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 7.7×10⁻⁷ for rs2715148 and 1.2×10⁻⁶ 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=6.4×10⁻⁸ 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.

The reported interaction between the length polymorphism (5HTTLPR) in the serotonin transporter gene (SLC6A4) and stressful life events on depression has led to many attempts to replicate but with inconsistent results. This inconsistency may reflect, in part, small sample size and the unknown contribution of the long allele SNP, rs25531. Using a large twin sample of 3,243 individuals from 2,230 families aged 18–95 years (mean = 32.3, SD = 13.6) we investigate the interaction between 5HTTLPR (subtyped with SNP rs25531) and stressful events on risk of depression and suicidality using both ordinal regressions and item response theory analyses. Participants reported via mailed questionnaire (82% response rate) both stressful events in the preceeding 12 months and symptoms of depression. Stressful events were defined as "personal" (affecting the individual), or "network" (affecting close family or friends). One to 10 years later (mean = 4.2 years), participants completed a comprehensive clinical psychiatric telephone interview (83% response rate) which assessed DSM-IV major depression and ideation of suicidality. Self-reports of depression and an increase in depression/suicidality assessed by clinical interview are significantly associated with prior personal events (P<0.001) after controlling for age and sex. However, they are inconsistently associated with prior network events (ranging, ns to P<0.01) and are not significantly associated with any of the genotype main effects (5HTTLPR, 5HTTLPR+rs25531) or interactions (stress×genotype). We find no evidence to support the hypothesis of any 5HTTLPR genotype by stress interaction.

Serotonergic neurotransmission impacts on a wide range of behaviors, including cognition and emotion (1,2), and drugs targeting serotonin reuptake are clinically effective antidepressants (3). As a result, one of the most studied polymorphisms for association with a broad range of psychiatric and personality phenotypes is the length polymorphism repeat (LPR) in the promoter region of the serotonin transporter gene (5HTT renamed SLC6A4) (5HTTLPR). The 5HTTLPR polymorphism comprises a 43-base pair (bp) (4–8) insertion or deletion (long, "L," with 16 repeat units or short, "S," with 14 repeat units, alleles, respectively). The S allele (frequency in Caucasians ~.45 [9]) reduces transcriptional efficiency, resulting in decreased SLC6A4expression and function (10). Association studies and subsequent meta-analyses (Table 1) (11–15) have shown conflicting results in support of an association between the S allele and anxiety, depression, and the personality trait neuroticism (a measure of emotional stability that is genetically correlated to both anxiety and depression [16–18]). Conflicting results have dogged candidate gene association studies for many complex disorders, attributable to small sample sizes of both primary and replication studies, heterogenous subject populations, association dependent on environmental conditions such as stressful life events (19), and differing instruments for assessment of phenotypic traits and statistical methods (e.g., [20,21]). However, an additional problem specific to 5HTTLPR relates to the genotyping assay, which has caused considerable bias toward S allele identification (22,23). Furthermore, association may have been compromised by the presence of an A/G single nucleotide polymorphism (SNP), rs25531, that lies within the L allele of 5HTTLPR (5,8); the L allele with the rarer G allele of rs25531 (denoted L) is functionally equivalent to the S allele because of changes to the activating protein 2 (AP2) transcription factor binding site altered by this SNP (5,8).