Background
Association type | Author | Year | Country | PMID | Subjects number | Key findings |
---|---|---|---|---|---|---|
Genome-wide association studies | Gelernter J et al. [7] | 2014 | USA | 24,166,409 | 16,087 | 1. They confirmed well-known risk loci mapped to alcohol-metabolizing enzyme genes, notably ADH1B in European-American (EA) and African-American (AA) populations and ADH1C in AAs, and identified novel risk loci mapping to the ADH gene cluster on chromosome 4 and extending centromerically beyond it to include GWS associations at LOC100507053 in AAs, PDLIM5 in EAs, and METAP in AAs. 2. They also identified a novel GWS association mapped to chromosome 2 at rs1437396, between MTIF2 and CCDC88A, across all of the EA and AA cohorts, with supportive gene expression evidence, and population-specific GWS for markers on chromosomes 5, 9 and 19. |
Xu K et al. [8] | 2015 | USA | 26,036,284 | 9500 | 1. The results confirmed significant associations of the well-known functional loci at ADH1B with MaxDrinks in EAs and AAs. The region of significant association on chromosome 4 was extended to LOC100507053 in AAs but not EAs. 2. They also identified potentially novel significant common SNPs for MaxDrinks in EAs: rs1799876 at SERPINC1 on chromosome 1 and rs2309169 close to ANKRD36 on chromosome 2. | |
Mbarek H et al. [5] | 2015 | Netherlands | 26,365,420 | 7842 | 1. GWAS SNP effect concordance analysis was performed between GWAS and a recent alcohol dependence GWAS using DSM-IV diagnosis. The twin-based heritability of alcohol dependence-AUDIT was estimated at 60% (55–69%). 2. GCTA showed that common SNPs jointly capture 33% of this heritability. 3. The top hits were positioned within 4 regions (4q31.1, 2p16.1, 6q25.1, 7p14.1) with the strongest association detected for rs55768019. | |
Polimanti R et al. [11] | 2017 | USA | 26,458,734 | 5546 | 1. In the stage 1 sample, they observed 3 GWS SNP associations, rs200889048 and rs12490016 in EAs and rs1630623 in AAs and EAs meta-analyzed. 2. In the stage 2 sample, they replicated 278, 253 and 168 of the stage 1 suggestive loci in AAs, EAs, and AAs and EAs meta-analyzed, respectively. A meta-analysis of stage 1 and stage 2 samples identified 2 additional GWS signals: rs28562191 in EAs and rs56950471 in AAs | |
Meyers JL et al. [9] | 2017 | USA | 28,070,124 | 2382 | 1. Ten correlated SNPs located in an intergenic region on chromosome 3q26 were associated with fast beta (20–28 Hz) EEG power at P < 5 × 10–8. The most significantly associated SNP, rs11720469 is an expression quantitative trait locus for butyrylcholinesterase, expressed in thalamus tissue. 2. Four of the genome-wide SNPs were also associated with alcohol dependence, and two (rs13093097, rs7428372) were replicated in an independent AA sample. 3. Analyses in the AA adolescent/young adult subsample indicated association of rs11720469 with heavy episodic drinking (frequency of consuming 5+ drinks within 24 h). | |
Phenome-wide association studies | Polimanti R et al. [10] | 2016 | USA | 27,187,070 | 26,394 | 1. They replicated prior associations with drinking behaviors and identified multiple novel phenome-wide significant and suggestive findings related to psychological traits, socioeconomic status, vascular/metabolic conditions, and reproductive health. 2. They applied Bayesian network learning algorithms to provide insight into the causative relationships of the novel ADH1B associations: ADH1B appears to affect phenotypic traits via both alcohol-mediated and alcohol-independent effects. They replicated the novel ADH1B associations related to socioeconomic status (household gross income and highest grade finished in school). 3. For CHRNA3-CHRNA5 risk alleles, they replicated association with smoking behaviors, lung cancer, and asthma. There were also novel suggestive CHRNA3-CHRNA5 findings with respect to high-cholesterol-medication use and distrustful attitude. |
Methods
Article search and selection criteria
Number | Inclusion criteria |
1 | Case-control studies. |
2 | The studies evaluated the associations between OPRM1 A118G polymorphism and alcohol dependence. |
3 | The studies included detailed genotyping data (total number of cases and controls, number of cases and controls with A/A, A/G, and G/G genotypes). |
4 | Studies focusing on human being. |
Number | Exclusion criteria |
1 | The design of the experiments was not case-control. |
2 | The source of cases and controls, and other essential information were not provided. |
3 | The genotype distribution of the control population was not in accordance with the Hardy–Weinberg equilibrium (HWE). |
4 | Reviews and duplicated publications. |
Data extraction
Methodological qualities
Criteria | Score |
---|---|
1. Representativeness of cases | |
RA diagnosed according to acknowledged criteria. | 2 |
Mentioned the diagnosed criteria but not specifically described. | 1 |
Not Mentioned. | 0 |
2. Source of controls | |
Population or community based | 3 |
Hospital-based RA-free controls | 2 |
Healthy volunteers without total description | 1 |
RA-free controls with related diseases | 0.5 |
Not described | 0 |
3. Sample size | |
> 300 | 2 |
200–300 | 1 |
< 200 | 0 |
4. Quality control of genotyping methods | |
Repetition of partial/total tested samples with a different method | 2 |
Repetition of partial/total tested samples with the same method | 1 |
Not described | 0 |
5. Hardy-Weinberg equilibrium (HWE) | |
Hardy-Weinberg equilibrium in control subjects | 1 |
Hardy-Weinberg disequilibrium in control subjects | 0 |
Statistical analysis
Statistic means | Goals and Usages | Explanation |
---|---|---|
Labbe plot | To evaluate heterogeneity between the included studies | In Labbe figure, if the points basically present as a linear distribution, it can be taken as an evidence of homogeneity. |
Cochran’s Q test | To evaluate heterogeneity between the included studies | Cochran’s Q test is an extension to the McNemar test for related samples that provides a method for testing for differences between three or more matched sets of frequencies or proportions. Heterogeneity was also considered significant if P < 0.05 using the Cochran’s Q test. |
I2 index test | To evaluate heterogeneity between the included studies | The I2 index measures the extent of true heterogeneity dividing the difference between the result of the Q test and its degrees of freedom (k – 1) by the Q value itself, and multiplied by 100. I2 values of 25%, 50% and 75% were used as evidence of low, moderate and high heterogeneity, respectively. |
Sensitivity analysis | To examine the stability of the pooled results | A sensitivity analysis was performed using the one-at-a-time method, which involved omitting one study at a time and repeating the meta-analysis. If the omission of one study significantly changed the result, it implied that the result was sensitive to the studies included. |
Contour-enhanced funnel plot | Publication bias test | Visual inspection of the Contour-enhanced funnel plots was used to assess potential publication bias. Asymmetry in the plots, which may be due to studies missing on the left-hand side of the plot that represents low statistical significance, suggested publication bias. If studies were missing in the high statistical significance areas (on the right-hand side of the plot), the funnel asymmetry was not considered to be due to publication bias |
Results
Search results and study characteristics
Author | Year | Country | Ethnicity | Disease type | Genotyping | Source of controls | Alcohol-dependence (n) | Controls (n) | P for HWE | Quality | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Total | AA | AG | GG | Total | AA | AG | GG | |||||||||
Bergen et al. | 1997 | USA | Caucasian | Alcohol-dependence | Direct sequencing and PCR-RFLP | Population-based | 160 | 123 | 35 | 2 | 264 | 204 | 59 | 1 | 0.1285 | 7 |
Sander et al. | 1998 | German | Caucasian | Alcohol-dependence | PCR-RFLP | Population-based | 327 | 261 | 62 | 4 | 340 | 289 | 49 | 2 | 0.9606 | 6 |
Franke et al. | 2001 | German | Caucasian | Alcohol-dependence | Direct sequencing and PCR-RFLP | Mixed | 221 | 170 | 50 | 1 | 365 | 284 | 74 | 7 | 0.4024 | 8 |
Schinka et al. | 2002 | USA | Caucasian | Alcohol-dependence | Puregene™ kit or standard phenol-chloroform method | Population-based | 179 | 152 | 27 | 0 | 297 | 220 | 73 | 4 | 0.4531 | 7 |
Kim et al. | 2004 | Korea | Asian | Alcohol-dependence | PCR-RFLP | Hospital-based | 100 | 46 | 47 | 7 | 128 | 54 | 53 | 21 | 0.2014 | 8 |
Kim et al. | 2004 | Korea | Asian | Alcohol-dependence | PCR-RFLP | Hospital-based | 112 | 37 | 61 | 14 | 140 | 68 | 57 | 15 | 0.5582 | 7 |
Loh et al. | 2004 | China Taiwan | Asian | Alcohol-dependence | PCR-RFLP | Mixed | 154 | 59 | 77 | 18 | 146 | 70 | 56 | 20 | 0.1136 | 8 |
Bart et al. | 2005 | USA | Caucasian | Alcohol-dependence | PCR-RFLP | Population-based | 389 | 299 | 90 | 170 | 147 | 23 | Not available | 8 | ||
Nishizawa et al. | 2006 | Japan | Asian | Alcohol-dependence | PCR-RFLP | Population-based | 64 | 12 | 37 | 15 | 74 | 26 | 33 | 15 | 0.4493 | 8 |
Zhang et al. | 2006 | USA and Russia | Caucasian | Alcohol-dependence | PCR-RFLP | Mixed | 318 | 246 | 68 | 4 | 338 | 256 | 78 | 4 | 0.4713 | 7 |
Deb et al. | 2010 | India | Asian | Alcohol-dependence | PCR-RFLP | Mixed | 53 | 16 | 32 | 5 | 82 | 44 | 30 | 8 | 0.3967 | 8 |
Miranda et al. | 2010 | USA | Caucasian | Alcohol-dependence | TaqMan assays | Population-based | 27 | 13 | 14 | 160 | 134 | 26 | > 0.05 | 8 | ||
Dou et al. | 2011 | China | Asian | Alcohol-dependence | PCR-RFLP | Population-based | 118 | 48 | 53 | 17 | 218 | 74 | 110 | 34 | 0.5127 | 6 |
Koller et al. | 2012 | Germany | Caucasian | Alcohol-dependence | Fluorescence resonance energy transfer method | Hospital-based | 1845 | 1461 | 353 | 31 | 1863 | 1417 | 419 | 27 | 0.5275 | 9 |
Huang et al. | 2012 | China | Asian | Alcohol-dependence | PCR-RFLP | Population-based | 45 | 33 | 11 | 1 | 45 | 33 | 12 | 0 | 0.3021 | 6 |
Francesc | 2015 | Spain | Caucasian | Alcohol-dependence | PCR-RFLP | Population-based | 630 | 425 | 190 | 15 | 133 | 101 | 30 | 2 | 0.893 | 7 |
Jin | 2015 | China | Asian | Alcohol-dependence | PCR-RFLP | Population-based | 58 | 41 | 12 | 5 | 50 | 39 | 9 | 2 | 0.1487 | 7 |
Meta-analysis results
Genetic model | Heterogeneity test | Test of Association | Publication bias | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Name | Explanation | Ethnicity | Q value | d.f. | I-squared | Tau-squared |
P Value | Heterogeneity | Effect model | Pooled OR | 95% CI | Z value |
P value | Statistical significance | |
Allele model | G vs. A | Caucasian | 17.38 | 6 | 65.5% | 0.0493 | 0.008 | Yes | Random | 0.985 | [0.797, 1.217] | 0.14 | 0.888 | No | No |
Asian | 14.90 | 7 | 53.0% | 0.0564 | 0.037 | Yes | Random | 1.100 | [0.871, 1.390] | 0.80 | 0.421 | No | |||
Total | 34.85 | 14 | 59.8% | 0.0487 | 0.002 | Yes | Random | 1.037 | [0.890, 1.210] | 0.47 | 0.640 | No | |||
Homozygote model | GG vs. AA | Caucasian | 5.60 | 6 | 0.0% | NA | 0.469 | No | Random | 1.119 | [0.731, 1.714] | 0.52 | 0.605 | No | No |
Asian | 10.22 | 7 | 31.5% | NA | 0.176 | No | Random | 1.146 | [0.743, 1.767] | 0.62 | 0.538 | No | |||
Total | 15.81 | 14 | 11.4% | NA | 0.325 | No | Random | 1.118 | [0.830, 1.506] | 0.74 | 0.462 | No | |||
Heterozygote model | AG vs. AA | Caucasian | 16.71 | 6 | 64.1% | 0.0575 | 0.010 | Yes | Random | 0.983 | [0.780, 1.237] | 0.15 | 0.882 | No | No |
Asian | 15.58 | 7 | 55.1% | 0.1296 | 0.029 | Yes | Random | 1.433 | [1.015, 2.023] | 2.04 | 0.041 | No | |||
Total | 42.72 | 14 | 67.2% | 0.1017 | 0.000 | Yes | Random | 1.155 | [0.935, 1.427] | 1.34 | 0.181 | No | |||
Dominant model | AG + GG vs. AA | Caucasian | 41.43 | 8 | 80.7% | 0.1518 | 0.000 | Yes | Random | 1.185 | [0.882, 1.593] | 1.13 | 0.259 | No | No |
Asian | 16.65 | 7 | 58.0% | 0.1310 | 0.020 | Yes | Random | 1.379 | [0.983, 1.934] | 1.86 | 0.063 | No | |||
Total | 63.64 | 16 | 74.9% | 0.1467 | 0.000 | Yes | Random | 1.261 | [1.008, 1.578] | 2.03 | 0.042 | No | |||
Recessive model | GG vs. AA + AG | Caucasian | 5.24 | 6 | 0.0% | NA | 0.513 | No | Random | 1.142 | [0.746, 1.747] | 0.61 | 0.542 | No | No |
Asian | 6.21 | 7 | 0.0% | NA | 0.516 | No | Random | 0.919 | [0.673, 1.255] | 0.53 | 0.595 | No | |||
Total | 12.06 | 14 | 0.0% | NA | 0.602 | No | Random | 0.991 | [0.771, 1.275] | 0.07 | 0.946 | No |