Genetic assessment of additional endophenotypes from the Consortium on the Genetics of Schizophrenia Family Study

Abstract

The Consortium on the Genetics of Schizophrenia Family Study (COGS-1) has previously reported our efforts to characterize the genetic architecture of 12 primary endophenotypes for schizophrenia. We now report the characterization of 13 additional measures derived from the same endophenotype test paradigms in the COGS-1 families. Nine of the measures were found to discriminate between schizophrenia patients and controls, were significantly heritable (31 to 62%), and were sufficiently independent of previously assessed endophenotypes, demonstrating utility as additional endophenotypes. Genotyping via a custom array of 1536 SNPs from 94 candidate genes identified associations for CTNNA2, ERBB4, GRID1, GRID2, GRIK3, GRIK4, GRIN2B, NOS1AP, NRG1, and RELN across multiple endophenotypes. An experiment-wide p value of 0.003 suggested that the associations across all SNPs and endophenotypes collectively exceeded chance. Linkage analyses performed using a genome-wide SNP array further identified significant or suggestive linkage for six of the candidate endophenotypes, with several genes of interest located beneath the linkage peaks (e.g., CSMD1, DISC1, DLGAP2, GRIK2, GRIN3A, and SLC6A3). While the partial convergence of the association and linkage likely reflects differences in density of gene coverage provided by the distinct genotyping platforms, it is also likely an indication of the differential contribution of rare and common variants for some genes and methodological differences in detection ability. Still, many of the genes implicated by COGS through endophenotypes have been identified by independent studies of common, rare, and de novo variation in schizophrenia, all converging on a functional genetic network related to glutamatergic neurotransmission that warrants further investigation.

Keywords: Association; Endophenotype; Genetics; Heritability; Linkage; Schizophrenia.

Figure 1

Summary of the candidate gene association results in the 130 families. The most significant p-value observed for each of the 39 genes with each of the eight candidate endophenotypes is shown using a minimum p-value of <0.01 as a threshold. Note that not all associations to the same gene across endophenotypes reflect associations to the same SNP, although many do. Genes associated with three or more endophenotypes are indicated in bold. An asterisk (*) indicates that at least one SNP in the gene associated with the specified phenotype has been previously associated with schizophrenia as follows: rs807759 in DGCR2 (Shifman et al., 2006), rs2793092 in DISC1 (Liu et al., 2006), rs1018381 in DTNBP1 (Funke et al., 2004; Stefanis et al., 2007), rs2814351 in GRID1 (Fallin et al., 2005), and rs175174 in ZDHHC8 (Mukai et al., 2004). The two SNPs in DTNBP1 are >100kb apart and represent two independent associations with startle but not N100-C1 where only rs1040410 is associated. Note that Stories-recall could not be evaluated for association with the custom array because data for this endophenotype was only present in 98 subjects from 29 of the 130 genotyped families.

Figure 2

Results of the genome-wide SNP linkage scan in the 296 families for each of the 9 candidate endophenotypes. The variance components multipoint results are shown in red, the pedigree-wide regression multipoint results are shown in blue, and the variance components two-point results are shown in grey. LOD scores are indicated on the y-axis, along with the name of the corresponding endophenotype. Chromosomes are aligned along the x-axis end to end with the p-terminus on the left and locations indicated at the top of the figure. Dashed horizontal lines indicate genome-wide significant and suggestive LOD scores of 3.6 and 2.2, respectively.

Figure 3

Pathway analysis of the genes identified through association and linkage. Genes are represented as nodes, and the molecular interactions between nodes are represented by lines and arrows, with solid lines representing direct protein-protein or protein-DNA interactions, solid arrows representing phosphorylation, and dashed arrows representing indirect effects on expression, activation, or inhibition. Gene functions and relationships were determined by Ingenuity Pathway Analysis. Genes and interactions shown in black represent those included on the custom array and directly evaluated for association, while those in gray represent those derived from the linkage studies or other interacting genes. Candidate genes from the custom array associated (p<0.01) with at least one additional endophenotype are highlighted in yellow, and genes identified through linkage analysis are indicated with a red box. Genes from the custom array associated (p<0.01) in with a primary endophenotype in our previous study are indicated with a blue box (Greenwood et al., 2011), and genes identified through linkage analysis of a primary endophenotype are indicated in a green box (Greenwood et al., 2013c). Genes from the custom array associated with ≥3 additional endophenotypes or ≥3 primary endophenotypes are shown in bold, and those further associated (p<0.01) in our independent case-control sample are identified with an asterisk (*) (Greenwood et al., 2012).