Author: "Claudia Schurmann" / Topic: biology - Searchworks@Jio Institute Digital Library Search Results

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1. Exome sequencing and characterization of 49,960 individuals in the UK Biobank

Author: David J. Carey, Cristen J. Willer, Anthony Marcketta, Claudia Schurmann, Leland Barnard, John Penn, Suganthi Balasubramanian, Daren Liu, Joseph B. Leader, Gonçalo R. Abecasis, Marcus B. Jones, John C. Whittaker, Ashutosh K. Pandey, Ida Surakka, David H. Ledbetter, Evan Maxwell, John D. Overton, Andrew Blumenfeld, Michael N. Cantor, Robert A. Scott, Wendy K. Chung, Alexander H. Li, Alexander Lopez, Joshua D. Backman, Matthew R. Nelson, Jeffrey Staples, Giovanni Coppola, Jonathan Marchini, Xiaodong Bai, Kavita Praveen, Alan R. Shuldiner, Claudia Gonzaga-Jauregui, Aris N. Economides, Shareef Khalid, William J Salerno, Bin Ye, Cristopher V. Van Hout, Kristian Hveem, Jeffrey G. Reid, Colm O'Dushlaine, Joshua D. Hoffman, Laura M. Yerges-Armstrong, Nilanjana Banerjee, Sean O'Keeffe, Ioanna Tachmazidou, Lon R. Cardon, Alicia Hawes, Aris Baras, Ashish Yadav, George D. Yancopoulos, and Lukas Habegger
Subjects: Male, 0301 basic medicine, Genes, BRCA2, Genes, BRCA1, Hasso-Plattner-Institut für Digital Engineering GmbH, Penetrance, 030204 cardiovascular system & hematology, Ion Channels, 0302 clinical medicine, Bone Density, Loss of Function Mutation, Neoplasms, Databases, Genetic, Genetics research, Genotype, Exome, Exome sequencing, Biological Specimen Banks, education.field_of_study, Multidisciplinary, Genomics, Middle Aged, Biobank, Pedigree, Phenotype, ras GTPase-Activating Proteins, Female, Kidney Diseases, Population, Collagen Type VI, Computational biology, Biology, Article, DNA sequencing, Varicose Veins, 03 medical and health sciences, Exome Sequencing, Humans, education, Alleles, Aged, Demography, Rare variants, Peptide Fragments, United Kingdom, 030104 developmental biology, ddc:000, Next-generation sequencing
Abstract: The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world1. Here we describe the release of exome-sequence data for the first 49,960 study participants, revealing approximately 4 million coding variants (of which around 98.6% have a frequency of less than 1%). The data include 198,269 autosomal predicted loss-of-function (LOF) variants, a more than 14-fold increase compared to the imputed sequence. Nearly all genes (more than 97%) had at least one carrier with a LOF variant, and most genes (more than 69%) had at least ten carriers with a LOF variant. We illustrate the power of characterizing LOF variants in this population through association analyses across 1,730 phenotypes. In addition to replicating established associations, we found novel LOF variants with large effects on disease traits, including PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on blood cell traits. We further demonstrate the value of exome sequencing by surveying the prevalence of pathogenic variants of clinical importance, and show that 2% of this population has a medically actionable variant. Furthermore, we characterize the penetrance of cancer in carriers of pathogenic BRCA1 and BRCA2 variants. Exome sequences from the first 49,960 participants highlight the promise of genome sequencing in large population-based studies and are now accessible to the scientific community., Exome sequences from the first 49,960 participants in the UK Biobank highlight the promise of genome sequencing in large population-based studies and are now accessible to the scientific community.
Published: 2020

2. Determinants of penetrance and variable expressivity in monogenic metabolic conditions across 77,184 exomes

Author: Julia K. Goodrich, Moriel Singer-Berk, Rachel Son, Abigail Sveden, Jordan Wood, Eleina England, Joanne B. Cole, Ben Weisburd, Nick Watts, Lizz Caulkins, Peter Dornbos, Ryan Koesterer, Zachary Zappala, Haichen Zhang, Kristin A. Maloney, Andy Dahl, Carlos A. Aguilar-Salinas, Gil Atzmon, Francisco Barajas-Olmos, Nir Barzilai, John Blangero, Eric Boerwinkle, Lori L. Bonnycastle, Erwin Bottinger, Donald W. Bowden, Federico Centeno-Cruz, John C. Chambers, Nathalie Chami, Edmund Chan, Juliana Chan, Ching-Yu Cheng, Yoon Shin Cho, Cecilia Contreras-Cubas, Emilio Córdova, Adolfo Correa, Ralph A. DeFronzo, Ravindranath Duggirala, Josée Dupuis, Ma Eugenia Garay-Sevilla, Humberto García-Ortiz, Christian Gieger, Benjamin Glaser, Clicerio González-Villalpando, Ma Elena Gonzalez, Niels Grarup, Leif Groop, Myron Gross, Christopher Haiman, Sohee Han, Craig L. Hanis, Torben Hansen, Nancy L. Heard-Costa, Brian E. Henderson, Juan Manuel Malacara Hernandez, Mi Yeong Hwang, Sergio Islas-Andrade, Marit E. Jørgensen, Hyun Min Kang, Bong-Jo Kim, Young Jin Kim, Heikki A. Koistinen, Jaspal Singh Kooner, Johanna Kuusisto, Soo-Heon Kwak, Markku Laakso, Leslie Lange, Jong-Young Lee, Juyoung Lee, Donna M. Lehman, Allan Linneberg, Jianjun Liu, Ruth J. F. Loos, Valeriya Lyssenko, Ronald C. W. Ma, Angélica Martínez-Hernández, James B. Meigs, Thomas Meitinger, Elvia Mendoza-Caamal, Karen L. Mohlke, Andrew D. Morris, Alanna C. Morrison, Maggie C. Y. Ng, Peter M. Nilsson, Christopher J. O’Donnell, Lorena Orozco, Colin N. A. Palmer, Kyong Soo Park, Wendy S. Post, Oluf Pedersen, Michael Preuss, Bruce M. Psaty, Alexander P. Reiner, Cristina Revilla-Monsalve, Stephen S. Rich, Jerome I. Rotter, Danish Saleheen, Claudia Schurmann, Xueling Sim, Rob Sladek, Kerrin S. Small, Wing Yee So, Timothy D. Spector, Konstantin Strauch, Tim M. Strom, E. Shyong Tai, Claudia H. T. Tam, Yik Ying Teo, Farook Thameem, Brian Tomlinson, Russell P. Tracy, Tiinamaija Tuomi, Jaakko Tuomilehto, Teresa Tusié-Luna, Rob M. van Dam, Ramachandran S. Vasan, James G. Wilson, Daniel R. Witte, Tien-Yin Wong, AMP-T2D-GENES Consortia, Noël P. Burtt, Noah Zaitlen, Mark I. McCarthy, Michael Boehnke, Toni I. Pollin, Jason Flannick, Josep M. Mercader, Anne O’Donnell-Luria, Samantha Baxter, Jose C. Florez, Daniel G. MacArthur, Miriam S. Udler, Institute for Molecular Medicine Finland, Clinicum, Centre of Excellence in Complex Disease Genetics, Leif Groop Research Group, HUS Abdominal Center, University of Helsinki, Department of Medicine, Tiinamaija Tuomi Research Group, Department of Public Health, NIH - National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) (Estados Unidos), NIH - National Institute of Child Health and Human Development (NICHD) (Estados Unidos), and American Diabetes Association
Subjects: 0301 basic medicine, Multifactorial Inheritance, LD SCORE REGRESSION, General Physics and Astronomy, MEDICAL GENETICS, Penetrance, Disease, DISEASE, 0302 clinical medicine, Genotype, Exome, Exome sequencing, Genetics, RISK, Multidisciplinary, Molecular medicine, Endocrine system and metabolic diseases, ASSOCIATION, RARE VARIANTS, LOW-FREQUENCY, Medical genomics, Adult, Science, Biology, AMERICAN-COLLEGE, Risk Assessment, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Diabetes mellitus, medicine, Humans, Genetic Predisposition to Disease, CLINICAL EXOME, Monogenic Diabetes, Dyslipidemias, MUTATIONS, Genetic variants, General Chemistry, medicine.disease, Biomarker (cell), 030104 developmental biology, Biological Variation, Population, Diabetes Mellitus, Type 2, 3121 General medicine, internal medicine and other clinical medicine, 030217 neurology & neurosurgery, Biomarkers
Abstract: Hundreds of thousands of genetic variants have been reported to cause severe monogenic diseases, but the probability that a variant carrier develops the disease (termed penetrance) is unknown for virtually all of them. Additionally, the clinical utility of common polygenetic variation remains uncertain. Using exome sequencing from 77,184 adult individuals (38,618 multi-ancestral individuals from a type 2 diabetes case-control study and 38,566 participants from the UK Biobank, for whom genotype array data were also available), we apply clinical standard-of-care gene variant curation for eight monogenic metabolic conditions. Rare variants causing monogenic diabetes and dyslipidemias display effect sizes significantly larger than the top 1% of the corresponding polygenic scores. Nevertheless, penetrance estimates for monogenic variant carriers average 60% or lower for most conditions. We assess epidemiologic and genetic factors contributing to risk prediction in monogenic variant carriers, demonstrating that inclusion of polygenic variation significantly improves biomarker estimation for two monogenic dyslipidemias., Penetrance of variants in monogenic disease and clinical utility of common polygenic variation has not been well explored on a large-scale. Here, the authors use exome sequencing data from 77,184 individuals to generate penetrance estimates and assess the utility of polygenic variation in risk prediction of monogenic variants.
Published: 2021

3. The trans-ancestral genomic architecture of glycemic traits

Author: Albertine J. Oldehinkel, Wieland Kiess, Xueling Sim, Norihiro Kato, Philippe Froguel, Astrid van Hylckama Vlieg, Josée Dupuis, Nanette R. Lee, Symen Ligthart, Harry Campbell, Marta E. Alarcón-Riquelme, P. Eline Slagboom, Massimo Mangino, Tian Xie, Niek Verweij, James B. Meigs, Chaolong Wang, Michael Y. Tsai, Erik Ingelsson, Colin N. A. Palmer, Erik B. van den Akker, Fumihiko Matsuda, Rainer Rauramaa, Yi-Cheng Chang, Lars Lind, Stefan R. Bornstein, Mandy Vogel, Sven Bergmann, Ya X. Wang, Ching-Ti Liu, Annette Schürmann, Michael Boehnke, David J. Porteous, Kazuya Setoh, Qibin Qi, Ayse Demirkan, Francesco Cucca, Allan Linneberg, Claire J. Steves, Jun Liu, Leslie A. Lange, Noël P. Burtt, Diana Kuh, Cassandra N. Spracklen, Ken K. Ong, Charumathi Sabanayagam, Jost B. Jonas, Ele Ferrannini, Lawrence J. Beilin, Qing Duan, Blair H. Smith, Isobel D. Stewart, Alexander P. Reiner, Simon P. Mooijaart, Tim D. Spector, Paul W. Franks, E. Shyong Tai, Mark I. McCarthy, Anna L. Gloyn, D.I. Boomsma, Dennis Raven, Nicholas J. Timpson, Rona J. Strawbridge, George Dedoussis, Susan Redline, Jaeyoung Hong, Harald Grallert, Jagadish Vangipurapu, Rico Rueedi, Diane M. Becker, Marian Beekman, Claudia P. Cabrera, Johannes Waage, Jin Fang Chai, Yii-Der Ida Chen, Graciela E. Delgado, Thibaud S. Boutin, Yang Hai, Yoriko Heianza, Wei Zhao, Andres Metspalu, Tien Yin Wong, Mila Desi Anasanti, Inger Njølstad, Hans Bisgaard, Valeriya Lyssenko, Denis Rybin, Wanqing Wen, Torben Hansen, James F. Wilson, Sameline Grimsgaard, Annette Peters, Michele K. Evans, Damia Noce, Sarah C. Nelson, May E. Montasser, Nan Wang, Geltrude Mingrone, Gudny Eiriksdottir, Nicholas J. Wareham, Fouad Kandeel, Linda S. Adair, Kelvin Lam, Jaana Lindström, Eco J. C. de Geus, Debbie A Lawlor, Sara M. Willems, Xu Lin, Harold Snieder, Matt J. Neville, Naveed Sattar, Chelsea K. Raulerson, Paul M. Ridker, Jer-Yuarn Wu, Weihua Zhang, H. Janaka de Silva, Jana V. van Vliet-Ostaptchouk, Elena Tremoli, Toru Nabika, Jing Hua Zhao, Vilmundur Gudnason, Tao Huang, Robert C. Kaplan, Sohee Han, Mohammad Hadi Zafarmand, Aaron Leong, Yen-Feng Chiu, Kumaraswamy Naidu Chitrala, Ivana Kolcic, Franco Giulianini, Tao Wang, Lu Qi, Stephan J. L. Bakker, Laura J Corbin, Zoltán Kutalik, Bruna Gigante, Willa A. Hsueh, Peter J. van der Most, Tin Louie, Yujie Wang, Stella Trompet, Fernando Rivideneira, Yasumasa Ohyagi, Lynne E. Wagenknecht, Jerry L. Nadler, Michael Stumvoll, Mark O. Goodarzi, Sahoko Ichihara, Jeffrey R. O'Connell, Tomohiro Katsuya, Giorgio Pistis, Alice Stanton, Sirkka Keinänen-Kiukaanniemi, Momoko Horikoshi, Honglan Li, Tanja G. M. Vrijkotte, Caroline Hayward, Karen L. Mohlke, Carola Marzi, Girish N. Nadkarni, Laura J. Rasmussen-Torvik, Alain G. Bertoni, Andrew R. Wood, Annique Claringbould, Mi Yeong Hwang, Hugh Watkins, Heikki A. Koistinen, Mattias Frånberg, Jani Heikkinen, Elizabeth Selvin, Donald W. Bowden, Abbas Dehghan, Christian Fuchsberger, Audrey Y. Chu, Kent D. Taylor, Katherine A. Kentistou, Johanna Kuusisto, Jingyi Tan, Huaixing Li, Eric Boerwinkle, Catharina A. Hartman, Archie Campbell, Kari E. North, Oluf Pedersen, Sölve Elmståhl, Emil V. R. Appel, Chang-Hsun Hsieh, Dennis O. Mook-Kanamori, Rob M. van Dam, Pontiano Kaleebu, Corri Black, Jennifer A. Brody, Bengt Sennblad, Shaofeng Huo, M. Larissa Avilés-Santa, Ruth J. F. Loos, Patricia B. Munroe, Chien-Hsiun Chen, Liang Sun, Zorayr Arzumanyan, Rebecca Rohde, Yasuharu Tabara, Albert V. Smith, Betina H. Thuesen, Niels Grarup, Jorgen Engmann, Tatijana Zemunik, M. Arfan Ikram, Marit E. Jørgensen, Christian Herder, Ching-Yu Cheng, Serena Sanna, Damiano Baldassarre, Tarunveer S. Ahluwalia, Mark J. Caulfield, Anne Ndungu, Carl D. Langefeld, Lisa R. Yanek, Luigi Ferrucci, Ananda R. Wickremasinghe, Raymond Noordam, Trevor A. Mori, Tom Wilsgaard, Mika Kivimäki, Rita R. Kalyani, Alan B. Zonderman, Veronique Vitart, Patricia A. Peyser, Shuiqing Lai, Richa Saxena, Li-Ching Chang, Karin Leander, Wei Huang, Peter Vollenweider, Tanya M. Teslovich, Ying Wu, Shufa Du, Brian E. Cade, Patrik K. E. Magnusson, John C. Chambers, Stephen C. J. Parker, Tamar Sofer, Winfried März, Sharon L.R. Kardia, Peter K. Joshi, Neil R. Robertson, Anny H. Xiang, Fumihiko Takeuchi, N. Amin, Jouke-Jan Hottenga, Carol A. Wang, Stefan Gustafsson, Jung Ho Gong, Penny Gordon-Larsen, Yu-Tang Gao, Abhishek Nag, Gonneke Willemsen, Michael A. Province, Aliki-Eleni Farmaki, Segun Fatumo, Antje Körner, Pim van der Harst, Marie Loh, Kei Hang Katie Chan, Gonçalo R. Abecasis, Nicholette D. Palmer, Simin Liu, Ishminder K. Kooner, Javier Gayán, Arne Astrup, Laura J. Scott, Erwin P. Bottinger, Andrew Wong, Inga Prokopenko, Ping An, Markku Laakso, Matthias Blüher, Susan R. Heckbert, Thomas A. Buchanan, Tatsuaki Matsubara, Andrew P. Morris, Brian H. Chen, Kristi Läll, Teresa Tusie, Timo A. Lakka, Jie Yao, Michael Preuss, Teemu Kuulasmaa, Carlos Lorenzo, Stephen S. Rich, Marie Lauzon, Laura M. Raffield, Pankow S. James, Takahisa Kawaguchi, Kathleen A. Ryan, Wei Zheng, Igor Rudan, Thomas Sparsø, Hugoline G. de Haan, Sandosh Padmanabhan, Richard M. Watanabe, Alicia Huerta-Chagoya, Anette P. Gjesing, Andrew A. Hicks, Richard N. Bergman, Mitsuhiro Yokota, Heather M. Stringham, Bruce M. Psaty, Jian'an Luan, Anuj Goel, Eleanor Wheeler, Masahiro Nakatochi, Young-Jin Kim, Xiao-Ou Shu, Mickaël Canouil, Robert A. Scott, Marika Kaakinen, Mari Nelis, Adolfo Correa, Jaspal S. Kooner, Michiya Igase, Anubha Mahajan, Peter E. H. Schwarz, Craig E. Pennell, Claudia Schurmann, Xiaoran Chai, Ji Chen, Lori L. Bonnycastle, Peter S. Sever, Thorkild I. A. Sørensen, André G. Uitterlinden, Ilja M. Nolte, Gaëlle Marenne, Timothy M. Frayling, Bong-Jo Kim, Kerrin S. Small, Cecilia M. Lindgren, Bernhard O. Böhm, Shih-Yi Lin, Katharina E. Schraut, Cornelia M. van Duijn, Sanghoon Moon, Mark Walker, Chiea Chuen Khor, Ruifang Li-Gao, Qiuyin Cai, Neil Schneiderman, Ko Willems van Dijk, Ozren Polasek, W. Craig Johnson, Dermot F. Reilly, Inês Barroso, Anke Tönjes, Manjinder S. Sandhu, Wen B. Wei, Jose C. Florez, Lorraine Southam, Leif Groop, Lawrence F. Bielak, Peter Kovacs, Jianjun Liu, Jouko Saramies, Helen R. Warren, Man Li, Daniel I. Chasman, Eleftheria Zeggini, Xiaoshuai Zhang, Loic Yengo, Shi Jinxiu, Jirong Long, Xiuqing Guo, Meena Kumari, Leslie J. Raffel, Jill M. Norris, Henrik Vestergaard, Jing He, Peter P. Pramstaller, Diana van Heemst, Kevin Sandow, Marjo-Ritta Jarvelin, Carlos A. Aguilar-Salinas, Peitao Wu, Hortensia Moreno-Macías, Jerome I. Rotter, Kathryn Roll, Frits R. Rosendaal, Bernardo L. Horta, Heming Wang, Fernando Pires Hartwig, Richard A. Jensen, Matti Uusitupa, Rozenn N. Lemaitre, Paul R. H. J. Timmers, Timo Saaristo, Jaakko Tuomilehto, Reedik Mägi, Debashree Ray, J. Wouter Jukema, Claudia Langenberg, Marcus E. Kleber, Francis S. Collins, Klaus Bønnelykke, Lenore J. Launer, Arushi Varshney, Anders Hamsten, European Commission, Génétique, génomique fonctionnelle et biotechnologies (UMR 1078) (GGB), Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO)-Université de Brest (UBO)-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM), Sanger Institute, Wellcome Trust, Marenne, Gaëlle [0000-0002-4363-7170], Varshney, Arushi [0000-0001-9177-9707], Corbin, Laura J [0000-0002-4032-9500], Parker, Stephen CJ [0000-0001-8122-0117], Langenberg, Claudia [0000-0002-5017-7344], Wheeler, Eleanor [0000-0002-8616-6444], Morris, Andrew P [0000-0002-6805-6014], Barroso, Inês [0000-0001-5800-4520], Apollo - University of Cambridge Repository, Lifelines Cohort Study, Meta-Analysis of Glucose and Insulin-related Traits Consortium (MAGIC), de Haan, H.G., van den Akker, E., van der Most, P.J., de Geus, EJC, van Dam, R.M., van Heemst, D., van Hylckama Vlieg, A., van Willems van Dijk, K., de Silva, H.J., van der Harst, P., van Duijn, C., Centre of Excellence in Complex Disease Genetics, HUS Abdominal Center, Institute for Molecular Medicine Finland, Leif Groop Research Group, HUS Internal Medicine and Rehabilitation, Department of Medicine, Department of Biochemistry and Developmental Biology, Helsinki University Hospital Area, University of Helsinki, Clinicum, Department of Public Health, Biological Psychology, APH - Health Behaviors & Chronic Diseases, APH - Personalized Medicine, Physiology, AMS - Musculoskeletal Health, AMS - Tissue Function & Regeneration, APH - Mental Health, Nutrition and Health, APH - Methodology, Epidemiology and Data Science, ACS - Atherosclerosis & ischemic syndromes, APH - Aging & Later Life, ARD - Amsterdam Reproduction and Development, Public and occupational health, Epidemiology, Internal Medicine, Life Course Epidemiology (LCE), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Groningen Institute for Organ Transplantation (GIOT), Groningen Kidney Center (GKC), Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Center for Liver, Digestive and Metabolic Diseases (CLDM), and Cardiovascular Centre (CVC)
Subjects: Blood Glucose, Disease risk, Multifactorial Inheritance, Glycated Hemoglobin A, [SDV]Life Sciences [q-bio], Meta-Analysis of Glucose and Insulin-related Traits Consortium (MAGIC), LOCI, Genome-wide association study, Type 2 diabetes, VARIANTS, GLUCOSE, Epigenesis, Genetic, chemistry.chemical_compound, 0302 clinical medicine, Mechanisms, WIDE ASSOCIATION, genetics, Gene-expression, HEMOGLOBIN, ComputingMilieux_MISCELLANEOUS, 11 Medical and Health Sciences, GENE-EXPRESSION, Genetics, Genetics & Heredity, 0303 health sciences, INSULIN-RESISTANCE, Genome, Loci, 1184 Genetics, developmental biology, physiology, Variants, ALSPAC, Physical Chromosome Mapping, Life Sciences & Biomedicine, Human, Quantitative Trait Loci, Wide association study, Biology, Quantitative trait locus, Article, White People, diseases, MECHANISMS, Quantitative Trait, 03 medical and health sciences, Insulin resistance, Quantitative Trait, Heritable, SDG 3 - Good Health and Well-being, Genetic, Lifelines Cohort Study, Diabetes mellitus, medicine, Humans, Hemoglobin, Heritable, METAANALYSIS, Alleles, 030304 developmental biology, Genetic association, Glycemic, Glycated Hemoglobin, Science & Technology, Genome, Human, Whites, Gene Expression Profiling, DISEASE RISK, Settore MED/13 - ENDOCRINOLOGIA, Insulin-resistance, 06 Biological Sciences, medicine.disease, Glucose, chemistry, Blood Glucose/genetics, European Continental Ancestry Group/genetics, Genome-Wide Association Study, Glycated Hemoglobin A/metabolism, Multifactorial Inheritance/genetics, Quantitative Trait Loci/genetics, Glycated hemoglobin, 030217 neurology & neurosurgery, Meta analysis, Epigenesis, Developmental Biology
Abstract: Glycemic traits are used to diagnose and monitor type 2 diabetes and cardiometabolic health. To date, most genetic studies of glycemic traits have focused on individuals of European ancestry. Here we aggregated genome-wide association studies comprising up to 281,416 individuals without diabetes (30% non-European ancestry) for whom fasting glucose, 2-h glucose after an oral glucose challenge, glycated hemoglobin and fasting insulin data were available. Trans-ancestry and single-ancestry meta-analyses identified 242 loci (99 novel; P-8), 80% of which had no significant evidence of between-ancestry heterogeneity. Analyses restricted to individuals of European ancestry with equivalent sample size would have led to 24 fewer new loci. Compared with single-ancestry analyses, equivalent-sized trans-ancestry fine-mapping reduced the number of estimated variants in 99% credible sets by a median of 37.5%. Genomic-feature, gene-expression and gene-set analyses revealed distinct biological signatures for each trait, highlighting different underlying biological pathways. Our results increase our understanding of diabetes pathophysiology by using trans-ancestry studies for improved power and resolution.A trans-ancestry meta-analysis of GWAS of glycemic traits in up to 281,416 individuals identifies 99 novel loci, of which one quarter was found due to the multi-ancestry approach, which also improves fine-mapping of credible variant sets.
Published: 2021

4. Genetic discovery and risk characterization in type 2 diabetes across diverse populations

Author: Eric Boerwinkle, Lisa R. Yanek, Teresa Tusié-Luna, Lynne R. Wikens, Charles Kooperberg, Richard A. Jensen, Ruth J. F. Loos, Ping An, Xin Sheng, Lauren E. Petty, Yingchang Lu, Girish N. Nadkarni, Martha L. Daviglus, Suhn K. Rhie, Pierre Fontanillas, Lawrence S. Phillips, Cassandra N. Spracklen, Wei-Min Chen, Jennifer E. Below, Maggie C.Y. Ng, Yoonjung Yoonie Joo, Aude Nicolas, Stephanie A. Bien, Mariaelisa Graff, Qibin Qi, Burcu F. Darst, Lawrence F. Bielak, Kari E. North, Salman M. Tajuddin, Brian E. Cade, Christopher A. Haiman, Xueling Sim, Linda M. Polfus, Loic Le Marchand, Steven Buyske, Heather M. Highland, Lorena Orozco, James S. Pankow, Ulrike Peters, Meng Sun, Xiuqing Guo, Michael Preuss, Yesha Patel, Laura M. Raffield, Joseph M. Mercader, Simin Liu, Christopher S. Carlson, Guanjie Chen, Zhaohui Du, Clicerio González-Villalpando, Daniel O. Stram, Ran Tao, Wei Wang, and Claudia Schurmann
Subjects: education.field_of_study, medicine.medical_specialty, Population, Genomics, European population, Type 2 diabetes, Odds ratio, QH426-470, Biology, medicine.disease, Control subjects, Article, Type 2 Diabetes, Risk variant, Epidemiology, Genetics, medicine, Molecular Medicine, education, Genetics (clinical), Genetic Risk Score, Demography
Abstract: Summary: Genomic discovery and characterization of risk loci for type 2 diabetes (T2D) have been conducted primarily in individuals of European ancestry. We conducted a multiethnic genome-wide association study of T2D among 53,102 cases and 193,679 control subjects from African, Hispanic, Asian, Native Hawaiian, and European population groups in the Population Architecture Genomics and Epidemiology (PAGE) and Diabetes Genetics Replication and Meta-analysis (DIAGRAM) Consortia. In individuals of African ancestry, we discovered a risk variant in the TGFB1 gene (rs11466334, risk allele frequency (RAF) = 6.8%, odds ratio [OR] = 1.27, p = 2.06 × 10−8), which replicated in independent studies of African ancestry (p = 6.26 × 10−23). We identified a multiethnic risk variant in the BACE2 gene (rs13052926, RAF = 14.1%, OR = 1.08, p = 5.75 × 10−9), which also replicated in independent studies (p = 3.45 × 10−4). We also observed a significant difference in the performance of a multiethnic genetic risk score (GRS) across population groups (pheterogeneity = 3.85 × 10−20). Comparing individuals in the top GRS risk category (40%–60%), the OR was highest in Asians (OR = 3.08) and European (OR = 2.94) ancestry populations, followed by Hispanic (OR = 2.39), Native Hawaiian (OR = 2.02), and African ancestry (OR = 1.57) populations. These findings underscore the importance of genetic discovery and risk characterization in diverse populations and the urgent need to further increase representation of non-European ancestry individuals in genetics research to improve genetic-based risk prediction across populations.
Published: 2021

5. Rare coding variants in 35 genes associate with circulating lipid levels – a multi-ancestry analysis of 170,000 exomes

Author: Marju Orho-Melander, Humberto García-Ortiz, Xueling Sim, Amp-T D-Genes, Cheol Joo Park, Gina M. Peloso, Jason Flannick, Brian Tomlinson, Hyun Min Kang, Emilio J. Cordova, Stephen S. Rich, Richard A. Gibbs, Angélica Martínez-Hernández, Lorena Orozco, Harsha Doddapaneni, Lisa R. Yanek, Jiwon Lee, Namrata Gupta, Valeriya Lyssenko, Sohee Han, James B. Meigs, Bong-Jo Kim, Bruce M. Psaty, Leslie S. Emery, Kerrin S. Small, Pradeep Natarajan, May E. Montasser, Christian Gieger, Sharon L.R. Kardia, Sarah C. Nelson, Craig L. Hanis, Heikki A. Koistinen, María Elena González-Villalpando, Edmund Chan, Michael Y. Tsai, Benjamin Glaser, Thomas Meitinger, Matthew J. Bown, Mariaelisa Graff, John Danesh, Sekar Kathiresan, Tiinamaija Tuomi, Ramachandran S. Vasan, Gil Atzmon, Alyna T. Khan, Diego Ardissino, Yii-Der Ida Chen, David Zhang, Rob M. van Dam, Wendy S. Post, Barry I. Freedman, D. C. Rao, Michael Preuss, Donna M. Lehman, L. Adrienne Cupples, Colin N. A. Palmer, Claudia H. T. Tam, Hortensia Moreno-Macías, Markku Laakso, Peter Dornbos, Teresa Tusié-Luna, Stella Aslibekyan, Marguerite R. Irvin, Daniel J. Rader, Jee-Young Moon, Eimear E. Kenny, Lisa W. Martin, Jennifer A. Brody, Amit Khera, Erwin P. Bottinger, Sarah E. Graham, Myriam Fornage, Ruth McPherson, Nancy L. Heard-Costa, Michael Boehnke, Clicerio Gonzalez, Ryan W. Kim, Yi-Cheng Chang, Peter M. Nilsson, Yik Ying Teo, Robert Sladek, Cristen J. Willer, Fei Fei Wang, Donna K. Arnett, Mark Chaffin, Karine A. Viaud Martinez, Alanna C. Morrison, Leslie A. Lange, Ravindranath Duggirala, Donna M. Muzny, Kent D. Taylor, Niels Grarup, Soren Germer, Patricia A. Peyser, Brian E. Cade, Lewis C. Becker, Steven A. Lubitz, Nicholette D. Palmer, Susan K. Dutcher, Ronald C.W. Ma, Xuenan Mi, Xiuqing Guo, Hugh Watkins, Eric Boerwinkle, Qibin Qi, Johanna Kuusisto, Christie M. Ballantyne, Tanika N. Kelly, Rajiv Chowdhury, Elvia Mendoza-Caamal, Wing-Yee So, Tien Yin Wong, Torben Hansen, Cecilia Contreras-Cubas, Jeong-Sun Seo, Mi Yeong Hwang, Daekwan Seo, Dajiang J. Liu, Cristina Revilla-Monsalve, Paul S. de Vries, Daniel R. Witte, Yi-Jen Hung, Olle Melander, Karen L. Mohlke, Lucinda Antonacci-Fulton, Francisco Barajas-Olmos, Soo Heon Kwak, Daniel E. Weeks, Claudia Schurmann, Ginger A. Metcalf, Young-Jin Kim, Adrienne M. Stilp, Lori L. Bonnycastle, John Blangero, Ralph A. DeFronzo, Donald W. Bowden, Rasika A. Mathias, Oluf Pedersen, Rozenn N. Lemaitre, Stephen T. McGarvey, Heribert Schunkert, Jaakko Tuomilehto, Farook Thameem, Valentin Fuster, Joshua C. Bis, George Hindy, Allan Linneberg, James G. Wilson, Kyong Soo Park, Sergio A. Islas-Andrade, Ching-Yu Cheng, Won Jung Choi, Minxian X. Wang, Xuzhi Wang, Adolfo Correa, Jai G. Broome, Gail P. Jarvik, Alexander P. Reiner, E. Shyong Tai, Juyoung Lee, Mark I. McCarthy, Nilesh J. Samani, Susan Redline, Carlos A. Aguilar-Salinas, Jerome I. Rotter, Ma. Eugenia Garay-Sevilla, Jiang He, Patrick T. Ellinor, Joseph Park, Joanne E. Curran, Nir Barzilai, Federico Centeno-Cruz, Seonwook Lee, Lawrence F. Bielak, Jianjun Liu, Charles Kooperberg, Juan M. Peralta, Jose C. Florez, Leif Groop, Noël P. Burtt, Margaret Sunitha Selvaraj, Jeffrey R. O'Connell, and Ruth J. F. Loos
Subjects: Genetics, 0303 health sciences, education.field_of_study, Population, Single-nucleotide polymorphism, Genome-wide association study, Biology, DNA sequencing, Minor allele frequency, 03 medical and health sciences, 0302 clinical medicine, SNP, education, Gene, 030217 neurology & neurosurgery, Exome sequencing, 030304 developmental biology
Abstract: Large-scale gene sequencing studies for complex traits have the potential to identify causal genes with therapeutic implications. We performed gene-based association testing of blood lipid levels with rare (minor allele frequency170,000 individuals from multiple ancestries: 97,493 European, 30,025 South Asian, 16,507 African, 16,440 Hispanic/Latino, 10,420 East Asian, and 1,182 Samoan. We identified 35 genes associated with circulating lipid levels. Ten of these: ALB, SRSF2, JAK2, CREB3L3, TMEM136, VARS, NR1H3, PLA2G12A, PPARG and STAB1 have not been implicated for lipid levels using rare coding variation in population-based samples. We prioritize 32 genes identified in array-based genome-wide association study (GWAS) loci based on gene-based associations, of which three: EVI5, SH2B3, and PLIN1, had no prior evidence of rare coding variant associations. Most of the associated genes showed evidence of association in multiple ancestries. Also, we observed an enrichment of gene-based associations for low-density lipoprotein cholesterol drug target genes, and for genes closest to GWAS index single nucleotide polymorphisms (SNP). Our results demonstrate that gene-based associations can be beneficial for drug target development and provide evidence that the gene closest to the array-based GWAS index SNP is often the functional gene for blood lipid levels.
Published: 2020

6. Genetic studies of leptin concentrations implicate leptin in the regulation of early adiposity

Author: Daniel I. Chasman, Torben Hansen, Rebecca S. Fine, Kari E. North, Harald Grallert, Jeffrey Haesser, Jie Yao, Arund D. Pradhan, Peter Kovacs, Mariaelisa Graff, Rebecca D. Jackson, Zoltán Kutalik, James G. Wilson, Neil Robertson, Mika Kähönen, Linda S. Adair, Jennifer Kriebel, Ruth J. F. Loos, Massimo Mangino, Jayne F. Martin Carli, Yiying Zhang, M. Arfan Ikram, Paraskevi Christofidou, Linda Broer, Paul M. Ridker, Barbara McKnight, Satu Männistö, Sophia Metz, Tea Skaaby, Jette Bork-Jensen, Craig E. Pennell, Sophie Molnos, Michael A. Province, Xiuqing Guo, Laura B. L. Wittemans, Stephen J. Lye, Cornelia M. van Duijn, Samuli Ripatti, Ko Willems van Dijk, Tim Kacprowski, America A. Sandoval-Zárate, Hermina Jakupović, Tuomas O. Kilpeläinen, Michael Preuss, Jaeyoung Hong, Cristina Venturini, Ying Wu, Germán D. Carrasquilla, Ivana Prokic, Mary F. Feitosa, Melissa E. Garcia, Paul L. Auer, Leslie A. Lange, Leo-Pekka Lyytikäinen, Kristin L. Young, Tugce Karaderi, Alexander P. Reiner, Tim D. Spector, Anubha Mahajan, Claudia Schurmann, Jerome I. Rotter, Rudolph L. Leibel, Georg Homuth, Claudia A. Doege, Hakon Hakonarson, Nicholas J. Wareham, Najaf Amin, Shuai Wang, Matthias Blüher, Ayse Demirkan, Andrew P. Morris, Charles A. LeDuc, Claudia Langenberg, Hanieh Yaghootkar, Mike A. Nalls, Erik Ingelsson, Dennis O. Mook-Kanamori, Jorge R. Kizer, Carolina Medina-Gomez, Timothy M. Frayling, Colleen M. Sitlani, David A. Mackey, Bruce M. Psaty, Matthias Nauck, Struan F.A. Grant, Konstantin Strauch, Olli T. Raitakari, Alexander Teumer, Mark Walker, Jonathan P. Bradfield, Judith B. Borja, Karen L. Mohlke, Lars Lind, André G. Uitterlinden, Renée de Mutsert, Ruifang Li-Gao, Cassandra N. Spracklen, Jin Li, Anne E. Justice, Cecilia M. Lindgren, Kaiying Guo, Terho Lehtimäki, Pekka Jousilahti, Yingchang Lu, Yii-Der Ida Chen, Sara M. Willems, Tamara B. Harris, Matthew A. Allison, Carol A. Wang, Niels Grarup, Lam Opal Huang, Veikko Salomaa, Jian'an Luan, Robert A. Scott, Kent D. Taylor, James B. Meigs, Ophthalmology, Epidemiology, Internal Medicine, Clinical Genetics, Department of Organisation and Personnel Management, Health Services Management & Organisation (HSMO), Yaghootkar, Hanieh [0000-0001-9672-9477], Kilpeläinen, Tuomas O [0000-0002-8349-3028], and Apollo - University of Cambridge Repository
Subjects: 0301 basic medicine, Leptin, Models, Molecular, medicine.medical_specialty, Genotype, Protein Conformation, Endocrinology, Diabetes and Metabolism, 030209 endocrinology & metabolism, Genome-wide association study, KLF14, Biology, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, Internal Medicine, medicine, Missense mutation, Humans, Allele, Exome, Adiposity, 2. Zero hunger, Racial Groups, digestive, oral, and skin physiology, Gene Expression Regulation, Developmental, Genetic Variation, Genetics/Genomes/Proteomics/Metabolomics, medicine.disease, Obesity, 030104 developmental biology, Endocrinology, hormones, hormone substitutes, and hormone antagonists
Abstract: Leptin influences food intake by informing the brain about the status of body fat stores. Rare LEP mutations associated with congenital leptin deficiency cause severe early-onset obesity that can be mitigated by administering leptin. However, the role of genetic regulation of leptin in polygenic obesity remains poorly understood. We performed an exome-based analysis in up to 57,232 individuals of diverse ancestries to identify genetic variants that influence adiposity-adjusted leptin concentrations. We identify five novel variants, including four missense variants, in LEP, ZNF800, KLHL31, and ACTL9, and one intergenic variant near KLF14. The missense variant Val94Met (rs17151919) in LEP was common in individuals of African ancestry only and its association with lower leptin concentrations was specific to this ancestry (P=2x10-16, n=3,901). Using in vitro analyses, we show that the Met94 allele decreases leptin secretion. We also show that the Met94 allele is associated with higher BMI in young African-ancestry children but not in adults, suggesting leptin regulates early adiposity.
Published: 2020

7. Determinants of penetrance and variable expressivity in monogenic metabolic conditions across 77,184 exomes

Author: Ma Elena Gonzalez, Marit E. Jørgensen, Edmund Chan, Eric Boerwinkle, Craig L. Hanis, Tim M. Strom, Young-Jin Kim, Alanna C. Morrison, Abigail Sveden, Zachary Zappala, Jianjun Liu, Markku Laakso, Russell P. Tracy, Andrew D. Morris, Farook Thameem, Ruth J. F. Loos, Robert Sladek, Moriel Singer-Berk, Jason Flannick, Stephen S. Rich, Angélica Martínez-Hernández, Rob M. van Dam, Wendy S. Post, Michael Boehnke, Peter M. Nilsson, Humberto García-Ortiz, Clicerio González-Villalpando, Samantha Baxter, Yoon Shin Cho, Sergio Islas-Andrade, Colin N. A. Palmer, Claudia H. T. Tam, Nicholas A. Watts, Lizz Caulkins, Rachel Son, Daniel G. MacArthur, Toni I. Pollin, Juan Manuel Malacara Hernandez, Jong-Young Lee, Bruce M. Psaty, Ravindranath Duggirala, Erwin P. Bottinger, Nancy L. Heard-Costa, Donna M. Lehman, Carlos A. Aguilar-Salinas, Juyoung Lee, Haichen Zhang, Mark I. McCarthy, Brian Tomlinson, Leslie A. Lange, Cecilia Contreras-Cubas, Johanna Kuusisto, Danish Saleheen, Juliana C.N. Chan, Andrew Dahl, Konstantin Strauch, Noël P. Burtt, Tien Yin Wong, Niels Grarup, Jerome I. Rotter, Ronald C.W. Ma, Julia K. Goodrich, Anne H. O’Donnell-Luria, Jose C. Florez, Miriam S. Udler-Aubrey, Kristin A. Maloney, James G. Wilson, Ramachandran S. Vasan, Bong-Jo Kim, Leif Groop, Noah Zaitlen, Kerrin S. Small, Heikki A. Koistinen, Donald W. Bowden, Wing-Yee So, Jaakko Tuomilehto, Oluf Pedersen, John C. Chambers, Mi Yeong Hwang, Karen L. Mohlke, John Blangero, Eleina M. England, Elvia Mendoza-Caamal, James B. Meigs, Federico Centeno-Cruz, Michael Preuss, Ralph A. DeFronzo, Joanne B. Cole, Jordan Wood, Allan Linneberg, Benjamin Glaser, Lorena Orozco, Jaspal S. Kooner, Valeriya Lyssenko, Sohee Han, Gil Atzmon, Ma. Eugenia Garay-Sevilla, Tiinamaija Tuomi, Brian E. Henderson, Christopher J. O'Donnell, Hyun Min Kang, Teresa Tusié-Luna, Nir Barzilai, Thomas Meitinger, Christian Gieger, Ben Weisburd, Alexander P. Reiner, Tim D. Spector, Myron D. Gross, E. Shyong Tai, Yik Ying Teo, for Amp-T D-Genes Consortia, Xueling Sim, Emilio J. Cordova, Cristina Revilla-Monsalve, Daniel R. Witte, Francisco Barajas-Olmos, Claudia Schurmann, Lori L. Bonnycastle, Josep M. Mercader, Adolfo Correa, Torben Hansen, Kyong Soo Park, Ching-Yu Cheng, Soo Heon Kwak, Nathalie Chami, Christopher A. Haiman, Xavier Soberón, Josée Dupuis, and Maggie C.Y. Ng
Subjects: Genetics, 0303 health sciences, Genetic variants, Disease, 030204 cardiovascular system & hematology, Biology, medicine.disease, Penetrance, 3. Good health, Biomarker (cell), 03 medical and health sciences, 0302 clinical medicine, Diabetes mellitus, Genotype, medicine, Exome sequencing, 030304 developmental biology, Monogenic Diabetes
Abstract: Hundreds of thousands of genetic variants have been reported to cause severe monogenic diseases, but the probability that a variant carrier will develop the disease (termed penetrance) is unknown for virtually all of them. Additionally, the clinical utility of common polygenetic variation remains uncertain. Using exome sequencing from 77,184 adult individuals (38,618 multi-ancestral individuals from a type 2 diabetes case-control study and 38,566 participants from the UK Biobank, for whom genotype array data were also available), we applied clinical standard-of-care gene variant curation for eight monogenic metabolic conditions. Rare variants causing monogenic diabetes and dyslipidemias displayed effect sizes significantly larger than the top 1% of the corresponding polygenic scores. Nevertheless, penetrance estimates for monogenic variant carriers averaged below 60% in both studies for all conditions except monogenic diabetes. We assessed additional epidemiologic and genetic factors contributing to risk prediction, demonstrating that inclusion of common polygenic variation significantly improved biomarker estimation for two monogenic dyslipidemias.
Published: 2020

8. Trans-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation

Author: Anubha Mahajan, Cassandra N Spracklen, Weihua Zhang, Maggie CY Ng, Lauren E Petty, Hidetoshi Kitajima, Grace Z Yu, Sina Rüeger, Leo Speidel, Young Jin Kim, Momoko Horikoshi, Josep M Mercader, Daniel Taliun, Sanghoon Moon, Soo-Heon Kwak, Neil R Robertson, Nigel W Rayner, Marie Loh, Bong-Jo Kim, Joshua Chiou, Irene Miguel-Escalada, Pietro della Briotta Parolo, Kuang Lin, Fiona Bragg, Michael H Preuss, Fumihiko Takeuchi, Jana Nano, Xiuqing Guo, Amel Lamri, Masahiro Nakatochi, Robert A Scott, Jung-Jin Lee, Alicia Huerta-Chagoya, Mariaelisa Graff, Jin-Fang Chai, Esteban J Parra, Jie Yao, Lawrence F Bielak, Yasuharu Tabara, Yang Hai, Valgerdur Steinthorsdottir, James P Cook, Mart Kals, Niels Grarup, Ellen M Schmidt, Ian Pan, Tamar Sofer, Matthias Wuttke, Chloe Sarnowski, Christian Gieger, Darryl Nousome, Stella Trompet, Jirong Long, Meng Sun, Lin Tong, Wei-Min Chen, Meraj Ahmad, Raymond Noordam, Victor JY Lim, Claudia HT Tam, Yoonjung Yoonie Joo, Chien-Hsiun Chen, Laura M Raffield, Cécile Lecoeur, Nisa M Maruthur, Bram Peter Prins, Aude Nicolas, Lisa R Yanek, Guanjie Chen, Richard A Jensen, Salman Tajuddin, Edmond Kabagambe, Ping An, Anny H Xiang, Hyeok Sun Choi, Brian E Cade, Jingyi Tan, Fernando Abaitua, Linda S Adair, Adebowale Adeyemo, Carlos A Aguilar-Salinas, Masato Akiyama, Sonia S Anand, Alain Bertoni, Zheng Bian, Jette Bork-Jensen, Ivan Brandslund, Jennifer A Brody, Chad M Brummett, Thomas A Buchanan, Mickaël Canouil, Juliana CN Chan, Li-Ching Chang, Miao-Li Chee, Ji Chen, Shyh-Huei Chen, Yuan-Tsong Chen, Zhengming Chen, Lee-Ming Chuang, Mary Cushman, Swapan K Das, H. Janaka de Silva, George Dedoussis, Latchezar Dimitrov, Ayo P Doumatey, Shufa Du, Qing Duan, Kai-Uwe Eckardt, Leslie S Emery, Daniel S Evans, Michele K Evans, Krista Fischer, James S Floyd, Ian Ford, Myriam Fornage, Oscar H Franco, Timothy M Frayling, Barry I Freedman, Christian Fuchsberger, Pauline Genter, Hertzel C Gerstein, Vilmantas Giedraitis, Clicerio González-Villalpando, Maria Elena González-Villalpando, Mark O Goodarzi, Penny Gordon-Larsen, David Gorkin, Myron Gross, Yu Guo, Sophie Hackinger, Sohee Han, Andrew T Hattersley, Christian Herder, Annie-Green Howard, Willa Hsueh, Mengna Huang, Wei Huang, Yi-Jen Hung, Mi Yeong Hwang, Chii-Min Hwu, Sahoko Ichihara, Mohammad Arfan Ikram, Martin Ingelsson, Md. Tariqul Islam, Masato Isono, Hye-Mi Jang, Farzana Jasmine, Guozhi Jiang, Jost B Jonas, Marit E Jørgensen, Torben Jørgensen, Yoichiro Kamatani, Fouad R Kandeel, Anuradhani Kasturiratne, Tomohiro Katsuya, Varinderpal Kaur, Takahisa Kawaguchi, Jacob M Keaton, Abel N Kho, Chiea-Chuen Khor, Muhammad G Kibriya, Duk-Hwan Kim, Katsuhiko Kohara, Jennifer Kriebel, Florian Kronenberg, Johanna Kuusisto, Kristi Läll, Leslie A Lange, Myung-Shik Lee, Nanette R Lee, Aaron Leong, Liming Li, Yun Li, Ruifang Li-Gao, Symen Ligthart, Cecilia M Lindgren, Allan Linneberg, Ching-Ti Liu, Jianjun Liu, Adam E Locke, Tin Louie, Jian’an Luan, Andrea O Luk, Xi Luo, Jun Lv, Valeriya Lyssenko, Vasiliki Mamakou, K Radha Mani, Thomas Meitinger, Andres Metspalu, Andrew D Morris, Girish N. Nadkarni, Jerry L Nadler, Michael A Nalls, Uma Nayak, Ioanna Ntalla, Yukinori Okada, Lorena Orozco, Sanjay R Patel, Mark A Pereira, Annette Peters, Fraser J Pirie, Bianca Porneala, Gauri Prasad, Sebastian Preissl, Laura J Rasmussen-Torvik, Alexander P Reiner, Michael Roden, Rebecca Rohde, Katheryn Roll, Charumathi Sabanayagam, Maike Sander, Kevin Sandow, Naveed Sattar, Sebastian Schönherr, Claudia Schurmann, Mohammad Shahriar, Jinxiu Shi, Dong Mun Shin, Daniel Shriner, Jennifer A Smith, Wing Yee So, Alena Stančáková, Adrienne M Stilp, Konstantin Strauch, Ken Suzuki, Atsushi Takahashi, Kent D Taylor, Barbara Thorand, Gudmar Thorleifsson, Unnur Thorsteinsdottir, Brian Tomlinson, Jason M Torres, Fuu-Jen Tsai, Jaakko Tuomilehto, Teresa Tusie-Luna, Miriam S Udler, Adan Valladares-Salgado, Rob M van Dam, Jan B van Klinken, Rohit Varma, Marijana Vujkovic, Niels Wacher-Rodarte, Ellie Wheeler, Eric A Whitsel, Ananda R Wickremasinghe, Konstantin Willems van Dijk, Daniel R Witte, Chittaranjan S Yajnik, Ken Yamamoto, Toshimasa Yamauchi, Loïc Yengo, Kyungheon Yoon, Canqing Yu, Jian-Min Yuan, Salim Yusuf, Liang Zhang, Wei Zheng, null FinnGen, Leslie J Raffel, Michiya Igase, Eli Ipp, Susan Redline, Yoon Shin Cho, Lars Lind, Michael A Province, Craig L Hanis, Patricia A Peyser, Erik Ingelsson, Alan B Zonderman, Bruce M Psaty, Ya-Xing Wang, Charles N Rotimi, Diane M Becker, Fumihiko Matsuda, Yongmei Liu, Eleftheria Zeggini, Mitsuhiro Yokota, Stephen S Rich, Charles Kooperberg, James S Pankow, James C Engert, Yii-Der Ida Chen, Philippe Froguel, James G Wilson, Wayne HH Sheu, Sharon LR Kardia, Jer-Yuarn Wu, M Geoffrey Hayes, Ronald CW Ma, Tien-Yin Wong, Leif Groop, Dennis O Mook-Kanamori, Giriraj R Chandak, Francis S Collins, Dwaipayan Bharadwaj, Guillaume Paré, Michèle M Sale, Habibul Ahsan, Ayesha A Motala, Xiao-Ou Shu, Kyong-Soo Park, J Wouter Jukema, Miguel Cruz, Roberta McKean-Cowdin, Harald Grallert, Ching-Yu Cheng, Erwin P Bottinger, Abbas Dehghan, E-Shyong Tai, Josee Dupuis, Norihiro Kato, Markku Laakso, Anna Köttgen, Woon-Puay Koh, Colin NA Palmer, Simin Liu, Goncalo Abecasis, Jaspal S Kooner, Ruth JF Loos, Kari E North, Christopher A Haiman, Jose C Florez, Danish Saleheen, Torben Hansen, Oluf Pedersen, Reedik Mägi, Claudia Langenberg, Nicholas J Wareham, Shiro Maeda, Takashi Kadowaki, Juyoung Lee, Iona Y Millwood, Robin G Walters, Kari Stefansson, Simon R Myers, Jorge Ferrer, Kyle J Gaulton, James B Meigs, Karen L Mohlke, Anna L Gloyn, Donald W Bowden, Jennifer E Below, John C Chambers, Xueling Sim, Michael Boehnke, Jerome I Rotter, Mark I McCarthy, and Andrew P Morris
Subjects: 0303 health sciences, Transferability, Translation (biology), Type 2 diabetes, Biology, medicine.disease, 03 medical and health sciences, 0302 clinical medicine, Evolutionary biology, Global health, medicine, Genetic risk, Gene, 030217 neurology & neurosurgery, 030304 developmental biology, Genetic association
Abstract: We assembled an ancestrally diverse collection of genome-wide association studies of type 2 diabetes (T2D) in 180,834 cases and 1,159,055 controls (48.9% non-European descent). We identified 277 loci at genome-wide significance (p-8), including 237 attaining a more stringent trans-ancestry threshold (p-9), which were delineated to 338 distinct association signals. Trans-ancestry meta-regression offered substantial enhancements to fine-mapping, with 58.6% of associations more precisely localised due to population diversity, and 54.4% of signals resolved to a single variant with >50% posterior probability. This improved fine-mapping enabled systematic assessment of candidate causal genes and molecular mechanisms through which T2D associations are mediated, laying foundations for functional investigations. Trans-ancestry genetic risk scores enhanced transferability across diverse populations, providing a step towards more effective clinical translation to improve global health.
Published: 2020

9. Discovery and fine-mapping of height loci via high-density imputation of GWASs in individuals of African ancestry

Author: Mariaelisa Graff, Zhaoming Wang, David R. Weir, Ann W. Hsing, Joel N. Hirschhorn, Rebecca S. Fine, Wei Zheng, William Maixner, Adebowale Adeyemo, Rick A. Kittles, Rebecca Rohde, Krista A. Zanetti, Elizabeth K. Speliotes, Keri L. Monda, Ingrid B. Borecki, Yaming Shao, Suhn K. Rhie, Sanjay R. Patel, Richard S. Cooper, Jerome I. Rotter, Michael J. Thun, William J. Blot, Brendan J. Keating, Michèle M. Sale, Scott M. Williams, Yingchang Lu, Margaret A. Tucker, Eric A. Klein, Uma Nayak, Curtis A. Pettaway, Yii-Der Ida Chen, Sailaja Vedantam, Pamela J. Schreiner, Phyllis J. Goodman, Babatunde L. Salako, Christine Neslund-Dudas, Andrew B. Singleton, Michael F. Press, Neil E. Caporaso, Maureen Sanderson, Diane M. Becker, Michele K. Evans, Margaret R. Spitz, Christopher I. Amos, Susan Redline, Kurt Lohman, Ching-Ti Liu, Hampton L. Leonard, Kris Monroe, Sun J. Kang, David Van Den Berg, Janet L. Stanford, Lewis H. Kuller, Traci M. Bartz, J. M. Zmuda, Christopher S. Carlson, Ruth J. F. Loos, Joanne M. Jordan, Guillaume Lettre, Youfang Liu, Lara Sucheston, Mike A. Nalls, Shad B. Smith, Suzanne Kolb, Lisa B. Signorello, Daniel Shriner, Tamara B. Harris, Larry D. Atwood, Wei-Min Chen, Oladosu Ojengbede, Kristin A. Rand, Claudia Schurmann, Guanjie Chen, Sharon L.R. Kardia, Graham Casey, Lawrence F. Bielak, Dena G. Hernandez, Talin Haritunians, Rajiv Nadukuru, Elisa V. Bandera, Matthew A. Allison, Amidou N'Diaye, Donna K. Arnett, Olufunmilayo I. Olopade, Ellen W. Demerath, Babette S. Zemel, Margaret Wrensch, Myriam Fornage, John K. Wiencke, George J. Papanicolaou, Sara S. Strom, Temidayo O. Ogundiran, Gregory L. Burke, Erin B. Ware, Marian L. Neuhouser, James G. Wilson, Dhananjay Vaidya, Nicholette D. Palmer, Marguerite R. Irvin, JoAnn E. Manson, Benjamin A. Rybicki, Laurence N. Kolonel, Chad D. Huff, Jennifer J. Hu, Jennifer A. Brody, L. Keoki Williams, Leslie A. Lange, Qing Duan, David S. Siscovick, Yongmei Liu, Leslie Bernstein, Jennifer A. Smith, Latchezar Dimitrov, Sarah J. Nyante, Sue A. Ingles, Yu Han H. Hsu, Xifeng Wu, Heather M. Ochs-Balcom, Jingzhong Ding, David V. Conti, L. Adrienne Cupples, Gerry A. Coetzee, Thomas H. Mosley, Kristin L. Young, Donald W. Bowden, Edmond K. Kabagambe, Christine B. Ambrosone, Karen C. Johnson, Patricia A. Peyser, Stefan Ambs, Victoria L. Stevens, Minhui Chen, Carl D. Langefeld, Sonja I. Berndt, Andrew F. Olshan, Qiuyin Cai, Jessica D. Faul, Mary F. Feitosa, Brian E. Cade, Esther M. John, Ann G. Schwartz, Yan V. Sun, Xinruo Zhang, Stephen J. Chanock, Jason H. Moore, Alexander P. Reiner, Caroline S. Fox, Charles Kooperberg, Anne E. Justice, Jin Li, Lorna H. McNeill, Alex Stram, Jie Yao, Xiuqing Guo, Mara Z. Vitolins, Edward A. Ruiz-Narváez, Abdullah Kutlar, Charleston W. K. Chiang, Jing Hua Zhao, Lisa R. Yanek, Poorva Mudgal, John D. Carpten, Barbara V. Howard, Anselm Hennis, Charles N. Rotimi, Ulrich Broeckel, Albert M. Levin, Jonathan P. Bradfield, Curtis C. Harris, Regina G. Ziegler, Brian E. Henderson, Bruce M. Psaty, Adeyinka G. Falusi, Katherine L. Nathanson, Barbara McKnight, Melinda C. Aldrich, Herman A. Taylor, Melissa Garcia, Degui Zhi, Dezheng Huo, Barry I. Freedman, D. C. Rao, Sylvia Wassertheil-Smoller, Jie Zhou, Adam B. Murphy, Eric E. Schadt, Sandra L. Deming, John S. Witte, Julie R. Palmer, Neil A. Zakai, Adesola Ogunniyi, Yun Li, Mary Cushman, Victoria L. Buchanan, Jorge L. Rodriguez-Gil, Struan F.A. Grant, Timothy D. Howard, Omri Gottesman, Wei Zhao, Kira C. Taylor, Yan Meng, Hayrettin Okut, Hakon Hakonarson, Xiaofeng Zhu, Elizabeth M. Gillanders, Alan B. Zonderman, Lisa Chu, Badri Padhukasahasram, Vaneet Lotay, W. Ryan Diver, Mary K. Wojczynski, Simin Liu, Erwin P. Bottinger, Cameron D. Palmer, Alessandra Chesi, Elise Lim, Laura J. Rasmussen-Torvik, Eirini Marouli, Kari E. North, Salman M. Tajuddin, Christopher A. Haiman, Barbara Nemesure, Loic Le Marchand, Bamidele O. Tayo, and Maggie C.Y. Ng
Subjects: Male, 0303 health sciences, 030305 genetics & heredity, High density, Black People, Single-nucleotide polymorphism, Genome-wide association study, Biology, Polymorphism, Single Nucleotide, Body Height, Article, Minor allele frequency, Black or African American, Europe, 03 medical and health sciences, Evolutionary biology, Africa, Genetics, Humans, Female, Genotyping, Genetics (clinical), Imputation (genetics), 030304 developmental biology, Genome-Wide Association Study
Abstract: Although many loci have been associated with height in European ancestry populations, very few have been identified in African ancestry individuals. Furthermore, many of the known loci have yet to be generalized to and fine-mapped within a large-scale African ancestry sample. We performed sex-combined and sex-stratified meta-analyses in up to 52,764 individuals with height and genome-wide genotyping data from the African Ancestry Anthropometry Genetics Consortium (AAAGC). We additionally combined our African ancestry meta-analysis results with published European genome-wide association study (GWAS) data. In the African ancestry analyses, we identified three novel loci (SLC4A3, NCOA2, ECD/FAM149B1) in sex-combined results and two loci (CRB1, KLF6) in women only. In the African plus European sex-combined GWAS, we identified an additional three novel loci (RCCD1, G6PC3, CEP95) which were equally driven by AAAGC and European results. Among 39 genome-wide significant signals at known loci, conditioning index SNPs from European studies identified 20 secondary signals. Two of the 20 new secondary signals and none of the 8 novel loci had minor allele frequencies (MAF) < 5%. Of 802 known European height signals, 643 displayed directionally consistent associations with height, of which 205 were nominally significant (p < 0.05) in the African ancestry sex-combined sample. Furthermore, 148 of 241 loci contained ≤20 variants in the credible sets that jointly account for 99% of the posterior probability of driving the associations. In summary, trans-ethnic meta-analyses revealed novel signals and further improved fine-mapping of putative causal variants in loci shared between African and European ancestry populations.
Published: 2020

10. Genetic and Pharmacologic Inactivation of ANGPTL3 and Cardiovascular Disease

Author: Alex Lopez, Jerome I. Rotter, Yii-Der Ida Chen, Lukas Habegger, Anders Berg Wulff, Richard L Dunbar, John Penn, Anita M. van den Hoek, An Zhao, Omri Gottesman, Cristopher V. Van Hout, Scott M. Damrauer, Tanya M. Teslovich, Aurelie Bouzelmat, Daniel J. Rader, Poulabi Banerjee, David J. Carey, Viktoria Gusarova, Shane McCarthy, Frederick E. Dewey, Kae-Woei Liang, David H. Ledbetter, Gary Herman, Rick Zhang, Alan R. Shuldiner, Svati H. Shah, Claudia Schurmann, Neil Stahl, Marylyn D. Ritchie, Sara Hamon, Colm O'Dushlaine, Ingrid B. Borecki, Daniel A. Gipe, Jesper Gromada, Hans M.G. Princen, Børge G. Nordestgaard, H. Lester Kirchner, Michael F. Murray, Shannon Bruse, Aris Baras, Jeffrey G. Reid, Wayne H-H Sheu, William E. Kraus, Xiuqing Guo, Aeron Small, Brad Shumel, William J. Sasiela, Anne Tybjærg-Hansen, Andrew J. Murphy, Joseph B. Leader, John D. Overton, Robert Pordy, Scott Mellis, Weiping Shao, George D. Yancopoulos, Hayes Dansky, and I-Te Lee
Subjects: 0301 basic medicine, medicine.medical_specialty, Evinacumab, Population, 030204 cardiovascular system & hematology, Pharmacology, Coronary artery disease, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Internal medicine, ANGPTL3, Medicine, education, education.field_of_study, biology, business.industry, Cholesterol, General Medicine, medicine.disease, Human genetics, 030104 developmental biology, Endocrinology, chemistry, biology.protein, lipids (amino acids, peptides, and proteins), Antibody, business, Lipoprotein
Abstract: BackgroundLoss-of-function variants in the angiopoietin-like 3 gene (ANGPTL3) have been associated with decreased plasma levels of triglycerides, low-density lipoprotein (LDL) cholesterol, and high-density lipoprotein (HDL) cholesterol. It is not known whether such variants or therapeutic antagonism of ANGPTL3 are associated with a reduced risk of atherosclerotic cardiovascular disease. MethodsWe sequenced the exons of ANGPTL3 in 58,335 participants in the DiscovEHR human genetics study. We performed tests of association for loss-of-function variants in ANGPTL3 with lipid levels and with coronary artery disease in 13,102 case patients and 40,430 controls from the DiscovEHR study, with follow-up studies involving 23,317 case patients and 107,166 controls from four population studies. We also tested the effects of a human monoclonal antibody, evinacumab, against Angptl3 in dyslipidemic mice and against ANGPTL3 in healthy human volunteers with elevated levels of triglycerides or LDL cholesterol. ResultsIn th...
Published: 2017

11. Genome-wide association analyses for lung function and chronic obstructive pulmonary disease identify new loci and potential druggable targets

Author: Stefan Enroth, Robert J. Hall, James D. Crapo, Frederick E. Dewey, Victoria E. Jackson, Eleftheria Zeggini, Gudmar Thorleifsson, Terho Lehtimäki, David J. Porteous, Nicole Probst-Hensch, Ian J. Deary, A. Mesut Erzurumluoglu, Bram P. Prins, Maarten van den Berge, Craig E. Pennell, Catherine John, Terri H. Beaty, Claudia Schurmann, Michael H. Cho, Veronique Vitart, Erwin P. Bottinger, Carol A. Wang, H. Lester Kirchner, Medea Imboden, David J. Carey, Archie Campbell, Kari Stefansson, Matthias Wielscher, Ida Surakka, Igor Rudan, Shona M. Kerr, Holger Schulz, Michael A. Portelli, Thorarinn Gislason, Peter D. Paré, James F. Wilson, Boris Noyvert, Beate Stubbe, Zhengming Chen, Ruth J. F. Loos, Ma'en Obeidat, María Soler Artigas, Philippe Joubert, Kathleen C. Barnes, Christian Gieger, Andrew P. Morris, Rajesh Rawal, Yohan Bossé, Peter K. Joshi, Nadia N. Hansel, Emily S. Wan, David M. Evans, David C. Nickle, Caroline Hayward, Stefan Karrasch, Ke Hao, Tracy L. Rimington, Don D. Sin, Alan James, Stefan Jonsson, Shannon Bruse, Amanda P. Henry, Iona Y Millwood, Lara Bossini-Castillo, Ian P. Hall, David Sparrow, Ulf Gyllensten, Ian Sayers, Edwin K. Silverman, Robert Busch, David P. Strachan, Martin D. Tobin, Nick Shrine, Louise V. Wain, Robin G. Walters, Ingileif Jonsdottir, Peter D. Sly, Liming Li, Charlotte K. Billington, Anna Hansell, Omri Gottesman, Om P Kurmi, Ingo Ruczinski, Nicholas J. Wareham, Amund Gulsvik, Per Bakke, Jennie Hui, Corry-Anke Brandsma, Gosia Trynka, Anthony G. Fenech, Brian D. Hobbs, A. John Henderson, Jonathan Marten, Olli T. Raitakari, Richard J. Allen, Augusto A. Litonjua, Sarah E. Harris, Ozren Polasek, Mika Kähönen, Tineka Blake, Marjo-Riitta Järvelin, Rasika A. Mathias, Jing Hua Zhao, Julien Vaucher, Girish N. Nadkarni, Christopher E. Brightling, Groningen Research Institute for Asthma and COPD (GRIAC), Wareham, Nicholas [0000-0003-1422-2993], Zhao, Jing Hua [0000-0003-4930-3582], Marten, Jonathan [0000-0001-6916-2014], and Apollo - University of Cambridge Repository
Subjects: Male, 0301 basic medicine, Oncology, Genome-wide association study, heart disease, VARIANTS, SUSCEPTIBILITY, Epigenesis, Genetic, AIR-FLOW OBSTRUCTION, Pulmonary Disease, Chronic Obstructive, Risk Factors, HISTORY, GWAS, EPIDEMIOLOGY, Lung, POPULATION, Cause of death, Genetics & Heredity, Aged, 80 and over, education.field_of_study, COPD, Framingham Risk Score, Chronic obstructive pulmonary disease, Heart, 11 Medical And Health Sciences, Middle Aged, 3. Good health, Female, HEALTH, Life Sciences & Biomedicine, Adult, medicine.medical_specialty, Population, genome-wide, lungs, target, Biology, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Internal medicine, Genetics, medicine, Humans, Genetic Predisposition to Disease, Allele, education, Alleles, Aged, Asthma, Science & Technology, ta1184, Odds ratio, 06 Biological Sciences, ta3121, medicine.disease, Lung function, respiratory tract diseases, 030104 developmental biology, Genetic Loci, FAM13A, Immunology, Lungs, Pulmonary disease, Developmental Biology, Genome-Wide Association Study
Abstract: Chronic obstructive pulmonary disease (COPD) is characterized by reduced lung function and is the third leading cause of death globally. Through genome-wide association discovery in 48,943 individuals, selected from extremes of the lung function distribution in UK Biobank, and follow-up in 95,375 individuals, we increased the yield of independent signals for lung function from 54 to 97. A genetic risk score was associated with COPD susceptibility (odds ratio per 1 s.d. of the risk score (similar to 6 alleles) (95% confidence interval) = 1.24 (1.20-1.27), P = 5.05 x 10(-49)), and we observed a 3.7-fold difference in COPD risk between individuals in the highest and lowest genetic risk score deciles in UK Biobank. The 97 signals show enrichment in genes for development, elastic fibers and epigenetic regulation pathways. We highlight targets for drugs and compounds in development for COPD and asthma (genes in the inositol phosphate metabolism pathway and CHRM3) and describe targets for potential drug repositioning from other clinical indications.
Published: 2017

12. Associations of autozygosity with a broad range of human phenotypes

Author: Dennis O. Mook-Kanamori, Salma M. Wakil, Lisa R. Yanek, Dominique P.V. de Kleijn, Gert J. de Borst, Alison D. Murray, Kamran Guity, Vincent W. V. Jaddoe, Mario Pirastu, Carole Ober, Giuseppe Matullo, Charles N. Rotimi, Daniela Ruggiero, Teresa Tusié-Luna, Wolfgang Lieb, Chew-Kiat Heng, John R. B. Perry, Hortensia Moreno-Macías, Jie Zhou, John M. Starr, Juhani Junttila, Lei Yu, Danielle Posthuma, Marcus Dörr, Yingchang Lu, Jonathan P. Bradfield, Einat Granot-Hershkovitz, Karina Meidtner, Wouter van Rheenen, T Esko, Maris Alver, Wen-Jane Lee, Zhengming Chen, Jennifer A. Brody, Paolo Gasparini, Yii-Der Ida Chen, Cinzia Sala, Peter P. Pramstaller, Gauri Prasad, Nana Matoba, Natalie Terzikhan, Simonetta Guarrera, Bjarke Feenstra, Peter Vollenweider, Smeeta Shrestha, Yi-Jen Hung, Lilja Stefansdottir, David R. Weir, Felix R. Day, Antonietta Robino, Liang Zhang, Lluis Quintana-Murci, Nicholas J. Timpson, Robyn E Wootton, Xue W. Mei, Dharambir K. Sanghera, Gisli Masson, Debbie A Lawlor, Thomas Meitinger, Sharon L.R. Kardia, Peter K. Joshi, Frank J. A. van Rooij, Claude Bouchard, Cassandra N. Spracklen, Ken K. Ong, Taulant Muka, Guanjie Chen, Laura J. Scott, Walter Palmas, Daniel I. Chasman, Sarah E. Medland, Krista Fischer, Blair H. Smith, Jon K. Sigurdsson, Leon Straker, Clara Viberti, Yuan Shi, Louis Pérusse, Peter J. van der Most, Timo Tõnis Sikka, Chris Haley, Kuang Lin, Leif Groop, Hester M. den Ruijter, Hakon Hakonarson, Masato Akiyama, Stephan J. L. Bakker, Sonja I. Berndt, Jeffery R. O'Connell, Cisca Wijmenga, Daniele Cusi, Lorena Orozco, Kristjan H. S. Moore, Kevin Sandow, Stephen S. Rich, Stephanie J. Loomis, George Davey Smith, Cornelia M. van Duijn, Sharvari Rahul Shukla, Agnar Helgason, Thorsten Kessler, Anuj Goel, Dan Mason, David W. Clark, James S. Pankow, Simona Vaccargiu, Uwe Völker, Tamara B. Harris, Matthew A. Allison, Clicerio Gonzalez, Sarju Ralhan, I-Te Lee, Matthias Laudes, Yen-Feng Chiu, Neil Poulter, Benjamin Lehne, John Wright, Lawrence F. Bielak, Philip L. De Jager, Reinhold Schmidt, Ya Xing Wang, Matthias Nauck, Diana L. Cousminer, Patrick Deelen, Ani Manichaikul, Stephen J. Chanock, Anders Hamsten, Barry I. Freedman, Gudmar Thorleifsson, Peter Kraft, Ozren Polasek, Jie Yao, Yoshinori Murakami, Paul M. Ridker, Anubha Mahajan, Struan F.A. Grant, Claudia Schurmann, Bjarni Gunnarsson, Catriona L. K. Barnes, Jessica van Setten, Sandosh Padmanabhan, Alena Stančáková, Markus M. Lerch, Anuradha Jagadeesan, Franco Giulianini, Daniel F. Gudbjartsson, Dwaipayan Bharadwaj, Shengchao Alfred Li, Peter S. Sever, Trevor A. Mori, Albertine J. Oldehinkel, Koichi Matsuda, Xueling Sim, Evangelos Evangelou, André G. Uitterlinden, Pekka Jousilahti, Yukihide Momozawa, Ioanna Tzoulaki, Chao A. Hsiung, Ginevra Biino, Murielle Bochud, Hannele Mattsson, Ilja M. Nolte, Sarah H. Wild, Patricia B. Munroe, Jianjun Liu, Bruce M. Psaty, Giriraj R. Chandak, Masahiro Kanai, Tony R. Merriman, Teemu Palviainen, Rodney A. Lea, Janie Corley, Nicholas J. Wareham, Alan B. Zonderman, Makoto Hirata, Matthew J. Bixley, Caroline Hayward, Nora Franceschini, Kristel R van Eijk, Etienne Patin, Daniel Shriner, Niek Verweij, Xiuqing Guo, Fredrik Karpe, Ruth J. F. Loos, Tiinamaija Tuomi, Ashley van der Spek, Patricia A. Peyser, Jessica D. Faul, Christian Fuchsberger, David Cesarini, Alex S. F. Doney, Janine F. Felix, Cornelius A. Rietveld, Jagadish Vangipurapu, Tanguy Corre, Line Skotte, Rajkumar Dorajoo, Catherine Igartua, Meena Kumari, Nona Sotoodehnia, Leonard H. van den Berg, Najaf Amin, Dale R. Nyholt, Harry Campbell, Massimiliano Cocca, Scott D. Gordon, Patrik K. E. Magnusson, John C. Chambers, Traci M. Bartz, Mike A. Nalls, Tin Aung, Nduna Dzimiri, Colin N. A. Palmer, Rob M. van Dam, Johanna Kuusisto, Russell P. Tracy, Anna Damulina, Pierre-Emmanuel Morange, Sylvain Foisy, Jing Hua Zhao, Nicholas G. Martin, Ching-Yu Cheng, Mariaelisa Graff, Rashmi B. Prasad, Alice Stanton, David-Alexandre Trégouët, Yu Guo, Helen R. Warren, Lyn R. Griffiths, Weihua Meng, Annika Tillander, Christa Meisinger, Albert V. Smith, Mark I. McCarthy, Jingyun Yang, Marine Germain, Neil Small, Linda Broer, Vilmundur Gudnason, Gunnar K. Pálsson, Michele K. Evans, Alexander Teumer, Mark J. Caulfield, Giorgia Girotto, Thomas Lumley, Tinca J. C. Polderman, Wei Zhao, Carlos A. Aguilar-Salinas, Jari Lahti, Matthew L. Albert, Yechiel Friedlander, Veikko Salomaa, Iona Y Millwood, Jan H. Veldink, Archie Campbell, Andres Metspalu, Ulf Gyllensten, Grant W. Montgomery, Veronique Vitart, Jai Rup Singh, Saima Afaq, Alan R. Shuldiner, Miao-Li Chee, Adebowale Adeyemo, Jennifer A. Smith, David A. van Heel, Jaspal S. Kooner, Daniela Toniolo, Cristian Pattaro, Jerome I. Rotter, John Whitfield, Melissa C. Smart, Kari E. North, Salman M. Tajuddin, Tallapragada Divya Sri Priyanka, Christopher A. Haiman, Diane M. Becker, Bernhard K. Krämer, Paul Elliott, Lihua Wang, He Gao, Patrick Sulem, Jinyan Huang, Chiea Chuen Khor, Ruifang Li-Gao, Åsa Johansson, Winfried März, Shai Carmi, Ilaria Gandin, Eric Boerwinkle, Gardar Sveinbjornsson, Saskia P. Hagenaars, Sander W. van der Laan, Gerard Pasterkamp, E-Shyong Tai, Hagit Hochner, Yih Chung Tham, Kent D. Taylor, Kari Stefansson, Matt J. Neville, Craig E. Pennell, Yanchun Bao, Annelot M. Dekker, Helena Schmidt, Mehdi Hedayati, Joshua Elliott, Ian J. Deary, Iris E. Jansen, Judith B. Borja, Edith Hofer, Martin Gögele, Igor Rudan, Lude Franke, Matthias Munz, Folkert W. Asselbergs, Bengt Sennblad, Imo Hofer, John D. Rioux, Pim van der Harst, Bahareh Sedaghati-khayat, Giovanni Cugliari, Morris A. Swertz, Francine Grodstein, Erwin P. Bottinger, Carol A. Wang, Andre Franke, Brian F. Meyer, Adele M. Taylor, Klodian Dhana, Jian'an Luan, Constance Turman, Robert A. Scott, May E. Montasser, Alison Pattie, Marco Brumat, Liming Li, Heiner Boeing, Karen L. Mohlke, Clemens Baumbach, Bishwa Raj Sapkota, Unnur Thorsteinsdottir, Naveed Sattar, Amy R. Bentley, Matthias B. Schulze, Ivana Kolcic, Stella Trompet, Sarah E. Harris, Ayo P. Doumatey, Charumathi Sabanayagam, David Eccles, Mary F. Feitosa, Jost B. Jonas, Massimo Mezzavilla, Mark O. Goodarzi, David Ellinghaus, Heribert Schunkert, Christian Gieger, Heikki V. Huikuri, Lingyao Zeng, Johan G. Eriksson, Woon-Puay Koh, Yucheng Jia, Gurpreet Singh Wander, James F. Wilson, Torgny Karlsson, Steven C. Hunt, Weihua Zhang, Maria Pina Concas, Zoltán Kutalik, Rebecca Rohde, Chittaranjan S. Yajnik, Yasaman Saba, Dabeeru C. Rao, Robin G. Walters, Reedik Mägi, Marie Loh, Eero Vuoksimaa, Josyf C. Mychaleckyj, Katri Räikkönen, Philippe Goyette, M. Arfan Ikram, Alicia Huerta-Chagoya, David J. Porteous, Teresa Nutile, J. Wouter Jukema, Noha A. Yousri, Yoichiro Kamatani, Maryam S. Daneshpour, Babette S. Zemel, Rona J. Strawbridge, Tien Yin Wong, Claudia Langenberg, Amy Moore, Marcus E. Kleber, Fereidoun Azizi, Avner Halevy, Erika Salvi, Francis S. Collins, Markku Laakso, Tim Kacprowski, S. Sunna Ebenesersdóttir, William R. Scott, Michael Boehnke, Jin-Fang Chai, Markus Perola, Nicola Pirastu, Wayne Huey-Herng Sheu, Robert Karlsson, Lenore J. Launer, Lili Milani, Renée de Mutsert, Fernando Rivadeneira, David A. Bennett, Nicola D. Kerrison, Paolo Manunta, Graciela E. Delgado, Magnus Johannesson, Carolina Medina-Gomez, Alanna C. Morrison, Kay-Tee Khaw, Jian-Min Yuan, Jaakko Kaprio, Melanie Waldenberger, Ralf Ewert, Hugoline G. de Haan, Andrew A. Hicks, Yukinori Okada, Maria Sabater-Lleal, Marilyn C. Cornelis, Stephanie J. London, Federica Rizzi, Jeanette Erdmann, Marina Ciullo, Michiaki Kubo, University of Edinburgh, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Osaka University Graduate School of Medicine, Laboratory for Cardiovascular Genomics and Informatics [Yokohama] (RIKEN IMS), RIKEN Center for Integrative Medical Sciences [Yokohama] (RIKEN IMS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN)-RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), deCODE genetics [Reykjavik], Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK (BIHR), Area Science Park, Università degli studi di Trieste = University of Trieste, MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Interfaculty Institute for Genetics and Functional Genomics, Universität Greifswald - University of Greifswald, Harbor UCLA Medical Center [Torrance, Ca.], Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, Department of Electrical and Computer Engineering [Waterloo] (ECE), University of Waterloo [Waterloo], Department of Medical Epidemiology and Biostatistics (MEB), Karolinska Institutet [Stockholm], Institute of Pop. Genetics, CNR, Sassari, Shardna life science Pula Cagliari, Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Medstar Research Institute, Florida State University [Tallahassee] (FSU), University Medical Center [Utrecht], Centre for Population Health Sciences, Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), California State University [Sacramento], Department of Thrombosis and Haemostasis, Leiden University Medical Center (LUMC), Universiteit Leiden-Universiteit Leiden, Medical University Graz, Department of Neurology, Alzheimer Centre, VU Medical Centre, Amsterdam, Vth Department of Medicine (Nephrology, Hypertensiology, Endocrinology, Diabetology, Rheumatology), Medical Faculty of Mannheim, University of Heidelberg, Heidelberg, Frederick National Laboratory for Cancer Research (FNLCR), Wellcome Trust Centre of Human Genetics, University of Oxford, Department of Epidemiology, German Institute of Human Nutrition, University Medical Center Groningen [Groningen] (UMCG), Institute of Genetics and Biophysics, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Department of Medicine, Surgery, and Dentistry, University of Milano, Icelandic Heart Association, Kopavogur, Iceland., Department of Epidemiology [Rotterdam], Erasmus University Medical Center [Rotterdam] (Erasmus MC), University of Glasgow, Department of Cardiology, Leiden University Medical Center, Leiden, Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, Queen Mary University of London (QMUL), General Internal Medicine, Johns Hopkins School of Medicine, Johns Hopkins University School of Medicine [Baltimore], Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Immunobiologie des Cellules dendritiques, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Institut Pasteur [Paris] (IP), Genentech, Inc., Genentech, Inc. [San Francisco], University of Tartu, Duke-NUS Medical School [Singapore], Deutsches Institut für Ernährungsforschung Potsdam-Rehbrücke (DifE), Leibniz Association, Human Genome Sequencing Center, Baylor College of Medicine, Baylor College of Medicine (BCM), Baylor University-Baylor University, University of San Carlos, Office of Population Studies Foundation, Icahn School of Medicine at Mount Sinai [New York] (MSSM), King‘s College London, Division of Cancer Epidemiology and Genetics, National Cancer Institute [Bethesda] (NCI-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), University of Oxford, Vth Department of Medicine (Nephrology, Hypertensiology, Endocrinology, Diabetology, Rheumatology), Medical Faculty of Mannheim, University of Heidelberg, Division of Molecular & Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Department of Internal Medicine B, University Medicine Greifswald, Greifswald, University of Chicago, University of Huddersfield, Infectious diseases division, Department of internal medicine, Washington University in Saint Louis (WUSTL), Section on Nephrology [Winston-Salem, NC, USA] (Department of Internal Medicine), Wake Forest School of Medicine [Winston-Salem], Wake Forest Baptist Medical Center-Wake Forest Baptist Medical Center, Radcliffe Department of Medicine [Oxford], Harvard School of Public Health, Kunming University of Science and Technology (KMUST), Sans affiliation, University of Southern California (USC), National Institute on Aging [Bethesda, USA] (NIA), National Institutes of Health [Bethesda] (NIH), Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), MRC Centrer for Nutritional Epidemiology and Cancer Prevention and Survival, University of Cambridge [UK] (CAM), National University of Singapore (NUS), Experimental Cardiology Laboratory (ECL), Unirversity Medical Center, Department of Medical Statistics, Epidemiology and Medical Informatics, University of Zagreb, Department of Medical Genetics, Department of Medicine, University of Eastern Finland-Kuopio University Hospital, MRC Epidemiology Unit, University of Cambridge [UK] (CAM)-Institute of Metabolic Science, Capital Normal University [Beijing], Saw Swee Hock School of Public Health, National Institute for Environmental Health Sciences Research Triangle Park, Brown University, MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, Toyota Research Institute, Helmholtz Zentrum München = German Research Center for Environmental Health, Department of Chemistry and Biochemistry [Boulder], University of Colorado [Boulder], Centre recherche en CardioVasculaire et Nutrition = Center for CardioVascular and Nutrition research (C2VN), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Hôpital de la Timone [CHU - APHM] (TIMONE), Metacohorts Consortium, Universiteit Leiden, Institute of Clinical Chemistry and Laboratory Medicine, University of Groningen [Groningen], Medical Research Concil Epidemiology Unit, Institute of Medical Science, Faculty of Medicine, Genetics and Pathology, Imperial College London, Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Brigham and Women's Hospital [Boston], Erasmus University Rotterdam, Department of Chronic Disease Prevention, National Institute for Health and Welfare [Helsinki], Department of Biostatistics and Center for Statistical Genetics, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System-School of public health, The University of Hong Kong (HKU)-The University of Hong Kong (HKU), Stockholm Bioinformatics Center (SBC), Stockholm University, Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, INRH, Department of Genetics, Los Angeles Biomedical Research Institute (LA BioMed), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán - National Institute of Medical Science and Nutrition Salvador Zubiran [Mexico], Western General Hospital, German Research Center for Environmental Health - Helmholtz Center München (GmbH), Medical Research Council, Division of Cancer Control and Population Sciences, University of Pittsburgh Cancer Institute-University of Pittsburgh Graduate School of Public Health, Zhengzhou University of Light Industry, Department of Electrical and Electronic Engineering [Niigata Univ.], Niigata University, Genetic Epidemiology Unit, University College of London [London] (UCL), Aston Business School, Aston University [Birmingham], Division of Cancer Epidemiology and Genetics [Bethesda, MD, États-Unis], Centre Hospitalier Universitaire Vaudois (CHUV), Pennington Biomedical Research Center, University of Washington [Seattle], Guy's and St Thomas' Hospitals, Northwestern Polytechnical University [Xi'an] (NPU), Department of Social Medicine, University of Bristol [Bristol], Department of Genomics of Common Disease [London, UK], Imperial College London-Hammersmith Hospital NHS Imperial College Healthcare, Department of Internal Medicine, Institute of Clinical Molecular Biology, Kiel University, Medizinische Klinik II, Universität zu Lübeck = University of Lübeck [Lübeck], Clinical and Molecular Epidemiology Unit, Department of Hygiene and Epidemiology, University of Ioannina, Institute for Social Research, University of Michigan System-University of Michigan System, Division of Statistical Genomics, Washington University School of Medicine, Institute for Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel (CAU), Department of Physics, RISSC-Lab-University of Naples Federico II = Università degli studi di Napoli Federico II, Lund University [Lund], Icelandic Heart Association, Heart Preventive Clinic and Research Institute, The Center for Applied Genomics, Children’s Hospital of Philadelphia (CHOP ), Génétique moléculaire de la neurotransmission et des processus neurodégénératifs (LGMNPN), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Medical Research Center Oulu, University of Oulu, University of Utah School of Medicine [Salt Lake City], The Generation R Study, Pediatrics, Epidemiology, Center for Translational and Computational Neuroimmunology [New York, NY, États-Unis] (CTCN), Department of Neurology [New York, NY, États-Unis], Columbia University Medical Center (CUMC), Columbia University [New York]-Columbia University [New York]-Columbia University Medical Center (CUMC), Columbia University [New York]-Columbia University [New York], Universität Heidelberg [Heidelberg] = Heidelberg University, Interuniversity Cardiology Institute Netherlands, School of Public Health, University of Michigan [Dearborn], Department of Epidemiology and Public Health, University of Kuopio, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Institute of Epidemiology and Biobank PopGen, Department of Biostatistics, University of Washington, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Clinical Institute of Medical and Chemical Laboratory Diagnostics, Karl-Franzens-Universität Graz, Department of Genetics, Biology and Biochemistry, Università degli studi di Torino = University of Turin (UNITO), Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), QIMR Berghofer Medical Research Institute, University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC)-University of North Carolina System (UNC), University of North Carolina System (UNC)-University of North Carolina System (UNC)-UNC Gillings School of Global Public Health-Carolina Center for Genome Sciences, University of Illinois [Chicago] (UIC), University of Illinois System, Experimental Cardiology Laboratory, Genetic Epidemiology and Clinical Research Group, Umea University Hospital, Functional Genomics, Erasmus Medical Centre, National Human Genome Research Institute (NHGRI), School of Medicine [Los Angeles], University of California [Los Angeles] (UCLA), University of California (UC)-University of California (UC), Department of Pathological Biochemistry, Royal Infirmary, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Institute of Metabolic Science, MRC, University of Maryland School of Medicine [Baltimore, MD, USA], Centre for Molecular Epidemiology, Centre for Causal Analyses in Translational Epidemiology, University of Bristol [Bristol]-Medical Research Council, IRCCS San Raffaele Scientific Institute [Milan, Italie], U937, Génomique cardiovasculaire, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire Vaudois [Lausanne] (CHUV), University of Michigan System, HMNC Brain Health, Singapore Eye Research Institute, Partenaires INRAE, Institut d'Électronique et des Technologies du numéRique (IETR), Université de Nantes (UN)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Institute for Molecular Medicine Finland [Helsinki] (FIMM), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Department of Psychiatry and Psychotherapy, Rheinische Friedrich-Wilhelms-Universität Bonn, University of Groningen, Department of Genomics of Common Disease, Department of Microbiology, The Freeman Hospital, Department Biostatistics University of North Carolina, Complex Trait Genetics, Amsterdam Neuroscience - Complex Trait Genetics, Clark, D. W., Okada, Y., Moore, K. H. S., Mason, D., Pirastu, N., Gandin, I., Mattsson, H., Barnes, C. L. K., Lin, K., Zhao, J. H., Deelen, P., Rohde, R., Schurmann, C., Guo, X., Giulianini, F., Zhang, W., Medina-Gomez, C., Karlsson, R., Bao, Y., Bartz, T. M., Baumbach, C., Biino, G., Bixley, M. J., Brumat, M., Chai, J. -F., Corre, T., Cousminer, D. L., Dekker, A. M., Eccles, D. A., van Eijk, K. R., Fuchsberger, C., Gao, H., Germain, M., Gordon, S. D., de Haan, H. G., Harris, S. E., Hofer, E., Huerta-Chagoya, A., Igartua, C., Jansen, I. E., Jia, Y., Kacprowski, T., Karlsson, T., Kleber, M. E., Li, S. A., Li-Gao, R., Mahajan, A., Matsuda, K., Meidtner, K., Meng, W., Montasser, M. E., van der Most, P. J., Munz, M., Nutile, T., Palviainen, T., Prasad, G., Prasad, R. B., Priyanka, T. D. S., Rizzi, F., Salvi, E., Sapkota, B. R., Shriner, D., Skotte, L., Smart, M. C., Smith, A. V., van der Spek, A., Spracklen, C. N., Strawbridge, R. J., Tajuddin, S. M., Trompet, S., Turman, C., Verweij, N., Viberti, C., Wang, L., Warren, H. R., Wootton, R. E., Yanek, L. R., Yao, J., Yousri, N. A., Zhao, W., Adeyemo, A. A., Afaq, S., Aguilar-Salinas, C. A., Akiyama, M., Albert, M. L., Allison, M. A., Alver, M., Aung, T., Azizi, F., Bentley, A. R., Boeing, H., Boerwinkle, E., Borja, J. B., de Borst, G. J., Bottinger, E. P., Broer, L., Campbell, H., Chanock, S., Chee, M. -L., Chen, G., Chen, Y. -D. I., Chen, Z., Chiu, Y. -F., Cocca, M., Collins, F. S., Concas, M. P., Corley, J., Cugliari, G., van Dam, R. M., Damulina, A., Daneshpour, M. S., Day, F. R., Delgado, G. E., Dhana, K., Doney, A. S. F., Dorr, M., Doumatey, A. P., Dzimiri, N., Ebenesersdottir, S. S., Elliott, J., Elliott, P., Ewert, R., Felix, J. F., Fischer, K., Freedman, B. I., Girotto, G., Goel, A., Gogele, M., Goodarzi, M. O., Graff, M., Granot-Hershkovitz, E., Grodstein, F., Guarrera, S., Gudbjartsson, D. F., Guity, K., Gunnarsson, B., Guo, Y., Hagenaars, S. P., Haiman, C. A., Halevy, A., Harris, T. B., Hedayati, M., van Heel, D. A., Hirata, M., Hofer, I., Hsiung, C. A., Huang, J., Hung, Y. -J., Ikram, M. A., Jagadeesan, A., Jousilahti, P., Kamatani, Y., Kanai, M., Kerrison, N. D., Kessler, T., Khaw, K. -T., Khor, C. C., de Kleijn, D. P. V., Koh, W. -P., Kolcic, I., Kraft, P., Kramer, B. K., Kutalik, Z., Kuusisto, J., Langenberg, C., Launer, L. J., Lawlor, D. A., Lee, I. -T., Lee, W. -J., Lerch, M. M., Li, L., Liu, J., Loh, M., London, S. J., Loomis, S., Lu, Y., Luan, J., Magi, R., Manichaikul, A. W., Manunta, P., Masson, G., Matoba, N., Mei, X. W., Meisinger, C., Meitinger, T., Mezzavilla, M., Milani, L., Millwood, I. Y., Momozawa, Y., Moore, A., Morange, P. -E., Moreno-Macias, H., Mori, T. A., Morrison, A. C., Muka, T., Murakami, Y., Murray, A. D., de Mutsert, R., Mychaleckyj, J. C., Nalls, M. A., Nauck, M., Neville, M. J., Nolte, I. M., Ong, K. K., Orozco, L., Padmanabhan, S., Palsson, G., Pankow, J. S., Pattaro, C., Pattie, A., Polasek, O., Poulter, N., Pramstaller, P. P., Quintana-Murci, L., Raikkonen, K., Ralhan, S., Rao, D. C., van Rheenen, W., Rich, S. S., Ridker, P. M., Rietveld, C. A., Robino, A., van Rooij, F. J. A., Ruggiero, D., Saba, Y., Sabanayagam, C., Sabater-Lleal, M., Sala, C. F., Salomaa, V., Sandow, K., Schmidt, H., Scott, L. J., Scott, W. R., Sedaghati-Khayat, B., Sennblad, B., van Setten, J., Sever, P. J., Sheu, W. H. -H., Shi, Y., Shrestha, S., Shukla, S. R., Sigurdsson, J. K., Sikka, T. T., Singh, J. R., Smith, B. H., Stancakova, A., Stanton, A., Starr, J. M., Stefansdottir, L., Straker, L., Sulem, P., Sveinbjornsson, G., Swertz, M. A., Taylor, A. M., Taylor, K. D., Terzikhan, N., Tham, Y. -C., Thorleifsson, G., Thorsteinsdottir, U., Tillander, A., Tracy, R. P., Tusie-Luna, T., Tzoulaki, I., Vaccargiu, S., Vangipurapu, J., Veldink, J. H., Vitart, V., Volker, U., Vuoksimaa, E., Wakil, S. M., Waldenberger, M., Wander, G. S., Wang, Y. X., Wareham, N. J., Wild, S., Yajnik, C. S., Yuan, J. -M., Zeng, L., Zhang, L., Zhou, J., Amin, N., Asselbergs, F. W., Bakker, S. J. L., Becker, D. M., Lehne, B., Bennett, D. A., van den Berg, L. H., Berndt, S. I., Bharadwaj, D., Bielak, L. F., Bochud, M., Boehnke, M., Bouchard, C., Bradfield, J. P., Brody, J. A., Campbell, A., Carmi, S., Caulfield, M. J., Cesarini, D., Chambers, J. C., Chandak, G. R., Cheng, C. -Y., Ciullo, M., Cornelis, M., Cusi, D., Smith, G. D., Deary, I. J., Dorajoo, R., van Duijn, C. M., Ellinghaus, D., Erdmann, J., Eriksson, J. G., Evangelou, E., Evans, M. K., Faul, J. D., Feenstra, B., Feitosa, M., Foisy, S., Franke, A., Friedlander, Y., Gasparini, P., Gieger, C., Gonzalez, C., Goyette, P., Grant, S. F. A., Griffiths, L. R., Groop, L., Gudnason, V., Gyllensten, U., Hakonarson, H., Hamsten, A., van der Harst, P., Heng, C. -K., Hicks, A. A., Hochner, H., Huikuri, H., Hunt, S. C., Jaddoe, V. W. V., De Jager, P. L., Johannesson, M., Johansson, A., Jonas, J. B., Jukema, J. W., Junttila, J., Kaprio, J., Kardia, S. L. R., Karpe, F., Kumari, M., Laakso, M., van der Laan, S. W., Lahti, J., Laudes, M., Lea, R. A., Lieb, W., Lumley, T., Martin, N. G., Marz, W., Matullo, G., Mccarthy, M. I., Medland, S. E., Merriman, T. R., Metspalu, A., Meyer, B. F., Mohlke, K. L., Montgomery, G. W., Mook-Kanamori, D., Munroe, P. B., North, K. E., Nyholt, D. R., O'Connell, J. R., Ober, C., Oldehinkel, A. J., Palmas, W., Palmer, C., Pasterkamp, G. G., Patin, E., Pennell, C. E., Perusse, L., Peyser, P. A., Pirastu, M., Polderman, T. J. C., Porteous, D. J., Posthuma, D., Psaty, B. M., Rioux, J. D., Rivadeneira, F., Rotimi, C., Rotter, J. I., Rudan, I., Den Ruijter, H. M., Sanghera, D. K., Sattar, N., Schmidt, R., Schulze, M. B., Schunkert, H., Scott, R. A., Shuldiner, A. R., Sim, X., Small, N., Smith, J. A., Sotoodehnia, N., Tai, E. -S., Teumer, A., Timpson, N. J., Toniolo, D., Tregouet, D. -A., Tuomi, T., Vollenweider, P., Wang, C. A., Weir, D. R., Whitfield, J. B., Wijmenga, C., Wong, T. -Y., Wright, J., Yang, J., Yu, L., Zemel, B. S., Zonderman, A. B., Perola, M., Magnusson, P. K. E., Uitterlinden, A. G., Kooner, J. S., Chasman, D. I., Loos, R. J. F., Franceschini, N., Franke, L., Haley, C. S., Hayward, C., Walters, R. G., Perry, J. R. B., Esko, T., Helgason, A., Stefansson, K., Joshi, P. K., Kubo, M., Wilson, J. F., Læknadeild (HÍ), Faculty of Medicine (UI), Félagsfræði-, mannfræði- og þjóðfræðideild (HÍ), Faculty of Sociology, Anthropology and Folkloristics (UI), Heilbrigðisvísindasvið (HÍ), School of Health Sciences (UI), School of Engineering and Natural Sciences (UI), Verkfræði- og náttúruvísindasvið (HÍ), Félagsvísindasvið (HÍ), School of Social Sciences (UI), Háskóli Íslands, University of Iceland, Clark, David W [0000-0002-1025-9185], Okada, Yukinori [0000-0002-0311-8472], Moore, Kristjan H S [0000-0002-9579-4362], Mason, Dan [0000-0002-0026-9216], Pirastu, Nicola [0000-0002-5363-3886], Gandin, Ilaria [0000-0003-3196-2491], Deelen, Patrick [0000-0002-5654-3966], Schurmann, Claudia [0000-0003-4158-9192], Medina-Gomez, Carolina [0000-0001-7999-5538], Karlsson, Robert [0000-0002-8949-2587], Bao, Yanchun [0000-0002-6102-5098], Biino, Ginevra [0000-0002-9936-946X], Brumat, Marco [0000-0003-3268-039X], Chai, Jin-Fang [0000-0003-3770-1137], Eccles, David A [0000-0003-4634-4995], Gordon, Scott D [0000-0001-7623-328X], Harris, Sarah E [0000-0002-4941-5106], Kacprowski, Tim [0000-0002-5393-2413], Karlsson, Torgny [0000-0001-8095-6149], Kleber, Marcus E [0000-0003-0663-7275], Mahajan, Anubha [0000-0001-5585-3420], Matsuda, Koichi [0000-0001-7292-2686], Meng, Weihua [0000-0001-5388-8494], van der Most, Peter J [0000-0001-8450-3518], Munz, Matthias [0000-0002-4728-3357], Palviainen, Teemu [0000-0002-7847-8384], Prasad, Rashmi B [0000-0002-4400-6741], Salvi, Erika [0000-0002-2724-2291], Skotte, Line [0000-0002-7398-1271], van der Spek, Ashley [0000-0001-7136-0159], Spracklen, Cassandra N [0000-0003-3590-7182], Strawbridge, Rona J [0000-0001-8506-3585], Tajuddin, Salman M [0000-0002-7919-8528], Verweij, Niek [0000-0002-4303-7685], Yanek, Lisa R [0000-0001-7117-1075], Zhao, Wei [0000-0001-7388-0692], Albert, Matthew L [0000-0001-7285-6973], Bentley, Amy R [0000-0002-0827-9101], Chanock, Stephen [0000-0002-2324-3393], Chen, Zhengming [0000-0001-6423-105X], Chiu, Yen-Feng [0000-0002-3352-4500], Cocca, Massimiliano [0000-0002-1127-7596], Collins, Francis S [0000-0002-1023-7410], Cugliari, Giovanni [0000-0002-6080-0718], Damulina, Anna [0000-0001-8241-2727], Day, Felix R [0000-0003-3789-7651], Dhana, Klodian [0000-0002-6397-7009], Dzimiri, Nduna [0000-0003-3395-5754], Elliott, Paul [0000-0002-7511-5684], Felix, Janine F [0000-0002-9801-5774], Freedman, Barry I [0000-0003-0275-5530], Girotto, Giorgia [0000-0003-4507-6589], Goel, Anuj [0000-0003-2307-4021], Goodarzi, Mark O [0000-0001-6364-5103], Gudbjartsson, Daniel F [0000-0002-5222-9857], Guity, Kamran [0000-0002-8379-9668], van Heel, David A [0000-0002-0637-2265], Hirata, Makoto [0000-0002-9994-9958], Ikram, M Arfan [0000-0003-0372-8585], Kamatani, Yoichiro [0000-0001-8748-5597], Kanai, Masahiro [0000-0001-5165-4408], Khor, Chiea Chuen [0000-0002-1128-4729], Kolcic, Ivana [0000-0001-7918-6052], Langenberg, Claudia [0000-0002-5017-7344], Lawlor, Deborah A [0000-0002-6793-2262], Liu, Jianjun [0000-0002-3255-3019], London, Stephanie J [0000-0003-4911-5290], Luan, Jian’an [0000-0003-3137-6337], Matoba, Nana [0000-0001-5329-0134], Mei, Xue W [0000-0002-6279-4884], Mezzavilla, Massimo [0000-0002-9000-4595], Milani, Lili [0000-0002-5323-3102], Mori, Trevor A [0000-0002-5264-9229], Murakami, Yoshinori [0000-0002-2826-4396], Murray, Alison D [0000-0003-4915-4847], Mychaleckyj, Josyf C [0000-0003-2595-0005], Neville, Matt J [0000-0002-6004-5433], Nolte, Ilja M [0000-0001-5047-4077], Ong, Ken K [0000-0003-4689-7530], Pálsson, Gunnar [0000-0002-8231-3961], Pankow, James S [0000-0001-7076-483X], Pattaro, Cristian [0000-0002-4119-0109], Quintana-Murci, Lluis [0000-0003-2429-6320], van Rheenen, Wouter [0000-0002-5860-1533], Rich, Stephen S [0000-0003-3872-7793], Rietveld, Cornelius A [0000-0003-4053-1861], Ruggiero, Daniela [0000-0003-3898-7827], Sabanayagam, Charumathi [0000-0002-4042-4719], Sabater-Lleal, Maria [0000-0002-0128-379X], Sala, Cinzia Felicita [0000-0003-2514-2075], Salomaa, Veikko [0000-0001-7563-5324], Scott, Laura J [0000-0002-4886-5084], Sedaghati-Khayat, Bahareh [0000-0002-7665-8648], Sennblad, Bengt [0000-0002-4360-8003], van Setten, Jessica [0000-0002-4934-7510], Smith, Blair H [0000-0002-5362-9430], Stančáková, Alena [0000-0002-1375-0252], Stanton, Alice [0000-0002-4961-165X], Straker, Leon [0000-0002-7786-4128], Sulem, Patrick [0000-0001-7123-6123], Swertz, Morris A [0000-0002-0979-3401], Taylor, Kent D [0000-0002-2756-4370], Tzoulaki, Ioanna [0000-0002-4275-9328], Veldink, Jan H [0000-0001-5572-9657], Vitart, Veronique [0000-0002-4991-3797], Völker, Uwe [0000-0002-5689-3448], Wander, Gurpreet S [0000-0002-4596-4247], Wang, Ya Xing [0000-0003-2749-7793], Wild, Sarah [0000-0001-7824-2569], Yuan, Jian-Min [0000-0002-4620-3108], Asselbergs, Folkert W [0000-0002-1692-8669], Boehnke, Mike [0000-0002-6442-7754], Bouchard, Claude [0000-0002-0048-491X], Brody, Jennifer A [0000-0001-8509-148X], Campbell, Archie [0000-0003-0198-5078], Caulfield, Mark J [0000-0001-9295-3594], Smith, George Davey [0000-0002-1407-8314], Dorajoo, Rajkumar [0000-0001-6608-2051], Ellinghaus, David [0000-0002-4332-6110], Erdmann, Jeanette [0000-0002-4486-6231], Evangelou, Evangelos [0000-0002-5488-2999], Feenstra, Bjarke [0000-0003-1478-649X], Feitosa, Mary [0000-0002-0933-2410], Franke, Andre [0000-0003-1530-5811], Grant, Struan F A [0000-0003-2025-5302], Griffiths, Lyn R [0000-0002-6774-5475], Groop, Leif [0000-0002-0187-3263], Gudnason, Vilmundur [0000-0001-5696-0084], van der Harst, Pim [0000-0002-2713-686X], Heng, Chew-Kiat [0000-0002-7309-9473], Hicks, Andrew A [0000-0001-6320-0411], Jaddoe, Vincent W V [0000-0003-2939-0041], De Jager, Philip L [0000-0002-8057-2505], Johannesson, Magnus [0000-0001-8759-6393], Johansson, Åsa [0000-0002-2915-4498], Jonas, Jost B [0000-0003-2972-5227], Jukema, J Wouter [0000-0002-3246-8359], Kaprio, Jaakko [0000-0002-3716-2455], Laakso, Markku [0000-0002-3394-7749], van der Laan, Sander W [0000-0001-6888-1404], Lahti, Jari [0000-0002-4310-5297], Martin, Nicholas G [0000-0003-4069-8020], Medland, Sarah E [0000-0003-1382-380X], Merriman, Tony R [0000-0003-0844-8726], Metspalu, Andres [0000-0002-3718-796X], Mohlke, Karen L [0000-0001-6721-153X], Montgomery, Grant W [0000-0002-4140-8139], Munroe, Patricia B [0000-0002-4176-2947], Nyholt, Dale R [0000-0001-7159-3040], Ober, Carole [0000-0003-4626-9809], Oldehinkel, Albertine J [0000-0003-3925-3913], Palmer, Colin [0000-0002-6415-6560], Perusse, Louis [0000-0001-6440-9698], Polderman, Tinca J. C. [0000-0001-5564-301X], Porteous, David J [0000-0003-1249-6106], Rioux, John D [0000-0001-7560-8326], Rivadeneira, Fernando [0000-0001-9435-9441], Rotimi, Charles [0000-0001-5759-053X], Rotter, Jerome I [0000-0001-7191-1723], Rudan, Igor [0000-0001-6993-6884], Sattar, Naveed [0000-0002-1604-2593], Sim, Xueling [0000-0002-1233-7642], Smith, Jennifer A [0000-0002-3575-5468], Teumer, Alexander [0000-0002-8309-094X], Timpson, Nicholas J [0000-0002-7141-9189], Tuomi, Tiinamaija [0000-0002-8306-6202], Wang, Carol A [0000-0002-4301-3974], Weir, David R [0000-0002-1661-2402], Whitfield, John B [0000-0002-1103-0876], Magnusson, Patrik K. E. [0000-0002-7315-7899], Uitterlinden, André G [0000-0002-7276-3387], Loos, Ruth J. F. [0000-0002-8532-5087], Franke, Lude [0000-0002-5159-8802], Haley, Chris S [0000-0002-9811-0210], Hayward, Caroline [0000-0002-9405-9550], Walters, Robin G [0000-0002-9179-0321], Joshi, Peter K [0000-0002-6361-5059], Wilson, James F [0000-0001-5751-9178], Apollo - University of Cambridge Repository, Moore, Kristjan HS [0000-0002-9579-4362], Luan, Jian'an [0000-0003-3137-6337], Grant, Struan FA [0000-0003-2025-5302], Jaddoe, Vincent WV [0000-0003-2939-0041], Polderman, Tinca JC [0000-0001-5564-301X], Magnusson, Patrik KE [0000-0002-7315-7899], Loos, Ruth JF [0000-0002-8532-5087], Neurology, Human genetics, Amsterdam Reproduction & Development (AR&D), Life Course Epidemiology (LCE), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Groningen Institute for Organ Transplantation (GIOT), Lifestyle Medicine (LM), Groningen Kidney Center (GKC), Cardiovascular Centre (CVC), Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Stem Cell Aging Leukemia and Lymphoma (SALL), Institute for Molecular Medicine Finland, Department of Psychology and Logopedics, University Management, Developmental Psychology Research Group, Staff Services, Cognitive and Brain Aging, Research Programs Unit, Diabetes and Obesity Research Program, Johan Eriksson / Principal Investigator, Department of General Practice and Primary Health Care, Clinicum, University of Helsinki, Centre of Excellence in Complex Disease Genetics, Department of Public Health, Genetic Epidemiology, Helsinki Collegium for Advanced Studies, HUS Abdominal Center, Endokrinologian yksikkö, Bradford Teaching Hospitals NHS Foundation Trust [Bradford, UK] (BTHFT), University of Trieste, Université de Lausanne (UNIL), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Consiglio Nazionale delle Ricerche (CNR), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris], Institut Pasteur [Paris], University of Oxford [Oxford], Medical Genetics, Dept. RSD and Public Health, IRCCS-Burlo Garofolo/University of Trieste, sans affiliation, Helmholtz-Zentrum München (HZM), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institute of Cardiovascular Science, University College London, Hammersmith Hospital NHS Imperial College Healthcare-Imperial College London, Universität zu Lübeck [Lübeck], University of Ioannina Medical School, Università degli studi di Napoli Federico II-RISSC-Lab, Universität Heidelberg [Heidelberg], University of Turin, University of California-University of California, Nantes Université (NU)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), University of Helsinki-University of Helsinki, Université de Nantes (UN)-Université de Rennes 1 (UR1), Erasmus MC other, Internal Medicine, and Applied Economics
Subjects: 0301 basic medicine, 631/208/1397, Chemistry(all), Health Status, [SDV]Life Sciences [q-bio], LOCI, General Physics and Astronomy, MESH: Haplotype, MESH: Cognition, 030105 genetics & heredity, Runs of Homozygosity, Biochemistry, Consanguinity, Cognition, Inbreeding depression, 2.1 Biological and endogenous factors, Body Size, Inbreeding, Skyldleikarækt, Aetiology, Human phenotypes, lcsh:Science, MESH: Health Status, Genetics, Multidisciplinary, Inbreeding Depression, Confounding, Homozygote, RUNS, 631/208/205, 631/208/721, 3. Good health, genomic inbreeding coefficients, MESH: Risk-Taking, 631/208/730, Autozygosit, homozygosity, Erfðarannsóknir, Medical Genetics, genomic inbreeding coefficient, MESH: Homozygote, Offspring, Science, Autozygosity, Blóðsifjar, 610 Medicine & health, Biology, INBREEDING DEPRESSION, HOMOZYGOSITY, FERTILITY, QUANTIFICATION, Physics and Astronomy(all), General Biochemistry, Genetics and Molecular Biology, Article, Association, 03 medical and health sciences, Risk-Taking, 360 Social problems & social services, Journal Article, Humans, ddc:610, Allele, Alleles, Medicinsk genetik, Genetic association study, MESH: Consanguinity, MESH: Body Size, MESH: Humans, Biochemistry, Genetics and Molecular Biology(all), MESH: Alleles, Haplotype, MESH: Fertility, General Chemistry, Brain Disorders, MESH: Inbreeding Depression, 030104 developmental biology, Fertility, Haplotypes, Genetic markers, lcsh:Q, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, 3111 Biomedicine, Genetics and Molecular Biology(all)
Abstract: Publisher's version (útgefin grein)., In many species, the offspring of related parents suffer reduced reproductive success, a phenomenon known as inbreeding depression. In humans, the importance of this effect has remained unclear, partly because reproduction between close relatives is both rare and frequently associated with confounding social factors. Here, using genomic inbreeding coefficients (FROH) for >1.4 million individuals, we show that FROH is significantly associated (p < 0.0005) with apparently deleterious changes in 32 out of 100 traits analysed. These changes are associated with runs of homozygosity (ROH), but not with common variant homozygosity, suggesting that genetic variants associated with inbreeding depression are predominantly rare. The effect on fertility is striking: FROH equivalent to the offspring of first cousins is associated with a 55% decrease [95% CI 44–66%] in the odds of having children. Finally, the effects of FROH are confirmed within full-sibling pairs, where the variation in FROH is independent of all environmental confounding., This paper is the work of the ROHgen consortium. We thank the Sigma T2D Consortium, whose members are detailed in Supplementary Note 3. We thank the UK Biobank Resource, approved under application 19655; we acknowledge funding from the UK Medical Research Council Human Genetics Unit and MRC Doctoral Training Programme in Precision Medicine. We also thank Neil Robertson, Wellcome Trust Centre for Human Genetics, Oxford, for use of his author details management software, Authorial. Finally, we thank all the participants, researchers and funders of ROHgen cohorts. Cohort-specific acknowledgements are in Supplementary Data 2; personal acknowledgements and disclosures are in Supplementary Note 2. We thank Rachel Edwards for administrative assistance.
Published: 2019

13. Whole exome sequencing and characterization of coding variation in 49,960 individuals in the UK Biobank

Author: Ida Surakka, Alexander Lopez, Lukas Habegger, Shareef Khalid, William J Salerno, Andrew Blumenfeld, Bin Ye, Jeffrey G. Reid, Ashutosh K. Pandey, Alicia Hawes, John D. Overton, Giovanni Coppola, Jonathan Marchini, Wendy K. Chung, David J. Carey, David H. Ledbetter, Kristian Hveem, Aris N. Economides, Cristopher V. Van Hout, Kavita Praveen, Cristen J. Willer, Joshua D. Backman, Anthony Marcketta, Ioanna Tachmazidou, Marcus B. Jones, O’Dushlaine Colm, John Penn, Joseph B. Leader, Leland Barnard, Daren Liu, George D. Yancopoulos, Michael N. Cantor, Suganthi Balasubramanian, Laura M. Yerges-Armstrong, Alan R. Shuldiner, Claudia Gonzaga-Jauregui, John C. Whittaker, Nilanjana Banerjee, Aris Baras, Gonçalo R. Abecasis, Claudia Schurmann, Robert A. Scott, Evan Maxwell, Matthew R. Nelson, Jeffrey Staples, Ashish Yadav, Joshua D. Hoffman, Lon R. Cardon, and Alexander H. Li
Subjects: education.field_of_study, Genotype, Population, Disease, Computational biology, Biology, education, Exome, Gene, Biobank, Exome sequencing, Loss function
Abstract: SUMMARYThe UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world. Here we describe the first tranche of large-scale exome sequence data for 49,960 study participants, revealing approximately 4 million coding variants (of which ~98.4% have frequency < 1%). The data includes 231,631 predicted loss of function variants, a >10-fold increase compared to imputed sequence for the same participants. Nearly all genes (>97%) had ≥1 predicted loss of function carrier, and most genes (>69%) had ≥10 loss of function carriers. We illustrate the power of characterizing loss of function variation in this large population through association analyses across 1,741 phenotypes. In addition to replicating a range of established associations, we discover novel loss of function variants with large effects on disease traits, including PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on blood cell traits. We further demonstrate the value of exome sequencing by surveying the prevalence of pathogenic variants of clinical significance in this population, finding that 2% of the population has a medically actionable variant. Additionally, we leverage the phenotypic data to characterize the relationship between rare BRCA1 and BRCA2 pathogenic variants and cancer risk. Exomes from the first 49,960 participants are now made accessible to the scientific community and highlight the promise offered by genomic sequencing in large-scale population-based studies.
Published: 2019

14. Exome-derived adiponectin-associated variants implicate obesity and lipid biology

Author: Peter Kovacs, Judith B. Borja, Karen L. Mohlke, Jennifer Kriebel, Kent D. Taylor, Stuart MacGregor, Ruth J. F. Loos, Carol A. Wang, Cornelia M. van Duijn, Samuli Ripatti, Ko Willems van Dijk, Jaeyoung Hong, Yingchang Lu, Leslie A. Lange, Terho Lehtimäki, Matthias Blüher, Cassandra N. Spracklen, Michael A. Province, Craig E. Pennell, Laura B. L. Wittemans, Yii-Der Ida Chen, Alex P. Reiner, Nicholas J. Wareham, Massimo Mangino, Kristin L. Young, Tuomas O. Kilpeläinen, David A. Mackey, Michael Preuss, Mika Kähönen, Sara M. Willems, Paraskevi Chirstofidou, Tamara B. Harris, Matthew A. Allison, Michael Boehnke, Jian'an Luan, Cristina Venturini, Kari E. North, Chelsea K. Raulerson, Linda Broer, Paul M. Ridker, Colleen M. Sitlani, Xiuqing Guo, Leo-Pekka Lyytikäinen, Neil Roberston, Pekka Jousilahti, Barbara McKnight, M. Arfan Ikram, Heather M. Highland, Torben Hansen, Niels Grarup, Satu Männistö, James G. Wilson, Konstantin Strauch, Mariaelisa Graff, Ayse Demirkan, Rebecca S. Fine, Tugce Karaderi, Linda S. Adair, Jie Yao, Olli T. Raitakari, Zoltán Kutalik, Jeffrey Haesser, Veikko Salomaa, Sophie Molnos, Rebecca D. Jackson, Renée de Mutsert, Markku Laakso, Mark I. McCarthy, Carolina Medina-Gomez, America A. Sandoval-Zárate, Anke Tönjes, Daniel I. Chasman, Shuai Wang, Michael Stumvoll, Jette Bork-Jensen, Claudia Langenberg, Paul L. Auer, Anubha Mahajan, Claudia Schurmann, Mary F. Feitosa, Melissa E. Garcia, Tim D. Spector, Aruna D. Pradhan, Jorge R. Kizer, Timothy M. Frayling, Ying Wu, James B. Meigs, Andrew P. Morris, Harald Grallert, André G. Uitterlinden, Cecilia M. Lindgren, Traci M. Bartz, Mike A. Nalls, Erik Ingelsson, Jerome I. Rotter, Mark Walker, Ruifang Li-Gao, Ivana Nedeljkovic, Najaf Amin, Hanieh Yaghootkar, Dennis O. Mook-Kanamori, Betina H. Thuesen, Lars Lind, Jin Li, Epidemiology, Internal Medicine, Centre of Excellence in Complex Disease Genetics, Department of Public Health, Samuli Olli Ripatti / Principal Investigator, University Management, Biostatistics Helsinki, University of Helsinki, Institute for Molecular Medicine Finland, Complex Disease Genetics, and Medical and Clinical Psychology
Subjects: Male, 0301 basic medicine, Candidate gene, Adipose tissue, Genome-wide association study, DISEASE, CANDIDATE GENES, 0302 clinical medicine, Cqardio metabolic traits, RARE, Exome, Genetics (clinical), Aged, 80 and over, Genetics, 0303 health sciences, 1184 Genetics, developmental biology, physiology, Hispanic or Latino, Middle Aged, Lipids, Phenotype, ADIPOSE-TISSUE, Adipose Tissue, 030220 oncology & carcinogenesis, Medical genetics, Female, CIRCULATING ADIPONECTIN, Adiponectin, Adult, EXPRESSION, medicine.medical_specialty, Adolescent, Quantitative Trait Loci, 030209 endocrinology & metabolism, Biology, Polymorphism, Single Nucleotide, Article, White People, Young Adult, 03 medical and health sciences, Cardio Metabolic Traits, Genome-wide Association Study, Obesity, SDG 3 - Good Health and Well-being, medicine, GLYCEMIC TRAITS, Humans, Genetic Predisposition to Disease, GENOME-WIDE ASSOCIATION, Gene, METAANALYSIS, 030304 developmental biology, Aged, PLASMA ADIPONECTIN, Correction, medicine.disease, Human genetics, Black or African American, 030104 developmental biology, Expression quantitative trait loci, 3111 Biomedicine
Abstract: Circulating levels of adiponectin, an adipocyte-secreted protein associated with cardiovascular and metabolic risk, are highly heritable. To gain insights into the biology that regulates adiponectin levels, we performed an exome array meta-analysis of 265,780 genetic variants in 67,739 individuals of European, Hispanic, African American, and East Asian ancestry. We identified 20 loci associated with adiponectin, including 11 that had been reported previously (p -7). Comparison of exome array variants to regional linkage disequilibrium (LD) patterns and prior genome-wide association study (GWAS) results detected candidate variants (r2 > .60) spanning as much as 900 kb. To identify potential genes and mechanisms through which the previously unreported association signals act to affect adiponectin levels, we assessed cross-trait associations, expression quantitative trait loci in subcutaneous adipose, and biological pathways of nearby genes. Eight of the nine loci were also associated (p -4) with at least one obesity or lipid trait. Candidate genes include PRKAR2A, PTH1R, and HDAC9, which have been suggested to play roles in adipocyte differentiation or bone marrow adipose tissue. Taken together, these findings provide further insights into the processes that influence circulating adiponectin levels.
Published: 2019

15. Coding Variant In LEP Associated with Lower Leptin Concentrations Implicates Leptin in the Regulation of Early Adiposity

Author: Rebecca D. Jackson, Jeffrey Haesser, Lars Lind, Germán D. Carrasquilla, Michael A. Province, Paraskevi Christofidou, Charles A. LeDuc, Neil R. Robertson, Tim Kacprowski, Michael Preuss, James G. Wilson, Paul L. Auer, Barbara McKnight, Tuomas O. Kilpeläinen, Satu Männistö, André G. Uitterlinden, Kent D. Taylor, Konstantin Strauch, Cristina Venturini, Mike A. Nalls, Erik Ingelsson, Daniel I. Chasman, Anubha Mahajan, Claudia Schurmann, Mary F. Feitosa, Melissa E. Garcia, Jin Li, Sophia Metz, Torben Hansen, Linda S. Adair, Alexander P. Reiner, Leo-Pekka Lyytikäinen, Cassandra N. Spracklen, Rebecca S. Fine, Tim D. Spector, Leslie A. Lange, Cecilia M. Lindgren, Timothy M. Frayling, Jaeyoung Hong, M. Arfan Ikram, Yingchang Lu, Jette Bork-Jensen, Mark Walker, Mariaelisa Graff, Craig E. Pennell, Paul M. Ridker, Kristin L. Young, Stephen J. Lye, Zoltán Kutalik, Yii-Der Ida Chen, Carolina Medina-Gomez, Ruifang Li-Gao, Cornelia M. van Duijn, Samuli Ripatti, Xiuqing Guo, Laura B. L. Wittemans, Nicholas J. Wareham, Sophie Molnos, Anne E. Justice, Ko Willems van Dijk, Sara M. Willems, Tugce Karaderi, Ivana Nedeljkovic, Massimo Mangino, Ying Wu, James B. Meigs, Matthias Blüher, Matthew A. Allison, Kari E. North, Peter Kovacs, Najaf Amin, Tamara Harris, Judith B. Borja, Karen L. Mohlke, Mika Kähönen, Colleen M. Sitlani, Jorge R. Kizer, David A. Mackey, Hanieh Yaghootkar, Niels Grarup, Dennis O. Mook-Kanamori, Matthias Nauck, Struan F.A. Grant, Lam Opal Huang, Jayne F. Martin Carli, Yiying Zhang, Kaiying Guo, Georg Homuth, Claudia A. Doege, Linda Broer, Ayse Demirkan, Veikko Salomaa, Harald Grallert, Tea Skaaby, Andrew P. Morris, Alexander Teumer, Olli T. Raitakari, Jerome I. Rotter, Jonathan P. Bradfield, Jennifer Kriebel, Rudolph L. Leibel, Hakon Hakonarson, Jian'an Luan, Robert A. Scott, Renée de Mutsert, America A. Sandoval-Zárate, Hermina Jakupović, Shuai Wang, Claudia Langenberg, Pekka Jousilahti, Arund D. Pradhan, Jie Yao, Terho Lehtimäki, Carol A. Wang, Bruce M. Psaty, and Ruth J. F. Loos
Subjects: 2. Zero hunger, medicine.medical_specialty, Food intake, Leptin, digestive, oral, and skin physiology, Genome-wide association study, Biology, medicine.disease, Obesity, Minor allele frequency, Endocrinology, Internal medicine, medicine, Missense mutation, Allele, Exome, hormones, hormone substitutes, and hormone antagonists
Abstract: Leptin influences food intake by informing the brain about the status of body fat stores. Rare LEP mutations associated with congenital leptin deficiency cause severe early-onset obesity that can be mitigated by administering leptin. However, the role of genetic regulation of leptin concentrations in polygenic obesity remains poorly understood. We performed an exome-based analysis in up to 57,232 individuals of diverse ancestries to identify genetic variants that influence adiposity-adjusted leptin concentrations. We confirmed five previously established and identified five novel variants, including four missense variants, in LEP, ZNF800, KLHL31, and ACTL9, and one intergenic variant near KLF14. The novel missense Val94Met (rs17151919) variant in LEP was common in individuals with African ancestry ( minor allele frequency ( MAF) AFR=8%; MAFEUR=0.02%) and was associated with 0.34 standard deviations lower leptin concentrations per Met94 allele in adults (P=2x10-16, n=3,901). Using in vitro analyses, we showed that the Met94 allele decreases leptin secretion (P=0.025). The Met94 allele was associated with higher BMI in young African-ancestry children (P=0.002, n=2,030) but not in adults, suggesting leptin regulates early adiposity.
Published: 2019

16. Platelet-Related Variants Identified by Exomechip Meta-analysis in 157,293 Individuals

Author: Anne-Claire Vergnaud, Nauder Faraday, Tim Kacprowski, Lisa R. Yanek, Oscar H. Franco, Yongmei Liu, Andreas Greinacher, Gina M. Peloso, Cristen J. Willer, Leslie A. Lange, Eric S. Torstenson, Reedik Mägi, Jeanette Erdmann, Ethan M. Lange, Deborah A. Nickerson, Henry Völzke, David R. Crosslin, Gunnar Engström, Albert V. Smith, André G. Uitterlinden, Salman M. Tajuddin, W. David Hill, Diane M. Becker, Paul Elliot, Caterina Vacchi-Suzzi, Linda M. Polfus, Traci M. Bartz, Nathalie Chami, Abbas Dehghan, Mike A. Nalls, John D. Eicher, Leo-Pekka Lyytikäinen, Evelin Mihailov, Uwe Völker, Caroline Hayward, Ioanna Tzoulaki, Myriam Fornage, Marju Orho-Melander, Mary Cushman, Lars Wallentin, Terho Lehtimäki, Ayush Giri, Laura M. Raffield, Lewis C. Becker, Yingchang Lu, Emma Raitoharju, Sekar Kathiresan, Simon de Denus, Ruth J. F. Loos, James S. Floyd, Dawn M. Waterworth, James G. Wilson, Nathan Pankratz, Lenore J. Launer, Andrew D. Johnson, Andrew J. Slater, Jean-Claude Tardif, Raha Pazoki, Evangelos Evangelou, Kenneth Rice, Harvey D. White, Marie-Pierre Dubé, Frank J. A. van Rooij, Akihiro Nomura, Tamara B. Harris, Vilmundur Gudnason, Gonçalo R. Abecasis, Alan B. Zonderman, Guillaume Lettre, Todd L. Edwards, Amber A. Burt, Ani Manichaikul, Heribert Schunkert, Ming-Huei Chen, Ian J. Deary, Michelle L. O'Donoghue, Jennifer A. Brody, Russell P. Tracy, Tõnu Esko, Mika Kähönen, Panos Deloukas, Eric Boerwinkle, Rasika A. Mathias, Dajiang J. Liu, Jin Li, Santhi K. Ganesh, David C. Liewald, Paul L. Auer, Digna R. Velez Edwards, Erwin P. Bottinger, Nina Mononen, Claudia Schurmann, Michele K. Evans, John M. Starr, Thomas Thiele, Jussi Hernesniemi, Jerome I. Rotter, Rakale C. Quarells, He Gao, Kjell Nikus, Stephen S. Rich, Heather M. Highland, Bruce M. Psaty, Ursula M. Schick, Andres Metspalu, Melissa A. Richard, Neil A. Zakai, Olle Melander, John D. Rioux, Olli T. Raitakari, Alexander P. Reiner, Joel N. Hirschhorn, Nilesh J. Samani, Epidemiology, Internal Medicine, Home Office, National Institute for Health Research, and Medical Research Council (MRC)
Subjects: 0301 basic medicine, Blood Platelets, Male, CARDIoGRAM Exome Consortium, Genome-wide association study, 030204 cardiovascular system & hematology, Biology, Myocardial Infarction Genetics Consortium, Article, 03 medical and health sciences, 0302 clinical medicine, Genetics, Humans, Platelet, Exome, Genetics(clinical), Mean platelet volume, Allele frequency, Genotyping, Genetics (clinical), Genetics & Heredity, Platelet Count, ta1184, Genetic Variation, Global Lipids Genetics Consortium, 11 Medical And Health Sciences, 06 Biological Sciences, FCER1A, Genetic architecture, 030104 developmental biology, Hemostasis, Immunology, Female, Mean Platelet Volume, Genome-Wide Association Study
Abstract: Platelet production, maintenance, and clearance are tightly controlled processes indicative of platelets' important roles in hemostasis and thrombosis. Platelets are common targets for primary and secondary prevention of several conditions. They are monitored clinically by complete blood counts, specifically with measurements of platelet count (PLT) and mean platelet volume (MPV). Identifying genetic effects on PLT and MPV can provide mechanistic insights into platelet biology and their role in disease. Therefore, we formed the Blood Cell Consortium (BCX) to perform a large-scale meta-analysis of Exomechip association results for PLT and MPV in 157,293 and 57,617 individuals, respectively. Using the low-frequency/rare coding variant-enriched Exomechip genotyping array, we sought to identify genetic variants associated with PLT and MPV. In addition to confirming 47 known PLT and 20 known MPV associations, we identified 32 PLT and 18 MPV associations not previously observed in the literature across the allele frequency spectrum, including rare large effect (FCER1A), low-frequency (IQGAP2, MAP1A, LY75), and common (ZMIZ2, SMG6, PEAR1, ARFGAP3/PACSIN2) variants. Several variants associated with PLT/MPV (PEAR1, MRVI1, PTGES3) were also associated with platelet reactivity. In concurrent BCX analyses, there was overlap of platelet-associated variants with red (MAP1A, TMPRSS6, ZMIZ2) and white (PEAR1, ZMIZ2, LY75) blood cell traits, suggesting common regulatory pathways with shared genetic architecture among these hematopoietic lineages. Our large-scale Exomechip analyses identified previously undocumented associations with platelet traits and further indicate that several complex quantitative hematological, lipid, and cardiovascular traits share genetic factors.
Published: 2016

17. Large-Scale Exome-wide Association Analysis Identifies Loci for White Blood Cell Traits and Pleiotropy with Immune-Mediated Diseases

Author: Yingchang Lu, Lisa R. Yanek, Evangelos Evangelou, Andreas Greinacher, Leslie A. Lange, Albert Hofman, Rakale C. Quarells, Christopher J. O'Donnell, Simon de Denus, Marcus Dörr, Tamara B. Harris, Mary Cushman, Lars Wallentin, Digna R. Velez Edwards, Michelle L. O'Donoghue, Deborah A. Nickerson, Lisa Bastarache, Caterina Vacchi-Suzzi, Harvey D. White, Rasika A. Mathias, Jin Li, Santhi K. Ganesh, Leo-Pekka Lyytikäinen, Kjell Nikus, Ayush Giri, Paul Elliott, John M. Starr, Ruth J. F. Loos, Vilmundur Gudnason, Ioanna Tzoulaki, Myriam Fornage, Joshua C. Denny, Alan B. Zonderman, Caroline Hayward, Lewis C. Becker, Raha Pazoki, Guillaume Lettre, Lenore J. Launer, Ursula M. Schick, Michele K. Evans, Andrew J. Slater, Diane M. Becker, Jean-Claude Tardif, Ethan M. Lange, John D. Eicher, He Gao, James S. Floyd, Eric Boerwinkle, Paul L. Auer, Nathalie Chami, Frank J. A. van Rooij, Claudia Schurmann, Nele Friedrich, Kent D. Taylor, Andres Metspalu, Todd L. Edwards, Anne-Claire Vergnaud, Yongmei Liu, W. David Hill, Nauder Faraday, Terho Lehtimäki, Amber A. Burt, Jerome I. Rotter, Albert V. Smith, Tõnu Esko, Traci M. Bartz, Tim Kacprowski, Mike A. Nalls, Alexander P. Reiner, Ani Manichaikul, Ian J. Deary, Eric S. Torstenson, Laura M. Raffield, David C. Liewald, Ming-Huei Chen, Erwin P. Bottinger, Reedik Mägi, Andrew D. Johnson, Melissa A. Richard, Neil A. Zakai, John D. Rioux, Mika Kähönen, Stephen S. Rich, Heather M. Highland, Bruce M. Psaty, Joel N. Hirschhorn, Salman M. Tajuddin, Linda M. Polfus, Dawn M. Waterworth, James G. Wilson, Nathan Pankratz, Abbas Dehghan, Evelin Mihailov, David R. Crosslin, André G. Uitterlinden, Georg Homuth, Jennifer A. Brody, Gastroenterology & Hepatology, Epidemiology, and Internal Medicine
Subjects: 0301 basic medicine, Quality Control, Myeloid, 1.1 Normal biological development and functioning, Genome-wide association study, Biology, Autoimmune Disease, Medical and Health Sciences, Article, 03 medical and health sciences, Underpinning research, White blood cell, medicine, Leukocytes, Genetics, Humans, 2.1 Biological and endogenous factors, Genetics(clinical), Exome, Aetiology, Genetics (clinical), Genetic association, Genetics & Heredity, Medical And Health Sciences, Neutrophil clearance, Hematopoietic stem cell differentiation, Inflammatory and immune system, Human Genome, Genetic Pleiotropy, Hematology, Biological Sciences, Acquired immune system, Stem Cell Research, 3. Good health, Blood Cell Count, 030104 developmental biology, medicine.anatomical_structure, Immune System Diseases, Genetic Loci, Immunology, Stem Cell Research - Nonembryonic - Non-Human, Genome-Wide Association Study
Abstract: White blood cells play diverse roles in innate and adaptive immunity. Genetic association analyses of phenotypic variation in circulating white blood cell (WBC) counts from large samples of otherwise healthy individuals can provide insights into genes and biologic pathways involved in production, differentiation, or clearance of particular WBC lineages (myeloid, lymphoid) and also potentially inform the genetic basis of autoimmune, allergic, and blood diseases. We performed an exome array-based meta-analysis of total WBC and subtype counts (neutrophils, monocytes, lymphocytes, basophils, and eosinophils) in a multi-ancestry discovery and replication sample of ∼157,622 individuals from 25 studies. We identified 16 common variants (8 of which were coding variants) associated with one or more WBC traits, the majority of which are pleiotropically associated with autoimmune diseases. Based on functional annotation, these loci included genes encoding surface markers of myeloid, lymphoid, or hematopoietic stem cell differentiation (CD69, CD33, CD87), transcription factors regulating lineage specification during hematopoiesis (ASXL1, IRF8, IKZF1, JMJD1C, ETS2-PSMG1), and molecules involved in neutrophil clearance/apoptosis (C10orf54, LTA), adhesion (TNXB), or centrosome and microtubule structure/function (KIF9, TUBD1). Together with recent reports of somatic ASXL1 mutations among individuals with idiopathic cytopenias or clonal hematopoiesis of undetermined significance, the identification of a common regulatory 3' UTR variant of ASXL1 suggests that both germline and somatic ASXL1 mutations contribute to lower blood counts in otherwise asymptomatic individuals. These association results shed light on genetic mechanisms that regulate circulating WBC counts and suggest a prominent shared genetic architecture with inflammatory and autoimmune diseases.
Published: 2016

18. Genome Analyses of >200,000 Individuals Identify 58 Loci for Chronic Inflammation and Highlight Pathways that Link Inflammation and Complex Disorders

Author: Symen Ligthart, Ahmad Vaez, Urmo Võsa, Maria G. Stathopoulou, Paul S. de Vries, Bram P. Prins, Peter J. Van der Most, Toshiko Tanaka, Elnaz Naderi, Lynda M. Rose, Ying Wu, Robert Karlsson, Maja Barbalic, Honghuang Lin, René Pool, Gu Zhu, Aurélien Macé, Carlo Sidore, Stella Trompet, Massimo Mangino, Maria Sabater-Lleal, John P. Kemp, Ali Abbasi, Tim Kacprowski, Niek Verweij, Albert V. Smith, Tao Huang, Carola Marzi, Mary F. Feitosa, Kurt K. Lohman, Marcus E. Kleber, Yuri Milaneschi, Christian Mueller, Mahmudul Huq, Efthymia Vlachopoulou, Leo-Pekka Lyytikäinen, Christopher Oldmeadow, Joris Deelen, Markus Perola, Jing Hua Zhao, Bjarke Feenstra, Marzyeh Amini, Jari Lahti, Katharina E. Schraut, Myriam Fornage, Bhoom Suktitipat, Wei-Min Chen, Xiaohui Li, Teresa Nutile, Giovanni Malerba, Jian’an Luan, Tom Bak, Nicholas Schork, Fabiola Del Greco M., Elisabeth Thiering, Anubha Mahajan, Riccardo E. Marioni, Evelin Mihailov, Joel Eriksson, Ayse Bilge Ozel, Weihua Zhang, Maria Nethander, Yu-Ching Cheng, Stella Aslibekyan, Wei Ang, Ilaria Gandin, Loïc Yengo, Laura Portas, Charles Kooperberg, Edith Hofer, Kumar B. Rajan, Claudia Schurmann, Wouter den Hollander, Tarunveer S. Ahluwalia, Jing Zhao, Harmen H.M. Draisma, Ian Ford, Nicholas Timpson, Alexander Teumer, Hongyan Huang, Simone Wahl, YongMei Liu, Jie Huang, Hae-Won Uh, Frank Geller, Peter K. Joshi, Lisa R. Yanek, Elisabetta Trabetti, Benjamin Lehne, Diego Vozzi, Marie Verbanck, Ginevra Biino, Yasaman Saba, Ingrid Meulenbelt, Jeff R. O’Connell, Markku Laakso, Franco Giulianini, Patrik K.E. Magnusson, Christie M. Ballantyne, Jouke Jan Hottenga, Grant W. Montgomery, Fernando Rivadineira, Rico Rueedi, Maristella Steri, Karl-Heinz Herzig, David J. Stott, Cristina Menni, Mattias Frånberg, Beate St. Pourcain, Stephan B. Felix, Tune H. Pers, Stephan J.L. Bakker, Peter Kraft, Annette Peters, Dhananjay Vaidya, Graciela Delgado, Johannes H. Smit, Vera Großmann, Juha Sinisalo, Ilkka Seppälä, Stephen R. Williams, Elizabeth G. Holliday, Matthijs Moed, Claudia Langenberg, Katri Räikkönen, Jingzhong Ding, Harry Campbell, Michele M. Sale, Yii-Der I. Chen, Alan L. James, Daniela Ruggiero, Nicole Soranzo, Catharina A. Hartman, Erin N. Smith, Gerald S. Berenson, Christian Fuchsberger, Dena Hernandez, Carla M.T. Tiesler, Vilmantas Giedraitis, David Liewald, Krista Fischer, Dan Mellström, Anders Larsson, Yunmei Wang, William R. Scott, Matthias Lorentzon, John Beilby, Kathleen A. Ryan, Craig E. Pennell, Dragana Vuckovic, Beverly Balkau, Maria Pina Concas, Reinhold Schmidt, Carlos F. Mendes de Leon, Erwin P. Bottinger, Margreet Kloppenburg, Lavinia Paternoster, Michael Boehnke, A.W. Musk, Gonneke Willemsen, David M. Evans, Pamela A.F. Madden, Mika Kähönen, Zoltán Kutalik, Magdalena Zoledziewska, Ville Karhunen, Stephen B. Kritchevsky, Naveed Sattar, Genevieve Lachance, Robert Clarke, Tamara B. Harris, Olli T. Raitakari, John R. Attia, Diana van Heemst, Eero Kajantie, Rossella Sorice, Giovanni Gambaro, Robert A. Scott, Andrew A. Hicks, Luigi Ferrucci, Marie Standl, Cecilia M. Lindgren, John M. Starr, Magnus Karlsson, Lars Lind, Jun Z. Li, John C. Chambers, Trevor A. Mori, Eco J.C.N. de Geus, Andrew C. Heath, Nicholas G. Martin, Juha Auvinen, Brendan M. Buckley, Anton J.M. de Craen, Melanie Waldenberger, Konstantin Strauch, Thomas Meitinger, Rodney J. Scott, Mark McEvoy, Marian Beekman, Cristina Bombieri, Paul M. Ridker, Karen L. Mohlke, Nancy L. Pedersen, Alanna C. Morrison, Dorret I. Boomsma, John B. Whitfield, David P. Strachan, Albert Hofman, Peter Vollenweider, Francesco Cucca, Marjo-Riitta Jarvelin, J. Wouter Jukema, Tim D. Spector, Anders Hamsten, Tanja Zeller, André G. Uitterlinden, Matthias Nauck, Vilmundur Gudnason, Lu Qi, Harald Grallert, Ingrid B. Borecki, Jerome I. Rotter, Winfried März, Philipp S. Wild, Marja-Liisa Lokki, Michael Boyle, Veikko Salomaa, Mads Melbye, Johan G. Eriksson, James F. Wilson, Brenda W.J.H. Penninx, Diane M. Becker, Bradford B. Worrall, Greg Gibson, Ronald M. Krauss, Marina Ciullo, Gianluigi Zaza, Nicholas J. Wareham, Albertine J. Oldehinkel, Lyle J. Palmer, Sarah S. Murray, Peter P. Pramstaller, Stefania Bandinelli, Joachim Heinrich, Erik Ingelsson, Ian J. Deary, Reedik Mägi, Liesbeth Vandenput, Pim van der Harst, Karl C. Desch, Jaspal S. Kooner, Claes Ohlsson, Caroline Hayward, Terho Lehtimäki, Alan R. Shuldiner, Donna K. Arnett, Lawrence J. Beilin, Antonietta Robino, Philippe Froguel, Mario Pirastu, Tine Jess, Wolfgang Koenig, Ruth J.F. Loos, Denis A. Evans, Helena Schmidt, George Davey Smith, P. Eline Slagboom, Gudny Eiriksdottir, Andrew P. Morris, Bruce M. Psaty, Russell P. Tracy, Ilja M. Nolte, Eric Boerwinkle, Sophie Visvikis-Siest, Alex P. Reiner, Myron Gross, Joshua C. Bis, Lude Franke, Oscar H. Franco, Emelia J. Benjamin, Daniel I. Chasman, Josée Dupuis, Harold Snieder, Abbas Dehghan, Behrooz Z. Alizadeh, H. Marike Boezen, Gerjan Navis, Marianne Rots, Morris Swertz, Bruce H.R. Wolffenbuttel, Cisca Wijmenga, Emelia Benjamin, Tarunveer Singh Ahluwalia, James Meigs, Russell Tracy, Josh Bis, Nathan Pankratz, Alex Rainer, James G. Wilson, Josee Dupuis, Bram Prins, Urmo Vaso, Maria Stathopoulou, Terho Lehtimaki, Yalda Jamshidi, Sophie Siest, Andre G. Uitterlinden, Mohammadreza Abdollahi, Renate Schnabel, Ursula M. Schick, Aldi Kraja, Yi-Hsiang Hsu, Daniel S. Tylee, Alyson Zwicker, Rudolf Uher, George Davey-Smith, Andrew Hicks, Cornelia M. van Duijn, Cavin Ward-Caviness, J. Rotter, Ken Rice, Leslie Lange, Eco de Geus, Kari Matti Makela, David Stacey, Johan Eriksson, Tim M. Frayling, Eline P. Slagboom, Erasmus University Medical Center [Rotterdam] (Erasmus MC), University Medical Center Groningen [Groningen] (UMCG), University of Isfahan, University of Tartu, Interactions Gène-Environnement en Physiopathologie Cardio-Vasculaire (IGE-PCV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL), The University of Texas Health Science Center at Houston (UTHealth), National Institute on Aging [Bethesda, USA] (NIA), National Institutes of Health [Bethesda] (NIH), Brigham and Women's Hospital [Boston], University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), Department of Medical Epidemiology and Biostatistics (MEB), Karolinska Institutet [Stockholm], University of Split, Boston University School of Medicine (BUSM), Boston University [Boston] (BU), Process & Energy Laboratory, Delft University of Technology (TU Delft), Grand Lyon : communauté urbaine de Lyon, Interuniversity Cardiology Institute Netherlands, Department of Twin Research and Genetic Epidemiology, King's College London, London, Huazhong University of Science and Technology [Wuhan] (HUST), Division of Statistical Genomics, Washington University School of Medicine, Department of Psychiatry, VU University Medical Center [Amsterdam], Institut fuer Theoretische Physik (Institut fuer Theoretische Physik), Universität Heidelberg [Heidelberg] = Heidelberg University, Molecular Epidemiology, MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Mahidol University [Bangkok], Northwest A and F University, Laboratoire d'Optimisation des Systèmes Industriels (LOSI), Institut Charles Delaunay (ICD), Université de Technologie de Troyes (UTT)-Centre National de la Recherche Scientifique (CNRS)-Université de Technologie de Troyes (UTT)-Centre National de la Recherche Scientifique (CNRS), Institute of Genetics and Biophysics, CNR, Naples, Università degli studi di Verona = University of Verona (UNIVR), Department of Molecular Medicine [Scripps Research Institute], The Scripps Research Institute [La Jolla, San Diego], Department of Physics, Indian Institute of Technology Kanpur (IIT Kanpur), Deptartment of Medical Biochemistry and Microbiology, Uppsala University, Department of Electrical and Computer Engineering [Waterloo] (ECE), University of Waterloo [Waterloo], University of Maryland School of Medicine, University of Maryland System, Institut National de l'Environnement Industriel et des Risques (INERIS), Institute of Pop. Genetics, CNR, Sassari, Interfaculty Institute for Genetics and Functional Genomics, Universität Greifswald - University of Greifswald, IT University of Copenhagen (ITU), Robertson Centre for Biostatistics, University of Glasgow, Centre for Causal Analyses in Translational Epidemiology, University of Bristol [Bristol]-Medical Research Council, King‘s College London, Jinan University [Guangzhou], Institute of Oceanology [China], School Medicine, University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE)-Pennsylvania Commonwealth System of Higher Education (PCSHE), General Internal Medicine, Johns Hopkins School of Medicine, Johns Hopkins University School of Medicine [Baltimore], Shardna life science Pula Cagliari, Section Molecular Epidemiology, Leiden University Medical Center (LUMC), Department of Medicine, University of Eastern Finland-Kuopio University Hospital, Medstar Research Institute, Department of Cardiology, Ernst-Moritz-Arndt University, Center for Biological Sequence Analysis [Lyngby], Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Department of Internal Medicine, University of Groningen and University Medical Center Groningen, Department of Epidemiology, Harvard School of Public Health, German Research Center for Environmental Health - Helmholtz Center München (GmbH), Metacohorts Consortium, INEOS Technologies (SWITZERLAND), MRC Epidemiology Unit, University of Cambridge [UK] (CAM)-Institute of Metabolic Science, University of Edinburgh, School of Population Health [Crawley, Western Australia], The University of Western Australia (UWA), Institute of Genetics and Biophysics, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), The Scripps Translational Science Institute and Scripps Health, Tulane Center for Cardiovascular Health, Tulane University Health Sciences Center, Centre for Population Health Sciences, Genomic Research Laboratory, Service of Infectious Disease, Hôpitaux Universitaires de Genève (HUG), Infectious diseases division, Department of internal medicine, Washington University in Saint Louis (WUSTL), Luleå University of Technology (LUT), Recherche en épidémiologie et biostatistique, Université Paris-Sud - Paris 11 (UP11)-Institut National de la Santé et de la Recherche Médicale (INSERM), Austrian Institute of Technology [Vienna] (AIT), Icahn School of Medicine at Mount Sinai [New York] (MSSM), Department of Rheumatology and Clinical Epidemiology, Leiden University Medical Center (LUMC), Department of Rheumatology and Clinical Epidemiology [Leiden University Medical Center] (LUMC), Leiden University Medical Center (LUMC), Universiteit Leiden-Universiteit Leiden-Leiden University Medical Center (LUMC), Universiteit Leiden-Universiteit Leiden, Department of Biostatistics and Center for Statistical Genetics, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, University of Virginia, Tampere University Hospital, Department of Medical Genetics, Université de Lausanne = University of Lausanne (UNIL), Department of Pathological Biochemistry, Royal Infirmary, Oxford University, University of Oxford, University of Newcastle [Callaghan, Australia] (UoN), Department of neurology, Institute of Metabolic Science, MRC, The Wellcome Trust Centre for Human Genetics [Oxford], Uppsala Universitet [Uppsala], QIMR Berghofer Medical Research Institute, Institute of Genetic Epidemiology [Neuherberg, Germany], Institute of Human Genetics, Helmholtz Zentrum München = German Research Center for Environmental Health, Schizophrenia Research Institute [Sydney], Department of Genetics, University of North Carolina System (UNC)-University of North Carolina System (UNC), Vrije Universiteit Brussel (VUB), Population Health Sciences and Education, St George's University of London, Centre Hospitalier Universitaire Vaudois [Lausanne] (CHUV), Institute of Health Sciences and Biocenter Oulu, University of Oulu, Medizinische Klinik und Poliklinik, Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), Institute of Clinical Chemistry and Laboratory Medicine, Icelandic Heart Association, Heart Preventive Clinic and Research Institute, Departments of Epidemiology and Nutrition, Institute of Epidemiology [Neuherberg] (EPI), Medical University Graz, Transplantation Laboratory [Helsinki], Haartman Institute [Helsinki], Faculty of Medecine [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Faculty of Medecine [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Department of Chronic Disease Prevention, National Institute for Health and Welfare [Helsinki], Dept. of Epidemiology Research, Statens Serum Institut [Copenhagen], CLinical Psychology, Genetics and Pathology, Geriatric Rehabilitation Unit, Azienda Sanitaria Firenze, Center For Narcolepsy, Stanford University, Centre for Bone and Arthritis Research, University of Gothenburg (GU)-Institute of Medicine, MRC Human Gentics Unit, Inst Genet and Mol Med, Western General Hospital, Edinburgh, University of Maryland School of Medicine [Baltimore, MD, USA], Génétique des maladies multifactorielles (GMM), Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Stockholm], Stockholm University, University of Bristol [Bristol], Universiteit Leiden, Department of Epidemiology, University of Washington, University of Washington [Seattle], Department of Epidemiology [Rotterdam], University of Groningen [Groningen], Dutch Initiative on Crohn and Colitis (ICC), Icelandic Heart Association [Kopavogur, Iceland] (IHA), Department of Physiology and Biophysics [Jackson, MS, USA], University of Southern Mississippi (USM), Human Genetics Branch, National Institutes of Health [Bethesda] (NIH)-National Institute of Mental Health (NIMH), Faculty of Medicine and Life Sciences [Tampere], University of Tampere [Finland], German Center for Cardiovascular Research (DZHK), Berlin Institute of Health (BIH), MRC Centre for Neuropsychiatric Genetics and Genomics, Medical Research Council-Cardiff University, Department of Social Medicine, School of Medicine [Los Angeles], University of California [Los Angeles] (UCLA), University of California (UC)-University of California (UC), Department of Medicine [Aurora, CO, USA], University of Colorado [Denver], Institute for Molecular Medicine Finland [Helsinki] (FIMM), Helsinki Institute of Life Science (HiLIFE), Mathematical Institute [Oxford] (MI), Institute of Psychiatry, Psychology & Neuroscience, King's College London, LifeLines Cohort Study, CHARGE Inflammation Working Group, Ligthart, S., Vaez, A., Vosa, U., Stathopoulou, M. G., de Vries, P. S., Prins, B. P., Van der Most, P. J., Tanaka, T., Naderi, E., Rose, L. M., Wu, Y., Karlsson, R., Barbalic, M., Lin, H., Pool, R., Zhu, G., Mace, A., Sidore, C., Trompet, S., Mangino, M., Sabater-Lleal, M., Kemp, J. P., Abbasi, A., Kacprowski, T., Verweij, N., Smith, A. V., Huang, T., Marzi, C., Feitosa, M. F., Lohman, K. K., Kleber, M. E., Milaneschi, Y., Mueller, C., Huq, M., Vlachopoulou, E., Lyytikainen, L. -P., Oldmeadow, C., Deelen, J., Perola, M., Zhao, J. H., Feenstra, B., Alizadeh, B. Z., Boezen, H. M., Franke, L., van der Harst, P., Navis, G., Rots, M., Snieder, H., Swertz, M., Wolffenbuttel, B. H. R., Wijmenga, C., Amini, M., Benjamin, E., Chasman, D. I., Dehghan, A., Ahluwalia, T. S., Meigs, J., Tracy, R., Bis, J., Eiriksdottir, G., Pankratz, N., Gross, M., Rainer, A., Wilson, J. G., Psaty, B. M., Dupuis, J., Prins, B., Vaso, U., Stathopoulou, M., Lehtimaki, T., Koenig, W., Jamshidi, Y., Siest, S., Uitterlinden, A. G., Abdollahi, M., Schnabel, R., Schick, U. M., Nolte, I. M., Kraja, A., Hsu, Y. -H., Tylee, D. S., Zwicker, A., Uher, R., Davey-Smith, G., Morrison, A. C., Hicks, A., van Duijn, C. M., Ward-Caviness, C., Boerwinkle, E., Rotter, J., Rice, K., Lange, L., de Geus, E., Morris, A. P., Makela, K. M., Stacey, D., Eriksson, J., Frayling, T. M., Slagboom, E. P., Lahti, J., Schraut, K. E., Fornage, M., Suktitipat, B., Chen, W. -M., Li, X., Nutile, T., Malerba, G., Luan, J., Bak, T., Schork, N., Del Greco, M. F., Thiering, E., Mahajan, A., Marioni, R. E., Mihailov, E., Ozel, A. B., Zhang, W., Nethander, M., Cheng, Y. -C., Aslibekyan, S., Ang, W., Gandin, I., Yengo, L., Portas, L., Kooperberg, C., Hofer, E., Rajan, K. B., Schurmann, C., den Hollander, W., Zhao, J., Draisma, H. H. M., Ford, I., Timpson, N., Teumer, A., Huang, H., Wahl, S., Liu, Y., Huang, J., Uh, H. -W., Geller, F., Joshi, P. K., Yanek, L. R., Trabetti, E., Lehne, B., Vozzi, D., Verbanck, M., Biino, G., Saba, Y., Meulenbelt, I., O'Connell, J. R., Laakso, M., Giulianini, F., Magnusson, P. K. E., Ballantyne, C. M., Hottenga, J. J., Montgomery, G. W., Rivadineira, F., Rueedi, R., Steri, M., Herzig, K. -H., Stott, D. J., Menni, C., Franberg, M., S, t. Pourcain B., Felix, S. B., Pers, T. H., Bakker, S. J. L., Kraft, P., Peters, A., Vaidya, D., Delgado, G., Smit, J. H., Grossmann, V., Sinisalo, J., Seppala, I., Williams, S. R., Holliday, E. G., Moed, M., Langenberg, C., Raikkonen, K., Ding, J., Campbell, H., Sale, M. M., Chen, Y. -D. I., James, A. L., Ruggiero, D., Soranzo, N., Hartman, C. A., Smith, E. N., Berenson, G. S., Fuchsberger, C., Hernandez, D., Tiesler, C. M. T., Giedraitis, V., Liewald, D., Fischer, K., Mellstrom, D., Larsson, A., Wang, Y., Scott, W. R., Lorentzon, M., Beilby, J., Ryan, K. A., Pennell, C. E., Vuckovic, D., Balkau, B., Concas, M. P., Schmidt, R., Mendes de Leon, C. F., Bottinger, E. P., Kloppenburg, M., Paternoster, L., Boehnke, M., Musk, A. W., Willemsen, G., Evans, D. M., Madden, P. A. F., Kahonen, M., Kutalik, Z., Zoledziewska, M., Karhunen, V., Kritchevsky, S. B., Sattar, N., Lachance, G., Clarke, R., Harris, T. B., Raitakari, O. T., Attia, J. R., van Heemst, D., Kajantie, E., Sorice, R., Gambaro, G., Scott, R. A., Hicks, A. A., Ferrucci, L., Standl, M., Lindgren, C. M., Starr, J. M., Karlsson, M., Lind, L., Li, J. Z., Chambers, J. C., Mori, T. A., de Geus, E. J. C. N., Heath, A. C., Martin, N. G., Auvinen, J., Buckley, B. M., de Craen, A. J. M., Waldenberger, M., Strauch, K., Meitinger, T., Scott, R. J., Mcevoy, M., Beekman, M., Bombieri, C., Ridker, P. M., Mohlke, K. L., Pedersen, N. L., Boomsma, D. I., Whitfield, J. B., Strachan, D. P., Hofman, A., Vollenweider, P., Cucca, F., Jarvelin, M. -R., Jukema, J. W., Spector, T. D., Hamsten, A., Zeller, T., Nauck, M., Gudnason, V., Qi, L., Grallert, H., Borecki, I. B., Rotter, J. I., Marz, W., Wild, P. S., Lokki, M. -L., Boyle, M., Salomaa, V., Melbye, M., Eriksson, J. G., Wilson, J. F., Penninx, B. W. J. H., Becker, D. M., Worrall, B. B., Gibson, G., Krauss, R. M., Ciullo, M., Zaza, G., Wareham, N. J., Oldehinkel, A. J., Palmer, L. J., Murray, S. S., Pramstaller, P. P., Bandinelli, S., Heinrich, J., Ingelsson, E., Deary, I. J., Magi, R., Vandenput, L., Desch, K. C., Kooner, J. S., Ohlsson, C., Hayward, C., Shuldiner, A. R., Arnett, D. K., Beilin, L. J., Robino, A., Froguel, P., Pirastu, M., Jess, T., Loos, R. J. F., Evans, D. A., Schmidt, H., Slagboom, P. E., Tracy, R. P., Visvikis-Siest, S., Reiner, A. P., Bis, J. C., Franco, O. H., Benjamin, E. J., AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, Graduate School, Epidemiology, Internal Medicine, Groningen Institute for Organ Transplantation (GIOT), Lifestyle Medicine (LM), Groningen Kidney Center (GKC), Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Cardiovascular Centre (CVC), Life Course Epidemiology (LCE), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Stem Cell Aging Leukemia and Lymphoma (SALL), Real World Studies in PharmacoEpidemiology, -Genetics, -Economics and -Therapy (PEGET), VU University medical center, Psychiatry, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, APH - Mental Health, APH - Methodology, APH - Digital Health, Biological Psychology, APH - Personalized Medicine, APH - Health Behaviors & Chronic Diseases, Universität Heidelberg [Heidelberg], University of Verona (UNIVR), Department of Molecular and Experimental Medicine, The Scripps Research Institute, The Scripps Research Institute, Université Grenoble Alpes - UFR Sciences de l'Homme et de la Société (UGA UFR SHS), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), IT University of Copenhagen, Technical University of Denmark [Lyngby] (DTU), Consiglio Nazionale delle Ricerche (CNR), University of Virginia [Charlottesville], Université de Lausanne (UNIL), University of Oxford [Oxford], University of Newcastle [Australia] (UoN), Centre d'économie industrielle i3 (CERNA i3), Centre National de la Recherche Scientifique (CNRS)-MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Helmholtz-Zentrum München (HZM), Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA (UMR_7583)), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Universitätsmedizin der Johannes-Gutenberg Universität Mainz, University of Helsinki-University of Helsinki-Faculty of Medecine [Helsinki], University of Helsinki-University of Helsinki, Cardiff University-Medical Research Council, University of California-University of California, and DE CARVALHO, Philippe
Subjects: 0301 basic medicine, Male, Netherlands Twin Register (NTR), Bipolar Disorder, LD SCORE REGRESSION, [SDV]Life Sciences [q-bio], Genome-wide association study, [SDV.GEN] Life Sciences [q-bio]/Genetics, Body Mass Index, inflammatory disorder, 80 and over, WIDE ASSOCIATION, EPIDEMIOLOGY, ta318, International HapMap Project, Child, Genetics (clinical), 2. Zero hunger, Genetics, Genetics & Heredity, Aged, 80 and over, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, C-reactive proteingenome-wide association studyinflammationMendelian randomizationinflammatory disordersDEPICTcoronary artery diseaseschizophreniasystem biology, system biology, DEPICT, Mendelian Randomization Analysis, 11 Medical And Health Sciences, Middle Aged, C-reactive protein, coronary artery disease, genome-wide association study, inflammation, inflammatory disorders, Mendelian randomization, schizophrenia, Adolescent, Adult, Aged, Biomarkers, C-Reactive Protein, Female, Genetic Loci, Genome-Wide Association Study, Humans, Inflammation, Liver, Metabolic Networks and Pathways, Schizophrenia, Young Adult, 3. Good health, [SDV] Life Sciences [q-bio], Medical genetics, Biomarker (medicine), Life Sciences & Biomedicine, Human, medicine.medical_specialty, CHARGE Inflammation Working Group, Biology, IMMUNITY, ta3111, Article, 03 medical and health sciences, SDG 3 - Good Health and Well-being, medicine, CORONARY-HEART-DISEASE, Mendelian Randomization Analysi, 1000 Genomes Project, METAANALYSIS, Genetic association, [SDV.GEN]Life Sciences [q-bio]/Genetics, Science & Technology, ta1184, Metabolic Networks and Pathway, Biomarker, INSTRUMENTS, 06 Biological Sciences, 030104 developmental biology, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, LifeLines Cohort Study
Abstract: International audience; C-reactive protein (CRP) is a sensitive biomarker of chronic low-grade inflammation and is associated with multiple complex diseases. The genetic determinants of chronic inflammation remain largely unknown, and the causal role of CRP in several clinical outcomes is debated. We performed two genome-wide association studies (GWASs), on HapMap and 1000 Genomes imputed data, of circulating amounts of CRP by using data from 88 studies comprising 204,402 European individuals. Additionally, we performed in silico functional analyses and Mendelian randomization analyses with several clinical outcomes. The GWAS meta-analyses of CRP revealed 58 distinct genetic loci (p < 5 × 10-8). After adjustment for body mass index in the regression analysis, the associations at all except three loci remained. The lead variants at the distinct loci explained up to 7.0% of the variance in circulating amounts of CRP. We identified 66 gene sets that were organized in two substantially correlated clusters, one mainly composed of immune pathways and the other characterized by metabolic pathways in the liver. Mendelian randomization analyses revealed a causal protective effect of CRP on schizophrenia and a risk-increasing effect on bipolar disorder. Our findings provide further insights into the biology of inflammation and could lead to interventions for treating inflammation and its clinical consequences.Copyright © 2018 American Society of Human Genetics. All rights reserved.
Published: 2018

19. Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps

Author: George Dedoussis, M. Arfan Ikram, Marit E. Jørgensen, Christian Herder, Gudmar Thorleifsson, Oscar H. Franco, Xueling Sim, Philippe Froguel, Symen Ligthart, Ellen M. Schmidt, Jason M. Torres, Karen L. Mohlke, Markku Laakso, Barbara Thorand, Erwin P. Bottinger, Matthias Thurner, Torben Hansen, Jerome I. Rotter, Weihua Zhang, Ching-Ti Liu, Michael Boehnke, Kristi Läll, Konstantin Strauch, Kent D. Taylor, Andrew D. Morris, Daniel R. Witte, Anna L. Gloyn, Jonathan Marchini, Andres Metspalu, Florian Kronenberg, Anubha Mahajan, Claudia Schurmann, Jennifer Kriebel, James S. Pankow, Matthias Wuttke, Valeriya Lyssenko, Jose C. Florez, Josée Dupuis, Patricia A. Peyser, Leif Groop, John C. Chambers, Torben Jørgensen, Timothy M. Frayling, Lawrence F. Bielak, Nicholas J. Wareham, Thomas Meitinger, Alena Stančáková, Vasiliki Mamakou, Cramer Christensen, Michael Preuss, Bram P. Prins, Niels Grarup, Amanda J. Bennett, Vilmantas Giedraitis, Jian'an Luan, Young-Jin Kim, Mickaël Canouil, Robert A. Scott, Kari Stefansson, Jana Nano, Donald W. Bowden, Oluf Pedersen, Cécile Lecoeur, Anna Köttgen, Jette Bork-Jensen, Francis S. Collins, Unnur Thorsteinsdottir, Naveed Sattar, Stella Trompet, Martin Ingelsson, Maggie C.Y. Ng, Jaakko Tuomilehto, Reedik Mägi, James B. Meigs, Lauren E. Petty, J. Wouter Jukema, Andrew T. Hattersley, Claudia Langenberg, Harald Grallert, Christian Gieger, Chad M. Brummett, Ian Ford, Andrew P. Morris, James P. Cook, Vibe Nylander, Sebastian Schönherr, Daniel Taliun, Xiuqing Guo, Valgerdur Steinthorsdottir, Cecilia M. Lindgren, Jennifer E. Below, Eleftheria Zeggini, Anthony Payne, Loic Yengo, Sharon L.R. Kardia, Neil R. Robertson, Abbas Dehghan, Ivan Brandslund, Erik Ingelsson, Colin N. A. Palmer, Ruth J. F. Loos, Girish N. Nadkarni, Gonçalo R. Abecasis, Adam E. Locke, Johanna Kuusisto, Lars Lind, Krista Fischer, Annette Peters, Kai-Uwe Ec Kardt, Ioanna Ntalla, Chloé Sarnowski, Mark I. McCarthy, N. William Rayner, Allan Linneberg, Sophie Hackinger, Centre of Excellence in Complex Disease Genetics, Institute for Molecular Medicine Finland, University of Helsinki, HUS Abdominal Center, Mahajan, Anubha [0000-0001-5585-3420], Morris, Andrew P [0000-0002-6805-6014], Boehnke, Michael [0000-0002-6442-7754], McCarthy, Mark I [0000-0002-4393-0510], Apollo - University of Cambridge Repository, Lee Kong Chian School of Medicine (LKCMedicine), and Epidemiology
Subjects: 0301 basic medicine, Male, Linkage disequilibrium, endocrine system diseases, Genome-wide association study, DISEASE, Linkage Disequilibrium, Body Mass Index, Epigenesis, Genetic, 0302 clinical medicine, Gene Frequency, High-Throughput Screening Assays/methods, European Continental Ancestry Group/genetics, Genetics & Heredity, 0303 health sciences, Chromosome Mapping, 11 Medical And Health Sciences, Functional Genomics, 3. Good health, Genetic Loci/genetics, Medical genetics, Female, Islets of Langerhans/metabolism, Life Sciences & Biomedicine, TRAITS, EXPRESSION, medicine.medical_specialty, SUSCEPTIBILITY LOCI, Genomics, 030209 endocrinology & metabolism, PHENOTYPES, Computational biology, Biology, Polymorphism, Single Nucleotide, White People, Article, GENETIC ARCHITECTURE, Islets of Langerhans, 03 medical and health sciences, Sex Factors, SDG 3 - Good Health and Well-being, Meta-Analysis as Topic, SCORE, Genetics, medicine, Humans, Medicine [Science], Genetic Predisposition to Disease, Allele, GENOME-WIDE ASSOCIATION, Genotyping, Allele frequency, METAANALYSIS, 030304 developmental biology, Science & Technology, IDENTIFICATION, Genome, Human, Haplotype, 06 Biological Sciences, Human genetics, Genetic architecture, High-Throughput Screening Assays, Minor allele frequency, 030104 developmental biology, Diabetes Mellitus, Type 2, Diabetes Mellitus, Type 2/epidemiology, Sample size determination, Genetic Loci, Case-Control Studies, Genome, Human/genetics, Genome-wide Association Studies, 3111 Biomedicine, Chromosome Mapping/methods, 030217 neurology & neurosurgery, Imputation (genetics), Developmental Biology, Genome-Wide Association Study
Abstract: We aggregated genome-wide genotyping data from 32 European-descent GWAS (74,124 T2D cases, 824,006 controls) imputed to high-density reference panels of >30,000 sequenced haplotypes. Analysis of ˜27M variants (˜21M with minor allele frequency [MAF]p−8; MAF 0.02%-50%; odds ratio [OR] 1.04-8.05), 135 not previously-implicated in T2D-predisposition. Conditional analyses revealed 160 additional distinct association signals (p−5) within the identified loci. The combined set of 403 T2D-risk signals includes 56 low-frequency (0.5%≤MAF2. Forty-one of the signals displayed effect-size heterogeneity between BMI-unadjusted and adjusted analyses. Increased sample size and improved imputation led to substantially more precise localisation of causal variants than previously attained: at 51 signals, the lead variant after fine-mapping accounted for >80% posterior probability of association (PPA) and at 18 of these, PPA exceeded 99%. Integration with islet regulatory annotations enriched for T2D association further reduced median credible set size (from 42 variants to 32) and extended the number of index variants with PPA>80% to 73. Although most signals mapped to regulatory sequence, we identified 18 genes as human validated therapeutic targets through coding variants that are causal for disease. Genome wide chip heritability accounted for 18% of T2D-risk, and individuals in the 2.5% extremes of a polygenic risk score generated from the GWAS data differed >9-fold in risk. Our observations highlight how increases in sample size and variant diversity deliver enhanced discovery and single-variant resolution of causal T2D-risk alleles, and the consequent impact on mechanistic insights and clinical translation.
Published: 2018

20. Genetic discovery and translational decision support from exome sequencing of 20,791 type 2 diabetes cases and 24,440 controls from five ancestries

Author: Humberto García-Ortiz, Loos R, Frederick E. Dewey, Farook Thameem, John C. Chambers, Mi Yeong Hwang, Nancy L. Heard-Costa, Danish Saleheen, Shuai Wang, Morris Ad, Josep M. Mercader, Noël P. Burtt, Laura J. Scott, Torben Hansen, Mark I. McCarthy, Clicerio Gonzalez, Matsuo K, Mark Seielstad, Marijana Vujkovic, Teresa Tusié-Luna, Alanna C. Morrison, Christian Gieger, Dana Dabelea, Colm O'Dushlaine, Niels Grarup, Elvia Mendoza-Caamal, Amanda F. Elliott, Ryan P. Welch, Craig L. Hanis, Kirchner Hl, Song Chen, Jennifer A. Brody, Maria L. Cortes, Asif Rasheed, Russel Tracy, Nancy J. Cox, Miriam S. Udler, Myron D. Gross, Donald W. Bowden, Oluf Pedersen, Marit E. Jørgensen, J. Tuomilehto, Yik Ying Teo, Andrew P. Morris, Zeitler P, T. M. Strom, Aris Baras, Colin N. A. Palmer, Shin Yc, Johanna Kuusisto, Lin Chen, Donna M. Lehman, Edmund Chan, Heikki A. Koistinen, Anthony Marcketta, Boehnke M, Francis S. Collins, Rayner Nw, Leslie A. Lange, Nir Barzilai, Brian E. Henderson, Jennifer Wessel, David J. Carey, Jaspal S. Kooner, Ralph A. DeFronzo, Anthony Payne, Carlos A. Aguilar-Salinas, Tien Yin Wong, Thomas Meitinger, Lyssenko, Claudia Ht Tam, Cristina Revilla-Monsalve, Daniel R. Witte, Jerome I. Rotter, Michael Preuss, Allan Linneberg, Jose C. Florez, Alisa K. Manning, Gonçalo R. Abecasis, Hyun Min Kang, van Dam Rm, Jason M. Torres, Anubha Mahajan, Claudia Schurmann, Markku Laakso, Leif Groop, Lori L. Bonnycastle, Sohee Han, Jason Flannick, Bong-Jo Kim, Lawrence M. Dolan, Brian Burke, Ma Elena Gonzalez, Kerrin S. Small, Ching-Ti Liu, Ronald C.W. Ma, Peter M. Nilsson, Eric Boerwinkle, Garay-Sevilla Me, Ravindranath Duggirala, Anne Ndungu, Cecilia Contreras-Cubas, Wendy S. Post, Tanya M. Teslovich, Brian Tomlinson, Kimberly L. Drews, Lizz Caulkins, Lee J, Philippe M. Frossard, Jianjun Liu, Hanks S, Ki-Sun Park, Tai Es, Kelsey M, S. Gabriel, Erwin P. Bottinger, Alexander P. Reiner, Tim D. Spector, Lorena Orozco, James S. Pankow, Juliana C.N. Chan, Wing-Yee So, Tiinamaija Tuomi, Malacara-Hernandez Jm, Karen L. Mohlke, S. S. Rich, de Vries Ps, Konstantin Strauch, Graeme I. Bell, Angélica Martínez-Hernández, Elizabeth J. Mayer-Davis, Thomas W. Blackwell, Heather M. Stringham, Bruce M. Psaty, Soo Heon Kwak, Catherine Pihoker, James S. Floyd, Christian Fuchsberger, Ching-Yu Cheng, Neil R. Robertson, Adolfo Correa, James G. Wilson, Ramachandran S. Vasan, Robert Sladek, James B. Meigs, Benjamin Glaser, Gil Atzmon, David Altshuler, Josée Dupuis, Xueling Sim, John Blangero, Emilio J. Cordova, C.J. O'Donnell, Maggie C.Y. Ng, Heckbert, Young-Jin Kim, Joseph B. Leader, Anne U. Jackson, Ryan Koesterer, Nicola Santoro, and Christopher A. Haiman
Subjects: Genetics, 0303 health sciences, Candidate gene, SLC30A8, Heritability, Biology, Minor allele frequency, 03 medical and health sciences, 0302 clinical medicine, Sample size determination, biology.protein, Allele, Gene, 030217 neurology & neurosurgery, Exome sequencing, 030304 developmental biology
Abstract: Protein-coding genetic variants that strongly affect disease risk can provide important clues into disease pathogenesis. Here we report an exome sequence analysis of 20,791 type 2 diabetes (T2D) cases and 24,440 controls from five ancestries. We identify rare (minor allele frequency30 SLC30A8 alleles, and (b) within 12 gene sets, including those corresponding to T2D drug targets (p=6.1×10−3) and candidate genes from knockout mice (p=5.2×10−3). Within our study, the strongest T2D rare variant gene-level signals explain at most 25% of the heritability of the strongest common single-variant signals, and the rare variant gene-level effect sizes we observe in established T2D drug targets will require 110K-180K sequenced cases to exceed exome-wide significance. To help prioritize genes using associations from current smaller sample sizes, we present a Bayesian framework to recalibrate association p-values as posterior probabilities of association, estimating that reaching ppwww.type2diabetesgenetics.org.
Published: 2018
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21. A Protein-Truncating HSD17B13 Variant and Protection from Chronic Liver Disease

Author: Shane McCarthy, Jonathan C. Cohen, Frederick E. Dewey, Claudia Schurmann, Matthew D. Still, Panayiotis Stevis, Xin Chu, Daniel J. Rader, David J. Carey, Alan R. Shuldiner, Noura S. Abul-Husn, Semanti Mukherjee, Jonathan S. Packer, Xiping Cheng, Ann Stepanchick, Brian Zambrowicz, Helen H. Hobbs, John Penn, Uyenlinh L. Mirshahi, Scott M. Damrauer, Ingrid B. Borecki, Yurong Xin, G. Craig Wood, Jesper Gromada, Suganthi Balasubramanian, Tanya M. Teslovich, Andrew J. Murphy, Erin D. Fuller, Christopher D. Still, Tooraj Mirshahi, Jonathan Z. Luo, John D. Overton, George D. Yancopoulos, Yashu Liu, Alexander H. Li, Aeron Small, Omri Gottesman, Julia Kozlitina, Jeffrey G. Reid, Stefan Stender, David Esopi, William C. Olson, Michael Feldman, Colm O'Dushlaine, Alexander E. Lopez, Nehal Gosalia, Sun Y. Kim, and Aris Baras
Subjects: 0301 basic medicine, Male, medicine.medical_specialty, 17-Hydroxysteroid Dehydrogenases, Genotype, Chronic liver disease, Gastroenterology, Article, 03 medical and health sciences, Liver disease, 0302 clinical medicine, Non-alcoholic Fatty Liver Disease, Loss of Function Mutation, Internal medicine, Exome Sequencing, Medicine, Humans, Exome, Genetic Predisposition to Disease, Aspartate Aminotransferases, Exome sequencing, biology, business.industry, Sequence Analysis, RNA, Liver Diseases, Fatty liver, Genetic Variation, Alanine Transaminase, General Medicine, medicine.disease, Human genetics, Fatty Liver, 030104 developmental biology, Alanine transaminase, Liver, Chronic Disease, biology.protein, Disease Progression, Linear Models, 030211 gastroenterology & hepatology, Female, business, Biomarkers, TM6SF2
Abstract: BACKGROUND: Elucidation of the genetic factors underlying chronic liver disease may reveal new therapeutic targets. METHODS: We used exome sequence data and electronic health records from 46,544 participants in the DiscovEHR human genetics study to identify genetic variants associated with serum levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST). Variants that were replicated in three additional cohorts (12,527 persons) were evaluated for association with clinical diagnoses of chronic liver disease in DiscovEHR study participants and two independent cohorts (total of 37,173 persons) and with histopathological severity of liver disease in 2391 human liver samples. RESULTS: A splice variant (rs72613567:TA) in HSD17B13, encoding the hepatic lipid droplet protein hydroxysteroid 17-beta dehydrogenase 13, was found to be associated with reduced levels of ALT (P=4.20×10(−12)) and AST (P=6.2×10(−10)). Among DiscovEHR study participants, this variant was found to be associated with a reduced risk of alcoholic liver disease (by 42% [95% confidence interval {CI}, 20 to 58] among heterozygotes and by 53% [95% CI, 3 to 77] among homozygotes), nonalcoholic liver disease (by 17% [95% CI, 8 to 25] among heterozygotes and by 30% [95% CI, 13 to 43] among homozygotes), alcoholic cirrhosis (by 42% [95% CI, 14 to 61] among heterozygotes and by 73% [95% CI, 15 to 91] among homozygotes), and nonalcoholic cirrhosis (by 26% [95% CI, 7 to 40] among heterozygotes and by 49% [95% CI, 15 to 69] among homozygotes). Associations were confirmed in two independent cohorts. The rs72613567:TA variant was associated with a reduced risk of nonalcoholic steatohepatitis, but not steatosis, in human liver samples. The rs72613567:TA variant mitigated liver injury associated with the risk-increasing PNPLA3 p.I148M allele and resulted in an unstable and truncated protein with reduced enzymatic activity. CONCLUSIONS: A loss-of-function variant in HSD17B13 is associated with a reduced risk of chronic liver disease and of progression from steatosis to steatohepatitis. (Funded by Regeneron Pharmaceuticals and others.)
Published: 2018

22. Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity

Author: Alison Pattie, Ailith Pirie, Francis S. Collins, Charles Kooperberg, Nienke van Leeuwen, Carmel Moore, Sharon L.R. Kardia, Neil R. Robertson, Lisa Bastarache, Allan Linneberg, Peter T. Campbell, Helena Kuivaniemi, Struan F.A. Grant, Sascha Fauser, Sekar Kathiresan, Lars Lind, Erin B. Ware, Olli T. Raitakari, Dawn M. Waterworth, James G. Wilson, Markus Perola, Chris J. Packard, Michelle L. O'Donoghue, Fredrik Karpe, Roel A. Ophoff, Sailaja Vedantam, Artitaya Lophatananon, Uwe Völker, Emmanouil Tsafantakis, Hakon Hakonarson, Dajiang J. Liu, Craig E. Pennell, Xueling Sim, Jennifer E. Huffman, Sandosh Padmanabhan, Digna R. Velez Edwards, Michiel L. Bots, Ayush Giri, Renée de Mutsert, Emanuele Di Angelantonio, Nicholas J. Wareham, Jin Li, Gail P. Jarvik, Evangelos Evangelou, Anne Tybjærg-Hansen, Patricia B. Munroe, Penny Gordon-Larsen, Lia E. Bang, Ivan Brandslund, Hester M. den Ruijter, Jussi Hernesniemi, Nancy L. Heard-Costa, Angela L. Mazul, Jonathan Tyrer, Danish Saleheen, Mark J. Caulfield, John Andrew Pospisilik, Annette Peters, Caroline Hayward, Iris M. Heid, J. Wouter Jukema, Valérie Turcot, Matt Neville, Rudolf Uher, Patricia A. Peyser, Jessica D. Faul, Asif Rasheed, Shuai Wang, John C. Chambers, Jordi Corominas Galbany, Murray H. Brilliant, Yucheng Jia, Torben Hansen, Veikko Salomaa, Mary F. Feitosa, Mathias Gorski, Li-An Lin, George Dedoussis, Honghuang Lin, Ethan M. Lange, Veronique Vitart, Bratati Kahali, Alexander Teumer, Jerome I. Rotter, Wayne H-H Sheu, Vilmantas Giedraitis, Aliki-Eleni Farmaki, Lorraine Southam, Ele Ferrannini, Anette P. Gjesing, Krina T. Zondervan, Stavroula Kanoni, David J. Roberts, Rebecca S. Fine, Svati H. Shah, Tugce Karaderi, Claudia Langenberg, Stefan Johansson, Elizabeth K. Speliotes, Alexander P. Reiner, Ching-Ti Liu, Yiqin Wang, Pål R. Njølstad, Gabriel Cuellar-Partida, Amanda J. Cox, Tim D. Spector, Paul W. Franks, Anke Tönjes, John D. Rioux, Jeffrey Haessler, Paul L. Auer, Ingrid B. Borecki, Deborah J. Thompson, Weihua Zhang, John R. B. Perry, Paul Elliott, Folkert W. Asselbergs, Myriam Fornage, Ken Sin Lo, Marie Moitry, Paul Mitchell, Martin den Heijer, Zoltán Kutalik, Tune H. Pers, Kari Stefansson, Kari Kuulasmaa, Robert E. Schoen, Mark C.H. De Groot, Laura M. Yerges-Armstrong, Jing Hua Zhao, Beverley Balkau, Peggy L. Peissig, Michael Boehnke, Janie Corley, Katharine R. Owen, Unnur Thorsteinsdottir, Naveed Sattar, Sita H. Vermeulen, Thomas N. Person, Mark I. McCarthy, Paul I.W. de Bakker, David Lamparter, Poorva Mudgal, Nicholette D. Palmer, Maria Karaleftheri, Jan-Håkan Jansson, Ozren Polasek, Ruth J. F. Loos, Daniel R. Witte, Dermot F. Reilly, Anubha Mahajan, Stella Trompet, James A. Perry, Yingchang Lu, Claudia Schurmann, Yii-Der Ida Chen, Hidetoshi Kitajima, Dale R. Nyholt, John Danesh, Pamela J. Schreiner, Narisu Narisu, Jose C. Florez, Adelheid Lempradl, Gerome Breen, Torben Jørgensen, Anu Loukola, Joe Dennis, Hans-Jörgen Grabe, Vilmundur Gudnason, Timo A. Lakka, Heather M. Highland, Sven Bergmann, Marie-Pierre Dubé, Giovanni Veronesi, Martina Müller-Nurasyid, Jaakko Tuomilehto, Nele Friedrich, Joel N. Hirschhorn, Pia R. Kamstrup, Nilesh J. Samani, Josh C. Denny, Mika Kähönen, Massimiliano Cocca, Liang Sun, Karina Meidtner, Carsten A. Böger, Sara M. Willems, Marcelo P. Segura-Lepe, Johanna Kuusisto, Hanieh Yaghootkar, Konstantin Strauch, Ruth Frikke-Schmidt, Jane Gibson, Matti Uusitupa, Oscar H. Franco, Yongmei Liu, Heather M. Stringham, Rohit Varma, Grant W. Montgomery, Dennis O. Mook-Kanamori, Stefania Cappellani, Paul L. Huang, Albert V. Smith, Eric Kim, Anke R. Hammerschlag, Katherine S. Ruth, Carolina Medina-Gomez, Gerard Pasterkamp, Cristen J. Willer, Alisa K. Manning, Frida Renström, René S. Kahn, Lili Milani, Feijie Wang, Tessel E. Galesloot, Fernando Rivadeneira, Leo-Pekka Lyytikäinen, Adam S. Butterworth, Tamara B. Harris, Matthew A. Allison, Paul M. Ridker, David J. Carey, Todd L. Edwards, Panos Deloukas, Xiuqing Guo, Lawrence F. Bielak, Leena Moilanen, Heiner Boeing, Peter Kovacs, Karen L. Mohlke, Myriam Rheinberger, Cramer Christensen, Betina H. Thuesen, Mike A. Nalls, Erik Ingelsson, Nicholas G. D. Masca, Colin N. A. Palmer, Audrey E. Hendricks, Linda Broer, Vanisha Mistry, Praveen Surendran, Audrey Y. Chu, Rainer Rauramaa, Angela D'Eustacchio, Helen Griffiths, Satu Männistö, Patrick T. Ellinor, Terho Lehtimäki, Katherine E. Tansey, I. Sadaf Farooqi, Gaëlle Marenne, Anneke I. den Hollander, Jessica van Setten, Hannu Puolijoki, Tinca J. C. Polderman, Timothy M. Frayling, Niels Grarup, Eric Boerwinkle, Gonçalo R. Abecasis, Adam E. Locke, Mengmeng Du, Manuel A. Rivas, Philippe Amouyel, Jaakko Kaprio, Leslie A. Lange, Loes M. Olde Loohuis, Trevor A. Mori, Lambertus A. Kiemeney, Wei Zhao, Eva Rb Petersen, Huaixing Li, Thomas W. Winkler, Tellervo Korhonen, Kathleen Stirrups, Jean Ferrières, Wei Zhou, Ian J. Deary, Guillaume Lettre, M. Arfan Ikram, Alex W. Hewitt, Marit E. Jørgensen, Ian Ford, Liang He, Mark Walker, Stefan Gustafsson, Andre Franke, Yao Hu, Jaana Lindström, Jonathan P. Bradfield, Anne E. Justice, Kristin L. Young, Sander W. van der Laan, Shuang Feng, Yadav Sapkota, Douglas F. Easton, Cornelia M. van Duijn, Amy J. Swift, Kjell Nikus, Helen R. Warren, Christian Theil Have, Wei Gan, Steven A. Lubitz, Harvey D. White, Pirjo Komulainen, John M. Starr, Jeffrey R. O'Connel, Anette Varbo, Daniel I. Chasman, Ruifang Li-Gao, Lynne E. Wagenknecht, Matthias Blüher, Xiaowei Zhan, Thomas F. Vogt, Eleftheria Zeggini, Tamuno Alfred, Katja K.H. Aben, Lars Wallentin, Joanna M. M. Howson, Jie Yao, Eulalia Catamo, Henrik Vestergaard, Gina M. Peloso, Markku Laakso, Matthias B. Schulze, Hayato Tada, Jennifer Wessel, Andrew R. Wood, Erwin P. Bottinger, Cora E. Lewis, Robin Young, Carol A. Wang, Oddgeir L. Holmen, Andrew J. Slater, Jean-Claude Tardif, Xu Lin, Inês Barroso, Gail Davies, Tibor V. Varga, Andrew J. Lotery, Igor Rudan, Andrew T. Hattersley, Michael Stumvoll, David Ellinghaus, Andrew C. Heath, Frank Kee, Christopher P. Nelson, Donald W. Bowden, Alison M. Dunning, Marianne Benn, Oluf Pedersen, Amber A. Burt, Aniruddh P. Patel, G. Kees Hovingh, David S. Crosslin, Gorm B. Jensen, Keng-Hung Lin, Dewan S. Alam, Jian'an Luan, Ying Wu, Tõnu Esko, Kathleen Mullan Harris, Antonietta Robino, Anne U. Jackson, Eirini Marouli, Robert A. Scott, Jette Bork-Jensen, Olov Rolandsson, Nanette R. Lee, Gerard Tromp, Megan L. Grove, Suthesh Sivapalaratnam, Sameer E. Al-Harthi, Roberta McKean-Cowdin, Paolo Gasparini, Ellen W. Demerath, Marco Brumat, Maggie C.Y. Ng, Børge G. Nordestgaard, Kari E. North, Rajiv Chowdhury, Mauno Vanhala, Andrew P. Morris, Sarah E. Medland, Sune F. Nielsen, Ilaria Gandin, Øyvind Helgeland, James P. Cook, Kent D. Taylor, Andrew D. Morris, Gudmar Thorleifsson, André G. Uitterlinden, Pang Yao, Valgerdur Steinthorsdottir, Eric B. Larson, Kerrin S. Small, Cecilia M. Lindgren, Dragana Vuckovic, Mariaelisa Graff, Fotios Drenos, Jaspal S. Kooner, Schurmann, Claudia [0000-0003-4158-9192], Justice, Anne E [0000-0002-8903-8712], Giri, Ayush [0000-0002-7786-4670], Locke, Adam E [0000-0001-6227-198X], Young, Kristin L [0000-0003-0070-6145], Medina-Gomez, Carolina [0000-0001-7999-5538], Winkler, Thomas W [0000-0003-0292-5421], Zeggini, Eleftheria [0000-0003-4238-659X], Zhao, Wei [0000-0002-8301-9297], Zondervan, Krina T [0000-0002-0275-9905], Pospisilik, John A [0000-0002-9745-0977], Rivadeneira, Fernando [0000-0001-9435-9441], Deloukas, Panos [0000-0001-9251-070X], Apollo - University of Cambridge Repository, Vascular Medicine, ACS - Amsterdam Cardiovascular Sciences, ACS - Atherosclerosis & ischemic syndromes, Internal Medicine, Epidemiology, Obstetrics & Gynecology, Radiology & Nuclear Medicine, CHD Exome+ Consortium, EPIC-CVD Consortium, ExomeBP Consortium, Global Lipids Genetic Consortium, GoT2D Genes Consortium, EPIC InterAct Consortium, INTERVAL Study, ReproGen Consortium, T2D-Genes Consortium, MAGIC Investigators, Understanding Society Scientific Group, Biological Psychology, Complex Trait Genetics, Amsterdam Neuroscience - Complex Trait Genetics, British Heart Foundation, Wellcome Trust, Medical Research Council (MRC), National Institute for Health Research, Home Office, National Institutes of Health, Imperial College Healthcare NHS Trust- BRC Funding, Turcot, Valérie, Lu, Yingchang, Highland, Heather M., Schurmann, Claudia, Justice, Anne E., Fine, Rebecca S., Bradfield, Jonathan P., Esko, Tõnu, Giri, Ayush, Graff, Mariaelisa, Guo, Xiuqing, Hendricks, Audrey E., Karaderi, Tugce, Lempradl, Adelheid, Locke, Adam E., Mahajan, Anubha, Marouli, Eirini, Sivapalaratnam, Suthesh, Young, Kristin L., Alfred, Tamuno, Feitosa, Mary F., Masca, Nicholas G. D., Manning, Alisa K., Medina-Gomez, Carolina, Mudgal, Poorva, Ng, Maggie C. Y., Reiner, Alex P., Vedantam, Sailaja, Willems, Sara M., Winkler, Thomas W., Abecasis, Gonçalo, Aben, Katja K., Alam, Dewan S., Alharthi, Sameer E., Allison, Matthew, Amouyel, Philippe, Asselbergs, Folkert W., Auer, Paul L., Balkau, Beverley, Bang, Lia E., Barroso, Inê, Bastarache, Lisa, Benn, Marianne, Bergmann, Sven, Bielak, Lawrence F., Blüher, Matthia, Boehnke, Michael, Boeing, Heiner, Boerwinkle, Eric, Böger, Carsten A., Bork-Jensen, Jette, Bots, Michiel L., Bottinger, Erwin P., Bowden, Donald W., Brandslund, Ivan, Breen, Gerome, Brilliant, Murray H., Broer, Linda, Brumat, Marco, Burt, Amber A., Butterworth, Adam S., Campbell, Peter T., Cappellani, Stefania, Carey, David J., Catamo, Eulalia, Caulfield, Mark J., Chambers, John C., Chasman, Daniel I., Chen, Yii-Der I., Chowdhury, Rajiv, Christensen, Cramer, Chu, Audrey Y., Cocca, Massimiliano, Collins, Francis S., Cook, James P., Corley, Janie, Corominas Galbany, Jordi, Cox, Amanda J., Crosslin, David S., Cuellar-Partida, Gabriel, D'Eustacchio, Angela, Danesh, John, Davies, Gail, Bakker, Paul I. W., Groot, Mark C. H., Mutsert, Renée, Deary, Ian J., Dedoussis, George, Demerath, Ellen W., Heijer, Martin, Hollander, Anneke I., Ruijter, Hester M., Dennis, Joe G., Denny, Josh C., Angelantonio, Emanuele, Drenos, Fotio, Du, Mengmeng, Dubé, Marie-Pierre, Dunning, Alison M., Easton, Douglas F., Edwards, Todd L., Ellinghaus, David, Ellinor, Patrick T., Elliott, Paul, Evangelou, Evangelo, Farmaki, Aliki-Eleni, Farooqi, I. Sadaf, Faul, Jessica D., Fauser, Sascha, Feng, Shuang, Ferrannini, Ele, Ferrieres, Jean, Florez, Jose C., Ford, Ian, Fornage, Myriam, Franco, Oscar H., Franke, Andre, Franks, Paul W., Friedrich, Nele, Frikke-Schmidt, Ruth, Galesloot, Tessel E., Gan, Wei, Gandin, Ilaria, Gasparini, Paolo, Gibson, Jane, Giedraitis, Vilmanta, Gjesing, Anette P., Gordon-Larsen, Penny, Gorski, Mathia, Grabe, Hans-Jörgen, Grant, Struan F. A., Grarup, Niel, Griffiths, Helen L., Grove, Megan L., Gudnason, Vilmundur, Gustafsson, Stefan, Haessler, Jeff, Hakonarson, Hakon, Hammerschlag, Anke R., Hansen, Torben, Harris, Kathleen Mullan, Harris, Tamara B., Hattersley, Andrew T., Have, Christian T., Hayward, Caroline, He, Liang, Heard-Costa, Nancy L., Heath, Andrew C., Heid, Iris M., Helgeland, Øyvind, Hernesniemi, Jussi, Hewitt, Alex W., Holmen, Oddgeir L., Hovingh, G. Kee, Howson, Joanna M. M., Hu, Yao, Huang, Paul L., Huffman, Jennifer E., Ikram, M. Arfan, Ingelsson, Erik, Jackson, Anne U., Jansson, Jan-Håkan, Jarvik, Gail P., Jensen, Gorm B., Jia, Yucheng, Johansson, Stefan, Jørgensen, Marit E., Jørgensen, Torben, Jukema, J. Wouter, Kahali, Bratati, Kahn, René S., Kähönen, Mika, Kamstrup, Pia R., Kanoni, Stavroula, Kaprio, Jaakko, Karaleftheri, Maria, Kardia, Sharon L. R., Karpe, Fredrik, Kathiresan, Sekar, Kee, Frank, Kiemeney, Lambertus A., Kim, Eric, Kitajima, Hidetoshi, Komulainen, Pirjo, Kooner, Jaspal S., Kooperberg, Charle, Korhonen, Tellervo, Kovacs, Peter, Kuivaniemi, Helena, Kutalik, Zoltán, Kuulasmaa, Kari, Kuusisto, Johanna, Laakso, Markku, Lakka, Timo A., Lamparter, David, Lange, Ethan M., Lange, Leslie A., Langenberg, Claudia, Larson, Eric B., Lee, Nanette R., Lehtimäki, Terho, Lewis, Cora E., Li, Huaixing, Li, Jin, Li-Gao, Ruifang, Lin, Honghuang, Lin, Keng-Hung, Lin, Li-An, Lin, Xu, Lind, Lar, Lindström, Jaana, Linneberg, Allan, Liu, Ching-Ti, Liu, Dajiang J., Liu, Yongmei, Lo, Ken S., Lophatananon, Artitaya, Lotery, Andrew J., Loukola, Anu, Luan, Jian'An, Lubitz, Steven A., Lyytikäinen, Leo-Pekka, Männistö, Satu, Marenne, Gaëlle, Mazul, Angela L., Mccarthy, Mark I., McKean-Cowdin, Roberta, Medland, Sarah E., Meidtner, Karina, Milani, Lili, Mistry, Vanisha, Mitchell, Paul, Mohlke, Karen L., Moilanen, Leena, Moitry, Marie, Montgomery, Grant W., Mook-Kanamori, Dennis O., Moore, Carmel, Mori, Trevor A., Morris, Andrew D., Morris, Andrew P., Müller-Nurasyid, Martina, Munroe, Patricia B., Nalls, Mike A., Narisu, Narisu, Nelson, Christopher P., Neville, Matt, Nielsen, Sune F., Nikus, Kjell, Njølstad, Pål R., Nordestgaard, Børge G., Nyholt, Dale R., O'Connel, Jeffrey R., O'Donoghue, Michelle L., Olde Loohuis, Loes M., Ophoff, Roel A., Owen, Katharine R., Packard, Chris J., Padmanabhan, Sandosh, Palmer, Colin N. A., Palmer, Nicholette D., Pasterkamp, Gerard, Patel, Aniruddh P., Pattie, Alison, Pedersen, Oluf, Peissig, Peggy L., Peloso, Gina M., Pennell, Craig E., Perola, Marku, Perry, James A., Perry, John R. B., Pers, Tune H., Person, Thomas N., Peters, Annette, Petersen, Eva R. B., Peyser, Patricia A., Pirie, Ailith, Polasek, Ozren, Polderman, Tinca J., Puolijoki, Hannu, Raitakari, Olli T., Rasheed, Asif, Rauramaa, Rainer, Reilly, Dermot F., Renström, Frida, Rheinberger, Myriam, Ridker, Paul M., Rioux, John D., Rivas, Manuel A., Roberts, David J., Robertson, Neil R., Robino, Antonietta, Rolandsson, Olov, Rudan, Igor, Ruth, Katherine S., Saleheen, Danish, Salomaa, Veikko, Samani, Nilesh J., Sapkota, Yadav, Sattar, Naveed, Schoen, Robert E., Schreiner, Pamela J., Schulze, Matthias B., Scott, Robert A., Segura-Lepe, Marcelo P., Shah, Svati H., Sheu, Wayne H. -H., Sim, Xueling, Slater, Andrew J., Small, Kerrin S., Smith, Albert V., Southam, Lorraine, Spector, Timothy D., Speliotes, Elizabeth K., Starr, John M., Stefansson, Kari, Steinthorsdottir, Valgerdur, Stirrups, Kathleen E., Strauch, Konstantin, Stringham, Heather M., Stumvoll, Michael, Sun, Liang, Surendran, Praveen, Swift, Amy J., Tada, Hayato, Tansey, Katherine E., Tardif, Jean-Claude, Taylor, Kent D., Teumer, Alexander, Thompson, Deborah J., Thorleifsson, Gudmar, Thorsteinsdottir, Unnur, Thuesen, Betina H., Tönjes, Anke, Tromp, Gerard, Trompet, Stella, Tsafantakis, Emmanouil, Tuomilehto, Jaakko, Tybjaerg-Hansen, Anne, Tyrer, Jonathan P., Uher, Rudolf, Uitterlinden, André G., Uusitupa, Matti, Laan, Sander W., Duijn, Cornelia M., Leeuwen, Nienke, Van Setten, Jessica, Vanhala, Mauno, Varbo, Anette, Varga, Tibor V., Varma, Rohit, Velez Edwards, Digna R., Vermeulen, Sita H., Veronesi, Giovanni, Vestergaard, Henrik, Vitart, Veronique, Vogt, Thomas F., Völker, Uwe, Vuckovic, Dragana, Wagenknecht, Lynne E., Walker, Mark, Wallentin, Lar, Wang, Feijie, Wang, Carol A., Wang, Shuai, Wang, Yiqin, Ware, Erin B., Wareham, Nicholas J., Warren, Helen R., Waterworth, Dawn M., Wessel, Jennifer, White, Harvey D., Willer, Cristen J., Wilson, James G., Witte, Daniel R., Wood, Andrew R., Wu, Ying, Yaghootkar, Hanieh, Yao, Jie, Yao, Pang, Yerges-Armstrong, Laura M., Young, Robin, Zeggini, Eleftheria, Zhan, Xiaowei, Zhang, Weihua, Zhao, Jing Hua, Zhao, Wei, Zhou, Wei, Zondervan, Krina T, Rotter, Jerome I., Pospisilik, John A., Rivadeneira, Fernando, Borecki, Ingrid B., Deloukas, Pano, Frayling, Timothy M., Lettre, Guillaume, North, Kari E., Lindgren, Cecilia M., Hirschhorn, Joel N., Loos, Ruth J. F., Internal medicine, AGEM - Endocrinology, metabolism and nutrition, Amsterdam Movement Sciences - Rehabilitation & Development, Amsterdam Movement Sciences - Restoration and Development, APH - Aging & Later Life, Physiology, and VU University medical center
Subjects: 0301 basic medicine, Male, ReproGen Consortium, MathematicsofComputing_GENERAL, Genome-wide association study, medicine.disease_cause, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], Body Mass Index, genetics [Obesity], 0302 clinical medicine, Gene Frequency, Glucose homeostasis, Adult, Animals, Drosophila/genetics, Energy Intake/genetics, Energy Metabolism/genetics, Female, Genetic Variation, Humans, Obesity/genetics, Proteins/genetics, Syndrome, 11 Medical and Health Sciences, 2. Zero hunger, Genetics, Genetics & Heredity, Mutation, CHD Exome+ Consortium, body mass index, TheoryofComputation_GENERAL, T2D-Genes Consortium, GENOME-WIDE ASSOCIATION, MELANOCORTIN-4 RECEPTOR GENE, DONEPEZIL 23 MG, FRAMESHIFT MUTATION, GLUCOSE-HOMEOSTASIS, HYPOTHALAMIC AMPK, CODING VARIANTS, BLOOD-PRESSURE, RARE, LOCI, Urological cancers Radboud Institute for Health Sciences [Radboudumc 15], Drosophila, ExomeBP Consortium, Life Sciences & Biomedicine, INTERVAL Study, Understanding Society Scientific Group, EPIC InterAct Consortium, genetics [Energy Metabolism], Biology, EPIC-CVD Consortium, Frameshift mutation, 03 medical and health sciences, MAGIC Investigators, All institutes and research themes of the Radboud University Medical Center, Genetic, SDG 3 - Good Health and Well-being, ddc:570, genetics [Drosophila], medicine, Journal Article, Global Lipids Genetic Consortium, Obesity, Gene, Allele frequency, Genetic association, Science & Technology, Proteins, 06 Biological Sciences, genetics [Proteins], Minor allele frequency, 030104 developmental biology, GoT2D Genes Consortium, Energy Intake, Energy Metabolism, genetics [Energy Intake], 030217 neurology & neurosurgery, Developmental Biology
Abstract: Genome-wide association studies (GWAS) have identified >250 loci for body mass index (BMI), implicating pathways related to neuronal biology. Most GWAS loci represent clusters of common, noncoding variants from which pinpointing causal genes remains challenging. Here we combined data from 718,734 individuals to discover rare and low-frequency (minor allele frequency (MAF) < 5%) coding variants associated with BMI. We identified 14 coding variants in 13 genes, of which 8 variants were in genes (ZBTB7B, ACHE, RAPGEF3, RAB21, ZFHX3, ENTPD6, ZFR2 and ZNF169) newly implicated in human obesity, 2 variants were in genes (MC4R and KSR2) previously observed to be mutated in extreme obesity and 2 variants were in GIPR. The effect sizes of rare variants are ~10 times larger than those of common variants, with the largest effect observed in carriers of an MC4R mutation introducing a stop codon (p.Tyr35Ter, MAF = 0.01%), who weighed ~7 kg more than non-carriers. Pathway analyses based on the variants associated with BMI confirm enrichment of neuronal genes and provide new evidence for adipocyte and energy expenditure biology, widening the potential of genetically supported therapeutic targets in obesity.
Published: 2018

23. Generalization and fine mapping of red blood cell trait genetic associations to multi-ethnic populations: The PAGE study

Author: Ran Tao, James S. Floyd, Charles Kooperberg, Kari E. North, Alexander P. Reiner, Christy L. Avery, Claudia Schurmann, Chani J. Hodonsky, Jonathan M. Kocarnik, Ursula M. Schick, Danyu Lin, Ruth J. F. Loos, Myriam Fornage, Santhi K. Ganesh, Frank J. A. van Rooij, Steven Buyske, Lucia A. Hindorff, Christina L. Wassel, and Epidemiology
Subjects: 0301 basic medicine, Genetics, education.field_of_study, Population, Locus (genetics), Single-nucleotide polymorphism, Hematology, Biology, Heritability, Genetic architecture, Article, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Trait, Population study, education, 030217 neurology & neurosurgery, Genetic association
Abstract: Red blood cell (RBC) traits provide insight into a wide range of physiological states and exhibit moderate to high heritability, making them excellent candidates for genetic studies to inform underlying biologic mechanisms. Previous RBC trait genome-wide association studies were performed primarily in European- or Asian-ancestry populations, missing opportunities to inform understanding of RBC genetic architecture in diverse populations and reduce intervals surrounding putative functional SNPs through fine-mapping. Here, we report the first fine-mapping of six correlated (Pearson's r range: |0.04 - 0.92|) RBC traits in up to 19,036 African Americans and 19,562 Hispanic/Latinos participants of the Population Architecture using Genomics and Epidemiology (PAGE) consortium. Trans-ethnic meta-analysis of race/ethnic- and study-specific estimates for approximately 11,000 SNPs flanking 13 previously identified association signals as well as 150,000 additional array-wide SNPs was performed using inverse-variance meta-analysis after adjusting for study and clinical covariates. Approximately half of previously reported index SNP-RBC trait associations generalized to the trans-ethnic study population (p
Published: 2018

24. Fucosyltransferase 2 (FUT2) non-secretor status and blood group B are associated with elevated serum lipase activity in asymptomatic subjects and an increased risk for chronic pancreatitis: a genetic association study

Author: Alexander Teumer, Uwe Völker, Henry Völzke, Martin Zenker, Markus M. Lerch, Florian Ernst, Peter Simon, Julia Mayerle, Dörte Radke, Georg Homuth, Jens-Peter Kuehn, F. Ulrich Weiss, Annett Guenther, Claudia Schurmann, and Andreas Greinacher
Subjects: Adult, Male, medicine.medical_specialty, Fucosyltransferase, Endocrinology, Diabetes and Metabolism, Population, Biology, Asymptomatic, Gastroenterology, Polymorphism, Single Nucleotide, Risk Assessment, ABO Blood-Group System, Elevated serum, Young Adult, Internal medicine, ABO blood group system, Pancreatitis, Chronic, medicine, Humans, Lipase, Pancreatitis, chronic, education, Genetic Association Studies, Genetic association, Subclinical infection, Aged, Aged, 80 and over, education.field_of_study, Hepatology, business.industry, Middle Aged, medicine.disease, Fucosyltransferases, 3. Good health, Increased risk, Immunology, biology.protein, Acute pancreatitis, Pancreatitis, Female, medicine.symptom, business, Genome-Wide Association Study
Abstract: Objective Serum lipase activities above the threefold upper reference limit indicate acute pancreatitis. We investigated whether high lipase activity—within the reference range and in the absence of pancreatitis—are associated with genetic single nucleotide polymorphisms (SNP), and whether these identified SNPs are also associated with clinical pancreatitis. Methods Genome-wide association studies (GWAS) on phenotypes ‘serum lipase activity’ and ‘high serum lipase activity’ were conducted including 3966 German volunteers from the population-based Study-of-Health-in-Pomerania (SHIP). Lead SNPs associated on a genome-wide significance level were replicated in two cohorts, 1444 blood donors and 1042 pancreatitis patients. Results Initial discovery GWAS detected SNPs within or near genes encoding the ABO blood group specifying transferases A/B ( ABO ), Fucosyltransferase-2 ( FUT2 ), and Chymotrypsinogen-B2 ( CTRB2 ), to be significantly associated with lipase activity levels in asymptomatic subjects. Replication analyses in blood donors confirmed the association of FUT-2 non-secretor status (OR=1.49; p=0.012) and ABO blood-type-B (OR=2.48; p=7.29×10 −8 ) with high lipase activity levels. In pancreatitis patients, significant associations were found for FUT-2 non-secretor status (OR=1.53; p=8.56×10 −4 ) and ABO -B (OR=1.69, p=1.0×10 −4 ) with chronic pancreatitis, but not with acute pancreatitis. Conversely, carriers of blood group O were less frequently affected by chronic pancreatitis (OR=0.62; p=1.22×10 −05) and less likely to have high lipase activity levels (OR=0.59; p=8.14×10 −05 ). Conclusions These are the first results indicating that ABO blood type-B as well as FUT2 non-secretor status are common population-wide risk factors for developing chronic pancreatitis. They also imply that, even within the reference range, elevated lipase activities may indicate subclinical pancreatic injury in asymptomatic subjects.
Published: 2015
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25. Transcriptome-Wide Analysis Identifies Novel Associations With Blood Pressure

Author: Christian P. Müller, Thomas Meitinger, Francisco Ojeda, Holger Prokisch, Marcus Dörr, Xiuqing Guo, Licia Iacoviello, Philipp S. Wild, Katharina Schramm, Johannes T Neumann, Stefan Blankenberg, Arne Schillert, Kari Kuulasmaa, Uwe Völker, Maren Carstensen-Kirberg, Georg Homuth, Walter Palmas, Claudia Schurmann, Alexander Teumer, Simone Wahl, Adelheid Kratzer, Renate B. Schnabel, Jerome I. Rotter, Mahir Karakas, Tanja Zeller, Stephan B. Felix, Andreas Ziegler, Simona Costanzo, David-Alexandre Trégouët, Yongmei Liu, Jingzhong Ding, Karl J. Lackner, Christian Gieger, Petra Wolf, Ulf Landmesser, Annika Jagodzinski, Tim Kacprowski, Michael Roden, Soonil Kwon, David M. Herrington, and Christian Herder
Subjects: 0301 basic medicine, Male, Candidate gene, Gene Expression, Genome-wide association study, Blood Pressure, 030204 cardiovascular system & hematology, Cardiorespiratory Medicine and Haematology, Cardiovascular, LMNA, Transcriptome, 0302 clinical medicine, Risk Factors, CEBPA, Gene expression, 2.1 Biological and endogenous factors, Aetiology, Genetics, Myelin and Lymphocyte-Associated Proteolipid Proteins, Genome-wide Association Study, Hypertension, blood pressure, Genomics, Single Nucleotide, LIM Domain Proteins, gene expression, genome-wide association study, hypertension, transcriptome, Stroke, Heart Disease, Public Health and Health Services, Biomarker (medicine), Female, Essential Hypertension, Poly(ADP-ribose) Polymerases, Biotechnology, Adult, Clinical Sciences, Nucleoside Transport Proteins, Biology, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Clinical Research, Internal Medicine, Humans, Polymorphism, Gene Expression Profiling, Human Genome, Blood Pressure Determination, Gene expression profiling, 030104 developmental biology, Good Health and Well Being, Cardiovascular System & Hematology, CCAAT-Enhancer-Binding Proteins, Carrier Proteins, Transcription Factors
Abstract: Hypertension represents a major cardiovascular risk factor. The pathophysiology of increased blood pressure (BP) is not yet completely understood. Transcriptome profiling offers possibilities to uncover genetics effects on BP. Based on 2 populations including 2549 individuals, a meta-analyses of monocytic transcriptome-wide profiles were performed to identify transcripts associated with BP. Replication was performed in 2 independent studies of whole-blood transcriptome data including 1990 individuals. For identified candidate genes, a direct link between long-term changes in BP and gene expression over time and by treatment with BP-lowering therapy was assessed. The predictive value of protein levels encoded by candidate genes for subsequent cardiovascular disease was investigated. Eight transcripts ( CRIP1 , MYADM , TIPARP , TSC22D3 , CEBPA , F12, LMNA , and TPPP3 ) were identified jointly accounting for up to 13% (95% confidence interval, 8.7–16.2) of BP variability. Changes in CRIP1 , MYADM , TIPARP , LMNA , TSC22D3 , CEBPA , and TPPP3 expression associated with BP changes—among these, CRIP1 gene expression was additionally correlated to measures of cardiac hypertrophy. Assessment of circulating CRIP1 (cystein-rich protein 1) levels as biomarkers showed a strong association with increased risk for incident stroke (hazard ratio, 1.06; 95% confidence interval, 1.03–1.09; P =5.0×10 –5 ). Our comprehensive analysis of global gene expression highlights 8 novel transcripts significantly associated with BP, providing a link between gene expression and BP. Translational approaches further established evidence for the potential use of CRIP1 as emerging disease-related biomarker.
Published: 2017

26. The PAGE Study: How Genetic Diversity Improves Our Understanding of the Architecture of Complex Traits

Author: Steve Buyske, Claudia Schurmann, Andrés Moreno-Estrada, Cathy C. Laurie, Ulrike Peters, Yesha Patel, Eimear E. Kenny, Michael Preuss, Hannah Poisner, Kari E. North, Carlos Bustamante, Christopher A. Haiman, Stephanie A. Bien, Anne E. Justice, Katherine K. Nishimura, Yuqing Li, Loic Le Marchand, Unhee Lim, E Stahl, Christopher R. Gignoux, Alexandra Sockell, Paul Norman, Ewa Deelman, Yingchang Lu, Rebecca D. Jackson, Huckins Lm, Gerardo Heiss, Kimberly F. Doheny, Chani J. Hodonsky, Brenna M. Henn, Benyam Hailu, Genevieve L. Wojcik, Jane Romm, Misa Graff, Loos R, Christy L. Avery, Danyu Lin, José Luis Ambite, Kris Young, Eric Boerwinkle, Kathleen C. Barnes, Gillian M. Belbin, Bridget M Lin, Lindsay Fernández-Rhodes, Cecilia A. Laurie, Christian Caberto, Sung-Hyuk Park, Tara C. Matise, Abhishek Vishnu, Loreall Pooler, Ran Tao, Elena P. Sorokin, Ron Do, Lucia A. Hindorff, Sarah C. Nelson, Heather M. Highland, L R Wilkens, Cheryl A. Winkler, Iona Cheng, Acuna-Alonso, Matthew P. Conomos, Myriam Fornage, Xin Sheng, Girish N. Nadkarni, Christopher S. Carlson, Ruth H. Walker, Janina M. Jeff, Jeffrey Haessler, Daniel O. Stram, Sabati C, Sachiko Yoneyama, Jonathan M. Kocarnik, Christina L. Wassel, Timothy A. Thornton, Charles Kooperberg, Veronica Wendy Setiawan, Yao Hu, Sinead Cullina, Canizales-Quinteroes S, Niha Zubair, Melissa A. Richard, Karan Vahi, Karla Sandoval, Marie Verbanck, Erwin P. Bottinger, and Alexander P. Reiner
Subjects: 0303 health sciences, medicine.medical_specialty, education.field_of_study, Genetic diversity, Public health, Population, Genomics, Genome-wide association study, Disease, Biology, Health equity, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, Evolutionary biology, 030220 oncology & carcinogenesis, medicine, education, 030304 developmental biology, Genetic association
Abstract: Summary/AbstractGenome-wide association studies (GWAS) have laid the foundation for investigations into the biology of complex traits, drug development, and clinical guidelines. However, the dominance of European-ancestry populations in GWAS creates a biased view of the role of human variation in disease, and hinders the equitable translation of genetic associations into clinical and public health applications. The Population Architecture using Genomics and Epidemiology (PAGE) study conducted a GWAS of 26 clinical and behavioral phenotypes in 49,839 non-European individuals. Using strategies designed for analysis of multi-ethnic and admixed populations, we confirm 574 GWAS catalog variants across these traits, and find 38 secondary signals in known loci and 27 novel loci. Our data shows strong evidence of effect-size heterogeneity across ancestries for published GWAS associations, substantial benefits for fine-mapping using diverse cohorts, and insights into clinical implications. We strongly advocate for continued, large genome-wide efforts in diverse populations to reduce health disparities.
Published: 2017
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27. Genetic identification of a common collagen disease in Puerto Ricans via identity-by-descent mapping in a health system

Author: Omri Gottesman, Ruth J. F. Loos, Elena P. Sorokin, Jacqueline A. Odgis, Lisa Edelmann, Muh-Ching Yee, Janina M. Jeff, Eimear E. Kenny, Claudia Schurmann, Ruth Kornreich, Amanda Merkelson, Douglas M. Ruderfer, Benjamin S. Glicksberg, Michael D. Linderman, Sumita Kohli, Kristin L. Young, Regina James, Misa Graff, Christopher R. Gignoux, Kari E. North, Lucia A. Hindorff, Anne E. Justice, Judy H. Cho, Tielman Van Vleck, Noura S. Abul-Husn, Genevieve L. Wojcik, Gillian M. Belbin, Ulrike Peters, Erwin P. Bottinger, Girish N. Nadkarni, Xiaoqiang Cai, and Eli A. Stahl
Subjects: Male, 0301 basic medicine, Fibrillar Collagens, Population genetics, Pedigree chart, Genome-wide association study, Disease, Identity by descent, 0302 clinical medicine, GWAS, Electronic Health Records, Musculoskeletal Diseases, Biology (General), Child, Ancestor, Genetics, Bone growth, Molecular Epidemiology, 0303 health sciences, General Neuroscience, Homozygote, Genetic disorder, Hispanic or Latino, General Medicine, Middle Aged, Pedigree, 3. Good health, Genomics and Evolutionary Biology, Statistical genetics, Multigene Family, Mutation (genetic algorithm), Medical genetics, Medicine, Female, Research Article, Human, Adult, Heterozygote, medicine.medical_specialty, medical genetics, Adolescent, Genotype, QH301-705.5, Science, Genomics, Locus (genetics), Biology, General Biochemistry, Genetics and Molecular Biology, Young Adult, 03 medical and health sciences, medicine, Humans, Human Biology and Medicine, Aged, 030304 developmental biology, Whole Genome Sequencing, General Immunology and Microbiology, Collagen Diseases, population genetics, medicine.disease, 030104 developmental biology, Evolutionary biology, collagen disorder, Collagen disorder, New York City, 030217 neurology & neurosurgery
Abstract: Achieving confidence in the causality of a disease locus is a complex task that often requires supporting data from both statistical genetics and clinical genomics. Here we describe a combined approach to identify and characterize a genetic disorder that leverages distantly related patients in a health system and population-scale mapping. We utilize genomic data to uncover components of distant pedigrees, in the absence of recorded pedigree information, in the multi-ethnic BioMe biobank in New York City. By linking to medical records, we discover a locus associated with both elevated genetic relatedness and extreme short stature. We link the gene, COL27A1, with a little-known genetic disease, previously thought to be rare and recessive. We demonstrate that disease manifests in both heterozygotes and homozygotes, indicating a common collagen disorder impacting up to 2% of individuals of Puerto Rican ancestry, leading to a better understanding of the continuum of complex and Mendelian disease., eLife digest Diseases often run in families. These disease are frequently linked to changes in DNA that are passed down through generations. Close family members may share these disease-causing mutations; so may distant relatives who inherited the same mutation from a common ancestor long ago. Geneticists use a method called linkage mapping to trace a disease found in multiple members of a family over generations to genetic changes in a shared ancestor. This allows scientists to pinpoint the exact place in the genome the disease-causing mutation occurred. Using computer algorithms, scientists can apply the same technique to identify mutations that distant relatives inherited from a common ancestor. Belbin et al. used this computational technique to identify a mutation that may cause unusually short stature or bone and joint problems in up to 2% of people of Puerto Rican descent. In the experiments, the genomes of about 32,000 New Yorkers who have volunteered to participate in the BioMe Biobank and their health records were used to search for genetic changes linked to extremely short stature. The search revealed that people who inherited two copies of this mutation from their parents were likely to be extremely short or to have bone and joint problems. People who inherited one copy had an increased likelihood of joint or bone problems. This mutation affects a gene responsible for making a form of protein called collagen that is important for bone growth. The analysis suggests the mutation first arose in a Native American ancestor living in Puerto Rico around the time that European colonization began. The mutation had previously been linked to a disorder called Steel syndrome that was thought to be rare. Belbin et al. showed this condition is actually fairly common in people whose ancestors recently came from Puerto Rico, but may often go undiagnosed by their physicians. The experiments emphasize the importance of including diverse populations in genetic studies, as studies of people of predominantly European descent would likely have missed the link between this disease and mutation.
Published: 2017

28. Genetic analyses of diverse populations improves discovery for complex traits

Author: Paul Norman, Mariaelisa Graff, Elena P. Sorokin, Michael Preuss, Ron Do, Victor Acuña-Alonso, Lucia A. Hindorff, Yingchang Lu, Eli A. Stahl, Ruth J. F. Loos, Steven Buyske, Tara C. Matise, José Luis Ambite, Lindsay Fernández-Rhodes, Abhishek Vishnu, Matthew P. Conomos, Chiara Sabatti, Katherine K. Nishimura, Myriam Fornage, Xin Sheng, Samuel Canizales-Quinteros, Carlos Bustamante, Christopher R. Gignoux, Girish N. Nadkarni, Christopher S. Carlson, Daniel O. Stram, Sachi Yoneyama, Christian Caberto, Stephanie A. Bien, Gerardo Heiss, Iona Cheng, Janina M. Jeff, Timothy A. Thornton, Charles Kooperberg, Lynne R. Wilkens, Alexandra Sockell, Loreall Pooler, Ryan W. Walker, Cheryl A. Winkler, Christy L. Avery, Ran Tao, Rebecca D. Jackson, Heather M. Highland, Kathleen C. Barnes, Sungshim L. Park, Yesha Patel, Christina L. Wassel, Sinead Cullina, Jonathan M. Kocarnik, Claudia Schurmann, Eimear E. Kenny, Jeffrey Haessler, Yuqing Li, Cathy C. Laurie, Benyam Hailu, Kristin L. Young, Jane Romm, Danyu Lin, Brenna M. Henn, Gillian M. Belbin, Anne E. Justice, Alexander P. Reiner, Bridget M Lin, Yao Hu, Cecelia A. Laurie, Niha Zubair, Veronica Wendy Setiawan, Andrés Moreno-Estrada, Melissa A. Richard, Kari E. North, Karan Vahi, Christopher A. Haiman, Loic Le Marchand, Ulrike Peters, Chani J. Hodonsky, Eric Boerwinkle, Laura M. Huckins, Sarah C. Nelson, Hannah Poisner, Unhee Lim, Ewa Deelman, Genevieve L. Wojcik, Kimberly F. Doheny, Karla Sandoval, Marie Verbanck, and Erwin P. Bottinger
Subjects: 0301 basic medicine, Asian Continental Ancestry Group, Male, Multifactorial Inheritance, General Science & Technology, Genetics, Medical, Population, Black People, Genomics, Genome-wide association study, Disease, Biology, Article, Cohort Studies, 03 medical and health sciences, 0302 clinical medicine, Asian People, 2.5 Research design and methodologies (aetiology), Medical, Genetics, Humans, Genetic Testing, education, Minority Groups, Genetic association, African Continental Ancestry Group, education.field_of_study, Multidisciplinary, Health Equity, Prevention, Human Genome, Health Status Disparities, Hispanic or Latino, Blacks, Precision medicine, Genetic architecture, Health equity, Body Height, United States, Asians, 030104 developmental biology, Evolutionary biology, Women's Health, Female, Hispanic Americans, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: Genome-wide association studies (GWAS) have laid the foundation for investigations into the biology of complex traits, drug development and clinical guidelines. However, the majority of discovery efforts are based on data from populations of European ancestry1–3. In light of the differential genetic architecture that is known to exist between populations, bias in representation can exacerbate existing disease and healthcare disparities. Critical variants may be missed if they have a low frequency or are completely absent in European populations, especially as the field shifts its attention towards rare variants, which are more likely to be population-specific4–10. Additionally, effect sizes and their derived risk prediction scores derived in one population may not accurately extrapolate to other populations11,12. Here we demonstrate the value of diverse, multi-ethnic participants in large-scale genomic studies. The Population Architecture using Genomics and Epidemiology (PAGE) study conducted a GWAS of 26 clinical and behavioural phenotypes in 49,839 non-European individuals. Using strategies tailored for analysis of multi-ethnic and admixed populations, we describe a framework for analysing diverse populations, identify 27 novel loci and 38 secondary signals at known loci, as well as replicate 1,444 GWAS catalogue associations across these traits. Our data show evidence of effect-size heterogeneity across ancestries for published GWAS associations, substantial benefits for fine-mapping using diverse cohorts and insights into clinical implications. In the United States—where minority populations have a disproportionately higher burden of chronic conditions13—the lack of representation of diverse populations in genetic research will result in inequitable access to precision medicine for those with the highest burden of disease. We strongly advocate for continued, large genome-wide efforts in diverse populations to maximize genetic discovery and reduce health disparities. © 2019, The Author(s), under exclusive licence to Springer Nature Limited.
Published: 2017

29. Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation

Author: Joshua C. Bis, Daniel I. Chasman, Archie Campbell, J. Wouter Jukema, Yoichiro Kamatani, Joylene E. Siland, Siegfried Perz, Jie Huang, Jorge A. Wong, Jared W. Magnani, Stefan Weiss, Caroline Hayward, Christopher D. Anderson, Carolina Roselli, Alexander P. Reiner, Maartje N. Niemeijer, Efthymia Vlachopoulou, David R. Van Wagoner, Elsayed Z. Soliman, Lenore J. Launer, Claudia Schurmann, Jeffrey Haessler, Joshua C. Denny, Qiong Yang, Mika Kähönen, Henry J. Lin, Lu-Chen Weng, Molong Li, Paul L. Huang, Terho Lehtimäki, Bruno H. Stricker, Lewin Eisele, Christopher Newton-Cheh, Marcus E. Kleber, Alexander Teumer, Rainer Malik, Juha Sinisalo, Siew-Kee Low, Xiaoyan Yin, Stéphanie Debette, Jennifer A. Brody, Marco V Perez, Derek Klarin, Farid Radmanesh, Ian Ford, Dan M. Roden, Paul M. Ridker, Jan Heeringa, Jonathan Rosand, Andrew P. Morris, Winfried März, Stefan Gustafsson, Xiuqing Guo, Nathan R. Tucker, Dawood Darbar, Daniel J. Rader, Martin Dichgans, Stefan Kääb, Lars Lind, Patrick T. Ellinor, Nancy L. Pedersen, Stefanie Aeschbacher, Erwin B. Bottinger, Leo-Pekka Lyytikäinen, Peter Lichtner, Marcus Dörr, Svati H. Shah, Lin Y. Chen, Alvaro Alonso, Marja-Liisa Lokki, Albert V. Smith, Guillaume Paré, Ruth J. F. Loos, Christine M. Albert, Markku Eskola, Jonathan D. Smith, Kjell Nikus, Martina Müller-Nurasyid, Yanick Hagemeijer, Lorenz Risch, Nona Sotoodehnia, Jussi Hernesniemi, Albert Y. Sun, Man Li, Jemma C. Hopewell, Olle Melander, Albert Hofman, Annette Peters, Pim van der Harst, Michiel Rienstra, Ilkka Seppälä, Kent D. Taylor, Charles Kooperberg, Moritz F. Sinner, Jerome I. Rotter, Stuart A. Scott, Toshihiro Tanaka, Steven A. Lubitz, Uwe Völker, Marju Orho-Melander, Patrik K. E. Magnusson, Jari Laurikka, M. Benjamin Shoemaker, Niek Verweij, J. Gustav Smith, José Eduardo Krieger, Sébastien Thériault, Andrea R. V. R. Horimoto, Natalia S. Rost, André G. Uitterlinden, Oscar H. Franco, David Conen, Cecilia M. Lindgren, Sekar Kathiresan, Michiaki Kubo, Marina Arendt, Graciela Delgado, Anders Hamsten, Rajat Deo, Lars Lannfelt, Sebastian Clauss, Sandosh Padmanabhan, Emelia J. Benjamin, Roopinder K. Sandhu, Bruce M. Psaty, Peter Weeke, Mark Chaffin, Traci M. Bartz, Erik Ingelsson, Alfredo José Mansur, Nathan A. Bihlmeyer, Christian M. Shaffer, Lynne J. Hocking, Stella Trompet, Melanie Waldenberger, Honghuang Lin, Stephan B. Felix, David J. Porteous, Vilmundur Gudnason, Eric Boerwinkle, Dan E. Arking, Alexandre C. Pereira, Bastiaan Geelhoed, Susan R. Heckbert, Jie Yao, Bradford B. Worrall, Ingrid E. Christophersen, Jennifer Kriebel, Peter Almgren, Blair H. Smith, Jennifer E. Huffman, Seung Hoan Choi, Mina K. Chung, Karl-Heinz Jöckel, Yingchang Lu, Yii-Der Ida Chen, Peter W. Macfarlane, John Barnard, Tamara B. Harris, Kathryn L. Lunetta, Stefanie Heilmann-Heimbach, Ganesh Chauhan, Epidemiology, Internal Medicine, and Cardiovascular Centre (CVC)
Subjects: 0301 basic medicine, Quantitative Trait Loci, Medizin, genetics [White People], SNP, Genome-wide association study, 030204 cardiovascular system & hematology, Biology, SUSCEPTIBILITY, Bioinformatics, GENOMAS, ANNOTATION, White People, 03 medical and health sciences, 0302 clinical medicine, ddc:570, Genetic variation, Atrial Fibrillation, Genetics, medicine, Journal Article, TOOL, Humans, Genetic Predisposition to Disease, genetics [Atrial Fibrillation], GENOME-WIDE ASSOCIATION, Stroke, METAANALYSIS, Genetic association, RISK, genetics [Black or African American], GENETIC-VARIATION, Atrial fibrillation, medicine.disease, R1, 3. Good health, Black or African American, genetics [European Continental Ancestry Group], 030104 developmental biology, Genetic Loci, Heart failure, Meta-analysis, VISUALIZATION, genetics [African Americans], BURDEN, Genome-Wide Association Study
Abstract: Atrial fibrillation affects more than 33 million people worldwide and increases the risk of stroke, heart failure, and death(1,2). Fourteen genetic loci have been associated with atrial fibrillation in European and Asian ancestry groups(3-7). To further define the genetic basis of atrial fibrillation, we performed large-scale, trans-ancestry meta-analyses of common and rare variant association studies. The genome-wide association studies (GWAS) included 17,931 individuals with atrial fibrillation and 115,142 referents; the exome-wide association studies (ExWAS) and rare variant association studies (RVAS) involved 22,346 cases and 132,086 referents. We identified 12 new genetic loci that exceeded genome-wide significance, implicating genes involved in cardiac electrical and structural remodeling. Our results nearly double the number of known genetic loci for atrial fibrillation, provide insights into the molecular basis of atrial fibrillation, and may facilitate the identification of new potential targets for drug discovery(8).
Published: 2017

30. Author response: Genetic identification of a common collagen disease in Puerto Ricans via identity-by-descent mapping in a health system

Author: Kristin L. Young, Misa Graff, Douglas M. Ruderfer, Janina M. Jeff, Ruth J. F. Loos, Amanda Merkelson, Kari E. North, Benjamin S. Glicksberg, Eli Ea Stahl, Elena P. Sorokin, Regina James, Girish N. Nadkarni, Jacqueline A. Odgis, Lisa Edelmann, Noura S. Abul-Husn, Judy H. Cho, Tielman Van Vleck, Genevieve L. Wojcik, Sumita Kohli, Ulrike Peters, Christopher R. Gignoux, Ruth Kornreich, Gillian M. Belbin, Eimear E. Kenny, Lucia A. Hindorff, Erwin P. Bottinger, Michael D. Linderman, Muh-Ching Yee, Anne E. Justice, Claudia Schurmann, Xiaoqiang Cai, and Omri Gottesman
Subjects: Collagen disease, medicine, Identification (biology), Computational biology, Biology, medicine.disease, Identity by descent
Published: 2017

31. Genome-Wide Association Study of Heavy Smoking and Daily/Nondaily Smoking in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

Author: Weimin Duan, Erwin P. Bottinger, Dana B. Hancock, Adam A. Szpiro, Tin Louie, Nancy L. Saccone, Eric O. Johnson, Gregory A. Talavera, Krista M. Perreira, Robert C. Kaplan, Leslie S. Emery, Lisa R. Yanek, Tamar Sofer, Laura J. Bierut, Adrienne M. Stilp, Ruth J. F. Loos, Claudia Schurmann, Robert Culverhouse, H. Dean Hosgood, Cathy C. Laurie, Li-Shiun Chen, George Papanicolaou, James F. Thrasher, Kent D. Taylor, Erik J. Rodriquez, Diane M. Becker, Eliseo J. Pérez-Stable, and Stephanie M. Gogarten
Subjects: 0301 basic medicine, Adult, Male, Genotype, Population, Original Investigations, Genome-wide association study, Nerve Tissue Proteins, Receptors, Nicotinic, 03 medical and health sciences, Gene Frequency, Environmental health, Medicine, Humans, 1000 Genomes Project, education, Genetic association, education.field_of_study, biology, business.industry, CHRNA5, Smoking, Public Health, Environmental and Occupational Health, Odds ratio, Hispanic or Latino, Middle Aged, United States, Minor allele frequency, 030104 developmental biology, Cohort, biology.protein, Female, Public Health, business, Genome-Wide Association Study
Abstract: INTRODUCTION: Genetic variants associated with nicotine dependence have previously been identified, primarily in European-ancestry populations. No genome-wide association studies (GWAS) have been reported for smoking behaviors in Hispanics/Latinos in the United States and Latin America, who are of mixed ancestry with European, African, and American Indigenous components. METHODS: We examined genetic associations with smoking behaviors in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) (N = 12 741 with smoking data, 5119 ever-smokers), using ~2.3 million genotyped variants imputed to the 1000 Genomes Project phase 3. Mixed logistic regression models accounted for population structure, sampling, relatedness, sex, and age. RESULTS: The known region of CHRNA5, which encodes the α5 cholinergic nicotinic receptor subunit, was associated with heavy smoking at genome-wide significance (p ≤ 5 × 10(–8)) in a comparison of 1929 ever-smokers reporting cigarettes per day (CPD) > 10 versus 3156 reporting CPD ≤ 10. The functional variant rs16969968 in CHRNA5 had a p value of 2.20 × 10(–7) and odds ratio (OR) of 1.32 for the minor allele (A); its minor allele frequency was 0.22 overall and similar across Hispanic/Latino background groups (Central American = 0.17; South American = 0.19; Mexican = 0.18; Puerto Rican = 0.22; Cuban = 0.29; Dominican = 0.19). CHRNA4 on chromosome 20 attained p < 10(–4), supporting prior findings in non-Hispanics. For nondaily smoking, which is prevalent in Hispanic/Latino smokers, compared to daily smoking, loci on chromosomes 2 and 4 achieved genome-wide significance; replication attempts were limited by small Hispanic/Latino sample sizes. CONCLUSIONS: Associations of nicotinic receptor gene variants with smoking, first reported in non-Hispanic European-ancestry populations, generalized to Hispanics/Latinos despite different patterns of smoking behavior. IMPLICATIONS: We conducted the first large-scale genome-wide association study (GWAS) of smoking behavior in a US Hispanic/Latino cohort, and the first GWAS of daily/nondaily smoking in any population. Results show that the region of the nicotinic receptor subunit gene CHRNA5, which in non-Hispanic European-ancestry smokers has been associated with heavy smoking as well as cessation and treatment efficacy, is also significantly associated with heavy smoking in this Hispanic/Latino cohort. The results are an important addition to understanding the impact of genetic variants in understudied Hispanic/Latino smokers.
Published: 2017

32. Genome-wide association study of red blood cell traits in Hispanics/Latinos: The Hispanic Community Health Study/Study of Latinos

Author: Deepti Jain, Alex P. Reiner, Kent D. Taylor, Jean Morrison, Timothy A. Thornton, Diane D. Chen, Jerome I. Rotter, Ruth J. F. Loos, Yun Li, Yukio Nakamura, Cecilia A. Laurie, Paul L. Auer, Sharon R. Browning, George Papanicolaou, Kari E. North, Brian L. Browning, Claudia Schurmann, Lisa M. Brown, Tamar Sofer, Chani J. Hodonsky, Caitlin P. McHugh, Cathy C. Laurie, Ursula M. Schick, Ryo Kurita, Nathan Pankratz, Yongmei Liu, and Daniel E. Bauer
Subjects: Male, 0301 basic medicine, Cancer Research, Erythrocytes, Genome-wide association study, beta-Globins, Biochemistry, Hemoglobins, Animal Cells, Red Blood Cells, Solute Carrier Family 12, Member 2, Copy-number variation, Genetics (clinical), Genetics, Sex Chromosomes, medicine.diagnostic_test, Chromosome Biology, X Chromosomes, Genomics, Hispanic or Latino, Female, RNA, Long Noncoding, Cellular Types, Research Article, Proteasome Endopeptidase Complex, lcsh:QH426-470, Quantitative Trait Loci, Mean corpuscular hemoglobin, Locus (genetics), Biology, Quantitative trait locus, Polymorphism, Single Nucleotide, Chromosomes, 03 medical and health sciences, alpha-Globins, Genome-Wide Association Studies, medicine, Humans, Hemoglobin, Allele, 1000 Genomes Project, Molecular Biology, Alleles, Ecology, Evolution, Behavior and Systematics, Homeodomain Proteins, Blood Cells, Tumor Suppressor Proteins, Biology and Life Sciences, Proteins, Computational Biology, Human Genetics, Cell Biology, Genome Analysis, lcsh:Genetics, 030104 developmental biology, Genetic Loci, Erythrocyte Count, Imputation (genetics), Genome-Wide Association Study
Abstract: Prior GWAS have identified loci associated with red blood cell (RBC) traits in populations of European, African, and Asian ancestry. These studies have not included individuals with an Amerindian ancestral background, such as Hispanics/Latinos, nor evaluated the full spectrum of genomic variation beyond single nucleotide variants. Using a custom genotyping array enriched for Amerindian ancestral content and 1000 Genomes imputation, we performed GWAS in 12,502 participants of Hispanic Community Health Study and Study of Latinos (HCHS/SOL) for hematocrit, hemoglobin, RBC count, RBC distribution width (RDW), and RBC indices. Approximately 60% of previously reported RBC trait loci generalized to HCHS/SOL Hispanics/Latinos, including African ancestral alpha- and beta-globin gene variants. In addition to the known 3.8kb alpha-globin copy number variant, we identified an Amerindian ancestral association in an alpha-globin regulatory region on chromosome 16p13.3 for mean corpuscular volume and mean corpuscular hemoglobin. We also discovered and replicated three genome-wide significant variants in previously unreported loci for RDW (SLC12A2 rs17764730, PSMB5 rs941718), and hematocrit (PROX1 rs3754140). Among the proxy variants at the SLC12A2 locus we identified rs3812049, located in a bi-directional promoter between SLC12A2 (which encodes a red cell membrane ion-transport protein) and an upstream anti-sense long-noncoding RNA, LINC01184, as the likely causal variant. We further demonstrate that disruption of the regulatory element harboring rs3812049 affects transcription of SLC12A2 and LINC01184 in human erythroid progenitor cells. Together, these results reinforce the importance of genetic study of diverse ancestral populations, in particular Hispanics/Latinos., Author summary Red blood cells (RBC) are important for transport of oxygen to tissues throughout the body. Distribution of RBC traits differs by ethnicity and gender, and both genetic and acquired factors likely contribute to these differences. Prior genetic studies have identified physical regions of the genome associated with RBC traits in populations with European, African, and Asian ancestry. These studies have not included individuals with ancestry from the American continents (Amerindian ancestry), such as Hispanics/Latinos. In an analysis of RBC traits in up to 19,608 Hispanics/Latinos, we identified an Amerindian-ancestry genetic association in a known alpha-globin regulatory region. We also identified three new RBC trait associations, including a regulatory variant of SLC12A2 that encodes a RBC membrane ion-transport protein. Experimental disruption of this regulatory element led to reduced expression of both SLC12A2 and an adjacent long non-coding RNA in human erythroid progenitor cells. These results contribute to understanding the physiology of red blood cells and reinforce the importance of genetic study of diverse ancestry populations, in particular Hispanics/Latinos.
Published: 2017

33. Genome-wide association of white blood cell counts in Hispanic/Latino Americans: the Hispanic Community Health Study/Study of Latinos

Author: Sharon R. Minnerath, Ursula M. Schick, Cecelia A. Laurie, Bharat Thyagarajan, Paul L. Auer, Claudia Schurmann, Yongmei Liu, Alexander P. Reiner, Timothy A. Thornton, Brian L. Browning, Kent D. Taylor, Cathy C. Laurie, Tamar Sofer, Deepti Jain, Jean Morrison, Sharon R. Browning, Kari E. North, Lisa M. Brown, Chani J. Hodonsky, George Papanicolaou, and Ruth J. F. Loos
Subjects: 0301 basic medicine, Male, Neutrophils, Genome-wide association study, Biology, Monocytes, White People, 03 medical and health sciences, Leukocyte Count, 0302 clinical medicine, Gene Frequency, White blood cell, hemic and lymphatic diseases, CEBPA, Genetics, medicine, Humans, Lymphocytes, Allele, Molecular Biology, Allele frequency, Genetics (clinical), Association Studies Articles, General Medicine, CEBPE, Hispanic or Latino, medicine.disease, United States, Basophils, Minor allele frequency, Black or African American, Leukemia, 030104 developmental biology, medicine.anatomical_structure, fms-Like Tyrosine Kinase 3, 030220 oncology & carcinogenesis, Immunology, CCAAT-Enhancer-Binding Proteins, Female, Genome-Wide Association Study
Abstract: Circulating white blood cell (WBC) counts (neutrophils, monocytes, lymphocytes, eosinophils, basophils) differ by ethnicity. The genetic factors underlying basal WBC traits in Hispanics/Latinos are unknown. We performed a genome-wide association study of total WBC and differential counts in a large, ethnically diverse US population sample of Hispanics/Latinos ascertained by the Hispanic Community Health Study and Study of Latinos (HCHS/SOL). We demonstrate that several previously known WBC-associated genetic loci (e.g. the African Duffy antigen receptor for chemokines null variant for neutrophil count) are generalizable to WBC traits in Hispanics/Latinos. We identified and replicated common and rare germ-line variants at FLT3 (a gene often somatically mutated in leukemia) associated with monocyte count. The common FLT3 variant rs76428106 has a large allele frequency differential between African and non-African populations. We also identified several novel genetic loci involving or regulating hematopoietic transcription factors (CEBPE-SLC7A7, CEBPA and CRBN-TRNT1) associated with basophil count. The minor allele of the CEBPE variant associated with lower basophil count has been previously associated with Amerindian ancestry and higher risk of acute lymphoblastic leukemia in Hispanics. Together, these data suggest that germline genetic variation affecting transcriptional and signaling pathways that underlie WBC development and lineage specification can contribute to inter-individual as well as ethnic differences in peripheral blood cell counts (normal hematopoiesis) in addition to susceptibility to leukemia (malignant hematopoiesis).
Published: 2017
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34. Genome-wide meta-analysis of 241,258 adults accounting for smoking behaviour identifies novel loci for obesity traits

Author: P. Eline Slagboom, Massimo Mangino, David J. Porteous, Karin Leander, Nancy L. Heard-Costa, Sharon L.R. Kardia, Jennifer Bragg, Ken K. Ong, Igor Rudan, Blair H. Smith, Mark A. Sarzynski, Torben Hansen, James F. Wilson, Weihua Zhang, Zoltán Kutalik, Karl Gertow, Yii-Der Ida Chen, Daniele Cusi, Lu Qi, Nicholas G. Martin, Peter Vollenweider, Thomas W. Winkler, Graciela E. Delgado, Thorkild I. A. Sørensen, André G. Uitterlinden, J. Wouter Jukema, Rajesh Rawal, Dena G. Hernandez, Amy J. Swift, Naveed Sattar, Ruth J. F. Loos, George Dedoussis, Ani Manichaikul, Henrik Vestergaard, Jian'an Luan, Luting Xue, Charles Kooperberg, Rona J. Strawbridge, John-Olov Jansson, Jian Gong, Martina Müller-Nurasyid, L. Adrienne Cupples, Frida Renström, Stephan J. L. Bakker, Ivana Kolcic, Mathias Gorski, Tamara B. Harris, Sandosh Padmanabhan, Stephanie A. Bien, Arthur W. Musk, Cristina Menni, Steve Buyske, Anubha Mahajan, Claudia Schurmann, John Blangero, Natalia Pervjakova, Inês Barroso, Kristin L. Young, Momoko Horikoshi, Robert A. Scott, Ozren Polasek, Shafqat Ahmad, Jeremiah Perez, Stella Trompet, Claude Bouchard, Claudia Langenberg, Paul M. Ridker, Tuomas O. Kilpeläinen, Oddgeir L. Holmen, Tarunveer S. Ahluwalia, Alan F. Wright, Ulf de Faire, Cecilia M. Lindgren, Misa Graff, Jie Huang, Liesbeth Vandenput, Marcel Bruinenberg, Luigi Ferrucci, Johanne Marie Justesen, Audrey Y. Chu, Melanie Waldenberger, Karen L. Mohlke, Ching-Ti Liu, Barbara Thorand, Joseph Hung, Pim van der Harst, Colin A. McKenzie, Sailaja Vedantam, Gitta H. Lubke, Bruna Gigante, Göran Hallmans, Sara Lupoli, Anja Ludolph-Donislawski, Michael Boehnke, Treva Rice, Lori L. Bonnycastle, Daniele Braga, Mika Kähönen, Joel Eriksson, Gonçalo R. Abecasis, Joseph M. Wu, Niels Grarup, Ilja M. Nolte, Jonathan Marchini, Georg Homuth, Pamela A. F. Madden, John Beilby, Andrew D. Johnson, Nanette R. Lee, Caroline Hayward, Unhee Lim, Bamidele O. Tayo, Peter S. Chines, Lynda M. Rose, Amélie Bonnefond, Elena Tremoli, Serena Sanna, David P. Strachan, Barbara McKnight, Narisu Narisu, Anton J. M. de Craen, David R. Weir, Albertine J. Oldehinkel, Jessica Tyrrell, Beverley Balkau, Kirsti Kvaløy, Marie-Claude Vohl, Jennifer A. Smith, Rainer Rauramaa, Andrew C. Heath, Erwin P. Bottinger, Andrew Wong, Günther Silbernagel, Mattias Lorentzon, Philippe Froguel, Uzma Afzal, Tanja B. Grammer, Dabeeru C. Rao, Charlotta Pisinger, Nicola Glorioso, Najaf Amin, Andrew P. Morris, Tanguy Corre, Alan James, Julius S. Ngwa, Jennifer E. Huffman, Gudny Eiriksdottir, Maija Hassinen, Lenore J. Launer, Marit E. Jørgensen, Dorret I. Boomsma, Harry Campbell, Scott Coggeshall, Timothy M. Frayling, Konstantin Strauch, Johanna Kuusisto, David Hadley, Penny Gordon-Larsen, Xuan Deng, Dorothée Thuillier, Albert V. Smith, Jaakko Tuomilehto, Harald Grallert, Lynne J. Hocking, Dan Mellström, M. Carola Zillikens, Lars Lind, Hester M. den Ruijter, Gemma Cadby, Joanne E. Curran, Richard N. Bergman, David J. Stott, Matthias Olden, Veronique Vitart, Robert Luben, Cinzia Sarti, Gert J. de Borst, Lyle J. Palmer, Sven Bergmann, Alexander Teumer, John D. Eicher, Marcus E. Kleber, Marie Loh, Genovefa Kolovou, Iris M. Heid, Gonneke Willemsen, Marie Neergaard Harder, David J. Hunter, Stefania Bandinelli, Francis S. Collins, Hans J. Grabe, Virginia Fisher, John Whitfield, Leo-Pekka Lyytikäinen, Salome Scholtens, Tamuno Alfred, Richard S. Cooper, Jouke-Jan Hottenga, Martina Chittani, Jan A. Staessen, Bernhard K. Krämer, Markku Laakso, Min A. Jhun, Marjo-Riitta Järvelin, Saima Afaq, Rita P. S. Middelberg, Jing Hua Zhao, Toshiko Tanaka, Kent D. Taylor, Rudi G. J. Westendorp, Panagiotis Deloukas, Nina Hutri-Kähönen, Reiner Biffar, Krista Fischer, Leena Kinnunen, Diana Kuh, Jaspal S. Kooner, Caroline S. Fox, Harold Snieder, Pau Navarro, Stéphane Lobbens, Tao Huang, Vilmundur Gudnason, Jacqueline M. Vink, Terrence Forrester, Kari E. North, Annette Peters, Mika Kivimäki, David Schlessinger, Ian Ford, Kristian Hveem, Christopher A. Haiman, Lucia A. Hindorff, Oluf Pedersen, Ingrid B. Borecki, Bruce H. R. Wolffenbuttel, Nicholas J. Wareham, Cornelia M. van Duijn, Lawrence F. Bielak, Loic Le Marchand, Linda S. Adair, Tõnu Esko, Anne U. Jackson, Ying Wu, Eco J. C. de Geus, Jana V. van Vliet-Ostaptchouk, Louis Pérusse, Peter J. van der Most, Ulrike Peters, Magnus Karlsson, Anders Hamsten, Anne E. Justice, Alena Stančáková, Henning Tiemeier, Eric Boerwinkle, Catharina A. Hartman, Claes Ohlsson, Grant W. Montgomery, Elise Lim, Traci M. Bartz, Erik Ingelsson, Martina E. Zimmermann, Laura J. Rasmussen-Torvik, Terho Lehtimäki, Heikki A. Koistinen, Pirjo Komulainen, Damiano Baldassarre, Marten A. Siemelink, Niek Verweij, Gerard Pasterkamp, Markus Juonala, Wei Zhao, Andres Metspalu, Sander W. van der Laan, Tuomo Rankinen, Timo A. Lakka, Yun Ju Sung, Heather M. Stringham, Bruce M. Psaty, Niha Zubair, Stavroula Kanoni, Saskia Haitjema, Bengt Sennblad, Llilda Barata, Morris A. Swertz, Mary F. Feitosa, Tim D. Spector, Paul W. Franks, Qibin Qi, Francesco Cucca, Allan Linneberg, Reija Männikkö, Jonathan Marten, Olli T. Raitakari, Mark I. McCarthy, Joel N. Hirschhorn, Winfried März, Sarah H. Wild, Meena Kumari, Nese Direk, Patricia A. Peyser, Jessica D. Faul, John C. Chambers, Nicholas D. Hastie, Mette Hollensted, Jacek Czajkowski, Daniel I. Chasman, Matthias Nauck, Gérard Waeber, Brendan M. Buckley, Kai Savonen, Judith M. Vonk, Carsten A. Böger, Loic Yengo, Anna Eriksson, Henry Völzke, Pedro Marques-Vidal, Center for Liver, Digestive and Metabolic Diseases (CLDM), Groningen Institute for Organ Transplantation (GIOT), Lifestyle Medicine (LM), Groningen Kidney Center (GKC), Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Life Course Epidemiology (LCE), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Groningen Research Institute for Asthma and COPD (GRIAC), Cardiovascular Centre (CVC), Clinicum, Department of Medicine, University of Helsinki, Endokrinologian yksikkö, HUS Internal Medicine and Rehabilitation, Luan, Jian'an [0000-0003-3137-6337], Marten, Jonathan [0000-0001-6916-2014], Langenberg, Claudia [0000-0002-5017-7344], Luben, Robert [0000-0002-5088-6343], Ong, Kenneth [0000-0003-4689-7530], Wareham, Nicholas [0000-0003-1422-2993], Barroso, Ines [0000-0001-5800-4520], Apollo - University of Cambridge Repository, Læknadeild (HÍ), Faculty of Medicine (UI), Heilbrigðisvísindasvið (HÍ), School of Health Sciences (UI), Háskóli Íslands, University of Iceland, Biological Psychology, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, APH - Mental Health, APH - Health Behaviors & Chronic Diseases, APH - Methodology, APH - Personalized Medicine, Epidemiology, Erasmus MC other, Medical Microbiology & Infectious Diseases, Internal Medicine, Child and Adolescent Psychiatry / Psychology, and Psychiatry
Subjects: 0301 basic medicine, Netherlands Twin Register (NTR), Medicin och hälsovetenskap, Offita, Chemistry(all), Epidemiology, General Physics and Astronomy, Genome-wide association study, methods [Genome-Wide Association Study], Biochemistry, Genome-wide association studies, Medical and Health Sciences, Body Mass Index, genetics [Obesity], Genetics research, IMPUTATION, Body Fat Distribution, genetics [Genetic Predisposition to Disease], OXIDATIVE STRESS, POPULATION, Adiposity, METABOLIC SYNDROME, Genetics, education.field_of_study, Multidisciplinary, Smoking, Public Health, Global Health, Social Medicine and Epidemiology, genetics [Smoking], ASSOCIATION, 3142 Public health care science, environmental and occupational health, 3. Good health, Multidisciplinary Sciences, DEFICIENCY, Phenotype, ADDICTION, Science & Technology - Other Topics, Medical genetics, ddc:500, Waist Circumference, Reykingar, genetics [Adiposity], Adult, medicine.medical_specialty, Science, Quantitative Trait Loci, Population, genetics [Waist Circumference], Accounting, Biology, Quantitative trait locus, Physics and Astronomy(all), Polymorphism, Single Nucleotide, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, SDG 3 - Good Health and Well-being, GWAS, obesity, smoking, MD Multidisciplinary, Genetic predisposition, medicine, Journal Article, Erfðafræði, Humans, Genetic Predisposition to Disease, Obesity, education, Genetic association, Science & Technology, VITAMIN-C, genetics [Quantitative Trait Loci], Waist-Hip Ratio, business.industry, Biochemistry, Genetics and Molecular Biology(all), Epistasis, Genetic, Rannsóknir, General Chemistry, ta3121, R1, GENE, Folkhälsovetenskap, global hälsa, socialmedicin och epidemiologi, MICE, 030104 developmental biology, 3121 General medicine, internal medicine and other clinical medicine, business, Body mass index, Developmental Psychopathology, Imputation (genetics), Genetics and Molecular Biology(all), Genome-Wide Association Study
Abstract: Few genome-wide association studies (GWAS) account for environmental exposures, like smoking, potentially impacting the overall trait variance when investigating the genetic contribution to obesity-related traits. Here, we use GWAS data from 51,080 current smokers and 190,178 nonsmokers (87% European descent) to identify loci influencing BMI and central adiposity, measured as waist circumference and waist-to-hip ratio both adjusted for BMI. We identify 23 novel genetic loci, and 9 loci with convincing evidence of gene-smoking interaction (GxSMK) on obesity-related traits. We show consistent direction of effect for all identified loci and significance for 18 novel and for 5 interaction loci in an independent study sample. These loci highlight novel biological functions, including response to oxidative stress, addictive behaviour, and regulatory functions emphasizing the importance of accounting for environment in genetic analyses. Our results suggest that tobacco smoking may alter the genetic susceptibility to overall adiposity and body fat distribution., A full list of acknowledgments appears in the Supplementary Note 4. Co-author A.J.M.d.C. recently passed away while this work was in process. This work was performed under the auspices of the Genetic Investigation of ANthropometric Traits (GIANT) consortium. We acknowledge the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium for encouraging CHARGE studies to participate in this effort and for the contributions of CHARGE members to the analyses conducted for this research. Funding for this study was provided by the Aase and Ejner Danielsens Foundation; Academy of Finland (41071, 77299, 102318, 110413, 117787, 121584, 123885, 124243, 124282, 126925, 129378, 134309, 286284); Accare Center for Child and Adolescent Psychiatry; Action on Hearing Loss (G51); Agence Nationale de la 359 Recherche; Agency for Health Care Policy Research (HS06516); ALF/LUA research grant in Gothenburg; ALFEDIAM; ALK-Abelló A/S; Althingi; American Heart Association (13POST16500011); Amgen; Andrea and Charles Bronfman Philanthropies; Ardix Medical; Arthritis Research UK; Association Diabète Risque Vasculaire; Australian National Health and Medical Research Council (241944, 339462, 389875, 389891, 389892, 389927, 389938, 442915, 442981, 496739, 552485, 552498); Avera Institute; Bayer Diagnostics; Becton Dickinson; BHF (RG/14/5/30893); Boston Obesity Nutrition Research Center (DK46200), Bristol-Myers Squibb; British Heart Foundation (RG/10/12/28456, RG2008/08, RG2008/014, SP/04/002); Medical Research Council of Canada; Canadian Institutes for Health Research (FRCN-CCT-83028); Cancer Research UK; Cardionics; Cavadis B.V., Center for Medical Systems Biology; Center of Excellence in Genomics; CFI; CIHR; City of Kuopio; CNAMTS; Cohortes Santé TGIR; Contrat de Projets État-Région; Croatian Science Foundation (8875); Danish Agency for Science, Technology and Innovation; Danish Council for Independent Research (DFF-1333-00124, DFF-1331-00730B); County Council of Dalarna; Dalarna University; Danish Council for Strategic Research; Danish Diabetes Academy; Danish Medical Research Council; Department of Health, UK; Development Fund from the University of Tartu (SP1GVARENG); Diabetes Hilfs- und Forschungsfonds Deutschland; Diabetes UK; Diabetes Research and Wellness Foundation Fellowship; Donald W. Reynolds Foundation; Dr Robert Pfleger-Stiftung; Dutch Brain Foundation; Dutch Diabetes Research Foundation; Dutch Inter University Cardiology Institute; Dutch Kidney Foundation (E033); Dutch Ministry of Justice; the DynaHEALTH action No. 633595, Economic Structure Enhancing Fund of the Dutch Government; Else Kröner-Fresenius-Stiftung (2012_A147, P48/08//A11/08); Emil Aaltonen Foundation; Erasmus University Medical Center Rotterdam; Erasmus MC and Erasmus University Rotterdam; the Municipality of Rotterdam; Estonian Government (IUT20-60, IUT24-6); Estonian Research Roadmap through the Estonian Ministry of Education and Research (3.2.0304.11-0312); European Research Council (ERC Starting Grant and 323195:SZ-245 50371-GLUCOSEGENES-FP7-IDEAS-ERC); European Regional Development Fund; European Science Foundation (EU/QLRT-2001-01254); European Commission (018947, 018996, 201668, 223004, 230374, 279143, 284167, 305739, BBMRI-LPC-313010, HEALTH-2011.2.4.2-2-EU-MASCARA, HEALTH-2011-278913, HEALTH-2011-294713-EPLORE, HEALTH-F2-2008-201865-GEFOS, HEALTH-F2-2013-601456, HEALTH-F4-2007-201413, HEALTH-F4-2007-201550-HYPERGENES, HEALTH-F7-305507 HOMAGE, IMI/115006, LSHG-CT-2006-018947, LSHG-CT-2006-01947, LSHM-CT-2004-005272, LSHM-CT-2006-037697, LSHM-CT-2007-037273, QLG1-CT-2002-00896, QLG2-CT-2002-01254); Faculty of Biology and Medicine of Lausanne; Federal Ministry of Education and Research (01ZZ0103, 01ZZ0403, 01ZZ9603, 03IS2061A, 03ZIK012); Federal State of Mecklenburg-West Pomerania; Fédération Française de Cardiologie; Finnish Cultural Foundation; Finnish Diabetes Association; Finnish Foundation of Cardiovascular Research; Finnish Heart Association; Fondation Leducq; Food Standards Agency; Foundation for Strategic Research; French Ministry of Research; FRSQ; Genetic Association Information Network (GAIN) of the Foundation for the NIH; German Federal Ministry of Education and Research (BMBF, 01ER1206, 01ER1507); GlaxoSmithKline; Greek General Secretary of Research and Technology; Göteborg Medical Society; Health and Safety Executive; Healthcare NHS Trust; Healthway; Western Australia; Heart Foundation of Northern Sweden; Helmholtz Zentrum München—German Research Center for Environmental Health; Hjartavernd; Ingrid Thurings Foundation; INSERM; InterOmics (PB05 MIUR-CNR); INTERREG IV Oberrhein Program (A28); Interuniversity Cardiology Institute of the Netherlands (ICIN, 09.001); Italian Ministry of Health (ICS110.1/RF97.71); Italian Ministry of Economy and Finance (FaReBio di Qualità); Marianne and Marcus Wallenberg Foundation; the Ministry of Health, Welfare and Sports, the Netherlands; J.D.E. and Catherine T, MacArthur Foundation Research Networks on Successful Midlife Development and Socioeconomic Status and Health; Juho Vainio Foundation; Juvenile Diabetes Research Foundation International; KfH Stiftung Präventivmedizin e.V.; King's College London; Knut and Alice Wallenberg Foundation; Kuopio University Hospital; Kuopio, Tampere and Turku University Hospital Medical Funds (X51001); La Fondation de France; Leenaards Foundation; Lilly; LMUinnovativ; Lundberg Foundation; Magnus Bergvall Foundation; MDEIE; Medical Research Council UK (G0000934, G0601966, G0700931, MC_U106179471, MC_UU_12019/1); MEKOS Laboratories; Merck Santé; Ministry for Health, Welfare and Sports, The Netherlands; Ministry of Cultural Affairs of Mecklenburg-West Pomerania; Ministry of Economic Affairs, The Netherlands; Ministry of Education and Culture of Finland (627;2004-2011); Ministry of Education, Culture and Science, The Netherlands; Ministry of Science, Education and Sport in the Republic of Croatia (108-1080315-0302); MRC centre for Causal Analyses in Translational Epidemiology; MRC Human Genetics Unit; MRC-GlaxoSmithKline pilot programme (G0701863); MSD Stipend Diabetes; National Institute for Health Research; Netherlands Brain Foundation (F2013(1)-28); Netherlands CardioVascular Research Initiative (CVON2011-19); Netherlands Genomics Initiative (050-060-810); Netherlands Heart Foundation (2001 D 032, NHS2010B280); Netherlands Organization for Scientific Research (NWO) and Netherlands Organisation for Health Research and Development (ZonMW) (56-464-14192, 60-60600-97-118, 100-001-004, 261-98-710, 400-05-717, 480-04-004, 480-05-003, 481-08-013, 904-61-090, 904-61-193, 911-11-025, 985-10-002, Addiction-31160008, BBMRI–NL 184.021.007, GB-MaGW 452-04-314, GB-MaGW 452-06-004, GB-MaGW 480-01-006, GB-MaGW 480-07-001, GB-MW 940-38-011, Middelgroot-911-09-032, NBIC/BioAssist/RK 2008.024, Spinozapremie 175.010.2003.005, 175.010.2007.006); Neuroscience Campus Amsterdam; NHS Foundation Trust; National Institutes of Health (1RC2MH089951, 1Z01HG000024, 24152, 263MD9164, 263MD821336, 2R01LM010098, 32100-2, 32122, 32108, 5K99HL130580-02, AA07535, AA10248, AA11998, AA13320, AA13321, AA13326, AA14041, AA17688, AG13196, CA047988, DA12854, DK56350, DK063491, DK078150, DK091718, DK100383, DK078616, ES10126, HG004790, HHSN268200625226C, HHSN268200800007C, HHSN268201200036C, HHSN268201500001I, HHSN268201100046C, HHSN268201100001C, HHSN268201100002C, HHSN268201100003C, HHSN268201100004C, HHSN271201100004C, HL043851, HL45670, HL080467, HL085144, HL087660, HL054457, HL119443, HL118305, HL071981, HL034594, HL126024, HL130114, KL2TR001109, MH66206, MH081802, N01AG12100, N01HC55015, N01HC55016, N01C55018, N01HC55019, N01HC55020, N01HC55021, N01HC55022, N01HC85079, N01HC85080, N01HC85081, N01HC85082, N01HC85083, N01HC85086, N01HC95159, N01HC95160, N01HC95161, N01HC95162, N01HC95163, N01HC95164, N01HC95165, N01HC95166, N01HC95167, N01HC95168, N01HC95169, N01HG65403, N01WH22110, N02HL6‐4278, N01-HC-25195, P01CA33619, R01HD057194, R01HD057194, R01AG023629, R01CA63, R01D004215701A, R01DK075787, R01DK062370, R01DK072193, R01DK075787, R01DK089256, R01HL53353, R01HL59367, R01HL086694, R01HL087641, R01HL087652, R01HL103612, R01HL105756, R01HL117078, R01HL120393, R03 AG046389, R37CA54281, RC2AG036495, RC4AG039029, RPPG040710371, RR20649, TW008288, TW05596, U01AG009740, U01CA98758, U01CA136792, U01DK062418, U01HG004402, U01HG004802, U01HG007376, U01HL080295, UL1RR025005, UL1TR000040, UL1TR000124, UL1TR001079, 2T32HL007055-36, T32GM074905, HG002651, HL084729, N01-HC-25195, UM1CA182913); NIH, National Institute on Aging (Intramural funding, NO1-AG-1-2109); Northern Netherlands Collaboration of Provinces; Novartis Pharma; Novo Nordisk; Novo Nordisk Foundation; Nutricia Research Foundation (2016-T1); ONIVINS; Parnassia Bavo group; Pierre Fabre; Province of Groningen; Päivikki and Sakari Sohlberg Foundation; Påhlssons Foundation; Paavo Nurmi Foundation; Radboud Medical Center Nijmegen; Research Centre for Prevention and Health, the Capital Region of Denmark; the Research Institute for Diseases in the Elderly; Research into Ageing; Robert Dawson Evans Endowment of the Department of Medicine at Boston University School of Medicine and Boston Medical Center; Roche; Royal Society; Russian Foundation for Basic Research (NWO-RFBR 047.017.043); Rutgers University Cell and DNA Repository (NIMH U24 MH068457-06); Sanofi-Aventis; Scottish Government Health Directorates, Chief Scientist Office (CZD/16/6); Siemens Healthcare; Social Insurance Institution of Finland (4/26/2010); Social Ministry of the Federal State of Mecklenburg-West Pomerania; Société Francophone du 358 Diabète; State of Bavaria; Stiftelsen för Gamla Tjänarinnor; Stockholm County Council (560183, 592229); Strategic Cardiovascular and Diabetes Programmes of Karolinska Institutet and Stockholm County Council; Stroke Association; Swedish Diabetes Association; Swedish Diabetes Foundation (2013-024); Swedish Foundation for Strategic Research; Swedish Heart-Lung Foundation (20120197, 20150711); Swedish Research Council (0593, 8691, 2012-1397, 2012-1727, and 2012-2215); Swedish Society for Medical Research; Swiss Institute of Bioinformatics; Swiss National Science Foundation (3100AO-116323/1, 31003A-143914, 33CSCO-122661, 33CS30-139468, 33CS30-148401, 51RTP0_151019); Tampere Tuberculosis Foundation; Technology Foundation STW (11679); The Fonds voor Wetenschappelijk Onderzoek Vlaanderen, Ministry of the Flemish Community (G.0880.13, G.0881.13); The Great Wine Estates of the Margaret River Region of Western Australia; Timber Merchant Vilhelm Bangs Foundation; Topcon; Tore Nilsson Foundation; Torsten and Ragnar Söderberg's Foundation; United States – Israel Binational Science Foundation (Grant 2011036), Umeå University; University Hospital of Regensburg; University of Groningen; University Medical Center Groningen; University of Michigan; University of Utrecht; Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) (b2011036); Velux Foundation; VU University’s Institute for Health and Care Research; Västra Götaland Foundation; Wellcome Trust (068545, 076113, 079895, 084723, 088869, WT064890, WT086596, WT098017, WT090532, WT098051, 098381); Wissenschaftsoffensive TMO; Yrjö Jahnsson Foundation; and Åke Wiberg Foundation. The views expressed in this manuscript are those of the authors and do not necessarily represent the views of the National Heart, Lung, and Blood Institute (NHLBI); the National Institutes of Health (NIH); or the U.S. Department of Health and Human Services.
Published: 2017

35. Helicobacter pylori colonization and obesity - a Mendelian randomization study

Author: David Meyre, Markus M. Lerch, Georg Homuth, Claudia Schurmann, Julia Mayerle, Wouter den Hollander, Albert Hofman, André G. Uitterlinden, Linda Broer, Caroline M. den Hoed, Ernst J. Kuipers, Erasmus MC other, Internal Medicine, Gastroenterology & Hepatology, and Epidemiology
Subjects: 0301 basic medicine, Male, medicine.medical_specialty, Pathology, Cross-sectional study, Population, lcsh:Medicine, Polymorphism, Single Nucleotide, Article, Body Mass Index, Helicobacter Infections, Cohort Studies, 03 medical and health sciences, Random Allocation, 0302 clinical medicine, SDG 3 - Good Health and Well-being, Risk Factors, Internal medicine, Germany, Mendelian randomization, Epidemiology, medicine, Humans, Obesity, education, lcsh:Science, Aged, Netherlands, Aged, 80 and over, education.field_of_study, Multidisciplinary, biology, Helicobacter pylori, business.industry, lcsh:R, Mendelian Randomization Analysis, Middle Aged, medicine.disease, biology.organism_classification, 030104 developmental biology, Cross-Sectional Studies, 030211 gastroenterology & hepatology, Female, lcsh:Q, business, Body mass index, Cohort study
Abstract: Obesity is associated with substantial morbidity, costs, and decreased life expectancy, and continues to rise worldwide. While etiological understanding is needed for prevention, epidemiological studies indicated that colonization with Helicobacter pylori (H. pylori) may affect body mass index (BMI), but with inconsistent results. Here, we examine the relationship between H. pylori colonization and BMI/obesity. Cross-sectional analyses were performed in two independent population-based cohorts of elderly from the Netherlands and Germany (n = 13,044). Genetic risk scores were conducted based on genetic loci associated with either H. pylori colonization or BMI/obesity. We performed a bi-directional Mendelian randomization. Meta-analysis of cross-sectional data revealed no association between anti-H. pylori IgG titer and BMI, nor of H. pylori positivity and BMI. Anti-H. pylori IgG titer was negatively associated with obesity (OR 0.99972; 95% CI 0.99946-0.99997, p = 0.03) and with obesity classes (Beta −6.91 •10−5; 95% CI −1.38•10−4, −5.49•10−7, p = 0.048), but the magnitude of these effects was limited. Mendelian randomization showed no causal relation between H. pylori genetic risk score and BMI/obesity, nor between BMI or obesity genetic risk scores and H. pylori positivity. This study provides no evidence for a clinically relevant association between H. pylori and BMI/obesity.
Published: 2017

36. A proteomics workflow for quantitative and time-resolved analysis of adaptation reactions of internalized bacteria

Author: Claudia Schurmann, Vishnu M. Dhople, Maren Depke, Ulrike Jehmlich, Petra Hildebrandt, Melanie Gutjahr, Leif Steil, Sandra Ernst, Jörg Bernhardt, Frank Schmidt, Elke Hammer, Kristin Surmann, Uwe Völker, Henrike Pförtner, and Juliane Wagner
Subjects: Proteomics, Staphylococcus aureus, Time Factors, Host–pathogen interaction, media_common.quotation_subject, Bronchi, Biology, Arginine, Mass Spectrometry, General Biochemistry, Genetics and Molecular Biology, Cell Line, Bacterial Proteins, Stable isotope labeling by amino acids in cell culture, Protein purification, Humans, Internalization, Molecular Biology, media_common, Carbon Isotopes, Lysine, Epithelial Cells, Cell sorting, biology.organism_classification, Adaptation, Physiological, Molecular biology, Biochemistry, Isotope Labeling, Host-Pathogen Interactions, Proteome, Peptides, Bacteria
Abstract: The development of a mass spectrometric workflow for the sensitive identification and quantitation of the kinetics of changes in metaproteomes, or in particular bacterial pathogens after internalization by host cells, is described. This procedure employs three essential stages: (i) SILAC pulse-chase labeling and infection assay; (ii) isolation of bacteria by GFP-assisted cell sorting; (iii) mass spectrometry-based proteome analysis. This approach displays greater sensitivity than techniques relying on conventional cell sorting and protein separation, due to an efficient combination of a filtration-based purification and an on-membrane digestion. We exemplary describe the use of the workflow for the identification and quantitation of the proteome of 10⁶ cells of Staphylococcus aureus after internalization by S9 human bronchial epithelial cells. With minor modifications, the workflow described can be applied for the characterization of other host-pathogen pairs, permitting identification and quantitation of hundreds of bacterial proteins over a time range of several hours post infection.
Published: 2013

37. Apolipoprotein L1 Variants and Blood Pressure Traits in African Americans

Author: Rajiv Nadukuru, Claudia Schurmann, Laura J. Rasmussen-Torvik, Geneviève Galarneau, Stephen B. Ellis, Dan M. Roden, Joshua C. Denny, Eimear E. Kenny, Stuart A. Scott, Jennifer A. Pacheco, Rongling Li, Teri A. Manolio, Jinglan Zhang, Abel N. Kho, Girish N. Nadkarni, Erwin P. Bottinger, M. Geoffrey Hayes, and Rex L. Chisholm
Subjects: 0301 basic medicine, Adult, Male, medicine.medical_specialty, Apolipoprotein L1, Single-nucleotide polymorphism, Blood Pressure, 030204 cardiovascular system & hematology, Article, Cohort Studies, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Internal medicine, medicine, Humans, Allele, Aged, biology, business.industry, Proportional hazards model, Middle Aged, Black or African American, 030104 developmental biology, Endocrinology, Blood pressure, Apolipoproteins, Cohort, Hypertension, biology.protein, Female, Cardiology and Cardiovascular Medicine, business, Lipoproteins, HDL, Body mass index, Biomarkers, Cohort study
Abstract: Background African Americans (AA) are disproportionately affected by hypertension-related health disparities. Apolipoprotein L1 (APOL1) risk variants are associated with kidney disease in hypertensive AAs. Objectives This study assessed the APOL1 risk alleles’ association with blood pressure traits in AAs. Methods The discovery cohort included 5,204 AA participants from Mount Sinai’s BioMe biobank. Replication cohorts included additional BioMe (n = 1,623), Vanderbilt BioVU (n = 1,809), and Northwestern NUgene (n = 567) AA biobank participants. Single nucleotide polymorphisms determining APOL1 G1 and G2 risk alleles were genotyped in BioMe and imputed in BioVU/NUgene participants. APOL1 risk alleles’ association with blood pressure–related traits was tested in the discovery cohort, a meta-analysis of replication cohorts, and a combined meta-analysis under recessive and additive models after adjusting for age, sex, body mass index, and estimated glomerular filtration rate. Results There were 14% to 16% of APOL1 variant allele homozygotes (2 copies of G1/G2) across cohorts. APOL1 risk alleles were associated under an additive model with systolic blood pressure (SBP) and age at diagnosis of hypertension, which was 2 to 5 years younger in the APOL1 variant allele homozygotes (Cox proportional hazards analysis, p value for combined meta-analysis [pcom] = 1.9 × 10−5). APOL1 risk alleles were associated with overall SBP (pcom = 7.0 × 10−8) and diastolic blood pressure (pcom = 2.8 × 10−4). After adjustment for all covariates, those in the 20- to 29-year age range showed an increase in SBP of 0.94 ± 0.44 mm Hg (pcom = 0.01) per risk variant copy. APOL1-associated estimated glomerular filtration rate decline was observed starting a decade later in life in the 30- to 39-year age range. Conclusions APOL1 risk alleles are associated with higher SBP and earlier hypertension diagnoses in young AAs; this relationship appears to follow an additive model.
Published: 2016

38. Exome Genotyping Identifies Pleiotropic Variants Associated with Red Blood Cell Traits

Author: Torben Hansen, Marie-Pierre Dubé, Frank J. A. van Rooij, Todd L. Edwards, Michele K. Evans, Tõnu Esko, Paul Elliott, Leslie A. Lange, Kjell Nikus, Jette Bork-Jensen, Caterina Vacchi-Suzzi, Mika Kähönen, John M. Starr, Jennifer A. Brody, Ethan M. Lange, Christopher J. O'Donnell, John D. Eicher, Marju Orho-Melander, Kent D. Taylor, Vilmundur Gudnason, Yingchang Lu, Betina H. Thuesen, Amber A. Burt, Lisa R. Yanek, Andreas Greinacher, Leo-Pekka Lyytikäinen, Albert V. Smith, Eric Boerwinkle, Ming-Huei Chen, Paul L. Auer, Laura M. Raffield, Ani Manichaikul, Kenneth Rice, Frank Schmidt, Evangelos Evangelou, Russell P. Tracy, Nathalie Chami, Ayush Giri, Jussi Hernesniemi, Andrew D. Johnson, Ruth J. F. Loos, Sekar Kathiresan, Salman M. Tajuddin, Nina Mononen, Emma Raitoharju, Dawn M. Waterworth, James G. Wilson, Linda M. Polfus, Akihiro Nomura, Tamara B. Harris, Guillaume Lettre, Astrid Petersmann, Marguerite R. Irvin, Jerome I. Rotter, Alexander P. Reiner, Niels Grarup, Latisha Love-Gregory, Claudia Schurmann, Michelle L. O'Donoghue, Ursula M. Schick, Raha Pazoki, Lars Wallentin, Anne-Claire Vergnaud, Nauder Faraday, W. David Hill, Cornelia M. van Duijn, Nathan Pankratz, Rasika A. Mathias, Joel N. Hirschhorn, Jin Li, Santhi K. Ganesh, Tim Kacprowski, Traci M. Bartz, Mike A. Nalls, Samuel Lessard, Albert Hofman, Reedik Mägi, Ioanna Tzoulaki, Myriam Fornage, Evelin Mihailov, He Gao, Lewis C. Becker, Lenore J. Launer, Fernando Rivadeneira, Deborah A. Nickerson, Simon de Denus, Andrew J. Slater, Allan Linneberg, Andres Metspalu, Oluf Pedersen, Olli T. Raitakari, Harvey D. White, Yongmei Liu, Heather M. Highland, Bruce M. Psaty, Melissa A. Richard, Neil A. Zakai, Olle Melander, David R. Crosslin, Gunnar Engström, Ian J. Deary, Digna R. Velez Edwards, David C. Liewald, Mary Cushman, Erwin P. Bottinger, Eric S. Torstenson, Alan B. Zonderman, Nada A. Abumrad, Diane M. Becker, Terho Lehtimäki, Caroline Hayward, James S. Floyd, Alexander Teumer, Epidemiology, and Internal Medicine
Subjects: 0301 basic medicine, Hemolytic anemia, Erythrocyte Indices, Erythrocytes, Genotype, Quantitative Trait Loci, Mean corpuscular hemoglobin, 030204 cardiovascular system & hematology, Biology, Allelic Imbalance, Article, 03 medical and health sciences, Hemoglobins, 0302 clinical medicine, Sideroblastic anemia, Gene Frequency, Pleiotropy, hemic and lymphatic diseases, Genetics, medicine, Humans, Genetics(clinical), Erythropoiesis, Exome, Allele frequency, Mean corpuscular volume, Genetics (clinical), Genetics & Heredity, Medical And Health Sciences, medicine.diagnostic_test, ta1184, Genetic Variation, Genetic Pleiotropy, Biological Sciences, ta3121, medicine.disease, 3. Good health, Minor allele frequency, Black or African American, 030104 developmental biology, Hematocrit
Abstract: Red blood cell (RBC) traits are important heritable clinical biomarkers and modifiers of disease severity. To identify coding genetic variants associated with these traits, we conducted meta-analyses of seven RBC phenotypes in 130,273 multi-ethnic individuals from studies genotyped on an exome array. After conditional analyses and replication in 27,480 independent individuals, we identified 16 new RBC variants. We found low-frequency missense variants in MAP1A (rs55707100, minor allele frequency [MAF] = 3.3%, p = 2 × 10(-10) for hemoglobin [HGB]) and HNF4A (rs1800961, MAF = 2.4%, p < 3 × 10(-8) for hematocrit [HCT] and HGB). In African Americans, we identified a nonsense variant in CD36 associated with higher RBC distribution width (rs3211938, MAF = 8.7%, p = 7 × 10(-11)) and showed that it is associated with lower CD36 expression and strong allelic imbalance in ex vivo differentiated human erythroblasts. We also identified a rare missense variant in ALAS2 (rs201062903, MAF = 0.2%) associated with lower mean corpuscular volume and mean corpuscular hemoglobin (p < 8 × 10(-9)). Mendelian mutations in ALAS2 are a cause of sideroblastic anemia and erythropoietic protoporphyria. Gene-based testing highlighted three rare missense variants in PKLR, a gene mutated in Mendelian non-spherocytic hemolytic anemia, associated with HGB and HCT (SKAT p < 8 × 10(-7)). These rare, low-frequency, and common RBC variants showed pleiotropy, being also associated with platelet, white blood cell, and lipid traits. Our association results and functional annotation suggest the involvement of new genes in human erythropoiesis. We also confirm that rare and low-frequency variants play a role in the architecture of complex human traits, although their phenotypic effect is generally smaller than originally anticipated.
Published: 2016

39. Genome-wide association study of copy number variation with lung function identifies a novel signal of association near BANP for forced vital capacity

Author: Claudia Schurmann, Jennie Hui, UK BiLEVE, Nick Shrine, Generation Scotland, John Henderson, Sven Gläser, David P. Strachan, Martin D. Tobin, Raquel Granell, Jennifer E. Huffman, María Soler Artigas, Caroline Hayward, Lyle J. Palmer, Louise V. Wain, Craig E. Pennell, Alan L. James, Anders Mälarstig, Stephan B. Felix, David M. Evans, Olli T. Raitakari, Bill Musk, Terho Lehtimäki, Georg Homuth, and Qi Wei Ang
Subjects: 0301 basic medicine, Adult, Genome-wide association study, Adolescent, DNA Copy Number Variations, Genotype, Vital Capacity, Single-nucleotide polymorphism, Cell Cycle Proteins, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, Young Adult, Missing heritability problem, Genetics, SNP, Humans, Genetics(clinical), Copy-number variation, Lung, Genetics (clinical), Genetic association, Aged, Aged, 80 and over, genome-wide association study, Copy number variation, copy number variation, Nuclear Proteins, lung function, Tag SNP, Middle Aged, Lung function, 3. Good health, SNP genotyping, Respiratory Function Tests, DNA-Binding Proteins, 030104 developmental biology, Phenotype, Population Surveillance, Research Article
Abstract: Background Genome-wide association studies of Single Nucleotide Polymorphisms (SNPs) have identified 55 SNPs associated with lung function. However, little is known about the effect of copy number variants (CNVs) on lung function, although CNVs represent a significant proportion of human genetic polymorphism. To assess the effect of CNVs on lung function quantitative traits, we measured copy number at 2788 previously characterised, common copy number variable regions in 6 independent cohorts (n = 24,237) using intensity data from SNP genotyping experiments. We developed a pipeline for genome-wide association analysis and meta-analysis of CNV genotypes measured across multiple studies using SNP genotype array intensity data from different platform technologies. We then undertook cohort-level genome-wide association studies of CNV with lung function in a subset of 4 cohorts (n
Published: 2016

40. Genome-wide Association Study of Platelet Count Identifies Ancestry-Specific Loci in Hispanic/Latino Americans

Author: Nora Franceschini, Lisa M. Brown, Chani J. Hodonsky, Karen L. Mohlke, George Papanicolaou, Jerome I. Rotter, Adam A. Szpiro, Jean Morrison, Robert L. Hanson, Kari E. North, Paul L. Auer, Claudia Schurmann, Adrienne M. Stilp, Sharon R. Browning, Stephanie A. Bien, Brian L. Browning, Swarooparani Vadlamudi, Leslie J. Baier, Kenneth Rice, Ruth J. F. Loos, Cathy C. Laurie, Anna Plantinga, Timothy A. Thornton, Kathleen F. Kerr, Caitlin P. McHugh, Ursula M. Schick, Stephanie M. Gogarten, Tamar Sofer, Deepti Jain, Stephen S. Rich, Kent D. Taylor, Cecelia A. Laurie, Yongmei Liu, Bruce S. Weir, James P. Davis, Sarah C. Nelson, Alex P. Reiner, and Matthew P. Conomos
Subjects: 0301 basic medicine, Genotyping Techniques, Genome-wide association study, Medical and Health Sciences, 0302 clinical medicine, Gene Frequency, Receptors, Genotype, Genetics(clinical), Actinin, Platelet, Genetics (clinical), Genetics & Heredity, Genetics, MEF2 Transcription Factors, Single Nucleotide, Hispanic or Latino, Hematology, Middle Aged, Biological Sciences, Phenotype, Blood, Adult, Adolescent, 1.1 Normal biological development and functioning, Biology, Polymorphism, Single Nucleotide, Article, Young Adult, 03 medical and health sciences, Clinical Research, Underpinning research, Humans, Polymorphism, Allele, Allele frequency, Gene, Alleles, Genetic Association Studies, Aged, Platelet Count, GABA-B, Human Genome, Membrane Proteins, 030104 developmental biology, Receptors, GABA-B, Genetic Loci, Hemostasis, 030217 neurology & neurosurgery
Abstract: Platelets play an essential role in hemostasis and thrombosis. We performed a genome-wide association study of platelet count in 12,491 participants of the Hispanic Community Health Study/Study of Latinos by using a mixed-model method that accounts for admixture and family relationships. We discovered and replicated associations with five genes (ACTN1, ETV7, GABBR1-MOG, MEF2C, and ZBTB9-BAK1). Our strongest association was with Amerindian-specific variant rs117672662 (p value = 1.16× 10(-28)) in ACTN1, agene implicated in congenital macrothrombocytopenia. rs117672662 exhibited allelic differences in transcriptional activity and protein binding in hematopoietic cells. Our results underscore the value of diverse populations to extend insights into the allelic architecture of complex traits.
Published: 2016
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41. Quantitative analysis of the intra- and inter-subject variability of the whole salivary proteome

Author: K. H. D. Dinh, Manuela Gesell-Salazar, Elke Hammer, Birte Holtfreter, Uwe Völker, Claudia Schurmann, Nico Jehmlich, Leif Steil, Vishnu M. Dhople, and Thomas Kocher
Subjects: Adult, Male, Proteomics, Saliva, Difference gel electrophoresis, Coefficient of variation, Biology, Bioinformatics, Statistics, Nonparametric, Liquid chromatography–mass spectrometry, Humans, Electrophoresis, Gel, Two-Dimensional, Salivary Proteins and Peptides, Whole saliva, Biomarker discovery, Analysis of Variance, Chromatography, Gene Expression Profiling, Genetic Variation, Middle Aged, Evaluation Studies as Topic, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Proteome, Periodontics, Female
Abstract: Background and Objective Interest in human saliva is increasing for disease-specific biomarker discovery studies. However, protein composition of whole saliva can grossly vary with physiological and environmental factors over time and it comprises human as well as bacterial proteins. Material and Methods We compared intra- and inter-subject variabilities using complementary gel-based (two-dimensional difference gel electrophoresis, 2-D DIGE) and gel-free (liquid chromatography tandem mass spectrometry, LC-MS/MS) proteomics profiling of saliva. Unstimulated whole saliva of four subjects was examined at three different time-points (08.00 h, 12.00 h and 17.00 h) and variability of the saliva proteome was analyzed on two successive days by LC-MS/MS. Results In the 2-D DIGE experiment, the median coefficient of variation (CV) for intra-subject variability was significantly lower (CV of 0.39) than that for inter-subject variability (CV of 0.57; CV of technical replicates 0.17). LC-MS/MS data confirmed the significantly lower variation within subjects over time (CV of 0.37) than the inter-subject variability (CV of 0.53; CV of technical replicates 0.11), and that the inter-subject variability was not time-dependent. Conclusion Both techniques revealed similar trends of variations on technical, intra- and inter-subject level but provided peptide and protein focused information and should thus be used as complementary approaches. The data presented indicate that 2-D DIGE as well as LC-MS/MS approaches are suitable for biomarker screening in saliva.
Published: 2012

42. Life and Death of Proteins: A Case Study of Glucose-starved Staphylococcus aureus

Author: Michael Hecker, Ulf Gerth, Rabea Schlüter, Martin Moche, Claudia Schurmann, Andreas Otto, Dörte Becher, Holger Kock, Michael Lalk, Hanna Meyer, Stephan Michalik, and Jörg Bernhardt
Subjects: Staphylococcus aureus, medicine.medical_treatment, Proteolysis, Citric Acid Cycle, Biology, Protein degradation, Biochemistry, Analytical Chemistry, Bacterial Proteins, medicine, Protein biosynthesis, Molecular Biology, chemistry.chemical_classification, Protease, medicine.diagnostic_test, Catabolism, Research, Gluconeogenesis, Wild type, Endopeptidase Clp, Gene Expression Regulation, Bacterial, Repressor Proteins, Citric acid cycle, Oxidative Stress, Glucose, Enzyme, chemistry, Protein Biosynthesis, Mutation
Abstract: The cellular amount of proteins not only depends on synthesis but also on degradation. Here, we expand the understanding of differential protein levels by complementing synthesis data with a proteome-wide, mass spectrometry-based stable isotope labeling with amino acids in cell culture analysis of protein degradation in the human pathogen Staphylococcus aureus during glucose starvation. Monitoring protein stability profiles in a wild type and an isogenic clpP protease mutant revealed that 1) proteolysis mainly affected proteins with vegetative functions, anabolic and selected catabolic enzymes, whereas the expression of TCA cycle and gluconeogenesis enzymes increased; 2) most proteins were prone to aggregation in the clpP mutant; 3) the absence of ClpP correlated with protein denaturation and oxidative stress responses, deregulation of virulence factors and a CodY repression. We suggest that degradation of redundant, inactive proteins disintegrated from functional complexes and thereby amenable to proteolytic attack is a fundamental cellular process in all organisms to regain nutrients and guarantee protein homeostasis.
Published: 2012

43. The androgen receptor CAG repeat polymorphism as a risk factor of low serum testosterone and its cardiometabolic effects in men

Author: Henri Wallaschofski, Florian Ernst, Claudia Schurmann, Henry Völzke, M Nauck, Georg Homuth, Uwe Völker, and Robin Haring
Subjects: medicine.medical_specialty, education.field_of_study, biology, Urology, Endocrinology, Diabetes and Metabolism, Population, Confidence interval, Sex hormone-binding globulin, Endocrinology, Reproductive Medicine, Quartile, Internal medicine, Relative risk, Study of Health in Pomerania, biology.protein, medicine, Risk factor, education, Body mass index
Abstract: Summary Previous studies reported correlations of CAG repeat length with sex hormone serum concentrations and cardiometabolic risk factors, but were limited by small cross-sectional samples. We used data of 1859 men aged 20–79 years from the population-based Study of Health in Pomerania (SHIP) to investigate the direct and modulating effects of CAG repeat length on androgen action and cardiometabolic risk factors. We performed cross-sectional and longitudinal linear and Poisson regression models adjusted for age, smoking, physical activity, alcohol consumption and body mass index. The CAG repeat length was categorized into quartiles and low total testosterone (TT) defined according to the age-specific (by decades) 10th percentile, respectively. Age-adjusted cross-sectional linear regression models showed a positive association between CAG repeat length and serum testosterone concentrations [β coefficient for TT, 0.099 (p = 0.028) and for free T, 0.002 (p = 0.001), respectively]. After a 5.0 year median follow-up period, men with CAG repeat length in the lowest quartile had an increased risk of incident low TT concentrations [relative risk (RR), 2.31; 95% confidence interval (CI), 1.18–4.55]. We found no direct association between CAG repeat length and cardiometabolic risk factors in cross-sectional and longitudinal multivariable linear regression analyses; whereas men with longer CAG repeat length and low TT concentrations showed the highest risk of incident MetS (RR, 1.51; 95% CI, 1.05–2.16). CAG repeat length is a risk factor of incident low TT concentrations and a contributing factor of testosterone-related cardiometabolic effects. The added clinical value of a combined assessment of CAG repeat length and serum TT concentrations merits further investigation.
Published: 2011

44. Extensive alterations of the whole-blood transcriptome are associated with body mass index: results of an mRNA profiling study involving two large population-based cohorts

Author: Katharina Schramm, Andreas Ziegler, Philipp S. Wild, Henry Völzke, Harald Grallert, Jochen Kruppa, Tanja Zeller, Julia Mayerle, Leif Steil, Christian Englbrecht, Claudia Schurmann, Carola Marzi, Eva Reinmaa, Simone Wahl, Henri Wallaschofski, Andres Metspalu, Annette Peters, Wolfgang Rathmann, Karlhans Endlich, Marcus Dörr, Christian P. Müller, Michael Roden, Stephan B. Felix, Arne Schillert, Christian Herder, Maren Carstensen, Matthias Nauck, Thomas Illig, Alexander Teumer, Christian Gieger, Uwe Völker, Rainer Rettig, Thomas Meitinger, Stefan Blankenberg, Georg Homuth, Holger Prokisch, Konstantin Strauch, and Ulrike Mäder
Subjects: Male, Reticulocytes, medicine.medical_treatment, Type 2 diabetes, Bioinformatics, Body Mass Index, Cohort Studies, Transcriptome, 0302 clinical medicine, Obesity, Oxidative stress, Insulin resistance, Insulin signaling, Transcriptome-wide association study (TWAS), Transcriptomics, BMI, Insulin, Genetics(clinical), Genetics (clinical), Aged, 80 and over, 2. Zero hunger, 0303 health sciences, education.field_of_study, biology, Middle Aged, ddc, 3. Good health, Blood, Female, Research Article, Signal Transduction, Population, 030209 endocrinology & metabolism, 03 medical and health sciences, Transcriptome-wide Association Study (twas), Bmi, Insulin Resistance, Type 2 Diabetes, Oxidative Stress, Insulin Signaling, Genetics, medicine, Humans, RNA, Messenger, education, Aged, 030304 developmental biology, Gene Expression Profiling, medicine.disease, Gene expression profiling, Insulin receptor, biology.protein, Metabolic syndrome, Reactive Oxygen Species
Abstract: Background Obesity, defined as pathologically increased body mass index (BMI), is strongly related to an increased risk for numerous common cardiovascular and metabolic diseases. It is particularly associated with insulin resistance, hyperglycemia, and systemic oxidative stress and represents the most important risk factor for type 2 diabetes (T2D). However, the pathophysiological mechanisms underlying these associations are still not completely understood. Therefore, in order to identify potentially disease-relevant BMI-associated gene expression signatures, a transcriptome-wide association study (TWAS) on BMI was performed. Methods Whole-blood mRNA levels determined by array-based transcriptional profiling were correlated with BMI in two large independent population-based cohort studies (KORA F4 and SHIP-TREND) comprising a total of 1977 individuals. Results Extensive alterations of the whole-blood transcriptome were associated with BMI: More than 3500 transcripts exhibited significant positive or negative BMI-correlation. Three major whole-blood gene expression signatures associated with increased BMI were identified. The three signatures suggested: i) a ratio shift from mature erythrocytes towards reticulocytes, ii) decreased expression of several genes essentially involved in the transmission and amplification of the insulin signal, and iii) reduced expression of several key genes involved in the defence against reactive oxygen species (ROS). Conclusions Whereas the first signature confirms published results, the other two provide possible mechanistic explanations for well-known epidemiological findings under conditions of increased BMI, namely attenuated insulin signaling and increased oxidative stress. The putatively causative BMI-dependent down-regulation of the expression of numerous genes on the mRNA level represents a novel finding. BMI-associated negative transcriptional regulation of insulin signaling and oxidative stress management provide new insights into the pathogenesis of metabolic syndrome and T2D. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0141-x) contains supplementary material, which is available to authorized users.
Published: 2015

45. A functional brain-derived neurotrophic factor (BDNF) gene variant increases the risk of moderate-to-severe allergic rhinitis

Author: Yang Yie Sio, Peng Jin, Tõnu Esko, Hans Joergen Grabe, Jianjun Liu, Furen Zhang, Jia Min Quek, Hong Liu, Fook Tim Chew, Liangdan Sun, Anis Larbi, Sri Anusha Matta, Bijin Au, Harm-Jan Westra, Li Shi, De Yun Wang, Claudia Schurmann, Anand Kumar Andiappan, Bani Kaur Suri, Xuejun Zhang, Astrid Irwanto, Michael Poidinger, Olaf Rötzschke, Lude Franke, Xin Xu, Bernett Lee, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), and Stem Cell Aging Leukemia and Lymphoma (SALL)
Subjects: Male, genetic association, AIRWAY INFLAMMATION, Gene Expression, neurotrophins, Severity of Illness Index, Cohort Studies, Neurotrophic factors, Genotype, Odds Ratio, Immunology and Allergy, ATOPIC-DERMATITIS, Child, Singapore, EPITHELIAL-CELLS, Middle Aged, Child, Preschool, DISEASES, Female, rs6265, PRODUCE NEUROTROPHINS, Adult, Risk, China, Adolescent, Immunology, Quantitative Trait Loci, moderate-to-severe allergic rhinitis, Single-nucleotide polymorphism, Biology, Polymorphism, Single Nucleotide, Brain-derived neurotrophic factor, Asian People, SNP, Humans, Genetic Predisposition to Disease, RNA, Messenger, Genetic association, CHINESE POPULATION, EOSINOPHILS, Singapore Chinese, ACTIVITY-DEPENDENT SECRETION, Immunoglobulin E, Rhinitis, Allergic, ASSOCIATION ANALYSIS, nervous system, Expression quantitative trait loci, ASTHMA
Abstract: Background Brain-derived neurotrophic factor (BDNF) is a secretory protein that has been implicated in the pathogenesis of allergic rhinitis (AR), atopic asthma, and eczema, but it is currently unknown whether BDNF polymorphisms influence susceptibility to moderate-to-severe AR. Objective We sought to identify disease associations and the functional effect of BDNF genetic variants in patients with moderate-to-severe AR. Methods Tagging single nucleotide polymorphisms (SNPs) spanning the BDNF gene were selected from the human HapMap Han Chinese from Beijing (CHB) data set, and associations with moderate-to-severe AR were assessed in 2 independent cohorts of Chinese patients (2216 from Shandong province and 1239 living in Singapore). The functional effects of the BDNF genetic variants were determined by using both in vitro and ex vivo assays. Results The tagging SNP rs10767664 was significantly associated with the risk of moderate-to-severe AR in both Singapore Chinese ( P = .0017; odds ratio, 1.324) and Shandong Chinese populations ( P = .039; odds ratio, 1.180). The coding nonsynonymous SNP rs6265 was in perfect linkage with rs10767664 and conferred increased BDNF protein secretion by a human cell line in vitro . Subjects bearing the AA genotype of rs10767664 exhibited increased risk of moderate-to-severe AR and displayed increased BDNF protein and total IgE levels in plasma. Using a large-scale expression quantitative trait locus study, we demonstrated that BDNF SNPs are significantly associated with altered BDNF concentrations in peripheral blood. Conclusion A common genetic variant of the BDNF gene is associated with increased risk of moderate-to-severe AR, and the AA genotype is associated with increased BDNF mRNA levels in peripheral blood. Together, these data indicate that functional BDNF gene variants increase the risk of moderate-to-severe AR.
Published: 2015

46. Cell Specific eQTL Analysis without Sorting Cells

Author: Julian C. Knight, Harm-Jan Westra, Joyce B. J. van Meurs, Ritsert C. Jansen, De Yun Wang, Christian Herder, Francesca Zolezzi, Uwe Völker, Michael Roden, Georg Homuth, Rinse K. Weersma, Jan H. Veldink, Konstantin Strauch, Benjamin P. Fairfax, Silva Kasela, Anis Larbi, Jingyuan Fu, Anand Kumar Andiappan, Veikko Salomaa, Markus Perola, Samuli Ripatti, Leonard H. van den Berg, Marjolein J. Peters, Yang Li, Olaf Rötzschke, Danny Arends, Tõnu Esko, Lili Milani, Bernett Lee, Harald Grallert, David Melzer, Fernando Rivadeneira, Albert Hofman, Eva Reinmaa, Andrew B. Singleton, Marijn C. Visschedijk, Astrid Petersmann, Lude Franke, Luigi Ferrucci, Andres Metspalu, Michael Poidinger, Holger Prokisch, Liina Tserel, Thomas Meitinger, Andrew R. Wood, Mathieu Platteel, Roberto Lorbeer, Katharina Schramm, André G. Uitterlinden, Rossella Melchiotti, Dena G. Hernandez, Hanieh Yaghootkar, Johannes Kettunen, Juha Karjalainen, Cisca Wijmenga, Claudia Schurmann, Seiko Makino, Pärt Peterson, Bioinformatics, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Center for Liver, Digestive and Metabolic Diseases (CLDM), Stem Cell Aging Leukemia and Lymphoma (SALL), Internal Medicine, Epidemiology, Dermatology, Institute for Molecular Medicine Finland, Clinicum, Samuli Olli Ripatti / Principal Investigator, Department of Public Health, Biostatistics Helsinki, Quantitative Genetics, and Complex Disease Genetics
Subjects: Cancer Research, BLOOD, Neutrophils, Nod2 Signaling Adaptor Protein, Genome-wide association study, VARIANTS, Meta-analysis, Gene expression, Monocytes, Blood, Genome-wide association studies, Principal component analysis, Gene mapping, 0302 clinical medicine, Crohn Disease, WIDE ASSOCIATION, HETEROGENEITY, Lymphocytes, DNA METHYLATION, Genetics (clinical), GENE-EXPRESSION, Genetics, Regulation of gene expression, Principal Component Analysis, 0303 health sciences, C100, C700, ACTIVE CROHNS-DISEASE, 3142 Public health care science, environmental and occupational health, 3. Good health, ddc, Phenotype, DNA methylation, Research Article, Cell type, lcsh:QH426-470, Quantitative Trait Loci, Locus (genetics), Single-nucleotide polymorphism, Quantitative trait locus, Biology, Polymorphism, Single Nucleotide, Cell Line, 03 medical and health sciences, Humans, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Reproducibility of Results, lcsh:Genetics, Gene Expression Regulation, Expression quantitative trait loci, 3111 Biomedicine, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL) mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a genome-environment interaction (GxE) meta-analysis on data from 5,683 samples to infer the cell type specificity of whole blood cis-eQTLs. We demonstrate that this method is able to predict neutrophil and lymphocyte specific cis-eQTLs and replicate these predictions in independent cell-type specific datasets. Finally, we show that SNPs associated with Crohn’s disease preferentially affect gene expression within neutrophils, including the archetypal NOD2 locus., Author Summary Many variants in the genome, including variants associated with disease, affect the expression of genes. These so-called expression quantitative trait loci (eQTL) can be used to gain insight in the downstream consequences of disease. While it has been shown that many disease-associated variants alter gene expression in a cell-type dependent manner, eQTL datasets for specific cell types may not always be available and their sample size is often limited. We present a method that is able to detect cell type specific effects within eQTL datasets that have been generated from whole tissues (which may be composed of many cell types), in our case whole blood. By combining numerous whole blood datasets through meta-analysis, we show that we are able to detect eQTL effects that are specific for neutrophils and lymphocytes (two blood cell types). Additionally, we show that the variants associated with some diseases may preferentially alter the gene expression in one of these cell types. We conclude that our method is an alternative method to detect cell type specific eQTL effects, that may complement generating cell type specific eQTL datasets and that may be applied on other cell types and tissues as well.
Published: 2015

47. Burden analysis of rare microdeletions suggests a strong impact of neurodevelopmental genes in genetic generalised epilepsies

Author: Dennis Lal, Ann-Kathrin Ruppert, Holger Trucks, Herbert Schulz, Carolien G de Kovel, Dorothée Kasteleijn-Nolst Trenité, Anja C M Sonsma, Bobby P Koeleman, Dick Lindhout, Yvonne G Weber, Holger Lerche, Claudia Kapser, Christoph J Schankin, Wolfram S Kunz, Rainer Surges, Christian E Elger, Verena Gaus, Bettina Schmitz, Ingo Helbig, Hiltrud Muhle, Ulrich Stephani, Karl M Klein, Felix Rosenow, Bernd A Neubauer, Eva M Reinthaler, Fritz Zimprich, Martha Feucht, Rikke S Møller, Helle Hjalgrim, Peter De Jonghe, Arvid Suls, Wolfgang Lieb, Andre Franke, Konstantin Strauch, Christian Gieger, Claudia Schurmann, Ulf Schminke, Peter Nürnberg, EPICURE Consortium, Thomas Sander, and EPICURE Consortium
Subjects: Male, Cancer Research, INTELLECTUAL DISABILITY, Genome-wide association study, QH426-470, Bioinformatics, 16P13.11 PREDISPOSE, Cohort Studies, 0302 clinical medicine, OF-FUNCTION MUTATIONS, Copy-number variation, Child, Non-U.S. Gov't, Genetics (clinical), Sequence Deletion, Genetics, Gene Rearrangement, COPY NUMBER VARIANTS, 0303 health sciences, DEVELOPMENTAL DELAY, COMMON EPILEPSIES, Research Support, Non-U.S. Gov't, 3. Good health, Epilepsy, Generalized, Female, Research Article, Adult, medicine.medical_specialty, Adolescent, DNA Copy Number Variations, 15Q13.3 MICRODELETIONS, Biology, Research Support, Polymorphism, Single Nucleotide, 03 medical and health sciences, Young Adult, Molecular genetics, medicine, Genetic predisposition, Journal Article, SNP, Humans, Protein Interaction Domains and Motifs, ddc:610, GENOME-WIDE ASSOCIATION, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Genetic Association Studies, 030304 developmental biology, EPILEPTIC ENCEPHALOPATHY, Genome, Human, AUTISM SPECTRUM DISORDER, Case-control study, Gene rearrangement, Human genetics, Neurodevelopmental Disorders, Case-Control Studies, Human medicine, 030217 neurology & neurosurgery
Abstract: Genetic generalised epilepsy (GGE) is the most common form of genetic epilepsy, accounting for 20% of all epilepsies. Genomic copy number variations (CNVs) constitute important genetic risk factors of common GGE syndromes. In our present genome-wide burden analysis, large (≥ 400 kb) and rare (< 1%) autosomal microdeletions with high calling confidence (≥ 200 markers) were assessed by the Affymetrix SNP 6.0 array in European case-control cohorts of 1,366 GGE patients and 5,234 ancestry-matched controls. We aimed to: 1) assess the microdeletion burden in common GGE syndromes, 2) estimate the relative contribution of recurrent microdeletions at genomic rearrangement hotspots and non-recurrent microdeletions, and 3) identify potential candidate genes for GGE. We found a significant excess of microdeletions in 7.3% of GGE patients compared to 4.0% in controls (P = 1.8 x 10-7; OR = 1.9). Recurrent microdeletions at seven known genomic hotspots accounted for 36.9% of all microdeletions identified in the GGE cohort and showed a 7.5-fold increased burden (P = 2.6 x 10-17) relative to controls. Microdeletions affecting either a gene previously implicated in neurodevelopmental disorders (P = 8.0 x 10-18, OR = 4.6) or an evolutionarily conserved brain-expressed gene related to autism spectrum disorder (P = 1.3 x 10-12, OR = 4.1) were significantly enriched in the GGE patients. Microdeletions found only in GGE patients harboured a high proportion of genes previously associated with epilepsy and neuropsychiatric disorders (NRXN1, RBFOX1, PCDH7, KCNA2, EPM2A, RORB, PLCB1). Our results demonstrate that the significantly increased burden of large and rare microdeletions in GGE patients is largely confined to recurrent hotspot microdeletions and microdeletions affecting neurodevelopmental genes, suggesting a strong impact of fundamental neurodevelopmental processes in the pathogenesis of common GGE syndromes., Author Summary Epilepsy affects about 4% of the general population during lifetime. The genetic generalised epilepsies (GGEs) represent the most common group of epilepsies with predominant genetic aetiology, accounting for 20% of all epilepsies. Despite their strong heritability, the genetic basis of the majority of patients with GGE remains elusive. Genomic microdeletions constitute a significant source of genetic risk factors for epilepsies. The present genome-wide burden analysis in 1,366 European patients with GGE and 5,234 ancestry-matched controls explored the role of large and rare microdeletions (size ≥ 400 kb, frequency < 1%) in the complex genetic architecture of common GGE syndromes. Our results revealed a 2-fold excess of microdeletions in GGE patients relative to the population controls, 2) a 7-fold increased burden for known hotspot microdeletions (15q11.2, 15q13.3, 16p13.11, 22q11.2) previously associated with a wide range of neurodevelopmental disorders, and 3) a more than 4-fold enrichment of microdeletions carrying a gene implicated in neurodevelopmental disorders. Our findings reinforce emerging evidence that genes affected by microdeletions in GGE patients have a strong impact in fundamental neurodevelopmental processes and dissect novel candidate genes involved in epileptogenesis.
Published: 2015

48. A Meta-analysis of Gene Expression Signatures of Blood Pressure and Hypertension

Author: Benjamin Voight, Mark Caulfield, Wiek Van Gilst, Ruth Loos, Cristiano FAVA, Joyce Van Meurs, Nicole Glazer, Valur Emilsson, Alan Shuldiner, Andrew Taylor, Nicole Soranzo, Ozren Polasek, Stefania Bandinelli, Jan A. Staessen, ROBERTO ELOSUA, FULVIO RICCERI, Peter P Pramstaller, Lili Milani, ANGELO SCUTERI, Maris Laan, Gavin Lucas, E Shyong Tai, Aroon Hingorani, Michael Marmot, Thor Aspelund, Mika Kivimaki, María Soler Artigas, Mika Ala-Korpela, Uwe Völker, Mika Kähönen, Tomonori Okamura, Marcus Dörr, Giuseppe MATULLO, Yvonne Van der Schouw, Luke Pilling, Andrew Wong, Alanna Morrison, George Davey Smith, Holger Prokisch, Francesco Mattace-Raso, Margus Viigimaa, Peter Würtz, Fadi Charchar, Alena Yaluri, Annette Peters, Janoš Terzić, Jeanette Erdmann, Maciej Tomaszewski, Tonu Esko, Martin Tobin, David Melzer, Dorairaj Prabhakaran, Sudha Seshadri, Tom Gaunt, Giriraj Ratan Chandak, Takayoshi Ohkubo, Louise Wain, Tanja Zeller, Mark Seielstad, Jemma Hopewell, Thomas Meitinger, Thomas Wang, Abbas Dehghan, Albert Vernon Smith, Pankaj Arora, Susana Eyheramendy, Ioanna Tzoulaki, Vasan Ramachandran, Najaf Amin, Claudia Schurmann, Xueling Sim, Daniel Levy, Internal Medicine, Epidemiology, Dermatology, Esko, Tõnu [0000-0003-1982-6569], Pilling, Luke C [0000-0002-3332-8454], Schurmann, Claudia [0000-0003-4158-9192], Milani, Lili [0000-0002-5323-3102], Wang, Richard [0000-0003-4063-6508], Dehghan, Abbas [0000-0001-6403-016X], Melzer, David [0000-0002-0170-3838], Meitinger, Thomas [0000-0002-8838-8403], Dörr, Marcus [0000-0001-7471-475X], Zeller, Tanja [0000-0003-3379-2641], Prokisch, Holger [0000-0003-2379-6286], Völker, Uwe [0000-0002-5689-3448], Levy, Daniel [0000-0003-1843-8724], Apollo - University of Cambridge Repository, McCarthy, Mark I, Department of Neuroscience and Biomedical Engineering, Aalto-yliopisto, and Aalto University
Subjects: Aging, Cancer Research, Genome-wide association study, Blood Pressure, 030204 cardiovascular system & hematology, Cardiovascular, 0302 clinical medicine, Clinical genetics, Medicine and health sciences, Drug research and development, Genome-wide association studies, Gene expression, Research laboratories, Cardiology, Genetic epidemiology, 2.1 Biological and endogenous factors, Aetiology, Genetics (clinical), Genetics, Regulation of gene expression, Genetics & Heredity, 0303 health sciences, International Consortium for Blood Pressure GWAS (ICBP), Single Nucleotide, Phenotype, POTASSIUM, 3. Good health, ddc, TRIALS, Hypertension, Life Sciences & Biomedicine, Biotechnology, Research Article, International Consortium for Blood Pressure GWAS, lcsh:QH426-470, Genotype, Single-nucleotide polymorphism, Biology, PERIPHERAL-BLOOD, PROFILE, Polymorphism, Single Nucleotide, 03 medical and health sciences, MICROARRAY ANALYSIS, Humans, Genetic Predisposition to Disease, Polymorphism, GENOME-WIDE ASSOCIATION, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Genetic association, 0604 Genetics, Science & Technology, Prevention, Human Genome, ta1182, PREVENTION, gene expression, blood pressure, hypertension, SODIUM, lcsh:Genetics, MICE, Gene Expression Regulation, CELLS, Transcriptome, Developmental Biology, Genome-Wide Association Study
Abstract: Genome-wide association studies (GWAS) have uncovered numerous genetic variants (SNPs) that are associated with blood pressure (BP). Genetic variants may lead to BP changes by acting on intermediate molecular phenotypes such as coded protein sequence or gene expression, which in turn affect BP variability. Therefore, characterizing genes whose expression is associated with BP may reveal cellular processes involved in BP regulation and uncover how transcripts mediate genetic and environmental effects on BP variability. A meta-analysis of results from six studies of global gene expression profiles of BP and hypertension in whole blood was performed in 7017 individuals who were not receiving antihypertensive drug treatment. We identified 34 genes that were differentially expressed in relation to BP (Bonferroni-corrected p, Author Summary The focus of blood pressure (BP) GWAS has been the identification of common DNA sequence variants associated with the phenotype; this approach provides only one dimension of molecular information about BP. While it is a critical dimension, analyzing DNA variation alone is not sufficient for achieving an understanding of the multidimensional complexity of BP physiology. The top loci identified by GWAS explain only about 1 percent of inter-individual BP variability. In this study, we performed a meta-analysis of gene expression profiles in relation to BP and hypertension in 7017 individuals from six studies. We identified 34 differentially expressed genes for BP, and discovered that the top BP signature genes explain 5%–9% of BP variability. We further linked BP gene expression signature genes with BP GWAS results by integrating expression associated SNPs (eSNPs) and discovered that one of the top BP loci from GWAS, rs3184504 in SH2B3, is a trans regulator of expression of 6 of the top 34 BP signature genes. Our study, in conjunction with prior GWAS, provides a deeper understanding of the molecular and genetic basis of BP regulation, and identifies several potential targets and pathways for the treatment and prevention of hypertension and its sequelae.
Published: 2015
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49. Associations between Serum Sex Hormone Concentrations and Whole Blood Gene Expression Profiles in the General Population

Author: Henri Wallaschofski, Robin Haring, Henry Völzke, Leif Steil, Georg Homuth, Uwe Völker, Brian G. Keevil, Claudia Schurmann, and Matthias Nauck
Subjects: Adult, Male, Estrone, Population, lcsh:Medicine, Genome-wide association study, Bioinformatics, Body Mass Index, Transcriptome, Young Adult, Sex hormone-binding globulin, Sex Hormone-Binding Globulin, Medicine, Humans, Testosterone, education, lcsh:Science, Whole blood, Aged, education.field_of_study, Multidisciplinary, biology, Estradiol, business.industry, Dehydroepiandrosterone Sulfate, lcsh:R, Age Factors, Androstenedione, Middle Aged, biology.protein, Female, lcsh:Q, business, Body mass index, Hormone, Research Article
Abstract: Background Despite observational evidence from epidemiological and clinical studies associating sex hormones with various cardiometabolic risk factors or diseases, pathophysiological explanations are sparse to date. To reveal putative functional insights, we analyzed associations between sex hormone levels and whole blood gene expression profiles. Methods We used data of 991 individuals from the population-based Study of Health in Pomerania (SHIP-TREND) with whole blood gene expression levels determined by array-based transcriptional profiling and serum concentrations of total testosterone (TT), sex hormone-binding globulin (SHBG), free testosterone (free T), dehydroepiandrosterone sulfate (DHEAS), androstenedione (AD), estradiol (E2), and estrone (E1) measured by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and immunoassay. Associations between sex hormone concentrations and gene expression profiles were analyzed using sex-specific regression models adjusted for age, body mass index, and technical covariables. Results In men, positive correlations were detected between AD and DDIT4 mRNA levels, as well as between SHBG and the mRNA levels of RPIA, RIOK3, GYPB, BPGM, and RAB2B. No additional significant associations were observed. Conclusions Besides the associations between AD and DDIT4 expression and SHBG and the transcript levels of RPIA, RIOK3, GYPB, BPGM, and RAB2B, the present study did not indicate any association between sex hormone concentrations and whole blood gene expression profiles in men and women from the general population.
Published: 2015

50. The transcriptional landscape of age in human peripheral blood

Author: Russell P. Tracy, Nilesh J. Samani, Pascal P. Arp, Stefania Bandinelli, Anjali K. Henders, Karen N. Conneely, Sarah Williams-Blangero, John Hardy, Ingrid Meulenbelt, Henry Völzke, Stephen T. Turner, Astrid Suchy-Dicey, Peter M. Visscher, Yongmei Liu, Robert L. Johnson, Hans J. Grabe, Robert Walker, Dena G. Hernandez, Mike A. Nalls, Matthew P. Johnson, Katharina Schramm, Yolande F. M. Ramos, Jack W. Kent, Jingzhong Ding, Juan C. Troncoso, P. Eline Slagboom, Markus Perola, Sayuko Kobes, Michael Roden, Sharon L.R. Kardia, Lisa J. Oyston, Nicholas G. Martin, John Blangero, Mina Ryten, Quinta Helmer, Elisabeth B. Binder, Michael E. Weale, Mila Jhamai, Marjolein J. Peters, Pärt Peterson, Veryan Codd, Michael M. P. J. Verbiest, Yana A. Wilson, K. Maria Nylocks, Georg Homuth, Jennifer A. Brody, Daniel A. Enquobahrie, Allissa Dillman, Jerome I. Rotter, Joseph E. Powell, Thomas Kocher, Ronald H. Zielke, Taru Tukiainen, Daniah Trabzuni, Divya Mehta, Anna Murray, Lude Franke, Richard O'Brien, Philip L. De Jager, Torsten Klengel, David Melzer, Harald H H Göring, Holger Prokisch, George L. Sutphin, Peter J. Munson, Alan B. Zonderman, Luke C. Pilling, Sina A. Gharib, Noman Bakhshi, André G. Uitterlinden, Linda Broer, Adaikalavan Ramasamy, Qiao-Ping Wang, Elizabeth M. Kennedy, Paula Singmann, Cavin K. Ward-Caviness, Sonja Zeilinger, Joanne M. Murabito, Roby Joehanes, Jennifer A. Smith, Harm-Jan Westra, Colin Smith, Abraham Aviv, Bryan J. Traynor, Jeanine J. Houwing-Duistermaat, Thomas Illig, Dan L. Longo, Eric K. Moses, Claudia Schurmann, Liina Tserel, Albert Hofman, Wouter den Hollander, Grant W. Montgomery, Eva Reinmaa, Samuli Ripatti, Andrew B. Singleton, Alexandra Zhernakova, Marcel P. van der Brug, Annette Peters, Silva Kasela, Kerry J. Ressler, Alicia K. Smith, Joanne E. Curran, Lisette Stolk, Joyce B. J. van Meurs, Jeroen van Rooij, Tõnu Esko, Iiris Hovatta, Myriam Fornage, Barbara E. Stranger, Hanieh Yaghootkar, Leif Steil, Luigi Ferrucci, Johannes Kettunen, Mark R. Cookson, Alexander Teumer, Ron Korstanje, Bruce M. Psaty, Tianxiao Huan, Andres Metspalu, Christian Herder, Shannon Bean, Jian Yang, Lili Milani, Fernando Rivadeneira, Allan F. McRae, Veikko Salomaa, Towfique Raj, Yii-Der Ida Chen, Robert L. Hanson, G. Gregory Neely, Daniel Levy, Raphael Gibbs, Andrew D. Johnson, Sampath Arepalli, Margreet Kloppenburg, Melanie Waldenberger, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Translational Immunology Groningen (TRIGR), Stem Cell Aging Leukemia and Lymphoma (SALL), Internal Medicine, Epidemiology, Dermatology, Institute for Molecular Medicine Finland, Biosciences, Genetics, Iiris Hovatta / Principal Investigator, Clinicum, Samuli Olli Ripatti / Principal Investigator, Department of Public Health, Biostatistics Helsinki, Quantitative Genetics, and Complex Disease Genetics
Subjects: Aging, General Physics and Astronomy, Genome-wide association study, Biology, Article, White People, DISEASE, General Biochemistry, Genetics and Molecular Biology, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Gene expression, Humans, Epigenetics, GENOME-WIDE ASSOCIATION, OXIDATIVE STRESS, CELL-TYPES, Gene, LIFE-SPAN, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, Gene Expression Profiling, METHYLATION, General Chemistry, DNA Methylation, GENE-EXPRESSION CHANGES, ddc, Gene expression profiling, DROSOPHILA-MELANOGASTER, Ageing, DNA methylation, 3111 Biomedicine, CAENORHABDITIS-ELEGANS, Biomarkers, HUMAN LONGEVITY, 030217 neurology & neurosurgery
Abstract: Disease incidences increase with age, but the molecular characteristics of ageing that lead to increased disease susceptibility remain inadequately understood. Here we perform a whole-blood gene expression meta-analysis in 14,983 individuals of European ancestry (including replication) and identify 1,497 genes that are differentially expressed with chronological age. The age-associated genes do not harbor more age-associated CpG-methylation sites than other genes, but are instead enriched for the presence of potentially functional CpG-methylation sites in enhancer and insulator regions that associate with both chronological age and gene expression levels. We further used the gene expression profiles to calculate the ‘transcriptomic age' of an individual, and show that differences between transcriptomic age and chronological age are associated with biological features linked to ageing, such as blood pressure, cholesterol levels, fasting glucose, and body mass index. The transcriptomic prediction model adds biological relevance and complements existing epigenetic prediction models, and can be used by others to calculate transcriptomic age in external cohorts., Ageing increases the risk of many diseases. Here the authors compare blood cell transcriptomes of over 14,000 individuals and identify a set of about 1,500 genes that are differently expressed with age, shedding light on transcriptional programs linked to the ageing process and age-associated diseases.
Published: 2015

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