Analysis of Copy Number Variation within GABRA4

Background: Autism has a strong genetic component but studies over the past decade have demonstrated that the underlying genetics are complex. Previous studies suggest an important role for copy number variants (CNVs) in autism risk and indicate a strong association of de novo copy number mutations with autism. The GABRA4 gene is implicated in autism risk through both cytogenetic alterations in autism patients in the GABR chromosome 4p region and through association with SNPs in the GABRA4 gene in autistic families.  These data point to GABRA4 and potentially other GABR genes in this region as autism candidate genes.

Objectives: To examine the GABRA4 gene for possible disease associated CNVs within or near the GABRA4 gene.

Methods: Using DNA collected from 428 autism family probands and 190 controls, we performed quantitative real-time PCR (qPCR) with unique probes located within or near the GABRA4 gene spanning an area of almost 100 kb to identify the presence of duplications and deletions. We used qPCR of RNAse P as an internal control to measure deviation from diploid copy number.  Results were compared across assays to gauge the approximate CNV size.

Results: Preliminary results showed putative CNVs in GABRA4 in 75 individuals (17.5%).  14 of these individuals (3.3%) were found to have deletions, 49 (11.4%) appear to carry duplications and 12 individuals (2.8%) have potentially complex rearrangements in the region.  Evaluation of the same region in the 190 control individuals showed only 4 individuals with CNVs (2.1%), 2 with deletions and 2 carrying duplications.

Conclusions: Our preliminary results suggest that a larger number of both deletions and duplications occur within GABRA4 in autism probands when compared to controls, suggesting a role in autism etiology.  Validation studies are in progress as well as examination of segregation of the variations with disease status in multiplex families.