DOI: 10.5281/zenodo.12729266
title: devBrain_xQTL_sumstats_part1
title: Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain

description: Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain

This repository contains summary statistics for gene, isoform, and splicing quantitative trait loci (cis-xQTLs) in the developing human brain across 672 unique samples from 4 to 39 postconception weeks spanning European (EUR), African-American (AFR), and Latino/admixed American (AMR) ancestries.

 

Web Portal: https://devbrainhub.gandallab.org/

Github: https://github.com/gandallab/devBrain_xQTL

Citation:  Cindy Wen et al., Science 384, eadh0829(2024). DOI: 10.1126/science.adh0829

 

 
description: README.md

MJG 7/24/24

eQTLs

cis-eQTL Summary Statistics: All Samples combined





cis-eQTLs from nominal pass and permutation-based analysis (both FDR correcte) using 90 hidden covariates




see FastQTL and QTLtools papers & documentation for further details







devBrain_eQTL_ALL_nominal_90HCP_FDR_0.05.txt.gz





pid = ID of the tested molecular phenotype (in this particular case, the gene I)




sdi = ID of the tested variant (in this case a SN)




dist= Distance between the variant and the phenotype in bp




npval = The nominal p-value of association slope = The slope associated with the nominal p-value of association




fdr = fdr-corrected p-value






devBrain_eQTL_ALL_permutation_90HC_FDR_0.05.txt.gz





pid=ID of the tested molecular phenotype (in this particular case, the gene I)




nvar=Number of variants tested in cis for this phenotype




shape1=MLE of the shape1 parameter of the Beta distribution




shape2=MLE of the shape2 parameter of the Beta distribution




dummy=Dummy variable




sid=ID of the best variant found for this molecular phenotypes (i.e. with the smallest p-valu)




dist=Distance between the molecular phenotype - variant pair




npval=The nominal p-value of association that quantifies how significant from 0, the regression coefficient is




slope=The slope associated with the nominal p-value of association




ppval=A first permutation p-value directly obtained from the permutations with the direct method. This is basically a corrected version of the nominal p-value that accounts for the fact that multiple variants are tested per molecular phenotype.




bpval=A second permutation p-value obtained via beta approximation. We advice to use this one in any downstream analysis.




qval=fdr-corrected bpval




pval_nominal_threshold=npval corresponding to qval = 0.05






Variants_for_ALL_xQTLmapping_A1effect_A2other.hg19.sorted.removeRel.bim.gz







plink .bim file, A1 = effect allele



cis-eQTL Summary Statistics: Ancestry-Grouped Analyses





devBrain_eQTL_EUR_nominal_50HCP_FDR_0.05.txt.gz




devBrain_eQTL_EUR_permutation_50HCP_FDR_0.05.txt.gz




Variants_for_EUR_xQTLmapping_A1effect_A2other.hg19.sorted.removeRel.bim.gz




devBrain_eQTL_AFR_nominal_25HCP_FDR_0.05.txt.gz




devBrain_eQTL_AFR_permutation_25HCP_FDR_0.05.txt.gz




devBrain_eQTL_AMR_nominal_15HCP_FDR_0.05.txt.gz




devBrain_eQTL_AMR_permutation_15HCP_FDR_0.05.txt.gz



cis-eQTL Summary Statistics: Trimester 1 & 2 Specific Analyses (EUR onl)





trimester1_eQTL_EUR_nominal_FDR_0.05.txt.gz




trimester1_eQTL_EUR_permutation_FDR_0.05.txt




trimester2_eQTL_EUR_nominal_FDR_0.05.txt.gz




trimester2_eQTL_EUR_permutation_FDR_0.05.txt



TWAS (Fusion) and PrediXcan Weights from cis-eQTLs





predixcan_fetal_db.db




TWAS_WEIGHTS_multi_ancestry_LDREF.gz



 

isoQTLs (isoform-level)

cis-isoQTL Summary Statistics: All samples combined





devBrain_isoQTL_ALL_nominal_70HCP_FDR0.05.txt.gz




devBrain_isoQTL_ALL_grouped_permutation_70HCP_FDR0.05.txt.gz







uses grouped permutation scheme from QTLtools



cis-isoQTL Summary Statistics: Ancestry-Grouped Analyses (part 1)





devBrain_isoQTL_AFR_nominal_20HCP_FDR0.05.txt.gz




devBrain_isoQTL_AFR_permutation_20HCP_FDR0.05.txt.gz



(continued in next Zenodo Notebook)