John Seibert

Project Personnel, Geisinger Clinic

2 active projects

X and Y Chromosome Intensity

Not applicable - these notebooks demonstrate example analysis how to use Hail and PLINK to perform genome-wide association studies using the All of Us genomic data and phenotypic data.

Scientific Questions Being Studied

Not applicable - these notebooks demonstrate example analysis how to use Hail and PLINK to perform genome-wide association studies using the All of Us genomic data and phenotypic data.

Project Purpose(s)

  • Other Purpose (Demonstrate to the All of Us Researcher Workbench users how to get started with the All of Us genomic data and tools. It includes an overview of all the All of Us genomic data and shows some simple examples on how to use these data.)

Scientific Approaches

Not applicable - these notebooks demonstrate example analysis how to use Hail and PLINK to perform genome-wide association studies using the All of Us genomic data and phenotypic data.

Anticipated Findings

Not applicable - these notebooks demonstrate example analysis how to use Hail and PLINK to perform genome-wide association studies using the All of Us genomic data and phenotypic data.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

Sex Chromosome Aneuploidies and Neuropsychiatric Disorders

Some individuals are born with sex chromosome aneuploidies, an extra or loss of an X or Y chromosome. Sex chromosome aneuploidies are known to associate with cognitive impairment, but the full spectrum of brain disorders is not well described. The…

Scientific Questions Being Studied

Some individuals are born with sex chromosome aneuploidies, an extra or loss of an X or Y chromosome. Sex chromosome aneuploidies are known to associate with cognitive impairment, but the full spectrum of brain disorders is not well described. The primary question of this project is “What is the relationship between sex chromosome aneuploidies and neuropsychiatric disorders?”

Project Purpose(s)

  • Disease Focused Research (Sex chromosome aneuploidies)
  • Ancestry

Scientific Approaches

Sex-chromosome aneuploidies will be identified from the array of genotype data. We will screen for sex-chromosome imbalances by identifying outliers in the array intensity values. We will use whole-genome data to orthogonally confirm the presence of a sex-chromosome aneuploidy called from the genotype array data. We plan to use comprehensive EHR data, conditions, drug exposures, lab/measurements, and procedures to create NPD outcomes and exposure variables. We will primarily use regression analyses to compare the rates of NPD in those with a sex chromosome aneuploidy compared to those without a sex chromosome aneuploidy.

Anticipated Findings

We will derive population-based estimates for NPD risk caused by the presence of a sex chromosome aneuploidy. Our findings may demonstrate the importance of considering sex chromosome aneuploidies as a common cause of NPD.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

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