Strong association of de novo copy number mutations with autism

Abstract

We tested the hypothesis that de novo copy number variation (CNV) is associated with autism spectrum disorders (ASDs). We performed comparative genomic hybridization (CGH) on the genomic DNA of patients and unaffected subjects to detect copy number variants not present in their respective parents. Candidate genomic regions were validated by higher-resolution CGH, paternity testing, cytogenetics, fluorescence in situ hybridization, and microsatellite genotyping. Confirmed de novo CNVs were significantly associated with autism (P = 0.0005). Such CNVs were identified in 12 out of 118 (10%) of patients with sporadic autism, in 2 out of 77 (3%) of patients with an affected first-degree relative, and in 2 out of 196 (1%) of controls. Most de novo CNVs were smaller than microscopic resolution. Affected genomic regions were highly heterogeneous and included mutations of single genes. These findings establish de novo germline mutation as a more significant risk factor for ASD than previously recognized.

Fig. 1

Procedure for the detection of de novo CNVs. The flow diagram describes the step-by-step procedure for identifying regions of altered copy number that are present in a child and not in the biological parents.

Fig. 2

Detection and validation of a spontaneous deletion in a patient with Asperger syndrome. CNVs were detected in patient scans using the standard HMM. Parents were ascertained and determined to have no change in copy number using an algorithm with relaxed criteria. These second detection criteria included (1) detection by an HMM with reduced stringency (false-positive expectation set at 1%), and median probe ratio ≤0.91 or ≥1.1. Probe ratio data are shown for the patient SK-135 (blue) and the mother (red) and father (green) for 85K ROMA (A) and 244K Agilent CGH (B) platforms. The map of annotated known genes was obtained from the UCSC Genome Browser, May 2004 assembly (30). The genomic region estimated to be deleted is shown in (C) outlined in red.