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multiomics_analysis_for_dementia [2019/02/14 16:18] – [Data] adminmultiomics_analysis_for_dementia [2019/07/15 17:12] – [Related work] admin
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   - Exome Sequencing Project ([[http://evs.gs.washington.edu|ESP]]), richly-phenotyped for heart, lung and blood disorders.   - Exome Sequencing Project ([[http://evs.gs.washington.edu|ESP]]), richly-phenotyped for heart, lung and blood disorders.
   - Alzheimer's Disease Sequencing Project ([[https://www.niagads.org/adsp/content/study-design|ADSP]]), WES and WGS of thousands of AD and control samples.   - Alzheimer's Disease Sequencing Project ([[https://www.niagads.org/adsp/content/study-design|ADSP]]), WES and WGS of thousands of AD and control samples.
-  - Allen Brain [[http://portal.brain-map.org/|Atlases]] has many different data types, but from a few mouse and human samples. RNA-Seq data of hundreds of dementia cases+  - Allen Brain [[http://portal.brain-map.org/|Atlases]] has many different [[http://aging.brain-map.org/overview/home|downloadable]] data types, but from a few mouse and human samples. RNA-Seq data of hundreds of dementia cases.
-  - The Alzheimer's Disease Neuroimaging Initiative ([[http://adni.loni.usc.edu/data-samples/data-types/|ADNI]]) has genetic and imaging data of 1-3 K samples.+
   - The Image and Data Archive ([[https://ida.loni.usc.edu|IDA]]) contains mostly image data on 43,290 subjects from 119 studies.   - The Image and Data Archive ([[https://ida.loni.usc.edu|IDA]]) contains mostly image data on 43,290 subjects from 119 studies.
 +  - The Alzheimer's Disease Neuroimaging Initiative ([[http://adni.loni.usc.edu/data-samples/data-types/|ADNI]]) has genetic and imaging data of 1-3 K samples, which are available through [[https://ida.loni.usc.edu|IDA]].
   - Several studies share their data through Accelerating Medicines Partnership - Alzheimer's Disease ([[https://www.synapse.org/#!Synapse:syn5550382|AMP-AD]]) including:   - Several studies share their data through Accelerating Medicines Partnership - Alzheimer's Disease ([[https://www.synapse.org/#!Synapse:syn5550382|AMP-AD]]) including:
       - The Adult Changes in Thought ([[https://www.synapse.org/#!Synapse:syn5759376|ACT]]) measured ~4K __proteins__  in ~50 brains and performed WGCNA. Also, proteome data in BLSA (~100 brains), Banner (~200), and UPPpilot (~200).       - The Adult Changes in Thought ([[https://www.synapse.org/#!Synapse:syn5759376|ACT]]) measured ~4K __proteins__  in ~50 brains and performed WGCNA. Also, proteome data in BLSA (~100 brains), Banner (~200), and UPPpilot (~200).
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       - The Mount Sinai Brain Bank ([[https://www.synapse.org/#!Synapse:syn3159438|MSBB]]) includes proteome and gene expression profiles from hundreds of samples.       - The Mount Sinai Brain Bank ([[https://www.synapse.org/#!Synapse:syn3159438|MSBB]]) includes proteome and gene expression profiles from hundreds of samples.
       - The [[https://www.synapse.org/#!Synapse:syn5550404|MayoRNAseq]] includes WGS and RNA-Seq data from 275 Cerebellum (CBE) and 276 Temporal cortex (TCX) samples.       - The [[https://www.synapse.org/#!Synapse:syn5550404|MayoRNAseq]] includes WGS and RNA-Seq data from 275 Cerebellum (CBE) and 276 Temporal cortex (TCX) samples.
-  - The Religious Orders Study and Memory and Aging Project ([[https://www.synapse.org/#!Synapse:syn3219045|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 [[https://www.radc.rush.edu/docs/omics.htm|documented]].+  - The Religious Orders Study and Memory and Aging Project ([[https://www.synapse.org/#!Synapse:syn3219045|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 [[https://www.radc.rush.edu/docs/omics.htm|documented]], and was used to identify [[http://mostafavilab.stat.ubc.ca/xqtl/|xQTL]] by Philip De Jager.
  
  
 ===== Collaborators ===== ===== Collaborators =====
  
-Dr. [[http://gsbs.uthscsa.edu/faculty/sudha-seshadri-m.d.-dm|Sudha Seshadri]], the Founding Director of The Glenn [[https://biggsinstitute.org/|Biggs Institute]] for Alzheimer's & Neurodegenerative Diseases, and [[https://biggsinstitute.org/team-member/claudia-l-satizabal-phd/|Dr. Claudia Satizabal]].+Dr. [[http://gsbs.uthscsa.edu/faculty/sudha-seshadri-m.d.-dm|Sudha Seshadri]], the Founding Director of The Glenn [[https://biggsinstitute.org/|Biggs Institute]] for Alzheimer's & Neurodegenerative Diseases, [[https://biggsinstitute.org/team-member/claudia-l-satizabal-phd/|Dr. Claudia Satizabal]], and Dr. [[http://runewarkbiology.rutgers.edu/Dobrowolski Lab/index.html|Radek Dobrowolski]]. 
  
 ===== Subprojects ===== ===== Subprojects =====
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 ===== Related work ===== ===== Related work =====
  
-1- An interactive timeline of Alzheimer's disease by [[https://www.alzforum.org/timeline/alzheimers-disease#2010|AlzForum]].+  - An interactive **timeline**  of Alzheimer's disease by [[https://www.alzforum.org/timeline/alzheimers-disease#2010|AlzForum]]
 +  - Satizabal, Claudia L., et al. "Genetic architecture of subcortical brain structures in over 40,000 individuals worldwide." [[https://www.biorxiv.org/content/10.1101/173831v1.full|bioRxiv]] (2017): 173831. \\  They identified a set of genes that is "significantly enriched for //Drosophila//  orthologs associated with neurodevelopmental phenotypes".