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1. Discovery and prioritization of variants and genes for kidney function in >1.2 million individuals

Author

John Michael Gaziano, Snehal Patil, Cassiane Robinson-Cohen, Thomas W. Winkler, Humaira Rasheed, Anna Köttgen, Christopher J. O'Donnell, Sarah E. Graham, Stein Hallan, Brett R Vanderweff, Kira J Stanzick, Cristian Pattaro, Matthias Wuttke, Bjørn Olav Åsvold, Iris M. Heid, Adriana M. Hung, Bryce X Rowan, Pascal Schlosser, Klaus Stark, VA Million Veteran Program, Cristen J. Willer, André Gessner, Yong Li, Mathias Gorski, and Laurent F. Thomas

Subjects
0301 basic medicine, Science, Quantitative Trait Loci, 610 Medizin, General Physics and Astronomy, Renal function, Genome-wide association study, RNA-Seq, Computational biology, Biology, Quantitative trait locus, Kidney, Genome-wide association studies, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Risk Factors, Chronic kidney disease, Genetics research, Databases, Genetic, medicine, Humans, Genetic Predisposition to Disease, Renal Insufficiency, Chronic, Gene, Genetic association, ddc:610, Multidisciplinary, Kidney metabolism, General Chemistry, medicine.disease, Cystatins, Europe, 030104 developmental biology, Gene Expression Regulation, Organ Specificity, Creatinine, Single-Cell Analysis, Biomarkers, 030217 neurology & neurosurgery, Genome-Wide Association Study, Glomerular Filtration Rate, Kidney disease
Abstract

Genes underneath signals from genome-wide association studies (GWAS) for kidney function are promising targets for functional studies, but prioritizing variants and genes is challenging. By GWAS meta-analysis for creatinine-based estimated glomerular filtration rate (eGFR) from the Chronic Kidney Disease Genetics Consortium and UK Biobank (n = 1,201,909), we expand the number of eGFRcrea loci (424 loci, 201 novel; 9.8% eGFRcrea variance explained by 634 independent signal variants). Our increased sample size in fine-mapping (n = 1,004,040, European) more than doubles the number of signals with resolved fine-mapping (99% credible sets down to 1 variant for 44 signals, ≤5 variants for 138 signals). Cystatin-based eGFR and/or blood urea nitrogen association support 348 loci (n = 460,826 and 852,678, respectively). Our customizable tool for Gene PrioritiSation reveals 23 compelling genes including mechanistic insights and enables navigation through genes and variants likely relevant for kidney function in human to help select targets for experimental follow-up., Identifying causal variants and genes in genome-wide association studies remains a challenge, an issue that is ameliorated with larger sample sizes. Here the authors meta-analyze kidney function genome-wide association studies to identify new loci and fine-map loci to home in on variants and genes involved in kidney function.

Published
2021

2. Genetic analysis in European ancestry individuals identifies 517 loci associated with liver enzymes

Author

Stephen R. Atkinson, Philip S. Tsao, Evangelos Evangelou, VA Million Veteran Program, Karl-Heinz Herzig, David E. Kaplan, Marina Serper, Behrooz Z. Alizadeh, Benjamin F. Voight, Xiyun Jiang, Julie A. Lynch, Dipender Gill, Danish Saleheen, Marjo-Riitta Järvelin, André G. Uitterlinden, Rui Pinto, Raha Pazoki, Peter J. van der Most, Paul Elliott, Verena Zuber, Matthias Farlik, Ioanna Tzoulaki, Mark Thursz, Harold Snieder, Marijana Vujkovic, Christopher J. O'Donnell, Mohsen Ghanbari, Kyung Min Lee, Saredo Said, Matthias Wielscher, Kyong-Mi Chang, M. Arfan Ikram, Joshua Elliott, Rotonya M. Carr, Robert J. de Knegt, Abbas Dehghan, Life Course Epidemiology (LCE), Real World Studies in PharmacoEpidemiology, -Genetics, -Economics and -Therapy (PEGET), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Restoring Organ Function by Means of Regenerative Medicine (REGENERATE), Damage and Repair in Cancer Development and Cancer Treatment (DARE), Medical Research Council (MRC), Epidemiology, Gastroenterology & Hepatology, and Internal Medicine

Subjects
Enzymologic, Male, 0301 basic medicine, LD SCORE REGRESSION, General Physics and Astronomy, Physiology, Genome-wide association study, Cardiovascular, Oral and gastrointestinal, DISEASE, Cohort Studies, Rotterdam Study, 0302 clinical medicine, Risk Factors, Databases, Genetic, 2.1 Biological and endogenous factors, Aetiology, POPULATION, RISK, education.field_of_study, Multidisciplinary, biology, medicine.diagnostic_test, HERITABILITY, Liver Disease, Alanine Transaminase, gamma-Glutamyltransferase, Single Nucleotide, Middle Aged, Heart Disease, Liver, Cardiovascular Diseases, VA Million Veteran Program, MENDELIAN RANDOMIZATION, Female, 030211 gastroenterology & hepatology, HEALTH, Science, Population, Single-nucleotide polymorphism, BIOBANK, Polymorphism, Single Nucleotide, Gene Expression Regulation, Enzymologic, White People, General Biochemistry, Genetics and Molecular Biology, Databases, 03 medical and health sciences, Insulin resistance, Metabolic Diseases, Genetic, Lifelines Cohort Study, SDG 3 - Good Health and Well-being, Mendelian randomization, Genetics, medicine, Humans, Genetic Predisposition to Disease, Genetic Testing, Polymorphism, GENOME-WIDE ASSOCIATION, education, Metabolic and endocrine, METAANALYSIS, Aged, Genetic testing, business.industry, General Chemistry, Mendelian Randomization Analysis, Alkaline Phosphatase, Lipid Metabolism, medicine.disease, Good Health and Well Being, 030104 developmental biology, Gene Expression Regulation, Alanine transaminase, biology.protein, Insulin Resistance, Digestive Diseases, business, Genome-Wide Association Study
Abstract

Plasma levels of liver enzymes provide insights into hepatic function and related diseases. Here, the authors perform a genome-wide association study on three liver enzymes, identifying genetic variants associated with their plasma concentration as well as links to metabolic and cardiovascular diseases.Serum concentration of hepatic enzymes are linked to liver dysfunction, metabolic and cardiovascular diseases. We perform genetic analysis on serum levels of alanine transaminase (ALT), alkaline phosphatase (ALP) and gamma-glutamyl transferase (GGT) using data on 437,438 UK Biobank participants. Replication in 315,572 individuals from European descent from the Million Veteran Program, Rotterdam Study and Lifeline study confirms 517 liver enzyme SNPs. Genetic risk score analysis using the identified SNPs is strongly associated with serum activity of liver enzymes in two independent European descent studies (The Airwave Health Monitoring study and the Northern Finland Birth Cohort 1966). Gene-set enrichment analysis using the identified SNPs highlights involvement in liver development and function, lipid metabolism, insulin resistance, and vascular formation. Mendelian randomization analysis shows association of liver enzyme variants with coronary heart disease and ischemic stroke. Genetic risk score for elevated serum activity of liver enzymes is associated with higher fat percentage of body, trunk, and liver and body mass index. Our study highlights the role of molecular pathways regulated by the liver in metabolic disorders and cardiovascular disease.

Published
2021

3. Chromosome 1q21.2 and additional loci influence risk of spontaneous coronary artery dissection and myocardial infarction

Author

Liam R. Brunham, Chad M. Brummett, Natalia Fendrikova-Mahlay, Million Veteran Program, Chang Xu, Christopher J. O'Donnell, Catherine Tcheandjieu, Kristina L. Hunker, Ellen M. Schmidt, Kirby Swan, Jacqueline Saw, Heather L. Gornik, Themistocles L. Assimes, Dawn M. Coleman, Sebastian Zoellner, Mark Trinder, Isabelle Birt, Jun Li, Xiang Zhou, Andrew Starovoytov, Michael R. Mathis, Santhi K. Ganesh, Min-Lee Yang, Alexander Katz, Linda A. Jackson, James C. Stanley, and Matthew Zawistowski

Subjects
0301 basic medicine, Carotid Artery Diseases, Male, Coronary Vessel Anomalies, Myocardial Infarction, General Physics and Astronomy, 02 engineering and technology, Fibromuscular dysplasia, Coronary Artery Disease, Coronary artery disease, Cohort Studies, ADAMTS Proteins, Risk Factors, Fibromuscular Dysplasia, Myocardial infarction, Genetic risk, lcsh:Science, Multidisciplinary, Microfilament Proteins, 021001 nanoscience & nanotechnology, Cardiology, Female, 0210 nano-technology, Low Density Lipoprotein Receptor-Related Protein-1, medicine.medical_specialty, Science, Lower risk, General Biochemistry, Genetics and Molecular Biology, Article, Chromosomes, 03 medical and health sciences, Meta-Analysis as Topic, Internal medicine, medicine, Humans, Vascular Diseases, Artery dissection, business.industry, Chromosome, General Chemistry, Cardiovascular genetics, medicine.disease, Computational biology and bioinformatics, 030104 developmental biology, lcsh:Q, Scad, business, Genes, Neoplasm, Genome-Wide Association Study
Abstract

Spontaneous coronary artery dissection (SCAD) is a non-atherosclerotic cause of myocardial infarction (MI), typically in young women. We undertook a genome-wide association study of SCAD (Ncases = 270/Ncontrols = 5,263) and identified and replicated an association of rs12740679 at chromosome 1q21.2 (Pdiscovery+replication = 2.19 × 10−12, OR = 1.8) influencing ADAMTSL4 expression. Meta-analysis of discovery and replication samples identified associations with P, Spontaneous coronary artery dissection (SCAD) is a cause of myocardial infarction Here, the authors present a genome-wide association study of SCAD, finding an association at 1q21.2 which potentially affects expression of ADAMTSL4.

Published
2020
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4. Genetic architecture of heart failure with preserved versus reduced ejection fraction

Author

Jacob, Joseph, Chang, Liu, Qin, Hui, Krishna, Aragam, Zeyuan, Wang, Brian, Charest, Jennifer E, Huffman, Jacob M, Keaton, Todd L, Edwards, Serkalem, Demissie, Luc, Djousse, Juan P, Casas, J Michael, Gaziano, Kelly, Cho, Peter W F, Wilson, Lawrence S, Phillips, and Christopher J, O'Donnell

Abstract

Pharmacologic clinical trials for heart failure with preserved ejection fraction have been largely unsuccessful as compared to those for heart failure with reduced ejection fraction. Whether differences in the genetic underpinnings of these major heart failure subtypes may provide insights into the disparate outcomes of clinical trials remains unknown. We utilize a large, uniformly phenotyped, single cohort of heart failure sub-classified into heart failure with reduced and with preserved ejection fractions based on current clinical definitions, to conduct detailed genetic analyses of the two heart failure sub-types. We find different genetic architectures and distinct genetic association profiles between heart failure with reduced and with preserved ejection fraction suggesting differences in underlying pathobiology. The modest genetic discovery for heart failure with preserved ejection fraction (one locus) compared to heart failure with reduced ejection fraction (13 loci) despite comparable sample sizes indicates that clinically defined heart failure with preserved ejection fraction likely represents the amalgamation of several, distinct pathobiological entities. Development of consensus sub-phenotyping of heart failure with preserved ejection fraction is paramount to better dissect the underlying genetic signals and contributors to this highly prevalent condition.

Published
2022

5. 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
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6. Erratum

Author

Deepali Jaju, Melanie Neijts, Gabrielle Boucher, Arpi Minassian, James D. Stewart, Andreas Voss, Pim van der Harst, Duanping Liao, Joshua C. Bis, Kari E. North, Matteo Barcella, Michel G. Nivard, Jitender Kumar, Andrew Wong, Dewleen G. Baker, G. Ehret, Sulayma Albarwani, Kathleen F. Kerr, Quenna Wong, Ville Huikari, Alexander Kluttig, Andrew P. Morris, Eco J. C. de Geus, Albertine J. Oldehinkel, Ann-Christine Syvänen, Martina Mueller-Nurasyid, Yong Li, Marcel den Hoed, Henning Tiemeier, Henriette E. Meyer zu Schwabedissen, Dorret I. Boomsma, Joop D. Lefrandt, Mohammad Hadi Zafarmand, Victoria B. Risbrough, Halina Greiser, Bruce M. Psaty, Oscar H. Franco, Niek Verweij, Cees A. Swenne, Antti M. Kiviniemi, Konstantin Strauch, Markus Juonala, Zhu Ming Zhang, Nicholas L. Smith, Olli T. Raitakari, Daiane Hemerich, Daniel T. O'Connor, Christopher J. O'Donnell, Riad Bayoumi, Peter Friberg, Alvaro Alonso, Julian F. Thayer, Caroline M. Nievergelt, Delilah Zabaneh, Steven A. Lubitz, Tomas Axelsson, Terho Lehtimäki, Daniele Cusi, Eric A. Whitsel, Arie M. van Roon, Kjell Nikus, Bruno H. Stricker, Bouwe P. Krijthe, Stefan Kääb, Lars Lind, Abdel Abdellaoui, Timothy A. Thornton, Anubha Mahajan, Johan Sundström, Nona Sotoodehnia, Charles Kooperberg, Moritz F. Sinner, Leo-Pekka Lyytikäinen, Xavier Jouven, Tanja G. M. Vrijkotte, Sander W. van der Laan, Tatiana Kuznetsova, Patrick T. Ellinor, Alexander P. Reiner, Ilja M. Nolte, Marian C. Limacher, Paul I.W. de Bakker, Ahmad Vaez, Albert Hofman, Meena Kumari, Folkert W. Asselbergs, Juhani Junttila, Bram Dierckx, Marjo-Riitta Järvelin, Ingrid E. Christophersen, Annie Britton, Cathy C. Laurie, Phyllis K. Stein, Katarzyna Stolarz-Skrzypek, Juha Auvinen, Alexander Teumer, Vilmantas Giedraitis, Foram N. Ashar, Jenny van Dongen, David S. Siscovick, Markku Eskola, Jussi Hernesniemi, Janine F. Felix, M. Loretto Munoz, Jessica van Setten, Yun Li, Bianca J. J. M. Brundel, Christine M. Albert, Annette Peters, Jerome I. Rotter, Nina Hutri-Kähönen, Mark A. Geyer, Lesley E. Tinker, Vinicius Tragante, Susan R. Heckbert, Alan B. Zonderman, John D. Rioux, Kent D. Taylor, Shih-Jen Hwang, Johan Ormel, Mike A. Nalls, Erik Ingelsson, Kirk C. Wilhelmsen, John S. Floras, Diana Kuh, Elsayed Z. Soliman, Henry J. Lin, Brenda W.J.H. Penninx, Mika Kivimäki, Maaike G. J. Gademan, Jouke-Jan Hottenga, Mika Kähönen, Gerjan Navis, Siegfried Perz, Tamar Sofer, Catharina A. Hartman, Barbara McKnight, Jan A. Kors, Rick Jansen, Melanie Waldenberger, Nina Mononen, Heikki V. Huikuri, Azmeraw T. Amare, Mohammad L. Hassan, Jan A. Staessen, Adam X. Maihofer, Erika Salvi, Rob J. Bieringa, Benedikt von der Heyde, Andrea Dietrich, Peter J. van der Most, Philippe Goyette, Harriëtte Riese, Michele K. Evans, Stephanie M. Gogarten, Jean-Claude Tardif, Harold Snieder, Adrienne M. Stilp, Christy L. Avery, Johannes H. Smit, Gonneke Willemsen, Yuri Milaneschi, André G. Uitterlinden, Cecilia M. Lindgren, VU University medical center, APH - Mental Health, Psychiatry, Physiology, ACS - Heart failure & arrhythmias, APH - Methodology, and APH - Digital Health

Subjects
0301 basic medicine, Genetics, Multidisciplinary, Science, General Physics and Astronomy, General Chemistry, Biology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Disease risk, Heart rate variability, 030217 neurology & neurosurgery
Abstract

Nature Communications 8: Article number: 15805 (2017); Published: 14 June 2017; Updated: 2 August 2017 In Supplementary Fig. 10 of this Article, images for panels a and b were inadvertently omitted. The correct version of Supplementary Fig. 10 is provided as Supplementary Information associated withthis Erratum.

Published
2017
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7. Erratum: Distinct metabolomic signatures are associated with longevity in humans

Author

Paul F. Jacques, Christopher J. O'Donnell, Thomas J. Wang, Robert E. Gerszten, Jennifer E. Ho, Joanne M. Murabito, Olle Melander, Kerry A. Pierce, Susan Cheng, Eugene P. Rhee, Martin G. Larson, Kevin Bullock, Clary B. Clish, Amanda Souza, Martin Magnusson, Ramachandran S. Vasan, Elizabeth L. McCabe, Amy Deik, and Anahita Ghorbani

Subjects
Multidisciplinary, Metabolomics, media_common.quotation_subject, Published Erratum, Longevity, General Physics and Astronomy, General Chemistry, Computational biology, Biology, Aconitase, General Biochemistry, Genetics and Molecular Biology, media_common
Abstract

Nature Communications 6: Article number:6791 (2015); Published 13 April 2015; Updated 21 May 2015. In Fig. 1c,d of this Article, the y axis labels were inadvertently changed from ‘Log isocitrate’ to ‘Log aconitase’ during the production process. The correct version of Fig. 1 appears below.

Published
2015
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8. Genome-wide identification of microRNA expression quantitative trait loci

Author

Brian H. Chen, Nancy J. Cox, Paul Courchesne, Christopher J. O'Donnell, Daniel Levy, Andrew D. Johnson, Tianxiao Huan, Roby Joehanes, Jane E. Freedman, Kahraman Tanriverdi, Joanne M. Murabito, Peter J. Munson, Xiaoling Zhang, Chen Yao, Jian Rong, Martin G. Larson, and Chunyu Liu

Subjects
Adult, Male, Genotyping Techniques, Quantitative Trait Loci, General Physics and Astronomy, Genome-wide association study, Regulatory Sequences, Nucleic Acid, 030204 cardiovascular system & hematology, Biology, Polymorphism, Single Nucleotide, Genome, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Gene expression, microRNA, Humans, Aged, 030304 developmental biology, Genetics, 0303 health sciences, Multidisciplinary, Reverse Transcriptase Polymerase Chain Reaction, Gene Expression Profiling, Chromosome Mapping, General Chemistry, Middle Aged, Phenotype, Gene expression profiling, MicroRNAs, Regulatory sequence, Expression quantitative trait loci, Female, Genome-Wide Association Study
Abstract

Identification of microRNA expression quantitative trait loci (miR-eQTL) can yield insights into regulatory mechanisms of microRNA transcription, and can help elucidate the role of microRNA as mediators of complex traits. Here we present a miR-eQTL mapping study of whole blood from 5,239 individuals, and identify 5,269 cis-miR-eQTLs for 76 mature microRNAs. Forty-nine per cent of cis-miR-eQTLs are located 300-500 kb upstream of their associated intergenic microRNAs, suggesting that distal regulatory elements may affect the interindividual variability in microRNA expression levels. We find that cis-miR-eQTLs are highly enriched for cis-mRNA-eQTLs and regulatory single nucleotide polymorphisms. Among 243 cis-miR-eQTLs that were reported to be associated with complex traits in prior genome-wide association studies, many cis-miR-eQTLs miRNAs display differential expression in relation to the corresponding trait (for example, rs7115089, miR-125b-5p and high-density lipoprotein cholesterol). Our study provides a roadmap for understanding the genetic basis of miRNA expression, and sheds light on miRNA involvement in a variety of complex traits.

Published
2015
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9. Distinct Metabolomic Signatures Are Associated with Longevity in Humans

Author

Anahita Ghorbani, Kerry A. Pierce, Amanda Souza, Thomas J. Wang, Martin G. Larson, Paul F. Jacques, Olle Melander, Elizabeth L. McCabe, Jennifer E. Ho, Clary B. Clish, Martin Magnusson, Amy Deik, Susan Cheng, Joanne M. Murabito, Kevin Bullock, Eugene P. Rhee, Ramachandran S. Vasan, Robert E. Gerszten, and Christopher J. O'Donnell

Subjects
Male, Taurocholic Acid, medicine.medical_specialty, Isocitrates, medicine.drug_class, media_common.quotation_subject, Longevity, General Physics and Astronomy, Disease, Biology, General Biochemistry, Genetics and Molecular Biology, Mass Spectrometry, Article, Metabolomics, Internal medicine, Neoplasms, medicine, Metabolome, Odds Ratio, Humans, Longitudinal Studies, Survival analysis, media_common, Aged, Aged, 80 and over, Multidisciplinary, Bile acid, General Chemistry, Odds ratio, Middle Aged, Prognosis, Survival Analysis, 3. Good health, Metabolic pathway, Endocrinology, Cardiovascular Diseases, Female, Biomarkers, Chromatography, Liquid
Abstract

Alterations in metabolism influence lifespan in experimental models, but data in humans are lacking. Here we use liquid chromatography/mass spectrometry to quantify 217 plasma metabolites and examine their relation to longevity in a large cohort of men and women. In 647 individuals followed for up to 20 years, higher concentrations of the citric acid cycle intermediate, isocitrate, and the bile acid, taurocholate, are associated with lower odds of longevity, defined as attaining 80 years of age. In a larger cohort of 2,327 individuals with metabolite data available, higher concentrations of isocitrate but not taurocholate are also associated with worse cardiovascular health at baseline, as well as risk of future cardiovascular disease and death. None of the metabolites identified are associated with cancer risk. Our findings suggest that some, but not all, metabolic pathways to human longevity are dependent on modifying risk for the two most common causes of death.

Published
2015

10. Genetic insights into resting heart rate and its role in cardiovascular disease

Author

Yordi J. van de Vegte, Ruben N. Eppinga, M. Yldau van der Ende, Yanick P. Hagemeijer, Yuvaraj Mahendran, Elias Salfati, Albert V. Smith, Vanessa Y. Tan, Dan E. Arking, Ioanna Ntalla, Emil V. Appel, Claudia Schurmann, Jennifer A. Brody, Rico Rueedi, Ozren Polasek, Gardar Sveinbjornsson, Cecile Lecoeur, Claes Ladenvall, Jing Hua Zhao, Aaron Isaacs, Lihua Wang, Jian’an Luan, Shih-Jen Hwang, Nina Mononen, Kirsi Auro, Anne U. Jackson, Lawrence F. Bielak, Linyao Zeng, Nabi Shah, Maria Nethander, Archie Campbell, Tuomo Rankinen, Sonali Pechlivanis, Lu Qi, Wei Zhao, Federica Rizzi, Toshiko Tanaka, Antonietta Robino, Massimiliano Cocca, Leslie Lange, Martina Müller-Nurasyid, Carolina Roselli, Weihua Zhang, Marcus E. Kleber, Xiuqing Guo, Henry J. Lin, Francesca Pavani, Tessel E. Galesloot, Raymond Noordam, Yuri Milaneschi, Katharina E. Schraut, Marcel den Hoed, Frauke Degenhardt, Stella Trompet, Marten E. van den Berg, Giorgio Pistis, Yih-Chung Tham, Stefan Weiss, Xueling S. Sim, Hengtong L. Li, Peter J. van der Most, Ilja M. Nolte, Leo-Pekka Lyytikäinen, M. Abdullah Said, Daniel R. Witte, Carlos Iribarren, Lenore Launer, Susan M. Ring, Paul S. de Vries, Peter Sever, Allan Linneberg, Erwin P. Bottinger, Sandosh Padmanabhan, Bruce M. Psaty, Nona Sotoodehnia, Ivana Kolcic, The DCCT/EDIC Research Group, David O. Arnar, Daniel F. Gudbjartsson, Hilma Holm, Beverley Balkau, Claudia T. Silva, Christopher H. Newton-Cheh, Kjell Nikus, Perttu Salo, Karen L. Mohlke, Patricia A. Peyser, Heribert Schunkert, Mattias Lorentzon, Jari Lahti, Dabeeru C. Rao, Marilyn C. Cornelis, Jessica D. Faul, Jennifer A. Smith, Katarzyna Stolarz-Skrzypek, Stefania Bandinelli, Maria Pina Concas, Gianfranco Sinagra, Thomas Meitinger, Melanie Waldenberger, Moritz F. Sinner, Konstantin Strauch, Graciela E. Delgado, Kent D. Taylor, Jie Yao, Luisa Foco, Olle Melander, Jacqueline de Graaf, Renée de Mutsert, Eco J. C. de Geus, Åsa Johansson, Peter K. Joshi, Lars Lind, Andre Franke, Peter W. Macfarlane, Kirill V. Tarasov, Nicholas Tan, Stephan B. Felix, E-Shyong Tai, Debra Q. Quek, Harold Snieder, Johan Ormel, Martin Ingelsson, Cecilia Lindgren, Andrew P. Morris, Olli T. Raitakari, Torben Hansen, Themistocles Assimes, Vilmundur Gudnason, Nicholas J. Timpson, Alanna C. Morrison, Patricia B. Munroe, David P. Strachan, Niels Grarup, Ruth J. F. Loos, Susan R. Heckbert, Peter Vollenweider, Caroline Hayward, Kari Stefansson, Philippe Froguel, Leif Groop, Nicholas J. Wareham, Cornelia M. van Duijn, Mary F. Feitosa, Christopher J. O’Donnell, Mika Kähönen, Markus Perola, Michael Boehnke, Sharon L. R. Kardia, Jeanette Erdmann, Colin N. A. Palmer, Claes Ohlsson, David J. Porteous, Johan G. Eriksson, Claude Bouchard, Susanne Moebus, Peter Kraft, David R. Weir, Daniele Cusi, Luigi Ferrucci, Sheila Ulivi, Giorgia Girotto, Adolfo Correa, Stefan Kääb, Annette Peters, John C. Chambers, Jaspal S. Kooner, Winfried März, Jerome I. Rotter, Andrew A. Hicks, J. Gustav Smith, Lambertus A. L. M. Kiemeney, Dennis O. Mook-Kanamori, Brenda W. J. H. Penninx, Ulf Gyllensten, James F. Wilson, Stephen Burgess, Johan Sundström, Wolfgang Lieb, J. Wouter Jukema, Mark Eijgelsheim, Edward L. M. Lakatta, Ching-Yu Cheng, Marcus Dörr, Tien-Yin Wong, Charumathi Sabanayagam, Albertine J. Oldehinkel, Harriette Riese, Terho Lehtimäki, Niek Verweij, and Pim van der Harst

Subjects
Science
Abstract

Abstract Resting heart rate is associated with cardiovascular diseases and mortality in observational and Mendelian randomization studies. The aims of this study are to extend the number of resting heart rate associated genetic variants and to obtain further insights in resting heart rate biology and its clinical consequences. A genome-wide meta-analysis of 100 studies in up to 835,465 individuals reveals 493 independent genetic variants in 352 loci, including 68 genetic variants outside previously identified resting heart rate associated loci. We prioritize 670 genes and in silico annotations point to their enrichment in cardiomyocytes and provide insights in their ECG signature. Two-sample Mendelian randomization analyses indicate that higher genetically predicted resting heart rate increases risk of dilated cardiomyopathy, but decreases risk of developing atrial fibrillation, ischemic stroke, and cardio-embolic stroke. We do not find evidence for a linear or non-linear genetic association between resting heart rate and all-cause mortality in contrast to our previous Mendelian randomization study. Systematic alteration of key differences between the current and previous Mendelian randomization study indicates that the most likely cause of the discrepancy between these studies arises from false positive findings in previous one-sample MR analyses caused by weak-instrument bias at lower P-value thresholds. The results extend our understanding of resting heart rate biology and give additional insights in its role in cardiovascular disease development.

Published
2023
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11. Genomics and phenomics of body mass index reveals a complex disease network

Author

Jie Huang, Jennifer E. Huffman, Yunfeng Huang, Ítalo Do Valle, Themistocles L. Assimes, Sridharan Raghavan, Benjamin F. Voight, Chang Liu, Albert-László Barabási, Rose D. L. Huang, Qin Hui, Xuan-Mai T. Nguyen, Yuk-Lam Ho, Luc Djousse, Julie A. Lynch, Marijana Vujkovic, Catherine Tcheandjieu, Hua Tang, Scott M. Damrauer, Peter D. Reaven, Donald Miller, Lawrence S. Phillips, Maggie C. Y. Ng, Mariaelisa Graff, Christopher A. Haiman, Ruth J. F. Loos, Kari E. North, Loic Yengo, George Davey Smith, Danish Saleheen, J. Michael Gaziano, Daniel J. Rader, Philip S. Tsao, Kelly Cho, Kyong-Mi Chang, Peter W. F. Wilson, VA Million Veteran Program, Yan V. Sun, and Christopher J. O’Donnell

Subjects
Science
Abstract

Elevated body mass index is heritable and associated with many health conditions that impact morbidity and mortality. Here, the authors identify greater than 900 genetic loci for body mass index (BMI) and find over 300 diagnoses associated with increasing BMI.

Published
2022
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12. Cholesteryl ester transfer protein (CETP) as a drug target for cardiovascular disease

Author

Amand F. Schmidt, Nicholas B. Hunt, Maria Gordillo-Marañón, Pimphen Charoen, Fotios Drenos, Mika Kivimaki, Deborah A. Lawlor, Claudia Giambartolomei, Olia Papacosta, Nishi Chaturvedi, Joshua C. Bis, Christopher J. O’Donnell, Goya Wannamethee, Andrew Wong, Jackie F. Price, Alun D. Hughes, Tom R. Gaunt, Nora Franceschini, Dennis O. Mook-Kanamori, Magdalena Zwierzyna, Reecha Sofat, Aroon D. Hingorani, and Chris Finan

Subjects
Science
Abstract

Despite being studied in clinical trials, CETP inhibitors are not yet an approved treatment for coronary heart disease. Here, by analyzing results from clinical trials and drug target mendelian randomization studies, the authors demonstrate that previous failure of CETP inhibitors are likely compound and not drug target-related.

Published
2021
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13. Discovery and prioritization of variants and genes for kidney function in >1.2 million individuals

Author

Kira J. Stanzick, Yong Li, Pascal Schlosser, Mathias Gorski, Matthias Wuttke, Laurent F. Thomas, Humaira Rasheed, Bryce X. Rowan, Sarah E. Graham, Brett R. Vanderweff, Snehal B. Patil, VA Million Veteran Program, Cassiane Robinson-Cohen, John M. Gaziano, Christopher J. O’Donnell, Cristen J. Willer, Stein Hallan, Bjørn Olav Åsvold, Andre Gessner, Adriana M. Hung, Cristian Pattaro, Anna Köttgen, Klaus J. Stark, Iris M. Heid, and Thomas W. Winkler

Subjects
Science
Abstract

Identifying causal variants and genes in genome-wide association studies remains a challenge, an issue that is ameliorated with larger sample sizes. Here the authors meta-analyze kidney function genome-wide association studies to identify new loci and fine-map loci to home in on variants and genes involved in kidney function.

Published
2021
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14. Genetic analysis in European ancestry individuals identifies 517 loci associated with liver enzymes

Author

Raha Pazoki, Marijana Vujkovic, Joshua Elliott, Evangelos Evangelou, Dipender Gill, Mohsen Ghanbari, Peter J. van der Most, Rui Climaco Pinto, Matthias Wielscher, Matthias Farlik, Verena Zuber, Robert J. de Knegt, Harold Snieder, André G. Uitterlinden, Lifelines Cohort Study, Julie A. Lynch, Xiyun Jiang, Saredo Said, David E. Kaplan, Kyung Min Lee, Marina Serper, Rotonya M. Carr, Philip S. Tsao, Stephen R. Atkinson, Abbas Dehghan, Ioanna Tzoulaki, M. Arfan Ikram, Karl-Heinz Herzig, Marjo-Riitta Järvelin, Behrooz Z. Alizadeh, Christopher J. O’Donnell, Danish Saleheen, Benjamin F. Voight, Kyong-Mi Chang, Mark R. Thursz, Paul Elliott, and the VA Million Veteran Program

Subjects
Science
Abstract

Plasma levels of liver enzymes provide insights into hepatic function and related diseases. Here, the authors perform a genome-wide association study on three liver enzymes, identifying genetic variants associated with their plasma concentration as well as links to metabolic and cardiovascular diseases.

Published
2021
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15. Chromosome 1q21.2 and additional loci influence risk of spontaneous coronary artery dissection and myocardial infarction

Author

Jacqueline Saw, Min-Lee Yang, Mark Trinder, Catherine Tcheandjieu, Chang Xu, Andrew Starovoytov, Isabelle Birt, Michael R. Mathis, Kristina L. Hunker, Ellen M. Schmidt, Linda Jackson, Natalia Fendrikova-Mahlay, Matthew Zawistowski, Chad M. Brummett, Sebastian Zoellner, Alexander Katz, Dawn M. Coleman, Kirby Swan, Christopher J. O’Donnell, Million Veteran Program, Xiang Zhou, Jun Z. Li, Heather L. Gornik, Themistocles L. Assimes, James C. Stanley, Liam R. Brunham, and Santhi K. Ganesh

Subjects
Science
Abstract

Spontaneous coronary artery dissection (SCAD) is a cause of myocardial infarction Here, the authors present a genome-wide association study of SCAD, finding an association at 1q21.2 which potentially affects expression of ADAMTSL4.

Published
2020
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16. Mapping eGFR loci to the renal transcriptome and phenome in the VA Million Veteran Program

Author

Jacklyn N. Hellwege, Digna R. Velez Edwards, Ayush Giri, Chengxiang Qiu, Jihwan Park, Eric S. Torstenson, Jacob M. Keaton, O. D. Wilson, Cassianne Robinson-Cohen, Cecilia P. Chung, Christianne L. Roumie, Derek Klarin, Scott M. Damrauer, Scott L. DuVall, Edward Siew, Elvis A. Akwo, Matthias Wuttke, Mathias Gorski, Man Li, Yong Li, J. Michael Gaziano, Peter W. F. Wilson, Philip S. Tsao, Christopher J. O’Donnell, Csaba P. Kovesdy, Cristian Pattaro, Anna Köttgen, Katalin Susztak, Todd L. Edwards, and Adriana M. Hung

Subjects
Science
Abstract

Persistently low levels of estimated glomerular filtration rate (eGFR) are a biomarker of chronic kidney disease. Here, the authors reinterpret the genetic architecture of kidney function across ancestries, to identify not only genes, but the tissue and anatomical contexts of renal homeostasis.

Published
2019
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17. GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes

Author

Nora Franceschini, Claudia Giambartolomei, Paul S. de Vries, Chris Finan, Joshua C. Bis, Rachael P. Huntley, Ruth C. Lovering, Salman M. Tajuddin, Thomas W. Winkler, Misa Graff, Maryam Kavousi, Caroline Dale, Albert V. Smith, Edith Hofer, Elisabeth M. van Leeuwen, Ilja M. Nolte, Lingyi Lu, Markus Scholz, Muralidharan Sargurupremraj, Niina Pitkänen, Oscar Franzén, Peter K. Joshi, Raymond Noordam, Riccardo E. Marioni, Shih-Jen Hwang, Solomon K. Musani, Ulf Schminke, Walter Palmas, Aaron Isaacs, Adolfo Correa, Alan B. Zonderman, Albert Hofman, Alexander Teumer, Amanda J. Cox, André G. Uitterlinden, Andrew Wong, Andries J. Smit, Anne B. Newman, Annie Britton, Arno Ruusalepp, Bengt Sennblad, Bo Hedblad, Bogdan Pasaniuc, Brenda W. Penninx, Carl D. Langefeld, Christina L. Wassel, Christophe Tzourio, Cristiano Fava, Damiano Baldassarre, Daniel H. O’Leary, Daniel Teupser, Diana Kuh, Elena Tremoli, Elmo Mannarino, Enzo Grossi, Eric Boerwinkle, Eric E. Schadt, Erik Ingelsson, Fabrizio Veglia, Fernando Rivadeneira, Frank Beutner, Ganesh Chauhan, Gerardo Heiss, Harold Snieder, Harry Campbell, Henry Völzke, Hugh S. Markus, Ian J. Deary, J. Wouter Jukema, Jacqueline de Graaf, Jacqueline Price, Janne Pott, Jemma C. Hopewell, Jingjing Liang, Joachim Thiery, Jorgen Engmann, Karl Gertow, Kenneth Rice, Kent D. Taylor, Klodian Dhana, Lambertus A. L. M. Kiemeney, Lars Lind, Laura M. Raffield, Lenore J. Launer, Lesca M. Holdt, Marcus Dörr, Martin Dichgans, Matthew Traylor, Matthias Sitzer, Meena Kumari, Mika Kivimaki, Mike A. Nalls, Olle Melander, Olli Raitakari, Oscar H. Franco, Oscar L. Rueda-Ochoa, Panos Roussos, Peter H. Whincup, Philippe Amouyel, Philippe Giral, Pramod Anugu, Quenna Wong, Rainer Malik, Rainer Rauramaa, Ralph Burkhardt, Rebecca Hardy, Reinhold Schmidt, Renée de Mutsert, Richard W. Morris, Rona J. Strawbridge, S. Goya Wannamethee, Sara Hägg, Sonia Shah, Stela McLachlan, Stella Trompet, Sudha Seshadri, Sudhir Kurl, Susan R. Heckbert, Susan Ring, Tamara B. Harris, Terho Lehtimäki, Tessel E. Galesloot, Tina Shah, Ulf de Faire, Vincent Plagnol, Wayne D. Rosamond, Wendy Post, Xiaofeng Zhu, Xiaoling Zhang, Xiuqing Guo, Yasaman Saba, MEGASTROKE Consortium, Abbas Dehghan, Adrie Seldenrijk, Alanna C. Morrison, Anders Hamsten, Bruce M. Psaty, Cornelia M. van Duijn, Deborah A. Lawlor, Dennis O. Mook-Kanamori, Donald W. Bowden, Helena Schmidt, James F. Wilson, James G. Wilson, Jerome I. Rotter, Joanna M. Wardlaw, John Deanfield, Julian Halcox, Leo-Pekka Lyytikäinen, Markus Loeffler, Michele K. Evans, Stéphanie Debette, Steve E. Humphries, Uwe Völker, Vilmundur Gudnason, Aroon D. Hingorani, Johan L. M. Björkegren, Juan P. Casas, and Christopher J. O’Donnell

Subjects
Science
Abstract

Carotid intima-media thickness (cIMT) and plaque are associated with subclinical atherosclerosis and coronary heart disease (CHD). Here, the authors identify and prioritize genetic loci for cIMT and plaque by GWAS and colocalization approaches and further demonstrate genetic correlation with CHD and stroke.

Published
2018
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18. An exome array study of the plasma metabolome

Author

Eugene P. Rhee, Qiong Yang, Bing Yu, Xuan Liu, Susan Cheng, Amy Deik, Kerry A. Pierce, Kevin Bullock, Jennifer E. Ho, Daniel Levy, Jose C. Florez, Sek Kathiresan, Martin G. Larson, Ramachandran S. Vasan, Clary B. Clish, Thomas J. Wang, Eric Boerwinkle, Christopher J. O’Donnell, and Robert E. Gerszten

Subjects
Science
Abstract

Several GWAS have identified many common variants associated with blood metabolites. Here, the authors use an exome array to identify low frequency, potentially functional variants that impact human metabolism.

Published
2016
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