In 2009, the first genome-wide association study (GWAS) for major depressive disorder (MDD) highlighted an association with PCLO locus on chromosome 7, although not reaching genome-wide significance level. In the present study, we revisited the original GWAS after increasing the overall sample size and the number of interrogated SNPs. In an analysis comparing 1,942 cases with lifetime diagnosis of MDD and 4,565 controls, PCLO showed a genome-wide significant association with MDD at SNP (rs2715157, p = 2.91 × 10 −8 ) and gene-based (p = 1.48 × 10 −7 ) level. Our results confirm the potential role of the PCLO gene in MDD, which is worth further replication and functional studies.Keywords: major depressive disorder, genome-wide association study, genetics, PCLO In 2009, as part of the Genetic Association Information Network (GAIN) initiative, we published (Sullivan et al., 2009) the first genome-wide association study (GWAS) for major depressive disorder (MDD). The participants were assembled from two large Dutch cohorts: the Netherlands Study of Depression and Anxiety (NESDA) and the Netherlands Twin Registry (NTR). A comparison between 1,738 cases with lifetime diagnosis of DSM-IV MDD and 1,802 screened controls highlighted a signal overlapping the region of PCLO gene, although variants identified did not reach genome-wide significance. Importantly, our result received strong support (though not reaching formal significance) from Australian data similarly ascertained from a population twin registry (Sullivan et al., 2009). Based on the promising role of PCLO encoding a cytoskeletal protein located in the presynaptic active zone, the original finding was followed by replication efforts, with positive (Hek et al., 2010) and negative (Verbeek et al., 2013) results. In the present study, we revisited the original GWAS after introducing important improvements. The overall sample size was almost doubled, adding newly genotyped participants from the original cohorts, consisting mainly of a large number of controls carefully screened using several sources of information including longitudinal assessments and family history (Boomsma et al., 2008). The number of interrogated SNPs was increased by re-genotyping the majority of participants on a newer array and by imputing variants with a denser reference panel (1,000 Genomes Phase 3).The present sample consisted of 6,507 participants (63.1% females) of European ancestry from NESDA and NTR. Lifetime MDD diagnoses according to DSM-IV were ascertained using the Composite Interview Diagnostic Instrument. Healthy controls were screened based on absence of any lifetime psychiatric disorder (NESDA), no report of MDD, no known first-degree relatives with MDD, and a low factor score based on a multivariate analysis of depressive complaints, anxiety, neuroticism, and somatic anxiety (Boomsma et al., 2000). After applying stringent quality control criteria (Supplementary Methods), we performed a GWAS comparing 1,942 cases and 4,565 controls,
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