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multiomics_analysis_for_dementia [2019/08/01 00:31] – [Collaborators] adminmultiomics_analysis_for_dementia [2020/02/21 13:43] – [Related work] raheleh
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   - 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.
-  - The Trans-Omics for Precision Medicine ([[https://www.nhlbiwgs.org|TOPMed]]) program. The TOPMed Omics [[http://oncinfo.org/_media/wiki:topmed_omics_survey.pdf|Survey]] in 2017 includes Framingham Heart Study (FHS) details, which are described clearer in [[http://oncinfo.org/_media/wiki:omics_fhs.pdf|2016]]. [[https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/molecular.cgi?study_id=phs000363.v17.p11&phv=173423&phd=4119&pha=&pht=2941&phvf=&phdf=&phaf=&phtf=&dssp=1&consent=&temp=1|SABRe]] is a substudy of FHS and has mRNA and miRNA data.+  - The Trans-Omics for Precision Medicine ([[https://www.nhlbiwgs.org|TOPMed]]) program. The TOPMed Omics [[http://oncinfo.org/_media/wiki:topmed_omics_survey.pdf|Survey]] in 2017 includes Framingham Heart Study (FHS) details, which are described clearer in [[http://oncinfo.org/_media/wiki:omics_fhs.pdf|2016]]. [[https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/molecular.cgi?study_id=phs000363.v17.p11&phv=173423&phd=4119&pha=&pht=2941&phvf=&phdf=&phaf=&phtf=&dssp=1&consent=&temp=1|SABRe]] is a substudy of FHS and has mRNA and miRNA data. We obtained [[https://docs.google.com/document/d/1B8uKY2QBuJHAiPrv9y_cR9704RrI7nZM71oVc7jt5Q8/edit|these]] data in 2019.
   - 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.
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   - 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.   - 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."   - 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.
  
  
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 ===== 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 =====
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   - 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".   - 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".
 +  - Yamazaki, Yu., et al. "Apolipoprotein E and Alzheimer disease: pathobiology and targeting strategies." [[https://www.nature.com/articles/s41582-019-0228-7|Nat Rev Neurol ]](2019): 501–518.
 +  - Ferreira, Daniel., et al. Biological subtypes of Alzheimer disease: A systematic review and meta-analysis [[https://n.neurology.org/content/neurology/early/2020/02/11/WNL.0000000000009058.full.pdf|Neurology]] (2020):94:1-13.