Table 1
Descriptive statistics of the study group.
| Diagnosis | Number (n) | Mean age ± SEM | Females % | ||
|---|---|---|---|---|---|
| Depression or Dysthymia + Alcohol dependence or abuse diagnosis (AUD) | 76 | 46.6 ± 1.220 | 43.3 | ||
| Individuals with an alcohol dependence or abuse diagnosis (AUD) | 446 | 47.1 ± 0.550 | 15.1 | ||
| Individuals without an alcohol or dependence diagnosis (AUD) | 517 | 46.2 ± 0.494 | 19.5 | ||
| Total | 1039 | ||||
Table 2
The Sample sets used.
| Sample sets | Cases number n | Controls number n |
|---|---|---|
| 1. Depression or Dysthymia + AUD diagnosis vs individuals without psychiatric symptoms | 76 | 517 |
| 2. Individuals with an AUD diagnosis vs individuals without psychiatric symptoms | 446 | 517 |
| 3. Depression or Dysthymia + AUD diagnosis vs individuals with and without an AUD diagnosis | 76 | 963 |
The SNPs found nominally associated (P < 0.05) in Sample set 1 were investigated in Sample sets 2 and 3.
Table 3
Descriptive statistics of the continuous variables for Sample set 1.
| Variable name | Score range | Group | Total n | Min-Max | Median |
|---|---|---|---|---|---|
| 6-item Global Seasonality Score* (GSS) | 0-18 | Cases | 76 | 0-13 | 6.00 |
| Controls | 517 | 0-18 | 4.00 | ||
| 21-item Beck Depression Inventory* (BDI) | 0-55 | Cases | 76 | 0-44 | 18.50 |
| Controls | 517 | 0-24 | 3.00 | ||
| 12-item General Health Questionnaire* (GHQ) | 0-36 | Cases | 76 | 0-12 | 7.00 |
| Controls | 517 | 0-12 | 0.00 | ||
| Maslach Burnout Inventory-General* (MBI) | 0-16 | Cases | 76 | 0.26-4.73 | 2.18 |
| Controls | 517 | 0.00-3.88 | 0.79 | ||
| Length of night sleep (h) | 4-12 | Cases | 76 | 4-12 | 6.00 |
| Controls | 517 | 4-11 | 7.00 |
* GSS, BDI, GHQ and MBI scores were higher for cases than controls in Sample set 1 (P < 0.0001).
Table 4
The 19 circadian clockwork related genes and the 32 SNPs analyzed.
| Gene | Gene name | Location | ID (rs#) of SNPs genotyped |
|---|---|---|---|
| ARNTL | Aryl hydrocarbon receptor nuclear translocator-like | 11p15.2 | (rs2290035, rs3816360, rs2278749) |
| ARNTL2 | Aryl hydrocarbon receptor nuclear translocator-like 2 | 12p12.2-p11.2 | (rs4964057, rs2306074, rs7958822, rs1037921) |
| CLOCK | Clock homolog (mouse) | 4q12 | (rs3805151, rs2412648, rs11240, rs2412646) |
| NPAS2 | Neuronal PAS domain protein 2 | 2q11.2 | (rs11541353, rs2305160) |
| PER2 | Period homolog 2 (Drosophila) | 2q37.3 | (Spanagel/10870, rs2304672) |
| TIMELESS | Timeless homolog (Drosophila) | 12q13.2 | (rs2291739, rs2291738) |
| ACADS | Acyl-Coenzyme Adehydrogenase, C-2 to C-3 short chain | 12q22-qter | (rs1799958/rs17848088) |
| ADA | Adenosine deaminase | 20q12-q13.11 | (Asp8Asn) |
| ADCYAP1 | Adenylate cyclase activating polypeptide 1 (pituitary) | 18p11.32 | (rs2856966) |
| DRD2 | Dopamine receptor D2 | 11q23.1 | (rs6277) |
| ANKK1 | Ankyrin repeat and kinase domain containing 1 | 11q23.1 | (rs1800497) |
| FDFT1 | Farnesyl-diphosphate farnesyltransferase 1 | 8p23.1-p22 | (rs11549147) |
| GLO1 | Glyoxalase I | 6p21.3-p21.1 | (rs2736654) |
| OPN4 | LIM domain binding 3;opsin 4 (melanopsin) | 10q23.2 | (rs1079610) |
| NCOA3 | Nuclear receptor coactivator 3 | 20q13.12 | (rs6094752, rs2230782) |
| NPY | Neuropeptide Y | 7p15.1 | (rs16139) |
| PLCB4 | Phospholipase C, beta 4 | 20p12 | (rs6077510) |
| VIP | vasoactive intestinal peptide | 6q25.2 | (rs3823082, rs688136) |
| VIPR2 | Vasoactive intestinal peptide receptor 2 | 7q36.3 | (rsS885863) |
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database http://www.genenames.org/, the location and rs# were taken from the NCBI Entrez Gene and dbSNP BUILD 129 database respectively http://www.ncbi.nlm.nih.gov/. TagSNPs were selected using HapMap (The International HapMap Consortium, 2005). Note: Historically DRD2 Taq1A (rs1800497) has been assigned to DRD2 whereas more recent data have indicated that the SNP is actually located within the coding region of ANKK1.
Table 5
SNP allele and genotype frequency association analysis for the three Sample sets.
| Gene | Function | SNP | Alleles | Sample set | MAF A/U | OR (95% CI)* | P-values allele | P-values genotype | |||
|---|---|---|---|---|---|---|---|---|---|---|---|
| * | Empirical | Cochran- Armitage trend* | Dominant model* | Recessive model* | |||||||
| CLOCK | Intron | rs11240 | G/C | 1. | 0.44/0.33 | 1.65 (1.14-2.38) | 0.0077 | 0.0072 | 0.0077 | 0.055 | 0.013 |
| 2. | 0.33/0.33 | 1.02 (0.85-1.24) | Ns | Ns | Ns | Ns | Ns | ||||
| 3. | 0.44/0.33 | 1.59 (1.13-2.26) | 0.0084 | 0.0068 | 0.0082 | 0.048 | 0.016 | ||||
| ARNTL2 | Intron | rs2306074 | C/T | 1. | 0.30/0.35 | 0.77 (0.53-1.12) | Ns | Ns | Ns | 0.043 | Ns |
| 2. | 0.33/0.35 | 0.90 (0.74-1.09) | Ns | Ns | Ns | Ns | Ns | ||||
| 3. | 0.30/0.34 | 0.80 (0.55-1.15) | Ns | Ns | Ns | 0.056 | Ns | ||||
| ACADS | Mis-sense mutation | rs1799958 | A/G | 1. | 0.34/0.26 | 1.47 (1.01-2.15) | 0.045 | 0.044 | 0.045 | 0.097 | Ns |
| 2. | 0.28/0.26 | 1.11 (0.91-1.37) | Ns | Ns | Ns | Ns | Ns | ||||
| 3. | 0.34/0.27 | 1.44 (1.01-2.07) | 0.046 | 0.040 | 0.046 | 0.097 | Ns | ||||
SNPs which showed nominal association (allelic or genotypic) P < 0.05 for Sample set 1 are displayed as are the p-values P < 0.1. Ns = non significant. Analysis in Sample set 2 and 3 were then performed for these SNPs. Alleles: the minor allele first. Odds ratio (OR): the proportion of minor versus major allele in the affected (A) divided by the proportion of minor versus major allele in the non-affected (U) individuals. Empirical P is the point-wise P-value after 10,000 permutations.* gender was used as covariate.
Table 6
Haplotype association analysis of CLOCK.
| SNP block | Haplotype | Sample set | Overall frequency | OR (95% CI) | P-value | |
|---|---|---|---|---|---|---|
| rs3805151-rs2412648-rs11240-rs2412646 | TTGC | 1. | 0.34 | 1.65 (1.14-2.28) | 0.0077 | |
| 2. | 0.33 | Ns | Ns | |||
| 3. | 0.34 | 1.50 (1.14-2.27) | 0.0084 | |||
| rs11240-rs2412646 | GC | 1. | 0.34 | 1.65 (1.15-2.29) | 0.0077 | |
| 2. | 0.28 | Ns | Ns | |||
| 3. | 0.34 | 1.50 (1.14-2.27) | 0.0084 | |||
Ns = non significant (P > 0.1). Odds ratio (OR): the ratio specific haplotype versus all other haplotypes among the cases, relative to the ratio specific haplotype versus all other haplotypes among the controls. Gender was used as covariate.