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Yao S, Han JZ, Guo J, Wang X, Qian L, Wu H, Shi W, Zhu RJ, Wang JH, Dong SS, Cui LL, Wang Y, Guo Y, Yang TL. The Causal Relationships Between Gut Microbiota, Brain Volume, and Intelligence: A Two-Step Mendelian Randomization Analysis. Biol Psychiatry 2024; 96:463-472. [PMID: 38432522 DOI: 10.1016/j.biopsych.2024.02.1012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/05/2024] [Accepted: 02/23/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND Growing evidence indicates that dynamic changes in gut microbiome can affect intelligence; however, whether these relationships are causal remains elusive. We aimed to disentangle the poorly understood causal relationship between gut microbiota and intelligence. METHODS We performed a 2-sample Mendelian randomization (MR) analysis using genetic variants from the largest available genome-wide association studies of gut microbiota (N = 18,340) and intelligence (N = 269,867). The inverse-variance weighted method was used to conduct the MR analyses complemented by a range of sensitivity analyses to validate the robustness of the results. Considering the close relationship between brain volume and intelligence, we applied 2-step MR to evaluate whether the identified effect was mediated by regulating brain volume (N = 47,316). RESULTS We found a risk effect of the genus Oxalobacter on intelligence (odds ratio = 0.968 change in intelligence per standard deviation increase in taxa; 95% CI, 0.952-0.985; p = 1.88 × 10-4) and a protective effect of the genus Fusicatenibacter on intelligence (odds ratio = 1.053; 95% CI, 1.024-1.082; p = 3.03 × 10-4). The 2-step MR analysis further showed that the effect of genus Fusicatenibacter on intelligence was partially mediated by regulating brain volume, with a mediated proportion of 33.6% (95% CI, 6.8%-60.4%; p = .014). CONCLUSIONS Our results provide causal evidence indicating the role of the microbiome in intelligence. Our findings may help reshape our understanding of the microbiota-gut-brain axis and development of novel intervention approaches for preventing cognitive impairment.
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Affiliation(s)
- Shi Yao
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China; Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China; National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Ji-Zhou Han
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jing Guo
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xin Wang
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Long Qian
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hao Wu
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Wei Shi
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Ren-Jie Zhu
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jia-Hao Wang
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Li-Li Cui
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Yan Wang
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China; National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
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Urquiza-Martínez MV, Fabián-Avilés IM, Torner L, Servín-Campuzano H, González-Avilés M. Integrative Approach of Treating Early Undernutrition with an Enriched Black Corn Chip, Study on a Murine Model. Nutrients 2024; 16:2001. [PMID: 38999749 PMCID: PMC11243394 DOI: 10.3390/nu16132001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 06/12/2024] [Accepted: 06/15/2024] [Indexed: 07/14/2024] Open
Abstract
Undernutrition (UN) increases child vulnerability to illness and mortality. Caused by a low amount and/or poor quality of food intake, it impacts physical, cognitive, and social development. Modern types of food consumption have given highly processed food a higher cultural value compared to minimally processed food. OBJECTIVE The objective of this study was to evaluate the effect on growth, metabolism, physical activity (PA), memory, inflammation, and toxicity of an enriched black corn chip (BC) made with endemic ingredients on post-weaned UN mice. METHODS A chip was made with a mixture of black corn, fava beans, amaranth, and nopal cactus. To probe the effects of UN, UN was induced in 3wo post-weaned male C57Bl/6j mice through a low-protein diet (LPD-50% of the regular requirement of protein) for 3w. Then, the BC was introduced to the animals' diet (17%) for 5w; murinometric parameters were measured, as were postprandial glucose response, PA, and short-term memory. Histological analysis was conducted on the liver and kidneys to measure toxicity. Gene expression related to energy balance, thermogenesis, and inflammation was measured in adipose and hypothalamic tissues. RESULTS Treatment with the BC significantly improved mouse growth, even with a low protein intake, as evidenced by a significant increase in body weight, tail length, cerebral growth, memory improvement, physical activation, normalized energy expenditure (thermogenesis), and orexigenic peptides (AGRP and NPY). It decreased anorexigenic peptides (POMC), and there was no tissue toxicity. CONCLUSIONS BC treatment, even with persistent low protein intake, is a promising strategy against UN, as it showed efficacy in correcting growth deficiency, cognitive impairment, and metabolic problems linked to treatment by adjusting energy expenditure, which led to the promotion of energy intake and regulation of thermogenesis, all by using low-cost, accessible, and endemic ingredients.
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Affiliation(s)
- Mercedes-Victoria Urquiza-Martínez
- Master in Engineering for the Energetic Sustainability, Universidad Intercultural Indígena de Michoacán, Campus Tzipekua, Pátzcuaro 61614, Mexico
| | - Imelda M Fabián-Avilés
- Master in Engineering for the Energetic Sustainability, Universidad Intercultural Indígena de Michoacán, Campus Tzipekua, Pátzcuaro 61614, Mexico
| | - Luz Torner
- Centro de Investigación Biomédica de Michoacán, Instituto Mexicano del Seguro Social, Morelia 58330, Mexico
| | - Hermelinda Servín-Campuzano
- Master in Engineering for the Energetic Sustainability, Universidad Intercultural Indígena de Michoacán, Campus Tzipekua, Pátzcuaro 61614, Mexico
| | - Mauricio González-Avilés
- Master in Engineering for the Energetic Sustainability, Universidad Intercultural Indígena de Michoacán, Campus Tzipekua, Pátzcuaro 61614, Mexico
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3
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Knol MJ, Poot RA, Evans TE, Satizabal CL, Mishra A, Sargurupremraj M, van der Auwera S, Duperron MG, Jian X, Hostettler IC, van Dam-Nolen DHK, Lamballais S, Pawlak MA, Lewis CE, Carrion-Castillo A, van Erp TGM, Reinbold CS, Shin J, Scholz M, Håberg AK, Kämpe A, Li GHY, Avinun R, Atkins JR, Hsu FC, Amod AR, Lam M, Tsuchida A, Teunissen MWA, Aygün N, Patel Y, Liang D, Beiser AS, Beyer F, Bis JC, Bos D, Bryan RN, Bülow R, Caspers S, Catheline G, Cecil CAM, Dalvie S, Dartigues JF, DeCarli C, Enlund-Cerullo M, Ford JM, Franke B, Freedman BI, Friedrich N, Green MJ, Haworth S, Helmer C, Hoffmann P, Homuth G, Ikram MK, Jack CR, Jahanshad N, Jockwitz C, Kamatani Y, Knodt AR, Li S, Lim K, Longstreth WT, Macciardi F, Mäkitie O, Mazoyer B, Medland SE, Miyamoto S, Moebus S, Mosley TH, Muetzel R, Mühleisen TW, Nagata M, Nakahara S, Palmer ND, Pausova Z, Preda A, Quidé Y, Reay WR, Roshchupkin GV, Schmidt R, Schreiner PJ, Setoh K, Shapland CY, Sidney S, St Pourcain B, Stein JL, Tabara Y, Teumer A, Uhlmann A, van der Lugt A, Vernooij MW, Werring DJ, Windham BG, Witte AV, Wittfeld K, Yang Q, Yoshida K, Brunner HG, Le Grand Q, Sim K, Stein DJ, Bowden DW, Cairns MJ, Hariri AR, Cheung CL, Andersson S, Villringer A, Paus T, Cichon S, Calhoun VD, Crivello F, Launer LJ, White T, Koudstaal PJ, Houlden H, Fornage M, Matsuda F, Grabe HJ, Ikram MA, Debette S, Thompson PM, Seshadri S, Adams HHH. Genetic variants for head size share genes and pathways with cancer. Cell Rep Med 2024; 5:101529. [PMID: 38703765 PMCID: PMC11148644 DOI: 10.1016/j.xcrm.2024.101529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 09/18/2023] [Accepted: 04/04/2024] [Indexed: 05/06/2024]
Abstract
The size of the human head is highly heritable, but genetic drivers of its variation within the general population remain unmapped. We perform a genome-wide association study on head size (N = 80,890) and identify 67 genetic loci, of which 50 are novel. Neuroimaging studies show that 17 variants affect specific brain areas, but most have widespread effects. Gene set enrichment is observed for various cancers and the p53, Wnt, and ErbB signaling pathways. Genes harboring lead variants are enriched for macrocephaly syndrome genes (37-fold) and high-fidelity cancer genes (9-fold), which is not seen for human height variants. Head size variants are also near genes preferentially expressed in intermediate progenitor cells, neural cells linked to evolutionary brain expansion. Our results indicate that genes regulating early brain and cranial growth incline to neoplasia later in life, irrespective of height. This warrants investigation of clinical implications of the link between head size and cancer.
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Affiliation(s)
- Maria J Knol
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Raymond A Poot
- Department of Cell Biology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Tavia E Evans
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands; Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Claudia L Satizabal
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA; The Framingham Heart Study, Framingham, MA, USA; Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Aniket Mishra
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, Bordeaux, France
| | - Muralidharan Sargurupremraj
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
| | - Sandra van der Auwera
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany; German Centre of Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Greifswald, Germany
| | - Marie-Gabrielle Duperron
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, Bordeaux, France
| | - Xueqiu Jian
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Isabel C Hostettler
- Stroke Research Centre, University College London, Institute of Neurology, London, UK; Department of Neurosurgery, Klinikum rechts der Isar, University of Munich, Munich, Germany; Neurosurgical Department, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Dianne H K van Dam-Nolen
- Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Sander Lamballais
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Mikolaj A Pawlak
- Department of Neurology, Poznań University of Medical Sciences, Poznań, Poland; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cora E Lewis
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
| | - Amaia Carrion-Castillo
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Theo G M van Erp
- Clinical Translational Neuroscience Laboratory, Department of Psychiatry and Human Behavior, University of California, Irvine, Irvine, CA, USA; Center for the Neurobiology of Learning and Memory, University of California, Irvine, Irvine, CA, USA
| | - Céline S Reinbold
- Department of Biomedicine, University of Basel, Basel, Switzerland; Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland; Institute of Computational Life Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Jean Shin
- The Hospital for Sick Children, University of Toronto, Toronto, Canada; Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, Canada
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany; LIFE Research Center for Civilization Disease, Leipzig, Germany
| | - Asta K Håberg
- Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Department of Radiology and Nuclear Medicine, St. Olavs University Hospital, Trondheim, Norway
| | - Anders Kämpe
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Gloria H Y Li
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Reut Avinun
- Laboratory of NeuroGenetics, Department of Psychology & Neuroscience, Duke University, Durham, NC, USA
| | - Joshua R Atkins
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia; Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Fang-Chi Hsu
- Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Alyssa R Amod
- Department of Child and Adolescent Psychiatry, TU Dresden, Dresden, Germany
| | - Max Lam
- North Region, Institute of Mental Health, Singapore, Singapore; Population and Global Health, LKC Medicine, Nanyang Technological University, Singapore, Singapore
| | - Ami Tsuchida
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, Bordeaux, France; Groupe d'imagerie neurofonctionnelle, Institut des Maladies Neurodégénératives, UMR 5293, CNRS, CEA, Université de Bordeaux, Bordeaux, France
| | - Mariël W A Teunissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Neurology, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Nil Aygün
- Department of Genetics UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yash Patel
- Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - Dan Liang
- Department of Genetics UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexa S Beiser
- The Framingham Heart Study, Framingham, MA, USA; Department of Neurology, Boston University School of Medicine, Boston, MA, USA; Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Frauke Beyer
- Department of Neurology, Max Planck Institute for Cognitive and Brain Sciences, Leipzig, Germany; Collaborative Research Center 1052 Obesity Mechanisms, Faculty of Medicine, University of Leipzig, Leipzig, Germany; Day Clinic for Cognitive Neurology, University Hospital Leipzig, Leipzig, Germany
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Daniel Bos
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands; Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - R Nick Bryan
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Robin Bülow
- Institute of Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, Greifswald, Germany
| | - Svenja Caspers
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany; Institute for Anatomy I, Medical Faculty & University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Gwenaëlle Catheline
- University of Bordeaux, CNRS, INCIA, UMR 5287, team NeuroImagerie et Cognition Humaine, Bordeaux, France; EPHE-PSL University, Bordeaux, France
| | - Charlotte A M Cecil
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands; Department of Child and Adolescent Psychiatry, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Shareefa Dalvie
- Department of Child and Adolescent Psychiatry, TU Dresden, Dresden, Germany
| | - Jean-François Dartigues
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team SEPIA, UMR 1219, Bordeaux, France
| | - Charles DeCarli
- Department of Neurology and Center for Neuroscience, University of California at Davis, Sacramento, CA, USA
| | - Maria Enlund-Cerullo
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Folkhälsan Research Center, Helsinki, Finland
| | - Judith M Ford
- San Francisco Veterans Administration Medical Center, San Francisco, CA, USA; University of California, San Francisco, San Francisco, CA, USA
| | - Barbara Franke
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Psychiatry, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Nele Friedrich
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Melissa J Green
- School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia; Neuroscience Research Australia, Sydney, NSW, Australia
| | - Simon Haworth
- Bristol Dental School, University of Bristol, Bristol, UK
| | - Catherine Helmer
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team LEHA, UMR 1219, Bordeaux, France
| | - Per Hoffmann
- Department of Biomedicine, University of Basel, Basel, Switzerland; Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland; Institute of Human Genetics, University of Bonn Medical School, Bonn, Germany
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - M Kamran Ikram
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands; Department of Neurology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | | | - Neda Jahanshad
- Imaging Genetics Center, Mark & Mary Stevens Neuroimaging & Informatics Institute, Keck USC School of Medicine, Los Angeles, CA, USA
| | - Christiane Jockwitz
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany; Department of Psychiatry, Psychotherapy and Psychosomatics, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Yoichiro Kamatani
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Annchen R Knodt
- Laboratory of NeuroGenetics, Department of Psychology & Neuroscience, Duke University, Durham, NC, USA
| | - Shuo Li
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Keane Lim
- Research Division, Institute of Mental Health, Singapore, Singapore
| | - W T Longstreth
- Department of Neurology, University of Washington, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Fabio Macciardi
- Laboratory of Molecular Psychiatry, Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Outi Mäkitie
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden; Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Folkhälsan Research Center, Helsinki, Finland
| | - Bernard Mazoyer
- Groupe d'imagerie neurofonctionnelle, Institut des Maladies Neurodégénératives, UMR 5293, CNRS, CEA, Université de Bordeaux, Bordeaux, France; Centre Hospitalo-Universitaire de Bordeaux, Bordeaux, France
| | - Sarah E Medland
- Psychiatric Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; School of Psychology, University of Queensland, Brisbane, QLD, Australia; Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Susumu Miyamoto
- Department of Neurosurgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Susanne Moebus
- Institute for Urban Public Health, University of Duisburg-Essen, Essen, Germany
| | - Thomas H Mosley
- Department of Medicine, Division of Geriatrics, University of Mississippi Medical Center, Jackson, MS, USA; Memory Impairment and Neurodegenerative Dementia (MIND) Center, Jackson, MS, USA
| | - Ryan Muetzel
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands; Department of Child and Adolescent Psychiatry, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Thomas W Mühleisen
- Department of Biomedicine, University of Basel, Basel, Switzerland; Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany; C. and O. Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Manabu Nagata
- Department of Neurosurgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Soichiro Nakahara
- Clinical Translational Neuroscience Laboratory, Department of Psychiatry and Human Behavior, University of California, Irvine, Irvine, CA, USA; Unit 2, Candidate Discovery Science Labs, Drug Discovery Research, Astellas Pharma Inc, 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Zdenka Pausova
- The Hospital for Sick Children, University of Toronto, Toronto, Canada; Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, Canada
| | - Adrian Preda
- Department of Psychiatry, University of California, Irvine, Irvine, CA, USA
| | - Yann Quidé
- School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia; Neuroscience Research Australia, Sydney, NSW, Australia
| | - William R Reay
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia; Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Gennady V Roshchupkin
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands; Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Reinhold Schmidt
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, Austria
| | | | - Kazuya Setoh
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Chin Yang Shapland
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands; MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Population Health Sciences, University of Bristol, Bristol, UK
| | - Stephen Sidney
- Kaiser Permanente Division of Research, Oakland, CA, USA
| | - Beate St Pourcain
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Nijmegen, the Netherlands; MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Jason L Stein
- Department of Genetics UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Alexander Teumer
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany; Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Anne Uhlmann
- Department of Child and Adolescent Psychiatry, TU Dresden, Dresden, Germany
| | - Aad van der Lugt
- Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Meike W Vernooij
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands; Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - David J Werring
- Stroke Research Centre, University College London, Institute of Neurology, London, UK
| | - B Gwen Windham
- Department of Medicine, Division of Geriatrics, University of Mississippi Medical Center, Jackson, MS, USA; Memory Impairment and Neurodegenerative Dementia (MIND) Center, Jackson, MS, USA
| | - A Veronica Witte
- Department of Neurology, Max Planck Institute for Cognitive and Brain Sciences, Leipzig, Germany; Collaborative Research Center 1052 Obesity Mechanisms, Faculty of Medicine, University of Leipzig, Leipzig, Germany; Day Clinic for Cognitive Neurology, University Hospital Leipzig, Leipzig, Germany
| | - Katharina Wittfeld
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany; German Centre of Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Greifswald, Germany
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Kazumichi Yoshida
- Department of Neurosurgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Han G Brunner
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Clinical Genetics MUMC+, GROW School of Oncology and Developmental Biology, and MHeNs School of Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Quentin Le Grand
- Bordeaux Population Health, University of Bordeaux, INSERM U1219, Bordeaux, France
| | - Kang Sim
- West Region, Institute of Mental Health, Singapore, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Dan J Stein
- Department of Child and Adolescent Psychiatry, TU Dresden, Dresden, Germany; SAMRC Unit on Risk and Resilience, University of Cape Town, Cape Town, South Africa
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia; Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Ahmad R Hariri
- Laboratory of NeuroGenetics, Department of Psychology & Neuroscience, Duke University, Durham, NC, USA
| | - Ching-Lung Cheung
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Sture Andersson
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Arno Villringer
- Department of Neurology, Max Planck Institute for Cognitive and Brain Sciences, Leipzig, Germany; Day Clinic for Cognitive Neurology, University Hospital Leipzig, Leipzig, Germany
| | - Tomas Paus
- Departments of Psychiatry and Neuroscience, Faculty of Medicine and Centre Hospitalier Universitaire Sainte-Justine, University of Montreal, Montreal, QC, Canada; Department of Psychiatry, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Sven Cichon
- Department of Biomedicine, University of Basel, Basel, Switzerland; Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland; Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
| | - Vince D Calhoun
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS) {Georgia State, Georgia Tech, Emory}, Atlanta, GA, USA
| | - Fabrice Crivello
- Groupe d'imagerie neurofonctionnelle, Institut des Maladies Neurodégénératives, UMR 5293, CNRS, CEA, Université de Bordeaux, Bordeaux, France
| | - Lenore J Launer
- Laboratory of Epidemiology, Demography, and Biometry, Intramural Research Program, National Institute of Aging, The National Institutes of Health, Bethesda, MD, USA
| | - Tonya White
- Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands; Department of Child and Adolescent Psychiatry, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Peter J Koudstaal
- Department of Neurology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Henry Houlden
- Stroke Research Centre, University College London, Institute of Neurology, London, UK
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA; Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Stéphanie Debette
- Bordeaux Population Health, University of Bordeaux, INSERM U1219, Bordeaux, France; Department of Neurology, Bordeaux University Hospital, Bordeaux, France
| | - Paul M Thompson
- Imaging Genetics Center, Mark & Mary Stevens Neuroimaging & Informatics Institute, Keck USC School of Medicine, Los Angeles, CA, USA
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA; The Framingham Heart Study, Framingham, MA, USA; Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Hieab H H Adams
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Latin American Brain Health (BrainLat), Universidad Adolfo Ibáñez, Santiago, Chile.
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4
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Verhoef E, Allegrini AG, Jansen PR, Lange K, Wang CA, Morgan AT, Ahluwalia TS, Symeonides C, Eising E, Franken MC, Hypponen E, Mansell T, Olislagers M, Omerovic E, Rimfeld K, Schlag F, Selzam S, Shapland CY, Tiemeier H, Whitehouse AJO, Saffery R, Bønnelykke K, Reilly S, Pennell CE, Wake M, Cecil CAM, Plomin R, Fisher SE, St Pourcain B. Genome-Wide Analyses of Vocabulary Size in Infancy and Toddlerhood: Associations With Attention-Deficit/Hyperactivity Disorder, Literacy, and Cognition-Related Traits. Biol Psychiatry 2024; 95:859-869. [PMID: 38070845 DOI: 10.1016/j.biopsych.2023.11.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 11/26/2023] [Accepted: 11/29/2023] [Indexed: 02/17/2024]
Abstract
BACKGROUND The number of words children produce (expressive vocabulary) and understand (receptive vocabulary) changes rapidly during early development, partially due to genetic factors. Here, we performed a meta-genome-wide association study of vocabulary acquisition and investigated polygenic overlap with literacy, cognition, developmental phenotypes, and neurodevelopmental conditions, including attention-deficit/hyperactivity disorder (ADHD). METHODS We studied 37,913 parent-reported vocabulary size measures (English, Dutch, Danish) for 17,298 children of European descent. Meta-analyses were performed for early-phase expressive (infancy, 15-18 months), late-phase expressive (toddlerhood, 24-38 months), and late-phase receptive (toddlerhood, 24-38 months) vocabulary. Subsequently, we estimated single nucleotide polymorphism-based heritability (SNP-h2) and genetic correlations (rg) and modeled underlying factor structures with multivariate models. RESULTS Early-life vocabulary size was modestly heritable (SNP-h2 = 0.08-0.24). Genetic overlap between infant expressive and toddler receptive vocabulary was negligible (rg = 0.07), although each measure was moderately related to toddler expressive vocabulary (rg = 0.69 and rg = 0.67, respectively), suggesting a multifactorial genetic architecture. Both infant and toddler expressive vocabulary were genetically linked to literacy (e.g., spelling: rg = 0.58 and rg = 0.79, respectively), underlining genetic similarity. However, a genetic association of early-life vocabulary with educational attainment and intelligence emerged only during toddlerhood (e.g., receptive vocabulary and intelligence: rg = 0.36). Increased ADHD risk was genetically associated with larger infant expressive vocabulary (rg = 0.23). Multivariate genetic models in the ALSPAC (Avon Longitudinal Study of Parents and Children) cohort confirmed this finding for ADHD symptoms (e.g., at age 13; rg = 0.54) but showed that the association effect reversed for toddler receptive vocabulary (rg = -0.74), highlighting developmental heterogeneity. CONCLUSIONS The genetic architecture of early-life vocabulary changes during development, shaping polygenic association patterns with later-life ADHD, literacy, and cognition-related traits.
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Affiliation(s)
- Ellen Verhoef
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands.
| | - Andrea G Allegrini
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Philip R Jansen
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, the Netherlands; Section Clinical Genetics, Department Human Genetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Katherine Lange
- Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Carol A Wang
- School of Medicine and Public Health, The University of Newcastle, Newcastle, New South Wales, Australia; Mothers and Babies Research Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Angela T Morgan
- Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Department of Audiology and Speech Pathology, University of Melbourne, Parkville, Victoria, Australia; Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Tarunveer S Ahluwalia
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark; Steno Diabetes Center Copenhagen, Herlev, Denmark; Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Christos Symeonides
- Murdoch Children's Research Institute, Parkville, Victoria, Australia; Royal Children's Hospital, Melbourne, Victoria, Australia; Minderoo Foundation, Perth, Western Australia, Australia
| | - Else Eising
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Marie-Christine Franken
- Erasmus University Medical Center, Sophia Children's Hospital, Department of Otorhinolaryngology and Head and Neck Surgery, Rotterdam, the Netherlands
| | - Elina Hypponen
- Australian Centre for Precision Health, Unit of Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia; South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Toby Mansell
- Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Mitchell Olislagers
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands; Department of Urology, Erasmus University Medical Center, Erasmus University Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Emina Omerovic
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Kaili Rimfeld
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; Department of Psychology, Royal Holloway University of London, London, UK
| | - Fenja Schlag
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Saskia Selzam
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Chin Yang Shapland
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Population Health Sciences, University of Bristol, Bristol, UK
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Rotterdam, the Netherlands; Harvard, T.H. Chan School of Public Health, Boston, Massachusetts
| | - Andrew J O Whitehouse
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Chongqing Medical University, Chongqing, China
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Sheena Reilly
- Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Menzies Health Institute Queensland, Griffith University, Brisbane, Queensland, Australia
| | - Craig E Pennell
- School of Medicine and Public Health, The University of Newcastle, Newcastle, New South Wales, Australia; Mothers and Babies Research Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia; Maternity and Gynaecology John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Melissa Wake
- Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Liggins Institute, The University of Auckland, Grafton, New Zealand
| | - Charlotte A M Cecil
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands; Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Robert Plomin
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Beate St Pourcain
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands; Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands.
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5
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Seidlitz J, Mallard TT, Vogel JW, Lee YH, Warrier V, Ball G, Hansson O, Hernandez LM, Mandal AS, Wagstyl K, Lombardo MV, Courchesne E, Glessner JT, Satterthwaite TD, Bethlehem RAI, Bernstock JD, Tasaki S, Ng B, Gaiteri C, Smoller JW, Ge T, Gur RE, Gandal MJ, Alexander-Bloch AF. The molecular genetic landscape of human brain size variation. Cell Rep 2023; 42:113439. [PMID: 37963017 DOI: 10.1016/j.celrep.2023.113439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 06/13/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
Human brain size changes dynamically through early development, peaks in adolescence, and varies up to 2-fold among adults. However, the molecular genetic underpinnings of interindividual variation in brain size remain unknown. Here, we leveraged postmortem brain RNA sequencing and measurements of brain weight (BW) in 2,531 individuals across three independent datasets to identify 928 genome-wide significant associations with BW. Genes associated with higher or lower BW showed distinct neurodevelopmental trajectories and spatial patterns that mapped onto functional and cellular axes of brain organization. Expression of BW genes was predictive of interspecies differences in brain size, and bioinformatic annotation revealed enrichment for neurogenesis and cell-cell communication. Genome-wide, transcriptome-wide, and phenome-wide association analyses linked BW gene sets to neuroimaging measurements of brain size and brain-related clinical traits. Cumulatively, these results represent a major step toward delineating the molecular pathways underlying human brain size variation in health and disease.
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Affiliation(s)
- Jakob Seidlitz
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA 19104, USA; Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Travis T Mallard
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Boston, MA 02142, USA; Department of Psychiatry, Harvard Medical School, Boston, MA 02142, USA
| | - Jacob W Vogel
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA; Lifespan Informatics and Neuroimaging Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Younga H Lee
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Boston, MA 02142, USA; Department of Psychiatry, Harvard Medical School, Boston, MA 02142, USA
| | - Varun Warrier
- Department of Psychiatry, University of Cambridge, Cambridge CB2 1TN, UK; Department of Psychology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Gareth Ball
- Developmental Imaging, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Melbourne, VIC 3052, Australia
| | - Oskar Hansson
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Malmö P663+Q9, Sweden; Memory Clinic, Skåne University Hospital, Malmö P663+Q9, Sweden
| | - Leanna M Hernandez
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90024, USA
| | - Ayan S Mandal
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA 19104, USA; Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Konrad Wagstyl
- Wellcome Centre for Human Neuroimaging, University College London, London WC1N 3AR, UK
| | - Michael V Lombardo
- Laboratory for Autism and Neurodevelopmental Disorders, Center for Neuroscience and Cognitive Systems @UniTn, Istituto Italiano di Tecnologia, 38068 Rovereto, Italy
| | - Eric Courchesne
- Department of Neuroscience, University of California, San Diego, San Diego, CA 92093, USA; Autism Center of Excellence, University of California, San Diego, San Diego, CA 92093, USA
| | - Joseph T Glessner
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Theodore D Satterthwaite
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA 19104, USA; Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA; Lifespan Informatics and Neuroimaging Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | | | - Joshua D Bernstock
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard University, Boston, MA 02115, USA; Department of Neurosurgery, Boston Children's Hospital, Harvard University, Boston, MA 02115, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shinya Tasaki
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Bernard Ng
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Chris Gaiteri
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Jordan W Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Boston, MA 02142, USA; Department of Psychiatry, Harvard Medical School, Boston, MA 02142, USA; Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Boston, MA 02142, USA; Department of Psychiatry, Harvard Medical School, Boston, MA 02142, USA; Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Raquel E Gur
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA 19104, USA; Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael J Gandal
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA 19104, USA; Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aaron F Alexander-Bloch
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA 19104, USA; Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA
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6
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Goovaerts S, Hoskens H, Eller RJ, Herrick N, Musolf AM, Justice CM, Yuan M, Naqvi S, Lee MK, Vandermeulen D, Szabo-Rogers HL, Romitti PA, Boyadjiev SA, Marazita ML, Shaffer JR, Shriver MD, Wysocka J, Walsh S, Weinberg SM, Claes P. Joint multi-ancestry and admixed GWAS reveals the complex genetics behind human cranial vault shape. Nat Commun 2023; 14:7436. [PMID: 37973980 PMCID: PMC10654897 DOI: 10.1038/s41467-023-43237-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
The cranial vault in humans is highly variable, clinically relevant, and heritable, yet its genetic architecture remains poorly understood. Here, we conduct a joint multi-ancestry and admixed multivariate genome-wide association study on 3D cranial vault shape extracted from magnetic resonance images of 6772 children from the ABCD study cohort yielding 30 genome-wide significant loci. Follow-up analyses indicate that these loci overlap with genomic risk loci for sagittal craniosynostosis, show elevated activity cranial neural crest cells, are enriched for processes related to skeletal development, and are shared with the face and brain. We present supporting evidence of regional localization for several of the identified genes based on expression patterns in the cranial vault bones of E15.5 mice. Overall, our study provides a comprehensive overview of the genetics underlying normal-range cranial vault shape and its relevance for understanding modern human craniofacial diversity and the etiology of congenital malformations.
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Affiliation(s)
- Seppe Goovaerts
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium.
| | - Hanne Hoskens
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Ryan J Eller
- Department of Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Noah Herrick
- Department of Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Anthony M Musolf
- Statistical Genetics Section, Computational and Statistical Genomics Branch, NHGRI, NIH, MD, Baltimore, USA
| | - Cristina M Justice
- Genometrics Section, Computational and Statistical Genomics Branch, Division of Intramural Research, NHGRI, NIH, Baltimore, MD, USA
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Meng Yuan
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Genetics and Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Myoung Keun Lee
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dirk Vandermeulen
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Heather L Szabo-Rogers
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatchewan, Canada
| | - Paul A Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, IA, USA
| | - Simeon A Boyadjiev
- Department of Pediatrics, University of California Davis, Sacramento, CA, USA
| | - Mary L Marazita
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - John R Shaffer
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mark D Shriver
- Department of Anthropology, Pennsylvania State University, State College, PA, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Susan Walsh
- Department of Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Seth M Weinberg
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium.
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.
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7
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Gong S, Ge Y, Wei Y, Gao Y. Genomic insights into the genetic basis of eagle-beak jaw, large head, and long tail in the big-headed turtle. Ecol Evol 2023; 13:e10361. [PMID: 37502307 PMCID: PMC10368965 DOI: 10.1002/ece3.10361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/15/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
The big-headed turtle (Platysternon megacephalum) is an endemic chelonian species in Asia. Unlike most other turtles in the world, P. megacephalum is characterized with eagle-beak jaw, large head, and long tail. Although these unique characteristics are well recognized, the underlying genetic basis remains largely elusive. Here, we performed comparative genomic analysis between P. megacephalum and other representative species, aiming to reveal the genetic basis of the unique morphological features. Our results revealed that the eagle-beak jaw is most likely enabled by combined effects of expansion of SFRP5, extraction of FGF11, and mutation of both ZFYVE16 and PAX6. Large head is supported by mutations of SETD2 and FGRF2 and copy number variations of six head circumference modulation-related genes (TGFBR2, Twist2, Rdh10, Gas1, Chst11, and SNAP25). The long tail is probably involved in a genetic network comprising Gdf11, Lin 28, and HoxC12, two of which showed a consistent expression pattern with a model organism (mice). These findings suggest that expansion, extraction, and mutation of those genes may have profound effects on unique phenotypes of P. megacephalum.
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Affiliation(s)
- Shiping Gong
- College of Life Science and TechnologyJinan UniversityGuangzhouChina
| | - Yan Ge
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of ZoologyGuangdong Academy of SciencesGuangzhouChina
| | - Yufeng Wei
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of ZoologyGuangdong Academy of SciencesGuangzhouChina
| | - Yangchun Gao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of ZoologyGuangdong Academy of SciencesGuangzhouChina
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8
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Zhang W, Mu Y, Dong K, Zhang L, Yan B, Hu H, Liao Y, Zhao R, Shu W, Ye Z, Lu Y, Wan C, Sun Q, Li L, Wang H, Xiao X. PAM-independent ultra-specific activation of CRISPR-Cas12a via sticky-end dsDNA. Nucleic Acids Res 2022; 50:12674-12688. [PMID: 36484104 PMCID: PMC9825152 DOI: 10.1093/nar/gkac1144] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/04/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Although CRISPR-Cas12a [clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 12a] combining pre-amplification technology has the advantage of high sensitivity in biosensing, its generality and specificity are insufficient, which greatly restrains its application range. Here, we discovered a new targeting substrate for LbaCas12a (Lachnospiraceae bacterium Cas12a), namely double-stranded DNA (dsDNA) with a sticky-end region (PAM-SE+ dsDNA). We discovered that CRISPR-Cas12a had special enzymatic properties for this substrate DNA, including the ability to recognize and cleave it without needing a protospacer adjacent motif (PAM) sequence and a high sensitivity to single-base mismatches in that substrate. Further mechanism studies revealed that guide RNA (gRNA) formed a triple-stranded flap structure with the substrate dsDNA. We also discovered the property of low-temperature activation of CRISPR-Cas12a and, by coupling with the unique DNA hybridization kinetics at low temperature, we constructed a complete workflow for low-abundance point mutation detection in real samples, which was fast, convenient and free of single-stranded DNA (ssDNA) transformation. The detection limits were 0.005-0.01% for synthesized strands and 0.01-0.05% for plasmid genomic DNA, and the mutation abundances provided by our system for 28 clinical samples were in accordance with next-generation sequencing results. We believe that our work not only reveals novel information about the target recognition mechanism of the CRISPR-Cas12a system, but also greatly broadens its application scenarios.
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Affiliation(s)
| | | | - Kejun Dong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Lei Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Bei Yan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hao Hu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yangwei Liao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Rong Zhao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Wan Shu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Zhengxin Ye
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yaping Lu
- Sinopharm Genomics Technology Co., Ltd, Wuhan 430000, China
| | - Chong Wan
- Precision Medicine Center, Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, China
| | - Qiangqiang Sun
- Life Health Care Clinical Laboratories, Beijing 100000, China
| | - Longjie Li
- Correspondence may also be addressed to Longjie Li.
| | - Hongbo Wang
- Correspondence may also be addressed to Hongbo Wang.
| | - Xianjin Xiao
- To whom correspondence should be addressed. Tel: +86 027 8369 2651; Fax: +86 027 8369 2651;
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9
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Vogelezang S, Bradfield JP, Grant SFA, Felix JF, Jaddoe VWV. Genetics of early-life head circumference and genetic correlations with neurological, psychiatric and cognitive outcomes. BMC Med Genomics 2022; 15:124. [PMID: 35659227 PMCID: PMC9166310 DOI: 10.1186/s12920-022-01281-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 05/30/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Head circumference is associated with intelligence and tracks from childhood into adulthood. METHODS We performed a genome-wide association study meta-analysis and follow-up of head circumference in a total of 29,192 participants between 6 and 30 months of age. RESULTS Seven loci reached genome-wide significance in the combined discovery and replication analysis of which three loci near ARFGEF2, MYCL1, and TOP1, were novel. We observed positive genetic correlations for early-life head circumference with adult intracranial volume, years of schooling, childhood and adult intelligence, but not with adult psychiatric, neurological, or personality-related phenotypes. CONCLUSIONS The results of this study indicate that the biological processes underlying early-life head circumference overlap largely with those of adult head circumference. The associations of early-life head circumference with cognitive outcomes across the life course are partly explained by genetics.
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Affiliation(s)
- Suzanne Vogelezang
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jonathan P Bradfield
- Division of Human Genetics, Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Quantinuum Research LLC, San Diego, CA, USA
| | - Struan F A Grant
- Division of Human Genetics, Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Endocrinology and Diabetes, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
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10
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Inherited variants in CHD3 show variable expressivity in Snijders Blok-Campeau syndrome. Genet Med 2022; 24:1283-1296. [PMID: 35346573 DOI: 10.1016/j.gim.2022.02.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/22/2022] [Accepted: 02/22/2022] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Common diagnostic next-generation sequencing strategies are not optimized to identify inherited variants in genes associated with dominant neurodevelopmental disorders as causal when the transmitting parent is clinically unaffected, leaving a significant number of cases with neurodevelopmental disorders undiagnosed. METHODS We characterized 21 families with inherited heterozygous missense or protein-truncating variants in CHD3, a gene in which de novo variants cause Snijders Blok-Campeau syndrome. RESULTS Computational facial and Human Phenotype Ontology-based comparisons showed that the phenotype of probands with inherited CHD3 variants overlaps with the phenotype previously associated with de novo CHD3 variants, whereas heterozygote parents are mildly or not affected, suggesting variable expressivity. In addition, similarly reduced expression levels of CHD3 protein in cells of an affected proband and of healthy family members with a CHD3 protein-truncating variant suggested that compensation of expression from the wild-type allele is unlikely to be an underlying mechanism. Notably, most inherited CHD3 variants were maternally transmitted. CONCLUSION Our results point to a significant role of inherited variation in Snijders Blok-Campeau syndrome, a finding that is critical for correct variant interpretation and genetic counseling and warrants further investigation toward understanding the broader contributions of such variation to the landscape of human disease.
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11
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Nawaz MS, Einarsson G, Bustamante M, Gisladottir RS, Walters GB, Jonsdottir GA, Skuladottir AT, Bjornsdottir G, Magnusson SH, Asbjornsdottir B, Unnsteinsdottir U, Sigurdsson E, Jonsson PV, Palmadottir VK, Gudjonsson SA, Halldorsson GH, Ferkingstad E, Jonsdottir I, Thorleifsson G, Holm H, Thorsteinsdottir U, Sulem P, Gudbjartsson DF, Stefansson H, Thorgeirsson TE, Ulfarsson MO, Stefansson K. Thirty novel sequence variants impacting human intracranial volume. Brain Commun 2022; 4:fcac271. [PMID: 36415660 PMCID: PMC9677475 DOI: 10.1093/braincomms/fcac271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/16/2022] [Accepted: 10/20/2022] [Indexed: 11/14/2022] Open
Abstract
Intracranial volume, measured through magnetic resonance imaging and/or estimated from head circumference, is heritable and correlates with cognitive traits and several neurological disorders. We performed a genome-wide association study meta-analysis of intracranial volume (n = 79 174) and found 64 associating sequence variants explaining 5.0% of its variance. We used coding variation, transcript and protein levels, to uncover 12 genes likely mediating the effect of these variants, including GLI3 and CDK6 that affect cranial synostosis and microcephaly, respectively. Intracranial volume correlates genetically with volumes of cortical and sub-cortical regions, cognition, learning, neonatal and neurological traits. Parkinson's disease cases have greater and attention deficit hyperactivity disorder cases smaller intracranial volume than controls. Our Mendelian randomization studies indicate that intracranial volume associated variants either increase the risk of Parkinson's disease and decrease the risk of attention deficit hyperactivity disorder and neuroticism or correlate closely with a confounder.
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Affiliation(s)
- Muhammad Sulaman Nawaz
- deCODE genetics/Amgen Inc., Sturlugata 8, 102 Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland
| | | | | | - Rosa S Gisladottir
- deCODE genetics/Amgen Inc., Sturlugata 8, 102 Reykjavik, Iceland.,School of Humanities, University of Iceland, Saemundargata 2, 102 Reykjavik, Iceland
| | - G Bragi Walters
- deCODE genetics/Amgen Inc., Sturlugata 8, 102 Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland
| | | | | | | | | | | | | | - Engilbert Sigurdsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland.,Department of Psychiatry, Landspitali-National University Hospital, Hringbraut 101, 101 Reykjavik, Iceland
| | - Palmi V Jonsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland.,Department of Geriatric Medicine, Landspitali University Hospital, Hringbraut 101, 101 Reykjavik, Iceland
| | - Vala Kolbrun Palmadottir
- Department of Internal Medicine, Landspitali University Hospital, Hringbraut 101, 101 Reykjavik, Iceland
| | | | - Gisli H Halldorsson
- deCODE genetics/Amgen Inc., Sturlugata 8, 102 Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Taeknigardur, Dunhagi 5, 107 Reykjavik, Iceland
| | - Egil Ferkingstad
- deCODE genetics/Amgen Inc., Sturlugata 8, 102 Reykjavik, Iceland
| | | | | | - Hilma Holm
- deCODE genetics/Amgen Inc., Sturlugata 8, 102 Reykjavik, Iceland
| | | | - Patrick Sulem
- deCODE genetics/Amgen Inc., Sturlugata 8, 102 Reykjavik, Iceland
| | | | | | | | - Magnus O Ulfarsson
- deCODE genetics/Amgen Inc., Sturlugata 8, 102 Reykjavik, Iceland.,Faculty of Electrical and Computer Engineering, University of Iceland, Taeknigardur, Dunhagi 5, 107 Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen Inc., Sturlugata 8, 102 Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland
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12
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Di Giovannantonio M, Harris BH, Zhang P, Kitchen-Smith I, Xiong L, Sahgal N, Stracquadanio G, Wallace M, Blagden S, Lord S, Harris D, Harris AHL, Buffa FM, Bond GL. Heritable genetic variants in key cancer genes link cancer risk with anthropometric traits. J Med Genet 2021; 58:392-399. [PMID: 32591342 PMCID: PMC8142426 DOI: 10.1136/jmedgenet-2019-106799] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Height and other anthropometric measures are consistently found to associate with differential cancer risk. However, both genetic and mechanistic insights into these epidemiological associations are notably lacking. Conversely, inherited genetic variants in tumour suppressors and oncogenes increase cancer risk, but little is known about their influence on anthropometric traits. METHODS By integrating inherited and somatic cancer genetic data from the Genome-Wide Association Study Catalog, expression Quantitative Trait Loci databases and the Cancer Gene Census, we identify SNPs that associate with different cancer types and differential gene expression in at least one tissue type, and explore the potential pleiotropic associations of these SNPs with anthropometric traits through SNP-wise association in a cohort of 500,000 individuals. RESULTS We identify three regulatory SNPs for three important cancer genes, FANCA, MAP3K1 and TP53 that associate with both anthropometric traits and cancer risk. Of particular interest, we identify a previously unrecognised strong association between the rs78378222[C] SNP in the 3' untranslated region (3'-UTR) of TP53 and both increased risk for developing non-melanomatous skin cancer (OR=1.36 (95% 1.31 to 1.41), adjusted p=7.62E-63), brain malignancy (OR=3.12 (2.22 to 4.37), adjusted p=1.43E-12) and increased standing height (adjusted p=2.18E-24, beta=0.073±0.007), lean body mass (adjusted p=8.34E-37, beta=0.073±0.005) and basal metabolic rate (adjusted p=1.13E-31, beta=0.076±0.006), thus offering a novel genetic link between these anthropometric traits and cancer risk. CONCLUSION Our results clearly demonstrate that heritable variants in key cancer genes can associate with both differential cancer risk and anthropometric traits in the general population, thereby lending support for a genetic basis for linking these human phenotypes.
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Affiliation(s)
- Matteo Di Giovannantonio
- Computational Biology & Integrative Genomics Lab, Department of Oncology, Medical Science Division, University of Oxford, Oxford, UK
- Ludwig Cancer Institute, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Benjamin Hl Harris
- Computational Biology & Integrative Genomics Lab, Department of Oncology, Medical Science Division, University of Oxford, Oxford, UK
| | - Ping Zhang
- Ludwig Cancer Institute, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Isaac Kitchen-Smith
- Ludwig Cancer Institute, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Lingyun Xiong
- Ludwig Cancer Institute, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Natasha Sahgal
- Ludwig Cancer Institute, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Giovanni Stracquadanio
- Ludwig Cancer Institute, Medical Sciences Division, University of Oxford, Oxford, UK
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Marsha Wallace
- Ludwig Cancer Institute, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Sarah Blagden
- Cancer Therapeutics and mRNA Dysregulation, Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Simon Lord
- Early Phase Clinical Trials Unit, Department of Oncology, Medical Siences Division, University of Oxford, Oxford, UK
| | - David Harris
- St Anne's College, University of Oxford, Oxford, UK
| | - Adrian H L Harris
- Molecular Oncology Laboratories, Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Francesca M Buffa
- Computational Biology & Integrative Genomics Lab, Department of Oncology, Medical Science Division, University of Oxford, Oxford, UK
| | - Gareth L Bond
- Ludwig Cancer Institute, Medical Sciences Division, University of Oxford, Oxford, UK
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
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13
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Pinot de Moira A, Haakma S, Strandberg-Larsen K, van Enckevort E, Kooijman M, Cadman T, Cardol M, Corpeleijn E, Crozier S, Duijts L, Elhakeem A, Eriksson JG, Felix JF, Fernández-Barrés S, Foong RE, Forhan A, Grote V, Guerlich K, Heude B, Huang RC, Järvelin MR, Jørgensen AC, Mikkola TM, Nader JLT, Pedersen M, Popovic M, Rautio N, Richiardi L, Ronkainen J, Roumeliotaki T, Salika T, Sebert S, Vinther JL, Voerman E, Vrijheid M, Wright J, Yang TC, Zariouh F, Charles MA, Inskip H, Jaddoe VWV, Swertz MA, Nybo Andersen AM. The EU Child Cohort Network's core data: establishing a set of findable, accessible, interoperable and re-usable (FAIR) variables. Eur J Epidemiol 2021; 36:565-580. [PMID: 33884544 PMCID: PMC8159791 DOI: 10.1007/s10654-021-00733-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/14/2021] [Indexed: 10/24/2022]
Abstract
The Horizon2020 LifeCycle Project is a cross-cohort collaboration which brings together data from multiple birth cohorts from across Europe and Australia to facilitate studies on the influence of early-life exposures on later health outcomes. A major product of this collaboration has been the establishment of a FAIR (findable, accessible, interoperable and reusable) data resource known as the EU Child Cohort Network. Here we focus on the EU Child Cohort Network's core variables. These are a set of basic variables, derivable by the majority of participating cohorts and frequently used as covariates or exposures in lifecourse research. First, we describe the process by which the list of core variables was established. Second, we explain the protocol according to which these variables were harmonised in order to make them interoperable. Third, we describe the catalogue developed to ensure that the network's data are findable and reusable. Finally, we describe the core data, including the proportion of variables harmonised by each cohort and the number of children for whom harmonised core data are available. EU Child Cohort Network data will be analysed using a federated analysis platform, removing the need to physically transfer data and thus making the data more accessible to researchers. The network will add value to participating cohorts by increasing statistical power and exposure heterogeneity, as well as facilitating cross-cohort comparisons, cross-validation and replication. Our aim is to motivate other cohorts to join the network and encourage the use of the EU Child Cohort Network by the wider research community.
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Affiliation(s)
- Angela Pinot de Moira
- Section for Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
| | - Sido Haakma
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Katrine Strandberg-Larsen
- Section for Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Esther van Enckevort
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marjolein Kooijman
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Tim Cadman
- Population Health Science, Bristol Medical School, Bristol, BS8 2BN, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2PS, UK
| | - Marloes Cardol
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Eva Corpeleijn
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sarah Crozier
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK
- NIHR Applied Research Collaboration Wessex, Southampton Science Park, Innovation Centre, 2 Venture Road, Chilworth, Southampton, SO16 7NP, UK
| | - Liesbeth Duijts
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Ahmed Elhakeem
- Population Health Science, Bristol Medical School, Bristol, BS8 2BN, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2PS, UK
| | - Johan G Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Singapore Institute for Clinical Sciences (SICS), Agency for Science and Technology (A*STAR), Singapore, Singapore
| | - Janine F Felix
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Sílvia Fernández-Barrés
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Rachel E Foong
- Telethon Kids Institute, Perth, WA, Australia
- School of Physiotherapy and Exercise Science, Curtin University, Perth, WA, Australia
| | - Anne Forhan
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France
| | - Veit Grote
- Division of Metabolic and Nutritional Medicine, Department of Pediatrics, Dr. von Hauner Children's Hospital, LMU University Hospital Munich, Munich, Germany
| | - Kathrin Guerlich
- Division of Metabolic and Nutritional Medicine, Department of Pediatrics, Dr. von Hauner Children's Hospital, LMU University Hospital Munich, Munich, Germany
| | - Barbara Heude
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France
| | | | - Marjo-Riitta Järvelin
- Faculty of Medicine, Center for Life-Course Health Research, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Anne Cathrine Jørgensen
- Section for Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Tuija M Mikkola
- Folkhälsan Research Center, Helsinki, Finland
- Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Johanna L T Nader
- Department of Genetics and Bioinformatics, Division of Health Data and Digitalisation, Norwegian Institute of Public Health, Oslo, Norway
| | - Marie Pedersen
- Section for Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Maja Popovic
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Nina Rautio
- Faculty of Medicine, Center for Life-Course Health Research, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland
| | - Lorenzo Richiardi
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Justiina Ronkainen
- Faculty of Medicine, Center for Life-Course Health Research, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland
| | - Theano Roumeliotaki
- Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Theodosia Salika
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Sylvain Sebert
- Faculty of Medicine, Center for Life-Course Health Research, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland
| | - Johan L Vinther
- Section for Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Ellis Voerman
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Martine Vrijheid
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - John Wright
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Tiffany C Yang
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Faryal Zariouh
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France
| | - Marie-Aline Charles
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France
- ELFE Joint Unit, French Institute for Demographic Studies (Ined), French Institute for Medical Research and Health (INSERM), French Blood Agency, Aubervilliers, France
| | - Hazel Inskip
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Vincent W V Jaddoe
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Morris A Swertz
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anne-Marie Nybo Andersen
- Section for Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
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14
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Kirkpatrick RM, Pritikin JN, Hunter MD, Neale MC. Combining Structural-Equation Modeling with Genomic-Relatedness-Matrix Restricted Maximum Likelihood in OpenMx. Behav Genet 2021; 51:331-342. [PMID: 33439421 PMCID: PMC8096671 DOI: 10.1007/s10519-020-10037-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/07/2020] [Indexed: 11/29/2022]
Abstract
There is a long history of fitting biometrical structural-equation models (SEMs) in the pregenomic behavioral-genetics literature of twin, family, and adoption studies. Recently, a method has emerged for estimating biometrical variance-covariance components based not upon the expected degree of genetic resemblance among relatives, but upon the observed degree of genetic resemblance among unrelated individuals for whom genome-wide genotypes are available-genomic-relatedness-matrix restricted maximum-likelihood (GREML). However, most existing GREML software is concerned with quickly and efficiently estimating heritability coefficients, genetic correlations, and so on, rather than with allowing the user to fit SEMs to multitrait samples of genotyped participants. We therefore introduce a feature in the OpenMx package, "mxGREML", designed to fit the biometrical SEMs from the pregenomic era in present-day genomic study designs. We explain the additional functionality this new feature has brought to OpenMx, and how the new functionality works. We provide an illustrative example of its use. We discuss the feature's current limitations, and our plans for its further development.
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Affiliation(s)
- Robert M Kirkpatrick
- Virginia Commonwealth University, Richmond, USA.
- Virginia Institute for Psychiatric & Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, 23298-0126, USA.
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15
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16
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Jansen PR, Nagel M, Watanabe K, Wei Y, Savage JE, de Leeuw CA, van den Heuvel MP, van der Sluis S, Posthuma D. Genome-wide meta-analysis of brain volume identifies genomic loci and genes shared with intelligence. Nat Commun 2020; 11:5606. [PMID: 33154357 PMCID: PMC7644755 DOI: 10.1038/s41467-020-19378-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 10/06/2020] [Indexed: 12/22/2022] Open
Abstract
The phenotypic correlation between human intelligence and brain volume (BV) is considerable (r ≈ 0.40), and has been shown to be due to shared genetic factors. To further examine specific genetic factors driving this correlation, we present genomic analyses of the genetic overlap between intelligence and BV using genome-wide association study (GWAS) results. First, we conduct a large BV GWAS meta-analysis (N = 47,316 individuals), followed by functional annotation and gene-mapping. We identify 18 genomic loci (14 not previously associated), implicating 343 genes (270 not previously associated) and 18 biological pathways for BV. Second, we use an existing GWAS for intelligence (N = 269,867 individuals), and estimate the genetic correlation (rg) between BV and intelligence to be 0.24. We show that the rg is partly attributable to physical overlap of GWAS hits in 5 genomic loci. We identify 92 shared genes between BV and intelligence, which are mainly involved in signaling pathways regulating cell growth. Out of these 92, we prioritize 32 that are most likely to have functional impact. These results provide information on the genetics of BV and provide biological insight into BV's shared genetic etiology with intelligence.
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Affiliation(s)
- Philip R Jansen
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mats Nagel
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Kyoko Watanabe
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Yongbin Wei
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jeanne E Savage
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Christiaan A de Leeuw
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Martijn P van den Heuvel
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Child and Adolescent Psychiatry and Psychology, Section Complex Trait Genetics, Amsterdam Neuroscience, Vrije Universiteit Medical Center, Amsterdam UMC, Amsterdam, The Netherlands
| | - Sophie van der Sluis
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Child and Adolescent Psychiatry and Psychology, Section Complex Trait Genetics, Amsterdam Neuroscience, Vrije Universiteit Medical Center, Amsterdam UMC, Amsterdam, The Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
- Department of Child and Adolescent Psychiatry and Psychology, Section Complex Trait Genetics, Amsterdam Neuroscience, Vrije Universiteit Medical Center, Amsterdam UMC, Amsterdam, The Netherlands.
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17
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Vogelezang S, Bradfield JP, Ahluwalia TS, Curtin JA, Lakka TA, Grarup N, Scholz M, van der Most PJ, Monnereau C, Stergiakouli E, Heiskala A, Horikoshi M, Fedko IO, Vilor-Tejedor N, Cousminer DL, Standl M, Wang CA, Viikari J, Geller F, Íñiguez C, Pitkänen N, Chesi A, Bacelis J, Yengo L, Torrent M, Ntalla I, Helgeland Ø, Selzam S, Vonk JM, Zafarmand MH, Heude B, Farooqi IS, Alyass A, Beaumont RN, Have CT, Rzehak P, Bilbao JR, Schnurr TM, Barroso I, Bønnelykke K, Beilin LJ, Carstensen L, Charles MA, Chawes B, Clément K, Closa-Monasterolo R, Custovic A, Eriksson JG, Escribano J, Groen-Blokhuis M, Grote V, Gruszfeld D, Hakonarson H, Hansen T, Hattersley AT, Hollensted M, Hottenga JJ, Hyppönen E, Johansson S, Joro R, Kähönen M, Karhunen V, Kiess W, Knight BA, Koletzko B, Kühnapfel A, Landgraf K, Langhendries JP, Lehtimäki T, Leinonen JT, Li A, Lindi V, Lowry E, Bustamante M, Medina-Gomez C, Melbye M, Michaelsen KF, Morgen CS, Mori TA, Nielsen TRH, Niinikoski H, Oldehinkel AJ, Pahkala K, Panoutsopoulou K, Pedersen O, Pennell CE, Power C, Reijneveld SA, Rivadeneira F, Simpson A, Sly PD, Stokholm J, Teo KK, Thiering E, Timpson NJ, Uitterlinden AG, van Beijsterveldt CEM, van Schaik BDC, Vaudel M, Verduci E, Vinding RK, Vogel M, Zeggini E, Sebert S, Lind MV, Brown CD, Santa-Marina L, Reischl E, Frithioff-Bøjsøe C, Meyre D, Wheeler E, Ong K, Nohr EA, Vrijkotte TGM, Koppelman GH, Plomin R, Njølstad PR, Dedoussis GD, Froguel P, Sørensen TIA, Jacobsson B, Freathy RM, Zemel BS, Raitakari O, Vrijheid M, Feenstra B, Lyytikäinen LP, Snieder H, Kirsten H, Holt PG, Heinrich J, Widén E, Sunyer J, Boomsma DI, Järvelin MR, Körner A, Davey Smith G, Holm JC, Atalay M, Murray C, Bisgaard H, McCarthy MI, Jaddoe VWV, Grant SFA, Felix JF. Novel loci for childhood body mass index and shared heritability with adult cardiometabolic traits. PLoS Genet 2020; 16:e1008718. [PMID: 33045005 PMCID: PMC7581004 DOI: 10.1371/journal.pgen.1008718] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/22/2020] [Accepted: 03/16/2020] [Indexed: 01/22/2023] Open
Abstract
The genetic background of childhood body mass index (BMI), and the extent to which the well-known associations of childhood BMI with adult diseases are explained by shared genetic factors, are largely unknown. We performed a genome-wide association study meta-analysis of BMI in 61,111 children aged between 2 and 10 years. Twenty-five independent loci reached genome-wide significance in the combined discovery and replication analyses. Two of these, located near NEDD4L and SLC45A3, have not previously been reported in relation to either childhood or adult BMI. Positive genetic correlations of childhood BMI with birth weight and adult BMI, waist-to-hip ratio, diastolic blood pressure and type 2 diabetes were detected (Rg ranging from 0.11 to 0.76, P-values <0.002). A negative genetic correlation of childhood BMI with age at menarche was observed. Our results suggest that the biological processes underlying childhood BMI largely, but not completely, overlap with those underlying adult BMI. The well-known observational associations of BMI in childhood with cardio-metabolic diseases in adulthood may reflect partial genetic overlap, but in light of previous evidence, it is also likely that they are explained through phenotypic continuity of BMI from childhood into adulthood.
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Affiliation(s)
- Suzanne Vogelezang
- The Generation R Study Group, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jonathan P. Bradfield
- Quantinuum Research LLC, San Diego, California, United States of America
- Center for Applied Genomics, Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Tarunveer S. Ahluwalia
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - John A. Curtin
- Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre, and Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Timo A. Lakka
- Institute of Biomedicine, Physiology, University of Eastern Finland, Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Peter J. van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Claire Monnereau
- The Generation R Study Group, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Evie Stergiakouli
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- School of Oral and Dental Sciences, University of Bristol, Bristol, United Kingdom
| | - Anni Heiskala
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Momoko Horikoshi
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Iryna O. Fedko
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Natalia Vilor-Tejedor
- ISGlobal, Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
- BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Diana L. Cousminer
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marie Standl
- Institute of Epidemiology, Helmholtz Zentrum München- German Research Center for Environmental Health, Neuherberg, Germany
| | - Carol A. Wang
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Newcastle, Australia
| | - Jorma Viikari
- Department of Medicine, University of Turku, Turku, Finland
- Division of Medicine, Turku University Hospital, Turku, Finland
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Carmen Íñiguez
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Statistics and Computational Research–Universitat de València, València, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, València, Spain
| | - Niina Pitkänen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Alessandra Chesi
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Jonas Bacelis
- Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Obstetrics and Gynecology, Gothenburg Sweden
| | - Loic Yengo
- University Lille, Centre National de la Recherche Scientifique, Institut Pasteur de Lille, UMR 8199—European Genomic Institute for Diabetes, Lille, France
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Maties Torrent
- Area de Salut de Menorca ib-salut, Menorca, Spain
- Institut d'Investigacio Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Ioanna Ntalla
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Øyvind Helgeland
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Saskia Selzam
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Judith M. Vonk
- Department of Epidemiology, GRIAC (Groningen Research Institute for Asthma and COPD), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mohammed H. Zafarmand
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Obstetrics & Gynecology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Barbara Heude
- Université de Paris, CRESS, INSERM, INRA, Paris, France
| | - Ismaa Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Akram Alyass
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Robin N. Beaumont
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, United Kingdom
| | - Christian T. Have
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Rzehak
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Jose Ramon Bilbao
- University of the Basque Country (UPV/EHU), Leioa, Spain
- Biocrues-Bizkaia Health Research Institute, Barakaldo, Spain
- CIBER Diabetes y Enfermedades Metabólicas (CIBERDEM), Spain
| | - Theresia M. Schnurr
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Inês Barroso
- Wellcome Sanger Institute, Cambridge, United Kingdom
- MRC Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Lawrence J. Beilin
- Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Lisbeth Carstensen
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Bo Chawes
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Karine Clément
- Nutrition and Obesities; systemic approaches research unit, Sorbonne University, INSERM, Pitie- Salpêtrière Hospital, Assistance Publique hôpital de Paris, Paris, France
| | - Ricardo Closa-Monasterolo
- Pediatrics, Nutrition and Development Research Unit, Universitat Rovira i Virgili, IISPV, Reus, Spain
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Johan G. Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Obstetrics & Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Joaquin Escribano
- Pediatrics, Nutrition and Development Research Unit, Universitat Rovira i Virgili, IISPV, Reus, Spain
| | - Maria Groen-Blokhuis
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Veit Grote
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Dariusz Gruszfeld
- Neonatal Department, Children's Memorial Health Institute, Warsaw, Poland
| | - Hakon Hakonarson
- Center for Applied Genomics, Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States of America
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrew T. Hattersley
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, United Kingdom
- NIHR Exeter Clinical Research Facility, College of Medicine and Health, University of Exeter, and Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Mette Hollensted
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Danish Diabetes Academy, Odense, Denmark
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Elina Hyppönen
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, Adelaide, Australia
- Population, Policy and Practice, UCL Institute of Child Health, University College London, London, United Kingdom
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Stefan Johansson
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Raimo Joro
- Institute of Biomedicine, Physiology, University of Eastern Finland, Kuopio, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
- Department of Clinical Physiology, Finnish Cardiovascular Research Center—Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ville Karhunen
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, United Kingdom
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, United Kingdom
| | - Wieland Kiess
- Center for Pediatric Research, University Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
| | - Bridget A. Knight
- NIHR Exeter Clinical Research Facility, College of Medicine and Health, University of Exeter, and Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Berthold Koletzko
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Andreas Kühnapfel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Kathrin Landgraf
- Center for Pediatric Research, University Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
- Integrated Research and Treatment Center (IFB) Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | | | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center—Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jaakko T. Leinonen
- Institute For Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - Aihuali Li
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Virpi Lindi
- University of Eastern Finland Library Kuopio, Kuopio, Finland
| | - Estelle Lowry
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Biocenter Oulu, Oulu University Hospital, Oulu, Finland
| | - Mariona Bustamante
- ISGlobal, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carolina Medina-Gomez
- The Generation R Study Group, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Medicine, Stanford School of Medicine, Stanford, California, United States of America
| | - Kim F. Michaelsen
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Camilla S. Morgen
- Department of Public Health, Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark
- National Insitute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Trevor A. Mori
- Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Tenna R. H. Nielsen
- Department of Pediatrics, Hvidovre Hospital, Hvidovre, Denmark
- The Children’s Obesity Clinic, Department of Pediatrics, Copenhagen University Hospital Holbæk, Holbæk, Denmark
| | - Harri Niinikoski
- Department of Physiology, University of Turku, Turku, Finland
- Department of Pediatrics, University of Turku, Turku, Finland
| | - Albertine J. Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation, University of Groningen, University Medical Center, Groningen, the Netherlands
| | - Katja Pahkala
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Paavo Nurmi Centre, Sports and Exercise Medicine Unit, Department of Physical Activity and Health, University of Turku, Turku, Finland
| | - Kalliope Panoutsopoulou
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Craig E. Pennell
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Newcastle, Australia
| | - Christine Power
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Sijmen A. Reijneveld
- Department of Health Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Angela Simpson
- Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre, and Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Peter D. Sly
- Child Health Research Centre, University of Queensland, Brisbane, Australia
- World Health Organization, WHO Collaborating Centre for Children’s Health and Environment, Brisbane, Queensland, Australia
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Kook K. Teo
- Department of Medicine, McMaster University, Hamilton, Canada; Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Elisabeth Thiering
- Institute of Epidemiology, Helmholtz Zentrum München- German Research Center for Environmental Health, Neuherberg, Germany
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Nicholas J. Timpson
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging NCHA), Leiden, the Netherlands
| | | | - Barbera D. C. van Schaik
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Marc Vaudel
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Elvira Verduci
- Department of Pediatrics, San Paolo Hospital, University of Milan, Milan, Italy
| | - Rebecca K. Vinding
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Mandy Vogel
- Center for Pediatric Research, University Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
- Integrated Research and Treatment Center (IFB) Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Eleftheria Zeggini
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- Institute of Translational Genomics, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- TUM School of Medicine, Technical University of Munich and Klinikum Rechts der Isar, Munich, Germany
| | - Sylvain Sebert
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Biocenter Oulu, Oulu University Hospital, Oulu, Finland
- Section of Genomics of Common Disease, Department of Medicine, Imperial College London, London, United Kingdom
| | - Mads V. Lind
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Christopher D. Brown
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Loreto Santa-Marina
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiologia y Salud Publica-CIBERESP), Barcelona, Spain
- Biodonostia Health Research Institute, San Sebastian, Spain
- Subdirección Salud Pública de Gipuzkoa, San Sebastian, Spain
| | - Eva Reischl
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Muenchen, Munich, Germany
| | - Christine Frithioff-Bøjsøe
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, Department of Pediatrics, Copenhagen University Hospital Holbæk, Holbæk, Denmark
- University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen N, Denmark
| | - David Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Eleanor Wheeler
- Wellcome Sanger Institute, Cambridge, United Kingdom
- MRC Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Ken Ong
- Medical Research Council Epidemiology Unit & Department of Paediatrics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, England
| | - Ellen A. Nohr
- Research Unit for Gynaecology and Obstetrics, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Tanja G. M. Vrijkotte
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Gerard H. Koppelman
- University Medical Center Groningen, University of Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC (Groningen Research Institute for Asthma and COPD), Groningen, the Netherlands
| | - Robert Plomin
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Pål R. Njølstad
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics and Adolescents, Haukeland University Hospital, Bergen, Norway
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - George D. Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Philippe Froguel
- University Lille, Centre National de la Recherche Scientifique, Institut Pasteur de Lille, UMR 8199—European Genomic Institute for Diabetes, Lille, France
- Section of Genomics of Common Disease, Department of Medicine, Imperial College London, London, United Kingdom
| | - Thorkild I. A. Sørensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- Department of Public Health, Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Obstetrics and Gynecology, Gothenburg Sweden
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Rachel M. Freathy
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, United Kingdom
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Babette S. Zemel
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States of America
- Division of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Martine Vrijheid
- ISGlobal, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center—Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere, Finland
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Patrick G. Holt
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Joachim Heinrich
- Institute of Epidemiology, Helmholtz Zentrum München- German Research Center for Environmental Health, Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Inner City Clinic, University Hospital Munich, Ludwig-Maximilians-Universität of Munich, Munich, Germany
- Allergy and Lung Health Unit, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Elisabeth Widén
- Institute For Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - Jordi Sunyer
- ISGlobal, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Dorret I. Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health research institute and Amsterdam Reproduction & Development research Institute, Amsterdam, the Netherlands
| | - Marjo-Riitta Järvelin
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, United Kingdom
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, United Kingdom
| | - Antje Körner
- Center for Pediatric Research, University Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
- Integrated Research and Treatment Center (IFB) Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - George Davey Smith
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Jens-Christian Holm
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, Department of Pediatrics, Copenhagen University Hospital Holbæk, Holbæk, Denmark
- University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen N, Denmark
| | - Mustafa Atalay
- Institute of Biomedicine, Physiology, University of Eastern Finland, Kuopio, Finland
| | - Clare Murray
- Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre, and Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Mark I. McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom
- Oxford National Institute for Health Research (NIHR) Biomedical Research Centre, Churchill Hospital, Oxford, United Kingdom
| | | | - Vincent W. V. Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Struan F. A. Grant
- Center for Applied Genomics, Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Neonatal Department, Children's Memorial Health Institute, Warsaw, Poland
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Janine F. Felix
- The Generation R Study Group, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- * E-mail:
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18
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Genetic variation in APOE, GRN, and TP53 are phenotype modifiers in frontotemporal dementia. Neurobiol Aging 2020; 99:99.e15-99.e22. [PMID: 32972771 DOI: 10.1016/j.neurobiolaging.2020.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 11/21/2022]
Abstract
Frontotemporal dementia (FTD) is a clinical, genetic, and pathologic heterogeneous group of neurodegenerative diseases. In this study, we investigated the role of APOƐ4, rs5848 in GRN, and rs1042522 in TP53 gene as disease risk factors and/or phenotype modifiers in 440 FTD patients, including 175 C9orf72 expansion carriers. We found that the C9orf72 expansion carriers showing an earlier age at onset (p < 0.001). Among the clinical groups, the FTD-MND (motoneuron disease) showed the lowest survival (hazard ratio [HR] = 4.12), and the progressive nonfluent aphasia group showed the highest onset age (p = 0.03). In our cohort, the rs1042522 in TP53 was associated with disease onset (p = 0.02) and survival (HR = 1.73) and rs5848 GRN with a significantly shorter survival in CC homozygous patients (HR = 1.98). The frequency of APOƐ4 carriers was significantly increased in the C9orf72 noncarriers (p = 0.022). Although validation of our findings is necessary, our results suggest that TP53, GRN, and APOE genes may act as phenotype modifiers in FTD and should be considered in future clinical trials.
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19
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Jaddoe VWV, Felix JF, Andersen AMN, Charles MA, Chatzi L, Corpeleijn E, Donner N, Elhakeem A, Eriksson JG, Foong R, Grote V, Haakma S, Hanson M, Harris JR, Heude B, Huang RC, Inskip H, Järvelin MR, Koletzko B, Lawlor DA, Lindeboom M, McEachan RRC, Mikkola TM, Nader JLT, de Moira AP, Pizzi C, Richiardi L, Sebert S, Schwalber A, Sunyer J, Swertz MA, Vafeiadi M, Vrijheid M, Wright J, Duijts L. The LifeCycle Project-EU Child Cohort Network: a federated analysis infrastructure and harmonized data of more than 250,000 children and parents. Eur J Epidemiol 2020; 35:709-724. [PMID: 32705500 PMCID: PMC7387322 DOI: 10.1007/s10654-020-00662-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 07/04/2020] [Indexed: 12/15/2022]
Abstract
Early life is an important window of opportunity to improve health across the full lifecycle. An accumulating body of evidence suggests that exposure to adverse stressors during early life leads to developmental adaptations, which subsequently affect disease risk in later life. Also, geographical, socio-economic, and ethnic differences are related to health inequalities from early life onwards. To address these important public health challenges, many European pregnancy and childhood cohorts have been established over the last 30 years. The enormous wealth of data of these cohorts has led to important new biological insights and important impact for health from early life onwards. The impact of these cohorts and their data could be further increased by combining data from different cohorts. Combining data will lead to the possibility of identifying smaller effect estimates, and the opportunity to better identify risk groups and risk factors leading to disease across the lifecycle across countries. Also, it enables research on better causal understanding and modelling of life course health trajectories. The EU Child Cohort Network, established by the Horizon2020-funded LifeCycle Project, brings together nineteen pregnancy and childhood cohorts, together including more than 250,000 children and their parents. A large set of variables has been harmonised and standardized across these cohorts. The harmonized data are kept within each institution and can be accessed by external researchers through a shared federated data analysis platform using the R-based platform DataSHIELD, which takes relevant national and international data regulations into account. The EU Child Cohort Network has an open character. All protocols for data harmonization and setting up the data analysis platform are available online. The EU Child Cohort Network creates great opportunities for researchers to use data from different cohorts, during and beyond the LifeCycle Project duration. It also provides a novel model for collaborative research in large research infrastructures with individual-level data. The LifeCycle Project will translate results from research using the EU Child Cohort Network into recommendations for targeted prevention strategies to improve health trajectories for current and future generations by optimizing their earliest phases of life.
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Affiliation(s)
- Vincent W V Jaddoe
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, The Generation R Study Group, (Na 29-18), PO Box 2040, 3000 CA, Rotterdam, The Netherlands. .,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Janine F Felix
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, The Generation R Study Group, (Na 29-18), PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Anne-Marie Nybo Andersen
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Marie-Aline Charles
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France.,ELFE Joint Unit, French Institute for Demographic Studies (Ined), French Institute for Medical Research and Health (INSERM), French Blood Agency, Aubervilliers, France
| | - Leda Chatzi
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Eva Corpeleijn
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nina Donner
- Concentris Research Management GmbH, Fürstenfeldbruck, Germany
| | - Ahmed Elhakeem
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Johan G Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland.,Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore.,Singapore Institute for Clinical Sciences (SICS), Agency for Science and Technology (A*STAR), Singapore, Singapore
| | - Rachel Foong
- Telethon Kids Institute, Perth, WA, Australia.,School of Physiotherapy and Exercise Science, Curtin University, Perth, WA, Australia
| | - Veit Grote
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany
| | - Sido Haakma
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands
| | - Mark Hanson
- Institute of Developmental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Jennifer R Harris
- Centre for Fertility and Health, The Norwegian Institute of Public Health, Oslo, Norway.,Division of Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Barbara Heude
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France
| | | | - Hazel Inskip
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK.,MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Marjo-Riitta Järvelin
- Center for Life-Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.,Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK.,Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
| | - Berthold Koletzko
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Maarten Lindeboom
- Department of Economics, VU University Amsterdam, Amsterdam, The Netherlands
| | - Rosemary R C McEachan
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | | | - Johanna L T Nader
- Department of Genetics and Bioinformatics, Division of Health Data and Digitalisation, Norwegian Institute of Public Health, Oslo, Norway
| | - Angela Pinot de Moira
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Costanza Pizzi
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Lorenzo Richiardi
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Sylvain Sebert
- Center for Life-Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Ameli Schwalber
- Concentris Research Management GmbH, Fürstenfeldbruck, Germany
| | - Jordi Sunyer
- ISGlobal, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Morris A Swertz
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marina Vafeiadi
- Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Martine Vrijheid
- ISGlobal, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - John Wright
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Liesbeth Duijts
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, The Generation R Study Group, (Na 29-18), PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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20
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Valge M, Meitern R, Hõrak P. Morphometric traits predict educational attainment independently of socioeconomic background. BMC Public Health 2019; 19:1696. [PMID: 31852467 PMCID: PMC6921596 DOI: 10.1186/s12889-019-8072-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/11/2019] [Indexed: 02/08/2023] Open
Abstract
Background Aim of this study is to describe the relationship between anthropometric traits and educational attainment among Estonian schoolchildren born between 1937 and 1962. We asked whether height, cranial volume and face width (a testosterone-dependent trait), measured in childhood predict later educational attainment independently of each other, family socioeconomic position (SEP) and sex. Associations between morphometric traits and education and their interactions with biosocial variables are of scholarly importance because higher education is nearly universally associated with low fertility in women, and often with high fertility in men. Hence, morphometric traits associated with educational attainment are targeted by natural selection and describing the exact nature of these associations is relevant for understanding the current patterns of evolution of human body size. Methods Data on morphometric measurements and family background of 11,032 Estonian schoolchildren measured between seven and 19 years of age were obtained from the study performed by Juhan Aul between 1956 and 1969. Ordinal logistic regression was used for testing the effects of morphometric traits, biosocial variables and their interaction on the cumulative probability of obtaining education beyond primary level. Results Of biosocial variables, family SEP was the most important determinant of educational attainment, followed by the sex, rural vs urban origin and the number of siblings. No significant interactions with morphometric traits were detected, i.e., within each category of SEP, rural vs urban origin and sex, taller children and those with larger heads and relatively narrower faces were more likely to proceed to secondary and/or tertiary education. The effect of height on education was independent of cranial volume, indicating that taller children did not obtain more educations because their brains were larger than those of shorter children; height per se was important. Conclusions Our main finding – that adjusting for other morphometric traits and biosocial variables, morphometric traits still robustly predicted educational attainment, is relevant for understanding the current patterns of evolution of human body size. Our findings suggest that fecundity selection acting on educational attainment could be partly responsible for the concurrent selection for smaller stature and cranial volume in women and opposite trends in men.
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Affiliation(s)
- Markus Valge
- Department of Zoology, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
| | - Richard Meitern
- Department of Zoology, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
| | - Peeter Hõrak
- Department of Zoology, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia.
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21
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Chen X, Liu N, Liu L, Chen W, Chen N, Lin M, Xu J, Zhou X, Wang H, Zhao M, Xiao X. Thermodynamics and kinetics guided probe design for uniformly sensitive and specific DNA hybridization without optimization. Nat Commun 2019; 10:4675. [PMID: 31611572 PMCID: PMC6791858 DOI: 10.1038/s41467-019-12593-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/18/2019] [Indexed: 12/15/2022] Open
Abstract
Sensitive and specific DNA hybridization is essential for nucleic acid chemistry. Competitive composition of probe and blocker has been the most adopted probe design for its relatively high sensitivity and specificity. However, the sensitivity and specificity were inversely correlated over the length and concentration of the blocker strand, making the optimization process cumbersome. Herein, we construct a theoretical model for competitive DNA hybridization, which disclose that both the thermodynamics and kinetics contribute to the inverse correlation. Guided by this, we invent the 4-way Strand Exchange LEd Competitive DNA Testing (SELECT) system, which breaks up the inverse correlation. Using SELECT, we identified 16 hot-pot mutations in human genome under uniform conditions, without optimization at all. The specificities were all above 140. As a demonstration of the clinical practicability, we develop probe systems that detect mutations in human genomic DNA extracted from ovarian cancer patients with a detection limit of 0.1%. Optimisation of nucleic acid probes and blocker strands can be laborious. Here the authors construct a theoretical model of competitive DNA hybridisation to design DNA probes for optimisation-free mutation detection.
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Affiliation(s)
- Xin Chen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Na Liu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Liquan Liu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Wei Chen
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, PR China
| | - Na Chen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Meng Lin
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Jiaju Xu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Xing Zhou
- Department of Obstetrics and Gynaecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, PR China
| | - Hongbo Wang
- Department of Obstetrics and Gynaecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, PR China.
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, PR China.
| | - Xianjin Xiao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China. .,Department of Obstetrics and Gynaecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, PR China.
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22
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Yang XL, Zhang SY, Zhang H, Wei XT, Feng GJ, Pei YF, Zhang L. Three Novel Loci for Infant Head Circumference Identified by a Joint Association Analysis. Front Genet 2019; 10:947. [PMID: 31681408 PMCID: PMC6798153 DOI: 10.3389/fgene.2019.00947] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/05/2019] [Indexed: 01/02/2023] Open
Abstract
As an important trait at birth, infant head circumference (HC) is associated with a variety of intelligence- and mental-related conditions. Despite being dominated by genetics, the mechanism underlying the variation of HC is poorly understood. Aiming to uncover the genetic basis of HC, we performed a genome-wide joint association analysis by integrating the genome-wide association summary statistics of HC with that of its two related traits, birth length and birth weight, using a recently developed integrative method, multitrait analysis of genome-wide association (MTAG), and performed in silico replication in an independent sample of intracranial volume (N = 26,577). We then conducted a series of bioinformatic investigations on the identified loci. Combining the evidence from both the MTAG analysis and the in silico replication, we identified three novel loci at the genome-wide significance level (α = 5.0 × 10-8): 3q23 [lead single nucleotide polymorphism (SNP) rs9846396, p MTAG = 3.35 × 10-8, p replication = 0.01], 7p15.3 (rs12534093, p MTAG = 2.00 × 10-8, p replication = 0.004), and 9q33.3 (rs7048271 p MTAG = 9.23 × 10-10, p replication = 1.14 × 10-4). Each of the three lead SNPs was associated with at least one of eight brain-related traits including intelligence and educational attainment. Credible risk variants, defined as those SNPs located within 500 kb of the lead SNP and with p values within two orders of magnitude of the lead SNP, were enriched in DNase I hypersensitive site region in brain. Nine candidate genes were prioritized at the three novel loci using multiple sources of information. Gene set enrichment analysis identified one associated pathway GO:0048009, which participates in the development of nervous system. Our findings provide useful insights into the genetic basis of HC and the relationship between brain growth and mental health.
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Affiliation(s)
- Xiao-Lin Yang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College, Soochow University, Jiangsu, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College, Soochow University, Jiangsu, China
| | - Shao-Yan Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College, Soochow University, Jiangsu, China.,Department of Epidemiology and Health Statistics, School of Public Health, Medical College, Soochow University, Jiangsu, China
| | - Hong Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College, Soochow University, Jiangsu, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College, Soochow University, Jiangsu, China
| | - Xin-Tong Wei
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College, Soochow University, Jiangsu, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College, Soochow University, Jiangsu, China
| | - Gui-Juan Feng
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College, Soochow University, Jiangsu, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College, Soochow University, Jiangsu, China
| | - Yu-Fang Pei
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College, Soochow University, Jiangsu, China.,Department of Epidemiology and Health Statistics, School of Public Health, Medical College, Soochow University, Jiangsu, China
| | - Lei Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College, Soochow University, Jiangsu, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College, Soochow University, Jiangsu, China
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