Identifying Alzheimer's Disease Genetic Risk Factors By Integrated Genomic and Proteomic Analysis
- PI
- Wingo, Thomas
- DAR ID
- 10019
- Initial Approval Date
- September 17, 2019
- Current DAR Status
- Closed
- PI Institution
- Emory University
- PI Institution Country
- United States
- PI Institution Type
- Non-Profit
Requested Datasets (2)
Research Use Statement
We aim to uncover new genetic risk variants for Alzheimer’s disease (AD) by analysis of an integrated analysis of proteomics and genetic sequencing performed at Emory University. Results of these analyses will be used to weight analysis of whole-genome sequencing (WGS), whole-genome genotyping (WGG), and whole-exome sequencing (WES) data from dbGaP and ADSP. We plan to publish our findings, so they are shared with the scientific community.
Outcomes that will be tested include: (1) clinical disease status, (2) pathologic characterization (e.g., measures of beta-amylodi, tau, etc.), and (3) cognitive decline. For sequencing data, we will perform joint calling from samples previously mapped by ADSP using PECaller using default settings. Variant annotation will be performed using Bystro and quality control will follow Wingo et al., 2017. For rare variants, we will use burden- and variance-based tests to estimate association between genetic variants and each outcome for every gene in the genome. External weights from proteomic analyses will be optionally used, as well as measures of genomic conservation for each site. For common variants, we plan to test for differences in allele frequencies using maximum likelihood tests. For all analyses, we plan to control for population structure deriving principal components from the underlying sequencing or genotyping data.
Outcomes that will be tested include: (1) clinical disease status, (2) pathologic characterization (e.g., measures of beta-amylodi, tau, etc.), and (3) cognitive decline. For sequencing data, we will perform joint calling from samples previously mapped by ADSP using PECaller using default settings. Variant annotation will be performed using Bystro and quality control will follow Wingo et al., 2017. For rare variants, we will use burden- and variance-based tests to estimate association between genetic variants and each outcome for every gene in the genome. External weights from proteomic analyses will be optionally used, as well as measures of genomic conservation for each site. For common variants, we plan to test for differences in allele frequencies using maximum likelihood tests. For all analyses, we plan to control for population structure deriving principal components from the underlying sequencing or genotyping data.
Non-Technical Summary
Our aim is to identify genetic variants that are associated with Alzheimer's Disease (AD) either using genomic data (from dbGap or from Emory University) or brain protein sequencing data (from Emory University) as a starting point. Each center’s data will be analyzed separately, and we will determine whether the findings are consistent among the centers. Additionally, we will use protein data from brain or cerebrospinal fluid of individuals with or without AD to guide the analysis of the genomic data to identify genetic variants that influence AD risk. Our overarching aim is to use genetic discoveries to identify mechanisms of AD pathogenesis and creation of more meaningful models of the disease.
Reported Publications
Publications shown are those reported by investigators through NIAGADS DAR reporting and renewal processes and may not represent a complete list of publications associated with the project.
No publications have been reported for this DAR.