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multiomics_analysis_for_dementia [2019/12/12 20:08] – [Data] adminmultiomics_analysis_for_dementia [2021/01/28 16:23] – [Data] admin
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 Determine biomarkers for Alzheimer's and other neurodegenerative diseases using comprehensive analysis of multi-omics data including genomics, epigenomics, metabolomics, proteomics, etc. Determine biomarkers for Alzheimer's and other neurodegenerative diseases using comprehensive analysis of multi-omics data including genomics, epigenomics, metabolomics, proteomics, etc.
  
 +
 +====== Multiomics analysis for dementia ======
 +
 +===== Objectives =====
 +
 +Determine biomarkers for Alzheimer's and other neurodegenerative diseases using comprehensive analysis of multi-omics data including genomics, epigenomics, metabolomics, proteomics, etc.
  
 ===== Data ===== ===== Data =====
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   - 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.
 +  - [[https://bmbls.bmi.osumc.edu/scread/|scREAD]]: A Single-Cell RNA-Seq Database for Alzheimer’s Disease [[[https://www.cell.com/iscience/pdf/S2589-0042(20)30966-4.pdf|pdf]]].
 +
 +===== 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]], Dr. [[http://runewarkbiology.rutgers.edu/Dobrowolski Lab/index.html|Radek Dobrowolski]], and Dr. [[https://biggsinstitute.org/team-member/qitao-ran/|Qitao Ran]].
 +
 +===== Subprojects =====
 +
 +  - 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.
  
  
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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 38,851 individuals." //[[https://www.nature.com/articles/s41588-019-0511-y|Nature genetics]]// 51.11 (2019): 1624-1636. \\ 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. 
 +  - Sey, Nancy YA, et al. A computational tool (H-MAGMA) for improved prediction of brain-disorder risk genes by incorporating brain chromatin interaction profiles. [[https://www.nature.com/articles/s41593-020-0603-0|Nature Neuroscience]], 2020. 
 +  - Borghesan, M., et al. "A **Senescence**-Centric View of Aging: Implications for Longevity and Disease." [[https://www.sciencedirect.com/science/article/abs/pii/S0962892420301434|Trends in Cell Biology]] (2020). The review paper suggested by Christi.