of these diseases.

Project Purpose(s)

  • Disease Focused Research (VEXAS, adult onset Stills disease, and others)
  • Ancestry

Scientific Approaches

We will examine genetic sequencing data, diagnosis codes, and laboratory values to test whether any genetic variants that arise during adulthood may contribute to auto-immune or auto-inflammatory diseases as described above.

Anticipated Findings

We anticipate that we may discover some new genetic variants that can arise in adulthood and cause inflammation, either in one part of the body or throughout the whole body.

Demographic Categories of Interest

  • Age

Data Set Used

Controlled Tier

Research Team

Owner:

  • Robert Corty - Research Fellow, Vanderbilt University Medical Center
  • Brian Sharber - Project Personnel, Vanderbilt University Medical Center
  • Alexander Bick - Early Career Tenure-track Researcher, Vanderbilt University Medical Center

Collaborators:

  • Suebin Choi - Undergraduate Student, Vanderbilt University

CHIP in All of Us Genomes with Mutect2

The purpose of this workspace is to demonstrate how to use dsub within the Researcher Workbench. This workspace will demonstrate writing dsub jobs.

Scientific Questions Being Studied

The purpose of this workspace is to demonstrate how to use dsub within the Researcher Workbench. This workspace will demonstrate writing dsub jobs.

Project Purpose(s)

  • Educational

Scientific Approaches

The purpose of this workspace is to demonstrate how to use dsub within the Researcher Workbench. This workspace will demonstrate writing dsub jobs.

Anticipated Findings

N/A

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Brian Sharber - Project Personnel, Vanderbilt University Medical Center
  • Alexander Bick - Early Career Tenure-track Researcher, Vanderbilt University Medical Center

Collaborators:

  • Robert Corty - Research Fellow, Vanderbilt University Medical Center
  • Yash Pershad - Graduate Trainee, Vanderbilt University Medical Center
  • Taralynn Mack - Graduate Trainee, Vanderbilt University
  • Nicole Deflaux - Other, All of Us Program Operational Use
  • Caitlyn Vlasschaert - Graduate Trainee, Vanderbilt University Medical Center
  • Md Mesbah Uddin - Research Fellow, Broad Institute

Learning How to run WDLs using Cromwell in the Researcher Workbench (v7)

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:

  • Brian Sharber - Project Personnel, Vanderbilt University Medical Center

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

  • Educational
  • 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:

  • Yaomin Xu - Early Career Tenure-track Researcher, Vanderbilt University Medical Center
  • Brian Sharber - Project Personnel, Vanderbilt University Medical Center

Collaborators:

  • Yajing Li - Project Personnel, Vanderbilt University Medical Center

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

  • Brian Sharber - Project Personnel, Vanderbilt University Medical Center

Learning How to Work with Genomics Data (CRAM_Processing and IGV)

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…

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 Tier

Research Team

Owner:

  • Brian Sharber - Project Personnel, Vanderbilt University Medical Center

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:

  • Brian Sharber - Project Personnel, Vanderbilt University Medical Center

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

Validation of alpha 0 genomic data. Validation of alpha 0 genomic data. Validation of alpha 0 genomic data.

Scientific Questions Being Studied

Validation of alpha 0 genomic data. Validation of alpha 0 genomic data. Validation of alpha 0 genomic data.

Project Purpose(s)

  • Educational

Scientific Approaches

Validation of alpha 0 genomic data. Validation of alpha 0 genomic data. Validation of alpha 0 genomic data.

Anticipated Findings

Validation of alpha 0 genomic data. Validation of alpha 0 genomic data. Validation of alpha 0 genomic data.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Brian Sharber - Project Personnel, Vanderbilt University Medical Center

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

Validation of alpha 0 genomic data. Validation of alpha 0 genomic data. Validation of alpha 0 genomic data.

Scientific Questions Being Studied

Validation of alpha 0 genomic data. Validation of alpha 0 genomic data. Validation of alpha 0 genomic data.

Project Purpose(s)

  • Educational

Scientific Approaches

Validation of alpha 0 genomic data. Validation of alpha 0 genomic data. Validation of alpha 0 genomic data.

Anticipated Findings

Validation of alpha 0 genomic data. Validation of alpha 0 genomic data. Validation of alpha 0 genomic data.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Brian Sharber - Project Personnel, Vanderbilt University Medical Center
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