1201
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Díaz-Peña R, Boekstegers F, Silva RS, Jaime S, Hosgood HD, Miravitlles M, Agustí À, Lorenzo Bermejo J, Olloquequi J. Amerindian Ancestry Influences Genetic Susceptibility to Chronic Obstructive Pulmonary Disease. J Pers Med 2020; 10:jpm10030093. [PMID: 32824824 PMCID: PMC7565405 DOI: 10.3390/jpm10030093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 12/21/2022] Open
Abstract
The contribution of genetic ancestry on chronic obstructive pulmonary disease (COPD) predisposition remains unclear. To explore this relationship, we analyzed the associations between 754,159 single nucleotide polymorphisms (SNPs) and risk of COPD (n = 214 cases, 193 healthy controls) in Talca, Chile, considering the genetic ancestry and established risk factors. The proportion of Mapuche ancestry (PMA) was based on a panel of 45 Mapuche reference individuals. Five PRDM15 SNPs and two PPP1R12B SNPs were associate with COPD risk (p = 0.05 to 5×10-4) in those individuals with lower PMA. Based on linkage disequilibrium and sliding window analyses, an adjacent PRDM15 SNPs were associated with COPD risk in the lower PMA group (p = 10-3 to 3.77×10-8). Our study is the first to report an association between PPP1R12B and COPD risk, as well as effect modification between ethnicity and PRDM15 SNPs in determining COPD risk. Our results are biologically plausible given that PPP1R12B and PRDM15 are involved in immune dysfunction and autoimmunity, providing mechanistic evidence for COPD pathogenesis and highlighting the importance to conduct more genome wide association studies (GWAS) in admixed populations with Amerindian descent.
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Affiliation(s)
- Roberto Díaz-Peña
- Laboratory of Cellular and Molecular Pathology, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca 3460000, Chile;
- Liquid Biopsy Analysis Unit, Oncomet, Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
| | - Felix Boekstegers
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, 69126 Heidelberg, Germany; (F.B.); (J.L.B.)
| | - Rafael S. Silva
- Unidad Respiratorio, Centro de Diagnóstico Terapéutico, Hospital Regional de Talca, Talca 3460000, Chile; (R.S.S.); (S.J.)
| | - Sergio Jaime
- Unidad Respiratorio, Centro de Diagnóstico Terapéutico, Hospital Regional de Talca, Talca 3460000, Chile; (R.S.S.); (S.J.)
| | - H. Dean Hosgood
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
| | - Marc Miravitlles
- Pneumology Department, Hospital Universitari Vall d’Hebron/Vall d’Hebron Institut de Recerca (VHIR), CIBER Enfermedades Respiratorias (CIBERES), 08035 Barcelona, Spain;
| | - Àlvar Agustí
- Respiratory Institute, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, CIBER Enfermedades Respiratorias (CIBERES), 08036 Barcelona, Spain;
| | - Justo Lorenzo Bermejo
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, 69126 Heidelberg, Germany; (F.B.); (J.L.B.)
| | - Jordi Olloquequi
- Laboratory of Cellular and Molecular Pathology, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca 3460000, Chile;
- Correspondence: ; Tel.: +56-71-273-5728
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1202
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Lonardo A, Leoni S, Alswat KA, Fouad Y. History of Nonalcoholic Fatty Liver Disease. Int J Mol Sci 2020; 21:E5888. [PMID: 32824337 PMCID: PMC7460697 DOI: 10.3390/ijms21165888] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 12/15/2022] Open
Abstract
Based on the assumption that characterizing the history of a disease will help in improving practice while offering a clue to research, this article aims at reviewing the history of nonalcoholic fatty liver disease (NAFLD) in adults and children. To this end, we address the history of NAFLD histopathology, which begins in 1980 with Ludwig's seminal studies, although previous studies date back to the 19th century. Moreover, the principal milestones in the definition of genetic NAFLD are summarized. Next, a specific account is given of the evolution, over time, of our understanding of the association of NAFLD with metabolic syndrome, spanning from the outdated concept of "NAFLD as a manifestation of the Metabolic Syndrome", to the more appropriate consideration that NAFLD has, with metabolic syndrome, a mutual and bi-directional relationship. In addition, we also report on the evolution from first intuitions to more recent studies, supporting NAFLD as an independent risk factor for cardiovascular disease. This association probably has deep roots, going back to ancient Middle Eastern cultures, wherein the liver had a significance similar to that which the heart holds in contemporary society. Conversely, the notions that NAFLD is a forerunner of hepatocellular carcinoma and extra-hepatic cancers is definitely more modern. Interestingly, guidelines issued by hepatological societies have lagged behind the identification of NAFLD by decades. A comparative analysis of these documents defines both shared attitudes (e.g., ultrasonography and lifestyle changes as the first approaches) and diverging key points (e.g., the threshold of alcohol consumption, screening methods, optimal non-invasive assessment of liver fibrosis and drug treatment options). Finally, the principal historical steps in the general, cellular and molecular pathogenesis of NAFLD are reviewed. We conclude that an in-depth understanding of the history of the disease permits us to better comprehend the disease itself, as well as to anticipate the lines of development of future NAFLD research.
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Affiliation(s)
- Amedeo Lonardo
- Ospedale Civile di Baggiovara, UOC Medicina Metabolica, Dipartimento di Medicina Interna Generale, d’Urgenza e post Acuzie, Azienda Ospedaliero-Universitaria di Modena, Via Giardini 1135, 41125 Modena, Italy
| | - Simona Leoni
- Internal Medicine Unit, Department of Digestive Diseases, S.Orsola-Malpighi Hospital, Via Massarenti 9, 40136 Bologna, Italy;
| | - Khalid A. Alswat
- Liver Research Center, Department of Medicine, College of Medicine, King Saud University, Riyadh 11322, Saudi Arabia;
| | - Yasser Fouad
- Department of Gastroenterology, Hepatology and Endemic Medicine, Faculty of Medicine, Minia University, Minya 19111, Egypt;
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1203
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Mennigen E, Bearden CE. Psychosis Risk and Development: What Do We Know From Population-Based Studies? Biol Psychiatry 2020; 88:315-325. [PMID: 32061373 PMCID: PMC7305046 DOI: 10.1016/j.biopsych.2019.12.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 11/22/2019] [Accepted: 12/11/2019] [Indexed: 12/23/2022]
Abstract
Recent years have seen an advent in population-based studies in children, adolescents, and adults that examine the prevalence, etiology, and developmental trajectories of diverse subclinical psychopathological symptoms that pose a risk for the later development of severe mental illnesses. It is increasingly recognized that most categorically defined psychiatric disorders occur on a spectrum or continuum, show high heterogeneity and symptom overlap, and share genetic and environmental risk factors. We discuss neurodevelopmental underpinnings of psychosis spectrum symptoms and review brain morphometric and functional alterations as well as genetic liability for psychosis in individuals experiencing psychotic symptoms (PSs) in the general population. With regard to brain structure and function, findings of qualitatively similar alterations in individuals experiencing subthreshold PSs and individuals with overt psychotic disorders support the notion of a psychosis continuum. However, genetic and epidemiological studies have emphasized the overlap of PSs and other psychiatric illnesses. In particular, PSs during adolescence appear to be a nonspecific precursor of different psychopathological outcomes. Given the evidence presented in this review, we argue that findings from population-based studies are appropriate to guide policy-making to further emphasize public health efforts. Broadly accessible mental health programs are promising to make a difference in the field of adolescent mental health. However, the specific efficacy of these programs warrants further study, and caution is advised to not overpathologize potentially transient occurrence of mental health problems.
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Affiliation(s)
- Eva Mennigen
- Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, California; Department of Psychiatry and Psychotherapy, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Carrie E Bearden
- Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, California; Department of Psychology, University of California, Los Angeles, Los Angeles, California.
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1204
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Wang M, Menon R, Mishra S, Patel AP, Chaffin M, Tanneeru D, Deshmukh M, Mathew O, Apte S, Devanboo CS, Sundaram S, Lakshmipathy P, Murugan S, Sharma KK, Rajendran K, Santhosh S, Thachathodiyl R, Ahamed H, Balegadde AV, Alexander T, Swaminathan K, Gupta R, Mullasari AS, Sigamani A, Kanchi M, Peterson AS, Butterworth AS, Danesh J, Di Angelantonio E, Naheed A, Inouye M, Chowdhury R, Vedam RL, Kathiresan S, Gupta R, Khera AV. Validation of a Genome-Wide Polygenic Score for Coronary Artery Disease in South Asians. J Am Coll Cardiol 2020; 76:703-714. [PMID: 32762905 PMCID: PMC7592606 DOI: 10.1016/j.jacc.2020.06.024] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 12/26/2022]
Abstract
BACKGROUND Genome-wide polygenic scores (GPS) integrate information from many common DNA variants into a single number. Because rates of coronary artery disease (CAD) are substantially higher among South Asians, a GPS to identify high-risk individuals may be particularly useful in this population. OBJECTIVES This analysis used summary statistics from a prior genome-wide association study to derive a new GPSCAD for South Asians. METHODS This GPSCAD was validated in 7,244 South Asian UK Biobank participants and tested in 491 individuals from a case-control study in Bangladesh. Next, a static ancestry and GPSCAD reference distribution was built using whole-genome sequencing from 1,522 Indian individuals, and a framework was tested for projecting individuals onto this static ancestry and GPSCAD reference distribution using 1,800 CAD cases and 1,163 control subjects newly recruited in India. RESULTS The GPSCAD, containing 6,630,150 common DNA variants, had an odds ratio (OR) per SD of 1.58 in South Asian UK Biobank participants and 1.60 in the Bangladeshi study (p < 0.001 for each). Next, individuals of the Indian case-control study were projected onto static reference distributions, observing an OR/SD of 1.66 (p < 0.001). Compared with the middle quintile, risk for CAD was most pronounced for those in the top 5% of the GPSCAD distribution-ORs of 4.16, 2.46, and 3.22 in the South Asian UK Biobank, Bangladeshi, and Indian studies, respectively (p < 0.05 for each). CONCLUSIONS The new GPSCAD has been developed and tested using 3 distinct South Asian studies, and provides a generalizable framework for ancestry-specific GPS assessment.
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Affiliation(s)
- Minxian Wang
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | - Aniruddh P Patel
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts; Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Mark Chaffin
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Thomas Alexander
- Kovai Medical Center and Hospital Research Foundation, Coimbatore, India
| | | | | | | | | | | | | | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, United Kingdom
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, United Kingdom; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, United Kingdom; National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, United Kingdom; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, United Kingdom; Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Emanuele Di Angelantonio
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Aliya Naheed
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Melbourne, Victoria, Australia, and Cambridge, United Kingdom; Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom; Department of Clinical Pathology and School of BioSciences, University of Melbourne, Parkville, Victoria, Australia; The Alan Turing Institute, London, United Kingdom
| | - Rajiv Chowdhury
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom; Centre for Non-Communicable Disease Research, Dhaka, Bangladesh
| | | | - Sekar Kathiresan
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts; Verve Therapeutics, Cambridge, Massachusetts
| | | | - Amit V Khera
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts; Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts.
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1205
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Baker E, Escott-Price V. Polygenic Risk Scores in Alzheimer's Disease: Current Applications and Future Directions. Front Digit Health 2020; 2:14. [PMID: 34713027 PMCID: PMC8521998 DOI: 10.3389/fdgth.2020.00014] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/07/2020] [Indexed: 12/23/2022] Open
Abstract
Genome-wide association studies have identified nearly 40 genome-wide significant single nucleotide polymorphisms (SNPs) which are associated with Alzheimer's Disease (AD). Due to the polygenicity of AD, polygenic risk scores (PRS) have shown high potential for AD risk prediction. PRSs have been shown to successfully discriminate between AD cases and controls achieving a prediction accuracy of up to 84% based on area under the receiver operating curve. The prediction accuracy in AD is higher compared with other complex genetic disorders. PRS can be restricted to SNPs which reside in biologically relevant gene-sets; the predictive value of these gene-sets in the general population is not as high as genome-wide PRS, but they may play an important role to identify mechanisms of disease development and inform biological experiments. Multiple methods are available to derive PRSs, such as selecting SNPs based on statistical evidence of association with the disease or using prior evidence for SNP selection. All methods have advantages, but PRS produced using different methodologies are often not comparable, and results should be interpreted with care. Similarly, this is true when PRS is based on different background populations. With the exponential growth in development of digital electronic devices it is easy to calculate an individual's disease risk using public databases. A major limitation for the utility of PRSs is that the risk score is sample and method dependent. Therefore, replicability and interpretability of PRS is an important issue. PRS can be used to determine the probability of developing disease which incorporates information about disease risk in the general population or in a specific AD risk group. It is essential to consult with genetic counselors to ensure genetic risk is communicated appropriately.
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Affiliation(s)
- Emily Baker
- UK Dementia Research Institute at Cardiff University, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Valentina Escott-Price
- UK Dementia Research Institute at Cardiff University, School of Medicine, Cardiff University, Cardiff, United Kingdom.,MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
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1206
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Fuller ZL, Mocellin VJL, Morris LA, Cantin N, Shepherd J, Sarre L, Peng J, Liao Y, Pickrell J, Andolfatto P, Matz M, Bay LK, Przeworski M. Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching. Science 2020; 369:369/6501/eaba4674. [PMID: 32675347 DOI: 10.1126/science.aba4674] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/01/2020] [Indexed: 12/11/2022]
Abstract
Although reef-building corals are declining worldwide, responses to bleaching vary within and across species and are partly heritable. Toward predicting bleaching response from genomic data, we generated a chromosome-scale genome assembly for the coral Acropora millepora We obtained whole-genome sequences for 237 phenotyped samples collected at 12 reefs along the Great Barrier Reef, among which we inferred little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin We conducted a genome-wide association study of visual bleaching score for 213 samples, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for genomics-based approaches in conservation strategies.
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Affiliation(s)
- Zachary L Fuller
- Department of Biological Sciences, Columbia University, New York, NY, USA.
| | | | - Luke A Morris
- Australian Institute of Marine Science, Townsville, QLD, Australia.,AIMS@JCU, Australian Institute of Marine Science, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Neal Cantin
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Jihanne Shepherd
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Luke Sarre
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Julie Peng
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Yi Liao
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.,Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | | | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Mikhail Matz
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Line K Bay
- Australian Institute of Marine Science, Townsville, QLD, Australia.
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY, USA. .,Department of Systems Biology, Columbia University, New York, NY, USA.,Program for Mathematical Genomics, Columbia University, New York, NY, USA
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1207
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Lieb W, Vasan RS. An update on genetic risk scores for coronary artery disease: are they useful for predicting disease risk and guiding clinical decisions? Expert Rev Cardiovasc Ther 2020; 18:443-447. [PMID: 32672491 DOI: 10.1080/14779072.2020.1797489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Wolfgang Lieb
- Institute of Epidemiology, Kiel University , Kiel, Germany
| | - Ramachandran S Vasan
- The Framingham Heart Study , Framingham, MA, USA.,Sections of Preventive Medicine and Epidemiology, and Cardiovascular Medicine, Department of Medicine, Boston University School of Medicine , Boston, MA, USA.,Department of Epidemiology, Boston University School of Public Health
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1208
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Polygenic risk score as clinical utility in psychiatry: a clinical viewpoint. J Hum Genet 2020; 66:53-60. [PMID: 32770057 DOI: 10.1038/s10038-020-0814-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/21/2020] [Accepted: 07/19/2020] [Indexed: 01/06/2023]
Abstract
Genome-wide association studies (GWASs) have detected many susceptible variants for common diseases, including psychiatric disorders. However, because of the small effect size of each variant, clinical utility that aims for risk prediction and/or diagnostic assistance based on the individual "variants" is difficult to use. Therefore, to improve the statistical power, polygenic risk score (PRS) has been established and applied in the GWAS as a robust analytic tool. Although PRS has potential predictive ability, because of its current "insufficient" discriminative power at the individual level for clinical use, it remains limited solely in the research area, specifically in the psychiatric field. For a better understanding of the PRS, in this review, we (1) introduce the clinical features of psychiatric disorders, (2) summarize the recent GWAS/PRS findings in the psychiatric disorders, (3) evaluate the problems of PRS, and (4) propose its possible utility to apply PRS into the psychiatric clinical setting.
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1209
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Noé A, Cargill TN, Nielsen CM, Russell AJC, Barnes E. The Application of Single-Cell RNA Sequencing in Vaccinology. J Immunol Res 2020; 2020:8624963. [PMID: 32802896 PMCID: PMC7411487 DOI: 10.1155/2020/8624963] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023] Open
Abstract
Single-cell RNA sequencing allows highly detailed profiling of cellular immune responses from limited-volume samples, advancing prospects of a new era of systems immunology. The power of single-cell RNA sequencing offers various opportunities to decipher the immune response to infectious diseases and vaccines. Here, we describe the potential uses of single-cell RNA sequencing methods in prophylactic vaccine development, concentrating on infectious diseases including COVID-19. Using examples from several diseases, we review how single-cell RNA sequencing has been used to evaluate the immunological response to different vaccine platforms and regimens. By highlighting published and unpublished single-cell RNA sequencing studies relevant to vaccinology, we discuss some general considerations how the field could be enriched with the widespread adoption of this technology.
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MESH Headings
- Animals
- Betacoronavirus/immunology
- COVID-19
- Cell Line
- Clinical Trials as Topic
- Coronavirus Infections/epidemiology
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/virology
- Disease Models, Animal
- Drug Evaluation, Preclinical
- Host-Pathogen Interactions/genetics
- Host-Pathogen Interactions/immunology
- Humans
- Immunity, Cellular/genetics
- Immunity, Innate/genetics
- Immunogenicity, Vaccine
- Pandemics/prevention & control
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/immunology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/virology
- RNA, Viral/isolation & purification
- RNA-Seq/methods
- SARS-CoV-2
- Single-Cell Analysis
- Vaccinology/methods
- Viral Vaccines/administration & dosage
- Viral Vaccines/immunology
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Affiliation(s)
- Andrés Noé
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Tamsin N. Cargill
- Peter Medawar Building for Pathogen Research and Oxford NIHR Biomedical Research Centre, Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Carolyn M. Nielsen
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | | | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research and Oxford NIHR Biomedical Research Centre, Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
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1210
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Easteal S, Arkell RM, Balboa RF, Bellingham SA, Brown AD, Calma T, Cook MC, Davis M, Dawkins HJS, Dinger ME, Dobbie MS, Farlow A, Gwynne KG, Hermes A, Hoy WE, Jenkins MR, Jiang SH, Kaplan W, Leslie S, Llamas B, Mann GJ, McMorran BJ, McWhirter RE, Meldrum CJ, Nagaraj SH, Newman SJ, Nunn JS, Ormond-Parker L, Orr NJ, Paliwal D, Patel HR, Pearson G, Pratt GR, Rambaldini B, Russell LW, Savarirayan R, Silcocks M, Skinner JC, Souilmi Y, Vinuesa CG, Baynam G. Equitable Expanded Carrier Screening Needs Indigenous Clinical and Population Genomic Data. Am J Hum Genet 2020; 107:175-182. [PMID: 32763188 PMCID: PMC7413856 DOI: 10.1016/j.ajhg.2020.06.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Expanded carrier screening (ECS) for recessive monogenic diseases requires prior knowledge of genomic variation, including DNA variants that cause disease. The composition of pathogenic variants differs greatly among human populations, but historically, research about monogenic diseases has focused mainly on people with European ancestry. By comparison, less is known about pathogenic DNA variants in people from other parts of the world. Consequently, inclusion of currently underrepresented Indigenous and other minority population groups in genomic research is essential to enable equitable outcomes in ECS and other areas of genomic medicine. Here, we discuss this issue in relation to the implementation of ECS in Australia, which is currently being evaluated as part of the national Government's Genomics Health Futures Mission. We argue that significant effort is required to build an evidence base and genomic reference data so that ECS can bring significant clinical benefit for many Aboriginal and/or Torres Strait Islander Australians. These efforts are essential steps to achieving the Australian Government's objectives and its commitment "to leveraging the benefits of genomics in the health system for all Australians." They require culturally safe, community-led research and community involvement embedded within national health and medical genomics programs to ensure that new knowledge is integrated into medicine and health services in ways that address the specific and articulated cultural and health needs of Indigenous people. Until this occurs, people who do not have European ancestry are at risk of being, in relative terms, further disadvantaged.
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Affiliation(s)
- Simon Easteal
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia.
| | - Ruth M Arkell
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Renzo F Balboa
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia
| | - Shayne A Bellingham
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia
| | - Alex D Brown
- Aboriginal Health Equity, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia; Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Tom Calma
- Poche Centre for Indigenous Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Matthew C Cook
- Department of Immunology, Canberra Hospital, Canberra, ACT 2606, Australia
| | - Megan Davis
- UNSW Law, University of New South Wales, Sydney, NSW 2052, Australia
| | - Hugh J S Dawkins
- HBF Health Limited, Perth, WA 6000, Australia; School of Medicine, The University of Notre Dame Australia, Sydney, NSW 2010, Australia; Sir Walter Murdoch School of Policy and International Affairs, Murdoch University, Murdoch, WA 6150, Australia; Division of Genetics, School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6008, Australia; Centre for Population Health Research, Curtin University of Technology, Bentley, WA 6102, Australia
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Michael S Dobbie
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia; John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Ashley Farlow
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia; Melbourne Integrative Genomics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kylie G Gwynne
- Poche Centre for Indigenous Health, University of Sydney, Sydney, NSW 2006, Australia; Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2113, Australia
| | - Azure Hermes
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia
| | - Wendy E Hoy
- Faculty of Medicine, University of Queensland, Brisbane, QLD 4072, Australia
| | - Misty R Jenkins
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; La Trobe Institute of Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Simon H Jiang
- Department of Immunology, Canberra Hospital, Canberra, ACT 2606, Australia
| | - Warren Kaplan
- Informatics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Stephen Leslie
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia; Melbourne Integrative Genomics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Bastien Llamas
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia; Centre of Excellence in Australian Biodiversity and Heritage, School of Biological Sciences, The Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Graham J Mann
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Brendan J McMorran
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Rebekah E McWhirter
- Centre for Law and Genetics, Faculty of Law, University of Tasmania, Hobart, TAS 7001, Australia
| | | | - Shivashankar H Nagaraj
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Saul J Newman
- Biological Data Science Institute, Australian National University, Canberra, ACT 2600, Australia
| | - Jack S Nunn
- Public Health, La Trobe University, Melbourne, VIC 3086, Australia
| | - Lyndon Ormond-Parker
- Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Neil J Orr
- Poche Centre for Indigenous Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Devashi Paliwal
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia; John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Hardip R Patel
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia
| | - Glenn Pearson
- Aboriginal Health, Telethon Kids Institute, Perth, WA 6009, Australia
| | - Greg R Pratt
- Aboriginal and Torres Strait Islander Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Boe Rambaldini
- Poche Centre for Indigenous Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Lynette W Russell
- Centre of Excellence in Australian Biodiversity and Heritage, Monash Indigenous Studies Centre, Monash University, Melbourne, VIC 3800, Australia
| | - Ravi Savarirayan
- Victorian Clinical Genetic Services, Murdoch Children's Research Institute, and University of Melbourne, Parkville, VIC 3052, Australia
| | - Matthew Silcocks
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia; Melbourne Integrative Genomics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - John C Skinner
- Poche Centre for Indigenous Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Yassine Souilmi
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600, Australia; School of Biological Sciences, The Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Carola G Vinuesa
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Gareth Baynam
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA 6004, Australia; The Western Australian Register of Developmental Anomalies, Department of Health, Government of Western Australia, Perth, WA 6004, Australia; School of Medicine, Division of Paediatrics and Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia.
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1211
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Editorial: Polygenic Risk as a Biomarker for Attention-Deficit/Hyperactivity Disorder. J Am Acad Child Adolesc Psychiatry 2020; 59:926-928. [PMID: 32036035 DOI: 10.1016/j.jaac.2019.11.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/15/2019] [Indexed: 11/21/2022]
Abstract
Although the term has been relatively ill defined in psychiatric research, "biomarker" is typically considered a measurable objective characteristic that can predict clinical outcomes such as risk, diagnosis, subgroups, severity, prognosis, and response to treatment.1 Among several fields of medicine, such as cardiology and oncology, biomarkers have been used to aid clinicians during the various stages of decision-making processes, advancing toward precision medicine and health in which care is tailored based on specific characteristics of individuals. However, that has not been the case for psychiatry until now. Despite the remarkable advancements in our understanding of the etiology and pathophysiology of mental disorders over the past decades, there is no well-validated biomarker incorporated into our clinical practice. We as psychiatrists still find ourselves establishing diagnoses, allocating individuals to treatment, and predicting response without inputs from the accumulated knowledge from neuroscience.
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1212
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Andlauer TF, Nöthen MM. Polygenic scores for psychiatric disease: from research tool to clinical application. MED GENET-BERLIN 2020. [DOI: 10.1515/medgen-2020-2006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Abstract
Propensity to psychiatric disease involves the contribution of multiple genetic variants with small individual effects (i. e., polygenicity). This contribution can be summarized using polygenic scores (PGSs). The present article discusses the methodological foundations of PGS calculation, together with the limitations and caveats of their use. Furthermore, we show that in terms of using genetic information to address the complexities of mental disorders, PGSs have become a standard tool in psychiatric research. PGS also have the potential for translation into clinical practice. Although PGSs alone do not allow reliable disease prediction, they have major potential value in terms of risk stratification, the identification of disorder subtypes, functional investigations, and case selection for experimental models. However, given the stigma associated with mental illness and the limited availability of effective interventions, risk prediction for common psychiatric disorders must be approached with particular caution, particularly in the non-regulated consumer context.
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Affiliation(s)
- Till F. M. Andlauer
- Department of Neurology, Klinikum rechts der Isar, School of Medicine , Technical University of Munich , Ismaninger Str. 22 , Munich , Germany
| | - Markus M. Nöthen
- Institute of Human Genetics , University of Bonn, School of Medicine & University Hospital Bonn , Venusberg-Campus 1, Gebäude 13 , Bonn , Germany
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1213
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Wang Y, Guo J, Ni G, Yang J, Visscher PM, Yengo L. Theoretical and empirical quantification of the accuracy of polygenic scores in ancestry divergent populations. Nat Commun 2020; 11:3865. [PMID: 32737319 PMCID: PMC7395791 DOI: 10.1038/s41467-020-17719-y] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 07/10/2020] [Indexed: 02/03/2023] Open
Abstract
Polygenic scores (PGS) have been widely used to predict disease risk using variants identified from genome-wide association studies (GWAS). To date, most GWAS have been conducted in populations of European ancestry, which limits the use of GWAS-derived PGS in non-European ancestry populations. Here, we derive a theoretical model of the relative accuracy (RA) of PGS across ancestries. We show through extensive simulations that the RA of PGS based on genome-wide significant SNPs can be predicted accurately from modelling linkage disequilibrium (LD), minor allele frequencies (MAF), cross-population correlations of causal SNP effects and heritability. We find that LD and MAF differences between ancestries can explain between 70 and 80% of the loss of RA of European-based PGS in African ancestry for traits like body mass index and type 2 diabetes. Our results suggest that causal variants underlying common genetic variation identified in European ancestry GWAS are mostly shared across continents.
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Affiliation(s)
- Ying Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jing Guo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Guiyan Ni
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Advanced Research, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Loic Yengo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
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1214
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Abstract
Individuals of African ancestry have been starkly underrepresented in the pursuit of personalized medicine for brain illnesses. The African Ancestry Neuroscience Research Initiative will seek to generate much-needed brain gene and protein expression profiles for people of African ancestry.
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Affiliation(s)
- Daniel R Weinberger
- Lieber Institute for Brain Development, Maltz Research Laboratories, Departments of Psychiatry, Neurology, Neuroscience and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Kafui Dzirasa
- Department of Psychiatry and Behavioral Sciences, Departments of Neurobiology, Biomedical Engineering, Neurosurgery, Center for Neuroengineering, Duke University Medical Center, Durham, NC 27710, USA
| | - Lesia L Crumpton-Young
- Morgan State University, Provost and Senior Vice President for Academic Affairs, Professor of Engineering, Baltimore, MD 21251, USA
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1215
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Yong SY, Raben TG, Lello L, Hsu SDH. Genetic architecture of complex traits and disease risk predictors. Sci Rep 2020; 10:12055. [PMID: 32694572 PMCID: PMC7374622 DOI: 10.1038/s41598-020-68881-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/30/2020] [Indexed: 01/30/2023] Open
Abstract
Genomic prediction of complex human traits (e.g., height, cognitive ability, bone density) and disease risks (e.g., breast cancer, diabetes, heart disease, atrial fibrillation) has advanced considerably in recent years. Using data from the UK Biobank, predictors have been constructed using penalized algorithms that favor sparsity: i.e., which use as few genetic variants as possible. We analyze the specific genetic variants (SNPs) utilized in these predictors, which can vary from dozens to as many as thirty thousand. We find that the fraction of SNPs in or near genic regions varies widely by phenotype. For the majority of disease conditions studied, a large amount of the variance is accounted for by SNPs outside of coding regions. The state of these SNPs cannot be determined from exome-sequencing data. This suggests that exome data alone will miss much of the heritability for these traits-i.e., existing PRS cannot be computed from exome data alone. We also study the fraction of SNPs and of variance that is in common between pairs of predictors. The DNA regions used in disease risk predictors so far constructed seem to be largely disjoint (with a few interesting exceptions), suggesting that individual genetic disease risks are largely uncorrelated. It seems possible in theory for an individual to be a low-risk outlier in all conditions simultaneously.
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Affiliation(s)
- Soke Yuen Yong
- Department of Physics and Astronomy, Michigan State University, East Lansing, USA.
| | - Timothy G Raben
- Department of Physics and Astronomy, Michigan State University, East Lansing, USA
| | - Louis Lello
- Department of Physics and Astronomy, Michigan State University, East Lansing, USA.,Genomic Prediction, North Brunswick, NJ, USA
| | - Stephen D H Hsu
- Department of Physics and Astronomy, Michigan State University, East Lansing, USA.,Genomic Prediction, North Brunswick, NJ, USA
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1216
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Abstract
Understanding the influence of genetics on human disease is among the primary goals for biology and medicine. To this end, the direct study of natural human genetic variation has provided valuable insights into human physiology and disease as well as into the origins and migrations of humans. In this review, we discuss the foundations of population genetics, which provide a crucial context to the study of human genes and traits. In particular, genome-wide association studies and similar methods have revealed thousands of genetic loci associated with diseases and traits, providing invaluable information into the biology of these traits. Simultaneously, as the study of rare genetic variation has expanded, so-called human knockouts have elucidated the function of human genes and the therapeutic potential of targeting them.
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Affiliation(s)
- Konrad J. Karczewski
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA;,
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Alicia R. Martin
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA;,
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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1217
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Kang K, Sun X, Wang L, Yao X, Tang S, Deng J, Wu X, Yang C, Chen G. Direct-to-consumer genetic testing in China and its role in GWAS discovery and replication. QUANTITATIVE BIOLOGY 2020. [DOI: 10.1007/s40484-020-0209-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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1218
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Zhu Z, Hasegawa K, Camargo CA, Liang L. Investigating asthma heterogeneity through shared and distinct genetics: Insights from genome-wide cross-trait analysis. J Allergy Clin Immunol 2020; 147:796-807. [PMID: 32693092 PMCID: PMC7368660 DOI: 10.1016/j.jaci.2020.07.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 07/03/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022]
Abstract
Asthma is a heterogeneous respiratory disease reflecting distinct pathobiologic mechanisms. These mechanisms are based, at least partly, on different genetic factors shared by many other conditions, such as allergic diseases and obesity. Investigating the shared genetic effects enables better understanding of the mechanisms of phenotypic correlations and is less subject to confounding by environmental factors. The increasing availability of large-scale genome-wide association study (GWAS) for asthma has enabled researchers to examine the genetic contributions to the epidemiologic associations between asthma subtypes and those between coexisting diseases and/or traits and asthma. Studies have found not only shared but also distinct genetic components between asthma subtypes, indicating that the heterogeneity is related to distinct genetics. This review summarizes a recently compiled analytic approach-genome-wide cross-trait analysis-to determine shared and distinct genetic architecture. The genome-wide cross-trait analysis features in several analytic aspects: genetic correlation, cross-trait meta-analysis, Mendelian randomization, polygenic risk score, and functional analysis. In this article, we discuss in detail the scientific goals that can be achieved by these analyses, their advantages, and their limitations. We also make recommendations for future directions: (1) ethnicity-specific asthma GWASs and (2) application of cross-trait methods to multiomics data to dissect the heritability found in GWASs. Finally, these analytic approaches are also applicable to complex and heterogeneous traits beyond asthma.
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Affiliation(s)
- Zhaozhong Zhu
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Mass; Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Mass; Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| | - Carlos A Camargo
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Mass; Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| | - Liming Liang
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Mass; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Mass.
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1219
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Yanes T, McInerney-Leo AM, Law MH, Cummings S. The emerging field of polygenic risk scores and perspective for use in clinical care. Hum Mol Genet 2020; 29:R165-R176. [DOI: 10.1093/hmg/ddaa136] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023] Open
Abstract
Abstract
Genetic testing is used widely for diagnostic, carrier and predictive testing in monogenic diseases. Until recently, there were no genetic testing options available for multifactorial complex diseases like heart disease, diabetes and cancer. Genome-wide association studies (GWAS) have been invaluable in identifying single-nucleotide polymorphisms (SNPs) associated with increased or decreased risk for hundreds of complex disorders. For a given disease, SNPs can be combined to generate a cumulative estimation of risk known as a polygenic risk score (PRS). After years of research, PRSs are increasingly used in clinical settings. In this article, we will review the literature on how both genome-wide and restricted PRSs are developed and the relative merit of each. The validation and evaluation of PRSs will also be discussed, including the recognition that PRS validity is intrinsically linked to the methodological and analytical approach of the foundation GWAS together with the ethnic characteristics of that cohort. Specifically, population differences may affect imputation accuracy, risk magnitude and direction. Even as PRSs are being introduced into clinical practice, there is a push to combine them with clinical and demographic risk factors to develop a holistic disease risk. The existing evidence regarding the clinical utility of PRSs is considered across four different domains: informing population screening programs, guiding therapeutic interventions, refining risk for families at high risk, and facilitating diagnosis and predicting prognostic outcomes. The evidence for clinical utility in relation to five well-studied disorders is summarized. The potential ethical, legal and social implications are also highlighted.
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Affiliation(s)
- Tatiane Yanes
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Aideen M McInerney-Leo
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Matthew H Law
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Herston QLD 4006, Australia
- Faculty of Health, School of Biomedical Sciences, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove QLD 4059, Australia
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1220
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Chen M, Sidore C, Akiyama M, Ishigaki K, Kamatani Y, Schlessinger D, Cucca F, Okada Y, Chiang CWK. Evidence of Polygenic Adaptation in Sardinia at Height-Associated Loci Ascertained from the Biobank Japan. Am J Hum Genet 2020; 107:60-71. [PMID: 32533944 PMCID: PMC7332648 DOI: 10.1016/j.ajhg.2020.05.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 05/19/2020] [Indexed: 01/31/2023] Open
Abstract
Adult height is one of the earliest putative examples of polygenic adaptation in humans. However, this conclusion was recently challenged because residual uncorrected stratification from large-scale consortium studies was considered responsible for the previously noted genetic difference. It thus remains an open question whether height loci exhibit signals of polygenic adaptation in any human population. We re-examined this question, focusing on one of the shortest European populations, the Sardinians, in addition to mainland European populations. We utilized height-associated loci from the Biobank Japan (BBJ) dataset to further alleviate concerns of biased ascertainment of GWAS loci and showed that the Sardinians remain significantly shorter than expected under neutrality (∼0.22 standard deviation shorter than Utah residents with ancestry from northern and western Europe [CEU] on the basis of polygenic height scores, p = 3.89 × 10-4). We also found the trajectory of polygenic height scores between the Sardinian and the British populations diverged over at least the last 10,000 years (p = 0.0082), consistent with a signature of polygenic adaptation driven primarily by the Sardinian population. Although the polygenic score-based analysis showed a much subtler signature in mainland European populations, we found a clear and robust adaptive signature in the UK population by using a haplotype-based statistic, the trait singleton density score (tSDS), driven by the height-increasing alleles (p = 9.1 × 10-4). In summary, by ascertaining height loci in a distant East Asian population, we further supported the evidence of polygenic adaptation at height-associated loci among the Sardinians. In mainland Europeans, the adaptive signature was detected in haplotype-based analysis but not in polygenic score-based analysis.
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Affiliation(s)
- Minhui Chen
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
| | - Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato 09042, Cagliari, Italy
| | - Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Department of Ocular Pathology and Imaging Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Kyoto-McGill International Collaborative School in Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - David Schlessinger
- Laboratory of Genetics and Genomics, National Institute on Aging, US National Institutes of Health, Baltimore, MD 21224, USA
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato 09042, Cagliari, Italy
| | - Yukinori Okada
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Quantitative and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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1221
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Ajnakina O, Cadar D, Steptoe A. Interplay between Socioeconomic Markers and Polygenic Predisposition on Timing of Dementia Diagnosis. J Am Geriatr Soc 2020; 68:1529-1536. [PMID: 32187654 PMCID: PMC7363562 DOI: 10.1111/jgs.16406] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/08/2020] [Accepted: 02/14/2020] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Identifying the interplay between socioeconomic markers (education and financial resources) and polygenetic predisposition influencing the time of dementia and the diagnosis of clinical Alzheimer's disease (AD) dementia is of central relevance for preventive strategies. DESIGN Prospective cohort design. SETTING The English Longitudinal Study of Aging is a household survey data set of a representative sample. PARTICIPANTS A total of 7,039 individuals aged 50 years and older participated in the study. Of these, 320 (4.6%) were diagnosed with dementia over the 10-year follow-up. MEASUREMENTS Polygenic score (PGS) for Alzheimer's disease (AD-PGS) was calculated using summary statistics from the International Genomics of Alzheimer's Project. An accelerated failure time survival model was used to investigate interactions between AD-PGS and socioeconomic markers on the timing of dementia and clinical AD dementia diagnosis. RESULTS A one standard deviation increase in AD-PGS was associated with an accelerated time to dementia diagnosis by 4.8 months. The presence of the apolipoprotein E gene (APOE-ε4) was associated with an earlier dementia onset by approximately 24.9 months, whereas intermediate and low levels of wealth were associated with an accelerated time to dementia diagnosis by 12.0 months and 18.7 months, respectively. A multiplicative interaction between AD-PGS and years of completed schooling in decelerating the time to clinical AD dementia by 3.0 months suggests educational attainment may serve as a protective mechanism against AD diagnosis among older people with a higher polygenic risk. Interaction between AD-PGS and lower wealth accelerated the time to clinical AD dementia diagnosis by 21.1 to 24.1 months. CONCLUSION Socioeconomic markers influence the time to dementia and clinical AD dementia diagnosis, particularly in those with a higher polygenic predisposition. J Am Geriatr Soc 68:1529-1536, 2020.
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Affiliation(s)
- Olesya Ajnakina
- Department of Behavioural Science and HealthInstitute of Epidemiology and Health Care, University College LondonLondonUK
- Department of Biostatistics & Health InformaticsInstitute of Psychiatry, Psychology and Neuroscience, Kingʼs College LondonLondonUK
| | - Dorina Cadar
- Department of Behavioural Science and HealthInstitute of Epidemiology and Health Care, University College LondonLondonUK
| | - Andrew Steptoe
- Department of Behavioural Science and HealthInstitute of Epidemiology and Health Care, University College LondonLondonUK
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1222
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van Reij RRI, Voncken JW, Joosten EAJ, van den Hoogen NJ. Polygenic risk scores indicates genetic overlap between peripheral pain syndromes and chronic postsurgical pain. Neurogenetics 2020; 21:205-215. [PMID: 32377986 PMCID: PMC7283206 DOI: 10.1007/s10048-020-00614-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/21/2020] [Indexed: 02/08/2023]
Abstract
Chronic postsurgical pain (CPSP) is a debilitating chronic pain condition that has a substantial effect on quality of life. CPSP shows considerable clinical overlap with different chronic peripheral pain syndromes, suggesting a shared aetiology. This study aims to assess the genetic overlap between different chronic pain syndromes and CPSP, providing relevant biological context for potential chronic pain markers of CPSP. To analyse the genetic overlap between CPSP and chronic peripheral pain syndromes, recent GWAS studies were combined for polygenic risk scores (PRS) analysis, using a cohort of CPSP patients as starting point. Biological contextualisation of genetic marker, overlap between CPSP and chronic pain syndromes, was assessed through Gene Ontology (GO), using Pathway Scoring Algorithm (PASCAL) and REVIGO. PRS analyses suggest a significant genetic overlap between CPSP and 3 chronic pain disorders: chronic widespread pain (CWP, p value threshold = 0.003, R2 0.06, p = 0.003), rheumatoid arthritis (RA, p value threshold = 0.0177, R2 = 0.04, p = 0.017) and possibly sciatica (p value threshold = 0.00025, R2 = 0.03, p = 0.045). Whereas no significant genetic overlap was found with cluster headache and migraine, the outcome for osteoarthritis (OA) was inconsistent between the cohorts. This is likely related to cohort composition, as repeated random reallocation of patients' nullified CPSP/OA outcome variation between the discovery and replication cohorts. GO analyses suggested an aetiological involvement of genetic markers that control neurological signalling (specifically sodium channels) and inflammatory response. The current study reaffirms the impact of sample size, cohort composition and open data accessibility on the unbiased identification of genetic overlap across disorders. In conclusion, this study is the first to report genetic overlap between regulatory processes implicated in CPSP and chronic peripheral pain syndromes. Interaction between neurological signalling and inflammatory response may explain the genetic overlap between CPSP, CWP and RA. Enhanced understanding of mechanisms underlying chronification of pain will aid the development of new therapeutic strategies for CPSP with sodium channel biochemistry as a potential candidate.
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Affiliation(s)
- Roel R I van Reij
- Department of Anaesthesiology and Pain Management, Maastricht University Medical Center+, 6200, MD, Maastricht, The Netherlands.
- Department of Translational Neuroscience, School for Mental Health and Neuroscience (MHeNs), University of Maastricht, 6200, MD, Maastricht, The Netherlands.
| | - Jan Willem Voncken
- Department of Molecular Genetics, Maastricht University Medical Center+, 6200, MD, Maastricht, The Netherlands
| | - Elbert A J Joosten
- Department of Anaesthesiology and Pain Management, Maastricht University Medical Center+, 6200, MD, Maastricht, The Netherlands
- Department of Translational Neuroscience, School for Mental Health and Neuroscience (MHeNs), University of Maastricht, 6200, MD, Maastricht, The Netherlands
| | - Nynke J van den Hoogen
- Department of Anaesthesiology and Pain Management, Maastricht University Medical Center+, 6200, MD, Maastricht, The Netherlands
- Department of Translational Neuroscience, School for Mental Health and Neuroscience (MHeNs), University of Maastricht, 6200, MD, Maastricht, The Netherlands
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1223
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Forgetta V, Keller-Baruch J, Forest M, Durand A, Bhatnagar S, Kemp JP, Nethander M, Evans D, Morris JA, Kiel DP, Rivadeneira F, Johansson H, Harvey NC, Mellström D, Karlsson M, Cooper C, Evans DM, Clarke R, Kanis JA, Orwoll E, McCloskey EV, Ohlsson C, Pineau J, Leslie WD, Greenwood CMT, Richards JB. Development of a polygenic risk score to improve screening for fracture risk: A genetic risk prediction study. PLoS Med 2020; 17:e1003152. [PMID: 32614825 PMCID: PMC7331983 DOI: 10.1371/journal.pmed.1003152] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/03/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Since screening programs identify only a small proportion of the population as eligible for an intervention, genomic prediction of heritable risk factors could decrease the number needing to be screened by removing individuals at low genetic risk. We therefore tested whether a polygenic risk score for heel quantitative ultrasound speed of sound (SOS)-a heritable risk factor for osteoporotic fracture-can identify low-risk individuals who can safely be excluded from a fracture risk screening program. METHODS AND FINDINGS A polygenic risk score for SOS was trained and selected in 2 separate subsets of UK Biobank (comprising 341,449 and 5,335 individuals). The top-performing prediction model was termed "gSOS", and its utility in fracture risk screening was tested in 5 validation cohorts using the National Osteoporosis Guideline Group clinical guidelines (N = 10,522 eligible participants). All individuals were genome-wide genotyped and had measured fracture risk factors. Across the 5 cohorts, the average age ranged from 57 to 75 years, and 54% of studied individuals were women. The main outcomes were the sensitivity and specificity to correctly identify individuals requiring treatment with and without genetic prescreening. The reference standard was a bone mineral density (BMD)-based Fracture Risk Assessment Tool (FRAX) score. The secondary outcomes were the proportions of the screened population requiring clinical-risk-factor-based FRAX (CRF-FRAX) screening and BMD-based FRAX (BMD-FRAX) screening. gSOS was strongly correlated with measured SOS (r2 = 23.2%, 95% CI 22.7% to 23.7%). Without genetic prescreening, guideline recommendations achieved a sensitivity and specificity for correct treatment assignment of 99.6% and 97.1%, respectively, in the validation cohorts. However, 81% of the population required CRF-FRAX tests, and 37% required BMD-FRAX tests to achieve this accuracy. Using gSOS in prescreening and limiting further assessment to those with a low gSOS resulted in small changes to the sensitivity and specificity (93.4% and 98.5%, respectively), but the proportions of individuals requiring CRF-FRAX tests and BMD-FRAX tests were reduced by 37% and 41%, respectively. Study limitations include a reliance on cohorts of predominantly European ethnicity and use of a proxy of fracture risk. CONCLUSIONS Our results suggest that the use of a polygenic risk score in fracture risk screening could decrease the number of individuals requiring screening tests, including BMD measurement, while maintaining a high sensitivity and specificity to identify individuals who should be recommended an intervention.
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Affiliation(s)
- Vincenzo Forgetta
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | | | - Marie Forest
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Audrey Durand
- School of Computer Science, McGill University, Montréal, Québec, Canada
| | - Sahir Bhatnagar
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - John P. Kemp
- University of Queensland Diamantina Institute, University of Queensland, Woolloongabba, Queensland, Australia
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Maria Nethander
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute for Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Evans
- California Pacific Medical Center Research Institute, San Francisco, California, United States of America
| | - John A. Morris
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Douglas P. Kiel
- Institute for Aging Research, Hebrew SeniorLife, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Broad Institute of MIT & Harvard University, Boston, Massachusetts, United States of America
| | | | - Helena Johansson
- Centre for Metabolic Bone Diseases, University of Sheffield, Sheffield, United Kingdom
- Australian Catholic University, Melbourne, Victoria, Australia
| | - Nicholas C. Harvey
- Medical Research Council Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
- National Institute for Health Research Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Dan Mellström
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute for Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Karlsson
- Department of Orthopaedics and Clinical Sciences, Lund University, Skane University Hospital, Malmö, Sweden
| | - Cyrus Cooper
- Medical Research Council Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
- National Institute for Health Research Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - David M. Evans
- University of Queensland Diamantina Institute, University of Queensland, Woolloongabba, Queensland, Australia
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Robert Clarke
- Clinical Trial Service Unit and Epidemiological Studies Unit, University of Oxford, Oxford, United Kingdom
| | - John A. Kanis
- Centre for Metabolic Bone Diseases, University of Sheffield, Sheffield, United Kingdom
- Australian Catholic University, Melbourne, Victoria, Australia
| | - Eric Orwoll
- Bone and Mineral Unit, Oregon Health & Science University, Portland, Oregon, United States of America
- Department of Medicine, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Eugene V. McCloskey
- Mellanby Centre for Bone Research, Centre for Integrated Research in Musculoskeletal Ageing, University of Sheffield and Sheffield Teaching Hospitals Foundation Trust, Sheffield, United Kingdom
| | - Claes Ohlsson
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute for Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Joelle Pineau
- School of Computer Science, McGill University, Montréal, Québec, Canada
| | - William D. Leslie
- Department of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Celia M. T. Greenwood
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montréal, Québec, Canada
| | - J. Brent Richards
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
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1224
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Harlemon M, Ajayi O, Kachambwa P, Kim MS, Simonti CN, Quiver MH, Petersen DC, Mittal A, Fernandez PW, Hsing AW, Baichoo S, Agalliu I, Jalloh M, Gueye SM, Snyper NYF, Adusei B, Mensah JE, Abrahams AOD, Adebiyi AO, Orunmuyi AT, Aisuodionoe-Shadrach OI, Nwegbu MM, Joffe M, Chen WC, Irusen H, Neugut AI, Quintana Y, Seutloali M, Fadipe MB, Warren C, Woehrmann MH, Zhang P, Ongaco CM, Mawhinney M, McBride J, Andrews CV, Adams M, Pugh E, Rebbeck TR, Petersen LN, Lachance J. A Custom Genotyping Array Reveals Population-Level Heterogeneity for the Genetic Risks of Prostate Cancer and Other Cancers in Africa. Cancer Res 2020; 80:2956-2966. [PMID: 32393663 PMCID: PMC7335354 DOI: 10.1158/0008-5472.can-19-2165] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/03/2019] [Accepted: 05/06/2020] [Indexed: 12/25/2022]
Abstract
Although prostate cancer is the leading cause of cancer mortality for African men, the vast majority of known disease associations have been detected in European study cohorts. Furthermore, most genome-wide association studies have used genotyping arrays that are hindered by SNP ascertainment bias. To overcome these disparities in genomic medicine, the Men of African Descent and Carcinoma of the Prostate (MADCaP) Network has developed a genotyping array that is optimized for African populations. The MADCaP Array contains more than 1.5 million markers and an imputation backbone that successfully tags over 94% of common genetic variants in African populations. This array also has a high density of markers in genomic regions associated with cancer susceptibility, including 8q24. We assessed the effectiveness of the MADCaP Array by genotyping 399 prostate cancer cases and 403 controls from seven urban study sites in sub-Saharan Africa. Samples from Ghana and Nigeria clustered together, whereas samples from Senegal and South Africa yielded distinct ancestry clusters. Using the MADCaP array, we identified cancer-associated loci that have large allele frequency differences across African populations. Polygenic risk scores for prostate cancer were higher in Nigeria than in Senegal. In summary, individual and population-level differences in prostate cancer risk were revealed using a novel genotyping array. SIGNIFICANCE: This study presents an Africa-specific genotyping array, which enables investigators to identify novel disease associations and to fine-map genetic loci that are associated with prostate and other cancers.
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Affiliation(s)
- Maxine Harlemon
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
- Clark Atlanta University, Atlanta, Georgia
| | - Olabode Ajayi
- Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | | | - Michelle S Kim
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Corinne N Simonti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Melanie H Quiver
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | | | | | - Pedro W Fernandez
- Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Ann W Hsing
- Stanford Cancer Institute, Stanford University, Stanford, California
| | | | - Ilir Agalliu
- Albert Einstein College of Medicine, Bronx, New York
| | - Mohamed Jalloh
- Hôpital Général de Grand Yoff, Institut de Formation et de Recherche en Urologie et Santé Familiale, Dakar, Senegal
| | - Serigne M Gueye
- Hôpital Général de Grand Yoff, Institut de Formation et de Recherche en Urologie et Santé Familiale, Dakar, Senegal
| | | | | | - James E Mensah
- Korle-Bu Teaching Hospital and University of Ghana, Accra, Ghana
| | | | | | | | | | - Maxwell M Nwegbu
- College of Health Sciences, University of Abuja and University of Abuja Teaching Hospital, Abuja, Nigeria
| | - Maureen Joffe
- Non-Communicable Diseases Research Division, Wits Health Consortium (PTY) Ltd, Johannesburg, South Africa
- MRC Developmental Pathways to Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Wenlong C Chen
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Cancer Registry, National Health Laboratory Service, Johannesburg, South Africa
| | - Hayley Irusen
- Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Alfred I Neugut
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | - Yuri Quintana
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | | | - Mayowa B Fadipe
- Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | | | | | - Peng Zhang
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Chrissie M Ongaco
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Michelle Mawhinney
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Jo McBride
- Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | | | - Marcia Adams
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Timothy R Rebbeck
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | | | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.
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1225
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Roberts JS, Patterson AK, Uhlmann WR. Genetic testing for neurodegenerative diseases: Ethical and health communication challenges. Neurobiol Dis 2020; 141:104871. [PMID: 32302673 PMCID: PMC7311284 DOI: 10.1016/j.nbd.2020.104871] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/01/2020] [Accepted: 04/13/2020] [Indexed: 12/31/2022] Open
Abstract
Advances in genomic science are informing an expansion of genetic testing for neurodegenerative diseases, which can be used for diagnostic and predictive purposes and performed in both medical and consumer genomics settings. Such testing-which is often for severe and incurable conditions like Huntington's, Alzheimer's, and Parkinson's diseases-raises important ethical and health communication challenges. This review addresses such challenges in the contexts of clinical, research, and direct-to-consumer genetic testing; these include informed consent, risk estimation and communication, potential benefits and psychosocial harms of genetic information (e.g., genetic discrimination), access to services, education and workforce needs, and health policies. The review also highlights future areas of likely growth in the field, including polygenic risk scores, use of genetic testing in clinical trials, and return of individual research results.
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Affiliation(s)
- J Scott Roberts
- Department of Health Behavior & Health Education, University of Michigan School of Public Health, United States of America.
| | - Anne K Patterson
- University of Michigan School of Public Health, United States of America
| | - Wendy R Uhlmann
- Department of Internal Medicine, Division of Genetic Medicine, Department of Human Genetics, University of Michigan School of Medicine, United States of America
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1226
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Wimberley T, Agerbo E, Horsdal HT, Ottosen C, Brikell I, Als TD, Demontis D, Børglum AD, Nordentoft M, Mors O, Werge T, Hougaard D, Bybjerg-Grauholm J, Hansen MB, Mortensen PB, Thapar A, Riglin L, Langley K, Dalsgaard S. Genetic liability to ADHD and substance use disorders in individuals with ADHD. Addiction 2020; 115:1368-1377. [PMID: 31803957 DOI: 10.1111/add.14910] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 10/22/2019] [Accepted: 11/15/2019] [Indexed: 12/18/2022]
Abstract
AIMS 1) To investigate whether genetic liability to attention-deficit/hyperactivity disorder (ADHD), indexed by polygenic risk scores for ADHD (PRS-ADHD), is associated with substance use disorders (SUD) in individuals with ADHD. 2) To investigate whether other individual- or family-related risk factors for SUD could mediate or confound this association. DESIGN Population-based cohort study SETTING AND PARTICIPANTS: ADHD cases in the iPSYCH sample (a Danish case-cohort sample of genotyped cases with specific mental disorders), born in Denmark between 1981 and 2003 (N = 13 116). Register-based information on hospital diagnoses of SUD was available until December 31, 2016. MEASUREMENTS We estimated odds ratios (ORs) with 95% confidence intervals (CIs) for any SUD as well as for different SUD types (alcohol, cannabis, and other illicit drugs) and severities (use, abuse, and addiction), with effect sizes corresponding to a comparison of the highest PRS-ADHD decile to the lowest. FINDINGS PRS-ADHD were associated with any SUD (OR = 1.30, 95% CI: 1.11-1.51). Estimates were similar across different types and severity levels of SUD. Other risk factors for SUD (male sex, age at ADHD diagnosis, comorbid conduct problems, and parental factors including SUD, mental disorders, and socio-economic status) were independently associated with increased risk of SUD. PRS-ADHD explained a minor proportion of the variance in SUD (0.2% on the liability scale) compared to the other risk factors. The association between PRS-ADHD and any SUD was slightly attenuated (OR = 1.21, 95% CI: 1.03-1.41) after adjusting for the other risk factors for SUD. Furthermore, associations were nominally higher in females than in males (ORfemales = 1.59, 95% CI: 1.19-2.12, ORmales = 1.18, 95% CI: 0.98-1.42). CONCLUSIONS A higher genetic liability to attention-deficit/hyperactivity disorder appears to be associated with higher risks of substance use disorders in individuals with attention-deficit/hyperactivity disorder.
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Affiliation(s)
- Theresa Wimberley
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen and Aarhus, Denmark
- NCRR - National Centre for Register-based Research, Department of Economics and Business Economics, Aarhus University, Aarhus, Denmark
| | - Esben Agerbo
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen and Aarhus, Denmark
- NCRR - National Centre for Register-based Research, Department of Economics and Business Economics, Aarhus University, Aarhus, Denmark
- CIRRAU - Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Henriette Thisted Horsdal
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen and Aarhus, Denmark
- NCRR - National Centre for Register-based Research, Department of Economics and Business Economics, Aarhus University, Aarhus, Denmark
| | - Caecilie Ottosen
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen and Aarhus, Denmark
- NCRR - National Centre for Register-based Research, Department of Economics and Business Economics, Aarhus University, Aarhus, Denmark
| | - Isabell Brikell
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen and Aarhus, Denmark
- NCRR - National Centre for Register-based Research, Department of Economics and Business Economics, Aarhus University, Aarhus, Denmark
| | - Thomas Damm Als
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen and Aarhus, Denmark
- Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Central Region Denmark and Aarhus University, Aarhus, Denmark
| | - Ditte Demontis
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen and Aarhus, Denmark
- Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Central Region Denmark and Aarhus University, Aarhus, Denmark
| | - Anders D Børglum
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen and Aarhus, Denmark
- Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Central Region Denmark and Aarhus University, Aarhus, Denmark
| | - Merete Nordentoft
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen and Aarhus, Denmark
- Mental Health Center Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ole Mors
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen and Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital, Aarhus, Denmark
| | - Thomas Werge
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen and Aarhus, Denmark
- Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - David Hougaard
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen and Aarhus, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Danish Center for Neonatal Screening, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen and Aarhus, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Danish Center for Neonatal Screening, Copenhagen, Denmark
| | - Marie Baekvad Hansen
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen and Aarhus, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Danish Center for Neonatal Screening, Copenhagen, Denmark
| | - Preben Bo Mortensen
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen and Aarhus, Denmark
- NCRR - National Centre for Register-based Research, Department of Economics and Business Economics, Aarhus University, Aarhus, Denmark
- CIRRAU - Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Anita Thapar
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Lucy Riglin
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Kate Langley
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- School of Psychology, Cardiff University, Cardiff, UK
| | - Søren Dalsgaard
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen and Aarhus, Denmark
- NCRR - National Centre for Register-based Research, Department of Economics and Business Economics, Aarhus University, Aarhus, Denmark
- CIRRAU - Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
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1227
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Huggett SB, Stallings MC. Genetic Architecture and Molecular Neuropathology of Human Cocaine Addiction. J Neurosci 2020; 40:5300-5313. [PMID: 32457073 PMCID: PMC7329314 DOI: 10.1523/jneurosci.2879-19.2020] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 05/04/2020] [Accepted: 05/10/2020] [Indexed: 01/12/2023] Open
Abstract
We integrated genomic and bioinformatic analyses, using data from the largest genome-wide association study of cocaine dependence (CD; n = 6546; 82.37% with CD; 57.39% male) and the largest postmortem gene-expression sample of individuals with cocaine use disorder (CUD; n = 36; 51.35% with CUD; 100% male). Our genome-wide analyses identified one novel gene (NDUFB9) associated with the genetic predisposition to CD in African-Americans. The genetic architecture of CD was similar across ancestries. Individual genes associated with CD demonstrated modest overlap across European-Americans and African-Americans, but the genetic liability for CD converged on many similar tissue types (brain, heart, blood, liver) across ancestries. In a separate sample, we investigated the neuronal gene expression associated with CUD by using RNA sequencing of dorsal-lateral prefrontal cortex neurons. We identified 133 genes differentially expressed between CUD case patients and cocaine-free control subjects, including previously implicated candidates for cocaine use/addiction (FOSB, ARC, KCNJ9/GIRK3, NR4A2, JUNB, and MECP2). Differential expression analyses significantly correlated across European-Americans and African-Americans. While genes significantly associated with CD via genome-wide methods were not differentially expressed, two of these genes (NDUFB9 and C1qL2) were part of a robust gene coexpression network associated with CUD involved in neurotransmission (GABA, acetylcholine, serotonin, and dopamine) and drug addiction. We then used a "guilt-by-association" approach to unravel the biological relevance of NDUFB9 and C1qL2 in the context of CD. In sum, our study furthers the understanding of the genetic architecture and molecular neuropathology of human cocaine addiction and provides a framework for translating biological meaning into otherwise obscure genome-wide associations.SIGNIFICANCE STATEMENT Our study further clarifies the genetic and neurobiological contributions to cocaine addiction, provides a rapid approach for generating testable hypotheses for specific candidates identified by genome-wide research, and investigates the cross-ancestral biological contributions to cocaine use disorder/dependence for individuals of European-American and African-American ancestries.
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Affiliation(s)
- Spencer B Huggett
- Department of Psychology and Neuroscience, University of Colorado, Boulder, Colorado 80309-0345
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado 80309-0447
| | - Michael C Stallings
- Department of Psychology and Neuroscience, University of Colorado, Boulder, Colorado 80309-0345
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado 80309-0447
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1228
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Mann FD, Krueger RF, Clouston S, Cole S. Demographic correlates of inflammatory and antiviral gene expression in the study of Midlife in the United States (MIDUS). BIODEMOGRAPHY AND SOCIAL BIOLOGY 2020; 66:236-249. [PMID: 34622724 PMCID: PMC8702472 DOI: 10.1080/19485565.2021.1983761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The present study examined the demographic correlates of gene expression in a sample of adults (n = 543) from the Study of Midlife in the United States (MIDUS). Inflammatory and antiviral gene sets were operationalized using a priori composite scores and empirically derived co-regulatory gene sets. For both composite scores and co-regulatory gene sets, White/European Americans showed lower while Black/African Americans showed higher expression of genes involved in interferon responses and antibody synthesis. The effects of chronological age on gene expression varied by sex, such that pro-inflammatory gene expression increased with age more rapidly for females than males. The difference between the average expression of inflammatory and antiviral genes also increased with age for females but not males. Results shed light on differential gene expression as a potential physiological correlate for race/ethnicity, age, and sex-related health disparities in adulthood.
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Affiliation(s)
- Frank D. Mann
- Program in Public Health and the Department of Family, Population, and Preventive Medicine, Stony Brook University
| | | | - Sean Clouston
- Program in Public Health and the Department of Family, Population, and Preventive Medicine, Stony Brook University
| | - Steven Cole
- Department of Psychiatry & Biobehavioral Sciences and Medicine, University of California, Los Angeles
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1229
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Gaydosh L, Mitchell C, Notterman D, Schneper L, Brooks-Gunn J, Wagner B, Koss K, McLanahan S. Demographic and developmental patterns in telomere length across adolescence. BIODEMOGRAPHY AND SOCIAL BIOLOGY 2020; 66:208-219. [PMID: 34597213 PMCID: PMC8702463 DOI: 10.1080/19485565.2021.1983758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Telomere length is often used in studies of adults as a biomarker of cellular aging and an indicator of stress exposure. However, we know little about how telomeres change over time, particularly over the course of the important developmental period of adolescence. We use data on telomere length collected at two points in time spanning adolescence (Years 9 and 15) from the Fragile Families and Child Wellbeing Study to examine longitudinal patterns (n = 1,654) in telomere length. We find a quantitatively small but significant average lengthening in telomere length across adolescence and little evidence of associations between telomere length and pubertal development.
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Affiliation(s)
- Lauren Gaydosh
- Department of Sociology and Population Research Center, The University of Texas at Austin, Austin, Texas, USA
| | - Colter Mitchell
- Institute for Social Research and Department of Sociology, University of Michigan, Ann Arbor, Michigan, USA
| | - Daniel Notterman
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Lisa Schneper
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Jeanne Brooks-Gunn
- Teachers College and the College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Brandon Wagner
- Department of Sociology, Anthropology, and Social Work, Texas Tech University, Lubbock, Texas, USA
- Department of Sociology and School of Public and International Affairs, Princeton University, Princeton, New Jersey, USA
| | - Kalsea Koss
- Human Development and Family Science, University of Georgia, Athens, Georgia, USA
| | - Sara McLanahan
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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1230
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Unraveling the genetic contributions to complex traits across different ethnic groups. Nat Med 2020; 26:467-469. [PMID: 32231296 DOI: 10.1038/s41591-020-0834-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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1231
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Abstract
Susceptibility to atrial fibrillation (AF) is determined by well-recognized risk factors such as diabetes mellitus or hypertension, emerging risk factors such as sleep apnea or inflammation, and increasingly well-defined genetic variants. As discussed in detail in a companion article in this series, studies in families and in large populations have identified multiple genetic loci, specific genes, and specific variants increasing susceptibility to AF. Since it is becoming increasingly inexpensive to obtain genotype data and indeed whole genome sequence data, the question then becomes to define whether using emerging new genetics knowledge can improve care for patients both before and after development of AF. Examples of improvements in care could include identifying patients at increased risk for AF (and thus deploying increased surveillance or even low-risk preventive therapies should these be available), identifying patient subsets in whom specific therapies are likely to be effective or ineffective or in whom the driving biology could motivate the development of new mechanism-based therapies or identifying an underlying susceptibility to comorbid cardiovascular disease. While current guidelines for the care of patients with AF do not recommend routine genetic testing, this rapidly increasing knowledge base suggests that testing may now or soon have a place in the management of select patients. The opportunity is to generate, validate, and deploy clinical predictors (including family history) of AF risk, to assess the utility of incorporating genomic variants into those predictors, and to identify and validate interventions such as wearable or implantable device-based monitoring ultimately to intervene in patients with AF before they present with catastrophic complications like heart failure or stroke.
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Affiliation(s)
- M. Benjamin Shoemaker
- Department of Medicine (Cardiovascular Medicine), Vanderbilt University Medical Center, Nashville, TN
| | - Rajan L. Shah
- Department of Medicine (Cardiovascular Medicine), Stanford University Medical Center, Palo Alto, CA
| | - Dan M. Roden
- Departments of Medicine (Cardiovascular Medicine and Clinical Pharmacology), Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Marco V. Perez
- Stanford Center for Inherited Cardiovascular Diseases, Stanford University, Palo Alto, CA
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1232
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Using polygenic scores for identifying individuals at increased risk of substance use disorders in clinical and population samples. Transl Psychiatry 2020; 10:196. [PMID: 32555147 PMCID: PMC7303212 DOI: 10.1038/s41398-020-00865-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 11/11/2022] Open
Abstract
Genome-wide, polygenic risk scores (PRS) have emerged as a useful way to characterize genetic liability. There is growing evidence that PRS may prove useful for early identification of those at increased risk for certain diseases. The current potential of PRS for alcohol use disorders (AUD) remains an open question. Using data from both a population-based sample [the FinnTwin12 (FT12) study] and a high-risk sample [the Collaborative Study on the Genetics of Alcoholism (COGA)], we examined the association between PRSs derived from genome-wide association studies (GWASs) of (1) alcohol dependence/alcohol problems, (2) alcohol consumption, and (3) risky behaviors with AUD and other substance use disorder (SUD) criteria. These PRSs explain ~2.5-3.5% of the variance in AUD (across FT12 and COGA) when all PRSs are included in the same model. Calculations of area under the curve (AUC) show PRS provide only a slight improvement over a model with age, sex, and ancestral principal components as covariates. While individuals in the top 20, 10, and 5% of the PRS distribution had greater odds of having an AUD compared to the lower end of the continuum in both COGA and FT12, the point estimates at each threshold were statistically indistinguishable. Those in the top 5% reported greater levels of licit (alcohol and nicotine) and illicit (cannabis and opioid) SUD criteria. PRSs are associated with risk for SUD in independent samples. However, usefulness for identifying those at increased risk in their current form is modest, at best. Improvement in predictive ability will likely be dependent on increasing the size of well-phenotyped discovery samples.
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1233
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Efficient polygenic risk scores for biobank scale data by exploiting phenotypes from inferred relatives. Nat Commun 2020; 11:3074. [PMID: 32555176 PMCID: PMC7299943 DOI: 10.1038/s41467-020-16829-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/25/2020] [Indexed: 01/06/2023] Open
Abstract
Polygenic risk scores are emerging as a potentially powerful tool to predict future phenotypes of target individuals, typically using unrelated individuals, thereby devaluing information from relatives. Here, for 50 traits from the UK Biobank data, we show that a design of 5,000 individuals with first-degree relatives of target individuals can achieve a prediction accuracy similar to that of around 220,000 unrelated individuals (mean prediction accuracy = 0.26 vs. 0.24, mean fold-change = 1.06 (95% CI: 0.99-1.13), P-value = 0.08), despite a 44-fold difference in sample size. For lifestyle traits, the prediction accuracy with 5,000 individuals including first-degree relatives of target individuals is significantly higher than that with 220,000 unrelated individuals (mean prediction accuracy = 0.22 vs. 0.16, mean fold-change = 1.40 (1.17-1.62), P-value = 0.025). Our findings suggest that polygenic prediction integrating family information may help to accelerate precision health and clinical intervention. Genetic data from large cohorts of unrelated individuals can be used to create polygenic risk scores, which could be used to predict individual risk of developing a specific disease. Here the authors show that smaller cohorts of related individuals can provide similarly powerful predictive ability.
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1234
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Cheng W, Ramachandran S, Crawford L. Estimation of non-null SNP effect size distributions enables the detection of enriched genes underlying complex traits. PLoS Genet 2020; 16:e1008855. [PMID: 32542026 PMCID: PMC7316356 DOI: 10.1371/journal.pgen.1008855] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 06/25/2020] [Accepted: 05/13/2020] [Indexed: 12/22/2022] Open
Abstract
Traditional univariate genome-wide association studies generate false positives and negatives due to difficulties distinguishing associated variants from variants with spurious nonzero effects that do not directly influence the trait. Recent efforts have been directed at identifying genes or signaling pathways enriched for mutations in quantitative traits or case-control studies, but these can be computationally costly and hampered by strict model assumptions. Here, we present gene-ε, a new approach for identifying statistical associations between sets of variants and quantitative traits. Our key insight is that enrichment studies on the gene-level are improved when we reformulate the genome-wide SNP-level null hypothesis to identify spurious small-to-intermediate SNP effects and classify them as non-causal. gene-ε efficiently identifies enriched genes under a variety of simulated genetic architectures, achieving greater than a 90% true positive rate at 1% false positive rate for polygenic traits. Lastly, we apply gene-ε to summary statistics derived from six quantitative traits using European-ancestry individuals in the UK Biobank, and identify enriched genes that are in biologically relevant pathways.
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Affiliation(s)
- Wei Cheng
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Sohini Ramachandran
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (SR); (LC)
| | - Lorin Crawford
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
- Department of Biostatistics, Brown University, Providence, Rhode Island, United States of America
- Center for Statistical Sciences, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (SR); (LC)
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1235
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Dou J, Wu D, Ding L, Wang K, Jiang M, Chai X, Reilly DF, Tai ES, Liu J, Sim X, Cheng S, Wang C. Using off-target data from whole-exome sequencing to improve genotyping accuracy, association analysis and polygenic risk prediction. Brief Bioinform 2020; 22:5857014. [PMID: 32591784 DOI: 10.1093/bib/bbaa084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/09/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022] Open
Abstract
Whole-exome sequencing (WES) has been widely used to study the role of protein-coding variants in genetic diseases. Non-coding regions, typically covered by sparse off-target data, are often discarded by conventional WES analyses. Here, we develop a genotype calling pipeline named WEScall to analyse both target and off-target data. We leverage linkage disequilibrium shared within study samples and from an external reference panel to improve genotyping accuracy. In an application to WES of 2527 Chinese and Malays, WEScall can reduce the genotype discordance rate from 0.26% (SE= 6.4 × 10-6) to 0.08% (SE = 3.6 × 10-6) across 1.1 million single nucleotide polymorphisms (SNPs) in the deeply sequenced target regions. Furthermore, we obtain genotypes at 0.70% (SE = 3.0 × 10-6) discordance rate across 5.2 million off-target SNPs, which had ~1.2× mean sequencing depth. Using this dataset, we perform genome-wide association studies of 10 metabolic traits. Despite of our small sample size, we identify 10 loci at genome-wide significance (P < 5 × 10-8), including eight well-established loci. The two novel loci, both associated with glycated haemoglobin levels, are GPATCH8-SLC4A1 (rs369762319, P = 2.56 × 10-12) and ROR2 (rs1201042, P = 3.24 × 10-8). Finally, using summary statistics from UK Biobank and Biobank Japan, we show that polygenic risk prediction can be significantly improved for six out of nine traits by incorporating off-target data (P < 0.01). These results demonstrate WEScall as a useful tool to facilitate WES studies with decent amounts of off-target data.
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Affiliation(s)
- Jinzhuang Dou
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Degang Wu
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lin Ding
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Wang
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Minghui Jiang
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | | | | | - E Shyong Tai
- Saw Swee Hock School of Public Health, Duke-NUS Medical School, and Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jianjun Liu
- Genome Institute of Singapore and a professor at Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Shanshan Cheng
- Ministry of Education Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chaolong Wang
- Ministry of Education Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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1236
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Genetic control of non-genetic inheritance in mammals: state-of-the-art and perspectives. Mamm Genome 2020; 31:146-156. [PMID: 32529318 PMCID: PMC7369129 DOI: 10.1007/s00335-020-09841-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022]
Abstract
Thought to be directly and uniquely dependent from genotypes, the ontogeny of individual phenotypes is much more complicated. Individual genetics, environmental exposures, and their interaction are the three main determinants of individual's phenotype. This picture has been further complicated a decade ago when the Lamarckian theory of acquired inheritance has been rekindled with the discovery of epigenetic inheritance, according to which acquired phenotypes can be transmitted through fertilization and affect phenotypes across generations. The results of Genome-Wide Association Studies have also highlighted a big degree of missing heritability in genetics and have provided hints that not only acquired phenotypes, but also individual's genotypes affect phenotypes intergenerationally through indirect genetic effects. Here, we review available examples of indirect genetic effects in mammals, what is known of the underlying molecular mechanisms and their potential impact for our understanding of missing heritability, phenotypic variation. and individual disease risk.
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1237
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Smeland OB, Frei O, Dale AM, Andreassen OA. The polygenic architecture of schizophrenia — rethinking pathogenesis and nosology. Nat Rev Neurol 2020; 16:366-379. [DOI: 10.1038/s41582-020-0364-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2020] [Indexed: 02/07/2023]
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1238
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Shared polygenic risk for ADHD, executive dysfunction and other psychiatric disorders. Transl Psychiatry 2020; 10:182. [PMID: 32518222 PMCID: PMC7283259 DOI: 10.1038/s41398-020-00872-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/15/2020] [Accepted: 05/26/2020] [Indexed: 12/14/2022] Open
Abstract
Many psychiatric disorders are associated with impaired executive functioning (EF). The associated EF component varies by psychiatric disorders, and this variation might be due to genetic liability. We explored the genetic association between five psychiatric disorders and EF in clinically-recruited attention deficit hyperactivity disorder (ADHD) children using polygenic risk score (PRS) methodology. Genome-wide association study (GWAS) summary data for ADHD, major depressive disorder (MDD), schizophrenia (SZ), bipolar disorder (BIP) and autism were used to calculate the PRSs. EF was evaluated by the Stroop test for inhibitory control, the trail-making test for cognitive flexibility, and the digital span test for working memory in a Chinese ADHD cohort (n = 1147). Exploratory factor analysis of the three measures identified one principal component for EF (EF-PC). Linear regression models were used to analyze the association between each PRS and the EF measures. The role of EF measures in mediating the effects of the PRSs on ADHD symptoms was also analyzed. The result showed the PRSs for MDD, ADHD and BIP were all significantly associated with the EF-PC. For each EF component, the association results were different for the PRSs of the five psychiatric disorders: the PRSs for ADHD and MDD were associated with inhibitory control (adjusted P = 0.0183 and 0.0313, respectively), the PRS for BIP was associated with working memory (adjusted P = 0.0416), and the PRS for SZ was associated with cognitive flexibility (adjusted P = 0.0335). All three EF measures were significantly correlated with ADHD symptoms. In mediation analyses, the ADHD and MDD PRSs, which were associated with inhibitory control, had significant indirect effects on ADHD symptoms through the mediation of inhibitory control. These findings indicate that the polygenic risks for several psychiatric disorders influence specific executive dysfunction in children with ADHD. The results helped to clarify the relationship between risk genes of each mental disorder and the intermediate cognitive domain, which may further help elucidate the risk genes and motivate efforts to develop EF measures as a diagnostic marker and future treatment target.
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1239
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Aragam KG, Dobbyn A, Judy R, Chaffin M, Chaudhary K, Hindy G, Cagan A, Finneran P, Weng LC, Loos RJ, Nadkarni G, Cho JH, Kember RL, Baras A, Reid J, Overton J, Philippakis A, Ellinor PT, Weiss ST, Rader DJ, Lubitz SA, Smoller JW, Karlson EW, Khera AV, Kathiresan S, Do R, Damrauer SM, Natarajan P. Limitations of Contemporary Guidelines for Managing Patients at High Genetic Risk of Coronary Artery Disease. J Am Coll Cardiol 2020; 75:2769-2780. [PMID: 32498804 PMCID: PMC7346975 DOI: 10.1016/j.jacc.2020.04.027] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/31/2020] [Accepted: 04/07/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND Polygenic risk scores (PRS) for coronary artery disease (CAD) identify high-risk individuals more likely to benefit from primary prevention statin therapy. Whether polygenic CAD risk is captured by conventional paradigms for assessing clinical cardiovascular risk remains unclear. OBJECTIVES This study sought to intersect polygenic risk with guideline-based recommendations and management patterns for CAD primary prevention. METHODS A genome-wide CAD PRS was applied to 47,108 individuals across 3 U.S. health care systems. The authors then assessed whether primary prevention patients at high polygenic risk might be distinguished on the basis of greater guideline-recommended statin eligibility and higher rates of statin therapy. RESULTS Of 47,108 study participants, the mean age was 60 years, and 11,020 (23.4%) had CAD. The CAD PRS strongly associated with prevalent CAD (odds ratio: 1.4 per SD increase in PRS; p < 0.0001). High polygenic risk (top 20% of PRS) conferred 1.9-fold odds of developing CAD (p < 0.0001). However, among primary prevention patients (n = 33,251), high polygenic risk did not correspond with increased recommendations for statin therapy per the American College of Cardiology/American Heart Association (46.2% for those with high PRS vs. 46.8% for all others, p = 0.54) or U.S. Preventive Services Task Force (43.7% vs. 43.7%, p = 0.99) or higher rates of statin prescriptions (25.0% vs. 23.8%, p = 0.04). An additional 4.1% of primary prevention patients may be recommended for statin therapy if high CAD PRS were considered a guideline-based risk-enhancing factor. CONCLUSIONS Current paradigms for primary cardiovascular prevention incompletely capture a polygenic susceptibility to CAD. An opportunity may exist to improve CAD prevention efforts by integrating both genetic and clinical risk.
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Affiliation(s)
- Krishna G. Aragam
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, USA,Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Amanda Dobbyn
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Renae Judy
- Department of Surgery, Perlman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark Chaffin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Kumardeep Chaudhary
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - George Hindy
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Andrew Cagan
- Research Computing, Partners HealthCare, Charlestown, MA, USA
| | - Phoebe Finneran
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Lu-Chen Weng
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, USA,Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Girish Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Judy H. Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rachel L. Kember
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | - Anthony Philippakis
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Patrick T. Ellinor
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, USA,Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Scott T. Weiss
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Daniel J. Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Steven A. Lubitz
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, USA,Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
| | - Jordan W. Smoller
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA,Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA,Stanley Center for Psychiatric Research, Broad Institute, Boston, MA, USA
| | - Elizabeth W. Karlson
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, MA, USA
| | - Amit V. Khera
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Sekar Kathiresan
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Scott M. Damrauer
- Department of Surgery, Perlman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA,Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Pradeep Natarajan
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts; Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
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1240
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Ishigaki K, Akiyama M, Kanai M, Takahashi A, Kawakami E, Sugishita H, Sakaue S, Matoba N, Low SK, Okada Y, Terao C, Amariuta T, Gazal S, Kochi Y, Horikoshi M, Suzuki K, Ito K, Koyama S, Ozaki K, Niida S, Sakata Y, Sakata Y, Kohno T, Shiraishi K, Momozawa Y, Hirata M, Matsuda K, Ikeda M, Iwata N, Ikegawa S, Kou I, Tanaka T, Nakagawa H, Suzuki A, Hirota T, Tamari M, Chayama K, Miki D, Mori M, Nagayama S, Daigo Y, Miki Y, Katagiri T, Ogawa O, Obara W, Ito H, Yoshida T, Imoto I, Takahashi T, Tanikawa C, Suzuki T, Sinozaki N, Minami S, Yamaguchi H, Asai S, Takahashi Y, Yamaji K, Takahashi K, Fujioka T, Takata R, Yanai H, Masumoto A, Koretsune Y, Kutsumi H, Higashiyama M, Murayama S, Minegishi N, Suzuki K, Tanno K, Shimizu A, Yamaji T, Iwasaki M, Sawada N, Uemura H, Tanaka K, Naito M, Sasaki M, Wakai K, Tsugane S, Yamamoto M, Yamamoto K, Murakami Y, Nakamura Y, Raychaudhuri S, Inazawa J, Yamauchi T, Kadowaki T, Kubo M, Kamatani Y. Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases. Nat Genet 2020; 52:669-679. [PMID: 32514122 DOI: 10.1038/s41588-020-0640-3] [Citation(s) in RCA: 269] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/01/2020] [Indexed: 12/20/2022]
Abstract
The overwhelming majority of participants in current genetic studies are of European ancestry. To elucidate disease biology in the East Asian population, we conducted a genome-wide association study (GWAS) with 212,453 Japanese individuals across 42 diseases. We detected 320 independent signals in 276 loci for 27 diseases, with 25 novel loci (P < 9.58 × 10-9). East Asian-specific missense variants were identified as candidate causal variants for three novel loci, and we successfully replicated two of them by analyzing independent Japanese cohorts; p.R220W of ATG16L2 (associated with coronary artery disease) and p.V326A of POT1 (associated with lung cancer). We further investigated enrichment of heritability within 2,868 annotations of genome-wide transcription factor occupancy, and identified 378 significant enrichments across nine diseases (false discovery rate < 0.05) (for example, NKX3-1 for prostate cancer). This large-scale GWAS in a Japanese population provides insights into the etiology of complex diseases and highlights the importance of performing GWAS in non-European populations.
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Affiliation(s)
- Kazuyoshi Ishigaki
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Center for Data Sciences, Harvard Medical School, Boston, MA, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahiro Kanai
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Genomic Medicine, Research Institute, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Eiryo Kawakami
- Medical Sciences Innovation Hub Program (MIH), RIKEN, Yokohama, Japan.,Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroki Sugishita
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Saori Sakaue
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan.,Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nana Matoba
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Genetics and UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Siew-Kee Low
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yukinori Okada
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan.,Laboratory of Statistical Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tiffany Amariuta
- Center for Data Sciences, Harvard Medical School, Boston, MA, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Steven Gazal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yuta Kochi
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Momoko Horikoshi
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ken Suzuki
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan.,Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kaoru Ito
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Satoshi Koyama
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kouichi Ozaki
- Medical Genome Center, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Shumpei Niida
- Medical Genome Center, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yasuhiko Sakata
- Department of Cardiovascular Medicine, Tohoku University Graduate School of Medicine, Tohoku, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Makoto Hirata
- Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Koichi Matsuda
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Masashi Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Aichi, Japan
| | - Nakao Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Aichi, Japan
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Ikuyo Kou
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Toshihiro Tanaka
- Laboratory for Cardiovascular Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hidewaki Nakagawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tomomitsu Hirota
- Laboratory for Respiratory and Allergic Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mayumi Tamari
- Laboratory for Respiratory and Allergic Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Daiki Miki
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Masaki Mori
- Department of Surgery and Sciences, Graduate School of Medicine, Kyushu University, Fukuoka, Japan
| | - Satoshi Nagayama
- Department of Gastroenterological Surgery, The Cancer Institute Hospital of the Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yataro Daigo
- Department of Medical Oncology and Cancer Center, and Center for Advanced Medicine against Cancer, Shiga University of Medical Science, Shiga, Japan.,Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoshio Miki
- Department of Genetic Diagnosis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Toyomasa Katagiri
- Division of Genome Medicine, Institute for Genome Research, Tokushima University, Tokushima, Japan
| | - Osamu Ogawa
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Wataru Obara
- Department of Urology, Iwate Medical University School of Medicine, Iwate, Japan
| | - Hidemi Ito
- Division of Cancer Information and Control, Aichi Cancer Center Research Institute, Nagoya, Japan.,Division of Descriptive Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Teruhiko Yoshida
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Issei Imoto
- Division of Molecular Genetics, Aichi Cancer Center Research Institute, Nagoya, Japan.,Risk Assessment Center, Aichi Caner Center Hospital, Nagoya, Japan.,Division of Cancer Genetics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Chizu Tanikawa
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | | | - Shiro Minami
- Department of Bioregulation, Nippon Medical School, Kawasaki, Japan
| | | | - Satoshi Asai
- Division of Pharmacology, Department of Biomedical Science, Nihon University School of Medicine, Tokyo, Japan.,Division of Genomic Epidemiology and Clinical Trials, Clinical Trials Research Center, Nihon University School of Medicine, Tokyo, Japan
| | - Yasuo Takahashi
- Division of Genomic Epidemiology and Clinical Trials, Clinical Trials Research Center, Nihon University School of Medicine, Tokyo, Japan
| | - Ken Yamaji
- Department of Internal Medicine and Rheumatology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kazuhisa Takahashi
- Department of Respiratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tomoaki Fujioka
- Department of Urology, Iwate Medical University School of Medicine, Iwate, Japan
| | - Ryo Takata
- Department of Urology, Iwate Medical University School of Medicine, Iwate, Japan
| | - Hideki Yanai
- Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | | | | | - Hiromu Kutsumi
- Center for Clinical Research and Advanced Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Masahiko Higashiyama
- Department of General Thoracic Surgery, Osaka International Cancer Institute, Osaka, Japan
| | - Shigeo Murayama
- Department of Neurology and Neuropathology (the Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kichiya Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kozo Tanno
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Atsushi Shimizu
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Taiki Yamaji
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Norie Sawada
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Hirokazu Uemura
- Department of Preventive Medicine, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan.,College of Nursing Art and Science, University of Hyogo, Akashi, Japan
| | - Keitaro Tanaka
- Department of Preventive Medicine, Saga University Faculty of Medicine, Saga, Japan
| | - 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
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shoichiro Tsugane
- Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yusuke Nakamura
- Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Soumya Raychaudhuri
- Center for Data Sciences, Harvard Medical School, Boston, MA, USA. .,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. .,Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan. .,Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Toshimasa Yamauchi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Takashi Kadowaki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan. .,Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.
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1241
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Cho SK, Kim B, Myung W, Chang Y, Ryu S, Kim HN, Kim HL, Kuo PH, Winkler CA, Won HH. Polygenic analysis of the effect of common and low-frequency genetic variants on serum uric acid levels in Korean individuals. Sci Rep 2020; 10:9179. [PMID: 32514006 PMCID: PMC7280503 DOI: 10.1038/s41598-020-66064-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 05/05/2020] [Indexed: 01/28/2023] Open
Abstract
Increased serum uric acid (SUA) levels cause gout and are associated with multiple diseases, including chronic kidney disease. Previous genome-wide association studies (GWAS) have identified more than 180 loci that contribute to SUA levels. Here, we investigated genetic determinants of SUA level in the Korean population. We conducted a GWAS for SUA in 6,881 Korean individuals, calculated polygenic risk scores (PRSs) for common variants, and validated the association of low-frequency variants and PRS with SUA levels in 3,194 individuals. We identified two low-frequency and six common independent variants associated with SUA. Despite the overall similar effect sizes of variants in Korean and European populations, the proportion of variance for SUA levels explained by the variants was greater in the Korean population. A rare, nonsense variant SLC22A12 p.W258X showed the most significant association with reduced SUA levels, and PRSs of common variants associated with SUA levels were significant in multiple Korean cohorts. Interestingly, an East Asian-specific missense variant (rs671) in ALDH2 displayed a significant association on chromosome 12 with the SUA level. Further genetic epidemiological studies on SUA are needed in ethnically diverse cohorts to investigate rare or low-frequency variants and determine the influence of genetic and environmental factors on SUA.
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Affiliation(s)
- Sung Kweon Cho
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, Republic of Korea.,Molecular Genetic Epidemiology Section, Basic Research Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Beomsu Kim
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, Republic of Korea
| | - Woojae Myung
- Department of Neuropsychiatry, Seoul National University Bundang Hospital, Seongnam-si, Republic of Korea
| | - Yoosoo Chang
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seungho Ryu
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Han-Na Kim
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyung-Lae Kim
- Department of Biochemistry, Ewha Womans University, Seoul, Republic of Korea
| | - Po-Hsiu Kuo
- Department of Public Health & Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Cheryl A Winkler
- Molecular Genetic Epidemiology Section, Basic Research Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Hong-Hee Won
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, Republic of Korea.
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1242
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Fernandez-Rhodes L, Young KL, Lilly AG, Raffield LM, Highland HM, Wojcik GL, Agler C, M Love SA, Okello S, Petty LE, Graff M, Below JE, Divaris K, North KE. Importance of Genetic Studies of Cardiometabolic Disease in Diverse Populations. Circ Res 2020; 126:1816-1840. [PMID: 32496918 PMCID: PMC7285892 DOI: 10.1161/circresaha.120.315893] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies have revolutionized our understanding of the genetic underpinnings of cardiometabolic disease. Yet, the inadequate representation of individuals of diverse ancestral backgrounds in these studies may undercut their ultimate potential for both public health and precision medicine. The goal of this review is to describe the imperativeness of studying the populations who are most affected by cardiometabolic disease, to the aim of better understanding the genetic underpinnings of the disease. We support this premise by describing the current variation in the global burden of cardiometabolic disease and emphasize the importance of building a globally and ancestrally representative genetics evidence base for the identification of population-specific variants, fine-mapping, and polygenic risk score estimation. We discuss the important ethical, legal, and social implications of increasing ancestral diversity in genetic studies of cardiometabolic disease and the challenges that arise from the (1) lack of diversity in current reference populations and available analytic samples and the (2) unequal generation of health-associated genomic data and their prediction accuracies. Despite these challenges, we conclude that additional, unprecedented opportunities lie ahead for public health genomics and the realization of precision medicine, provided that the gap in diversity can be systematically addressed. Achieving this goal will require concerted efforts by social, academic, professional and regulatory stakeholders and communities, and these efforts must be based on principles of equity and social justice.
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Affiliation(s)
- Lindsay Fernandez-Rhodes
- Department of Biobehavioral Health, College of Health and Human Development, Pennsylvania State University, University Park, PA
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Adam G Lilly
- Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Heather M Highland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Cary Agler
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Shelly-Ann M Love
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Samson Okello
- Department of Internal Medicine, Mbarara University of Science and Technology, Uganda
- University of Virginia, Charlottesville, VA
- Harvard TH Chan School of Public Health, Boston, MA
| | - Lauren E Petty
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Vanderbilt, TN
- Department of Genetic Medicine, Vanderbilt University, Vanderbilt, TN
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Vanderbilt, TN
- Department of Genetic Medicine, Vanderbilt University, Vanderbilt, TN
| | - Kimon Divaris
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Carolina Center for Genome Sciences, Chapel Hill, NC
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1243
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Shi H, Burch KS, Johnson R, Freund MK, Kichaev G, Mancuso N, Manuel AM, Dong N, Pasaniuc B. Localizing Components of Shared Transethnic Genetic Architecture of Complex Traits from GWAS Summary Data. Am J Hum Genet 2020; 106:805-817. [PMID: 32442408 PMCID: PMC7273527 DOI: 10.1016/j.ajhg.2020.04.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/20/2020] [Indexed: 12/19/2022] Open
Abstract
Despite strong transethnic genetic correlations reported in the literature for many complex traits, the non-transferability of polygenic risk scores across populations suggests the presence of population-specific components of genetic architecture. We propose an approach that models GWAS summary data for one trait in two populations to estimate genome-wide proportions of population-specific/shared causal SNPs. In simulations across various genetic architectures, we show that our approach yields approximately unbiased estimates with in-sample LD and slight upward-bias with out-of-sample LD. We analyze nine complex traits in individuals of East Asian and European ancestry, restricting to common SNPs (MAF > 5%), and find that most common causal SNPs are shared by both populations. Using the genome-wide estimates as priors in an empirical Bayes framework, we perform fine-mapping and observe that high-posterior SNPs (for both the population-specific and shared causal configurations) have highly correlated effects in East Asians and Europeans. In population-specific GWAS risk regions, we observe a 2.8× enrichment of shared high-posterior SNPs, suggesting that population-specific GWAS risk regions harbor shared causal SNPs that are undetected in the other GWASs due to differences in LD, allele frequencies, and/or sample size. Finally, we report enrichments of shared high-posterior SNPs in 53 tissue-specific functional categories and find evidence that SNP-heritability enrichments are driven largely by many low-effect common SNPs.
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Affiliation(s)
- Huwenbo Shi
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Kathryn S Burch
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Ruth Johnson
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Malika K Freund
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gleb Kichaev
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Astrid M Manuel
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
| | - Natalie Dong
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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1244
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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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1245
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A positively selected FBN1 missense variant reduces height in Peruvian individuals. Nature 2020; 582:234-239. [PMID: 32499652 PMCID: PMC7410362 DOI: 10.1038/s41586-020-2302-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/10/2020] [Indexed: 01/21/2023]
Abstract
On average, Peruvian individuals are among the shortest in the world1. Here we show that Native American ancestry is associated with reduced height in an ethnically diverse group of Peruvian individuals, and identify a population-specific, missense variant in the FBN1 gene (E1297G) that is significantly associated with lower height. Each copy of the minor allele (frequency of 4.7%) reduces height by 2.2 cm (4.4 cm in homozygous individuals). To our knowledge, this is the largest effect size known for a common height-associated variant. FBN1 encodes the extracellular matrix protein fibrillin 1, which is a major structural component of microfibrils. We observed less densely packed fibrillin-1-rich microfibrils with irregular edges in the skin of individuals who were homozygous for G1297 compared with individuals who were homozygous for E1297. Moreover, we show that the E1297G locus is under positive selection in non-African populations, and that the E1297 variant shows subtle evidence of positive selection specifically within the Peruvian population. This variant is also significantly more frequent in coastal Peruvian populations than in populations from the Andes or the Amazon, which suggests that short stature might be the result of adaptation to factors that are associated with the coastal environment in Peru.
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1246
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Stein DJ, Lehner T, Lombard Z, Pringle B, Senthil G, Uddin M. Mental health delivery and neurogenetics discovery in Africa. Lancet Psychiatry 2020; 7:473-474. [PMID: 32445676 PMCID: PMC8214223 DOI: 10.1016/s2215-0366(20)30085-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 02/19/2020] [Indexed: 11/17/2022]
Affiliation(s)
- Dan J Stein
- SAMRC Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, 7925, South Africa.
| | - Thomas Lehner
- New York Genome Center, New York, NY, USA; National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA; New York Genome Center, New York, NY, USA
| | - Zane Lombard
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa
| | - Beverly Pringle
- Center for Global Mental Health Research, National Institutes of Health, Bethesda, MD, USA
| | - Geetha Senthil
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Monica Uddin
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
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1247
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Johnson EC, Chang Y, Agrawal A. An update on the role of common genetic variation underlying substance use disorders. CURRENT GENETIC MEDICINE REPORTS 2020; 8:35-46. [PMID: 33457110 PMCID: PMC7810203 DOI: 10.1007/s40142-020-00184-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PURPOSE OF THE REVIEW Sample size increases have resulted in novel and replicable loci for substance use disorders (SUDs). We summarize some of the latest insights into SUD genetics and discuss some next steps in addiction genetics. RECENT FINDINGS Genome-wide association studies have substantiated the role of previously known variants (e.g., rs1229984 in ADH1B for alcohol) and identified several novel loci for alcohol, tobacco, cannabis, opioid and cocaine use disorders. SUDs are genetically correlated with psychiatric outcomes, while liability to substance use is inconsistently associated with these outcomes and more closely associated with lifestyle factors. Specific variant associations appear to differ somewhat across populations, although similar genes and systems are implicated. SUMMARY The next decade of human genetic studies of addiction should focus on expanding to non-European populations, consider pleiotropy across SUD and with other psychiatric disorders, and leverage human and cross-species functional data to elucidate the biological mechanisms underlying SUDs.
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Affiliation(s)
- Emma C Johnson
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
| | - Yoonhoo Chang
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, Saint Louis, MO
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
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1248
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Schienda J, Stopfer J. Cancer Genetic Counseling-Current Practice and Future Challenges. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a036541. [PMID: 31548230 DOI: 10.1101/cshperspect.a036541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cancer genetic counseling practice is rapidly evolving, with services being provided in increasingly novel ways. Pretest counseling for cancer patients may be abbreviated from traditional models to cover the elements of informed consent in the broadest of strokes. Genetic testing may be ordered by a cancer genetics professional, oncology provider, or primary care provider. Increasingly, direct-to-consumer testing options are available and utilized by consumers anxious to take control of their genetic health. Finally, genetic information is being used to inform oncology care, from surgical decision-making to selection of chemotherapeutic agent. This review provides an overview of the current and evolving practice of cancer genetic counseling as well as opportunities and challenges for a wide variety of indications in both the adult and pediatric setting.
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Affiliation(s)
- Jaclyn Schienda
- Division of Cancer Genetics and Prevention, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Jill Stopfer
- Division of Cancer Genetics and Prevention, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
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1249
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Mathieson I. Human adaptation over the past 40,000 years. Curr Opin Genet Dev 2020; 62:97-104. [PMID: 32745952 PMCID: PMC7484260 DOI: 10.1016/j.gde.2020.06.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/10/2020] [Accepted: 06/01/2020] [Indexed: 02/07/2023]
Abstract
Over the past few years several methodological and data-driven advances have greatly improved our ability to robustly detect genomic signatures of selection in humans. New methods applied to large samples of present-day genomes provide increased power, while ancient DNA allows precise estimation of timing and tempo. However, despite these advances, we are still limited in our ability to translate these signatures into understanding about which traits were actually under selection, and why. Combining information from different populations and timescales may allow interpretation of selective sweeps. Other modes of selection have proved more difficult to detect. In particular, despite strong evidence of the polygenicity of most human traits, evidence for polygenic selection is weak, and its importance in recent human evolution remains unclear. Balancing selection and archaic introgression seem important for the maintenance of potentially adaptive immune diversity, but perhaps less so for other traits.
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Affiliation(s)
- Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, United States.
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Harden KP, Koellinger PD. Using genetics for social science. Nat Hum Behav 2020; 4:567-576. [PMID: 32393836 PMCID: PMC8240138 DOI: 10.1038/s41562-020-0862-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/16/2020] [Indexed: 02/06/2023]
Abstract
Social science genetics is concerned with understanding whether, how and why genetic differences between human beings are linked to differences in behaviours and socioeconomic outcomes. Our review discusses the goals, methods, challenges and implications of this research endeavour. We survey how the recent developments in genetics are beginning to provide social scientists with a powerful new toolbox they can use to better understand environmental effects, and we illustrate this with several substantive examples. Furthermore, we examine how medical research can benefit from genetic insights into social-scientific outcomes and vice versa. Finally, we discuss the ethical challenges of this work and clarify several common misunderstandings and misinterpretations of genetic research on individual differences.
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Affiliation(s)
- K Paige Harden
- Department of Psychology, University of Texas at Austin, Austin, Texas, USA.
| | - Philipp D Koellinger
- Department of Economics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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