Protein QTL (pQTL) Resources on FunGen-AD Resources

EFIGA CSF proteomics QTL

Mon, 01 Jan 0001 00:00:00 +0000

EFIGA CSF proteomics QTL#

Contact#

Zining Qi

Knight ADRC brain proteomics QTL

Mon, 01 Jan 0001 00:00:00 +0000

Knight ADRC brain proteomics QTL#

Charles F. And Joanne Knight Alzheimer’s Disease Research Center (Knight-ADRC)

Please refer to this document for an overview of the Knight project.

Contact#

Zining Qi(zq2209@cumc.columbia.edu)

Study Overview#

Study name : Knight ADRC brain proteomics QTL
Study Description : Charles F. And Joanne Knight Alzheimer’s Disease Research Center (Knight-ADRC) brain proteomics QTL analysis summary statistics using the FGC xQTL pipeline.

Samples’ phenotype information (sex, age, race etc.) can be found in Knight metadata, see “Other information” section in this document

Knight ADRC CSF proteomics QTL

Mon, 01 Jan 0001 00:00:00 +0000

Knight ADRC CSF proteomics QTL#

Contact#

Zining Qi

MSBB brain proteomics QTL

Mon, 01 Jan 0001 00:00:00 +0000

MSBB brain proteomics QTL#

Contact#

Minghui Wang

Links to QTL analysis notebooks#

See notebooks in:

https://github.com/cumc/xqtl-analysis/tree/main/analysis/Wang_Columbia/MSBB/pQTL

The notebooks in this folder contain the commands and data wrangling codes for analysis of the expression data in MSBB. (data wrangling exist because not all data are processed using the xqtl-pipeline from the beginning and need to be reformatted to fit one intermediate step of the pipeline).

Association data preprocessing#

genotype_preprocessing.ipynb shows the commands used for genotype processing and preparation steps.
phenotype_preprocessing.ipynb shows the commands used for the phenotype data processing and preparation steps.
covariate_preprocessing.ipynb shows the commands used for the covariate data processing and preparation steps. Genotype data and covariate data are the same for MSBB.

Association scan using TensorQTL and summary statistics standardization#

TensorQTL.ipynb provides the pipeline to generate TensorQTL cis association results for all QTLs.
MSBB_pQTL provides information about the input files for TensorQTL cis association in the base_params variable in [generate_command_1].

Path(s) to cis-QTL association testing#

output of TensorQTL.ipynb

ROSMAP DLPFC protein expression QTL

Mon, 01 Jan 0001 00:00:00 +0000

ROSMAP DLPFC protein expression QTL#

Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC protein expression.

Please refer to this document for an overview of the ROSMAP project.

Contact#

Zining Qi(zq2209@cumc.columbia.edu)

Study Overview#

Study name : ROSMAP DLPFC proteomics QTL
Study Description : Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) proteomics QTL analysis summary statistics using the FGC xQTL pipeline.

Samples’ phenotype information (sex, age, race etc.) can be found in ROSMAP metadata, see “Other information” section in this document