devBrain_xQTL_sumstats_part1 Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain

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: devbrainhub.gandallab.org Github: github.com Citation:  Cindy Wen et al., Science 384, eadh0829(2024). DOI: 10.1126/science.adh0829     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)