Identification of novel driver risk genes in CNV loci associated with neurodevelopmental disorders

Abstract

Copy-number variants (CNVs) are genome-wide structural variations involving the duplication or deletion of large nucleotide sequences. While these types of variations can be commonly found in humans, large and rare CNVs are known to contribute to the development of various neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD). Nevertheless, given that these NDD-risk CNVs cover broad regions of the genome, it is particularly challenging to pinpoint the critical gene(s) responsible for the manifestation of the phenotype. In this study, we performed a meta-analysis of CNV data from 11,614 affected individuals with NDDs and 4,031 control individuals from SFARI database to identify 41 NDD-risk CNV loci, including 24 novel regions. We also found evidence for dosage-sensitive genes within these regions being significantly enriched for known NDD-risk genes and pathways. In addition, a significant proportion of these genes was found to (1) converge in protein-protein interaction networks, (2) be among most expressed genes in the brain across all developmental stages, and (3) be hit by deletions that are significantly over-transmitted to individuals with ASD within multiplex ASD families from the iHART cohort. Finally, we conducted a burden analysis using 4,281 NDD cases from Decipher and iHART cohorts, and 2,504 neurotypical control individuals from 1000 Genomes and iHART, which resulted in the validation of the association of 162 dosage-sensitive genes driving risk for NDDs, including 22 novel NDD-risk genes. Importantly, most NDD-risk CNV loci entail multiple NDD-risk genes in agreement with a polygenic model associated with the majority of NDD cases.

Keywords: Copy number variants; Decipher database; SFARI database; autism spectrum disorder; burden testing; dosage-sensitive genes; iHART cohort; neurodevelopmental disorders; risk genes and pathways; structural variants.

Graphical abstract

Figure 1

Dosage-sensitive genes in NDD-risk regions overlap with ASD-risk genes Scatterplot A shows the dose sensitivity score values (pHI and pTS) for genes in regions identified as NDD-risk. Gray dots in the scatterplot stand for genes that do not meet the threshold to be considered HI genes, TS genes, or bHITS genes. Depicted in red are the genes that meet the threshold for haploinsufficiency, HI genes, and in blue the ones that meet the threshold for triplosensitivity, TS genes. Genes that surpass the threshold for both haploinsufficiency and triplosensitivity, bHITS genes, are depicted in yellow in the upper right quadrant of the grid. The circular bar plot (B) represents the 63 dosage-sensitive genes that are present in both our list of qDSGs and the SFARI curated catalog of ASD-risk genes, according to the degree of evidence of association.

Figure 2

Validation of NDD-risk for 162 qDSGs, 22 of them novel genes never associated before with risk for NDD Validation of qDSG in NDD-risk regions found associated to autism in affected individuals from iHART and Decipher compared with control individuals from 1000 Genomes. (A–C) Volcano plot depicting the p values and odds ratios for qDSGs genes in NDD-risk regions: (A) HI genes, (B) bHITS genes, and (C) TS genes. Vertical red line delimits odds ratio 1, whereas horizontal red line stands for the multiple test correction threshold. Dashed red line represents p = 0.05. (D) Bar plot describing the number of qDSG validated according to type of novelty. ∗Candidate and high confidence, ∗∗NDD-risk genes according to the GeneTrek catalog.

Figure 3

Pathways where qDSGs are involved, and their overlap with known NDD-risk pathways Subset of top GO terms enriched for HI genes (A), for TS genes (B), and for bHITS genes (C). In the lower half is depicted the overlap between the GO terms enriched for our qDSGs and the GO terms enriched for the genes in the SFARI catalog of ASD-risk genes, also divided according to their dosage type, for HI genes (D), for TS genes (E), and for bHITS genes (F).

Figure 4

qDSGs are significantly highly expressed in key areas of the brain across all developmental stages Surface and slice representation of odds ratio resulting from the enrichment analysis of qDSGs in the highly expressed ranking. Only statistically significant areas enriched with highly expressed qDSGs are colored.

Figure 5

PPI network depicting interactions between protein products of qDSGs Protein-protein interaction network depicting interactions of qDSGs where nodes are colored based on their evidence strength of NDD-risk. Circled nodes stand for validated NDD-risk for those genes in our analysis.

Figure 6

Phenotypes associated to most qDSGs are NDD-risk clinical signs and symptoms (A) Histogram listing the top 60 HPO terms associated with NDD-risk genes, according to the type and number of genes they are associated to. (B) Histogram listing the top 60 NDD-risk genes, according to the number of HPO phenotypes they are associated.

Figure 7

Pedigree for deleted CNVs on 3q29, affecting qDSG ACAP2, which was identified in four different families with a transmission rate of 1