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multiomics_analysis_for_dementia [2019/06/07 17:55]
admin [Related work]
multiomics_analysis_for_dementia [2019/08/01 03:31]
admin [Collaborators]
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 ===== Data ===== ===== Data =====
  
-Large cohorts with phenotype data on dementia are available through:+Large cohorts with phenotype data on dementia are available through ​the following resources (incomplete [[https://​docs.google.com/​spreadsheets/​d/​1NpWRjxwwCJp-AKci239fjCf2IDg-oJONdNAuBojsG9I/​edit#​gid=305034359|table]] of data types):
  
   - The Cohorts for Heart and Aging Research in Genomic Epidemiology ([[http://​www.chargeconsortium.com|CHARGE]]) Consortium.   - The Cohorts for Heart and Aging Research in Genomic Epidemiology ([[http://​www.chargeconsortium.com|CHARGE]]) Consortium.
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   - 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 [[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.   - 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. 
 +  - Mathys, Hansruedi, et al. "​**Single-cell** ​ transcriptomic analysis of Alzheimer’s disease."​ Nature ([[https://​www.nature.com/​articles/​s41586-019-1195-2|2019]]). \\  Radek'​s summary: "​Showing ~80K single cell transcriptomic analysis on brain tissues from ~50 patients with Alzheimer'​s disease. Subpopulations of glia and neurons expressed different gene signatures associated with AD. These enormous cataloging data may help to further pinpoint pathways associated with AD.", and his [[:plan|]]. Habil'​s [[https://​docs.google.com/​presentation/​d/​1u2rv9FExW44JfJsqPjenJcCsCFnOSUbJUxQwalviNHk/​edit#​slide=id.p|presentation]] in Biggs journal club on 2 July 2019. 
 +  - The Brain eQTL Almanac ([[http://​braineac.org/​|Braineac]]) generated by UK Brain Expression Consortium (UKBEC) "​comprises of genomic and transcriptome data of 134 brains from individuals free of neurodegenerative disorders. Up to 12 brain regions were extracted per brain in parallel for mRNA quantification."​
  
  
 ===== 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]], Dr. [[http://​runewarkbiology.rutgers.edu/​Dobrowolski Lab/​index.html|Radek Dobrowolski]],​ and Dr. [[https://​biggsinstitute.org/​team-member/​qitao-ran/​|Qitao Ran]]. 
  
 ===== Subprojects ===== ===== Subprojects =====
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 ===== Related work ===== ===== Related work =====
  
-  - 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]]. 
-  - MathysHansruedi, et al. "Single-cell transcriptomic analysis ​of Alzheimer’s disease." ​Nature ([[https://​www.nature.com/articles/s41586-019-1195-2|2019]]). \\  ​Radek'​s summary: ​"Showing single cell transcriptomic analysis on brain tissues from ~50 patients with Alzheimer'​s disease. Subpopulations of glia and neurons expressed different gene signatures ​associated with AD. These enormous cataloging data may help to further pinpoint pathways associated with AD.", and his {{:​wiki:​img_20190516_162440263.jpg?​linkonly|plan}}.+  - SatizabalClaudia 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".