GWAS ILAE 2018 16LOCI
This page contains 10 summary statistics files (3 METAL files and 7 BOLT-LMM files) to accompany the epilepsy GWAS paper by the International League Against Epilepsy Consortium on Complex Epilepsies, published in Nature Communications.
METAL files (trans-ethnic meta-analyses of 3 broad epilepsy phenotypes) with the following columns:
- - CHR - chromosome
- - BP - physical (base pair) position
- - MarkerName - rs number
- - Allele1 - the first allele for this marker in the first file where it occurs; used as the effect allele
- - Allele2 - the second allele for this marker in the first file where it occurs; used as the non-effect allele
- - Freq1 - frequency of the first allele
- - FreqSE - standard error of the frequency of the first allele
- - Weight - the sum of the individual study weights for this marker. Individual study weights are calculated with the formula: 4 / (1/[# of cases] + 1/[# of controls])
- - Z-score - the combined z-statistic for this marker
- - P-value - meta-analysis p-value
- - Direction - summary of effect direction for each study (see below), with one '+' or '-' per study
- - HetISq - I^2 statistic which measures heterogeneity on scale of 0-100%
- - HetChiSq - chi-squared statistic in simple test of heterogeneity
- - df - degrees of freedom for heterogeneity statistic
- - HetPVal - P-value for heterogeneity statistic
- - SNP - rs number
- - CHR - chromosome
- - BP - physical (base pair) position
- - GENPOS - genetic position either from bim file or interpolated from genetic map
- - ALLELE1 - first allele in bim file (usually the minor allele), used as the effect allele
- - ALLELE0 - second allele in bim file, used as the non-effect (reference) allele
- - A1FREQ - frequency of first allele
- - F_MISS - fraction of individuals with missing genotype at this SNP
- - BETA - effect size from BOLT-LMM approximation to infinitesimal mixed model
- - SE - standard error of effect size
- - P_BOLT_LMM_INF - infinitesimal mixed model association test p-value
- all_epilepsy_METAL.gz
- CAE_BOLT-LMM_final.gz
- focal_epilepsy_METAL.gz
- focal_HS_BOLT-LMM_final.gz
- focal_lesion_negative_BOLT-LMM_final.gz
- focal_other_lesion_BOLT-LMM_final.gz
- generalised_epilepsy_METAL.gz
- GTCS_BOLT-LMM_final.gz
- JAE_BOLT-LMM_final.gz
- JME_BOLT-LMM_final.gz
- README.txt
BOLT-LMM files (Caucasian-only analyses of 7 epilepsy subphenotypes) with the following columns: