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Gialluisi A, Reccia MG, Tirozzi A, Nutile T, Lombardi A, De Sanctis C, Varanese S, Pietracupa S, Modugno N, Simeone A, Ciullo M, Esposito T. Whole Exome Sequencing Study of Parkinson Disease and Related Endophenotypes in the Italian Population. Front Neurol 2020; 10:1362. [PMID: 31998221 PMCID: PMC6965311 DOI: 10.3389/fneur.2019.01362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 12/10/2019] [Indexed: 12/30/2022] Open
Abstract
Parkinson Disease (PD) is a complex neurodegenerative disorder characterized by large genetic heterogeneity and missing heritability. Since the genetic background of PD can partly vary among ethnicities and neurological scales have been scarcely investigated in a PD setting, we performed an exploratory Whole Exome Sequencing (WES) analysis of 123 PD patients from mainland Italy, investigating scales assessing motor (UPDRS), cognitive (MoCA), and other non-motor symptoms (NMS). We performed variant prioritization, followed by targeted association testing of prioritized variants in 446 PD cases and 211 controls. Then we ran Exome-Wide Association Scans (EWAS) within sequenced PD cases (N = 113), testing both motor and non-motor PD endophenotypes, as well as their associations with Polygenic Risk Scores (PRS) influencing brain subcortical volumes. We identified a variant associated with PD, rs201330591 in GTF2H2 (5q13; alternative T allele: OR [CI] = 8.16[1.08; 61.52], FDR = 0.048), which was not replicated in an independent cohort of European ancestry (1,148 PD cases, 503 controls). In the EWAS, polygenic analyses revealed statistically significant multivariable associations of amygdala- [β(SE) = -0.039(0.013); FDR = 0.039] and caudate-PRS [0.043(0.013); 0.028] with motor symptoms. All subcortical PRSs in a multivariable model notably increased the variance explained in motor (adjusted-R2 = 38.6%), cognitive (32.2%) and other non-motor symptoms (28.9%), compared to baseline models (~20%). Although, the small sample size warrants further replications, these findings suggest shared genetic architecture between PD symptoms and subcortical structures, and provide interesting clues on PD genetic and neuroimaging features.
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Affiliation(s)
| | | | | | - Teresa Nutile
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | | | | | | | | | | | | | - Antonio Simeone
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Marina Ciullo
- IRCCS Neuromed, Pozzilli, Italy
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Teresa Esposito
- IRCCS Neuromed, Pozzilli, Italy
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
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102
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Woodley Of Menie MA, Rindermann H, Pallesen J, Sarraf MA. How Intelligence Affects Fertility 30 Years On: Retherford and Sewell Revisited - With Polygenic Scores and Numbers of Grandchildren. Twin Res Hum Genet 2019; 22:147-53. [PMID: 31250786 DOI: 10.1017/thg.2019.25] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Using newly available polygenic scores for educational attainment and cognitive ability, this paper investigates the possible presence and causes of a negative association between IQ and fertility in the Wisconsin Longitudinal Study sample, an issue that Retherford and Sewell first addressed 30 years ago. The effect of the polygenic score on the sample's reproductive characteristics was indirect: a latent cognitive ability measure, comprised of both educational attainment and IQ, wholly mediated the relationship. Age at first birth mediated the negative effect of cognitive ability on sample fertility, which had a direct (positive) effect on the number of grandchildren. Significantly greater impacts of cognitive ability on the sample's fertility characteristics were found among the female subsample. This indicates that, in this sample, having a genetic disposition toward higher cognitive ability does not directly reduce number of offspring; instead, higher cognitive ability is a risk factor for prolonging reproductive debut, which, especially for women, reduces the fertility window and, thus, the number of children and grandchildren that can be produced. By estimating the effect of the sample's reproductive characteristics on the strength of polygenic selection, it was found that the genetic variance component of IQ should be declining at a rate between -.208 (95% CI [-.020, -.383]) and -.424 (95% CI [-.041, -.766]) points per decade, depending on whether GCTA-GREML or classical behavior genetic estimates of IQ heritability are used to correct for 'missing' heritability.
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103
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Ng CD, Weiss J. What your genes can (and can't) tell you about BMI and diabetes. Biodemography Soc Biol 2020; 66:40-49. [PMID: 33682573 PMCID: PMC9284979 DOI: 10.1080/19485565.2020.1806032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Body mass index (BMI) is commonly used as a proxy for adiposity in epidemiological and public health studies. However, BMI may suffer from issues of misreporting and, because it fluctuates over the life course, its association with morbidities such as diabetes is difficult to measure. We examined the associations between actual BMI, genetic propensity for high BMI, and diabetes to better understand whether a BMI polygenic score (PGS) explained more variation in diabetes than self-reported BMI. We used a sample of non-Hispanic white adults from the longitudinal Health and Retirement Study (1992-2016). Structural equation models were used to determine how much variation in BMI could be explained by a BMI PGS. Then, we used logistic regression models (n = 12,086) to study prevalent diabetes at baseline and Cox regression models (n = 11,129) to examine incident diabetes with up to 24 years of follow-up. We observed that while both actual BMI and the BMI PGS were significantly associated with diabetes, actual BMI had a stronger association than its genetic counterpart and resulted in better model performance. Moreover, actual BMI explained more variation in baseline and incident diabetes than its genetic counterpart which may suggest that actual BMI captures more than just adiposity as intended.
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Affiliation(s)
- Carmen D. Ng
- Hubert Department of Global Health and the Emory Global Diabetes Research Center, Emory University, Atlanta, GA, USA
| | - Jordan Weiss
- Population Studies Center and the Leonard Davis Institute of Health Economics, University of Pennsylvania, Philadelphia, PA, USA
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104
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Tilot AK, Vino A, Kucera KS, Carmichael DA, van den Heuvel L, den Hoed J, Sidoroff-Dorso AV, Campbell A, Porteous DJ, St Pourcain B, van Leeuwen TM, Ward J, Rouw R, Simner J, Fisher SE. Investigating genetic links between grapheme-colour synaesthesia and neuropsychiatric traits. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190026. [PMID: 31630655 PMCID: PMC6834005 DOI: 10.1098/rstb.2019.0026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2019] [Indexed: 12/22/2022] Open
Abstract
Synaesthesia is a neurological phenomenon affecting perception, where triggering stimuli (e.g. letters and numbers) elicit unusual secondary sensory experiences (e.g. colours). Family-based studies point to a role for genetic factors in the development of this trait. However, the contributions of common genomic variation to synaesthesia have not yet been investigated. Here, we present the SynGenes cohort, the largest genotyped collection of unrelated people with grapheme-colour synaesthesia (n = 723). Synaesthesia has been associated with a range of other neuropsychological traits, including enhanced memory and mental imagery, as well as greater sensory sensitivity. Motivated by the prior literature on putative trait overlaps, we investigated polygenic scores derived from published genome-wide scans of schizophrenia and autism spectrum disorder (ASD), comparing our SynGenes cohort to 2181 non-synaesthetic controls. We found a very slight association between schizophrenia polygenic scores and synaesthesia (Nagelkerke's R2 = 0.0047, empirical p = 0.0027) and no significant association for scores related to ASD (Nagelkerke's R2 = 0.00092, empirical p = 0.54) or body mass index (R2 = 0.00058, empirical p = 0.60), included as a negative control. As sample sizes for studying common genomic variation continue to increase, genetic investigations of the kind reported here may yield novel insights into the shared biology between synaesthesia and other traits, to complement findings from neuropsychology and brain imaging. This article is part of a discussion meeting issue 'Bridging senses: novel insights from synaesthesia'.
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Affiliation(s)
- Amanda K. Tilot
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90033, USA
| | - Arianna Vino
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands
| | - Katerina S. Kucera
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands
| | - Duncan A. Carmichael
- School of Applied Sciences, Edinburgh Napier University, Sighthill Court, Edinburgh EH11 4BN, UK
| | - Loes van den Heuvel
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands
| | - Joery den Hoed
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands
| | | | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh EH16 4UX, UK
| | - David J. Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Beate St Pourcain
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands
| | - Tessa M. van Leeuwen
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500 HE Nijmegen, The Netherlands
| | - Jamie Ward
- School of Psychology, University of Sussex, Brighton BN1 9RH, UK
| | - Romke Rouw
- Department of Psychology, University of Amsterdam, 1018 WT Amsterdam, The Netherlands
| | - Julia Simner
- School of Psychology, University of Sussex, Brighton BN1 9RH, UK
| | - Simon E. Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500 HE Nijmegen, The Netherlands
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105
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Karavani E, Zuk O, Zeevi D, Barzilai N, Stefanis NC, Hatzimanolis A, Smyrnis N, Avramopoulos D, Kruglyak L, Atzmon G, Lam M, Lencz T, Carmi S. Screening Human Embryos for Polygenic Traits Has Limited Utility. Cell 2019; 179:1424-1435.e8. [PMID: 31761530 PMCID: PMC6957074 DOI: 10.1016/j.cell.2019.10.033] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/11/2019] [Accepted: 10/25/2019] [Indexed: 12/19/2022]
Abstract
The increasing proportion of variance in human complex traits explained by polygenic scores, along with progress in preimplantation genetic diagnosis, suggests the possibility of screening embryos for traits such as height or cognitive ability. However, the expected outcomes of embryo screening are unclear, which undermines discussion of associated ethical concerns. Here, we use theory, simulations, and real data to evaluate the potential gain of embryo screening, defined as the difference in trait value between the top-scoring embryo and the average embryo. The gain increases very slowly with the number of embryos but more rapidly with the variance explained by the score. Given current technology, the average gain due to screening would be ≈2.5 cm for height and ≈2.5 IQ points for cognitive ability. These mean values are accompanied by wide prediction intervals, and indeed, in large nuclear families, the majority of children top-scoring for height are not the tallest.
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Affiliation(s)
- Ehud Karavani
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Or Zuk
- Department of Statistics, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Danny Zeevi
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nir Barzilai
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Genetics, Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nikos C Stefanis
- Department of Psychiatry, National and Kapodistrian University of Athens Medical School, Eginition Hospital, 115 28 Athens, Greece; University Mental Health Research Institute, 115 27 Athens, Greece; Neurobiology Research Institute, Theodor-Theohari Cozzika Foundation, 115 21 Athens, Greece
| | - Alex Hatzimanolis
- Department of Psychiatry, National and Kapodistrian University of Athens Medical School, Eginition Hospital, 115 28 Athens, Greece; Neurobiology Research Institute, Theodor-Theohari Cozzika Foundation, 115 21 Athens, Greece
| | - Nikolaos Smyrnis
- Department of Psychiatry, National and Kapodistrian University of Athens Medical School, Eginition Hospital, 115 28 Athens, Greece; University Mental Health Research Institute, 115 27 Athens, Greece
| | - Dimitrios Avramopoulos
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Leonid Kruglyak
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gil Atzmon
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Genetics, Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Biology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
| | - Max Lam
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY 11004, USA; Institute of Behavioral Science, Feinstein Institutes of Medical Research, Manhasset, NY 11030, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Todd Lencz
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY 11004, USA; Institute of Behavioral Science, Feinstein Institutes of Medical Research, Manhasset, NY 11030, USA; Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA.
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
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106
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Elliott ML, Belsky DW, Anderson K, Corcoran DL, Ge T, Knodt A, Prinz JA, Sugden K, Williams B, Ireland D, Poulton R, Caspi A, Holmes A, Moffitt T, Hariri AR. A Polygenic Score for Higher Educational Attainment is Associated with Larger Brains. Cereb Cortex 2019; 29:3496-3504. [PMID: 30215680 PMCID: PMC6645179 DOI: 10.1093/cercor/bhy219] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/09/2018] [Accepted: 08/16/2018] [Indexed: 01/20/2023] Open
Abstract
People who score higher on intelligence tests tend to have larger brains. Twin studies suggest the same genetic factors influence both brain size and intelligence. This has led to the hypothesis that genetics influence intelligence partly by contributing to the development of larger brains. We tested this hypothesis using four large imaging genetics studies (combined N = 7965) with polygenic scores derived from a genome-wide association study (GWAS) of educational attainment, a correlate of intelligence. We conducted meta-analysis to test associations among participants' genetics, total brain volume (i.e., brain size), and cognitive test performance. Consistent with previous findings, participants with higher polygenic scores achieved higher scores on cognitive tests, as did participants with larger brains. Participants with higher polygenic scores also had larger brains. We found some evidence that brain size partly mediated associations between participants' education polygenic scores and their cognitive test performance. Effect sizes were larger in the population-based samples than in the convenience-based samples. Recruitment and retention of population-representative samples should be a priority for neuroscience research. Findings suggest promise for studies integrating GWAS discoveries with brain imaging to understand neurobiology linking genetics with cognitive performance.
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Affiliation(s)
- Maxwell L Elliott
- Department of Psychology & Neuroscience, Duke University, Box 104410, Durham, NC, USA
| | - Daniel W Belsky
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA
- Social Science Research Institute, Duke University, Durham, NC, USA
| | - Kevin Anderson
- Department of Psychology, Yale University, New Haven, CT, USA
| | - David L Corcoran
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Tian Ge
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA, USA
| | - Annchen Knodt
- Department of Psychology & Neuroscience, Duke University, Box 104410, Durham, NC, USA
| | - Joseph A Prinz
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Karen Sugden
- Social Science Research Institute, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Benjamin Williams
- Social Science Research Institute, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - David Ireland
- Department of Psychology, Dunedin Multidisciplinary Health and Development Research Unit, University of Otago, 163 Union St E, Dunedin, New Zealand
| | - Richie Poulton
- Department of Psychology, Dunedin Multidisciplinary Health and Development Research Unit, University of Otago, 163 Union St E, Dunedin, New Zealand
| | - Avshalom Caspi
- Department of Psychology & Neuroscience, Duke University, Box 104410, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Social, Genetic, & Developmental Psychiatry Research Centre, Institute of Psychiatry, Psychology, & Neuroscience, King’s College London, De Crespigny Park, Denmark Hill, London, UK
- Department of Psychiatry & Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Avram Holmes
- Department of Psychology, Yale University, New Haven, CT, USA
| | - Terrie Moffitt
- Department of Psychology & Neuroscience, Duke University, Box 104410, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Social, Genetic, & Developmental Psychiatry Research Centre, Institute of Psychiatry, Psychology, & Neuroscience, King’s College London, De Crespigny Park, Denmark Hill, London, UK
- Department of Psychiatry & Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Ahmad R Hariri
- Department of Psychology & Neuroscience, Duke University, Box 104410, Durham, NC, USA
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107
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Tanksley PT, Motz RT, Kail RM, Barnes JC, Liu H. The Genome-Wide Study of Human Social Behavior and Its Application in Sociology. Front Sociol 2019; 4:53. [PMID: 33869376 PMCID: PMC8022812 DOI: 10.3389/fsoc.2019.00053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/07/2019] [Indexed: 06/12/2023]
Abstract
Recent years have seen a push for the integration of modern genomic methodologies with sociological inquiry. The inclusion of genomic approaches promises to help address long-standing issues in sociology (e.g., selection effects), as well as open up new avenues for future research. This article reviews the substantive findings of behavior genetic/genomic research, both from the recent past (e.g., twin/adoption studies, candidate gene studies) and from contemporary genomic analyses. The article primarily focuses on modern genomic methods available to sociologists (e.g., polygenic score analysis) and their various applications for answering sociological questions. The article concludes by considering a number of areas to which genomic researchers and sociologists should pay close attention if a consilience between genomic methods and sociological research is to be fully realized.
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Affiliation(s)
- Peter T. Tanksley
- School of Criminal Justice, University of Cincinnati, Cincinnati, OH, United States
| | - Ryan T. Motz
- School of Criminal Justice, University of Cincinnati, Cincinnati, OH, United States
| | - Rachel M. Kail
- School of Criminal Justice, University of Cincinnati, Cincinnati, OH, United States
| | - J. C. Barnes
- School of Criminal Justice, University of Cincinnati, Cincinnati, OH, United States
| | - Hexuan Liu
- School of Criminal Justice, University of Cincinnati, Cincinnati, OH, United States
- Institute for Interdisciplinary Data Science, University of Cincinnati, Cincinnati, OH, United States
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108
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Belsky DW, Harden KP. Phenotypic Annotation: Using Polygenic Scores to Translate Discoveries From Genome-Wide Association Studies From the Top Down. Curr Dir Psychol Sci 2019; 28:82-90. [PMID: 38736689 PMCID: PMC11086979 DOI: 10.1177/0963721418807729] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Genome-wide association studies (GWASs) have identified specific genetic variants associated with complex human traits and behaviors, such as educational attainment, mental disorders, and personality. However, small effect sizes for individual variants, uncertainty regarding the biological function of discovered genotypes, and potential "outside-the-skin" environmental mechanisms leave a translational gulf between GWAS results and scientific understanding that will improve human health and well-being. We propose a set of social, behavioral, and brain-science research activities that map discovered genotypes to neural, developmental, and social mechanisms and call this research program phenotypic annotation. Phenotypic annotation involves (a) elaborating the nomological network surrounding discovered genotypes, (b) shifting focus from individual genes to whole genomes, and (c) testing how discovered genotypes affect life-span development. Phenotypic-annotation research is already advancing the understanding of GWAS discoveries for educational attainment and schizophrenia. We review examples and discuss methodological considerations for psychologists taking up the phenotypic-annotation approach.
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Affiliation(s)
- Daniel W. Belsky
- Department of Epidemiology, Columbia University Mailman School of Public Health
- The Robert N. Butler Columbia Aging Center, Columbia University Mailman School of Public Health
| | - K. Paige Harden
- Department of Psychology, The University of Texas at Austin
- Population Research Center, The University of Texas at Austin
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109
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Rosenberg NA, Edge MD, Pritchard JK, Feldman MW. Interpreting polygenic scores, polygenic adaptation, and human phenotypic differences. Evol Med Public Health 2018; 2019:26-34. [PMID: 30838127 PMCID: PMC6393779 DOI: 10.1093/emph/eoy036] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 12/21/2018] [Indexed: 12/24/2022] Open
Abstract
Recent analyses of polygenic scores have opened new discussions concerning the genetic basis and evolutionary significance of differences among populations in distributions of phenotypes. Here, we highlight limitations in research on polygenic scores, polygenic adaptation and population differences. We show how genetic contributions to traits, as estimated by polygenic scores, combine with environmental contributions so that differences among populations in trait distributions need not reflect corresponding differences in genetic propensity. Under a null model in which phenotypes are selectively neutral, genetic propensity differences contributing to phenotypic differences among populations are predicted to be small. We illustrate this null hypothesis in relation to health disparities between African Americans and European Americans, discussing alternative hypotheses with selective and environmental effects. Close attention to the limitations of research on polygenic phenomena is important for the interpretation of their relationship to human population differences.
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Affiliation(s)
| | - Michael D Edge
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Jonathan K Pritchard
- Department of Biology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
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110
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DiPrete TA, Burik CAP, Koellinger PD. Genetic instrumental variable regression: Explaining socioeconomic and health outcomes in nonexperimental data. Proc Natl Acad Sci U S A 2018; 115:E4970-9. [PMID: 29686100 DOI: 10.1073/pnas.1707388115] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We propose genetic instrumental variable (GIV) regression—a method that controls for pleiotropic effects of genes on two variables. GIV regression is broadly applicable to study outcomes for which polygenic scores from large-scale genome-wide association studies are available. We explore the performance of GIV regression in the presence of pleiotropy across a range of scenarios and find that it yields more accurate estimates than alternative approaches such as ordinary least-squares regression or Mendelian randomization. When GIV regression is combined with proper controls for purely environmental sources of bias (e.g., using control variables and sibling fixed effects), it improves our understanding of the causal relationships between genetically correlated variables. Identifying causal effects in nonexperimental data is an enduring challenge. One proposed solution that recently gained popularity is the idea to use genes as instrumental variables [i.e., Mendelian randomization (MR)]. However, this approach is problematic because many variables of interest are genetically correlated, which implies the possibility that many genes could affect both the exposure and the outcome directly or via unobserved confounding factors. Thus, pleiotropic effects of genes are themselves a source of bias in nonexperimental data that would also undermine the ability of MR to correct for endogeneity bias from nongenetic sources. Here, we propose an alternative approach, genetic instrumental variable (GIV) regression, that provides estimates for the effect of an exposure on an outcome in the presence of pleiotropy. As a valuable byproduct, GIV regression also provides accurate estimates of the chip heritability of the outcome variable. GIV regression uses polygenic scores (PGSs) for the outcome of interest which can be constructed from genome-wide association study (GWAS) results. By splitting the GWAS sample for the outcome into nonoverlapping subsamples, we obtain multiple indicators of the outcome PGSs that can be used as instruments for each other and, in combination with other methods such as sibling fixed effects, can address endogeneity bias from both pleiotropy and the environment. In two empirical applications, we demonstrate that our approach produces reasonable estimates of the chip heritability of educational attainment (EA) and show that standard regression and MR provide upwardly biased estimates of the effect of body height on EA.
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111
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Abdellaoui A, Nivard MG, Hottenga JJ, Fedko I, Verweij KJH, Baselmans BML, Ehli EA, Davies GE, Bartels M, Boomsma DI, Cacioppo JT. Predicting loneliness with polygenic scores of social, psychological and psychiatric traits. Genes Brain Behav 2018; 17:e12472. [PMID: 29573219 DOI: 10.1111/gbb.12472] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 01/31/2018] [Accepted: 03/08/2018] [Indexed: 12/14/2022]
Abstract
Loneliness is a heritable trait that accompanies multiple disorders. The association between loneliness and mental health indices may partly be due to inherited biological factors. We constructed polygenic scores for 27 traits related to behavior, cognition and mental health and tested their prediction for self-reported loneliness in a population-based sample of 8798 Dutch individuals. Polygenic scores for major depressive disorder (MDD), schizophrenia and bipolar disorder were significantly associated with loneliness. Of the Big Five personality dimensions, polygenic scores for neuroticism and conscientiousness also significantly predicted loneliness, as did the polygenic scores for subjective well-being, tiredness and self-rated health. When including all polygenic scores simultaneously into one model, only 2 major depression polygenic scores remained as significant predictors of loneliness. When controlling only for these 2 MDD polygenic scores, only neuroticism and schizophrenia remain significant. The total variation explained by all polygenic scores collectively was 1.7%. The association between the propensity to feel lonely and the susceptibility to psychiatric disorders thus pointed to a shared genetic etiology. The predictive power of polygenic scores will increase as the power of the genome-wide association studies on which they are based increases and may lead to clinically useful polygenic scores that can inform on the genetic predisposition to loneliness and mental health.
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Affiliation(s)
- A Abdellaoui
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands.,Department of Psychiatry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - M G Nivard
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - J-J Hottenga
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - I Fedko
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - K J H Verweij
- Department of Psychiatry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - B M L Baselmans
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands.,Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - E A Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota
| | - G E Davies
- Avera Institute for Human Genetics, Sioux Falls, South Dakota
| | - M Bartels
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands.,Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - D I Boomsma
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands.,Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - J T Cacioppo
- Department of Psychology, University of Chicago, Chicago, Illinois
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112
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Abstract
We interrogate state-level clustering of polygenic scores at different points in the life course and variation in the association of mean polygenic scores in a respondent's state of birth with corresponding phenotypes. The polygenic scores for height and smoking show the most state-level clustering (2 to 4 percent) with relatively little clustering observed for the other scores. However, even the small amounts of observed clustering are potentially meaningful. The state-mean polygenic score for educational attainment is strongly associated with an individual's educational attainment net of that person's polygenic score. The ecological clustering of polygenic scores may denote a new environmental factor in gene-environment research. We conclude by discussing possible mechanisms that underlie this association and the implications of our findings for social and genetic research.
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Affiliation(s)
| | - David H Rehkopf
- is assistant professor of medicine at the Stanford University School of Medicine
| | | | - Jason D Boardman
- is professor in the Department of Sociology and director of the Health and Society Program in the Institute of Behavioral Science at the University of Colorado at Boulder
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113
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Reginsson GW, Ingason A, Euesden J, Bjornsdottir G, Olafsson S, Sigurdsson E, Oskarsson H, Tyrfingsson T, Runarsdottir V, Hansdottir I, Steinberg S, Stefansson H, Gudbjartsson DF, Thorgeirsson TE, Stefansson K. Polygenic risk scores for schizophrenia and bipolar disorder associate with addiction. Addict Biol 2018; 23:485-492. [PMID: 28231610 PMCID: PMC5811785 DOI: 10.1111/adb.12496] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 01/19/2017] [Accepted: 01/23/2017] [Indexed: 12/15/2022]
Abstract
We use polygenic risk scores (PRSs) for schizophrenia (SCZ) and bipolar disorder (BPD) to predict smoking, and addiction to nicotine, alcohol or drugs in individuals not diagnosed with psychotic disorders. Using PRSs for 144 609 subjects, including 10 036 individuals admitted for in‐patient addiction treatment and 35 754 smokers, we find that diagnoses of various substance use disorders and smoking associate strongly with PRSs for SCZ (P = 5.3 × 10−50–1.4 × 10−6) and BPD (P = 1.7 × 10−9–1.9 × 10−3), showing shared genetic etiology between psychosis and addiction. Using standardized scores for SCZ and BPD scaled to a unit increase doubling the risk of the corresponding disorder, the odds ratios for alcohol and substance use disorders range from 1.19 to 1.31 for the SCZ‐PRS, and from 1.07 to 1.29 for the BPD‐PRS. Furthermore, we show that as regular smoking becomes more stigmatized and less prevalent, these biological risk factors gain importance as determinants of the behavior.
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Affiliation(s)
| | | | - Jack Euesden
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience; King's College London; UK
- MRC Integrative Epidemiology Unit; Oakfield House, Oakfield Grove, University of Bristol; BS8 2EG UK
| | | | | | | | | | | | | | - Ingunn Hansdottir
- SAA-National Center of Addiction Medicine; Iceland
- Faculty of Psychology; University of Iceland; Iceland
| | | | | | - Daniel F. Gudbjartsson
- deCODE genetics/Amgen; Iceland
- Department of Engineering and Natural Sciences; University of Iceland; Iceland
| | | | - Kari Stefansson
- deCODE genetics/Amgen; Iceland
- Faculty of Medicine; University of Iceland; Iceland
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114
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Krapohl E, Hannigan LJ, Pingault JB, Patel H, Kadeva N, Curtis C, Breen G, Newhouse SJ, Eley TC, O'Reilly PF, Plomin R. Widespread covariation of early environmental exposures and trait-associated polygenic variation. Proc Natl Acad Sci U S A 2017; 114:11727-32. [PMID: 29078306 DOI: 10.1073/pnas.1707178114] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Although gene-environment correlation is recognized and investigated by family studies and recently by SNP-heritability studies, the possibility that genetic effects on traits capture environmental risk factors or protective factors has been neglected by polygenic prediction models. We investigated covariation between trait-associated polygenic variation identified by genome-wide association studies (GWASs) and specific environmental exposures, controlling for overall genetic relatedness using a genomic relatedness matrix restricted maximum-likelihood model. In a UK-representative sample (n = 6,710), we find widespread covariation between offspring trait-associated polygenic variation and parental behavior and characteristics relevant to children's developmental outcomes-independently of population stratification. For instance, offspring genetic risk for schizophrenia was associated with paternal age (R2 = 0.002; P = 1e-04), and offspring education-associated variation was associated with variance in breastfeeding (R2 = 0.021; P = 7e-30), maternal smoking during pregnancy (R2 = 0.008; P = 5e-13), parental smacking (R2 = 0.01; P = 4e-15), household income (R2 = 0.032; P = 1e-22), watching television (R2 = 0.034; P = 5e-47), and maternal education (R2 = 0.065; P = 3e-96). Education-associated polygenic variation also captured covariation between environmental exposures and children's inattention/hyperactivity, conduct problems, and educational achievement. The finding that genetic variation identified by trait GWASs partially captures environmental risk factors or protective factors has direct implications for risk prediction models and the interpretation of GWAS findings.
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115
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Abstract
Recent findings from molecular genetics now make it possible to test directly for natural selection by analyzing whether genetic variants associated with various phenotypes have been under selection. I leverage these findings to construct polygenic scores that use individuals' genotypes to predict their body mass index, educational attainment (EA), glucose concentration, height, schizophrenia, total cholesterol, and (in females) age at menarche. I then examine associations between these scores and fitness to test whether natural selection has been occurring. My study sample includes individuals of European ancestry born between 1931 and 1953 who participated in the Health and Retirement Study, a representative study of the US population. My results imply that natural selection has been slowly favoring lower EA in both females and males, and are suggestive that natural selection may have favored a higher age at menarche in females. For EA, my estimates imply a rate of selection of about -1.5 mo of education per generation (which pales in comparison with the increases in EA observed in contemporary times). Although they cannot be projected over more than one generation, my results provide additional evidence that humans are still evolving-albeit slowly, especially compared with the rapid changes that have occurred over the past few generations due to cultural and environmental factors.
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116
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Conley D, Laidley T, Belsky DW, Fletcher JM, Boardman JD, Domingue BW. Assortative mating and differential fertility by phenotype and genotype across the 20th century. Proc Natl Acad Sci U S A 2016; 113:6647-52. [PMID: 27247411 DOI: 10.1073/pnas.1523592113] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
This study asks two related questions about the shifting landscape of marriage and reproduction in US society over the course of the last century with respect to a range of health and behavioral phenotypes and their associated genetic architecture: (i) Has assortment on measured genetic factors influencing reproductive and social fitness traits changed over the course of the 20th century? (ii) Has the genetic covariance between fitness (as measured by total fertility) and other traits changed over time? The answers to these questions inform our understanding of how the genetic landscape of American society has changed over the past century and have implications for population trends. We show that husbands and wives carry similar loadings for genetic factors related to education and height. However, the magnitude of this similarity is modest and has been fairly consistent over the course of the 20th century. This consistency is particularly notable in the case of education, for which phenotypic similarity among spouses has increased in recent years. Likewise, changing patterns of the number of children ever born by phenotype are not matched by shifts in genotype-fertility relationships over time. Taken together, these trends provide no evidence that social sorting is becoming increasingly genetic in nature or that dysgenic dynamics have accelerated.
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117
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Groen-Blokhuis MM, Middeldorp CM, Kan KJ, Abdellaoui A, van Beijsterveldt CE, Ehli EA, Davies GE, Scheet PA, Xiao X, Hudziak JJ, Hottenga JJ, Neale BM, Boomsma DI; Psychiatric Genomics Consortium ADHD Working Group. Attention-deficit/hyperactivity disorder polygenic risk scores predict attention problems in a population-based sample of children. J Am Acad Child Adolesc Psychiatry 2014; 53:1123-9.e6. [PMID: 25245356 DOI: 10.1016/j.jaac.2014.06.014] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Revised: 06/23/2014] [Accepted: 08/12/2014] [Indexed: 10/24/2022]
Abstract
OBJECTIVE Clinically, attention-deficit/hyperactivity disorder (ADHD) is characterized by hyperactivity, impulsivity, and inattention and is among the most common childhood disorders. These same traits that define ADHD are variable in the general population, and the clinical diagnosis may represent the extreme end of a continuous distribution of inattentive and hyperactive behaviors. This hypothesis can be tested by assessing the predictive value of polygenic risk scores derived from a discovery sample of ADHD patients in a target sample from the general population with continuous scores of inattention and hyperactivity. In addition, the genetic overlap between ADHD and continuous ADHD scores can be tested across rater and age. METHOD The Psychiatric Genomics Consortium has performed the largest genome-wide analysis (GWA) study of ADHD so far, including 5,621 clinical patients and 13,589 controls. The effects sizes of single nucleotide polymorphisms (SNPs) estimated in this meta-analysis were used to obtain individual polygenic risk scores in an independent population-based cohort of 2,437 children from the Netherlands Twin Register. The variance explained in Attention Problems (AP) scale scores by the polygenic risk scores was estimated by linear mixed modeling. RESULTS The ADHD polygenic risk scores significantly predicted both parent and teacher ratings of AP in preschool- and school-aged children. CONCLUSION These results indicate genetic overlap between a diagnosis of ADHD and AP scale scores across raters and age groups and provides evidence for a dimensional model of ADHD. Future GWA studies on ADHD can likely benefit from the inclusion of population-based cohorts and the analysis of continuous scores.
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118
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de Zeeuw EL, van Beijsterveldt CEM, Glasner TJ, Bartels M, Ehli EA, Davies GE, Hudziak JJ, Rietveld CA, Groen-Blokhuis MM, Hottenga JJ, de Geus EJC, Boomsma DI. Polygenic scores associated with educational attainment in adults predict educational achievement and ADHD symptoms in children. Am J Med Genet B Neuropsychiatr Genet 2014; 165B:510-20. [PMID: 25044548 DOI: 10.1002/ajmg.b.32254] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 06/02/2014] [Indexed: 12/31/2022]
Abstract
The American Psychiatric Association estimates that 3 to 7 per cent of all school aged children are diagnosed with attention deficit hyperactivity disorder (ADHD). Even after correcting for general cognitive ability, numerous studies report a negative association between ADHD and educational achievement. With polygenic scores we examined whether genetic variants that have a positive influence on educational attainment have a protective effect against ADHD. The effect sizes from a large GWA meta-analysis of educational attainment in adults were used to calculate polygenic scores in an independent sample of 12-year-old children from the Netherlands Twin Register. Linear mixed models showed that the polygenic scores significantly predicted educational achievement, school performance, ADHD symptoms and attention problems in children. These results confirm the genetic overlap between ADHD and educational achievement, indicating that one way to gain insight into genetic variants responsible for variation in ADHD is to include data on educational achievement, which are available at a larger scale.
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Affiliation(s)
- Eveline L de Zeeuw
- Department of Biological Psychology, VU University, Amsterdam, the Netherlands; EMGO+ Institute for Health and Care Research, VU University Medical Centre, Amsterdam, the Netherlands
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