We also analyzed our data for association signals at candidate genes or regions with prior evidence of involvement in autism. Although there are few well-replicated associations of biological candidate genes, there are many rare genetic variants, diseases, and syndromes associated with autism. Most of these loci have not been systematically assessed to see whether common variation in the gene or region might contribute to autism. We assessed four categories of candidate loci: 1) genes with previous evidence for association with common variation, 2) genes implicated by rare variants leading to autism, 3) genes causing Mendelian diseases associated with autism, and 4) regions where microdeletion or microduplication syndromes are associated with autism. For each gene, we included all SNPs passing basic quality criteria within 2 kb of the transcript.
