Excess of rare, inherited truncating mutations in autism

Abstract

To assess the relative impact of inherited and de novo variants on autism risk, we generated a comprehensive set of exonic single-nucleotide variants (SNVs) and copy number variants (CNVs) from 2,377 families with autism. We find that private, inherited truncating SNVs in conserved genes are enriched in probands (odds ratio = 1.14, P = 0.0002) in comparison to unaffected siblings, an effect involving significant maternal transmission bias to sons. We also observe a bias for inherited CNVs, specifically for small (<100 kb), maternally inherited events (P = 0.01) that are enriched in CHD8 target genes (P = 7.4 × 10(-3)). Using a logistic regression model, we show that private truncating SNVs and rare, inherited CNVs are statistically independent risk factors for autism, with odds ratios of 1.11 (P = 0.0002) and 1.23 (P = 0.01), respectively. This analysis identifies a second class of candidate genes (for example, RIMS1, CUL7 and LZTR1) where transmitted mutations may create a sensitized background but are unlikely to be completely penetrant.

Figure 1. SNV quality assessment

SNVs were identified based on the intersection of FreeBayes and GATK variant callers. The panels display a) proband-sibling concordance for number of private SNVs (Pearson’s r² > 0.99) and stratified by population (calculated by PCA using EIGENSTRAT on SNV markers); b) the number and distribution of private, heterozygous genotypes that do not differ significantly between mothers, fathers, probands or siblings (p-values > 0.3 for all comparisons); c) the number of transmitted SNVs per exome in dbSNP (blue) or novel (green); d) concordance between exome and SNP microarray calls (Sanders unpublished); e) fraction of events per exome found in dbSNP; f) genotype concordance of SNVs found in dbSNP, per exome.

Figure 2. Transmission disequilibrium of SNVs in ASD

a) Private, inherited LGD (red bars) SNVs in genes not tolerant to functional variation were significantly enriched in probands. The analysis examines only SNVs in genes with an RVIS in the lower 50%. Non-private, rare variants or missense-inherited (gray bars) SNVs are not enriched in probands. Bar heights are Fisher’s exact test odds ratio and whiskers represent 95% confidence interval bounds. b) The RVIS is a critical determinant for enrichment in probands. Burden was highest (reaching OR = 1.4) for private, inherited LGD SNVs amongst genes with the lowest RVIS values (<1%). MAF = minor allele frequency.

Figure 3. Transmitted mutations and their effect on phenotype

a) Private, inherited LGD SNVs enriched in probands with autism and pervasive developmental disorder (PDD) diagnoses, but not Asperger’s syndrome (AS). b) Private, inherited LGD SNVs primarily enriched in probands with lower IQ than average (<100). c) We observe transmission disequilibrium of rare, inherited CNVs in SRS (Social Responsiveness Scale) discordant families (proband SRS score > 75, sibling < 50) but not in families where the SRS score is mild or more balanced between proband and sibling. d) Rare, inherited CNVs are enriched in probands (versus their siblings) with IQ < 70, but the effect is not significant in probands with IQ > 70. All tests and reported p-values are paired t-tests based on proband-sibling pairs. All analyses were restricted to genes with RVIS < 50.

Figure 4. Combined risk model for SNVs and CNVs: inherited and de novo

Integrative risk model for ASD, based on de novo and inherited events, and covering both SNVs and CNVs. The model used is a stratified logistic regression model, which utilizes proband-sibling pairs to estimate the odds ratio (i.e., risk of ASD) for each type of event (see also Supplementary Table 7).

Figure 5. Networks and pathways

A highly interconnected network was identified based on novel de novo mutations identified in this study (Note: one additional de novo missense mutation was recently identified in ). Gene ontology annotation of the genes in this network suggests involvement of the insulin-like growth factor signaling pathway (GIGYF1, GIGYF2, GRB10; accession GO:0048009), which has been previously implicated in the development of ASD . Furthermore, GIGYF2 and ZNF598 form part of the m4EHP mRNA binding complex and have widespread translational repression roles, especially in the brain and lungs . Red stars: de novo LGD mutations (frameshift, stop-gained, splice-site); Blue stars: de novo missense mutations; Purple star: CNV deletion.