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Alamin M, Sultana MH, Lou X, Jin W, Xu H. Dissecting Complex Traits Using Omics Data: A Review on the Linear Mixed Models and Their Application in GWAS. PLANTS (BASEL, SWITZERLAND) 2022; 11:3277. [PMID: 36501317 PMCID: PMC9739826 DOI: 10.3390/plants11233277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Genome-wide association study (GWAS) is the most popular approach to dissecting complex traits in plants, humans, and animals. Numerous methods and tools have been proposed to discover the causal variants for GWAS data analysis. Among them, linear mixed models (LMMs) are widely used statistical methods for regulating confounding factors, including population structure, resulting in increased computational proficiency and statistical power in GWAS studies. Recently more attention has been paid to pleiotropy, multi-trait, gene-gene interaction, gene-environment interaction, and multi-locus methods with the growing availability of large-scale GWAS data and relevant phenotype samples. In this review, we have demonstrated all possible LMMs-based methods available in the literature for GWAS. We briefly discuss the different LMM methods, software packages, and available open-source applications in GWAS. Then, we include the advantages and weaknesses of the LMMs in GWAS. Finally, we discuss the future perspective and conclusion. The present review paper would be helpful to the researchers for selecting appropriate LMM models and methods quickly for GWAS data analysis and would benefit the scientific society.
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Affiliation(s)
- Md. Alamin
- Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | | | - Xiangyang Lou
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Wenfei Jin
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Haiming Xu
- Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
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2
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Shashkova TI, Gorev DD, Pakhomov ED, Shadrina AS, Sharapov SZ, Tsepilov YA, Karssen LC, Aulchenko YS. The GWAS-MAP platform for aggregation of results of genome-wide association studies and the GWAS-MAP|homo database of 70 billion genetic associations of human traits. Vavilovskii Zhurnal Genet Selektsii 2020; 24:876-884. [PMID: 35088001 PMCID: PMC8763720 DOI: 10.18699/vj20.686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 11/23/2022] Open
Abstract
Hundreds of genome-wide association studies (GWAS) of human traits are performed each year. The
results of GWAS are often published in the form of summary statistics. Information from summary statistics can
be used for multiple purposes – from fundamental research in biology and genetics to the search for potential
biomarkers and therapeutic targets. While the amount of GWAS summary statistics collected by the scientific community is rapidly increasing, the use of this data is limited by the lack of generally accepted standards. In particular,
the researchers who would like to use GWAS summary statistics in their studies have to become aware that the data
are scattered across multiple websites, are presented in a variety of formats, and, often, were not quality controlled.
Moreover, each available summary statistics analysis tools will ask for data to be presented in their own internal
format. To address these issues, we developed GWAS-MAP, a high-throughput platform for aggregating, storing,
analyzing, visualizing and providing access to a database of big data that result from region- and genome-wide
association studies. The database currently contains information on more than 70 billion associations between
genetic variants and human diseases, quantitative traits, and “omics” traits. The GWAS-MAP platform and database
can be used for studying the etiology of human diseases, building predictive risk models and finding potential biomarkers and therapeutic interventions. In order to demonstrate a typical application of the platform as an approach
for extracting new biological knowledge and establishing mechanistic hypotheses, we analyzed varicose veins, a
disease affecting on average every third adult in Russia. The results of analysis confirmed known epidemiologic associations for this disease and led us to propose a hypothesis that increased levels of MICB and CD209 proteins in
human plasma may increase susceptibility to varicose veins.
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Affiliation(s)
- T. I. Shashkova
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University
| | - D. D. Gorev
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University
| | - E. D. Pakhomov
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University;
PolyKnomics BV
| | - A. S. Shadrina
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University
| | - S. Zh. Sharapov
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University
| | - Y. A. Tsepilov
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University
| | | | - Y. S. Aulchenko
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University
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3
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Colicino E, Marioni R, Ward-Caviness C, Gondalia R, Guan W, Chen B, Tsai PC, Huan T, Xu G, Golareh A, Schwartz J, Vokonas P, Just A, Starr JM, McRae AF, Wray NR, Visscher PM, Bressler J, Zhang W, Tanaka T, Moore AZ, Pilling LC, Zhang G, Stewart JD, Li Y, Hou L, Castillo-Fernandez J, Spector T, Kiel DP, Murabito JM, Liu C, Mendelson M, Assimes T, Absher D, Tsaho PS, Lu AT, Ferrucci L, Wilson R, Waldenberger M, Prokisch H, Bandinelli S, Bell JT, Levy D, Deary IJ, Horvath S, Pankow J, Peters A, Whitsel EA, Baccarelli A. Blood DNA methylation sites predict death risk in a longitudinal study of 12, 300 individuals. Aging (Albany NY) 2020; 12:14092-14124. [PMID: 32697766 PMCID: PMC7425458 DOI: 10.18632/aging.103408] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/25/2020] [Indexed: 12/22/2022]
Abstract
DNA methylation has fundamental roles in gene programming and aging that may help predict mortality. However, no large-scale study has investigated whether site-specific DNA methylation predicts all-cause mortality. We used the Illumina-HumanMethylation450-BeadChip to identify blood DNA methylation sites associated with all-cause mortality for 12, 300 participants in 12 Cohorts of the Heart and Aging Research in Genetic Epidemiology (CHARGE) Consortium. Over an average 10-year follow-up, there were 2,561 deaths across the cohorts. Nine sites mapping to three intergenic and six gene-specific regions were associated with mortality (P < 9.3x10-7) independently of age and other mortality predictors. Six sites (cg14866069, cg23666362, cg20045320, cg07839457, cg07677157, cg09615688)—mapping respectively to BMPR1B, MIR1973, IFITM3, NLRC5, and two intergenic regions—were associated with reduced mortality risk. The remaining three sites (cg17086398, cg12619262, cg18424841)—mapping respectively to SERINC2, CHST12, and an intergenic region—were associated with increased mortality risk. DNA methylation at each site predicted 5%–15% of all deaths. We also assessed the causal association of those sites to age-related chronic diseases by using Mendelian randomization, identifying weak causal relationship between cg18424841 and cg09615688 with coronary heart disease. Of the nine sites, three (cg20045320, cg07839457, cg07677157) were associated with lower incidence of heart disease risk and two (cg20045320, cg07839457) with smoking and inflammation in prior CHARGE analyses. Methylation of cg20045320, cg07839457, and cg17086398 was associated with decreased expression of nearby genes (IFITM3, IRF, NLRC5, MT1, MT2, MARCKSL1) linked to immune responses and cardiometabolic diseases. These sites may serve as useful clinical tools for mortality risk assessment and preventative care.
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Affiliation(s)
- Elena Colicino
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Riccardo Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Cavin Ward-Caviness
- US Environmental Protection Agency, Chapel Hill, NC 27514, USA.,Institute for Epidemiology II, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg D-85764, Germany
| | - Rahul Gondalia
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Brian Chen
- Longitudinal Study Section, Translational Gerontology Branch, National Institute of Aging, Bethesda, MD 20892, USA
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Tianxiao Huan
- National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
| | - Gao Xu
- Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Agha Golareh
- Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Joel Schwartz
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Pantel Vokonas
- VA Boston Healthcare System and Boston University Schools of Public Health and Medicine, Boston, MA 02115, USA
| | - Allan Just
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John M Starr
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Allan F McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Jan Bressler
- University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Wen Zhang
- Department of Biostatistics and Data Science, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Toshiko Tanaka
- Longitudinal Study Section, Translational Gerontology Branch, National Institute of Aging, Bethesda, MD 20892, USA
| | - Ann Zenobia Moore
- Longitudinal Study Section, Translational Gerontology Branch, National Institute of Aging, Bethesda, MD 20892, USA
| | - Luke C Pilling
- Epidemiology and Public Health Group, University of Exeter Medical School, Exeter, UK
| | - Guosheng Zhang
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - James D Stewart
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Yun Li
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Lifang Hou
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Juan Castillo-Fernandez
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Tim Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Douglas P Kiel
- Hebrew SeniorLife Institute for Aging Research and Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School Boston, MA 02215, USA
| | - Joanne M Murabito
- Section General Internal Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02215, USA
| | - Chunyu Liu
- Boston University School of Public Health, Boston, MA 02215, USA
| | - Mike Mendelson
- Boston University School of Medicine, Boston, MA 02215, USA
| | - Tim Assimes
- Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Devin Absher
- Hudson Alpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Phil S Tsaho
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | | | - Rory Wilson
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg D-85764, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg D-85764, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg S-85764, Germany
| | | | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Daniel Levy
- Framingham Heart Study, Framingham, MA 01702, USA
| | - Ian J Deary
- Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jim Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Annette Peters
- Institute for Epidemiology II, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg D-85764, Germany
| | - Eric A Whitsel
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Andrea Baccarelli
- Columbia University Mailman School of Public Health, New York, NY 10032, USA
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4
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Xia Y. Correlation and association analyses in microbiome study integrating multiomics in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 171:309-491. [PMID: 32475527 DOI: 10.1016/bs.pmbts.2020.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Correlation and association analyses are one of the most widely used statistical methods in research fields, including microbiome and integrative multiomics studies. Correlation and association have two implications: dependence and co-occurrence. Microbiome data are structured as phylogenetic tree and have several unique characteristics, including high dimensionality, compositionality, sparsity with excess zeros, and heterogeneity. These unique characteristics cause several statistical issues when analyzing microbiome data and integrating multiomics data, such as large p and small n, dependency, overdispersion, and zero-inflation. In microbiome research, on the one hand, classic correlation and association methods are still applied in real studies and used for the development of new methods; on the other hand, new methods have been developed to target statistical issues arising from unique characteristics of microbiome data. Here, we first provide a comprehensive view of classic and newly developed univariate correlation and association-based methods. We discuss the appropriateness and limitations of using classic methods and demonstrate how the newly developed methods mitigate the issues of microbiome data. Second, we emphasize that concepts of correlation and association analyses have been shifted by introducing network analysis, microbe-metabolite interactions, functional analysis, etc. Third, we introduce multivariate correlation and association-based methods, which are organized by the categories of exploratory, interpretive, and discriminatory analyses and classification methods. Fourth, we focus on the hypothesis testing of univariate and multivariate regression-based association methods, including alpha and beta diversities-based, count-based, and relative abundance (or compositional)-based association analyses. We demonstrate the characteristics and limitations of each approaches. Fifth, we introduce two specific microbiome-based methods: phylogenetic tree-based association analysis and testing for survival outcomes. Sixth, we provide an overall view of longitudinal methods in analysis of microbiome and omics data, which cover standard, static, regression-based time series methods, principal trend analysis, and newly developed univariate overdispersed and zero-inflated as well as multivariate distance/kernel-based longitudinal models. Finally, we comment on current association analysis and future direction of association analysis in microbiome and multiomics studies.
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Affiliation(s)
- Yinglin Xia
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States.
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5
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Köttgen A, Raffler J, Sekula P, Kastenmüller G. Genome-Wide Association Studies of Metabolite Concentrations (mGWAS): Relevance for Nephrology. Semin Nephrol 2019; 38:151-174. [PMID: 29602398 DOI: 10.1016/j.semnephrol.2018.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Metabolites are small molecules that are intermediates or products of metabolism, many of which are freely filtered by the kidneys. In addition, the kidneys have a central role in metabolite anabolism and catabolism, as well as in active metabolite reabsorption and/or secretion during tubular passage. This review article illustrates how the coupling of genomics and metabolomics in genome-wide association analyses of metabolites can be used to illuminate mechanisms underlying human metabolism, with a special focus on insights relevant to nephrology. First, genetic susceptibility loci for reduced kidney function and chronic kidney disease (CKD) were reviewed systematically for their associations with metabolite concentrations in metabolomics studies of blood and urine. Second, kidney function and CKD-associated metabolites reported from observational studies were interrogated for metabolite-associated genetic variants to generate and discuss complementary insights. Finally, insights originating from the simultaneous study of both blood and urine or by modeling intermetabolite relationships are summarized. We also discuss methodologic questions related to the study of metabolite concentrations in urine as well as among CKD patients. In summary, genome-wide association analyses of metabolites using metabolite concentrations quantified from blood and/or urine are a promising avenue of research to illuminate physiological and pathophysiological functions of the kidney.
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Affiliation(s)
- Anna Köttgen
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.
| | - Johannes Raffler
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Peggy Sekula
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
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6
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Tsepilov YA, Sharapov SZ, Zaytseva OO, Krumsiek J, Prehn C, Adamski J, Kastenmüller G, Wang-Sattler R, Strauch K, Gieger C, Aulchenko YS. A network-based conditional genetic association analysis of the human metabolome. Gigascience 2018; 7:5214749. [PMID: 30496450 PMCID: PMC6287100 DOI: 10.1093/gigascience/giy137] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 11/06/2018] [Indexed: 12/24/2022] Open
Abstract
Background Genome-wide association studies have identified hundreds of loci that influence a wide variety of complex human traits; however, little is known regarding the biological mechanism of action of these loci. The recent accumulation of functional genomics (“omics”), including metabolomics data, has created new opportunities for studying the functional role of specific changes in the genome. Functional genomic data are characterized by their high dimensionality, the presence of (strong) statistical dependency between traits, and, potentially, complex genetic control. Therefore, the analysis of such data requires specific statistical genetics methods. Results To facilitate our understanding of the genetic control of omics phenotypes, we propose a trait-centered, network-based conditional genetic association (cGAS) approach for identifying the direct effects of genetic variants on omics-based traits. For each trait of interest, we selected from a biological network a set of other traits to be used as covariates in the cGAS. The network can be reconstructed either from biological pathway databases (a mechanistic approach) or directly from the data, using a Gaussian graphical model applied to the metabolome (a data-driven approach). We derived mathematical expressions that allow comparison of the power of univariate analyses with conditional genetic association analyses. We then tested our approach using data from a population-based Cooperative Health Research in the region of Augsburg (KORA) study (n = 1,784 subjects, 1.7 million single-nucleotide polymorphisms) with measured data for 151 metabolites. Conclusions We found that compared to single-trait analysis, performing a genetic association analysis that includes biologically relevant covariates can either gain or lose power, depending on specific pleiotropic scenarios, for which we provide empirical examples. In the context of analyzed metabolomics data, the mechanistic network approach had more power compared to the data-driven approach. Nevertheless, we believe that our analysis shows that neither a prior-knowledge-only approach nor a phenotypic-data-only approach is optimal, and we discuss possibilities for improvement.
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Affiliation(s)
- Y A Tsepilov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Lavrentieva Ave. 10, 630090, Russia.,Natural Scince Department, Novosibirsk State University, Novosibirsk, Pirogova Str. 1, 630090, Russia
| | - S Z Sharapov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Lavrentieva Ave. 10, 630090, Russia.,Natural Scince Department, Novosibirsk State University, Novosibirsk, Pirogova Str. 1, 630090, Russia
| | - O O Zaytseva
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Lavrentieva Ave. 10, 630090, Russia.,Natural Scince Department, Novosibirsk State University, Novosibirsk, Pirogova Str. 1, 630090, Russia
| | - J Krumsiek
- Institute of Computational Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Ingolstadter Landtrasse 1, 85764, Germany
| | - C Prehn
- Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Ingolstadter Landtrasse 1, 85764, Germany
| | - J Adamski
- Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Ingolstadter Landtrasse 1, 85764, Germany.,Institute of Experimental Genetics, Life and Food Science Center Weihenstephan, Technical University of Munich, Freising-Weihenstephan, Arcisstrasse 21, 80333, Germany.,German Center for Diabetes Research, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Ingolstadter Landtrasse 1, 85764, Germany
| | - G Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Ingolstadter Landtrasse 1, 85764, Germany
| | - R Wang-Sattler
- German Center for Diabetes Research, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Ingolstadter Landtrasse 1, 85764, Germany.,Research Unit of Molecular Epidemiology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Ingolstadter Landtrasse 1, 85764, Germany.,Institute of Epidemiology II, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Ingolstadter Landtrasse 1, 85764, Germany
| | - K Strauch
- Institute of Genetic Epidemiology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Ingolstadter Landtrasse 1, 85764, Germany.,Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, Butenandstrasse 5, 81377, Germany
| | - C Gieger
- German Center for Diabetes Research, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Ingolstadter Landtrasse 1, 85764, Germany.,Research Unit of Molecular Epidemiology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Ingolstadter Landtrasse 1, 85764, Germany.,Institute of Epidemiology II, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Ingolstadter Landtrasse 1, 85764, Germany
| | - Y S Aulchenko
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Lavrentieva Ave. 10, 630090, Russia.,Natural Scince Department, Novosibirsk State University, Novosibirsk, Pirogova Str. 1, 630090, Russia.,PolyOmica, 's-Hertogenbosch, Het Vlaggeschip 61, 5237 PA, The Netherlands
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7
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Li Y, Sekula P, Wuttke M, Wahrheit J, Hausknecht B, Schultheiss UT, Gronwald W, Schlosser P, Tucci S, Ekici AB, Spiekerkoetter U, Kronenberg F, Eckardt KU, Oefner PJ, Köttgen A. Genome-Wide Association Studies of Metabolites in Patients with CKD Identify Multiple Loci and Illuminate Tubular Transport Mechanisms. J Am Soc Nephrol 2018; 29:1513-1524. [PMID: 29545352 DOI: 10.1681/asn.2017101099] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 02/09/2018] [Indexed: 12/24/2022] Open
Abstract
Background The kidneys have a central role in the generation, turnover, transport, and excretion of metabolites, and these functions can be altered in CKD. Genetic studies of metabolite concentrations can identify proteins performing these functions.Methods We conducted genome-wide association studies and aggregate rare variant tests of the concentrations of 139 serum metabolites and 41 urine metabolites, as well as their pairwise ratios and fractional excretions in up to 1168 patients with CKD.Results After correction for multiple testing, genome-wide significant associations were detected for 25 serum metabolites, two urine metabolites, and 259 serum and 14 urinary metabolite ratios. These included associations already known from population-based studies. Additional findings included an association for the uremic toxin putrescine and variants upstream of an enzyme catalyzing the oxidative deamination of polyamines (AOC1, P-min=2.4×10-12), a relatively high carrier frequency (2%) for rare deleterious missense variants in ACADM that are collectively associated with serum ratios of medium-chain acylcarnitines (P-burden=6.6×10-16), and associations of a common variant in SLC7A9 with several ratios of lysine to neutral amino acids in urine, including the lysine/glutamine ratio (P=2.2×10-23). The associations of this SLC7A9 variant with ratios of lysine to specific neutral amino acids were much stronger than the association with lysine concentration alone. This finding is consistent with SLC7A9 functioning as an exchanger of urinary cationic amino acids against specific intracellular neutral amino acids at the apical membrane of proximal tubular cells.Conclusions Metabolomic indices of specific kidney functions in genetic studies may provide insight into human renal physiology.
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Affiliation(s)
- Yong Li
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology, and Medical Bioinformatics, and
| | - Peggy Sekula
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology, and Medical Bioinformatics, and
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology, and Medical Bioinformatics, and
| | - Judith Wahrheit
- BIOCRATES Life Sciences Aktiengesellschaft, Innsbruck, Austria
| | | | - Ulla T Schultheiss
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology, and Medical Bioinformatics, and
| | - Wolfram Gronwald
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany; and
| | - Pascal Schlosser
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology, and Medical Bioinformatics, and
| | - Sara Tucci
- Department of General Pediatrics, Center for Pediatrics and Adolescent Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Arif B Ekici
- Insitute of Human Genetics, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Ute Spiekerkoetter
- Department of General Pediatrics, Center for Pediatrics and Adolescent Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Peter J Oefner
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany; and
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology, and Medical Bioinformatics, and
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8
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Wahl A, Kasela S, Carnero-Montoro E, van Iterson M, Štambuk J, Sharma S, van den Akker E, Klaric L, Benedetti E, Razdorov G, Trbojević-Akmačić I, Vučković F, Ugrina I, Beekman M, Deelen J, van Heemst D, Heijmans BT, B.I.O.S. Consortium, Wuhrer M, Plomp R, Keser T, Šimurina M, Pavić T, Gudelj I, Krištić J, Grallert H, Kunze S, Peters A, Bell JT, Spector TD, Milani L, Slagboom PE, Lauc G, Gieger C. IgG glycosylation and DNA methylation are interconnected with smoking. Biochim Biophys Acta Gen Subj 2018; 1862:637-648. [DOI: 10.1016/j.bbagen.2017.10.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/01/2017] [Accepted: 10/16/2017] [Indexed: 01/18/2023]
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Molnos S, Baumbach C, Wahl S, Müller-Nurasyid M, Strauch K, Wang-Sattler R, Waldenberger M, Meitinger T, Adamski J, Kastenmüller G, Suhre K, Peters A, Grallert H, Theis FJ, Gieger C. pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms. BMC Bioinformatics 2017; 18:429. [PMID: 28962546 PMCID: PMC5622569 DOI: 10.1186/s12859-017-1838-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 09/20/2017] [Indexed: 01/23/2023] Open
Abstract
Background Genome-wide association studies allow us to understand the genetics of complex diseases. Human metabolism provides information about the disease-causing mechanisms, so it is usual to investigate the associations between genetic variants and metabolite levels. However, only considering genetic variants and their effects on one trait ignores the possible interplay between different “omics” layers. Existing tools only consider single-nucleotide polymorphism (SNP)–SNP interactions, and no practical tool is available for large-scale investigations of the interactions between pairs of arbitrary quantitative variables. Results We developed an R package called pulver to compute p-values for the interaction term in a very large number of linear regression models. Comparisons based on simulated data showed that pulver is much faster than the existing tools. This is achieved by using the correlation coefficient to test the null-hypothesis, which avoids the costly computation of inversions. Additional tricks are a rearrangement of the order, when iterating through the different “omics” layers, and implementing this algorithm in the fast programming language C++. Furthermore, we applied our algorithm to data from the German KORA study to investigate a real-world problem involving the interplay among DNA methylation, genetic variants, and metabolite levels. Conclusions The pulver package is a convenient and rapid tool for screening huge numbers of linear regression models for significant interaction terms in arbitrary pairs of quantitative variables. pulver is written in R and C++, and can be downloaded freely from CRAN at https://cran.r-project.org/web/packages/pulver/. Electronic supplementary material The online version of this article (10.1186/s12859-017-1838-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sophie Molnos
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany. .,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany. .,German Center for Diabetes Research (DZD), Neuherberg, Germany.
| | - Clemens Baumbach
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Simone Wahl
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Martina Müller-Nurasyid
- Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, Munich, Germany.,Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Rui Wang-Sattler
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Jerzy Adamski
- German Center for Diabetes Research (DZD), Neuherberg, Germany.,Genome Analysis Center, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Experimental Genetics, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Twins Research and Genetic Epidemiology, Kings College, London, UK
| | - Karsten Suhre
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Biophysics and Physiology, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Mathematics, Technische Universitat München, Garching, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
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Abstract
Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the “core team”, facilitating agile statistical omics methodology development and fast dissemination.
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Affiliation(s)
- Lennart C Karssen
- PolyOmica, Groningen, 9722 HC, Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, 3000 CA, Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, 3000 CA, Netherlands
| | - Yurii S Aulchenko
- PolyOmica, Groningen, 9722 HC, Netherlands; Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Novosibirsk, 630090, Russian Federation; Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
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Wang Q, Cheng W, Li M, Ren H, Hu X, Deng W, Ma X, Zhao L, Wang Y, Xiang B, Wu HM, Sham PC, Feng J, Li T. The CHRM3 gene is implicated in abnormal thalamo-orbital frontal cortex functional connectivity in first-episode treatment-naive patients with schizophrenia. Psychol Med 2016; 46:1523-1534. [PMID: 26959877 DOI: 10.1017/s0033291716000167] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND The genetic influences in human brain structure and function and impaired functional connectivities are the hallmarks of the schizophrenic brain. To explore how common genetic variants affect the connectivities in schizophrenia, we applied genome-wide association studies assaying the abnormal neural connectivities in schizophrenia as quantitative traits. METHOD We recruited 161 first-onset and treatment-naive patients with schizophrenia and 150 healthy controls. All the participants underwent scanning with a 3 T-magnetic resonance imaging scanner to acquire structural and functional imaging data and genotyping using the HumanOmniZhongHua-8 BeadChip. The brain-wide association study approach was employed to account for the inherent modular nature of brain connectivities. RESULTS We found differences in four abnormal functional connectivities [left rectus to left thalamus (REC.L-THA.L), left rectus to right thalamus (REC.L-THA.R), left superior orbital cortex to left thalamus (ORBsup.L-THA.L) and left superior orbital cortex to right thalamus (ORBsup.L-THA.R)] between the two groups. Univariate single nucleotide polymorphism (SNP)-based association revealed that the SNP rs6800381, located nearest to the CHRM3 (cholinergic receptor, muscarinic 3) gene, reached genomic significance (p = 1.768 × 10-8) using REC.L-THA.R as the phenotype. Multivariate gene-based association revealed that the FAM12A (family with sequence similarity 12, member A) gene nearly reached genomic significance (nominal p = 2.22 × 10-6, corrected p = 0.05). CONCLUSIONS Overall, we identified the first evidence that the CHRM3 gene plays a role in abnormal thalamo-orbital frontal cortex functional connectivity in first-episode treatment-naive patients with schizophrenia. Identification of these genetic variants using neuroimaging genetics provides insights into the causes of variability in human brain development, and may help us determine the mechanisms of dysfunction in schizophrenia.
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Affiliation(s)
- Q Wang
- Mental Health Center,West China Hospital,Sichuan University,Chengdu,Sichuan,People's Republic of China
| | - W Cheng
- Centre for Computational Systems Biology,Fudan University,Shanghai,People's Republic of China
| | - M Li
- State Key Laboratory of Brain and Cognitive Sciences,Centre for Genomic Sciences and Department of Psychiatry,University of Hong Kong,Pokfulam,S.A.R.China
| | - H Ren
- Mental Health Center,West China Hospital,Sichuan University,Chengdu,Sichuan,People's Republic of China
| | - X Hu
- Biobank,West China Hospital,Sichuan University,Chengdu,Sichuan,People's Republic of China
| | - W Deng
- Mental Health Center,West China Hospital,Sichuan University,Chengdu,Sichuan,People's Republic of China
| | - X Ma
- State Key Laboratory of Biotherapy, Psychiatric Laboratory,West China Hospital,Sichuan University,Chengdu, Sichuan,People's Republic of China
| | - L Zhao
- State Key Laboratory of Biotherapy, Psychiatric Laboratory,West China Hospital,Sichuan University,Chengdu, Sichuan,People's Republic of China
| | - Y Wang
- State Key Laboratory of Biotherapy, Psychiatric Laboratory,West China Hospital,Sichuan University,Chengdu, Sichuan,People's Republic of China
| | - B Xiang
- Mental Health Center,West China Hospital,Sichuan University,Chengdu,Sichuan,People's Republic of China
| | - H-M Wu
- State Key Laboratory of Brain and Cognitive Sciences,Centre for Genomic Sciences and Department of Psychiatry,University of Hong Kong,Pokfulam,S.A.R.China
| | - P C Sham
- State Key Laboratory of Brain and Cognitive Sciences,Centre for Genomic Sciences and Department of Psychiatry,University of Hong Kong,Pokfulam,S.A.R.China
| | - J Feng
- Centre for Computational Systems Biology,Fudan University,Shanghai,People's Republic of China
| | - T Li
- Mental Health Center,West China Hospital,Sichuan University,Chengdu,Sichuan,People's Republic of China
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