Combining SNP-to-gene linking strategies to pinpoint disease genes and assess disease omnigenicity

Datasets and codes to replicate the results and Figures of "Combining SNP-to-gene linking strategies to pinpoint disease genes and assess disease omnigenicity".

#baselineS2Gannots.tgz
This compressed file contains S2G-derived and cS2G SNP annotations and LD scores for critical gene sets and all genes.
This compressed file contains s-ldsc outputs of the baseline-S2G model and the baseline-S2G model with the cS2G-derived SNP annotation.

#cS2G_1000GEUR.zip
This compressed file contains cS2G scores for 9,997,231 SNPs with a minor allele count >=5 in a 1000 Genomes Project European reference panel (same as reference SNPs used in S-LDSC) (see file allsnps.txt.gz for a complet list).
SNP: SNP ID
GENE: GENE ID
cS2G: cS2G score
INFO: S2G scores for the 10 main functional S2G (including the 7 cS2G constituent strategies)

#cS2G_UKBB.zip
This compressed file contains cS2G scores for 19,476,620 SNPs with a minor allele count ≥0.1% in the UK Biobank (see file allsnps.txt.gz for a complet list).
SNP: SNP ID
GENE: GENE ID
cS2G: cS2G score
INFO: S2G scores for the 10 main functional S2G (including the 7 cS2G constituent strategies)

#code.zip
This compressed file contain codes to replicate the results of Gazal et al. 2022 Nat Genet

#critical_gene_sets.zip
This compressed file contains genes of critical gene sets
list_genes_qc.txt.gz: contains information on all the 19,995 genes analyzed
training_constrained_conserved.txt.gz: training critical gene set; contains list of genes with constrained exons and conserved promoters
validation_popsexopro_*: validation critical gene sets; contain list of genes with highest pops score

#figures_paper.zip
This compressed file contains the code (figures.r) and datasets (figure*txt) to reproduce figures of the paper

#finemapping_cS2G_UKBB.zip
This compressed file contains cS2G score for 138,716 potentially causal SNP-gene-disease triplets inferred from causal SNP-disease pairs with PIP>0.05 from functionally informed fine-mapping of 49 UK Biobank diseases/traits.
CHR: Chromosome
BP: Position (hg19)
SNP: SNP ID
DISEASE.TRAIT: PHENOTYPE
PIP: Posterior inclusion probability
GENE: Gene ID
cS2G: cS2G score
INFO: S2G scores for the 10 main functional S2G (including the 7 cS2G constituent strategies)
This compressed file also contains a beta2 directory with PolyFun outputs for each traits (used in the omnigenicity analyses)

#gwas_catalog_cS2G.zip
This compressed file contains cS2G score for 78,499 potentially causal SNP-gene-disease triplets from the NHGRI-EBI GWAS catalog (accessed file: gwas_catalog_v1.0-associations_e100_r2021-02-25.txt)
PUBMEDID: PUBMED ID
DISEASE.TRAIT: PHENOTYPE
CHR: Chromosome
POS: Position (hg19)
SNP: SNP ID
GENE: Gene ID
cS2G: cS2G score
INFO: S2G scores for the 10 main functional S2G (including the 7 cS2G constituent strategies)

#pergeneh2_cS2G_UKBB.zip
This compressed file contains per gene heritability for 19,995 genes in 49 UK Biobank traits
GENE: name of the gene
h2gene: heritability linked to genes using cS2G
Mgene: sum of the linking scores for SNPs with a beta2>0
h2gene_common: heritability of common SNPs linked to genes using cS2G
Mgene_common: sum of the linking scores for common SNPs with a beta2>0
h2gene_lowfreq: heritability of low-frequency SNPs linked to genes using cS2G
Mgene_lowfreq: sum of the linking scores for low-frequency SNPs with a beta2>0

#S2G_original.zip
This compressed file contains original S2G startegies that we computed (fine-mapped eQTLs), obtained through personal coomunication (Cicero), or accessed online.

#sumstats_63.zip
This compressed file contains the 63 independent summary statistics, and additional blood/immune traits

#sumstats_UKBB122K.zip
This compressed file contains the 49 UK BiobanK summary statistics computed on N=122K and used in the omnigenicity analyses