shaghayegh beheshti

Graduate Trainee, Baylor College of Medicine

6 active projects

SOD cohort

Septo-optic dysplasia (SOD) is a rare congenital disorder with an estimated incidence of 1 in 10,000 newborns. SOD is a cerebral midline anomaly, and its classic triad of features includes optic nerve hypoplasia (ONH), agenesis of the septum pellucidum and…

Scientific Questions Being Studied

Septo-optic dysplasia (SOD) is a rare congenital disorder with an estimated incidence of 1 in 10,000 newborns. SOD is a cerebral midline anomaly, and its classic triad of features includes optic nerve hypoplasia (ONH), agenesis of the septum pellucidum and corpus callosum, and hypoplasia of the hypothalamo-pituitary axis. The presence of two or more components of the classic triad is “diagnostic” for SOD. Several genes, such as HESX1, SOX2/SOX3, OTX2, GLI2, PAX6, PROP1, and TAX1BP3 have been identified to play crucial roles in the embryonic development of the eyes, optic nerves, and pituitary gland, thereby influencing the expression of SOD. Despite these advancements in the underlying molecular mechanisms of SOD, a substantial number of SOD families still lack a molecular diagnosis.

Project Purpose(s)

  • Educational

Scientific Approaches

Septo-optic dysplasia (SOD) is a rare congenital disorder with an estimated incidence of 1 in 10,000 newborns. SOD is a cerebral midline anomaly, and its classic triad of features includes optic nerve hypoplasia (ONH), agenesis of the septum pellucidum and corpus callosum, and hypoplasia of the hypothalamo-pituitary axis. The presence of two or more components of the classic triad is “diagnostic” for SOD. Several genes, such as HESX1, SOX2/SOX3, OTX2, GLI2, PAX6, PROP1, and TAX1BP3 have been identified to play crucial roles in the embryonic development of the eyes, optic nerves, and pituitary gland, thereby influencing the expression of SOD. Despite these advancements in the underlying molecular mechanisms of SOD, a substantial number of SOD families still lack a molecular diagnosis.

Anticipated Findings

Septo-optic dysplasia (SOD) is a rare congenital disorder with an estimated incidence of 1 in 10,000 newborns. SOD is a cerebral midline anomaly, and its classic triad of features includes optic nerve hypoplasia (ONH), agenesis of the septum pellucidum and corpus callosum, and hypoplasia of the hypothalamo-pituitary axis. The presence of two or more components of the classic triad is “diagnostic” for SOD. Several genes, such as HESX1, SOX2/SOX3, OTX2, GLI2, PAX6, PROP1, and TAX1BP3 have been identified to play crucial roles in the embryonic development of the eyes, optic nerves, and pituitary gland, thereby influencing the expression of SOD. Despite these advancements in the underlying molecular mechanisms of SOD, a substantial number of SOD families still lack a molecular diagnosis.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Duplicate of Demo share workspace height and sex example python and R

N/A this is a demonstration workspace for education on how to use the AoU workspace This will demonstrate how to select a cohort of adult participants, search for height measurements and sex at birth data, plot a histogram of this…

Scientific Questions Being Studied

N/A this is a demonstration workspace for education on how to use the AoU workspace
This will demonstrate how to select a cohort of adult participants, search for height measurements and sex at birth data, plot a histogram of this data and perform a students t-test comparison of heights between males and females.
The intent is to create a "hello world" very simple example use of the AoU researchers workbench for beginners who have never used the workbench before, and have them perform their first analysis as rapidly as possible.

Project Purpose(s)

  • Educational

Scientific Approaches

N/A this is a demonstration workspace for education on how to use the AoU workspace
This will demonstrate how to select a cohort of adult participants, search for height measurements and sex at birth data, plot a histogram of this data and perform a students t-test comparison of heights between males and females.
The intent is to create a "hello world" very simple example use of the AoU researchers workbench for beginners who have never used the workbench before, and have them perform their first analysis as rapidly as possible.

Anticipated Findings

N/A this is a demonstration workspace for education on how to use the AoU workspace
This will demonstrate how to select a cohort of adult participants, search for height measurements and sex at birth data, plot a histogram of this data and perform a students t-test comparison of heights between males and females.
The intent is to create a "hello world" very simple example use of the AoU researchers workbench for beginners who have never used the workbench before, and have them perform their first analysis as rapidly as possible.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

SOD cohort

Septo-optic dysplasia (SOD) is a rare congenital disorder with an estimated incidence of 1 in 10,000 newborns. The full molecular etiology of SOD is not yet known; however, it is widely believed that a combination of genetic predisposition and prenatal…

Scientific Questions Being Studied

Septo-optic dysplasia (SOD) is a rare congenital disorder with an estimated incidence of 1 in 10,000 newborns. The full molecular etiology of SOD is not yet known; however, it is widely believed that a combination of genetic predisposition and prenatal environmental factors contribute substantially to its development. Several genes, such as HESX1, SOX2/SOX3, OTX2, GLI2, PAX6, PROP1, and TAX1BP3 have been identified to play crucial roles in the embryonic development of the eyes, optic nerves, and pituitary gland, thereby influencing the expression of SOD. Despite these advancements in the underlying molecular mechanisms of SOD, a substantial number of SOD families still lack a molecular diagnosis

Project Purpose(s)

  • Educational

Scientific Approaches

Through the Baylor Hopkins Center for Mendelian Genomics (BHCMG) and Baylor College of Medicine Genomic Research to Elucidate the Genetics of Rare (BCM-GREGoR) databases and All of Us database, we will identify unrelated SOD probands and their families for exome and genome sequencing (ES) data. Using a rare variant, family-based analysis approach leveraging existing genomic knowledge sources, we will identify putative candidate, rare variants (MAF ≤ 0.1%) predicted to impact protein function in four candidate disease genes that demonstrate biological roles relevant to the SOD phenotype.

Anticipated Findings

molecular findings in rare disease may inform septo-optic dysplasia molecular diagnosis and clinical presentation

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Registered Tier

Research Team

Owner:

Post-lab-7

to identify the rate of infection with viruses with people with depression. depression can lead to more susceptibility to viruses infections. I will be looking at diagnosis data and the clinical visits due to infection. Describe the phenotype and inclusion/exclusion…

Scientific Questions Being Studied

to identify the rate of infection with viruses with people with depression.
depression can lead to more susceptibility to viruses infections.
I will be looking at diagnosis data and the clinical visits due to infection.
Describe the phenotype and inclusion/exclusion criteria for your cohort

Project Purpose(s)

  • Disease Focused Research (mental depression)

Scientific Approaches

to compare the two criteria, depression and virology infection.
a. Describe the phenotype and inclusion/exclusion criteria for your cohort
b. What is the size of this cohort?
3. Create a new concept set with at least three concepts. (I recommend sticking to one domain, such as Measurements, for this exercise.)
a. Which concepts are you including? Why?
4. Create a dataset using your cohort and concept set.
a. Export your dataset to a Jupyter notebook (you can use R or Python)
b. Open the notebook in “Edit” mode
5. Perform a simple exploratory analysis (You can use code snippets, modify code copied from example workbooks, or write your own code)
a. Combine data frames from the different domains into one data frame
b. Create a table of summary statistics for your three concepts
c. Create a plot visualizing one of your concepts

Anticipated Findings

depression can lead to more susceptibility to viruses infections.
I will be looking at diagnosis data and the clinical visits due to infection.
Describe the phenotype and inclusion/exclusion criteria for your cohort
b. What is the size of this cohort?
3. Create a new concept set with at least three concepts. (I recommend sticking to one domain, such as Measurements, for this exercise.)
a. Which concepts are you including? Why?
4. Create a dataset using your cohort and concept set.
a. Export your dataset to a Jupyter notebook (you can use R or Python)
b. Open the notebook in “Edit” mode
5. Perform a simple exploratory analysis (You can use code snippets, modify code copied from example workbooks, or write your own code)
a. Combine data frames from the different domains into one data frame
b. Create a table of summary statistics for your three concepts
c. Create a plot visualizing one of your concepts

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Registered Tier

Research Team

Owner:

Duplicate of Phenotype - Depression (v7)

The Notebooks in this Workspace can be used to implement well-known phenotype algorithms in one’s own research.

Scientific Questions Being Studied

The Notebooks in this Workspace can be used to implement well-known phenotype algorithms in one’s own research.

Project Purpose(s)

  • Educational
  • Methods Development
  • Other Purpose (This is an All of Us Phenotype Library Workspace created by the Researcher Workbench Support team. It is meant to demonstrate the implementation of key phenotype algorithms within the All of Us Research Program cohort.)

Scientific Approaches

Not Applicable

Anticipated Findings

By reading and running the Notebooks in this Phenotype Library Workspace, researchers can implement the following phenotype algorithms:

This Workspace contains an implementation of a phenotype algorithm for depression: This algorithm was obtained from the eMERGE network. Citation: TBA. KPWA/UW. Depression. PheKB; 2018 Available from: https://phekb.org/phenotype/1095

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Registered Tier

Research Team

Owner:

Duplicate of Phenotype - Dementia (v7)

The Notebooks in this Workspace can be used to implement well-known phenotype algorithms in one’s own research.

Scientific Questions Being Studied

The Notebooks in this Workspace can be used to implement well-known phenotype algorithms in one’s own research.

Project Purpose(s)

  • Educational
  • Methods Development
  • Other Purpose (This is an All of Us Phenotype Library Workspace created by the Researcher Workbench Support team. It is meant to demonstrate the implementation of key phenotype algorithms within the All of Us Research Program cohort.)

Scientific Approaches

Not Applicable

Anticipated Findings

By reading and running the Notebooks in this Phenotype Library Workspace, researchers can implement the following phenotype algorithms:

Ritchie, M., Denny, J., Crawford, D., Ramirez, A., Weiner, J., … Roden, D. (2010). Robust replication of genotype-phenotype associations across multiple diseases in an electronic medical record. American Journal of Human Genetics. 87(2):310 doi: 10.1016/j.ajhg.2010.03.003

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Registered Tier

Research Team

Owner:

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