Brian Sharber
Project Personnel, Vanderbilt University Medical Center
11 active projects
Learning How to run WDLs using Cromwell in the Researcher Workbench (v7)
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
CHIP in All of Us Genomes with Mutect2 v7
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 TierResearch 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
- 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
- Uma Arora - Research Fellow, Broad Institute
- Alex Silver - Graduate Trainee, Vanderbilt University Medical Center
- 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
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 TierResearch 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
- 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
CHIP in All of Us Genomes with Mutect2
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 TierResearch 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
- 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
Clonal Hematopoiesis in All of Us Genomes
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 TierResearch 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:
- 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
- Brian Johnson - Graduate Trainee, University of California, San Diego
TBILab Learning of How to Work with All of Us Genomic Data (Hail - Plink)(v6)
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 TierResearch 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)
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 TierLearning How to Work with Genomics Data (CRAM_Processing and IGV)
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 TierDuplicate of How to use 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 TierDuplicate of How to Work with All of Us Genomic Data (Hail - Plink)
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 TierDuplicate of How to Work with All of Us Genomic Data (Hail - Plink)
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 TierRequest 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.
