README for GWAMA meta-analyses (performed for European, African, Hispanic/Latino, and East Asian specific, as well as trans-ethnic analyses (to obtain effect estimates))
Columns:
rs_number - unique marker identification across input files (chromosome:position_allele1_allele2, with alleles listed in lexicographical order or based on indel length)
reference_allele - Effect allele
other_allele - Non effect allele
eaf - effect allele frequency
beta - Overall effect size/beta value for meta-analysis
se - standard error
beta_95L - Lower 95% CI for beta
beta_95U - Upper 95% CI for beta
z - Z-score
p-value - Meta-analysis p-value
_-log10_p-value - Absolut value of logarithm of meta-analysis p-value to the base of 10.
q_statistic - Cochran's heterogeneity statistic
q_p-value - Cochran's heterogeneity statistic's p-value
i2 - Heterogeneity index I2 by Higgins et al 2003
n_studies - Number of studies with marker present
n_samples - Number of samples with marker present
effects - Summary of effect directions ('+' - positive effect of reference allele, '-' - negative effect of reference allele,'?' - missing data)
README for MR-MEGA meta-analyses (main trans-ethnic analyses)
Columns:
MarkerName - unique marker identification across input files (Chromosome:Position_allele1_allele2, with alleles listed in lexicographical order or based on indel length)
Chromosome - Marker chromosome
Position - Marker position (base pair), build 37
EA - Effect allele
NEA - Non effect allele
EAF - average effect allele frequency (weighted by the samplesize of each input file)
Nsample - total number of samples
Ncohort - total number of cohorts, where the marker was present
Effects - effect direction across cohorts (+ positive effect of effect allele, '-' - negative effect of effect allele,'?' - missing data)
beta_0 - effect of intercept meta-regression
se_0 - standard error of intercept meta-regression
beta_1 - effect of first PC of meta-regression
se_1 - standard error of the effect of first PC of meta-regression
beta_2 - effect of second PC of meta-regression
se_2 - standard error of the effect of second PC of meta-regression
beta_3 - effect of fourth PC of meta-regression
se_3 - standard error of the effect of fourth PC of meta-regression
beta_4 - effect of fourth PC of meta-regression
se_4 - standard error of the effect of fourth PC of meta-regression
chisq_association - chisq value of the association
ndf_association - number of degrees of freedom of the association
P.value_association - p-value of the association
chisq_ancestry_het - chisq value of the heterogeneity due to different ancestry
ndf_ancestry_het - ndf of the heterogeneity due to different ancestry
P.value_ancestry_het - p-value of the heterogeneity due to different ancestry
chisq_residual_het - chisq value of the residual heterogeneity
ndf_residual_het - ndf of the residual heterogeneity
P.value_residual_het - p-value of the residual heterogeneity
lnBF - log of Bayes factor
Comments - reason why marker was not analysed (blank for our analysis)
Please note that p-values in the uploaded MR-MEGA results have been corrected as suggested by MR-MEGA creators using the script below in R
data$P.value_association <- pchisq(data$chisq_association, data$ndf_association, lower.tail=FALSE)
data$P.value_ancestry_het <- pchisq(data$chisq_ancestry_het, data$ndf_ancestry_het, lower.tail=FALSE)
data$P.value_residual_het <- pchisq(data$chisq_residual_het, data$ndf_residual_het, lower.tail=FALSE)
UK Biobank South Asian analysis
The only South Asian participants in our BCX analyses were from UK Biobank, so these results are presented separately (single cohort, not a meta-analysis) and are included as a contributing cohort to the trans-ethnic analyses.
Columns:
cptid- Chromosome:Position ID
STRAND - strand, + or -
EFFECT_ALLELE - effect allele
OTHER_ALLELE - non-effect allele
EAF - effect allele frequency
IMPUTATION - imputation rsq (metric of imputation quality)
BETA - effect size
SE - standard error of effect size
PVAL - p-value
N - number of samples
MAC - minor allele count
Unique_ID- unique marker identification across input files (Chromosome:Position_allele1_allele2, with alleles listed in lexicographical order or based on indel length)
CHR - Marker chromosome
BP- Marker position (base pair), build 37
Chromosome - Marker chromosome
Position - Marker position (base pair), build 37