Genome-wide genotype data were derived from a previously published GWAS of sporadic ALS in seven countries (The Netherlands, Belgium, France, Ireland, United Kingdom, Sweden, United States) [7]. All patients fulfilled the 1994 El Escorial criteria for probable or definite ALS [27]. Cohorts for which genome-wide SNP data were available were included. For both the discovery and replication set, genotype files with Illumina Beadchip data (HumanHap 300K, HumanCNV 370K, HumanHap 550K or HumanHap 610K platforms) were merged and the following quality control measures were taken. Only SNPs common to all cohorts were used. Triallelic and C/G or A/T SNPs were excluded. Genotype files were merged, and after each merge, a flipscan (scan for possible allele swaps) was performed in PLINK v1.07 [28]. SNPs with call rate <95%, minor allele frequency <5%, deviation from Hardy-Weinberg equilibrium in controls (p<1×10−4), or with differing heterozygosity or missing rates between cases and controls were excluded. Duplicate samples, samples with a genotyping rate <95%, samples without gender information, or samples where the genotypic gender did not match the phenotype file gender were excluded. LD-based SNP pruning
