The Mount Sinai Brain Bank (MSBB) study info
The MSBB cohort generated large-scale, matched multi-omics data in AD and control brains to study the molecular basis of AD.
Access
Controlled access. Request data access for MSBB on the AD Knowledge Portal; you need a Synapse account. See How to get the data.
| Where | ID | Access | What you get |
|---|---|---|---|
| Synapse | syn69670592 | Controlled | Files described below |
Other Synapse IDs on this page syn69670600 syn69670597 syn69865816
pip install synapseclient
synapse login
synapse get -r syn69670592- PI : Prof. Bin Zhang
- Institution : Icahn School of Medicine at Mount Sinai
- Grant number : U01AG046170, RF1AG057440, RF1AG054014, R01AG057907
- Contact person : Minghui Wang (minghui.wang@mssm.edu)
- Publication : PMID: 30204156, 33238137
- Acknowledgement : This work was supported by the grants from the NIH/National Institute on Aging (NIA). U01AG046170 is a component of the AMP-AD Target Discovery and Preclinical Validation Project. Brain tissue collection and characterization was supported by NIH HHSN271201300031C.
- Study name : The Mount Sinai Brain Bank (MSBB) study
- Study Description : Brain specimens were obtained from the Mount Sinai/JJ Peters VA Medical Center Brain Bank (MSBB) which holds over 1,700 samples. This cohort was assembled after applying stringent inclusion/exclusion criteria and represents the full spectrum of disease severity. Neuropathological assessments are performed according to the Consortium to Establish a Registry for Alzheimer’s Disease (CERAD) protocol and include assessment by hematoxylin and eosin, modified Bielschowski, modified thioflavin S, and anti-β amyloid (4G8), anti-tau (AD2) and anti-ubiquitin (Daka Corp.). Each case is assigned a Braak AD-staging score for progression of neurofibrillary neuropathology. Quantitative data regarding the density of neuritic plaques in the middle frontal gyrus, orbital frontal cortex, superior temporal gyrus, inferior parietal cortex and calcarine cortex are also collected as described. Clinical dementia rating scale (CDR) and mini–mental state examination (MMSE) severity tests are conducted for assessment of dementia and cognitive status. Final diagnoses and CDR scores are conferred by consensus. Based on CDR classification, subjects are grouped as no cognitive deficits (CDR = 0), questionable dementia (CDR = 0.5), mild dementia (CDR = 1.0), moderate dementia (CDR = 2.0), and severe to terminal dementia (CDR = 3.0–5.0). Covariates including demographic and neuropathological data were collected on the samples used for this project including postmortem interval, race, age of death, clinical dementia rating, clinical neuropathology diagnosis, CERAD, Braak, sex, and a series of neuropathological variables. See the Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer’s disease for a detailed description of the study and the data.
- Disease : Alzheimer’s disease
- Website : https://www.synapse.org/#!Synapse:syn3159438
Contact
Xuanhe
QTL Analyses
The FunGen-xQTL flagship paper used MSBB datasets in these xQTL analyses.
| Dataset | Modality | QTL File |
|---|---|---|
| Brain bulk RNA-seq | eQTL | MSBB_brain_expression_qtl |
| Brain RNA splicing | sQTL | MSBB_brain_splicing_qtl |
| Brain methylation | mQTL | MSBB_brain_methylation_qtl |
| Brain proteomics | pQTL | MSBB_proteomics_qtl |
The flagship paper also used these datasets for fine-mapping (syn69670592), TWAS models (syn69670600) and colocalization (syn69670597, syn69865816).