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multiomics_analysis_for_dementia [2019/07/03 01:34] – [Related work] adminmultiomics_analysis_for_dementia [2019/08/01 00:41] – [Subprojects] admin
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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."
  
  
 ===== 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".