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multiomics_analysis_for_dementia [2019/07/03 04:34]
admin [Related work]
multiomics_analysis_for_dementia [2019/11/07 17:24] (current)
admin [Data]
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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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       - 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]],​ and was used to identify [[http://​mostafavilab.stat.ubc.ca/​xqtl/​|xQTL]] by Philip De Jager.   - 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."​
 +  - Omics data were generated in [[https://​www.neurodegenerationresearch.eu/​it/​cohort/​the-rhineland-study/​|Rhineland]] Study including DNA methylation from ~2K blood samples. ​ Aslam Imtiaz presented these data in the NeuroCHARGE call on 2019-11-07.
  
  
 ===== 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, [[https://​biggsinstitute.org/​team-member/​claudia-l-satizabal-phd/​|Dr. Claudia Satizabal]], ​and Dr. [[http://​runewarkbiology.rutgers.edu/​Dobrowolski Lab/​index.html|Radek Dobrowolski]].+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 =====
  
-Network analysis on [[https://​docs.google.com/​document/​d/​1K89u6OubQUXAycg6JaEqzNgv18ybRy4QWcG_3UVQBuQ/​edit|proteome]] data of Fremingham cohort+  - Network analysis on [[https://​docs.google.com/​document/​d/​1K89u6OubQUXAycg6JaEqzNgv18ybRy4QWcG_3UVQBuQ/​edit|proteome]] data of Fremingham cohort
 +  - [[https://​docs.google.com/​presentation/​d/​1gCs39bst5xqxbpLNybRkJg1hUxxWCspmhlvKfdjtTsw/​edit?​ts=5d41b329#​slide=id.g5e1f444b4f_0_0|DE]] analysis on RNA-Seq data of 5xFAD and Gpx4Tg mouse models for AD. Four biological replicates in each of the four conditions were generated in Ran's Lab. 
  
 ===== 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]].
-  - 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 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}}. Habil'​s [[https://​docs.google.com/​presentation/​d/​1u2rv9FExW44JfJsqPjenJcCsCFnOSUbJUxQwalviNHk/​edit#​slide=id.p|presentation]] in Biggs journal club on 2 July 2019. 
   - 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"​.   - 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"​.