Association and mutation analyses of 16p11.2 autism candidate genes

Abstract

Background: Autism is a complex childhood neurodevelopmental disorder with a strong genetic basis. Microdeletion or duplication of a approximately 500-700-kb genomic rearrangement on 16p11.2 that contains 24 genes represents the second most frequent chromosomal disorder associated with autism. The role of common and rare 16p11.2 sequence variants in autism etiology is unknown.

Methodology/principal findings: To identify common 16p11.2 variants with a potential role in autism, we performed association studies using existing data generated from three microarray platforms: Affymetrix 5.0 (777 families), Illumina 550 K (943 families), and Affymetrix 500 K (60 families). No common variants were identified that were significantly associated with autism. To look for rare variants, we performed resequencing of coding and promoter regions for eight candidate genes selected based on their known expression patterns and functions. In total, we identified 26 novel variants in autism: 13 exonic (nine non-synonymous, three synonymous, and one untranslated region) and 13 promoter variants. We found a significant association between autism and a coding variant in the seizure-related gene SEZ6L2 (12/1106 autism vs. 3/1161 controls; p = 0.018). Sez6l2 expression in mouse embryos was restricted to the spinal cord and brain. SEZ6L2 expression in human fetal brain was highest in post-mitotic cortical layers, hippocampus, amygdala, and thalamus. Association analysis of SEZ6L2 in an independent sample set failed to replicate our initial findings.

Conclusions/significance: We have identified sequence variation in at least one candidate gene in 16p11.2 that may represent a novel genetic risk factor for autism. However, further studies are required to substantiate these preliminary findings.

Figure 1. SEZ6L2 is expressed in mouse and human central nervous systems.

In situ analyses in whole mouse embryos demonstrate that Sez6l2 mRNA is expressed in the developing brain and spinal cord at e10.5 (A) and e12.5 (B). Human SEZ6L2 transcript distribution was assayed in 18- and 19-week-old human brains sectioned in either coronal orientation in subjects 1137 (C), 1110 (D, E) and in the sagittal orientation in subject 4889 (F). SEZ6L2 is enriched in the cortical plate in the post mitotic neuron, in the ventricular zone, in the hippocampus, thalamus, ganglionic eminence, basal ganglia, and amygdala and at lower levels in the pons and the putamen. Emulsion picture of the dentate gyrus showing cellular specificity within the hippocampus (K). Sense controls tested on adjacent sections (not shown) gave no signal. Am, Amygdala; BG, Basal ganglia; CP, Cortical plate; DG, Dentate gyrus; GE, Ganglionic eminence; Hi, Hippocampus; Pu, Putamen; Th, Thalamus.