rs10513025 and neighbors are on chromosome 5p15 in a region of LD containing several other ESTs and TAS2R1, a bitter taste receptor (Supplementary Figure 3). The SNPs are ~80 kb upstream of semaphorin 5A (SEMA5A), a gene implicated in axonal guidance and known to be down-regulated in lymphoblastoid cell lines of autism cases versus healthy controls 7. An independent study at Children’s Hospital Boston using whole blood (SWK, LK, ZK, manuscript in preparation) confirms this lower expression (P = 0.0034) of SEMA5A in autism cases versus controls. To more completely evaluate the role of this locus in autism pathogenesis, we evaluated the entirety of 5p15 for copy-number variation. Despite excellent probe coverage throughout the locus, no common or rare copy number variants were detected in the entire AGRE scan in the region of LD surrounding the associated SNPs and the entire SEMA5A locus including 250 kb up and downstream (see Methods).
