FunGen-xQTL Resources

ROSMAP DLPFC glycoproteomics QTL

This page documents the glycoproteomics QTL (glycoQTL) analysis of dorsolateral prefrontal cortex (DLPFC) tissue from the Religious Orders Study (ROS) and the Rush Memory and Aging Project (MAP). The ROSMAP study page gives an overview of the cohort.
Cohort
ROSMAPReligious Orders Study and Rush Memory and Aging Project
Modality
glycoQTLQTL results
Tissue or cell type
DLPFC
Sample size
Not recorded on this page
Release status
Stagednot yet verified
Access
ControlledData use certificate
Lead analysts
FunGen-xQTL Analysis Working GroupContact by name
Source data
ROSMAP DLPFC Glycoproteomics
Open syn69865744 in Synapse ↗ Query associations in the xQTL Atlas ↗

Access

Controlled access. Request data access for ROSMAP on the AD Knowledge Portal; you need a Synapse account. See How to get the data.

WhereIDAccessWhat you get
Synapsesyn69865744ControlledResults described below

Other Synapse IDs on this page syn70094703 syn76495192 syn77828034 syn76489398 syn76490205 syn75180848

shell
pip install synapseclient
synapse login
synapse get -r syn69865744

Study overview

  • Study name. ROSMAP glycoproteomics QTL.
  • Description. Summary statistics from the FGC xQTL pipeline for the ROSMAP proteomics QTL analysis.
  • Sample phenotypes. Sex, age, race and other sample information are in the ROSMAP metadata, described under “Other information” on the ROSMAP study page.

Analysis notebooks

Association scan with TensorQTL and summary statistics standardization

  • TensorQTL.ipynb generates the TensorQTL cis association results for all QTL types.
  • ROSMAP_gpQTL lists the input files for the adjusted and unadjusted glycoproteomics cis association, in the base_params variable of generate_command_1.

Where to find the results

Analyses

  • cis-QTLDone
  • SuSiEDone
  • ColocBoostDone
  • TWASDone

Read from the methods: map in this page's metadata header, the same data as the analysis coverage grid.