Meta-analysis and imputation refines the association of 15q25 with smoking quantity
Jonathan Marchini and colleagues with the Ox-GSK consortium report a meta-analysis for smoking phenotypes from 20 studies including 41,150 individuals, confirming an association at the CHRNA5 – CHRNA3 locus on 15q25 to smoking quantity. They use imputation based on 1,000 Genomes Project Pilot 1 data...
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Published in | Nature genetics Vol. 42; no. 5; pp. 436 - 440 |
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Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
New York
Nature Publishing Group US
01.05.2010
Nature Publishing Group |
Subjects | |
Online Access | Get full text |
ISSN | 1061-4036 1546-1718 1546-1718 |
DOI | 10.1038/ng.572 |
Cover
Abstract | Jonathan Marchini and colleagues with the Ox-GSK consortium report a meta-analysis for smoking phenotypes from 20 studies including 41,150 individuals, confirming an association at the
CHRNA5
–
CHRNA3
locus on 15q25 to smoking quantity. They use imputation based on 1,000 Genomes Project Pilot 1 data to refine the association at this locus.
Smoking is a leading global cause of disease and mortality
1
. 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 × 10
−19
) that includes
CHRNA5
,
CHRNA3
and
CHRNB4
, three genes encoding neuronal nicotinic acetylcholine receptor subunits. We used data from the 1000 Genomes project to investigate the region using imputation, which allowed for analysis of virtually all common SNPs in the region and offered a fivefold increase in marker density over HapMap2 (ref.
2
) as an imputation reference panel. Our fine-mapping approach identified a SNP showing the highest significance, rs55853698, located within the promoter region of
CHRNA5
. Conditional analysis also identified a secondary locus (rs6495308) in
CHRNA3
. |
---|---|
AbstractList | 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 × 10^sup -19^) that includes CHRNA5, CHRNA3 and CHRNB4, three genes encoding neuronal nicotinic acetylcholine receptor subunits. We used data from the 1000 Genomes project to investigate the region using imputation, which allowed for analysis of virtually all common SNPs in the region and offered a fivefold increase in marker density over HapMap2 (ref. 2) as an imputation reference panel. Our fine-mapping approach identified a SNP showing the highest significance, rs55853698, located within the promoter region of CHRNA5. Conditional analysis also identified a secondary locus (rs6495308) in CHRNA3. [PUBLICATION ABSTRACT] 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 acetylcholine receptor subunits. We used data from the 1000 Genomes project to investigate the region using imputation, which allowed for analysis of virtually all common SNPs in the region and offered a fivefold increase in marker density over HapMap2 (ref. 2) as an imputation reference panel. Our fine-mapping approach identified a SNP showing the highest significance, rs55853698, located within the promoter region of CHRNA5. Conditional analysis also identified a secondary locus (rs6495308) in CHRNA3.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 acetylcholine receptor subunits. We used data from the 1000 Genomes project to investigate the region using imputation, which allowed for analysis of virtually all common SNPs in the region and offered a fivefold increase in marker density over HapMap2 (ref. 2) as an imputation reference panel. Our fine-mapping approach identified a SNP showing the highest significance, rs55853698, located within the promoter region of CHRNA5. Conditional analysis also identified a secondary locus (rs6495308) in CHRNA3. Jonathan Marchini and colleagues with the Ox-GSK consortium report a meta-analysis for smoking phenotypes from 20 studies including 41,150 individuals, confirming an association at the CHRNA5 – CHRNA3 locus on 15q25 to smoking quantity. They use imputation based on 1,000 Genomes Project Pilot 1 data to refine the association at this locus. Smoking is a leading global cause of disease and mortality 1 . 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 × 10 −19 ) that includes CHRNA5 , CHRNA3 and CHRNB4 , three genes encoding neuronal nicotinic acetylcholine receptor subunits. We used data from the 1000 Genomes project to investigate the region using imputation, which allowed for analysis of virtually all common SNPs in the region and offered a fivefold increase in marker density over HapMap2 (ref. 2 ) as an imputation reference panel. Our fine-mapping approach identified a SNP showing the highest significance, rs55853698, located within the promoter region of CHRNA5 . Conditional analysis also identified a secondary locus (rs6495308) in CHRNA3 . 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 10 super(-19)) that includes CHRNA5, CHRNA3 and CHRNB4, three genes encoding neuronal nicotinic acetylcholine receptor subunits. We used data from the 1000 Genomes project to investigate the region using imputation, which allowed for analysis of virtually all common SNPs in the region and offered a fivefold increase in marker density over HapMap2 (ref. 2) as an imputation reference panel. Our fine-mapping approach identified a SNP showing the highest significance, rs55853698, located within the promoter region of CHRNA5. Conditional analysis also identified a secondary locus (rs6495308) in CHRNA3. Smoking is a leading global cause of disease and mortality (1). 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.sup.-19]) that includes CHRNA5, CHRNA3 and CHRNB4, three genes encoding neuronal nicotinic acetylcholine receptor subunits. We used data from the 1000 Genomes project to investigate the region using imputation, which allowed for analysis of virtually all common SNPs in the region and offered a fivefold increase in marker density over HapMap2 (ref. 2) as an imputation reference panel. Our fine-mapping approach identified a SNP showing the highest significance, rs55853698, located within the promoter region of CHRNA5. Conditional analysis also identified a secondary locus (rs6495308) in CHRNA3. 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 acetylcholine receptor subunits. We used data from the 1000 Genomes project to investigate the region using imputation, which allowed for analysis of virtually all common SNPs in the region and offered a fivefold increase in marker density over HapMap2 (ref. 2) as an imputation reference panel. Our fine-mapping approach identified a SNP showing the highest significance, rs55853698, located within the promoter region of CHRNA5. Conditional analysis also identified a secondary locus (rs6495308) in CHRNA3. Smoking is a leading global cause of disease and mortality 1 . We performed a genomewide meta-analytic association study of smoking-related behavioral traits in a total sample of 41,150 individuals drawn from 20 disease, population, and control cohorts. Our analysis confirmed an effect on smoking quantity (SQ) at a locus on 15q25 (P=9.45e-19) that includes three genes encoding neuronal nicotinic acetylcholine receptor subunits (CHRNA5, CHRNA3, CHRNB4). We used data from the 1000 Genomes project to investigate the region using imputation, which allowed analysis of virtually all common variants in the region and offered a five-fold increase in coverage over the HapMap. This increased the spectrum of potentially causal single nucleotide polymorphisms (SNPs), which included a novel SNP that showed the highest significance, rs55853698, located within the promoter region of CHRNA5. Conditional analysis also identified a secondary locus (rs6495308) in CHRNA3. |
Audience | Academic |
Author | Lindsay, Joseph M Kent, Kenneth M Worthington, Jane Barton, Anne Thompson, John R Epstein, Stephen Middleton, Lefkos Tozzi, Federica Khaw, Kay-Tee Farrall, Martin Munroe, Patricia B Farmer, Anne Knouff, Christopher W Zgaga, Lina Anderson, Carl A Rudan, Igor Berrettini, Wade Franke, Andre Samani, Nilesh J Satsangi, Jack Terracciano, Antonio Rader, Daniel J Mathew, Christopher G Dahmen, Norbert Vollenweider, Peter Kooner, Jaspal Wittig, Michael Schäfer, Arne Parkes, Miles Balmforth, Anthony J Wilson, James F Hayward, Caroline Campbell, Harry Eyre, Steve Pichard, Augusto D Devaney, Joseph M Barroso, Inês Waeber, Gérard Loos, Ruth J F Caulfield, Mark Xiao, Xiangjun Busonero, Fabio Chambers, John C Mooser, Vincent Grabe, Hans Jörgen Lucae, Susanne Preisig, Martin Muglia, Pierandrea Ising, Marcus Liu, Jason Z Wichmann, H-Erich Burnett, Mary Susan Li, Mingyao Rawal, Rajesh Rujescu, Dan Strauss, John Waterworth, Dawn M Wright, Alan F Huffman, Jennifer Satler, Lowell Qu, Liming Mahley, Robert Polasek, Ozren Wareham, Nicholas J Barter, Philip Bakke, Per Horstm |
AuthorAffiliation | 19 Division of Cardiology, University of Ottawa Heart Institute, Ottawa, Ontario, Canada 31 Centre for Population Health Sciences, University of Edinburgh, UK 17 Department of Internal Medicine, University of Oulu, Oulu, Finland 5 Department of Psychiatry, University of Pennsylvania School of Medicine, Philadelphia, PA, USA 23 Institute of Medicine, University of Bergen, Bergen, Norway 34 Division of Epidemiology, Imperial College London, UK 16 American Hospital, Istanbul, Turkey 55 Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, UK 58 Gastroenterology Research Unit, Addenbrooke's Hospital, Cambridge, UK 6 Genetics Division, GlaxoSmithKline, Research Triangle Park, NC, USA 46 Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA 13 Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, Texas, USA 21 Medical Research Council Social, Genetic and Developmental Ps |
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of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK – name: 58 Gastroenterology Research Unit, Addenbrooke's Hospital, Cambridge, UK – name: 50 Institute of Clinical Chemistry and Laboratory Medicine, University of Greifswald, Germany – name: 4 Division of Neurosciences and Mental Health, Imperial College London, UK – name: 56 Peninsula College of Medicine and Dentistry, Exeter, UK – name: 31 Centre for Population Health Sciences, University of Edinburgh, UK – name: 3 Genetics Division, GlaxoSmithKline, Upper Merion, PA, USA – name: 15 Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, California, USA – name: 44 Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom – name: 19 Division of Cardiology, University of Ottawa Heart Institute, Ottawa, Ontario, Canada – name: 26 Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany – name: 37 The Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, PA, USA |
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Wellcome Trust Sanger Institute – sequence: 92 givenname: Tariq surname: Ahmad fullname: Ahmad, Tariq organization: Peninsula College of Medicine and Dentistry – sequence: 93 givenname: Christopher G surname: Mathew fullname: Mathew, Christopher G organization: Department of Medical and Molecular Genetics, King's College London School of Medicine, Guy's Hospital – sequence: 94 givenname: Miles surname: Parkes fullname: Parkes, Miles organization: Gastroenterology Research Unit, Addenbrooke's Hospital – sequence: 95 givenname: Jack surname: Satsangi fullname: Satsangi, Jack organization: Gastrointestinal Unit, Molecular Medicine Centre, University of Edinburgh, Western General Hospital – sequence: 96 givenname: Mark surname: Caulfield fullname: Caulfield, Mark organization: Clinical Pharmacology and Barts and the London Genome Centre, William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University of London – sequence: 97 givenname: Patricia B surname: Munroe fullname: Munroe, Patricia B organization: Clinical Pharmacology and Barts and the London Genome Centre, William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University of London – sequence: 98 givenname: Martin surname: Farrall fullname: Farrall, Martin organization: Department of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human Genetics – sequence: 99 givenname: Anna surname: Dominiczak fullname: Dominiczak, Anna organization: Division of Cardiovascular and Medical Sciences, British Heart Foundation Glasgow Cardiovascular Research Centre, University of Glasgow, Western Infirmary, Glasgow, UK – sequence: 100 givenname: Jane surname: Worthington fullname: Worthington, Jane organization: arc Epidemiology Research Unit, School of Translational Medicine, Faculty of Medical and Human Sciences, University of Manchester – sequence: 101 givenname: Wendy surname: Thomson fullname: Thomson, Wendy organization: arc Epidemiology Research Unit, School of Translational Medicine, Faculty of Medical and Human Sciences, University of Manchester – sequence: 102 givenname: Steve surname: Eyre fullname: Eyre, Steve organization: arc Epidemiology Research Unit, School of Translational Medicine, Faculty of Medical and Human Sciences, University of Manchester – sequence: 103 givenname: Anne surname: Barton fullname: Barton, Anne organization: arc Epidemiology Research Unit, School of Translational Medicine, Faculty of Medical and Human Sciences, University of Manchester – sequence: 105 givenname: Vincent surname: Mooser fullname: Mooser, Vincent organization: Genetics Division, GlaxoSmithKline – sequence: 106 givenname: Clyde surname: Francks fullname: Francks, Clyde email: clyde.francks@well.ox.ac.uk organization: Genetics Division, GlaxoSmithKline, Wellcome Trust Centre for Human Genetics, University of Oxford – sequence: 107 givenname: Jonathan surname: Marchini fullname: Marchini, Jonathan email: marchini@stats.ox.ac.uk organization: Department of Statistics, University of Oxford |
BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=23092431$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/20418889$$D View this record in MEDLINE/PubMed |
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CODEN | NGENEC |
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Snippet | Jonathan Marchini and colleagues with the Ox-GSK consortium report a meta-analysis for smoking phenotypes from 20 studies including 41,150 individuals,... 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... Smoking is a leading global cause of disease and mortality (1). We established the Oxford-GlaxoSmithKline study (Ox-GSK) to perform a genome-wide meta-analysis... Smoking is a leading global cause of disease and mortality 1 . We performed a genomewide meta-analytic association study of smoking-related behavioral traits... |
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SubjectTerms | 631/208/205/2138 631/208/729/743 692/699/476/5 Adult Aged Agriculture Alleles Animal Genetics and Genomics Biological and medical sciences Biomedical and Life Sciences Biomedicine Cancer Research Chromosome Mapping - methods Chromosomes Chromosomes, Human, Pair 15 Cohort Studies Confidence intervals Female Fundamental and applied biological sciences. Psychology Gene Function Genetic aspects Genetic Markers - genetics Genetic susceptibility Genetics of eukaryotes. Biological and molecular evolution Genome, Human Human Genetics Humans letter Male Medical sciences Meta-analysis Middle Aged Models, Genetic Neurons - metabolism Neurosciences Nicotine Polymorphism, Single Nucleotide Receptors, Nicotinic - metabolism Risk factors Single nucleotide polymorphisms Smoking Software Tobacco habit Tobacco, tobacco smoking Toxicology |
Title | Meta-analysis and imputation refines the association of 15q25 with smoking quantity |
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