An integrated analysis of rare CNV and exome variation in Autism Spectrum Disorder using the Infinium PsychArray

Abstract

Autism spectrum disorder (ASD) is a neurodevelopmental condition with a complex and heterogeneous genetic etiology. While a proportion of ASD risk is attributable to common variants, rare copy-number variants (CNVs) and protein-disrupting single-nucleotide variants (SNVs) have been shown to significantly contribute to ASD etiology. We analyzed a homogeneous cohort of 127 ASD Italian families genotyped with the Illumina PsychArray, to perform an integrated analysis of CNVs and SNVs and to assess their contribution to ASD risk. We observed a higher burden of rare CNVs, especially deletions, in ASD individuals versus unaffected controls. Furthermore, we identified a significant enrichment of rare CNVs intersecting ASD candidate genes reported in the SFARI database. Family-based analysis of rare SNVs genotyped by the PsychArray also indicated an increased transmission of rare SNV variants from heterozygous parents to probands, supporting a multigenic model of ASD risk with significant contributions of both variant types. Moreover, our study reinforced the evidence for a significant role of VPS13B, WWOX, CNTNAP2, RBFOX1, MACROD2, APBA2, PARK2, GPHN, and RNF113A genes in ASD susceptibility. Finally, we showed that the PsychArray, besides providing useful genotyping data in psychiatric disorders, is a valuable and cost-efficient tool for genic CNV detection, down to 10 kb.

Figure 1

Schematic of the experimental design.

Figure 2

VPS13B deletion. (a) UCSC hg19 screenshot showing the 200 kb maternally inherited deletion impacting the VPS13B gene identified in case AB151. No CNVs in VPS13B have been detected in our control cohort. qPCR probes used to test VPS13B expression are shown in green; (b) VPS13B expression levels in the deletion carriers (AB151 and the mother of AB151) and in two controls.

Figure 3

Most notable CNVs intersecting SFARI genes. UCSC hg19 screenshots reporting the most notable CNVs impacting SFARI genes identified in our ASD sample and in controls. PsychArray probes are shown. (a) A 128 kb maternally inherited intronic deletion in the CNTNAP2 gene in case AB87. No CNVs in CNTNAP2 have been detected in our control cohort; (b) PARK2 CNVs in 2 cases (AB47 and AB156) and 5 controls; (c) RBFOX1 deletions in 2 cases (AB74 and AB86) and 2 controls; (d) WWOX non overlapping deletions in case AB139 and in one control subject; (e) A 236 kb paternally inherited deletion in the MACROD2 gene in case AB81. No CNVs in MACROD2 have been detected in our control cohort; (f) A 1.4–2.2 Mb paternally inherited deletion mapping in 15q13.1-q13.2 locus and impacting at least nine genes, including NDNL2 and APBA2. No CNVs in this locus have been found in our control sample; (g) CTNNA3 deletions in 2 cases (AB35 and AB119), one non-transmitting mother (mother of case AB145) and 6 controls.