Nandita Mukhopadhyay
Project Personnel, University of Pittsburgh
4 active projects
Cleft_regions_stomach_cancer_Aug10_2023
Scientific Questions Being Studied
The goal of this research is to test whether variants in orofacial cleft risk genes are associated with risk of cancer.
Project Purpose(s)
- Ancestry
Scientific Approaches
Subjects with a known cancer status will be extracted and analyzed using logistic regression to their array genotypes in selected regions. HAIL and/or PLINK will be used. Following single variant association on common variants, we will also run rare-variant association and gene-set analysis.
Anticipated Findings
Prior studies have reported increased risk of certain types of cancer in individuals born with an orofacial cleft defect, as well as higher rates of cancer in the relatives of affected subjects. This indicates that the two phenotypes may share a common genetic etilogy We intend to study if this is true in the All of Us research subjects.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled Tier
Cleft_regions_stomach_cancer
Scientific Questions Being Studied
The goal of this research is to test whether variants in orofacial cleft rish genes are associated with risk of cancer.
Project Purpose(s)
- Ancestry
Scientific Approaches
Subjects with a known cancer status will be extracted and analyzed using logistic regression to their array genotypes in selected regions. HAIL and/or PLINK will be used. Following single variant association on common variants, we will also run rare-variant association and gene-set analysis.
Anticipated Findings
Prior studies have reported increased risk of certain types of cancer in individuals born with an orofacial cleft defect, as well as higher rates of cancer in the relatives of affected subjects. This indicates that the two phenotypes may share a common genetic etilogy We intend to study if this is true in the All of Us research subjects.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierGenomic Data (Hail - Plink)(v7) copy
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)
- Ancestry
- 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 TierExtraction of Stomach tumor Data (Hail - Plink)
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)
- Ancestry
- 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 TierResearch Team
Owner:
- Nandita Mukhopadhyay - Project Personnel, University of Pittsburgh
- Jun Qian - Other, All of Us Program Operational Use
- Jennifer Zhang - Project Personnel, All of Us Program Operational Use
- Will Dolbeer - Other, All of Us Program Operational Use
Collaborators:
- Henry Condon - Project Personnel, All of Us Program Operational Use
Request a Review of this Research Project
You can request that the All of Us Resource Access Board (RAB) review a research purpose description if you have concerns that this research project may stigmatize All of Us participants or violate the Data User Code of Conduct in some other way. To request a review, you must fill in a form, which you can access by selecting ‘request a review’ below.
