MSBB brain methylation QTL · FunGen-xQTL Resources

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	Results described below

shell

pip install synapseclient
synapse login
synapse get -r syn69670592

Contact

Alexandre Pelletier

Links to QTL analysis notebooks

See notebooks in:

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

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 provides steps for PCA analysis for genotype data. Phenotype_preprocessing shows the commands used for the phenotype data processing and preparation steps. Covariates_preprocessing shows the commands used for the covariate data processing and preparation steps. details please see https://github.com/cumc/xqtl-analysis/tree/main/analysis/TCW_BU/MSBB/mqtl/scripts

Association scan using TensorQTL and summary statistics standardization

TensorQTL.ipynb provides the pipeline to generate TensorQTL cis association results for all QTLs.
MSBB_mQTL 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

Path(s) to fine-mapping with fSuSiE / SuSiE RSS model

Fine-mapping model objects (fSuSiE/SuSiE-RSS, .rds) are available in the finemapping models folder (syn69670592).

Path(s) to colocalization

Pairwise colocalization models (SuSiE-coloc): syn69670597

AD GWAS–xQTL colocalization results: syn69865816

AD GWAS–xQTL colocalization models: syn69670630