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serum_biomarkers_for_neurodegeneration [2019/12/11 23:32] – admin | serum_biomarkers_for_neurodegeneration [2019/12/19 23:47] – [Data] admin |
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===== Objectives ===== | ===== Objectives ===== |
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Identify novel serum biomarkers for neurodegeneration that allow accurate diagnosis of Alzheimer's disease (AD) in Hispanic and non-Hispanic white populations. | Identify novel serum biomarkers for neurodegeneration that allow accurate diagnosis of Alzheimer's disease (AD) in Hispanic and non-Hispanic white populations (Specific {{:analysis_plan.docx|Aims}} ). |
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===== Data ===== | ===== Data ===== |
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- DNA methylation data of [[29 subjects|]] were measured in 2019 using Infinium [[https://support.illumina.com/downloads/infinium-methylationepic-v1-0-product-files.html|MethylationEpic]] V1 Array. PBMC samples were collected before and after Rapamycin (16 subjects) and placebo (13 subjects) treatment for 6-8 weeks. | - Six proteins were measured in blood samples of ~1200 Hispanic and ~500 non-Hispanic white participants. Covariates include gender, education, and age. |
| - The cognitive status of participants were assessed in several visits over years. The number of visits and time intervals between visits vary across participants. |
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===== Collaborators ===== | ===== Collaborators ===== |
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Dr. [[https://wp.uthscsa.edu/mimg/team-member/ellen-kraig-ph-d/|Ellen Kraig]], an immunologist, and Dr. [[https://www.uthscsa.edu/academics/biomedical-sciences/faculty/profile/0V71EU5IM/Kellogg,-Dean-L.-Jr.|Dean Kellogg]], a physiologist, both from the University of Texas Health Science Center at San Antonio. | Dr. Sudha [[https://www.uthscsa.edu/academics/biomedical-sciences/faculty/profile/53266/Seshadri,-Sudha|Seshadri]], the Founding director of the Glenn [[https://biggsinstitute.org/|Biggs]] Institute for Alzheimer's & Neurodegenerative Diseases, and Dr. Mitzi [[https://biggsinstitute.org/team-member/mitzi-m-gonzales-ph-d/|Gonzales]] from the Department of Neurology at University of Texas Health Science Center in San Antonio. This study is supported by Texas Alzheimer's Research and Care Consortium (TARCC). |
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| ===== Analysis ===== |
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===== DNA methylation analysis ===== | - Linear models. |
| - Regularized regression, e.g., the LASSO. |
| - Hidden Markov Models (HMM). |
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We follow the Bioconductor [[https://www.bioconductor.org/packages/release/workflows/vignettes/methylationArrayAnalysis/inst/doc/methylationArrayAnalysis.html#differential-methylation-analysis|workflow]] to identify the probes and regions that are differentially methylation due to Rapamycin treatment. | |
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===== Related work ===== | ===== Related work ===== |
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- Kraig, Ellen, et al. "A randomized control trial to establish the feasibility and safety of rapamycin treatment in an older human cohort: Immunological, physical performance, and cognitive effects." [[https://www.sciencedirect.com/science/article/pii/S0531556517309130|Experimental gerontology]] 105 (2018): 53-69. | - Eagan, Danielle E., et al. "Elevated serum C-reactive protein relates to increased cerebral myoinositol levels in middle-aged adults." Cardiovascular psychiatry and neurology 2012 ([[https://www.hindawi.com/journals/cpn/2012/120540/|2012]]). |
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