Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia

Abstract

By analyzing the exomes of 12,332 unrelated Swedish individuals, including 4,877 individuals affected with schizophrenia, in ways informed by exome sequences from 45,376 other individuals, we identified 244,246 coding-sequence and splice-site ultra-rare variants (URVs) that were unique to individual Swedes. We found that gene-disruptive and putatively protein-damaging URVs (but not synonymous URVs) were more abundant among individuals with schizophrenia than among controls (P = 1.3 × 10^-10). This elevation of protein-compromising URVs was several times larger than an analogously elevated rate for de novo mutations, suggesting that most rare-variant effects on schizophrenia risk are inherited. Among individuals with schizophrenia, the elevated frequency of protein-compromising URVs was concentrated in brain-expressed genes, particularly in neuronally expressed genes; most of this elevation arose from large sets of genes whose RNAs have been found to interact with synaptically localized proteins. Our results suggest that synaptic dysfunction may mediate a large fraction of strong, individually rare genetic influences on schizophrenia risk.

Figure 1. Ultra-rare variants distribution and association with schizophrenia

(a-b) Counts across coding-sequence and splice-site rare variants stratified by minor allele count across exome sequencing data from 12,332 individuals indicating (a) how many variants were observed in the ExAC cohort and (b) how many variants were classified as disruptive, damaging, missense non-damaging, and synonymous. (c) Observed enrichment in schizophrenia cases compared to controls for coding-sequence and splice-site URVs across the main four annotation types. Enrichment and P values were computed using a linear regression model (left panel) and a logistic regression model (right panel). Horizontal bars indicate 95% confidence intervals.

Figure 2. dURVs enrichement in schizophrenia cases across selected gene sets

Excess per case and odds ratios for dURVs across loss-of-function intolerant (LoF-intolerant) genes, missense constrained genes, protein complexes genes, genes associated through common variants, predicted microRNA-137 targets, and intellectual disability genes. Enrichment and P values were computed using a linear regression model (left panel) and a logistic regression model (right panel) using exome-wide dURV count as a covariate to correct for average exome-wide burden (dot-dashed line). Horizontal bars indicate 95% confidence intervals.

Figure 3. dURVs enrichment in schizophrenia cases across tissue, brain cell type, and synaptic gene sets

Excess per case and odds ratios for dURVs across genes with higher expression in a given tissue (a), genes with higher expression in a given cell type (b), and genes expected to localize to synapses (c). Enrichment and P values were computed using a linear regression model (left panels) and a logistic regression model (right panels) using exome-wide dURV count as a covariate to correct for average exome-wide burden (dot-dashed line). Horizontal bars indicate 95% confidence intervals.

Figure 4. dURVs enrichment in schizophrenia cases across brain cell type gene sets stratified by synaptic localization

Odds ratios for enrichment of dURVs across genes expressed in brain tissue, neuronal cells, inhibitory neurons, and excitatory neurons, stratified between genes recognized as synaptic and genes recognized as non-synaptic. Synaptic genes were defined as genes part of either the FMRP, RBFOX2, CELF4, or SynaptomeDB gene sets. Enrichment and P values were computed using a logistic regression model using exome-wide dURV count as a covariate to correct for average exome-wide burden (dot-dashed line). Horizontal bars indicate 95% confidence intervals. Across each gene set, synaptic genes are clearly more enriched for variants in schizophrenia cases than non-synaptic genes.

Figure 5. dURVs enrichment in schizophrenia cases across genes previously observed as affected by de novo mutations

Odds ratios for enrichment of dURVs across (a) genes overlapping de novo deletions and duplications in schizophrenia, bipolar disorder, and autism trios, and across (b) loss-of-function intolerant (LoF-intolerant) genes with observed de novo mutations in schizophrenia, intellectual disability, congenital heart disease, epilepsy, and autism trios. Enrichment and P values were computed using a logistic regression model using exome-wide dURV count (a) and dURV count across LoF-intolerant genes (b) as a covariate to correct for average burden (dot-dashed line). Horizontal bars indicate 95% confidence intervals.

Figure 6. Dissection of the dURVs enrichment in schizophrenia cases

An enrichment of URVs in the exomes of individuals affected with schizophrenia (relative to variants in control exomes) is observed exclusively in dURVs. After correcting for exome-wide dURV count, this enrichment is observed as concentrated in brain-specific genes while not in other tissue-specific genes, in neuron-specific genes while not in other brain-cell type-specific genes, and finally in potentially synaptic genes while not in other neuronally expressed genes.