Margaret Sunitha Selvaraj

Research Fellow, Broad Institute

14 active projects

cad_rarevariant_analysis

Coronary Artery Disease (CAD) is the leading cause of death worldwide. Despite previous research efforts, the underlying mechanisms and processes involved in CAD remain incompletely understood. Furthermore, CAD has been observed to have a heritable component, showing a higher prevalence…

Scientific Questions Being Studied

Coronary Artery Disease (CAD) is the leading cause of death worldwide. Despite previous research efforts, the underlying mechanisms and processes involved in CAD remain incompletely understood. Furthermore, CAD has been observed to have a heritable component, showing a higher prevalence within certain families. Previous genetic studies have identified specific genes or variants associated with CAD by analyzing DNA sequences. This project aims to utilize the world's largest dataset of whole genome sequencing data to expand our current understanding of the genetic factors contributing to CAD. By analyzing this extensive dataset, we seek to enhance our knowledge of CAD genetics, including the identification of additional causal genes or variants. The findings from this research have the potential to shed light on the underlying genetic basis of CAD, leading to improved risk assessment, prevention strategies, and personalized treatment approaches for individuals affected by this disease.

Project Purpose(s)

  • Disease Focused Research (Coronary artery disease)

Scientific Approaches

Our strategy involves curating prevalent and incident cases of Coronary Artery Disease (CAD) using clinical follow-up data. By associating genetic data obtained from whole genome sequencing, we will identify the causal genes or variants associated with CAD within the dataset. To increase the statistical power, we aggregate disruptive variants in the gene. To validate and expand our findings, we will seek external datasets for replication and meta-analysis. Furthermore, we will conduct data analysis based on ancestry to identify ancestry-specific genetic factors and compare the results across different ancestries. This approach will provide a comprehensive understanding of CAD genetics while considering potential ancestry-related variations in the disease etiology.

Anticipated Findings

The primary goal of this study is to identify genes associated with CAD by leveraging a larger sample size. By expanding the scope of the research, we anticipate making significant scientific discoveries that will enhance our understanding of the pathophysiology of CAD. Additionally, the diverse ancestral backgrounds represented in the All of Us research cohort will enable us to gain novel insights into ancestrally specific causal genes or variants related to CAD. The identification of these genes and variants will not only contribute to our knowledge of CAD but also offer potential novel drug targets for the treatment and prevention of this disease.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Collaborators:

  • Sumaiya Nazeen - Research Fellow, Mass General Brigham

LipidsAOUdata_WithVersion7DataSets_CODING

The purpose of this work space is to curate lipids from AOU data and analyze the aggregate association for certain variant sets.

Scientific Questions Being Studied

The purpose of this work space is to curate lipids from AOU data and analyze the aggregate association for certain variant sets.

Project Purpose(s)

  • Ancestry

Scientific Approaches

We plan to use AOU alpha3 genomic data to aggregate to defined variant sets based on prior knowledge and test its association to lipids.

Anticipated Findings

The anticipated findings include replicating the lipid findings from other cohorts in AOU WGS data by implementing rare variant aggregate tests.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Collaborators:

  • Buu Truong - Research Fellow, Broad Institute

GLGC_lipid

Coronary artery disease (CAD) is one the leading causes of death worldwide. Among many risk factors established, serum lipids are well recognized causal risk factors for CAD. Serum lipid traits are also known as heritable. Scientists had conducted a series…

Scientific Questions Being Studied

Coronary artery disease (CAD) is one the leading causes of death worldwide. Among many risk factors established, serum lipids are well recognized causal risk factors for CAD. Serum lipid traits are also known as heritable. Scientists had conducted a series of genetic studies, but not all the genetic component (heritability) was not explained yet. Recent research indicates that such unexplained heritability is enriched in rare to very-rare variants only captured by large-scale sequencing efforts. Using All of Us data, we will associate the genetic variants across the entire allele frequency spectrum and serum lipid traits to fill the missing in the heritability of the serum lipid traits.

Project Purpose(s)

  • Ancestry

Scientific Approaches

We will use whole genome sequencing data in All of Us dataset and associate it with serum lipid traits (cholesterols or triglycerides) curated from electric health records.

Anticipated Findings

By associating genetic variants determined by whole genome sequencing and serum lipid traits, we will characterize the associations of genetic variation across the entire allele frequency spectrum with serum lipid traits. Leveraging the population/ancestral diversity in the All of Us study participants, we will gain a broader perspective of the associated alleles in human genetic variation. The list of genetic variants associated with lipids will be an essential resource for clinical diagnosis, drug development, and understanding of the disease.

Demographic Categories of Interest

  • Race / Ethnicity

Data Set Used

Controlled Tier

Research Team

Owner:

AOU_PAD_for_Alyssa_Version7

We would like to conduct Genome wide association studies (GWAS) on PAD case and control data. Individual PAD GWAS will be meta analyzed to identify important loci associated with PAD. We will conduct GWAS using Regenie an meta analyze the…

Scientific Questions Being Studied

We would like to conduct Genome wide association studies (GWAS) on PAD case and control data. Individual PAD GWAS will be meta analyzed to identify important loci associated with PAD. We will conduct GWAS using Regenie an meta analyze the results using Metal.

Project Purpose(s)

  • Disease Focused Research (peripheral artery disease)
  • Ancestry

Scientific Approaches

We will curate PAD case and controls and we will conduct GWAS using Regenie an meta analyze the results using Metal.

Anticipated Findings

We aim to meta-analyse the data with other cohorts and plan to identify new loci associated with PAD

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

LipidsAOUdata_WithVersion7DataSets_ACAF

The purpose of this work space is to curate lipids from AOU data and analyze the aggregate association for certain variant sets.

Scientific Questions Being Studied

The purpose of this work space is to curate lipids from AOU data and analyze the aggregate association for certain variant sets.

Project Purpose(s)

  • Ancestry

Scientific Approaches

We plan to use AOU alpha3 genomic data to aggregate to defined variant sets based on prior knowledge and test its association to lipids.

Anticipated Findings

The anticipated findings include replicating the lipid findings from other cohorts in AOU WGS data by implementing rare variant aggregate tests.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

LipidsAOUdata_WithVersion7DataSets_NONCODING

The purpose of this work space is to curate lipids from AOU data and analyze the aggregate association for certain variant sets.

Scientific Questions Being Studied

The purpose of this work space is to curate lipids from AOU data and analyze the aggregate association for certain variant sets.

Project Purpose(s)

  • Ancestry

Scientific Approaches

We plan to use AOU alpha3 genomic data to aggregate to defined variant sets based on prior knowledge and test its association to lipids.

Anticipated Findings

The anticipated findings include replicating the lipid findings from other cohorts in AOU WGS data by implementing rare variant aggregate tests.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

LipidsAOUdata_WithVersion7DataSets

The purpose of this work space is to curate lipids from AOU data and analyze the aggregate association for certain variant sets.

Scientific Questions Being Studied

The purpose of this work space is to curate lipids from AOU data and analyze the aggregate association for certain variant sets.

Project Purpose(s)

  • Ancestry

Scientific Approaches

We plan to use AOU alpha3 genomic data to aggregate to defined variant sets based on prior knowledge and test its association to lipids.

Anticipated Findings

The anticipated findings include replicating the lipid findings from other cohorts in AOU WGS data by implementing rare variant aggregate tests.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

AOU_PAD_for_Alyssa

We would like to conduct Genome wide association studies (GWAS) on PAD case and control data. Individual PAD GWAS will be meta analyzed to identify important loci associated with PAD. We will conduct GWAS using Regenie an meta analyze the…

Scientific Questions Being Studied

We would like to conduct Genome wide association studies (GWAS) on PAD case and control data. Individual PAD GWAS will be meta analyzed to identify important loci associated with PAD. We will conduct GWAS using Regenie an meta analyze the results using Metal.

Project Purpose(s)

  • Disease Focused Research (peripheral artery disease)
  • Ancestry

Scientific Approaches

We will curate PAD case and controls and we will conduct GWAS using Regenie an meta analyze the results using Metal.

Anticipated Findings

We aim to meta-analyse the data with other cohorts and plan to identify new loci associated with PAD

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

LipidsAOUdata_Collaboration_Workspace

The purpose of this work space is to curate lipids from AOU data and analyze the aggregate association for certain variant sets.

Scientific Questions Being Studied

The purpose of this work space is to curate lipids from AOU data and analyze the aggregate association for certain variant sets.

Project Purpose(s)

  • Ancestry

Scientific Approaches

We plan to use AOU alpha3 genomic data to aggregate to defined variant sets based on prior knowledge and test its association to lipids.

Anticipated Findings

The anticipated findings include replicating the lipid findings from other cohorts in AOU WGS data by implementing rare variant aggregate tests.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Collaborators:

  • Rohan Bhukar - Project Personnel, Broad Institute

AOU_PAD

We would like to conduct Genome wide association studies (GWAS) on PAD case and control data. Individual PAD GWAS will be meta analyzed to identify important loci associated with PAD. We will conduct GWAS using Regenie an meta analyze the…

Scientific Questions Being Studied

We would like to conduct Genome wide association studies (GWAS) on PAD case and control data. Individual PAD GWAS will be meta analyzed to identify important loci associated with PAD. We will conduct GWAS using Regenie an meta analyze the results using Metal.

Project Purpose(s)

  • Disease Focused Research (peripheral artery disease)
  • Ancestry

Scientific Approaches

We will curate PAD case and controls and we will conduct GWAS using Regenie an meta analyze the results using Metal.

Anticipated Findings

We aim to meta-analyse the data with other cohorts and plan to identify new loci associated with PAD

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Collaborators:

  • Buu Truong - Research Fellow, Broad Institute

LipidsAOUdata

The purpose of this work space is to curate lipids from AOU data and analyze the aggregate association for certain variant sets.

Scientific Questions Being Studied

The purpose of this work space is to curate lipids from AOU data and analyze the aggregate association for certain variant sets.

Project Purpose(s)

  • Ancestry

Scientific Approaches

We plan to use AOU alpha3 genomic data to aggregate to defined variant sets based on prior knowledge and test its association to lipids.

Anticipated Findings

The anticipated findings include replicating the lipid findings from other cohorts in AOU WGS data by implementing rare variant aggregate tests.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

AOU_Hail_to_Bgen

We would like to conduct Genome wide association studies (GWAS) on PAD case and control data. Individual PAD GWAS will be meta analyzed to identify important loci associated with PAD. We will conduct GWAS using Regenie an meta analyze the…

Scientific Questions Being Studied

We would like to conduct Genome wide association studies (GWAS) on PAD case and control data. Individual PAD GWAS will be meta analyzed to identify important loci associated with PAD. We will conduct GWAS using Regenie an meta analyze the results using Metal.

Project Purpose(s)

  • Disease Focused Research (peripheral artery disease)
  • Ancestry

Scientific Approaches

We will curate PAD case and controls and we will conduct GWAS using Regenie an meta analyze the results using Metal.

Anticipated Findings

We aim to meta-analyse the data with other cohorts and plan to identify new loci associated with PAD

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

AOU_DATAPROD_CLUSTER

We would like to conduct Genome wide association studies (GWAS) on PAD case and control data. Individual PAD GWAS will be meta analyzed to identify important loci associated with PAD. We will conduct GWAS using Regenie an meta analyze the…

Scientific Questions Being Studied

We would like to conduct Genome wide association studies (GWAS) on PAD case and control data. Individual PAD GWAS will be meta analyzed to identify important loci associated with PAD. We will conduct GWAS using Regenie an meta analyze the results using Metal.

Project Purpose(s)

  • Disease Focused Research (peripheral artery disease)
  • Ancestry

Scientific Approaches

We will curate PAD case and controls and we will conduct GWAS using Regenie an meta analyze the results using Metal.

Anticipated Findings

We aim to meta-analyse the data with other cohorts and plan to identify new loci associated with PAD

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Collaborators:

  • Henry Condon - Project Personnel, All of Us Program Operational Use
  • Buu Truong - Research Fellow, Broad Institute

OGTT

We are planning to investigate how genetic variation is associated with impaired glucose response after an oral glucose tolerance test.

Scientific Questions Being Studied

We are planning to investigate how genetic variation is associated with impaired glucose response after an oral glucose tolerance test.

Project Purpose(s)

  • Disease Focused Research (impaired glucose tolerance)
  • Ancestry

Scientific Approaches

We are planning to use genetic and phenotypic information. We will use two h glucose as the outcome variable. We will use genetic data to identify genetic variants associated with two h glucose after accounting for age, sex, and BMI. We will conduct analyses stratified by genetically-derived ethnicity.

Anticipated Findings

This study will help us identify genetic variants associated with impaired glucose response. These results could shed light on molecular processes underlying dysglycemia and inform future studies to investigate whether genetic susceptibility to impaired glucose could be attenuated by specific lifestyle or dietary modifications.

Demographic Categories of Interest

  • Race / Ethnicity
  • Age
  • Sex at Birth
  • Gender Identity
  • Sexual Orientation
  • Geography
  • Access to Care
  • Education Level
  • Income Level

Data Set Used

Controlled Tier

Research Team

Owner:

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