To replicate our genome-wide significant association signals at the 5p14.1 locus, we examined the association statistics for these markers in a third independently generated and analysed cohort, including 1,390 subjects from 447 autism families genotyped with ~1 million markers on the Illumina HumanHap1M BeadChip (CAP cohort, Table 1). The association signals for all the aforementioned SNPs were replicated in this cohort with the same direction of association, with Pvalues ranging from 0.01 to 2.8 × 10−5 (Table 2). To seek further evidence of replication, we examined association statistics from a fourth independent cohort of 108 ASD cases and 540 genetically matched control subjects, genotyped on the Illumina HumanCNV370 BeadChip, an array with over 300,000 SNP markers (CART cohort, Table 1). Because rs7704909 and rs10038113 were not present in this array platform, we analysed association on imputed genotypes. Most of the SNPs were replicated (P < 0.05) in the CART cohort with the same direction of association (Table 2). Combined analysis on all four data sets indicates that all six SNPs are associated with ASDs, with Pvalues ranging from 7.4 ×
