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multiomics_analysis_for_dementia [2019/11/07 17:24]
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multiomics_analysis_for_dementia [2019/12/12 22:08] (current)
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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.+  - 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.