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multiomics_analysis_for_dementia [2018/11/01 19:19] – [Data] admin | multiomics_analysis_for_dementia [2019/02/14 16:18] – [Data] admin |
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===== Objectives ===== | ===== Objectives ===== |
Determine biomarkers for Alzheimer's and other neurodegenerative diseases using comprehensive analysis of various 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. |
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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]]. | - 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. |
- 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. |
- The Mount Sinai Brain Bank ([[https://www.synapse.org/#!Synapse:syn3159438|MSBB]]) includes proteome and gene expression profiles from hundreds of samples. | - The Mount Sinai Brain Bank ([[https://www.synapse.org/#!Synapse:syn3159438|MSBB]]) includes proteome and gene expression profiles from hundreds of 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 [[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]]. | - 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]]. |
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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 |
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| ===== Related work ===== |
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===== ===== | 1- An interactive timeline of Alzheimer's disease by [[https://www.alzforum.org/timeline/alzheimers-disease#2010|AlzForum]]. |
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