To explore the converging biology hypothesis of ASD we examined enrichment within gene-sets derived from previously implicated genes and pathways (candidate gene-set) using the Interval-based Enrichment Analysis Tool for Genome Wide Association Studies (INRICH) method [38]. To identify new biology, we examined gene-set enrichment using established canonical gene-sets including gene ontology and the Kyoto Encyclopedia of Genes and Genomes (KEGG) gene-sets. INRICH is a pathway-based GWAS tool that tests for enrichment of association signals against predefined gene-sets across independent genomic intervals. INRICH analysis was performed in interval mode. The interval mode describes an enrichment statistic E for each gene-set that is the number of intervals that overlap at least one target gene in the gene-set. The significance of E is approximated using permutation and an empirical P value is generated from a null set of intervals which match the interval size, overlapping gene, and SNP number to the original input intervals. A detailed description of the gene-set compositions for the candidate gene-set and canonical gene-sets is reported in the Additional file 1. A summary of the sources of each candidate gene-set are also reported in Additional file 1: Table S1.
