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
  • BOLT-LMM files (Caucasian-only analyses of 7 epilepsy subphenotypes) with the following columns:

  • - 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
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