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Bhattacharya D, Bhattacharya S. Effects of gene–environment and gene–gene interactions in case-control studies: A novel Bayesian semiparametric approach. BRAZ J PROBAB STAT 2020. [DOI: 10.1214/18-bjps413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Bhattacharya D, Bhattacharya S. A Bayesian semiparametric approach to learning about gene–gene interactions in case-control studies. J Appl Stat 2018. [DOI: 10.1080/02664763.2018.1444741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Durba Bhattacharya
- St. Xavier's College, Kolkata, India
- Interdisciplinary Statistical Research Unit, Indian Statistical Institute, Kolkata, India
| | - Sourabh Bhattacharya
- Interdisciplinary Statistical Research Unit, Indian Statistical Institute, Kolkata, India
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Pathway-induced allelic spectra of diseases in the presence of strong genetic effects. Hum Genet 2018; 137:215-230. [DOI: 10.1007/s00439-018-1872-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 01/31/2018] [Indexed: 12/15/2022]
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The importance of gene-environment interactions in human obesity. Clin Sci (Lond) 2017; 130:1571-97. [PMID: 27503943 DOI: 10.1042/cs20160221] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/23/2016] [Indexed: 12/16/2022]
Abstract
The worldwide obesity epidemic has been mainly attributed to lifestyle changes. However, who becomes obese in an obesity-prone environment is largely determined by genetic factors. In the last 20 years, important progress has been made in the elucidation of the genetic architecture of obesity. In parallel with successful gene identifications, the number of gene-environment interaction (GEI) studies has grown rapidly. This paper reviews the growing body of evidence supporting gene-environment interactions in the field of obesity. Heritability, monogenic and polygenic obesity studies provide converging evidence that obesity-predisposing genes interact with a variety of environmental, lifestyle and treatment exposures. However, some skepticism remains regarding the validity of these studies based on several issues, which include statistical modelling, confounding, low replication rate, underpowered analyses, biological assumptions and measurement precision. What follows in this review includes (1) an introduction to the study of GEI, (2) the evidence of GEI in the field of obesity, (3) an outline of the biological mechanisms that may explain these interaction effects, (4) methodological challenges associated with GEI studies and potential solutions, and (5) future directions of GEI research. Thus far, this growing body of evidence has provided a deeper understanding of GEI influencing obesity and may have tremendous applications in the emerging field of personalized medicine and individualized lifestyle recommendations.
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Evans J, Swart M, Soko N, Wonkam A, Huzair F, Dandara C. A Global Health Diagnostic for Personalized Medicine in Resource-Constrained World Settings: A Simple PCR-RFLP Method for Genotyping CYP2B6 g.15582C>T and Science and Policy Relevance for Optimal Use of Antiretroviral Drug Efavirenz. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 19:332-8. [PMID: 26415139 DOI: 10.1089/omi.2015.0039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The use of pharmacogenomics (PGx) knowledge in treatment of individual patients is becoming a common phenomenon in the developed world. However, poorly resourced countries have thus far been constrained for three main reasons. First, the cost of whole genome sequencing is still considerably high in comparison to other (non-genomics) diagnostics in the developing world where both science and social dynamics create a dynamic and fragile healthcare ecosystem. Second, studies correlating genomic differences with drug pharmacokinetics and pharmacodynamics have not been consistent, and more importantly, often not indexed to impact on societal end-points, beyond clinical practice. Third, ethics regulatory frames over PGx testing require improvements based on nested accountability systems and in ways that address the user community needs. Thus, CYP2B6 is a crucial enzyme in the metabolism of antiretroviral drugs, efavirenz and nevirapine. More than 40 genetic variants have been reported, but only a few contribute to differences in plasma EFV and NVP concentrations. The most widely reported CYP2B6 variants affecting plasma drug levels include c.516G>T, c.983T>C, and to a lesser extent, g.15582C>T, which should be considered in future PGx tests. While the first two variants are easily characterized, the g.15582C>T detection has been performed primarily by sequencing, which is costly, labor intensive, and requires access to barely available expertise in the developing world. We report here on a simple, practical PCR-RFLP method with vast potentials for use in resource-constrained world regions to detect the g.15582C>T variation among South African and Cameroonian persons. The effects of CYP2B6 g.15582C>T on plasma EFV concentration were further evaluated among HIV/AIDS patients. We report no differences in the frequency of the g.15582T variant between the South African (0.08) and Cameroonian (0.06) groups, which are significantly lower than reported in Asians (0.39) and Caucasians (0.31). The g.15582C/T and T/T genotypes were associated with significantly reduced EFV levels (p=0.006). This article additionally presents the policy relevance of the PGX global health diagnostics and therefore, collectively makes an original interdisciplinary contribution to the field of integrative biology and personalized medicine in developing world. Such studies are, in fact, broadly important because resource-constrained regions exist not only in developing world but also in major geographical parts of the G20 nations and the developed countries.
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Affiliation(s)
- Jonathan Evans
- 1 Pharmacogenetics and Cancer Research Group, Division of Human Genetics, Department of Clinical Laboratory Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
| | - Marelize Swart
- 1 Pharmacogenetics and Cancer Research Group, Division of Human Genetics, Department of Clinical Laboratory Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
| | - Nyarai Soko
- 1 Pharmacogenetics and Cancer Research Group, Division of Human Genetics, Department of Clinical Laboratory Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
| | - Ambroise Wonkam
- 1 Pharmacogenetics and Cancer Research Group, Division of Human Genetics, Department of Clinical Laboratory Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
| | - Farah Huzair
- 2 Science, Technology and Innovation Studies, School of Social and Political Science, University of Edinburgh , Edinburgh, United Kingdom
| | - Collet Dandara
- 1 Pharmacogenetics and Cancer Research Group, Division of Human Genetics, Department of Clinical Laboratory Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
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Nagaie S, Ogishima S, Nakaya J, Tanaka H. A method to associate all possible combinations of genetic and environmental factors using GxE landscape plot. Bioinformation 2015; 11:161-4. [PMID: 25914450 PMCID: PMC4404419 DOI: 10.6026/97320630011161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 03/21/2015] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED Genome-wide association studies (GWAS) and linkage analysis has identified many single nucleotide polymorphisms (SNPs) related to disease. There are many unknown SNPs whose minor allele frequencies (MAFs) as low as 0.005 having intermediate effects with odds ratio between 1.5~3.0. Low frequency variants having intermediate effects on disease pathogenesis are believed to have complex interactions with environmental factors called gene-environment interactions (GxE). Hence, we describe a model using 3D Manhattan plot called GxE landscape plot to visualize the association of p-values for gene-environment interactions (GxE). We used the Gene-Environment iNteraction Simulator 2 (GENS2) program to simulate interactions between two genetic loci and one environmental factor in this exercise. The dataset used for training contains disease status, gender, 20 environmental exposures and 100 genotypes for 170 subjects, and p-values were calculated by Cochran-Mantel-Haenszel chi-squared test on known data. Subsequently, we created a 3D GxE landscape plot of negative logarithm of the association of p-values for all the possible combinations of genetic and environmental factors with their hierarchical clustering. Thus, the GxE landscape plot is a valuable model to predict association of p-values for GxE and similarity among genotypes and environments in the context of disease pathogenesis. ABBREVIATIONS GxE - Gene-environment interactions, GWAS - Genome-wide association study, MAFs - Minor allele frequencies, SNPs - Single nucleotide polymorphisms, EWAS - Environment-wide association study, FDR - False discovery rate, JPT+CHB - HapMap population of Japanese in Tokyo, Japan - Han Chinese in Beijing.
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Affiliation(s)
- Satoshi Nagaie
- Dept of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University
| | - Soichi Ogishima
- Dept of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University
| | - Jun Nakaya
- Dept of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University
- Medical IT Center, School of Medicine, Tohoku University
| | - Hiroshi Tanaka
- Dept of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University
- Dept. of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University
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Peng B, Chen HS, Mechanic LE, Racine B, Clarke J, Gillanders E, Feuer EJ. Genetic data simulators and their applications: an overview. Genet Epidemiol 2014; 39:2-10. [PMID: 25504286 DOI: 10.1002/gepi.21876] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Revised: 09/14/2014] [Accepted: 10/31/2014] [Indexed: 11/10/2022]
Abstract
Computer simulations have played an indispensable role in the development and applications of statistical models and methods for genetic studies across multiple disciplines. The need to simulate complex evolutionary scenarios and pseudo-datasets for various studies has fueled the development of dozens of computer programs with varying reliability, performance, and application areas. To help researchers compare and choose the most appropriate simulators for their studies, we have created the genetic simulation resources (GSR) website, which allows authors of simulation software to register their applications and describe them with more than 160 defined attributes. This article summarizes the properties of 93 simulators currently registered at GSR and provides an overview of the development and applications of genetic simulators. Unlike other review articles that address technical issues or compare simulators for particular application areas, we focus on software development, maintenance, and features of simulators, often from a historical perspective. Publications that cite these simulators are used to summarize both the applications of genetic simulations and the utilization of simulators.
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Affiliation(s)
- Bo Peng
- Department of Bioinformatics and Computational Biology, The University of Texas, MD Anderson Cancer Center, Houston, Texas, United States of America
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A C++ template library for efficient forward-time population genetic simulation of large populations. Genetics 2014; 198:157-66. [PMID: 24950894 DOI: 10.1534/genetics.114.165019] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
fwdpp is a C++ library of routines intended to facilitate the development of forward-time simulations under arbitrary mutation and fitness models. The library design provides a combination of speed, low memory overhead, and modeling flexibility not currently available from other forward simulation tools. The library is particularly useful when the simulation of large populations is required, as programs implemented using the library are much more efficient than other available forward simulation programs.
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Yang W, Gu C. A whole-genome simulator capable of modeling high-order epistasis for complex disease. Genet Epidemiol 2013; 37:686-94. [PMID: 24114848 PMCID: PMC4143152 DOI: 10.1002/gepi.21761] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 08/09/2013] [Accepted: 08/14/2013] [Indexed: 11/10/2022]
Abstract
Genome-wide association studies (GWAS) have been successful in finding numerous new risk variants for complex diseases, but the results almost exclusively rely on single-marker scans. Methods that can analyze joint effects of many variants in GWAS data are still being developed and trialed. To evaluate the performance of such methods it is essential to have a GWAS data simulator that can rapidly simulate a large number of samples, and capture key features of real GWAS data such as linkage disequilibrium (LD) among single-nucleotide polymorphisms (SNPs) and joint effects of multiple loci (multilocus epistasis). In the current study, we combine techniques for specifying high-order epistasis among risk SNPs with an existing program GWAsimulator [Li and Li, 2008] to achieve rapid whole-genome simulation with accurate modeling of complex interactions. We considered various approaches to specifying interaction models including the following: departure from product of marginal effects for pairwise interactions, product terms in logistic regression models for low-order interactions, and penetrance tables conforming to marginal effect constraints for high-order interactions or prescribing known biological interactions. Methods for conversion among different model specifications are developed using penetrance table as the fundamental characterization of disease models. The new program, called simGWA, is capable of efficiently generating large samples of GWAS data with high precision. We show that data simulated by simGWA are faithful to template LD structures, and conform to prespecified diseases models with (or without) interactions.
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Affiliation(s)
- Wei Yang
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO
| | - Charles Gu
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
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Kitchen JL, Allaby RG. Systems Modeling at Multiple Levels of Regulation: Linking Systems and Genetic Networks to Spatially Explicit Plant Populations. PLANTS (BASEL, SWITZERLAND) 2013; 2:16-49. [PMID: 27137364 PMCID: PMC4844292 DOI: 10.3390/plants2010016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/21/2012] [Accepted: 01/16/2013] [Indexed: 11/16/2022]
Abstract
Selection and adaptation of individuals to their underlying environments are highly dynamical processes, encompassing interactions between the individual and its seasonally changing environment, synergistic or antagonistic interactions between individuals and interactions amongst the regulatory genes within the individual. Plants are useful organisms to study within systems modeling because their sedentary nature simplifies interactions between individuals and the environment, and many important plant processes such as germination or flowering are dependent on annual cycles which can be disrupted by climate behavior. Sedentism makes plants relevant candidates for spatially explicit modeling that is tied in with dynamical environments. We propose that in order to fully understand the complexities behind plant adaptation, a system that couples aspects from systems biology with population and landscape genetics is required. A suitable system could be represented by spatially explicit individual-based models where the virtual individuals are located within time-variable heterogeneous environments and contain mutable regulatory gene networks. These networks could directly interact with the environment, and should provide a useful approach to studying plant adaptation.
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Affiliation(s)
- James L Kitchen
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Robin G Allaby
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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Schwartzer JJ, Koenig CM, Berman RF. Using mouse models of autism spectrum disorders to study the neurotoxicology of gene-environment interactions. Neurotoxicol Teratol 2012; 36:17-35. [PMID: 23010509 DOI: 10.1016/j.ntt.2012.08.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 08/28/2012] [Accepted: 08/30/2012] [Indexed: 10/27/2022]
Abstract
To better study the role of genetics in autism, mouse models have been developed which mimic the genetics of specific autism spectrum and related disorders. These models have facilitated research on the role genetic susceptibility factors in the pathogenesis of autism in the absence of environmental factors. Inbred mouse strains have been similarly studied to assess the role of environmental agents on neurodevelopment, typically without the complications of genetic heterogeneity of the human population. What has not been as actively pursued, however, is the methodical study of the interaction between these factors (e.g., gene and environmental interactions in neurodevelopment). This review suggests that a genetic predisposition paired with exposure to environmental toxicants plays an important role in the etiology of neurodevelopmental disorders including autism, and may contribute to the largely unexplained rise in the number of children diagnosed with autism worldwide. Specifically, descriptions of the major mouse models of autism and toxic mechanisms of prevalent environmental chemicals are provided followed by a discussion of current and future research strategies to evaluate the role of gene and environment interactions in neurodevelopmental disorders.
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Affiliation(s)
- Jared J Schwartzer
- Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California, Davis, Davis, CA 95618, United States.
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Pinelli M, Scala G, Amato R, Cocozza S, Miele G. Simulating gene-gene and gene-environment interactions in complex diseases: Gene-Environment iNteraction Simulator 2. BMC Bioinformatics 2012; 13:132. [PMID: 22698142 PMCID: PMC3538511 DOI: 10.1186/1471-2105-13-132] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 05/10/2012] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The analysis of complex diseases is an important problem in human genetics. Because multifactoriality is expected to play a pivotal role, many studies are currently focused on collecting information on the genetic and environmental factors that potentially influence these diseases. However, there is still a lack of efficient and thoroughly tested statistical models that can be used to identify implicated features and their interactions. Simulations using large biologically realistic data sets with known gene-gene and gene-environment interactions that influence the risk of a complex disease are a convenient and useful way to assess the performance of statistical methods. RESULTS The Gene-Environment iNteraction Simulator 2 (GENS2) simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. GENS2 is based on data with realistic patterns of linkage disequilibrium, and imposes no limitations either on the number of individuals to be simulated or on number of non-predisposing genetic/environmental factors to be considered. The GENS2 tool is able to simulate gene-environment and gene-gene interactions. To make the Simulator more intuitive, the input parameters are expressed as standard epidemiological quantities. GENS2 is written in Python language and takes advantage of operators and modules provided by the simuPOP simulation environment. It can be used through a graphical or a command-line interface and is freely available from http://sourceforge.net/projects/gensim. The software is released under the GNU General Public License version 3.0. CONCLUSIONS Data produced by GENS2 can be used as a benchmark for evaluating statistical tools designed for the identification of gene-gene and gene-environment interactions.
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Affiliation(s)
- Michele Pinelli
- Gruppo Interdipartimentale di Bioinformatica e Biologia Computazionale, Università di Napoli “Federico II” - Università di Salerno, Italy
- Dipartimento di Biologia e Patologia Cellulare e Molecolare “L. Califano”, Università di Napoli “Federico II”, Napoli, Italy
| | - Giovanni Scala
- Gruppo Interdipartimentale di Bioinformatica e Biologia Computazionale, Università di Napoli “Federico II” - Università di Salerno, Italy
- Dipartimento di Scienze Fisiche, Università di Napoli “Federico II”, Complesso Universitario di Monte S.Angelo, Napoli, Italy
| | - Roberto Amato
- Gruppo Interdipartimentale di Bioinformatica e Biologia Computazionale, Università di Napoli “Federico II” - Università di Salerno, Italy
- Dipartimento di Scienze Fisiche, Università di Napoli “Federico II”, Complesso Universitario di Monte S.Angelo, Napoli, Italy
- INFN Sezione di Napoli, Napoli, Italy
| | - Sergio Cocozza
- Gruppo Interdipartimentale di Bioinformatica e Biologia Computazionale, Università di Napoli “Federico II” - Università di Salerno, Italy
- Dipartimento di Biologia e Patologia Cellulare e Molecolare “L. Califano”, Università di Napoli “Federico II”, Napoli, Italy
| | - Gennaro Miele
- Gruppo Interdipartimentale di Bioinformatica e Biologia Computazionale, Università di Napoli “Federico II” - Università di Salerno, Italy
- Dipartimento di Scienze Fisiche, Università di Napoli “Federico II”, Complesso Universitario di Monte S.Angelo, Napoli, Italy
- INFN Sezione di Napoli, Napoli, Italy
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