Additional file 2.

Allele frequencies of variants detected by resequencing in four DLX genes and DLX1/2 intergenic enhancers. The allele frequency of the minor allele is presented for 161 autism probands (autism sample), 58 normal siblings of 58 autism probands (non-autism sample), and 188 samples from the NIGMS/NHGRI Polymorphism Discovery Resource (PDR sample). Selected variants were assayed in the PD sample, as described in the text. Variants from other autism studies are designated in the Variant column, with numbers of samples tested shown in the Autism Sample column. *, Bacchelli et al., 2003. [reference [32] **, Nabi et al., 2003 [reference [40]. The "intron 1 C/T" SNP currently maps to intron 2, and is also known as rs3801290, and was assayed in 221 affected sibling pairs and 210 discordant sibling pairs in 196 AGRE families. †, a variant reported at dbSNP within the region we sequenced, but that was not seen in our dataset. Of note, DLX2 SNP-1, a common SNP (rs743605) was found to differ significantly in allele frequency between the autistic probands and the polymorphism discovery sample (χ2 = 4.43, df = 1, p = 0.04). However, this SNP has also been genotyped as part of the HapMap project in a sample of 30 CEPH trios, and the minor allele frequency was found to be 0.47, essentially identical to our autism sample. This discrepancy is likely due to the heterogeneous population composition of the polymorphism discovery sample, which is approximately 26% each of European-American, African-American, and Asian-American populations, with smaller contributions of Mexican-American and Native-American samples (Collins, et al., 1998, Genome Res. 8, 1229–1231).

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Hamilton et al. BMC Genetics 2005 6:52   doi:10.1186/1471-2156-6-52