Transmission disequilibrium of small CNVs in simplex autism

Abstract

We searched for disruptive, genic rare copy-number variants (CNVs) among 411 families affected by sporadic autism spectrum disorder (ASD) from the Simons Simplex Collection by using available exome sequence data and CoNIFER (Copy Number Inference from Exome Reads). Compared to high-density SNP microarrays, our approach yielded ∼2× more smaller genic rare CNVs. We found that affected probands inherited more CNVs than did their siblings (453 versus 394, p = 0.004; odds ratio [OR] = 1.19) and that the probands' CNVs affected more genes (921 versus 726, p = 0.02; OR = 1.30). These smaller CNVs (median size 18 kb) were transmitted preferentially from the mother (136 maternal versus 100 paternal, p = 0.02), although this bias occurred irrespective of affected status. The excess burden of inherited CNVs among probands was driven primarily by sibling pairs with discordant social-behavior phenotypes (p < 0.0002, measured by Social Responsiveness Scale [SRS] score), which contrasts with families where the phenotypes were more closely matched or less extreme (p > 0.5). Finally, we found enrichment of brain-expressed genes unique to probands, especially in the SRS-discordant group (p = 0.0035). In a combined model, our inherited CNVs, de novo CNVs, and de novo single-nucleotide variants all independently contributed to the risk of autism (p < 0.05). Taken together, these results suggest that small transmitted rare CNVs play a role in the etiology of simplex autism. Importantly, the small size of these variants aids in the identification of specific genes as additional risk factors associated with ASD.

Figure 1

Discovery and Validation of CNVs with the Use of Exomes (A) Fraction of CNVs previously identified via Illumina 1M SNP microarray (gray, “known true positives”), the fraction of CNVs identified and confirmed by targeted array CGH in this study (green, “CNVs identified in this study”), confirmed processed pseudogenes (hatched green), and the overall FPR for unconfirmed CNVs (gray). (B) The majority (73% [152/207]) of all calls (green) identified in this study with the use of exomes were smaller than 20 kb. (C–D and F) Three examples of CNVs in this study. Top: CoNIFER output and normalized coverage at each exon. Middle: targeted array CGH at CNV locus; the threshold for deletion or duplication (dotted red line) was determined by ROC-curve analysis of known CNVs (Supplemental Data). Bottom: Illumina 1M SNP microarray data for locus shows poor probe coverage (C and D only). (E) Exome-based CNV discovery affords high exon-level specificity, as indicated by duplication of NETO1 exons (†, CoNIFER call). Previous work (Sanders et al.²) discovered this CNV (^∗), but the (incorrect) breakpoints did not extend into NETO1.

Figure 2

Increased Inherited CNV Burden in ASD Probands for Large and Small CNVs (A) Total number of rare (observed in fewer than ten families) inherited CNVs (at least two exons) for 411 ASD probands (Pro) and their unaffected siblings (Sib). (B) Total number of affected genes in rare inherited CNVs. p values refer to two-tailed paired t tests between proband and sibling counts. (C) Burden of inherited CNVs across six size categories.

Figure 3

Inherited CNV Burden Correlates with SRS Phenotype (A) The SRS measures autism features in social settings via parent report on 65 items. We classified proband-sibling pairs with severely affected probands but mildly or unaffected siblings as SRS-discordant quads (276 quads) and all other quads as SRS-concordant quads (115 quads). Strikingly, the SRS-discordant quads fully recapitulated the inherited CNV transmission bias, whereas the SRS-concordant quads did not show a differential burden. (B) CNV burden was independent of FSIQ, and probands with either low FSIQ (≤70) or high FSIQ had more CNVs than did their siblings. p values refer to two-tailed paired t tests between probands and siblings.

Figure 4

Genes in Proband-Only CNVs from SRS-Discordant Quads Are More Likely Brain-Expressed Genes We defined a gene to be expressed in a tissue if it ranked in the top 5% of all genes in that tissue and calculated the fold enrichment of proband and sibling genes expressed in each tissue. The tissues with the strongest proband enrichment were part of brain structures (black bars), as was the computed average of expression across 18 brain regions (“brain average”). However, the particular brain tissues with the strongest apparent enrichment should not be considered as independently enriched, given that expression values for individual genes between brain regions are highly correlated. Asterisks indicate a FDR-corrected p value < 0.05. See Figure S9 for results from all 411 quads.

Figure 5

A Combined Model of Inherited and De Novo Mutations Reveals Independent Risk for Both A logistic regression model estimates the OR for each inherited CNV (blue), de novo CNV (red), or disruptive de novo SNV (gray; nonsense and splice mutations and indels only) in probands and siblings. ORs and burden (proband-sibling ratio) given in the accompanying table reveal independent risk for each type of mutation. The line width for each type of mutation in the figure indicates whether a bias was observed for new mutations arising on the maternal or paternal haplotypes (see also O’Roak et al. for SNVs and Hehir-Kwa et al., for CNVs).