Genome-wide study of association and interaction with maternal cytomegalovirus infection suggests new schizophrenia loci

Abstract

Genetic and environmental components as well as their interaction contribute to the risk of schizophrenia, making it highly relevant to include environmental factors in genetic studies of schizophrenia. This study comprises genome-wide association (GWA) and follow-up analyses of all individuals born in Denmark since 1981 and diagnosed with schizophrenia as well as controls from the same birth cohort. Furthermore, we present the first genome-wide interaction survey of single nucleotide polymorphisms (SNPs) and maternal cytomegalovirus (CMV) infection. The GWA analysis included 888 cases and 882 controls, and the follow-up investigation of the top GWA results was performed in independent Danish (1396 cases and 1803 controls) and German-Dutch (1169 cases, 3714 controls) samples. The SNPs most strongly associated in the single-marker analysis of the combined Danish samples were rs4757144 in ARNTL (P=3.78 × 10(-6)) and rs8057927 in CDH13 (P=1.39 × 10(-5)). Both genes have previously been linked to schizophrenia or other psychiatric disorders. The strongest associated SNP in the combined analysis, including Danish and German-Dutch samples, was rs12922317 in RUNDC2A (P=9.04 × 10(-7)). A region-based analysis summarizing independent signals in segments of 100 kb identified a new region-based genome-wide significant locus overlapping the gene ZEB1 (P=7.0 × 10(-7)). This signal was replicated in the follow-up analysis (P=2.3 × 10(-2)). Significant interaction with maternal CMV infection was found for rs7902091 (P(SNP × CMV)=7.3 × 10(-7)) in CTNNA3, a gene not previously implicated in schizophrenia, stressing the importance of including environmental factors in genetic studies.

Figure 1

(a) Manhattan plot of genome-wide association (GWA) analysis. The blue line indicates P=1 × 10⁻⁴. (b) Regional association plot of rs4757144 located in ARNTL. (c) Regional association plot of rs8057927 located in CDH13. (d) Regional association plot of rs12922317 located in RUNDC2A. The P-values in green are from the GWA analysis, P-values marked in blue are from the combined analysis of Danish individuals, P-values marked in purple are from the extended meta-analysis. The linkage disequilibrium (LD; r²) between the SNP in focus and its flanking markers genotyped in the GWA study are demonstrated in red (high LD) to white (low LD). The recombination rate is plotted in blue according to HapMap (CEU).

Figure 2

(a) Manhattan plot of region-wise association analysis. The blue line indicates genome-wide significance (P=9.0 × 10⁻⁷). (b) Regional association plot of rs3123688 located upstream of ZEB1. The P-values in green are from the genome-wide association (GWA) analysis and P-values marked in blue are from the combined analysis of Danish individuals. The vertical lines represent the region-wise P-values. The linkage disequilibrium (LD; r²) between the single nucleotide polymorphism in focus and its flanking markers genotyped in the GWA study are demonstrated in red (high LD) to white (low LD). The recombination rate is plotted in blue according to HapMap (CEU).

Figure 3

Regional association plot of rs7902091. P-values of interaction between single nucleotide polymorphisms (SNPs) and maternal cytomegalovirus infection. The linkage disequilibrium (LD; r²) between the SNP in focus and its flanking markers genotyped in the genome-wide association study are demonstrated in red (high LD) to white (low LD). The recombination rate is plotted in blue according to HapMap (CEU).