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serum_biomarkers_for_neurodegeneration [2019/12/11 23:32] – adminserum_biomarkers_for_neurodegeneration [2019/12/25 01:51] (current) – [Analysis] admin
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 ===== Objectives ===== ===== Objectives =====
  
-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}} ).
  
 ===== Data ===== ===== Data =====
  
-  - 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. 
  
 ===== Collaborators ===== ===== Collaborators =====
  
-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). 
 + 
 + 
 +===== Analysis =====
  
-===== DNA methylation analysis =====+  - Linear models. 
 +  - Regularized regression, e.g., the LASSO and [[https://cran.r-project.org/web/packages/FeaLect/index.html|FeaLect]]. 
 +  - Hidden Markov Models (HMM).
  
-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. 
  
 ===== Related work ===== ===== Related work =====
  
-  - 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]]).