1251
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Mendelian randomization analysis using mixture models for robust and efficient estimation of causal effects. Nat Commun 2019; 10:1941. [PMID: 31028273 PMCID: PMC6486646 DOI: 10.1038/s41467-019-09432-2] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 03/07/2019] [Indexed: 12/22/2022] Open
Abstract
Mendelian randomization (MR) has emerged as a major tool for the investigation of causal relationship among traits, utilizing results from large-scale genome-wide association studies. Bias due to horizontal pleiotropy, however, remains a major concern. We propose a novel approach for robust and efficient MR analysis using large number of genetic instruments, based on a novel spike-detection algorithm under a normal-mixture model for underlying effect-size distributions. Simulations show that the new method, MRMix, provides nearly unbiased or/and less biased estimates of causal effects compared to alternative methods and can achieve higher efficiency than comparably robust estimators. Application of MRMix to publicly available datasets leads to notable observations, including identification of causal effects of BMI and age-at-menarche on the risk of breast cancer; no causal effect of HDL and triglycerides on the risk of coronary artery disease; a strong detrimental effect of BMI on the risk of major depressive disorder. Mendelian randomization (MR) is a powerful and widely used method for causal inference leveraging genetic information. Here, the authors develop MRMix, an MR method using mixture models for more robust and efficient estimation of causal effects.
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1252
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Ge T, Chen CY, Ni Y, Feng YCA, Smoller JW. Polygenic prediction via Bayesian regression and continuous shrinkage priors. Nat Commun 2019; 10:1776. [PMID: 30992449 PMCID: PMC6467998 DOI: 10.1038/s41467-019-09718-5] [Citation(s) in RCA: 763] [Impact Index Per Article: 152.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/25/2019] [Indexed: 01/23/2023] Open
Abstract
Polygenic risk scores (PRS) have shown promise in predicting human complex traits and diseases. Here, we present PRS-CS, a polygenic prediction method that infers posterior effect sizes of single nucleotide polymorphisms (SNPs) using genome-wide association summary statistics and an external linkage disequilibrium (LD) reference panel. PRS-CS utilizes a high-dimensional Bayesian regression framework, and is distinct from previous work by placing a continuous shrinkage (CS) prior on SNP effect sizes, which is robust to varying genetic architectures, provides substantial computational advantages, and enables multivariate modeling of local LD patterns. Simulation studies using data from the UK Biobank show that PRS-CS outperforms existing methods across a wide range of genetic architectures, especially when the training sample size is large. We apply PRS-CS to predict six common complex diseases and six quantitative traits in the Partners HealthCare Biobank, and further demonstrate the improvement of PRS-CS in prediction accuracy over alternative methods.
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Affiliation(s)
- Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Chia-Yen Chen
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Yang Ni
- Department of Statistics, Texas A&M University, College Station, TX, 77843, USA
| | - Yen-Chen Anne Feng
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Jordan W Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
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1253
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Wang DX, Kaur Y, Alyass A, Meyre D. A Candidate-Gene Approach Identifies Novel Associations Between Common Variants in/Near Syndromic Obesity Genes and BMI in Pediatric and Adult European Populations. Diabetes 2019; 68:724-732. [PMID: 30692245 DOI: 10.2337/db18-0986] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/24/2019] [Indexed: 11/13/2022]
Abstract
We hypothesized that monogenic syndromic obesity genes are also involved in the polygenic variation of BMI. Single-marker, tag single nucleotide polymorphism (tagSNP) and gene-based analysis were performed on common variants near 54 syndromic obesity genes. We used publicly available data from meta-analyses of European BMI genome-wide association studies conducted by the Genetic Investigation of ANthropometric Traits (GIANT) Consortium and the UK Biobank (UKB) (N = 681,275 adults). A total of 33 loci were identified, of which 19 of 33 (57.6%) were located at SNPs previously identified by the GIANT Consortium and UKB meta-analysis, 11 of 33 (33.3%) were located at novel SNPs, and 3 of 33 (9.1%) were novel genes identified with gene-based analysis. Both single-marker and tagSNP analyses mapped the previously identified 19 SNPs by the GIANT Consortium and UKB meta-analysis. Gene-based analysis confirmed 15 of 19 (78.9%) of the novel SNPs' associated genes. Of the 11 novel loci, 8 were identified with single-marker analysis and the remaining 3 were identified with tagSNP analysis. Gene-based analysis confirmed 4 of 11 (36.3%) of these loci. Meta-analysis with the Early Growth Genetics (EGG) Consortium (N = 35,668 children) was conducted post hoc for top SNPs, confirming 17 of 33 (51.5%) loci, of which 5 were novel. This study supports evidence for a continuum between rare monogenic syndromic and common polygenic forms of obesity.
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Affiliation(s)
- Dominic X Wang
- Department of Health Research, Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
- Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Yuvreet Kaur
- Department of Health Research, Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Akram Alyass
- Department of Health Research, Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
| | - David Meyre
- Department of Health Research, Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
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1254
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Wray NR, Kemper KE, Hayes BJ, Goddard ME, Visscher PM. Complex Trait Prediction from Genome Data: Contrasting EBV in Livestock to PRS in Humans: Genomic Prediction. Genetics 2019; 211:1131-1141. [PMID: 30967442 PMCID: PMC6456317 DOI: 10.1534/genetics.119.301859] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/20/2019] [Indexed: 12/20/2022] Open
Abstract
In this Review, we focus on the similarity of the concepts underlying prediction of estimated breeding values (EBVs) in livestock and polygenic risk scores (PRS) in humans. Our research spans both fields and so we recognize factors that are very obvious for those in one field, but less so for those in the other. Differences in family size between species is the wedge that drives the different viewpoints and approaches. Large family size achievable in nonhuman species accompanied by selection generates a smaller effective population size, increased linkage disequilibrium and a higher average genetic relationship between individuals within a population. In human genetic analyses, we select individuals unrelated in the classical sense (coefficient of relationship <0.05) to estimate heritability captured by common SNPs. In livestock data, all animals within a breed are to some extent "related," and so it is not possible to select unrelated individuals and retain a data set of sufficient size to analyze. These differences directly or indirectly impact the way data analyses are undertaken. In livestock, genetic segregation variance exposed through samplings of parental genomes within families is directly observable and taken for granted. In humans, this genomic variation is under-recognized for its contribution to variation in polygenic risk of common disease, in both those with and without family history of disease. We explore the equation that predicts the expected proportion of variance explained using PRS, and quantify how GWAS sample size is the key factor for maximizing accuracy of prediction in both humans and livestock. Last, we bring together the concepts discussed to address some frequently asked questions.
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Affiliation(s)
- Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Kathryn E Kemper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
| | - Benjamin J Hayes
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Michael E Goddard
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia
- Faculty of Land and Food Resources, University of Melbourne, Parkville, Victoria, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4067, Australia
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1255
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Visscher PM, Goddard ME. From R.A. Fisher's 1918 Paper to GWAS a Century Later. Genetics 2019; 211:1125-1130. [PMID: 30967441 PMCID: PMC6456325 DOI: 10.1534/genetics.118.301594] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/26/2018] [Indexed: 11/18/2022] Open
Abstract
The genetics and evolution of complex traits, including quantitative traits and disease, have been hotly debated ever since Darwin. A century ago, a paper from R.A. Fisher reconciled Mendelian and biometrical genetics in a landmark contribution that is now accepted as the main foundation stone of the field of quantitative genetics. Here, we give our perspective on Fisher's 1918 paper in the context of how and why it is relevant in today's genome era. We mostly focus on human trait variation, in part because Fisher did so too, but the conclusions are general and extend to other natural populations, and to populations undergoing artificial selection.
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Affiliation(s)
- Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia 4072
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Michael E Goddard
- Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia 3083
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia 3004
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1256
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Abstract
Great care is needed when interpreting claims about the genetic basis of human variation based on data from genome-wide association studies.
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Affiliation(s)
| | - Joachim Hermisson
- Department of Mathematics, University of Vienna, Vienna, Austria.,Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
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1257
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Sohail M, Maier RM, Ganna A, Bloemendal A, Martin AR, Turchin MC, Chiang CWK, Hirschhorn J, Daly MJ, Patterson N, Neale B, Mathieson I, Reich D, Sunyaev SR. Polygenic adaptation on height is overestimated due to uncorrected stratification in genome-wide association studies. eLife 2019; 8:e39702. [PMID: 30895926 PMCID: PMC6428571 DOI: 10.7554/elife.39702] [Citation(s) in RCA: 213] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 01/15/2019] [Indexed: 01/03/2023] Open
Abstract
Genetic predictions of height differ among human populations and these differences have been interpreted as evidence of polygenic adaptation. These differences were first detected using SNPs genome-wide significantly associated with height, and shown to grow stronger when large numbers of sub-significant SNPs were included, leading to excitement about the prospect of analyzing large fractions of the genome to detect polygenic adaptation for multiple traits. Previous studies of height have been based on SNP effect size measurements in the GIANT Consortium meta-analysis. Here we repeat the analyses in the UK Biobank, a much more homogeneously designed study. We show that polygenic adaptation signals based on large numbers of SNPs below genome-wide significance are extremely sensitive to biases due to uncorrected population stratification. More generally, our results imply that typical constructions of polygenic scores are sensitive to population stratification and that population-level differences should be interpreted with caution. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Mashaal Sohail
- Division of Genetics, Department of MedicineBrigham and Women’s Hospital and Harvard Medical SchoolBostonUnited States
- Department of Biomedical InformaticsHarvard Medical SchoolBostonUnited States
- Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeUnited States
| | - Robert M Maier
- Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeUnited States
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeUnited States
- Analytical and Translational Genetics UnitMassachusetts General HospitalBostonUnited States
| | - Andrea Ganna
- Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeUnited States
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeUnited States
- Analytical and Translational Genetics UnitMassachusetts General HospitalBostonUnited States
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
- Institute for Molecular Medicine FinlandUniversity of HelsinkiHelsinkiFinland
| | - Alex Bloemendal
- Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeUnited States
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeUnited States
- Analytical and Translational Genetics UnitMassachusetts General HospitalBostonUnited States
| | - Alicia R Martin
- Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeUnited States
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeUnited States
- Analytical and Translational Genetics UnitMassachusetts General HospitalBostonUnited States
| | - Michael C Turchin
- Center for Computational Molecular BiologyBrown UniversityProvidenceUnited States
- Department of Ecology and Evolutionary BiologyBrown UniversityProvidenceUnited States
| | - Charleston WK Chiang
- Department of Preventive Medicine, Center for Genetic Epidemiology, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | - Joel Hirschhorn
- Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeUnited States
- Departments of Pediatrics and GeneticsHarvard Medical SchoolBostonUnited States
- Division of Endocrinology and Center for Basic and Translational Obesity ResearchBoston Children’s HospitalBostonUnited States
| | - Mark J Daly
- Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeUnited States
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeUnited States
- Analytical and Translational Genetics UnitMassachusetts General HospitalBostonUnited States
- Institute for Molecular Medicine FinlandUniversity of HelsinkiHelsinkiFinland
| | - Nick Patterson
- Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Benjamin Neale
- Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeUnited States
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeUnited States
- Analytical and Translational Genetics UnitMassachusetts General HospitalBostonUnited States
| | - Iain Mathieson
- Department of Genetics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaUnited States
| | - David Reich
- Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
- Howard Hughes Medical Institute, Harvard Medical SchoolBostonUnited States
| | - Shamil R Sunyaev
- Department of Biomedical InformaticsHarvard Medical SchoolBostonUnited States
- Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeUnited States
- Division of Genetics, Department of MedicineBrigham and Women’s Hospital and Harvard Medical SchoolBostonUnited States
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1258
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Wiberg A, Ng M, Schmid AB, Smillie RW, Baskozos G, Holmes MV, Künnapuu K, Mägi R, Bennett DL, Furniss D. A genome-wide association analysis identifies 16 novel susceptibility loci for carpal tunnel syndrome. Nat Commun 2019; 10:1030. [PMID: 30833571 PMCID: PMC6399342 DOI: 10.1038/s41467-019-08993-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 02/13/2019] [Indexed: 01/07/2023] Open
Abstract
Carpal tunnel syndrome (CTS) is a common and disabling condition of the hand caused by entrapment of the median nerve at the level of the wrist. It is the commonest entrapment neuropathy, with estimates of prevalence ranging between 5-10%. Here, we undertake a genome-wide association study (GWAS) of an entrapment neuropathy, using 12,312 CTS cases and 389,344 controls identified in UK Biobank. We discover 16 susceptibility loci for CTS with p < 5 × 10-8. We identify likely causal genes in the pathogenesis of CTS, including ADAMTS17, ADAMTS10 and EFEMP1, and using RNA sequencing demonstrate expression of these genes in surgically resected tenosynovium from CTS patients. We perform Mendelian randomisation and demonstrate a causal relationship between short stature and higher risk of CTS. We suggest that variants within genes implicated in growth and extracellular matrix architecture contribute to the genetic predisposition to CTS by altering the environment through which the median nerve transits.
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Affiliation(s)
- Akira Wiberg
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, OX3 7LD, UK.,Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Michael Ng
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, OX3 7LD, UK
| | - Annina B Schmid
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Robert W Smillie
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, OX3 7LD, UK
| | - Georgios Baskozos
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Michael V Holmes
- Medical Research Council Population Health Research Unit at the University of Oxford, Oxford, OX3 7LF, UK.,Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Richard Doll Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7LF, UK
| | - K Künnapuu
- Institute of Technology, University of Tartu, Nooruse 1, 50411, Tartu, Estonia
| | - R Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Riia 23 B, 51010, Tartu, Estonia
| | - David L Bennett
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.
| | - Dominic Furniss
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, OX3 7LD, UK. .,Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, OX3 9DU, UK.
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1259
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Mace E, Innes D, Hunt C, Wang X, Tao Y, Baxter J, Hassall M, Hathorn A, Jordan D. The Sorghum QTL Atlas: a powerful tool for trait dissection, comparative genomics and crop improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:751-766. [PMID: 30343386 DOI: 10.1007/s00122-018-3212-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/11/2018] [Indexed: 05/20/2023]
Abstract
We describe the development and application of the Sorghum QTL Atlas, a high-resolution, open-access research platform to facilitate candidate gene identification across three cereal species, sorghum, maize and rice. The mechanisms governing the genetic control of many quantitative traits are only poorly understood and have yet to be fully exploited. Over the last two decades, over a thousand QTL and GWAS studies have been published in the major cereal crops including sorghum, maize and rice. A large body of information has been generated on the genetic basis of quantitative traits, their genomic location, allelic effects and epistatic interactions. However, such QTL information has not been widely applied by cereal improvement programs and genetic researchers worldwide. In part this is due to the heterogeneous nature of QTL studies which leads QTL reliability variation from study to study. Using approaches to adjust the QTL confidence interval, this platform provides access to the most updated sorghum QTL information than any database available, spanning 23 years of research since 1995. The QTL database provides information on the predicted gene models underlying the QTL CI, across all sorghum genome assembly gene sets and maize and rice genome assemblies and also provides information on the diversity of the underlying genes and information on signatures of selection in sorghum. The resulting high-resolution, open-access research platform facilitates candidate gene identification across 3 cereal species, sorghum, maize and rice. Using a number of trait examples, we demonstrate the power and resolution of the resource to facilitate comparative genomics approaches to provide a bridge between genomics and applied breeding.
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Affiliation(s)
- Emma Mace
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia.
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia.
| | - David Innes
- Department of Agriculture and Fisheries, Ecosciences Precinct, Brisbane, QLD, 4102, Australia
| | - Colleen Hunt
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Xuemin Wang
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia
| | - Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia
| | - Jared Baxter
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Michael Hassall
- Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, QLD, 4350, Australia
| | - Adrian Hathorn
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia
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1260
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Shrine N, Guyatt AL, Erzurumluoglu AM, Jackson VE, Hobbs BD, Melbourne CA, Batini C, Fawcett KA, Song K, Sakornsakolpat P, Li X, Boxall R, Reeve NF, Obeidat M, Zhao JH, Wielscher M, Weiss S, Kentistou KA, Cook JP, Sun BB, Zhou J, Hui J, Karrasch S, Imboden M, Harris SE, Marten J, Enroth S, Kerr SM, Surakka I, Vitart V, Lehtimäki T, Allen RJ, Bakke PS, Beaty TH, Bleecker ER, Bossé Y, Brandsma CA, Chen Z, Crapo JD, Danesh J, DeMeo DL, Dudbridge F, Ewert R, Gieger C, Gulsvik A, Hansell AL, Hao K, Hoffman JD, Hokanson JE, Homuth G, Joshi PK, Joubert P, Langenberg C, Li X, Li L, Lin K, Lind L, Locantore N, Luan J, Mahajan A, Maranville JC, Murray A, Nickle DC, Packer R, Parker MM, Paynton ML, Porteous DJ, Prokopenko D, Qiao D, Rawal R, Runz H, Sayers I, Sin DD, Smith BH, Soler Artigas M, Sparrow D, Tal-Singer R, Timmers PRHJ, Van den Berge M, Whittaker JC, Woodruff PG, Yerges-Armstrong LM, Troyanskaya OG, Raitakari OT, Kähönen M, Polašek O, Gyllensten U, Rudan I, Deary IJ, Probst-Hensch NM, Schulz H, James AL, Wilson JF, Stubbe B, Zeggini E, Jarvelin MR, Wareham N, Silverman EK, Hayward C, Morris AP, Butterworth AS, Scott RA, Walters RG, Meyers DA, Cho MH, Strachan DP, Hall IP, Tobin MD, Wain LV. New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries. Nat Genet 2019; 51:481-493. [PMID: 30804560 PMCID: PMC6397078 DOI: 10.1038/s41588-018-0321-7] [Citation(s) in RCA: 285] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/27/2018] [Indexed: 02/02/2023]
Abstract
Reduced lung function predicts mortality and is key to the diagnosis of chronic obstructive pulmonary disease (COPD). In a genome-wide association study in 400,102 individuals of European ancestry, we define 279 lung function signals, 139 of which are new. In combination, these variants strongly predict COPD in independent populations. Furthermore, the combined effect of these variants showed generalizability across smokers and never smokers, and across ancestral groups. We highlight biological pathways, known and potential drug targets for COPD and, in phenome-wide association studies, autoimmune-related and other pleiotropic effects of lung function-associated variants. This new genetic evidence has potential to improve future preventive and therapeutic strategies for COPD.
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Affiliation(s)
- Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anna L Guyatt
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Victoria E Jackson
- Department of Health Sciences, University of Leicester, Leicester, UK
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Carl A Melbourne
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Kijoung Song
- Target Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | - Phuwanat Sakornsakolpat
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Xingnan Li
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Ruth Boxall
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Nicola F Reeve
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Jing Hua Zhao
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Katherine A Kentistou
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - James P Cook
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Benjamin B Sun
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jian Zhou
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Jennie Hui
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- School of Population Health, The University of Western Australia, Crawley, Western Australia, Australia
- PathWest Laboratory Medicine of WA, Sir Charles Gairdner Hospital, Crawley, Western Australia, Australia
- School of Pathology and Laboratory Medicine, The University of Western Australia, Crawley, Western Australia, Australia
| | - Stefan Karrasch
- Institute of Epidemiology, Helmholtz Zentrum Muenchen-German Research Center for Environmental Health, Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Stefan Enroth
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala Universitet, Uppsala, Sweden
| | - Shona M Kerr
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ida Surakka
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- The National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Richard J Allen
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Per S Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins University School of Public Health, Baltimore, MD, USA
| | - Eugene R Bleecker
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Québec, Canada
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, Canada
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - James D Crapo
- National Jewish Health, Denver, CO, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - John Danesh
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK
- Department of Human Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ralf Ewert
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Anna L Hansell
- Centre for Environmental Health & Sustainability, University of Leicester, Leicester, UK
- UK Small Area Health Statistics Unit, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, St Mary's Hospital, London, UK
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, Canada
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University, Québec, Canada
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Xuan Li
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Liming Li
- Department of Epidemiology & Biostatistics, Peking University Health Science Center, Beijing, China
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Lars Lind
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University, Uppsala, Sweden
| | | | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Alison Murray
- The Institute of Medical Sciences, Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, UK
| | - David C Nickle
- MRL, Merck & Co., Inc, Kenilworth, NJ, USA
- Gossamer Bio, San Diego, CA, USA
| | - Richard Packer
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Megan L Paynton
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - David J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Heiko Runz
- MRL, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Ian Sayers
- Division of Respiratory Medicine and NIHR-Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Don D Sin
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - María Soler Artigas
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Barcelona, Spain
| | - David Sparrow
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | | | - Paul R H J Timmers
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Maarten Van den Berge
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - John C Whittaker
- Target Sciences - R&D, GSK Medicines Research Centre, Stevenage, UK
| | - Prescott G Woodruff
- UCSF Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
| | | | - Olga G Troyanskaya
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Ozren Polašek
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- University of Split School of Medicine, Split, Croatia
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala Universitet, Uppsala, Sweden
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Nicole M Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Holger Schulz
- Institute of Epidemiology, Helmholtz Zentrum Muenchen-German Research Center for Environmental Health, Neuherberg, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Alan L James
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia, Australia
| | - James F Wilson
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Beate Stubbe
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany
| | - Eleftheria Zeggini
- Wellcome Sanger Institute, Hinxton, UK
- Institute of Translational Genomics, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Nick Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Robert A Scott
- Target Sciences - R&D, GSK Medicines Research Centre, Stevenage, UK
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Deborah A Meyers
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, UK
| | - Ian P Hall
- Division of Respiratory Medicine and NIHR-Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK.
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK.
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
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Nimptsch K, Konigorski S, Pischon T. Diagnosis of obesity and use of obesity biomarkers in science and clinical medicine. Metabolism 2019; 92:61-70. [PMID: 30586573 DOI: 10.1016/j.metabol.2018.12.006] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/10/2018] [Accepted: 12/20/2018] [Indexed: 12/19/2022]
Abstract
The global epidemic of obesity is a major public health problem today. Obesity increases the risk of many chronic diseases, such as type 2 diabetes, coronary heart disease, and certain types of cancer, and is associated with lower life expectancy. The body mass index (BMI), which is currently used to classify obesity, is only an imperfect measure of abnormal or excessive body fat accumulation. Studies have shown that waist circumference as a measure of fat distribution may improve disease prediction. More elaborate techniques such as magnetic resonance imaging are increasingly available to assess body fat distribution, but these measures are not readily available in routine clinical practice, and health-relevant cut-offs not yet been established. The measurement of biomarkers that reflect the underlying biological mechanisms for the increased disease risk may be an alternative approach to characterize the relevant obesity phenotype. The insulin/insulin-like growth factor (IGF) axis and chronic low-grade inflammation have been identified as major pathways. In addition, specific adipokines such as leptin, adiponectin and resistin have been related to obesity-associated health outcomes. This biomarker research, which is currently further developed with the application of high throughput methods, gives important insights in obesity-related disease etiology and pathophysiological pathways and may be used to better characterize obese persons at high risk of disease development and target disease-causing biomarkers in personalized prevention strategies.
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Affiliation(s)
- Katharina Nimptsch
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany.
| | - Stefan Konigorski
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany; Digital Health - Machine Learning Group, Hasso-Plattner-Institute for Digital Engineering, Potsdam, Germany
| | - Tobias Pischon
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany; Charité Universitätsmedizin, Berlin, Germany; Berlin Institute of Health, Berlin, Germany; DZHK (German Center for Cardiovascular Research), partner site Berlin, Berlin, Germany
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1262
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Cheung CL, Tan KCB, Au PCM, Li GHY, Cheung BMY. Evaluation of GDF15 as a therapeutic target of cardiometabolic diseases in human: A Mendelian randomization study. EBioMedicine 2019; 41:85-90. [PMID: 30772304 PMCID: PMC6442643 DOI: 10.1016/j.ebiom.2019.02.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/01/2019] [Accepted: 02/08/2019] [Indexed: 11/29/2022] Open
Abstract
Background Growth differentiation factor 15 (GDF15) is a key regulator of body weight in animals by regulating food intake. Its receptor, glial cell-derived neurotrophic factor receptor alpha-like (GFRAL), was identified recently. Pre-clinical studies showed that it is a promising therapeutic target for cardiometabolic diseases and anorexia/cachexia. Although many pharmaceutical companies are developing drugs targeting GFRAL, whether the findings from animal studies can be extrapolated to man is unknown. Mendelian randomization (MR) is useful in investigating the relationship between risk factors and disease outcomes. We aimed to use a two-sample MR approach to evaluate the clinical usefulness of targeting GDF15 for cardiometabolic diseases. Methods Genetic instruments and summary statistics for MR analyses were obtained from a large genome-wide association study (GWAS) of GDF15 and cardiometabolic outcomes (n = 27,394 to 644,875), including body mass index, waist-hip ratio, waist circumference, whole-body lean mass, fat percentage, Type 2 Diabetes, fasting glucose, glycated haemoglobin, fasting insulin, LDL-cholesterol, HDL-cholesterol, total cholesterol, triglycerides, coronary artery disease, and estimated BMD (eBMD). Conventional inverse variance weighted (IVW) method was adopted to obtain the causal estimates of GDF-15 with different outcomes; weighted median and MR-egger were used for sensitivity analyses. Findings There was null association between GDF15 levels and anthropometric outcomes. One SD increase in genetically-determined GDF15 was significantly associated with reduced HDL-C (beta: -0.048SD; SE: 0.014; P = .001) but the result was not significant in sensitivity analyses. A consistent significant causal association was observed between GDF15 and eBMD in IVW (beta: 0.026 SD; SE: 0.005; P < .001) and subsequent sensitivity analyses. Interpretation This study sheds lights on the potential of drugs targeting the GDF15/GFRAL axis. It suggested that the effect of targeting GDF15/GFRAL axis for weight control in human may be different from the effects observed in animal studies. GDF15 treatment may improve BMD in humans. Fund No specific funding was received for this study.
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Affiliation(s)
- Ching-Lung Cheung
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong; Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong.
| | - Kathryn C B Tan
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Philip C M Au
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Gloria H Y Li
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Bernard M Y Cheung
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
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Rotwein P. Variation in the repulsive guidance molecule family in human populations. Physiol Rep 2019; 7:e13959. [PMID: 30746893 PMCID: PMC6370684 DOI: 10.14814/phy2.13959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 01/17/2023] Open
Abstract
Repulsive guidance molecules, RGMA, RGMB, and RGMC, are related proteins discovered independently through different experimental paradigms. They are encoded by single copy genes in mammalian and other vertebrate genomes, and are ~50% identical in amino acid sequence. The importance of RGM actions in human physiology has not been realized, as most research has focused on non-human models, although mutations in RGMC are the cause of the severe iron storage disorder, juvenile hemochromatosis. Here I show that repositories of human genomic and population genetic data can be used as starting points for discovery and for developing new testable hypotheses about each of these paralogs in human biology and disease susceptibility. Information was extracted, aggregated, and analyzed from the Ensembl and UCSC Genome Browsers, the Exome Aggregation Consortium, the Genotype-Tissue Expression project portal, the cBio portal for Cancer Genomics, and the National Cancer Institute Genomic Data Commons data site. Results identify extensive variation in gene expression patterns, substantial alternative RNA splicing, and possible missense alterations and other modifications in the coding regions of each of the three genes, with many putative mutations being detected in individuals with different types of cancers. Moreover, selected amino acid substitutions are highly prevalent in the world population, with minor allele frequencies of up to 37% for RGMA and up to 8% for RGMB. These results indicate that protein sequence variation is common in the human RGM family, and raises the possibility that individual variants will have a significant population impact on human physiology and/or disease predisposition.
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Affiliation(s)
- Peter Rotwein
- Department of Biomedical SciencesPaul L. Foster School of MedicineTexas Tech Health University Health Sciences CenterEl PasoTexas
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1264
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Genome-wide gene-based analyses of weight loss interventions identify a potential role for NKX6.3 in metabolism. Nat Commun 2019; 10:540. [PMID: 30710084 PMCID: PMC6358625 DOI: 10.1038/s41467-019-08492-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 01/07/2019] [Indexed: 12/31/2022] Open
Abstract
Hundreds of genetic variants have been associated with Body Mass Index (BMI) through genome-wide association studies (GWAS) using observational cohorts. However, the genetic contribution to efficient weight loss in response to dietary intervention remains unknown. We perform a GWAS in two large low-caloric diet intervention cohorts of obese participants. Two loci close to NKX6.3/MIR486 and RBSG4 are identified in the Canadian discovery cohort (n = 1166) and replicated in the DiOGenes cohort (n = 789). Modulation of HGTX (NKX6.3 ortholog) levels in Drosophila melanogaster leads to significantly altered triglyceride levels. Additional tissue-specific experiments demonstrate an action through the oenocytes, fly hepatocyte-like cells that regulate lipid metabolism. Our results identify genetic variants associated with the efficacy of weight loss in obese subjects and identify a role for NKX6.3 in lipid metabolism, and thereby possibly weight control. Individuals show large variability in their capacity to lose weight and maintain this weight. Here, the authors perform GWAS in two weight loss intervention cohorts and identify two genetic loci associated with weight loss that are taken forward for Bayesian fine-mapping and functional assessment in flies.
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1265
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Dissecting the genetic relationship between cardiovascular risk factors and Alzheimer's disease. Acta Neuropathol 2019; 137:209-226. [PMID: 30413934 PMCID: PMC6358498 DOI: 10.1007/s00401-018-1928-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 10/28/2018] [Accepted: 10/28/2018] [Indexed: 01/01/2023]
Abstract
Cardiovascular (CV)- and lifestyle-associated risk factors (RFs) are increasingly recognized as important for Alzheimer's disease (AD) pathogenesis. Beyond the ε4 allele of apolipoprotein E (APOE), comparatively little is known about whether CV-associated genes also increase risk for AD. Using large genome-wide association studies and validated tools to quantify genetic overlap, we systematically identified single nucleotide polymorphisms (SNPs) jointly associated with AD and one or more CV-associated RFs, namely body mass index (BMI), type 2 diabetes (T2D), coronary artery disease (CAD), waist hip ratio (WHR), total cholesterol (TC), triglycerides (TG), low-density (LDL) and high-density lipoprotein (HDL). In fold enrichment plots, we observed robust genetic enrichment in AD as a function of plasma lipids (TG, TC, LDL, and HDL); we found minimal AD genetic enrichment conditional on BMI, T2D, CAD, and WHR. Beyond APOE, at conjunction FDR < 0.05 we identified 90 SNPs on 19 different chromosomes that were jointly associated with AD and CV-associated outcomes. In meta-analyses across three independent cohorts, we found four novel loci within MBLAC1 (chromosome 7, meta-p = 1.44 × 10-9), MINK1 (chromosome 17, meta-p = 1.98 × 10-7) and two chromosome 11 SNPs within the MTCH2/SPI1 region (closest gene = DDB2, meta-p = 7.01 × 10-7 and closest gene = MYBPC3, meta-p = 5.62 × 10-8). In a large 'AD-by-proxy' cohort from the UK Biobank, we replicated three of the four novel AD/CV pleiotropic SNPs, namely variants within MINK1, MBLAC1, and DDB2. Expression of MBLAC1, SPI1, MINK1 and DDB2 was differentially altered within postmortem AD brains. Beyond APOE, we show that the polygenic component of AD is enriched for lipid-associated RFs. We pinpoint a subset of cardiovascular-associated genes that strongly increase the risk for AD. Our collective findings support a disease model in which cardiovascular biology is integral to the development of clinical AD in a subset of individuals.
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Hannon E, Marzi SJ, Schalkwyk LS, Mill J. Genetic risk variants for brain disorders are enriched in cortical H3K27ac domains. Mol Brain 2019; 12:7. [PMID: 30691483 PMCID: PMC6348673 DOI: 10.1186/s13041-019-0429-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 01/21/2019] [Indexed: 12/20/2022] Open
Abstract
Most variants associated with complex phenotypes in genome-wide association studies (GWAS) do not directly index coding changes affecting protein structure. Instead they are hypothesized to influence gene regulation, with common variants associated with disease being enriched in regulatory domains including enhancers and regions of open chromatin. There is interest, therefore, in using epigenomic annotation data to identify the specific regulatory mechanisms involved and prioritize risk variants. We quantified lysine H3K27 acetylation (H3K27ac) - a robust mark of active enhancers and promoters that is strongly correlated with gene expression and transcription factor binding - across the genome in entorhinal cortex samples using chromatin immunoprecipitation followed by highly parallel sequencing (ChIP-seq). H3K27ac peaks were called using high quality reads combined across all samples and formed the basis of partitioned heritability analysis using LD score regression along with publicly-available GWAS results for seven psychiatric and neurodegenerative traits. Heritability for all seven brain traits was significantly enriched in these H3K27ac peaks (enrichment ranging from 1.09-2.13) compared to regions of the genome containing other active regulatory and functional elements across multiple cell types and tissues. The strongest enrichments were for amyotrophic lateral sclerosis (ALS) (enrichment = 2.19; 95% CI = 2.12-2.27), autism (enrichment = 2.11; 95% CI = 2.05-2.16) and major depressive disorder (enrichment = 2.04; 95% CI = 1.92-2.16). Much lower enrichments were observed for 14 non-brain disorders, although we identified enrichment in cortical H3K27ac domains for body mass index (enrichment = 1.16; 95% CI = 1.13-1.19), ever smoked (enrichment = 2.07; 95% CI = 2.04-2.10), HDL (enrichment = 1.53; 95% CI = 1.45-1.62) and trigylcerides (enrichment = 1.33; 95% CI = 1.24-1.42). These results indicate that risk alleles for brain disorders are preferentially located in regions of regulatory/enhancer function in the cortex, further supporting the hypothesis that genetic variants for these phenotypes influence gene regulation in the brain.
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Affiliation(s)
- Eilis Hannon
- University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, University of Exeter, Barrack Rd, Exeter, EX2 5DW UK
| | - Sarah J. Marzi
- Blizard Institute, Queen Mary University of London, London, E1 2AD UK
| | | | - Jonathan Mill
- University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, University of Exeter, Barrack Rd, Exeter, EX2 5DW UK
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Hu Y, Zhao T, Zang T, Zhang Y, Cheng L. Identification of Alzheimer's Disease-Related Genes Based on Data Integration Method. Front Genet 2019; 9:703. [PMID: 30740125 PMCID: PMC6355707 DOI: 10.3389/fgene.2018.00703] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/14/2018] [Indexed: 01/18/2023] Open
Abstract
Alzheimer disease (AD) is the fourth major cause of death in the elderly following cancer, heart disease and cerebrovascular disease. Finding candidate causal genes can help in the design of Gene targeted drugs and effectively reduce the risk of the disease. Complex diseases such as AD are usually caused by multiple genes. The Genome-wide association study (GWAS), has identified the potential genetic variants for most diseases. However, because of linkage disequilibrium (LD), it is difficult to identify the causative mutations that directly cause diseases. In this study, we combined expression quantitative trait locus (eQTL) studies with the GWAS, to comprehensively define the genes that cause Alzheimer disease. The method used was the Summary Mendelian randomization (SMR), which is a novel method to integrate summarized data. Two GWAS studies and five eQTL studies were referenced in this paper. We found several candidate SNPs that have a strong relationship with AD. Most of these SNPs overlap in different data sets, providing relatively strong reliability. We also explain the function of the novel AD-related genes we have discovered.
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Affiliation(s)
- Yang Hu
- Department of Computer Science and Technology, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Tianyi Zhao
- Department of Computer Science and Technology, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Tianyi Zang
- Department of Computer Science and Technology, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Ying Zhang
- Department of Rehabilitation, Heilongjiang Province Land Reclamation Headquarters General Hospital, Harbin, China
| | - Liang Cheng
- Department of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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1268
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Mendelian randomization provides support for obesity as a risk factor for meningioma. Sci Rep 2019; 9:309. [PMID: 30670737 PMCID: PMC6343031 DOI: 10.1038/s41598-018-36186-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/16/2018] [Indexed: 02/07/2023] Open
Abstract
Little is known about the causes of meningioma. Obesity and obesity-related traits have been reported in several epidemiological observational studies to be risk factors for meningioma. We performed an analysis of genetic variants associated with obesity-related traits to assess the relationship with meningioma risk using Mendelian randomization (MR), an approach unaffected by biases from temporal variability and reverse causation that might have affected earlier investigations. We considered 11 obesity-related traits, identified genetic instruments for these factors, and assessed their association with meningioma risk using data from a genome-wide association study comprising 1,606 meningioma patients and 9,823 controls. To evaluate the causal relationship between the obesity-related traits and meningioma risk, we consider the estimated odds ratio (OR) of meningioma for each genetic instrument. We identified positive associations between body mass index (odds ratio [ORSD] = 1.27, 95% confidence interval [CI] = 1.03–1.56, P = 0.028) and body fat percentage (ORSD = 1.28, 95% CI = 1.01–1.63, P = 0.042) with meningioma risk, albeit non-significant after correction for multiple testing. Associations for basal metabolic rate, diastolic blood pressure, fasting glucose, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, systolic blood pressure, total cholesterol, triglycerides and waist circumference with risk of meningioma were non-significant. Our analysis provides additional support for obesity being associated with an increased risk of meningioma.
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1269
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Rasooly D, Patel CJ. Conducting a Reproducible Mendelian Randomization Analysis Using the R Analytic Statistical Environment. ACTA ACUST UNITED AC 2019; 101:e82. [PMID: 30645041 DOI: 10.1002/cphg.82] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Mendelian randomization (MR) is defined as the utilization of genetic variants as instrumental variables to assess the causal relationship between an exposure and an outcome. By leveraging genetic polymorphisms as proxy for an exposure, the causal effect of an exposure on an outcome can be assessed while addressing susceptibility to biases prone to conventional observational studies, including confounding and reverse causation, where the outcome causes the exposure. Analogous to a randomized controlled trial where patients are randomly assigned to subgroups based on different treatments, in an MR analysis, the random allocation of alleles during meiosis from parent to offspring assigns individuals to different subgroups based on genetic variants. Recent methods use summary statistics from genome-wide association studies to perform MR, bypassing the need for individual-level data. Here, we provide a straightforward protocol for using summary-level data to perform MR and provide guidance for utilizing available software. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Danielle Rasooly
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Chirag J Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
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1270
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Budu-Aggrey A, Brumpton B, Tyrrell J, Watkins S, Modalsli EH, Celis-Morales C, Ferguson LD, Vie GÅ, Palmer T, Fritsche LG, Løset M, Nielsen JB, Zhou W, Tsoi LC, Wood AR, Jones SE, Beaumont R, Saunes M, Romundstad PR, Siebert S, McInnes IB, Elder JT, Davey Smith G, Frayling TM, Åsvold BO, Brown SJ, Sattar N, Paternoster L. Evidence of a causal relationship between body mass index and psoriasis: A mendelian randomization study. PLoS Med 2019; 16:e1002739. [PMID: 30703100 PMCID: PMC6354959 DOI: 10.1371/journal.pmed.1002739] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/27/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Psoriasis is a common inflammatory skin disease that has been reported to be associated with obesity. We aimed to investigate a possible causal relationship between body mass index (BMI) and psoriasis. METHODS AND FINDINGS Following a review of published epidemiological evidence of the association between obesity and psoriasis, mendelian randomization (MR) was used to test for a causal relationship with BMI. We used a genetic instrument comprising 97 single-nucleotide polymorphisms (SNPs) associated with BMI as a proxy for BMI (expected to be much less confounded than measured BMI). One-sample MR was conducted using individual-level data (396,495 individuals) from the UK Biobank and the Nord-Trøndelag Health Study (HUNT), Norway. Two-sample MR was performed with summary-level data (356,926 individuals) from published BMI and psoriasis genome-wide association studies (GWASs). The one-sample and two-sample MR estimates were meta-analysed using a fixed-effect model. To test for a potential reverse causal effect, MR analysis with genetic instruments comprising variants from recent genome-wide analyses for psoriasis were used to test whether genetic risk for this skin disease has a causal effect on BMI. Published observational data showed an association of higher BMI with psoriasis. A mean difference in BMI of 1.26 kg/m2 (95% CI 1.02-1.51) between psoriasis cases and controls was observed in adults, while a 1.55 kg/m2 mean difference (95% CI 1.13-1.98) was observed in children. The observational association was confirmed in UK Biobank and HUNT data sets. Overall, a 1 kg/m2 increase in BMI was associated with 4% higher odds of psoriasis (meta-analysis odds ratio [OR] = 1.04; 95% CI 1.03-1.04; P = 1.73 × 10(-60)). MR analyses provided evidence that higher BMI causally increases the odds of psoriasis (by 9% per 1 unit increase in BMI; OR = 1.09 (1.06-1.12) per 1 kg/m2; P = 4.67 × 10(-9)). In contrast, MR estimates gave little support to a possible causal effect of psoriasis genetic risk on BMI (0.004 kg/m2 change in BMI per doubling odds of psoriasis (-0.003 to 0.011). Limitations of our study include possible misreporting of psoriasis by patients, as well as potential misdiagnosis by clinicians. In addition, there is also limited ethnic variation in the cohorts studied. CONCLUSIONS Our study, using genetic variants as instrumental variables for BMI, provides evidence that higher BMI leads to a higher risk of psoriasis. This supports the prioritization of therapies and lifestyle interventions aimed at controlling weight for the prevention or treatment of this common skin disease. Mechanistic studies are required to improve understanding of this relationship.
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Affiliation(s)
- Ashley Budu-Aggrey
- Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, United Kingdom
- * E-mail:
| | - Ben Brumpton
- Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Thoracic Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jess Tyrrell
- Genetics of Complex Traits, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon and Exeter Hospital, Exeter, United Kingdom
- European Centre for Environment and Human Health, University of Exeter Medical School, The Knowledge Spa, Truro, United Kingdom
| | - Sarah Watkins
- Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Ellen H. Modalsli
- Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Dermatology, St. Olav’s Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Carlos Celis-Morales
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Lyn D. Ferguson
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Gunnhild Åberge Vie
- Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tom Palmer
- Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom
| | - Lars G. Fritsche
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Mari Løset
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Dermatology, St. Olav’s Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jonas Bille Nielsen
- Department of Internal Medicine, Division of Cardiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Wei Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lam C. Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrew R. Wood
- Genetics of Complex Traits, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Samuel E. Jones
- Genetics of Complex Traits, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Robin Beaumont
- Genetics of Complex Traits, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Marit Saunes
- Department of Dermatology, St. Olav’s Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Pål Richard Romundstad
- Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Stefan Siebert
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Iain B. McInnes
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - James T. Elder
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, United States of America
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, United States of America
| | - George Davey Smith
- Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Timothy M. Frayling
- Genetics of Complex Traits, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Bjørn Olav Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Endocrinology, St. Olav’s Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Sara J. Brown
- Skin Research Group, School of Medicine, University of Dundee, Dundee, United Kingdom
- Department of Dermatology, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - Naveed Sattar
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Lavinia Paternoster
- Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, United Kingdom
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1271
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Kleinendorst L, van Haelst MM, van den Akker ELT. Genetics of Obesity. EXPERIENTIA SUPPLEMENTUM (2012) 2019; 111:419-441. [PMID: 31588542 DOI: 10.1007/978-3-030-25905-1_19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Obesity is caused by an imbalance between energy intake and output, influenced by numerous environmental, biological, and genetic factors. Only a minority of people with obesity have a genetic defect that is the main cause of their obesity. A key symptom for most of these disorders is early-onset obesity and hyperphagia. For some genetic obesity disorders, the hyperphagia is the main characteristic, often caused by disruptions of the leptin-melanocortin pathway, the central pathway that regulates the body's satiety and energy balance. For other disorders, obesity is part of a distinct combination of other clinical features such as intellectual disability, dysmorphic facial features, or organ abnormalities. This chapter focuses on genetic obesity disorders and also summarizes the present knowledge on the genetics of the more common polygenic/multifactorial obesity.
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Affiliation(s)
- Lotte Kleinendorst
- Obesity Center CGG, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Amsterdam UMC, Location AMC, Amsterdam, The Netherlands
- Department of Clinical Genetics, Amsterdam UMC, Location VUmc, Amsterdam, The Netherlands
| | - Mieke M van Haelst
- Department of Clinical Genetics, Amsterdam UMC, Location AMC, Amsterdam, The Netherlands
- Department of Clinical Genetics, Amsterdam UMC, Location VUmc, Amsterdam, The Netherlands
| | - Erica L T van den Akker
- Obesity Center CGG, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
- Division of Endocrinology, Department of Pediatrics, Erasmus MC-Sophia Children's Hospital, University Medical Center, Rotterdam, The Netherlands.
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1272
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Gene expression variation and parental allele inheritance in a Xiphophorus interspecies hybridization model. PLoS Genet 2018; 14:e1007875. [PMID: 30586357 PMCID: PMC6324826 DOI: 10.1371/journal.pgen.1007875] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/08/2019] [Accepted: 12/04/2018] [Indexed: 01/06/2023] Open
Abstract
Understanding the genetic mechanisms underlying segregation of phenotypic variation through successive generations is important for understanding physiological changes and disease risk. Tracing the etiology of variation in gene expression enables identification of genetic interactions, and may uncover molecular mechanisms leading to the phenotypic expression of a trait, especially when utilizing model organisms that have well-defined genetic lineages. There are a plethora of studies that describe relationships between gene expression and genotype, however, the idea that global variations in gene expression are also controlled by genotype remains novel. Despite the identification of loci that control gene expression variation, the global understanding of how genome constitution affects trait variability is unknown. To study this question, we utilized Xiphophorus fish of different, but tractable genetic backgrounds (inbred, F1 interspecies hybrids, and backcross hybrid progeny), and measured each individual’s gene expression concurrent with the degrees of inter-individual expression variation. We found, (a) F1 interspecies hybrids exhibited less variability than inbred animals, indicting gene expression variation is not affected by the fraction of heterozygous loci within an individual genome, and (b), that mixing genotypes in backcross populations led to higher levels of gene expression variability, supporting the idea that expression variability is caused by heterogeneity of genotypes of cis or trans loci. In conclusion, heterogeneity of genotype, introduced by inheritance of different alleles, accounts for the largest effects on global phenotypical variability. Phenotypical variability is a multi-factorial phenomenon. Although it has been shown that inheriting certain gene is associated with lower phenotypical variability, how genome complexity affect phenotypical variability is still unclear. To study this question, we used inbred Xiphophorus fish, backcross interspecies hybrids, and F1 interspecies hybrids between select Xiphophorus species to model genetic composition with minimum, medium, and maximum heterozygosity respectively, and measured their global gene expression variability. We found gene expression variation is not affected by the percentage of heterozygous loci in individual genome, but instead related to heterogeneity of genotype at local or remote loci.
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1273
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Yengo L, Robinson MR, Keller MC, Kemper KE, Yang Y, Trzaskowski M, Gratten J, Turley P, Cesarini D, Benjamin DJ, Wray NR, Goddard ME, Yang J, Visscher PM. Imprint of assortative mating on the human genome. Nat Hum Behav 2018; 2:948-954. [PMID: 30988446 PMCID: PMC6705135 DOI: 10.1038/s41562-018-0476-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 10/22/2018] [Indexed: 11/09/2022]
Abstract
Preference for mates with similar phenotypes; that is, assortative mating, is widely observed in humans1-5 and has evolutionary consequences6-8. Under Fisher's classical theory6, assortative mating is predicted to induce a signature in the genome at trait-associated loci that can be detected and quantified. Here, we develop and apply a method to quantify assortative mating on a specific trait by estimating the correlation (θ) between genetic predictors of the trait from single nucleotide polymorphisms on odd- versus even-numbered chromosomes. We show by theory and simulation that the effect of assortative mating can be quantified in the presence of population stratification. We applied this approach to 32 complex traits and diseases using single nucleotide polymorphism data from ~400,000 unrelated individuals of European ancestry. We found significant evidence of assortative mating for height (θ = 3.2%) and educational attainment (θ = 2.7%), both of which were consistent with theoretical predictions. Overall, our results imply that assortative mating involves multiple traits and affects the genomic architecture of loci that are associated with these traits, and that the consequence of mate choice can be detected from a random sample of genomes.
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Affiliation(s)
- Loic Yengo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
| | - Matthew R Robinson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Matthew C Keller
- Department of Psychology and Neuroscience, Institute for Behavioral Genetics, University of Colorado at Boulder, Boulder, CO, USA
| | - Kathryn E Kemper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Yuanhao Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Maciej Trzaskowski
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Jacob Gratten
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Mater Research, Translational Research Institute, Brisbane, Queensland, Australia
| | - Patrick Turley
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Cesarini
- National Bureau of Economic Research, Cambridge, MA, USA
- Department of Economics, New York University, New York, NY, USA
- Center for Experimental Social Science, New York University, New York, NY, USA
| | - Daniel J Benjamin
- National Bureau of Economic Research, Cambridge, MA, USA
- Center for Economic and Social Research, University of Southern California, Los Angeles, CA, USA
- Department of Economics, University of Southern California, Los Angeles, CA, USA
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael E Goddard
- Faculty of Veterinary and Agricultural Science, University of Melbourne, Melbourne, Victoria, Australia
- Biosciences Research Division, Department of Economic Development, Jobs, Transport and Resources Government of Victoria, Bundoora, Victoria, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.
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1274
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Bowden J, Hemani G, Davey Smith G. Invited Commentary: Detecting Individual and Global Horizontal Pleiotropy in Mendelian Randomization-A Job for the Humble Heterogeneity Statistic? Am J Epidemiol 2018; 187:2681-2685. [PMID: 30188969 PMCID: PMC6269239 DOI: 10.1093/aje/kwy185] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 12/17/2022] Open
Abstract
Mendelian randomization (MR) is gaining in recognition and popularity as a method for strengthening causal inference in epidemiology by utilizing genetic variants as instrumental variables. Concurrently with the explosion in empirical MR studies, there has been the steady production of new approaches for MR analysis. The recently proposed "global and individual tests for direct effects" (GLIDE) approach fits into a family of methods that aim to detect horizontal pleiotropy-at the individual single nucleotide polymorphism level and at the global level-and to adjust the analysis by removing outlying single nucleotide polymorphisms. In this commentary, we explain how existing methods can (and indeed are) being used to detect pleiotropy at the individual and global levels, although not explicitly using this terminology. By doing so, we show that the true comparator for GLIDE is not MR-Egger regression (as Dai et al., the authors of the accompanying article (Am J Epidemiol. 2018;187(12):2672-2680), claim) but rather the humble heterogeneity statistic.
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Affiliation(s)
- Jack Bowden
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
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1275
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Saini S, Mitra I, Mousavi N, Fotsing SF, Gymrek M. A reference haplotype panel for genome-wide imputation of short tandem repeats. Nat Commun 2018; 9:4397. [PMID: 30353011 PMCID: PMC6199332 DOI: 10.1038/s41467-018-06694-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 09/18/2018] [Indexed: 12/14/2022] Open
Abstract
Short tandem repeats (STRs) are involved in dozens of Mendelian disorders and have been implicated in complex traits. However, genotyping arrays used in genome-wide association studies focus on single nucleotide polymorphisms (SNPs) and do not readily allow identification of STR associations. We leverage next-generation sequencing (NGS) from 479 families to create a SNP + STR reference haplotype panel. Our panel enables imputing STR genotypes into SNP array data when NGS is not available for directly genotyping STRs. Imputed genotypes achieve mean concordance of 97% with observed genotypes in an external dataset compared to 71% expected under a naive model. Performance varies widely across STRs, with near perfect concordance at bi-allelic STRs vs. 70% at highly polymorphic repeats. Imputation increases power over individual SNPs to detect STR associations with gene expression. Imputing STRs into existing SNP datasets will enable the first large-scale STR association studies across a range of complex traits.
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Affiliation(s)
- Shubham Saini
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Ileena Mitra
- Bioinformatics and Systems Biology Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Nima Mousavi
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Stephanie Feupe Fotsing
- Bioinformatics and Systems Biology Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Biomedical Informatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Melissa Gymrek
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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1276
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Reis A, Spinath FM. Genetik der allgemeinen kognitiven Fähigkeit. MED GENET-BERLIN 2018. [DOI: 10.1007/s11825-018-0201-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Zusammenfassung
Intelligenz ist eines der bestuntersuchten Konstrukte der empirischen Verhaltenswissenschaften und stellt eine allgemeine geistige Kapazität dar, die unter anderem die Fähigkeit zum schlussfolgernden Denken, zum Lösen neuartiger Probleme, zum abstrakten Denken sowie zum schnellen Lernen umfasst. Diese kognitiven Fähigkeiten spielen eine große Rolle in der Erklärung und Vorhersage individueller Unterschiede in zentralen Bereichen des gesellschaftlichen Lebens, wie Schul- und Bildungserfolg, Berufserfolg, sozioökonomischer Status und Gesundheitsverhalten. Verhaltensgenetische Studien zeigen konsistent, dass genetische Einflüsse einen substanziellen Beitrag zur Erklärung individueller Unterschiede leisten, die über 60 % der Intelligenzunterschiede im Erwachsenenalter erklären. In den letzten Jahren konnten in großen genomweiten Assoziationsstudien mit häufigen genetischen Varianten Hunderte mit Intelligenz assoziierte Loci identifiziert werden sowie über 1300 assoziierte Gene mit differentieller Expression überwiegend im Gehirn. Mehrere Signalwege waren angereichert, vor allen für Neurogenese, Regulation der Entwicklung des Nervensystems sowie der synaptischen Struktur und Aktivität. Die Mehrzahl der assoziierten Loci betraf regulatorische Regionen und interessanterweise lag die Hälfte intronisch. Von den über 1300 Genen überlappen nur 9,2 % mit solchen, die mit monogenen neurokognitiven Störungen assoziiert sind. Insgesamt bestätigen die Befunde ein polygenes Modell Tausender additiver Faktoren, wobei die einzelnen Loci eine sehr geringe Effektstärke aufweisen. Insgesamt erklären die jetzigen Befunde ca. 10 % der Gesamtvarianz des Merkmals. Diese Ergebnisse sind ein wichtiger Ausgangspunkt für zukünftige Forschung sowohl in der Genetik als auch den Verhaltenswissenschaften.
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Affiliation(s)
- André Reis
- Aff1 0000 0001 2107 3311 grid.5330.5 Humangenetisches Institut, Universitätsklinikum Erlangen Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Schwabachanlage 10 91054 Erlangen Deutschland
| | - Frank M. Spinath
- Aff2 0000 0001 2167 7588 grid.11749.3a Fachbereich Psychologie Universität des Saarlandes Saarbrücken Deutschland
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1277
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Robinson-Cohen C, Bartz TM, Lai D, Ikizler TA, Peacock M, Imel EA, Michos ED, Foroud TM, Akesson K, Taylor KD, Malmgren L, Matsushita K, Nethander M, Eriksson J, Ohlsson C, Mellström D, Wolf M, Ljunggren O, McGuigan F, Rotter JI, Karlsson M, Econs MJ, Ix JH, Lutsey PL, Psaty BM, de Boer IH, Kestenbaum BR. Genetic Variants Associated with Circulating Fibroblast Growth Factor 23. J Am Soc Nephrol 2018; 29:2583-2592. [PMID: 30217807 PMCID: PMC6171267 DOI: 10.1681/asn.2018020192] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/06/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Fibroblast growth factor 23 (FGF23), a bone-derived hormone that regulates phosphorus and vitamin D metabolism, contributes to the pathogenesis of mineral and bone disorders in CKD and is an emerging cardiovascular risk factor. Central elements of FGF23 regulation remain incompletely understood; genetic variation may help explain interindividual differences. METHODS We performed a meta-analysis of genome-wide association studies of circulating FGF23 concentrations among 16,624 participants of European ancestry from seven cohort studies, excluding participants with eGFR<30 ml/min per 1.73 m2 to focus on FGF23 under normal conditions. We evaluated the association of single-nucleotide polymorphisms (SNPs) with natural log-transformed FGF23 concentration, adjusted for age, sex, study site, and principal components of ancestry. A second model additionally adjusted for BMI and eGFR. RESULTS We discovered 154 SNPs from five independent regions associated with FGF23 concentration. The SNP with the strongest association, rs17216707 (P=3.0×10-24), lies upstream of CYP24A1, which encodes the primary catabolic enzyme for 1,25-dihydroxyvitamin D and 25-hydroxyvitamin D. Each additional copy of the T allele at this locus is associated with 5% higher FGF23 concentration. Another locus strongly associated with variations in FGF23 concentration is rs11741640, within RGS14 and upstream of SLC34A1 (a gene involved in renal phosphate transport). Additional adjustment for BMI and eGFR did not materially alter the magnitude of these associations. Another top locus (within ABO, the ABO blood group transferase gene) was no longer statistically significant at the genome-wide level. CONCLUSIONS Common genetic variants located near genes involved in vitamin D metabolism and renal phosphate transport are associated with differences in circulating FGF23 concentrations.
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Affiliation(s)
- Cassianne Robinson-Cohen
- Division of Nephrology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee;
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Departments of Biostatistics and Medicine
| | - Dongbing Lai
- Departments of Medical and Molecular Genetics and
| | - T Alp Ikizler
- Division of Nephrology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Erik A Imel
- Medicine, Indiana University, Indianapolis, Indiana
| | - Erin D Michos
- Division of Cardiology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | | | - Kristina Akesson
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Science Malmö, Lund University, Malmö, Sweden
- Department of Orthopaedics, Skåne University Hospital, Malmö, Sweden
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-University of California, Los Angeles Medical Center, Torrance, California
| | - Linnea Malmgren
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Science Malmö, Lund University, Malmö, Sweden
- Department of Orthopaedics, Skåne University Hospital, Malmö, Sweden
| | - Kunihiro Matsushita
- Division of Cardiology, Johns Hopkins School of Medicine, Baltimore, Maryland
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, and
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland
| | | | - Joel Eriksson
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Claes Ohlsson
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Mellström
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Myles Wolf
- Division of Nephrology, Department of Medicine, and Duke Clinical Research Institute, Duke University School of Medicine, Durham, North Carolina
| | - Osten Ljunggren
- Department of Medical Sciences, Endocrinology and Mineral Metabolism, Uppsala University, Uppsala, Sweden
| | - Fiona McGuigan
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Science Malmö, Lund University, Malmö, Sweden
- Department of Orthopaedics, Skåne University Hospital, Malmö, Sweden
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-University of California, Los Angeles Medical Center, Torrance, California
| | - Magnus Karlsson
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Science Malmö, Lund University, Malmö, Sweden
- Department of Orthopaedics, Skåne University Hospital, Malmö, Sweden
| | - Michael J Econs
- Departments of Medical and Molecular Genetics and
- Medicine, Indiana University, Indianapolis, Indiana
| | - Joachim H Ix
- Division of Nephrology-Hypertension, Department of Medicine, University of California San Diego, San Diego, California
- Nephrology Section, Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Pamela L Lutsey
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Epidemiology, Health Services and Medicine, and
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington
| | - Ian H de Boer
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
| | - Bryan R Kestenbaum
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
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1278
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Barbitoff YA, Serebryakova EA, Nasykhova YA, Predeus AV, Polev DE, Shuvalova AR, Vasiliev EV, Urazov SP, Sarana AM, Scherbak SG, Gladyshev DV, Pokrovskaya MS, Sivakova OV, Meshkov AN, Drapkina OM, Glotov OS, Glotov AS. Identification of Novel Candidate Markers of Type 2 Diabetes and Obesity in Russia by Exome Sequencing with a Limited Sample Size. Genes (Basel) 2018; 9:genes9080415. [PMID: 30126146 PMCID: PMC6115942 DOI: 10.3390/genes9080415] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/11/2018] [Accepted: 08/13/2018] [Indexed: 12/22/2022] Open
Abstract
Type 2 diabetes (T2D) and obesity are common chronic disorders with multifactorial etiology. In our study, we performed an exome sequencing analysis of 110 patients of Russian ethnicity together with a multi-perspective approach based on biologically meaningful filtering criteria to detect novel candidate variants and loci for T2D and obesity. We have identified several known single nucleotide polymorphisms (SNPs) as markers for obesity (rs11960429), T2D (rs9379084, rs1126930), and body mass index (BMI) (rs11553746, rs1956549 and rs7195386) (p < 0.05). We show that a method based on scoring of case-specific variants together with selection of protein-altering variants can allow for the interrogation of novel and known candidate markers of T2D and obesity in small samples. Using this method, we identified rs328 in LPL (p = 0.023), rs11863726 in HBQ1 (p = 8 × 10−5), rs112984085 in VAV3 (p = 4.8 × 10−4) for T2D and obesity, rs6271 in DBH (p = 0.043), rs62618693 in QSER1 (p = 0.021), rs61758785 in RAD51B (p = 1.7 × 10−4), rs34042554 in PCDHA1 (p = 1 × 10−4), and rs144183813 in PLEKHA5 (p = 1.7 × 10−4) for obesity; and rs9379084 in RREB1 (p = 0.042), rs2233984 in C6orf15 (p = 0.030), rs61737764 in ITGB6 (p = 0.035), rs17801742 in COL2A1 (p = 8.5 × 10−5), and rs685523 in ADAMTS13 (p = 1 × 10−6) for T2D as important susceptibility loci in Russian population. Our results demonstrate the effectiveness of whole exome sequencing (WES) technologies for searching for novel markers of multifactorial diseases in cohorts of limited size in poorly studied populations.
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Affiliation(s)
- Yury A Barbitoff
- Biobank of the Research Park, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
- Bioinformatics Institute, 194100 Saint Petersburg, Russia.
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
- Institute of Translation Biomedicine, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
| | - Elena A Serebryakova
- Biobank of the Research Park, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
- Laboratory of Prenatal Diagnostics of Hereditary Diseases, FSBSI «The Research Institute of Obstetrics, Gynaecology and Reproductology Named after D.O. Ott», 199034 Saint Petersburg, Russia.
- City Hospital No. 40, Sestroretsk, 197706 Saint Petersburg, Russia.
| | - Yulia A Nasykhova
- Biobank of the Research Park, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
- Laboratory of Prenatal Diagnostics of Hereditary Diseases, FSBSI «The Research Institute of Obstetrics, Gynaecology and Reproductology Named after D.O. Ott», 199034 Saint Petersburg, Russia.
| | | | - Dmitrii E Polev
- Biobank of the Research Park, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
| | - Anna R Shuvalova
- Biobank of the Research Park, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
| | | | | | - Andrey M Sarana
- Institute of Translation Biomedicine, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
- City Hospital No. 40, Sestroretsk, 197706 Saint Petersburg, Russia.
| | - Sergey G Scherbak
- Institute of Translation Biomedicine, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
- City Hospital No. 40, Sestroretsk, 197706 Saint Petersburg, Russia.
| | | | - Maria S Pokrovskaya
- Federal State Institution «National Medical Research Center for Preventive Medicine» of the Ministry of Healthcare of the Russian Federation, 101990 Moscow, Russia.
| | - Oksana V Sivakova
- Federal State Institution «National Medical Research Center for Preventive Medicine» of the Ministry of Healthcare of the Russian Federation, 101990 Moscow, Russia.
| | - Aleksey N Meshkov
- Federal State Institution «National Medical Research Center for Preventive Medicine» of the Ministry of Healthcare of the Russian Federation, 101990 Moscow, Russia.
| | - Oxana M Drapkina
- Federal State Institution «National Medical Research Center for Preventive Medicine» of the Ministry of Healthcare of the Russian Federation, 101990 Moscow, Russia.
| | - Oleg S Glotov
- Laboratory of Prenatal Diagnostics of Hereditary Diseases, FSBSI «The Research Institute of Obstetrics, Gynaecology and Reproductology Named after D.O. Ott», 199034 Saint Petersburg, Russia.
- City Hospital No. 40, Sestroretsk, 197706 Saint Petersburg, Russia.
| | - Andrey S Glotov
- Biobank of the Research Park, Saint Petersburg State University, 199034 Saint Petersburg, Russia.
- Laboratory of Prenatal Diagnostics of Hereditary Diseases, FSBSI «The Research Institute of Obstetrics, Gynaecology and Reproductology Named after D.O. Ott», 199034 Saint Petersburg, Russia.
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1279
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Li Z, Chen P, Chen J, Xu Y, Wang Q, Li X, Li C, He L, Shi Y. Glucose and Insulin-Related Traits, Type 2 Diabetes and Risk of Schizophrenia: A Mendelian Randomization Study. EBioMedicine 2018; 34:182-188. [PMID: 30100396 PMCID: PMC6116472 DOI: 10.1016/j.ebiom.2018.07.037] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The link between schizophrenia and diabetes mellitus is well established by observational studies; however, the cause-effect relationship remains unclear. METHODS Here, we conducted Mendelian randomization analyses to assess a causal relationship of the genetic variants related to elevated fasting glucose levels, hemoglobin A1c (HbA1c), fasting insulin levels, and type 2 diabetes with the risk of schizophrenia. The analyses were performed using summary statistics obtained for the variants identified from the genome-wide association meta-analyses of fasting glucose levels (up to 133,010 individuals), HbA1c (up to 153,377 individuals), fasting insulin levels (up to 108,557 individuals), type 2 diabetes (up to 659,316 individuals), and schizophrenia (up to 108,341 individuals). The association between each variant and schizophrenia was weighted by its association with each studied condition, and estimates were combined using an inverse-variance weighted meta-analysis. FINDINGS Using information from thirteen variants related to fasting insulin levels, the causal effect of fasting insulin levels increases (per 1-SD) on the risk of schizophrenia was estimated at an odds ratio (OR) of 2·33 (p = 0·001), which is consistent with findings from the observational studies. The fasting glucose associated single nucleotide polymorphisms (SNPs) had no effect on the risk of schizophrenia in Europeans and East Asians (p > 0·05). Nonsignificant effects on the risk of schizophrenia was observed with raised HbA1c and type 2 diabetes, and consistent estimates were obtained across different populations. INTERPRETATION Our results suggest a causal role of elevated fasting insulin levels in schizophrenia pathogenesis.
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Affiliation(s)
- Zhiqiang Li
- The Affiliated Hospital of Qingdao University, The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, No. 16 Jiangsu Road, Qingdao 266003, PR China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, No. 1954 Huashan Road, Shanghai 200030, PR China; Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, PR China; Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, No. 1954 Huashan Road, Shanghai 200030, PR China.
| | - Peng Chen
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, No. 45 Chaoyang Xi Road, Changchun 130021, PR China; College of Basic Medical Sciences, Jilin University, No. 126 Xinmin Street, Changchun 130021, PR China; National Institute of Digestive, Diabetes and Kidney Diseases, National Institutes of Health, 445 N 5th St, Phoenix, AZ 85004, USA
| | - Jianhua Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, No. 1954 Huashan Road, Shanghai 200030, PR China; Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, PR China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, No. 600 Wanping Nan Road, Shanghai 200030, PR China
| | - Yifeng Xu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, No. 600 Wanping Nan Road, Shanghai 200030, PR China
| | - Qingzhong Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, No. 1954 Huashan Road, Shanghai 200030, PR China
| | - Xingwang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, No. 1954 Huashan Road, Shanghai 200030, PR China
| | - Changgui Li
- Shandong Provincial Key Laboratory of Metabolic Disease, The Metabolic Disease Institute of Qingdao University, No. 16 Jiangsu Road, Qingdao 266003, PR China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, No. 1954 Huashan Road, Shanghai 200030, PR China; Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, No. 1954 Huashan Road, Shanghai 200030, PR China
| | - Yongyong Shi
- The Affiliated Hospital of Qingdao University, The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, No. 16 Jiangsu Road, Qingdao 266003, PR China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, No. 1954 Huashan Road, Shanghai 200030, PR China; Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, PR China; Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, No. 1954 Huashan Road, Shanghai 200030, PR China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, No. 600 Wanping Nan Road, Shanghai 200030, PR China.
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1280
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Trejo S, Domingue BW. Genetic nature or genetic nurture? Introducing social genetic parameters to quantify bias in polygenic score analyses. BIODEMOGRAPHY AND SOCIAL BIOLOGY 2018; 64:187-215. [PMID: 31852332 DOI: 10.1080/19485565.2019.1681257] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Results from a genome-wide association study (GWAS) can be used to generate a polygenic score (PGS), an individual-level measure summarizing identified genetic influence on a trait dispersed across the genome. For complex, behavioral traits, the association between an individual's PGS and their phenotype may contain bias (from geographic, ancestral, and/or socioeconomic confounding) alongside the causal effect of the individual's genes. We formalize the introduction of a different source of bias in regression models using PGSs: the effects of parental genes on offspring outcomes, known as genetic nurture. GWAS do not discriminate between the various pathways through which genes become associated with outcomes, meaning existing PGSs capture both direct genetic effects and genetic nurture effects. We construct a theoretical model for genetic effects and show that the presence of genetic nurture biases PGS coefficients from both naïve OLS (between-family) and family fixed effects (within-family) regressions. This bias is in opposite directions; while naïve OLS estimates are biased away from zero, family fixed effects estimates are biased toward zero. We quantify this bias using two novel parameters: (1) the genetic correlation between the direct and nurture effects and (2) the ratio of the SNP heritabilities for the direct and nurture effects.
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Affiliation(s)
- Sam Trejo
- Graduate School of Education, Stanford University, Stanford, CA, USA
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