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Bowler A, Arichi T, Fearon P, Meaburn E, Begum-Ali J, Pascoe G, Johnson MH, Jones EJH, Ronald A. Phenotypic and Genetic Associations Between Preschool Fine Motor Skills and Later Neurodevelopment, Psychopathology, and Educational Achievement. Biol Psychiatry 2024; 95:849-858. [PMID: 38043695 DOI: 10.1016/j.biopsych.2023.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
BACKGROUND Fine motor skills are heritable and comprise important milestones in development, and some evidence suggests that impairments in fine motor skills are associated with neurodevelopmental conditions, psychiatric disorders, and poor educational outcomes. METHODS In a preregistered study of 9625 preschool children from TEDS (Twins Early Development Study), fine motor assessments (drawing, block building, folding, and questionnaires) were conducted at 2, 3, and 4 years of age. A cross-age fine motor score was derived using principal component analysis. Multivariate regression analysis was used to examine the relationships between the fine motor score and neurodevelopmental traits, psychopathology, and educational outcomes at 3 later ages (7-8, 12, and 16 years) and cross-age psychopathology composite scores. Polygenic scores (PGSs) were created for attention-deficit/hyperactivity disorder (ADHD), autism, schizophrenia, anxiety, major depressive disorder, obsessive-compulsive disorder, and years of education. We ran single-PGS models and a multi-PGS model. RESULTS Fine motor skills were negatively associated with neurodevelopmental traits and psychopathology across childhood and adolescence and positively associated with educational achievement in adolescence (β = 0.25, p < .001). Superior fine motor skills were associated with a higher years-of-education PGS (β = 0.07, p < .001), a lower ADHD PGS (β = -0.04, p = .011), and a higher anxiety PGS (β = 0.03, p = .040). Similarly, the multi-PGS model retained the PGSs for years of education (β = 0.07), ADHD (β = -0.03), and anxiety (β = 0.01). A non-preregistered analysis in an independent preschool sample replicated the ADHD PGS association, but not the years of education or anxiety PGS associations. CONCLUSIONS Fine motor skills are linked genetically and phenotypically to later neurodevelopment, psychopathology, and educational outcomes. Future work should investigate the mechanisms that underlie the role of fine motor development in later outcomes.
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Affiliation(s)
- Aislinn Bowler
- Centre for Brain and Cognitive Development, Birkbeck, University of London, London, United Kingdom.
| | - Tomoki Arichi
- Centre for the Developing Brain, School of Imaging Sciences and Biomedical Engineering, King's College London, London, United Kingdom; Pediatric Neurosciences, Evelina London Children's Hospital, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Pasco Fearon
- Centre for Family Research, Department of Psychology, University of Cambridge, Cambridge, United Kingdom; Research Department of Clinical, Educational and Health Psychology, University College London, London, United Kingdom
| | - Emma Meaburn
- Centre for Brain and Cognitive Development, Birkbeck, University of London, London, United Kingdom
| | - Jannath Begum-Ali
- Centre for Brain and Cognitive Development, Birkbeck, University of London, London, United Kingdom
| | - Greg Pascoe
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Mark H Johnson
- Centre for Brain and Cognitive Development, Birkbeck, University of London, London, United Kingdom; Department of Psychology, University of Cambridge, Cambridge, United Kingdom
| | - Emily J H Jones
- Centre for Brain and Cognitive Development, Birkbeck, University of London, London, United Kingdom
| | - Angelica Ronald
- Centre for Brain and Cognitive Development, Birkbeck, University of London, London, United Kingdom; School of Psychology, University of Surrey, Guildford, United Kingdom
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Grinde KE, Browning BL, Reiner AP, Thornton TA, Browning SR. Adjusting for principal components can induce spurious associations in genome-wide association studies in admixed populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587682. [PMID: 38617337 PMCID: PMC11014513 DOI: 10.1101/2024.04.02.587682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/24/2024]
Abstract
Principal component analysis (PCA) is widely used to control for population structure in genome-wide association studies (GWAS). Top principal components (PCs) typically reflect population structure, but challenges arise in deciding how many PCs are needed and ensuring that PCs do not capture other artifacts such as regions with atypical linkage disequilibrium (LD). In response to the latter, many groups suggest performing LD pruning or excluding known high LD regions prior to PCA. However, these suggestions are not universally implemented and the implications for GWAS are not fully understood, especially in the context of admixed populations. In this paper, we investigate the impact of pre-processing and the number of PCs included in GWAS models in African American samples from the Women's Women's Health Initiative SNP Health Association Resource and two Trans-Omics for Precision Medicine Whole Genome Sequencing Project contributing studies (Jackson Heart Study and Genetic Epidemiology of Chronic Obstructive Pulmonary Disease Study). In all three samples, we find the first PC is highly correlated with genome-wide ancestry whereas later PCs often capture local genomic features. The pattern of which, and how many, genetic variants are highly correlated with individual PCs differs from what has been observed in prior studies focused on European populations and leads to distinct downstream consequences: adjusting for such PCs yields biased effect size estimates and elevated rates of spurious associations due to the phenomenon of collider bias. Excluding high LD regions identified in previous studies does not resolve these issues. LD pruning proves more effective, but the optimal choice of thresholds varies across datasets. Altogether, our work highlights unique issues that arise when using PCA to control for ancestral heterogeneity in admixed populations and demonstrates the importance of careful pre-processing and diagnostics to ensure that PCs capturing multiple local genomic features are not included in GWAS models.
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Affiliation(s)
- Kelsey E. Grinde
- Department of Mathematics, Statistics, and Computer Science, Macalester College, Saint Paul, Minnesota, 55105, USA
| | - Brian L. Browning
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, 98195, USA
| | - Alexander P. Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, 98195, USA
| | - Timothy A. Thornton
- Regeneron Genetics Center, Tarrytown, New York, 10591, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, 98195, USA
| | - Sharon R. Browning
- Department of Biostatistics, University of Washington, Seattle, Washington, 98195, USA
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Lu J, Gong S, Zhu J, Fang Q. Relationships between obesity and functional outcome after ischemic stroke: a Mendelian randomization study. Neurol Sci 2024:10.1007/s10072-024-07415-w. [PMID: 38466476 DOI: 10.1007/s10072-024-07415-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 02/17/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND AND OBJECTIVES Most previous studies suggested obesity deteriorates the functional outcome after ischemic stroke. But there are researches claiming that obesity is associated with lower mortality, recurrence, and readmission rates, which is known as the obesity paradox. Our current research aimed to investigate the correlation between genetically obesity and the post-stroke outcome with the Mendelian randomization (MR) method. METHODS The UK Biobank and the GIANT consortium provided instrumental variables for body mass index (BMI, 806,834 individuals) and waist-to-hip ratio (WHR, 697,734 individuals). Data of functional outcome after ischemic stroke were obtained from the Genetics of Ischemic Stroke Functional Outcome network (6012 individuals). Inverse-variance weighted approach was utilized as the primary analyses. Sensitivity analyses involved the utilization of different MR methods. The heterogeneity among genetic variants was assessed by I2 and Q value statistics. RESULTS In univariable analysis, there was a significant connection between genetic susceptibility to WHR and worse functional outcome (modified Rankin Scale 3) after ischemic stroke (OR [95%CI] = 1.47 [1.07, 2.02], P = 0.016). Genetic liability to BMI and was not associated with post-stroke functional outcome (all P > 0.05). The overall patterns between genetic liability to WHR and functional outcome post-ischemic outcome no longer existed in the multivariable MR analysis after adjusting for BMI (OR [95%CI] = 1.26[0.76,1.67], P = 0.56). CONCLUSION The current MR study provided evidence that WHR was correlated to unfavorable outcome post-ischemic stroke. Exploring interventions against obesity may potentially improve recovery after ischemic stroke.
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Affiliation(s)
- Jieyi Lu
- Department of Neurology, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou, 215006, China
- Medical College of Soochow University, 199 Renai Road, Suzhou, 215123, China
| | - Siqi Gong
- Department of Neurology, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou, 215006, China
- Medical College of Soochow University, 199 Renai Road, Suzhou, 215123, China
| | - Juehua Zhu
- Department of Neurology, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou, 215006, China.
| | - Qi Fang
- Department of Neurology, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou, 215006, China.
- Department of Neurology, Dushu Lake Hospital Affiliated to Soochow University, 9 Chongwen Road, Suzhou, 215125, China.
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Waller C, Ho A, Batzler A, Geske J, Karpyak V, Biernacka J, Winham S. Genetic correlations of alcohol consumption and alcohol use disorder with sex hormone levels in females and males. RESEARCH SQUARE 2024:rs.3.rs-3944066. [PMID: 38464231 PMCID: PMC10925434 DOI: 10.21203/rs.3.rs-3944066/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Background Alcohol consumption behaviors and alcohol use disorder risk and presentation differ by sex, and these complex traits are associated with blood concentrations of the steroid sex hormones, testosterone and estradiol, and their regulatory binding proteins, sex hormone binding globulin (SHBG) and albumin. Genetic variation is associated with alcohol consumption and alcohol use disorder, as well as levels of steroid sex hormones and their binding proteins. Methods To assess the contribution of genetic factors to previously described phenotypic associations between alcohol-use traits and sex-hormone levels, we estimated genetic correlations (rg) using summary statistics from prior published, large sample size genome-wide association studies (GWAS) of alcohol consumption, alcohol dependence, testosterone, estradiol, SHBG, and albumin. Results For alcohol consumption, we observed positive genetic correlation (i.e. genetic effects in the same direction) with total testosterone in males (rg = 0.084, p = 0.007) and trends toward positive genetic correlation with bioavailable testosterone (rg = 0.060, p = 0.084) and SHBG in males (rg = 0.056, p = 0.086) and with albumin in a sex-combined cohort (rg = 0.082, p = 0.015); however in females, we observed positive genetic correlation with SHBG (rg = 0.089, p = 0.004) and a trend toward negative genetic correlation (i.e. genetic effects in opposite directions) with bioavailable testosterone (rg = -0.064, p = 0.032). For alcohol dependence, we observed a trend toward negative genetic correlation with total testosterone in females (rg = -0.106, p = 0.024) and positive genetic correlation with BMI-adjusted SHBG in males (rg = 0.119, p = 0.017). Several of these genetic correlations differed between females and males and were not in the same direction as the corresponding phenotypic associations. Conclusions Findings suggest that shared genetic effects may contribute to positive associations of alcohol consumption with albumin in both sexes, as well as positive associations between alcohol consumption and bioavailable testosterone and between alcohol dependence and SHBG in males. However, relative contributions of heritable and environmental factors to associations between alcohol-use traits and sex-hormone levels may differ by sex, with genetic factors contributing more in males and environmental factors contributing more in females.
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Agrawal V, Manouchehri A, Vaitinadin NS, Shi M, Bagheri M, Gupta DK, Kullo IJ, Luo Y, McNally EM, Puckelwartz MJ, Ferguson JF, Wells QS, Mosley JD. Identification of Clinical Drivers of Left Atrial Enlargement Through Genomics of Left Atrial Size. Circ Heart Fail 2024; 17:e010557. [PMID: 38126226 PMCID: PMC10842187 DOI: 10.1161/circheartfailure.123.010557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 10/24/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Greater left atrial size is associated with a higher incidence of cardiovascular disease and mortality, but the full spectrum of diagnoses associated with left atrial enlargement in sex-stratified clinical populations is not well known. Our study sought to identify genetic risk mechanisms affecting left atrial diameter (LAD) in a clinical cohort. METHODS Using Vanderbilt deidentified electronic health record, we studied 6163 females and 5993 males of European ancestry who had at least 1 LAD measure and available genotyping. A sex-stratified polygenic score was constructed for LAD variation and tested for association against 1680 International Classification of Diseases code-based phenotypes. Two-sample univariable and multivariable Mendelian randomization approaches were used to assess etiologic relationships between candidate associations and LAD. RESULTS A phenome-wide association study identified 25 International Classification of Diseases code-based diagnoses in females and 11 in males associated with a polygenic score of LAD (false discovery rate q<0.01), 5 of which were further evaluated by Mendelian randomization (waist circumference [WC], atrial fibrillation, heart failure, systolic blood pressure, and coronary artery disease). Sex-stratified differences in the genetic associations between risk factors and a polygenic score for LAD were observed (WC for females; heart failure, systolic blood pressure, atrial fibrillation, and WC for males). By multivariable Mendelian randomization, higher WC remained significantly associated with larger LAD in females, whereas coronary artery disease, WC, and atrial fibrillation remained significantly associated with larger LAD in males. CONCLUSIONS In a clinical population, we identified, by genomic approaches, potential etiologic risk factors for larger LAD. Further studies are needed to confirm the extent to which these risk factors may be modified to prevent or reverse adverse left atrial remodeling and the extent to which sex modifies these risk factors.
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Affiliation(s)
- Vineet Agrawal
- Vanderbilt Translational and Clinical Cardiovascular Research Center and Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs, Nashville, TN, USA
| | - Ali Manouchehri
- Vanderbilt Translational and Clinical Cardiovascular Research Center and Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nataraja Sarma Vaitinadin
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mingjian Shi
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Minoo Bagheri
- Vanderbilt Translational and Clinical Cardiovascular Research Center and Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Deepak K. Gupta
- Vanderbilt Translational and Clinical Cardiovascular Research Center and Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Iftikhar J. Kullo
- Department of Cardiovascular Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Yuan Luo
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Elizabeth M. McNally
- Center for Genetic Medicine, Northwestern Feinberg School of Medicine, Chicago, IL, USA
| | - Megan J. Puckelwartz
- Center for Genetic Medicine, Northwestern Feinberg School of Medicine, Chicago, IL, USA
- Department of Pharmacology, Northwestern Feinberg School of Medicine, Chicago, IL, USA
| | - Jane F. Ferguson
- Vanderbilt Translational and Clinical Cardiovascular Research Center and Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Quinn S. Wells
- Vanderbilt Translational and Clinical Cardiovascular Research Center and Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan D. Mosley
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
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Dahl A, Thompson M, An U, Krebs M, Appadurai V, Border R, Bacanu SA, Werge T, Flint J, Schork AJ, Sankararaman S, Kendler KS, Cai N. Phenotype integration improves power and preserves specificity in biobank-based genetic studies of major depressive disorder. Nat Genet 2023; 55:2082-2093. [PMID: 37985818 PMCID: PMC10703686 DOI: 10.1038/s41588-023-01559-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/18/2023] [Indexed: 11/22/2023]
Abstract
Biobanks often contain several phenotypes relevant to diseases such as major depressive disorder (MDD), with partly distinct genetic architectures. Researchers face complex tradeoffs between shallow (large sample size, low specificity/sensitivity) and deep (small sample size, high specificity/sensitivity) phenotypes, and the optimal choices are often unclear. Here we propose to integrate these phenotypes to combine the benefits of each. We use phenotype imputation to integrate information across hundreds of MDD-relevant phenotypes, which significantly increases genome-wide association study (GWAS) power and polygenic risk score (PRS) prediction accuracy of the deepest available MDD phenotype in UK Biobank, LifetimeMDD. We demonstrate that imputation preserves specificity in its genetic architecture using a novel PRS-based pleiotropy metric. We further find that integration via summary statistics also enhances GWAS power and PRS predictions, but can introduce nonspecific genetic effects depending on input. Our work provides a simple and scalable approach to improve genetic studies in large biobanks by integrating shallow and deep phenotypes.
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Affiliation(s)
- Andrew Dahl
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA.
| | - Michael Thompson
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ulzee An
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Morten Krebs
- Institute of Biological Psychiatry, Mental Health Center-Sct Hans, Copenhagen University Hospital-Mental Health Services CPH, Copenhagen, Denmark
| | - Vivek Appadurai
- Institute of Biological Psychiatry, Mental Health Center-Sct Hans, Copenhagen University Hospital-Mental Health Services CPH, Copenhagen, Denmark
| | - Richard Border
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Silviu-Alin Bacanu
- Virginia Institute for Psychiatric and Behavioral Genetics and Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Center-Sct Hans, Copenhagen University Hospital-Mental Health Services CPH, Copenhagen, Denmark
- Lundbeck Foundation GeoGenetics Centre, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Flint
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Andrew J Schork
- Institute of Biological Psychiatry, Mental Health Center-Sct Hans, Copenhagen University Hospital-Mental Health Services CPH, Copenhagen, Denmark
- Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA
- Section for Geogenetics, GLOBE Institute, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
| | - Sriram Sankararaman
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kenneth S Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics and Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Na Cai
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany.
- Computational Health Centre, Helmholtz Zentrum München, Neuherberg, Germany.
- School of Medicine, Technical University of Munich, Munich, Germany.
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7
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Sun K, Ming Y, Xu J, Wu Y, Zeng Y, Wu L, Li M, Shen B. Assessing the Casual Association between Sex Hormone Levels and Fracture Risk: A Two-Sample Mendelian Randomization Study. Orthop Surg 2023; 15:3065-3074. [PMID: 37771125 PMCID: PMC10694015 DOI: 10.1111/os.13881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 09/30/2023] Open
Abstract
OBJECTIVE Prior observational studies have reported that levels of sex hormones constitute a risk factor for the fracture. The aim of this study was to ascertain whether there is a causal relationship between the levels of sex hormones and the risk of fracture through Mendelian randomization (MR). METHODS Single-nucleotide polymorphisms (SNPs) associated with two indicators of sex hormone levels, circulating sex hormone-binding globulin (SHBG) and bioavailable testosterone levels, as exposures were selected from a large genome-wide association study (GWAS) from UK Biobank. The summary statistics for 11 different types of fracture as outcomes from the FinnGen consortium. This study employed the two-sample MR approach. For the main analysis, the inverse-variance-weighted (IVW) method was utilized. To assess the heterogeneity of MR results, the IVW method and MR-Egger method were utilized. To evaluate potential pleiotropy, MR-Egger regression was conducted. Additionally, a leave-one-SNP-out test was performed to assess the robustness of MR results to the exclusion of any individual SNP. RESULTS The MR analyses demonstrated a conspicuous impact of SHBG on the risk of pathological fracture with osteoporosis (OP). We found that an increase of one standard deviation (SD) in SHBG correspondingly increased the risk of pathological fracture with OP [odds ratio (OR) 2.42, 95% confidence interval (CI), 1.52-3.85; p = 1.93 × 10-4 ]. The bioavailable testosterone showed the negative casual genetic associations with fractures of foot and forearm. An increase of one SD in the genetically predetermined bioavailable testosterone was associated with a reduction of 37% in the risk of fracture of foot (OR 0.63, 95% Cl 0.49 to 0.81; p = 3.37 × 10-4 ), as well as a 39% decrease in the risk of fracture of forearm (OR 0.61, 95% Cl 0.50 to 0.76; p = 5.40 × 10-6 ). CONCLUSIONS Our study confirms that individuals experiencing elevated SHBG concentrations showed a major causal effect on pathological fracture with OP. High bioavailable testosterone levels play an important role in preventing the fractures of foot and forearm. Although increasing bioavailable testosterone and decreasing SHBG levels had no casual effect on most fractures in the general population, they are likely to have the most clinically relevant effect on certain fracture risk reduction.
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Affiliation(s)
- Kaibo Sun
- Department of Orthopaedics SurgeryOrthopedic Research Institute, West China Hospital, Sichuan UniversityChengduChina
| | - Yue Ming
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease‐related Molecular NetworksWest China Hospital, Sichuan UniversityChengduChina
| | - Jiawen Xu
- Department of Orthopaedics SurgeryOrthopedic Research Institute, West China Hospital, Sichuan UniversityChengduChina
| | - Yuangang Wu
- Department of Orthopaedics SurgeryOrthopedic Research Institute, West China Hospital, Sichuan UniversityChengduChina
| | - Yi Zeng
- Department of Orthopaedics SurgeryOrthopedic Research Institute, West China Hospital, Sichuan UniversityChengduChina
| | - Limin Wu
- Department of Orthopaedics SurgeryOrthopedic Research Institute, West China Hospital, Sichuan UniversityChengduChina
| | - Mingyang Li
- Department of Orthopaedics SurgeryOrthopedic Research Institute, West China Hospital, Sichuan UniversityChengduChina
| | - Bin Shen
- Department of Orthopaedics SurgeryOrthopedic Research Institute, West China Hospital, Sichuan UniversityChengduChina
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Pedersen EM, Agerbo E, Plana-Ripoll O, Steinbach J, Krebs MD, Hougaard DM, Werge T, Nordentoft M, Børglum AD, Musliner KL, Ganna A, Schork AJ, Mortensen PB, McGrath JJ, Privé F, Vilhjálmsson BJ. ADuLT: An efficient and robust time-to-event GWAS. Nat Commun 2023; 14:5553. [PMID: 37689771 PMCID: PMC10492844 DOI: 10.1038/s41467-023-41210-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 08/28/2023] [Indexed: 09/11/2023] Open
Abstract
Proportional hazards models have been proposed to analyse time-to-event phenotypes in genome-wide association studies (GWAS). However, little is known about the ability of proportional hazards models to identify genetic associations under different generative models and when ascertainment is present. Here we propose the age-dependent liability threshold (ADuLT) model as an alternative to a Cox regression based GWAS, here represented by SPACox. We compare ADuLT, SPACox, and standard case-control GWAS in simulations under two generative models and with varying degrees of ascertainment as well as in the iPSYCH cohort. We find Cox regression GWAS to be underpowered when cases are strongly ascertained (cases are oversampled by a factor 5), regardless of the generative model used. ADuLT is robust to ascertainment in all simulated scenarios. Then, we analyse four psychiatric disorders in iPSYCH, ADHD, Autism, Depression, and Schizophrenia, with a strong case-ascertainment. Across these psychiatric disorders, ADuLT identifies 20 independent genome-wide significant associations, case-control GWAS finds 17, and SPACox finds 8, which is consistent with simulation results. As more genetic data are being linked to electronic health records, robust GWAS methods that can make use of age-of-onset information will help increase power in analyses for common health outcomes.
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Affiliation(s)
- Emil M Pedersen
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark.
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.
| | - Esben Agerbo
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrated Register-based Research at Aarhus University, Aarhus, Denmark
| | - Oleguer Plana-Ripoll
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Department of Clinical Epidemiology, Aarhus University and Aarhus University Hospital, Aarhus, Denmark
| | - Jette Steinbach
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Morten D Krebs
- Institute of Biological Psychiatry, Mental Health Center - Sct Hans, Copenhagen University Hospital - Mental Health Services CPH, Copenhagen, Denmark
| | - David M Hougaard
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Center - Sct Hans, Copenhagen University Hospital - Mental Health Services CPH, Copenhagen, Denmark
- Department of Clinical Sciences, Copenhagen University, Copenhagen, Denmark
- Section for Geogenetics, GLOBE Institute, Faculty of Health and Medical Science, Copenhagen University, Copenhagen, Denmark
| | - Merete Nordentoft
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- CORE- Copenhagen Centre for Research in Mental Health, Mental Health Center-Copenhagen, Copenhagen University Hospital - Mental Health Services CPH, Copenhagen, Denmark
| | - Anders D Børglum
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine and iSEQ Centre, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, CGPM, Aarhus University, Aarhus, Denmark
| | - Katherine L Musliner
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Department of Affective Disorders, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Andrew J Schork
- Institute of Biological Psychiatry, Mental Health Center - Sct Hans, Copenhagen University Hospital - Mental Health Services CPH, Copenhagen, Denmark
- Section for Geogenetics, GLOBE Institute, Faculty of Health and Medical Science, Copenhagen University, Copenhagen, Denmark
- Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA
| | - Preben B Mortensen
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - John J McGrath
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD, Australia
| | - Florian Privé
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Bjarni J Vilhjálmsson
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark.
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, the Broad Institute of MIT and Harvard, Massachusetts, USA.
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9
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Warrier V, Stauffer EM, Huang QQ, Wigdor EM, Slob EAW, Seidlitz J, Ronan L, Valk SL, Mallard TT, Grotzinger AD, Romero-Garcia R, Baron-Cohen S, Geschwind DH, Lancaster MA, Murray GK, Gandal MJ, Alexander-Bloch A, Won H, Martin HC, Bullmore ET, Bethlehem RAI. Genetic insights into human cortical organization and development through genome-wide analyses of 2,347 neuroimaging phenotypes. Nat Genet 2023; 55:1483-1493. [PMID: 37592024 PMCID: PMC10600728 DOI: 10.1038/s41588-023-01475-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 07/13/2023] [Indexed: 08/19/2023]
Abstract
Our understanding of the genetics of the human cerebral cortex is limited both in terms of the diversity and the anatomical granularity of brain structural phenotypes. Here we conducted a genome-wide association meta-analysis of 13 structural and diffusion magnetic resonance imaging-derived cortical phenotypes, measured globally and at 180 bilaterally averaged regions in 36,663 individuals and identified 4,349 experiment-wide significant loci. These phenotypes include cortical thickness, surface area, gray matter volume, measures of folding, neurite density and water diffusion. We identified four genetic latent structures and causal relationships between surface area and some measures of cortical folding. These latent structures partly relate to different underlying gene expression trajectories during development and are enriched for different cell types. We also identified differential enrichment for neurodevelopmental and constrained genes and demonstrate that common genetic variants associated with cortical expansion are associated with cephalic disorders. Finally, we identified complex interphenotype and inter-regional genetic relationships among the 13 phenotypes, reflecting the developmental differences among them. Together, these analyses identify distinct genetic organizational principles of the cortex and their correlates with neurodevelopment.
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Affiliation(s)
- Varun Warrier
- Department of Psychiatry, University of Cambridge, Cambridge, UK.
- Department of Psychology, University of Cambridge, Cambridge, UK.
| | | | | | | | - Eric A W Slob
- Medical Research Council Biostatistics Unit, University of Cambridge, Cambridge, UK
- Department of Applied Economics, Erasmus School of Economics, Erasmus University Rotterdam, Rotterdam, the Netherlands
- Erasmus University Rotterdam Institute for Behavior and Biology, Erasmus University Rotterdam, Rotterdam, the Netherlands
| | - Jakob Seidlitz
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Lisa Ronan
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Sofie L Valk
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, FZ Jülich, Jülich, Germany
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Otto Hahn Group Cognitive Neurogenetics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Travis T Mallard
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Andrew D Grotzinger
- Department of Psychology and Neuroscience, University of Colorado at Boulder, Boulder, CO, USA
- Institute for Behavioral Genetics, University of Colorado at Boulder, Boulder, CO, USA
| | - Rafael Romero-Garcia
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Instituto de Biomedicina de Sevilla (IBiS) HUVR/CSIC/Universidad de Sevilla/CIBERSAM, ISCIII, Dpto. de Fisiología Médica y Biofísica, Seville, Spain
| | - Simon Baron-Cohen
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Department of Psychology, University of Cambridge, Cambridge, UK
| | - Daniel H Geschwind
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Program in Neurogenetics, Department of Neurology, University of California, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Jane and TerrySemel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
- Institute of Precision Health, University of California, Los Angeles, CA, USA
| | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK
| | - Graham K Murray
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Cambridgeshire and Peterborough NHS Trust, Cambridge, UK
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Michael J Gandal
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - Aaron Alexander-Bloch
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Hyejung Won
- Department of Genetics and the Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Edward T Bullmore
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Cambridgeshire and Peterborough NHS Trust, Cambridge, UK
| | - Richard A I Bethlehem
- Department of Psychiatry, University of Cambridge, Cambridge, UK.
- Department of Psychology, University of Cambridge, Cambridge, UK.
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10
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Gomez L, Díaz-Torres S, Colodro-Conde L, Garcia-Marin LM, Yap CX, Byrne EM, Yengo L, Lind PA, Wray NR, Medland SE, Hickie IB, Lupton MK, Rentería ME, Martin NG, Campos AI. Phenotypic and genetic factors associated with donation of DNA and consent to record linkage for prescription history in the Australian Genetics of Depression Study. Eur Arch Psychiatry Clin Neurosci 2023; 273:1359-1368. [PMID: 36422680 DOI: 10.1007/s00406-022-01527-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 11/15/2022] [Indexed: 11/27/2022]
Abstract
Samples can be prone to ascertainment and attrition biases. The Australian Genetics of Depression Study is a large publicly recruited cohort (n = 20,689) established to increase the understanding of depression and antidepressant treatment response. This study investigates differences between participants who donated a saliva sample or agreed to linkage of their records compared to those who did not. We observed that older, male participants with higher education were more likely to donate a saliva sample. Self-reported bipolar disorder, ADHD, panic disorder, PTSD, substance use disorder, and social anxiety disorder were associated with lower odds of donating a saliva sample, whereas anorexia was associated with higher odds of donation. Male and younger participants showed higher odds of agreeing to record linkage. Participants with higher neuroticism scores and those with a history of bipolar disorder were also more likely to agree to record linkage whereas participants with a diagnosis of anorexia were less likely to agree. Increased likelihood of consent was associated with increased genetic susceptibility to anorexia and reduced genetic risk for depression, and schizophrenia. Overall, our results show moderate differences among these subsamples. Most current epidemiological studies do not search for attrition biases at the genetic level. The possibility to do so is a strength of samples such as the AGDS. Our results suggest that analyses can be made more robust by identifying attrition biases both on the phenotypic and genetic level, and either contextualising them as a potential limitation or performing sensitivity analyses adjusting for them.
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Affiliation(s)
- Lina Gomez
- Genetic Epidemiology Lab, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Santiago Díaz-Torres
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Statistical Genetics Lab, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Lucía Colodro-Conde
- Psychiatric Genetics Lab, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Luis M Garcia-Marin
- Genetic Epidemiology Lab, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Chloe X Yap
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Enda M Byrne
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Loic Yengo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Penelope A Lind
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Psychiatric Genetics Lab, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Queensland Institute of Technology, Brisbane, QLD, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Sarah E Medland
- Psychiatric Genetics Lab, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Ian B Hickie
- Brain and Mind Centre, University of Sydney, Camperdown, NSW, Australia
| | - Michelle K Lupton
- Genetic Epidemiology Lab, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Miguel E Rentería
- Genetic Epidemiology Lab, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Nicholas G Martin
- Genetic Epidemiology Lab, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Adrian I Campos
- Genetic Epidemiology Lab, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
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11
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Kun E, Javan EM, Smith O, Gulamali F, de la Fuente J, Flynn BI, Vajrala K, Trutner Z, Jayakumar P, Tucker-Drob EM, Sohail M, Singh T, Narasimhan VM. The genetic architecture and evolution of the human skeletal form. Science 2023; 381:eadf8009. [PMID: 37471560 PMCID: PMC11075689 DOI: 10.1126/science.adf8009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/20/2023] [Indexed: 07/22/2023]
Abstract
The human skeletal form underlies bipedalism, but the genetic basis of skeletal proportions (SPs) is not well characterized. We applied deep-learning models to 31,221 x-rays from the UK Biobank to extract a comprehensive set of SPs, which were associated with 145 independent loci genome-wide. Structural equation modeling suggested that limb proportions exhibited strong genetic sharing but were independent of width and torso proportions. Polygenic score analysis identified specific associations between osteoarthritis and hip and knee SPs. In contrast to other traits, SP loci were enriched in human accelerated regions and in regulatory elements of genes that are differentially expressed between humans and great apes. Combined, our work identifies specific genetic variants that affect the skeletal form and ties a major evolutionary facet of human anatomical change to pathogenesis.
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Affiliation(s)
- Eucharist Kun
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Emily M. Javan
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Olivia Smith
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Faris Gulamali
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Javier de la Fuente
- Department of Psychology, The University of Texas at Austin, Austin, TX, USA
| | - Brianna I. Flynn
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Kushal Vajrala
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Zoe Trutner
- Department of Surgery and Perioperative Care, The University of Texas at Austin, Austin, TX, USA
| | - Prakash Jayakumar
- Department of Surgery and Perioperative Care, The University of Texas at Austin, Austin, TX, USA
| | | | - Mashaal Sohail
- Centro de Ciencias Genómicas (CCG), Universidad Nacional Autónoma de México (UNAM), 62209 Cuernavaca, Mexico
| | - Tarjinder Singh
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- The New York Genome Center, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute at Columbia University, New York, NY, USA
| | - Vagheesh M. Narasimhan
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
- Department of Statistics and Data Science, The University of Texas at Austin, Austin, TX, USA
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12
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Boatwright JL, Sapkota S, Kresovich S. Functional genomic effects of indels using Bayesian genome-phenome wide association studies in sorghum. Front Genet 2023; 14:1143395. [PMID: 37065477 PMCID: PMC10102435 DOI: 10.3389/fgene.2023.1143395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
High-throughput genomic and phenomic data have enhanced the ability to detect genotype-to-phenotype associations that can resolve broad pleiotropic effects of mutations on plant phenotypes. As the scale of genotyping and phenotyping has advanced, rigorous methodologies have been developed to accommodate larger datasets and maintain statistical precision. However, determining the functional effects of associated genes/loci is expensive and limited due to the complexity associated with cloning and subsequent characterization. Here, we utilized phenomic imputation of a multi-year, multi-environment dataset using PHENIX which imputes missing data using kinship and correlated traits, and we screened insertions and deletions (InDels) from the recently whole-genome sequenced Sorghum Association Panel for putative loss-of-function effects. Candidate loci from genome-wide association results were screened for potential loss of function using a Bayesian Genome-Phenome Wide Association Study (BGPWAS) model across both functionally characterized and uncharacterized loci. Our approach is designed to facilitate in silico validation of associations beyond traditional candidate gene and literature-search approaches and to facilitate the identification of putative variants for functional analysis and reduce the incidence of false-positive candidates in current functional validation methods. Using this Bayesian GPWAS model, we identified associations for previously characterized genes with known loss-of-function alleles, specific genes falling within known quantitative trait loci, and genes without any previous genome-wide associations while additionally detecting putative pleiotropic effects. In particular, we were able to identify the major tannin haplotypes at the Tan1 locus and effects of InDels on the protein folding. Depending on the haplotype present, heterodimer formation with Tan2 was significantly affected. We also identified major effect InDels in Dw2 and Ma1, where proteins were truncated due to frameshift mutations that resulted in early stop codons. These truncated proteins also lost most of their functional domains, suggesting that these indels likely result in loss of function. Here, we show that the Bayesian GPWAS model is able to identify loss-of-function alleles that can have significant effects upon protein structure and folding as well as multimer formation. Our approach to characterize loss-of-function mutations and their functional repercussions will facilitate precision genomics and breeding by identifying key targets for gene editing and trait integration.
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Affiliation(s)
- J. Lucas Boatwright
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- *Correspondence: J. Lucas Boatwright,
| | - Sirjan Sapkota
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
| | - Stephen Kresovich
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Feed the Future Innovation Lab for Crop Improvement, Cornell University, Ithaca, NY, United States
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13
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Song X, Wang C, Wang T, Zhang S, Qin J. Obesity and risk of gestational diabetes mellitus: A two-sample Mendelian randomization study. Diabetes Res Clin Pract 2023; 197:110561. [PMID: 36738839 DOI: 10.1016/j.diabres.2023.110561] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/29/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
AIMS To estimate genetically predicted causal associations of general and central obesity with GDM, and to determine the mediating role of circulating lipids. METHODS Summary-level data was obtained from the largest available genome-wide association studies of five obesity traits, five lipid traits and GDM. Two-sample univariate Mendelian randomization (MR), multivariate MR, and MR-based mediation analysis was applied to determine the total effect, direct effect and the mediating effect, respectively. RESULTS Univariate MR showed that the odds of GDM increased per 1-SD increase in body mass index (BMI) (OR = 1.64, P = 5.05 × 10-17), waist-to-hip ratio (WHR) (OR = 1.57, P = 2.27 × 10-14) and WHR adjusted for BMI (OR = 1.42, P = 6.11 × 10-15). The heterogeneous associations of waist circumference (OR = 1.64, P = 5.57 × 10-14) and hip circumference (OR = 1.20, P = 0.002) on GDM further reflected that body fat distribution could influence GDM risk. Mediation analysis suggested that triglycerides, high-density lipoprotein-cholesterol and apolipoprotein A-I each mediated between 5% and 10% of the association between obesity and GDM. CONCLUSION Our findings supported a deleterious causal effect of obesity on GDM risk, where lipid metabolism acted as potential drivers of the relationships between both general and central obesity and GDM.
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Affiliation(s)
- Xinli Song
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, Hunan, China
| | - Cheng Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Tingting Wang
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, Hunan, China
| | - Senmao Zhang
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, Hunan, China
| | - Jiabi Qin
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, Hunan, China; National Health Committee Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China; Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China; Hunan Provincial Key Laboratory of clinical epidemiology, Changsha, Hunan, China.
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14
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Kun E, Javan EM, Smith O, Gulamali F, de la Fuente J, Flynn BI, Vajrala K, Trutner Z, Jayakumar P, Tucker-Drob EM, Sohail M, Singh T, Narasimhan VM. The genetic architecture of the human skeletal form. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.521284. [PMID: 36712136 PMCID: PMC9881884 DOI: 10.1101/2023.01.03.521284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The human skeletal form underlies our ability to walk on two legs, but unlike standing height, the genetic basis of limb lengths and skeletal proportions is less well understood. Here we applied a deep learning model to 31,221 whole body dual-energy X-ray absorptiometry (DXA) images from the UK Biobank (UKB) to extract 23 different image-derived phenotypes (IDPs) that include all long bone lengths as well as hip and shoulder width, which we analyzed while controlling for height. All skeletal proportions are highly heritable (∼40-50%), and genome-wide association studies (GWAS) of these traits identified 179 independent loci, of which 102 loci were not associated with height. These loci are enriched in genes regulating skeletal development as well as associated with rare human skeletal diseases and abnormal mouse skeletal phenotypes. Genetic correlation and genomic structural equation modeling indicated that limb proportions exhibited strong genetic sharing but were genetically independent of width and torso proportions. Phenotypic and polygenic risk score analyses identified specific associations between osteoarthritis (OA) of the hip and knee, the leading causes of adult disability in the United States, and skeletal proportions of the corresponding regions. We also found genomic evidence of evolutionary change in arm-to-leg and hip-width proportions in humans consistent with striking anatomical changes in these skeletal proportions in the hominin fossil record. In contrast to cardiovascular, auto-immune, metabolic, and other categories of traits, loci associated with these skeletal proportions are significantly enriched in human accelerated regions (HARs), and regulatory elements of genes differentially expressed through development between humans and the great apes. Taken together, our work validates the use of deep learning models on DXA images to identify novel and specific genetic variants affecting the human skeletal form and ties a major evolutionary facet of human anatomical change to pathogenesis.
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Affiliation(s)
- Eucharist Kun
- Department of Integrative Biology, The University of Texas at Austin
| | - Emily M Javan
- Department of Integrative Biology, The University of Texas at Austin
| | - Olivia Smith
- Department of Integrative Biology, The University of Texas at Austin
| | | | | | - Brianna I Flynn
- Department of Integrative Biology, The University of Texas at Austin
| | - Kushal Vajrala
- Department of Integrative Biology, The University of Texas at Austin
| | - Zoe Trutner
- Department of Surgery and Perioperative Care, The University of Texas at Austin
| | - Prakash Jayakumar
- Department of Surgery and Perioperative Care, The University of Texas at Austin
| | | | - Mashaal Sohail
- Centro de Ciencias Genómicas (CCG), Universidad Nacional Autónoma de México (UNAM)
| | - Tarjinder Singh
- The Department of Psychiatry at Columbia University Irving Medical Center
- The New York Genome Center
- Mortimer B. Zuckerman Mind Brain Behavior Institute at Columbia University
| | - Vagheesh M Narasimhan
- Department of Integrative Biology, The University of Texas at Austin
- Department of Statistics and Data Science, The University of Texas at Austin
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15
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Lai D, Zhang M, Li R, Zhang C, Zhang P, Liu Y, Gao S, Foroud T. Identifying Genes Associated with Alzheimer's Disease Using Gene-Based Polygenic Risk Score. J Alzheimers Dis 2023; 96:1639-1649. [PMID: 38007651 DOI: 10.3233/jad-230510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2023]
Abstract
BACKGROUND Except APOE, Alzheimer's disease (AD) associated genes identified in recent large-scale genome-wide association studies (GWAS) had small effects and explained a small portion of heritability. Many AD-associated genes have even smaller effects thereby sub-threshold p-values in large-scale GWAS and remain to be identified. For some AD-associated genes, drug targeting them may have limited efficacies due to their small effect sizes. OBJECTIVE The purpose of this study is to identify AD-associated genes with sub-threshold p-values and prioritize drugs targeting AD-associated genes that have large efficacies. METHODS We developed a gene-based polygenic risk score (PRS) to identify AD genes. It was calculated using SNPs located within genes and having the same directions of effects in different study cohorts to exclude cohort-specific findings and false positives. Gene co-expression modules and protein-protein interaction networks were used to identify AD-associated genes that interact with multiple other genes, as drugs targeting them have large efficacies via co-regulation or interactions. RESULTS Gene-based PRS identified 389 genes with 164 of them not previously reported as AD-associated. These 389 genes explained 56.12% -97.46% SNP heritability; and they were enriched in brain tissues and 164 biological processes, most of which are related to AD and other neurodegenerative diseases. We prioritized 688 drugs targeting 64 genes that were in the same co-expression modules and/or PPI networks. CONCLUSIONS Gene-based PRS is a cost-effective way to identify AD-associated genes without substantially increasing the sample size. Co-expression modules and PPI networks can be used to identify drugs having large efficacies.
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Affiliation(s)
- Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michael Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Rudong Li
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Chi Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Pengyue Zhang
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sujuan Gao
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
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16
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Li Z, Chen H, Chen T. Genetic liability to obesity and peptic ulcer disease: a Mendelian randomization study. BMC Med Genomics 2022; 15:209. [PMID: 36195910 PMCID: PMC9533532 DOI: 10.1186/s12920-022-01366-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/27/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Epidemiological evidence relating obesity to peptic ulcer disease (PUD) has been mixed. Here we sought to determine the causality in the association of obesity with PUD risk using the Mendelian randomization (MR) approach. METHODS This study was based on summary-level data for body mass index (BMI), waist-to-hip ratio (WHR), and PUD derived from large genome-wide association studies (GWASs). Single nucleotide polymorphisms significantly associated with BMI and WHR (P < 5 × 10-8) were leveraged as instrumental variables. Causal estimates were pooled using several meta-analysis methods. In addition, multivariable MR was employed to account for covariation between BMI and WHR, as well as to explore potential mediators. RESULTS Genetically predicted higher BMI has a causal effect on PUD, with an OR of 1.34 per SD increase in BMI (~ 4.8 kg/m2) (P = 9.72 × 10-16). Likewise, there was a 35% higher risk of PUD (P = 2.35 × 10-10) for each SD increase in WHR (0.09 ratio). Complementary analyses returned consistent results. Multivariable MR demonstrated that adjustment for WHR largely attenuated the BMI-PUD association. However, the causal association of WHR with PUD risk survived adjustment for BMI. Both the associations remained robust upon adjustment for several traditional risk factors. Replication analyses using different instrumental variants further strengthened the causal inference. Besides, we found no evidence for the causal association in the reverse analyses from PUD to BMI/WHR. CONCLUSIONS This MR study revealed that obesity (notably abdominal obesity) is causally associated with higher PUD risk. Programs aimed at weight loss may represent therapeutic opportunities for PUD.
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Affiliation(s)
- Zhoubin Li
- Department of Lung Transplantation and General Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, Zhejiang Province
| | - Heng Chen
- Department of Cardiology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, Zhejiang Province, China
| | - Ting Chen
- Department of Cardiology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, Zhejiang Province, China. .,Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, China.
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Gorski M, Rasheed H, Teumer A, Thomas LF, Graham SE, Sveinbjornsson G, Winkler TW, Günther F, Stark KJ, Chai JF, Tayo BO, Wuttke M, Li Y, Tin A, Ahluwalia TS, Ärnlöv J, Åsvold BO, Bakker SJL, Banas B, Bansal N, Biggs ML, Biino G, Böhnke M, Boerwinkle E, Bottinger EP, Brenner H, Brumpton B, Carroll RJ, Chaker L, Chalmers J, Chee ML, Chee ML, Cheng CY, Chu AY, Ciullo M, Cocca M, Cook JP, Coresh J, Cusi D, de Borst MH, Degenhardt F, Eckardt KU, Endlich K, Evans MK, Feitosa MF, Franke A, Freitag-Wolf S, Fuchsberger C, Gampawar P, Gansevoort RT, Ghanbari M, Ghasemi S, Giedraitis V, Gieger C, Gudbjartsson DF, Hallan S, Hamet P, Hishida A, Ho K, Hofer E, Holleczek B, Holm H, Hoppmann A, Horn K, Hutri-Kähönen N, Hveem K, Hwang SJ, Ikram MA, Josyula NS, Jung B, Kähönen M, Karabegović I, Khor CC, Koenig W, Kramer H, Krämer BK, Kühnel B, Kuusisto J, Laakso M, Lange LA, Lehtimäki T, Li M, Lieb W, Lind L, Lindgren CM, Loos RJF, Lukas MA, Lyytikäinen LP, Mahajan A, Matias-Garcia PR, Meisinger C, Meitinger T, Melander O, Milaneschi Y, Mishra PP, Mononen N, Morris AP, Mychaleckyj JC, Nadkarni GN, Naito M, Nakatochi M, Nalls MA, Nauck M, Nikus K, Ning B, Nolte IM, Nutile T, O'Donoghue ML, O'Connell J, Olafsson I, Orho-Melander M, Parsa A, Pendergrass SA, Penninx BWJH, Pirastu M, Preuss MH, Psaty BM, Raffield LM, Raitakari OT, Rheinberger M, Rice KM, Rizzi F, Rosenkranz AR, Rossing P, Rotter JI, Ruggiero D, Ryan KA, Sabanayagam C, Salvi E, Schmidt H, Schmidt R, Scholz M, Schöttker B, Schulz CA, Sedaghat S, Shaffer CM, Sieber KB, Sim X, Sims M, Snieder H, Stanzick KJ, Thorsteinsdottir U, Stocker H, Strauch K, Stringham HM, Sulem P, Szymczak S, Taylor KD, Thio CHL, Tremblay J, Vaccargiu S, van der Harst P, van der Most PJ, Verweij N, Völker U, Wakai K, Waldenberger M, Wallentin L, Wallner S, Wang J, Waterworth DM, White HD, Willer CJ, Wong TY, Woodward M, Yang Q, Yerges-Armstrong LM, Zimmermann M, Zonderman AB, Bergler T, Stefansson K, Böger CA, Pattaro C, Köttgen A, Kronenberg F, Heid IM. Genetic loci and prioritization of genes for kidney function decline derived from a meta-analysis of 62 longitudinal genome-wide association studies. Kidney Int 2022; 102:624-639. [PMID: 35716955 PMCID: PMC10034922 DOI: 10.1016/j.kint.2022.05.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 04/19/2022] [Accepted: 05/11/2022] [Indexed: 12/15/2022]
Abstract
Estimated glomerular filtration rate (eGFR) reflects kidney function. Progressive eGFR-decline can lead to kidney failure, necessitating dialysis or transplantation. Hundreds of loci from genome-wide association studies (GWAS) for eGFR help explain population cross section variability. Since the contribution of these or other loci to eGFR-decline remains largely unknown, we derived GWAS for annual eGFR-decline and meta-analyzed 62 longitudinal studies with eGFR assessed twice over time in all 343,339 individuals and in high-risk groups. We also explored different covariate adjustment. Twelve genome-wide significant independent variants for eGFR-decline unadjusted or adjusted for eGFR-baseline (11 novel, one known for this phenotype), including nine variants robustly associated across models were identified. All loci for eGFR-decline were known for cross-sectional eGFR and thus distinguished a subgroup of eGFR loci. Seven of the nine variants showed variant-by-age interaction on eGFR cross section (further about 350,000 individuals), which linked genetic associations for eGFR-decline with age-dependency of genetic cross-section associations. Clinically important were two to four-fold greater genetic effects on eGFR-decline in high-risk subgroups. Five variants associated also with chronic kidney disease progression mapped to genes with functional in-silico evidence (UMOD, SPATA7, GALNTL5, TPPP). An unfavorable versus favorable nine-variant genetic profile showed increased risk odds ratios of 1.35 for kidney failure (95% confidence intervals 1.03-1.77) and 1.27 for acute kidney injury (95% confidence intervals 1.08-1.50) in over 2000 cases each, with matched controls). Thus, we provide a large data resource, genetic loci, and prioritized genes for kidney function decline, which help inform drug development pipelines revealing important insights into the age-dependency of kidney function genetics.
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Affiliation(s)
- Mathias Gorski
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany; Department of Nephrology, University Hospital Regensburg, Regensburg, Germany.
| | - Humaira Rasheed
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany; DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany; Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, Bialystok, Poland
| | - Laurent F Thomas
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; BioCore-Bioinformatics Core Facility, Norwegian University of Science and Technology, Trondheim, Norway
| | - Sarah E Graham
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Felix Günther
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany; Statistical Consulting Unit StaBLab, Department of Statistics, LMU Munich, Munich, Germany
| | - Klaus J Stark
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Jin-Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Bamidele O Tayo
- Department of Public Health Sciences, Loyola University Chicago, Maywood, Illinois, USA
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany; Renal Division, Department of Medicine IV, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Yong Li
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Adrienne Tin
- Memory Impairment and Neurodegenerative Dementia (MIND) Center, University of Mississippi Medical Center, Jackson, Mississippi, USA; Division of Nephrology, Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Tarunveer S Ahluwalia
- Steno Diabetes Center Copenhagen, Gentofte, Denmark; The Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Johan Ärnlöv
- Division of Family Medicine and Primary Care, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden; School of Health and Social Studies, Dalarna University, Stockholm, Sweden
| | - Bjørn Olav Åsvold
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Endocrinology, Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Stephan J L Bakker
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bernhard Banas
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Nisha Bansal
- Division of Nephrology, University of Washington, Seattle, Washington, USA; Kidney Research Institute, University of Washington, Seattle, Washington, USA
| | - Mary L Biggs
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, USA; Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Ginevra Biino
- Institute of Molecular Genetics, National Research Council of Italy, Pavia, Italy
| | - Michael Böhnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas, USA
| | - Erwin P Bottinger
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Digital Health Center, Hasso Plattner Institute and University of Potsdam, Potsdam, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Network Aging Research, Heidelberg University, Heidelberg, Germany
| | - Ben Brumpton
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Clinic of Thoracic and Occupational Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Robert J Carroll
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Layal Chaker
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - John Chalmers
- The George Institute for Global Health, University of New South Wales, Sydney, Australia
| | - Miao-Li Chee
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - Miao-Ling Chee
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore; Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore; Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Audrey Y Chu
- Genetics, Merck & Co, Inc., Kenilworth, New Jersey, USA
| | - Marina Ciullo
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso"-CNR, Naples, Italy; IRCCS Neuromed, Pozzilli, Italy
| | - Massimiliano Cocca
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," Trieste, Italy
| | - James P Cook
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Daniele Cusi
- Institute of Biomedical Technologies, National Research Council of Italy, Milan, Italy; Bio4Dreams-Business Nursery for Life Sciences, Milan, Italy
| | - Martin H de Borst
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany; Department of Nephrology and Hypertension, Friedrich Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Karlhans Endlich
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany; Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, US National Institutes of Health, Baltimore, Maryland, USA
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Sandra Freitag-Wolf
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Christian Fuchsberger
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA; Eurac Research, Institute for Biomedicine (affiliated with the University of Lübeck), Bolzano, Italy
| | - Piyush Gampawar
- Institute of Molecular Biology and Biochemistry, Center for Molecular Medicine, Medical University of Graz, Graz, Austria
| | - Ron T Gansevoort
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sahar Ghasemi
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany; DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Vilmantas Giedraitis
- Molecular Geriatrics, Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland; Iceland School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Stein Hallan
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Nephrology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Pavel Hamet
- Montreal University Hospital Research Center, CHUM, Montreal, Quebec, Canada; Medpharmgene, Montreal, Quebec, Canada; CRCHUM, Montreal, Quebec, Canada
| | - Asahi Hishida
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kevin Ho
- Kidney Health Research Institute (KHRI), Geisinger, Danville, Pennsylvania, USA; Department of Nephrology, Geisinger, Danville, Pennsylvania, USA
| | - Edith Hofer
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, Austria; Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Bernd Holleczek
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hilma Holm
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
| | - Anselm Hoppmann
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Katrin Horn
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany; LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Nina Hutri-Kähönen
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland; Department of Pediatrics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kristian Hveem
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Shih-Jen Hwang
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, USA; Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Navya Shilpa Josyula
- Geisinger Research, Biomedical and Translational Informatics Institute, Rockville, Maryland, USA
| | - Bettina Jung
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany; Department of Nephrology and Rheumatology, Kliniken Südostbayern, Traunstein, Germany; KfH Kidney Centre Traunstein, Traunstein, Germany
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland; Department of Clinical Physiology, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Irma Karabegović
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Chiea-Chuen Khor
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore; Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Wolfgang Koenig
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany; Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm, Germany
| | - Holly Kramer
- Department of Public Health Sciences, Loyola University Chicago, Maywood, Illinois, USA; Division of Nephrology and Hypertension, Loyola University Chicago, Chicago, Illinois, USA
| | - Bernhard K Krämer
- Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Brigitte Kühnel
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Johanna Kuusisto
- Department of Medicine, Kuopio University Hospital, Kuopio, Finland; Centre for Medicine and Clinical Research, University of Eastern Finland School of Medicine, Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, Kuopio University Hospital, Kuopio, Finland; Centre for Medicine and Clinical Research, University of Eastern Finland School of Medicine, Kuopio, Finland
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado, USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Man Li
- Division of Nephrology and Hypertension, Department of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank Popgen, Kiel University, Kiel, Germany
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Cecilia M Lindgren
- Nuffield Department of Population Health, University of Oxford, Oxford, UK; Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA; Wellcome Center for Human Genetics, University of Oxford, Oxford, UK; Nuffield Department of Women's and Reproductive Health, University of Oxford, Level 3, Women's Centre, John Radcliffe Hospital, Oxford, UK; Li Ka Shing Centre for Health Information and Discovery, The Big Data Institute, University of Oxford, Oxford, UK
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mary Ann Lukas
- Clinical Sciences, GlaxoSmithKline, Albuquerque, New Mexico, USA
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anubha Mahajan
- Wellcome Center for Human Genetics, University of Oxford, Oxford, UK; Oxford Center for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Pamela R Matias-Garcia
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Christa Meisinger
- Independent Research Group Clinical Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Chair of Epidemiology, University of Augsburg, University Hospital Augsburg, Augsburg, Germany
| | - Thomas Meitinger
- DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Olle Melander
- Hypertension and Cardiovascular Disease, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Public Health and Amsterdam Neuroscience, Amsterdam UMC/Vrije Universiteit and GGZ inGeest, Amsterdam, the Netherlands
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Nina Mononen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Andrew P Morris
- Department of Health Data Science, University of Liverpool, Liverpool, UK; Wellcome Center for Human Genetics, University of Oxford, Oxford, UK; Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, Charlottesville, Virginia, USA
| | - Girish N Nadkarni
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mariko Naito
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan; Department of Oral Epidemiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA; Data Tecnica International, Glen Echo, Maryland, USA
| | - Matthias Nauck
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany; Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Kjell Nikus
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere, Finland; Department of Cardiology, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Boting Ning
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Teresa Nutile
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso"-CNR, Naples, Italy
| | - Michelle L O'Donoghue
- Cardiovascular Division, Brigham and Women's Hospital, Boston, Massachusetts, USA; TIMI Study Group, Boston, Massachusetts, USA
| | | | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali University Hospital, Reykjavik, Iceland
| | - Marju Orho-Melander
- Diabetes and Cardiovascular Disease-Genetic Epidemiology, Department of Clinical Sciences in Malmö, Lund University, Malmö, Sweden
| | - Afshin Parsa
- Division of Kidney, Urologic and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sarah A Pendergrass
- Geisinger Research, Biomedical and Translational Informatics Institute, Danville, Pennsylvania, USA
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Public Health and Amsterdam Neuroscience, Amsterdam UMC/Vrije Universiteit and GGZ inGeest, Amsterdam, the Netherlands
| | - Mario Pirastu
- Institute of Genetic and Biomedical Research, National Research Council of Italy, UOS of Sassari, Li Punti, Sassari, Italy
| | - Michael H Preuss
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, Department of Epidemiology, Department of Health Services, University of Washington, Seattle, Washington, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland; Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland; Research Center of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Myriam Rheinberger
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany; Department of Nephrology and Rheumatology, Kliniken Südostbayern, Traunstein, Germany; KfH Kidney Centre Traunstein, Traunstein, Germany
| | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Federica Rizzi
- Department of Health Sciences, University of Milan, Milano, Italy; ePhood Scientific Unit, ePhood SRL, Milano, Italy
| | - Alexander R Rosenkranz
- Division of Nephrology, Department of Internal Medicine, Medical University Graz, Graz, Austria
| | - Peter Rossing
- Steno Diabetes Center Copenhagen, Gentofte, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Daniela Ruggiero
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso"-CNR, Naples, Italy; IRCCS Neuromed, Pozzilli, Italy
| | - Kathleen A Ryan
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Charumathi Sabanayagam
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore; Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Erika Salvi
- Department of Health Sciences, University of Milan, Milano, Italy; Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta," Milan, Italy
| | - Helena Schmidt
- Institute of Molecular Biology and Biochemistry, Center for Molecular Medicine, Medical University of Graz, Graz, Austria
| | - Reinhold Schmidt
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, Austria
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany; LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Network Aging Research, Heidelberg University, Heidelberg, Germany
| | - Christina-Alexandra Schulz
- Diabetes and Cardiovascular Disease-Genetic Epidemiology, Department of Clinical Sciences in Malmö, Lund University, Malmö, Sweden
| | - Sanaz Sedaghat
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Preventive Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Christian M Shaffer
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Karsten B Sieber
- Human Genetics, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Mario Sims
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Kira J Stanzick
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Hannah Stocker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Network Aging Research, Heidelberg University, Heidelberg, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Chair of Genetic Epidemiology, IBE, Faculty of Medicine, Ludwig-Maximilians-Universität München, München, Germany; Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Heather M Stringham
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Silke Szymczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany; Institute of Medical Biometry and Statistics, University of Lübeck, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Chris H L Thio
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Johanne Tremblay
- Montreal University Hospital Research Center, CHUM, Montreal, Quebec, Canada; CRCHUM, Montreal, Quebec, Canada; Medpharmgene, Montreal, Quebec, Canada
| | - Simona Vaccargiu
- Institute of Genetic and Biomedical Research, National Research Council of Italy, UOS of Sassari, Li Punti, Sassari, Italy
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Durrer Center for Cardiovascular Research, The Netherlands Heart Institute, Utrecht, the Netherlands
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Uwe Völker
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany; Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Lars Wallentin
- Cardiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden; Uppsala Clinical Research Center, Uppsala University, Uppsala, Sweden
| | - Stefan Wallner
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Judy Wang
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | - Harvey D White
- Green Lane Cardiovascular Service, Auckland City Hospital and University of Auckland, Auckland, New Zealand
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA; Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore; Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Mark Woodward
- The George Institute for Global Health, University of New South Wales, Sydney, Australia; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA; The George Institute for Global Health, University of Oxford, Oxford, UK
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | | | - Martina Zimmermann
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, US National Institutes of Health, Baltimore, Maryland, USA
| | - Tobias Bergler
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Carsten A Böger
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany; Department of Nephrology and Rheumatology, Kliniken Südostbayern, Traunstein, Germany; KfH Kidney Centre Traunstein, Traunstein, Germany
| | - Cristian Pattaro
- Eurac Research, Institute for Biomedicine (affiliated with the University of Lübeck), Bolzano, Italy
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany.
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18
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Timmers PRHJ, Wilson JF. Limited Effect of Y Chromosome Variation on Coronary Artery Disease and Mortality in UK Biobank-Brief Report. Arterioscler Thromb Vasc Biol 2022; 42:1198-1206. [PMID: 35861954 PMCID: PMC9394501 DOI: 10.1161/atvbaha.122.317664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND The effect of genetic variation in the male-specific region of the Y chromosome (MSY) on coronary artery disease and cardiovascular risk factors has been disputed. In this study, we systematically assessed the association of MSY genetic variation on these traits using a kin-cohort analysis of family disease history in the largest sample to date. METHODS We tested 90 MSY haplogroups against coronary artery disease, hypertension, blood pressure, classical lipid levels, and all-cause mortality in up to 152 186 unrelated, genomically British individuals from UK Biobank. Unlike previous studies, we did not adjust for heritable lifestyle factors (to avoid collider bias) and instead adjusted for geographic variables and socioeconomic deprivation, given the link between MSY haplogroups and geography. For family history traits, subject MSY haplogroups were tested against father and mother disease as validation and negative control, respectively. RESULTS Our models find little evidence for an effect of any MSY haplogroup on cardiovascular risk in participants. Parental models confirm these findings. CONCLUSIONS Kin-cohort analysis of the Y chromosome uniquely allows for discoveries in subjects to be validated using family history data. Despite our large sample size, improved models, and parental validation, there is little evidence to suggest cardiovascular risk in UK Biobank is influenced by genetic variation in MSY.
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Affiliation(s)
- Paul R H J Timmers
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer (P.R.H.J.T., J.F.W.), University of Edinburgh, United Kingdom.,Centre for Global Health Research, Usher Institute (P.R.H.J.T., J.F.W.), University of Edinburgh, United Kingdom
| | - James F Wilson
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer (P.R.H.J.T., J.F.W.), University of Edinburgh, United Kingdom.,Centre for Global Health Research, Usher Institute (P.R.H.J.T., J.F.W.), University of Edinburgh, United Kingdom
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19
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Akbari P, Sosina OA, Bovijn J, Landheer K, Nielsen JB, Kim M, Aykul S, De T, Haas ME, Hindy G, Lin N, Dinsmore IR, Luo JZ, Hectors S, Geraghty B, Germino M, Panagis L, Parasoglou P, Walls JR, Halasz G, Atwal GS, Jones M, LeBlanc MG, Still CD, Carey DJ, Giontella A, Orho-Melander M, Berumen J, Kuri-Morales P, Alegre-Díaz J, Torres JM, Emberson JR, Collins R, Rader DJ, Zambrowicz B, Murphy AJ, Balasubramanian S, Overton JD, Reid JG, Shuldiner AR, Cantor M, Abecasis GR, Ferreira MAR, Sleeman MW, Gusarova V, Altarejos J, Harris C, Economides AN, Idone V, Karalis K, Della Gatta G, Mirshahi T, Yancopoulos GD, Melander O, Marchini J, Tapia-Conyer R, Locke AE, Baras A, Verweij N, Lotta LA. Multiancestry exome sequencing reveals INHBE mutations associated with favorable fat distribution and protection from diabetes. Nat Commun 2022; 13:4844. [PMID: 35999217 PMCID: PMC9399235 DOI: 10.1038/s41467-022-32398-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/28/2022] [Indexed: 12/13/2022] Open
Abstract
Body fat distribution is a major, heritable risk factor for cardiometabolic disease, independent of overall adiposity. Using exome-sequencing in 618,375 individuals (including 160,058 non-Europeans) from the UK, Sweden and Mexico, we identify 16 genes associated with fat distribution at exome-wide significance. We show 6-fold larger effect for fat-distribution associated rare coding variants compared with fine-mapped common alleles, enrichment for genes expressed in adipose tissue and causal genes for partial lipodystrophies, and evidence of sex-dimorphism. We describe an association with favorable fat distribution (p = 1.8 × 10-09), favorable metabolic profile and protection from type 2 diabetes (~28% lower odds; p = 0.004) for heterozygous protein-truncating mutations in INHBE, which encodes a circulating growth factor of the activin family, highly and specifically expressed in hepatocytes. Our results suggest that inhibin βE is a liver-expressed negative regulator of adipose storage whose blockade may be beneficial in fat distribution-associated metabolic disease.
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Affiliation(s)
- Parsa Akbari
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Olukayode A. Sosina
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Jonas Bovijn
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Karl Landheer
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Jonas B. Nielsen
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Minhee Kim
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Senem Aykul
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Tanima De
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Mary E. Haas
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - George Hindy
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Nan Lin
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Ian R. Dinsmore
- grid.280776.c0000 0004 0394 1447Department of Molecular and Functional Genomics, Geisinger Health System, Danville, PA USA
| | - Jonathan Z. Luo
- grid.280776.c0000 0004 0394 1447Department of Molecular and Functional Genomics, Geisinger Health System, Danville, PA USA
| | - Stefanie Hectors
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Benjamin Geraghty
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Mary Germino
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Lampros Panagis
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Prodromos Parasoglou
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Johnathon R. Walls
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Gabor Halasz
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Gurinder S. Atwal
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | | | | | - Marcus Jones
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Michelle G. LeBlanc
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Christopher D. Still
- grid.280776.c0000 0004 0394 1447Geisinger Obesity Institute, Geisinger Health System, Danville, PA USA
| | - David J. Carey
- grid.280776.c0000 0004 0394 1447Geisinger Obesity Institute, Geisinger Health System, Danville, PA USA
| | - Alice Giontella
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden ,grid.5611.30000 0004 1763 1124Department of Medicine, University of Verona, Verona, Italy
| | - Marju Orho-Melander
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Jaime Berumen
- grid.9486.30000 0001 2159 0001Unidad de Medicina Experimental de la Facultad de Medicina de la Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Pablo Kuri-Morales
- grid.9486.30000 0001 2159 0001Unidad de Medicina Experimental de la Facultad de Medicina de la Universidad Nacional Autónoma de México, Mexico City, Mexico ,grid.419886.a0000 0001 2203 4701Instituto Tecnológico y de Estudios Superiores de Monterrey, Monterrey, Mexico
| | - Jesus Alegre-Díaz
- grid.9486.30000 0001 2159 0001Unidad de Medicina Experimental de la Facultad de Medicina de la Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jason M. Torres
- grid.4991.50000 0004 1936 8948MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK ,grid.4991.50000 0004 1936 8948Clinical Trial Service Unit & Epidemiological Studies Unit Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jonathan R. Emberson
- grid.4991.50000 0004 1936 8948MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK ,grid.4991.50000 0004 1936 8948Clinical Trial Service Unit & Epidemiological Studies Unit Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Rory Collins
- grid.4991.50000 0004 1936 8948Clinical Trial Service Unit & Epidemiological Studies Unit Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Daniel J. Rader
- grid.25879.310000 0004 1936 8972Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Brian Zambrowicz
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Andrew J. Murphy
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Suganthi Balasubramanian
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - John D. Overton
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Jeffrey G. Reid
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Alan R. Shuldiner
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Michael Cantor
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Goncalo R. Abecasis
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Manuel A. R. Ferreira
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Mark W. Sleeman
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Viktoria Gusarova
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Judith Altarejos
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Charles Harris
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Aris N. Economides
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA ,grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Vincent Idone
- grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Katia Karalis
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Giusy Della Gatta
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Tooraj Mirshahi
- grid.280776.c0000 0004 0394 1447Geisinger Obesity Institute, Geisinger Health System, Danville, PA USA
| | | | - Olle Melander
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden ,grid.411843.b0000 0004 0623 9987Department of Emergency and Internal Medicine, Skåne University Hospital, Malmö, Sweden
| | - Jonathan Marchini
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Roberto Tapia-Conyer
- grid.419886.a0000 0001 2203 4701Instituto Tecnológico y de Estudios Superiores de Monterrey, Monterrey, Mexico
| | - Adam E. Locke
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Aris Baras
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA.
| | - Niek Verweij
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
| | - Luca A. Lotta
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY USA
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20
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Agrawal S, Wang M, Klarqvist MDR, Smith K, Shin J, Dashti H, Diamant N, Choi SH, Jurgens SJ, Ellinor PT, Philippakis A, Claussnitzer M, Ng K, Udler MS, Batra P, Khera AV. Inherited basis of visceral, abdominal subcutaneous and gluteofemoral fat depots. Nat Commun 2022; 13:3771. [PMID: 35773277 PMCID: PMC9247093 DOI: 10.1038/s41467-022-30931-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/25/2022] [Indexed: 12/11/2022] Open
Abstract
For any given level of overall adiposity, individuals vary considerably in fat distribution. The inherited basis of fat distribution in the general population is not fully understood. Here, we study up to 38,965 UK Biobank participants with MRI-derived visceral (VAT), abdominal subcutaneous (ASAT), and gluteofemoral (GFAT) adipose tissue volumes. Because these fat depot volumes are highly correlated with BMI, we additionally study six local adiposity traits: VAT adjusted for BMI and height (VATadj), ASATadj, GFATadj, VAT/ASAT, VAT/GFAT, and ASAT/GFAT. We identify 250 independent common variants (39 newly-identified) associated with at least one trait, with many associations more pronounced in female participants. Rare variant association studies extend prior evidence for PDE3B as an important modulator of fat distribution. Local adiposity traits (1) highlight depot-specific genetic architecture and (2) enable construction of depot-specific polygenic scores that have divergent associations with type 2 diabetes and coronary artery disease. These results - using MRI-derived, BMI-independent measures of local adiposity - confirm fat distribution as a highly heritable trait with important implications for cardiometabolic health outcomes.
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Affiliation(s)
- Saaket Agrawal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Minxian Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | | | - Kirk Smith
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Joseph Shin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Hesam Dashti
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathaniel Diamant
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Seung Hoan Choi
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sean J Jurgens
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Experimental Cardiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Patrick T Ellinor
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Anthony Philippakis
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Melina Claussnitzer
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kenney Ng
- Center for Computational Health, IBM Research, Cambridge, MA, USA
| | - Miriam S Udler
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Puneet Batra
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amit V Khera
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Verve Therapeutics, Cambridge, MA, USA.
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21
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Lee H, Han B. A theory-based practical solution to correct for sex-differential participation bias. Genome Biol 2022; 23:138. [PMID: 35761388 PMCID: PMC9238114 DOI: 10.1186/s13059-022-02703-0] [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: 09/22/2021] [Accepted: 06/13/2022] [Indexed: 11/24/2022] Open
Abstract
Most genomic cohorts are retrospective where the exposures and outcomes are predetermined prior to sample collection. Therefore, a spurious association between an exposure and an outcome can arise if both variables affect study participation. Such concerns were raised in previous studies questioning the representativeness of the UK Biobank. Recently, a genome-wide association study (GWAS) on biological sex found many autosomal hits and non-negligible autosomal heritability which the authors attribute to selection bias. In this study, we propose a simple and a practical method that can overcome sex-driven selection bias based on theoretical analysis and simulations.
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Affiliation(s)
- Hanbin Lee
- Department of Medicine, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
| | - Buhm Han
- Department of Medicine, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea. .,Department of Biomedical Sciences, BK21 Plus Biomedical Science Project, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea. .,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea.
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22
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Dam V, Onland-Moret NC, Burgess S, Chirlaque MD, Peters SAE, Schuit E, Tikk K, Weiderpass E, Oliver-Williams C, Wood AM, Tjønneland A, Dahm CC, Overvad K, Boutron-Ruault MC, Schulze MB, Trichopoulou A, Ferrari P, Masala G, Krogh V, Tumino R, Matullo G, Panico S, Boer JMA, Verschuren WMM, Waaseth M, Pérez MJS, Amiano P, Imaz L, Moreno-Iribas C, Melander O, Harlid S, Nordendahl M, Wennberg P, Key TJ, Riboli E, Santiuste C, Kaaks R, Katzke V, Langenberg C, Wareham NJ, Schunkert H, Erdmann J, Willenborg C, Hengstenberg C, Kleber ME, Delgado G, März W, Kanoni S, Dedoussis G, Deloukas P, Nikpay M, McPherson R, Scholz M, Teren A, Butterworth AS, van der Schouw YT. Genetically Determined Reproductive Aging and Coronary Heart Disease: A Bidirectional 2-sample Mendelian Randomization. J Clin Endocrinol Metab 2022; 107:e2952-e2961. [PMID: 35306566 PMCID: PMC9202700 DOI: 10.1210/clinem/dgac171] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND Accelerated reproductive aging, in women indicated by early natural menopause, is associated with increased coronary heart disease (CHD) risk in observational studies. Conversely, an adverse CHD risk profile has been suggested to accelerate menopause. OBJECTIVES To study the direction and evidence for causality of the relationship between reproductive aging and (non-)fatal CHD and CHD risk factors in a bidirectional Mendelian randomization (MR) approach, using age at natural menopause (ANM) genetic variants as a measure for genetically determined reproductive aging in women. We also studied the association of these variants with CHD risk (factors) in men. DESIGN Two-sample MR, using both cohort data as well as summary statistics, with 4 methods: simple and weighted median-based, standard inverse-variance weighted (IVW) regression, and MR-Egger regression. PARTICIPANTS Data from EPIC-CVD and summary statistics from UK Biobank and publicly available genome-wide association studies were pooled for the different analyses. MAIN OUTCOME MEASURES CHD, CHD risk factors, and ANM. RESULTS Across different methods of MR, no association was found between genetically determined reproductive aging and CHD risk in women (relative risk estimateIVW = 0.99; 95% confidence interval (CI), 0.97-1.01), or any of the CHD risk factors. Similarly, no associations were found in men. Neither did the reversed analyses show evidence for an association between CHD (risk factors) and reproductive aging. CONCLUSION Genetically determined reproductive aging is not causally associated with CHD risk (factors) in women, nor were the genetic variants associated in men. We found no evidence for a reverse association in a combined sample of women and men.
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Affiliation(s)
- Veerle Dam
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, GA 3508 Utrecht, the Netherlands
- Netherlands Heart Institute, DG 3501 Utrecht, the Netherlands
| | - N Charlotte Onland-Moret
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, GA 3508 Utrecht, the Netherlands
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Homerton College, Cambridge, UK
| | - Maria-Dolores Chirlaque
- Department of Epidemiology, Regional Health Authority, IMIB-Arrixaca, Murcia University, 30001 Murcia, Spain
- Department of Public Health and Clinical Medicine, Umea University, 901 87 Umea, Sweden
| | - Sanne A E Peters
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, GA 3508 Utrecht, the Netherlands
- The George Institute for Global Health, Imperial College London, London W12 0BZ, UK
| | - Ewoud Schuit
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, GA 3508 Utrecht, the Netherlands
| | - Kaja Tikk
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium, DKFZ, 69120 Heidelberg, Germany
| | - Elisabete Weiderpass
- International Agency for Research on Cancer, World Health Organization, 69372 Lyon, France
| | - Clare Oliver-Williams
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Homerton College, Cambridge, UK
| | - Angela M Wood
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Anne Tjønneland
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
- Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Christina C Dahm
- Department of Public Health, Aarhus University, 8000 Aarhus, Denmark
| | - Kim Overvad
- Department of Public Health, Aarhus University, 8000 Aarhus, Denmark
- Department of Cardiology, Aalborg University Hospital, 9000 Aalborg, Denmark
| | - Marie-Christine Boutron-Ruault
- INSERM, Centre for Research in Epidemiology and Population Health, U1018, Nutrition, Hormones, and Women’s Health Team, Institut Gustave Roussy, 94 805 Villejuif, France
| | - Matthias B Schulze
- Department of Epidemiology, German Institute of Human Nutrition, Potsdam-Rehbruecke, Nuthetal, Germany; Institute of Nutritional Science, University of Potsdam, 14558 Nuthetal, Germany
| | - Antonia Trichopoulou
- Hellenic Health Foundation, 115 27 Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens 115 27, Greece
| | - Pietro Ferrari
- International Agency for Research on Cancer, World Health Organization, 69372 Lyon, France
| | - Giovanna Masala
- Cancer Risk Factors and Life-Style Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network - ISPRO, 50139 Florence, Italy
| | - Vittorio Krogh
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Rosario Tumino
- Cancer Registry and Histopathology Department, “Civic - M.P. Arezzo” hospital, ASPRagusa, 97100 Ragusa, Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Torino, 10124 Torino, Italy
- Italian Institute for Genomic Medicine–IIGM/HuGeF, 10126 Torino, Italy
| | - Salvatore Panico
- Dipartimento di medicina clinica e chirurgia, Federico II University, 80126 Naples, Italy
| | - Jolanda M A Boer
- National Institute for Public Health and the Environment, 3720 BA Bilthoven, the Netherlands
| | - W M Monique Verschuren
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, GA 3508 Utrecht, the Netherlands
- National Institute for Public Health and the Environment, 3720 BA Bilthoven, the Netherlands
| | - Marit Waaseth
- Department of Pharmacy, Faculty of Health Sciences, UiT the Arctic University of Norway, N-9037 Tromsø, Norway
| | - Maria José Sánchez Pérez
- Escuela Andaluza de Salud Pública. Instituto de Investigación Biosanitaria ibs.GRANADA, Universidad de Granada, 18011 Granada, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
| | - Pilar Amiano
- CIBER de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
- Public Health Division of Gipuzkoa, Biodonostia Research Institute, 20014 San Sebastian, Spain
| | - Liher Imaz
- CIBER de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
- Public Health Division of Gipuzkoa, Biodonostia Research Institute, 20014 San Sebastian, Spain
| | - Conchi Moreno-Iribas
- Instituto de Salud Pública de Navarra, IdiSNA, Navarre Institute for Health Research, REDISSEC, 31008, Pamplona, Spain
| | - Olle Melander
- Department of Clinical Sciences, Lund University, SE-221 00 Malmö, Sweden
| | - Sophia Harlid
- Department of Radiation Sciences, Oncology, Umea University, 901 87 Umea, Sweden
| | - Maria Nordendahl
- Department of Public Health and Clinical Medicine, Umea University, 901 87 Umea, Sweden
| | - Patrik Wennberg
- Department of Public Health and Clinical Medicine, Umea University, 901 87 Umea, Sweden
| | - Timothy J Key
- Nuffield Department of Population Health, University of Oxford, OX3 7LF Oxford, England
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, SW7 2AZ London, UK
| | - Carmen Santiuste
- CIBER de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
- Department of Epidemiology, Murcia Regional Health Authority, IMIB-Arrixaca, 30001 Murcia, Spain
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, DKFZ, Foundation under Public Law, D-69120 Heidelberg, Germany
| | - Verena Katzke
- Division of Cancer Epidemiology, DKFZ, Foundation under Public Law, D-69120 Heidelberg, Germany
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, CB2 0SL Cambridge, UK
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, CB2 0SL Cambridge, UK
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Technische Universität München, 80636 Munich, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, 80636 Munich, Germany
| | - Jeanette Erdmann
- Institute for Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany
| | | | - Christian Hengstenberg
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, 1090 Vienna, Austria
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Graciela Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Synlab Academy, Synlab Holding Deutschland GmbH, 68167 Mannheim, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, 8036 Graz, Austria
| | - Stavroula Kanoni
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
| | - George Dedoussis
- Department of Nutrition-Dietetics/Harokopio University, 17671 Athens, Greece
| | - Panos Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
- Centre for Genomic Health, Queen Mary University of London, London E1 4NS, UK
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Majid Nikpay
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Ontario K1Y 4W7, Canada
| | - Ruth McPherson
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Ontario K1Y 4W7, Canada
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04107 Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, 04103 Leipzig, Germany
| | - Andrej Teren
- LIFE Research Center for Civilization Diseases, University of Leipzig, 04103 Leipzig, Germany
- Heart Center Leipzig, 04289 Leipzig, Germany
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Yvonne T van der Schouw
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, GA 3508 Utrecht, the Netherlands
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23
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Said S, Pazoki R, Karhunen V, Võsa U, Ligthart S, Bodinier B, Koskeridis F, Welsh P, Alizadeh BZ, Chasman DI, Sattar N, Chadeau-Hyam M, Evangelou E, Jarvelin MR, Elliott P, Tzoulaki I, Dehghan A. Genetic analysis of over half a million people characterises C-reactive protein loci. Nat Commun 2022; 13:2198. [PMID: 35459240 PMCID: PMC9033829 DOI: 10.1038/s41467-022-29650-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 03/25/2022] [Indexed: 01/08/2023] Open
Abstract
Chronic low-grade inflammation is linked to a multitude of chronic diseases. We report the largest genome-wide association study (GWAS) on C-reactive protein (CRP), a marker of systemic inflammation, in UK Biobank participants (N = 427,367, European descent) and the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium (total N = 575,531 European descent). We identify 266 independent loci, of which 211 are not previously reported. Gene-set analysis highlighted 42 gene sets associated with CRP levels (p ≤ 3.2 ×10-6) and tissue expression analysis indicated a strong association of CRP related genes with liver and whole blood gene expression. Phenome-wide association study identified 27 clinical outcomes associated with genetically determined CRP and subsequent Mendelian randomisation analyses supported a causal association with schizophrenia, chronic airway obstruction and prostate cancer. Our findings identified genetic loci and functional properties of chronic low-grade inflammation and provided evidence for causal associations with a range of diseases.
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Affiliation(s)
- Saredo Said
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Raha Pazoki
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Cardiovascular and Metabolic Research Group, Department of Life Sciences, Brunel University London, London, UK
- The Centre for Inflammation Research and Translational Medicine (CIRTM), Brunel University London, London, UK
- Centre for Health and Well-being Across the Life Course, Brunel University London, London, UK
| | - Ville Karhunen
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Centre for Life Course Health Research, University of Oulu, Oulu, Finland
- Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland
| | - Urmo Võsa
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Symen Ligthart
- Department of Intensive Care, University Hospital Antwerp, Antwerp, Belgium
| | - Barbara Bodinier
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Fotios Koskeridis
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Paul Welsh
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Behrooz Z Alizadeh
- Department of Epidemiology, University of Groningen and University Medical Centre Groningen, Groningen, the Netherlands
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham & Women's Hospital, Boston, MA, 02115, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Naveed Sattar
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Evangelos Evangelou
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Centre for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, W2 1PG, UK
- UK Dementia Research Institute at Imperial College London, Burlington Danes Building, Hammersmith Hospital, DuCane Road, London, W12 0NN, UK
- National Institute for Health Research Imperial Biomedical Research Centre, Imperial College London, London, W2 1PG, UK
| | - Ioanna Tzoulaki
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, W2 1PG, UK
- UK Dementia Research Institute at Imperial College London, Burlington Danes Building, Hammersmith Hospital, DuCane Road, London, W12 0NN, UK
| | - Abbas Dehghan
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK.
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, W2 1PG, UK.
- UK Dementia Research Institute at Imperial College London, Burlington Danes Building, Hammersmith Hospital, DuCane Road, London, W12 0NN, UK.
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24
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Neumann A, Küçükali F, Bos I, Vos SJB, Engelborghs S, De Pooter T, Joris G, De Rijk P, De Roeck E, Tsolaki M, Verhey F, Martinez-Lage P, Tainta M, Frisoni G, Blin O, Richardson J, Bordet R, Scheltens P, Popp J, Peyratout G, Johannsen P, Frölich L, Vandenberghe R, Freund-Levi Y, Streffer J, Lovestone S, Legido-Quigley C, Ten Kate M, Barkhof F, Strazisar M, Zetterberg H, Bertram L, Visser PJ, van Broeckhoven C, Sleegers K. Rare variants in IFFO1, DTNB, NLRC3 and SLC22A10 associate with Alzheimer's disease CSF profile of neuronal injury and inflammation. Mol Psychiatry 2022; 27:1990-1999. [PMID: 35173266 PMCID: PMC9126805 DOI: 10.1038/s41380-022-01437-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/04/2021] [Accepted: 01/05/2022] [Indexed: 11/30/2022]
Abstract
Alzheimer's disease (AD) biomarkers represent several neurodegenerative processes, such as synaptic dysfunction, neuronal inflammation and injury, as well as amyloid pathology. We performed an exome-wide rare variant analysis of six AD biomarkers (β-amyloid, total/phosphorylated tau, NfL, YKL-40, and Neurogranin) to discover genes associated with these markers. Genetic and biomarker information was available for 480 participants from two studies: EMIF-AD and ADNI. We applied a principal component (PC) analysis to derive biomarkers combinations, which represent statistically independent biological processes. We then tested whether rare variants in 9576 protein-coding genes associate with these PCs using a Meta-SKAT test. We also tested whether the PCs are intermediary to gene effects on AD symptoms with a SMUT test. One PC loaded on NfL and YKL-40, indicators of neuronal injury and inflammation. Four genes were associated with this PC: IFFO1, DTNB, NLRC3, and SLC22A10. Mediation tests suggest, that these genes also affect dementia symptoms via inflammation/injury. We also observed an association between a PC loading on Neurogranin, a marker for synaptic functioning, with GABBR2 and CASZ1, but no mediation effects. The results suggest that rare variants in IFFO1, DTNB, NLRC3, and SLC22A10 heighten susceptibility to neuronal injury and inflammation, potentially by altering cytoskeleton structure and immune activity disinhibition, resulting in an elevated dementia risk. GABBR2 and CASZ1 were associated with synaptic functioning, but mediation analyses suggest that the effect of these two genes on synaptic functioning is not consequential for AD development.
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Affiliation(s)
- Alexander Neumann
- Complex Genetics of Alzheimer's Disease Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - Fahri Küçükali
- Complex Genetics of Alzheimer's Disease Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Isabelle Bos
- Netherlands Institute for Health Services Research, Utrecht, the Netherlands
| | - Stephanie J B Vos
- Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands
| | - Sebastiaan Engelborghs
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Memory Clinic, Universitair Ziekenhuis Brussel (UZ Brussel) and Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Tim De Pooter
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
| | - Geert Joris
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
| | - Peter De Rijk
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
| | - Ellen De Roeck
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA) Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Magda Tsolaki
- 1st Department of Neurology, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Makedonia, Thessaloniki, Greece
| | - Frans Verhey
- Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands
- Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Pablo Martinez-Lage
- Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, San Sebastian, Spain
| | - Mikel Tainta
- Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, San Sebastian, Spain
| | - Giovanni Frisoni
- Department of Psychiatry, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
- RCCS Instituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Oliver Blin
- Clinical Pharmacology & Pharmacovigilance Department, Marseille University Hospital, Marseille, France
| | - Jill Richardson
- Neurosciences Therapeutic Area, GlaxoSmithKline R&D, Stevanage, UK
| | - Régis Bordet
- Neuroscience & Cognition, CHU de Lille, University of Lille, Inserm, France
| | - Philip Scheltens
- Alzheimer Center and Department of Neurology, VU University Medical Center, Amsterdam, the Netherlands
| | - Julius Popp
- Department of Geriatric Psychiatry, University Hospital of Psychiatry Zürich, Zürich, Switzerland
- Old Age Psychiatry, Department of Psychiatry, University Hospital of Lausanne, Lausanne, Switzerland
| | - Gwendoline Peyratout
- Department of Psychiatry, University Hospital of Lausanne, Lausanne, Switzerland
| | - Peter Johannsen
- Clinical Drug Development, Novo Nordisk, Copenhagen, Denmark
| | - Lutz Frölich
- Department of Geriatric Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Rik Vandenberghe
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Yvonne Freund-Levi
- Center for Alzheimer Research, Division of Clinical Geriatrics, Department of Neurobiology, Care Sciences and Society Karolinska Institute Stockholm Sweden, Stockholm, Sweden
- School of Medical Sciences Örebro, University Örebro, Örebro, Sweden
| | - Johannes Streffer
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Simon Lovestone
- Department of Psychiatry, University of Oxford, Oxford, UK
- Janssen Medical Ltd, High Wycombe, UK
| | - Cristina Legido-Quigley
- Steno Diabetes Center, Copenhagen, Denmark
- Institute of Pharmaceutical Sciences, King's College London, London, UK
| | - Mara Ten Kate
- Alzheimer Center and Department of Neurology, VU University Medical Center, Amsterdam, the Netherlands
- Department of Radiology and Nuclear Medicine, VU University Medical Center, Amsterdam, the Netherlands
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, VU University Medical Center, Amsterdam, the Netherlands
- Institutes of Neurology and Healthcare Engineering, University College London, London, UK
| | - Mojca Strazisar
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, University of Gothenburg, Gothenburg, Sweden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- UK Dementia Research Institute, University College London, London, UK
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
- Centre for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway
| | - Pieter Jelle Visser
- Alzheimer Centrum Limburg, Maastricht University, Maastricht, the Netherlands
- Alzheimer Center and Department of Neurology, VU University Medical Center, Amsterdam, the Netherlands
| | - Christine van Broeckhoven
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
| | - Kristel Sleegers
- Complex Genetics of Alzheimer's Disease Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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25
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Bouras E, Karhunen V, Gill D, Huang J, Haycock PC, Gunter MJ, Johansson M, Brennan P, Key T, Lewis SJ, Martin RM, Murphy N, Platz EA, Travis R, Yarmolinsky J, Zuber V, Martin P, Katsoulis M, Freisling H, Nøst TH, Schulze MB, Dossus L, Hung RJ, Amos CI, Ahola-Olli A, Palaniswamy S, Männikkö M, Auvinen J, Herzig KH, Keinänen-Kiukaanniemi S, Lehtimäki T, Salomaa V, Raitakari O, Salmi M, Jalkanen S, Jarvelin MR, Dehghan A, Tsilidis KK. Circulating inflammatory cytokines and risk of five cancers: a Mendelian randomization analysis. BMC Med 2022; 20:3. [PMID: 35012533 PMCID: PMC8750876 DOI: 10.1186/s12916-021-02193-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/18/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Epidemiological and experimental evidence has linked chronic inflammation to cancer aetiology. It is unclear whether associations for specific inflammatory biomarkers are causal or due to bias. In order to examine whether altered genetically predicted concentration of circulating cytokines are associated with cancer development, we performed a two-sample Mendelian randomisation (MR) analysis. METHODS Up to 31,112 individuals of European descent were included in genome-wide association study (GWAS) meta-analyses of 47 circulating cytokines. Single nucleotide polymorphisms (SNPs) robustly associated with the cytokines, located in or close to their coding gene (cis), were used as instrumental variables. Inverse-variance weighted MR was used as the primary analysis, and the MR assumptions were evaluated in sensitivity and colocalization analyses and a false discovery rate (FDR) correction for multiple comparisons was applied. Corresponding germline GWAS summary data for five cancer outcomes (breast, endometrial, lung, ovarian, and prostate), and their subtypes were selected from the largest cancer-specific GWASs available (cases ranging from 12,906 for endometrial to 133,384 for breast cancer). RESULTS There was evidence of inverse associations of macrophage migration inhibitory factor with breast cancer (OR per SD = 0.88, 95% CI 0.83 to 0.94), interleukin-1 receptor antagonist with endometrial cancer (0.86, 0.80 to 0.93), interleukin-18 with lung cancer (0.87, 0.81 to 0.93), and beta-chemokine-RANTES with ovarian cancer (0.70, 0.57 to 0.85) and positive associations of monokine induced by gamma interferon with endometrial cancer (3.73, 1.86 to 7.47) and cutaneous T-cell attracting chemokine with lung cancer (1.51, 1.22 to 1.87). These associations were similar in sensitivity analyses and supported in colocalization analyses. CONCLUSIONS Our study adds to current knowledge on the role of specific inflammatory biomarker pathways in cancer aetiology. Further validation is needed to assess the potential of these cytokines as pharmacological or lifestyle targets for cancer prevention.
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Affiliation(s)
- Emmanouil Bouras
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Ville Karhunen
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London, W2 1PG, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London, W2 1PG, UK
- Novo Nordisk Research Centre Oxford, Old Road Campus, Oxford, UK
- Clinical Pharmacology Group, Pharmacy and Medicines Directorate, St George's University Hospitals NHS Foundation Trust, London, UK
- Clinical Pharmacology and Therapeutics Section, Institute for Infection and Immunity, St George's, University of London, London, UK
| | - Jian Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London, W2 1PG, UK
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Philip C Haycock
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Marc J Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Mattias Johansson
- Genomics Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Paul Brennan
- Genomics Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Tim Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Sarah J Lewis
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Richard M Martin
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol NHS Foundation Trust and the University of Bristol, Bristol, UK
| | - Neil Murphy
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ruth Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - James Yarmolinsky
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Verena Zuber
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London, W2 1PG, UK
| | - Paul Martin
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Michail Katsoulis
- Institute of Health Informatics, University College London, London, UK
- Health Data Research UK, London, UK
| | - Heinz Freisling
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Therese Haugdahl Nøst
- Department of Community Medicine, Faculty of Health Sciences, Arctic University of Norway, Tromsø, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nutehtal, Germany
- Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
| | - Laure Dossus
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute of Sinai Health System, Toronto, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | | | - Ari Ahola-Olli
- The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Saranya Palaniswamy
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London, W2 1PG, UK
| | - Minna Männikkö
- Northern Finland Birth Cohorts, Infrastructure for Population Studies, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Juha Auvinen
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Karl-Heinz Herzig
- Research Unit of Biomedicine, Medical Research Center, Faculty of Medicine, University of Oulu, and Oulu University Hospital, Oulu, Finland
| | | | - Terho Lehtimäki
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Marko Salmi
- MediCity Research Laboratory, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Sirpa Jalkanen
- MediCity Research Laboratory, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London, W2 1PG, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Abbas Dehghan
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London, W2 1PG, UK
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- UK Dementia Research Institute at Imperial College London, London, UK
| | - Konstantinos K Tsilidis
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece.
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London, W2 1PG, UK.
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Escott-Price V, Hardy J. Genome-wide association studies for Alzheimer's disease: bigger is not always better. Brain Commun 2022; 4:fcac125. [PMID: 35663382 PMCID: PMC9155614 DOI: 10.1093/braincomms/fcac125] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/15/2022] [Accepted: 05/13/2022] [Indexed: 11/25/2022] Open
Abstract
As the size of genome-wide association studies increase, the number of associated trait loci identified inevitably increase. One welcomes this if it allows the better delineation of the pathways to disease and increases the accuracy of genetic prediction of disease risk through polygenic risk score analysis. However, there are several problems in the continuing increase in the genome-wide analysis of 'Alzheimer's disease'. In this review, we have systematically assessed the history of Alzheimer's disease genome-wide association studies, including their sample sizes, age and selection/assessment criteria of cases and controls and heritability explained by these disease genome-wide association studies. We observe that nearly all earlier disease genome-wide association studies are now part of all current disease genome-wide association studies. In addition, the latest disease genome-wide association studies include (i) only a small fraction (∼10%) of clinically screened controls, substituting for them population-based samples which are systematically younger than cases, and (ii) around 50% of Alzheimer's disease cases are in fact 'proxy dementia cases'. As a consequence, the more genes the field finds, the less the heritability they explain. We highlight potential caveats this situation creates and discuss some of the consequences occurring when translating the newest Alzheimer's disease genome-wide association study results into basic research and/or clinical practice.
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Affiliation(s)
- Valentina Escott-Price
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
- Dementia Research Institute at Cardiff, Cardiff University, Cardiff, UK
- Correspondence to: Valentina Escott-Price Cardiff University, Hadyn Ellis Building Maindy Road, Cardiff CF24 4HQ, UK E-mail:
| | - John Hardy
- UCL Institute of Neurology, Queen Square, London, UK
- UCL Dementia Research Institute, UCL, London, UK
- Correspondence may also be addressed to: John Hardy UCL Institute of Neurology, Queen Square London WC1N 3BG, UK E-mail:
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Mills MC, Tropf FC, Brazel DM, van Zuydam N, Vaez A, Pers TH, Snieder H, Perry JRB, Ong KK, den Hoed M, Barban N, Day FR. Identification of 371 genetic variants for age at first sex and birth linked to externalising behaviour. Nat Hum Behav 2021; 5:1717-1730. [PMID: 34211149 PMCID: PMC7612120 DOI: 10.1038/s41562-021-01135-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 05/14/2021] [Indexed: 02/06/2023]
Abstract
Age at first sexual intercourse and age at first birth have implications for health and evolutionary fitness. In this genome-wide association study (age at first sexual intercourse, N = 387,338; age at first birth, N = 542,901), we identify 371 single-nucleotide polymorphisms, 11 sex-specific, with a 5-6% polygenic score prediction. Heritability of age at first birth shifted from 9% [CI = 4-14%] for women born in 1940 to 22% [CI = 19-25%] for those born in 1965. Signals are driven by the genetics of reproductive biology and externalising behaviour, with key genes related to follicle stimulating hormone (FSHB), implantation (ESR1), infertility and spermatid differentiation. Our findings suggest that polycystic ovarian syndrome may lead to later age at first birth, linking with infertility. Late age at first birth is associated with parental longevity and reduced incidence of type 2 diabetes and cardiovascular disease. Higher childhood socioeconomic circumstances and those in the highest polygenic score decile (90%+) experience markedly later reproductive onset. Results are relevant for improving teenage and late-life health, understanding longevity and guiding experimentation into mechanisms of infertility.
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Affiliation(s)
- Melinda C Mills
- Leverhulme Centre for Demographic Science, University of Oxford, Oxford, United Kingdom.
- Nuffield College, University of Oxford, Oxford, United Kingdom.
| | - Felix C Tropf
- Leverhulme Centre for Demographic Science, University of Oxford, Oxford, United Kingdom
- Nuffield College, University of Oxford, Oxford, United Kingdom
- École Nationale de la Statistique et de L'administration Économique (ENSAE), Paris, France
- Center for Research in Economics and Statistics (CREST), Paris, France
| | - David M Brazel
- Leverhulme Centre for Demographic Science, University of Oxford, Oxford, United Kingdom
- Nuffield College, University of Oxford, Oxford, United Kingdom
| | - Natalie van Zuydam
- The Beijer Laboratory and Department of Immunology, Genetics and Pathology, Uppsala University and SciLifeLab, Uppsala, Sweden
| | - Ahmad Vaez
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Bioinformatics, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Tune H Pers
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - John R B Perry
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Ken K Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Marcel den Hoed
- The Beijer Laboratory and Department of Immunology, Genetics and Pathology, Uppsala University and SciLifeLab, Uppsala, Sweden
| | - Nicola Barban
- Department of Statistical Sciences, University of Bologna, Bologna, Italy
| | - Felix R Day
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom.
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28
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Hernáez Á, Rogne T, Skåra KH, Håberg SE, Page CM, Fraser A, Burgess S, Lawlor DA, Magnus MC. Body mass index and subfertility: multivariable regression and Mendelian randomization analyses in the Norwegian Mother, Father and Child Cohort Study. Hum Reprod 2021; 36:3141-3151. [PMID: 34668019 PMCID: PMC8600658 DOI: 10.1093/humrep/deab224] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/10/2021] [Indexed: 01/29/2023] Open
Abstract
STUDY QUESTION What is the association between BMI and subfertility? SUMMARY ANSWER We observed a J-shaped relationship between BMI and subfertility in both sexes, when using both a standard multivariable regression and Mendelian randomization (MR) analysis. WHAT IS KNOWN ALREADY High BMI in both women and men is associated with subfertility in observational studies and this relationship is further substantiated by a few small randomized controlled trials of weight reduction and success of assisted reproduction. Women with low BMI also have lower conception rates with assisted reproduction technologies. STUDY DESIGN, SIZE, DURATION Cohort study (the Norwegian Mother, Father and Child Cohort Study), 28 341 women and 26 252 men, recruited from all over Norway between 1999 and 2008. PARTICIPANTS/MATERIALS, SETTING, METHODS Women (average age 30, average BMI 23.1 kg/m2) and men (average age 33, average BMI 25.5 kg/m2) had available genotype data and provided self-reported information on time-to-pregnancy and BMI. A total of 10% of couples were subfertile (time-to-pregnancy ≥12 months). MAIN RESULTS AND THE ROLE OF CHANCE Our findings support a J-shaped association between BMI and subfertility in both sexes using multivariable logistic regression models. Non-linear MR validated this relationship. A 1 kg/m2 greater genetically predicted BMI was linked to 18% greater odds of subfertility (95% CI 5% to 31%) in obese women (≥30.0 kg/m2) and 15% lower odds of subfertility (-24% to -2%) in women with BMI <20.0 kg/m2. A 1 kg/m2 higher genetically predicted BMI was linked to 26% greater odds of subfertility (8-48%) among obese men. Low genetically predicted BMI values were also related to greater subfertility risk in men at the lower end of the BMI distribution. A genetically predicted BMI of 23 and 25 kg/m2 was linked to the lowest subfertility risk in women and men, respectively. LIMITATIONS, REASONS FOR CAUTION The main limitations of our study were that we did not know whether the subfertility was driven by the women, men or both; the exclusive consideration of individuals of northern European ancestry; and the limited amount of participants with obesity or BMI values <20.0 kg/m2. WIDER IMPLICATIONS OF THE FINDINGS Our results support a causal effect of obesity on subfertility in women and men. Our findings also expand the current evidence by indicating that individuals with BMI values <20 kg/m2 may have an increased risk of subfertility. These results suggest that BMI values between 20 and 25 kg/m2 are optimal for a minimal risk of subfertility. STUDY FUNDING/COMPETING INTEREST(S) The MoBa Cohort Study is supported by the Norwegian Ministry of Health and Care Services and the Norwegian Ministry of Education and Research. This project received funding from the European Research Council under the European Union's Horizon 2020 research and innovation program (grant agreement No 947684). It was also partly supported by the Research Council of Norway through its Centres of Excellence funding scheme, project number 262700. Open Access funding was provided by the Folkehelseinstituttet/Norwegian Institute of Public Health. D.A.L. is a UK National Institute for Health Research Senior Investigator (NF-SI-0611-10196) and is supported by the US National Institutes of Health (R01 DK10324) and a European Research Council Advanced Grant (DevelopObese; 669545). The funders had no role in the collection, analysis and interpretation of data; in the writing of the report; or in the decision to submit the article for publication. D.A.L. receives (or has received in the last 10 years) research support from National and International government and charitable bodies, Roche Diagnostics and Medtronic for research unrelated to the current work. The rest of the authors declare that no competing interests exist. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Álvaro Hernáez
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Consorcio CIBER, M.P. Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
- Blanquerna School of Health Sciences, Universitat Ramon Llull, Barcelona, Spain
| | - Tormod Rogne
- Department of Chronic Disease Epidemiology, Yale University School of Public Health, New Haven, CT, USA
- Department of Circulation and Medical Imaging, Gemini Center for Sepsis Research, NTNU Norwegian University of Science and Technology, Trondheim, Norway
- Clinic of Anaesthesia and Intensive Care, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Karoline H Skåra
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Mathematics, University of Oslo, Oslo, Norway
| | - Abigail Fraser
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Maria Christine Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
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Mullee A, Dimou N, Allen N, O'Mara T, Gunter MJ, Murphy N. Testosterone, sex hormone-binding globulin, insulin-like growth factor-1 and endometrial cancer risk: observational and Mendelian randomization analyses. Br J Cancer 2021; 125:1308-1317. [PMID: 34363033 PMCID: PMC8548546 DOI: 10.1038/s41416-021-01518-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 06/04/2021] [Accepted: 07/26/2021] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Dysregulation of endocrine pathways related to steroid and growth hormones may modify endometrial cancer risk; however, prospective data on testosterone, sex hormone-binding globulin (SHBG) and insulin-like growth factor (IGF)-1 are limited. To elucidate the role of these hormones in endometrial cancer risk we conducted complementary observational and Mendelian randomization (MR) analyses. METHODS The observational analyses included 159,702 women (80% postmenopausal) enrolled in the UK Biobank. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated using Cox proportional hazards models. For MR analyses, genetic variants associated with hormone levels were identified and their association with endometrial cancer (12,906 cases/108,979 controls) was examined using two-sample MR. RESULTS In the observational analysis, higher circulating concentrations of total (HR per unit inverse normal scale = 1.38, 95% CI = 1.22-1.57) and free testosterone (HR per unit log scale = 2.07, 95% CI = 1.66-2.58) were associated with higher endometrial cancer risk. An inverse association was found for SHBG (HR per unit inverse normal scale = 0.76, 95% CI = 0.67-0.86). Results for testosterone and SHBG were supported by the MR analyses. No association was found between genetically predicted IGF-1 concentration and endometrial cancer risk. CONCLUSIONS Our results support probable causal associations between circulating concentrations of testosterone and SHBG with endometrial cancer risk.
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Affiliation(s)
- Amy Mullee
- School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Niki Dimou
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Naomi Allen
- Clinical Trial Service Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Tracy O'Mara
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Marc J Gunter
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Neil Murphy
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France.
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30
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Ohukainen P, Virtanen JK, Ala-Korpela M. Vexed causal inferences in nutritional epidemiology-call for genetic help. Int J Epidemiol 2021; 51:6-15. [PMID: 34387668 PMCID: PMC8856007 DOI: 10.1093/ije/dyab152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2021] [Indexed: 12/31/2022] Open
Affiliation(s)
- Pauli Ohukainen
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland.,Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Jyrki K Virtanen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Mika Ala-Korpela
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland.,Center for Life Course Health Research, University of Oulu, Oulu, Finland.,NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
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31
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Rask-Andersen M, Karlsson T, Ek WE, Johansson Å. Modification of Heritability for Educational Attainment and Fluid Intelligence by Socioeconomic Deprivation in the UK Biobank. Am J Psychiatry 2021; 178:625-634. [PMID: 33900812 DOI: 10.1176/appi.ajp.2020.20040462] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Socioeconomic factors have been suggested to influence the effect of education- and intelligence-associated genetic variants. However, results from previous studies on the interaction between socioeconomic status and education or intelligence have been inconsistent. The authors sought to assess these interactions in the UK Biobank cohort of 500,000 participants. METHODS The authors assessed the effect of socioeconomic deprivation on education- and intelligence-associated genetic variants by estimating the single-nucleotide polymorphism (SNP) heritability for fluid intelligence, educational attainment, and years of education in subsets of UK Biobank participants with different degrees of social deprivation, using linkage disequilibrium score regression. They also generated polygenic scores with LDpred and tested for interactions with social deprivation. RESULTS SNP heritability increased with socioeconomic deprivation for fluid intelligence, educational attainment, and years of education. Polygenic scores were also found to interact with socioeconomic deprivation, where the effects of the scores increased with increasing deprivation for all traits. CONCLUSIONS These results indicate that genetics have a larger influence on educational and cognitive outcomes in more socioeconomically deprived U.K. citizens, which has serious implications for equality of opportunity.
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Affiliation(s)
- Mathias Rask-Andersen
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Torgny Karlsson
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Weronica E Ek
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Åsa Johansson
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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32
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Dimou N, Mori N, Harlid S, Harbs J, Martin RM, Smith-Byrne K, Papadimitriou N, Bishop DT, Casey G, Colorado-Yohar SM, Cotterchio M, Cross AJ, Marchand LL, Lin Y, Offit K, Onland-Moret NC, Peters U, Potter JD, Rohan TE, Weiderpass E, Gunter MJ, Murphy N. Circulating Levels of Testosterone, Sex Hormone Binding Globulin and Colorectal Cancer Risk: Observational and Mendelian Randomization Analyses. Cancer Epidemiol Biomarkers Prev 2021; 30:1336-1348. [PMID: 33879453 PMCID: PMC8914241 DOI: 10.1158/1055-9965.epi-20-1690] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/22/2021] [Accepted: 04/07/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Epidemiologic studies evaluating associations between sex steroid hormones and colorectal cancer risk have yielded inconsistent results. To elucidate the role of circulating levels of testosterone, and sex hormone-binding globulin (SHBG) in colorectal cancer risk, we conducted observational and Mendelian randomization (MR) analyses. METHODS The observational analyses included 333,530 participants enrolled in the UK Biobank with testosterone and SHBG measured. HRs and 95% confidence intervals (CI) were estimated using multivariable Cox proportional hazards models. For MR analyses, genetic variants robustly associated with hormone levels were identified and their association with colorectal cancer (42,866 cases/42,752 controls) was examined using two-sample MR. RESULTS In the observational analysis, there was little evidence that circulating levels of total testosterone were associated with colorectal cancer risk; the MR analyses showed a greater risk for women (OR per 1-SD = 1.09; 95% CI, 1.01-1.17), although pleiotropy may have biased this result. Higher SHBG concentrations were associated with greater colorectal cancer risk for women (HR per 1-SD = 1.16; 95% CI, 1.05-1.29), but was unsupported by the MR analysis. There was little evidence of associations between free testosterone and colorectal cancer in observational and MR analyses. CONCLUSIONS Circulating concentrations of sex hormones are unlikely to be causally associated with colorectal cancer. Additional experimental studies are required to better understand the possible role of androgens in colorectal cancer development. IMPACT Our results from large-scale analyses provide little evidence for sex hormone pathways playing a causal role in colorectal cancer development.See related commentary by Hang and Shen, p. 1302.
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Affiliation(s)
- Niki Dimou
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France.
| | - Nagisa Mori
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Sophia Harlid
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Justin Harbs
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Richard M Martin
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol NHS Foundation Trust and the University of Bristol, Bristol, United Kingdom
| | - Karl Smith-Byrne
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Nikos Papadimitriou
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - D Timothy Bishop
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Sandra M Colorado-Yohar
- Department of Epidemiology, Murcia Regional Health Council, IMIB-Arrixaca, Murcia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Spain
- Research Group on Demography and Health, National Faculty of Public Health, University of Antioquia, Medellín, Colombia
| | - Michelle Cotterchio
- Ontario Health (Cancer Care Ontario), Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Amanda J Cross
- Department of Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London, United Kingdom
| | | | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - N Charlotte Onland-Moret
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
- Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Thomas E Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Elisabete Weiderpass
- Office of the Director, International Agency for Research on Cancer, Lyon, France
| | - Marc J Gunter
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Neil Murphy
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
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Carry PM, Vanderlinden LA, Dong F, Buckner T, Litkowski E, Vigers T, Norris JM, Kechris K. Inverse probability weighting is an effective method to address selection bias during the analysis of high dimensional data. Genet Epidemiol 2021; 45:593-603. [PMID: 34130352 DOI: 10.1002/gepi.22418] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/05/2021] [Accepted: 05/17/2021] [Indexed: 11/11/2022]
Abstract
Omics studies frequently use samples collected during cohort studies. Conditioning on sample availability can cause selection bias if sample availability is nonrandom. Inverse probability weighting (IPW) is purported to reduce this bias. We evaluated IPW in an epigenome-wide analysis testing the association between DNA methylation (261,435 probes) and age in healthy adolescent subjects (n = 114). We simulated age and sex to be correlated with sample selection and then evaluated four conditions: complete population/no selection bias (all subjects), naïve selection bias (no adjustment), and IPW selection bias (selection bias with IPW adjustment). Assuming the complete population condition represented the "truth," we compared each condition to the complete population condition. Bias or difference in associations between age and methylation was reduced in the IPW condition versus the naïve condition. However, genomic inflation and type 1 error were higher in the IPW condition relative to the naïve condition. Postadjustment using bacon, type 1 error and inflation were similar across all conditions. Power was higher under the IPW condition compared with the naïve condition before and after inflation adjustment. IPW methods can reduce bias in genome-wide analyses. Genomic inflation is a potential concern that can be minimized using methods that adjust for inflation.
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Affiliation(s)
- Patrick M Carry
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA.,Department of Orthopedics, Musculoskeletal Research Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Lauren A Vanderlinden
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA.,Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
| | - Fran Dong
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Teresa Buckner
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA
| | - Elizabeth Litkowski
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA
| | - Timothy Vigers
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
| | - Jill M Norris
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
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34
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Akimova ET, Breen R, Brazel DM, Mills MC. Gene-environment dependencies lead to collider bias in models with polygenic scores. Sci Rep 2021; 11:9457. [PMID: 33947934 PMCID: PMC8097011 DOI: 10.1038/s41598-021-89020-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/20/2021] [Indexed: 11/09/2022] Open
Abstract
The application of polygenic scores has transformed our ability to investigate whether and how genetic and environmental factors jointly contribute to the variation of complex traits. Modelling the complex interplay between genes and environment, however, raises serious methodological challenges. Here we illustrate the largely unrecognised impact of gene-environment dependencies on the identification of the effects of genes and their variation across environments. We show that controlling for heritable covariates in regression models that include polygenic scores as independent variables introduces endogenous selection bias when one or more of these covariates depends on unmeasured factors that also affect the outcome. This results in the problem of conditioning on a collider, which in turn leads to spurious associations and effect sizes. Using graphical and simulation methods we demonstrate that the degree of bias depends on the strength of the gene-covariate correlation and of hidden heterogeneity linking covariates with outcomes, regardless of whether the main analytic focus is mediation, confounding, or gene × covariate (commonly gene × environment) interactions. We offer potential solutions, highlighting the importance of causal inference. We also urge further caution when fitting and interpreting models with polygenic scores and non-exogenous environments or phenotypes and demonstrate how spurious associations are likely to arise, advancing our understanding of such results.
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Affiliation(s)
- Evelina T Akimova
- Department of Sociology, University of Oxford, Oxford, OX1 1JD, UK. .,Leverhulme Centre for Demographic Science, University of Oxford, Oxford, OX1 1JD, UK.
| | - Richard Breen
- Department of Sociology, University of Oxford, Oxford, OX1 1JD, UK.,Nuffield College, University of Oxford, Oxford, OX1 1NF, UK
| | - David M Brazel
- Leverhulme Centre for Demographic Science, University of Oxford, Oxford, OX1 1JD, UK.,Nuffield College, University of Oxford, Oxford, OX1 1NF, UK
| | - Melinda C Mills
- Leverhulme Centre for Demographic Science, University of Oxford, Oxford, OX1 1JD, UK.,Nuffield College, University of Oxford, Oxford, OX1 1NF, UK
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35
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Werme J, van der Sluis S, Posthuma D, de Leeuw CA. Genome-wide gene-environment interactions in neuroticism: an exploratory study across 25 environments. Transl Psychiatry 2021; 11:180. [PMID: 33753719 PMCID: PMC7985503 DOI: 10.1038/s41398-021-01288-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 01/25/2021] [Accepted: 02/15/2021] [Indexed: 11/20/2022] Open
Abstract
Gene-environment interactions (GxE) are often suggested to play an important role in the aetiology of psychiatric phenotypes, yet so far, only a handful of genome-wide environment interaction studies (GWEIS) of psychiatric phenotypes have been conducted. Representing the most comprehensive effort of its kind to date, we used data from the UK Biobank to perform a series of GWEIS for neuroticism across 25 broadly conceptualised environmental risk factors (trauma, social support, drug use, physical health). We investigated interactions on the level of SNPs, genes, and gene-sets, and computed interaction-based polygenic risk scores (PRS) to predict neuroticism in an independent sample subset (N = 10,000). We found that the predictive ability of the interaction-based PRSs did not significantly improve beyond that of a traditional PRS based on SNP main effects from GWAS, but detected one variant and two gene-sets showing significant interaction signal after correction for the number of analysed environments. This study illustrates the possibilities and limitations of a comprehensive GWEIS in currently available sample sizes.
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Affiliation(s)
- Josefin Werme
- Department of Complex Trait Genetics, Centre for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands.
| | - Sophie van der Sluis
- grid.16872.3a0000 0004 0435 165XDepartment of Child and Adolescent Psychology and Psychiatry, section Complex Trait Genetics, Amsterdam Neuroscience, VU University Medical Center, Amsterdam, The Netherlands
| | - Danielle Posthuma
- grid.12380.380000 0004 1754 9227Department of Complex Trait Genetics, Centre for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands ,grid.16872.3a0000 0004 0435 165XDepartment of Child and Adolescent Psychology and Psychiatry, section Complex Trait Genetics, Amsterdam Neuroscience, VU University Medical Center, Amsterdam, The Netherlands
| | - Christiaan A. de Leeuw
- grid.12380.380000 0004 1754 9227Department of Complex Trait Genetics, Centre for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
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36
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Papadimitriou N, Dimou N, Gill D, Tzoulaki I, Murphy N, Riboli E, Lewis SJ, Martin RM, Gunter MJ, Tsilidis KK. Genetically predicted circulating concentrations of micronutrients and risk of breast cancer: A Mendelian randomization study. Int J Cancer 2021; 148:646-653. [PMID: 32761610 PMCID: PMC8268064 DOI: 10.1002/ijc.33246] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/08/2020] [Accepted: 07/27/2020] [Indexed: 02/06/2023]
Abstract
The epidemiological literature reports inconsistent associations between consumption or circulating concentrations of micronutrients and breast cancer risk. We investigated associations between genetically predicted concentrations of 11 micronutrients (beta-carotene, calcium, copper, folate, iron, magnesium, phosphorus, selenium, vitamin B6 , vitamin B12 and zinc) and breast cancer risk using Mendelian randomization (MR). A two-sample MR study was conducted using 122 977 women with breast cancer and 105 974 controls from the Breast Cancer Association Consortium. MR analyses were conducted using the inverse variance-weighted approach, and sensitivity analyses were conducted to assess the impact of potential violations of MR assumptions. A value of 1 SD (SD: 0.08 mmol/L) higher genetically predicted concentration of magnesium was associated with a 17% (odds ratio [OR]: 1.17, 95% confidence interval [CI]: 1.10-1.25, P value = 9.1 × 10-7 ) and 20% (OR: 1.20, 95% CI: 1.08-1.34, P value = 3.2 × 10-6 ) higher risk of overall and ER+ve breast cancer, respectively. An inverse association was observed for a SD (0.5 mg/dL) higher genetically predicted phosphorus concentration and ER-ve breast cancer (OR: 0.84, 95% CI: 0.72-0.98, P value = .03). There was little evidence that any other nutrient was associated with breast cancer. The results for magnesium were robust under all sensitivity analyses and survived correction for multiple comparisons. Higher circulating concentrations of magnesium and potentially phosphorus may affect breast cancer risk. Further work is required to replicate these findings and investigate underlying mechanisms.
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Affiliation(s)
- Nikos Papadimitriou
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Niki Dimou
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Ioanna Tzoulaki
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Neil Murphy
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Sarah J Lewis
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Richard M Martin
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- University Hospitals Bristol NHS Foundation Trust National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, Bristol, UK
| | - Marc J Gunter
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Konstantinos K Tsilidis
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
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37
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Nguyen TV. Common methodological issues and suggested solutions in bone research. Osteoporos Sarcopenia 2021; 6:161-167. [PMID: 33426303 PMCID: PMC7783208 DOI: 10.1016/j.afos.2020.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 11/12/2020] [Accepted: 11/19/2020] [Indexed: 11/30/2022] Open
Abstract
Bone research is a dynamic area of scientific investigation that usually encompasses multidisciplines. Virtually all basic cellular research, clinical research and epidemiologic research rely on statistical concepts and methodology for inference. This paper discusses common issues and suggested solutions concerning the application of statistical thinking in bone research, particularly in clinical and epidemiological investigations. The issues are sample size estimation, biases and confounders, analysis of longitudinal data, categorization of continuous data, selection of significant variables, over-fitting, P-values, false positive finding, confidence interval, and Bayesian inference. It is hoped that by adopting the suggested measures the scientific quality of bone research can improve.
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Affiliation(s)
- Tuan V Nguyen
- Garvan Institute of Medical Research, St Vincent's Clinical School, UNSW Medicine, UNSW Sydney, School of Biomedical Engineering, University of Technology Sydney, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia
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38
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Polimanti R, Levey DF, Pathak GA, Wendt FR, Nunez YZ, Ursano RJ, Kessler RC, Kranzler HR, Stein MB, Gelernter J. Multi-environment gene interactions linked to the interplay between polysubstance dependence and suicidality. Transl Psychiatry 2021; 11:34. [PMID: 33431810 PMCID: PMC7801457 DOI: 10.1038/s41398-020-01153-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 11/27/2020] [Accepted: 12/03/2020] [Indexed: 12/19/2022] Open
Abstract
Substance dependence diagnoses (SDs) are important risk factors for suicidality. We investigated the associations of multiple SDs with different suicidality outcomes, testing how genetic background moderates these associations. The Yale-Penn cohort (N = 15,557) was recruited to investigate the genetics of SDs. The Army STARRS (Study to Assess Risk and Resilience in Servicemembers) cohort (N = 11,236) was recruited to evaluate mental health risk and resilience among Army personnel. We applied multivariate logistic regression to investigate the associations of SDs with suicidality and, in the Yale-Penn cohort, we used the structured linear mixed model (StructLMM) to study multivariate gene-environment interactions. In Yale-Penn, lifetime polysubstance dependence was strongly associated with lifetime suicidality: having five SDs showed an association with suicidality, from odds ratio (OR) = 6.77 (95% confidence interval, CI = 5.74-7.99) for suicidal ideation (SI) to OR = 3.61 (95% CI = 2.7-4.86) for suicide attempt (SA). In Army STARRS, having multiple substance use disorders for alcohol and/or drugs was associated with increased suicidality ranging from OR = 2.88 (95% CI = 2.6-3.19) for SI to OR = 3.92 (95% CI = 3.19-4.81) for SA. In Yale-Penn, we identified multivariate gene-environment interactions (Bayes factors, BF > 0) of SI with respect to a gene cluster on chromosome 16 (LCAT, p = 1.82 × 10-7; TSNAXIP1, p = 2.13 × 10-7; CENPT, p = 2.32 × 10-7; PARD6A, p = 5.57 × 10-7) for opioid dependence (BF = 12.2), cocaine dependence (BF = 12.1), nicotine dependence (BF = 9.2), and polysubstance dependence (BF = 2.1). Comorbidity of multiple SDs is a significant associated with suicidality and heritability of suicidality is partially moderated by multivariate gene interactions.
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Affiliation(s)
- Renato Polimanti
- Department of Psychiatry, Yale School of Medicine, Yale University, West Haven, CT, USA. .,Veteran Affairs CT Healthcare System, West Haven, CT, USA.
| | - Daniel F. Levey
- grid.47100.320000000419368710Department of Psychiatry, Yale School of Medicine, Yale University, West Haven, CT USA ,Veteran Affairs CT Healthcare System, West Haven, CT USA
| | - Gita A. Pathak
- grid.47100.320000000419368710Department of Psychiatry, Yale School of Medicine, Yale University, West Haven, CT USA ,Veteran Affairs CT Healthcare System, West Haven, CT USA
| | - Frank R. Wendt
- grid.47100.320000000419368710Department of Psychiatry, Yale School of Medicine, Yale University, West Haven, CT USA ,Veteran Affairs CT Healthcare System, West Haven, CT USA
| | - Yaira Z. Nunez
- grid.47100.320000000419368710Department of Psychiatry, Yale School of Medicine, Yale University, West Haven, CT USA ,Veteran Affairs CT Healthcare System, West Haven, CT USA
| | - Robert J. Ursano
- grid.265436.00000 0001 0421 5525Center for the Study of Traumatic Stress, Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD USA
| | - Ronald C. Kessler
- grid.38142.3c000000041936754XDepartment of Health Care Policy, Harvard Medical School, Boston, MA USA
| | - Henry R. Kranzler
- grid.25879.310000 0004 1936 8972University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA ,grid.410355.60000 0004 0420 350XCrescenz Veterans Affairs Medical Center, Philadelphia, PA USA
| | - Murray B. Stein
- grid.266100.30000 0001 2107 4242Department of Psychiatry, School of Medicine, University of California, San Diego, La Jolla, CA USA ,grid.410371.00000 0004 0419 2708Psychiatry Service, Veterans Affairs San Diego Healthcare System, San Diego, CA USA
| | - Joel Gelernter
- grid.47100.320000000419368710Department of Psychiatry, Yale School of Medicine, Yale University, West Haven, CT USA ,Veteran Affairs CT Healthcare System, West Haven, CT USA ,grid.47100.320000000419368710Departments of Genetics and Neuroscience, Yale University School of Medicine, New Haven, CT 06510 USA
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Suzuki H, Nakamura Y, Matsuo K, Imaeda N, Goto C, Narita A, Shimizu A, Takashima N, Matsui K, Miura K, Nakatochi M, Hishida A, Tamura T, Kadomatsu Y, Okada R, Nishida Y, Shimanoe C, Nishimoto D, Takezaki T, Oze I, Ito H, Ikezaki H, Murata M, Matsui D, Ozaki E, Mikami H, Nakamura Y, Suzuki S, Watanabe M, Arisawa K, Uemura H, Kuriki K, Momozawa Y, Kubo M, Kita Y, Takeuchi K, Wakai K. A genome-wide association study in Japanese identified one variant associated with a preference for a Japanese dietary pattern. Eur J Clin Nutr 2020; 75:937-945. [PMID: 33281188 DOI: 10.1038/s41430-020-00823-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 11/02/2020] [Accepted: 11/19/2020] [Indexed: 01/23/2023]
Abstract
BACKGROUND/OBJECTIVES Individual eating habits may be influenced by genetic factors, in addition to environmental factors. Previous studies suggested that adherence to Japanese food patterns was associated with a decreased risk of all-cause and cardiovascular disease mortality. We conducted a genome-wide association study (GWAS) in a Japanese population to find genetic variations that affect adherence to a Japanese food pattern. SUBJECTS/METHODS We analyzed GWAS data using 14,079 participants from the Japan Multi-Institutional Collaborative Cohort study. We made a Japanese food score based on six food groups. Association of the imputed variants with the Japanese food score was performed by linear regression analysis with adjustments for age, sex, total energy intake, alcohol intake (g/day), and principal components 1-10 omitting variants in the major histocompatibility region. RESULTS We found one SNP in the 14q11.2 locus that was significantly associated with the Japanese food score with P values <5 × 10-8. Functional annotation revealed that the expression levels of two genes (BCL2L2, SLC22A17) were significantly inversely associated with this SNP. These genes are known to be related to olfaction and obesity. CONCLUSION We found a new SNP that was associated with the Japanese food score in a Japanese population. This SNP is inversely associated with genes link to olfaction and obesity.
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Affiliation(s)
- Harumitsu Suzuki
- Center for Epidemiologic Research in Asia, Shiga University of Medical Science, Otsu, Japan.,Department of Hygiene, Wakayama Medical University, Wakayama, Japan
| | - Yasuyuki Nakamura
- Yamashina Racto Clinic and Medical Examination Center, Kyoto, Japan. .,Department of Public Health, Shiga University of Medical Science, Otsu, Japan.
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nahomi Imaeda
- Department of Nutrition, Faculty of Wellness, Shigakkan University, Obu, Japan.,Department of Public Health, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Chiho Goto
- Department of Public Health, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan.,Department of Health and Nutrition, School of Health and Human Life, Nagoya Bunri University, Inazawa, Japan
| | - Akira Narita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Atsushi Shimizu
- Division of Biomedical Information Analysis, Institute for Biomedical Sciences, Iwate Medical University, Shiwa-gun, Iwate, Japan
| | - Naoyuki Takashima
- Department of Public Health, Shiga University of Medical Science, Otsu, Japan.,Department of Public Health, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Kenji Matsui
- Division of Bioethics and Healthcare Law, the National Cancer Center, Tokyo, Japan
| | - Katsuyuki Miura
- Center for Epidemiologic Research in Asia, Shiga University of Medical Science, Otsu, Japan.,Department of Public Health, Shiga University of Medical Science, Otsu, Japan
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Asahi Hishida
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takashi Tamura
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Kadomatsu
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Rieko Okada
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuichiro Nishida
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | | | - Daisaku Nishimoto
- School of Health Sciences, Faculty of Medicine, Kagoshima University, Kagoshima, Japan
| | - Toshiro Takezaki
- Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Isao Oze
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Hidemi Ito
- Division of Cancer Information and Control, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Descriptive Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroaki Ikezaki
- Department of General Internal Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Masayuki Murata
- Department of General Internal Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Daisuke Matsui
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Etsuko Ozaki
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Haruo Mikami
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Yohko Nakamura
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Sadao Suzuki
- Department of Public Health, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Miki Watanabe
- Department of Public Health, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Kokichi Arisawa
- Department of Preventive Medicine, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Hirokazu Uemura
- Department of Preventive Medicine, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan.,Department of Health and Welfare System, College of Nursing Art and Science, University of Hyogo, Akashi, Japan
| | - Kiyonori Kuriki
- Laboratory of Public Health, School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Yoshikuni Kita
- Department of Public Health, Shiga University of Medical Science, Otsu, Japan.,Faculty of Nursing Science, Tsuruga Nursing University, Tsuruga, Japan
| | - Kenji Takeuchi
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
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40
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Stovitz SD, Banack HR, Kaufman JS. Selection bias can creep into unselected cohorts and produce counterintuitive findings. Int J Obes (Lond) 2020; 45:276-277. [PMID: 33235356 DOI: 10.1038/s41366-020-00720-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 09/27/2020] [Accepted: 11/05/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Steven D Stovitz
- Department of Family Medicine and Community Health, University of Minnesota, Minneapolis, Minnesota, USA.
| | - Hailey R Banack
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, The State University of New York, New York, New York, USA
| | - Jay S Kaufman
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
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41
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Mangantig E, MacGregor S, Iles MM, Scolyer RA, Cust AE, Hayward NK, Montgomery GW, Duffy DL, Thompson JF, Henders A, Bowdler L, Rowe C, Cadby G, Mann GJ, Whiteman DC, Long GV, Ward SV, Khosrotehrani K, Barrett JH, Law MH. Germline variants are associated with increased primary melanoma tumor thickness at diagnosis. Hum Mol Genet 2020; 29:3578-3587. [PMID: 33410475 PMCID: PMC7788289 DOI: 10.1093/hmg/ddaa222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/29/2020] [Accepted: 10/08/2020] [Indexed: 11/13/2022] Open
Abstract
Germline genetic variants have been identified, which predispose individuals and families to develop melanoma. Tumor thickness is the strongest predictor of outcome for clinically localized primary melanoma patients. We sought to determine whether there is a heritable genetic contribution to variation in tumor thickness. If confirmed, this will justify the search for specific genetic variants influencing tumor thickness. To address this, we estimated the proportion of variation in tumor thickness attributable to genome-wide genetic variation (variant-based heritability) using unrelated patients with measured primary cutaneous melanoma thickness. As a secondary analysis, we conducted a genome-wide association study (GWAS) of tumor thickness. The analyses utilized 10 604 individuals with primary cutaneous melanoma drawn from nine GWAS datasets from eight cohorts recruited from the general population, primary care and melanoma treatment centers. Following quality control and filtering to unrelated individuals with study phenotypes, 8125 patients were used in the primary analysis to test whether tumor thickness is heritable. An expanded set of 8505 individuals (47.6% female) were analyzed for the secondary GWAS meta-analysis. Analyses were adjusted for participant age, sex, cohort and ancestry. We found that 26.6% (SE 11.9%, P = 0.0128) of variation in tumor thickness is attributable to genome-wide genetic variation. While requiring replication, a chromosome 11 locus was associated (P < 5 × 10−8) with tumor thickness. Our work indicates that sufficiently large datasets will enable the discovery of genetic variants associated with greater tumor thickness, and this will lead to the identification of host biological processes influencing melanoma growth and invasion.
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Affiliation(s)
- Ernest Mangantig
- Regenerative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200, Pulau Pinang, Malaysia
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
| | - Mark M Iles
- Leeds Institute for Data Analytics, University of Leeds, Leeds LS2 9JT, UK
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, 2065, Australia.,Department of Tissue Oncology and Diagnostic Pathology, Royal Prince Alfred Hospital, Sydney, New South Wales, 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2050, Australia.,Department of Tissue Oncology and Diagnostic Pathology, New South Wales Health Pathology, Sydney, New South Wales, 2000, Australia
| | - Anne E Cust
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, 2065, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2050, Australia.,School of Public Health, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Nicholas K Hayward
- Oncogenomics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
| | - Grant W Montgomery
- Molecular Biology, The University of Queensland, Brisbane, Queensland, 4102, Australia
| | - David L Duffy
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
| | - John F Thompson
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, 2065, Australia.,Department of Tissue Oncology and Diagnostic Pathology, Royal Prince Alfred Hospital, Sydney, New South Wales, 2050, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2050, Australia
| | - Anjali Henders
- Molecular Biology, The University of Queensland, Brisbane, Queensland, 4102, Australia.,Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
| | - Lisa Bowdler
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
| | - Casey Rowe
- Experimental Dermatology Group, Diamantina Institute, The University of Queensland, Brisbane, Queensland, 4102, Australia.,Department of Dermatology, Princess Alexandra Hospital, Brisbane, Queensland, 4102, Australia
| | - Gemma Cadby
- School of Population and Global Health, The University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Graham J Mann
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, 2065, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, University of Sydney, New South Wales, 2145, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - David C Whiteman
- Cancer Control, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, 2065, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, 2050, Australia.,Department of Medical Oncology, Mater Hospital, North Sydney, NSW, 2060, Australia.,Department of Medical Oncology, Royal North Shore Hospital, St Leonards, New South Wales, 2065, Australia
| | - Sarah V Ward
- School of Population and Global Health, The University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Kiarash Khosrotehrani
- Experimental Dermatology Group, Diamantina Institute, The University of Queensland, Brisbane, Queensland, 4102, Australia.,Department of Dermatology, Princess Alexandra Hospital, Brisbane, Queensland, 4102, Australia
| | - Jennifer H Barrett
- Leeds Institute for Data Analytics, University of Leeds, Leeds LS2 9JT, UK
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
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42
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Kraft P, Chen H, Lindström S. The Use Of Genetic Correlation And Mendelian Randomization Studies To Increase Our Understanding of Relationships Between Complex Traits. CURR EPIDEMIOL REP 2020; 7:104-112. [PMID: 33552841 PMCID: PMC7863746 DOI: 10.1007/s40471-020-00233-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF THE REVIEW Increasing access to large-scale genetic datasets in population-based studies allows for genetic association studies as a means to examine previously known and novel relationships among complex traits. In this review, we discuss two widely used approaches to leverage genetic data to study the links between traits: Genome-wide genetic correlation and Mendelian Randomization (MR) studies. RECENT FINDINGS Both genetic correlation and MR studies have provided important novel insights. However, although they are less sensitive to many sources of bias present in traditional, observational epidemiology, they still rely on assumptions that in practice might be difficult to assess. To overcome this, development of novel methods less sensitive to these assumptions is an active area of research. SUMMARY We believe that as population-based genetic datasets grow larger and novel methods allowing for weaker forms of current assumptions become available, genetic correlation and MR studies will become an integral part of genetic epidemiology studies.
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Affiliation(s)
- Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Hongjie Chen
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Sara Lindström
- Department of Epidemiology, University of Washington, Seattle, WA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
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43
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Mosley JD, Levinson RT, Farber-Eger E, Edwards TL, Hellwege JN, Hung AM, Giri A, Shuey MM, Shaffer CM, Shi M, Brittain EL, Chung WK, Kullo IJ, Arruda-Olson AM, Jarvik GP, Larson EB, Crosslin DR, Williams MS, Borthwick KM, Hakonarson H, Denny JC, Wang TJ, Stein CM, Roden DM, Wells QS. The polygenic architecture of left ventricular mass mirrors the clinical epidemiology. Sci Rep 2020; 10:7561. [PMID: 32372017 PMCID: PMC7200691 DOI: 10.1038/s41598-020-64525-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 04/16/2020] [Indexed: 02/07/2023] Open
Abstract
Left ventricular (LV) mass is a prognostic biomarker for incident heart disease and all-cause mortality. Large-scale genome-wide association studies have identified few SNPs associated with LV mass. We hypothesized that a polygenic discovery approach using LV mass measurements made in a clinical population would identify risk factors and diseases associated with adverse LV remodeling. We developed a polygenic single nucleotide polymorphism-based predictor of LV mass in 7,601 individuals with LV mass measurements made during routine clinical care. We tested for associations between this predictor and 894 clinical diagnoses measured in 58,838 unrelated genotyped individuals. There were 29 clinical phenotypes associated with the LV mass genetic predictor at FDR q < 0.05. Genetically predicted higher LV mass was associated with modifiable cardiac risk factors, diagnoses related to organ dysfunction and conditions associated with abnormal cardiac structure including heart failure and atrial fibrillation. Secondary analyses using polygenic predictors confirmed a significant association between higher LV mass and body mass index and, in men, associations with coronary atherosclerosis and systolic blood pressure. In summary, these analyses show that LV mass-associated genetic variability associates with diagnoses of cardiac diseases and with modifiable risk factors which contribute to these diseases.
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Affiliation(s)
- Jonathan D Mosley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Rebecca T Levinson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric Farber-Eger
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Todd L Edwards
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jacklyn N Hellwege
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Tennessee Valley Healthcare System (626), Vanderbilt University, Nashville, TN, USA
| | - Adriana M Hung
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Tennessee Valley Healthcare System (626), Vanderbilt University, Nashville, TN, USA
| | - Ayush Giri
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA
- Institute for Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Megan M Shuey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christian M Shaffer
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mingjian Shi
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Evan L Brittain
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wendy K Chung
- Office of Research & Development, Department of Veterans Affairs, Washington DC, DC, USA
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | | | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA, USA
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute and Department of Medicine, University of Washington, Seattle, WA, USA
| | - David R Crosslin
- Departments of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | | | - Ken M Borthwick
- Biomedical and Translational Informatics, Geisinger, Danville, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Joshua C Denny
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Institute for Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Thomas J Wang
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Charles M Stein
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Quinn S Wells
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
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44
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Persyn E, Hanscombe KB, Howson JMM, Lewis CM, Traylor M, Markus HS. Genome-wide association study of MRI markers of cerebral small vessel disease in 42,310 participants. Nat Commun 2020; 11:2175. [PMID: 32358547 PMCID: PMC7195435 DOI: 10.1038/s41467-020-15932-3] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 03/24/2020] [Indexed: 12/24/2022] Open
Abstract
Cerebral small vessel disease is a major cause of stroke and dementia, but its genetic basis is incompletely understood. We perform a genetic study of three MRI markers of the disease in UK Biobank imaging data and other sources: white matter hyperintensities (N = 42,310), fractional anisotropy (N = 17,663) and mean diffusivity (N = 17,467). Our aim is to better understand the disease pathophysiology. Across the three traits, we identify 31 loci, of which 21 were previously unreported. We perform a transcriptome-wide association study to identify associations with gene expression in relevant tissues, identifying 66 associated genes across the three traits. This genetic study provides insights into the understanding of the biological mechanisms underlying small vessel disease.
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Affiliation(s)
- Elodie Persyn
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Ken B Hanscombe
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Joanna M M Howson
- BHF, Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Novo Nordisk Research Centre Oxford, Innovation Building, Old Road Campus, Roosevelt Drive, Oxford, UK
| | - Cathryn M Lewis
- Department of Medical and Molecular Genetics, King's College London, London, UK
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Matthew Traylor
- Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Hugh S Markus
- Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
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45
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Revez JA, Lin T, Qiao Z, Xue A, Holtz Y, Zhu Z, Zeng J, Wang H, Sidorenko J, Kemper KE, Vinkhuyzen AAE, Frater J, Eyles D, Burne THJ, Mitchell B, Martin NG, Zhu G, Visscher PM, Yang J, Wray NR, McGrath JJ. Genome-wide association study identifies 143 loci associated with 25 hydroxyvitamin D concentration. Nat Commun 2020; 11:1647. [PMID: 32242144 PMCID: PMC7118120 DOI: 10.1038/s41467-020-15421-7] [Citation(s) in RCA: 204] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/03/2020] [Indexed: 02/07/2023] Open
Abstract
Vitamin D deficiency is a candidate risk factor for a range of adverse health outcomes. In a genome-wide association study of 25 hydroxyvitamin D (25OHD) concentration in 417,580 Europeans we identify 143 independent loci in 112 1-Mb regions, providing insights into the physiology of vitamin D and implicating genes involved in lipid and lipoprotein metabolism, dermal tissue properties, and the sulphonation and glucuronidation of 25OHD. Mendelian randomization models find no robust evidence that 25OHD concentration has causal effects on candidate phenotypes (e.g. BMI, psychiatric disorders), but many phenotypes have (direct or indirect) causal effects on 25OHD concentration, clarifying the epidemiological relationship between 25OHD status and the health outcomes examined in this study.
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Affiliation(s)
- Joana A Revez
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Zhen Qiao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Angli Xue
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Yan Holtz
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Zhihong Zhu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Huanwei Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Julia Sidorenko
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Kathryn E Kemper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Anna A E Vinkhuyzen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Julanne Frater
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Darryl Eyles
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD, Australia
| | - Thomas H J Burne
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD, Australia
| | - Brittany Mitchell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | | | - Gu Zhu
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Institute for Advanced Research, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
| | - John J McGrath
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD, Australia.
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.
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46
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Marini S, Merino J, Montgomery BE, Malik R, Sudlow CL, Dichgans M, Florez JC, Rosand J, Gill D, Anderson CD. Mendelian Randomization Study of Obesity and Cerebrovascular Disease. Ann Neurol 2020; 87:516-524. [PMID: 31975536 PMCID: PMC7392199 DOI: 10.1002/ana.25686] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 01/19/2020] [Accepted: 01/20/2020] [Indexed: 01/05/2023]
Abstract
OBJECTIVE To systematically investigate causal relationships between obesity and cerebrovascular disease and the extent to which hypertension and hyperglycemia mediate the effect of obesity on cerebrovascular disease. METHODS We used summary statistics from genome-wide association studies for body mass index (BMI), waist-to-hip ratio (WHR), and multiple cerebrovascular disease phenotypes. We explored causal associations with 2-sample Mendelian randomization (MR) accounting for genetic covariation between BMI and WHR, and we assessed what proportion of the association between obesity and cerebrovascular disease was mediated by systolic blood pressure (SBP) and blood glucose levels, respectively. RESULTS Genetic predisposition to higher BMI did not increase the risk of cerebrovascular disease. In contrast, for each 10% increase in WHR there was a 75% increase (95% confidence interval [CI] = 44-113%) in risk for large artery ischemic stroke, a 57% (95% CI = 29-91%) increase in risk for small vessel ischemic stroke, a 197% increase (95% CI = 59-457%) in risk of intracerebral hemorrhage, and an increase in white matter hyperintensity volume (β = 0.11, 95% CI = 0.01-0.21). These WHR associations persisted after adjusting for genetic determinants of BMI. Approximately one-tenth of the observed effect of WHR was mediated by SBP for ischemic stroke (proportion mediated: 12%, 95% CI = 4-20%), but no evidence of mediation was found for average blood glucose. INTERPRETATION Abdominal adiposity may trigger causal pathological processes, partially independent from blood pressure and totally independent from glucose levels, that lead to cerebrovascular disease. Potential targets of these pathological processes could represent novel therapeutic opportunities for stroke. ANN NEUROL 2020;87:516-524.
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Affiliation(s)
- Sandro Marini
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Boston University Medical Center, Boston, MA, USA
| | - Jordi Merino
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Vascular Medicine and Metabolism Unit, Research Unit on Lipids and Atherosclerosis, Sant Joan University Hospital, Universitat Rovira i Virgili, IISPV, CIBERDEM, Reus, Spain
| | | | - Rainer Malik
- Institute for Stroke and Dementia Research (ISD), University Hospital of Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Catherine L. Sudlow
- Centre for Medical Informatics, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), University Hospital of Ludwig-Maximilians-University (LMU), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- German Centre for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Jose C. Florez
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jonathan Rosand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Henry and Allison McCance Center for Brain Health, Massachusetts General Hospital, Boston, MA, USA
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Christopher D. Anderson
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Henry and Allison McCance Center for Brain Health, Massachusetts General Hospital, Boston, MA, USA
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47
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Agler CS, Divaris K. Sources of bias in genomics research of oral and dental traits. COMMUNITY DENTAL HEALTH 2020; 37:102-106. [PMID: 32031351 PMCID: PMC7316399 DOI: 10.1922/cdh_specialissue_divaris05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Evidence regarding the genomic basis of oral/dental traits and diseases is a fundamental pillar of the emerging notion of precision health. During the last decade, technological advances have improved the feasibility and affordability of conducting genome-wide association studies (GWAS) and studying the associations of emanating data with both common and rare oral conditions. Most evidence thus far emanates from GWAS of dental caries and periodontal disease that have tested the associations of several million single nucleotide polymorphisms (SNPs) with typically binary, health vs. disease phenotypes. GWAS offer advantages over the previous candidate-gene studies, mainly owing to their agnostic (i.e., unbiased, or hypothesis-free) nature. Nevertheless, GWAS are prone to virtually all sources of random and systematic error. Here, we review common sources of bias in genomics research with focus on GWAS including: type I and II errors, population stratification and heterogeneity, selection bias, adjustment for heritable covariates, appropriate reference panels for imputation, and gene annotation. We argue that valid and precise phenotype measurement is a key requirement, as GWAS sample sizes and thus statistical power increase. Finally, we stress that the lack of diversity of populations with phenotypes and genotypes is a major limitation for the generalizability and ultimate translation of the emerging genomics evidence-base into oral health promotion for all.
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Affiliation(s)
- Cary S Agler
- Adams School of Dentistry, University of North Carolina Chapel Hill, Chapel Hill, NC, United States
| | - Kimon Divaris
- Adams School of Dentistry, University of North Carolina Chapel Hill, Chapel Hill, NC, United States
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48
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Ruth KS, Day FR, Tyrrell J, Thompson DJ, Wood AR, Mahajan A, Beaumont RN, Wittemans L, Martin S, Busch AS, Erzurumluoglu AM, Hollis B, O'Mara TA, McCarthy MI, Langenberg C, Easton DF, Wareham NJ, Burgess S, Murray A, Ong KK, Frayling TM, Perry JRB. Using human genetics to understand the disease impacts of testosterone in men and women. Nat Med 2020; 26:252-258. [PMID: 32042192 PMCID: PMC7025895 DOI: 10.1038/s41591-020-0751-5] [Citation(s) in RCA: 338] [Impact Index Per Article: 84.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/03/2020] [Indexed: 11/20/2022]
Abstract
Testosterone supplementation is commonly used for its effects on sexual function, bone health and body composition, yet its effects on disease outcomes are unknown. To better understand this, we identified genetic determinants of testosterone levels and related sex hormone traits in 425,097 UK Biobank study participants. Using 2,571 genome-wide significant associations, we demonstrate that the genetic determinants of testosterone levels are substantially different between sexes and that genetically higher testosterone is harmful for metabolic diseases in women but beneficial in men. For example, a genetically determined 1 s.d. higher testosterone increases the risks of type 2 diabetes (odds ratio (OR) = 1.37 (95% confidence interval (95% CI): 1.22-1.53)) and polycystic ovary syndrome (OR = 1.51 (95% CI: 1.33-1.72)) in women, but reduces type 2 diabetes risk in men (OR = 0.86 (95% CI: 0.76-0.98)). We also show adverse effects of higher testosterone on breast and endometrial cancers in women and prostate cancer in men. Our findings provide insights into the disease impacts of testosterone and highlight the importance of sex-specific genetic analyses.
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Affiliation(s)
- Katherine S Ruth
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Felix R Day
- Medical Research Council (MRC) Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Jessica Tyrrell
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Andrew R Wood
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Robin N Beaumont
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Laura Wittemans
- Medical Research Council (MRC) Epidemiology Unit, University of Cambridge, Cambridge, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Susan Martin
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Alexander S Busch
- Medical Research Council (MRC) Epidemiology Unit, University of Cambridge, Cambridge, UK
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health, University of Copenhagen, Copenhagen, Denmark
- Department of Growth and Reproduction, University of Copenhagen, Copenhagen, Denmark
| | - A Mesut Erzurumluoglu
- Medical Research Council (MRC) Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Benjamin Hollis
- Medical Research Council (MRC) Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Tracy A O'Mara
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- Genentech, San Francisco, CA, USA
| | - Claudia Langenberg
- Medical Research Council (MRC) Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Nicholas J Wareham
- Medical Research Council (MRC) Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- BHF Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Anna Murray
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Ken K Ong
- Medical Research Council (MRC) Epidemiology Unit, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | | | - John R B Perry
- Medical Research Council (MRC) Epidemiology Unit, University of Cambridge, Cambridge, UK.
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Martin AR, Daly MJ, Robinson EB, Hyman SE, Neale BM. Predicting Polygenic Risk of Psychiatric Disorders. Biol Psychiatry 2019; 86:97-109. [PMID: 30737014 PMCID: PMC6599546 DOI: 10.1016/j.biopsych.2018.12.015] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 11/18/2018] [Accepted: 12/08/2018] [Indexed: 12/27/2022]
Abstract
Genetics provides two major opportunities for understanding human disease-as a transformative line of etiological inquiry and as a biomarker for heritable diseases. In psychiatry, biomarkers are very much needed for both research and treatment, given the heterogenous populations identified by current phenomenologically based diagnostic systems. To date, however, useful and valid biomarkers have been scant owing to the inaccessibility and complexity of human brain tissue and consequent lack of insight into disease mechanisms. Genetic biomarkers are therefore especially promising for psychiatric disorders. Genome-wide association studies of common diseases have matured over the last decade, generating the knowledge base for increasingly informative individual-level genetic risk prediction. In this review, we discuss fundamental concepts involved in computing genetic risk with current methods, strengths and weaknesses of various approaches, assessments of utility, and applications to various psychiatric disorders and related traits. Although genetic risk prediction has become increasingly straightforward to apply and common in published studies, there are important pitfalls to avoid. At present, the clinical utility of genetic risk prediction is still low; however, there is significant promise for future clinical applications as the ancestral diversity and sample sizes of genome-wide association studies increase. We discuss emerging data and methods aimed at improving the value of genetic risk prediction for disentangling disease mechanisms and stratifying subjects for epidemiological and clinical studies. For all applications, it is absolutely critical that polygenic risk prediction is applied with appropriate methodology and control for confounding to avoid repeating some mistakes of the candidate gene era.
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Affiliation(s)
- Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts.
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Elise B Robinson
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Steven E Hyman
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
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50
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Spracklen CN, Karaderi T, Yaghootkar H, Schurmann C, Fine RS, Kutalik Z, Preuss MH, Lu Y, Wittemans LBL, Adair LS, Allison M, Amin N, Auer PL, Bartz TM, Blüher M, Boehnke M, Borja JB, Bork-Jensen J, Broer L, Chasman DI, Chen YDI, Chirstofidou P, Demirkan A, van Duijn CM, Feitosa MF, Garcia ME, Graff M, Grallert H, Grarup N, Guo X, Haesser J, Hansen T, Harris TB, Highland HM, Hong J, Ikram MA, Ingelsson E, Jackson R, Jousilahti P, Kähönen M, Kizer JR, Kovacs P, Kriebel J, Laakso M, Lange LA, Lehtimäki T, Li J, Li-Gao R, Lind L, Luan J, Lyytikäinen LP, MacGregor S, Mackey DA, Mahajan A, Mangino M, Männistö S, McCarthy MI, McKnight B, Medina-Gomez C, Meigs JB, Molnos S, Mook-Kanamori D, Morris AP, de Mutsert R, Nalls MA, Nedeljkovic I, North KE, Pennell CE, Pradhan AD, Province MA, Raitakari OT, Raulerson CK, Reiner AP, Ridker PM, Ripatti S, Roberston N, Rotter JI, Salomaa V, Sandoval-Zárate AA, Sitlani CM, Spector TD, Strauch K, Stumvoll M, Taylor KD, Thuesen B, Tönjes A, Uitterlinden AG, Venturini C, Walker M, Wang CA, Wang S, Wareham NJ, Willems SM, Willems van Dijk K, Wilson JG, Wu Y, Yao J, Young KL, Langenberg C, Frayling TM, Kilpeläinen TO, Lindgren CM, Loos RJF, Mohlke KL. Exome-Derived Adiponectin-Associated Variants Implicate Obesity and Lipid Biology. Am J Hum Genet 2019; 105:15-28. [PMID: 31178129 DOI: 10.1016/j.ajhg.2019.05.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/30/2019] [Indexed: 12/25/2022] Open
Abstract
Circulating levels of adiponectin, an adipocyte-secreted protein associated with cardiovascular and metabolic risk, are highly heritable. To gain insights into the biology that regulates adiponectin levels, we performed an exome array meta-analysis of 265,780 genetic variants in 67,739 individuals of European, Hispanic, African American, and East Asian ancestry. We identified 20 loci associated with adiponectin, including 11 that had been reported previously (p < 2 × 10-7). Comparison of exome array variants to regional linkage disequilibrium (LD) patterns and prior genome-wide association study (GWAS) results detected candidate variants (r2 > .60) spanning as much as 900 kb. To identify potential genes and mechanisms through which the previously unreported association signals act to affect adiponectin levels, we assessed cross-trait associations, expression quantitative trait loci in subcutaneous adipose, and biological pathways of nearby genes. Eight of the nine loci were also associated (p < 1 × 10-4) with at least one obesity or lipid trait. Candidate genes include PRKAR2A, PTH1R, and HDAC9, which have been suggested to play roles in adipocyte differentiation or bone marrow adipose tissue. Taken together, these findings provide further insights into the processes that influence circulating adiponectin levels.
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Affiliation(s)
- Cassandra N Spracklen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tugce Karaderi
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7FZ, UK; Department of Biological Sciences, Faculty of Arts and Sciences, Eastern Mediterranean University, Famagusta, Cyprus; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; DTU Health Technology, Technical University of Denmark, Lyngby 2800, Denmark
| | - Hanieh Yaghootkar
- Genetics of Complex Traits, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter EX2 5DW, UK; Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, UK
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rebecca S Fine
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zoltan Kutalik
- Genetics of Complex Traits, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter EX2 5DW, UK; University Center for Primary Care and Public Health, University of Lausanne, Lausanne 1010, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN 37203-1738, USA; Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura B L Wittemans
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7FZ, UK; MRC Epidemiology Unit, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Linda S Adair
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Matthew Allison
- Department of Family Medicine and Public Health, University of California, San Diego, CA 92093, USA
| | - Najaf Amin
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Paul L Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA; Department of Biostatistics, University of Washington, Seattle, WA 98101, USA
| | - Matthias Blüher
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig, Leipzig 4103, Germany
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Judith B Borja
- Office of Population Studies Foundation, Inc, Cebu City, Philippines; Department of Nutrition and Dietetics, University of San Carlos, Cebu City, Philippines
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Linda Broer
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Paraskevi Chirstofidou
- Department of Twin Research and Genetic Epidemiology, Kings College London, London SE1 7EH, UK
| | - Ayse Demirkan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Melissa E Garcia
- National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Carolina Center for Genome Sciences, Chapel Hill, NC 27599, USA
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, München-Neuherberg 85764, Germany; German Center for Diabetes Research, München-Neuherberg 85765, Germany
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Jeffrey Haesser
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Tamara B Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIH, Bethesda, MD 20892, USA
| | - Heather M Highland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jaeyoung Hong
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 2118, USA
| | - M Arfan Ikram
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands
| | - Erik Ingelsson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Palo Alto, CA 94304, USA; Stanford Cardiovascular Institute, Stanford University of Medicine, Palo Alto, CA 94304, USA; Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala 75185, Sweden; Stanford Diabetes Research Center, Stanford University, Stanford, CA 94305, USA
| | - Rebecca Jackson
- Division of Endocrinology, Diabetes, and Metabolism, Ohio State University, Columbus, OH 43210, USA
| | - Pekka Jousilahti
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere 33522, Finland; Department of Clinical Physiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33522, Finland
| | - Jorge R Kizer
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig, Leipzig 4103, Germany
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, München-Neuherberg 85764, Germany; German Center for Diabetes Research, München-Neuherberg 85765, Germany
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University of Hospital, Kuopio 70029 KYS, Finland
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado-Denver, Denver, CO 80045, USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33522, Finland
| | - Jin Li
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala 75185, Sweden
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33522, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33521, Finland
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - David A Mackey
- Faculty of Health and Medical Sciences, The University of Western Australia, Perth, WA 6009, Australia; Centre for Ophthalmology and Visual Science, Lions Eye Institute, The University of Western Australia, Perth, WA 6009, Australia
| | - Anubha Mahajan
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7FZ, UK; Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, Kings College London, London SE1 7EH, UK; NIHR Biomedical Research Centre, Guy's and St Thomas' Foundation Trust, London SE1 9RT, UK
| | - Satu Männistö
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Mark I McCarthy
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7FZ, UK; Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford OX3 7FZ, UK
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, WA 98101, USA
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands
| | - James B Meigs
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Program in Population and Medical Genetics, Broad Institute, Cambridge, MA 02114, USA
| | - Sophie Molnos
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, München-Neuherberg 85764, Germany; German Center for Diabetes Research, München-Neuherberg 85765, Germany
| | - Dennis Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands; Department of Public Health and Primary Care, Leiden University Medical Center, Leiden 2334 ZA, the Netherlands
| | - Andrew P Morris
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7FZ, UK; Department of Biostatistics, University of Liverpool, Liverpool L69 3GL, UK
| | - Renee de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA; Data Tecnica International, Glen Echo, MD 20812, USA
| | - Ivana Nedeljkovic
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Craig E Pennell
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Newcastle, NSW 2305, Australia
| | - Aruna D Pradhan
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland; Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Chelsea K Raulerson
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alex P Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Samuli Ripatti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Public Health, University of Helsinki, Helsinki 00014, Finland; Institute for Molecular Medicine Finland, Helsinki 00014, Finland
| | - Neil Roberston
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7FZ, UK; Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Veikko Salomaa
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki 00271, Finland
| | | | - Colleen M Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, Kings College London, London SE1 7EH, UK
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany; Chair of Genetic Epidemiology, Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich 81377, Germany
| | - Michael Stumvoll
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig, Leipzig 4103, Germany
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Betina Thuesen
- Center for Clinical Research and Disease Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen 2400, Denmark
| | - Anke Tönjes
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig, Leipzig 4103, Germany
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands
| | - Cristina Venturini
- Department of Twin Research and Genetic Epidemiology, Kings College London, London SE1 7EH, UK
| | - Mark Walker
- Institute of Cellular Medicine, The Medical School, Newcastle University, Newcastle, UK
| | - Carol A Wang
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Newcastle, NSW 2305, Australia
| | - Shuai Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 2118, USA
| | | | - Sara M Willems
- MRC Epidemiology Unit, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Ko Willems van Dijk
- Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden 2333 ZA, the Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Ying Wu
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter EX2 5DW, UK
| | - Tuomas O Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Cecilia M Lindgren
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7FZ, UK; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Ichan School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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