FunGen-xQTL Resources

ROSMAP DLPFC gene expression QTL

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

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

Cohort
ROSMAPReligious Orders Study and Rush Memory and Aging Project
Modality
eQTLQTL results
Tissue or cell type
DLPFC
Sample size
839 samples
Release status
Stagednot yet verified
Access
ControlledData use certificate
Lead analysts
Shrishtee Kandoi, Frank GrennSelect a name to email them
Source data
ROSMAP DLPFC Expression
Open syn69670592 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
Synapsesyn69670592ControlledResults described below

Other Synapse IDs on this page syn69670600 syn69670611 syn69670597 syn69865816 syn69670630

shell
pip install synapseclient
synapse login
synapse get -r syn69670592

Contact

Shrishtee Kandoi; Frank Grenn

Study Overview

  • Study name : ROSMAP DLPFC eQTL
  • Study Description : Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) eQTL 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

Analysis Details

Analysis Status

TransQTL association: Finished.

Sample size tracking through the analysis workflow

StepSample Size
Raw data1141
After overlapping with ROSMAP WGS839

QC and Normalization Details for Phenotype Data

Brain multi-region RNA-seq data was processed with the xQTL-pipeline, for analysis details please check records here: eQTL

Genotype parameters

  • Kinship coefficient for related individuals: 0.0625
  • Minor allele count cutoff for single variant analysis: 5
  • Variant level missingness threshold: 0.1
  • Sample level missingness threshold: 0.1
  • HWE filter: 1e-06

Covariate parameters

PCA analysis:

  • MAF for PCA: 0.01
  • LD pruning via PLINK for PCA analysis: window 50, shift 10, r2 0.1
  • Tolerance of missingness in covariates: 0.3
  • number of pc that captured more than 70% PVE were kept

PEER analysis (Default values from PEER software):

  • The number of max iteration: 1000
  • Prior parameter Alpha_a: 0.001
  • Prior parameter Alpha_b: 0.1
  • Prior parameter Eps_a: 0.1
  • Prior parameter Eps_b: 10.0
  • Tolerance parameter tol: 0.001
  • Tolerance parameter var_tol: 0.00001
  • minimum variance explained criteria to drop factors while training r2_tol: False
  • Convergence mode: “fast”

Final covariates: Sex, Age at death, PMI, PCs(13), PEER factors(60)

TensorQTL association scan parameters

  • cis window for the up and downstream radius to analyze around the region of interest, in units of bp: 1000000
  • Minor allele count cutoff: 5
  • Minor allele frequency cutoff: 5/(2N), where N is the number of samples in the analysis. The pipeline computes N from the covariate file, so the cutoff differs between datasets.

See notebooks in:

The notebooks in this folder contain the commands, data wrangling codes for analysis of the eQTL and sQTL data in ROSMAP (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), log files and some of the results visualizations produced by the pipeline when processing and analyzing the RNA-seq expression in the Dorsolateral Prefrontal Cortex region of the ROSMAP brain data (DLPFC-ROSMAP).

Association data preprocessing

phenotype preprocessing and genotype preprocessing can be run in parallel but covariate preprocessing needs to be done last since it requires both phenotype data and PCs from PCA in genotype preprocessing.

  • genotype_qc.ipynb shows the commands used for genotype processing and preparation steps, including why we decided not to remove any outliers.
    • Mostly contains the commands used to run the pipeline, but includes some pre-pipeline data wrangling.
    • This includes QC, PCA, and GRM steps
  • phenotype_preprocessing_eqtl.ipynb shows the commands used for the phenotype data processing and preparation steps.
    • As above, it mostly contains the commands used to run the pipeline, but includes some pre-pipeline data wrangling.
    • This includes quantification steps, QC, annotation, and residual expression steps
  • covariate_preprocessing_eQTL.ipynb shows the commands used for the covariate data processing and preparation steps.
    • This includes PEER factor analysis steps and merging the PEER factors to covariates in raw data and PCA.
  • rnaSeq_PEER.diag.pdf PEER factor analysis result

Association scan using TensorQTL and summary statistics standardization

  • association_scan_eQTL.ipynb provides information about the TensorQTL cis association scan.(might be confused when there are multiple versions)
  • TensorQTL.ipynb provides the pipeline to generate TensorQTL cis association results for all QTLs.
  • ROSMAP_CUIMC1_bulk_eQTLprovides information about the input files for AC/DLPFC/PCC TensorQTL cis association in the base_params variable in [generate_command_1].

SuSiE univariate fine mapping

Dataset Details

Path(s) to genotype matrix

output of genotype_qc.ipynb

Path(s) to QTL results

empirical_files:

text
$ls -lh *.txt
-rw-r--r-- 1 xc2610 xc2610 235K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.10.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 312K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.11.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 324K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.12.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 124K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.13.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 186K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.14.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 214K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.15.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 287K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.16.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 349K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.17.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 104K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.18.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 378K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.19.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 573K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.1.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 151K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.20.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610  62K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.21.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 150K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.22.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 392K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.2.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 330K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.3.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 218K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.4.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 282K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.5.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 304K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.6.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 279K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.7.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 220K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.8.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 230K Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.9.emprical.cis_sumstats.txt
-rw-r--r-- 1 xc2610 xc2610 7.6M Mar  2 00:02 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.emprical.cis_sumstats.txt

norminal_qced_files:

text
ls -lh *.txt
-rw-r--r-- 1 xc2610 xc2610 1.8G Jan 23 12:05 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.10.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 2.1G Jan 23 12:08 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.11.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 2.4G Jan 23 12:13 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.12.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 936M Jan 23 12:15 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.13.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 1.4G Jan 23 12:17 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.14.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 1.4G Jan 23 12:19 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.15.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 2.1G Jan 23 12:23 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.16.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 2.6G Jan 23 12:27 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.17.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 735M Jan 23 12:30 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.18.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 3.2G Jan 23 12:35 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.19.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 3.8G Jan 23 11:28 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.1.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 1.2G Jan 23 12:37 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.20.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 485M Jan 23 12:38 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.21.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 1.3G Jan 23 12:40 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.22.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 2.6G Jan 23 11:36 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.2.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 2.2G Jan 23 11:41 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.3.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 1.6G Jan 23 11:44 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.4.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 1.9G Jan 23 11:48 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.5.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 2.7G Jan 23 11:52 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.6.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 2.0G Jan 23 11:56 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.7.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 1.6G Jan 23 11:58 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.8.norminal.cis_long_table.txt
-rw-r--r-- 1 xc2610 xc2610 1.7G Jan 23 12:01 dlpfc_batch_all.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.processed_phenotype.per_chrom_dlpfc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.9.norminal.cis_long_table.txt

Path(s) to cis-QTL association testing

output of TensorQTL.ipynb

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

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

Path(s) to TWAS models

Pre-trained TWAS weight models for this context: syn69670600

Quantile TWAS (qTWAS) models: syn69670611

Path(s) to colocalization with SuSiE-coloc / ColocBoost

Multi-context colocalization models (ColocBoost): syn69670597

AD GWAS–xQTL colocalization results: syn69865816

AD GWAS–xQTL colocalization models: syn69670630

Analyses

  • cis-QTLDone
  • cTWASDone

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