Trevor Bowman

Project Personnel, Mass General Brigham

4 active projects

Naxerova Lab Cardiovascular Disease Evolution (v6 dataset)

We intend to study somatic evolution in the blood as evidenced by the presence or absence of driver mutations and the rate at which specific mutations expand over time (on average). We will then correlate these data with the presence…

Scientific Questions Being Studied

We intend to study somatic evolution in the blood as evidenced by the presence or absence of driver mutations and the rate at which specific mutations expand over time (on average). We will then correlate these data with the presence or absence of cardiovascular disease risk factors. The extent to which this will be possible depends on the sequencing depth of the dataset. However, if we can perform this research, it will be relevant to understanding how cardiovascular disease evolves.

Project Purpose(s)

  • Disease Focused Research (arteriosclerotic cardiovascular disease)
  • Ancestry

Scientific Approaches

We plan to model our methods on those published in Heyde et al., “Increased stem cell proliferation in atherosclerosis accelerates clonal hematopoiesis” (Cell 2021). We will use somatic variants in whole genome sequencing data and mathematical modeling to study the behavior of hematopoietic clones and link these results to clinical variables within the All of Us dataset. However, our approach depends on the sequencing depth and clinical variables that are accessible through All of Us, so a more specific description of the planned approaches will only be possible once we have studied the details of the data set.

Anticipated Findings

It is difficult to anticipate the study results without knowing more specifics about the available data, but we expect that our findings will contribute to our understanding of the interconnections between hematopoietic somatic evolution and cardiovascular disease. As such, this research is of a broad public health relevance.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Duplicate of How to Run Notebooks in the Background

Some analyses take some time to run. Currently, the researcher has to wait for their job to run because if they are logged out of the system, their code will stop working and will not be executed. This is problematic…

Scientific Questions Being Studied

Some analyses take some time to run. Currently, the researcher has to wait for their job to run because if they are logged out of the system, their code will stop working and will not be executed. This is problematic for users working on datatypes such as Fitbit and Genomics.

To avoid this interruption, this notebook will run codes in the background.

Project Purpose(s)

  • Educational
  • Other Purpose (The notebook in this workspace shows how to run notebooks in the background even if the user is logged out of the workbench.)

Scientific Approaches

To run notebooks in the background, we use a special Python library called nbconvert. Users will specify the name of the notebook that they need to be executed. After that, they just need to run every cell in this notebook.

Anticipated Findings

There is no anticipated findings as this is for educational purpose only.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Registered Tier

Research Team

Owner:

Duplicate of How to use dsub in the Researcher Workbench

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:

Naxerova Lab Cardiovascular Disease Evolution (v5 dataset)

We intend to study somatic evolution in the blood as evidenced by the presence or absence of driver mutations and the rate at which specific mutations expand over time (on average). We will then correlate these data with the presence…

Scientific Questions Being Studied

We intend to study somatic evolution in the blood as evidenced by the presence or absence of driver mutations and the rate at which specific mutations expand over time (on average). We will then correlate these data with the presence or absence of cardiovascular disease risk factors. The extent to which this will be possible depends on the sequencing depth of the dataset, though if we are able to perform this research, it will be relevant to our understanding of how cardiovascular disease evolves.

Project Purpose(s)

  • Disease Focused Research (arteriosclerotic cardiovascular disease)
  • Ancestry

Scientific Approaches

We plan to model our methods on those published in Heyde et al., “Increased stem cell proliferation in atherosclerosis accelerates clonal hematopoiesis” (Cell 2021). We will use somatic variants in whole genome sequencing data and mathematical modeling to study the behavior of hematopoietic clones and link these results to clinical variables within the All of Us dataset. However, our approach depends on the sequencing depth and clinical variables that are accessible through All of Us, so a more specific description of the planned approaches will only be possible once we have studied the details of the data set.

Anticipated Findings

It is difficult to anticipate the study results without knowing more specifics about the available data, but we expect that our findings will contribute to our understanding of the interconnections between hematopoietic somatic evolution and cardiovascular disease. As such, this research is of a broad public health relevance.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

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