Rare apoptosis-promoting functional variants in the apoptosis protease activating factor 1 (APAF1) gene were recently reported to co-segregate with major depression in male members of families from Utah. In order to estimate the impact of these variants on risk for major depressive disorder (MDD) in the general population, we surveyed the frequency of the APAF1 putative MDD risk alleles using re-sequencing in a large sample of northern European and European-American subjects, including a large number of males with MDD. The E777K and N782T APAF1 variants previously described by Harlan et al. [Harlan et al. (2006) Mol Psychiatry 11(1):76–85] were found at low frequencies in affected individuals and population controls. The C450W and Q465R variants were not detected in any of the 632 subjects sequenced. These results show that the APAF1 variants associated with risk for MDD in the Utah pedigrees are very rare in Northern European and European-American populations. In addition, the E777K and N782T variants were found at low frequencies both in patients and population controls, suggesting that these variants have limited impact on risk for MDD.
apoptosis; apoptotic protease-activating factor 1; genetic predisposition; mood disorders; single nucleotide polymorphism
The relative importance of specific genetic and environmental factors in regulating nicotine dependence (ND) risk, including the effects on specific forms of childhood adversity on smoking risk, have been understudied. Genome-wide association studies and rodent models have demonstrated that the α5 nicotinic acetylcholine receptor gene (CHRNA5) is important in regulating nicotine intake. Childhood adversity increases the methylation level of the CHRNA5 promoter region in European Americans (EAs), an effect that was observed only in males (Zhang et al, submitted for publication). In view of this potential sex difference in the effects of early life experience on smoking, we investigated the presence of a sex-specific gene-by-environment effect of this marker on ND risk. A nonsynonymous SNP in CHRNA5 previously associated to ND and several related traits, rs16969968, was genotyped in 2206 EAs (1301 men and 905 women). The main and interactive effects of childhood adversity and rs16969968 genotype on diagnosis of ND and ND defined by dichotomized Fagerstrom test for ND (FTND) scores were explored. Men and women were analyzed separately to test for sex differences. Childhood adversity significantly increased ND risk in both sexes, and the effect in women was twice than that in men. Significant interactive effects of childhood adversity and rs16969968 genotype were observed in men (ND: OR=1.80, 95% CI=1.18–2.73, P=0.0044; FTND: OR=1.79, 95% CI=1.11–2.88, P=0.012). No interaction was found in women. This study provides evidence of a sex-specific gene × environment effect of CHRNA5 and childhood adversity on the risk for ND.
CHRNA5; childhood adversity; gene–environment interaction; nicotine dependence; Fagerstrom test for nicotine dependence score; acetylcholine; addiction & substance abuse; neurogenetics; psychiatry & behavioral sciences; CHRNA5; childhood adversity; gene–environment interaction; nicotine dependence; Fagerstrom test for nicotine dependence score
Summary: Genotype calling from high-throughput platforms such as Illumina and Affymetrix is a critical step in data processing, so that accurate information on genetic variants can be obtained for phenotype–genotype association studies. A number of algorithms have been developed to infer genotypes from data generated through the Illumina BeadStation platform, including GenCall, GenoSNP, Illuminus and CRLMM. Most of these algorithms are built on population-based statistical models to genotype every SNP in turn, such as GenCall with the GenTrain clustering algorithm, and require a large reference population to perform well. These approaches may not work well for rare variants where only a small proportion of the individuals carry the variant. A fundamentally different approach, implemented in GenoSNP, adopts a single nucleotide polymorphism (SNP)-based model to infer genotypes of all the SNPs in one individual, making it an appealing alternative to call rare variants. However, compared to the population-based strategies, more SNPs in GenoSNP may fail the Hardy–Weinberg Equilibrium test. To take advantage of both strategies, we propose a two-stage SNP calling procedure, named the modified mixture model (M3), to improve call accuracy for both common and rare variants. The effectiveness of our approach is demonstrated through applications to genotype calling on a set of HapMap samples used for quality control purpose in a large case–control study of cocaine dependence. The increase in power with M3 is greater for rare variants than for common variants depending on the model.
Availability: M3 algorithm: http://bioinformatics.med.yale.edu/group.
Contact: email@example.com; firstname.lastname@example.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Personality correlates highly with both cocaine and nicotine dependencies (CD, ND), and their co-morbid psychopathologies. However, little is known about the nature of these relationships. This study examined if environment (marriage) or genetics (a single SNP, CHRNA5*rs16969968) would moderate the correlation of personality with CD, ND and cocaine-induced paranoia (CIP) in African and European Americans (AAs, EAs).
1432 EAs and 1513 AAs were examined using logistic regression. Personality was assessed by NEO-PI-R, while CD, ND and CIP were diagnosed according to DSM-IV. ND and CD were examined as binary traits and for the analysis of CIP, subjects were divided into 3 groups: (A) Controls with no CIP; (B) CD cases without CIP; and (C) CD cases with CIP. Multiple testing was Bonferroni-corrected.
For CD and ND in the EA population, marital status proved to be a significant moderator in their relationship with openness only (OR = 1.90, 95%CI = 1.36–2.64, p = 1.54e-04 and OR = 2.12, 95%CI = 1.52–2.90, p = 4.65e-06 respectively). For CIP, marriage was observed to moderate its correlation with openness and neuroticism (OR = 1.39, 95%CI = 1.18–1.63, p = 7.64e-04 and OR = 1.26, 95%CI = 1.12–1.42, p = 1.27e-03 respectively). The correlations moderated by rs16969968 were those of conscientiousness and CD (OR = 1.62, 95%CI: 1.23–2.12, p = 8.94e-04) as well as CIP (OR = 1.21, 95%CI: 1.11–1.32, p = 4.93e-04 when comparing group A versus group C). No significant interactions were observed in AA population. The Bonferroni-corrected significance threshold was set to be 1.67e-03.
The role of personality in CD and CIP may be interceded by both environment and genetics, while in ND by environment only.
Previous studies using SAGE (the Study of Addiction: Genetics and Environment) and COGA (the Collaborative Study on the Genetics of Alcoholism) genome-wide association study (GWAS) data sets reported several risk loci for alcohol dependence (AD), which have not yet been well replicated independently or confirmed by functional studies. We combined these two data sets, now publicly available, to increase the study power, in order to identify replicable, functional, and significant risk regions for AD. A total of 4116 subjects (1409 European-American (EA) cases with AD, 1518 EA controls, 681 African-American (AA) cases, and 508 AA controls) underwent association analysis. An additional 443 subjects underwent expression quantitative trait locus (eQTL) analysis. Genome-wide association analysis was performed in EAs to identify significant risk genes. All available markers in the genome-wide significant risk genes were tested in AAs for associations with AD, and in six HapMap populations and two European samples for associations with gene expression levels. We identified a unique genome-wide significant gene—KIAA0040—that was enriched with many replicable risk SNPs for AD, all of which had significant cis-acting regulatory effects. The distributions of −log(p) values for SNP-disease and SNP-expression associations for all markers in the TNN–KIAA0040 region were consistent across EAs, AAs, and five HapMap populations (0.369⩽r⩽0.824; 2.8 × 10−9⩽p⩽0.032). The most significant SNPs in these populations were in high LD, concentrating in KIAA0040. Finally, expression of KIAA0040 was significantly (1.2 × 10−11⩽p⩽1.5 × 10−6) associated with the expression of numerous genes in the neurotransmitter systems or metabolic pathways previously associated with AD. We concluded that KIAA0040 might harbor a causal variant for AD and thus might directly contribute to risk for this disorder. KIAA0040 might also contribute to the risk of AD via neurotransmitter systems or metabolic pathways that have previously been implicated in the pathophysiology of AD. Alternatively, KIAA0040 might regulate the risk via some interactions with flanking genes TNN and TNR. TNN is involved in neurite outgrowth and cell migration in hippocampal explants, and TNR is an extracellular matrix protein expressed primarily in the central nervous system.
risk region; alcohol dependence; cis-eQTL; GWAS; alcohol & alcoholism; neurogenetics; addiction & substance abuse; biological psychiatry; GWAScis-eQTL; risk region
Adverse childhood experiences (ACEs) increase the risk for adult depression and substance dependence, possibly mediated by the corticotropin-releasing hormone type 1 receptor (CRHR1). In some studies, a three-SNP “T-A-T” haplotype in CRHR1, which encodes CRHR1, exerted a protective moderating effect on risk of depression in adults with ACEs. Other studies have shown a main or moderating effect of SNPs in CRHR1 on alcohol consumption.
We tested the moderating effects of the three-SNP haplotype on lifetime risk of a major depressive episode (MDE) and alcohol dependence (AD) in 1,211 European Americans (EAs) and 1,869 African Americans (AAs), most of whom had a lifetime substance use disorder.
There were no significant main or interaction effects of the TAT haplotype on AD. There was a significant interaction of ACE by TAT on risk of depression only in AA women (p=0.005); each copy of the TAT haplotype reduced the odds of MDE by almost 40% (OR = 0.63). In AA women without an ACE and two TAT haplotypes, the risk of MDE was increased (OR=1.51).
Our findings in relation to the TAT haplotype of CRHR1 extend those obtained in other populations to a largely substance-dependent one. The complex structure of CRHR1 may help to explain why some variants in the gene moderate the effects of an ACE only on depression risk while others moderate the effect of an ACE only on AD risk.
Childhood maltreatment; Association analysis; Genetic risk; Gene by environment interaction; Depression; Alcoholism
Cocaine dependence (CD) and major depressive episode (MDE) frequently co-occur with poorer treatment outcome and higher relapse risk. Shared genetic risk was affirmed; to date, there have been no reports of genomewide linkage scans (GWLSs) surveying the susceptibility regions for comorbid CD and MDE (CD–MDE). We aimed to identify chromosomal regions and candidate genes susceptible to CD, MDE, and CD–MDE in African Americans (AAs) and European Americans (EAs). A total of 1896 individuals were recruited from 384 AA and 355 EA families, each with at least a sibling-pair with CD and/or opioid dependence. Array-based genotyping of about 6000 single-nucleotide polymorphisms was completed for all individuals. Parametric and non-parametric genomewide linkage analyses were performed. We found a genomewide-significant linkage peak on chromosome 7 at 183.4 cM for non-parametric analysis of CD–MDE in AAs (lod=3.8, genomewide empirical p=0.016; point-wise p=0.00001). A nearly genomewide significant linkage was identified for CD–MDE in EAs on chromosome 5 at 14.3 cM (logarithm of odds (lod)=2.95, genomewide empirical p=0.055; point-wise p=0.00012). Parametric analysis corroborated the findings in these two regions and improved the support for the peak on chromosome 5 so that it reached genomewide significance (heterogeneity lod=3.28, genomewide empirical p=0.046; point-wise p=0.00053). This is the first GWLS for CD–MDE. The genomewide significant linkage regions on chromosomes 5 and 7 harbor four particularly promising candidate genes: SRD5A1, UBE3C, PTPRN2, and VIPR2. Replication of the linkage findings in other populations is warranted, as is a focused analysis of the genes located in the linkage regions implicated here.
genomewide linkage scan; affected sib-pair; comorbidity; cocaine dependence; depression; drug dependence; addiction and substance abuse; depression, unipolar/bipolar; neurogenetics; biological psychiatry; genomewide linkage scan; affected sib-pair; comorbidity; cocaine dependence; depression
A single nucleotide polymorphism at the CACNA1C gene (rs1006737) has been reported in genome-wide association studies to be associated with bipolar disorder (BD) with genome-wide significance. However, the neural system effects of CACNA1C that mediate the association are not known. In this study, we assessed associations between rs1006737 variation and both morphology and functional connectivity within a corticolimbic frontotemporal neural system implicated in BD.
A total of 55 European Americans were divided into two groups: a GG group homozygous for the 'G' allele (n = 30) and carriers of the high risk A allele ('A-carrier' group, AA/AG genotypes; n = 25). The subjects participated in both high-resolution structural magnetic resonance imaging (MRI) scans and functional MRI scans during emotional face-processing. Voxel-based morphometry and functional connectivity analyses were performed.
Compared to the GG group, the A-carrier group showed significantly increased gray matter volume and reduced functional connectivity within a corticolimbic frontotemporal neural system (p < 0.05, corrected).
The findings support effects of the rs1006737 variation on the frontotemporal neural system implicated in BD, both in gray matter morphology and functional connectivity. This suggests that influence of CACNA1C variation on corticolimbic structure and function may be a mechanism contributing to the neural circuitry of BD.
bipolar disorder; calcium channels; genetic polymorphism; magnetic resonance imaging; functional magnetic resonance imaging; prefrontal cortex
Next generation sequencing is widely used to study complex diseases because of its ability to identify both common and rare variants without prior single nucleotide polymorphism (SNP) information. Pooled sequencing of implicated target regions can lower costs and allow more samples to be analyzed, thus improving statistical power for disease-associated variant detection. Several methods for disease association tests of pooled data and for optimal pooling designs have been developed under certain assumptions of the pooling process, e.g. equal/unequal contributions to the pool, sequencing depth variation, and error rate. However, these simplified assumptions may not portray the many factors affecting pooled sequencing data quality, such as PCR amplification during target capture and sequencing, reference allele preferential bias, and others. As a result, the properties of the observed data may differ substantially from those expected under the simplified assumptions. Here, we use real datasets from targeted sequencing of pooled samples, together with microarray SNP genotypes of the same subjects, to identify and quantify factors (biases and errors) affecting the observed sequencing data. Through simulations, we find that these factors have a significant impact on the accuracy of allele frequency estimation and the power of association tests. Furthermore, we develop a workflow protocol to incorporate these factors in data analysis to reduce the potential biases and errors in pooled sequencing data and to gain better estimation of allele frequencies. The workflow, Psafe, is available at http://bioinformatics.med.yale.edu/group/.
pooled sequencing; allele frequency estimation; next-generation sequencing; disease association tests
Antisocial personality disorder (ASPD) frequently co-occurs with substance dependence (SD). A functional polymorphism (5-HTTLPR) in the serotonin transporter gene has been widely studied as a risk factor for a variety of psychopathologic conditions, including aggressive/violent behavior. Childhood abuse is an important predictor of ASPD. We examined 5-HTTLPR genotype and adverse childhood events (ACEs) as risk factors for ASPD in a SD sample.
Study participants [602 European Americans (EAs) and 779 African Americans (AAs)] were interviewed to obtain lifetime diagnoses of ASPD and SD and information on ACEs. Tri-allelic genotypes for 5-HTTLPR were obtained using standard methods. We used logistic generalized estimating equations (GEE) regression to examine ACEs and 5-HTTLPR genotype and their interaction as predictors of ASPD, separately by population group.
There were 203 (14.7%) participants diagnosed with ASPD. The frequency of the low-activity 5-HTTLPR S’ allele did not differ by ASPD diagnosis, and there was no overall 5-HTTLPR × ACE interaction. However, among EAs, male sex (OR=3.36; p<0.001) and ACE history (OR=1.47; p=0.002) were significant predictors of ASPD. Among AAs, there was a significant interaction of sex × 5-HTTLPR genotype × ACEs (χ2=13.92, p<0.001). Among AA men, each additional ACE significantly increased the odds of ASPD irrespective of genotype, while among AA women, the effect of ACEs on ASPD was significant only among S’ homozygotes. However, these results are limited by the small sample size in each subgroup, (particularly AA women with S’S’ genotype; N=7) and require replication.
Childhood maltreatment contributes to the risk of antisocial personality disorder, an effect for which there is preliminary evidence of moderation by 5-HTTLPR genotype in AA women.
Serotonin Transporter Gene; SLC6A4; Child Abuse; Antisocial Personality Disorder; gene × environment
Risk of substance dependence (SD) and obesity has been linked to the function of melanocortin peptides encoded by the proopiomelanocortin gene (POMC).
Methods and Results
POMC exons were Sanger sequenced in 280 African Americans (AAs) and 308 European Americans (EAs). Among them, 311 (167 AAs and 114 EAs) were affected with substance (alcohol, cocaine, opioid and/or marijuana) dependence and 277 (113 AAs and164 EAs) were screened controls. We identified 23 variants, including two common polymorphisms (rs10654394 and rs1042571) and 21 rare variants; 12 of which were novel. We used logistic regression to analyze the association between the two common variants and SD or body mass index (BMI), with sex, age, and ancestry proportion as covariates. The common variant rs1042571 in the 3′UTR was significantly associated with BMI in EAs (Overweight: Padj = 0.005; Obese: Padj = 0.018; Overweight+Obese: Padj = 0.002) but not in AAs. The common variant, rs10654394, was not associated with BMI and neither common variant was associated with SD in either population. To evaluate the association between the rare variants and SD or BMI, we collapsed rare variants and tested their prevalence using Fisher’s exact test. In AAs, rare variants were nominally associated with SD overall and with specific SD traits (SD: PFET,1df = 0.026; alcohol dependence: PFET,1df = 0.027; cocaine dependence: PFET,1df = 0.007; marijuana dependence: PFET,1df = 0.050) (the P-value from cocaine dependence analysis survived Bonferroni correction). There was no such effect in EAs. Although the frequency of the rare variants did not differ significantly between the normal-weight group and the overweight or obese group in either population, certain rare exonic variants occurred only in overweight or obese subjects without SD.
These findings suggest that POMC exonic variants may influence risk for both SD and elevated BMI, in a population-specific manner. However, common and rare variants in this gene may exert different effects on these two phenotypes.
The alcohol dehydrogenase 1B gene (ADH1B) is hypothesized to affect predisposition to alcohol dependence (AD) and abuse. A variant of the ADH1B gene (rs1229984 or Arg48His; previously referred to as Arg (*1) and His (*2)) has been reported to be associated with reduced rates of alcohol and drug dependence. Different studies have produced inconclusive results regarding association between rs1229984 (or rs2066702) and substance dependence.
Using the cumulative association study literature from the past 21 years from both English and Chinese-language publications, this meta-analysis seeks to clarify the contradictory findings and to examine whether the aggregate data provide new evidence of significant association.
The results, based on a large sample size (9,638 cases and 9,517 controls), suggested strong associations with alcohol dependence and abuse as well as alcohol-induced liver diseases, with an allelic (Arg vs. His) P value being 1×10−36 and odds ratio (OR) 2.06 (1.84, 2.31) under the random effects model. The dominant and recessive models produced larger ORs of 2.17 and 3.05, respectively. When more stringent criteria and sub-group analyses were imposed, the associations remained consistent, and were strongest in various Asian groups (allelic P = 7×10−42 and OR = 2.24 (1.99, 2.51) with ORs of 2.16 and 4.11 for dominant and recessive models, respectively).
Our findings provide further strong evidence for the involvement of the ADH1B gene in the pathogenesis of alcohol dependence and abuse as well as for some alcohol-induced medical diseases in the multiple ethnic populations, in particular, in certain Asian populations.
Meta-analysis; Addiction; Ethanol Metabolism; Drinking; Liver Disease
There are several studies reporting association of alpha-4 nicotinic acetylcholine receptors (encoded by CHRNA4) with nicotine dependence (ND). A meta-analysis of genomewide linkage studies for ND implicated a single chromosomal region, which includes CHRNA4, as genomewide significant.
After establishing that common variants are unlikely to completely account for this linkage, we investigated the distribution of CHRNA4 rare variants by sequencing the coding exons and flanking intronic regions of CHRNA4 in 209 European American (EA) ND cases and 183 EA controls. Because most of the rare variants that we detected (and all nonsynonymous changes) were in exon 5, we sequenced exon 5 in an additional 1000 ND cases and 1000 non-ND comparison subjects, both of which included equal numbers of EAs and African Americans (AAs).
Comparison subjects had a higher frequency of rare nonsynonymous variants in the exon 5 region (encoding the large intercellular loop of the α4 subunit) (Fisher’s exact test p=0.009; association test p=0.009, OR=0.43; weighted-sum method p=0.014), indicating a protective effect against ND. Considering data from the two stages combined and only nonsynonymous variants predicted to alter protein function, the association was stronger (Fisher’s exact test p=0.005; association test p=0.008, OR=0.29). SPECT imaging results were consistent with functionality.
CHRNA4 functional rare variants may reduce ND risk. This is the first demonstration that rare functional variants at a candidate locus protect against substance dependence, suggesting a novel mechanism of substance dependence heritability that is potentially of general importance.
Nicotine dependence; rare variants; nonsynonymous; CHRNA4; imaging genetics; deep sequencing
Cocaine and opioid dependence are common, complex disorders with high heritability that commonly co-occur with other substance dependence disorders. Improved insight into the genetic basis of substance dependence would help elucidate its etiology and could inform its prevention and treatment. To generate new hypotheses about the genetics of substance dependence, we genotyped 5633 tagging single nucleotide polymorphism (SNP) markers in 1699 subjects from 339 African American (AA) families and 334 European American (EA) families ascertained through a sib pair meeting DSM-IV criteria for either cocaine or opioid dependence. The associations between genetic markers and five substance dependence traits (cocaine dependence, opioid dependence, cocaine-induced paranoia, alcohol dependence, and nicotine dependence) were assessed by family based association tests (FBAT). Results were ranked according to several criteria including statistical significance, concordance of results across population samples, and potential biological relevance of the implicated gene. The top-ranked result was an association of SNP rs1133503 in the MANEA gene with cocaine-induced paranoia (CIP). Our study provides an initial substance dependence trait-specific blue-print of associated regions for future candidate gene studies.
family-based association tests; genomewide association; cocaine dependence; alcohol dependence; nicotine dependence; cocaine-induced paranoia
Depression with psychomotor agitation (PMA; “agitated depression”) is a putative psychiatric phenotype that appears to associate with some forms of substance dependence. However, it is unclear whether such relationships extend across different substances and independent (I-MDE) versus substance-induced (SI-MDE) subtypes of major depressive episodes.
We examined whether lifetime depression with (vs. without) PMA was associated with lifetime substance dependence across individuals with lifetime: (1) I-MDE only (n = 575); and (2) SI-MDE only (n = 1683). Data were pooled from several family and genetic studies of substance dependence in which participants received identical structured interviews to diagnose DSM-IV mental disorders.
In I-MDE, PMA was significantly associated with alcohol, cocaine, opioid, other drug (hallucinogen, inhalant, speed-ball), and sedative dependence. After controlling for demographic and clinical co-factors, PMA's relationship to dependence on opioids, other drugs, and sedatives remained significant, but not its relationship to alcohol or cocaine. In SI-MDE, PMA was significantly associated with alcohol, cocaine, opioid, and other drug dependence. After adjusting for co-factors, associations remained significant for dependence on cocaine and opioids, but not alcohol or other drugs. Relationships between PMA and opioid dependence were stronger in I-MDE than SI-MDE. Depression subtype (I-MDE vs. SI-MDE) did not moderate relations between PMA and non-opioid forms of substance dependence.
Agitated depression associates with certain forms of substance dependence, particularly opioid dependence. MDE subtype did not alter most PMA-dependence associations, which suggests that the mechanisms underlying this comorbidity are complex and potentially bidirectional.
Major Depression; Psychomotor Agitation; Substance Dependence; Agitated Depression; Substance-Induced Depression
Affective disorders (AFDs) are highly comorbid with substance dependence (SD) and both are genetically influenced. However, the specific etiology of the comorbidity is not well understood. We genotyped an array of 1,350 single nucleotide polymorphisms (SNPs) in or near 130 genes in 868 European-Americans (EAs), including 182 individuals with primary AFDs (PAFDs), 214 with SD comorbid with AFD (CAFD), and 472 screened controls. NGFB, which encodes nerve growth factor β and was represented in the array by 15 SNPs, showed the strongest evidence of association, but only among women with PAFDs. Six of the SNPs showed a nominally significant association with PAFDs in women (Ps = 0.0007–0.01); three (rs2856813, rs4332358, and rs10776799) were empirically significant based on 1,000,000 permutations (Ps = 0.008–0.015). Seven haplotypes were significantly associated with PAFDs in women (Ps = 0.0014–0.01), of which six were significant based on empirical permutation analysis (minimal P = 0.0045). Four diplotypes were significantly associated with PAFDs in women (global Ps = 0.001–0.01). The specific diplotype GG-TC, reconstructed from rs2856813 and rs6678788, showed the strongest evidence of association with PAFDs in women (OR = 4.07, P = 4.2E-05). No SNPs or haplotypes were associated with PAFDs in men or with CAFDs in either sex. We conclude that variation in NGFB is a risk factor for PAFDs in women, but not for CAFD.
nerve growth factor β; NGFB; affective disorder; substance dependence; association study; sex-specific
To identify and validate homogeneous subtypes of opioid use and related behaviors.
Family-based and case-control genetic studies of opioid and/or cocaine dependence.
Clinical and general community samples from Connecticut, Massachusetts, Pennsylvania, and South Carolina.
4,061 individuals (2,003 individuals from 835 families and 2,058 unrelated individuals) recruited to participate in genetic studies.
The computer-assisted Semi-Structured Assessment for Drug Dependence and Alcoholism (SSADDA) was used to assess participants’ demographics, medical history, substance use behaviors, and other psychiatric disorders.
Five homogeneous subtypes were identified, which differed on opioid-related measures, demographics, and prevalence rates of co-morbid substance use and psychiatric disorders. Heritability estimates for the two most severely affected subtypes exceeded 0.60.
An empirical approach based on opioid use and related behaviors can yield homogeneous subtypes that could be of value in gene finding for opioid dependence.
Opioid dependence; Subtypes; Phenotype; Multiple correspondence analysis; K-means clustering; Hierarchical clustering; Heritability
Selective mutism (SM), considered an early-onset variant of social anxiety disorder (SAD), shares features of impaired social interaction and communication with autism spectrum disorders (ASDs) that suggest a possible shared pathophysiology. We examined the association of a susceptibility gene, contactin-associated protein-like 2 (CNTNAP2), for ASDs and specific language impairment (SLI) with SM and social anxiety-related traits.
Sample 1 subjects were 99 nuclear families including 106 children with SM. Sample 2 subjects were young adults who completed measures of social interactional anxiety (SIAS; N = 1028) and childhood behavioral inhibition (RSRI; N = 920). Five SNPs in CNTNAP2 (including rs7794745 and rs2710102, previously associated with ASDs) were genotyped.
FBAT analyses revealed nominal significance (p = 0.018) for association of SM with rs2710102 which, with rs6944808, was part of a common haplotype associated with SM (permutation p = 0.022). Adjusting for sex and ancestral proportion, each copy of the rs2710102*a risk allele in the young adults was associated with increased odds of being >1SD above the mean on the SIAS (OR = 1.33, p = 0.015) and RSRI (OR = 1.40, p = 0.010).
Although association was found with rs2710102, the risk allele (“a”) for the traits studied here is the non-risk allele for ASD and SLI (“g”). These findings suggest a partially shared etiology between ASDs and SM, but raise additional questions about specific aspects of these syndromes (i.e., language impairment and/or social anxiety) potentially influenced by CNTNAP2 and mechanism(s) by which these influences may be conveyed.
genetics; anxiety disorders; speech; childhood; autism; autism spectrum; social anxiety; behavioral inhibition
Studies of alcohol effects in rodents and in vitro implicate endogenous neuroactive steroids as key mediators of alcohol effects at GABAA receptors. We used a case-control sample to test the association with alcohol dependence (AD) of single nucleotide polymorphisms (SNPs) in the genes encoding two key enzymes required for the generation of endogenous neuroactive steroids: 5α–reductase, type I (5α-R) and 3α-hydroxysteroid dehydrogenase, type 2 (3α-HSD), both of which are expressed in human brain.
We focused on markers previously associated with a biological phenotype. For 5α-R, we examined the synonymous SRD5A1 exon 1 SNP rs248793, which has been associated with the ratio of dihydrotestosterone to testosterone. For 3α-HSD, we examined the non-synonymous AKR1C3 SNP rs12529 (H5Q), which has been associated with bladder cancer. The SNPs were genotyped in a sample of 1,083 non-Hispanic Caucasians including 552 controls and 531 subjects with AD.
The minor allele for both SNPs was more common among controls than subjects with AD: SRD5A1 rs248793 C-allele (χ2(1)=7.6, p=0.006) and AKR1C3 rs12529 G-allele (χ2(1)=14.6, p=0.0001). There was also an interaction of these alleles such that the “protective” effect of the minor allele at each marker for AD was conditional on the genotype of the second marker.
We found evidence of an association with AD of polymorphisms in two genes encoding neuroactive steroid biosynthetic enzymes, providing indirect evidence that neuroactive steroids are important mediators of alcohol effects in humans.
psychiatric genetics; neuroactive steroids; 5α-reductase; 3α-HSD; alcohol dependence; polymorphism
Recent studies have indicated a gene by environment interaction between serotonin transporter gene (5-HTTLPR) polymorphism and childhood abuse on depressive symptoms. In addition, persistent elevation of cerebrospinal fluid (CSF) corticotropin-releasing factor (CRF) concentrations following early-life adversity has been posited to underlie the subsequent development of major depression. This pilot study tested the hypothesis that elevations of juvenile CSF CRF concentrations are, in part, determined by an interaction between polymorphisms of the 5-HTTLPR and early-life stress. Nine juvenile male bonnet macaques (Macaca radiata) had been raised under variable foraging demand (VFD) conditions, a nonhuman primate model of early-life stress, whereas nine subjects were normatively raised under LFD (low foraging demand) conditions. Genotyping revealed that four (44.4%) of the VFD-reared monkeys possessed at least one “s” allele whereas five VFD monkeys were of the l/l genotype. Of the nine LFD subjects, two (22%) had the s/l genotype and seven had the l/l genotype. A “juvenile” CSF sample was obtained at approximately three years of age. CSF CRF concentrations were elevated specifically in the VFD “s/s” and “s/l” allele group in comparison to each of the remaining three groups, indicating a gene by environment (GxE) interaction.
Nonhuman primates; corticotropin-releasing hormone; early-life stress; serotonin transporter gene; major depression; anxiety disorders; gene by environment interaction
The present study examined the association between a measure of sociopathy and 5-HTTLPR genotype in a sample of individuals from Project MATCH, a multi-center alcohol treatment trial. 5-HTTLPR, an insertion/deletion polymorphism in SLC6A4, the gene encoding the serotonin transporter protein, results in functionally distinct long (L) and short (S) alleles. The S allele has been associated with a variety of psychiatric disorders and symptoms including alcohol dependence, but it is unknown whether 5-HTTLPR increases the risk for co-morbid sociopathy among those with alcohol dependence.
862 subjects diagnosed with alcohol dependence completed the California Psychological Inventory, a psychological assessment that includes a measure of socialization, which was used as a proxy measure of sociopathy. Subjects were genotyped for the insertion/deletion polymorphism, as well as a single nucleotide polymorphism (A→G) that is located in the inserted region.
Regression analysis revealed that, after controlling for age, which was negatively related to socialization score, 5-HTTLPR genotype interacted with sex to determine socialization score (p<0.001). Males with the L′L′ genotype (i.e., those homozygous for the LA allele) had lower socialization scores (i.e., greater sociopathy) than males who were carries of the S′ allele (p=0.03). In contrast, women with the S′S′ genotype had lower socialization scores than women with two L′ alleles (p=0.002) and tended to have lower CPI-So scores than women with one copy of the L′ allele (p=0.07).
Among individuals with AUDs, the tri-allelic 5-HTTLPR polymorphism had opposite effects on socialization scores in men than women. The basis for this finding is unknown, but it may have implications for subtyping alcoholics.
5-HTTLPR; Antisocial Behavior; Behavioral Genetics; Sociopathy
Because isolated populations offer relative genetic and environmental homogeneity, they are important resources for mapping genes for complex traits. Reliable and valid phenotypic characterization of the disease in the population studied is essential. We examined diagnostic reliability and concurrent validity of DSM-IV opioid dependence (OD) in a Hmong population in Thailand with historically high rates of opium (and heroin) use.
578 Thai-speaking Hmong individuals were assessed for lifetime OD, using Thai versions of both the Semi-Structured Assessment for Drug Dependence and Alcoholism (Thai SSADDA) and the Mini-Neuropsychiatric Interview (Thai MINI; adapted for lifetime diagnoses). In a subsample of 123 individuals, two raters interviewed each subject independently within a 2-week period. Chance-corrected agreement on the OD diagnosis was assessed between raters and instruments.
Results showed excellent agreement for the DSM-IV diagnosis of OD both for the SSADDA (κ=0.97) and MINI: (κ=1.00) and between the SSADDA and MINI (κ=0.97).
Consistent with reliability assessments of English versions, our data demonstrate high reliability for Thai versions of the SSADDA and MINI in the diagnosis of OD. The high concordance between instruments supports the concurrent validity of the diagnosis.
Either interview provides reliable, valid OD diagnoses in Thai-speaking Hmong individuals.