Genome-wide association for major depressive disorder: a possible role for the presynaptic protein piccolo

Abstract

Major depressive disorder (MDD) is a common complex trait with enormous public health significance. As part of the Genetic Association Information Network initiative of the US Foundation for the National Institutes of Health, we conducted a genome-wide association study of 435 291 single nucleotide polymorphisms (SNPs) genotyped in 1738 MDD cases and 1802 controls selected to be at low liability for MDD. Of the top 200, 11 signals localized to a 167 kb region overlapping the gene piccolo (PCLO, whose protein product localizes to the cytomatrix of the presynaptic active zone and is important in monoaminergic neurotransmission in the brain) with P-values of 7.7 x 10(-7) for rs2715148 and 1.2 x 10(-6) for rs2522833. We undertook replication of SNPs in this region in five independent samples (6079 MDD independent cases and 5893 controls) but no SNP exceeded the replication significance threshold when all replication samples were analyzed together. However, there was heterogeneity in the replication samples, and secondary analysis of the original sample with the sample of greatest similarity yielded P=6.4 x 10(-8) for the nonsynonymous SNP rs2522833 that gives rise to a serine to alanine substitution near a C2 calcium-binding domain of the PCLO protein. With the integrated replication effort, we present a specific hypothesis for further studies.

Figure 1

GWAS results for MDD in cases versus controls. Panel a shows the quantile-quantile plots and lambda estimates for the primary analysis using the Cochran-Armitage trend test and confirmatory analyses using logistic regressions and Cochran-Mantel-Haenszel stratified tests. The dashed lines show the expected 95% probability interval for ordered p-values, and the circles show the observed versus expected values for all SNPs. The λ values are the median Χ² from all association tests divided by the expected value under the null hypothesis of no association. If λ is large (e.g., >1.2), there is evidence that the observed test statistics deviate from the expected. This could be due to true associations but is more likely due to a systematic bias (e.g., population stratification effects). The λ values in Panel a are not consistent with the presence of stematic biases in the results. Panel b depicts −log₁₀(p) by genomic location for chr1-chr22 plus chrX. Odd-numbered chromosomes are in light blue and even-numbered chromosomes in orange. The 25 smallest p-values are shown with green crosses.

Figure 2

Plot of the PCLO region (NCBI build 35, UCSC hg17, chr7:82,000,000-82,500,000). P-values in this figure are all from SNPMstat. The x-axis is chromosomal position, the left y-axis −log₁₀(p) for genotyped SNPs (colored diamonds) and imputed SNPs (grey diamonds), and the right y-axis the recombination rate from the HapMap EUR panel (light blue curve). The color of the genotyped SNPs corresponds to LD with the SNP with smallest p-value (rs2715148): red 0.8 ≤ r² ≤ 1.0, orange 0.5 ≤ r² < 0.8, yellow 0.2 ≤ r² < 0.5, and white r² < 0.2. The significant and extent of all 3-SNP haplotypes with p<0.0001 in this region are colored light green. The transcripts for two PCLO isoforms are shown in dark green at the bottom. Graph adapted from an R function by the Broad DGI group.

Figure 3

PCLO region replication results for MDD showing genomic context and forest plots for the top 12 SNPs in the original sample. The backbone of the graph is the region of PCLO targeted for follow-up. SNP locations are given by the grey triangles. There are 12 forest plots for the SNPs with p<0.001 in the original sample. Each forest plot is for one SNP and shows the odds ratio (square) and 95% confidence intervals (horizontal line) for a particular sample with the area of the square proportional to sample size.