NG00102 - Genomic atlas of the proteome from brain, CSF and plasma prioritizes proteins implicated in neurological disorders


Understanding the tissue-specific genetic controls of protein levels is essential to uncover mechanisms of post-transcriptional gene regulation. In this study, we generated a genomic atlas of protein levels in three tissues relevant to neurological disorders (brain, cerebrospinal fluid and plasma) by profiling thousands of proteins from participants with and without Alzheimer’s disease. We identified 274, 127 and 32 protein quantitative trait loci (pQTLs) for cerebrospinal fluid, plasma and brain, respectively. cis-pQTLs were more likely to be tissue shared, but trans-pQTLs tended to be tissue specific. Between 48.0% and 76.6% of pQTLs did not co-localize with expression, splicing, DNA methylation or histone acetylation QTLs. Using Mendelian randomization, we nominated proteins implicated in neurological diseases, including Alzheimer’s disease, Parkinson’s disease and stroke. This first multi-tissue study will be instrumental to map signals from genome-wide association studies onto functional genes, to discover pathways and to identify drug targets for neurological diseases.

This dataset includes Individual-level data (proteomics + array-based genotype data after imputation), consent information, and summary statistics, below are the README files
Individual-level data README 
Summary statistics README

Individual-level data (size - 5GB) is accessible through formal data request.

Summary statistics (pQTL) data is freely available. The data exceeds 500Gb, so please email to set up an FTP transfer of the data.

This dataset is part of the Knight ADRC Collection. Other datasets in this collection can be found at:

The summary statistics for all the analyses can be easily explored in the ONTIME (Online Neurodegenerative Trait Integrative Multi-Omics Explorer) pheweb (

Peer-reviewed publication available via:

Molecular Data Type

Submission date: 



(used in pQTL analysis/manuscript)
(giving consent to share with public)
 CSF [total=835] 217 / 614 / 4 [total=817] 201 / 612 / 4
Plasma [total=529] 168 / 357 / 4 [total=528] 167 / 357 / 4
Brain [total=380] 248 / 24 / 108 [total=343] 234 / 22 / 87


PI Information