Methods: The participants included 190 cases of DSM-IV-TR diagnosed autistic disorder, and 918 controls of unrelated healthy volunteers recruited from community. Three single nucleotide polymorphisms (SNP) (rs3824067, rs1861972, rs1861973) at the EN2 gene that have been reported to be associated with autism underwent analysis among our studied cohorts. Both UNPHASE and PHASE statistical programs were utilized for evaluating the association of EN2 SNPs to autism base on allelic, genotypic frequencies and haplotype compositions accompanied with goodness of fit method of Chi-square test.Results: Both allelic and genotypic distributions of three polymorphisms were concordant to Hardy-Weinberg equilibrium. Significant differences were found for case vs. community and overall controls. Three-marker haplotype A-A-C of EN2 was identified to have a protective effect for the autism by using UNPHASE (OR=0.23) and PHASE (OR=0.36) programs, indicating the racial difference might confound for EN2 association with autism.
Conclusions: Therefore, more EN2 gene association studies of Han Chinese populations are warranted to confirm this finding.