A Genome-Wide Significant Linkage for Severe Depression on Chromosome 3: The Depression Network Study

Sibling pairs affected with recurrent unipolar depression were recruited from eight clinical sites (Aarhus, Denmark; Bonn, Germany; Dublin; Lausanne, Switzerland; St. Louis; London; Cardiff, United Kingdom; and Birmingham, United Kingdom). Probands were all of European ancestry. Eligibility criteria were as follows: age ≥18 years; at least one affected sibling, not a monozygotic twin, also age ≥18 years; and both siblings experiencing ≥2 depressive episodes of at least moderate severity separated by at least 2 months of remission as defined by DSM-IV (14) or ICD-10-DCR (15) criteria. Pairs were excluded if either sibling had ever fulfilled criteria for mania, hypomania, or schizophrenia or if either experienced psychotic symptoms that were mood incongruent or present when there was no evidence of a mood disturbance. Other exclusion criteria were intravenous drug dependency and depression occurring solely in relation to alcohol use. All participants gave written informed consent for participation in the study. For further details regarding the study sample, see Farmer et al. (16).

All participants were interviewed using the Schedules for Clinical Assessment in Neuropsychiatry (15, 17). Items of psychopathology in the interview were rated for presence and severity according to the worst and second worst episodes of depression identified by the participant. For rating severity, individuals were asked about the 4- to 6-week period when their symptoms were at their worst during each episode (peak intensity). The majority of items in the interview are coded as follows: 0=absence of the item; 1=present but to a mild degree or intermittently; 2=moderately severe and present for >50% of the peak intensity period or severe but present for <50% of the peak intensity period; and 3=severe for >50% of the peak intensity period. The computerized version of the interview (18) provides diagnoses according to DSM-IV and ICD-10-DCR. All interviewers from each site attended a 4-day training course, and all took part in a joint interrater reliability exercise. Further details regarding clinical assessment are provided by Farmer et al. (16).

At the time of interview, 25 ml of whole blood was collected in (ethylenediaminetetraacetic acid containing) Monovette tubes. In addition, drops of blood were placed on a Guthrie blood spot card. The blood samples were labeled with a bar code, gently mixed, and stored frozen upright in a –20°C freezer pending DNA extraction.

Genotyping was performed using standard methods by deCODE Genetics (Reykjavik, Iceland). Briefly, 1,130 microsatellite markers were typed in two waves of genotyping. A total of 350 individuals from wave 1 were regenotyped to ensure marker allele calling consistency. Seventy-five markers with Hardy-Weinberg equilibrium p values <0.001 were excluded. After exclusions, marker density was 3.3 cM, with a maximum gap of 10.2 cM. The average heterozygosity was 72.4%.

All phenotypic information from interviews and questionnaires was coded and all blood samples were bar coded by assigning a number to each participant and removing any personal identifying information. The software program MERLIN (Multipoint Engine for Rapid Likelihood INference [19]) was used to perform nonparametric dichotomous linkage analysis. The deCODE, version 5, map was used for all analyses. Allele frequencies were estimated with the maximum likelihood option in MERLIN, using the entire sample. MERLIN multipoint LOD scores were calculated at each marker and at 10 positions between them. Specifically, we used MERLIN's algorithm for calculation of the Whittemore and Halpern nonparametric linkage pairs statistics (Z scores) (20), which the algorithm converts to LOD scores using the model described by Kong and Cox (21).

Relationships were examined using the graphical representation of relationships application (22), which detected half-siblings coded as full siblings (N=5), duplicate samples or monozygotic twins (N=3), and unexpected relatedness (N=14). PEDSTATS (23) was used to detect mendelization errors (N=674), which were found in 201 families (range: 1–18) across 303 markers (range: 1–54), with all genotypes (N=3,194) for the specific marker within the family showing the error recoded as fails. In addition, the “error” procedure was used to remove unlikely recombinants, while the “simulate” procedure was used to empirically estimate the false positive rate (1,000 simulations with the largest single family dropped to speed computation).

The general structure of the cohort consisted of sibling pairs without parents (58%) or sibling trios (16%). The average size of informative families was 2.45 persons, with the majority (82.1%) having one generation with two or more affected offspring. Families with three, four, and five or more affected offspring represented 17.7%, 5.4%, and 1.5% of the sample, respectively. Details of the number of probands and affected relatives genotyped from each collection site are presented in Table 1. Table 2 shows the clinical characteristics for each phenotype. Three different phenotypes were analyzed. In addition to affected status based on recurrent depression, two additional and more restrictive diagnostic categories were generated (severe recurrent depression and very severe recurrent depression). These categories were based on severity as measured by impairment. It should be noted that the minimum score for items on the Schedules for Clinical Assessment in Neuropsychiatry for each episode was 2, with a potential range of 0–3 (i.e., the sample was selected to have a certain minimum impairment severity for each episode). To generate the phenotypes, the impairment severity scores for the worst and second worst episodes from the assessment scale were summed. To be considered affected in the recurrent depression, severe recurrent depression, or very severe recurrent depression categories, participants needed to have summed severity scores of at least 4, 5, or 6, respectively, in addition to meeting diagnostic criteria for depression in each episode. Since the categories were based on a minimum score, the phenotypes were nested.

Case patients and comparison subjects were drawn from two studies of recurrent depression (the Depression Case Control study and the Depression Network Study) using identical methods of case definition and the aforementioned phenotyping. The studies were approved by the local ethical committees, and written informed consent was obtained from all participants. The Depression Case Control sample consists of 1,346 recurrent depression patients (women: 69.3%) fulfilling DSM-IV and/or ICD-10 criteria of at least moderate severity and who were ascertained from the three clinical centers in the United Kingdom (London, Cardiff, and Birmingham). The mean age at onset was 22.9 years (SD=11.3; range: 1–62). Probands from the Depression Network Study were also analyzed (ascertained from all eight clinical sites). For a detailed description of these two samples, see the genome-wide association study (GWAS) conducted by Lewis et al. (24).

Comparison subjects (N=1,288) were contacted via the Medical Research Council general practice research framework and screened using a composite index of depressive and anxiety symptoms and with a telephone interview using the Past History Schedule. The proportion of women in this comparison group was 58.4%, and the mean age was 47.24 years (SD=12.2; range: 20–69). An additional 457 healthy volunteers (women, 61.4%), consisting of staff and students at King's College London, were also screened for mental health disorders using the Past History Schedule.

Genotyping for case patients and comparison subjects was performed by the Centre National de Génotypage using the Illumina HumanHap610-Quad BeadChips (Illumina, Inc., San Diego), which contains 598,723 single nucleotide polymorphism (SNP) markers. Bar-coded DNA samples were received by the Centre National de Génotypage DNA banking facility in standard tubes, together with the sample information. All DNA samples were subjected to stringent quality control, and all processing was carried out under full laboratory information management system control.

The concentrations of all samples were adjusted to 50 ng/μl, and 15 μl of each sample was robotically dispensed into bar-coded 96-well plates. Samples from both case patients and comparison subjects were randomly distributed on the plates. The plates were processed in a fully automated Illumina BeadLab equipped with liquid-handling robots, Illumina BeadArray readers, and Illumina iScans. Genotyping was carried out using the Illumina Human610 quad array according to the manufacturer's recommendations. The raw data were analyzed using Illumina BeadStudio and extracted for statistical analysis.

Stringent quality control procedures were applied to individual and SNP data. Individuals were excluded if their genotypic data showed a missing rate >1%, abnormal heterozygosity, or a sex assignment that conflicted with phenotypic data or that they were related (up to second-degree relatives) to other study participants or were of non-European ancestry. SNPs with a minor allele frequency <1% or showing departure from Hardy-Weinberg equilibrium (p<1×10^–5) were excluded. EIGENSTRAT analysis was performed again following quality control procedures, and the principal components showing significant differences in ancestry between case patients and comparison subjects were used as covariates in association testing (five components for case patients versus screened comparison subjects).

Markers were selected for analysis if they were within the one-LOD interval of a genome-wide significant linkage. The primary test for association between SNPs and depression was logistic regression, including ancestry principal components, assuming a log-additive genetic model but also fitting a dominance-deviance model to allow for recessive or dominant effects. Analyses were carried out for all participants meeting the impairment severity restricted diagnosis (a summed Schedules for Clinical Assessment in Neuropsychiatry item score ≥4), with case patients not meeting these criteria being redefined as comparison subjects. Analysis was carried out using PLINK, version 1.07 (25).

The genome scan results for all three nested phenotypes are shown in Figure 1 and were generated using all available informative families. The most significant results were observed on chromosome 3 for the impairment restricted diagnostic categories, with maximum LOD scores of 4.01 (for severe recurrent and very severe recurrent depression, respectively). The highest LOD score for recurrent depression was on chromosome 11 (LOD=1.79), and the highest LOD score for very severe recurrent depression was on chromosome 7 (LOD=1.91). One peak was genome-wide significant after correction for multiple testing at both the phenotype and marker level, with two adjacent markers achieving an empirical p value <0.05 after simulations. From the simulations, the 5% significance threshold was a LOD score of 3.53, and the suggestive threshold was a LOD score of 2.23, after accounting for the three phenotypes and 1,065 markers examined.

The most significant result observed in our combined analysis was on chromosome 3 using the severe recurrent depression diagnosis, which had a LOD of 4.0 at 19.9 cM (6.4 Mb [National Center for Biotechnology Information Build 36.1]) at marker D3S1515. In this analysis, affected was defined as depression with a minimum total impairment severity score of 5 (Figure 2). A LOD score of 4.0 corresponded with an empirical genome-wide p value of 0.015 after accounting for multiple testing at both markers and phenotypes via simulation of linkage (the proportion of times the observed LOD was exceeded by the maximum LOD scores from 1,000 simulations using MERLIN). Overall, the strongest marker was D3S1515 at 19.9 cM, with a LOD score of 4.0 and an empirical p value of 0.015, while its proximal flanking marker (D3S3591) at 23.9 cM had a LOD score of 3.567 and an empirical p value of 0.038. The distal flanking marker of D3S1515 was D3S2397, with a LOD score of 3.093 and an empirical p value of 0.254, which was the third most significant result. There is only modest support for linkage and reduced allele sharing in the same region for the recurrent depression phenotype, with a LOD score of 1.54, as well as the very severe recurrent depression phenotype, with a LOD score of 1.06. The one-LOD region extends 17.4 cM between markers D3S3706 (multipoint LOD: 2.674) and D3S1263 (multipoint LOD: 2.844) and covers approximately 7.3 Mb on hg18.

In examining allele sharing in the sample at the maximum LOD marker (D3S1515) using the standardized Kong and Cox (21) allele sharing parameter delta, which MERLIN outputs, the model demonstrated that allele sharing increased when restricting to severe recurrent depression and remained the same when restricting further. Specifically, the Kong and Cox delta was 0.125 for recurrent depression, 0.229 for severe recurrent depression, and 0.234 for very severe recurrent depression. We note that while the allele sharing was similar between the two restricted diagnoses, the severe recurrent depression diagnosis had a much larger number of concordant sibling pairs and thus greater power.

No other peaks approached significance. The next most significant result after that observed on chromosome 3 was for very severe recurrent depression on chromosome 7, with a LOD score of 1.91 at 23.2 cM at marker D7S513 (11.6 Mb on hg18). This was the narrowest criteria used, and affected status was restricted to individuals with a maximum severity score for both their worst and second worst episodes. When taking into account the other two dichotomous phenotypes, the empirical genome-wide p value was 0.77. There was little support for linkage in the same region for the other diagnostic definitions, with an empirical p value of 1.0 for both phenotypes at this marker.

Selected regions such as chromosomes 1p, 12q, 13q, and 15q, which showed evidence for linkage in wave 1, were examined in detail for the recurrent depression phenotype (7). For chromosome 1p36, wave 1 showed a maximum multipoint LOD of approximately 2 at D1S450. However, there was no evidence for linkage in wave 2, and there was a maximum LOD of 0.75 in the combined wave 1 and 2 analysis (empirical p=1.0). Similar patterns of results were seen for chromosomes 12q and 13q, which showed no evidence for linkage in the combined sample. For chromosome 15, wave 1 had a maximum LOD of 2.44 at 91.8 cM (at marker D15S999), while the combined sample gave a maximum LOD of 1.41 (empirical p=0.98). Additional significant evidence for 15q has been reported after fine mapping with SNPs (26). However, this reported peak is approximately 21 cM distant.

Genome-wide association data were available from 2,960 case patients and 1,594 screened comparison subjects (Figure 3). Logistic regression for SNP case-comparison association was performed in PLINK, version 1.06, adjusting for population stratification and dominance deviance for the severe recurrent depression phenotype, with a restriction to 5% minor allele frequency. After phenotype restriction, there were 1,590 case patients and 1,589 comparison subjects, meaning we compared intermediate severe case patients with screened comparison subjects and with other case patients being dropped from the analysis. There were 214 genes (including isoforms) in the University of California, Santa Cruz, genome browser annotation in the one-LOD interval between (hg18 coordinates) 3,895,145 and 11,636,572 on chromosome 3, as well as 1,878 SNPs, in our annotation. To allow for multiple testing and correlation between SNPs, empirical significance was calculated using the PLINK “mperm” procedure (100,000 case-comparison label permutations). Prior to permutation, no region-wide significant SNP or region-wide excess was observed, with 92 SNPs (4.89%/N=1,878) reaching a nominal level of significance (p<0.05). This remained the case after permutations, with the best SNPs being rs904467 and rs17050210, situated near SETD5, with an uncorrected p value <0.001 and lowest family-wise-corrected empirical p value of 0.19 for rs904467.