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101. A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans

Author

Nicholas J. Timpson, Klaudia Walter, Josine L. Min, Ioanna Tachmazidou, Giovanni Malerba, So Youn Shin, Lu Chen, Marta Futema, Lorraine Southam, Valentina Iotchkova, Jie Huang, Yasin Memari, Shane McCarthy, Petr Danecek, Dawn Muddyman, Massimo Mangino, Cristina Menni, John R. B. Perry, Susan M. Ring, Amadou Gaye, George Dedoussis, Aliki Eleni Farmaki, Paul Burton, Philippa J. Talmud, Giovanni Gambaro, Tim D. Spector, George Davey Smith, Richard Durbin, J. Brent Richards, Steve E. Humphries, Eleftheria Zeggini, Nicole Soranzo, Saeed Al Turki, Carl Anderson, Richard Anney, Dinu Antony, Maria Soler Artigas, Muhammad Ayub, Senduran Balasubramaniam, Jeffrey C. Barrett, Inês Barroso, Phil Beales, Jamie Bentham, Shoumo Bhattacharya, Ewan Birney, Douglas Blackwood, Martin Bobrow, Elena Bochukova, Patrick Bolton, Rebecca Bounds, Chris Boustred, Gerome Breen, Mattia Calissano, Keren Carss, Krishna Chatterjee, Antonio Ciampi, Sebhattin Cirak, Peter Clapham, Gail Clement, Guy Coates, David Collier, Catherine Cosgrove, Tony Cox, Nick Craddock, Lucy Crooks, Sarah Curran, David Curtis, Allan Daly, Aaron Day Williams, Ian N. M. Day, Thomas Down, Yuanping Du, Ian Dunham, Sarah Edkins, Peter Ellis, David Evans, Sadaf Faroogi, Ghazaleh Fatemifar, David R. Fitzpatrick, Paul Flicek, James Flyod, A. Reghan Foley, Christopher S. Franklin, Louise Gallagher, Tom Gaunt, Matthias Geihs, Daniel Geschwind, Celia Greenwood, Heather Griffin, Detelina Grozeva, Xueqin Guo, Xiaosen Guo, Hugh Gurling, Deborah Hart, Audrey Hendricks, Peter Holmans, Bryan Howie, Liren Huang, Tim Hubbard, Matthew E. Hurles, Pirro Hysi, David K. Jackson, Yalda Jamshidi, Tian Jing, Chris Joyce, Jane Kaye, Thomas Keane, Julia Keogh, John Kemp, Karen Kennedy, Anja Kolb Kokocinski, Genevieve Lachance, Cordelia Langford, Daniel Lawson, Irene Lee, Monkol Lek, Jieqin Liang, Hong Lin, Rui Li, Yingrui Li, Ryan Liu, Jouko Lönnqvist, Margarida Lopes, Valentina Lotchkova, Daniel MacArthur, Jonathan Marchini, John Maslen, Mangino Massimo, Iain Mathieson, Gaëlle Marenne, Peter McGuffin, Andrew McIntosh, Andrew G. McKechanie, Andrew McQuillin, Sarah Metrustry, Josine Min, Hannah Mitchison, Alireza Moayyeri, James Morris, Francesco Muntoni, Kate Northstone, Michael O'Donnovan, Alexandros Onoufriadis, Stephen O'Rahilly, Karim Oualkacha, Michael J. Owen, Aarno Palotie, Kalliope Panoutsopoulou, Victoria Parker, Jeremy R. Parr, Lavinia Paternoster, Tiina Paunio, Felicity Payne, John Perry, Olli Pietilainen, Vincent Plagnol, Lydia Quaye, Michael A. Quail, Lucy Raymond, Karola Rehnström, Brent Richards, Susan Ring, Graham R. S. Ritchie, Nicola Roberts, David B. Savage, Peter Scambler, Stephen Schiffels, Miriam Schmidts, Nadia Schoenmakers, Robert K. Semple, Eva Serra, Sally I. Sharp, Hasheem Shihab, David Skuse, Kerrin Small, Olivera Spasic Boskovic, Tim Spector, David St Clair, Jim Stalker, Elizabeth Stevens, Beate St Pourcian, Jianping Sun, Gabriela Surdulescu, Jaana Suvisaari, Ionna Tachmazidou, Nicholas Timpson, Martin D. Tobin, Ana Valdes, Margriet Van Kogelenberg, Parthiban Vijayarangakannan, Peter M. Visscher, Louise V. Wain, James T. R. Walters, Guangbiao Wang, Jun Wang, Yu Wang, Kirsten Ward, Elanor Wheeler, Tamieka Whyte, Hywel Williams, Kathleen A. Williamson, Crispian Wilson, Scott G. Wilson, Kim Wong, ChangJiang Xu, Jian Yang, Fend Zhang, Pingbo Zhang, Hou Feng Zheng, COCCA, MASSIMILIANO, Nicholas J., Timpson, Klaudia, Walter, Josine L., Min, Ioanna, Tachmazidou, Giovanni, Malerba, So Youn, Shin, Lu, Chen, Marta, Futema, Lorraine, Southam, Valentina, Iotchkova, Cocca, Massimiliano, Jie, Huang, Yasin, Memari, Shane, Mccarthy, Petr, Danecek, Dawn, Muddyman, Massimo, Mangino, Cristina, Menni, John R. B., Perry, Susan M., Ring, Amadou, Gaye, George, Dedoussi, Aliki Eleni, Farmaki, Paul, Burton, Philippa J., Talmud, Giovanni, Gambaro, Tim D., Spector, George Davey, Smith, Richard, Durbin, J., Brent Richard, Steve E., Humphrie, Eleftheria, Zeggini, Nicole, Soranzo, Saeed Al, Turki, Carl, Anderson, Richard, Anney, Dinu, Antony, Maria Soler, Artiga, Muhammad, Ayub, Senduran, Balasubramaniam, Jeffrey C., Barrett, Inês, Barroso, Phil, Beale, Jamie, Bentham, Shoumo, Bhattacharya, Ewan, Birney, Douglas, Blackwood, Martin, Bobrow, Elena, Bochukova, Patrick, Bolton, Rebecca, Bound, Chris, Boustred, Gerome, Breen, Mattia, Calissano, Keren, Car, Krishna, Chatterjee, Antonio, Ciampi, Sebhattin, Cirak, Peter, Clapham, Gail, Clement, Guy, Coate, David, Collier, Catherine, Cosgrove, Tony, Cox, Nick, Craddock, Lucy, Crook, Sarah, Curran, David, Curti, Allan, Daly, Aaron Day, William, Ian N. M., Day, Thomas, Down, Yuanping, Du, Ian, Dunham, Sarah, Edkin, Peter, Elli, David, Evan, Sadaf, Faroogi, Ghazaleh, Fatemifar, David R., Fitzpatrick, Paul, Flicek, James, Flyod, A., Reghan Foley, Christopher S., Franklin, Louise, Gallagher, Tom, Gaunt, Matthias, Geih, Daniel, Geschwind, Celia, Greenwood, Heather, Griffin, Detelina, Grozeva, Xueqin, Guo, Xiaosen, Guo, Hugh, Gurling, Deborah, Hart, Audrey, Hendrick, Peter, Holman, Bryan, Howie, Liren, Huang, Tim, Hubbard, Matthew E., Hurle, Pirro, Hysi, David K., Jackson, Yalda, Jamshidi, Tian, Jing, Chris, Joyce, Jane, Kaye, Thomas, Keane, Julia, Keogh, John, Kemp, Karen, Kennedy, Anja Kolb, Kokocinski, Genevieve, Lachance, Cordelia, Langford, Daniel, Lawson, Irene, Lee, Monkol, Lek, Jieqin, Liang, Hong, Lin, Rui, Li, Yingrui, Li, Ryan, Liu, Jouko, Lönnqvist, Margarida, Lope, Valentina, Lotchkova, Daniel, Macarthur, Jonathan, Marchini, John, Maslen, Mangino, Massimo, Iain, Mathieson, Gaëlle, Marenne, Peter, Mcguffin, Andrew, Mcintosh, Andrew G., Mckechanie, Andrew, Mcquillin, Sarah, Metrustry, Josine, Min, Hannah, Mitchison, Alireza, Moayyeri, James, Morri, Francesco, Muntoni, Kate, Northstone, Michael, O'Donnovan, Alexandros, Onoufriadi, Stephen, O'Rahilly, Karim, Oualkacha, Michael J., Owen, Aarno, Palotie, Kalliope, Panoutsopoulou, Victoria, Parker, Jeremy R., Parr, Lavinia, Paternoster, Tiina, Paunio, Felicity, Payne, John, Perry, Olli, Pietilainen, Vincent, Plagnol, Lydia, Quaye, Michael A., Quail, Lucy, Raymond, Karola, Rehnström, Brent, Richard, Susan, Ring, Graham R. S., Ritchie, Nicola, Robert, David B., Savage, Peter, Scambler, Stephen, Schiffel, Miriam, Schmidt, Nadia, Schoenmaker, Robert K., Semple, Eva, Serra, Sally I., Sharp, Hasheem, Shihab, David, Skuse, Kerrin, Small, Olivera Spasic, Boskovic, Tim, Spector, David St, Clair, Jim, Stalker, Elizabeth, Steven, Beate St, Pourcian, Jianping, Sun, Gabriela, Surdulescu, Jaana, Suvisaari, Ionna, Tachmazidou, Nicholas, Timpson, Martin D., Tobin, Ana, Valde, Margriet Van, Kogelenberg, Parthiban, Vijayarangakannan, Peter M., Visscher, Louise V., Wain, James T. R., Walter, Guangbiao, Wang, Jun, Wang, Yu, Wang, Kirsten, Ward, Elanor, Wheeler, Tamieka, Whyte, Hywel, William, Kathleen A., Williamson, Crispian, Wilson, Scott G., Wilson, Kim, Wong, Changjiang, Xu, Jian, Yang, Fend, Zhang, Pingbo, Zhang, and Hou Feng, Zheng

Subjects
Very low-density lipoprotein, Population, vldl, apoc3, General Physics and Astronomy, Genome-wide association study, 030204 cardiovascular system & hematology, Biology, rare mutations, Bioinformatics, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, genome-wide association study (GWAS), plasma lipids, 0302 clinical medicine, Polymorphism (computer science), Genetic variation, Settore MED/14 - NEFROLOGIA, Allele, education, Allele frequency, 030304 developmental biology, Genetics, 0303 health sciences, education.field_of_study, Multidisciplinary, cholesterol, General Chemistry, Minor allele frequency
Abstract

The analysis of rich catalogues of genetic variation from population-based sequencing provides an opportunity to screen for functional effects. Here we report a rare variant in APOC3 (rs138326449-A, minor allele frequency ~0.25% (UK)) associated with plasma triglyceride (TG) levels (−1.43 s.d. (s.e.=0.27 per minor allele (P-value=8.0 × 10−8)) discovered in 3,202 individuals with low read-depth, whole-genome sequence. We replicate this in 12,831 participants from five additional samples of Northern and Southern European origin (−1.0 s.d. (s.e.=0.173), P-value=7.32 × 10−9). This is consistent with an effect between 0.5 and 1.5 mmol l−1 dependent on population. We show that a single predicted splice donor variant is responsible for association signals and is independent of known common variants. Analyses suggest an independent relationship between rs138326449 and high-density lipoprotein (HDL) levels. This represents one of the first examples of a rare, large effect variant identified from whole-genome sequencing at a population scale., Population-based genome sequencing provides an increasingly rich resource for the identification of low-frequency, large effect variants associated with clinically important phenotypes. Timpson et al. use UK10K data to identify a variant of the APOC3 gene strongly associated with plasma triglyceride levels.

Published
2014

102. Genome-wide associations for birth weight and correlations with adult disease

Author

Anubha Mahajan, George McMahon, Charlotta Pisinger, Timothy M. Frayling, Elisabeth M. van Leeuwen, Felix R. Day, Virpi Lindi, Allan Vaag, Debbie A Lawlor, Natalie R. van Zuydam, Peter Kovacs, David Torrents, Bjarke Feenstra, Peter Vollenweider, David P. Strachan, Krina T. Zondervan, John R. B. Perry, Jorma Viikari, Pedro Marques-Vidal, Kalliope Panoutsopoulou, Ruifang Li-Gao, Juan Fernández-Tajes, Carolina Medina-Gomez, Nicole M. Warrington, Josep M. Mercader, Antje Körner, David M. Evans, Albert Hofman, Hans Bisgaard, Amanda J. Bennett, Eleanor Davies, Linda S. Adair, Oluf Pedersen, Mustafa Atalay, Sylvain Sebert, Ying Wu, Haja N. Kadarmideen, Ronald C.W. Ma, Lawrence J. Beilin, David M. Hougaard, Diana L. Cousminer, Louise A. Diver, Jing Hua Zhao, Nilufer Rahmioglu, Peter K. Joshi, Neil R. Robertson, Johannes Waage, Hugoline G. de Haan, Jens-Christian Holm, Dale R. Nyholt, Torben Hansen, Sara M. Willems, Sílvia Bonàs-Guarch, Carol A. Wang, Rico Rueedi, Lavinia Paternoster, James F. Wilson, Cilius Esmann Fonvig, Leo-Pekka Lyytikäinen, Hanieh Yaghootkar, Momoko Horikoshi, Gonneke Willemsen, Dennis O. Mook-Kanamori, Lisbeth Carstensen, Mariona Bustamante, Emil V. R. Appel, Christian Theil Have, Rebecca M. Reynolds, Niels Grarup, Seang-Mei Saw, Yik Ying Teo, Brian R. Walker, Anke Tönjes, Christopher J. Groves, Andrew P. Morris, Katja Pahkala, Marjolein N. Kooijman, Kyle J. Gaulton, Eskil Kreiner, Michael Stumvoll, Eleftheria Zeggini, Vincent W. V. Jaddoe, Zoltán Kutalik, Scott M. MacKenzie, George Davey Smith, Christine Power, Denise M. Scholtens, Joachim Heinrich, Samuel E. Jones, William L. Lowe, Eco J. C. de Geus, Jonathan P. Bradfield, Andrew T. Hattersley, Janine F. Felix, Wing Hung Tam, Frits R. Rosendaal, Wieland Kiess, Claudia H. T. Tam, Inga Prokopenko, Terho Lehtimäki, Frank D. Mentch, Marjo-Riitta Järvelin, Struan F.A. Grant, Santhi K. Ganesh, Fernando Rivadeneira, Thorkild I. A. Sørensen, André G. Uitterlinden, Marie Standl, Jian'an Luan, Gibran Hemani, Marcus A. Tuke, Andrew R. Wood, Robert A. Scott, Cæcilie Trier, Tarunveer S. Ahluwalia, Michael Nodzenski, Jouke-Jan Hottenga, Ken K. Ong, Po-Ru Loh, Nicholas J. Timpson, George Dedoussis, Friman Sánchez, Mark I. McCarthy, Frank Geller, Harri Niinikoski, Martine Vrijheid, Hakon Hakonarson, John P. Newnham, Xu Wang, Elina Hyppönen, Johan G. Eriksson, Craig E. Pennell, Niina Pitkänen, Rachel M. Freathy, Elisabeth Widen, Judith B. Borja, Karen L. Mohlke, Mads Melbye, Carla M. T. Tiesler, Susan M. Ring, Jessica Tyrrell, Elisabeth Thiering, Timo A. Lakka, Eileen Tai-Hui Boh, Olli T. Raitakari, Nicholas J. Wareham, Mario Murcia, Natalia Vilor-Tejedor, Katherine S. Ruth, Dorret I. Boomsma, Harry Campbell, Vasiliki Lagou, Robin N Beaumont, Klaus Bønnelykke, Claudia Langenberg, Catharina E. M. van Beijsterveldt, Mika Kähönen, Mads V. Hollegaard, Frank J.A. van Rooij, Katharina E. Schraut, Ioanna Ntalla, Raimo Joro, Cornelia M. van Duijn, Biological Psychology, EMGO+ - Lifestyle, Overweight and Diabetes, Day, Felix [0000-0003-3789-7651], Langenberg, Claudia [0000-0002-5017-7344], Luan, Jian'an [0000-0003-3137-6337], Zhao, Jing Hua [0000-0003-4930-3582], Wareham, Nicholas [0000-0003-1422-2993], Ong, Kenneth [0000-0003-4689-7530], Perry, John [0000-0001-6483-3771], Apollo - University of Cambridge Repository, Erasmus MC other, Medical Microbiology & Infectious Diseases, Epidemiology, Medical Oncology, Child and Adolescent Psychiatry / Psychology, Public Health, Internal Medicine, Pediatrics, Horikoshi, Momoko, Beaumont, Robin N, Day, Felix R, Warrington, Nicole, Hyppönen, Elina, and Freathy, Rachel M

Subjects
Male, 0301 basic medicine, Netherlands Twin Register (NTR), Aging, Datasets as Topic, Physiology, Blood Pressure, Genome-wide association study, Coronary Artery Disease, Type 2 diabetes, Bioinformatics, CHARGE Consortium Hematology Working Group, Cohort Studies, 0302 clinical medicine, Birth Weight, Insulin, Glucose homeostasis, 030212 general & internal medicine, education.field_of_study, Multidisciplinary, Anthropometry, 3. Good health, Phenotype, Female, Glycogen, Signal Transduction, Adult, hypertension, Genotype, General Science & Technology, Birth weight, intrauterine growth, Population, Quantitative trait locus, Biology, Article, quantitative trait, Genomic Imprinting, 03 medical and health sciences, Fetus, SDG 3 - Good Health and Well-being, Early Growth Genetics (EGG) Consortium, MD Multidisciplinary, Genetic variation, medicine, Humans, metabolic disorders, Genetic Predisposition to Disease, education, genome, Genetic association, Genetic Variation, birth weight, ta3121, Chromatin Assembly and Disassembly, medicine.disease, ta3123, Glucose, 030104 developmental biology, Diabetes Mellitus, Type 2, Genetic Loci, genome-wide association studies, adult disease, Genome-Wide Association Study
Abstract

Birth weight (BW) has been shown to be influenced by both fetal and maternal factors and in observational studies is reproducibly associated with future risk of adult metabolic diseases including type 2 diabetes (T2D) and cardiovascular disease. These life-course associations have often been attributed to the impact of an adverse early life environment. Here, we performed a multi-ancestry genome-wide association study (GWAS) meta-analysis of BW in 153,781 individuals, identifying 60 loci where fetal genotype was associated with BW (P&thinsp

Published
2016

103. Genetic variants associated with mosaic Y chromosome loss highlight cell cycle genes and overlap with cancer susceptibility

Author

Svanhvit Sigurjonsdottir, Kari Stefansson, Unnur Thorsteindottir, Alexia Cardona, Daniel F. Gudbjartsson, Nicholas J. Wareham, J. Ross Chapman, Nicola D. Kerrison, John R. B. Perry, Felix R. Day, Steve P Jackson, Deborah J. Thompson, Daniel J Wright, Agnar Helgason, Patrick Sulem, Florian Zink, Ken K. Ong, Robert A. Scott, Claudia Langenberg, Wright, Daniel J [0000-0003-3983-2093], Day, Felix R [0000-0003-3789-7651], Thompson, Deborah J [0000-0003-1465-5799], Chapman, J Ross [0000-0002-6477-4254], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Male, Genotype, Mosaic (geodemography), Biology, Y chromosome, Polymorphism, Single Nucleotide, Genomic Instability, Article, 03 medical and health sciences, INDEL Mutation, Neoplasms, Genetics, Humans, Genetic Predisposition to Disease, Chromosomes, Human, X, Chromosomes, Human, Y, Genome, Human, Cell Cycle, Genetic variants, Cancer susceptibility, Genetic Variation, DNA Methylation, Biobank, 3. Good health, 030104 developmental biology, Female, Chromosome Deletion, Genome-Wide Association Study
Abstract

The Y chromosome is frequently lost in hematopoietic cells, which represents the most common somatic alteration in men. However, the mechanisms that regulate mosaic loss of chromosome Y (mLOY), and its clinical relevance, are unknown. We used genotype-array-intensity data and sequence reads from 85,542 men to identify 19 genomic regions (P < 5 × 10-8) that are associated with mLOY. Cumulatively, these loci also predicted X chromosome loss in women (n = 96,123; P = 4 × 10-6). Additional epigenome-wide methylation analyses using whole blood highlighted 36 differentially methylated sites associated with mLOY. The genes identified converge on aspects of cell proliferation and cell cycle regulation, including DNA synthesis (NPAT), DNA damage response (ATM), mitosis (PMF1, CENPN and MAD1L1) and apoptosis (TP53). We highlight the shared genetic architecture between mLOY and cancer susceptibility, in addition to inferring a causal effect of smoking on mLOY. Collectively, our results demonstrate that genotype-array-intensity data enables a measure of cell cycle efficiency at population scale and identifies genes implicated in aneuploidy, genome instability and cancer susceptibility.

Published
2016

104. Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

Author

Steven A. McCarroll, John R. B. Perry, Jason D. Buenrostro, Caleb A. Lareau, Alexander Gusev, Kamil Slowikowski, Yakir A. Reshef, Bradley E. Bernstein, Po-Ru Loh, Evan Z. Macosko, Samuela Pollack, Soumya Raychaudhuri, Verneri Anttila, Hilary K. Finucane, Alkes L. Price, Benjamin M. Neale, Giulio Genovese, Noam Shoresh, Andrea Byrnes, Steven Gazal, and Arpiar Saunders

Subjects
0301 basic medicine, False discovery rate, Linkage disequilibrium, Multifactorial Inheritance, Schizophrenia/genetics, Bipolar Disorder, Neurons/metabolism, Gene Expression, Genome-wide association study, PREFRONTAL CORTEX, Disease, Linkage Disequilibrium, Body Mass Index, Epigenesis, Genetic, 0302 clinical medicine, SCHIZOPHRENIA, Gene expression, Tissue Distribution, PARTITIONING HERITABILITY, Epigenesis, 2. Zero hunger, Genetics, Neurons, 0303 health sciences, Chromatin/genetics, Bipolar Disorder/genetics, Brain, BIPOLAR DISORDER, Chromatin, Immune System Diseases, Cell type, SUSCEPTIBILITY LOCI, Immune System Diseases/genetics, Biology, Tissue Distribution/genetics, 03 medical and health sciences, Genome-Wide Association Study/statistics & numerical data, Brain/metabolism, Humans, Genetic Predisposition to Disease, Gene Expression Profiling/statistics & numerical data, GENOME-WIDE ASSOCIATION, Allele, Gene, METAANALYSIS, 030304 developmental biology, Models, Genetic, COMPLEX TRAITS, Gene Expression Profiling, Heritability, RISK LOCI, BODY-MASS INDEX, 030104 developmental biology, Schizophrenia, 030217 neurology & neurosurgery, Function (biology), Genome-Wide Association Study
Abstract

Genetics can provide a systematic approach to discovering the tissues and cell types relevant for a complex disease or trait. Identifying these tissues and cell types is critical for following up on non-coding allelic function, developing ex-vivo models, and identifying therapeutic targets. Here, we analyze gene expression data from several sources, including the GTEx and PsychENCODE consortia, together with genome-wide association study (GWAS) summary statistics for 48 diseases and traits with an average sample size of 169,331, to identify disease-relevant tissues and cell types. We develop and apply an approach that uses stratified LD score regression to test whether disease heritability is enriched in regions surrounding genes with the highest specific expression in a given tissue. We detect tissue-specific enrichments at FDR < 5% for 34 diseases and traits across a broad range of tissues that recapitulate known biology. In our analysis of traits with observed central nervous system enrichment, we detect an enrichment of neurons over other brain cell types for several brain-related traits, enrichment of inhibitory over excitatory neurons for bipolar disorder but excitatory over inhibitory neurons for schizophrenia and body mass index, and enrichments in the cortex for schizophrenia and in the striatum for migraine. In our analysis of traits with observed immunological enrichment, we identify enrichments of T cells for asthma and eczema, B cells for primary biliary cirrhosis, and myeloid cells for Alzheimer's disease, which we validated with independent chromatin data. Our results demonstrate that our polygenic approach is a powerful way to leverage gene expression data for interpreting GWAS signal.

Published
2016

105. Genetic evidence that raised sex hormone binding globulin (SHBG) levels reduce the risk of type 2 diabetes

Author

Amanda J. Bennett, Lori L. Bonnycastle, Inês Barroso, Gudmar Thorleifsson, Charlotta Pisinger, Timothy M. Frayling, Laura J. Scott, Christian Herder, Mark Walker, Markku Laakso, Laura Pascoe, Beverley M. Shields, Thomas Sparsø, Ele Ferrannini, John R. B. Perry, Torsten Lauritzen, Felicity Payne, Thomas Illig, Michael N. Weedon, Beatrice Knight, Luigi Ferrucci, Giuseppe Paolisso, Claudia Langenberg, Andrew D. Morris, Torben Hansen, Ewan R. Pearson, Oluf Pedersen, Annelli Sandbæk, Peter Schwarz, Mario A. Morken, Colin N. A. Palmer, Peter Nilsson, Marcello Maggio, Narisu Narisu, Katharine R. Owen, Stefan R. Bornstein, Michael Boehnke, Mike Sampson, Leif Groop, Marjo-Riitta Järvelin, Aimo Ruokonen, Andrew T. Hattersley, Valgerdur Steinthorsdottir, Unnur Thorsteinsdottir, Ele Zeggini Magic, Mark I. McCarthy, Cecilia M. Lindgren, Christopher J. Groves, Elizabeth H. Young, Johanna Kuusisto, Harald Grallert, Valeriya Lyssenko, Anette P. Gjesing, Malin Neptin, Anne U. Jackson, Kari Stefansson, Nicholas J. Wareham, Heather M. Stringham, Perry, Jr, Weedon, Mn, Langenberg, C, Jackson, Au, Lyssenko, V, Sparsø, T, Thorleifsson, G, Grallert, H, Ferrucci, L, Maggio, M, Paolisso, Giuseppe, Walker, M, Palmer, Cn, Payne, F, Young, E, Herder, C, Narisu, N, Morken, Ma, Bonnycastle, Ll, Owen, Kr, Shields, B, Knight, B, Bennett, A, Groves, Cj, Ruokonen, A, Jarvelin, Mr, Pearson, E, Pascoe, L, Ferrannini, E, Bornstein, Sr, Stringham, Hm, Scott, Lj, Kuusisto, J, Nilsson, P, Neptin, M, Gjesing, Ap, Pisinger, C, Lauritzen, T, Sandbaek, A, Sampson, M, Zeggini, Me, Lindgren, Cm, Steinthorsdottir, V, Thorsteinsdottir, U, Hansen, T, Schwarz, P, Illig, T, Laakso, M, Stefansson, K, Morris, Ad, Groop, L, Pedersen, O, Boehnke, M, Barroso, I, Wareham, Nj, Hattersley, At, Mccarthy, Mi, and Frayling, Tm

Subjects
Male, AUGSBURG CASE-COHORT, Genome-wide association study, Type 2 diabetes, 0302 clinical medicine, Sex hormone-binding globulin, Risk Factors, Sex Hormone-Binding Globulin, polycyclic compounds, Gonadal Steroid Hormones, 11 Medical and Health Sciences, Genetics (clinical), reproductive and urinary physiology, Genetics & Heredity, 0303 health sciences, biology, INSULIN SENSITIVITY, Association Studies Articles, General Medicine, Middle Aged, PROSTATE-CANCER, 3. Good health, POSTMENOPAUSAL WOMEN, MENDELIAN RANDOMIZATION, Female, TESTOSTERONE TREATMENT, Life Sciences & Biomedicine, hormones, hormone substitutes, and hormone antagonists, Adult, Biochemistry & Molecular Biology, medicine.medical_specialty, BODY-COMPOSITION, 030209 endocrinology & metabolism, Single-nucleotide polymorphism, STEROID-HORMONES, Polymorphism, Single Nucleotide, 03 medical and health sciences, Diabetes mellitus, Internal medicine, Mendelian randomization, Genetics, medicine, Humans, GENOME-WIDE ASSOCIATION, Molecular Biology, 030304 developmental biology, Aged, Science & Technology, Case-control study, Odds ratio, 06 Biological Sciences, medicine.disease, MAGIC, SERUM CONCENTRATIONS, Endocrinology, Diabetes Mellitus, Type 2, Case-Control Studies, biology.protein
Abstract

Udgivelsesdato: 2010-Feb-1 Epidemiological studies consistently show that circulating sex hormone binding globulin (SHBG) levels are lower in type 2 diabetes patients than non-diabetic individuals, but the causal nature of this association is controversial. Genetic studies can help dissect causal directions of epidemiological associations because genotypes are much less likely to be confounded, biased or influenced by disease processes. Using this Mendelian randomization principle, we selected a common single nucleotide polymorphism (SNP) near the SHBG gene, rs1799941, that is strongly associated with SHBG levels. We used data from this SNP, or closely correlated SNPs, in 27 657 type 2 diabetes patients and 58 481 controls from 15 studies. We then used data from additional studies to estimate the difference in SHBG levels between type 2 diabetes patients and controls. The SHBG SNP rs1799941 was associated with type 2 diabetes [odds ratio (OR) 0.94, 95% CI: 0.91, 0.97; P = 2 x 10(-5)], with the SHBG raising allele associated with reduced risk of type 2 diabetes. This effect was very similar to that expected (OR 0.92, 95% CI: 0.88, 0.96), given the SHBG-SNP versus SHBG levels association (SHBG levels are 0.2 standard deviations higher per copy of the A allele) and the SHBG levels versus type 2 diabetes association (SHBG levels are 0.23 standard deviations lower in type 2 diabetic patients compared to controls). Results were very similar in men and women. There was no evidence that this variant is associated with diabetes-related intermediate traits, including several measures of insulin secretion and resistance. Our results, together with those from another recent genetic study, strengthen evidence that SHBG and sex hormones are involved in the aetiology of type 2 diabetes.

Published
2016

106. Circulating beta-carotene levels and type 2 diabetes-cause or effect?

Author

Eleftheria Zeggini, Timothy M. Frayling, Laura J. Scott, J. M. Guralnik, Richard D. Semba, Michael N. Weedon, John R. B. Perry, Luigi Ferrucci, N. Rice, Mark I. McCarthy, David Melzer, Andrew T. Hattersley, Stefania Bandinelli, and Richa Saxena

Subjects
Vitamin, medicine.medical_specialty, Antioxidant, Endocrinology, Diabetes and Metabolism, medicine.medical_treatment, Type 2 diabetes, Polymorphism, Single Nucleotide, Article, chemistry.chemical_compound, beta-Carotene, Polymorphism (computer science), Diabetes mellitus, Internal medicine, Internal Medicine, Humans, Medicine, beta-Carotene 15,15'-Monooxygenase, business.industry, Carotene, Human physiology, beta Carotene, medicine.disease, Endocrinology, Diabetes Mellitus, Type 2, chemistry, business
Abstract

AIMS/HYPOTHESIS: Circulating beta-carotene levels are inversely associated with risk of type 2 diabetes, but the causal direction of this association is not certain. In this study we used a Mendelian randomisation approach to provide evidence for or against the causal role of the antioxidant vitamin beta-carotene in type 2 diabetes. METHODS: We used a common polymorphism (rs6564851) near the BCMO1 gene, which is strongly associated with circulating beta-carotene levels (p = 2 x 10(-24)), with each G allele associated with a 0.27 standard deviation increase in levels. We used data from the InCHIANTI and Uppsala Longitudinal Study of Adult Men (ULSAM) studies to estimate the association between beta-carotene levels and type 2 diabetes. We next used a triangulation approach to estimate the expected effect of rs6564851 on type 2 diabetes risk and compared this with the observed effect using data from 4549 type 2 diabetes patients and 5579 controls from the Diabetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium. RESULTS: A 0.27 standard deviation increase in beta-carotene levels was associated with an OR of 0.90 (95% CI 0.86-0.95) for type 2 diabetes in the InCHIANTI study. This association was similar to that of the ULSAM study (OR 0.90 [0.84-0.97]). In contrast, there was no association between rs6564851 and type 2 diabetes (OR 0.98 [0.93-1.04], p = 0.58); this effect size was also smaller than that expected, given the known associations between rs6564851 and beta-carotene levels, and the associations between beta-carotene levels and type 2 diabetes. CONCLUSIONS/INTERPRETATION: Our findings in this Mendelian randomisation study are in keeping with randomised controlled trials suggesting that beta-carotene is not causally protective against type 2 diabetes.

Published
2016

107. Type 2 diabetes risk alleles are associated with reduced size at birth

Author

Nicholas J. Timpson, George Davey Smith, Andrew T. Hattersley, Timothy M. Frayling, Beverley M. Shields, John R. B. Perry, Amanda J. Bennett, Eleftheria Zeggini, Chris Power, David P. Strachan, Michael N. Weedon, Paul Elliott, Elina Hyppönen, Marjo-Riitta Järvelin, Christopher J. Groves, Rachel M. Freathy, Susan M. Ring, Anneli Pouta, Mark I. McCarthy, Aimo Ruokonen, Hana Lango, Cecilia M. Lindgren, Freathy, Rachel M, Bennett, Amanda J, Ring, Susan M, Shields, Beverly, Hypponen, Elina, and Hattersley, Andrew T

Subjects
medicine.medical_specialty, Offspring, Endocrinology, Diabetes and Metabolism, Birth weight, Mothers, Apoptosis, 030209 endocrinology & metabolism, Type 2 diabetes, Biology, risk alleles, fetal insulin, 03 medical and health sciences, Fetus, 0302 clinical medicine, Insulin resistance, Risk Factors, Insulin-Secreting Cells, Internal medicine, Insulin Secretion, Genotype, Genetics, Internal Medicine, medicine, Birth Weight, Humans, Insulin, low birth weight, CDKAL1, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, SLC30A8, Infant, Newborn, DNA, Infant, Low Birth Weight, medicine.disease, 3. Good health, Low birth weight, Endocrinology, Diabetes Mellitus, Type 2, biology.protein, Original Article, type 2 diabetes, medicine.symptom
Abstract

OBJECTIVE Low birth weight is associated with an increased risk of type 2 diabetes. The mechanisms underlying this association are unknown and may represent intrauterine programming or two phenotypes of one genotype. The fetal insulin hypothesis proposes that common genetic variants that reduce insulin secretion or action may predispose to type 2 diabetes and also reduce birth weight, since insulin is a key fetal growth factor. We tested whether common genetic variants that predispose to type 2 diabetes also reduce birth weight. RESEARCH DESIGN AND METHODS We genotyped single-nucleotide polymorphisms (SNPs) at five recently identified type 2 diabetes loci (CDKAL1, CDKN2A/B, HHEX-IDE, IGF2BP2, and SLC30A8) in 7,986 mothers and 19,200 offspring from four studies of white Europeans. We tested the association between maternal or fetal genotype at each locus and birth weight of the offspring. RESULTS We found that type 2 diabetes risk alleles at the CDKAL1 and HHEX-IDE loci were associated with reduced birth weight when inherited by the fetus (21 g [95% CI 11–31], P = 2 × 10−5, and 14 g [4–23], P = 0.004, lower birth weight per risk allele, respectively). The 4% of offspring carrying four risk alleles at these two loci were 80 g (95% CI 39–120) lighter at birth than the 8% carrying none (Ptrend = 5 × 10−7). There were no associations between birth weight and fetal genotypes at the three other loci or maternal genotypes at any locus. CONCLUSIONS Our results are in keeping with the fetal insulin hypothesis and provide robust evidence that common disease-associated variants can alter size at birth directly through the fetal genotype.

Published
2016

108. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls

Author

Morris J. Brown, Sanjeev S. Bhaskar, Alison J. Coffey, Suzanne Rafelt, Kirsten McLay, John Bowes, Francesca Bredin, Alastair Compston, John C. Mansfield, Elaine R. Nimmo, Kate Downes, Peter McGuffin, Neil Walker, Anthony J. Balmforth, Philip Howard, Detelina Grozeva, Helen Stevens, Kate L. Lee, Richard D. Pearson, Gerome Breen, T. Daniel Andrews, Sheila Seal, Anna Elliot, Beverley M. Shields, Andrew T. Hattersley, Sarah Edkins, Ann E. Morgan, Gil McVean, Julian Maller, Millicent A. Stone, Adam Auton, Carol Scott, Michael R. Stratton, Matthew Woodburn, John R. B. Perry, Michael Conlon O'Donovan, Nigel P. Carter, Vincent Plagnol, Stephen Sawcer, Sarah Hines, Mahim Jain, Allan H. Young, Steve Eyre, Elilan Somaskantharajah, Alexander J. Mentzer, Niall Cardin, Eleanor Howard, Inês Barroso, Stephen C. L. Gough, Toby Johnson, Deborah P M Symmons, Christopher Holmes, David St Clair, Patricia B. Munroe, Sue Shaw-Hawkins, Emma Gray, Stephen W. Scherer, Tariq Ahmad, Jaswinder Bull, Debbie Hughes, E. Russell, Timothy M. Frayling, Chris Clee, I. Nicol Ferrier, James Lee, Dominic P. Kwiatkowski, Husam Hebaishi, Anne Hinks, Simon Myers, Gareth Evans, Eleftheria Zeggini, Katarina Spanova, Michael L. Mimmack, David M. Reid, Amanda J. Bennett, Richard T. Scott, Armand Valsesia, Derek P. Jewell, Andrew P. Morris, Peter Donnelly, Mark J. Caulfield, Jake K. Byrnes, Lars Feuk, Pile Harrison, Anna F. Dominiczak, Cathryn Edwards, Andrew Dunham, Dalila Pinto, Inga Prokopenko, Ian Jones, Craig Mowat, Nigel R. Ovington, Willem H. Ouwehand, Edward Flynn, Jason D. Cooper, Louise V. Wain, Alistair Forbes, Bernadette Ebbs, Jennifer Jolley, Jonathan Marchini, Peter S. Braund, Ifejinelo Onyiah, Mark Walker, Adrian V. S. Hill, Cordelia Langford, Anne M. Phillips, George Kirov, David P. Strachan, Oliver S. Burren, Martin D. Tobin, Anthony G. Wilson, Ian N. Bruce, Hana Lango-Allen, Alistair S. Hall, Natalie J. Prescott, Charles Lee, Clare Turnbull, Cecilia M. Lindgren, John D. Isaacs, Jack Satsangi, Liz Forty, John M. C. Connell, Neelam Hassanali, Hazel E. Drummond, Matthew A. Brown, John A. Todd, Joanna M. M. Howson, Jennifer G. Sambrook, Graham A. Hitman, Michael N. Weedon, Christopher Yau, Abiodun Onipinla, Kathy Stirrups, Chris Tyler-Smith, Darshna Dudakia, G. Mark Lathrop, Katherine Gordon-Smith, Nazneen Rahman, Christopher J. Groves, William G. Newman, Kirstie Parnell, Stephen G. Ball, Tomas W Fitzgerald, Paul Gilbert, Kevin Lewis, Charlie W. Lees, Polly Gibbs, Rachel M. Freathy, Aarno Palotie, Katarzyna Blaszczyk, Matthew E. Hurles, Jonathan Stephens, Lynne J. Hocking, Nicholas A. Watkins, Christopher G. Mathew, Helen Schuilenburg, David Pernet, Eleni Giannoulatou, Kimmo Palin, Nigel W. Rayner, Donald F. Conrad, Susan M. Ring, John R. Thompson, Debbie J. Smyth, Wendy L. McArdle, B. Paul Wordsworth, David M. Evans, Dunecan Massey, Naomi Hammond, Diana Eccles, Panos Deloukas, Sian Caesar, Chris P. Barnes, Sophia Steer, Anthony Attwood, Chris Wallace, Richard Redon, Paul Burton, Anne Barton, Marcus Pembrey, Michael John Owen, Jane Worthington, Mary E. Travers, Jeremy D. Sanderson, Meeta Maisuria-Armer, Elaine K. Green, Michael A. Quail, Oliver J. Brand, Anne Farmer, Matthew J. Simmonds, Neil Robertson, Nicholas John Craddock, Zhan Su, Jan Aerts, Martin Farrall, Hazel Arbury, Damjan Vukcevic, Paul Emery, Omer Gokumen, A Hall, Wendy Thomson, Jeffrey C. Barrett, Margaret Warren-Perry, Rhian Gwilliam, Sarah E. Hunt, Samuel Robson, Paul Martin, Audrey Duncanson, Anthony Renwick, John Webster, Lisa Jones, Mark I. McCarthy, Nilesh J. Samani, Matthew Hardy, Miles Parkes, John Burton, Jayne A. Franklyn, Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Statistics [Oxford], University of Oxford, The Wellcome Trust Centre for Human Genetics [Oxford], The Wellcome Trust Case Control Consortium, Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, University of Oxford [Oxford], and Medical Research Council (MRC)

Subjects
endocrine system diseases, [SDV]Life Sciences [q-bio], Genome-wide association study, Pilot Projects, CCL3L1, SUSCEPTIBILITY, Arthritis, Rheumatoid, Diabetes mellitus genetics, 0302 clinical medicine, Crohn Disease, Gene Frequency, DUPLICATIONS, SCHIZOPHRENIA, Disease, Copy-number variation, Oligonucleotide Array Sequence Analysis, Genetics, 0303 health sciences, Multidisciplinary, PSORIASIS, HERITABILITY, LARGE-SCALE, Nucleic Acid Hybridization, Science & Technology - Other Topics, Wellcome Trust Case Control Consortium, Quality Control, DNA Copy Number Variations, General Science & Technology, Single-nucleotide polymorphism, COPY-NUMBER VARIATION, Biology, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, MD Multidisciplinary, mental disorders, Genetic predisposition, Diabetes Mellitus, SNP, Humans, Genetic Predisposition to Disease, Allele frequency, POLYMORPHISMS, 030304 developmental biology, Genetic association, Science & Technology, MULTIDISCIPLINARY SCIENCES, DELETION, C431 Medical Genetics, Case-Control Studies, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed 19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with diseaseIRGM for Crohns disease, HLA for Crohns disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetesalthough in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases. © 2010 Macmillan Publishers Limited. All rights reserved.

Published
2016

109. Association between low-density lipoprotein cholesterol-lowering genetic variants and risk of type 2 diabetes: a meta-analysis

Author

Kim Overvad, Mark I. McCarthy, Larraitz Arriola, Olov Rolandsson, Heiner Boeing, Rudolf Kaaks, John R. B. Perry, Carmen Navarro, Peter M. Nilsson, Elena Salamanca-Fernández, Inês Barroso, Sara Grioni, Elio Riboli, Sara M. Willems, Claudia Langenberg, Timothy J. Key, David B. Savage, Beverley Balkau, Luca A. Lotta, Domenico Palli, Nadia Slimani, Isobel D. Stewart, Paul W. Franks, Anne Tjønneland, Stephen Burgess, Jian'an Luan, Annemieke M.W. Spijkerman, Robert A. Scott, Stephen J. Sharp, Salvatore Panico, Rosario Tumino, Yvonne T. van der Schouw, Eva Ardanaz, Nicholas J. Wareham, Panos Deloukas, Daphne L. van der A, Naveed Sattar, Carlotta Sacerdote, José Ramón Quirós, Stephen O'Rahilly, Nita G. Forouhi, Sharp, Stephen [0000-0003-2375-1440], Burgess, Stephen [0000-0001-5365-8760], Perry, John [0000-0001-6483-3771], Luan, Jian'an [0000-0003-3137-6337], Forouhi, Nita [0000-0002-5041-248X], Barroso, Ines [0000-0001-5800-4520], O'Rahilly, Stephen [0000-0003-2199-4449], Savage, David [0000-0002-7857-7032], Langenberg, Claudia [0000-0002-5017-7344], Wareham, Nicholas [0000-0003-1422-2993], Apollo - University of Cambridge Repository, Lotta, Luca A, Sharp, Stephen J, Burgess, Stephen, Perry, John R. B, Stewart, Isobel D, Willems, Sara M, Luan, Jian'An, Ardanaz, Eva, Arriola, Larraitz, Balkau, Beverley, Boeing, Heiner, Deloukas, Pano, Forouhi, Nita G, Franks, Paul W, Grioni, Sara, Kaaks, Rudolf, Key, Timothy J, Navarro, Carmen, Nilsson, Peter M, Overvad, Kim, Palli, Domenico, Panico, Salvatore, Quirós, Jose Ramón, Riboli, Elio, Rolandsson, Olov, Sacerdote, Carlotta, Salamanca Fernandez, Elena, Slimani, Nadia, Spijkerman, Annemieke M. W, Tjonneland, Anne, Tumino, Rosario, van der A, Daphne L, van der Schouw, Yvonne T, Mccarthy, Mark I, Barroso, Inê, O'Rahilly, Stephen, Savage, David B, Sattar, Naveed, Langenberg, Claudia, Scott, Robert A, and Wareham, Nicholas J.

Subjects
0301 basic medicine, Oncology, Simvastatin, Type 2 diabetes, Coronary Artery Disease, 030204 cardiovascular system & hematology, Coronary artery disease, Cohort Studies, 0302 clinical medicine, Odds Ratio, ATP Binding Cassette Transporter, Subfamily G, Member 5, Non-U.S. Gov't, Medicine(all), Research Support, Non-U.S. Gov't, 11 Medical And Health Sciences, General Medicine, Middle Aged, 3. Good health, Drug Therapy, Combination, lipids (amino acids, peptides, and proteins), Proprotein Convertase 9, Adult, Risk, medicine.medical_specialty, Lipoproteins, Research Support, 03 medical and health sciences, General & Internal Medicine, Internal medicine, Diabetes mellitus, Genetic variation, medicine, Journal Article, Humans, Allele, Genetic Association Studies, Genetic association, Aged, Polymorphism, Genetic, business.industry, PCSK9, Genetic Variation, Membrane Proteins, Membrane Transport Proteins, Odds ratio, Cholesterol, LDL, medicine.disease, Ezetimibe, 030104 developmental biology, Endocrinology, Diabetes Mellitus, Type 2, Receptors, LDL, Hydroxymethylglutaryl CoA Reductases, Hydroxymethylglutaryl-CoA Reductase Inhibitors, business, Meta-Analysis
Abstract

IMPORTANCE: Low-density lipoprotein cholesterol (LDL-C)-lowering alleles in or near $\textit{NPC1L1}$ or $\textit{HMGCR}$, encoding the respective molecular targets of ezetimibe and statins, have previously been used as proxies to study the efficacy of these lipid-lowering drugs. Alleles near $\textit{HMGCR}$ are associated with a higher risk of type 2 diabetes, similar to the increased incidence of new-onset diabetes associated with statin treatment in randomized clinical trials. It is unknown whether alleles near $\textit{NPC1L1}$ are associated with the risk of type 2 diabetes. OBJECTIVE: To investigate whether LDL-C-lowering alleles in or near $\textit{NPC1L1}$ and other genes encoding current or prospective molecular targets of lipid-lowering therapy (ie, $\textit{HMGCR}$, $\textit{PCSK9}$, $\textit{ABCG5/G8}$, $\textit{LDLR}$) are associated with the risk of type 2 diabetes. DESIGN, SETTING, AND PARTICIPANTS: The associations with type 2 diabetes and coronary artery disease of LDL-C-lowering genetic variants were investigated in meta-analyses of genetic association studies. Meta-analyses included 50 775 individuals with type 2 diabetes and 270 269 controls and 60 801 individuals with coronary artery disease and 123 504 controls. Data collection took place in Europe and the United States between 1991 and 2016. EXPOSURES: Low-density lipoprotein cholesterol-lowering alleles in or near $\textit{NPC1L1}$, $\textit{HMGCR}$, $\textit{PCSK9}$, $\textit{ABCG5/G8}$, and $\textit{LDLR}$. MAIN OUTCOMES AND MEASURES: Odds ratios (ORs) for type 2 diabetes and coronary artery disease. RESULTS: Low-density lipoprotein cholesterol-lowering genetic variants at $\textit{NPC1L1}$ were inversely associated with coronary artery disease (OR for a genetically predicted 1-mmol/L [38.7-mg/dL] reduction in LDL-C of 0.61 [95% CI, 0.42-0.88]; $P$ = .008) and directly associated with type 2 diabetes (OR for a genetically predicted 1-mmol/L reduction in LDL-C of 2.42 [95% CI, 1.70-3.43]; $P$ < .001). For $\textit{PCSK9}$ genetic variants, the OR for type 2 diabetes per 1-mmol/L genetically predicted reduction in LDL-C was 1.19 (95% CI, 1.02-1.38; $P$ = .03). For a given reduction in LDL-C, genetic variants were associated with a similar reduction in coronary artery disease risk ($I^2$ = 0% for heterogeneity in genetic associations; $P$ = .93). However, associations with type 2 diabetes were heterogeneous ($I^2$ = 77.2%; $P$ = .002), indicating gene-specific associations with metabolic risk of LDL-C-lowering alleles. CONCLUSIONS AND RELEVANCE: In this meta-analysis, exposure to LDL-C-lowering genetic variants in or near $\textit{NPC1L1}$ and other genes was associated with a higher risk of type 2 diabetes. These data provide insights into potential adverse effects of LDL-C-lowering therapy.

Published
2016

110. Genome-wide analysis identifies 12 loci influencing human reproductive behavior

Author

Ozren Polasek, Bo Jacobsson, Eleonora Porcu, Vinicius Tragante, Joel Eriksson, Jie Yao, Mika Kähönen, Mark Alan Fontana, Stefania Cappellani, J. Viikari, Rick Jansen, Crysovalanto Mamasoula, Linda Broer, Tamara B. Harris, Ellen A. Nohr, Genevieve Lachance, Johan G. Eriksson, Nicholas Eriksson, Rico Rueedi, Francesco Cucca, Jaakko Kaprio, Nicholas J. Timpson, George Dedoussis, Matt McGue, Per Magnus, Klaus Berger, Olli T. Raitakari, Cornelia M. van Duijn, Brenda W.J.H. Penninx, Jing Hua Zhao, Peter Eibich, Sheila Ulivi, Hugoline G. de Haan, Ronny Myhre, Ruth McQuillan, Florian Kronenberg, Markus Perola, Klaus Bønnelykke, Robert Karlsson, Martina La Bianca, Paul Mitchell, Ian J. Deary, Melinda Mills, Teresa Nutile, Patrick J. F. Groenen, Stacey A. Missmer, Nicholas G. Martin, Panos Deloukas, Mario Pirastu, Lindsay K. Matteson, Robert Luben, Veikko Salomaa, Renée de Mutsert, Chris Power, Nir Barzilai, Annette Kifley, Hamdi Mbarek, Denis A. Evans, Erica P. Gunderson, Tim D. Spector, Anke Tönjes, Michela Traglia, Claire Monnereau, Karin Halina Greiser, Sharon L.R. Kardia, John M. Starr, Peter K. Joshi, Sandra Lai, Doris Stöckl, James J. Lee, Heather J. Cordell, Andrew Bakshi, Nicholas J. Wareham, David C. Liewald, P Koponen, Paul M. Ridker, Joyce Y. Tung, Ilaria Gandin, Kauko Heikkilä, Johannes Haerting, Gonneke Willemsen, Janet W. Rich-Edwards, Andrew C. Heath, Astanand Jugessur, John L. Hopper, Stefan Kiechl, Henry Völzke, Daniela Ruggiero, John R. B. Perry, Dan Mellström, Simon R. Cox, Yasaman Saba, Magnus Johannesson, Ginevra Biino, David Schlessinger, Kirsi Auro, Dennis O. Mook-Kanamori, Christa Meisinger, Igor Rudan, Audrey J. Gaskins, Lars Bertram, Roy Thurik, Laura M. Yerges-Armstrong, Caterina Barbieri, Katri Räikkönen, Lawrence F. Bielak, Aviv Bergman, Philipp Koellinger, Ronald de Vlaming, Tian Liu, Johannes W. A. Smit, Peter Kovacs, Vincent W. V. Jaddoe, Jennifer A. Smith, Sven Bergmann, Inga Prokopenko, Xiuqing Guo, Marina Ciullo, Krina T. Zondervan, Marcel den Hoed, Daniel J. Benjamin, Kathryn Roll, Alan F. Wright, Helena Schmidt, William G. Iacono, Jie Jin Wang, Harold Snieder, Juho Wedenoja, Tarunveer S. Ahluwalia, David R. Weir, Ken K. Ong, Daniela Toniolo, Ruifang Li-Gao, Evelin Mihailov, Edith Hofer, Leslie J. Raffel, Daniel I. Chasman, Alexander Kluttig, Bernard Keavney, Eco J. C. de Geus, Kathleen A. Ryan, Kristin L. Ayers, Lude Franke, S. Fleur W. Meddens, Alison Pattie, Jornt J. Mandemakers, Eva Albrecht, David Cesarini, Beverley Balkau, Grant W. Montgomery, Michael Stumvoll, Ahmad Vaez, Michael B. Miller, Najaf Amin, Gyda Bjornsdottir, Cecile Lecoeur, Enes Makalic, Marc Jan Bonder, Terho Lehtimäki, Albert Hofman, Loic Yengo, Lynda M. Rose, Lisette Stolk, Juergen Wellmann, Gail Davies, Eero Kajantie, Nicole Schupf, Hans Bisgaard, Unnur Thorsteinsdottir, Konstantin Strauch, Ivana Kolcic, Lili Milani, Chunyan He, Claes Ohlsson, Yongmei Liu, Gil Atzmon, Janine F. Felix, Christian Gieger, Mike A. Nalls, Riitta Luoto, Nicola Barban, Philippe Froguel, Daniel F. Schmidt, Dorret I. Boomsma, Harry Campbell, Xia Shen, Vasiliki Lagou, Danny Ben-Avraham, Veronique Vitart, Ioanna P. Kalafati, Kari Stefansson, Daria V. Zhernakova, Constance Turman, Julie E. Buring, Johannes Waage, James F. Wilson, Maria Pina Concas, Zoltán Kutalik, Peter Willeit, Jørn Olsen, Dan Rujescu, Caroline Hayward, Penelope A. Lind, George McMahon, Elizabeth G. Holliday, Ilja M. Nolte, Fahimeh Falahi, Minh Bui, Gudmar Thorleifsson, Patrick F. McArdle, Cinzia Sala, Alana Cavadino, Rossella Sorice, Wei Zhao, Andres Metspalu, Sander W. van der Laan, Stavroula Kanoni, Elina Hyppönen, Morris A. Swertz, Simona Vaccargiu, Felix C. Tropf, Michael Lucht, Susan M. Ring, Elizabeth A. Streeten, Reinhold Schmidt, Augustine Kong, Johann Willeit, Patricia A. Peyser, Jessica D. Faul, Patrik K. E. Magnusson, Tõnu Esko, Antonietta Robino, Lavinia Paternoster, Peter J. van der Most, Kumar B. Rajan, George Davey-Smith, Dragana Vuckovic, Hans J. Grabe, Jari Lahti, Giorgia Girotto, Jorge E. Chavarro, Robert F. Krueger, Hongyan Huang, Georg Homuth, Paolo Gasparini, Sarah E. Medland, Gert G. Wagner, Peter Kraft, André G. Uitterlinden, Cornelius A. Rietveld, Howard Andrews, Cecilia M. Lindgren, Peter Vollenweider, Perry, John [0000-0001-6483-3771], Zhao, Jing Hua [0000-0003-4930-3582], Luben, Robert [0000-0002-5088-6343], Ong, Kenneth [0000-0003-4689-7530], Wareham, Nicholas [0000-0003-1422-2993], Apollo - University of Cambridge Repository, BARBAN N, Rick Jansen, Ronald de Vlaming, Ahmad Vaez, Jornt J Mandemaker, Felix C Tropf, Xia Shen, James F Wilson, Daniel I Chasman, Ilja M Nolte, Vinicius Tragante, Sander W van der Laan, John R B Perry, Augustine Kong, BIOS Consortium, Tarunveer S Ahluwalia, Eva Albrecht, Laura Yerges-Armstrong, Gil Atzmon, Kirsi Auro, Kristin Ayer, Andrew Bakshi, Danny Ben-Avraham, Klaus Berger, Aviv Bergman, Lars Bertram, Lawrence F Bielak, Gyda Bjornsdottir, Marc Jan Bonder, Linda Broer, Minh Bui, Caterina Barbieri, Alana Cavadino, Jorge E Chavarro, Constance Turman, Maria Pina Conca, Heather J Cordell, Gail Davie, Peter Eibich, Nicholas Eriksson, Tõnu Esko, Joel Eriksson, Fahimeh Falahi, Janine F Felix, Mark Alan Fontana, Lude Franke, Ilaria Gandin, Audrey J Gaskin, Christian Gieger, Erica P Gunderson, Xiuqing Guo, Caroline Hayward, Chunyan He, Edith Hofer, Hongyan Huang, Peter K Joshi, Stavroula Kanoni, Robert Karlsson, Stefan Kiechl, Annette Kifley, Alexander Kluttig, Peter Kraft, Vasiliki Lagou, Cecile Lecoeur, Jari Lahti, Ruifang Li-Gao, Penelope A Lind, Tian Liu, Enes Makalic, Crysovalanto Mamasoula, Lindsay Matteson, Hamdi Mbarek, Patrick F McArdle, George McMahon, S Fleur W Medden, Evelin Mihailov, Mike Miller, Stacey A Missmer, Claire Monnereau, Peter J van der Most, Ronny Myhre, Mike A Nall, Teresa Nutile, Ioanna Panagiota Kalafati, Eleonora Porcu, Inga Prokopenko, Kumar B Rajan, Janet Rich-Edward, Cornelius A Rietveld, Antonietta Robino, Lynda M Rose, Rico Rueedi, Kathleen A Ryan, Yasaman Saba, Daniel Schmidt, Jennifer A Smith, Lisette Stolk, Elizabeth Streeten, Anke Tönje, Gudmar Thorleifsson, Sheila Ulivi, Juho Wedenoja, Juergen Wellmann, Peter Willeit, Jie Yao, Loic Yengo, Jing Hua Zhao, Wei Zhao, Daria V Zhernakova, Najaf Amin, Howard Andrew, Beverley Balkau, Nir Barzilai, Sven Bergmann, Ginevra Biino, Hans Bisgaard, Klaus Bønnelykke, Dorret I Boomsma, Julie E Buring, Harry Campbell, Stefania Cappellani, Marina Ciullo, Simon R Cox, Francesco Cucca, Daniela Toniolo, George Davey-Smith, Ian J Deary, George Dedoussi, Panos Delouka, Cornelia M van Duijn, Eco J C de Geu, Johan G Eriksson, Denis A Evan, Jessica D Faul, Cinzia Felicita Sala, Philippe Froguel, Paolo Gasparini, Giorgia Girotto, Hans-Jörgen Grabe, Karin Halina Greiser, Patrick J F Groenen, Hugoline G de Haan, Johannes Haerting, Tamara B Harri, Andrew C Heath, Kauko Heikkilä, Albert Hofman, Georg Homuth, Elizabeth G Holliday, John Hopper, Elina Hyppönen, Bo Jacobsson, Vincent W V Jaddoe, Magnus Johannesson, Astanand Jugessur, Mika Kähönen, Eero Kajantie, Sharon L R Kardia, Bernard Keavney, Ivana Kolcic, Päivikki Koponen, Peter Kovac, Florian Kronenberg, Zoltan Kutalik, Martina La Bianca, Genevieve Lachance, William G Iacono, Sandra Lai, Terho Lehtimäki, David C Liewald, LifeLines Cohort Study, Cecilia M Lindgren, Yongmei Liu, Robert Luben, Michael Lucht, Riitta Luoto, Per Magnu, Patrik K E Magnusson, Nicholas G Martin, Matt McGue, Ruth McQuillan, Sarah E Medland, Christa Meisinger, Dan Mellström, Andres Metspalu, Michela Traglia, Lili Milani, Paul Mitchell, Grant W Montgomery, Dennis Mook-Kanamori, Renée de Mutsert, Ellen A Nohr, Claes Ohlsson, Jørn Olsen, Ken K Ong, Lavinia Paternoster, Alison Pattie, Brenda W J H Penninx, Markus Perola, Patricia A Peyser, Mario Pirastu, Ozren Polasek, Chris Power, Jaakko Kaprio, Leslie J Raffel, Katri Räikkönen, Olli Raitakari, Paul M Ridker, Susan M Ring, Kathryn Roll, Igor Rudan, Daniela Ruggiero, Dan Rujescu, Veikko Salomaa, David Schlessinger, Helena Schmidt, Reinhold Schmidt, Nicole Schupf, Johannes Smit, Rossella Sorice, Tim D Spector, John M Starr, Doris Stöckl, Konstantin Strauch, Michael Stumvoll, Morris A Swertz, Unnur Thorsteinsdottir, A Roy Thurik, Nicholas J Timpson, Joyce Y Tung, André G Uitterlinden, Simona Vaccargiu, Jorma Viikari, Veronique Vitart, Henry Völzke, Peter Vollenweider, Dragana Vuckovic, Johannes Waage, Gert G Wagner, Jie Jin Wang, Nicholas J Wareham, David R Weir, Gonneke Willemsen, Johann Willeit, Alan F Wright, Krina T Zondervan, Kari Stefansson, Robert F Krueger, James J Lee, Daniel J Benjamin, David Cesarini, Philipp D Koellinger, Marcel den Hoed, Harold Snieder & Melinda C Mills, Barban, N, Jansen, R, de Vlaming, R, Vaez, A, Mandemakers, Jj, Tropf, Fc, Shen, X, Wilson, Jf, Chasman, Di, Nolte, Im, Tragante, V, van der Laan, Sw, Perry, Jr, Kong, A, Ahluwalia, T, Albrecht, E, Yerges Armstrong, L, Atzmon, G, Auro, K, Ayers, K, Bakshi, A, Ben Avraham, D, Berger, K, Bergman, A, Bertram, L, Bielak, Lf, Bjornsdottir, G, Bonder, Mj, Broer, L, Bui, M, Barbieri, CATERINA MARIA, Cavadino, A, Chavarro, Je, Turman, C, Concas, MARIA PINA, Cordell, Hj, Davies, G, Eibich, P, Eriksson, N, Esko, T, Eriksson, J, Falahi, F, Felix, Jf, Fontana, Ma, Franke, L, Gandin, Ilaria, Gaskins, Aj, Gieger, C, Gunderson, Ep, Guo, X, Hayward, C, He, C, Hofer, E, Huang, H, Joshi, Pk, Kanoni, S, Karlsson, R, Kiechl, S, Kifley, A, Kluttig, A, Kraft, P, Lagou, V, Lecoeur, C, Lahti, J, Li Gao, R, Lind, Pa, Liu, T, Makalic, E, Mamasoula, C, Matteson, L, Mbarek, H, Mcardle, Pf, Mcmahon, G, Meddens, Sf, Mihailov, E, Miller, M, Missmer, Sa, Monnereau, C, van der Most, Pj, Myhre, R, Nalls, Ma, Nutile, T, Kalafati, Ip, Porcu, E, Prokopenko, I, Rajan, Kb, Rich Edwards, J, Rietveld, Ca, Robino, Antonietta, Rose, Lm, Rueedi, R, Ryan, Ka, Saba, Y, Schmidt, D, Smith, Ja, Stolk, L, Streeten, E, Tönjes, A, Thorleifsson, G, Ulivi, Sheila, Wedenoja, J, Wellmann, J, Willeit, P, Yao, J, Yengo, L, Zhao, Jh, Zhao, W, Zhernakova, Dv, Amin, N, Andrews, H, Balkau, B, Barzilai, N, Bergmann, S, Biino, G, Bisgaard, H, Bønnelykke, K, Boomsma, Di, Buring, Je, Campbell, H, Cappellani, Stefania, Ciullo, M, Cox, Sr, Cucca, F, Toniolo, D, Davey Smith, G, Deary, Ij, Dedoussis, G, Deloukas, P, van Duijn, Cm, de Geus, Ej, Eriksson, Jg, Evans, Da, Faul, Jd, Sala, Cf, Froguel, P, Gasparini, Paolo, Girotto, Giorgia, Grabe, Hj, Greiser, Kh, Groenen, Pj, de Haan, Hg, Haerting, J, Harris, Tb, Heath, Ac, Heikkilä, K, Hofman, A, Homuth, G, Holliday, Eg, Hopper, J, Hyppönen, E, Jacobsson, B, Jaddoe, Vw, Johannesson, M, Jugessur, A, Kähönen, M, Kajantie, E, Kardia, Sl, Keavney, B, Kolcic, I, Koponen, P, Kovacs, P, Kronenberg, F, Kutalik, Z, LA BIANCA, Martina, Lachance, G, Iacono, Wg, Lai, S, Lehtimäki, T, Liewald, Dc, Lindgren, Cm, Liu, Y, Luben, R, Lucht, M, Luoto, R, Magnus, P, Magnusson, Pk, Martin, Ng, Mcgue, M, Mcquillan, R, Medland, Se, Meisinger, C, Mellström, D, Metspalu, A, Traglia, Michela, Milani, L, Mitchell, P, Montgomery, Gw, Mook Kanamori, D, de Mutsert, R, Nohr, Ea, Ohlsson, C, Olsen, J, Ong, Kk, Paternoster, L, Pattie, A, Penninx, Bw, Perola, M, Peyser, Pa, Pirastu, M, Polasek, O, Power, C, Kaprio, J, Raffel, Lj, Räikkönen, K, Raitakari, O, Ridker, Pm, Ring, Sm, Roll, K, Rudan, I, Ruggiero, D, Rujescu, D, Salomaa, V, Schlessinger, D, Schmidt, H, Schmidt, R, Schupf, N, Smit, J, Sorice, R, Spector, Td, Starr, Jm, Stöckl, D, Strauch, K, Stumvoll, M, Swertz, Ma, Thorsteinsdottir, U, Thurik, Ar, Timpson, Nj, Tung, Jy, Uitterlinden, Ag, Vaccargiu, S, Viikari, J, Vitart, V, Völzke, H, Vollenweider, P, Vuckovic, Dragana, Waage, J, Wagner, Gg, Wang, Jj, Wareham, Nj, Weir, Dr, Willemsen, G, Willeit, J, Wright, Af, Zondervan, Kt, Stefansson, K, Krueger, Rf, Lee, Jj, Benjamin, Dj, Cesarini, D, Koellinger, Pd, den Hoed, M, Snieder, H, Mills, Mc, Sociology/ICS, Life Course Epidemiology (LCE), Isotope Research, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Stem Cell Aging Leukemia and Lymphoma (SALL), Barban, Nicola, Jansen, Rick, De Vlaming, Ronald, Vaez, Ahmad, Hyppönen, Elina, Mills, Melinda C, Psychiatry, Amsterdam Neuroscience - Complex Trait Genetics, EMGO - Mental health, Applied Economics, Public Health, Internal Medicine, Erasmus MC other, Epidemiology, Econometrics, Pediatrics, EMGO+ - Lifestyle, Overweight and Diabetes, Complex Trait Genetics, and Biological Psychology

Subjects
0301 basic medicine, Netherlands Twin Register (NTR), PROTEIN, WASS, Genome-wide association study, Reproductive Behavior, MOUSE, Genome-wide association studies, GWAS, reproductive behavior, fertility, 0302 clinical medicine, G1 PHASE, Pregnancy, Genetics & Heredity, Genetics, HUMAN-DISEASES, Reproduction, Human Reproduction, 11 Medical And Health Sciences, ASSOCIATION, Genome-Wide, POLYCYSTIC-OVARY-SYNDROME, Sociologie van Consumptie en Huishoudens, Parity, Phenotype, Behavioural genetics, Medical genetics, Female, BIOS Consortium, FOS: Medical biotechnology, Life Sciences & Biomedicine, Maternal Age, Infertility, medicine.medical_specialty, GENE PRIORITIZATION, Quantitative Trait Loci, Sociology of Consumption and Households, Quantitative trait locus, Biology, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, AGE, QUALITY-CONTROL, medicine, Journal Article, Life Science, SNP, Humans, gene, reproductive, behaviour, Science & Technology, ta1184, 06 Biological Sciences, medicine.disease, Genetic architecture, human reproductive behavior, 030104 developmental biology, Fertility, Human genome, Birth Order, 030217 neurology & neurosurgery, LifeLines Cohort Study, Developmental Biology, genome-wide analysis, Genome-Wide Association Study
Abstract

Barban N, Jansen R, de Vlaming R, Vaez A, Mandemakers JJ, Tropf FC, Shen X, Wilson JF, Chasman DI, Nolte IM, Tragante V, van der Laan SW, Perry JR, Kong A; BIOS Consortium, Ahluwalia TS, Albrecht E, Yerges-Armstrong L, Atzmon G, Auro K, Ayers K, Bakshi A, Ben-Avraham D, Berger K, Bergman A, Bertram L, Bielak LF, Bjornsdottir G, Bonder MJ, Broer L, Bui M, Barbieri C, Cavadino A, Chavarro JE, Turman C, Concas MP, Cordell HJ, Davies G, Eibich P, Eriksson N, Esko T, Eriksson J, Falahi F, Felix JF, Fontana MA, Franke L, Gandin I, Gaskins AJ, Gieger C, Gunderson EP, Guo X, Hayward C, He C, Hofer E, Huang H, Joshi PK, Kanoni S, Karlsson R, Kiechl S, Kifley A, Kluttig A, Kraft P, Lagou V, Lecoeur C, Lahti J, Li-Gao R, Lind PA, Liu T, Makalic E, Mamasoula C, Matteson L, Mbarek H, McArdle PF, McMahon G, Meddens SF, Mihailov E, Miller M, Missmer SA, Monnereau C, van der Most PJ, Myhre R, Nalls MA, Nutile T, Kalafati IP, Porcu E, Prokopenko I, Rajan KB, Rich-Edwards J, Rietveld CA, Robino A, Rose LM, Rueedi R, Ryan KA, Saba Y, Schmidt D, Smith JA, Stolk L, Streeten E, Tönjes A, Thorleifsson G, Ulivi S, Wedenoja J, Wellmann J, Willeit P, Yao J, Yengo L, Zhao JH, Zhao W, Zhernakova DV, Amin N, Andrews H, Balkau B, Barzilai N, Bergmann S, Biino G, Bisgaard H, Bønnelykke K, Boomsma DI, Buring JE, Campbell H, Cappellani S, Ciullo M, Cox SR, Cucca F, Toniolo D, Davey-Smith G, Deary IJ, Dedoussis G, Deloukas P, van Duijn CM, de Geus EJ, Eriksson JG, Evans DA, Faul JD, Sala CF, Froguel P, Gasparini P, Girotto G, Grabe HJ, Greiser KH, Groenen PJ, de Haan HG, Haerting J, Harris TB, Heath AC, Heikkilä K, Hofman A, Homuth G, Holliday EG, Hopper J, Hyppönen E, Jacobsson B, Jaddoe VW, Johannesson M, Jugessur A, Kähönen M, Kajantie E, Kardia SL, Keavney B, Kolcic I, Koponen P, Kovacs P, Kronenberg F, Kutalik Z, La Bianca M, Lachance G, Iacono WG, Lai S, Lehtimäki T, Liewald DC; LifeLines Cohort Study, Lindgren CM, Liu Y, Luben R, Lucht M, Luoto R, Magnus P, Magnusson PK, Martin NG, McGue M, McQuillan R, Medland SE, Meisinger C, Mellström D, Metspalu A, Traglia M, Milani L, Mitchell P, Montgomery GW, Mook-Kanamori D, de Mutsert R, Nohr EA, Ohlsson C, Olsen J, Ong KK, Paternoster L, Pattie A, Penninx BW, Perola M, Peyser PA, Pirastu M, Polasek O, Power C, Kaprio J, Raffel LJ, Räikkönen K, Raitakari O, Ridker PM, Ring SM, Roll K, Rudan I, Ruggiero D, Rujescu D, Salomaa V, Schlessinger D, Schmidt H, Schmidt R, Schupf N, Smit J, Sorice R, Spector TD, Starr JM, Stöckl D, Strauch K, Stumvoll M, Swertz MA, Thorsteinsdottir U, Thurik AR, Timpson NJ, Tung JY, Uitterlinden AG, Vaccargiu S, Viikari J, Vitart V, Völzke H, Vollenweider P, Vuckovic D, Waage J, Wagner GG, Wang JJ, Wareham NJ, Weir DR, Willemsen G, Willeit J, Wright AF, Zondervan KT, Stefansson K, Krueger RF, Lee JJ, Benjamin DJ, Cesarini D, Koellinger PD, den Hoed M, Snieder H, Mills MC.

Published
2016

111. A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance

Author

John R. B. Perry, James B. Meigs, José Dupuis, Luigi Ferrucci, Johan G. Eriksson, Vilmundur Gudnason, Eric J.G. Sijbrands, Jeanette S. Andrews, Jonna L. Grimsby, Lawrence F. Bielak, Peter Kovacs, Panos Deloukas, Marijana Peričić, Johannes H. Smit, Ruth J. F. Loos, Gonneke Willemsen, Eric Boerwinkle, Ben A. Oostra, Manuel Serrano-Ríos, Alena Stančáková, Meena Kumari, Antti Jula, Michael Marmot, Caroline S. Fox, Simon Heath, Guo Li, Ola Hansson, Gerard Waeber, Anne U. Jackson, Nicholas L. Smith, Markku Laakso, George Dedoussis, Aarno Palotie, Sara M. Willems, John F. Peden, Elisabeth Widen, Caroline Hayward, Alan F. Wright, Claes Ladenvall, May E. Montasser, María Teresa Martínez-Larrad, Peter Vollenweider, Louis Pérusse, Tamara B. Harris, Wen Hong L. Kao, Danijela Budimir, Denis Rybin, David B. Savage, Michael A. Province, Alisa K. Manning, Bruna Gigante, Najaf Amin, Lenore J. Launer, Naveed Sattar, Lori L. Bonnycastle, Göran Hallmans, Jeffrey R. O'Connell, Stéphane Lobbens, Jacques S. Beckmann, Gemma Cadby, J. Wouter Jukema, Maria Dimitriou, Michael Stumvoll, Max Vikström, Rona J. Strawbridge, Hugh Watkins, Lyle J. Palmer, Johanna Kuusisto, Aimo Ruokonen, Hanieh Yaghootkar, Yan V. Sun, Inês Barroso, Amy J. Swift, Nancy L. Pedersen, Lars Lind, Mladen Boban, Nita G. Forouhi, Ken K. Ong, Ivana Kolcic, Anke Tönjes, Timothy M. Frayling, Paul W. Franks, Narisu Narisu, Karin Leander, Serge Hercberg, Diana Zelenika, Sharon L.R. Kardia, Min A. Jhun, Marjo-Riitta Järvelin, Stella Trompet, Jaakko Kaprio, Toshiko Tanaka, David S. Siscovick, Toby Johnson, Cornelia M. van Duijn, Veikko Salomaa, Jose C. Florez, James F. Wilson, Leena Peltonen, Pilar Galan, Robert Clarke, Andrew A. Hicks, Claudia Langenberg, Anders Hamsten, David Couper, Albert Hofman, Dawn M. Waterworth, John Blangero, James S. Pankow, Nabila Bouatia-Naji, Sirkka Keinänen-Kiukaanniemi, Mark I. McCarthy, Valeriya Lyssenko, Leif Groop, Brenda W.J.H. Penninx, Ching-Ti Liu, Anuj Goel, Marina Pehlić, Michael Boehnke, Mika Kivimäki, Maria Sabater-Lleal, Emil Rehnberg, Ingrid B. Borecki, Ozren Polasek, Eco J. C. de Geus, Peter P. Pramstaller, Igor Rudan, Richard M. Watanabe, Pierre Meneton, Iva Miljkovic, Vincent Mooser, G. Mark Lathrop, John Beilby, Laura J. Rasmussen-Torvik, Arturo Corbató-Anchuelo, Yvonne Böttcher, Richard N. Bergman, Daniel R. Barnes, Paul C. D. Johnson, Mustafa Atalay, Aroon D. Hingorani, Olga D. Carlson, Perttu Salo, Jacqueline C.M. Witteman, Udo Seedorf, Timo Saaristo, Jian'an Luan, Nicholas J. Wareham, Gudny Eiriksdottir, Matti Uusitupa, Yongmei Liu, Jaakko Tuomilehto, Yurii S. Aulchenko, Peter Schwarz, Robert A. Scott, Lina Zgaga, Joseph Hung, Reedik Mägi, Maria Grazia Franzosi, Eric J. Brunner, Claude Bouchard, Ian Ford, Francis S. Collins, Ulf de Faire, Benjamin F. Voight, Erik Ingelsson, Mario A. Morken, Stefania Bandinelli, Nicole L. Glazer, Dmitry Shungin, Lars Lannfelt, André G. Uitterlinden, Tatijana Zemunik, Markus Perola, Kenneth Rice, Veronique Vitart, Kerrin S. Small, Jouke-Jan Hottenga, Han Chen, Jerome I. Rotter, Philippe Froguel, Karen L. Mohlke, Marie-Claude Vohl, Dorret I. Boomsma, Harry Campbell, Peter S. Chines, Pau Navarro, Vasiliki Lagou, Albert V. Smith, Kathleen Stirrups, Josephine M. Egan, Alan R. Shuldiner, Katri Räikkönen, Inga Prokopenko, Ping An, Rainer Rauramaa, Beverley Balkau, Thor Aspelund, Eleanor Wheeler, Mariza de Andrade, Richa Saxena, Jari Lahti, Cécile Lecoeur, Timo A. Lakka, Jennie Hui, Michael R. Erdos, Stavroula Kanoni, Kirsten Ohm Kyvik, Bengt Sennblad, Sarah H. Wild, Patricia A. Peyser, Patrik K. E. Magnusson, Claire Bellis, Elodie Eury, Jaana Lindström, Boston University [Boston] (BU), Broad Institute of Harvard and MIT, Partenaires INRAE, Massachusetts General Hospital, Massachusetts General Hospital [Boston], Department of Genetics [Boston], Harvard Medical School [Boston] (HMS), Department of Medicine, Université de Sherbrooke (UdeS), Addenbrooke's Hospital, Harvard Medical School [Boston] (HMS)-Beth Israel Deaconess Medical Center [Boston] (BIDMC), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP), Université Lille Nord de France (COMUE), Department of Epidemiology, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System-Center for Social Epidemiology and Population Health, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford [Oxford], The Wellcome Trust Centre for Human Genetics [Oxford], The Netherlands Cancer Institute, Ontario Institute for Cancer Research, Mount Sinai Hospital [Toronto, Canada] (MSH), VU University Amsterdam, Department of Medical Epidemiology and Biostatistics (MEB), Karolinska Institutet [Stockholm], University of Michigan System, Queen Mary University of London (QMUL), The Wellcome Trust Sanger Institute [Cambridge], Lund University [Lund], Diabetes Centre, Lund University, University of Helsinki, Wake Forest School of Medicine, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, University of Maryland School of Medicine, University of Maryland System, University of Edinburgh, University of Exeter, Department of Twin Research and Genetic Epidemiology, King's College London, London, Northwestern University [Evanston], National Institute of Health and Welfare, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Lund University Diabetes Centre, Umeå University, National Institutes of Health, Centre for Medical Systems Biology, Netherlands Genomics Initiative, Washington University in Saint Louis (WUSTL), Department of Health Sciences Research, Mayo Clinic, Wake Forest University, Icelandic Heart Association, Heart Preventive Clinic and Research Institute, University of Iceland, Institute of Biomedicine, Physiology, University of Eastern Finland, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR S 1018, Université Paris-Sud - Paris 11 (UP11), Azienda Sanitaria Firenze, Department of Medical Genetics, Université de Lausanne (UNIL), Centre Hospitalier Universitaire Vaudois (CHUV), Queen Elizabeth II Medical Centre, Research Institute, University of Southern California (USC), University of Split, The University of Texas Health Science Center at Houston (UTHealth), Leipzig University, Pennington Biomedical Research Center, Department of Epidemiology & Public Health, University College of London [London] (UCL), San Carlos Clinical Hospital, University of North Carolina, Harokopio University, National Institute on Aging, Folkhälsan Research Centre, Vaasa Central Hospital, Unité de Recherche en Epidémiologie Nutritionnelle (UREN), Université Paris 13 (UP13)-Institut National de la Recherche Agronomique (INRA)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Psychiatry, EMGO - Lifestyle, overweight and diabetes, Epidemiology, Immunology, Erasmus School of Social and Behavioural Sciences, Clinical Genetics, Ophthalmology, Internal Medicine, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium, Multiple Tissue Human Expression Resource (MUTHER) Consortium, Ahmadi, K.R., Ainali, C., Barrett, A., Bataille, V., Bell, J.T., Buil, A., Deloukas, P., Dermitzakis, E.T., Dimas, A.S., Durbin, R., Glass, D., Grundberg, E., Hassanali, N., Hedman, Å.K., Ingle, C., Knowles, D., Krestyaninova, M., Lindgren, C.M., Lowe, C.E., McCarthy, M.I., Meduri, E., di Meglio, P., Min, J.L., Montgomery, S.B., Nestle, F.O., Nica, A.C., Nisbet, J., O'Rahilly, S., Parts, L., Potter, S., Sekowska, M., Shin, S.Y., Small, K.S., Soranzo, N., Spector, T.D., Surdulescu, G., Travers, M.E., Tsaprouni, L., Tsoka, S., Wilk, A., Yang, T.P., Zondervan, K.T., Voight, B.F., Scott, L.J., Steinthorsdottir, V., Morris, A.P., Dina, C., Welch, R.P., Zeggini, E., Huth, C., Aulchenko, Y.S., Thorleifsson, G., McCulloch, L.J., Ferreira, T., Grallert, H., Amin, N., Wu, G., Willer, C.J., Raychaudhuri, S., McCarroll, S.A., Langenberg, C., Hofmann, O.M., Dupuis, J., Qi, L., Segrè, A.V., van Hoek, M., Navarro, P., Ardlie, K., Balkau, B., Benediktsson, R., Bennett, A.J., Blagieva, R., Boerwinkle, E., Bonnycastle, L.L., Boström, K.B., Bravenboer, B., Bumpstead, S., Burtt, N.P., Charpentier, G., Chines, P.S., Cornelis, M., Couper, D.J., Crawford, G., Doney, A.S., Elliott, K.S., Elliott, A.L., Erdos, M.R., Fox, C.S., Franklin, C.S., Ganser, M., Gieger, C., Grarup, N., Green, T., Griffin, S., Groves, C.J., Guiducci, C., Hadjadj, S., Herder, C., Isomaa, B., Jackson, A.U., Johnson, P.R., Jørgensen, T., Kao, W.H., Klopp, N., Kong, A., Kraft, P., Kuusisto, J., Lauritzen, T., Li, M., Lieverse, A., Lyssenko, V., Marre, M., Meitinger, T., Midthjell, K., Morken, M.A., Narisu, N., Nilsson, P., Owen, K.R., Payne, F., Perry, J.R., Petersen, A.K., Platou, C., Proença, C., Prokopenko, I., Rathmann, W., Rayner, N.W., Robertson, N.R., Rocheleau, G., Roden, M., Sampson, M.J., Saxena, R., Shields, B.M., Shrader, P., Sigurdsson, G., Sparsø, T., Strassburger, K., Stringham, H.M., Sun, Q., Swift, A.J., Thorand, B., Tichet, J., Tuomi, T., van Dam, R.M., van Haeften, T.W., van Herpt, T., van Vliet-Ostaptchouk, J.V., Walters, G.B., Weedon, M.N., Wijmenga, C., Witteman, J., Bergman, R.N., Cauchi, S., Collins, F.S., Gloyn, A.L., Gyllensten, U., Hansen, T., Hide, W.A., Hitman, G.A., Hofman, A., Hunter, D.J., Hveem, K., Laakso, M., Mohlke, K.L., Morris, A.D., Palmer, C.N., Pramstaller, P.P., Rudan, I., Sijbrands, E., Stein, L.D., Tuomilehto, J., Uitterlinden, A., Walker, M., Wareham, N.J., Watanabe, R.M., Abecasis, G.R., Boehm, B.O., Campbell, H., Daly, M.J., Hattersley, A.T., Hu, F.B., Meigs, J.B., Pankow, J.S., Pedersen, O., Wichmann, H.E., Barroso, I., Florez, J.C., Frayling, T.M., Groop, L., Sladek, R., Thorsteinsdottir, U., Wilson, J.F., Illig, T., Froguel, P., van Duijn, C.M., Stefansson, K., Altshuler, D., Boehnke, M., Biological Psychology, EMGO+ - Lifestyle, Overweight and Diabetes, Vrije universiteit = Free university of Amsterdam [Amsterdam] (VU), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Sorbonne Paris Cité (USPC)-Université Paris 13 (UP13)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut National de la Recherche Agronomique (INRA)

Subjects
Blood Glucose, Netherlands Twin Register (NTR), medicine.medical_treatment, [SDV]Life Sciences [q-bio], LOCI, Genome-wide association study, Type 2 diabetes, SUSCEPTIBILITY, Body Mass Index, GLUCOSE, Blood Glucose/metabolism, Cholesterol, HDL/metabolism, Diabetes Mellitus, Type 2/genetics, Genome-Wide Association Study, Humans, Insulin/metabolism, Insulin Resistance/genetics, Polymorphism, Single Nucleotide, 0302 clinical medicine, Insulin, 2. Zero hunger, Genetics, 0303 health sciences, COMMON VARIANTS, 3. Good health, ENVIRONMENT INTERACTION, OBESITY, CORONARY-ARTERY-DISEASE, medicine.medical_specialty, 030209 endocrinology & metabolism, Accounting, Biology, Article, 03 medical and health sciences, Insulin resistance, SDG 3 - Good Health and Well-being, Internal medicine, Diabetes mellitus, medicine, 030304 developmental biology, Genetic association, Glycemic, loci, SNP, insulin, business.industry, Cholesterol, HDL, medicine.disease, Obesity, POLYMORPHISM, ASSOCIATION ANALYSIS, Endocrinology, Diabetes Mellitus, Type 2, TYPE-2 DIABETES RISK, Insulin Resistance, business
Abstract

Group Authors : DIAGRAM Consortium MUTHER Consortium variants influencing fasting glycemic traits and insulin resistance Seuls les 100 premiers auteurs ont été conservés dans la publication. La liste complète des auteurs et des des affiliations est disponible sur la publication https://www.nature.com/articles/ng.2274.pdf p. 667-669.; International audience; Recent genome-wide association studies have described many loci implicated in type 2 diabetes (T2D) pathophysiology and beta-cell dysfunction but have contributed little to the understanding of the genetic basis of insulin resistance. We hypothesized that genes implicated in insulin resistance pathways might be uncovered by accounting for differences in body mass index (BMI) and potential interactions between BMI and genetic variants. We applied a joint meta-analysis approach to test associations with fasting insulin and glucose on a genome-wide scale. We present six previously unknown loci associated with fasting insulin at P < 5 x 10(-8) in combined discovery and follow-up analyses of 52 studies comprising up to 96,496 non-diabetic individuals. Risk variants were associated with higher triglyceride and lower high-density lipoprotein (HDL) cholesterol levels, suggesting a role for these loci in insulin resistance pathways. The discovery of these loci will aid further characterization of the role of insulin resistance in T2D pathophysiology.

Published
2012

112. Ant colony optimisation to identify genetic variant association with type 2 diabetes

Author

Edward Keedwell, Jacqueline Christmas, John R. B. Perry, and Timothy M. Frayling

Subjects
Information Systems and Management, Single-nucleotide polymorphism, Genome-wide association study, Computational biology, Biology, Heritability, Bioinformatics, Computer Science Applications, Theoretical Computer Science, Minor allele frequency, Chromosome 16, Chromosome (genetic algorithm), Artificial Intelligence, Control and Systems Engineering, Epistasis, SNP, Software
Abstract

Around 1.8 million people in the UK have type 2 diabetes, representing about 90% of all diabetes cases in the UK. Genome wide association studies have recently implicated several new genes that are likely to be associated with this disease. However, common genetic variants so far identified only explain a small proportion of the heritability of type 2 diabetes. The interaction of two or more gene variants, may explain a further element of this heritability but full interaction analyses are currently highly computationally burdensome or infeasible. For this reason this study investigates an ant colony optimisation (ACO) approach for its ability to identify common gene variants associated with type 2 diabetes, including putative epistatic interactions. This study uses a dataset comprising 15,309 common (>5% minor allele frequency) SNPs from chromosome 16, genotyped in 1924 type 2 diabetes cases and 2938 controls. This chromosome contains two previously determined associations, one of which is replicated in additional samples. Although no epistatic interactions have been previously reported on this dataset, we demonstrate that ACO can be used to discover single SNP and plausible epistatic associations from this dataset and is shown to be both accurate and computationally tractable on large, real datasets of SNPs with no expert knowledge included in the algorithm.

Published
2011

113. Abstract 230: Joint genome-wide association study of endometrial cancer and ovarian cancer identifies a novel genetic risk region at 14q23.3

Author

Paul L. Auer, Douglas F. Easton, Ellen L. Goode, Emma Tham, Daniel D. Buchanan, Peter A. Fasching, Dylan M. Glubb, Diether Lambrechts, Thilo Dörk, Graham G. Giles, Per Hall, Immaculata De Vivo, Bcac, Roger L. Milne, Ocac, John R. B. Perry, Ecac, Tracy A. O'Mara, Rodney J. Scott, Jone Trovik, Amanda B. Spurdle, Ian Tomlinson, and Deborah J. Thompson

Subjects
Oncology, Cancer Research, medicine.medical_specialty, business.industry, Endometrial cancer, Internal medicine, medicine, Genome-wide association study, Genetic risk, Ovarian cancer, medicine.disease, business
Abstract

Ovarian cancer is the most lethal gynecologic malignancy and the sixth most common cause of death from all cancer in women, with an estimated 140,000 deaths per year worldwide. Endometrial cancer (cancer of the uterine lining) is the most commonly diagnosed gynecologic cancer, ranking sixth in incident cancer in women. Ovarian and endometrial cancer share many epidemiologic, histopathologic, and tumor genetic characteristics. Meta-analyses of genome-wide association study (GWAS) datasets across etiologically related diseases have successfully been used to increase statistical power and identify novel genetic risk regions. We hypothesised that joint meta-analysis of ovarian and endometrial cancer GWAS datasets would identify novel genetic loci for both cancers. Following quality control, summary statistics for >11 million genetic variants were available from the largest genome-wide association studies performed by the Ovarian Cancer Association Consortium (OCAC, Phelan et al., Nature Genetics 2017) and the Endometrial Cancer Association Consortium (ECAC, unpublished). A total of 35,312 cancer cases from all histologic subtypes (22,406 ovarian and 12,906 endometrial cancer cases) and 149,920 controls were included in the analysis. Summary statistics were combined using an inverse-variance, fixed-effects model in METAL and identified ten loci at genome-wide significance (P < 5 x 10-8), of which one locus at 14q23.3 (rs4072776 combined OR 0.94; 95% CI 0.92-0.96; P = 8.0 x 10-9) had not been previously associated with the risk of either cancer. Integration with chromatin conformation data (RNAPolII HiChIP) from the Ishikawa endometrial cancer cell line suggests interaction between the risk signal and the promoter of FUT8. FUT8 encodes a fucosyltransferase and its expression has been implicated in breast, stomach, and melanoma and lung cancer. Interestingly, FUT8 is a downstream target regulated by the loss of PAX2 and mutated p53, which is the earliest known molecular aberration in the progression of the fallopian tissue epithelial to serous ovarian cancer. Further functional evaluation of the 14q23.3 risk region is required to determine the regulatory effect of genetic risk variants on FUT8. Future meta-analyses of datasets, stratifying results by histologic subtypes, will be undertaken. Citation Format: Tracy A. O'Mara, Dylan M. Glubb, Daniel D. Buchanan, Diether Lambrechts, Per Hall, Emma Tham, Jone Trovik, Ellen L. Goode, Peter Fasching, Thilo Dörk, Rodney J. Scott, Paul L. Auer, Roger L. Milne, Graham G. Giles, John Perry, Immaculata de Vivo, Ian Tomlinson, Douglas F. Easton, Deborah J. Thompson, Amanda B. Spurdle, E2C2, BCAC, OCAC, ECAC. Joint genome-wide association study of endometrial cancer and ovarian cancer identifies a novel genetic risk region at 14q23.3 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 230.

Published
2018

114. New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk

Author

Kenneth Rice, Amy J. Swift, Veronique Vitart, Lu Qi, Kaisa Silander, Olivier Le Bacquer, Laura Crisponi, David S. Siscovick, Bo Isomaa, Anne U. Jackson, Anke Tönjes, Richard N. Bergman, Rosa Maria Roccasecca, Luigi Ferrucci, Narisu Narisu, Kari Stefansson, Holly E. Syddall, Giuseppe Paolisso, Kim L. Ward, Paul Elliott, Scott M. Grundy, Paul Johnson, Jerome I. Rotter, Philippe Froguel, James B. Meigs, George Davey Smith, Andrew T. Hattersley, Leena Peltonen, Eric J.G. Sijbrands, Serena Sanna, María TeresaMartínez-Larrad, David Altshuler, Harald Grallert, Caroline S. Fox, Nita G. Forouhi, Dorret I. Boomsma, Harry Campbell, Jean Tichet, Angelo Scuteri, Aroon D. Hingorani, Daniel S. Pearson, Meena Kumari, Silvia Naitza, Shah Ebrahim, Manjinder S. Sandhu, Jose C. Florez, Cyrus Cooper, David M. Nathan, Joseph Hung, Fredrik Karpe, Ozren Polasek, Philip J. Barter, Ruth McPherson, Benjamin F. Voight, Wolfgang Rathmann, Abbas Dehghan, Udo Seedorf, Beverley M. Shields, Antti Jula, Pau Navarro, Josephine M. Egan, Rune R. Frants, Leif Groop, Gunnar Sigursson, Seppo Koskinen, Vincent Mooser, François Pattou, Jing Hua Zhao, Irene Pichler, John F. Peden, Göran Hallmans, Toshiko Tanaka, Ruth J. F. Loos, Peter Kovacs, Andrew D. Morris, Cécile Lecoeur, Jeffrey R. O'Connell, Massimo Mangino, Nicole Vogelzangs, Rhian Gwilliam, Gordon H. Williams, Carina Zabena, Naomi Hammond, Amélie Bonnefond, Björn Zethelius, Joachim Spranger, Nancy L. Pedersen, Christopher J. Groves, Nicholas J. Timpson, George Dedoussis, Veikko Salomaa, Peter Henneman, Andrew Walley, Serge Hercberg, Ian N. M. Day, Simon Heath, Matt Neville, Alex S. F. Doney, Robert Clarke, Olov Rolandsson, Panos Deloukas, Eric Boerwinkle, Y. AnteroKesaniemi, Mike Sampson, Gerard Waeber, Sven Bergmann, Ben A. Oostra, Manuel Serrano-Ríos, Mandy van Hoek, Christine Cavalcanti-Proença, Anna L. Gloyn, Ulla Sovio, Andrew P. Morris, Anneli Pouta, Amanda J. Bennett, Paul Scheet, Peter Schwarz, Jaakko Tuomilehto, Hugh Watkins, Johanna Kuusisto, Denis Rybin, Anna LiisaHartikainen, Maria GraziaFranzosi, Unnur Thorsteinsdottir, Rafn Benediktsson, Alan F. Wright, Colin N. Apalmer, Anuj Goel, Yavuz Ariyurek, Lars Lind, Robert Sladek, Stefan R. Bornstein, Reedik Mägi, Laila Simpson, Tim D. Spector, Paul W. Franks, Nicholas L. Smith, John R. B. Perry, Peter Vollenweider, Suzannah Bumpstead, Ruth E. Pakyz, Christa Meisinger, Alan R. Shuldiner, Josée Dupuis, Man Li, Eric J. Brunner, Francis S. Collins, Torben Hansen, James F. Wilson, Guangju Zhai, Igor Rudan, Nicole L. Glazer, Marco Orrù, Pierre Meneton, Knut Borch-Johnsen, Eleanor Wheeler, Gonçalo R. Abecasis, Mark I. McCarthy, Jouke JanHottenga, Inga Prokopenko, Ping An, Jérôme Delplanque, Albert Hofman, Andrew B. Singleton, Gabe Crawford, Thomas A. Buchanan, Avan Aihie Sayer, Richard M. Watanabe, David Schlessinger, A C Fedson, André G. Uitterlinden, Frank B. Hu, Jaqueline C. MWitteman, Dhiraj Varma, Ingrid B. Borecki, Sutapa Mukherjee, Murielle Bochud, Barbara Thorand, Christian Gieger, Lori L. Bonnycastle, Stephen J. Sharp, Markus Perola, Caroline Hayward, Kristin Ardlie, J. Graessler, Robert W. Mahley, Toby Johnson, Jian'an Luan, Joshua C. Randall, Cornelia M. van Duijn, Samuli Ripatti, Ko Willems van Dijk, Valgerdur Steinthorsdottir, Yurii S. Aulchenko, G. Mark Lathrop, Christian Dina, Eleftheria Zeggini, Cecilia M. Lindgren, Stavroula Kanoni, Timothy M. Frayling, Dawn M. Waterworth, Marika Kaakinen, Timo T. Valle, Diana Zelenika, Yii Der IdaChen, Angela Silveira, Nigel W. Rayner, Aimo Ruokonen, Yun Li, Cristian Pattaro, Annelli Sandbæk, Richa Saxena, Danielle Posthuma, Steven A. McCarroll, Niels Grarup, Samy Hadjadj, Pilar Galan, Xijing Han, Lyle J. Palmer, Ulf Gyllensten, Peter P. Pramstaller, Manuela Uda, Jarred B. McAteer, Brenda W.J.H. Penninx, Debbie A Lawlor, Torben Jørgensen, Beatrice Knight, Yvonne Böttcher, Claudia Langenberg, Nicole Soranzo, Ghislain Rocheleau, Erik Ingelsson, Mario A. Morken, Michael Roden, Felicity Payne, David R. Hillman, Michael Marmot, Karen L. Mohlke, Heather M. Stringham, Bruce M. Psaty, Gudmar Thorleifsson, Yoav Ben-Shlomo, Inês Barroso, W. H. Linda Kao, James S. Pankow, Valeriya Lyssenko, Nicholas J. Wareham, Tiinamaija Tuomi, Ann ChristineSyvänen, Braxton D. Mitchell, Alisa K. Manning, Mika Kivimäki, Peter Wagner, Praveen Sethupathy, G. BragiWalters, Jaakko Kaprio, Kijoung Song, Marjo Riitta-Järvelin, Michael A. Province, Andrew A. Hicks, Marilyn C. Cornelis, Sarah H. Wild, David Meyre, Guillaume Charpentier, Patrik K. E. Magnusson, David Melzer, Jennie Hui, Peter Shrader, Michael Stumvoll, Mark O. Goodarzi, Michael R. Erdos, Oluf Pedersen, Andreas Pfeiffer, Augustine Kong, Christian Herder, Laura J. Scott, John W. GYarnell, Kirsten Ohm Kyvik, Beverley Balkau, Antje Fischer-Rosinsky, Gonneke Willemsen, Thomas Illig, Neelam Hassanali, Markku Laakso, Michael Boehnke, John Beilby, Christopher S. Franklin, Fernando Rivadeneira, M. Carola Zillikens, Michael N. Weedon, Antonio Cao, Mark E. Cooper, Simon C. Potter, Eco J. C. de Geus, H.-Erich Wichmann, Amanda F. Elliott, Lachlan J. McOin, Sophie Visvikis-Siest, Thomas Sparsø, Laura J. McCulloch, Taina K. Lajunen, Peter S. Chines, Nabila Bouatia-Naji, Medical Research Council (MRC), Biological Psychology, Functional Genomics, Neuroscience Campus Amsterdam - Anxiety & Depression, Neuroscience Campus Amsterdam - Attention & Cognition, EMGO+ - Mental Health, Ophthalmology, Epidemiology, Clinical Genetics, Dermatology, Internal Medicine, DIAGRAM Consortium, GIANT Consortium, Global BPgen Consortium, Anders Hamsten on behalf of Procardis Consortium, MAGIC investigators, Human genetics, Psychiatry, EMGO - Mental health, NCA - Attention & Cognition, and NCA - Anxiety & Depression

Subjects
Blood Glucose, Netherlands Twin Register (NTR), Candidate gene, Genome-wide association study, Type 2 diabetes, CIRCADIAN CLOCK, TRIGLYCERIDE LEVELS, 0302 clinical medicine, Delta-5 Fatty Acid Desaturase, Databases, Genetic, Homeostasis, GENETICS & HEREDITY, Anders Hamsten on behalf of Procardis Consortium, Child, Genetics, PLASMA-GLUCOSE, 0303 health sciences, Glucokinase regulatory protein, COMMON VARIANTS, 11 Medical And Health Sciences, Fasting, MAGIC investigators, 3. Good health, MODEL ASSESSMENT, Life Sciences & Biomedicine, Adult, medicine.medical_specialty, ESSENTIAL COMPONENTS, Adolescent, DNA Copy Number Variations, Alleles, Blood Glucose/genetics, Blood Glucose/metabolism, DNA Copy Number Variations/genetics, Diabetes Mellitus, Type 2/genetics, Fasting/blood, Gene Expression Regulation, Genetic Loci/genetics, Genetic Predisposition to Disease, Genome-Wide Association Study, Homeostasis/genetics, Humans, Meta-Analysis as Topic, Polymorphism, Single Nucleotide/genetics, Quantitative Trait Loci/genetics, Quantitative Trait, Heritable, Reproducibility of Results, Quantitative Trait Loci, 030209 endocrinology & metabolism, Biology, DIAGRAM Consortium, INSULIN-SECRETION, Polymorphism, Single Nucleotide, Article, Fasting glucose, 03 medical and health sciences, Insulin resistance, SDG 3 - Good Health and Well-being, Diabetes mellitus, Internal medicine, genome wide association study, glucose, diabetes type 2, medicine, GIANT Consortium, Allele, GENOME-WIDE ASSOCIATION, Global BPgen Consortium, 030304 developmental biology, Glycemic, Science & Technology, genome-wide association beta-cell dysfunction plasma-glucose insulin-secretion triglyceride levels essential components model assessment common variants circadian clock disease risk, DISEASE RISK, 06 Biological Sciences, medicine.disease, Endocrinology, Diabetes Mellitus, Type 2, Genetic Loci, biology.protein, BETA-CELL DYSFUNCTION, Developmental Biology
Abstract

Levels of circulating glucose are tightly regulated. To identify new loci influencing glycemic traits, we performed meta-analyses of 21 genome-wide association studies informative for fasting glucose, fasting insulin and indices of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR) in up to 46, 186 nondiabetic participants. Follow-up of 25 loci in up to 76, 558 additional subjects identified 16 loci associated with fasting glucose and HOMA-B and two loci associated with fasting insulin and HOMA-IR. These include nine loci newly associated with fasting glucose (in or near ADCY5, MADD, ADRA2A, CRY2, FADS1, GLIS3, SLC2A2, PROX1 and C2CD4B) and one influencing fasting insulin and HOMA-IR (near IGF1). We also demonstrated association of ADCY5, PROX1, GCK, GCKR and DGKB-TMEM195 with type 2 diabetes. Within these loci, likely biological candidate genes influence signal transduction, cell proliferation, development, glucose-sensing and circadian regulation. Our results demonstrate that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes.

Published
2010
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115. Genome-wide association study identifies eight loci associated with blood pressure

Author

Peter Holmans, Udo Seedorf, Beverley M. Shields, Peter McGruffin, Arne Pfeufer, Steve Eyre, Nathalie J. Prescott, Michael Boehnke, Valentina Moskovina, Abiodun Onipinla, Leena Peltonen, Nadira Yuldasheva, Peter M. Nilsson, Valeria Romanazzi, Vincent Mooser, Göran Berglund, Alistair S. Hall, Dominic P. Kwiatkowski, Barry Widmer, Benjamin F. Voight, Stefania Bandinelli, Mark M. Iles, Sven Bergmann, Thomas Meitinger, James P. Boorman, Simonetta Guarrera, Nazneen Rahman, Murielle Bochud, Graham A. Hitman, Emma Keniry, Nelson B. Freimer, Richard Dobson, Francis S. Collins, Gerjan Navis, Jennifer L. Pointon, Richard N. Bergman, Ruth J. F. Loos, Roberto Lorbeer, Carolina A. Braga Marcano, Christian Gieger, Florian Ernst, Xin Yuan, Catherine Potter, Hazel E. Drummond, Allan H. Young, George Kirov, John F. Peden, Helen Stevens, David Clayton, Mattijs E. Numans, Katherine Gordon-Smith, Anne Farmer, Alastair Forbes, M. Khalid Mohiuddin, John A. Todd, Christopher G. Mathew, David A. Collier, Mark I. McCarthy, Francesca Bredin, Clive M. Onnie, Dan Davidson, Markus Perola, Pamela Whittaker, Yvonne T. van der Schouw, Rathi Ravindrarajan, I. C.A. Spencer, Teresa Ferreira, Nilesh J. Samani, Serge Hercberg, Gonçalo R. Abecasis, Christopher J. Groves, Nicholas John Craddock, Angela Döring, Edward G. Lakatta, Muminatou Jallow, Wendy L. McArdle, David Bentley, Susana Eyheramendy, Uwe Völker, Christopher Newton-Cheh, Jaspal S. Kooner, Hugh Watkins, Gavin Lucas, H. T. Leung, Marjo Ritta Jarvelin, Johanna Kuusisto, Wiek H. van Gilst, Wendy Thomson, Lou R. Cardon, Harold Snieder, Marju Orho-Melander, Patricia B. Munroe, Toshiko Tanaka, Jeffrey C. Barrett, Azhar Maqbool, Henry Völzke, John M. C. Connell, Elaine R. Nimmo, John R. B. Perry, Michael R. Stratton, Ralph McGinnis, Pekka Jousilahti, Michiel L. Bots, Ian Jones, Elizabeth Meech, Matthew A. Brown, Johannie Gungadoo, Jian'an Luan, Jilur Ghori, Richard J. Dixon, N. Charlotte Onland-Moret, Fulvio Ricceri, Anthony J. Balmforth, Catherine E. Todhunter, Inês Barroso, Sheila Bingham, Timo T. Valle, Fredrik O. Vannberg, Diana Zelenika, Stephen Sawcer, Anneli Pouta, David M. Evans, Cuno S. P. M. Uiterwaal, Pilar Galan, Georg Homuth, Hannah Donovan, David J. Conway, Paul Elliott, Alessandra Allione, Paul E. de Jong, Miles Parkes, Amy Chaney, John C. Chambers, Toby Johnson, Isaac Subirana, Vesela Gateva, Cathryn M. Lewis, Christopher J. O'Donnell, Hana Lango, David Schlessinger, Mark J. Caulfield, Thorsten Reffelmann, Jamie Barbour, Karen L. Mohlke, Sarah E. Hunt, Thilo Winzer, Frances M K Williams, Christopher Mathew, I. Wallace, Anuj Goel, Jaakko Tuomilehto, Louise V. Wain, Gabriel Crawford, Samantha L. Hider, Detelinea Grozeva, Elaine K. Green, Paul D. Gilbert, Peter S. Braund, Jaume Marrugat, Rainer Rettig, Pim van der Harst, Yik Ying Teo, Andrew P. Morris, Guiseppe Matullo, Serena Sanna, Cristen J. Willer, Suzannah Bumpstead, Niall C. Taylor, Jacques S. Beckmann, Pierre Meneton, Elin Org, Luigi Ferrucci, Doug Easton, Sheila Seal, Joanne M. Heward, Anne U. Jackson, Eleftheria Zeggini, Rachel M. Freathy, Maris Laan, Paul Wordsworth, Sarah Nutland, Kerstin Koch, Sian Ceasar, Anders Hamsten, Judith M. Hussey, Tariq Ahmad, Derek P. Jewell, Paul Scheet, Charlie W. Lees, C Farrar, Christopher Prowse, Markku Laakso, David St Clair, Kate Downes, Diederick E. Grobbee, Paul Burton, Simon C. Potter, Ian N. Bruce, Tim D. Spector, Anne Barton, H.-Erich Wichmann, Matthew J. Simmonds, David Hadley, Cecilia M. Lindgren, Gérard Waeber, Nigel W. Rayner, Melanie J. Newport, Manjinder S. Sandhu, Audrey Duncanson, Guangju Zhai, Simon Heath, Susan M. Ring, Alessandra Di Gregorio, Richard Williamson, Nicholas J. Wareham, Zhan Su, Olle Melander, John R. Thompson, Alexander Teumer, Sheila A. Fisher, Lachlan J. M. Coin, Leif Groop, Giovanni Tognoni, Amanda Elkin, Alan J. Silman, Jack Satsangi, Jane Worthington, Martin Farrall, John Webster, Niall Cardin, Neil Walker, Anna F. Dominiczak, Jeremy D. Sanderson, Damjan Vukcevic, Bryan Howie, Silvia Polidoro, Stephen G. Ball, Mark Tremelling, Stephen Newhouse, Stephen M. Schwartz, Lori L. Bonnycastle, Chris Wallace, Kijoung Song, Mario A. Morken, I. Nicol Ferrier, Beverley Barke, Paolo Vineis, Manuela Uda, Deborah P M Symmons, Emily J. Lyons, Mingzhan Xue, Timothy M. Frayling, Stephen C.L. Cough, David Withers, Adrian V. S. Hill, Suzanne Stevens, Jennifer Jolley, Marcus Dörr, Kirk A. Rockett, David B. Dunger, Mark Walker, Jayne A. Franklyn, Lisa Jones, David S. Siscovick, Ann-Christine Syvänen, Laura J. Scott, Morris J. Brown, Barbera Cant, Michael Inouye, Feng Zhang, Carlotta Sacerdote, Katherine S. Elliott, Jonathan Marchini, Peter Donnely, Michael John Owen, An Goris, Marcus Prembey, Andrew T. Hattersley, Gerome Breen, Marian L. Hamshere, Thomas Illig, Samer S. Najjar, Nicole Soranzo, Kay-Tee Khaw, Graham R. Walters, Willem H. Ouwehand, David P. Strachan, Martin D. Tobin, Alastair Compston, John C. Mansfield, David Altshuler, Salvatore Panico, Sekar Kathiresan, Dawn M. Waterworth, Michael N. Weedon, D. Timothy Bishop, Claire Bryan, Alexandra S. Knight, Kate L. Lee, Paul F. O'Reilly, Massimo Mangino, Michael Conlon O'Donovan, Jing Hua Zhao, Konstantinos A. Papadakis, Jennifer H. Barrett, Joanne Pereira-Gale, N J Timpson, Stephan B. Felix, Panos Deloukas, Nicholas A. Watkins, Anna-Liisa Hartikainen, Peter Vollenweider, Richard Jones, Anne Hinks, Fraser Cummings, Noha Lim, Linda A. Bradbury, Rhian G. William, Nita G. Forouhi, Roberto Eluosa, Ingeleif B. Hallgrimsdottir, Giorgio Sirugo, Robert Luben, Veikko Salomaa, Robert Clarke, Sally John, Ursula Everson, Emma King, Ivan Nikolov, Heather M. Stringham, Antony P. Attwood, Angelo Scuteri, Wellcome Trust Case Control Consortium, Burton, PR., Clayton, DG., Cardon, LR., Craddock, N., Deloukas, P., Duncanson, A., Kwiatkowski, DP., McCarthy, MI., Ouwehand, WH., Samani, NJ., Todd, JA., Donnelly, P., Barrett, JC., Davison, D., Easton, D., Evans, D., Leung, HT., Marchini, JL., Morris, AP., Spencer, IC., Tobin, MD., Attwood, AP., Boorman, JP., Cant, B., Everson, U., Hussey, JM., Jolley, JD., Knight, AS., Koch, K., Meech, E., Nutland, S., Prowse, CV., Stevens, HE., Taylor, NC., Walters, GR., Walker, NM., Watkins, NA., Winzer, T., Jones, RW., McArdle, WL., Ring, SM., Strachan, DP., Pembrey, M., Breen, G., St Clair, D., Caesar, S., Gordon-Smith, K., Jones, L., Fraser, C., Green, EK., Grozeva, D., Hamshere, ML., Holmans, PA., Jones, IR., Kirov, G., Moskvina, V., Nikolov, I., O'Donovan, MC., Owen, MJ., Collier, DA., Elkin, A., Farmer, A., Williamson, R., McGuffin, P., Young, AH., Ferrier, IN., Ball, SG., Balmforth, AJ., Barrett, JH., Bishop, DT., Iles, MM., Maqbool, A., Yuldasheva, N., Hall, AS., Braund, PS., Dixon, RJ., Mangino, M., Stevens, S., Thompson, JR., Bredin, F., Tremelling, M., Parkes, M., Drummond, H., Lees, CW., Nimmo, ER., Satsangi, J., Fisher, SA., Forbes, A., Lewis, CM., Onnie, CM., Prescott, NJ., Sanderson, J., Mathew, CG., Barbour, J., Mohiuddin, MK., Todhunter, CE., Mansfield, JC., Ahmad, T., Cummings, FR., Jewell, DP., Webster, J., Brown, MJ., Lathrop, GM., Connell, J., Dominiczak, A., Braga Marcano, CA., Burke, B., Dobson, R., Gungadoo, J., Lee, KL., Munroe, PB., Newhouse, SJ., Onipinla, A., Wallace, I., Xue, M., Caulfield, M., Farrall, M., Barton, A., Bruce, IN., Donovan, H., Eyre, S., Gilbert, PD., Hider, SL., Hinks, AM., John, SL., Potter, C., Silman, AJ., Symmons, DP., Thomson, W., Worthington, J., Dunger, DB., Widmer, B., Frayling, TM., Freathy, RM., Lango, H., Perry, JR., Shields, BM., Weedon, MN., Hattersley, AT., Hitman, GA., Walker, M., Elliott, KS., Groves, CJ., Lindgren, CM., Rayner, NW., Timpson, NJ., Zeggini, E., Newport, M., Sirugo, G., Lyons, E., Vannberg, F., Hill, AV., Bradbury, LA., Farrar, C., Pointon, JJ., Wordsworth, P., Brown, MA., Franklyn, JA., Heward, JM., Simmonds, MJ., Gough, SC., Seal, S., Stratton, MR., Rahman, N., Ban, M., Goris, A., Sawcer, SJ., Compston, A., Conway, D., Jallow, M., Rockett, KA., Bryan, C., Bumpstead, SJ., Chaney, A., Downes, K., Ghori, J., Gwilliam, R., Hunt, SE., Inouye, M., Keniry, A., King, E., McGinnis, R., Potter, S., Ravindrarajah, R., Whittaker, P., Withers, D., Cardin, NJ., Ferreira, T., Pereira-Gale, J., Hallgrimsdóttir, IB., Howie, BN., Su, Z., Teo, YY., Vukcevic, D., Bentley, D., Life Course Epidemiology (LCE), Cardiovascular Centre (CVC), Lifestyle Medicine (LM), Groningen Kidney Center (GKC), Vascular Ageing Programme (VAP), and Medical Research Council (MRC)

Subjects
Hemodynamics, Genome-wide association study, Blood Pressure, 030204 cardiovascular system & hematology, 0302 clinical medicine, Diastole, 11 Medical and Health Sciences, POPULATION, Genetics, Genetics & Heredity, RISK, 0303 health sciences, education.field_of_study, Econometric and Statistical Methods: General, CELL-DIFFERENTIATION, biology, Intracellular Signaling Peptides and Proteins, Chromosome Mapping, Steroid 17-alpha-Hydroxylase, COMMON VARIANTS, 3. Good health, DNA-Binding Proteins, Europe, Cardiovascular Diseases, PUBLIC-HEALTH, BARTTERS-SYNDROME, Blood Pressure/genetics, Cardiovascular Diseases/genetics, Cardiovascular Diseases/physiopathology, Cytochrome P-450 CYP1A2/genetics, DNA-Binding Proteins/genetics, Diastole/genetics, European Continental Ancestry Group/genetics, Fibroblast Growth Factor 5/genetics, Genetic Variation, Genome-Wide Association Study, Humans, India, Methylenetetrahydrofolate Reductase (NADPH2)/genetics, Open Reading Frames/genetics, Phospholipase C delta/genetics, Polymorphism, Single Nucleotide, Proteins/genetics, Steroid 17-alpha-Hydroxylase/genetics, Systole/genetics, Wellcome Trust Case Control Consortium, Life Sciences & Biomedicine, hypertension, Fibroblast Growth Factor 5, Systole, Population, European Continental Ancestry Group, METHYLENETETRAHYDROFOLATE REDUCTASE GENE, Single-nucleotide polymorphism, LOW-RENIN HYPERTENSION, White People, Article, 03 medical and health sciences, Open Reading Frames, Fibroblast growth factor-5, Cytochrome P-450 CYP1A2, Geneeskunde(GENK), education, Methylenetetrahydrofolate Reductase (NADPH2), Adaptor Proteins, Signal Transducing, 030304 developmental biology, Genetic association, genome-wide association, Science & Technology, MUTATIONS, Proteins, 06 Biological Sciences, POLYMORPHISM, Blood pressure, Methylenetetrahydrofolate reductase, biology.protein, biology.gene, Phospholipase C delta, Developmental Biology
Abstract

Elevated blood pressure is a common, heritable cause of cardiovascular disease worldwide. To date, identification of common genetic variants influencing blood pressure has proven challenging. We tested 2.5 million genotyped and imputed SNPs for association with systolic and diastolic blood pressure in 34,433 subjects of European ancestry from the Global BPgen consortium and followed up findings with direct genotyping (N ≤ 71,225 European ancestry, N ≤ 12,889 Indian Asian ancestry) and in silico comparison (CHARGE consortium, N = 29,136). We identified association between systolic or diastolic blood pressure and common variants in eight regions near the CYP17A1 (P = 7 × 10(-24)), CYP1A2 (P = 1 × 10(-23)), FGF5 (P = 1 × 10(-21)), SH2B3 (P = 3 × 10(-18)), MTHFR (P = 2 × 10(-13)), c10orf107 (P = 1 × 10(-9)), ZNF652 (P = 5 × 10(-9)) and PLCD3 (P = 1 × 10(-8)) genes. All variants associated with continuous blood pressure were associated with dichotomous hypertension. These associations between common variants and blood pressure and hypertension offer mechanistic insights into the regulation of blood pressure and may point to novel targets for interventions to prevent cardiovascular disease.

Published
2009

116. Interrogating Type 2 Diabetes Genome-Wide Association Data Using a Biological Pathway-Based Approach

Author

Michael N. Weedon, Mark I. McCarthy, Andrew T. Hattersley, Timothy M. Frayling, John R. B. Perry, and Eleftheria Zeggini

Subjects
Endocrinology, Diabetes and Metabolism, Single-nucleotide polymorphism, Genome-wide association study, Type 2 diabetes, Biology, Genome, Polymorphism, Single Nucleotide, Biological pathway, 03 medical and health sciences, 0302 clinical medicine, Reference Values, Internal Medicine, medicine, Odds Ratio, Genetics, Humans, KEGG, 030304 developmental biology, Genetic association, 0303 health sciences, Models, Genetic, Chromosome Mapping, Genetic Variation, medicine.disease, 3. Good health, Diabetes Mellitus, Type 2, Case-Control Studies, TCF7L2, 030217 neurology & neurosurgery, Algorithms, Genome-Wide Association Study
Abstract

OBJECTIVE Recent genome-wide association studies have resulted in a dramatic increase in our knowledge of the genetic loci involved in type 2 diabetes. In a complementary approach to these single-marker studies, we attempted to identify biological pathways associated with type 2 diabetes. This approach could allow us to identify additional risk loci. RESEARCH DESIGN AND METHODS We used individual level genotype data generated from the Wellcome Trust Case Control Consortium (WTCCC) type 2 diabetes study, consisting of 393,143 autosomal SNPs, genotyped across 1,924 case subjects and 2,938 control subjects. We sought additional evidence from summary level data available from the Diabetes Genetics Initiative (DGI) and the Finland-United States Investigation of NIDDM Genetics (FUSION) studies. Statistical analysis of pathways was performed using a modification of the Gene Set Enrichment Algorithm (GSEA). A total of 439 pathways were analyzed from the Kyoto Encyclopedia of Genes and Genomes, Gene Ontology, and BioCarta databases. RESULTS After correcting for the number of pathways tested, we found no strong evidence for any pathway showing association with type 2 diabetes (top Padj = 0.31). The candidate WNT-signaling pathway ranked top (nominal P = 0.0007, excluding TCF7L2; P = 0.002), containing a number of promising single gene associations. These include CCND2 (rs11833537; P = 0.003), SMAD3 (rs7178347; P = 0.0006), and PRICKLE1 (rs1796390; P = 0.001), all expressed in the pancreas. CONCLUSIONS Common variants involved in type 2 diabetes risk are likely to occur in or near genes in multiple pathways. Pathway-based approaches to genome-wide association data may be more successful for some complex traits than others, depending on the nature of the underlying disease physiology.

Published
2009

117. A Common Variation in Deiodinase 1 Gene DIO1 Is Associated with the Relative Levels of Free Thyroxine and Triiodothyronine

Author

Bijay Vaidya, Vijay Panicker, Colin M. Dayan, Dena G. Hernandez, John R. B. Perry, Jonathan Evans, Claire Durant, Anna Murray, David Melzer, Michael N. Weedon, Christie Cluett, Andrew T. Hattersley, Luigi Ferrucci, Theo J. Visser, Timothy M. Frayling, Beverley M. Shields, Andrew B. Singleton, Kirstie Parnell, Graziano Ceresini, Ponnusamy Saravanan, and Internal Medicine

Subjects
Adult, Male, endocrine system, medicine.medical_specialty, endocrine system diseases, Hormone Replacement Therapy, Endocrinology, Diabetes and Metabolism, Clinical Biochemistry, Deiodinase, Thyrotropin, Single-nucleotide polymorphism, Iodide Peroxidase, Polymorphism, Single Nucleotide, Biochemistry, Endocrinology, Internal medicine, Genetic variation, medicine, Humans, SNP, Gene, Aged, Triiodothyronine, biology, Biochemistry (medical), Thyroid, Middle Aged, Thyroxine, medicine.anatomical_structure, biology.protein, Female, Original Article, Hormone
Abstract

Introduction: Genetic factors influence circulating thyroid hormone levels, but the common gene variants involved have not been conclusively identified. The genes encoding the iodothyronine deiodinases are good candidates because they alter the balance of thyroid hormones. We aimed to thoroughly examine the role of common variation across the three deiodinase genes in relation to thyroid hormones. Methods: We used HapMap data to select single-nucleotide polymorphisms (SNPs) that captured a large proportion of the common genetic variation across the three deiodinase genes. We analyzed these initially in a cohort of 552 people on T4 replacement. Suggestive findings were taken forward into three additional studies in people not on T4 (total n = 2513) and metaanalyzed for confirmation. Results: A SNP in the DIO1 gene, rs2235544, was associated with the free T3 to free T4 ratio with genome-wide levels of significance (P = 3.6 × 10−13). The C-allele of this SNP was associated with increased deiodinase 1 (D1) function with resulting increase in free T3/T4 ratio and free T3 and decrease in free T4 and rT3. There was no effect on serum TSH levels. None of the SNPs in the genes coding for D2 or D3 had any influence on hormone levels. Conclusions: This study provides convincing evidence that common genetic variation in DIO1 alters deiodinase function, resulting in an alteration in the balance of circulating free T3 to free T4. This should prove a valuable tool to assess the relative effects of circulating free T3vs. free T4 on a wide range of biological parameters.

Published
2008

118. New gene variants alter type 2 diabetes risk predominantly through reduced beta-cell function

Author

John R. B. Perry and Timothy M. Frayling

Subjects
Genetics, Nutrition and Dietetics, Genome, Human, Genetic Variation, Medicine (miscellaneous), Beta-cell Function, Type 2 diabetes, Biology, medicine.disease, Genome, Diabetes Mellitus, Type 2, Insulin-Secreting Cells, Diabetes mellitus, Insulin Secretion, Genetic variation, medicine, Humans, Insulin, Genetic Predisposition to Disease, Insulin secretion, TCF7L2, Gene
Abstract

Over the past 18 months, the number of gene loci robustly associated with type 2 diabetes has risen from three to 18. In this study, we focus on explaining the genome-wide approach that has led to most of these discoveries and discuss some of the early insights the new gene loci have provided into the aetiology of type 2 diabetes.Recent genome-wide association studies have provided an important resource for furthering our understanding of type 2 diabetes disease mechanisms. Genes previously unsuspected of playing a role in diabetes are now implicated in the disease process. These include genes in cell cycling control (CDKN2A/2B, CDKAL1), transcription factors (TCF7L2, HHEX), and ion channels (SLC30A8). These variants are all associated with insulin-secretory defects in the general population and show little if any relationship to insulin resistance. Two common variants (near or in FTO and MC4R) alter diabetes risk through a primary effect on obesity.Recent genome-wide association studies show that there are now 18 gene loci associated with the risk of type 2 diabetes. Most of these T2D gene loci affect insulin secretion.

Published
2008

119. Shared genetic aetiology of puberty timing between sexes and with health-related outcomes

Author

Ken K. Ong, Joyce Y. Tung, Joanne M. Murabito, Felix R. Day, John R. B. Perry, David A. Hinds, Hilary K. Finucane, Brendan Bulik-Sullivan, Day, Felix [0000-0003-3789-7651], Ong, Kenneth [0000-0003-4689-7530], Perry, John [0000-0001-6483-3771], Apollo - University of Cambridge Repository, Massachusetts Institute of Technology. Department of Mathematics, and Finucane, Hilary Kiyo

Subjects
Male, Time Factors, General Physics and Astronomy, Genome-wide association study, Disease, Type 2 diabetes, Body Mass Index, Receptors, G-Protein-Coupled, 0302 clinical medicine, Bone Density, Basic Helix-Loop-Helix Transcription Factors, Insulin, Young adult, Child, 0303 health sciences, education.field_of_study, Extracellular Matrix Proteins, Multidisciplinary, Lumbar Vertebrae, Nuclear Receptor Subfamily 1, Group F, Member 2, 3. Good health, Cardiovascular Diseases, Receptors, Leptin, Female, Polycystic Ovary Syndrome, medicine.medical_specialty, Adolescent, Population, 030209 endocrinology & metabolism, Locus (genetics), Nerve Tissue Proteins, Biology, Genetic correlation, Article, General Biochemistry, Genetics and Molecular Biology, White People, 03 medical and health sciences, Young Adult, Sex Factors, Internal medicine, medicine, Humans, Receptors, Pituitary Hormone, education, Triglycerides, 030304 developmental biology, Retinoid X Receptor alpha, Cholesterol, HDL, Puberty, General Chemistry, medicine.disease, Body Height, Radiography, Repressor Proteins, Endocrinology, Diabetes Mellitus, Type 2, Body mass index, Genome-Wide Association Study
Abstract

Understanding of the genetic regulation of puberty timing has come largely from studies of rare disorders and population-based studies in women. Here, we report the largest genomic analysis for puberty timing in 55,871 men, based on recalled age at voice breaking. Analysis across all genomic variants reveals strong genetic correlation (0.74, P=2.7 × 10[superscript −70]) between male and female puberty timing. However, some loci show sex-divergent effects, including directionally opposite effects between sexes at the SIM1/MCHR2 locus (P[subscript heterogeneity]=1.6 × 10[superscript −12]). We find five novel loci for puberty timing (P, Medical Research Council (Great Britain) (U106179472), Medical Research Council (Great Britain) (MC_U106179472), Medical Research Council (Great Britain) (U106179471), Medical Research Council (Great Britain) (MC_U106179471), National Human Genome Research Institute (U.S.) Grant R44HG006981)

Published
2015

120. Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci

Author

Laura J. Scott, Neil Robertson, Anders Hamsten, Domenico Palli, Susanne Moebus, Bernhard O. Boehm, Gunnar Sigurðsson, Paul W. Franks, C. N. A. Palmer, Sonali Pechlivanis, Katharine R. Owen, Michael E. Reschen, Sarah Edkins, Jason Carey, Christopher A. O’Callaghan, Norman Klopp, Caroline S. Fox, Petter Storm, N. William Rayner, Johan G. Eriksson, Thomas Illig, Anubha Mahajan, Erik Ingelsson, Allan Linneberg, Andrew R. Wood, Oddgeir L. Holmen, Nicola L. Beer, Mark I. McCarthy, Frank B. Hu, Peter Almgren, Heiner Boeing, Peter Donnelly, Carl Platou, Veikko Salomaa, Karl-Heinz Jöcke, Wen-Hong L. Kao, Lori L. Bonnycastle, Denis Rybin, Benjamin F. Voight, Peter Kraft, Inês Barroso, Claudia Langenberg, Teresa Ferreira, Peter Kovacs, Anne Raimondo, Christian Theil Have, Ulf de Faire, Torben Hansen, Han Chen, James B. Meigs, Timothy M. Frayling, Noël P. Burtt, Gerald Steinbach, Eric Boerwinkle, Michael Stumvoll, Stefan Gustafsson, Lars Lind, Andrew D. Morris, Alena Stančáková, Panagiotis Deloukas, Kari Stefansson, Augustine Kong, Hans A. Kestler, Andrew T. Hattersley, Beverley Balkau, Lorenzo Pasquali, Yingchang Lu, Nicola D. Kerrison, George B. Grant, Eeva Korpi-Hyövälti, Steven Wiltshire, Karl Gertow, Jorge Ferrer, Barbara Thorand, Inga Prokopenko, Matthias Blüher, Yvonne T. van der Schouw, Olga McLeod, Oluf Pedersen, Leena Peltonen, Anil Chalisey, Eleftheria Zeggini, Joseph Trakalo, Eric J.G. Sijbrands, Rainer Rauramaa, Guillaume Charpentier, Satu Männistö, Cordelia Langford, Lewin Eisele, Damiano Baldassarre, Lennart C. Karssen, Rona J. Strawbridge, Ghazala Mirza, Peter S. Chines, Roman Wennauer, Sara M. Willems, Erwin P. Bottinger, Timo Saaristo, Stéphane Cauchi, Ching-Ti Liu, Martijn van de Bunt, Valgerdur Steinthorsdottir, David Altshuler, Hyun Min Kang, Michael Boehnke, Jaakko Tuomilehto, Peter M. Nilsson, Kyle J. Gaulton, Jian'an Luan, Loic Yengo, David Couper, Reedik Mägi, Harald Grallert, Simone Wahl, Juha Saltevo, Phoenix Kwan, Cecilia M. Lindgren, Peter Lichtner, Richard N. Bergman, Andrew Crenshaw, João Fadista, Michael Roden, Annette Peters, Robert A. Scott, Unnur Thorsteinsdottir, James S. Pankow, Yeji Lee, Cornelia M. van Duijn, Samuli Ripatti, Francis S. Collins, Stéphane Lobbens, Niels Grarup, Ruth J. F. Loos, Julia Meyer, Marit E. Jørgensen, Christian Herder, Inger Njølstad, John R. B. Perry, Markus M. Nöthen, Man Li, Martina Müller-Nurasyid, Valeriya Lyssenko, Pierre Fontanillas, Michael D. Linderman, Leena Kinnunen, Jana K. Rundle, Elena Tremoli, Marilyn C. Cornelis, Tanya M. Teslovich, Todd Green, Raimund Erbel, Elisabeth M. van Leeuwen, Bengt Sennblad, Olle Melander, Sirkka Keinänen-Kiukaanniemi, Markku Laakso, Eero Lindholm, Alex S. F. Doney, Anke Tönjes, Maija Hassinen, Thomas W. Mühleisen, Gonçalo R. Abecasis, Nancy L. Pedersen, Thomas Sparsø, Johanna Kuusisto, Dorothée Thuillier, Qi Sun, Ian Dunham, Himanshu Chheda, Adam E. Locke, Philippe Froguel, Nicholas J. Wareham, Bruna Gigante, Jose C. Florez, Mozhgan Dorkhan, Omri Gottesman, Liming Liang, Anna Jonsson, Tiinamaija Tuomi, Leif Groop, Steve E. Humphries, Heikki A. Koistinen, Kristian Hveem, Astradur B. Hreidarsson, Jason Flannick, Torben Jørgensen, Clement Ma, Mattias Frånberg, Ewan Birney, Andrew P. Morris, Timo A. Lakka, Rob M. van Dam, Heather M. Stringham, Christian Gieger, Elodie Eury, Konstantin Strauch, Anna L. Gloyn, Rafn Benediktsson, Andres Metspalu, David J. Hunter, Karen L. Mohlke, Gudmar Thorleifsson, Josée Dupuis, Emmi Tikkanen, Christian Fuchsberger, Evelin Mihailov, Christopher J. Groves, Soren K. Thomsen, Tõnu Esko, Anne U. Jackson, Karin Leander, Douglas M. Ruderfer, Nikolay Oskolkov, Sekar Kathiresan, Robert Sladek, Lu Qi, Jasmina Kravic, Carmen Navarro, Epidemiology, Dermatology, Internal Medicine, ACS - Amsterdam Cardiovascular Sciences, Vascular Medicine, Cardiology, Wellcome Trust, Imperial College Healthcare NHS Trust- BRC Funding, Medical Research Council (MRC), [ 1 ] Univ Oxford, Wellcome Trust Ctr Human Genet, Oxford, England [ 2 ] Stanford Univ, Dept Genet, Stanford, CA 94305 USA [ 3 ] Univ Michigan, Dept Biostat, Ann Arbor, MI 48109 USA [ 4 ] Univ Oxford, Oxford Ctr Diabet Endocrinol & Metab, Oxford, England [ 5 ] Univ Tartu, Estonian Genome Ctr, EE-50090 Tartu, Estonia [ 6 ] Univ Oxford, Nuffield Dept Med, Ctr Cellular & Mol Physiol, Oxford, England [ 7 ] Wellcome Trust Sanger Inst, Hinxton, England [ 8 ] Univ Cambridge, Sch Clin Med, Inst Metab Sci, Med Res Council MRC Epidemiol Unit, Cambridge, England [ 9 ] Univ London Imperial Coll Sci Technol & Med, Genom Common Dis, London, England [ 10 ] Broad Inst Harvard & MIT, Cambridge, MA USA [ 11 ] Univ Copenhagen, Fac Hlth & Med Sci, Novo Nordisk Fdn Ctr Basic Metab Res, Copenhagen, Denmark [ 12 ] European Genom Inst Diabet, Lille Inst Biol, Lille, France [ 13 ] German Res Ctr Environm Hlth, Helmholtz Zentrum Munchen, Res Unit Mol Epidemiol, Neuherberg, Germany [ 14 ] German Res Ctr Environm Hlth, Helmholtz Zentrum Munchen, Inst Epidemiol 2, Neuherberg, Germany [ 15 ] German Ctr Diabet Res, Neuherberg, Germany [ 16 ] Karolinska Inst, Dept Med Solna, Atherosclerosis Res Unit, Stockholm, Sweden [ 17 ] Sci Life Lab, Stockholm, Sweden [ 18 ] Stockholm Univ, Dept Numer Anal & Comp Sci, S-10691 Stockholm, Sweden [ 19 ] Fritz Lipmann Inst, Leibniz Inst Age Res, Jena, Germany [ 20 ] Univ Ulm, Med Syst Biol, D-89069 Ulm, Germany [ 21 ] Finnish Inst Mol Med, Helsinki, Finland [ 22 ] Univ Hosp Essen, Inst Med Informat Biometry & Epidemiol, Essen, Germany [ 23 ] Uppsala Univ, Dept Med Sci, Mol Epidemiol & Sci Life Lab, Uppsala, Sweden [ 24 ] deCODE Genet Amgen Inc, Reykjavik, Iceland [ 25 ] Harvard Univ, Sch Publ Hlth, Dept Epidemiol, Boston, MA 02115 USA [ 26 ] Harvard Univ, Sch Publ Hlth, Dept Nutr, Boston, MA 02115 USA [ 27 ] Brigham & Womens Hosp, Dept Med, Channing Div Network Med, Boston, MA 02115 USA [ 28 ] Harvard Univ, Sch Publ Hlth, Boston, MA 02115 USA [ 29 ] Tulane Univ, Sch Publ Hlth & Trop Med, Dept Epidemiol, New Orleans, LA USA [ 30 ] Erasmus Univ, Med Ctr, Dept Epidemiol, Rotterdam, Netherlands [ 31 ] Johns Hopkins Bloomberg Sch Publ Hlth, Dept Epidemiol, Baltimore, MD USA [ 32 ] Boston Univ, Sch Publ Hlth, Dept Biostat, Boston, MA USA [ 33 ] Harvard Univ, Sch Publ Hlth, Dept Biostat, Boston, MA 02115 USA [ 34 ] Icahn Sch Med Mt Sinai, Icahn Inst Genom & Multiscale Biol, New York, NY 10029 USA [ 35 ] Icahn Sch Med Mt Sinai, Genet Obes & Related Metab Traits Program, New York, NY 10029 USA [ 36 ] Univ Penn, Perelman Sch Med, Dept Pharmacol, Philadelphia, PA 19104 USA [ 37 ] Lund Univ, Scania Univ Hosp, Dept Clin Sci Malmo, Ctr Diabet, Malmo, Sweden [ 38 ] IRCCS, Ctr Cardiol Monzino, Milan, Italy [ 39 ] Univ Milan, Dipartimento Sci Farmacol & Biomol, Milan, Italy [ 40 ] Ctr Rech Epidemiol & Sante Populat CESP, INSERM, U1018, Villejuif, France [ 41 ] Univ Paris 11, UMRS 1018, Villejuif, France [ 42 ] Univ Iceland, Fac Med, Reykjavik, Iceland [ 43 ] Landspitali Univ Hosp, Reykjavik, Iceland Organization-Enhanced Name(s) Landspitali National University Hospital [ 44 ] Univ Leipzig, Integrated Treatment & Res IFB Ctr Adipos Dis, D-04109 Leipzig, Germany [ 45 ] Univ Leipzig, Dept Med, D-04109 Leipzig, Germany [ 46 ] German Inst Human Nutr, Potsdam, Germany [ 47 ] NHGRI, US NIH, Bethesda, MD 20892 USA [ 48 ] Icahn Sch Med Mt Sinai, Charles Bronfman Inst Personalized Med, New York, NY 10029 USA [ 49 ] Corbeil Essonnes Hosp, Endocrinol Diabetol Unit, Corbeil Essonnes, France [ 50 ] Northwestern Univ, Feinberg Sch Med, Dept Prevent Med, Chicago, IL 60611 USA [ 51 ] Univ N Carolina, Dept Biostat, Collaborat Studies Coordinating Ctr, Chapel Hill, NC USA [ 52 ] Natl Univ Singapore, Saw Swee Hock Sch Publ Hlth, Singapore 117548, Singapore [ 53 ] Univ Dundee, Ninewells Hosp, Biomed Res Inst, Ctr Diabet Res, Dundee, Scotland [ 54 ] Univ Dundee, Ninewells Hosp, Biomed Res Inst, Pharmacogen Ctr, Dundee, Scotland [ 55 ] Lund Univ, Ctr Diabet, Dept Clin Sci Malmo, Novo Nordisk Scandinavia, Malmo, Sweden [ 56 ] Natl Inst Hlth & Welf, Dept Chron Dis Prevent, Helsinki, Finland [ 57 ] Univ Helsinki, Dept Gen Practice & Primary Hlth Care, Helsinki, Finland [ 58 ] Univ Helsinki, Cent Hosp, Unit Gen Practice, Helsinki, Finland [ 59 ] Folkhalsan Res Ctr, Helsinki, Finland [ 60 ] Childrens Hosp, Div Endocrinol, Boston, MA 02115 USA [ 61 ] Broad Inst Harvard & MIT, Program Med & Populat Genet, Cambridge, MA USA [ 62 ] CNRS, UMR 8199, Inst Biol, Lille, France [ 63 ] Univ Lille 2, Inst Pasteur, Lille, France [ 64 ] NHLBI, Framingham Heart Study, Framingham, MA USA [ 65 ] Brigham & Womens Hosp, Div Endocrinol & Metab, Boston, MA 02115 USA [ 66 ] Harvard Univ, Sch Med, Boston, MA USA [ 67 ] Lund Univ, Dept Clin Sci, Malmo, Sweden [ 68 ] Umea Univ, Dept Publ Hlth & Clin Med, Umea, Sweden [ 69 ] Karolinska Inst, Inst Environm Med, Div Cardiovasc Epidemiol, S-10401 Stockholm, Sweden [ 70 ] Kuopio Res Inst Exercise Med, Kuopio, Finland [ 71 ] Univ Dusseldorf, Leibniz Ctr Diabet Res, German Diabet Ctr, Inst Clin Diabetol, Dusseldorf, Germany [ 72 ] Partner Site Dusseldorf, German Ctr Diabet Res, Dusseldorf, Germany [ 73 ] Norwegian Univ Sci & Technol, Dept Publ Hlth & Gen Practice, Nord Trondelag Hlth Study HUNT Res Ctr, Levanger, Norway [ 74 ] UCL, Inst Cardiovasc Sci, British Heart Fdn BHF Labs, Cardiovasc Genet, London, England [ 75 ] Harvard Univ, Sch Publ Hlth, Program Genet Epidemiol & Stat Genet, Boston, MA 02115 USA [ 76 ] Steno Diabet Ctr, DK-2820 Gentofte, Denmark [ 77 ] Capital Reg Denmark, Res Ctr Prevent & Hlth, Copenhagen, Denmark [ 78 ] Univ Copenhagen, Fac Hlth & Med Sci, Copenhagen, Denmark [ 79 ] Aalborg Univ, Fac Med, Aalborg, Denmark [ 80 ] Hannover Med Sch, Hannover Unified Biobank, Hannover, Germany [ 81 ] German Res Ctr Environm Hlth, Helmholtz Zentrum Munchen, Inst Human Genet, Neuherberg, Germany [ 82 ] Rigshosp, Copenhagen Univ Hosp, DK-2100 Copenhagen, Denmark [ 83 ] Univ Copenhagen, Fac Hlth & Med Sci, Dept Clin Med, Copenhagen, Denmark [ 84 ] German Res Ctr Environm Hlth, Helmholtz Zentrum Munchen, Inst Genet Epidemiol, Neuherberg, Germany [ 85 ] Guys & St Thomas Natl Hlth Serv NHS Fdn Trust, Guys & St Thomas Hosp, Genom Core Facil, Biomed Res Ctr, London, England [ 86 ] Univ Bonn, Inst Human Genet, Bonn, Germany [ 87 ] Univ Bonn, Life & Brain Ctr, Dept Genom, Bonn, Germany [ 88 ] Res Ctr Julich, Inst Neurosci & Med INM 1, Julich, Germany [ 89 ] Univ Munich, Univ Hosp Grosshadern, Dept Med 1, Munich, Germany [ 90 ] Univ Munich, Chair Genet Epidemiol, Inst Med Informat Biometry & Epidemiol, Neuherberg, Germany [ 91 ] Partner Site Munich Heart Alliance, DZHK German Ctr Cardiovasc Res, Munich, Germany [ 92 ] Inst Murciano Invest Biosanitaria Virgen de la Ar, Murcia Reg Hlth Council, Dept Epidemiol, Murcia, Spain [ 93 ] CIBERESP, Madrid, Spain [ 94 ] Univ Murcia, Dept Hlth & Social Sci, Murcia, Spain [ 95 ] Churchill Hosp, Biomed Res Ctr, Oxford Natl Inst Hlth Res, Oxford OX3 7LJ, England [ 96 ] Canc Res & Prevent Inst ISPO, Florence, Italy [ 97 ] Nord Trondelag Hlth Trust, Levanger Hosp, Dept Internal Med, Levanger, Norway [ 98 ] Univ Hosp Dusseldorf, Dept Endocrinol & Diabetol, Dusseldorf, Germany [ 99 ] Icahn Sch Med Mt Sinai, Dept Psychiat, Div Psychiat Genom, New York, NY 10029 USA [ 100 ] Boston Univ, Data Coordinating Ctr, Boston, MA 02215 USA [ 101 ] Univ Med Ctr Utrecht, Utrecht, Netherlands [ 102 ] Iceland Heart Assoc, Kopavogur, Iceland [ 103 ] Univ Eastern Finland, Dept Med, Kuopio, Finland [ 104 ] Kuopio Univ Hosp, SF-70210 Kuopio, Finland [ 105 ] Univ Ulm, Dept Clin Chem & Cent Lab, D-89069 Ulm, Germany [ 106 ] Univ Helsinki, Dept Publ Hlth, Hjelt Inst, Helsinki, Finland [ 107 ] Helsinki Univ Hosp, Abdominal Ctr, Dept Endocrinol, Helsinki, Finland [ 108 ] Univ Helsinki, Res Program Diabet & Obes, Helsinki, Finland [ 109 ] Erasmus Univ, Med Ctr, Dept Internal Med, Rotterdam, Netherlands [ 110 ] Univ Exeter, Sch Med, Genet Complex Traits, Exeter, Devon, England [ 111 ] European Mol Biol Lab, EBI, Hinxton, England [ 112 ] Germans Trias & Pujol Univ Hosp & Res Inst, Div Endocrinol, Badalona, Spain [ 113 ] Josep Carreras Leukaemia Res Inst, Badalona, Spain [ 114 ] CIBERDEM, Barcelona, Spain [ 115 ] Univ London Imperial Coll Sci Technol & Med, Dept Med, London, England [ 116 ] Inst Invest Biomed August Pi & Sunyer, Ctr Esther Koplowitz, Barcelona, Spain [ 117 ] Icahn Sch Med Mt Sinai, Mindich Child Hlth & Dev Inst, New York, NY 10029 USA [ 118 ] Harvard Univ, Sch Med, Dept Med, Boston, MA USA [ 119 ] Massachusetts Gen Hosp, Ctr Human Genet Res, Boston, MA 02114 USA [ 120 ] Massachusetts Gen Hosp, Diabet Res Ctr, Boston, MA 02114 USA [ 121 ] Univ Texas Hlth Sci Ctr Houston, Human Genet Ctr, Houston, TX 77030 USA [ 122 ] Baylor Coll Med, Human Genome Sequencing Ctr, Houston, TX 77030 USA [ 123 ] Univ Minnesota, Div Epidemiol & Community Hlth, Minneapolis, MN USA [ 124 ] Netherlands Consortium Hlth Ageing, Netherlands Genom Initiat, Rotterdam, Netherlands [ 125 ] Ctr Med Syst Biol, Rotterdam, Netherlands [ 126 ] Massachusetts Gen Hosp, Gen Med Div, Boston, MA 02114 USA [ 127 ] Univ Eastern Finland, Inst Biomed Physiol, Kuopio, Finland [ 128 ] Kuopio Univ Hosp, Dept Clin Physiol & Nucl Med, SF-70210 Kuopio, Finland [ 129 ] Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden [ 130 ] Univ Uppsala Hosp, Dept Med Sci, Uppsala, Sweden [ 131 ] Univ Oulu, Inst Hlth Sci, Fac Med, Oulu, Finland [ 132 ] Oulu Univ Hosp, Unit Gen Practice, Oulu, Finland [ 133 ] South Ostrobothnia Cent Hosp, Seinajoki, Finland [ 134 ] Finnish Diabet Assoc, Tampere, Finland [ 135 ] Pirkanmaa Dist Hosp, Tampere, Finland [ 136 ] Cent Finland Cent Hosp, Dept Med, Jyvasklya, Finland [ 137 ] Univ Tartu, Inst Mol & Cell Biol, EE-50090 Tartu, Estonia [ 138 ] Univ Duisdurg Essen, Univ Hosp Essen, West German Heart Ctr, Clin Cardiol, Essen, Germany [ 139 ] Natl Inst Hlth & Welf, Publ Hlth Genom Unit, Helsinki, Finland [ 140 ] Univ Med Ctr Ulm, Dept Internal Med, Div Endocrinol & Diabet, Ulm, Germany [ 141 ] Univ London Imperial Coll Sci Technol & Med, Lee Kong Chian Sch Med, London SW7 2AZ, England [ 142 ] Nanyang Technol Univ, Singapore 639798, Singapore [ 143 ] Cedars Sinai Med Ctr, Diabet & Obes Res Inst, Los Angeles, CA 90048 USA [ 144 ] Univ N Carolina, Dept Genet, Chapel Hill, NC USA [ 145 ] Univ Helsinki, Cent Hosp, Dept Med, Div Endocrinol, Helsinki, Finland [ 146 ] Minerva Fdn, Helsinki, Finland [ 147 ] Hosp Univ La Paz, Inst Invest Sanitaria, Madrid, Spain [ 148 ] Danube Univ Krems, Ctr Vasc Prevent, Krems, Austria [ 149 ] King Abdulaziz Univ, Diabet Res Grp, Jeddah 21413, Saudi Arabia [ 150 ] Univ Tromso, Fac Hlth Sci, Dept Community Med, Tromso, Norway [ 151 ] Queen Mary Univ London, Barts & London Sch Med & Dent, William Harvey Res Inst, London, England [ 152 ] Univ Oxford, Dept Stat, Oxford OX1 3TG, England [ 153 ] Univ Exeter, Sch Med, Inst Biomed & Clin Sci, Exeter, Devon, England [ 154 ] Ctr Hosp Univ Montreal, Ctr Rech, Montreal Diabet Res Ctr, Montreal, PQ, Canada [ 155 ] McGill Univ, Montreal, PQ, Canada [ 156 ] Genome Quebec Innovat Ctr, Montreal, PQ, Canada [ 157 ] Univ Southern Denmark, Fac Hlth Sci, Odense, Denmark [ 158 ] Univ Edinburgh, Usher Inst Populat Hlth Sci & Informat, Edinburgh, Midlothian, Scotland [ 159 ] Massachusetts Gen Hosp, Cardiovasc Res Ctr, Boston, MA 02114 USA [ 160 ] Univ Cambridge, Metab Res Labs, Wellcome Trust MRC Inst Metab Sci, Cambridge, England [ 161 ] Cambridge Biomed Res Ctr, Natl Inst Hlth Res, Cambridge, England [ 162 ] Harvard Univ, Sch Med, Dept Genet, Boston, MA USA [ 163 ] Harvard Univ, Sch Med, Dept Mol Biol, Boston, MA USA [ 164 ] Univ Liverpool, Dept Biostat, Liverpool L69 3BX, Merseyside, England [ 165 ] Univ Liverpool, Dept Mol & Clin Pharmacol, Liverpool L69 3BX, Merseyside, England, Luan, Jian'an [0000-0003-3137-6337], Perry, John [0000-0001-6483-3771], Barroso, Ines [0000-0001-5800-4520], Langenberg, Claudia [0000-0002-5017-7344], Wareham, Nicholas [0000-0003-1422-2993], and Apollo - University of Cambridge Repository

Subjects
endocrine system diseases, Medizin, Genome-wide association study, Glucose homeostasis, WIDE ASSOCIATION, Association mapping, Non-U.S. Gov't, Genome-Wide Association Study, Regulation of gene expression, Genetics, Genetics & Heredity, LARGE-SCALE ASSOCIATION, Research Support, Non-U.S. Gov't, COMMON VARIANTS, Chromosome Mapping, 11 Medical And Health Sciences, Genomics, 3. Good health, TRANSCRIPTION FACTORS, Liver, Hepatocyte Nuclear Factor 3-beta, Medical Genetics, Life Sciences & Biomedicine, Chromatin Immunoprecipitation, endocrine system, European Continental Ancestry Group/genetics, Biology, GENOTYPE IMPUTATION, Research Support, INSULIN-SECRETION, Polymorphism, Single Nucleotide, Article, N.I.H, Sykursýki, Islets of Langerhans, SDG 3 - Good Health and Well-being, Research Support, N.I.H., Extramural, HUMAN PANCREATIC-ISLETS, GLYCEMIC TRAITS, Journal Article, SNP, Humans, Genetic Predisposition to Disease, Comparative Study, Enhancer, Medicinsk genetik, Science & Technology, Binding Sites, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium, Receptor, Melatonin, MT2, Extramural, Molecular Sequence Annotation, Arfgengi, 06 Biological Sciences, Genetic Predisposition to Disease/genetics, BETA-CELL, Diabetes Mellitus, Type 2/genetics, Diabetes Mellitus, Type 2, Gene Expression Regulation, Genetic Loci, Case-Control Studies, Gene-Environment Interaction, GLUCOSE-HOMEOSTASIS, Chromatin immunoprecipitation, Developmental Biology
Abstract

To access publisher's full text version of this article click on the hyperlink at the bottom of the page We performed fine mapping of 39 established type 2 diabetes (T2D) loci in 27,206 cases and 57,574 controls of European ancestry. We identified 49 distinct association signals at these loci, including five mapping in or near KCNQ1. 'Credible sets' of the variants most likely to drive each distinct signal mapped predominantly to noncoding sequence, implying that association with T2D is mediated through gene regulation. Credible set variants were enriched for overlap with FOXA2 chromatin immunoprecipitation binding sites in human islet and liver cells, including at MTNR1B, where fine mapping implicated rs10830963 as driving T2D association. We confirmed that the T2D risk allele for this SNP increases FOXA2-bound enhancer activity in islet- and liver-derived cells. We observed allele-specific differences in NEUROD1 binding in islet-derived cells, consistent with evidence that the T2D risk allele increases islet MTNR1B expression. Our study demonstrates how integration of genetic and genomic information can define molecular mechanisms through which variants underlying association signals exert their effects on disease. cademy of Finland 77299 102318 10493 118065 123885 124243 129293 129680 136895 139635 211119 213506 251217 263836 Agence National de la Recherche Association de Langue Francaise pour l'Etude du Diabete et des Maladies Metaboliques Association Diabeete Risque Vasculaire Association Francaise des Diabetiques Association of Danish Pharmacies Augustinus Foundation Becket Foundation British Diabetes Association (BDA) Research British Heart Foundation Central Norway Health Authority Central Finland Hospital District Center for Inherited Disease Research (CIDR) City of Kuopio City of Leutkirch Copenhagen County Danish Centre for Evaluation and Health Technology Assessment Danish Council for Independent Research Danish Heart Foundation Danish Research Councils Deutsche Forschungsgemeinschaft ER 155/6-2 Diabetes Research Foundation Diabetes UK Doris Duke Charitable Foundation Erasmus Medical Center Erasmus University Estonian government SF0180142s08 European Commission ENGAGE HEALTH-F4-2007-201413 FP7-201413 FP7-245536 EXGENESIS LSHM-CT-2004-005272 FP6 LSHM_CT_2006_037197 LSHM-CT-2007-037273 C-Public Health 2004310 European Regional Development Fund Federal Ministry of Education and Research, Germany FKZ 01GI1128 FKZ 01EO1001 Federal Ministry of Health, Germany Finnish Diabetes Association Finnish Diabetes Research Foundation Finnish Foundation for Cardiovascular Research Finnish Medical Society Folkhalsan Research Foundation Foundation for Life and Health in Finland Foundation for Old Servants Fredrick och Ingrid Thuring Foundation French region of Nord-Pas-de-Calais (Contrat de Projets Etat-Region) German Center for Diabetes Research German Research Council GRK1041 German National Genome Research Network Groupe d'Etude des Maladies Metaboliques et Systemiques Health Care Centers in Vasa, Narpes and Korsholm, Finland Health Foundation Heinz Nixdorf Foundation Helmholtz Zentrum Munchen Helsinki University Central Hospital Research Foundation Hospital District of Southwest Finland Ib Henriksens Foundation IngaBritt and Arne Lundberg's Research Foundation 359 Karolinska Institutet Knut and Alice Wallenberg Foundation KAW 2009.0243 Kuopio University Hospital Lundbeck Foundation Magnus Bergvall Foundation Medical Faculty of University Duisburg-Essen Medical Research Council, UK G0000649 G0601261 Ministry for Health, Welfare and Sports, the Netherlands Ministry of Education and Culture, Finland 722 627 Ministry of Education, Culture and Science, the Netherlands Ministry of Health and Prevention, Denmark Ministry of Social Affairs and Health, Finland Ministry of Innovation, Science, Research and Technology of North Rhine-Westphalia, Germany Munich Center of Health Sciences Municipal Health Care Center and Hospital in Jakobstad, Finland municipality of Rotterdam, the Netherlands Narpes Health Care Foundation National Health Screening Service of Norway National Heart, Lung, and Blood Institute, USA HHSN268201100005C HHSN268201100006C HHSN268201100007C HHSN268201100008C HHSN268201100009C HHSN268201100010C HHSN268201100011C HHSN268201100012C N01HC25195 N02HL64278 R01HL087641 R01HL59367 R01HL086694 National Human Genome Research Institute, USA U01HG004402 N01HG65403 National Institute for Diabetes and Digestive and Kidney Diseases, USA R01DK078616 U01DK085526 K24DK080140 R01DK073490 National Institute for Health and Welfare, Finland National Institutes of Health, USA HHSN268200625226C UL1RR025005 R01DK062370 R01DK072193 1Z01HG000024 AG028555 AG08724 AG04563 AG10175 AG08861 U01HG004399 DK58845 CA055075 DK085545 DK098032 Netherlands Genomics Initiative Netherlands Organisation for Health Research and Development Netherlands Organisation of Scientific Research NOW Investments 175.010.2005.011 911-03-012 050-060-810 Nord-Trondelag County Council Nordic Center of Excellence in Disease Genetics Norwegian Institute of Public Health Norwegian Research Council Novo Nordisk Foundation Ollquist Foundation Oxford National Institute for Health Research (NIHR) Biomedical Research Centre Paavo Nurmi Foundation Paivikki and Sakari Sohlberg Foundation Perklen Foundation Pirkanmaa Hospital District, Finland Programme Hospitalier de Recherche Clinique Programme National de Recherche sur la Diabete Research Institute for Diseases in the Elderly 014-93-015 Robert Dawson Evans Endowment, Department of Medicine, Boston University School of Medicine and Boston Medical Center Royal Swedish Academy of Sciences Sarstedt, Germany Signe and Ane Gyllenberg Foundation Sigrid Juselius Foundation Slottery Machine Association, Finland Social Insurance Institution of Finland South OstroBothnia Hospital District state of Baden-Wurttemberg, Germany Stockholm County Council 560183 Swedish Cultural Foundation, Finland Swedish Diabetes Foundation Swedish e-science Research Center Swedish Foundation for Strategic Research Swedish Heart-Lung Foundation Swedish Research Council SFO EXODIAB 2009-1039 521-2010-3490 521-2007-4037 521-2008-2974 ANDIS 825-2010-5983 LUDC 349-2008-6589 8691 Swedish Society of Medicine Tore Nilsson Foundation Torsten and Ragnar Soderbergs Stiftelser MT33/09 University Hospital Essen University of Tromso University College London NIHR Biomedical Research Centre UK NIHR Cambridge Biomedical Research Centre Uppsala University Uppsala University Hospital Vaasa Hospital District Velux Foundation Wellcome Trust GR072960 076113 083948 090367 090532 083270 086596 098017 095101 098051 098381

Published
2015

121. An atlas of genetic correlations across human diseases and traits

Author

Felix R. Day, Verneri Anttila, John R. B. Perry, Alkes L. Price, Alexander Gusev, Nick Patterson, Brendan Bulik-Sullivan, Elise B. Robinson, Mark J. Daly, Hilary K. Finucane, Po-Ru Loh, Laramie E. Duncan, Benjamin M. Neale, Internal Medicine, Epidemiology, and Obstetrics & Gynecology

Subjects
Male, Linkage disequilibrium, Genotype, Quantitative Trait Loci, Single-nucleotide polymorphism, Genome-wide association study, Disease, Anorexia, Quantitative trait locus, Biology, Genetic correlation, Polymorphism, Single Nucleotide, Linkage Disequilibrium, Article, 03 medical and health sciences, 0302 clinical medicine, SDG 3 - Good Health and Well-being, mental disorders, Genetics, medicine, Humans, Computer Simulation, Genetic Predisposition to Disease, Genetic Association Studies, 030304 developmental biology, 0303 health sciences, Models, Genetic, Educational attainment, 3. Good health, Phenotype, Evolutionary biology, Regression Analysis, Female, medicine.symptom, 030217 neurology & neurosurgery, Algorithms, Genome-Wide Association Study
Abstract

Identifying genetic correlations between complex traits and diseases can provide useful etiological insights and help prioritize likely causal relationships. The major challenges preventing estimation of genetic correlation from genome-wide association study (GWAS) data with current methods are the lack of availability of individual genotype data and widespread sample overlap among meta-analyses. We circumvent these difficulties by introducing a technique – cross-trait LD Score regression – for estimating genetic correlation that requires only GWAS summary statistics and is not biased by sample overlap. We use this method to estimate 276 genetic correlations among 24 traits. The results include genetic correlations between anorexia nervosa and schizophrenia, anorexia and obesity and associations between educational attainment and several diseases. These results highlight the power of genome-wide analyses, since there currently are no significantly associated SNPs for anorexia nervosa and only three for educational attainment.

Published
2015

122. A robust example of collider bias in a genetic association study

Author

Felix R. Day, John R. B. Perry, Robert A. Scott, and Ken K. Ong

Subjects
Evolutionary biology, Causal inference, Covariate, Collider (epidemiology), Genetic variants, Genomics, Biology, Spurious relationship, Biobank, Genetic association
Abstract

Recent studies have described the potential for ″collider bias″ to modify the magnitude of genotype-phenotype associations, however the extent to which this effect can induce a completely false-positive association remains unclear. In a sample of 142,630 individuals from the UK Biobank study, inclusion of height (a ″collider″) as a covariate induces biologically spurious, but genome-wide significant, associations between autosomal genetic variants and sex. These associations are non-significant in models unadjusted for height. Our study underpins the importance of causal inference modeling in the design and interpretation of genetic (and non-genetic) association studies.

Published
2015
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123. New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk

Author

Philippe Froguel, Pekka Jousilahti, Harry Campbell, Ellen M. Schmidt, Vasiliki Lagou, John Andrew Pospisilik, Ivana Kolcic, Igor Rudan, Mark A. Sarzynski, Brigitte Kühnel, Robin Haring, Paul Knekt, Christian Gieger, Eero Kajantie, Jian Yang, Tuomas O. Kilpeläinen, Hans L. Hillege, Niek Verweij, Sarah H Wild, Torben Hansen, Leena Taittonen, Michael Boehnke, Mark I. McCarthy, Joel N. Hirschhorn, Åsa K. Hedman, D. Timothy Bishop, James F. Wilson, Jian'an Luan, Leo-Pekka Lyytikäinen, Nita G. Forouhi, Mark Walker, Elodie Eury, Konstantin Strauch, Aroon D. Hingorani, Nam H. Cho, Peter Vollenweider, Erkki Vartiainen, Jong-Young Lee, Fredrik Karpe, Jiali Han, Joanne M. Jordan, Chen Lu, Henri Wallaschofski, Anna A. E. Vinkhuyzen, Alan R. Shuldiner, David J. Hunter, Mario Falchi, Aron S. Buchman, Caroline S. Fox, Robert A. Scott, Chan Soo Shin, Fernando Rivadeneira, Zari Dastani, Veikko Salomaa, Weihua Zhang, Rui Li, John C. Chambers, Thorkild I. A. Sørensen, André G. Uitterlinden, David A. Bennett, Marianna Sanna, Claire Bellis, Lars Bertram, Karl Michaëlsson, Yingchang Lu, Marie Loh, Loic Yengo, Bok-Ghee Han, Priya Srikanth, Laura Pascoe, Peter Wagner, Philip L. De Jager, Oscar H. Franco, Yongmei Liu, Stavroula Kanoni, Simone Gärtner, Ruth J. F. Loos, Eric E. Schadt, Claes Ohlsson, Cornelia M. van Duijn, Jorma S. A. Viikari, Stephan J. L. Bakker, Tamara B. Harris, Pirro G. Hysi, Samuli Ripatti, John R. B. Perry, Stefan A. Czerwinski, Tune H. Pers, Angela Döring, Ghazaleh Fatemifar, Tarunveer S. Ahluwalia, Liesbeth Vandenput, Carrie M. Nielson, Claudia Langenberg, Carolina Medina-Gomez, Mike A. Nalls, Erik Ingelsson, Barbara McKnight, Niels Grarup, L. Adrienne Cupples, Torben Jørgensen, Satu Männistö, Jianbo Na, Cristen J. Willer, Tuomo Rankinen, Irene Mateo Leach, Cecilia M. Lindgren, Marie-Claude Vohl, Ryan W. Walker, Yun Ju Sung, Joanne M. Murabito, Natasja M. van Schoor, Mika Kivimäki, Nicholas J. Wareham, Lei Yu, Markku Laakso, Julia A. Newton Bishop, Pim van der Harst, Qibin Qi, Veronique Bataille, Clive Osmond, Alan F. Wright, Audrey C. Choh, Charles C. White, Felix R. Day, Ron T. Gansevoort, Tiina Laatikainen, Ozren Polasek, Johan G. Eriksson, Mark M. Iles, Dena G. Hernandez, Meena Kumari, Dmitry Shungin, Jeffrey R. O'Connell, Joseph M. Zmuda, Antti Jula, Hyung Jin Choi, Albert Hofman, Steven R. Cummings, Youfang Liu, Vilmundur Gudnason, J. Brent Richards, Michael Stumvoll, Ayse Demirkan, Teresa Ferreira, Rosalie A. M. Dhonukshe-Rutten, Rahel Eckardt, Lude Franke, Karen L. Mohlke, Uzma Afzal, Kijoung Song, Till Ittermann, Janina S. Ried, Allan Linneberg, Nicholas D. Hastie, Laticia Oozageer, Johanna Kuusisto, John Blangero, Amélie Bonnefond, Panos Deloukas, Andrew P. Morris, Oluf Pedersen, Adam E. Locke, Emmi Tikkanen, Veronique Vitart, Aki S. Havulinna, Olli T. Raitakari, Inga Prokopenko, Peter Lichtner, Harm-Jan Westra, Katja Borodulin, Teemu Kuulasmaa, Lars Lind, Bradford Towne, Christine G. Lee, Mika Kähönen, Anke W. Enneman, Terrence S. Furey, Treva Rice, Abbas Dehghan, Jaspal S. Kooner, Dabeeru C. Rao, Terrence Forrester, Jing Hua Zhao, Xin Li, Mary F. Feitosa, Melissa E. Garcia, Tian Liu, Aarno Palotie, Eric S. Orwoll, Reedik Mägi, Daniel S. Evans, Elisabeth Widen, Tim D. Spector, Caroline Hayward, Annette Peters, Markku Heliövaara, Harald Grallert, Niina Eklund, Robert C. Kaplan, Ilja Demuth, Luigi Ferrucci, Kati Kristiansson, Amy Luke, Tõnu Esko, Ken K. Ong, Gregory J. Tranah, Angelo Tremblay, Ben A. Oostra, Stefan Gustafsson, Zhihong Zhu, Nina Smolej Narančić, Cameron D. Palmer, William R. Scott, Alexander Teumer, Anne U. Jackson, Markus Perola, Toshiko Tanaka, Lavinia Paternoster, Henry Völzke, Terho Lehtimäki, Dominik Spira, Karin M. A. Swart, Louis Pérusse, Matthias Blüher, Jari Lahti, M. Carola Zillikens, Kari E. North, Yvonne Boettcher, Douglas P. Kiel, Bamidele O. Tayo, Elisabeth Steinhagen-Thiessen, Diana L. Cousminer, Joanne E. Curran, Peter Kovacs, David M. Evans, Claude Bouchard, Alena Stančáková, Seppo Koskinen, Jack W. Kent, Alexander W. Drong, Massimo Mangino, Frédéric Fumeron, Richard S. Cooper, Juha Karjalainen, Nathalie van der Velde, Martin L. Buchkovich, Stéphane Lobbens, Cristina Menni, Anubha Mahajan, Nele Friedrich, Anke Tönjes, Colin A. McKenzie, Tom Forsén, Anne E. Justice, Lisette C. P. G. M. de Groot, Ingrid B. Borecki, Mingfeng Zhang, Tommy Cederholm, IOO, Internal medicine, Epidemiology and Data Science, EMGO - Musculoskeletal health, APH - Amsterdam Public Health, AMS - Amsterdam Movement Sciences, Geriatrics, Internal Medicine, Erasmus MC other, Epidemiology, Clinical Genetics, Institute for Molecular Medicine Finland, Clinicum, Department of General Practice and Primary Health Care, Behavioural Sciences, Samuli Olli Ripatti / Principal Investigator, Department of Public Health, Aarno Palotie / Principal Investigator, Johan Eriksson / Principal Investigator, Children's Hospital, Lastentautien yksikkö, University of Helsinki, Elisabeth Ingrid Maria Widen / Principal Investigator, Biostatistics Helsinki, Quantitative Genetics, Developmental Psychology Research Group, Complex Disease Genetics, Genomics of Neurological and Neuropsychiatric Disorders, Genomic Discoveries and Clinical Translation, Groningen Institute for Organ Transplantation (GIOT), Lifestyle Medicine (LM), Groningen Kidney Center (GKC), Life Course Epidemiology (LCE), Cardiovascular Centre (CVC), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), and Stem Cell Aging Leukemia and Lymphoma (SALL)

Subjects
0301 basic medicine, Medicin och hälsovetenskap, Drosophila melanogaster/genetics, Nutrition and Disease, General Physics and Astronomy, Genome-wide association study, Medical and Health Sciences, Body fat percentage, Voeding en Ziekte, CUTANEOUS NEVI, Mass index, Human Nutrition & Health, Adiposity, INSULIN-RESISTANCE, Multidisciplinary, body fat, cardiometabolic traits, genome-wide association study, meta-analysis, biology, Disease genetics, Leptin, Humane Voeding & Gezondheid, COMMON VARIANTS, Public Health, Global Health, Social Medicine and Epidemiology, 3. Good health, Biological sciences, Cardiovascular diseases, Drosophila melanogaster, Gene Knockdown Techniques, ENERGY-BALANCE, Medical Genetics, medicine.medical_specialty, SUSCEPTIBILITY LOCI, Heart Diseases, 515 Psychology, Science, Quantitative Trait Loci, PROVIDES INSIGHTS, Quantitative trait locus, General Biochemistry, Genetics and Molecular Biology, Article, GENETIC ARCHITECTURE, 03 medical and health sciences, MASS INDEX, Insulin resistance, Internal medicine, MD Multidisciplinary, Genetics, medicine, Life Science, Animals, Humans, Genetic Predisposition to Disease, GENOME-WIDE ASSOCIATION, Medicinsk genetik, VLAG, Global Nutrition, Wereldvoeding, Gene Expression Regulation/physiology, C-reactive protein, Metabolic diseases, General Chemistry, ta3121, medicine.disease, Onderwijsinstituut, Folkhälsovetenskap, global hälsa, socialmedicin och epidemiologi, Adiposity/genetics, Drosophila melanogaster/metabolism, Genome-Wide Association Study, Heart Diseases/genetics, Quantitative Trait Loci/genetics, 030104 developmental biology, Endocrinology, Gene Expression Regulation, 3121 General medicine, internal medicine and other clinical medicine, biology.protein, Lean body mass, IDENTIFIES COMMON
Abstract

To increase our understanding of the genetic basis of adiposity and its links to cardiometabolic disease risk, we conducted a genome-wide association meta-analysis of body fat percentage (BF%) in up to 100,716 individuals. Twelve loci reached genome-wide significance (P, A genome-wide association meta-analysis study here shows novel genetic loci to be associated to body fat percentage, and describes cross-phenotype association that further demonstrate a close relationship between adiposity and cardiovascular disease risk.

Published
2015

124. Erratum: Whole-genome sequence-based analysis of thyroid function

Author

Benjamin H. Mullin, Jennie Hui, Pimphen Charoen, Dawn Muddyman, David Schlessinger, Scott Wilson, Peter N. Taylor, Tim D. Spector, Suzanne J. Brown, Silvia Naitza, Andrew D. Johnson, Eleonora Porcu, Nicholas J. Timpson, Shelby Chew, Vijay Panicker, Klaudia Walter, Wei Yuan, J. Brent Richards, Hou-Feng Zheng, Frank Dudbridge, J L Min, George Davey Smith, Jie Huang, Colin M. Dayan, Gonçalo R. Abecasis, Purdey J Campbell, Francesco Cucca, Gabriela L. Surdulescu, Michela Traglia, Hashem A. Shihab, Celia M. T. Greenwood, Jordana T. Bell, Ee Mun Lim, Daniela Toniolo, Shane A. McCarthy, Michael R. Barnes, Serena Sanna, Richard Durbin, Vincenzo Forgetta, John P. Walsh, Tom R. Gaunt, Petr Danecek, Caroline L Relton, John Beilby, Wolfram Woltersdorf, Elin Grundberg, Nicole Soranzo, Yasin Memari, Eleftheria Zeggini, and John R. B. Perry

Subjects
Computer science, Thyroid Gland, Thyrotropin, General Physics and Astronomy, computer.software_genre, Bioinformatics, General Biochemistry, Genetics and Molecular Biology, Cohort Studies, Humans, Typographical error, Genetic Association Studies, Whole genome sequencing, Multidisciplinary, business.industry, Genomics, General Chemistry, DNA Methylation, Synapsins, United Kingdom, Spelling, Thyroxine, 3',5'-Cyclic-AMP Phosphodiesterases, Artificial intelligence, Erratum, Thyroid function, business, computer, Natural language processing
Abstract

Normal thyroid function is essential for health, but its genetic architecture remains poorly understood. Here, for the heritable thyroid traits thyrotropin (TSH) and free thyroxine (FT4), we analyse whole-genome sequence data from the UK10K project (N=2,287). Using additional whole-genome sequence and deeply imputed data sets, we report meta-analysis results for common variants (MAF≥1%) associated with TSH and FT4 (N=16,335). For TSH, we identify a novel variant in SYN2 (MAF=23.5%, P=6.15 × 10(-9)) and a new independent variant in PDE8B (MAF=10.4%, P=5.94 × 10(-14)). For FT4, we report a low-frequency variant near B4GALT6/SLC25A52 (MAF=3.2%, P=1.27 × 10(-9)) tagging a rare TTR variant (MAF=0.4%, P=2.14 × 10(-11)). All common variants explain ≥20% of the variance in TSH and FT4. Analysis of rare variants (MAF1%) using sequence kernel association testing reveals a novel association with FT4 in NRG1. Our results demonstrate that increased coverage in whole-genome sequence association studies identifies novel variants associated with thyroid function.

Published
2015

125. Large-scale genomic analyses link reproductive aging to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair

Author

Lynne J. Hocking, Caterina Barbieri, Jenny Chang-Claude, David Karasik, Dieter Flesch-Janys, James F. Wilson, Mark S. Goldberg, Henry Voelzke, Archie Campbell, Stig E. Bojesen, David R. Weir, Ailith Pirie, Megan L. Grove, Melissa Wellons, Georg Homuth, Corrado Masciullo, Jennifer A. Brody, Hermann Brenner, Paolo Gasparini, Andrew D. Johnson, Patrick Neven, Graham G. Giles, Peter Kraft, André G. Uitterlinden, Wei Zheng, Alkes L. Price, Anja Rudolph, Arto Mannermaa, Nicholas G. Martin, Christopher A. Haiman, Massimo Mangino, Melissa C. Southey, Daniela Ruggiero, Toshiko Tanaka, Kathryn L. Lunetta, Julie E. Buring, John R. B. Perry, Robert Winqvist, Laufey Tryggvadottir, Angela Cox, Serena Sanna, Nicola Pirastu, Anna Jakubowska, Paul D.P. Pharoah, David J. Porteous, Dragana Vuckovic, Andrea D. Coviello, Giorgia Girotto, Sara Lindstroem, Patrick Sulem, Astrid Petersmann, Xin Li, Maartje J. Hooning, Lili Milani, Sven Bergmann, Marek Zygmunt, Javier Benitez, Vilmundur Gudnason, Fernando Rivadeneira, Volker Arndt, Marina Ciullo, Caroline Hayward, Sheila Ulivi, Janet E. Olson, Hoda Anton-Culver, Maria Kabisch, Sara Margolin, Vessela N. Kristensen, Patrick F. McArdle, Tanguy Corre, Nora Franceschini, Veli-Matti Kosma, Hiltrud Brauch, Roger L. Milne, Eric Boerwinkle, Matthias W. Beckmann, Charles Kooperberg, Qin Wang, Jessica D. Faul, Stephen J. Chanock, Alexander Teumer, Mark O. Goodarzi, Unnur Thorsteinsdottir, R Maegi, Paul M. Ridker, Antonis C. Antoniou, Ozren Polasek, Daniel F. Gudbjartsson, Barbara McKnight, Melissa E. Garcia, Manjeet K. Bolla, Alanna C. Morrison, Paolo Radice, Xiuqing Guo, Lude L. Franke, Michela Traglia, Marjanka K. Schmidt, Heli Nevanlinna, Teresa Nutile, Cinzia Sala, Pascal Guénel, Jennifer E. Huffman, Stephen T. Turner, Anna Murray, Carl Blomqvist, Margaux F. Keller, Samuel E. Jones, Montserrat Garcia-Closas, Ivana Kolcic, Anne B. Newman, Jan Lubinski, Albert Hofman, Isabel dos-Santos-Silva, Hilary K. Finucane, Anne Lise Børresen-Dale, Alexander P. Reiner, Tim D. Spector, Gonneke Willemsen, John D. Eicher, Douglas F. Easton, Claudia Langenberg, Anthony J. Swerdlow, Natalia Bogdanova, Alison M. Dunning, Giorgio Pistis, Tõnu Esko, Behrooz Z. Alizadeh, Martina Mueller-Nurasyid, Eleonora Porcu, Laura M. Yerges-Armstrong, Leslie J. Raffel, Laura Crisponi, Gonçalo R. Abecasis, Jerome I. Rotter, Yii-Der Ida Chen, Antonietta Robino, Katri Pylkaes, Ken K. Ong, Thibaud Boutin, Elinor J. Sawyer, Daniel I. Chasman, Brian E. Henderson, Frank B. Hu, Leslie Bernstein, Drakoulis Yannoukakos, Tamara B. Harris, Dorret I. Boomsma, Katherine S. Ruth, Jie Yao, Keith Humphreys, Jennifer A. Smith, Elisabeth Altmaier, Ulrike Peters, Doris Stoeckl, Eva Albrecht, Tatijana Zemunik, Jenny A. Visser, Minouk J. Schoemaker, Diego Vozzi, Thilo Doerk, J. Ross Chapman, Irene L. Andrulis, Joanne M. Murabito, Alan F. Wright, Lisette Stolk, Jonathan Marten, Alice M. Arnold, Paolo Peterlongo, Harry Campbell, Natalia Pervjakova, Jingmei Li, Jennifer Kriebel, Alicia Beeghly-Fadiel, Immaculata De Vivo, Jouke-Jan Hottenga, Kari Stefansson, Cornelia M. van Duijn, Brendan Bulik-Sullivan, Evelin Mihailov, Chunyan He, Joe Dennis, Nicholas J. Wareham, Yongmei Liu, Sharon L.R. Kardia, Lynda M. Rose, Felix R. Day, Georgia Chenevix-Trench, Albert V. Smith, David J. Hunter, Sandosh Padmanabhan, Christian Gieger, Konstantin Strauch, Igor Rudan, Jacques Simard, Jian'an Luan, Robert A. Scott, Kyriaki Michailidou, Bruce M. Psaty, Per Hall, Suzette J. Bielinski, Rita K. Schmutzler, Julian Peto, Ellen W. Demerath, Ursula M. Schick, Rossella Sorice, Wei Zhao, Børge G. Nordestgaard, Andres Metspalu, Jonine D. Figueroa, Julia A. Knight, Barbara Burwinkel, Thomas Bruening, Judith Manz, Anna González-Neira, Ilaria Gandin, Ian Tomlinson, Thérèse Truong, Kent D. Taylor, Amanda E. Toland, Deborah J. Thompson, Alfons Meindl, Caroline M. Seynaeve, Benjamin M. Neale, Fergus J. Couch, Mike A. Nalls, Ute Hamann, Kamila Czene, John L. Hopper, Bruce H. R. Wolffenbuttel, Grant W. Montgomery, Hatef Darabi, Daniela Toniolo, Jinyan Huang, Peter Devilee, Cathy E. Elks, David Schlessinger, Luigi Ferrucci, Frank Schmidt, Peter A. Fasching, Diether Lambrechts, Najaf Amin, Day, Felix R, Ruth, Katherine S, Thompson, Deborah J, Lunetta, Kathryn L, Pervjakova, Natalia, Chasman, Daniel I, Stolk, Lisette, Finucane, Hilary K, Sulem, Patrick, Bulik Sullivan, Brendan, Esko, Tõnu, Johnson, Andrew D, Elks, Cathy E, Franceschini, Nora, He, Chunyan, Altmaier, Elisabeth, Brody, Jennifer A, Franke, Lude L, Huffman, Jennifer E, Keller, Margaux F, Mcardle, Patrick F, Nutile, Teresa, Porcu, Eleonora, Robino, Antonietta, Rose, Lynda M, Schick, Ursula M, Smith, Jennifer A, Teumer, Alexander, Traglia, Michela, Vuckovic, Dragana, Yao, Jie, Zhao, Wei, Albrecht, Eva, Amin, Najaf, Corre, Tanguy, Hottenga, Jouke Jan, Mangino, Massimo, Smith, Albert V, Tanaka, Toshiko, Abecasis, Gonçalo R, Andrulis, Irene L, Anton Culver, Hoda, Antoniou, Antonis C, Arndt, Volker, Arnold, Alice M, Barbieri, CATERINA MARIA, Beckmann, Matthias W, Beeghly Fadiel, Alicia, Benitez, Javier, Bernstein, Leslie, Bielinski, Suzette J, Blomqvist, Carl, Boerwinkle, Eric, Bogdanova, Natalia V, Bojesen, Stig E, Bolla, Manjeet K, Borresen Dale, Anne Lise, Boutin, Thibaud S, Brauch, Hiltrud, Brenner, Hermann, Brüning, Thoma, Burwinkel, Barbara, Campbell, Archie, Campbell, Harry, Chanock, Stephen J, Chapman, J. Ro, Chen, Yii Der Ida, Chenevix Trench, Georgia, Couch, Fergus J, Coviello, Andrea D, Cox, Angela, Czene, Kamila, Darabi, Hatef, De Vivo, Immaculata, Demerath, Ellen W, Dennis, Joe, Devilee, Peter, Dörk, Thilo, Dos Santos Silva, Isabel, Dunning, Alison M, Eicher, John D, Fasching, Peter A, Faul, Jessica D, Figueroa, Jonine, Flesch Janys, Dieter, Gandin, Ilaria, Garcia, Melissa E, García Closas, Montserrat, Giles, Graham G, Girotto, Giorgia, Goldberg, Mark S, González Neira, Anna, Goodarzi, Mark O, Grove, Megan L, Gudbjartsson, Daniel F, Guénel, Pascal, Guo, Xiuqing, Haiman, Christopher A, Hall, Per, Hamann, Ute, Henderson, Brian E, Hocking, Lynne J, Hofman, Albert, Homuth, Georg, Hooning, Maartje J, Hopper, John L, Hu, Frank B, Huang, Jinyan, Humphreys, Keith, Hunter, David J, Jakubowska, Anna, Jones, Samuel E, Kabisch, Maria, Karasik, David, Knight, Julia A, Kolcic, Ivana, Kooperberg, Charle, Kosma, Veli Matti, Kriebel, Jennifer, Kristensen, Vessela, Lambrechts, Diether, Langenberg, Claudia, Li, Jingmei, Li, Xin, Lindström, Sara, Liu, Yongmei, Luan, Jian'An, Lubinski, Jan, Mägi, Reedik, Mannermaa, Arto, Manz, Judith, Margolin, Sara, Marten, Jonathan, Martin, Nicholas G, Masciullo, Corrado, Meindl, Alfon, Michailidou, Kyriaki, Mihailov, Evelin, Milani, Lili, Milne, Roger L, Müller Nurasyid, Martina, Nalls, Michael, Neale, Benjamin M, Nevanlinna, Heli, Neven, Patrick, Newman, Anne B, Nordestgaard, Børge G, Olson, Janet E, Padmanabhan, Sandosh, Peterlongo, Paolo, Peters, Ulrike, Petersmann, Astrid, Peto, Julian, Pharoah, Paul D. P, Pirastu, Nicola, Pirie, Ailith, Pistis, Giorgio, Polasek, Ozren, Porteous, David, Psaty, Bruce M, Pylkäs, Katri, Radice, Paolo, Raffel, Leslie J, Rivadeneira, Fernando, Rudan, Igor, Rudolph, Anja, Ruggiero, Daniela, Sala, Cinzia F, Sanna, Serena, Sawyer, Elinor J, Schlessinger, David, Schmidt, Marjanka K, Schmidt, Frank, Schmutzler, Rita K, Schoemaker, Minouk J, Scott, Robert A, Seynaeve, Caroline M, Simard, Jacque, Sorice, Rossella, Southey, Melissa C, Stöckl, Dori, Strauch, Konstantin, Swerdlow, Anthony, Taylor, Kent D, Thorsteinsdottir, Unnur, Toland, Amanda E, Tomlinson, Ian, Truong, Thérèse, Tryggvadottir, Laufey, Turner, Stephen T, Vozzi, Diego, Wang, Qin, Wellons, Melissa, Willemsen, Gonneke, Wilson, James F, Winqvist, Robert, Wolffenbuttel, Bruce B. H. R, Wright, Alan F, Yannoukakos, Drakouli, Zemunik, Tatijana, Zheng, Wei, Zygmunt, Marek, Bergmann, Sven, Boomsma, Dorret I, Buring, Julie E, Ferrucci, Luigi, Montgomery, Grant W, Gudnason, Vilmundur, Spector, Tim D, van Duijn, Cornelia M, Alizadeh, Behrooz Z, Ciullo, Marina, Crisponi, Laura, Easton, Douglas F, Gasparini, Paolo, Gieger, Christian, Harris, Tamara B, Hayward, Caroline, Kardia, Sharon L. R, Kraft, Peter, Mcknight, Barbara, Metspalu, Andre, Morrison, Alanna C, Reiner, Alex P, Ridker, Paul M, Rotter, Jerome I, Toniolo, Daniela, Uitterlinden, André G, Ulivi, Sheila, Völzke, Henry, Wareham, Nicholas J, Weir, David R, Yerges Armstrong, Laura M, Price, Alkes L, Stefansson, Kari, Visser, Jenny A, Ong, Ken K, Chang Claude, Jenny, Murabito, Joanne M, Perry, John R. B, Murray, Anna, Internal Medicine, Epidemiology, Medical Oncology, Clinical Genetics, Biological Psychology, Neuroscience Campus Amsterdam - Neurobiology of Mental Health, EMGO+ - Lifestyle, Overweight and Diabetes, PRACTICAL Consortium, kConFab Investigators, AOCS Investigators, EPIC-InterAct Consortium, LifeLines Cohort Study, Generation, Scotland, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Lifestyle Medicine (LM), Life Course Epidemiology (LCE), Center for Liver, Digestive and Metabolic Diseases (CLDM), Stem Cell Aging Leukemia and Lymphoma (SALL), and Real World Studies in PharmacoEpidemiology, -Genetics, -Economics and -Therapy (PEGET)

Subjects
Netherlands Twin Register (NTR), Aging, DNA Repair, LOCI, Genome-wide association study, BLOOD-PRESSURE, Disease, CHROMOSOMAL INSTABILITY, Bioinformatics, HOMOLOGOUS RECOMBINATION, PREMATURE OVARIAN FAILURE, Genotype, BRCA2 MUTATION CARRIERS, WIDE ASSOCIATION, Gene Regulatory Networks, NATURAL MENOPAUSE, Genetics, education.field_of_study, menopause, DDR, BODY-MASS INDEX, CELL-TYPES, BRCA1 Protein, Reproduction, BRCA1-mediated DNA repair, Age Factors, Obstetrics and Gynecology, General Medicine, Genomics, Middle Aged, 3. Good health, Menopause, Phenotype, Female, medicine.symptom, Signal Transduction, Delayed puberty, Adult, DNA repair, Population, Hypothalamus, Single-nucleotide polymorphism, Breast Neoplasms, Biology, Lower risk, DDR, Article, Breast cancer, SDG 3 - Good Health and Well-being, Mendelian randomization, medicine, Humans, Genetic Predisposition to Disease, Allele, education, Genetic association, Models, Genetic, business.industry, Genetic Variation, medicine.disease, Aging/genetics, BRCA1 Protein/genetics, Breast Neoplasms/genetics, Gene Regulatory Networks/genetics, Genetic Predisposition to Disease/genetics, Genome-Wide Association Study/methods, Genomics/methods, Hypothalamus/metabolism, Menopause/genetics, Reproduction/genetics, Signal Transduction/genetics, business, Genome-Wide Association Study
Abstract

Menopause timing has a major impact on infertility and risk of disease. Younger age at natural (nonsurgical) menopause (ANM) is associated with a higher risk of osteoporosis, cardiovascular disease, and type 2 diabetes and a lower risk of breast cancer. Late menopause is associated with a higher risk of breast cancer. It is well known that the age at which women go through menopause is partly determined by genes, but the underlying mechanisms are poorly understood. Genome-wide association studies have identified 18 common genetic variants associated with ANM. These variants explain less than 5% of the variation in ANM compared with the 21% explained by all common variants on genome-wide association study arrays. This genome-wide association study was the collaborative effort of researchers from 177 institutions worldwide. The study was designed to investigate genetic variants associated with timing of menopause among a population of approximately 70,000 women of European ancestry. A dual strategy was used to identify both common and, for the first time, low-frequency coding variants associated with ANM. The causal relationship between ANM and breast cancer was investigated using a Mendelian randomization approach. Combined analysis identified 1208 single-nucleotide polymorphisms (SNPs) of a total of approximately 2.6 million that reached the genome-wide significance threshold for association with ANM. Forty-four regions with common variants were identified; among these 44 loci were 2 rare low-frequency missense alleles of large effect. A majority of ANM SNPs were enriched in DNA damage response (DDR) genes, including the first common coding variant in BRCA1 associated with any complex trait. Mendelian randomization analyses supported a causal relationship between delayed ANM and breast cancer risk; there was approximately 6% increase in risk per year; P = 3 × 10-14); increased risk with delayed menopause appeared to be mediated primarily by prolonged sex hormone exposure in a woman’s lifetime, not DDR mechanisms. This is the first study to confirm the link between early and late menopause and breast cancer risk using genetic information. Age at natural menopause genetic variants influence breast cancer risk primarily through variation in menopause timing. Although carrying higher numbers of ANM-increasing variants and enrichment in DDR genes are associated with a modest increase in breast cancer risk, the major mechanism for increased risk appears to be prolonged estrogen and/or progesterone exposure due to delayed menopause.

Published
2015

126. Genetic Regulation of Puberty Timing in Humans

Author

Felix R. Day, Ken K. Ong, John R. B. Perry, Day, Felix [0000-0003-3789-7651], Perry, John [0000-0001-6483-3771], Ong, Kenneth [0000-0003-4689-7530], and Apollo - University of Cambridge Repository

Subjects
medicine.medical_specialty, Imprinted genes, Endocrinology, Diabetes and Metabolism, Population, Biology, Article, Cellular and Molecular Neuroscience, Endocrinology, Internal medicine, Human biology, medicine, Genetics, Obesity, Allele, education, Body mass index, Genetic association, Menarche, education.field_of_study, Reproductive function, Endocrine and Autonomic Systems, Puberty, medicine.disease
Abstract

Understanding the regulation of puberty timing has relevance to developmental and human biology and to the pathogenesis of various diseases. Recent large-scale genome-wide association studies on puberty timing and adult height, body mass index (BMI) and central body shape provide evidence for shared biological mechanisms that regulate these traits. There is a substantial genetic overlap between age at menarche in women and BMI, with almost invariable directional consistency with the epidemiological associations between earlier menarche and higher BMI. By contrast, the genetic loci identified for age at menarche are largely distinct from those identified for central body shape, while alleles that confer earlier menarche can be associated with taller or shorter adult height. The findings of population-based studies on age at menarche show increasing relevance for other studies of rare monogenic disorders and enrich our understanding of the mechanisms that regulate the timing of puberty and reproductive function.

Published
2015

127. Rare coding variants and X-linked loci associated with age at menarche

Author

Kathryn L. Lunetta, Felix R. Day, Patrick Sulem, Katherine S. Ruth, Joyce Y. Tung, David A. Hinds, Tõnu Esko, Cathy E. Elks, Elisabeth Altmaier, Chunyan He, Jennifer E. Huffman, Evelin Mihailov, Eleonora Porcu, Antonietta Robino, Lynda M. Rose, Ursula M. Schick, Lisette Stolk, Alexander Teumer, Deborah J. Thompson, Michela Traglia, Carol A. Wang, Laura M. Yerges-Armstrong, Antonis C. Antoniou, Caterina Barbieri, Andrea D. Coviello, Francesco Cucca, Ellen W. Demerath, Alison M. Dunning, Ilaria Gandin, Megan L. Grove, Daniel F. Gudbjartsson, Lynne J. Hocking, Albert Hofman, Jinyan Huang, Rebecca D. Jackson, David Karasik, Jennifer Kriebel, Ethan M. Lange, Leslie A. Lange, Claudia Langenberg, Xin Li, Jian'an Luan, Reedik Mägi, Alanna C. Morrison, Sandosh Padmanabhan, Ailith Pirie, Ozren Polasek, David Porteous, Alex P. Reiner, Fernando Rivadeneira, Igor Rudan, Cinzia F. Sala, David Schlessinger, Robert A. Scott, Doris Stöckl, Jenny A. Visser, Uwe Völker, Diego Vozzi, James G. Wilson, Marek Zygmunt, Nita G. Forouhi, Nicola D. Kerrison, Stephen J. Sharp, Matt Sims, Inês Barroso, Panos Deloukas, Mark I. McCarthy, Larraitz Arriola, Beverley Balkau, Aurelio Barricarte, Heiner Boeing, Paul W. Franks, Carlos Gonzalez, Sara Grioni, Rudolf Kaaks, Timothy J. Key, Carmen Navarro, Peter M. Nilsson, Kim Overvad, Domenico Palli, Salvatore Panico, J Ramón Quirós, Olov Rolandsson, Carlotta Sacerdote, María‐José Sánchez, Nadia Slimani, Anne Tjonneland, Rosario Tumino, Daphne L. van der A, Yvonne T. van der Schouw, Elio Riboli, Blair H. Smith, Archie Campbell, Ian J. Deary, Andrew M. McIntosh, Eric Boerwinkle, Julie E. Buring, Laura Crisponi, Douglas F. Easton, Caroline Hayward, Frank B. Hu, Simin Liu, Andres Metspalu, Craig E. Pennell, Paul M. Ridker, Konstantin Strauch, Elizabeth A. Streeten, Daniela Toniolo, André G. Uitterlinden, Sheila Ulivi, Henry Völzke, Nicholas J. Wareham, Melissa Wellons, Nora Franceschini, Daniel I. Chasman, Unnur Thorsteinsdottir, Anna Murray, Kari Stefansson, Joanne M. Murabito, Ken K. Ong, John R. B. Perry

Published
2015
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128. Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index

Author

Jian Yang, Lili Milani, Andrew Bakshi, Harold Snieder, Nancy L. Pedersen, Matthew C. Keller, Gibran Hemani, Patrik K. E. Magnusson, Sang Hong Lee, John R. B. Perry, Ilja M. Nolte, Anders Hamsten, Peter M. Visscher, Naomi R. Wray, Erik Ingelsson, Michael E. Goddard, Nicole Soranzo, Matthew R. Robinson, Anna A. E. Vinkhuyzen, Andres Metspalu, Zhihong Zhu, Tõnu Esko, Jana V. van Vliet-Ostaptchouk, Reedik Mägi, Yang, Jian, Bakshi, Andrew, Zhu, Zhihong, Hemani, Gibran, Lee, Sang Hong, Visscher, Peter M, LifeLines Cohort Study, Life Course Epidemiology (LCE), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), and Center for Liver, Digestive and Metabolic Diseases (CLDM)

Subjects
COMPLEX DISEASES, LOCI, Genome-wide association study, Biology, heritability, Genetic correlation, Article, Body Mass Index, COMMON SNPS, Missing heritability problem, Statistics, Genetics, Humans, GWAS, Human height, GENOME-WIDE ASSOCIATION, 2. Zero hunger, PROPORTION, Genetics & Heredity, ARCHITECTURE, phenotypic variance, SNP arrays, Genome, Human, Genetic Variation, Heritability, Body Height, TRAIT, Standard error, GENOTYPE-IMPUTATION, whole-genome sequencing, genome-wide association studies, Body mass index, Imputation (genetics)
Abstract

We propose a method (GREML-LDMS) to estimate heritability for human complex traits in unrelated individuals using whole-genome sequencing data. We demonstrate using simulations based on whole-genome sequencing data that similar to 97% and similar to 68% of variation at common and rare variants, respectively, can be captured by imputation. Using the GREML-LDMS method, we estimate from 44,126 unrelated individuals that all similar to 17 million imputed variants explain 56% (standard error (s.e.) = 2.3%) of variance for height and 27% (s.e. = 2.5%) of variance for body mass index (BMI), and we find evidence that height- and BMI-associated variants have been under natural selection. Considering the imperfect tagging of imputation and potential overestimation of heritability from previous family-based studies, heritability is likely to be 60-70% for height and 30-40% for BMI. Therefore, the missing heritability is small for both traits. For further discovery of genes associated with complex traits, a study design with SNP arrays followed by imputation is more cost-effective than whole-genome sequencing at current prices. Refereed/Peer-reviewed

Published
2015
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129. Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways

Author

Sophie H. Van Wingerden, Wei V. Zhuang, Mladen Boban, John R. B. Perry, Joop S.E. Laven, Shah Ebrahim, Andrea D. Coviello, Barbara McKnight, Laura Crisponi, Sharon L.R. Kardia, Daniel I. Chasman, Lorna M. Lopez, George Dedoussis, Stefania Bandinelli, Nora Franceschini, Florian Ernst, A. Cecile J.W. Janssens, Yvonne T. van der Schouw, Henri Wallaschofski, Jari Lahti, Triin Laisk, Elizabeth A. Streeten, Joanne M. Murabito, Liana Ferreli, Harold Snieder, Dale R. Nyholt, Lenore J. Launer, Panagiotis Deloukas, Melissa E. Garcia, Eco J. C. de Geus, H.-Erich Wichmann, John M. Starr, Eva Albrecht, Paul M. Ridker, N. Charlotte Onland-Moret, Petra H.M. Peeters, Massimo Mangino, Jacques S. Beckmann, Stephen J. Chanock, Grant W. Montgomery, Julie E. Buring, Barbara Thorand, Diederick E. Grobbee, Irena Martinović Klarić, Constance Chen, So-Youn Shin, Ozren Polasek, Daniel F. Gudbjartsson, Patrick Sulem, Carla H. van Gils, Eleonora Porcu, Cinzia Sala, Tim D. Spector, Alexander N. Parker, Ellen W. Demerath, Guillaume Paré, Krista Fischer, Simon N. Stacey, Mara Marongiu, Lina Zgaga, Jouke-Jan Hottenga, Unnur Styrkarsdottir, Debbie A Lawlor, Douglas P. Kiel, Guangju Zhai, Kari Stefansson, Lisette Stolk, Igor Rudan, David Schlessinger, Katri R Currency Signikkönen, Z. Kutalik, Ian J. Deary, Frank J.M. Broekmans, Ulf de Faire, Vincent Mooser, Luigi Ferrucci, Maria G. Stathopoulou, Pio D'Adamo, Marek Zygmunt, Linda Broer, James F. Wilson, Lovorka Barać Lauc, Angelo Scuteri, Patrik K. E. Magnusson, Frank B. Hu, Jennifer A. Smith, Toomas Haller, Giorgio Pistis, Colette J M Wijnands-van Gent, Emil Rehnberg, Marlies Voorhuis, Anna Murray, David Melzer, Chunyan He, Tamara B. Harris, Merli Hass, Patrick F. McArdle, Valur Emilsson, Gérard Waeber, Manuela Uda, Nancy L. Pedersen, Jenny A. Visser, Behrooz Z. Alizadeh, Andres Salumets, Andrew D. Johnson, Gonneke Willemsen, Sheila Ulivi, Tmu Esko, Vilmundur Gudnason, Bart C.J.M. Fauser, Maja Barbalić, Henry Völzke, Ronald P. Stolk, Aarno Palotie, Peter Van Nierop, Thor Aspelund, Elisabeth Widen, Caroline Hayward, Johan G. Eriksson, Alan F. Wright, Marilyn C. Cornelis, Tanguy Corre, Eric Boerwinkle, Ben A. Oostra, Alice M. Arnold, Kathleen Stirrups, Yvonne V. Louwers, M. Carola Zillikens, Anne B. Newman, Jerome I. Rotter, Jianjun Liu, Per Hall, Aaron R. Folsom, David Karasik, Yan V. Sun, Albert Hofman, Gudny Eiriksdottir, Andrew B. Singleton, Victor J M Pop, Pau Navarro, Tatijana Zemunik, Andres Metspalu, Andrew S. Plump, Cornelia M. van Duijn, Dorret I. Boomsma, Harry Campbell, Nicole Soranzo, Bruce M. Psaty, Enda M. Byrne, Christian Gieger, Albert Tenesa, Nicholas G. Martin, Unnur Thorsteinsdottir, Kathryn L. Lunetta, Laufey Tryggvadottir, Serena Sanna, Kim Tsui, Ivana Kolcic, Laura M. Yerges-Armstrong, Jacqueline M. Vink, Bruce H. R. Wolffenbuttel, Daniela Toniolo, Peter M. Visscher, Rob M. van Dam, Erik Ingelsson, Sandra Lai, Corrado Masciullo, Albert V. Smith, Paolo Gasparini, Sarah E. Medland, Nicole L. Glazer, Peter Kraft, André G. Uitterlinden, David J. Hunter, Andrea Burri, Jules J. Keyzer, Susan E. Hankinson, Gail Davies, Andrew C. Heath, Biological Psychology, EMGO+ - Mental Health, Internal Medicine, Epidemiology, Obstetrics & Gynecology, Surgery, Hematology, Clinical Genetics, Study T.L., Lisette, Stolk, John R. B., Perry, Daniel I., Chasman, Chunyan, He, Massimo, Mangino, Patrick, Sulem, Maja, Barbalic, Linda, Broer, Enda M., Byrne, Florian, Ernst, Tõnu, Esko, Nora, Franceschini, Daniel F., Gudbjartsson, Jouke Jan, Hottenga, Peter, Kraft, Patrick F., Mcardle, Eleonora, Porcu, So Youn, Shin, Albert V., Smith, Sophie van, Wingerden, Guangju, Zhai, Wei V., Zhuang, Eva, Albrecht, Behrooz Z., Alizadeh, Thor, Aspelund, Stefania, Bandinelli, Lovorka Barac, Lauc, Jacques S., Beckmann, Mladen, Boban, Eric, Boerwinkle, Frank J., Broekman, Andrea, Burri, Harry, Campbell, Stephen J., Chanock, Constance, Chen, Marilyn C., Corneli, Tanguy, Corre, Andrea D., Coviello, D'Adamo, ADAMO PIO, Gail, Davie, Ulf de, Faire, Eco J. C., de Geu, Ian J., Deary, George V. Z., Dedoussi, Panagiotis, Delouka, Shah, Ebrahim, Gudny, Eiriksdottir, Valur, Emilsson, Johan G., Eriksson, Bart C. J. M., Fauser, Liana, Ferreli, Luigi, Ferrucci, Krista, Fischer, Aaron R., Folsom, Melissa E., Garcia, Gasparini, Paolo, Christian, Gieger, Nicole, Glazer, Diederick E., Grobbee, Per, Hall, Toomas, Haller, Susan E., Hankinson, Merli, Ha, Caroline, Hayward, Andrew C., Heath, Albert, Hofman, Erik, Ingelsson, A. Cecile J. W., Janssen, Andrew D., Johnson, David, Karasik, Sharon L. R., Kardia, Jules, Keyzer, Douglas P., Kiel, Ivana, Kolcic, Zoltán, Kutalik, Jari, Lahti, Sandra, Lai, Triin, Laisk, Joop S. E., Laven, Debbie A., Lawlor, Jianjun, Liu, Lorna M., Lopez, Yvonne V., Louwer, Patrik K. E., Magnusson, Mara, Marongiu, Nicholas G., Martin, Irena Martinovic, Klaric, Corrado, Masciullo, Barbara, Mcknight, Sarah E., Medland, David, Melzer, Vincent, Mooser, Pau, Navarro, Anne B., Newman, Dale R., Nyholt, N., Charlotte Onland Moret, Aarno, Palotie, Guillaume, Paré, Alex N., Parker, Nancy L., Pedersen, Petra H. M., Peeter, Giorgio, Pisti, Andrew S., Plump, Ozren, Polasek, Victor J. M., Pop, Bruce M., Psaty, Katri, Räikkönen, Emil, Rehnberg, Jerome I., Rotter, Igor, Rudan, Cinzia, Sala, Andres, Salumet, Angelo, Scuteri, Andrew, Singleton, Jennifer A., Smith, Harold, Snieder, Nicole, Soranzo, Simon N., Stacey, John M., Starr, Maria G., Stathopoulou, Kathleen, Stirrup, Ronald P., Stolk, Unnur, Styrkarsdottir, Yan V., Sun, Albert, Tenesa, Barbara, Thorand, Daniela, Toniolo, Laufey, Tryggvadottir, Kim, Tsui, Sheila, Ulivi, Rob M., van Dam, Yvonne T., van der Schouw, Carla H., van Gil, Peter van, Nierop, Jacqueline M., Vink, Peter M., Visscher, Marlies, Voorhui, Gérard, Waeber, Henri, Wallaschofski, H., Erich Wichmann, Elisabeth, Widen, Colette J. M., Wijnands van Gent, Gonneke, Willemsen, James F., Wilson, Bruce H. R., Wolffenbuttel, Alan F., Wright, Laura M., Yerges Armstrong, Tatijana, Zemunik, Lina, Zgaga, M., Carola Zilliken, Marek, Zygmunt, The LifeLines Cohort, Study, Alice M., Arnold, Dorret I., Boomsma, Julie E., Buring, Laura, Crisponi, Ellen W., Demerath, Vilmundur, Gudnason, Tamara B., Harri, Frank B., Hu, David J., Hunter, Lenore J., Launer, Andres, Metspalu, Grant W., Montgomery, Ben A., Oostra, Paul M., Ridker, Serena, Sanna, David, Schlessinger, Tim D., Spector, Kari, Stefansson, Elizabeth A., Streeten, Unnur, Thorsteinsdottir, Manuela, Uda, André G., Uitterlinden, Cornelia M., van Duijn, Henry, Völzke, Anna, Murray, Joanne M., Murabito, Jenny A., Visser, Kathryn L., Lunetta, Faculteit Medische Wetenschappen/UMCG, Life Course Epidemiology (LCE), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Lifestyle Medicine (LM), and Center for Liver, Digestive and Metabolic Diseases (CLDM)

Subjects
Netherlands Twin Register (NTR), Candidate gene, Menopause, dna repair, DNA Repair, PROTEIN, Genome-wide association study, DNA-Directed DNA Polymerase, medicine.disease_cause, Bioinformatics, DISEASE, PREMATURE OVARIAN FAILURE, 0302 clinical medicine, NATURAL MENOPAUSE, MUTATION, GENE-EXPRESSION, Genetics, 0303 health sciences, Mutation, 030219 obstetrics & reproductive medicine, Age Factors, 3. Good health, Premature ovarian failure, DNA Polymerase gamma, menopause, loci, genetics, Female, DNA repair, DNA Primase, Biology, Polymorphism, Single Nucleotide, White People, Article, 03 medical and health sciences, FOLLICLE-STIMULATING-HORMONEPREMATURE OVARIAN FAILUREGENOME-WIDE ASSOCIATIONGENE-EXPRESSIONONSETPOLYMORPHISMSMUTATIONHERITABILITYCHROMOSOMEMENARCHE, medicine, Humans, GENOME-WIDE ASSOCIATION, Gene, POLYMORPHISMS, 030304 developmental biology, Genetic association, DNA Helicases, Immunity, Proteins, medicine.disease, FOLLICLE-STIMULATING-HORMONE, DNA Repair Enzymes, Exodeoxyribonucleases, Genetic Loci, ONSET, Genome-Wide Association Study
Abstract

To newly identify loci for age at natural menopause, we carried out a meta-analysis of 22 genome-wide association studies (GWAS) in 38,968 women of European descent, with replication in up to 14,435 women. In addition to four known loci, we identified 13 loci newly associated with age at natural menopause (at P < 5 - 10 g8). Candidate genes located at these newly associated loci include genes implicated in DNA repair (EXO1, HELQ, UIMC1, FAM175A, FANCI, TLK1, POLG and PRIM1) and immune function (IL11, NLRP11 and PRRC2A (also known as BAT2)). Gene-set enrichment pathway analyses using the full GWAS data set identified exoDNase, NF-I °B signaling and mitochondrial dysfunction as biological processes related to timing of menopause. © 2012 Nature America, Inc. All rights reserved.

Published
2012

130. A Robust Example of Collider Bias in a Genetic Association Study

Author

Po-Ru Loh, Ken K. Ong, Robert A. Scott, Felix R. Day, and John R. B. Perry

Subjects
0301 basic medicine, Genetics, Models, Genetic, Association (object-oriented programming), Genetic Variation, Genome-wide association study, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Quantitative Trait, Heritable, Evolutionary biology, Genetic variation, Covariate, Humans, Genetics(clinical), Psychology, Letters to the Editor, 030217 neurology & neurosurgery, Genetics (clinical), Genetic association, Genome-Wide Association Study
Abstract

To the Editor: “Collider bias” (also referred to as the “reversal paradox”)1 describes the artificial association created between two exposures (A and B) when a shared outcome (X) is included in the model as a covariate (Figure 1). A recent paper by Aschard et al. described the potential for collider bias when adjusting for heritable covariates in genetic association studies.2 However, in their examples, the authors acknowledged that they could not exclude the possibility of a true biological explanation for the genetic association seen only in the adjusted model.

Published
2016
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131. Identifying genetic variants that affect viability in large cohorts

Author

Molly Przeworski, John R. B. Perry, Tomaz Berisa, Hakhamanesh Mostafavi, Joseph K. Pickrell, Felix R. Day, Day, Felix [0000-0003-3789-7651], Perry, John [0000-0001-6483-3771], and Apollo - University of Cambridge Repository

Subjects
Male, 0301 basic medicine, Heredity, Physiology, Epidemiology, Vascular Medicine, Cohort Studies, Families, Fathers, Endocrinology, 0302 clinical medicine, Gene Frequency, APOE*4 Allele, Medicine and Health Sciences, Coronary Heart Disease, Biology (General), Genetics, 2. Zero hunger, 0303 health sciences, Natural selection, General Neuroscience, Biobank, 3. Good health, Genetic Mapping, Genetic Epidemiology, Cohort, Female, General Agricultural and Biological Sciences, Research Article, Common disease-common variant, QH301-705.5, Cardiology, Mothers, Variant Genotypes, Single-nucleotide polymorphism, Biology, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, 03 medical and health sciences, Genetic variation, Humans, Selection, Genetic, Allele, Allele frequency, Alleles, 030304 developmental biology, Endocrine Physiology, Models, Genetic, General Immunology and Microbiology, Human evolutionary genetics, Puberty, Biology and Life Sciences, Genetic Variation, Genetic architecture, Genetics, Population, 030104 developmental biology, Genetic epidemiology, Genetic Loci, People and Places, Population Groupings, Genetic Fitness, 030217 neurology & neurosurgery, Demography
Abstract

A number of open questions in human evolutionary genetics would become tractable if we were able to directly measure evolutionary fitness. As a step towards this goal, we developed a method to examine whether individual genetic variants, or sets of genetic variants, currently influence viability. The approach consists in testing whether the frequency of an allele varies across ages, accounting for variation in ancestry. We applied it to the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort and to the parents of participants in the UK Biobank. Across the genome, we found only a few common variants with large effects on age-specific mortality: tagging the APOE ε4 allele and near CHRNA3. These results suggest that when large, even late-onset effects are kept at low frequency by purifying selection. Testing viability effects of sets of genetic variants that jointly influence 1 of 42 traits, we detected a number of strong signals. In participants of the UK Biobank of British ancestry, we found that variants that delay puberty timing are associated with a longer parental life span (P~6.2 × 10−6 for fathers and P~2.0 × 10−3 for mothers), consistent with epidemiological studies. Similarly, variants associated with later age at first birth are associated with a longer maternal life span (P~1.4 × 10−3). Signals are also observed for variants influencing cholesterol levels, risk of coronary artery disease (CAD), body mass index, as well as risk of asthma. These signals exhibit consistent effects in the GERA cohort and among participants of the UK Biobank of non-British ancestry. We also found marked differences between males and females, most notably at the CHRNA3 locus, and variants associated with risk of CAD and cholesterol levels. Beyond our findings, the analysis serves as a proof of principle for how upcoming biomedical data sets can be used to learn about selection effects in contemporary humans., Author summary Our global understanding of adaptation in humans is limited to indirect statistical inferences from patterns of genetic variation, which are sensitive to past selection pressures. We introduced a method that allowed us to directly observe ongoing selection in humans by identifying genetic variants that affect survival to a given age (i.e., viability selection). We applied our approach to the GERA cohort and parents of the UK Biobank participants. We found viability effects of variants near the APOE and CHRNA3 genes, which are associated with the risk of Alzheimer disease and smoking behavior, respectively. We also tested for the joint effect of sets of genetic variants that influence quantitative traits. We uncovered an association between longer life span and genetic variants that delay puberty timing and age at first birth. We also detected detrimental effects of higher genetically predicted cholesterol levels, body mass index, risk of coronary artery disease (CAD), and risk of asthma on survival. Some of the observed effects differ between males and females, most notably those at the CHRNA3 gene and variants associated with risk of CAD and cholesterol levels. Beyond this application, our analysis shows how large biomedical data sets can be used to study natural selection in humans.

Published
2017

132. Associations between Potentially Modifiable Risk Factors and Alzheimer Disease: A Mendelian Randomization Study

Author

Søren D, Østergaard, Shubhabrata, Mukherjee, Stephen J, Sharp, Petroula, Proitsi, Luca A, Lotta, Felix, Day, John R B, Perry, Kevin L, Boehme, Stefan, Walter, John S, Kauwe, Laura E, Gibbons, Eric B, Larson, John F, Powell, Claudia, Langenberg, Paul K, Crane, and Nicholas J, Wareham

Subjects
Male, Alzheimer Disease, Risk Factors, Humans, Female, Genetic Predisposition to Disease, Mendelian Randomization Analysis, Polymorphism, Single Nucleotide, Research Article
Abstract

Background Potentially modifiable risk factors including obesity, diabetes, hypertension, and smoking are associated with Alzheimer disease (AD) and represent promising targets for intervention. However, the causality of these associations is unclear. We sought to assess the causal nature of these associations using Mendelian randomization (MR). Methods and Findings We used SNPs associated with each risk factor as instrumental variables in MR analyses. We considered type 2 diabetes (T2D, N SNPs = 49), fasting glucose (N SNPs = 36), insulin resistance (N SNPs = 10), body mass index (BMI, N SNPs = 32), total cholesterol (N SNPs = 73), HDL-cholesterol (N SNPs = 71), LDL-cholesterol (N SNPs = 57), triglycerides (N SNPs = 39), systolic blood pressure (SBP, N SNPs = 24), smoking initiation (N SNPs = 1), smoking quantity (N SNPs = 3), university completion (N SNPs = 2), and years of education (N SNPs = 1). We calculated MR estimates of associations between each exposure and AD risk using an inverse-variance weighted approach, with summary statistics of SNP–AD associations from the International Genomics of Alzheimer’s Project, comprising a total of 17,008 individuals with AD and 37,154 cognitively normal elderly controls. We found that genetically predicted higher SBP was associated with lower AD risk (odds ratio [OR] per standard deviation [15.4 mm Hg] of SBP [95% CI]: 0.75 [0.62–0.91]; p = 3.4 × 10−3). Genetically predicted higher SBP was also associated with a higher probability of taking antihypertensive medication (p = 6.7 × 10−8). Genetically predicted smoking quantity was associated with lower AD risk (OR per ten cigarettes per day [95% CI]: 0.67 [0.51–0.89]; p = 6.5 × 10−3), although we were unable to stratify by smoking history; genetically predicted smoking initiation was not associated with AD risk (OR = 0.70 [0.37, 1.33]; p = 0.28). We saw no evidence of causal associations between glycemic traits, T2D, BMI, or educational attainment and risk of AD (all p > 0.1). Potential limitations of this study include the small proportion of intermediate trait variance explained by genetic variants and other implicit limitations of MR analyses. Conclusions Inherited lifetime exposure to higher SBP is associated with lower AD risk. These findings suggest that higher blood pressure—or some environmental exposure associated with higher blood pressure, such as use of antihypertensive medications—may reduce AD risk., Robert A. Scott and colleagues use genetic instruments to identify causal associations between known risk factors and Alzheimer's disease., Editors' Summary Background Worldwide, about 44 million people have dementia, a group of brain degeneration disorders characterized by an irreversible decline in memory, communication, and other “cognitive” functions. Dementia mainly affects older people, and because people are living longer, experts estimate that more than 135 million people will have dementia by 2050. The most common form of dementia, which accounts for 60%–70% of cases, is Alzheimer disease (AD). The earliest sign of AD is often increasing forgetfulness. As the disease progresses, affected individuals gradually lose the ability to look after themselves, they may become anxious or aggressive, and they may have difficulty recognizing friends and relatives. People with late stage disease may lose control of their bladder and of other physical functions. At present, there is no cure for AD, although some of its symptoms can be managed with drugs. Most people with AD are initially cared for at home by relatives and other caregivers, but many affected individuals end their days in a care home or specialist nursing home. Why Was This Study Done? Researchers are interested in identifying risk factors for AD, particularly modifiable risk factors, because if such risk factors exist, it might be possible to limit the predicted increase in future AD cases. Epidemiological studies (investigations that examine patterns of disease in populations) have identified several potential risk factors for AD, including hypertension (high blood pressure), obesity, smoking, and dyslipidemia (changes in how the body handles fats). However, epidemiological studies cannot prove that a specific risk factor causes AD. For example, people with hypertension might share another characteristic that causes both hypertension and AD (confounding) or AD might cause hypertension (reverse causation). Information on causality is needed to decide which risk factors to target to help prevent AD. Here, the researchers use “Mendelian randomization” to examine whether differences in several epidemiologically identified risk factors for AD have a causal impact on AD risk. In Mendelian randomization, causal associations are inferred from the effects of genetic variants (which predict levels of modifiable risk factors) on the outcome of interest. Because gene variants are inherited randomly, they are not prone to confounding and are free from reverse causation. So, if hypertension actually causes AD, genetic variants that affect hypertension should be associated with an altered risk of AD. What Did the Researchers Do and Find? The researchers identified causal associations between potentially modifiable risk factors and AD risk by analyzing the occurrence of single nucleotide polymorphisms (SNPs, a type of gene variant) known to predict levels of each risk factor, in genetic data from 17,008 individuals with AD and 37,154 cognitively normal elderly controls collected by the International Genomics of Alzheimer’s Project. They report that genetically predicted higher systolic blood pressure (SBP; the pressure exerted on the inside of large blood vessels when the heart is pumping out blood) was associated with lower AD risk (and with a higher probability of taking antihypertensive medication). Predicted smoking quantity was also associated with lower AD risk, but there was no evidence of causal associations between any of the other risk factors investigated and AD risk. What Do These Findings Mean? In contrast to some epidemiological studies, these findings suggest that hypertension is associated with lower AD risk. However, because genetically predicted higher SBP was also associated with a higher probability of taking antihypertensive medication, it could be that exposure to such drugs, rather than having hypertension, reduces AD risk. Like all Mendelian randomization studies, the reliability of these findings depends on the validity of several assumptions made by the researchers and on the ability of the SNPs used in the analyses to explain variations in exposure to the various risk factors. Moreover, because all the participants in the International Genomics of Alzheimer’s Project are of European ancestry, these findings may not be valid for other ethnic groups. Given that hypertension is a risk factor for cardiovascular disease, the researchers do not advocate raising blood pressure as a measure to prevent AD (neither do they advocate that people smoke more cigarettes to lower AD risk). Rather, given the strong association between higher SBP gene scores and the probability of exposure to antihypertensive treatment, they suggest that the possibility that antihypertensive drugs might reduce AD risk independently of their effects on blood pressure should be investigated as a priority. Additional Information This list of resources contains links that can be accessed when viewing the PDF on a device or via the online version of the article at http://dx.doi.org/10.1371/journal.pmed.1001841. The UK National Health Service Choices website provides information (including personal stories) about Alzheimer disease The UK not-for-profit organization Alzheimer’s Society provides information for patients and carers about dementia, including personal experiences of living with Alzheimer disease The US not-for-profit organization Alzheimer’s Association also provides information for patients and carers about dementia and personal stories about dementia Alzheimer’s Disease International is the federation of Alzheimer disease associations around the world; it provides links to individual Alzheimer associations, information about dementia, and links to world Alzheimer reports MedlinePlus provides links to additional resources about Alzheimer disease (in English and Spanish) Wikipedia has a page on Mendelian randomization (note: Wikipedia is a free online encyclopedia that anyone can edit; available in several languages) A PLOS Medicine Research Article by Proitsi et al. describes a Mendelian randomization study that looked for a causal association between dyslipidemia and Alzheimer disease

Published
2014

133. Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche

Author

John R. B. Perry, Felix Day, Cathy E. Elks, Patrick Sulem, Deborah J. Thompson, Teresa Ferreira, Chunyan He, Daniel I. Chasman, Txf5nu Esko, Gudmar Thorleifsson, Jouke-Jan Hottenga, Eco E. J. de Geus, Gonneke Willemsen, Dorret I. Boomsma, Cornelia M. van Duijn, Thorkild I. A. Sxf8rensen, Tim D. Spector, David P. Strachan, Andrxe9 G. Uitterlinden, Nicholas J. Wareham, Elisabeth Widen, Marek Zygmunt, Anna Murray, Douglas F. Easton, Kari Stefansson, Joanne M. Murabito, and Ken K. Ong

Published
2014

134. The RSNA Image Sharing Network

Author

W. Zhu, Steve G. Langer, Wyatt M. Tellis, Mark Daly, Chris Carr, Max Warnock, Bradley J. Erickson, K. Shastri, John R. B. Perry, David S. Mendelson, and Stephen M. Moore

Subjects
Knowledge management, Physical media, Radiological and Ultrasound Technology, business.industry, Information Dissemination, Medical record, Image sharing, Article, Computer Science Applications, Systems Integration, Computer Communication Networks, Health care, North America, Information system, Medicine, System integration, Electronic Health Records, Humans, Radiology, Nuclear Medicine and imaging, business, Radiology, Societies, Medical, Private network
Abstract

In the era of health information exchanges, there are trade-offs to consider when sharing a patient’s medical record among all providers that a patient might choose. Exchange among in-network partners on the same electronic medical records (EMR) and other integrated information systems is trivial. The patient identifier is common, as are the relevant departmental systems, to all providers. Difficulties arise when patient records including images (and reports) must be shared among different networks and even with the patients themselves. The National Institutes of Health (NIH) challenged Radiological Society of North America (RSNA) to develop a transport method that could supersede the need for physical media (for patients or other providers), replace point-to-point private networks among providers, and enable image exchange on an ad hoc basis between arbitrary health networks without long legal delays. In concert with the evolving US health care paradigm, patient engagement was to be fundamental. With Integrating Healthcare Enterprise’s (IHE’s) help, the challenge has been met with an operational system.

Published
2014

135. Genome-wide association study with 1000 genomes imputation identifies signals for nine sex hormone-related phenotypes

Author

Katherine S, Ruth, Purdey J, Campbell, Shelby, Chew, Ee Mun, Lim, Narelle, Hadlow, Bronwyn G A, Stuckey, Suzanne J, Brown, Bjarke, Feenstra, John, Joseph, Gabriela L, Surdulescu, Hou Feng, Zheng, J Brent, Richards, Anna, Murray, Tim D, Spector, Scott G, Wilson, and John R B, Perry

Subjects
Male, Estradiol, Genotype, Dehydroepiandrosterone Sulfate, Genome, Human, Luteinizing Hormone, Polymorphism, Single Nucleotide, Article, Prolactin, Phenotype, Sex Hormone-Binding Globulin, Humans, Female, Testosterone, Follicle Stimulating Hormone, Gonadal Steroid Hormones, Progesterone, Genome-Wide Association Study
Abstract

Genetic factors contribute strongly to sex hormone levels, yet knowledge of the regulatory mechanisms remains incomplete. Genome-wide association studies (GWAS) have identified only a small number of loci associated with sex hormone levels, with several reproductive hormones yet to be assessed. The aim of the study was to identify novel genetic variants contributing to the regulation of sex hormones. We performed GWAS using genotypes imputed from the 1000 Genomes reference panel. The study used genotype and phenotype data from a UK twin register. We included 2913 individuals (up to 294 males) from the Twins UK study, excluding individuals receiving hormone treatment. Phenotypes were standardised for age, sex, BMI, stage of menstrual cycle and menopausal status. We tested 7,879,351 autosomal SNPs for association with levels of dehydroepiandrosterone sulphate (DHEAS), oestradiol, free androgen index (FAI), follicle-stimulating hormone (FSH), luteinizing hormone (LH), prolactin, progesterone, sex hormone-binding globulin and testosterone. Eight independent genetic variants reached genome-wide significance (P5 × 10(-8)), with minor allele frequencies of 1.3-23.9%. Novel signals included variants for progesterone (P=7.68 × 10(-12)), oestradiol (P=1.63 × 10(-8)) and FAI (P=1.50 × 10(-8)). A genetic variant near the FSHB gene was identified which influenced both FSH (P=1.74 × 10(-8)) and LH (P=3.94 × 10(-9)) levels. A separate locus on chromosome 7 was associated with both DHEAS (P=1.82 × 10(-14)) and progesterone (P=6.09 × 10(-14)). This study highlights loci that are relevant to reproductive function and suggests overlap in the genetic basis of hormone regulation.

Published
2014

137. Meta-analysis of genome-wide association data identifies two loci influencing age at menarche

Author

Vivian Zhuang, Albert V. Smith, Luigi Ferrucci, Karol Estrada, Alan R. Shuldiner, Toshiko Tanaka, Aaron R. Folsom, Vilmundur Gudnason, Lenore J. Launer, Nicole Soranzo, Douglas P. Kiel, Eric Boerwinkle, Lisette Stolk, Joyce B. J. van Meurs, Tamara B. Harris, Jenny A. Visser, Scott Wilson, Nora Franceschini, Kathryn L. Lunetta, David Karasik, John R. B. Perry, Thor Aspelund, Michael N. Weedon, Melissa E. Garcia, André G. Uitterlinden, Mike A. Nalls, Tim D. Spector, Guangju Zhai, Stefania Bandinelli, Elizabeth A. Streeten, Joanne M. Murabito, Fernando Rivadeneira, Gudny Eiriksdottir, Ellen W. Demerath, Anna Murray, Albert Hofman, Andrew B. Singleton, Patrick F. McArdle, Lynn Cherkas, Internal Medicine, and Epidemiology

Subjects
Genetics, Meta-analysis, Genetic variation, Menarche, Sexual maturity, Locus (genetics), Genome-wide association study, Biology, Body mass index, Gene, Article
Abstract

We conducted a meta-analysis of genome-wide association data to detect genes influencing age at menarche in 17,510 women. The strongest signal was at 9q31.2 (P = 1.7 x 10(-9)), where the nearest genes include TMEM38B, FKTN, FSD1L, TAL2 and ZNF462. The next best signal was near the LIN28B gene (rs7759938; P = 7.0 x 10(-9)), which also influences adult height. We provide the first evidence for common genetic variants influencing female sexual maturation.

Published
2009

138. Simulation of Finnish population history, guided by empirical genetic data, to assess power of rare-variant tests in Finland

Author

Mark A. DePristo, Gil McVean, Jacquelyn Murphy, Kyle J. Gaulton, Jasmina Kravic, Martin Hrabé de Angelis, Noël P. Burtt, Ryan Poplin, Jeff Chen, Peter S. Chines, Tiinamaija Toumi, David Buck, Khalid Shakir, Pierre Fontanillas, Richard N. Bergman, Neil Robertson, Leif Groop, Tim M. Strom, Martina Müller-Nurasyid, Loukas Moutsianas, Christian Fuchsberger, Charleston W. K. Chiang, Thomas Meitinger, Jennifer Kriebel, Richard D. Pearson, Christa Meisinger, Gonçalo R. Abecasis, Jaakko Tuomilehto, Ashok Kumar, Janina S. Ried, Anubha Mahajan, Andrew T. Hattersley, Adam E. Locke, Wolfgang Rathmann, Inga Prokopenko, Adrian Tan, Annette Peters, Lori L. Bonnycastle, Andrew D. Morris, Christopher Hartl, Peter Donnelly, Vineeta Agarwala, Will Rayner, Jason Flannick, Timothy M. Frayling, Cornelia Huth, Martijn van de Bunt, David Altshuler, Harald Grallert, Stacey Gabriel, Michael Boehnke, Laura J. Scott, Tim D. Spector, Thomas W. Blackwell, Heather M. Stringham, Phoenix Kwan, Alisa Manning, Tanya M. Teslovich, Sophie R. Wang, Jeroen R. Huyghe, Francis S. Collins, Kerrin S. Small, Cecilia M. Lindgren, Gerton Lunter, Mark I. McCarthy, Joel N. Hirschhorn, Timothy Fennell, Todd Green, Clement Ma, Manny Rivas, Claes Ladenvall, Bo Isomaa, Anne U. Jackson, Hyun Min Kang, Eric Banks, Michael L. Stitzel, Xueling Sim, John R. B. Perry, Bryan Howie, Konstantin Strauch, Goo Jun, Karen L. Mohlke, and Christian Gieger

Subjects
Genetics, Multifactorial Inheritance, Models, Genetic, Population, Population genetics, Biology, Genetic architecture, Founder Effect, White People, Article, Diabetes Mellitus, Type 2, Evolutionary biology, Genetic model, Humans, Genetics(clinical), Computer Simulation, Exome, Genotyping, Genetics (clinical), Exome sequencing, Finland, Genetic association, Founder effect
Abstract

Finnish samples have been extensively utilized in studying single-gene disorders, where the founder effect has clearly aided in discovery, and more recently in genome-wide association studies of complex traits, where the founder effect has had less obvious impacts. As the field starts to explore rare variants' contribution to polygenic traits, it is of great importance to characterize and confirm the Finnish founder effect in sequencing data and to assess its implications for rare-variant association studies. Here, we employ forward simulation, guided by empirical deep resequencing data, to model the genetic architecture of quantitative polygenic traits in both the general European and the Finnish populations simultaneously. We demonstrate that power of rare-variant association tests is higher in the Finnish population, especially when variants' phenotypic effects are tightly coupled with fitness effects and therefore reflect a greater contribution of rarer variants. SKAT-O, variable-threshold tests, and single-variant tests are more powerful than other rare-variant methods in the Finnish population across a range of genetic models. We also compare the relative power and efficiency of exome array genotyping to those of high-coverage exome sequencing. At a fixed cost, less expensive genotyping strategies have far greater power than sequencing; in a fixed number of samples, however, genotyping arrays miss a substantial portion of genetic signals detected in sequencing, even in the Finnish founder population. As genetic studies probe sequence variation at greater depth in more diverse populations, our simulation approach provides a framework for evaluating various study designs for gene discovery.

Published
2013

139. Imputation of variants from the 1000 Genomes Project modestly improves known associations and can identify low-frequency variant-phenotype associations undetected by HapMap based imputation

Author

Hou-Feng Zheng, Stefania Bandinelli, David Melzer, Toshiko Tanaka, Andrew R. Wood, J. Brent Richards, J. Raphael Gibbs, John R. B. Perry, Tim D. Spector, Luigi Ferrucci, Dena G. Hernandez, Mike A. Nalls, Michael N. Weedon, Andrew B. Singleton, and Timothy M. Frayling

Subjects
Adult, Male, Genotype, Population, lcsh:Medicine, Genome-wide association study, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Genome Analysis Tools, Genome-Wide Association Studies, Genetics, Humans, International HapMap Project, 1000 Genomes Project, education, lcsh:Science, 030304 developmental biology, Aged, Aged, 80 and over, 0303 health sciences, education.field_of_study, Multidisciplinary, Population Biology, Genome, Human, Haplotype, lcsh:R, Computational Biology, Human Genetics, Genomics, Middle Aged, Phenotype, Haplotypes, Genetic Polymorphism, Human genome, lcsh:Q, Female, Haplotype estimation, 030217 neurology & neurosurgery, Imputation (genetics), Population Genetics, Genome-Wide Association Study, Research Article
Abstract

Genome-wide association (GWA) studies have been limited by the reliance on common variants present on microarrays or imputable from the HapMap Project data. More recently, the completion of the 1000 Genomes Project has provided variant and haplotype information for several million variants derived from sequencing over 1,000 individuals. To help understand the extent to which more variants (including low frequency (1% ≤ MAF

Published
2013

140. Shared genetic factors for age at natural menopause in Iranian and European women

Author

Jackson Wu, Fereidoun Azizi, Angela Brooks-Wilson, Madalene Earp, Joanne M. Murabito, Martin Treml, Fahimeh Ramezani Tehrani, Mehran Ataee, John R. B. Perry, Maziar Rahmani, Sara P-Behnami, Ramona Nudischer, and Radiology & Nuclear Medicine

Subjects
Genotype, Population, Genome-wide association study, Single-nucleotide polymorphism, Biology, Iran, Polymorphism, Single Nucleotide, SNP, Humans, education, Genotyping, Genetic Association Studies, Genetic association, Aged, Genetics, education.field_of_study, Rehabilitation, Age Factors, Obstetrics and Gynecology, Middle Aged, SNP genotyping, Europe, Reproductive Medicine, Linear Models, Female, Menopause, Demography
Abstract

Study question Do differences in heritable genetic factors explain some of the difference in age at natural menopause (ANM) among populations? Summary answer One single nucleotide polymorphism (SNP)-ANM association (rs16991615) detected in European women was replicated in Iranian women. What is known already Genetics plays an important role in ANM, and well-powered genome-wide association studies (GWAS) of ANM performed in European women have discovered many statistically significant SNP-ANM associations. Average ANM varies by ethnicity, and population-specific differences in ANM-associated alleles may in part explain these differences. Study design, size, duration After quality control procedures, 97 SNPs were analyzed in genotype data of 828 Iranian women who experienced natural menopause. SNP genotyping data were used to perform linear regression analyses with ANM as a quantitative trait. Study participants were drawn from the population-based Tehran Lipid and Glucose Study based in Tehran, Iran. This study was performed between February 2009 and March 2012. Participants/materials, setting and methods Based on an ANM-GWAS literature review, eight SNPs at four loci previously associated with ANM in European women were tested for replication in Iranian women. Linear regression analyses were performed including (n = 828) and excluding (n = 783) women who experience premature ovarian failure (ANM before 40 years of age). In addition, to search for novel population-specific ANM risk alleles, a pool-based GWAS was performed using this collection of Iranian women. Two DNA pools were constructed and compared: an 'early' ANM pool (lower 20(th) percentile of menopause ages, 40-45 years, n = 165) and a 'late' ANM pool (upper 20(th) percentile of menopause ages, 54-65 years, n = 187). Each DNA pool was assayed on four Illumina Human1M-Duo arrays, and allele-based tests of association were used to rank SNPs. One hundred and two highly ranked SNPs were chosen for individual genotyping by Sequenom MassARRAY and association analysis in the Iranian women. Main results and the role of chance One SNP-ANM association previously detected in European women was replicated in Iranian women (rs16991615; β = 1.07, standard error (SE): 0.49, P = 0.02). SNPs at the previously reported 19q13.42 and 6p24.2 loci also approached statistical significance and had consistent SNP effects (magnitude and direction) in Iranian women (rs1172822; β = -0.39, SE: 0.22, P = 0.08; and rs2153157, β = 0.41, SE: 0.21, P = 0.05). We found little evidence for novel SNP-ANM associations in Iranian women; no SNP selected based on the pool-based GWAS achieved genome-wide significance. Limitations, reasons for caution Due to small sample size this study was powered to reliably detect only moderate-to-large SNP effect sizes. This limited our ability to replicate many of the previously reported SNP-ANM risk alleles and to discover novel SNP-ANM associations' specific to the Iranian population. In performing our pool-based GWAS, a reduction in power was introduced relative to a conventional GWAS. Wider implications of the findings Our results imply that European and Iranian women share ANM-associated genetic variants. Our study was underpowered but for all SNPs tested the direction of the effect was consistent with data from the European study. Therefore, we anticipate that many (if not all) of the ANM-associated SNPs discovered in European women will replicate in Iranian women upon genotyping a sufficient number of women. Our data do not support the hypothesis that population-specific SNP-ANM associations explain population-specific differences in the mean ANM.

Published
2013

141. A common biological basis of obesity and nicotine addiction

Author

Peter Kovacs, Angela Döring, Frank Geller, Lenka Foretova, Dana Mates, Paul M. Ridker, Francesco Mauri, Mark J. Caulfield, Nora Franceschini, Neonilia Szeszenia-Dabrowska, Toshiko Tanaka, Pagona Lagiou, Jennifer E. Huffman, Paul Scheet, Gudmar Thorleifsson, Jacqueline M. Vink, Nicole Vogelzangs, Ida Surakka, Jeffrey R. Gulcher, Ulrich John, Veikko Salomaa, Eco J. C. de Geus, Hakon Hakonarson, Anne Barton, Luigi Barzan, H.-Erich Wichmann, Anneli Pouta, Peter Vollenweider, Kristina Kjærheim, Jed E. Rose, Ruth J. F. Loos, Susanne Lucae, Danielle Posthuma, Henning Tiemeier, Fangyi Gu, Mark I. McCarthy, Unnur Styrkarsdottir, James McKay, Talin Haritunians, Martin Preisig, Olle Melander, Xavier Castellsagué, William H. Matthai, Piera Angelica Merlini, Daniel I. Chasman, Michael Stumvoll, Ozren Polasek, Nilesh J. Samani, Søren Besenbacher, Jane Worthington, Daniel F. Gudbjartsson, Alistair S. Hall, Antonio Agudo, Keith Matthews, Gonçalo R. Abecasis, Jaana Laitinen, Norbert Dahmen, Robert W. Mahley, Mari Nelis, Inga Prokopenko, Anke Tönjes, Iris H Gudjonsdottir, Joshua W. Knowles, Jing Hua Zhao, Jouke-Jan Hottenga, Vincent Mooser, Jack Satsangi, Cristina Canova, Stephen P. Fortmann, Hreinn Stefansson, Manuela Uda, T. Brueckl, Mary Susan Burnett, Michael Boehnke, Veronique Vitart, Philip J. Barter, Ruth McPherson, Benjamin F. Voight, Patrick F. Sullivan, Pier Mannuccio Mannucci, Michael Wittig, Kari Stefansson, Lowell F. Satler, Eric Boerwinkle, Benjamin J. Wright, Ben A. Oostra, John Strauss, Stefania Bandinelli, S. Horstmann, Jonathan Marchini, Simone Benhamou, Stephen E. Epstein, Rajesh Rawal, Vladimir Janout, Miles Parkes, Liming Qu, Yuri Milaneschi, Peter Almgren, Kaisu Keskitalo, Matti Isohanni, Dan Rujescu, John P. A. Ioannidis, Peter Rudnai, Stefan Walter, Diego Ardissino, John B. Vincent, Leif Groop, Kent D. Taylor, Christopher J. O'Donnell, Christopher W. Knouff, David I. Conway, Thomas Quertermous, Joseph M. Lindsay, Stephen M. Schwartz, Tariq Ahmed, Jolanta Lissowska, Evan L. Thacker, Igor Rudan, Sreekumar G. Pillai, Janet Audrain-McGovern, Daniel Levy, S. Kathiresan, Timothy M. Frayling, Brenda W.J.H. Penninx, Shen Huei-Yi, Johannes H. Smit, Gonneke Willemsen, Henry Völzke, John R. B. Perry, Federica Tozzi, Roberto Elosua, Devin Absher, G B Walters, Augusto D. Pichard, Stephen J. Chanock, Katja K.H. Aben, Anna-Liisa Hartikainen, Maria Krestyaninova, Ivana Holcatova, Tim D. Spector, Ming D. Li, Xiangjun Xiao, Barbara McKnight, Hans J. Grabe, Martin den Heijer, Caroline Hayward, Unnur Thorsteinsdottir, Douglas F. Levinson, Claes Ladenvall, Robert L. Wilensky, Danyu Lin, Nicole Soranzo, Lefkos T. Middleton, Jason S. Liu, Wade H. Berrettini, Laura M. Thornton, Muredach P. Reilly, Jack M. Guralnik, Ron Waksman, Per Bakke, Alan F. Wright, Andre Franke, Thorgeir E. Thorgeirsson, Barbara Nitz, Anthony J. Balmforth, Jaspal S. Kooner, Gavin Lucas, Esther H. Lips, Helena Furberg, Albert Hofman, Patrick Sulem, Astrid Petersmann, Ivana Kolcic, Jaakko Tuomilehto, Lorenzo Richiardi, Pablo V. Gejman, Claire J. Steves, Thorarinn Tyrfingsson, Yurii S. Aulchenko, Brendan M. Everett, Ariana Znaor, Maxine Allen, Thorunn Rafnar, Mark Lathrop, Reedik Mägi, Kenneth M. Kent, M. Perola, Nicholas J. Wareham, Daniel J. Rader, John R. Thompson, Sarah R. Preis, Peter Kraft, Caryn Lerman, Hogni Oskarsson, Alan R. Sanders, Alexander Teumer, Xin Yuan, Cornelia M. van Duijn, Samuli Ripatti, André G. Uitterlinden, Carl A. Anderson, Martin Farrall, Kay-Tee Khaw, Joachim Heinrich, Heather M. Stringham, Bruce M. Psaty, Jaakko Kaprio, Valgerdur Steinthorsdottir, Steve Eyre, James F. Wilson, David J. Hunter, Johannes Kettunen, Wendy Thomson, Antero Kesäniemi, Karen L. Mohlke, Christian Gieger, Tatiana V. Macfarlane, Jubao Duan, Anne Farmer, Clyde Francks, Joshua C. Bis, Harry Campbell, Pierandrea Muglia, Andres Metspalu, Dawn M. Waterworth, Ramachandran S. Vasan, Hermine H. Maes, David Zaridze, Luisa Bernardinelli, Vladimir Bencko, Massimo Mangino, Lambertus A. Kiemeney, Solveig Gretarsdottir, Tõnu Esko, Anne U. Jackson, Claire M. Healy, Scott M. Grundy, David St Clair, Curt D. Furberg, Mingyao Li, Peter McGuffin, Christopher G. Mathew, David Altshuler, Dorret I. Boomsma, Susan Campbell, Jianxin Shi, Najaf Amin, James L. Kennedy, Ana M. Valdes, Anna F. Dominiczak, Themistocles L. Assimes, Susan E. Hankinson, Inês Barroso, Marjo-Riitta Järvelin, Guillaume Paré, Joe Devaney, Antonio Terracciano, David Schlessinger, Paul Brennan, Shih-Jen Hwang, Luigi Ferrucci, Ray Lowry, Jennifer Dackor, Eleonora Fabianova, Lina Zgaga, Emelia J. Benjamin, Fabio Busonero, Sarah H. Wild, Patricia B. Munroe, John C. Chambers, Carlos Iribarren, Marcus Ising, Yunjung Kim, Richard O. Day, Amund Gulsvik, Gérard Waeber, Claudia Lamina, Arne Schäfer, Functional Genomics, Neuroscience Campus Amsterdam - Neurobiology of Mental Health, Hjelt Institute (-2014), Department of Public Health, Institute for Molecular Medicine Finland, Genetic Epidemiology, Human genetics, and NCA - Neurobiology of mental health

Subjects
obesity, FOOD-INTAKE, TAG Consortium, medicine.medical_treatment, Oxford-GSK Consortium, LOCI, Iceland, Aetiology, screening and detection [ONCOL 5], VARIANTS, 3124 Neurology and psychiatry, Nicotine, 0302 clinical medicine, DEPENDENCE, 030212 general & internal medicine, Age of Onset, ENGAGE consortium, POPULATION, Addiction, Body Mass Index, Nicotine dependence, Smoking, media_common, Psychiatry, 2. Zero hunger, 0303 health sciences, education.field_of_study, ASSOCIATION, Tobacco Use Disorder, DSM-V, CANCER, 3142 Public health care science, environmental and occupational health, 3. Good health, Psychiatry and Mental health, Meta-analysis, Original Article, addiction, Life Sciences & Biomedicine, medicine.drug, medicine.medical_specialty, media_common.quotation_subject, Population, body mass index, Polymorphism, Single Nucleotide, smoking, 03 medical and health sciences, Cellular and Molecular Neuroscience, SDG 3 - Good Health and Well-being, Internal medicine, medicine, Humans, SMOKING-BEHAVIOR, nicotine dependence, education, Biological Psychiatry, Molecular epidemiology Aetiology, screening and detection [NCEBP 1], 030304 developmental biology, Science & Technology, business.industry, Appetite, medicine.disease, Obesity, BODY-MASS INDEX, Behavior, Addictive, Endocrinology, Smoking cessation, business, Body mass index
Abstract

Contains fulltext : 128630.pdf (Publisher’s version ) (Open Access) Smoking influences body weight such that smokers weigh less than non-smokers and smoking cessation often leads to weight increase. The relationship between body weight and smoking is partly explained by the effect of nicotine on appetite and metabolism. However, the brain reward system is involved in the control of the intake of both food and tobacco. We evaluated the effect of single-nucleotide polymorphisms (SNPs) affecting body mass index (BMI) on smoking behavior, and tested the 32 SNPs identified in a meta-analysis for association with two smoking phenotypes, smoking initiation (SI) and the number of cigarettes smoked per day (CPD) in an Icelandic sample (N=34,216 smokers). Combined according to their effect on BMI, the SNPs correlate with both SI (r=0.019, P=0.00054) and CPD (r=0.032, P=8.0 x 10(-7)). These findings replicate in a second large data set (N=127,274, thereof 76,242 smokers) for both SI (P=1.2 x 10(-5)) and CPD (P=9.3 x 10(-5)). Notably, the variant most strongly associated with BMI (rs1558902-A in FTO) did not associate with smoking behavior. The association with smoking behavior is not due to the effect of the SNPs on BMI. Our results strongly point to a common biological basis of the regulation of our appetite for tobacco and food, and thus the vulnerability to nicotine addiction and obesity.

Published
2013

142. A Genome-Wide Association Meta-Analysis of Circulating Sex Hormone-Binding Globulin Reveals Multiple Loci Implicated in Sex Steroid Hormone Regulation

Author

Massimo Mangino, Magnus Karlsson, Wei Vivian Zhuang, Laure Morin Papunen, Nicole Soranzo, Martin Reincke, Leo-Pekka Lyytikäinen, Andrea D. Coviello, Petra H.M. Peeters, Daniel B. Mirel, Myriam Fornage, Carla H. van Gils, Kurt Lohman, Tamara B. Harris, Martin Bidlingmaier, Leslie J. Raffel, Marc J. Gunter, Liesbeth Vandenput, M. Maggio, Pamela Ouyang, Sarah Keildson, Iva Miljkovic, Annemarie Koster, Simin Liu, Steven R. Cummings, John-Olov Jansson, Mattias Lorentzon, Mika Kähönen, Stephen J. Chanock, Yuhui Chen, Luigi Ferrucci, David G. Cox, Johannes Kettunen, Henri Wallaschofski, Anneli Pouta, Marcello Ricardo Paulista Markus, Steve Franks, Jorma Viikari, Frank De Jong, Melissa Wellons, Susan E. Hankinson, Georg Homuth, Hannu Martikainen, Albert Hofman, Alexander P. Reiner, Andrew D. Johnson, Douglas P. Kiel, Marjo-Riitta Järvelin, Reiner Biffar, Fernando Rivadeneira, Joel Eriksson, Inga Prokopenko, Ann-Kristin Petersen, Kathryn M. Rexrode, H.-Erich Wichmann, Stephen M. Schwartz, Chunyan He, John R. B. Perry, Shelley S. Tworoger, N. Charlotte Onland-Moret, Yongmei Liu, David S. Siscovick, Terho Lehtimäki, Peter Kraft, Georg Brabant, André G. Uitterlinden, Alexander Teumer, Östen Ljunggren, Dan Mellström, Stefania Bandinelli, Dhananjay Vaidya, Claes Ohlsson, David Karasik, Lisette Stolk, Anna-Liisa Hartikainen, Andrew R. Wood, Shalender Bhasin, Mark I. McCarthy, Jennifer Prescott, Anna Murray, Tim D. Spector, Guangju Zhai, Olli T. Raitakari, Joanne M. Murabito, Kathryn L. Lunetta, Thomas Illig, Jingmin Liu, Melissa Garcia, Brian H. Chen, Ramachandran S. Vasan, David J. Hunter, Robin Haring, Sarah C. Nelson, Vasiliki Lagou, Aimo Ruokonen, Immaculata De Vivo, Doris Stöckl, Timothy M. Frayling, Yvonne T. van der Schouw, Interne Geneeskunde, RS: CARIM School for Cardiovascular Diseases, Public Health, Internal Medicine, Epidemiology, Urology, Medical Research Council (MRC), and Institute for Molecular Medicine Finland

Subjects
MEDICAL PROGRESS, Male, Cancer Research, Medicin och hälsovetenskap, Epidemiology, HAN CHINESE POPULATION, Genome-wide association study, RECEPTOR TYROSINE KINASE, QH426-470, HAN CHINESE, Medical and Health Sciences, 0302 clinical medicine, Sex hormone-binding globulin, Endocrinology, Sex Hormone-Binding Globulin, GENETICS & HEREDITY, Gonadal Steroid Hormones, POPULATION, Genetics (clinical), GENE-EXPRESSION, RISK, 0303 health sciences, education.field_of_study, Sex Characteristics, POLYCYSTIC-OVARY-SYNDROME, INSULIN-RECEPTOR, 3. Good health, 030220 oncology & carcinogenesis, Genetic Epidemiology, MEDICAL, Medicine, Allelic heterogeneity, Female, Life Sciences & Biomedicine, Metabolic Networks and Pathways, Research Article, medicine.medical_specialty, medicine.drug_class, Population, Single-nucleotide polymorphism, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, Genetic Heterogeneity, SDG 3 - Good Health and Well-being, Internal medicine, medicine, Genetics, Humans, Reproductive Endocrinology, education, PROGRESS, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Alleles, 030304 developmental biology, 0604 Genetics, Science & Technology, GCKR RS780094, Endocrine Physiology, Genetic heterogeneity, ta3121, Androgen, SHBG GENE, POLYMORPHISM, Orthopedics, Sex steroid, biology.protein, 3111 Biomedicine, Developmental Biology, Genome-Wide Association Study
Abstract

Sex hormone-binding globulin (SHBG) is a glycoprotein responsible for the transport and biologic availability of sex steroid hormones, primarily testosterone and estradiol. SHBG has been associated with chronic diseases including type 2 diabetes (T2D) and with hormone-sensitive cancers such as breast and prostate cancer. We performed a genome-wide association study (GWAS) meta-analysis of 21,791 individuals from 10 epidemiologic studies and validated these findings in 7,046 individuals in an additional six studies. We identified twelve genomic regions (SNPs) associated with circulating SHBG concentrations. Loci near the identified SNPs included SHBG (rs12150660, 17p13.1, p = 1.8×10−106), PRMT6 (rs17496332, 1p13.3, p = 1.4×10−11), GCKR (rs780093, 2p23.3, p = 2.2×10−16), ZBTB10 (rs440837, 8q21.13, p = 3.4×10−09), JMJD1C (rs7910927, 10q21.3, p = 6.1×10−35), SLCO1B1 (rs4149056, 12p12.1, p = 1.9×10−08), NR2F2 (rs8023580, 15q26.2, p = 8.3×10−12), ZNF652 (rs2411984, 17q21.32, p = 3.5×10−14), TDGF3 (rs1573036, Xq22.3, p = 4.1×10−14), LHCGR (rs10454142, 2p16.3, p = 1.3×10−07), BAIAP2L1 (rs3779195, 7q21.3, p = 2.7×10−08), and UGT2B15 (rs293428, 4q13.2, p = 5.5×10−06). These genes encompass multiple biologic pathways, including hepatic function, lipid metabolism, carbohydrate metabolism and T2D, androgen and estrogen receptor function, epigenetic effects, and the biology of sex steroid hormone-responsive cancers including breast and prostate cancer. We found evidence of sex-differentiated genetic influences on SHBG. In a sex-specific GWAS, the loci 4q13.2-UGT2B15 was significant in men only (men p = 2.5×10−08, women p = 0.66, heterogeneity p = 0.003). Additionally, three loci showed strong sex-differentiated effects: 17p13.1-SHBG and Xq22.3-TDGF3 were stronger in men, whereas 8q21.12-ZBTB10 was stronger in women. Conditional analyses identified additional signals at the SHBG gene that together almost double the proportion of variance explained at the locus. Using an independent study of 1,129 individuals, all SNPs identified in the overall or sex-differentiated or conditional analyses explained ∼15.6% and ∼8.4% of the genetic variation of SHBG concentrations in men and women, respectively. The evidence for sex-differentiated effects and allelic heterogeneity highlight the importance of considering these features when estimating complex trait variance., Author Summary Sex hormone-binding globulin (SHBG) is the key protein responsible for binding and transporting the sex steroid hormones, testosterone and estradiol, in the circulatory system. SHBG regulates their bioavailability and therefore their effects in the body. SHBG has been linked to chronic diseases including type 2 diabetes and to hormone-sensitive cancers such as breast and prostate cancer. SHBG concentrations are approximately 50% heritable in family studies, suggesting SHBG concentrations are under significant genetic control; yet, little is known about the specific genes that influence SHBG. We conducted a large study of the association of SHBG concentrations with markers in the human genome in ∼22,000 white men and women to determine which loci influence SHBG concentrations. Genes near the identified genomic markers in addition to the SHBG protein coding gene included PRMT6, GCKR, ZBTB10, JMJD1C, SLCO1B1, NR2F2, ZNF652, TDGF3, LHCGR, BAIAP2L1, and UGT2B15. These genes represent a wide range of biologic pathways that may relate to SHBG function and sex steroid hormone biology, including liver function, lipid metabolism, carbohydrate metabolism and type 2 diabetes, and the development and progression of sex steroid hormone-responsive cancers.

Published
2012

143. Stratifying type 2 diabetes cases by BMI identifies genetic risk variants in LAMA1 and enrichment for risk variants in lean compared to obese cases

Author

David Altschuler, Cornelia M. van Duijn, Igor Rudan, Denis Rybin, Yann Labrune, Francis S. Collins, Martha Ganser, Lu Qi, Michael Roden, Unnur Thorsteinsdottir, Inga Prokopenko, Albert Hofman, Guillaume Charpentier, Mark I. McCarthy, Robert Sladek, James F. Wilson, Stéphane Cauchi, Yurii S. Aulchenko, Christian Herder, Robert A. Scott, Man Li, Peter P. Pramstaller, Rafn Benediktsson, Frank B. Hu, Samy Hadjadj, Peter Almgren, Andrew D. Johnson, Beverley Balkau, Pau Navarro, Michael Boehnke, Michael N. Weedon, Leif Groop, John R. B. Perry, Lori L. Bonnycastle, Noël P. Burtt, Alisa K. Manning, Claudia Langenberg, W Rayner, Benjamin F. Voight, Wolfgang Rathmann, Timothy M. Frayling, Gunnar Sigurdsson, Eric Boerwinkle, James S. Pankow, Ben A. Oostra, Andrew D. Morris, Philippe Froguel, Linda Kao, Dan E. Arking, Kari Stefansson, Harry Campbell, Loic Yengo, Colin N. A. Palmer, Nicholas J. Wareham, James B. Meigs, Karen L. Mohlke, Gudmar Thorleifsson, Andrew T. Hattersley, Alan F. Wright, Laura J. Scott, Harald Grallert, Jaakko Tuomilehto, Najaf Amin, Christian Gieger, Thomas Illig, Anna Köttgen, Todd Green, Josée Dupuis, Sidonie Vivequin, Richard N. Bergman, Peter Kraft, André G. Uitterlinden, Valgerdur Steinthorsdottir, Andrew P. Morris, Ann-Kristin Petersen, Epidemiology, Dermatology, Clinical Genetics, and Internal Medicine

Subjects
Male, Cancer Research, Heredity, Epidemiology, PROTEIN, Type 2 diabetes, QH426-470, Overweight, MOUSE, Bioinformatics, DISEASE, GLUCOSE, Body Mass Index, Endocrinology, 0302 clinical medicine, Risk Factors, GENETICS & HEREDITY, Genetics (clinical), 2. Zero hunger, Molecular Epidemiology, 0303 health sciences, High Mobility Group Proteins, Middle Aged, INSULIN, 3. Good health, Phenotypes, DIFFERENTIATION, Genetic Epidemiology, Medicine, Female, medicine.symptom, Life Sciences & Biomedicine, Research Article, EXPRESSION, Asian Continental Ancestry Group, medicine.medical_specialty, SUSCEPTIBILITY LOCI, European Continental Ancestry Group, 030209 endocrinology & metabolism, DIAGRAM Consortium, Biology, Endocrinology and Diabetes, Polymorphism, Single Nucleotide, White People, 03 medical and health sciences, Asian People, SDG 3 - Good Health and Well-being, Internal medicine, GIANT Consortium, Genome-Wide Association Studies, Genetics, medicine, Genetic predisposition, Humans, Genetic Predisposition to Disease, Obesity, GENOME-WIDE ASSOCIATION, Risk factor, Molecular Biology, Alleles, Ecology, Evolution, Behavior and Systematics, Aged, 030304 developmental biology, Diabetic Endocrinology, 0604 Genetics, Science & Technology, Complex Traits, Case-control study, Human Genetics, Odds ratio, Diabetes Mellitus Type 2, medicine.disease, MAGIC, Diabetes Mellitus, Type 2, Case-Control Studies, CELLS, Laminin, Body mass index, Developmental Biology, Genome-Wide Association Study
Abstract

Common diseases such as type 2 diabetes are phenotypically heterogeneous. Obesity is a major risk factor for type 2 diabetes, but patients vary appreciably in body mass index. We hypothesized that the genetic predisposition to the disease may be different in lean (BMI, Author Summary Individuals with Type 2 diabetes (T2D) can present with variable clinical characteristics. It is well known that obesity is a major risk factor for type 2 diabetes, yet patients can vary considerably—there are many lean diabetes patients and many overweight people without diabetes. We hypothesized that the genetic predisposition to the disease may be different in lean (BMI

Published
2012

144. Genome-Wide Association Study to Identify Common Variants Associated with Brachial Circumference: A Meta-Analysis of 14 Cohorts

Author

Daniele Cusi, Juho Wedenoja, Beate St Pourcain, Kirsi H. Pietiläinen, Ping An, Verneri Anttila, Ozren Polasek, Jennifer E. Huffman, Nicholas J. Timpson, George Dedoussis, Timothy M. Frayling, Harry Campbell, Florian Ernst, Vesna Boraska, Jostein Holmen, Ingrid B. Borecki, Zoltán Kutalik, Jan A. Staessen, Henry Völzke, John R. B. Perry, Peter P. Pramstaller, Ioanna Ntalla, Craig E. Pennell, Debbie A Lawlor, Katherine S. Elliott, Murielle Bochud, Christian Gieger, Marina Pehlić, Ivana Kolcic, Cornelia Huth, Aarno Palotie, Caroline Hayward, Norman Klopp, David M. Evans, Lina Zgaga, Alan James, Gemma Cadby, Eleftheria Zeggini, Arthur W. Musk, Igor Rudan, Susan M. Ring, Lyle J. Palmer, Alexander Teumer, Aaron G. Day-Williams, Annette Peters, Hanieh Yaghootkar, Michel Burnier, Stefania Bandinelli, Lawrence J. Beilin, John-Anker Zwart, H.-Erich Wichmann, Ioanna Tachmazidou, George Davey Smith, Alan F. Wright, Kalliope Panoutsopoulou, Bendik S. Winsvold, Sabine Schipf, Tatijana Zemunik, Veronique Vitart, Nicole M. Warrington, Jaakko Kaprio, Andrew A. Hicks, Michael A. Province, Eva Albrecht, Erika Salvi, Christopher S. Franklin, Epidemiologie, RS: CARIM School for Cardiovascular Diseases, Department of Medicine, Institute for Molecular Medicine Finland, Haartman Institute (-2014), Department of Medical and Clinical Genetics, Department of Public Health, Hjelt Institute (-2014), Genomics of Neurological and Neuropsychiatric Disorders, and Genetic Epidemiology

Subjects
Male, Heredity, Anatomy and Physiology, Epidemiology, lcsh:Medicine, Genome-wide association study, Overweight, Bioinformatics, FTO gene, FAMILIES, Body Mass Index, Cohort Studies, 0302 clinical medicine, STRENGTH, ARM CIRCUMFERENCE, 030212 general & internal medicine, lcsh:Science, Aged, 80 and over, 0303 health sciences, Multidisciplinary, Anthropometry, WOMEN, Chromosome Mapping, MEN, Genomics, Middle Aged, BODY-FAT DISTRIBUTION, Meta-analysis, Arm, Medicine, SEX, Female, medicine.symptom, Research Article, Adult, Adolescent, Genotype, education, European Continental Ancestry Group, Alpha-Ketoglutarate-Dependent Dioxygenase FTO, Biology, Polymorphism, Single Nucleotide, White People, 03 medical and health sciences, AGE, Genome Analysis Tools, Genetic model, medicine, Genetics, Humans, Genetic Predisposition to Disease, Obesity, FTO GENE, 030304 developmental biology, Nutrition, Aged, lcsh:R, Proteins, Human Genetics, medicine.disease, Metabolic Disorders, lcsh:Q, 3111 Biomedicine, Body mass index, Population Genetics, Demography, Genome-Wide Association Study
Abstract

Brachial circumference (BC), also known as upper arm or mid arm circumference, can be used as an indicator of muscle mass and fat tissue, which are distributed differently in men and women. Analysis of anthropometric measures of peripheral fat distribution such as BC could help in understanding the complex pathophysiology behind overweight and obesity. The purpose of this study is to identify genetic variants associated with BC through a large-scale genome-wide association scan (GWAS) meta-analysis. We used fixed-effects meta-analysis to synthesise summary results across 14 GWAS discovery and 4 replication cohorts comprising overall 22,376 individuals (12,031 women and 10,345 men) of European ancestry. Individual analyses were carried out for men, women, and combined across sexes using linear regression and an additive genetic model: adjusted for age and adjusted for age and BMI. We prioritised signals for follow-up in two-stages. We did not detect any signals reaching genome-wide significance. The FTO rs9939609 SNP showed nominal evidence for association (p

Published
2012

145. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes

Author

Sarah Edkins, Anubha Mahajan, Nita G. Forouhi, Danish Saleheen, Lori L. Bonnycastle, Jackie F. Price, Lu Qi, Jasmina Kravic, Laura J. Scott, Susanne Moebus, Timothy M. Frayling, Stéphane Cauchi, Ching-Ti Liu, Michael Boehnke, Peter M. Nilsson, Lars Lind, James F. Wilson, John Beilby, Emil Rehnberg, Veikko Salomaa, Richard N. Bergman, Thomas Illig, Ruth J. F. Loos, Martina Müller-Nurasyid, Andrew Crenshaw, Karl-Heinz Jöckel, Krista Fischer, James B. Meigs, Rob M. van Dam, George Dedoussis, Christopher J. Groves, Julia Meyer, Valur Emilsson, Timo Saaristo, Kees Hovingh, Joseph Trakalo, Peter Kraft, André G. Uitterlinden, Valgerdur Steinthorsdottir, Cecilia M. Lindgren, Denis Rybin, Gonçalo R. Abecasis, Andrew T. Hattersley, Sonia Shah, Bruna Gigante, Jaakko Tuomilehto, Pierre Fontanillas, Kay-Tee Khaw, Annette Peters, Andrew D. Johnson, Rafn Benediktsson, Candace Guiducci, Andrew P. Morris, Tõnu Esko, Bo Isomaa, Anne U. Jackson, Beverley Balkau, Peter Donnelly, Thomas W. Mühleisen, Barbara Thorand, Tom Wilsgaard, Alan R. Shuldiner, David J. Hunter, Roman Wennauer, Karl Gertow, Wen Hong L. Kao, Alan James, Cordelia Langford, Christian Herder, Timo A. Lakka, Soumya Raychaudhuri, Jian'an Luan, Katharine R. Owen, Jennie Hui, Francis S. Collins, Juha Saltevo, David Couper, Bernhard O. Boehm, Sonali Pechlivanis, Raimund Erbel, Suthesh Sivapalaratnam, Markku Laakso, Augustine Kong, Heather M. Stringham, Leena Kinnunen, Kathleen Stirrups, Markus M. Nöthen, Ashok Kumar, Andrew R. Wood, Delilah Zabaneh, Rona J. Strawbridge, Bill Musk, Noël P. Burtt, Eeva Korpi-Hyövälti, Oddgeir L. Holmen, Inga Prokopenko, Marilyn C. Cornelis, Elodie Eury, Angela Silveira, Inês Barroso, Michael Roden, Unnur Thorsteinsdottir, Josée Dupuis, Han Chen, Cornelia M. van Duijn, Samuli Ripatti, Anna Jonsson, Gerald Steinbach, George B. Grant, Kristian Hveem, Andres Metspalu, Astradur B. Hreidarsson, Guillaume Charpentier, John Danesh, Claudia Langenberg, Sirkka Keinänen-Kiukaanniemi, Christian Dina, James S. Pankow, Panos Deloukas, Rainer Rauramaa, Satu Männistö, Kaarel Krjutškov, Eric Boerwinkle, Wendy Winckler, Valeriya Lyssenko, Anders Hamsten, Philippe Froguel, Nancy L. Pedersen, Harry Campbell, Sailaja Vedantam, Nicholas J. Wareham, Hassan Khan, Simon C. Potter, Damiano Baldassarre, Tiinamaija Tuomi, Vasiliki Lagou, Mozhgan Dorkhan, Stavroula Kanoni, Benjamin F. Voight, Wolfgang Rathmann, Tanya M. Teslovich, Antigone S. Dimas, Bengt Sennblad, Olle Melander, Albert Hofman, Mark I. McCarthy, Andrew D. Morris, Fabrizio Veglia, Karen L. Mohlke, Melissa Parkin, Sarah E. Hunt, Frank B. Hu, Elena Tremoli, Gudmar Thorleifsson, Steve E. Humphries, Jason Carey, Eero Lindholm, Alex S. F. Doney, Peter Almgren, Erik Ingelsson, Colin N. A. Palmer, Johanna Kuusisto, Inger Njølstad, Ann-Christine Syvänen, Leena Peltonen, Eric J.G. Sijbrands, Ross M. Fraser, Mieke D. Trip, Ghazala Mirza, Robert W. Lawrence, Neil Robertson, David Altshuler, Harald Grallert, Gunnar Sigurðsson, Kari Stefansson, N. William Rayner, Johan G. Eriksson, Christian Gieger, Emmi Tikkanen, Mustafa Atalay, S Wiltshire, Eleftheria Zeggini, Alena Stančáková, Loukianos S. Rallidis, Jouko Saramies, Stéphane Lobbens, Man Li, Hyun Min Kang, Loic Yengo, Norman Klopp, Ayellet V. Segrè, Carl G. P. Platou, Tom Forsén, Qi Sun, Karin Leander, Caroline S. Fox, Sekar Kathiresan, Jose C. Florez, Leif Groop, Teresa Ferreira, John R. B. Perry, Ulf de Faire, Peter S. Chines, Elizabeth J. Rossin, Vascular Medicine, ACS - Amsterdam Cardiovascular Sciences, Cardiology, Surgery, Dermatology, Epidemiology, and Internal Medicine

Subjects
Male, Linkage disequilibrium, Medizin, 030209 endocrinology & metabolism, Single-nucleotide polymorphism, Genome-wide association study, Type 2 diabetes, Biology, Polymorphism, Single Nucleotide, Article, Linkage Disequilibrium, 03 medical and health sciences, Sex Factors, 0302 clinical medicine, SDG 3 - Good Health and Well-being, Genetics, medicine, Humans, Genetic Predisposition to Disease, Pakistan, Gene, 030304 developmental biology, Genetic association, 0303 health sciences, Case-control study, medicine.disease, Genetic architecture, 3. Good health, Diabetes Mellitus, Type 2, Genes, Evolutionary biology, Case-Control Studies, Female, Genome-Wide Association Study
Abstract

To extend understanding of the genetic architecture and molecular basis of type 2 diabetes (T2D), we conducted a meta-analysis of genetic variants on the Metabochip, including 34,840 cases and 114,981 controls, overwhelmingly of European descent. We identified ten previously unreported T2D susceptibility loci, including two showing sex-differentiated association. Genome-wide analyses of these data are consistent with a long tail of additional common variant loci explaining much of the variation in susceptibility to T2D. Exploration of the enlarged set of susceptibility loci implicates several processes, including CREBBP-related transcription, adipocytokine signaling and cell cycle regulation, in diabetes pathogenesis. © 2012 Nature America, Inc. All rights reserved.

Published
2012

146. Genome-wide meta-analysis of common variant differences between men and women

Author

Igor Rudan, Nora Franceschini, Sheila Ulivi, Maja Barbalić, Gérard Waeber, Jouke-Jan Hottenga, Jian'an Luan, James F. Wilson, Veikko Salomaa, Jacqueline M. Vink, Juan R. González, Aarno Palotie, Elisabeth Widen, Johan G. Eriksson, Alan F. Wright, Michael Stumvoll, Zoltán Kutalik, Caroline Hayward, Mathieu Lemire, Thomas J. Hudson, Johannes H. Smit, Gonneke Willemsen, Daniela Toniolo, Michael Boehnke, Olli T. Raitakari, Tanguy Corre, Dorret I. Boomsma, Harry Campbell, Stefania Bandinelli, Wiek H. van Gilst, Nigel W. Rayner, Kalliope Panoutsopoulou, Albert Hofman, Vasiliki Lagou, Alexander Teumer, Nicholas G. Martin, Dorine W. Swinkels, Jorma Viikari, Tamara B. Harris, Momoko Horikoshi, Massimo Mangino, Nicole M. Warrington, Kay-Tee Khaw, Adamo Pio D'Adamo, Lambertus A. Kiemeney, Tim D. Spector, Martin den Heijer, Evelin Mihailov, Wei Ang, Samuli Ripatti, Markus Perola, Nicola Pirastu, Ozren Polasek, Mika Kähönen, Albert V. Smith, Anke Tönjes, Michela Traglia, Jing Hua Zhao, Gerjan Navis, Christian Gieger, Stefan Schreiber, André G. Uitterlinden, Eva Albrecht, Inês Barroso, Marja-Liisa Lokki, Andrew C. Heath, Eco J. C. de Geus, H.-Erich Wichmann, Grant W. Montgomery, Armand Valsesia, Marjo-Riitta Järvelin, Reiner Biffar, Krista Fischer, Markku S. Nieminen, Jacques S. Beckmann, Ellen W. Demerath, Fernando Rivadeneira, Yali Xue, Vilmundur Gudnason, Christina Loley, Graham R. S. Ritchie, Giorgia Girotto, Lisette Stolk, Terho Lehtimäki, Annette Peters, Jeanette Erdmann, Lorraine Southam, Vincenza Colonna, So-Youn Shin, Andres Metspalu, Tõnu Esko, Craig E. Pennell, Jaakko Tuomilehto, Vesna Boraska, Nilesh J. Samani, Karola Rehnström, Antonietta Robino, Anne U. Jackson, Irene Mateo Leach, Nicholas J. Wareham, Manolis Kogevinas, Toshiko Tanaka, Heribert Schunkert, Sarah E. Medland, Juha Sinisalo, Wolfgang Hoffmann, John P. Newnham, Peter Vollenweider, Dale R. Nyholt, Lenore J. Launer, Luigi Ferrucci, Brent W. Zanke, Pim van der Harst, Ana Jerončić, Nicole Soranzo, Joyce B. J. van Meurs, Lina Zgaga, Christian Hengstenberg, Timothy M. Frayling, Eleftheria Zeggini, Iris M. Heid, Brenda W.J.H. Penninx, Norman Klopp, Ruth J. F. Loos, Antti Jula, Henry Völzke, John R. B. Perry, V., Boraska, A., Jeroncic, V., Colonna, L., Southam, D. R., Nyholt, N., William Rayner, J. R. B., Perry, D., Toniolo, E., Albrecht, W., Ang, S., Bandinelli, M., Barbalic, I., Barroso, J. S., Beckmann, R., Biffar, D., Boomsma, H., Campbell, T., Corre, J., Erdmann, T., Esko, K., Fischer, N., Franceschini, T. M., Frayling, Girotto, Giorgia, J. R., Gonzalez, T. B., Harri, A. C., Heath, I. M., Heid, W., Hoffmann, A., Hofman, M., Horikoshi, J., Hua Zhao, A. U., Jackson, J. J., Hottenga, A., Jula, M., Kahonen, K. T., Khaw, L. A., Kiemeney, N., Klopp, Z., Kutalik, V., Lagou, L. J., Launer, T., Lehtimaki, M., Lemire, M. L., Lokki, C., Loley, J., Luan, M., Mangino, I., Mateo Leach, S. E., Medland, E., Mihailov, G. W., Montgomery, G., Navi, J., Newnham, M. S., Nieminen, A., Palotie, K., Panoutsopoulou, A., Peter, Pirastu, Nicola, O., Polasek, K., Rehnstrom, S., Ripatti, G. R. S., Ritchie, F., Rivadeneira, Robino, Antonietta, N. J., Samani, S. Y., Shin, J., Sinisalo, J. H., Smit, N., Soranzo, L., Stolk, D. W., Swinkel, T., Tanaka, A., Teumer, A., Tonje, Traglia, Michela, J., Tuomilehto, A., Valsesia, W. H., van Gilst, J. B. J., van Meur, A. V., Smith, J., Viikari, J. M., Vink, G., Waeber, N. M., Warrington, E., Widen, G., Willemsen, A. F., Wright, B. W., Zanke, L., Zgaga, M., Boehnke, D'Adamo, ADAMO PIO, E., de Geu, E. W., Demerath, M., den Heijer, J. G., Eriksson, L., Ferrucci, C., Gieger, V., Gudnason, C., Hayward, C., Hengstenberg, T. J., Hudson, M. R., Jarvelin, M., Kogevina, R. J. F., Loo, N. G., Martin, A., Metspalu, C. E., Pennell, B. W., Penninx, M., Perola, O., Raitakari, V., Salomaa, S., Schreiber, H., Schunkert, T. D., Spector, M., Stumvoll, A. G., Uitterlinden, S., Ulivi, P., van der Harst, P., Vollenweider, H., Volzke, N. J., Wareham, H. E., Wichmann, J. F., Wilson, I., Rudan, Y., Xue, E., Zeggini, Biological Psychology, EMGO+ - Musculoskeletal Health, Medical Research Council (MRC), Psychiatry, Internal medicine, EMGO - Musculoskeletal health, Cardiovascular Centre (CVC), Lifestyle Medicine (LM), Groningen Kidney Center (GKC), Vascular Ageing Programme (VAP), Wellcome Trust Case Control Consortium, Surgery, Epidemiology, Medical Oncology, Internal Medicine, Hematology, Immunology, and Clinical Genetics

Subjects
Male, Netherlands Twin Register (NTR), sex differences, Iron metabolism Pathogenesis and modulation of inflammation [IGMD 7], Genome-wide association study, Aetiology, screening and detection [ONCOL 5], DISEASE, meta-analysi, 0302 clinical medicine, 5. Gender equality, Gene Frequency, Gender differences, GWAS, Genetics (clinical), SEX-RATIO, 11 Medical and Health Sciences, Genetics, Genetics & Heredity, 0303 health sciences, Association Studies Articles, General Medicine, ASSOCIATION, male-to-female sex ratio, meta-analysis, TIME, HUMAN SEX-RATIO, 030220 oncology & carcinogenesis, SIMULATION, Female, Wellcome Trust Case Control Consortium, Life Sciences & Biomedicine, Sex ratio, Biochemistry & Molecular Biology, GENES, BIRTH, European Continental Ancestry Group, Sexism, Single-nucleotide polymorphism, Biology, Human sex ratio, Polymorphism, Single Nucleotide, White People, 03 medical and health sciences, Sex Factors, Humans, Sex Ratio, Allele, Molecular Biology, Allele frequency, Health aging / healthy living Cardiovascular diseases [IGMD 5], 030304 developmental biology, Genetic association, Molecular epidemiology Aetiology, screening and detection [NCEBP 1], Science & Technology, Models, Genetic, ta3121, 06 Biological Sciences, Minor allele frequency, Genome-Wide Association Study
Abstract

Item does not contain fulltext The male-to-female sex ratio at birth is constant across world populations with an average of 1.06 (106 male to 100 female live births) for populations of European descent. The sex ratio is considered to be affected by numerous biological and environmental factors and to have a heritable component. The aim of this study was to investigate the presence of common allele modest effects at autosomal and chromosome X variants that could explain the observed sex ratio at birth. We conducted a large-scale genome-wide association scan (GWAS) meta-analysis across 51 studies, comprising overall 114 863 individuals (61 094 women and 53 769 men) of European ancestry and 2 623 828 common (minor allele frequency >0.05) single-nucleotide polymorphisms (SNPs). Allele frequencies were compared between men and women for directly-typed and imputed variants within each study. Forward-time simulations for unlinked, neutral, autosomal, common loci were performed under the demographic model for European populations with a fixed sex ratio and a random mating scheme to assess the probability of detecting significant allele frequency differences. We do not detect any genome-wide significant (P < 5 x 10(-8)) common SNP differences between men and women in this well-powered meta-analysis. The simulated data provided results entirely consistent with these findings. This large-scale investigation across approximately 115 000 individuals shows no detectable contribution from common genetic variants to the observed skew in the sex ratio. The absence of sex-specific differences is useful in guiding genetic association study design, for example when using mixed controls for sex-biased traits.

Published
2012

147. Deep resequencing unveils genetic architecture of ADIPOQ and identifies a novel low-frequency variant strongly associated with adiponectin variation

Author

Dana Fraser, Margaret G. Ehm, Vincent Mooser, Xin Yuan, Matthew R. Nelson, Stephanie L. Chissoe, Lon R. Cardon, John C. Whittaker, Li Li, Andrew J. Slater, Dawn Waterworth, Liling Warren, John R. B. Perry, Peter Woollard, Andrew D. Morris, Colin N. A. Palmer, Keith Nangle, Simon Topp, Judong Shen, Jennifer L. Aponte, Matthew D. Hall, and Timothy M. Frayling

Subjects
Endocrinology, Diabetes and Metabolism, 030209 endocrinology & metabolism, Single-nucleotide polymorphism, Type 2 diabetes, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, 0302 clinical medicine, Diabetes mellitus, Mendelian randomization, Genetic variation, medicine, Internal Medicine, Humans, SNP, Genetic Predisposition to Disease, 030304 developmental biology, Genetics, 0303 health sciences, Base Sequence, Adiponectin, Racial Groups, Computational Biology, Genetics/Genomes/Proteomics/Metabolomics, Odds ratio, medicine.disease, 3. Good health, Diabetes Mellitus, Type 2
Abstract

Increased adiponectin levels have been shown to be associated with a lower risk of type 2 diabetes. To understand the relations between genetic variation at the adiponectin-encoding gene, ADIPOQ, and adiponectin levels, and subsequently its role in disease, we conducted a deep resequencing experiment of ADIPOQ in 14,002 subjects, including 12,514 Europeans, 594 African Americans, and 567 Indian Asians. We identified 296 single nucleotide polymorphisms (SNPs), including 30 amino acid changes, and carried out association analyses in a subset of 3,665 subjects from two independent studies. We confirmed multiple genome-wide association study findings and identified a novel association between a low-frequency SNP (rs17366653) and adiponectin levels (P = 2.2E–17). We show that seven SNPs exert independent effects on adiponectin levels. Together, they explained 6% of adiponectin variation in our samples. We subsequently assessed association between these SNPs and type 2 diabetes in the Genetics of Diabetes Audit and Research in Tayside Scotland (GO-DARTS) study, comprised of 5,145 case and 6,374 control subjects. No evidence of association with type 2 diabetes was found, but we were also unable to exclude the possibility of substantial effects (e.g., odds ratio 95% CI for rs7366653 [0.91–1.58]). Further investigation by large-scale and well-powered Mendelian randomization studies is warranted.

Published
2012

148. Abdominal Aortic Aneurysm Is Associated with a Variant in Low-Density Lipoprotein Receptor-Related Protein 1

Author

Wolfgang Lieb, Bruna Gigante, Thodur M. Vasudevan, Georg Homuth, Joseph B. Muhlestein, Mark J. Daly, Andrew P. Morris, Jacqueline de Graaf, Peter Kraft, Ann-Kristin Petersen, André G. Uitterlinden, Jaqueline C M Witteman, Valgerdur Steinthorsdottir, Jutta Palmen, Amanda L. Elliott, Cecilia M. Lindgren, Richard N. Bergman, Benjamin D. Horne, Tony R. Merriman, Robert W. Davies, Jaspal S. Kooner, Gavin Lucas, Carl G. P. Platou, Diederick E. Grobbee, Ruth J. F. Loos, Fulvio Ricceri, Karin Leander, Wen H. L. Kao, Torsten Lauritzen, Qi Sun, Narisu Narisu, Stephan B. Felix, N. William Rayner, Aaron R. Folsom, Robert D. Sayers, Ross D. Blair, John F. Carlquist, Jing Hua Zhao, L. Vicky Phillips, Gabe Crawford, Anne Johnson, Chris Wallace, Paul F. O'Reilly, Jose C. Florez, Andreas Ziegler, Salvatore Panico, Neil R. Robertson, Ruth Frikke-Schmidt, Leif Groop, Pier Mannuccio Mannucci, Stanley L. Hazen, Gerjan Navis, Peter P. Pramstaller, Laura J. Scott, Niels Grarup, Klaus Berger, Christian Gieger, Stephen E. Epstein, Cornelia Huth, Stephanie Tennstedt, Morris J. Brown, Timothy A. Barnes, Naomi Hammond, Ulf de Faire, Vilmundur Gudnason, Marcus Fischer, Nita G. Forouhi, Paolo Vineis, Thomas Quertermous, Christopher Patterson, W.H. Wilson Tang, Konstantinos A. Papadakis, Lincoln Stein, Maciej Tomaszewski, Suthesh Sivapalaratnam, M. S. Sandhu, Feng Zhang, Christa Meisinger, David R. Lewis, Norman Klopp, Roza Blagieva, Gonçalo R. Abecasis, Jeffrey L. Anderson, Lu Qi, Amy J. Swift, Albert Hofman, George Dedoussis, Robert Luben, Daniel J. Rader, Thomas Münzel, Bert Bravenboer, Christopher J. O'Donnell, Elin Org, Veikko Salomaa, Philipp S. Wild, Stephen G. Ellis, Dawn M. Waterworth, Vesela Gateva, Loukianos S. Rallidis, Joseph M. Devaney, kevin Burnand, Robert Clarke, George A. Wells, Harold Snieder, Kay-Tee Khaw, Panos Deloukas, Jaakko Tuomilehto, Louise V. Wain, Eric Boerwinkle, Inke R. König, Amanda J. Bennett, Uwe Völker, Florian Ernst, Markus M. Nöthen, Thomas Sparsø, Jean Tichet, Inga Prokopenko, Paul Johnson, Jaume Marrugat, Marju Orho-Melander, Aloysius G Lieverse, Ian Thomson, Vincent Mooser, Teresa Ferreira, Man Li, Benjamin J. Wright, Ryan P. Welch, Alessandra Allione, Stefan Blankenberg, Veryan Codd, Philippe Froguel, James C. Engert, Pekka Jousilahti, Klaus Stark, Toby Johnson, Cornelia M. van Duijn, Ivo Gut, John J.P. Kastelein, Thomas M. Morgan, Noël P. Burtt, Laura J. McCulloch, Tim D. Spector, Peter S. Chines, Timo T. Valle, Peter Shrader, Christian Dina, Diana Zelenika, Monika Stoll, Peter S. Braund, Harry Campbell, Rainer Rettig, Joep A.W. Teijink, Thomas Illig, Anne Tybjærg-Hansen, Peter Vollenweider, Guangju Zhai, Frits R. Rosendaal, Pau Navarro, James B. Meigs, Ghislain Rocheleau, Li Chen, Pilar Galan, Giuseppe Matullo, Henry Völzke, Samer S. Najjar, Christina Loley, N. Charlotte Onland-Moret, Alison H. Goodall, Riyaz S. Patel, S. Matthijs Boekholdt, Pim van der Harst, John R. B. Perry, Angela Doering, James S. Pankow, Gudmundur Thorgeirsson, Xin Yuan, Patricia B. Munroe, Abbas Dehghan, Tamara B. Smith, Valeriya Lyssenko, Mark I. McCarthy, Andrew T. Hattersley, Simon Futers, Barbara Thorand, Andre G. Uitterlinden, Simon J. Griffin, Winfried März, Nilesh J. Samani, Frank B. Hu, Valeria Romanazzi, Michael N. Weedon, Zouhair Aherrahrou, Ruth McPherson, Benjamin F. Voight, Wolfgang Rathmann, Markus Perola, Stefania Bandinelli, Kathy Stirrups, Hilma Holm, Maja Barbalić, Kiran Musunuru, David Couper, David S. Siscovick, Guillaume Charpentier, Alexandre F.R. Stewart, Patrick Diemert, Leena Peltonen, Serge Hercberg, Robert Roberts, Michael Roden, Rhian Gwilliam, Guillaume Lettre, Eric J.G. Sijbrands, Lambertus A. Kiemeney, Martha Ganser, Silvia Polidoro, Kristin G. Ardlie, Stephen G. Ball, Kristina Bengtsson Boström, Katharine R. Owen, Paul E. de Jong, Felicity Payne, Wendy L. McArdle, Frances M K Williams, Paul Elliott, Roberto Elosua, Devin Absher, Kristian Midthjell, Jan D. Blankensteijn, Nelson B. Freimer, John C. Chambers, G. Kolovou, Karl Andersen, John Webster, Nicholas J. Wareham, Eric E. Schadt, Simon Heath, Diana Rubin, Solveig Gretarsdottir, Willem H. Ouwehand, Oluf Pedersen, Liming Qu, Sandra Eifert, Mary Susan Burnett, Paul Burton, Frank M. van Bockxmeer, Eleftheria Zeggini, Stephen M. Schwartz, Simon C. Potter, Tiinamaija Tuomi, Jeffrey R. Gulcher, David Altshuler, Harald Grallert, Hooman Allayee, Kari Stefansson, Anne H. Child, Sekar Kathiresan, Torben Hansen, Unnur Thorsteinsdottir, Isaac Subirana, Serena Sanna, Muredach P. Reilly, J. Wouter Jukema, H.-Erich Wichmann, François Cambien, Pier Angelica Merlini, Wiek H. van Gilst, Caroline S. Fox, Andrew Smith, Oliviero Olivieri, S Sohrabi, James F. Wilson, Gillian W. Cockerill, Guanming Wu, Andrew D. Morris, Carlos Iribarren, Joshua W. Knowles, Angelo Scuteri, Göran Berglund, Marilyn C. Cornelis, Pascal P. McKeown, Thorsten Reffelmann, Gérard Waeber, Les McNoe, Maris Laan, Dilip K. Naik, Karen L. Mohlke, Matthew Waltham, Rachel E. Clough, Claudia Langenberg, Seamus C. Harrison, Hany Hafez, Timon W. van Haeften, Carlotta Sacerdote, Robert Sladek, Nicola Martinelli, Declan Bradley, Cristen J. Willer, Sarah E. Hunt, Sven Cichon, Udo Seedorf, Winston Hide, Arne Schillert, Cuno S.P.M. Uiterwaal, Steve E. Humphries, Andre A van Rij, Stéphane Cauchi, Michael Boehnke, Beverley M. Shields, Suzannah Bumpstead, Diane M. Becker, Ron Do, Heribert Schunkert, Jacques S. Beckmann, Alistair S. Hall, Mike Sampson, Christine Proença, Lachlan J. M. Coin, Rob M. van Dam, Mohan U. Sivananthan, Martin Farrall, B. Gerry Hill, Simonetta Guarrera, Thijs T. W. van Herpt, Sonia S. Anand, Peter M. Nilsson, Arne Pfeufer, Rafn Benediktsson, Candace Guiducci, Lee M. Kaplan, Michel Marre, Thomas Meitinger, Annette F. Baas, Graham A. Hitman, Roberto Lorbeer, Flora Peyvandi, David J. Hunter, Seraya Maouche, G. Mark Lathrop, Michael R. Erdos, Thomas W. Mühleisen, L. Adrienne Cupples, Anne E. Hughes, Ayellet V. Segrè, Igor Rudan, Kijoung Song, Reijo Laaksonen, G. Bragi Walters, Christopher P. Nelson, Christopher S. Franklin, Richard M. Watanabe, Mattijs E. Numans, Christina Willenborg, Jeanette Erdmann, Alessandra Di Gregorio, John M. C. Connell, Soumya Raychaudhuri, Jian'an Luan, Anthony J. Balmforth, Yurii S. Aulchenko, Arne Schäfer, Catherine M. Rice, Tanja Zeller, Grace Yu, Augustine Kong, Matthew M Thompson, Diego Ardissino, Oliver Hofmann, John R. Thompson, J.B. Wild, Alexander Teumer, Ulf Gyllensten, David P. Strachan, Martin D. Tobin, Michael A. Kaiser, Steve McCarroll, Beverley Balkau, Stephen J. Newhouse, Michael Preuss, John A. Spertus, Janja Nahrstaedt, Neelam Hassanali, Gunnar Sigurdsson, Jaapjan D. Snoep, Angela Döring, Todd Green, D. Julian A. Scott, Christian Herder, Bo Isomaa, Anne U. Jackson, David Hadley, Domenico Girelli, Jes S. Lindholt, Toshiko Tanaka, Ruth Topless, Bernhard O. Boehm, Jana V. van Vliet-Ostaptchouk, Anna-Liisa Hartikainen, Anneli Pouta, Anuj Goel, Stefan Schreiber, Kristian Hveem, Gabriel Crawford, Pierre Meneton, Jürgen Schrezenmeir, Andre M. van Rij, Markku Laakso, Richa Saxena, Joshua C. Bis, Samy Hadjadj, Anders Franco-Cereceda, Noha Lim, Christopher J. Groves, Klaus Strassburger, Stefan E Matthiasson, M. Lourdes Sampietro, Josée Dupuis, Morris J. Bown, Cisca Wijmenga, Shu Ye, Jennifer Freyer, Anders Hamsten, Christian Hengstenberg, Olle Melander, Sarah Edkins, Alberto Smith, Luigi Ferrucci, Murielle Bochud, Lori L. Bonnycastle, Gregory T. Jones, Manuela Uda, Lasse Folkersen, Timothy M. Frayling, Giovanni Tognoni, Torben Jørgensen, Anna F. Dominiczak, Michiel L. Bots, Mario A. Morken, Ian Buysschaert, Colin N. A. Palmer, Andrew Hill, Mark J. Caulfield, Nicolas Sylvius, Nicole Soranzo, Susana Eyheramendy, Christopher Newton-Cheh, Eran Halperin, Mandy van Hoek, Stephen A. Badger, Paul Scheet, Gudmar Thorleifsson, Themistocles L. Assimes, Inês Barroso, Sheila Bingham, Nour Eddine El Mokhtari, Yvonne T. van der Schouw, Andrew J. Lotery, Heather M. Stringham, Marcus Dörr, Per Eriksson, Mark Walker, Mette Refstrup, Anna L. Gloyn, Ann-Christine Syvänen, John F. Peden, Diether Lambrechts, Arshed A. Quyyumi, Katherine S. Elliott, Jonathan Golledge, Edward G. Lakatta, Serkalem Demissie, Lewis C. Becker, Alex S. F. Doney, Najaf Amin, Hugh Watkins, Johanna Kuusisto, Paul Norman, Marjo-Riitta Järvelin, Annette Peters, David Schlessinger, Janet T. Powell, Surgery, ICaR - Ischemia and repair, and Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)

Subjects
Male, VASCULAR WALL, Genome-wide association study, 030204 cardiovascular system & hematology, Bioinformatics, Aortic aneurysm, 0302 clinical medicine, Risk Factors, Odds Ratio, Genetics(clinical), Genetics (clinical), Aorta, 0303 health sciences, Cardiovascular diseases [NCEBP 14], Homozygote, Abdominal aortic aneurysm, Organ Specificity, Data Interpretation, Statistical, CORONARY-ARTERY-DISEASE, Female, METALLOPROTEINASE, Sterol Regulatory Element Binding Protein 1, Low Density Lipoprotein Receptor-Related Protein-1, medicine.medical_specialty, SUSCEPTIBILITY LOCI, Locus (genetics), Biology, Polymorphism, Single Nucleotide, DISSECTIONS, Article, Molecular epidemiology [NCEBP 1], 03 medical and health sciences, SDG 3 - Good Health and Well-being, Genome-wide associaton, Coronary-artery-disease, Susceptibility loci, Sequence variant, Vascular wall, Metalloproteinase, Atherosclerosis, Identification, Metaanalysis, Dissections, medicine.artery, Internal medicine, Cell Line, Tumor, medicine, Genetics, Humans, Genetic Predisposition to Disease, ddc:610, GENOME-WIDE ASSOCIATION, METAANALYSIS, 030304 developmental biology, Genetic association, Molecular epidemiology Aetiology, screening and detection [NCEBP 1], Aged, IDENTIFICATION, Case-control study, Odds ratio, medicine.disease, Endocrinology, ATHEROSCLEROSIS, SEQUENCE VARIANT, Genetic Loci, Case-Control Studies, Aortic Aneurysm, Abdominal, Follow-Up Studies, Genome-Wide Association Study
Abstract

Contains fulltext : 97601.pdf (Publisher’s version ) (Closed access) Abdominal aortic aneurysm (AAA) is a common cause of morbidity and mortality and has a significant heritability. We carried out a genome-wide association discovery study of 1866 patients with AAA and 5435 controls and replication of promising signals (lead SNP with a p value < 1 x 10(-5)) in 2871 additional cases and 32,687 controls and performed further follow-up in 1491 AAA and 11,060 controls. In the discovery study, nine loci demonstrated association with AAA (p < 1 x 10(-5)). In the replication sample, the lead SNP at one of these loci, rs1466535, located within intron 1 of low-density-lipoprotein receptor-related protein 1 (LRP1) demonstrated significant association (p = 0.0042). We confirmed the association of rs1466535 and AAA in our follow-up study (p = 0.035). In a combined analysis (6228 AAA and 49182 controls), rs1466535 had a consistent effect size and direction in all sample sets (combined p = 4.52 x 10(-10), odds ratio 1.15 [1.10-1.21]). No associations were seen for either rs1466535 or the 12q13.3 locus in independent association studies of coronary artery disease, blood pressure, diabetes, or hyperlipidaemia, suggesting that this locus is specific to AAA. Gene-expression studies demonstrated a trend toward increased LRP1 expression for the rs1466535 CC genotype in arterial tissues; there was a significant (p = 0.029) 1.19-fold (1.04-1.36) increase in LRP1 expression in CC homozygotes compared to TT homozygotes in aortic adventitia. Functional studies demonstrated that rs1466535 might alter a SREBP-1 binding site and influence enhancer activity at the locus. In conclusion, this study has identified a biologically plausible genetic variant associated specifically with AAA, and we suggest that this variant has a possible functional role in LRP1 expression. 9 p.

Published
2011

149. Eight common genetic variants associated with serum DHEAS levels suggest a key role in ageing mechanisms

Author

Timothy M. Frayling, Anna Murray, Massimo Mangino, David Melzer, Florian Ernst, Marcello Maggio, Åsa K. Hedman, Frank H. de Jong, Robin Haring, Alexander Teumer, Jordana T. Bell, Fernando Rivadeneira, Li Xi, Albert Hofman, Claes Ohlsson, Joel Eriksson, Lisette Stolk, Mattias Lorentzon, Iva Miljkovic, Wei Vivian Zhuang, Luigi Ferrucci, Elin Grundberg, Nicole Soranzo, Yongmei Liu, Liesbeth Vandenput, Shalender Bhasin, Joanne M. Murabito, Annemarie Koster, Brenda W.J.H. Penninx, Henri Wallaschofski, Tim D. Spector, Guangju Zhai, Anna Eriksson, Daniel Glass, Henry Völzke, John R. B. Perry, Douglas P. Kiel, Alexandra C. Nica, Ramachandran S. Vasan, Kathryn L. Lunetta, Heyo K. Kroemer, Tamara B. Harris, Andrea D. Coviello, Scott Wilson, André G. Uitterlinden, Kerrin S. Small, Internal Medicine, Public Health, Epidemiology, Psychiatry, EMGO - Mental health, and EMGO+ - Mental Health

Subjects
Male, Cancer Research, Linkage disequilibrium, Aging, Epidemiology, Gene Expression, Genome-wide association study, Type 2 diabetes, QH426-470, Linkage Disequilibrium, chemistry.chemical_compound, 0302 clinical medicine, Endocrinology, Gene expression, Genetics (clinical), 0303 health sciences, Bcl-2-Like Protein 11, Dehydroepiandrosterone Sulfate, Genomics, Middle Aged, 3. Good health, DNA-Binding Proteins, Liver, 030220 oncology & carcinogenesis, Medicine, Female, Aryl Hydrocarbon Hydroxylases, Sulfotransferases, Research Article, Adult, medicine.medical_specialty, Kruppel-Like Transcription Factors, Single-nucleotide polymorphism, Biology, Polymorphism, Single Nucleotide, Actin-Related Protein 2-3 Complex, White People, Biological pathway, 03 medical and health sciences, Young Adult, Dehydroepiandrosterone sulfate, SDG 3 - Good Health and Well-being, Internal medicine, Proto-Oncogene Proteins, medicine, Genetics, Humans, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Adaptor Proteins, Signal Transducing, Aged, Cytochrome P-450 CYP2C9, Homeodomain Proteins, Membrane Proteins, medicine.disease, chemistry, Ageing, Geriatrics, Apoptosis Regulatory Proteins, Genome-Wide Association Study, Transcription Factors
Abstract

Dehydroepiandrosterone sulphate (DHEAS) is the most abundant circulating steroid secreted by adrenal glands—yet its function is unknown. Its serum concentration declines significantly with increasing age, which has led to speculation that a relative DHEAS deficiency may contribute to the development of common age-related diseases or diminished longevity. We conducted a meta-analysis of genome-wide association data with 14,846 individuals and identified eight independent common SNPs associated with serum DHEAS concentrations. Genes at or near the identified loci include ZKSCAN5 (rs11761528; p = 3.15×10−36), SULT2A1 (rs2637125; p = 2.61×10−19), ARPC1A (rs740160; p = 1.56×10−16), TRIM4 (rs17277546; p = 4.50×10−11), BMF (rs7181230; p = 5.44×10−11), HHEX (rs2497306; p = 4.64×10−9), BCL2L11 (rs6738028; p = 1.72×10−8), and CYP2C9 (rs2185570; p = 2.29×10−8). These genes are associated with type 2 diabetes, lymphoma, actin filament assembly, drug and xenobiotic metabolism, and zinc finger proteins. Several SNPs were associated with changes in gene expression levels, and the related genes are connected to biological pathways linking DHEAS with ageing. This study provides much needed insight into the function of DHEAS., Author Summary Dehydroepiandrosterone sulphate (DHEAS), mainly secreted by the adrenal gland, is the most abundant circulating steroid in humans. It shows a significant physiological decline after the age of 25 and diminishes about 95% by the age of 85 years, which has led to speculation that a relative DHEAS deficiency may contribute to the development of common age-related diseases or diminished longevity. Twin- and family-based studies have shown that there is a substantial genetic effect with heritability estimate of 60%, but no specific genes regulating serum DHEAS concentration have been identified to date. Here we take advantage of recent technical and methodological advances to examine the effects of common genetic variants on serum DHEAS concentrations. By examining 14,846 Caucasian individuals, we show that eight common genetic variants are associated with serum DHEAS concentrations. Genes at or near these genetic variants include BCL2L11, ARPC1A, ZKSCAN5, TRIM4, HHEX, CYP2C9, BMF, and SULT2A1. These genes have various associations with steroid hormone metabolism—co-morbidities of ageing including type 2 diabetes, lymphoma, actin filament assembly, drug and xenobiotic metabolism, and zinc finger proteins—suggesting a wider functional role for DHEAS than previously thought.

Published
2011

150. Genetic determinants of serum testosterone concentrations in men

Author

Uwe Völker, Brenda W.J.H. Penninx, André G. Uitterlinden, Douglas P. Kiel, Abdelouahid Tajar, John-Olov Jansson, Frederick C. W. Wu, Yongmei Liu, Tsung Sheng Wu, Andrea D. Coviello, Robin Haring, Stephen R Pye, Luigi Ferrucci, Kathryn L. Lunetta, Henry Völzke, John R. B. Perry, Iva Miljkovic, Tamara B. Harris, Ilpo Huhtaniemi, Mika Kähönen, Albert Hofman, Östen Ljunggren, Maria Nilsson, Ann-Kristin Petersen, Thomas Meitinger, Alexander Teumer, Ramachandran S. Vasan, Joel Eriksson, Magnus Karlsson, Geoffrey L. Hammond, Claes Ohlsson, Henri Wallaschofski, Lisette Stolk, Kate L. Holliday, Frank H. de Jong, Anna Eriksson, Elad Ziv, Olli T. Raitakari, Martin Bidlingmaier, Liesbeth Vandenput, Annemarie Koster, Margit Heier, Wei Vivian Zhuang, Martin Reincke, Marcello Maggio, Joanne M. Murabito, Matthias Nauck, Shalender Bhasin, Anna Murray, David Melzer, J. Viikari, Fernando Rivadeneira, Dan Mellström, David Karasik, Mattias Lorentzon, H.-Erich Wichmann, Terho Lehtimäki, Leo-Pekka Lyytikäinen, Jagadish Ulloor, Abecasis, Gonçalo R, EMGO+ - Mental Health, Internal Medicine, Public Health, Epidemiology, Psychiatry, and EMGO - Mental health

Subjects
Male, Cancer Research, Aging, Epidemiology, Genome-wide association study, QH426-470, Cardiovascular, Body Mass Index, 0302 clinical medicine, Sex hormone-binding globulin, Endocrinology, Sex Hormone-Binding Globulin, 80 and over, 2.1 Biological and endogenous factors, Testosterone, Aetiology, Genetics (clinical), Aged, 80 and over, 0303 health sciences, Nuclear Proteins, Single Nucleotide, Middle Aged, 3. Good health, Genetic Epidemiology, Medicine, Research Article, Human, Adult, medicine.medical_specialty, Globulin, 030209 endocrinology & metabolism, Single-nucleotide polymorphism, and over, Biology, Polymorphism, Single Nucleotide, Chromosomes, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Clinical Research, Internal medicine, hormone-binding globulin, population-based cohort, elderly-men, older men, androgen deficiency, metabolic syndrome, risk-factors, shbg gene, mortality, health, medicine, Genetics, Reproductive Endocrinology, Humans, Allele, Polymorphism, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Alleles, 030304 developmental biology, Aged, Clinical Genetics, Chromosomes, Human, X, Endocrine Physiology, Human Genome, Personalized Medicine, Heritability, medicine.disease, Obesity, EMAS Study Group, Orthopedics, biology.protein, Body mass index, Genome-Wide Association Study, Developmental Biology
Abstract

Testosterone concentrations in men are associated with cardiovascular morbidity, osteoporosis, and mortality and are affected by age, smoking, and obesity. Because of serum testosterone's high heritability, we performed a meta-analysis of genome-wide association data in 8,938 men from seven cohorts and followed up the genome-wide significant findings in one in silico (n = 871) and two de novo replication cohorts (n = 4,620) to identify genetic loci significantly associated with serum testosterone concentration in men. All these loci were also associated with low serum testosterone concentration defined as, Author Summary Testosterone is the most important testicular androgen in men. Low serum testosterone concentrations are associated with cardiovascular morbidity, metabolic syndrome, type 2 diabetes mellitus, atherosclerosis, osteoporosis, sarcopenia, and increased mortality risk. Thus, there is growing evidence that serum testosterone is a valuable biomarker of men's overall health status. Studies in male twins indicate that there is a strong heritability of serum testosterone. Here we perform a large-scale genome-wide association study to examine the effects of common genetic variants on serum testosterone concentrations. By examining 14,429 men, we show that genetic variants in the sex hormone-binding globulin (SHBG) locus and on the X chromosome are associated with a substantial variation in serum testosterone concentrations and increased risk of low testosterone. The reported associations may now be used in order to better understand the functional background of recently identified disease associations related to low testosterone. Importantly, we identified the first known genetic variant, which affects SHBG's affinity for binding testosterone and the free testosterone fraction and could therefore influence the calculation of free testosterone. This finding suggests that individual-based SHBG-testosterone affinity constants are required depending on the genotype of this single-nucleotide polymorphism.

Published
2011

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