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Hüls A, Ickstadt K, Schikowski T, Krämer U. Detection of gene-environment interactions in the presence of linkage disequilibrium and noise by using genetic risk scores with internal weights from elastic net regression. BMC Genet 2017; 18:55. [PMID: 28606108 PMCID: PMC5469185 DOI: 10.1186/s12863-017-0519-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 05/23/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND For the analysis of gene-environment (GxE) interactions commonly single nucleotide polymorphisms (SNPs) are used to characterize genetic susceptibility, an approach that mostly lacks power and has poor reproducibility. One promising approach to overcome this problem might be the use of weighted genetic risk scores (GRS), which are defined as weighted sums of risk alleles of gene variants. The gold-standard is to use external weights from published meta-analyses. METHODS In this study, we used internal weights from the marginal genetic effects of the SNPs estimated by a multivariate elastic net regression and thereby provided a method that can be used if there are no external weights available. We conducted a simulation study for the detection of GxE interactions and compared power and type I error of single SNPs analyses with Bonferroni correction and corresponding analysis with unweighted and our weighted GRS approach in scenarios with six risk SNPs and an increasing number of highly correlated (up to 210) and noise SNPs (up to 840). RESULTS Applying weighted GRS increased the power enormously in comparison to the common single SNPs approach (e.g. 94.2% vs. 35.4%, respectively, to detect a weak interaction with an OR ≈ 1.04 for six uncorrelated risk SNPs and n = 700 with a well-controlled type I error). Furthermore, weighted GRS outperformed the unweighted GRS, in particular in the presence of SNPs without any effect on the phenotype (e.g. 90.1% vs. 43.9%, respectively, when 20 noise SNPs were added to the six risk SNPs). This outperforming of the weighted GRS was confirmed in a real data application on lung inflammation in the SALIA cohort (n = 402). However, in scenarios with a high number of noise SNPs (>200 vs. 6 risk SNPs), larger sample sizes are needed to avoid an increased type I error, whereas a high number of correlated SNPs can be handled even in small samples (e.g. n = 400). CONCLUSION In conclusion, weighted GRS with weights from the marginal genetic effects of the SNPs estimated by a multivariate elastic net regression were shown to be a powerful tool to detect gene-environment interactions in scenarios of high Linkage disequilibrium and noise.
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Affiliation(s)
- Anke Hüls
- IUF-Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, 40225, Düsseldorf, Germany.
- Faculty of Statistics, TU Dortmund University, Dortmund, Germany.
| | - Katja Ickstadt
- Faculty of Statistics, TU Dortmund University, Dortmund, Germany
| | - Tamara Schikowski
- IUF-Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, 40225, Düsseldorf, Germany
| | - Ursula Krämer
- IUF-Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, 40225, Düsseldorf, Germany
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Moons KGM, de Groot JAH, Bouwmeester W, Vergouwe Y, Mallett S, Altman DG, Reitsma JB, Collins GS. Critical appraisal and data extraction for systematic reviews of prediction modelling studies: the CHARMS checklist. PLoS Med 2014; 11:e1001744. [PMID: 25314315 PMCID: PMC4196729 DOI: 10.1371/journal.pmed.1001744] [Citation(s) in RCA: 981] [Impact Index Per Article: 98.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Carl Moons and colleagues provide a checklist and background explanation for critically appraising and extracting data from systematic reviews of prognostic and diagnostic prediction modelling studies. Please see later in the article for the Editors' Summary.
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Affiliation(s)
- Karel G. M. Moons
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht, The Netherlands
| | - Joris A. H. de Groot
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht, The Netherlands
| | - Walter Bouwmeester
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht, The Netherlands
| | - Yvonne Vergouwe
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht, The Netherlands
| | - Susan Mallett
- Department of Primary Care Health Sciences, New Radcliffe House, University of Oxford, Oxford, United Kingdom
| | - Douglas G. Altman
- Centre for Statistics in Medicine, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, United Kingdom
| | - Johannes B. Reitsma
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht, The Netherlands
| | - Gary S. Collins
- Centre for Statistics in Medicine, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, United Kingdom
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Buitendijk GHS, Rochtchina E, Myers C, van Duijn CM, Lee KE, Klein BEK, Meuer SM, de Jong PTVM, Holliday EG, Tan AG, Uitterlinden AG, Sivakumaran TS, Attia J, Hofman A, Mitchell P, Vingerling JR, Iyengar SK, Janssens ACJW, Wang JJ, Klein R, Klaver CCW. Prediction of age-related macular degeneration in the general population: the Three Continent AMD Consortium. Ophthalmology 2013; 120:2644-2655. [PMID: 24120328 PMCID: PMC3986722 DOI: 10.1016/j.ophtha.2013.07.053] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 07/31/2013] [Accepted: 07/31/2013] [Indexed: 11/28/2022] Open
Abstract
PURPOSE Prediction models for age-related macular degeneration (AMD) based on case-control studies have a tendency to overestimate risks. The aim of this study is to develop a prediction model for late AMD based on data from population-based studies. DESIGN Three population-based studies: the Rotterdam Study (RS), the Beaver Dam Eye Study (BDES), and the Blue Mountains Eye Study (BMES) from the Three Continent AMD Consortium (3CC). PARTICIPANTS People (n = 10,106) with gradable fundus photographs, genotype data, and follow-up data without late AMD at baseline. METHODS Features of AMD were graded on fundus photographs using the 3CC AMD severity scale. Associations with known genetic and environmental AMD risk factors were tested using Cox proportional hazard analysis. In the RS, the prediction of AMD was estimated for multivariate models by area under receiver operating characteristic curves (AUCs). The best model was validated in the BDES and BMES, and associations of variables were re-estimated in the pooled data set. Beta coefficients were used to construct a risk score, and risk of incident late AMD was calculated using Cox proportional hazard analysis. Cumulative incident risks were estimated using Kaplan-Meier product-limit analysis. MAIN OUTCOME MEASURES Incident late AMD determined per visit during a median follow-up period of 11.1 years with a total of 4 to 5 visits. RESULTS Overall, 363 participants developed incident late AMD, 3378 participants developed early AMD, and 6365 participants remained free of any AMD. The highest AUC was achieved with a model including age, sex, 26 single nucleotide polymorphisms in AMD risk genes, smoking, body mass index, and baseline AMD phenotype. The AUC of this model was 0.88 in the RS, 0.85 in the BDES and BMES at validation, and 0.87 in the pooled analysis. Individuals with low-risk scores had a hazard ratio (HR) of 0.02 (95% confidence interval [CI], 0.01-0.04) to develop late AMD, and individuals with high-risk scores had an HR of 22.0 (95% CI, 15.2-31.8). Cumulative risk of incident late AMD ranged from virtually 0 to more than 65% for those with the highest risk scores. CONCLUSIONS Our prediction model is robust and distinguishes well between those who will develop late AMD and those who will not. Estimated risks were lower in these population-based studies than in previous case-control studies.
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Affiliation(s)
- Gabriëlle H S Buitendijk
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Elena Rochtchina
- Centre for Vision Research, Department of Ophthalmology and Westmead Millennium Institute, University of Sydney, Sydney, Australia
| | - Chelsea Myers
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | | | - Kristine E Lee
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Barbara E K Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Stacy M Meuer
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Paulus T V M de Jong
- Department of Ophthalmogenetics, Netherlands Institute of Neurosciences, An Institute of the Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands; Department of Ophthalmology, Academic Medical Center, Amsterdam, The Netherlands; Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Elizabeth G Holliday
- Centre for Clinical Epidemiology and Biostatistics, and School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Ava G Tan
- Centre for Vision Research, Department of Ophthalmology and Westmead Millennium Institute, University of Sydney, Sydney, Australia
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands; Netherlands Consortium for Healthy Aging, Netherlands Genomics Initiative, the Hague, The Netherlands
| | - Theru S Sivakumaran
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio
| | - John Attia
- Centre for Clinical Epidemiology and Biostatistics, and School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia; Department of Medicine, John Hunter Hospital and Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands; Netherlands Consortium for Healthy Aging, Netherlands Genomics Initiative, the Hague, The Netherlands
| | - Paul Mitchell
- Centre for Vision Research, Department of Ophthalmology and Westmead Millennium Institute, University of Sydney, Sydney, Australia
| | - Johannes R Vingerling
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sudha K Iyengar
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio
| | - A Cecile J W Janssens
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Jie Jin Wang
- Centre for Vision Research, Department of Ophthalmology and Westmead Millennium Institute, University of Sydney, Sydney, Australia; Centre for Eye Research Australia, University of Melbourne, Melbourne, Australia
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.
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Hofman A, Darwish Murad S, van Duijn CM, Franco OH, Goedegebure A, Ikram MA, Klaver CCW, Nijsten TEC, Peeters RP, Stricker BHC, Tiemeier HW, Uitterlinden AG, Vernooij MW. The Rotterdam Study: 2014 objectives and design update. Eur J Epidemiol 2013; 28:889-926. [PMID: 24258680 DOI: 10.1007/s10654-013-9866-z] [Citation(s) in RCA: 259] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 11/08/2013] [Indexed: 02/06/2023]
Abstract
The Rotterdam Study is a prospective cohort study ongoing since 1990 in the city of Rotterdam in The Netherlands. The study targets cardiovascular, endocrine, hepatic, neurological, ophthalmic, psychiatric, dermatological, oncological, and respiratory diseases. As of 2008, 14,926 subjects aged 45 years or over comprise the Rotterdam Study cohort. The findings of the Rotterdam Study have been presented in over a 1,000 research articles and reports (see www.erasmus-epidemiology.nl/rotterdamstudy ). This article gives the rationale of the study and its design. It also presents a summary of the major findings and an update of the objectives and methods.
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Affiliation(s)
- Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands,
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Tuteja S, Rader DJ. Genomic medicine in the prevention and treatment of atherosclerotic cardiovascular disease. Per Med 2012; 9:395-404. [DOI: 10.2217/pme.12.34] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cardiovascular disease (CVD) is the leading cause of death in the world. Over the past decade considerable progress has been made in understanding the genomic basis of polygenic disorders including CVD. The future application of genomic medicine to the prevention and treatment of CVDs will ultimately lessen the burden of CVD. Given the complex nature of CVD, information derived from newer evolving fields, such as transcriptomics, proteomics and metabolomics, will allow us to fully interrogate features of the human genome to better understand disease pathogenesis and to identify new drug targets. In this article, we will review how genomics will allow enhanced risk prediction of cardiovascular events, provide personalized treatment options and hasten the drug development process, with a particular focus on atherosclerotic CVD.
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Affiliation(s)
- Sony Tuteja
- Perelman School of Medicine at the University of Pennsylvania, Division of Translational Medicine & Human Genetics, 11-125 Translational Research Center, 3400 Civic Center Blvd, Building 421, Philadelphia, PA 19104-5158, USA
| | - Daniel J Rader
- Perelman School of Medicine at the University of Pennsylvania, Division of Translational Medicine & Human Genetics, 11-125 Translational Research Center, 3400 Civic Center Blvd, Building 421, Philadelphia, PA 19104-5158, USA
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Kundu S, Aulchenko YS, van Duijn CM, Janssens ACJW. PredictABEL: an R package for the assessment of risk prediction models. Eur J Epidemiol 2011; 26:261-4. [PMID: 21431839 PMCID: PMC3088798 DOI: 10.1007/s10654-011-9567-4] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 03/08/2011] [Indexed: 08/09/2024]
Abstract
The rapid identification of genetic markers for multifactorial diseases from genome-wide association studies is fuelling interest in investigating the predictive ability and health care utility of genetic risk models. Various measures are available for the assessment of risk prediction models, each addressing a different aspect of performance and utility. We developed PredictABEL, a package in R that covers descriptive tables, measures and figures that are used in the analysis of risk prediction studies such as measures of model fit, predictive ability and clinical utility, and risk distributions, calibration plot and the receiver operating characteristic plot. Tables and figures are saved as separate files in a user-specified format, which include publication-quality EPS and TIFF formats. All figures are available in a ready-made layout, but they can be customized to the preferences of the user. The package has been developed for the analysis of genetic risk prediction studies, but can also be used for studies that only include non-genetic risk factors. PredictABEL is freely available at the websites of GenABEL ( http://www.genabel.org ) and CRAN ( http://cran.r-project.org/).
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Affiliation(s)
- Suman Kundu
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Yurii S. Aulchenko
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Cornelia M. van Duijn
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - A. Cecile J. W. Janssens
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
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