Alireza Majd

Research Fellow, University of California, San Francisco

7 active projects

G2H_AllofUSs

investigating the relationship between genetics, vaccinology and immunology, with an effort to describe the heterogeneity of immune response to measles vaccine among individuals from different genetic backgrounds.

Scientific Questions Being Studied

investigating the relationship between genetics, vaccinology and immunology, with an effort to describe the heterogeneity of immune response to measles vaccine among individuals from different genetic backgrounds.

Project Purpose(s)

  • Disease Focused Research (measles)
  • Ancestry

Scientific Approaches

investigate genetic variants that impact the response to the measles vaccine and testing the hypothesis that structural variants influence the generation of antibodies against the measles vaccine.

Anticipated Findings

This project will have a significant impact on the current state of the field by advancing our understanding of the genetic factors, i.e. both SNPs and SVs, influencing the response to the measles vaccine. Despite the vaccine's overall effectiveness, a considerable percentage of individuals fail to develop sufficient protective antibodies, leading to outbreaks and potential fatalities. By exploring the complex interplay between genetics and vaccine efficacy, this project aims to fill the existing knowledge gaps.

Demographic Categories of Interest

  • Race / Ethnicity

Data Set Used

Controlled Tier

Research Team

Owner:

Duplicate of Demo - Polygenic_Risk_Score_Genetic_Ancestry_Calibration

Polygenic risk scores (PRS) are available for a wide array of traits and conditions, offering many potential applications. There is a serious concern that clinical use of PRS could contribute to health disparities due to the poorer performance of PRS…

Scientific Questions Being Studied

Polygenic risk scores (PRS) are available for a wide array of traits and conditions, offering many potential applications. There is a serious concern that clinical use of PRS could contribute to health disparities due to the poorer performance of PRS in non-European ancestry individuals. We aim to improve our ability to correct the genetic ancestry-dependent bias in PRS for 10 conditions (Asthma, Atrial fibrillation, Breast Cancer, Chronic Kidney Disease, Coronary heart disease, Hypercholesterolemia, Obesity/BMI, Prostate cancer, Type 1 Diabetes, Type 2 Diabetes). We will use the AoU dataset to produce a resource that can be used to reduce the ancestry-dependent bias in these 10 PRS. The citation for this work is:
Lennon, N.J., Kottyan, L.C., Kachulis, C. et al. Selection, optimization and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse US populations. Nat Med 30, 480–487 (2024). https://doi.org/10.1038/s41591-024-02796-z

Project Purpose(s)

  • Educational
  • Ancestry

Scientific Approaches

Polygenic risk scores (PRS) are available for a wide array of traits and conditions, offering many potential applications. There is a serious concern that clinical use of PRS could contribute to health disparities due to the poorer performance of PRS in non-European ancestry individuals. Here with running the featrued workspace , we try to understand how the Polygenic Risk Scoring works on AllofUs

Anticipated Findings

We will produce a set of fitted parameters for a simple model which attempts to describe the macroscopic relationship between genetic ancestry and observed polygenic scores. The fitted parameters of this model can then be used as a resource to reduce genetic ancestry-dependent bias when calculating these scores in a clinical setting.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Alireza Majd - Research Fellow, University of California, San Francisco

DGBIs_On_AllofUs

This workspace is intended to be an starting point for developing a genome-wide association study pipeline on the All of Us genomic data studying Disorders of Gut-Brain Interactions. Also with using electronic health records, we will try to find potential…

Scientific Questions Being Studied

This workspace is intended to be an starting point for developing a genome-wide association study pipeline on the All of Us genomic data studying Disorders of Gut-Brain Interactions. Also with using electronic health records, we will try to find potential mechanisms underlying functional gastrointestinal disorders as a side effect of some medications like chemotherapy medications.

Project Purpose(s)

  • Ancestry

Scientific Approaches

This workspace is exploration of data and testing the GWAS pipeline on AllofUs, and we will look into the outcome of functional gastrointestinal problems in patients receiving chemotherapy. We will use multivariable regression as the main statistical method to find the most associated factor for predicting the risk of developing side effects.

Anticipated Findings

Outcomes of this workspace are educational purposes and also a specified GWAS pipeline for DGBIs. We will try to find potential associated genomic variations that can play role in mechanism of these diseases. Also we hope to gain knowledge about the mechanism underlying the gastrointestinal side effects of chemotherapy medications.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Tutorial

In this workshop, I am trying to get familiar with the gastrointestinal dataset at All of Us. In doing so I'll explore the distribution of the diseases across the US, and compare the relevance of these diseases amongst different ages…

Scientific Questions Being Studied

In this workshop, I am trying to get familiar with the gastrointestinal dataset at All of Us. In doing so I'll explore the distribution of the diseases across the US, and compare the relevance of these diseases amongst different ages and groups.

Project Purpose(s)

  • Educational

Scientific Approaches

In this workshop, the scientific approach I am planning to use is to use descriptive statistics to get familiar with the distribution of the gastrointestinal dataset at All of Us. In doing so I'll explore the distribution of the diseases across the US, and compare the relevance of these diseases amongst different ages and groups.

Anticipated Findings

Anticipated findings from the study could show where these diseases are staggered in the nation and ultimately help motivate allocating resources to those areas.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Alireza Majd - Research Fellow, University of California, San Francisco
  • Ali Kalantari - Graduate Trainee, University of California, San Francisco

DGBIs_On_AllofUs

Not applicable - this workspace is intended to be an starting point for developing a genome-wide association study pipeline on the All of Us genomic data studying Disorders of Gut-Brain Interactions.

Scientific Questions Being Studied

Not applicable - this workspace is intended to be an starting point for developing a genome-wide association study pipeline on the All of Us genomic data studying Disorders of Gut-Brain Interactions.

Project Purpose(s)

  • Educational

Scientific Approaches

Not applicable - This workspace is more exploration of data and testing the GWAS pipeline on AllofUs.

Anticipated Findings

Not applicable - outcome of this workspace would be educational purposes and also a specified GWAS pipeline for DGBIs.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Registered Tier

Research Team

Owner:

  • Alireza Majd - Research Fellow, University of California, San Francisco
  • Ali Kalantari - Graduate Trainee, University of California, San Francisco

Duplicate of Introductory example of GWAS with type 2 diabetes phenotype

Not applicable - this workspace is intended to be an introductory example of how to do a genome-wide association study on the All of Us genomic data that individuals can easily click through and understand.

Scientific Questions Being Studied

Not applicable - this workspace is intended to be an introductory example of how to do a genome-wide association study on the All of Us genomic data that individuals can easily click through and understand.

Project Purpose(s)

  • Educational

Scientific Approaches

Not applicable - this workspace is intended to be an introductory example of how to do a genome-wide association study on the All of Us genomic data that individuals can easily click through and understand.

Anticipated Findings

Not applicable - this workspace is intended to be an introductory example of how to do a genome-wide association study on the All of Us genomic data that individuals can easily click through and understand.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Alireza Majd - Research Fellow, University of California, San Francisco

Dup of Studies of Autosomal Dominant Polycystic Kidney Disease

Not applicable - this workspace is intended to be an example of how use the Researcher Workbench by studying participants with Autosomal Polycystic Kidney Disease (ADPKD)

Scientific Questions Being Studied

Not applicable - this workspace is intended to be an example of how use the Researcher Workbench by studying participants with Autosomal Polycystic Kidney Disease (ADPKD)

Project Purpose(s)

  • Educational

Scientific Approaches

Not applicable - this workspace is intended to be an example of how use the Researcher Workbench by studying participants with Autosomal Polycystic Kidney Disease (ADPKD)

Anticipated Findings

Not applicable - this workspace is intended to be an example of how use the Researcher Workbench by studying participants with Autosomal Polycystic Kidney Disease (ADPKD)

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Registered Tier

Research Team

Owner:

  • Alireza Majd - Research Fellow, University of California, San Francisco
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