Genetic contributors to risk of schizophrenia in the presence of a 22q11.2 deletion

Abstract

Schizophrenia occurs in about one in four individuals with 22q11.2 deletion syndrome (22q11.2DS). The aim of this International Brain and Behavior 22q11.2DS Consortium (IBBC) study was to identify genetic factors that contribute to schizophrenia, in addition to the ~20-fold increased risk conveyed by the 22q11.2 deletion. Using whole-genome sequencing data from 519 unrelated individuals with 22q11.2DS, we conducted genome-wide comparisons of common and rare variants between those with schizophrenia and those with no psychotic disorder at age ≥25 years. Available microarray data enabled direct comparison of polygenic risk for schizophrenia between 22q11.2DS and independent population samples with no 22q11.2 deletion, with and without schizophrenia (total n = 35,182). Polygenic risk for schizophrenia within 22q11.2DS was significantly greater for those with schizophrenia (p_adj = 6.73 × 10^-6). Novel reciprocal case-control comparisons between the 22q11.2DS and population-based cohorts showed that polygenic risk score was significantly greater in individuals with psychotic illness, regardless of the presence of the 22q11.2 deletion. Within the 22q11.2DS cohort, results of gene-set analyses showed some support for rare variants affecting synaptic genes. No common or rare variants within the 22q11.2 deletion region were significantly associated with schizophrenia. These findings suggest that in addition to the deletion conferring a greatly increased risk to schizophrenia, the risk is higher when the 22q11.2 deletion and common polygenic risk factors that contribute to schizophrenia in the general population are both present.

Figure 1:. IBBC 22q11.2 DS cohort overview and schematic of data generation and analyses performed.

The full IBBC cohort and European subset are illustrated as yellow circles, broken down by numbers with or without schizophrenia, as well as sex and 22q11.2 deletion extent for individuals of European Ancestry. Whole-genome sequencing methods and data are represented by blue boxes and microarray data represented by green boxes (lighter for IBBC 22q11.2DS data, darker for schizophrenia case-control study data (15)). i to vi represent the comparisons presented in Fig. 3 for novel reciprocal case-control comparisons of schizophrenia PRS between the 22q11.2DS and population-based cohorts.

Figure 2.. Polygenic risk score analyses of schizophrenia in 22q11.2DS.

Analysis of schizophrenia PRS in 432 individuals of European ancestry with 22q11.2DS, with (n=212) or without (n=220) schizophrenia. Variants from the 22q11.2 deletion, MHC regions and X chromosome were excluded and results adjusted for sex, top 3 ancestry PCs. P-values were adjusted using P-ACT for the 13 p-value thresholds (pT) used for PRS construction (13). Details on the number of SNPs used (maximum 68,966 SNPs for polygenic risk scoring at pT=1, minimum 202 SNPs at pT=1×10⁻⁶) are shown in Table S9. Figure 2a. The proportion of variance in schizophrenia explained by PRS (Nagelkerke’s R2) across different pT thresholds. At pT=0.05, Nagelkerke’s pseudo-R2= 0.077 (adjusted p=6.73×10⁻⁶). Figure 2b. Odds ratio and 95% confidence interval bars per one standard deviation increase in PRS across different pT thresholds. At pT=0.05 a one standard deviation increase in PRS corresponded to a 1.77-fold higher odds for schizophrenia in 22q11.2DS.

Figure 3.. Polygenic risk score analyses in 22q11.2DS individuals with or without schizophrenia, and a case-control cohort without 22q11.2DS.

PRS analyses were performed for 322 individuals with 22q11.2DS (147 with schizophrenia, 175 without) and 35,182 individuals with no 22q11.2 deletion (10,791 schizophrenia CLOZUK cases, 24,391 WTCCC controls) (6); all subjects were of European ancestry. Six comparisons of schizophrenia PRS were considered (Figure 1) between: (i) individuals with 22q11.2DS, with and without schizophrenia (ii) 22q11.2DS-schizophrenia and WTCCC controls (iii) 22q11.2DS-non-psychotic and WTCCC controls (iv) the CLOZUK schizophrenia cohort and 22q11.2DS-schizophrenia, (v) the CLOZUK schizophrenia cohort and 22q11.2DS-non-psychotic, and (vi) the CLOZUK schizophrenia cohort and WTCCC controls. Figure 3a shows the proportion of variance explained by PRS (Nagelkerke’s R2) for each of the six comparisons (clockwise: i to vi). Figure 3b shows the odds ratio and 95% confidence interval bars per PRS standard deviation constructed for these six PRS analyses (left to right: i to vi). Taken as a whole, these results demonstrate that the PRS in the CLOZUK-schizophrenia is significantly greater than that seen in 22q11.2DS individuals with schizophrenia, which itself is significantly greater than that seen in the WTCCC-controls and the 22q11.2DS non-psychotic groups.

Figure 4.. Representation of 46 genes spanning the 22q11.2 LCR22A-LCR22D deletion region annotated for contextual information and results from the current study:

Representation of 46 genes spanning the 22q11.2 low copy repeat (LCR) LCR22A-LCR22D deletion region annotated for contextual information and, on grey background, results from the current study. The sections numbered 1–11 indicate the following: 1) Gene expression in brain, ranging from none to low (white) to low-medium (yellow) to medium-high (orange) to very high (red) according to BrainSpan (BrainSpan: Atlas of the Developing Human Brain [[http://developinghumanbrain.org]]http://developinghumanbrain.org]) and as previously processed by (10); 2 & 3) Exome Aggregation Consortium (ExAC) (48) calculated probability (ranging from 0 to 1.00, shown as a spectrum from white to deep violet) that the gene is intolerant to (2) two LOF variants (recessive; pRec), or (3) a single LOF variant (haploinsufficient; pLI); 4 & 5) Neuro-phenotype data availability, (4) from mouse in the form of mouse homologues from MGI (49) as a union of two MPO-based gene-sets [MP:0005386 behavior/neurological phenotype, MP:0003631 nervous system phenotype] as used in (10), and (5) for human neurologic disease genes from the Clinical Genomic Database (CGD) (CGD: Clinical Genomic Database. [https://research.nhgri.nih.gov/CGD/]); 6) Clusters of small rare deletions in the general population per the Database of Genomic Variants (DGV) (50), indicating presumed tolerance to hemizygosity, where an aqua circle/oval represents a single deletion cluster of ≤1% frequency; 7) Rare LOF variants found in this 22q11.2DS cohort, thus representing a presumed null mutation, each variant observed in a single individual either within the schizophrenia (magenta) or non-psychotic (green) subgroups; number indicates the number of individuals (1, 2, or 3) in the schizophrenia or non-psychotic group with a LOF variant identified; 8) Genes in the 22q11.2 deletion region that show nominal significance for rare variants (in yellow, p-values ranged between 7.92E-03 and 4.75E-02 based on SKAT or Burden test) or for common variants (in red, p-values ranged between 3.63E-03 and 4.23E-02 based on SKAT test) in gene-based association tests for schizophrenia in this study using data for the subset of European ancestry. All results for the SKAT gene-based test for common variants can be found in Table S19. Note that all genes with nominal significance for rare variants are indicated in yellow, but that only CDC45, PI4KA, CLTCL1 and TRMT2A comply with the n≥5 rare variants criterion (see Table S15 for exact number of rare variants). 9) Schematic of gene positions in the 22q11.2 region. 10) Schematic of the positions, relative to genes, of the main 22q11.2 deletion region LCR22s A, B, C, and D. 11) Approximate genomic extents of the two most common 22q11.2 deletion sizes. NA = Data not available.