Milovan Suvakov

Research Fellow, Mayo Clinic

6 active projects

Detecting somatic CNAs in AoU (V7)

Genomic variants in an individual may be either inherited (i.e., transmitted through the germline) or generated by mutagenesis in post-zygotic cells. Widespread genomic mosaicism in somatic cells of phenotypically normal individuals is now well established. Mutations occur in each cell…

Scientific Questions Being Studied

Genomic variants in an individual may be either inherited (i.e., transmitted through the germline) or generated by mutagenesis in post-zygotic cells. Widespread genomic mosaicism in somatic cells of phenotypically normal individuals is now well established. Mutations occur in each cell during development and aging. This project is aimed at studying large structural rearrangements, called copy number alterations (CNA), in genomes of AoU participants. Discovered CNAs in AoU cohort will be compared to CNAs discovered in external cohorts of people with autism and their relatives.

Project Purpose(s)

  • Ancestry
  • Other Purpose (Fulfilling aims of the award R03 AG085705)

Scientific Approaches

We will use whole genome sequencing (WGS) data and personal genome polymorphisms inferred from WGS. The method to discover CNA was previously developed by us and tested in the frames of Brain Somatic Mosaicism Network (DOI: 10.1126/science.abm6222). The method was implemented in the software tool called CNVpytor (https://github.com/abyzovlab/CNVpytor).

Anticipated Findings

The result of the study will contribute to understanding the frequency and spectrum of somatic CNAs during life span in human populations . Results of the study may then be used by us or other researcher to associate somatic CNAs with various diseases, conditions, and early diagnosis of malignancies and age-associated diseases.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

3. Duplicate of Detecting somatic CNAs in AoU (V7)

Genomic variants in an individual may be either inherited (i.e., transmitted through the germline) or generated by mutagenesis in post-zygotic cells. Widespread genomic mosaicism in somatic cells of phenotypically normal individuals is now well established. Mutations occur in each cell…

Scientific Questions Being Studied

Genomic variants in an individual may be either inherited (i.e., transmitted through the germline) or generated by mutagenesis in post-zygotic cells. Widespread genomic mosaicism in somatic cells of phenotypically normal individuals is now well established. Mutations occur in each cell during development and aging. This project is aimed at studying large structural rearrangements, called copy number alterations (CNA), in genomes of AoU participants. Discovered CNAs in AoU cohort will be compared to CNAs discovered in external cohorts of people with autism and their relatives.

Project Purpose(s)

  • Ancestry
  • Other Purpose (Fulfilling aims of the award R0 3AG085705)

Scientific Approaches

We will use whole genome sequencing (WGS) data and personal genome polymorphisms inferred from WGS. The method to discover CNA was previously developed by us and tested in the frames of Brain Somatic Mosaicism Network (DOI: 10.1126/science.abm6222). The method was implemented in the software tool called CNVpytor (https://github.com/abyzovlab/CNVpytor).

Anticipated Findings

The result of the study will contribute to understanding the frequency and spectrum of somatic CNAs during life span in human populations . Results of the study may then be used by us or other researcher to associate somatic CNAs with various diseases, conditions, and early diagnosis of malignancies and age-associated diseases.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

2. Duplicate of Detecting somatic CNAs in AoU (V7)

Genomic variants in an individual may be either inherited (i.e., transmitted through the germline) or generated by mutagenesis in post-zygotic cells. Widespread genomic mosaicism in somatic cells of phenotypically normal individuals is now well established. Mutations occur in each cell…

Scientific Questions Being Studied

Genomic variants in an individual may be either inherited (i.e., transmitted through the germline) or generated by mutagenesis in post-zygotic cells. Widespread genomic mosaicism in somatic cells of phenotypically normal individuals is now well established. Mutations occur in each cell during development and aging. This project is aimed at studying large structural rearrangements, called copy number alterations (CNA), in genomes of AoU participants. Discovered CNAs in AoU cohort will be compared to CNAs discovered in external cohorts of people with autism and their relatives.

Project Purpose(s)

  • Ancestry
  • Other Purpose (Fulfilling aims of the award R0 3AG085705)

Scientific Approaches

We will use whole genome sequencing (WGS) data and personal genome polymorphisms inferred from WGS. The method to discover CNA was previously developed by us and tested in the frames of Brain Somatic Mosaicism Network (DOI: 10.1126/science.abm6222). The method was implemented in the software tool called CNVpytor (https://github.com/abyzovlab/CNVpytor).

Anticipated Findings

The result of the study will contribute to understanding the frequency and spectrum of somatic CNAs during life span in human populations . Results of the study may then be used by us or other researcher to associate somatic CNAs with various diseases, conditions, and early diagnosis of malignancies and age-associated diseases.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Duplicate of How to Work with Genomics Data (CRAM_Processing and IGV) v7

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:

Duplicate of Detecting somatic CNAs in AoU (V7)

Genomic variants in an individual may be either inherited (i.e., transmitted through the germline) or generated by mutagenesis in post-zygotic cells. Widespread genomic mosaicism in somatic cells of phenotypically normal individuals is now well established. Mutations occur in each cell…

Scientific Questions Being Studied

Genomic variants in an individual may be either inherited (i.e., transmitted through the germline) or generated by mutagenesis in post-zygotic cells. Widespread genomic mosaicism in somatic cells of phenotypically normal individuals is now well established. Mutations occur in each cell during development and aging. This project is aimed at studying large structural rearrangements, called copy number alterations (CNA), in genomes of AoU participants. Discovered CNAs in AoU cohort will be compared to CNAs discovered in external cohorts of people with autism and their relatives.

Project Purpose(s)

  • Ancestry
  • Other Purpose (Fulfilling aims of the award R0 3AG085705)

Scientific Approaches

We will use whole genome sequencing (WGS) data and personal genome polymorphisms inferred from WGS. The method to discover CNA was previously developed by us and tested in the frames of Brain Somatic Mosaicism Network (DOI: 10.1126/science.abm6222). The method was implemented in the software tool called CNVpytor (https://github.com/abyzovlab/CNVpytor).

Anticipated Findings

The result of the study will contribute to understanding the frequency and spectrum of somatic CNAs during life span in human populations . Results of the study may then be used by us or other researcher to associate somatic CNAs with various diseases, conditions, and early diagnosis of malignancies and age-associated diseases.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Duplicate of 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:

Collaborators:

  • Alexej Abyzov - Early Career Tenure-track Researcher, Mayo Clinic
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