Pleiotropy-informed risk loci for ALS

Using an adapted cFDR method⁹ that allows shared controls between cohorts²², we estimated per-SNP cFDR given LD score-corrected⁸ schizophrenia GWAS P-values for ALS mixed linear model summary statistics calculated in a dataset excluding Finnish and German cohorts (in which suspected control overlap could not be determined), but including all other overlapping samples (totalling 5,582). To correct for the relationship between LD and GWAS test statistics, schizophrenia summary statistics were residualized on LD score by subtracting the product of each SNP's LD score and the univariate LD score regression coefficient for schizophrenia. cFDR values conditioned on these residualized schizophrenia GWAS P-values were calculated for mixed linear model association statistics calculated at 6,843,670 SNPs genotyped in 10,147 ALS cases and 22,094 controls. Pleiotropic genomic loci were considered statistically significant if cFDR<0.01 (following Andreassen et al.⁹) and were clumped with all neighbouring SNPs based on LD (r²>0.1) in the complete ALS dataset. Associated cFDR genomic regions were then mapped to the locations of known RefSeq transcripts in human genome build GRCh37. Genome-wide cFDR values were also tested for enrichment in 9,711 gene sets included in the MAGENTA software package (version 2.4, July 2011) and derived from databases such as Gene Ontology (GO, http://geneontology.org/), Kyoto Encyclopedia of Genes and Genomes (KEGG, http://www.kegg.jp/), Protein ANalysis THrough Evolutionary Relationships (PANTHER, http://www.pantherdb.org/) and INGENUITY (http://www.ingenuity.com/). SNPs were mapped to genes including 20 kb up- and downstream regions to include regulatory elements. The enrichment cutoff applied in our analysis was based on the 95th percentile of gene scores for all genes in the genome. The null distribution of gene scores for each gene set was based on 10,000 randomly sampled gene sets with equal size. MAGENTA uses a Mann–Whitney rank-sum test to assess gene-set enrichment³⁹.