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1. Exome Chip Meta-analysis Fine Maps Causal Variants and Elucidates the Genetic Architecture of Rare Coding Variants in Smoking and Alcohol Use

Author

Michael Boehnke, Anke R. Hammerschlag, Stavroula Kanoni, Nilesh J. Samani, Stefan Blankenberg, Arpana Agrawal, Ersin Yavas, Chris Hsu, Dominique Arveiler, Giovanni Veronesi, Sarah E. Harris, Guillaume Lettre, Leah Wetherill, Helen R. Warren, M Samuel, Manav Kapoor, Praveen Surendran, Mengzhen Liu, Massimo Mangino, Abdulla Al Shafi Majumder, Chiara Batini, Jeff Haessler, Anton J. M. De Craen, Matt McGue, Laura J. Bierut, Yi Ling Chou, Markku Laakso, Ian J. Deary, Rebecca Rohde, Nhung Le, David Schlessinger, J. Dylan Weissenkampen, Claudia Langenberg, Tim D. Spector, Paul W. Franks, John P. Rice, Philippe M. Frossard, Hanieh Yaghootkar, Janie Corley, Frank Kee, J. Wouter Jukema, Pim van der Harst, Dermot F. Reily, Jenny Chang-Claude, Nicholas G. Martin, Tatiana Foroud, Sune F. Nielsen, Charles Kooperberg, Rudolf A. de Boer, Francesco Cucca, Paul D.P. Pharoah, Alex P. Reiner, Daniel R. Barnes, Anders Mälarstig, Jonathan Marten, Henry Völzke, Yu Jiang, Jukka Kontto, J Danesh, Antonis C. Antoniou, Andrew C. Heath, Nicholas J. Wareham, Joanna M. M. Howson, Alison Goate, Olov Rolandsson, Frida Renström, Chu Chen, Vinicius Tragante, Matt J. Neville, Kathleen Stirrups, Clemens Baumbach, Colin N. A. Palmer, Adam S. Butterworth, William G. Iacono, Naveed Sattar, Ian P. Hall, Daniel O. Stram, Giorgio Pistis, Jan-Håkan Jansson, Jaakko Kaprio, David R. Weir, David P. Strachan, Martin D. Tobin, Folkert W. Asselbergs, John M. Starr, Stefan Weiss, Thomas F. Vogt, Riccardo E. Marioni, Maarten Hoek, Jessica Tyrrell, Hilary A. Tindle, Alison M. Dunning, Anu Loukola, Joe Dennis, Victoria E. Jackson, Louise V. Wain, Eleftheria Zeggini, Weihua Zhang, Yaming Shao, Kari Kuulasmaa, Elisabeth Altmaier, Jean-Claude Tardif, Jian Gong, A. Mesut Erzurumluoglu, Andries R. van der Leij, Kari E. North, Anna F. Dominiczak, Martina Müller-Nurasyid, Scott I. Vrieze, Sarah Bertelsen, Markus Perola, Evangelos Evangelou, Chris J. Packard, Gonçalo R. Abecasis, Robert A. Scott, S. Trompet, Jennifer A. Smith, H. Steven Scholte, Timothy M. Frayling, Danielle Posthuma, Ian Ford, Douglas F. Easton, Børge Grønne Nordestgaard, Michiel L. Bots, Charles B. Eaton, Sharon L.R. Kardia, Dewan S. Alam, Xiaowei Zhan, Sean P. David, Maria Uria-Nickelsen, Dongbing Lai, Ilonca Vaartjes, Mark J. Caulfield, Valérie Turcot, Jean Ferrières, Emanuele Di Angelantonio, Robin Young, Pamela A. F. Madden, Tibor V. Varga, Asif Rasheed, Peter van der Meer, Dajiang J. Liu, Ioanna Tachmazidou, Panos Deloukas, Danish Saleheen, Evelin Mihailov, Caroline Hayward, Patricia B. Munroe, Beenish Qaiser, Jessica D. Faul, John C. Chambers, Matthias Nauck, Niek Verweij, Jordan M. Hughey, Christopher A. Haiman, Hans J. Grabe, Muriel Caslake, Saima Afaq, Jaspal S. Kooner, Tinca J. C. Polderman, Philippe Amouyel, Wei Zhao, Göran Hallmans, Andres Metspalu, Jarmo Virtamo, Carl A. Melbourne, Kaixin Zhou, Christiaan de Leeuw, Peter S. Sever, Eirini Marouli, Neil Poulter, Rajiv Chowdhury, Jian'an Luan, Deborah J. Thompson, F Karpe, Kyriaki Michailidou, David M. Brazel, Heather M. Stringham, Brein en Cognitie (Psychologie, FMG), Psychology Other Research (FMG), Human genetics, Amsterdam Neuroscience - Compulsivity, Impulsivity & Attention, Amsterdam Reproduction & Development (AR&D), Cardiovascular Centre (CVC), Restoring Organ Function by Means of Regenerative Medicine (REGENERATE), Graduate School, Experimental Vascular Medicine, ACS - Diabetes & metabolism, Amsterdam Cardiovascular Sciences, ACS - Atherosclerosis & ischemic syndromes, AGEM - Digestive immunity, AGEM - Endocrinology, metabolism and nutrition, Laboratory Genetic Metabolic Diseases, Gastroenterology and Hepatology, Experimental Immunology, Radiotherapy, Cardiology, HUSLAB, Institute for Molecular Medicine Finland, Department of Public Health, Genetic Epidemiology, Barnes, Daniel [0000-0002-3781-7570], Erzurumluoglu, Mesut [0000-0003-1322-8138], Apollo - University of Cambridge Repository, Biological Psychology, and Complex Trait Genetics

Subjects
0301 basic medicine, Nonsynonymous substitution, Genome-wide association study, 3124 Neurology and psychiatry, 0302 clinical medicine, DEPENDENCE, Genotype, Databases, Genetic, SEQUENCE VARIANTS, GWAS, Exome, Non-U.S. Gov't, Oligonucleotide Array Sequence Analysis, Genetics, RISK, HERITABILITY, Research Support, Non-U.S. Gov't, Smoking, ASSOCIATION, 3. Good health, ADH1B, Phenotype, Behavioral genetics, LOW-FREQUENCY, Alcohol, Heritability, Nicotine, Tobacco, Alcohol Drinking, Non-P.H.S, Single-nucleotide polymorphism, Biology, Research Support, Polymorphism, Single Nucleotide, N.I.H, 03 medical and health sciences, Research Support, N.I.H., Extramural, SDG 3 - Good Health and Well-being, Genetic variation, Journal Article, Humans, Genetic Predisposition to Disease, COMMON, Biological Psychiatry, 3112 Neurosciences, Genetic Variation, Extramural, MISSENSE VARIANTS, R1, Genetic architecture, 030104 developmental biology, U.S. Gov't, 030217 neurology & neurosurgery, Research Support, U.S. Gov't, Non-P.H.S, Genome-Wide Association Study
Abstract

BackgroundSmoking and alcohol use have been associated with common genetic variants in multiple loci. Rare variants within these loci hold promise in the identification of biological mechanisms in substance use. Exome arrays and genotype imputation can now efficiently genotype rare nonsynonymous and loss of function variants. Such variants are expected to have deleterious functional consequences and to contribute to disease risk.MethodsWe analyzed ∼250,000 rare variants from 16 independent studies genotyped with exome arrays and augmented this dataset with imputed data from the UK Biobank. Associations were tested for five phenotypes: cigarettes per day, pack-years, smoking initiation, age of smoking initiation, and alcoholic drinks per week. We conducted stratified heritability analyses, single-variant tests, and gene-based burden tests of nonsynonymous/loss-of-function coding variants. We performed a novel fine-mapping analysis to winnow the number of putative causal variants within associated loci.ResultsMeta-analytic sample sizes ranged from 152,348 to 433,216, depending on the phenotype. Rare coding variation explained 1.1% to 2.2% of phenotypic variance, reflecting 11% to 18% of the total single nucleotide polymorphism heritability of these phenotypes. We identified 171 genome-wide associated loci across all phenotypes. Fine mapping identified putative causal variants with double base-pair resolution at 24 of these loci, and between three and 10 variants for 65 loci. Twenty loci contained rare coding variants in the 95% credible intervals.ConclusionsRare coding variation significantly contributes to the heritability of smoking and alcohol use. Fine-mapping genome-wide association study loci identifies specific variants contributing to the biological etiology of substance use behavior.

Published
2019
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2. Fifteen new risk loci for coronary artery disease highlight arterial-wall-specific mechanisms

Author

Pia R. Kamstrup, Nilesh J. Samani, Daniel F. Freitag, Nora Franceschini, Børge G. Nordestgaard, Chao A. Hsiung, Charles Kooperberg, Elias Salfati, Rajiv Chowdhury, Kristin L. Young, Wayne Huey-Herng Sheu, Asif Rasheed, Cara L. Carty, I-Te Lee, Jemma B. Wilk, Ying-Hsiang Chen, Lucia A. Hindorff, Praveen Surendran, Alexander P. Reiner, Ren-Hua Chung, Dewan S. Alam, Andrew D. Johnson, Jeanette Erdmann, Sune F. Nielsen, Adam S. Butterworth, Heribert Schunkert, Thomas Quertermous, Abdulla Al Shafi Majumder, Julie A. Johnson, Sekar Kathiresan, Robin Young, Themistocles L. Assimes, CARDIoGRAMplusC D, Xiuqing Guo, Katrine L. Rasmussen, John A. Spertus, Daniel J. Rader, Joanna M. M. Howson, John D. Eicher, Anne E. Justice, Stanley L. Hazen, Panos Deloukas, Eric B. Fauman, Devin Absher, Eric Boerwinkle, Danish Saleheen, John Danesh, Daniel R. Barnes, Epic-Cvd, Weang Kee Ho, Philippe M. Frossard, Hugh Watkins, Yi-Jen Hung, Anne Tybjærg-Hansen, Anders Mälarstig, Jyh-Ming Jimmy Juang, Ulrike Peters, Jerome I. Rotter, Emanuele Di Angelantonio, Tzung-Dau Wang, Ron Do, Carl J. Pepine, Wei-Yu Lin, Wen-Jane Lee, Benjamin B. Sun, Kari E. North, Lindsay L. Waite, Mariaelisa Graff, Steven Buyske, Yii-Der Ida Chen, Wei Zhao, Arshed A. Quyyumi, Kent D. Taylor, and Dirk S. Paul

Subjects
0301 basic medicine, Male, Leukocyte migration, Genotype, Quantitative Trait Loci, Single-nucleotide polymorphism, Genome-wide association study, Coronary Artery Disease, 030204 cardiovascular system & hematology, Quantitative trait locus, Biology, Bioinformatics, Polymorphism, Single Nucleotide, Article, Muscle, Smooth, Vascular, Coronary artery disease, 03 medical and health sciences, 0302 clinical medicine, Risk Factors, Genetics, medicine, Cell Adhesion, Humans, Genetic Predisposition to Disease, Genetic association, Arteries, medicine.disease, Atherosclerosis, 3. Good health, Histone Code, Chemotaxis, Leukocyte, 030104 developmental biology, Vascular smooth muscle cell differentiation, Female, Energy Metabolism, Genome-Wide Association Study
Abstract

Coronary artery disease (CAD) is a leading cause of morbidity and mortality worldwide1,2. Although 58 genomic regions have been associated with CAD thus far3-9, most of the heritability is unexplained9, indicating that additional susceptibility loci await identification. An efficient discovery strategy may be larger-scale evaluation of promising associations suggested by genome-wide association studies (GWAS). Hence, we genotyped 56,309 participants using a targeted gene array derived from earlier GWAS results and performed metaanalysis of results with 194,427 participants previously genotyped, totaling 88,192 CAD cases and 162,544 controls. We identified 25 new SNP-CAD associations (P < 5 x 10(-8), in fixed-effects meta-analysis) from 15 genomic regions, including SNPs in or near genes involved in cellular adhesion, leukocyte migration and atherosclerosis (PECAM1, rs1867624), coagulation and inflammation (PROCR, rs867186 (p. Ser219Gly)) and vascular smooth muscle cell differentiation (LMOD1, rs2820315). Correlation of these regions with celltype- specific gene expression and plasma protein levels sheds light on potential disease mechanisms.

Published
2017

3. Genetic invalidation of Lp-PLA

Author

John M, Gregson, Daniel F, Freitag, Praveen, Surendran, Nathan O, Stitziel, Rajiv, Chowdhury, Stephen, Burgess, Stephen, Kaptoge, Pei, Gao, James R, Staley, Peter, Willeit, Sune F, Nielsen, Muriel, Caslake, Stella, Trompet, Linda M, Polfus, Kari, Kuulasmaa, Jukka, Kontto, Markus, Perola, Stefan, Blankenberg, Giovanni, Veronesi, Francesco, Gianfagna, Satu, Männistö, Akinori, Kimura, Honghuang, Lin, Dermot F, Reilly, Mathias, Gorski, Vladan, Mijatovic, Patricia B, Munroe, Georg B, Ehret, Alex, Thompson, Maria, Uria-Nickelsen, Anders, Malarstig, Abbas, Dehghan, Thomas F, Vogt, Taishi, Sasaoka, Fumihiko, Takeuchi, Norihiro, Kato, Yoshiji, Yamada, Frank, Kee, Martina, Müller-Nurasyid, Jean, Ferrières, Dominique, Arveiler, Philippe, Amouyel, Veikko, Salomaa, Eric, Boerwinkle, Simon G, Thompson, Ian, Ford, J, Wouter Jukema, Naveed, Sattar, Chris J, Packard, Abdulla Al, Shafi Majumder, Dewan S, Alam, Panos, Deloukas, Heribert, Schunkert, Nilesh J, Samani, Sekar, Kathiresan, Børge G, Nordestgaard, Danish, Saleheen, Joanna Mm, Howson, Emanuele, Di Angelantonio, Adam S, Butterworth, and John, Danesh

Subjects
Adult, Male, Genotype, Phospholipase A2 Inhibitors, Reproducibility of Results, Coronary Disease, Middle Aged, Polymorphism, Single Nucleotide, Risk Assessment, Treatment Outcome, Gene Expression Regulation, Reference Values, Benzaldehydes, Case-Control Studies, 1-Alkyl-2-acetylglycerophosphocholine Esterase, Oximes, Humans, Female, Molecular Targeted Therapy, Alleles, Aged, Randomized Controlled Trials as Topic
Abstract

Aims Darapladib, a potent inhibitor of lipoprotein-associated phospholipase A

Published
2016

4. Genetic invalidation of Lp-PLA2 as a therapeutic target: Large-scale study of five functional Lp-PLA2-lowering alleles

Author

Dewan S. Alam, Martina Müller-Nurasyid, Pei Gao, Akinori Kimura, Danish Saleheen, Emanuele Di Angelantonio, Stefan Blankenberg, Taishi Sasaoka, Jean Ferrières, Børge G. Nordestgaard, Panos Deloukas, Abbas Dehghan, Eric Boerwinkle, Maria Uria-Nickelsen, Simon G. Thompson, Markus Perola, Chris J. Packard, Giovanni Veronesi, Dominique Arveiler, Dermot F. Reilly, Patricia B. Munroe, Stephen Burgess, Rajiv Chowdhury, Philippe Amouyel, J. Wouter Jukema, Alex Thompson, Francesco Gianfagna, Satu Männistö, Honghuang Lin, Nathan O. Stitziel, Heribert Schunkert, Naveed Sattar, Vladan Mijatovic, Abdulla Al Shafi Majumder, Nilesh J. Samani, Daniel F. Freitag, Stephen Kaptoge, Sekar Kathiresan, Stella Trompet, Peter Willeit, Jukka Kontto, John Danesh, Georg Ehret, Veikko Salomaa, Adam S. Butterworth, Joanna M. M. Howson, Ian Ford, Mathias Gorski, Kari Kuulasmaa, Yoshiji Yamada, Norihiro Kato, John M. Gregson, Frank Kee, Fumihiko Takeuchi, Praveen Surendran, James R Staley, Linda M. Polfus, Sune F. Nielsen, Anders Mälarstig, Thomas F. Vogt, Muriel J. Caslake, CKDGen consortium, International Consortium for Blood Pressure, CHARGE inflammation working group, MICAD Exome consortium, EPIC-CVD consortium and the CHD Exome+ consortium, Epidemiology, Surendran, Praveen [0000-0002-4911-6077], Chowdhury, Rajiv [0000-0003-4881-5690], Burgess, Stephen [0000-0001-5365-8760], Kaptoge, Stephen [0000-0002-1155-4872], Thompson, Simon [0000-0002-5274-7814], Howson, Joanna [0000-0001-7618-0050], Di Angelantonio, Emanuele [0000-0001-8776-6719], Butterworth, Adam [0000-0002-6915-9015], Danesh, John [0000-0003-1158-6791], Apollo - University of Cambridge Repository, Institute for Molecular Medicine Finland, University of Helsinki, and Quantitative Genetics

Subjects
0301 basic medicine, Pathology, Epidemiology, 030204 cardiovascular system & hematology, VARIANTS, Gastroenterology, law.invention, CHARGE inflammation working group, 0302 clinical medicine, Randomized controlled trial, Human genetics, law, Medicine, ARTERY-DISEASE, RISK, 1184 Genetics, developmental biology, physiology, 3. Good health, CARDIOVASCULAR-DISEASE, International Consortium for Blood Pressure, MICAD Exome consortium, lipids (amino acids, peptides, and proteins), Cardiology and Cardiovascular Medicine, medicine.medical_specialty, coronary heart disease, darapladib, lipoprotein-associated phospholipase A2, target validation, ACTIVATING-FACTOR ACETYLHYDROLASE, EVENTS, 03 medical and health sciences, Internal medicine, Darapladib, health services administration, lipoprotein-associated phospholipase A(2), CORONARY-HEART-DISEASE, Allele, Risk factor, GENOME-WIDE ASSOCIATION, Genotyping, PHOSPHOLIPASE A(2) ACTIVITY, business.industry, Lipoprotein-associated phospholipase A2, EPIC-CVD consortium and the CHD Exome+ consortium, R1, 030104 developmental biology, CKDGen consortium, Relative risk, 3121 General medicine, internal medicine and other clinical medicine, 1-Alkyl-2-acetylglycerophosphocholine Esterase/drug effects, 1-Alkyl-2-acetylglycerophosphocholine Esterase/genetics, Adult, Aged, Alleles, Benzaldehydes/therapeutic use, Case-Control Studies, Coronary Disease/diagnosis, Coronary Disease/drug therapy, Coronary Disease/genetics, Female, Gene Expression Regulation, Genotype, Humans, Male, Middle Aged, Molecular Targeted Therapy, Oximes/therapeutic use, Phospholipase A2 Inhibitors/therapeutic use, Polymorphism, Single Nucleotide, Randomized Controlled Trials as Topic, Reference Values, Reproducibility of Results, Risk Assessment, Treatment Outcome, 3111 Biomedicine, business
Abstract

Aims Darapladib, a potent inhibitor of lipoprotein-associated phospholipase A javax.xml.bind.JAXBElement@3ed2b341 (Lp-PLA javax.xml.bind.JAXBElement@3d94c871 ), has not reduced risk of cardiovascular disease outcomes in recent randomized trials. We aimed to test whether Lp-PLA javax.xml.bind.JAXBElement@ab2bb75 enzyme activity is causally relevant to coronary heart disease. Methods In 72,657 patients with coronary heart disease and 110,218 controls in 23 epidemiological studies, we genotyped five functional variants: four rare loss-of-function mutations (c.109+2T > C (rs142974898), Arg82His (rs144983904), Val279Phe (rs76863441), Gln287Ter (rs140020965)) and one common modest-impact variant (Val379Ala (rs1051931)) in PLA2G7, the gene encoding Lp-PLA javax.xml.bind.JAXBElement@77eb0872 . We supplemented de-novo genotyping with information on a further 45,823 coronary heart disease patients and 88,680 controls in publicly available databases and other previous studies. We conducted a systematic review of randomized trials to compare effects of darapladib treatment on soluble Lp-PLA javax.xml.bind.JAXBElement@5c08e575 activity, conventional cardiovascular risk factors, and coronary heart disease risk with corresponding effects of Lp-PLA javax.xml.bind.JAXBElement@474479c5 -lowering alleles. Results Lp-PLA javax.xml.bind.JAXBElement@58b21b4b activity was decreased by 64% ( p = 2.4 × 10 javax.xml.bind.JAXBElement@77b520b7 ) with carriage of any of the four loss-of-function variants, by 45% ( p < 10 javax.xml.bind.JAXBElement@6c8d5079 ) for every allele inherited at Val279Phe, and by 2.7% ( p = 1.9 × 10 javax.xml.bind.JAXBElement@8e3967c ) for every allele inherited at Val379Ala. Darapladib 160 mg once-daily reduced Lp-PLA javax.xml.bind.JAXBElement@4043bc68 activity by 65% ( p < 10 javax.xml.bind.JAXBElement@1ead8c4f ). Causal risk ratios for coronary heart disease per 65% lower Lp-PLA javax.xml.bind.JAXBElement@1825097b activity were: 0.95 (0.88-1.03) with Val279Phe; 0.92 (0.74-1.16) with carriage of any loss-of-function variant; 1.01 (0.68-1.51) with Val379Ala; and 0.95 (0.89-1.02) with darapladib treatment. Conclusions In a large-scale human genetic study, none of a series of Lp-PLA javax.xml.bind.JAXBElement@c612c75 -lowering alleles was related to coronary heart disease risk, suggesting that Lp-PLA javax.xml.bind.JAXBElement@511c716d is unlikely to be a causal risk factor.

Published
2016
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