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1.  Common biological networks underlie genetic risk for alcoholism in African- and European-American populations 
Genes, brain, and behavior  2013;12(5):532-542.
Alcohol dependence (AD) is a heritable substance addiction with adverse physical and psychological consequences, representing a major health and economic burden on societies worldwide. Genes thus far implicated via linkage, candidate gene and genome-wide association studies (GWAS) account for only a small fraction of its overall risk, with effects varying across ethnic groups. Here we investigate the genetic architecture of alcoholism and report on the extent to which common, genome-wide SNPs collectively account for risk of AD in two US populations, African-Americans (AAs) and European-Americans (EAs). Analyzing GWAS data for two independent case-control sample sets, we compute polymarker scores that are significantly associated with alcoholism (P=1.64 × 10−3 and 2.08 × 10−4 for EAs and AAs, respectively), reflecting the small individual effects of thousands of variants derived from patterns of allelic architecture that are population-specific. Simulations show that disease models based on rare and uncommon causal variants (MAF<0.05) best fit the observed distribution of polymarker signals. When scoring bins were annotated for gene location and examined for constituent biological networks, gene enrichment is observed for several cellular processes and functions in both EA and AA populations, transcending their underlying allelic differences. Our results reveal key insights into the complex etiology of AD, raising the possibility of an important role for rare and uncommon variants, and identify polygenic mechanisms that encompass a spectrum of disease liability, with some, such as chloride transporters and glycine metabolism genes, displaying subtle, modifying effects that are likely to escape detection in most GWAS designs.
doi:10.1111/gbb.12043
PMCID: PMC3709451  PMID: 23607416
alcohol dependence; GWAS; polymarker scores; synthetic association; rare variants; pathway analysis
2.  The Persistent Effects of Minimum Legal Drinking Age Laws on Drinking Patterns Later in Life 
Background
Exposure to permissive minimum legal drinking age (MLDA) laws not only affects young adults in the short term, but also later in life; for example, individuals who could legally purchase alcohol before age 21 are more likely to suffer from drinking problems as older adults, long after the laws had been changed. However, it is not known how permissive MLDA exposure affects specific drinking behavior. This present study uses changes in MLDA laws during the 1970s and 1980s as a natural experiment to investigate the potential impact of permissive MLDA exposure on average alcohol consumption, frequency of drinking, and on patterns of binging and more moderate, non-heavy drinking.
Methods
Policy exposure data were paired with alcohol use data from the 1991–1992 National Longitudinal Alcohol Epidemiologic Survey and the 2001–2002 National Epidemiologic Survey on Alcohol and Related Conditions. Past-year drinkers born between 1949 and 1972 (n = 24,088) were included. Average daily intake, overall drinking frequency, and frequency of both binge episodes (5+ drinks) and days without a binge episode (non-heavy drinking) for the previous year at the time of interview were tracked for each respondent.
Results
Exposure to permissive MLDAs was associated with higher odds to report frequent binging and lower odds to report any moderate drinking; these associations were largely driven by men and those who did not attend college. Overall drinking frequency and average alcohol consumption were not affected by MLDA exposure.
Conclusions
The ability to legally purchase alcohol before age 21 does not seem to increase overall drinking frequency, but our findings suggest that it is associated with certain types of problematic drinking behaviors that persist into later adulthood: more frequent binge episodes and less frequent non-heavy drinking. We also propose that policymakers and critics should not focus on college drinking when evaluating the effectiveness of MLDAs.
doi:10.1111/j.1530-0277.2012.01945.x
PMCID: PMC3586293  PMID: 23347177
Minimum legal drinking age; binge drinking; drinking patterns; moderate drinking
3.  Genetic influences on craving for alcohol 
Addictive behaviors  2012;38(2):1501-1508.
Introduction
Craving is being considered for inclusion in the Diagnostic and Statistical Manual (DSM) DSM-5. However, little is known of its genetic underpinnings – specifically, whether genetic influences on craving are distinct from those influencing DSM-IV alcohol dependence.
Method
Analyses were conducted in a sample of unrelated adults ascertained for alcohol dependence (N=3976). Factor analysis was performed to examine how alcohol craving loaded with the existing DSM-IV alcohol dependence criteria. For genetic analyses, we first examined whether genes in the dopamine pathway, including dopamine receptor genes (DRD1, DRD2, DRD3, DRD4) and the dopamine transporter gene (SLC6A3), which have been implicated in neurobiological studies of craving, as well as alpha-synuclein (SNCA), which has been previously found to be associated with craving, were associated with alcohol craving in this sample. Second, in an effort to identify novel genetic variants associated with craving, we conducted a genomewide association study (GWAS). For variants that were implicated in the primary analysis of craving, we conducted additional comparisons - to determine if these variants were uniquely associated with alcohol craving as compared with alcohol dependence. We contrasted our results to those obtained for DSM-IV alcohol dependence, and also compared alcohol dependent individuals without craving to non-dependent individuals who also did not crave alcohol.
Results
Twenty-one percent of the full sample reported craving alcohol. Of those reporting craving, 97.3% met criteria for DSM-IV alcohol dependence with 48% endorsing all 7 dependence criteria. Factor analysis found a high factor loading (0.89) for alcohol craving. When examining genes in the dopamine pathway, single nucleotide polymorphisms (SNPs) in DRD3 and SNCA were associated with craving (p<0.05). There was evidence for association of these SNPs with DSM-IV alcohol dependence (p<0.05) but less evidence for dependence without craving (p>0.05), suggesting that the association was due in part to craving. In the GWAS, the greatest evidence of association with craving was for a SNP in the integrin alpha D (ITGAD) gene on chromosome 7 (rs2454908; p=1.8×10−6). The corresponding p-value for this SNP with DSM-IV alcohol dependence was similar (p=4.0×10−5) but was far less with dependence without craving (p=0.02), again suggesting the association was due to alcohol craving. Adjusting for dependence severity (number of endorsed criteria) attenuated p-values but did not eliminate association.
Conclusions
Craving is frequently reported by those who report multiple other alcohol dependence symptoms. We found that genes providing evidence of association with craving were also associated with alcohol dependence; however, these same SNPs were not associated with alcohol dependence in the absence of alcohol craving. These results suggest that there may be unique genetic factors affecting craving among those with alcohol dependence.
doi:10.1016/j.addbeh.2012.03.021
PMCID: PMC3394913  PMID: 22481050
4.  CYP2B6 Non-Coding Variation Associated with Smoking Cessation Is Also Associated with Differences in Allelic Expression, Splicing, and Nicotine Metabolism Independent of Common Amino-Acid Changes 
PLoS ONE  2013;8(11):e79700.
The Cytochrome P450 2B6 (CYP2B6) enzyme makes a small contribution to hepatic nicotine metabolism relative to CYP2A6, but CYP2B6 is the primary enzyme responsible for metabolism of the smoking cessation drug bupropion. Using CYP2A6 genotype as a covariate, we find that a non-coding polymorphism in CYP2B6 previously associated with smoking cessation (rs8109525) is also significantly associated with nicotine metabolism. The association is independent of the well-studied non-synonymous variants rs3211371, rs3745274, and rs2279343 (CYP2B6*5 and *6). Expression studies demonstrate that rs8109525 is also associated with differences in CYP2B6 mRNA expression in liver biopsy samples. Splicing assays demonstrate that specific splice forms of CYP2B6 are associated with haplotypes defined by variants including rs3745274 and rs8109525. These results indicate differences in mRNA expression and splicing as potential molecular mechanisms by which non-coding variation in CYP2B6 may affect enzymatic activity leading to differences in metabolism and smoking cessation.
doi:10.1371/journal.pone.0079700
PMCID: PMC3829832  PMID: 24260284
5.  Inclusion of African Americans in Genetic Studies: What Is the Barrier? 
American Journal of Epidemiology  2011;174(3):336-344.
To facilitate an increase in the amount of data on minority subjects collected for genetic databases, the authors attempted to clarify barriers to African-American participation in genetic studies. They randomly sampled 78,072 subjects from the community (Missouri Family Registry, 2002–2007). Of these, 28,658 participated in a telephone screening interview, 3,179 were eligible to participate in the genetic study, and 1,919 participated in the genetic study. Response rates were examined in relation to the proportion of subjects in the area who were African-American according to US Census 2000 zip code demographic data. Compared with zip codes with fewer than 5% African Americans (average = 2% African-American), zip codes with at least 60% African Americans (average = 87% African-American) had higher proportions of subjects with an incorrect address or telephone number but lower proportions of subjects who did not answer the telephone and subjects who refused the telephone interview (P < 0.0001). Based on reported race from the telephone screening, 71% of eligible African Americans and 57% of eligible European Americans participated in the genetic study (P < 0.0001). The results of this study suggest that increasing the number of African Americans in genetic databases may be achieved by increasing efforts to locate and contact them.
doi:10.1093/aje/kwr084
PMCID: PMC3202157  PMID: 21633120
African Americans; consumer participation; data collection; genetic association studies; genetics; minority groups
6.  Identifying Genetic Variation for Alcohol Dependence 
Researchers are using various strategies to identify the genes that may be associated with alcoholism. The initial efforts primarily relied on candidate gene and linkage studies; more recently, however, modern advances in genotyping have resulted in widespread use of genome-wide association studies for alcohol dependence. The key findings of the earlier studies were that variations (i.e., polymorphisms) in the DNA sequences of the genes encoding alcohol dehydrogenase 1B (i.e., the ADH1B gene), aldehyde dehydrogenase 2 (i.e., the ALDH2 gene), and other alcohol-metabolizing enzymes mediate the risk for alcoholism; moreover, these polymorphisms also have an impact on the risk of alcohol-related cancers, such as esophageal cancer. In addition, a gene encoding one of the receptors for the neurotransmitter γ-aminobutyric acid (GABA) known as GABRA2 seems to have a role in the development of alcohol dependence. Genome-wide association studies now offer a host of emerging opportunities, as well as challenges, for discovering the genetic etiology of alcohol dependence and for unveiling new treatment strategies.
PMCID: PMC3662475  PMID: 23134043
Alcoholism; alcohol dependence; alcohol-metabolizing genes; genetic factors; genetic mapping; genome-wide association studies; candidate gene studies; genetic variants; alcohol dehydrogenase (ADH), aldehyde dehydrogenase (ALDH); alcohol-related cancers; esophageal cancer; γ-aminobutyric acid (GABA); DNA
8.  Use of a predictive model derived from in vivo endophenotype measurements to demonstrate associations with a complex locus, CYP2A6 
Human Molecular Genetics  2012;21(13):3050-3062.
This study demonstrates a novel approach to test associations between highly heterogeneous genetic loci and complex phenotypes. Previous investigations of the relationship between Cytochrome P450 2A6 (CYP2A6) genotype and smoking phenotypes made comparisons by dividing subjects into broad categories based on assumptions that simplify the range of function of different CYP2A6 alleles, their numerous possible diplotype combinations and non-additive allele effects. A predictive model that translates CYP2A6 diplotype into a single continuous variable was previously derived from an in vivo metabolism experiment in 189 European Americans. Here, we apply this model to assess associations between genotype, inferred nicotine metabolism and smoking behaviors in larger samples without direct nicotine metabolism measurements. CYP2A6 genotype is not associated with nicotine dependence, as defined by the Fagerström Test of Nicotine Dependence, demonstrating that cigarettes smoked per day (CPD) and nicotine dependence have distinct genetic correlates. The predicted metric is significantly associated with CPD among African Americans and European American dependent smokers. Individual slow metabolizing genotypes are associated with lower CPD, but the predicted metric is the best predictor of CPD. Furthermore, optimizing the predictive model by including additional CYP2A6 alleles improves the fit of the model in an independent data set and provides a novel method of predicting the functional impact of alleles without direct metabolism measurements. Lastly, comprehensive genotyping and in vivo metabolism data are used to demonstrate that genome-wide significant associations between CPD and single nucleotide polymorphisms are the result of synthetic associations.
doi:10.1093/hmg/dds114
PMCID: PMC3373237  PMID: 22451501
9.  Nicotine Dependence and Comorbid Psychiatric Disorders: Examination of Specific Genetic Variants in the CHRNA5-A3-B4 Nicotinic Receptor Genes* 
Drug and Alcohol Dependence  2012;123S1:S42-S51.
Background
The associations between nicotine dependence and specific variants in the nicotinic receptor CHRNA5-A3-B4 subunit genes are irrefutable with replications in many studies. The relationship between the newly identified genetic risk variants for nicotine dependence and comorbid psychiatric disorders is unclear. We examined whether these genetic variants were associated with comorbid disorders and whether comorbid psychiatric disorders modified the genetic risk of nicotine dependence.
Methods
In a case control study of nicotine dependence with 2032 subjects of European descent, we used logistic regression models to examine the pleiotropy and risk moderation. Comorbid disorders examined were alcohol dependence, cannabis dependence, major depressive disorder, panic attack, social phobia, posttraumatic stress disorder (PTSD), attention deficit hyperactivity disorder (ADHD), conduct disorder, and antisocial personality disorder (ASPD).
Results
Nicotine dependence was associated with every examined comorbid psychiatric disorders, with odds ratio varying from 1.75 to 3.33. No evidence supported the associations between the genetic variants and the comorbid disorders (pleiotropy). No evidence suggested that the risks for nicotine dependence associated with the genetic variants vary with comorbid psychiatric disorders in general, but the power was limited in detecting interactions.
Conclusions
The genetic risks of nicotine dependence associated with the CHRNA5-A3-B4 subunit genes are specific, and not shared among commonly comorbid psychiatric disorders. The risks for nicotine dependence associated with these genetic variants are not modified by comorbid psychiatric disorders such as major depressive disorder or alcohol dependence. However, the power is an important limitation in studying the interplay of comorbidity and genetic variants.
doi:10.1016/j.drugalcdep.2012.01.014
PMCID: PMC3376673  PMID: 22336398
nicotine dependence; nicotinic receptor genes; case control study; comorbidity; pleiotropy; genetic epidemiology
10.  Identifying Genetic Variation for Alcohol Dependence 
Various strategies are employed by researchers to identify the genes that may be associated with alcoholism. While prior studies have primarily relied on candidate gene methods and linkage studies, modern advances in genotyping have resulted in widespread use of genome-wide association studies for alcohol dependence. In this review, we revisit the key association findings between risk for alcoholism and candidate polymorphisms in ADH1B, ALDH2 and other alcohol metabolizing genes, and examine the impact of these polymorphisms on alcohol-related cancers, such as esophageal cancer. We also discuss the putative role of GABRA2 in the development of alcohol dependence. The emerging opportunities and challenges of genome-wide association studies are presented along with future directions for studies to discover the genetic etiology of alcohol dependence.
PMCID: PMC3662475  PMID: 23134043
12.  The legacy of minimum legal drinking age law changes: Long-term effects on suicide and homicide deaths among women 
Background
Prior to the establishment of the uniform drinking age of 21 in the United States, many states permitted legal purchase of alcohol at younger ages. Lower drinking ages were associated with several adverse outcomes, including elevated rates of suicide and homicide among youth. The objective of this study is to examine whether individuals who were legally permitted to drink prior to age 21 remained at elevated risk in adulthood.
Methods
Analysis of data from the U.S. Multiple Cause of Death files, 1990–2004, combined with data on the living population from the U.S. Census and American Community Survey. The assembled data contained records on over 200,000 suicides and 130,000 homicides for individuals born between 1949 and 1972, the years during which the drinking age was in flux. Logistic regression models were used to evaluate whether adults who were legally permitted to drink prior to age 21 were at elevated risk for death by these causes. A quasi-experimental analytical approach was employed which incorporated state and birth year fixed effects to account for unobserved covariates associated with policy exposure.
Results
In the population as a whole, we found no association between minimum drinking age and homicide or suicide. However, significant policy-by-sex interactions were observed for both outcomes, such that women exposed to permissive drinking age laws were at higher risk for both suicide (OR=1.12; 95% CI 1.05, 1.18, p=0.0003) and homicide (OR=1.15; 95% CI 1.04, 1.25; p=0.0028). Effect sizes were stronger for the portion of the cohort born after 1960, whereas no significant effects were observed for women born prior to 1960.
Conclusions
Lower drinking ages may result in persistent elevated risk for suicide and homicide among women born after 1960. The national drinking age of 21 may be preventing about 600 suicides and 600 homicides annually.
doi:10.1111/j.1530-0277.2011.01608.x
PMCID: PMC3587149  PMID: 22085045
suicide; homicide; policy; women; epidemiology
13.  Genome-wide association study of comorbid depressive syndrome and alcohol dependence 
Psychiatric genetics  2012;22(1):31-41.
Objective
Depression and alcohol dependence are common psychiatric disorders that often co-occur. Both disorders are genetically influenced, with heritability estimates in the range of 35–60%. In addition, evidence from twin studies suggests that alcohol dependence and depression are genetically correlated. Here we report results from a genome-wide association study (GWAS) of a comorbid phenotype in which cases meet the DSM-IV symptom threshold for major depressive symptomatology and DSM-IV criteria for alcohol dependence.
Methods
Samples (N=467 cases and N=407 controls) were of European-American descent, and were genotyped using the Illumina Human 1M BeadChip array.
Results
Although no SNP meets genome-wide significance criteria, we identify ten markers with p-values < 1 × 10−5, seven of which are located in known genes, which have not been previously implicated in either disorder. Genes harboring SNPs yielding p<1 × 10−3 are functionally enriched for a number of gene ontology categories, notably several related to glutamatergic function. Investigation of expression localization using online resources suggests that these genes are expressed across a variety of tissues, including behaviorally relevant brain regions. Genes that have been previously associated with depression, alcohol dependence, or other addiction-related phenotypes – such as CDH13, CSMD2, GRID1, and HTR1B – were implicated by nominally significant SNPs. Finally, the degree of overlap of significant SNPs between a comorbid phenotype and an alcohol dependence-only phenotype is modest.
Conclusions
These results underscore the complex genomic influences on psychiatric phenotypes, and suggest that a comorbid phenotype is partially influenced by genetic variants that do not affect alcohol dependence alone.
doi:10.1097/YPG.0b013e32834acd07
PMCID: PMC3241912  PMID: 22064162
genetics of alcoholism; comorbidity; genetic risk; depressive syndrome
14.  Rare missense variants in CHRNB4 are associated with reduced risk of nicotine dependence 
Human Molecular Genetics  2011;21(3):647-655.
Genome-wide association studies have identified common variation in the CHRNA5–CHRNA3–CHRNB4 and CHRNA6–CHRNB3 gene clusters that contribute to nicotine dependence. However, the role of rare variation in risk for nicotine dependence in these nicotinic receptor genes has not been studied. We undertook pooled sequencing of the coding regions and flanking sequence of the CHRNA5, CHRNA3, CHRNB4, CHRNA6 and CHRNB3 genes in African American and European American nicotine-dependent smokers and smokers without symptoms of dependence. Carrier status of individuals harboring rare missense variants at conserved sites in each of these genes was then compared in cases and controls to test for an association with nicotine dependence. Missense variants at conserved residues in CHRNB4 are associated with lower risk for nicotine dependence in African Americans and European Americans (AA P = 0.0025, odds-ratio (OR) = 0.31, 95% confidence-interval (CI) = 0.31–0.72; EA P = 0.023, OR = 0.69, 95% CI = 0.50–0.95). Furthermore, these individuals were found to smoke fewer cigarettes per day than non-carriers (AA P = 6.6 × 10−5, EA P = 0.021). Given the possibility of stochastic differences in rare allele frequencies between groups replication of this association is necessary to confirm these findings. The functional effects of the two CHRNB4 variants contributing most to this association (T375I and T91I) and a missense variant in CHRNA3 (R37H) in strong linkage disequilibrium with T91I were examined in vitro. The minor allele of each polymorphism increased cellular response to nicotine (T375I P = 0.01, T91I P = 0.02, R37H P = 0.003), but the largest effect on in vitro receptor activity was seen in the presence of both CHRNB4 T91I and CHRNA3 R37H (P = 2 × 10−6).
doi:10.1093/hmg/ddr498
PMCID: PMC3259016  PMID: 22042774
15.  Occupation and Workplace Policies Predict Smoking Behaviors: Analysis of National Data from the Current Population Survey 
Objective
Describe differences in smoking behaviors associated with occupation, workplace rules against smoking, and workplace smoking cessation programs.
Methods
We analyzed data from the Current Population Survey- Tobacco Use Supplement surveys from 1992 through 2007.
Results
After adjusting for demographic factors, blue-collar workers were at higher risk than white-collar workers for ever smoking, current smoking, and persistent smoking (current smoking among ever smokers). Construction workers were more likely to be current daily smokers than other blue-collar workers. Among ever smokers, current daily smoking was more common in the absence of both workplace rules against smoking and workplace smoking cessation programs.
Conclusions
Social or cultural effects related to occupation are important determinants of smoking. More aggressive promotion of smoking cessation programs and workplace rules prohibiting smoking could have a significant public health impact.
doi:10.1097/JOM.0b013e3182337778
PMCID: PMC3217081  PMID: 21988795
16.  Non-replication of an association of SGIP1 SNPs with alcohol dependence and resting theta EEG power 
Psychiatric genetics  2011;21(5):265-266.
OBJECTIVE
A recent study in a sample of Plains Indians showed association between eight SNPs located in the SGIP1 gene and resting theta electroencephalogram (EEG) power (Hodgkinson et al., 2010). This association appeared to generalize to alcohol use disorders, for which EEG power is a potential endophenotype.
METHODS
We analyzed a large, diverse sample for replication of the association of these implicated SGIP1 SNPs (genotyped on the Illumina 1M platform) with alcohol dependence (N = 3988) and theta EEG power (N = 1066).
RESULTS
We found no evidence of association of the previously implicated SGIP1 SNPs with either alcohol dependence or theta EEG power (all p > 0.15) in the current sample.
CONCLUSIONS
The previously implicated SNPs located in SGIP1 showed no association with alcohol dependence or theta EEG power in the present sample of individuals with European and/or African ancestry. This failure to replicate may be the result of differences in ancestry between the current and original samples.
doi:10.1097/YPG.0b013e32834371fd
PMCID: PMC3139721  PMID: 21317682
alcoholism; electroencephalogram; candidate gene association study
17.  Identification of a Novel Tumor Suppressor Gene p34 on Human Chromosome 6q25.1 
Cancer research  2007;67(1):93-99.
In this study, we observed loss of heterozygosity (LOH) in human chromosomal fragment 6q25.1 in sporadic lung cancer patients. LOH was observed in 65% of the 26 lung tumors examined and was narrowed down to a 2.2-Mb region. Single-nucleotide polymorphism (SNP) analysis of genes located within this region identified a candidate gene, termed p34. This gene, also designated as ZC3H12D, C6orf95, FLJ46041, or dJ281H8.1, carries an A/G nonsynonymous SNP at codon 106, which alters the amino acid from lysine to arginine. Nearly 73% of heterozygous lung cancer tissues with LOH and the A/G SNP also exhibited loss of the A allele. In vitro clonogenic and in vivo nude mouse studies showed that overexpression of the A allele exerts tumor suppressor function compared with the G allele. p34 is located within a recently mapped human lung cancer susceptibility locus, and association of the p34 A/G SNP was tested among these families. No significant association between the less frequent G allele and lung cancer susceptibility was found. Our results suggest that p34 may be a novel tumor suppressor gene involved in sporadic lung cancer but it seems not to be the candidate familial lung cancer susceptibility gene linked to chromosomal region 6q23-25.
doi:10.1158/0008-5472.CAN-06-2723
PMCID: PMC3461257  PMID: 17210687
18.  The Contribution of Common CYP2A6 Alleles to Variation in Nicotine Metabolism Among European Americans 
Pharmacogenetics and genomics  2011;21(7):403-416.
Cytochrome P450 2A6 (CYP2A6) is the primary catalyst of nicotine metabolism. To develop a predictive genetic model of nicotine metabolism, the conversion of deuterated (D2)-nicotine to D2-cotinine was quantified in 189 European Americans and the contribution of CYP2A6 genotype to variability in first-pass nicotine metabolism was assessed. Specifically, 1) single time-point measures of D2-cotinine/(D2-cotinine + D2-nicotine) following oral administration were used as a metric of CYP2A6 activity; 2) the impact of CYP2A6 haplotype was treated as acting multiplicatively; 3) parameter estimates were calculated for all haplotypes in the subject pool, defined by a set of polymorphisms previously reported to affect function, including gene copy number; and 4) a minimum number of predictive polymorphisms are justified to be included in the model based on statistical evidence of differences between haplotypes. The final model includes seven polymorphisms and fits the phenotype, 30 minutes following D2-nicotine oral administration, with R2=0.719. The predictive power of the model is robust: parameter estimates calculated in men (n=89) predict the phenotype in women (n=100) with R2=0.758 and vice versa with R2=0.617; estimates calculated in current smokers (n=102) predict phenotype in former smokers (n=86) with R2=0.690 and vice versa with R2=0.703. Comparisons of haplotypes also demonstrate that CYP2A6*12 is a loss of function allele indistinguishable from CYP2A6*4 and CYP2A6*2 and that the CYP2A6*1B 5′ UTR conversion has negligible impact on metabolism. After controlling for CYP2A6 genotype modest associations were found between increased metabolism and both female gender (p= 4.8×10−4) and current smoking (p=0.02).
doi:10.1097/FPC.0b013e328346e8c0
PMCID: PMC3116045  PMID: 21597399
CYP2A6; nicotine metabolism; cotinine
19.  Common polymorphisms in FMO1 are associated with nicotine dependence 
Pharmacogenetics and genomics  2011;21(7):397-402.
BACKGROUND
Cigarette smoking and other forms of tobacco use are the leading cause of preventable mortality in the world. A better understanding of the etiology of nicotine addiction may help increase the success rate of cessation and decrease the massive morbidity and mortality associated with smoking.
METHODS
In order to identify genetic polymorphisms that contribute to nicotine dependence, our group undertook a genetic association study including three enzyme families that potentially influence nicotine metabolism: cytochrome P450 enzymes (CYP P450s), flavin monooxygenases (FMOs) and UDP-glucuronosyl transferases (UGTs).
RESULTS
Several polymorphisms in FMO1 showed association in a discovery sample and were tested in an independent replication sample. One polymorphism, rs10912765, showed association that remained significant after Bonferroni correction (nominal p=0.0067, corrected p=0.0134). Several additional polymorphisms in linkage disequilibrium with this SNP also showed association. Subsequent in vitro experiments characterized FMO1 as a more efficient catalyst of nicotine N-oxidation than FMO3. In adult humans, FMO1 is primarily expressed in the kidney and is likely to be a major contributor to the renal metabolism and clearance of therapeutic drugs. FMO1 is also expressed in the brain and could contribute to the nicotine concentration in this tissue.
CONCLUSIONS
These findings suggest that polymorphisms in FMO1 are significant risk factors in the development of nicotine dependence and that the mechanism may involve variation in nicotine pharmacology.
doi:10.1097/FPC.0b013e328346886f
PMCID: PMC3248052  PMID: 21540762
FMO1; nicotine dependence; nicotine metabolism
20.  Cigarette Smoking Reduction and Changes in Nicotine Dependence 
Nicotine & Tobacco Research  2011;13(6):426-430.
Introduction:
The relationship of nicotine dependence (ND) to smoking behavior and cessation has been well characterized. However, little is known about the association between smoking reduction (SR) and ND.
Methods:
We retrospectively evaluated the lifetime prevalence and extent of SR and whether ND as assessed by a modified Fagerström Test for Nicotine Dependence (FTND) score without cigarettes per day (CPD) and time-to-first cigarette changed with reductions in CPD. As part of the Collaborative Study of the Genetics of Nicotine Dependence (COGEND), 47,777 individuals from 2 mid-Western metropolitan areas were identified for a community-based telephone screening, yielding 6,955 current daily smokers ages 25–44 years (European-American, n = 5,135 and Black, n = 1,820). The FTND was administered to measure current ND and peak ND in respondents whose current daily CPD is lower than their reported lifetime peak.
Results:
About 44% (n = 3,077) of the sample reported reducing their smoking from their lifetime peak, with a mean reduction of 14.4 CPD (SD = 8.9) or a 54.0% reduction compared with peak smoking. Controlling for peak smoking and years smoked, the magnitude of SR was associated with declines in ND excluding the direct contribution of CPD.
Conclusions:
Self-reported SR was associated with reduced levels of ND. The impact of this reduction on smoking cessation and health risks and smoking cessation requires further study, particularly given the retrospective nature of the present dataset.
doi:10.1093/ntr/ntr019
PMCID: PMC3103717  PMID: 21367813
21.  Genome-Wide Association Study of Theta Band Event-Related Oscillations Identifies Serotonin Receptor Gene HTR7 Influencing Risk of Alcohol Dependence 
Event-related brain oscillations (EROs) represent highly heritable neuroelectrical correlates of human perception and cognitive performance that exhibit marked deficits in patients with various psychiatric disorders. We report the results of the first genome-wide association study (GWAS) of an ERO endophenotype – frontal theta ERO evoked by visual oddball targets during P300 response in 1,064 unrelated individuals drawn from a study of alcohol dependence. Forty-two SNPs of the Illumina HumanHap 1M microarray were selected from the theta ERO GWAS for replication in family-based samples (N = 1,095), with four markers revealing nominally significant association. The most significant marker from the two-stage study is rs4907240 located within ARID protein 5A gene (ARID5A) on chromosome 2q11 (unadjusted, Fisher’s combined P = 3.68 × 10−6). However, the most intriguing association to emerge is with rs7916403 in serotonin receptor gene HTR7 on chromosome 10q23 (combined P = 1.53 × 10−4), implicating the serotonergic system in the neurophysiological underpinnings of theta EROs. Moreover, promising SNPs were tested for association with diagnoses of alcohol dependence (DSM-IV), revealing a significant relationship with the HTR7 polymorphism among GWAS case-controls (P = 0.008). Significant recessive genetic effects were also detected for alcohol dependence in both case-control and family-based samples (P = 0.031 and 0.042, respectively), with the HTR7 risk allele corresponding to theta ERO reductions among homozygotes. These results suggest a role of the serotonergic system in the biological basis of alcohol dependence and underscore the utility of analyzing brain oscillations as a powerful approach to understanding complex genetic psychiatric disorders.
doi:10.1002/ajmg.b.31136
PMCID: PMC3139811  PMID: 21184583
serotonin receptor gene (HTR7); serotonin receptor (5-HT7); event-related oscillation (ERO); alcohol dependence; genome-wide association study (GWAS)
22.  Smoking Cessation Pharmacogenetics: Analysis of Varenicline and Bupropion in Placebo-Controlled Clinical Trials 
Neuropsychopharmacology  2011;37(3):641-650.
Despite effective therapies for smoking cessation, most smokers find quitting difficult and most successful quitters relapse. Considerable evidence supports a genetic risk for nicotine dependence; however, less is known about the pharmacogenetics of smoking cessation. In the first pharmacogenetic investigation of the efficacy of varenicline and bupropion, we examined whether genes important in the pharmacodynamics and pharmacokinetics of these drugs and nicotine predict medication efficacy and adverse events. Subjects participated in randomized, double-blind, placebo-controlled smoking cessation clinical trials, comparing varenicline, a nicotinic acetylcholine receptor (nAChR) partial agonist, with bupropion, a norepinephrine/dopamine reuptake inhibitor, and placebo. Primary analysis included 1175 smokers of European ancestry, and 785 single nucleotide polymorphisms from 24 genes, representing 254 linkage disequilibrium (LD) bins (genes included nAChR subunits, additional varenicline-specific genes, and genes involved in nicotine or bupropion metabolism). For varenicline, continuous abstinence (weeks 9–12) was associated with multiple nAChR subunit genes (including CHRNB2, CHRNA5, and CHRNA4) (OR=1.76; 95% CI: 1.23–2.52) (p<0.005); for bupropion, abstinence was associated with CYP2B6 (OR=1.78; 95% CI: 1.27–2.50) (p<0.001). Incidence of nausea was associated with several nAChR subunit genes (OR=0.50; 95% CI: 0.36–0.70) (p<0.0001) and time to relapse after quitting was associated with HTR3B (HR=1.97; 95% CI: 1.45–2.68) (p<0.0001). These data provide evidence for multiple genetic loci contributing to smoking cessation and therapeutic response. Different loci are associated with varenicline vs bupropion response, suggesting that additional research may identify clinically useful markers to guide treatment decisions.
doi:10.1038/npp.2011.232
PMCID: PMC3260990  PMID: 22048466
varenicline; bupropion; pharmacogenetics; nicotine; nicotinic receptor; CYP2B6; pharmacogenetics/pharmacogenomics; addiction and substance abuse; clinical pharmacology/clinical trials; neuropharmacology; varenicline; bupropion; nicotine; smoking cessation; nicotinic receptors
23.  Nicotinic α5 receptor subunit mRNA expression is associated with distant 5′ upstream polymorphisms 
CHRNA5, encoding the nicotinic α5 subunit, is implicated in multiple disorders, including nicotine addiction and lung cancer. Previous studies demonstrate significant associations between promoter polymorphisms and CHRNA5 mRNA expression, but the responsible sequence variants remain uncertain. To search for cis-regulatory variants, we measured allele-specific mRNA expression of CHRNA5 in human prefrontal cortex autopsy tissues and scanned the CHRNA5 locus for regulatory variants. A cluster of six frequent single nucleotide polymorphisms (rs1979905, rs1979906, rs1979907, rs880395, rs905740, and rs7164030), in complete linkage disequilibrium, fully account for a >2.5-fold allelic expression difference and a fourfold increase in overall CHRNA5 mRNA expression. This proposed enhancer region resides more than 13 kilobases upstream of the CHRNA5 transcription start site. The same upstream variants failed to affect CHRNA5 mRNA expression in peripheral blood lymphocytes, indicating tissue-specific gene regulation. Other promoter polymorphisms were also correlated with overall CHRNA5 mRNA expression in the brain, but were inconsistent with allelic mRNA expression ratios, a robust and proximate measure of cis-regulatory variants. The enhancer region and the nonsynonymous polymorphism rs16969968 generate three main haplotypes that alter the risk of developing nicotine dependence. Ethnic differences in linkage disequilibrium across the CHRNA5 locus require consideration of the upstream enhancer variants when testing clinical associations.
doi:10.1038/ejhg.2010.120
PMCID: PMC2995013  PMID: 20700147
Nicotinic receptor; alpha5 subunit; gene expression; nicotine dependence; lung cancer; enhancer
24.  Nicotinic α5 receptor subunit mRNA expression is associated with distant 5′ upstream polymorphisms 
CHRNA5, encoding the nicotinic α5 subunit, is implicated in multiple disorders, including nicotine addiction and lung cancer. Previous studies demonstrate significant associations between promoter polymorphisms and CHRNA5 mRNA expression, but the responsible sequence variants remain uncertain. To search for cis-regulatory variants, we measured allele-specific mRNA expression of CHRNA5 in human prefrontal cortex autopsy tissues and scanned the CHRNA5 locus for regulatory variants. A cluster of six frequent single-nucleotide polymorphisms (rs1979905, rs1979906, rs1979907, rs880395, rs905740, and rs7164030), in complete linkage disequilibrium (LD), fully account for a >2.5-fold allelic expression difference and a fourfold increase in overall CHRNA5 mRNA expression. This proposed enhancer region resides more than 13 kilobases upstream of the CHRNA5 transcription start site. The same upstream variants failed to affect CHRNA5 mRNA expression in peripheral blood lymphocytes, indicating tissue-specific gene regulation. Other promoter polymorphisms were also correlated with overall CHRNA5 mRNA expression in the brain, but were inconsistent with allelic mRNA expression ratios, a robust and proximate measure of cis-regulatory variants. The enhancer region and the nonsynonymous polymorphism rs16969968 generate three main haplotypes that alter the risk of developing nicotine dependence. Ethnic differences in LD across the CHRNA5 locus require consideration of upstream enhancer variants when testing clinical associations.
doi:10.1038/ejhg.2010.120
PMCID: PMC2995013  PMID: 20700147
nicotinic receptor; α5 subunit; gene expression; nicotine dependence; lung cancer; enhancer
25.  Single-Nucleotide Polymorphisms in Corticotropin Releasing Hormone Receptor 1 Gene (CRHR1) Are Associated With Quantitative Trait of Event-Related Potential and Alcohol Dependence 
Background
Endophenotypes reflect more proximal effects of genes than diagnostic categories, hence providing a more powerful strategy in searching for genes involved in complex psychiatric disorders. There is strong evidence suggesting the P3 amplitude of the event-related potential (ERP) as an endophenotype for the risk of alcoholism and other disinhibitory disorders. Recent studies demonstrated a crucial role of corticotropin releasing hormone receptor 1 (CRHR1) in the environmental stress response and ethanol self-administration in animal models. The aim of the present study was to test the potential associations between single-nucleotide polymorphisms (SNPs) in the CRHR1 gene and the quantitative trait, P3 amplitude during the processing of visual target signals in an oddball paradigm, as well as alcohol dependence diagnosis.
Methods
We analyzed a sample from the Collaborative Study on the Genetics of Alcoholism (COGA) comprising 1049 Caucasian subjects from 209 families (including 472 alcohol-dependent individuals). Quantitative transmission disequilibrium test (QTDT) and family-based association test (FBAT) were used to test the association, and false discovery rate (FDR) was applied to correct for multiple comparisons.
Results
Significant associations (p < 0.05) were found between the P3 amplitude and alcohol dependence with multiple SNPs in the CRHR1 gene.
Conclusions
Our results suggest that CRHR1 may be involved in modulating the P3 component of the ERP during information processing and in vulnerability to alcoholism. These findings underscore the utility of electrophysiology and the endophenotype approach in the genetic study of psychiatric disorders.
doi:10.1111/j.1530-0277.2010.01173.x
PMCID: PMC3248053  PMID: 20374216
P3; Disinhibition; Endophenotype; Stress; Corticotropin Releasing Factor (CRF)

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