Meta-analysis and imputation refines the association of 15q25 with smoking quantity.
Ontology highlight
ABSTRACT:
SUBMITTER: Liu JZ
PROVIDER: S-EPMC3612983 | biostudies-literature | 2010 May
REPOSITORIES: biostudies-literature
Publications
Meta-analysis and imputation refines the association of 15q25 with smoking quantity.
Liu Jason Z JZ Tozzi Federica F Waterworth Dawn M DM Pillai Sreekumar G SG Muglia Pierandrea P Middleton Lefkos L Berrettini Wade W Knouff Christopher W CW Yuan Xin X Waeber Gérard G Vollenweider Peter P Preisig Martin M Wareham Nicholas J NJ Zhao Jing Hua JH Loos Ruth J F RJ Barroso Inês I Khaw Kay-Tee KT Grundy Scott S Barter Philip P Mahley Robert R Kesaniemi Antero A McPherson Ruth R Vincent John B JB Strauss John J Kennedy James L JL Farmer Anne A McGuffin Peter P Day Richard R Matthews Keith K Bakke Per P Gulsvik Amund A Lucae Susanne S Ising Marcus M Brueckl Tanja T Horstmann Sonja S Wichmann H-Erich HE Rawal Rajesh R Dahmen Norbert N Lamina Claudia C Polasek Ozren O Zgaga Lina L Huffman Jennifer J Campbell Susan S Kooner Jaspal J Chambers John C JC Burnett Mary Susan MS Devaney Joseph M JM Pichard Augusto D AD Kent Kenneth M KM Satler Lowell L Lindsay Joseph M JM Waksman Ron R Epstein Stephen S Wilson James F JF Wild Sarah H SH Campbell Harry H Vitart Veronique V Reilly Muredach P MP Li Mingyao M Qu Liming L Wilensky Robert R Matthai William W Hakonarson Hakon H HH Rader Daniel J DJ Franke Andre A Wittig Michael M Schäfer Arne A Uda Manuela M Terracciano Antonio A Xiao Xiangjun X Busonero Fabio F Scheet Paul P Schlessinger David D St Clair David D Rujescu Dan D Abecasis Gonçalo R GR Grabe Hans Jörgen HJ Teumer Alexander A Völzke Henry H Petersmann Astrid A John Ulrich U Rudan Igor I Hayward Caroline C Wright Alan F AF Kolcic Ivana I Wright Benjamin J BJ Thompson John R JR Balmforth Anthony J AJ Hall Alistair S AS Samani Nilesh J NJ Anderson Carl A CA Ahmad Tariq T Mathew Christopher G CG Parkes Miles M Satsangi Jack J Caulfield Mark M Munroe Patricia B PB Farrall Martin M Dominiczak Anna A Worthington Jane J Thomson Wendy W Eyre Steve S Barton Anne A Mooser Vincent V Francks Clyde C Marchini Jonathan J
Nature genetics 20100425 5
Smoking is a leading global cause of disease and mortality. We established the Oxford-GlaxoSmithKline study (Ox-GSK) to perform a genome-wide meta-analysis of SNP association with smoking-related behavioral traits. Our final data set included 41,150 individuals drawn from 20 disease, population and control cohorts. Our analysis confirmed an effect on smoking quantity at a locus on 15q25 (P = 9.45 x 10(-19)) that includes CHRNA5, CHRNA3 and CHRNB4, three genes encoding neuronal nicotinic acetylch ...[more]
Similar Datasets
Project description:Genetic variants in 15q25 have been identified as potential risk markers for lung cancer (LC), but controversy exists as to whether this is a direct association, or whether the 15q variant is simply a proxy for increased exposure to tobacco carcinogens.We performed a detailed analysis of one 15q single nucleotide polymorphism (SNP) (rs16969968) with smoking behaviour and cancer risk in a total of 17 300 subjects from five LC studies and four upper aerodigestive tract (UADT) cancer studies.Subjects with one minor allele smoked on average 0.3 cigarettes per day (CPD) more, whereas subjects with the homozygous minor AA genotype smoked on average 1.2 CPD more than subjects with a GG genotype (P < 0.001). The variant was associated with heavy smoking (>20 CPD) [odds ratio (OR) = 1.13, 95% confidence interval (CI) 0.96-1.34, P = 0.13 for heterozygotes and 1.81, 95% CI 1.39-2.35 for homozygotes, P < 0.0001]. The strong association between the variant and LC risk (OR = 1.30, 95% CI 1.23-1.38, P = 1 x 10(-18)), was virtually unchanged after adjusting for this smoking association (smoking adjusted OR = 1.27, 95% CI 1.19-1.35, P = 5 x 10(-13)). Furthermore, we found an association between the variant allele and an earlier age of LC onset (P = 0.02). The association was also noted in UADT cancers (OR = 1.08, 95% CI 1.01-1.15, P = 0.02). Genome wide association (GWA) analysis of over 300 000 SNPs on 11 219 subjects did not identify any additional variants related to smoking behaviour.This study confirms the strong association between 15q gene variants and LC and shows an independent association with smoking quantity, as well as an association with UADT cancers.
| S-EPMC2913450 | biostudies-literature
Project description:Cigarette smokers with schizophrenia consume more cigarettes than smokers in the general population. Schizophrenia and smoking quantity may have shared genetic liability. Genome-wide association studies (GWASs) of schizophrenia and smoking quantity have highlighted a biological pleiotropy in which a robust 15q25 locus affects both traits. To identify the genetic variants shared between these traits on 15q25, we used summary statistics from large-scale GWAS meta-analyses of schizophrenia in the Psychiatric Genomics Consortium 2 and smoking quantity assessed by cigarettes smoked per day in the Tobacco and Genetics Consortium. To evaluate the regulatory potential of the shared genetic variants, expression quantitative trait loci analysis in 10 postmortem brain regions was performed using the BRAINEAC dataset in 134 neuropathologically normal individuals. Twenty-two genetic variants on 15q25 were associated with both smoking quantity and schizophrenia at the genome-wide significance level (P < 5.00 × 10-8). Major alleles of all variants were associated with higher smoking quantity and risk of schizophrenia. These genetic variants were associated with PSMA4, CHRNA3, and CHRNB4 expression in specific brain regions (lowest P = 4.81 × 10-4) and with CHRNA5 expression in multiple brain regions (lowest P = 8.70 × 10-6). Risk-associated major alleles of these variants were commonly associated with higher expression in several brain regions, excluding the medulla, at the transcript level. In addition, the risk-associated major allele at rs637137 was associated with higher CHRNA5 expression at the specific exon level in multiple brain regions (lowest P = 2.37 × 10-5). Our findings suggest that genome-wide variants shared between smoking quantity and schizophrenia contribute to a common pathophysiology underlying these traits involving altered CHRNA5 expression in the brain.
| S-EPMC6581148 | biostudies-literature
Project description:Recent meta-analyses of European ancestry subjects show strong evidence for association between smoking quantity and multiple genetic variants on chromosome 15q25. This meta-analysis extends the examination of association between distinct genes in the CHRNA5-CHRNA3-CHRNB4 region and smoking quantity to Asian and African American populations to confirm and refine specific reported associations. Association results for a dichotomized cigarettes smoked per day phenotype in 27 datasets (European ancestry (N = 14,786), Asian (N = 6,889), and African American (N = 10,912) for a total of 32,587 smokers) were meta-analyzed by population and results were compared across all three populations. We demonstrate association between smoking quantity and markers in the chromosome 15q25 region across all three populations, and narrow the region of association. Of the variants tested, only rs16969968 is associated with smoking (P < 0.01) in each of these three populations (odds ratio [OR] = 1.33, 95% CI = 1.25-1.42, P = 1.1 × 10(-17) in meta-analysis across all population samples). Additional variants displayed a consistent signal in both European ancestry and Asian datasets, but not in African Americans. The observed consistent association of rs16969968 with heavy smoking across multiple populations, combined with its known biological significance, suggests rs16969968 is most likely a functional variant that alters risk for heavy smoking. We interpret additional association results that differ across populations as providing evidence for additional functional variants, but we are unable to further localize the source of this association. Using the cross-population study paradigm provides valuable insights to narrow regions of interest and inform future biological experiments.
| S-EPMC3387741 | biostudies-literature
Project description:Results of basic science studies demonstrate shared actions of endogenous neuroactive steroid hormones and drugs of abuse on neurotransmission. As such, premenstrual syndrome (PMS) may be associated with smoking, however, results from studies examining this relationship have been mixed. Following PRISMA guidelines, we extracted unique studies examining the relationship between smoking and PMS. We used the escalc () function in R to compute the log odds ratios and corresponding sampling variance for each study. We based quality assessment on the nature of PMS diagnosis and smoking estimation, confounding adjustment, participation rate, and a priori specification of target population. Our final sample included 13 studies, involving 25,828 study participants. Smoking was associated with an increased risk for PMS [OR = 1.56 (95% CI: 1.25-1.93), p < 0.0001]. Stratified by diagnosis, the effect size estimate was higher for Premenstrual Dysphoric Disorder (PMDD) [OR = 3.15 (95% CI: 2.20-4.52), p < 0.0001] than for PMS [OR = 1.27 (95% CI: 1.16-1.39), p < 0.0001]. We review some of the basic mechanisms for the observed association between smoking and PMS. Given nicotine's rewarding effects, increased smoking behavior may be a mechanism to alleviate affective symptoms of PMS. However, smoking may lead to worsening of PMS symptoms because nicotine has effects on neurocircuitry that increases susceptibility to environmental stressors. Indeed, prior evidence shows that the hypothalamic-pituitary-adrenal (HPA) axis is already sub-optimal in PMS, hence, smoking likely further deteriorates it. Combined, this complicates the clinical course for the treatment of both PMS and Tobacco Use Disorder in this population.
| S-EPMC7725748 | biostudies-literature
Project description:Recently, genetic association findings for nicotine dependence, smoking behavior, and smoking-related diseases converged to implicate the chromosome 15q25.1 region, which includes the CHRNA5-CHRNA3-CHRNB4 cholinergic nicotinic receptor subunit genes. In particular, association with the nonsynonymous CHRNA5 SNP rs16969968 and correlates has been replicated in several independent studies. Extensive genotyping of this region has suggested additional statistically distinct signals for nicotine dependence, tagged by rs578776 and rs588765. One goal of the Consortium for the Genetic Analysis of Smoking Phenotypes (CGASP) is to elucidate the associations among these markers and dichotomous smoking quantity (heavy versus light smoking), lung cancer, and chronic obstructive pulmonary disease (COPD). We performed a meta-analysis across 34 datasets of European-ancestry subjects, including 38,617 smokers who were assessed for cigarettes-per-day, 7,700 lung cancer cases and 5,914 lung-cancer-free controls (all smokers), and 2,614 COPD cases and 3,568 COPD-free controls (all smokers). We demonstrate statistically independent associations of rs16969968 and rs588765 with smoking (mutually adjusted p-values<10(-35) and <10(-8) respectively). Because the risk alleles at these loci are negatively correlated, their association with smoking is stronger in the joint model than when each SNP is analyzed alone. Rs578776 also demonstrates association with smoking after adjustment for rs16969968 (p<10(-6)). In models adjusting for cigarettes-per-day, we confirm the association between rs16969968 and lung cancer (p<10(-20)) and observe a nominally significant association with COPD (p = 0.01); the other loci are not significantly associated with either lung cancer or COPD after adjusting for rs16969968. This study provides strong evidence that multiple statistically distinct loci in this region affect smoking behavior. This study is also the first report of association between rs588765 (and correlates) and smoking that achieves genome-wide significance; these SNPs have previously been associated with mRNA levels of CHRNA5 in brain and lung tissue.
| S-EPMC2916847 | biostudies-literature
Project description:Here we report a large genome-wide association study (GWAS) for longitudinal smoking phenotypes in 286,118 individuals from the Million Veteran Program (MVP) where we identified 18 loci for smoking trajectory of current versus never in European Americans, one locus in African Americans, and one in Hispanic Americans. Functional annotations prioritized several dozen genes where significant loci co-localized with either expression quantitative trait loci or chromatin interactions. The smoking trajectories were genetically correlated with 209 complex traits, for 33 of which smoking was either a causal or a consequential factor. We also performed European-ancestry meta-analyses for smoking status in the MVP and GWAS & Sequencing Consortium of Alcohol and Nicotine use (GSCAN) (Ntotal?=?842,717) and identified 99 loci for smoking initiation and 13 loci for smoking cessation. Overall, this large GWAS of longitudinal smoking phenotype in multiple populations, combined with a meta-GWAS for smoking status, adds new insights into the genetic vulnerability for smoking behavior.
| S-EPMC7598939 | biostudies-literature
Project description:BACKGROUND: Meta-analysis (MA) is widely used to pool genome-wide association studies (GWASes) in order to a) increase the power to detect strong or weak genotype effects or b) as a result verification method. As a consequence of differing SNP panels among genotyping chips, imputation is the method of choice within GWAS consortia to avoid losing too many SNPs in a MA. YAMAS (Yet Another Meta Analysis Software), however, enables cross-GWAS conclusions prior to finished and polished imputation runs, which eventually are time-consuming. RESULTS: Here we present a fast method to avoid forfeiting SNPs present in only a subset of studies, without relying on imputation. This is accomplished by using reference linkage disequilibrium data from 1,000 Genomes/HapMap projects to find proxy-SNPs together with in-phase alleles for SNPs missing in at least one study. MA is conducted by combining association effect estimates of a SNP and those of its proxy-SNPs. Our algorithm is implemented in the MA software YAMAS. Association results from GWAS analysis applications can be used as input files for MA, tremendously speeding up MA compared to the conventional imputation approach. We show that our proxy algorithm is well-powered and yields valuable ad hoc results, possibly providing an incentive for follow-up studies. We propose our method as a quick screening step prior to imputation-based MA, as well as an additional main approach for studies without available reference data matching the ethnicities of study participants. As a proof of principle, we analyzed six dbGaP Type II Diabetes GWAS and found that the proxy algorithm clearly outperforms naïve MA on the p-value level: for 17 out of 23 we observe an improvement on the p-value level by a factor of more than two, and a maximum improvement by a factor of 2127. CONCLUSIONS: YAMAS is an efficient and fast meta-analysis program which offers various methods, including conventional MA as well as inserting proxy-SNPs for missing markers to avoid unnecessary power loss. MA with YAMAS can be readily conducted as YAMAS provides a generic parser for heterogeneous tabulated file formats within the GWAS field and avoids cumbersome setups. In this way, it supplements the meta-analysis process.
| S-EPMC3472171 | biostudies-literature
Project description:BackgroundGenes encoding the receptors involved in the dopaminergic and serotonergic pathways are potential candidates in the mechanisms of nicotine addiction.AimsTo identify genetic variants in the promoter regions and exons of the DRD4 and HTR2A genes associated with tobacco smoking and the degree of nicotine addiction in Mexican mestizos.MethodsThe study included 438 non-smokers (NS) and 1,157 current smokers, ranked based on their consumption of cigarettes per day (cpd): 574 heavy smokers (HS, >20 cpd) and 583 light smokers (LS, 1-10 cpd). Genotyping was performed for 4 and 8 single nucleotide polymorphisms (SNPs) in the DRD4 and HTR2A genes, respectively.ResultsThe C allele of rs1800955 in DRD4 was found to be associated with cigarette smoking in the HS vs. NS and LS vs. NS comparisons (p = 2.34E-03 and p = 1.13E-03, respectively); the association was maintained in the homozygous CC genotype (p = 5.00E-04 and p = 2.00E-04, respectively). The T allele of rs6313 in HTR2A was significantly associated with cigarette smoking and a greater degree of nicotine addiction (p = 4.77E-03, OR = 1.55); the association was maintained in the homozygous genotype (TT) (p = 4.90E-03, OR = 1.96). The A allele of rs6313 was associated with cigarette smoking in the HS vs. NS comparison (p = 1.53E-02, OR = 1.36); the risk was nearly doubled in the homozygous AA genotype (p = 1.30E-03, OR = 1.83) compared with the heterozygous GA genotype (OR = 1.38).ConclusionsAmong Mexican mestizos, the C allele of rs1800955 in the DRD4 gene and the A allele of rs6311 in the HTR2A gene are associated with cigarette smoking, whereas the T allele of rs6313 in HTR2A is associated with cigarette smoking and the degree of nicotine addiction.
| S-EPMC5245876 | biostudies-literature
Project description:BackgroundTobacco exposure might be a modifiable risk factor for atopic dermatitis (AD).ObjectiveWe examine the association between AD and exposure to tobacco smoke.MethodsWe performed a systematic review and meta-analysis of observational studies (n = 86) in MEDLINE, EMBASE, Scopus, and Cochrane Library (1823-2015). Quality of evidence was assessed using the Newcastle-Ottawa Scale (NOS). A meta-analysis was performed using random-effects models to estimate pooled odds ratios (OR). Subset analyses were performed for different ages (children, adult), regions, study designs (cross-sectional, longitudinal), study sizes (<5000, ≥5000), study quality (NOS score <6, ≥6), and amount of smoking (mild, extensive).ResultsA diagnosis of AD was associated with higher odds of active smoking (OR 1.87, 95% confidence interval 1.32-2.63) and exposure to passive smoke (OR 1.18, 95% confidence interval 1.01-1.38), but not maternal smoking during pregnancy (OR 1.06, 95% confidence interval 0.80-1.40). The association between active smoking and AD remained significant in children and adults, all continents studied, and study sizes, but all were cross-sectional designs and had NOS score 6 or greater. Passive smoke was associated with AD in children and adults, cross-sectional studies, South/Central American and African studies, study size less than 5000, and NOS score less than 6.LimitationsAD severity and distribution were not assessed.ConclusionsActive and passive exposure to smoke are associated with increased AD prevalence.
| S-EPMC5216172 | biostudies-literature
Project description:Cigarette smoking is a common addiction that increases the risk for many diseases, including lung cancer and chronic obstructive pulmonary disease. Genome-wide association studies (GWAS) have successfully identified and validated several susceptibility loci for nicotine consumption and dependence. However, the trait variance explained by these genes is only a small fraction of the estimated genetic risk. Pathway analysis complements single marker methods by including biological knowledge into the evaluation of GWAS, under the assumption that causal variants lie in functionally related genes, enabling the evaluation of a broad range of signals. Our approach to the identification of pathways enriched for multiple genes associated with smoking quantity includes the analysis of two studies and the replication of common findings in a third dataset. This study identified pathways for the cholinergic receptors, which included SNPs known to be genome-wide significant; as well as novel pathways, such as genes involved in the sensory perception of smell, that do not contain any single SNP that achieves that stringent threshold.
| S-EPMC3515482 | biostudies-literature