Association analysis of 94 candidate genes and schizophrenia-related endophenotypes

Abstract

While it is clear that schizophrenia is highly heritable, the genetic basis of this heritability is complex. Human genetic, brain imaging, and model organism studies have met with only modest gains. A complementary research tactic is to evaluate the genetic substrates of quantitative endophenotypes with demonstrated deficits in schizophrenia patients. We used an Illumina custom 1,536-SNP array to interrogate 94 functionally relevant candidate genes for schizophrenia and evaluate association with both the qualitative diagnosis of schizophrenia and quantitative endophenotypes for schizophrenia. Subjects included 219 schizophrenia patients and normal comparison subjects of European ancestry and 76 schizophrenia patients and normal comparison subjects of African ancestry, all ascertained by the UCSD Schizophrenia Research Program. Six neurophysiological and neurocognitive endophenotype test paradigms were assessed: prepulse inhibition (PPI), P50 suppression, the antisaccade oculomotor task, the Letter-Number Span Test, the California Verbal Learning Test-II, and the Wisconsin Card Sorting Test-64 Card Version. These endophenotype test paradigms yielded six primary endophenotypes with prior evidence of heritability and demonstrated schizophrenia-related impairments, as well as eight secondary measures investigated as candidate endophenotypes. Schizophrenia patients showed significant deficits on ten of the endophenotypic measures, replicating prior studies and facilitating genetic analyses of these phenotypes. A total of 38 genes were found to be associated with at least one endophenotypic measure or schizophrenia with an empirical p-value<0.01. Many of these genes have been shown to interact on a molecular level, and eleven genes displayed evidence for pleiotropy, revealing associations with three or more endophenotypic measures. Among these genes were ERBB4 and NRG1, providing further support for a role of these genes in schizophrenia susceptibility. The observation of extensive pleiotropy for some genes and singular associations for others in our data may suggest both converging and independent genetic (and neural) pathways mediating schizophrenia risk and pathogenesis.

Figure 1. Summary of the most significant associations observed in the European ancestry sample.

Empirical p-values are presented for each of the 38 genes with each of the 10 phenotypes and schizophrenia using a minimum empirical p-value of <0.01 as a threshold. Note that not all associations to the same gene across phenotypes reflect associations to the same SNP, although many do. An asterisk (*) indicates that at least one SNP in the gene associated with the specified phenotype has been previously associated with schizophrenia as follows: rs963468 in DRD3 , rs2344485 in NEUROG1 ; rs520692 in NOTCH4 , ; rs1954787 in GRIK4 ; rs1805247 in GRIN2B , ; and rs2267341 and rs2283981 in CACNG2 . Genes associated with three or more phenotypes are indicated in bold.

Figure 2. Distribution of the 94 candidate genes in known biological pathways.

Associated (empirical p<0.01) genes are indicated in bold, and those associated with more than one phenotype are additionally indicated with an asterisk (*).

Figure 3. Genetic network detailing the types of interactions between a subset of the 94 candidate genes.

Genes associated (empirical p<0.01) with at least one neurophysiological phenotype (PPI, startle habituation, and P50 S1) are highlighted in yellow in (A), and genes associated (empirical p<0.01) with the neurocognitive phenotypes (antisaccade, LNS forward, LNS re-order, CVLT-II immediate recall, CVLT-II delayed recall, WCST-64 perseverative responses, or WCST-64 categories) are highlighted in (B). Note that antisaccade was grouped with the neurocognitive phenotypes based on its demonstrated correlations with these measures (see Table 2). Genes are represented as nodes, and the biological relationship between two nodes is represented as an edge (line or arrow) supported by at least one reference from the literature, a textbook, or canonical information derived from the human, mouse, and rat orthologs of the gene that are stored in the Ingenuity Pathways Knowledge Base. Solid and dashed lines/arrows indicate direct and indirect interactions, respectively.

Figure 4. Summary of the most significant associations observed in the African ancestry sample.

Empirical p-values are presented for each of the 11 genes exhibiting pleiotropy in the analyses of the European ancestry sample with each of the 10 phenotypes and schizophrenia using a minimum empirical p-value of <0.01 as a threshold. Note that not all associations to the same gene across phenotypes reflect associations to the same SNP, although many do.