Alexander Bick
Early Career Tenure-track Researcher, Vanderbilt University Medical Center
8 active projects
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
AGBT 2023: Intro to All of Us Genomics Data
Scientific Questions Being Studied
This workspace is meant to help researchers get familiar with the All of Us Researcher Workbench. There are five hands-on exercises during the workshop, each with a specific notebook.
Exercise 1: Duplicate the workspace & start the cloud environment
Exercise 2: Looking at the genomic data (notebook)
Exercise 3: GWAS - extracting phenotypic data (notebook)
Exercise 4: GWAS - running Hail GWAS (notebook)
Exercise 5: Advanced GWAS (2 notebooks)
By running the exercises in this workspace, researchers will become more familiar with the genomic data, know how to access the genomic data, see how the genomic data and tools can be used in the Researcher Workbench, and be able to start their own genomic data project.
Project Purpose(s)
- Other Purpose (This workspace is meant for use during the Introduction to Analyzing All of Us Genomic Data workshop. In this workshop, participants will get hands-on experience using the genomics data running a genome-wide association study (GWAS) using Hail. )
Scientific Approaches
We are using the All of Us dataset in order to run a genome-wide association study (GWAS) using Hail. In the workshop, we will give an introduction to the All of Us Researcher Workbench and demonstrate how to use the Cohort Builder and Jupyter Notebooks to set up a research project. Using Jupyter notebooks, we will create a dataset linking the All of Us phenotypic data to the short read whole genome sequencing (srWGS) data. After running the GWAS steps using Hail, we will visualize the results.
Anticipated Findings
This study is running a genome-wide association study (GWAS) using Hail, using height as the selected phenotypic data. We do not anticipate findings from this example workspace but we expect that workshop participants will be able to apply similar methods to their future research.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierResearch Team
Owner:
- Alexander Bick - Early Career Tenure-track Researcher, 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
Using REGENIE with dsub in All of Us
Scientific Questions Being Studied
This workspace is intended to show researchers how to run REGENIE to perform a GWAS on All of Us whole genome data for educational purposes.
Project Purpose(s)
- Educational
Scientific Approaches
We will show how to use the whole genome datasets (in bgen format) to perform a GWAS. In the tutorial, we use PLINK to filter the genetic data and REGENIE to run the GWAS itself.
Anticipated Findings
This educational workspace will provide the framework for researchers to perform their own GWAS on their phenotype of interest within their own workspaces.
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
- Alexander Bick - Early Career Tenure-track Researcher, Vanderbilt University Medical Center
Collaborators:
- Jun Qian - Other, All of Us Program Operational Use
- Jennifer Zhang - Project Personnel, All of Us Program Operational Use
- Hannah Poisner - Graduate Trainee, Vanderbilt University
- Nicole Deflaux - Other, All of Us Program Operational Use
- Brian Sharber - Project Personnel, Vanderbilt University Medical Center
- Margaret Sunitha Selvaraj - Research Fellow, Broad Institute
- Laura Raffield - Other, University of North Carolina, Chapel Hill
- Nikita Pozdeyev - Early Career Tenure-track Researcher, University of Colorado, Denver
- Kelsy Alaine Broadaway - Project Personnel, University of North Carolina, Chapel Hill
- Henry Condon - Project Personnel, All of Us Program Operational Use
- Bjoernar Tuftin - Project Personnel, University of North Carolina, Chapel Hill
- Aaron Eisman - Graduate Trainee, Brown University
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
ASHG22 - 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 TierResearch Team
Owner:
- Alexander Bick - Early Career Tenure-track Researcher, Vanderbilt University Medical Center
Kidney disease workspace – controlled tier V6
Scientific Questions Being Studied
We seek to identify genetic or environmental factors that modify kidney disease risk in individuals with APOL1 mutations.
In the United States, African American patients who are of West-African descent have a fourfold increase in the risk of end stage kidney disease (ESKD) compared to patients of other ancestry background. Although some of this difference can be attributed to socioeconomic and clinical risk, previous studies have also identified genetic mutations in apolipoprotein L1 (APOL1) that significantly increase risk of kidney disease. The two APOL1 high-risk mutations (G1 & G2) are common as they confer resistance to lethal Trypanosoma brucei infections, which is a pathogen endemic to West Africa. While just one copy of APOL1 G1 or G2 confers protection against T. brucei rhodesiense, two copies confer increased risk of kidney disease. Although ~13% of individuals of African Americans carry two APOL1 high-risk mutations; the majority do not develop kidney disease.
Project Purpose(s)
- Disease Focused Research (kidney disease)
- Ancestry
Scientific Approaches
Population: Subset of AoU Data set with available genetic data that is of West African Ancestry as determined by ancestry informative genetic markers
Outcome: Kidney disease phenotypes including chronic kidney disease (CKD), end stage renal disease (ESRD) or other kidney diseases or kidney disease markers as defined in the electronic health record or other AoU datasets.
Analysis plan: We will begin by identifying which individuals have APOL1 high-risk variants G1 (rs73885319 p.S342G; rs60910145 p.I384M) and G2 (rs71785313, a 6–base pair deletion that removes amino acids N388 and Y389). We will then determine whether carrying two of these high risk variants are associated with kidney disease (recessive genetic model). We will identify whether additional genetic mutations or environmental factors modify the association between APOL1 genetic risk variants and kidney disease using multivariate logistic regression.
Anticipated Findings
The identification of genetic or environmental factors that modify kidney disease risk, might guide lifestyle modification strategies or therapeutic development for individuals with APOL1 high risk mutations.
Demographic Categories of Interest
- Race / Ethnicity
Data Set Used
Controlled TierResearch Team
Owner:
- Caitlyn Vlasschaert - Graduate Trainee, Vanderbilt University Medical Center
- Alexander Bick - Early Career Tenure-track Researcher, Vanderbilt University Medical Center
Collaborators:
- Sarah Reed - Graduate Trainee, Vanderbilt University
- Taralynn Mack - Graduate Trainee, Vanderbilt University
APOL1 gene mutations and Kidney Disease
Scientific Questions Being Studied
We seek to identify genetic or environmental factors that modify kidney disease risk in individuals with APOL1 mutations.
In the United States, African American patients who are of West-African descent have a fourfold increase in the risk of end stage kidney disease (ESKD) compared to patients of other ancestry background. Although some of this difference can be attributed to socioeconomic and clinical risk, previous studies have also identified genetic mutations in apolipoprotein L1 (APOL1) that significantly increase risk of kidney disease. The two APOL1 high-risk mutations (G1 & G2) are common as they confer resistance to lethal Trypanosoma brucei infections, which is a pathogen endemic to West Africa. While just one copy of APOL1 G1 or G2 confers protection against T. brucei rhodesiense, two copies confer increased risk of kidney disease. Although ~13% of individuals of African Americans carry two APOL1 high-risk mutations; the majority do not develop kidney disease.
Project Purpose(s)
- Disease Focused Research (kidney disease)
- Ancestry
Scientific Approaches
Population: Subset of AoU Data set with available genetic data that is of West African Ancestry as determined by ancestry informative genetic markers
Outcome: Kidney disease phenotypes including chronic kidney disease (CKD), end stage renal disease (ESRD) or other kidney diseases or kidney disease markers as defined in the electronic health record or other AoU datasets.
Analysis plan: We will begin by identifying which individuals have APOL1 high-risk variants G1 (rs73885319 p.S342G; rs60910145 p.I384M) and G2 (rs71785313, a 6–base pair deletion that removes amino acids N388 and Y389). We will then determine whether carrying two of these high risk variants are associated with kidney disease (recessive genetic model). We will identify whether additional genetic mutations or environmental factors modify the association between APOL1 genetic risk variants and kidney disease using multivariate logistic regression.
Anticipated Findings
The identification of genetic or environmental factors that modify kidney disease risk, might guide lifestyle modification strategies or therapeutic development for individuals with APOL1 high risk mutations.
Demographic Categories of Interest
- Race / Ethnicity
Data Set Used
Controlled TierResearch Team
Owner:
- Alexander Bick - Early Career Tenure-track Researcher, Vanderbilt University Medical Center
Collaborators:
- Caitlyn Vlasschaert - Graduate Trainee, Vanderbilt University Medical Center
- Megan Lancaster - Research Fellow, Vanderbilt University Medical Center
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.
