Multiomics analysis for dementia

Objectives

Determine biomarkers for Alzheimer's and other neurodegenerative diseases using comprehensive analysis of multi-omics data including genomics, epigenomics, metabolomics, proteomics, etc.

Data

Large cohorts with phenotype data on dementia are available through:

  1. The Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium.
  2. The Trans-Omics for Precision Medicine (TOPMed) program. The TOPMed Omics Survey in 2017 includes Framingham Heart Study (FHS) details, which are described clearer in 2016.
  3. Exome Sequencing Project (ESP), richly-phenotyped for heart, lung and blood disorders.
  4. Alzheimer's Disease Sequencing Project (ADSP), WES and WGS of thousands of AD and control samples.
  5. Allen Brain Atlases has many different data types, but from a few mouse and human samples. RNA-Seq data of hundreds of dementia cases.
  6. The Alzheimer's Disease Neuroimaging Initiative (ADNI) has genetic and imaging data of 1-3 K samples.
  7. The Image and Data Archive (IDA) contains mostly image data on 43,290 subjects from 119 studies.
  8. Several studies share their data through Accelerating Medicines Partnership - Alzheimer's Disease (AMP-AD) including:
    1. The Adult Changes in Thought (ACT) measured ~4K proteins in ~50 brains and performed WGCNA. Also, proteome data in BLSA (~100 brains), Banner (~200), and UPPpilot (~200).
    2. CHDWB and HBTRC, each has a gene expression profile from ~500 brains, MC-CAA (75), MCADGS (~100 RNA-Seq and GWAS samples).
    3. The Mount Sinai Brain Bank (MSBB) includes proteome and gene expression profiles from hundreds of samples.
    4. The MayoRNAseq includes WGS and RNA-Seq data from 275 Cerebellum (CBE) and 276 Temporal cortex (TCX) samples.
  9. The Religious Orders Study and Memory and Aging Project (ROSMAP) is the richest dataset in AMP-AD in terms of variety of data types, which include gene expression, genome, proteome, metabolome, and image data. Also, DNA methylation, miRNA, WGS, WES, and even H3K9Ac are available for ~1K samples. The dataset is very well documented.

Collaborators

Dr. Sudha Seshadri, the Founding Director of The Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, and Dr. Claudia Satizabal.

Subprojects

Network analysis on proteome data of Fremingham cohort