README:
Meta-analysis of genome-wide association studies for neuroticism in 449,484 individuals identifies novel genetic loci and pathways (Nagel et al., Nature Genetics, 2018).
# Neuroticism
We performed GWAS in PLINK using a linear regression model. Subsequently, we conducted meta-analyses on these UKB neuroticism results, the 23andMe neuroticism data and neuroticism data from the GPC1. Note that the GWAS meta-analysis summary statistics presented here do NOT include the 23andMe data (due to 23andMe data-sharing policy).
# Depression
We performed GWAS on a depressive symptoms phenotype in PLINK using a linear regression model. Subsequently, we conducted meta-analyses on these UKB results, the 23andMe depression data and depression data from the PGC. Note that the GWAS meta-analysis summary statistics presented here do NOT include the 23andMe data (due to 23andMe data-sharing policy).
# Neuroticism subclusters
Results are based on UKB data only. GWAS was conducted in PLINK using a linear regression model.
# Four summary statistics files:
- neuroticism (N = 449,484 - 59,206 = 390,278 individuals)
- depression (N = 688,809 - 307,354 = 381,455 individuals)
- depressed affect subcluster (N = 357,957 individuals)
- worry subcluster (N = 348,219 individuals)
Columns (not all are present for each sumstats file, see note bottom of file):
SNP: rsID of the variant
UNIQUE_ID: unique SNP ID based on chromosome, position and alleles
CHR: chromosome number
POS: base pair position reported on GRCh37
A1: effect allele
A2: non-effect allele
EAF: effect allele frequency (the neuroticism and depression meta-analyses have: EAF_UKB, indicating the EAF for a given variant in the UKB data exclusively)
MAF: Minor allele frequency (the neuroticism and depression meta-analyses have: MAF_UKB, indicating the MAF for a given variant in the UKB data exclusively)
Z: z-score from the meta-analysis
BETA: beta coefficient *
SE: standard error of the beta *
P: P-value
N_analyzed: per-SNP sample size
INFO: info score (SNP quality measure)
* Beta/SE were calculated from METAL Z-scores using the formula from Zhu et al (Nature Genetics, 2016):
Beta = Zscore / sqrt( 2 * MAF * ( 1 - MAF) * ( N + Zscore^2 ) )
SE = 1 / sqrt( 2 * MAF * ( 1 - MAF ) * ( N + Zscore^2 ) )
NOTE. For the neuroticism sum-score and the depression meta-analysis results, no BETA/SE are given.
METAL only provides Z-statistics, and since we only have MAF for the individual samples the BETAs
could not be calculated.