The Australian Imaging Biomarkers and Lifestyle (AIBL) Flagship Study of Ageing: Detecting and Preventing Alzheimer’s disease: Towards Lifestyle Interventions-Somatic mutation in Alzheimer's Disease
- PI
- Masters, Colin
- DAR ID
- 10591
- Initial Approval Date
- December 23, 2022
- Current DAR Status
- Expired
- PI Institution
- The Florey Institute, The University of Melbourne
- PI Institution Country
- Australia
- PI Institution Type
- Non-Profit
Requested Datasets (3)
Research Use Statement
Project Title: The Australian Imaging Biomarkers and Lifestyle (AIBL) Flagship Study of Ageing: Detecting and Preventing Alzheimer’s disease: Towards Lifestyle Interventions - Somatic mutation in Alzheimer's Disease (sub-project)
Objectives -- Somatic Mutation in AD is a project to identify non-congenitally acquired genetic risks associated with disease onset of sporadic Alzheimer’s disease (AD). Somatic mutation can be any form of alteration in DNA that occur after conception. As opposed to congenital, it’s generally not hereditary unless the germ cells are involved. These alterations can (but do not always) cause disease. We aim to identify somatic variants that contribute to sporadic AD. We believe that the detection of somatic mutations can overcome the flaws of the large genome-wide multiple testing and increase the signal-to-noise ratio to pinpoint the rare genetic determinants that were largely neglected by current genetic association studies.
Study design -- We have collected 20 paired human brain microglial DNAs (treated as “tumour”) and whole blood DNAs (treated as “normal”) to call somatic mutations by a tumour-normal mode using a software, MuTect2 (Broad Institute). The sequence has been obtained from the whole genome. Hundreds of rare genetic variants have been identified to connect with AD.
Analysis plan -- We’d like to validate our results using datasets like NG00067, NG00105 and NG00106. However, it’s ideal if we could access the alignment data (i.e., BAM files) as well. Because technically somatic calling is not simply a difference between normal (germline) and reference; but also calls for tumour against normal (germline) alongside alignment. MuTect2 is developed to identify somatic mutations. It works with or without matching normal. Once we get access to the alignment data, we will reprocess all samples using the MuTect2 without matching the normal pipeline. We'll call somatic mutations using those datasets and validate the rare genetic determinants that contribute to sporadic AD.
Objectives -- Somatic Mutation in AD is a project to identify non-congenitally acquired genetic risks associated with disease onset of sporadic Alzheimer’s disease (AD). Somatic mutation can be any form of alteration in DNA that occur after conception. As opposed to congenital, it’s generally not hereditary unless the germ cells are involved. These alterations can (but do not always) cause disease. We aim to identify somatic variants that contribute to sporadic AD. We believe that the detection of somatic mutations can overcome the flaws of the large genome-wide multiple testing and increase the signal-to-noise ratio to pinpoint the rare genetic determinants that were largely neglected by current genetic association studies.
Study design -- We have collected 20 paired human brain microglial DNAs (treated as “tumour”) and whole blood DNAs (treated as “normal”) to call somatic mutations by a tumour-normal mode using a software, MuTect2 (Broad Institute). The sequence has been obtained from the whole genome. Hundreds of rare genetic variants have been identified to connect with AD.
Analysis plan -- We’d like to validate our results using datasets like NG00067, NG00105 and NG00106. However, it’s ideal if we could access the alignment data (i.e., BAM files) as well. Because technically somatic calling is not simply a difference between normal (germline) and reference; but also calls for tumour against normal (germline) alongside alignment. MuTect2 is developed to identify somatic mutations. It works with or without matching normal. Once we get access to the alignment data, we will reprocess all samples using the MuTect2 without matching the normal pipeline. We'll call somatic mutations using those datasets and validate the rare genetic determinants that contribute to sporadic AD.
Non-Technical Summary
Somatic Mutation in Alzheimer's disease is a project to identify non-congenitally acquired genetic risks associated disease onset of a sporadic Alzheimer’s disease (AD). We believe that detection of somatic mutations can pinpoint the rare genetic determinants that were largely neglected by current genetic association studies. In our pilot study, we have identified hundreds of rare genetic mutations that are strongly associated with AD. We'd like to validate our results using an independent cohort. We plan to reprocess NIH datasets using our own pipeline. But we would need to access the raw data rather than the processed data. This research will greatly accelerate the research on the molecular genetics of AD.
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.