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multiomics_analysis_for_dementia [2021/09/16 18:22] – [Related work] adminmultiomics_analysis_for_dementia [2024/07/24 19:53] (current) – [Data] admin
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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. We obtained [[https://docs.google.com/document/d/1B8uKY2QBuJHAiPrv9y_cR9704RrI7nZM71oVc7jt5Q8/edit|these]] data in 2019. On 2021-04-23, {{:fhs_multiomics_meeting_msevilla_april21.pdf|Magdalena}}  Sevilla presented a collection of FHS and other omics datasets and some methods for analyzing them.+  - 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. On 2021-04-23, {{:fhs_multiomics_meeting_msevilla_april21.pdf|Magdalena}}  Sevilla presented a collection of FHS, MESA, and WHI omics datasets and some statistical methods for analyzing them.
   - 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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   - 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]]). It covers 73 datasets from 15 studies, 10 brain regions, 713640 cells.Useful for: a) listing available datasets, b) easy preliminary DE analysis across cell types and disease vs. control conditions.   - [[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]]). It covers 73 datasets from 15 studies, 10 brain regions, 713640 cells.Useful for: a) listing available datasets, b) easy preliminary DE analysis across cell types and disease vs. control conditions.
 +  - [[https://www.nature.com/articles/s41586-021-03910-8|Bhaduri]] 's 2021 snRNASeq of the developing human brain.
 +  - Leonenko, et al. (2021). Identifying individuals with high risk of Alzheimer’s disease using polygenic risk scores. [[https://www.nature.com/articles/s41467-021-24082-z#Sec8|Nature communications]]. A comprehensive list of large dementia cohorts in the Methods.
 +  - Gabitto, Mariano I., et al. "Integrated multimodal cell atlas of Alzheimer’s disease." //bioRxiv//  (2023). Seattle Alzheimer’s Disease Brain Cell [[https://portal.brain-map.org/explore/seattle-alzheimers-disease|Atlas]], [[https://knowledge.brain-map.org/data/5IU4U8BP711TR6KZ843/2CD0HDC5PS6A58T0P6E/compare?cellType=Whole Taxonomy&geneOption=IL1B&metadata=Cognitive Status&comparison=dotplot|browsable]] from knowledge.brain-map.org.
 +  - Sun, Na, et al. … Manolis Kellis. "Single-cell multi-region dissection of brain vasculature in Alzheimer’s Disease." //[[https://www.nature.com/articles/s41586-024-07606-7|Nature]]// (2024). snRNA-seq data of 1.3 million cells from 6 brain regions across 48 individuals with and without Alzheimer’s disease.
  
  
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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]].
 +  - [[https://www.nia.nih.gov/research/blog/2022/05/napa-at-10?utm_source=NIA+Main&utm_campaign=3c45f80fa9-20220516_blog&utm_medium=email&utm_term=0_ffe42fdac3-3c45f80fa9-18446435|NAPA]] at 10: A decade of Alzheimer’s and related dementias research progress, 2022.
   - 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".   - 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.   - 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.
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   - 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.   - 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.   - 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.
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