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Kullo IJ. Promoting equity in polygenic risk assessment through global collaboration. Nat Genet 2024; 56:1780-1787. [PMID: 39103647 DOI: 10.1038/s41588-024-01843-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 06/24/2024] [Indexed: 08/07/2024]
Abstract
The long delay before genomic technologies become available in low- and middle-income countries is a concern from both scientific and ethical standpoints. Polygenic risk scores (PRSs), a relatively recent advance in genomics, could have a substantial impact on promoting health by improving disease risk prediction and guiding preventive strategies. However, clinical use of PRSs in their current forms might widen global health disparities, as their portability to diverse groups is limited. This Perspective highlights the need for global collaboration to develop and implement PRSs that perform equitably across the world. Such collaboration requires capacity building and the generation of new data in low-resource settings, the sharing of harmonized genotype and phenotype data securely across borders, novel population genetics and statistical methods to improve PRS performance, and thoughtful clinical implementation in diverse settings. All this needs to occur while considering the ethical, legal and social implications, with support from regulatory and funding agencies and policymakers.
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Affiliation(s)
- Iftikhar J Kullo
- Department of Cardiovascular Medicine and the Gonda Vascular Center, Mayo Clinic, Rochester, MN, USA.
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2
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Biddanda A, Bandyopadhyay E, de la Fuente Castro C, Witonsky D, Urban Aragon JA, Pasupuleti N, Moots HM, Fonseca R, Freilich S, Stanisavic J, Willis T, Menon A, Mustak MS, Kodira CD, Naren AP, Sikdar M, Rai N, Raghavan M. Distinct positions of genetic and oral histories: Perspectives from India. HGG ADVANCES 2024; 5:100305. [PMID: 38720459 PMCID: PMC11153255 DOI: 10.1016/j.xhgg.2024.100305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/04/2024] [Accepted: 05/04/2024] [Indexed: 05/16/2024] Open
Abstract
Over the past decade, genomic data have contributed to several insights on global human population histories. These studies have been met both with interest and critically, particularly by populations with oral histories that are records of their past and often reference their origins. While several studies have reported concordance between oral and genetic histories, there is potential for tension that may stem from genetic histories being prioritized or used to confirm community-based knowledge and ethnography, especially if they differ. To investigate the interplay between oral and genetic histories, we focused on the southwestern region of India and analyzed whole-genome sequence data from 156 individuals identifying as Bunt, Kodava, Nair, and Kapla. We supplemented limited anthropological records on these populations with oral history accounts from community members and historical literature, focusing on references to non-local origins such as the ancient Scythians in the case of Bunt, Kodava, and Nair, members of Alexander the Great's army for the Kodava, and an African-related source for Kapla. We found these populations to be genetically most similar to other Indian populations, with the Kapla more similar to South Indian tribal populations that maximize a genetic ancestry related to Ancient Ancestral South Indians. We did not find evidence of additional genetic sources in the study populations than those known to have contributed to many other present-day South Asian populations. Our results demonstrate that oral and genetic histories may not always provide consistent accounts of population origins and motivate further community-engaged, multi-disciplinary investigations of non-local origin stories in these communities.
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Affiliation(s)
- Arjun Biddanda
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Esha Bandyopadhyay
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Constanza de la Fuente Castro
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA; Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - David Witonsky
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | | | - Nagarjuna Pasupuleti
- Department of Applied Zoology, Mangalore University, Mangalagangothri, Karnataka 574199, India
| | - Hannah M Moots
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA; Institute for the Study of Ancient Cultures Museum, University of Chicago, Chicago, IL, USA
| | - Renée Fonseca
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Suzanne Freilich
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA; Department of Evolutionary Anthropology, University of Vienna, Vienna 1090, Austria
| | - Jovan Stanisavic
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Tabitha Willis
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Anoushka Menon
- Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK
| | - Mohammed S Mustak
- Department of Applied Zoology, Mangalore University, Mangalagangothri, Karnataka 574199, India
| | | | - Anjaparavanda P Naren
- Division of Pulmonary Medicine, Cystic Fibrosis Research Center, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Mithun Sikdar
- Anthropological Survey of India, Mysore, Karnataka 570026, India
| | - Niraj Rai
- Birbal Sahni Institute of Palaeosciences, Uttar Pradesh, Lucknow, Uttar Pradesh 226007, India.
| | - Maanasa Raghavan
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
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3
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Monti R, Eick L, Hudjashov G, Läll K, Kanoni S, Wolford BN, Wingfield B, Pain O, Wharrie S, Jermy B, McMahon A, Hartonen T, Heyne H, Mars N, Lambert S, Hveem K, Inouye M, van Heel DA, Mägi R, Marttinen P, Ripatti S, Ganna A, Lippert C. Evaluation of polygenic scoring methods in five biobanks shows larger variation between biobanks than methods and finds benefits of ensemble learning. Am J Hum Genet 2024; 111:1431-1447. [PMID: 38908374 PMCID: PMC11267524 DOI: 10.1016/j.ajhg.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/24/2024] Open
Abstract
Methods of estimating polygenic scores (PGSs) from genome-wide association studies are increasingly utilized. However, independent method evaluation is lacking, and method comparisons are often limited. Here, we evaluate polygenic scores derived via seven methods in five biobank studies (totaling about 1.2 million participants) across 16 diseases and quantitative traits, building on a reference-standardized framework. We conducted meta-analyses to quantify the effects of method choice, hyperparameter tuning, method ensembling, and the target biobank on PGS performance. We found that no single method consistently outperformed all others. PGS effect sizes were more variable between biobanks than between methods within biobanks when methods were well tuned. Differences between methods were largest for the two investigated autoimmune diseases, seropositive rheumatoid arthritis and type 1 diabetes. For most methods, cross-validation was more reliable for tuning hyperparameters than automatic tuning (without the use of target data). For a given target phenotype, elastic net models combining PGS across methods (ensemble PGS) tuned in the UK Biobank provided consistent, high, and cross-biobank transferable performance, increasing PGS effect sizes (β coefficients) by a median of 5.0% relative to LDpred2 and MegaPRS (the two best-performing single methods when tuned with cross-validation). Our interactively browsable online-results and open-source workflow prspipe provide a rich resource and reference for the analysis of polygenic scoring methods across biobanks.
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Affiliation(s)
- Remo Monti
- Hasso Plattner Institute, University of Potsdam, Digital Engineering Faculty, Potsdam, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Lisa Eick
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Georgi Hudjashov
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Kristi Läll
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Stavroula Kanoni
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Brooke N Wolford
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health, Norwegian University of Science and Technology, Trondheim, Norway
| | - Benjamin Wingfield
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Oliver Pain
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience; Institute of Psychiatry, Psychology and Neuroscience; King's College London, London, UK
| | - Sophie Wharrie
- Aalto University, Department of Computer Science, Espoo, Finland
| | - Bradley Jermy
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tuomo Hartonen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Henrike Heyne
- Hasso Plattner Institute, University of Potsdam, Digital Engineering Faculty, Potsdam, Germany
| | - Nina Mars
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samuel Lambert
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway; Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; British Heart Foundation Cambridge Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health, Norwegian University of Science and Technology, Trondheim, Norway; Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; British Heart Foundation Cambridge Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | | | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Pekka Marttinen
- Aalto University, Department of Computer Science, Espoo, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Department of Public Health, University of Helsinki, Helsinki, Finland; Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Massachusetts General Hospital and Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christoph Lippert
- Hasso Plattner Institute, University of Potsdam, Digital Engineering Faculty, Potsdam, Germany; Windreich Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Diagnostic, Molecular, and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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4
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Lassen FH, Venkatesh SS, Baya N, Hill B, Zhou W, Bloemendal A, Neale BM, Kessler BM, Whiffin N, Lindgren CM, Palmer DS. Exome-wide evidence of compound heterozygous effects across common phenotypes in the UK Biobank. CELL GENOMICS 2024; 4:100602. [PMID: 38944039 PMCID: PMC11293579 DOI: 10.1016/j.xgen.2024.100602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 03/11/2024] [Accepted: 06/07/2024] [Indexed: 07/01/2024]
Abstract
The phenotypic impact of compound heterozygous (CH) variation has not been investigated at the population scale. We phased rare variants (MAF ∼0.001%) in the UK Biobank (UKBB) exome-sequencing data to characterize recessive effects in 175,587 individuals across 311 common diseases. A total of 6.5% of individuals carry putatively damaging CH variants, 90% of which are only identifiable upon phasing rare variants (MAF < 0.38%). We identify six recessive gene-trait associations (p < 1.68 × 10-7) after accounting for relatedness, polygenicity, nearby common variants, and rare variant burden. Of these, just one is discovered when considering homozygosity alone. Using longitudinal health records, we additionally identify and replicate a novel association between bi-allelic variation in ATP2C2 and an earlier age at onset of chronic obstructive pulmonary disease (COPD) (p < 3.58 × 10-8). Genetic phase contributes to disease risk for gene-trait pairs: ATP2C2-COPD (p = 0.000238), FLG-asthma (p = 0.00205), and USH2A-visual impairment (p = 0.0084). We demonstrate the power of phasing large-scale genetic cohorts to discover phenome-wide consequences of compound heterozygosity.
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Affiliation(s)
- Frederik H Lassen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
| | - Samvida S Venkatesh
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Nikolas Baya
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Barney Hill
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Wei Zhou
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alex Bloemendal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Novo Nordisk Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin M Neale
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicola Whiffin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cecilia M Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK; Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, UK.
| | - Duncan S Palmer
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, UK.
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5
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Wenteler A, Cabrera CP, Wei W, Neduva V, Barnes MR. AI approaches for the discovery and validation of drug targets. CAMBRIDGE PRISMS. PRECISION MEDICINE 2024; 2:e7. [PMID: 39258224 PMCID: PMC11383977 DOI: 10.1017/pcm.2024.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 09/12/2024]
Abstract
Artificial intelligence (AI) holds immense promise for accelerating and improving all aspects of drug discovery, not least target discovery and validation. By integrating a diverse range of biological data modalities, AI enables the accurate prediction of drug target properties, ultimately illuminating biological mechanisms of disease and guiding drug discovery strategies. Despite the indisputable potential of AI in drug target discovery, there are many challenges and obstacles yet to be overcome, including dealing with data biases, model interpretability and generalisability, and the validation of predicted drug targets, to name a few. By exploring recent advancements in AI, this review showcases current applications of AI for drug target discovery and offers perspectives on the future of AI for the discovery and validation of drug targets, paving the way for the generation of novel and safer pharmaceuticals.
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Affiliation(s)
- Aaron Wenteler
- Digital Environment Research Institute, Queen Mary University of London, London, United Kingdom
- Centre for Translational Bioinformatics, William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
- MSD Discovery Centre, London, United Kingdom
| | - Claudia P Cabrera
- Digital Environment Research Institute, Queen Mary University of London, London, United Kingdom
- Centre for Translational Bioinformatics, William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Wei Wei
- MSD Discovery Centre, London, United Kingdom
| | | | - Michael R Barnes
- Digital Environment Research Institute, Queen Mary University of London, London, United Kingdom
- Centre for Translational Bioinformatics, William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- The Alan Turing Institute, London, United Kingdom
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6
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Truong B, Hull LE, Ruan Y, Huang QQ, Hornsby W, Martin H, van Heel DA, Wang Y, Martin AR, Lee SH, Natarajan P. Integrative polygenic risk score improves the prediction accuracy of complex traits and diseases. CELL GENOMICS 2024; 4:100523. [PMID: 38508198 PMCID: PMC11019356 DOI: 10.1016/j.xgen.2024.100523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/15/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
Polygenic risk scores (PRSs) are an emerging tool to predict the clinical phenotypes and outcomes of individuals. We propose PRSmix, a framework that leverages the PRS corpus of a target trait to improve prediction accuracy, and PRSmix+, which incorporates genetically correlated traits to better capture the human genetic architecture for 47 and 32 diseases/traits in European and South Asian ancestries, respectively. PRSmix demonstrated a mean prediction accuracy improvement of 1.20-fold (95% confidence interval [CI], [1.10; 1.3]; p = 9.17 × 10-5) and 1.19-fold (95% CI, [1.11; 1.27]; p = 1.92 × 10-6), and PRSmix+ improved the prediction accuracy by 1.72-fold (95% CI, [1.40; 2.04]; p = 7.58 × 10-6) and 1.42-fold (95% CI, [1.25; 1.59]; p = 8.01 × 10-7) in European and South Asian ancestries, respectively. Compared to the previously cross-trait-combination methods with scores from pre-defined correlated traits, we demonstrated that our method improved prediction accuracy for coronary artery disease up to 3.27-fold (95% CI, [2.1; 4.44]; p value after false discovery rate (FDR) correction = 2.6 × 10-4). Our method provides a comprehensive framework to benchmark and leverage the combined power of PRS for maximal performance in a desired target population.
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Affiliation(s)
- Buu Truong
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA; Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - Leland E Hull
- Division of General Internal Medicine, Massachusetts General Hospital, 100 Cambridge Street, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Yunfeng Ruan
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA; Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - Qin Qin Huang
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Whitney Hornsby
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA; Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - Hilary Martin
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - David A van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Ying Wang
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Alicia R Martin
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - S Hong Lee
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, University of South Australia, Adelaide, SA 5000, Australia
| | - Pradeep Natarajan
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA; Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.
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7
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Braat S, Fielding KL, Han J, Jackson VE, Zaloumis S, Xu JXH, Moir-Meyer G, Blaauwendraad SM, Jaddoe VWV, Gaillard R, Parkin PC, Borkhoff CM, Keown-Stoneman CDG, Birken CS, Maguire JL, Bahlo M, Davidson EM, Pasricha SR. Haemoglobin thresholds to define anaemia from age 6 months to 65 years: estimates from international data sources. Lancet Haematol 2024; 11:e253-e264. [PMID: 38432242 PMCID: PMC10983828 DOI: 10.1016/s2352-3026(24)00030-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND Detection of anaemia is crucial for clinical medicine and public health. Current WHO anaemia definitions are based on statistical thresholds (fifth centiles) set more than 50 years ago. We sought to establish evidence for the statistical haemoglobin thresholds for anaemia that can be applied globally and inform WHO and clinical guidelines. METHODS In this analysis we identified international data sources from populations in the USA, England, Australia, China, the Netherlands, Canada, Ecuador, and Bangladesh with sufficient clinical and laboratory information collected between 1998 and 2020 to obtain a healthy reference sample. Individuals with clinical or biochemical evidence of a condition that could reduce haemoglobin concentrations were excluded. We estimated haemoglobin thresholds (ie, 5th centiles) for children aged 6-23 months, 24-59 months, 5-11 years, and 12-17 years, and adults aged 18-65 years (including during pregnancy) for individual datasets and pooled across data sources. We also collated findings from three large-scale genetic studies to summarise genetic variants affecting haemoglobin concentrations in different ancestral populations. FINDINGS We identified eight data sources comprising 18 individual datasets that were eligible for inclusion in the analysis. In pooled analyses, the haemoglobin fifth centile was 104·4 g/L (90% CI 103·5-105·3) in 924 children aged 6-23 months, 110·2 g/L (109·5-110·9) in 1874 children aged 24-59 months, and 114·4 g/L (113·6-115·2) in 1839 children aged 5-11 years. Values diverged by sex in adolescents and adults. In pooled analyses, the fifth centile was 122·2 g/L (90% CI 121·3-123·1) in 1741 female adolescents aged 12-17 years and 128·2 g/L (126·4-130·0) in 1103 male adolescents aged 12-17 years. In pooled analyses of adults aged 18-65 years, the fifth centile was 119·7 g/L (90% CI 119·1-120·3) in 3640 non-pregnant females and 134·9 g/L (134·2-135·6) in 2377 males. Fifth centiles in pregnancy were 110·3 g/L (90% CI 109·5-111·0) in the first trimester (n=772) and 105·9 g/L (104·0-107·7) in the second trimester (n=111), with insufficient data for analysis in the third trimester. There were insufficient data for adults older than 65 years. We did not identify ancestry-specific high prevalence of non-clinically relevant genetic variants that influence haemoglobin concentrations. INTERPRETATION Our results enable global harmonisation of clinical and public health haemoglobin thresholds for diagnosis of anaemia. Haemoglobin thresholds are similar between sexes until adolescence, after which males have higher thresholds than females. We did not find any evidence that thresholds should differ between people of differering ancestries. FUNDING World Health Organization and the Bill & Melinda Gates Foundation.
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Affiliation(s)
- Sabine Braat
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Methods and Implementation Support for Clinical and Health research Hub, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Katherine L Fielding
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia; Clinical Haematology, The Austin Hospital, Heidelberg, VIC, Australia
| | - Jiru Han
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Victoria E Jackson
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Sophie Zaloumis
- Methods and Implementation Support for Clinical and Health research Hub, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Jessica Xu Hui Xu
- Methods and Implementation Support for Clinical and Health research Hub, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Gemma Moir-Meyer
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Sophia M Blaauwendraad
- Generation R Study Group, and Department of Pediatrics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Vincent W V Jaddoe
- Generation R Study Group, and Department of Pediatrics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Romy Gaillard
- Generation R Study Group, and Department of Pediatrics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Patricia C Parkin
- Division of Pediatric Medicine and the Pediatric Outcomes Research Team, The Hospital for Sick Children, Toronto, ON, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Cornelia M Borkhoff
- Division of Pediatric Medicine and the Pediatric Outcomes Research Team, The Hospital for Sick Children, Toronto, ON, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Charles D G Keown-Stoneman
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada; Unity Health Toronto, Toronto, ON, Canada
| | - Catherine S Birken
- Division of Pediatric Medicine and the Pediatric Outcomes Research Team, The Hospital for Sick Children, Toronto, ON, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Jonathon L Maguire
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada; Unity Health Toronto, Toronto, ON, Canada
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Eliza M Davidson
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Sant-Rayn Pasricha
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia; Diagnostic Haematology, The Royal Melbourne Hospital, Parkville, VIC, Australia; Clinical Haematology, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Parkville, VIC, Australia.
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8
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Venkatesh SS, Wittemans LBL, Palmer DS, Baya NA, Ferreira T, Hill B, Lassen FH, Parker MJ, Reibe S, Elhakeem A, Banasik K, Bruun MT, Erikstrup C, Jensen BA, Juul A, Mikkelsen C, Nielsen HS, Ostrowski SR, Pedersen OB, Rohde PD, Sorensen E, Ullum H, Westergaard D, Haraldsson A, Holm H, Jonsdottir I, Olafsson I, Steingrimsdottir T, Steinthorsdottir V, Thorleifsson G, Figueredo J, Karjalainen MK, Pasanen A, Jacobs BM, Hubers N, Lippincott M, Fraser A, Lawlor DA, Timpson NJ, Nyegaard M, Stefansson K, Magi R, Laivuori H, van Heel DA, Boomsma DI, Balasubramanian R, Seminara SB, Chan YM, Laisk T, Lindgren CM. Genome-wide analyses identify 21 infertility loci and over 400 reproductive hormone loci across the allele frequency spectrum. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.19.24304530. [PMID: 38562841 PMCID: PMC10984039 DOI: 10.1101/2024.03.19.24304530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Genome-wide association studies (GWASs) may help inform treatments for infertility, whose causes remain unknown in many cases. Here we present GWAS meta-analyses across six cohorts for male and female infertility in up to 41,200 cases and 687,005 controls. We identified 21 genetic risk loci for infertility (P≤5E-08), of which 12 have not been reported for any reproductive condition. We found positive genetic correlations between endometriosis and all-cause female infertility (rg=0.585, P=8.98E-14), and between polycystic ovary syndrome and anovulatory infertility (rg=0.403, P=2.16E-03). The evolutionary persistence of female infertility-risk alleles in EBAG9 may be explained by recent directional selection. We additionally identified up to 269 genetic loci associated with follicle-stimulating hormone (FSH), luteinising hormone, oestradiol, and testosterone through sex-specific GWAS meta-analyses (N=6,095-246,862). While hormone-associated variants near FSHB and ARL14EP colocalised with signals for anovulatory infertility, we found no rg between female infertility and reproductive hormones (P>0.05). Exome sequencing analyses in the UK Biobank (N=197,340) revealed that women carrying testosterone-lowering rare variants in GPC2 were at higher risk of infertility (OR=2.63, P=1.25E-03). Taken together, our results suggest that while individual genes associated with hormone regulation may be relevant for fertility, there is limited genetic evidence for correlation between reproductive hormones and infertility at the population level. We provide the first comprehensive view of the genetic architecture of infertility across multiple diagnostic criteria in men and women, and characterise its relationship to other health conditions.
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Affiliation(s)
- Samvida S Venkatesh
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Laura B L Wittemans
- Novo Nordisk Research Centre Oxford, Oxford, United Kingdom
- Nuffield Department of Women's and Reproductive Health, Medical Sciences Division, University of Oxford, United Kingdom
| | - Duncan S Palmer
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
- Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Nikolas A Baya
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Teresa Ferreira
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Barney Hill
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
- Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Frederik Heymann Lassen
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Melody J Parker
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Saskia Reibe
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
- Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Ahmed Elhakeem
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Copenhagen, Denmark
| | - Mie T Bruun
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Health, Aarhus University, Aarhus, Denmark
| | - Bitten A Jensen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Anders Juul
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen; Copenhagen, Denmark
- Department of Growth and Reproduction, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Christina Mikkelsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, Copenhagen University, Copenhagen, Denmark
| | - Henriette S Nielsen
- Department of Obstetrics and Gynecology, The Fertility Clinic, Hvidovre University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sisse R Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole B Pedersen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Kge, Denmark
| | - Palle D Rohde
- Genomic Medicine, Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Erik Sorensen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Copenhagen, Denmark
| | - Asgeir Haraldsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Children's Hospital Iceland, Landspitali University Hospital, Reykjavik, Iceland
| | - Hilma Holm
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
| | - Ingileif Jonsdottir
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
| | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali University Hospital, Reykjavik, Iceland
| | - Thora Steingrimsdottir
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Department of Obstetrics and Gynecology, Landspitali University Hospital, Reykjavik, Iceland
| | | | | | - Jessica Figueredo
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Minna K Karjalainen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Finland
- Northern Finland Birth Cohorts, Arctic Biobank, Infrastructure for Population Studies, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Anu Pasanen
- Research Unit of Clinical Medicine, Medical Research Center Oulu, University of Oulu, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Benjamin M Jacobs
- Centre for Preventive Neurology, Wolfson Institute of Population Health, Queen Mary University London, London, EC1M 6BQ, United Kingdom
| | - Nikki Hubers
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Institute, Amsterdam, The Netherlands
| | - Margaret Lippincott
- Harvard Reproductive Sciences Center and Reproductive Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Abigail Fraser
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Mette Nyegaard
- Genomic Medicine, Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Kari Stefansson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
| | - Reedik Magi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Hannele Laivuori
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Obstetrics and Gynecology, Tampere University Hospital, Finland
- Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - David A van Heel
- Blizard Institute, Queen Mary University London, London, E1 2AT, United Kingdom
| | - Dorret I Boomsma
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Institute, Amsterdam, The Netherlands
| | - Ravikumar Balasubramanian
- Harvard Reproductive Sciences Center and Reproductive Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Stephanie B Seminara
- Harvard Reproductive Sciences Center and Reproductive Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yee-Ming Chan
- Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Endocrinology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, United States of America
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Cecilia M Lindgren
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
- Nuffield Department of Women's and Reproductive Health, Medical Sciences Division, University of Oxford, United Kingdom
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
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9
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Islam A, Manjarrez-González JC, Song X, Gore T, Draviam VM. Search for chromosomal instability aiding variants reveal naturally occurring kinetochore gene variants that perturb chromosome segregation. iScience 2024; 27:109007. [PMID: 38361632 PMCID: PMC10867425 DOI: 10.1016/j.isci.2024.109007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/15/2023] [Accepted: 01/19/2024] [Indexed: 02/17/2024] Open
Abstract
Chromosomal instability (CIN) is a hallmark of cancers, and CIN-promoting mutations are not fully understood. Here, we report 141 chromosomal instability aiding variant (CIVa) candidates by assessing the prevalence of loss-of-function (LoF) variants in 135 chromosome segregation genes from over 150,000 humans. Unexpectedly, we observe both heterozygous and homozygous CIVa in Astrin and SKA3, two evolutionarily conserved kinetochore and microtubule-associated proteins essential for chromosome segregation. To stratify harmful versus harmless variants, we combine live-cell microscopy and controlled protein expression. We find the naturally occurring Astrin p.Q1012∗ variant is harmful as it fails to localize normally and induces chromosome misalignment and missegregation, in a dominant negative manner. In contrast, the Astrin p.L7Qfs∗21 variant generates a shorter isoform that localizes and functions normally, and the SKA3 p.Q70Kfs∗7 variant allows wild-type SKA complex localisation and function, revealing distinct resilience mechanisms that render these variants harmless. Thus, we present a scalable framework to predict and stratify naturally occurring CIVa, and provide insight into resilience mechanisms that compensate for naturally occurring CIVa.
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Affiliation(s)
- Asifa Islam
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
| | | | - Xinhong Song
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
| | - Trupti Gore
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
- London Interdisciplinary Doctoral Program, University College London, London, UK
| | - Viji M. Draviam
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
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10
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Nickolls BJ, Relton C, Hemkens L, Zwarenstein M, Eldridge S, McCall SJ, Griffin XL, Sohanpal R, Verkooijen HM, Maguire JL, McCord KA. Randomised trials conducted using cohorts: a scoping review. BMJ Open 2024; 14:e075601. [PMID: 38458814 PMCID: PMC10928784 DOI: 10.1136/bmjopen-2023-075601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 11/24/2023] [Indexed: 03/10/2024] Open
Abstract
INTRODUCTION Cohort studies generate and collect longitudinal data for a variety of research purposes. Randomised controlled trials (RCTs) increasingly use cohort studies as data infrastructures to help identify and recruit trial participants and assess outcomes. OBJECTIVE To examine the extent, range and nature of research using cohorts for RCTs and describe the varied definitions and conceptual boundaries for RCTs using cohorts. DESIGN Scoping review. DATA SOURCES Searches were undertaken in January 2021 in MEDLINE (Ovid) and EBM Reviews-Cochrane Methodology Registry (Final issue, third Quarter 2012). ELIGIBILITY CRITERIA Reports published between January 2007 and December 2021 of (a) cohorts used or planned to be used, to conduct RCTs, or (b) RCTs which use cohorts to recruit participants and/or collect trial outcomes, or (c) methodological studies discussing the use of cohorts for RCTs. DATA EXTRACTION AND SYNTHESIS Data were extracted on the condition being studied, age group, setting, country/continent, intervention(s) and comparators planned or received, unit of randomisation, timing of randomisation, approach to informed consent, study design and terminology. RESULTS A total of 175 full-text articles were assessed for eligibility. We identified 61 protocols, 9 descriptions of stand-alone cohorts intended to be used for future RCTs, 39 RCTs using cohorts and 34 methodological papers.The use and scope of this approach is growing. The thematics of study are far-ranging, including population health, oncology, mental and behavioural disorders, and musculoskeletal conditions.Authors reported that this approach can lead to more efficient recruitment, more representative samples, and lessen disappointment bias and crossovers. CONCLUSION This review outlines the development of cohorts to conduct RCTs including the range of use and innovative changes and adaptations. Inconsistencies in the use of terminology and concepts are highlighted. Guidance now needs to be developed to support the design and reporting of RCTs conducted using cohorts.
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Affiliation(s)
- Beverley Jane Nickolls
- Centre for Evaluation and Methods, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Clare Relton
- Centre for Evaluation and Methods, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Lars Hemkens
- Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel, Basel, Switzerland
- Department of Clinical Research, University of Basel, Basel, Switzerland
- Meta-Research Innovation Center at Stanford (METRICS), Stanford University, Stanford, California, USA
- Meta-Research Innovation Center Berlin (METRICS-B), Berlin Institute of Health, Berlin, Germany
| | - Merrick Zwarenstein
- Department of Family Medicine, Western University, London, Ontario, Canada
- Institute for Clinical Evaluative Sciences, Toronto, Ontario, Canada
| | - Sandra Eldridge
- Centre for Evaluation and Methods, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Stephen J McCall
- National Perinatal Epidemiology Unit, Clinical Trials Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Center for Research on Population and Health, Faculty of Health Sciences, American University of Beirut, Ras Beirut, Lebanon
| | - Xavier Luke Griffin
- Bone and Joint Health, Blizard Institute, Queen Mary University of London, London, UK
- Barts Health NHS Trust, Royal London Hospital, London, UK
| | - Ratna Sohanpal
- Centre for Primary Care, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Helena M Verkooijen
- University Medical Centre Utrecht, Utrecht, The Netherlands
- University of Utrecht, Utrecht, The Netherlands
| | - Jonathon L Maguire
- University of Toronto Institute of Health Policy Management and Evaluation, Toronto, Ontario, Canada
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11
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Dokuru DR, Horwitz TB, Freis SM, Stallings MC, Ehringer MA. South Asia: The Missing Diverse in Diversity. Behav Genet 2024; 54:51-62. [PMID: 37917228 PMCID: PMC11129896 DOI: 10.1007/s10519-023-10161-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 09/26/2023] [Indexed: 11/04/2023]
Abstract
South Asia, making up around 25% of the world's population, encompasses a wide range of individuals with tremendous genetic and environmental diversity. This region, which spans eight countries, is home to over 4500 anthropologically defined groups that speak numerous languages and have an array of religious beliefs and cultures, making it one of the most diverse places in the world. Much of the region's rich genetic diversity and structure is the result of a complex combination of population history, migration patterns, and endogamous practices. Despite the overwhelming size and diversity, South Asians have often been underrepresented in genetic research, making up less than 2% of the participants in genetic studies. This has led to a lack of population specific understanding of genetic disease risks. We aim to raise awareness about underlying genetic diversity in this ancestry group, call attention to the lack of representation of the group, and to highlight strategies for future studies in South Asians.
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Affiliation(s)
- Deepika R Dokuru
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA.
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA.
| | - Tanya B Horwitz
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Samantha M Freis
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Michael C Stallings
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Marissa A Ehringer
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
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12
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Sleiman PM, Qu HQ, Connolly JJ, Mentch F, Pereira A, Lotufo PA, Tollman S, Choudhury A, Ramsay M, Kato N, Ozaki K, Mitsumori R, Jeon JP, Hong CH, Son SJ, Roh HW, Lee DG, Mukadam N, Foote IF, Marshall CR, Butterworth A, Prins BP, Glessner JT, Hakonarson H. Trans-ethnic genomic informed risk assessment for Alzheimer's disease: An International Hundred K+ Cohorts Consortium study. Alzheimers Dement 2023; 19:5765-5772. [PMID: 37450379 PMCID: PMC10854406 DOI: 10.1002/alz.13378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/26/2023] [Accepted: 05/05/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND As a collaboration model between the International HundredK+ Cohorts Consortium (IHCC) and the Davos Alzheimer's Collaborative (DAC), our aim was to develop a trans-ethnic genomic informed risk assessment (GIRA) algorithm for Alzheimer's disease (AD). METHODS The GIRA model was created to include polygenic risk score calculated from the AD genome-wide association study loci, the apolipoprotein E haplotypes, and non-genetic covariates including age, sex, and the first three principal components of population substructure. RESULTS We validated the performance of the GIRA model in different populations. The proteomic study in the participant sites identified proteins related to female infertility and autoimmune thyroiditis and associated with the risk scores of AD. CONCLUSIONS As the initial effort by the IHCC to leverage existing large-scale datasets in a collaborative setting with DAC, we developed a trans-ethnic GIRA for AD with the potential of identifying individuals at high risk of developing AD for future clinical applications.
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Affiliation(s)
- Patrick M. Sleiman
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Hui-Qi Qu
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - John J Connolly
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Frank Mentch
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Alexandre Pereira
- Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Centro de Pesquisas Clínicas e Epidemiológicas, Hospital Universitário, Universidade de São Paulo, São Paulo, Brazil
| | - Paulo A Lotufo
- Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Centro de Pesquisas Clínicas e Epidemiológicas, Hospital Universitário, Universidade de São Paulo, São Paulo, Brazil
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michele Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Norihiro Kato
- National Center for Global Health and Medicine, Tokyo, 1628655, Japan
| | - Kouichi Ozaki
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology (NCGG), Obu City, Aichi Prefecture, Japan
| | - Risa Mitsumori
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology (NCGG), Obu City, Aichi Prefecture, Japan
| | - Jae-Pil Jeon
- Korea Biobank Project, Korea National Institute of Health, Osong, Korea
| | - Chang Hyung Hong
- Department of Psychiatry, Ajou University School of Medicine, Suwon, Korea
| | - Sang Joon Son
- Department of Psychiatry, Ajou University School of Medicine, Suwon, Korea
| | - Hyun Woong Roh
- Department of Psychiatry, Ajou University School of Medicine, Suwon, Korea
| | - Dong-gi Lee
- Department of Psychiatry, Ajou University School of Medicine, Suwon, Korea
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Naaheed Mukadam
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, UK
| | - Isabelle F Foote
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, UK
- Genes & Health, Blizard Institute, Queen Mary University of London, UK
| | - Charles R Marshall
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, UK
- Genes & Health, Blizard Institute, Queen Mary University of London, UK
| | - Adam Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Bram P Prins
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joseph T Glessner
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
- Division of Pulmonary Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
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13
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Magavern EF, Durrani F, Raza M, Lerner R, Islam MR, Clinch M, Caulfield MJ. British South Asian ancestry participants views of pharmacogenomics clinical implementation and research: a thematic analysis. THE PHARMACOGENOMICS JOURNAL 2023; 23:185-194. [PMID: 37907686 PMCID: PMC10661738 DOI: 10.1038/s41397-023-00317-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 11/02/2023]
Abstract
BACKGROUND South Asian ancestry populations are underrepresented in genomic studies and therapeutics trials. British South Asians suffer from multi-morbidity leading to polypharmacy. Our objective was to elucidate British South Asian ancestry community perspectives on pharmacogenomic implementation and sharing pharmacogenomic clinical data for research. METHODS Four focus groups were conducted (9-12 participants in each). Two groups were mixed gender, while one group was male only and one was female only. Simultaneous interpretation was available to participants in Urdu and Bengali. Focus groups were recorded and abridged transcription and thematic analysis were undertaken. RESULTS There were 42 participants, 64% female. 26% were born in the UK or Europe. 52% were born in Bangladesh and 17% in Pakistan. 36% reported university level education. Implementation of pharmacogenomics was perceived to be beneficial to individuals but pose a risk of overburdening resource limited systems. Pharmacogenomic research was perceived to be beneficial to the community, with concerns about data privacy and misuse. Data sharing was desirable if the researchers did not have a financial stake, and benefits would be shared. Trust was the key condition for the acceptability of both clinical implementation and research. Trust was linked with medication compliance. Education, outreach, and communication facilitate trust. CONCLUSIONS (SIGNIFICANCE AND IMPACT OF THE STUDY) Pharmacogenomics implementation with appropriate education and communication has the potential to enhance trust and contribute to increased medication compliance. Trust drives data sharing, which would enable enhanced representation in research. Representation in scientific evidence base could cyclically enhance trust and compliance.
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Grants
- Wellcome Trust
- This work forms part of the portfolio and was funded by the National Institute for Health Research Barts Biomedical Research Centre. EFM is funded by Barts Charity. Genes & Health is/has recently been core-funded by Wellcome (WT102627, WT210561), the Medical Research Council (UK) (M009017, MR/X009777/1, MR/X009920/1), Higher Education Funding Council for England Catalyst, Barts Charity (845/1796), Health Data Research UK (for London substantive site), and research delivery support from the NHS National Institute for Health Research Clinical Research Network (North Thames). Genes & Health is/has recently been funded by Alnylam Pharmaceuticals, Genomics PLC; and a Life Sciences Industry Consortium of Astra Zeneca PLC, Bristol-Myers Squibb Company, GlaxoSmithKline Research and Development Limited, Maze Therapeutics Inc, Merck Sharp & Dohme LLC, Novo Nordisk A/S, Pfizer Inc, Takeda Development Centre Americas Inc. We thank Social Action for Health, Centre of The Cell, members of our Community Advisory Group, and staff who have recruited and collected data from volunteers. We thank the NIHR National Biosample Centre (UK Biocentre), the Social Genetic & Developmental Psychiatry Centre (King’ College London), Wellcome Sanger Institute, and Broad Institute for sample processing, genotyping, sequencing and variant annotation.
- Genes & Health is/has recently been core-funded by Wellcome (WT102627, WT210561), the Medical Research Council (UK) (M009017, MR/X009777/1, MR/X009920/1), Higher Education Funding Council for England Catalyst, Barts Charity (845/1796), Health Data Research UK (for London substantive site), and research delivery support from the NHS National Institute for Health Research Clinical Research Network (North Thames). Genes & Health is/has recently been funded by Alnylam Pharmaceuticals, Genomics PLC; and a Life Sciences Industry Consortium of Astra Zeneca PLC, Bristol-Myers Squibb Company, GlaxoSmithKline Research and Development Limited, Maze Therapeutics Inc, Merck Sharp & Dohme LLC, Novo Nordisk A/S, Pfizer Inc, Takeda Development Centre Americas Inc. We thank Social Action for Health, Centre of The Cell, members of our Community Advisory Group, and staff who have recruited and collected data from volunteers. We thank the NIHR National Biosample Centre (UK Biocentre), the Social Genetic & Developmental Psychiatry Centre (King’ College London), Wellcome Sanger Institute, and Broad Institute for sample processing, genotyping, sequencing and variant annotation.
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Affiliation(s)
- Emma F Magavern
- William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Faiza Durrani
- Genes & Health, Blizard Institute, Queen Mary University of London, London, E1 2AB, UK
| | - Mehru Raza
- Genes & Health, Blizard Institute, Queen Mary University of London, London, E1 2AB, UK
| | - Robin Lerner
- Genes & Health, Blizard Institute, Queen Mary University of London, London, E1 2AB, UK
| | | | - Megan Clinch
- Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Mark J Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK.
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14
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Magavern EF, van Heel DA, Smedley D, Caulfield MJ. CYP2C19 loss-of-function alleles are not associated with higher prevalence of gastrointestinal bleeds in those who have been prescribed antidepressants: Analysis in a British-South Asian cohort. Br J Clin Pharmacol 2023; 89:3432-3438. [PMID: 37143396 DOI: 10.1111/bcp.15762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023] Open
Abstract
AIMS CYP2C19 is a hepatic enzyme involved in the metabolism of antidepressants associated with increased gastrointestinal bleed (GIB) risk. The aim of our study was to explore a possible association between loss-of-function CYP2C19 genotypes and GIB in South Asian ancestry participants prescribed antidepressants. METHODS Genes & Health participants with a record in Barts Health NHS Trust (N 22 753) were studied using a cross-sectional approach. CYP2C19 diplotypes were assessed and metabolizer type inferred from consortia guidance. Fisher's exact test was used to compare the prevalence of GIB in different metabolizer categories. Multivariable regression was used to test for association between antidepressant prescriptions and GIB, and between CYP2C19 metabolizer state and GIB in the subcohort prescribed antidepressants. RESULTS Antidepressants were frequently prescribed (47%, N = 10 612). A total of 864 participants (4%) had a GIB; 534 (62%) had been prescribed a CYP2C19 metabolized antidepressant. There was an independent association between antidepressant prescriptions and GIB events (odds ratio 1.8, confidence interval 1.5-2.0, P < 0.0001). There was no relationship between CYP2C19 inferred poor (P 0.56) or intermediate (P 0.53) metabolizer status and GIB in those prescribed an antidepressant in unadjusted analysis. A multivariable logistic regression model did not show an independent association between poor (P 0.54) or intermediate (P 0.62) CYP2C19 metabolizers and GIB in the subcohort prescribed antidepressants. CONCLUSIONS CYP2C19 dependent antidepressants are associated with increased GIB prevalence. GIB appeared independent from CYP2C19 metabolizer genotype in individuals who had been prescribed antidepressants. Precision dosing based on CYP2C19 genetic information alone is unlikely to reduce GIB prevalence.
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Affiliation(s)
- Emma F Magavern
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Mark J Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, UK
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15
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Williams AT, Chen J, Coley K, Batini C, Izquierdo A, Packer R, Abner E, Kanoni S, Shepherd DJ, Free RC, Hollox EJ, Brunskill NJ, Ntalla I, Reeve N, Brightling CE, Venn L, Adams E, Bee C, Wallace SE, Pareek M, Hansell AL, Esko T, Stow D, Jacobs BM, van Heel DA, Hennah W, Rao BS, Dudbridge F, Wain LV, Shrine N, Tobin MD, John C. Genome-wide association study of thyroid-stimulating hormone highlights new genes, pathways and associations with thyroid disease. Nat Commun 2023; 14:6713. [PMID: 37872160 PMCID: PMC10593800 DOI: 10.1038/s41467-023-42284-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 10/05/2023] [Indexed: 10/25/2023] Open
Abstract
Thyroid hormones play a critical role in regulation of multiple physiological functions and thyroid dysfunction is associated with substantial morbidity. Here, we use electronic health records to undertake a genome-wide association study of thyroid-stimulating hormone (TSH) levels, with a total sample size of 247,107. We identify 158 novel genetic associations, more than doubling the number of known associations with TSH, and implicate 112 putative causal genes, of which 76 are not previously implicated. A polygenic score for TSH is associated with TSH levels in African, South Asian, East Asian, Middle Eastern and admixed American ancestries, and associated with hypothyroidism and other thyroid disease in South Asians. In Europeans, the TSH polygenic score is associated with thyroid disease, including thyroid cancer and age-of-onset of hypothyroidism and hyperthyroidism. We develop pathway-specific genetic risk scores for TSH levels and use these in phenome-wide association studies to identify potential consequences of pathway perturbation. Together, these findings demonstrate the potential utility of genetic associations to inform future therapeutics and risk prediction for thyroid diseases.
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Affiliation(s)
- Alexander T Williams
- Department of Population Health Sciences, University of Leicester, Leicester, UK.
| | - Jing Chen
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Kayesha Coley
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK
| | - Abril Izquierdo
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK
| | - Richard Packer
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK
| | - Erik Abner
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Stavroula Kanoni
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - David J Shepherd
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Robert C Free
- University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK
- School of Computing and Mathematical Sciences, University of Leicester, Leicester, UK
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Nigel J Brunskill
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Ioanna Ntalla
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Nicola Reeve
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Division of Population Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - Christopher E Brightling
- University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK
- Institute for Lung Health, Leicester NIHR BRC, University of Leicester, Leicester, UK
| | - Laura Venn
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Emma Adams
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Catherine Bee
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Susan E Wallace
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Manish Pareek
- University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Anna L Hansell
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Daniel Stow
- Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Benjamin M Jacobs
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
- Department of Neurology, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - David A van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - William Hennah
- Orion Pharma, Espoo, Finland
- Neuroscience Center, HiLIFE, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | | | - Frank Dudbridge
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Louise V Wain
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK
| | - Nick Shrine
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Martin D Tobin
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK
| | - Catherine John
- Department of Population Health Sciences, University of Leicester, Leicester, UK.
- University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK.
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16
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Magavern EF, Smedley D, Caulfield MJ. Factor V Leiden, estrogen, and multimorbidity association with venous thromboembolism in a British-South Asian cohort. iScience 2023; 26:107795. [PMID: 37810217 PMCID: PMC10550715 DOI: 10.1016/j.isci.2023.107795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/06/2023] [Accepted: 08/29/2023] [Indexed: 10/10/2023] Open
Abstract
Multimorbidity, estrogen use, and Factor V Leiden (FVL) are known independent risk factors for venous thromboembolism (VTE). This cross-sectional analysis of women in the Genes & Health British-South Asian cohort (N 20,048) linked the F5 SNP rs6025 with estrogen prescribing data and VTE events. Multivariable logistic regression was used to test the association between estrogen use, FVL, common medical co-morbidities, and VTE. Estrogens were prescribed to 30% of women. 3% of participants were FVL carriers. 439 participants had a VTE event (2.2%), and VTE prevalence increased with obesity, hypertension, dyslipidemia, chronic kidney disease, estrogen use, and in the presence of FVL. One medical condition above was independently associated with VTE with an OR 1.6 (CI 1.2-2.0, p 0.001); two medical conditions OR 2.7 (CI 2.0-3.7, p < 0.001); three OR 5.3 (CI 3.8-7.4, p < 0.001); four OR 8.1 (CI 4.9-13.0, p < 0.001). Multimorbidity and FVL compound risk of VTE with estrogen use.
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Affiliation(s)
- Emma F Magavern
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Mark J Caulfield
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
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17
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Malawsky DS, van Walree E, Jacobs BM, Heng TH, Huang QQ, Sabir AH, Rahman S, Sharif SM, Khan A, Mirkov MU, Kuwahara H, Gao X, Alkuraya FS, Posthuma D, Newman WG, Griffiths CJ, Mathur R, van Heel DA, Finer S, O'Connell J, Martin HC. Influence of autozygosity on common disease risk across the phenotypic spectrum. Cell 2023; 186:4514-4527.e14. [PMID: 37757828 PMCID: PMC10580289 DOI: 10.1016/j.cell.2023.08.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 07/11/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023]
Abstract
Autozygosity is associated with rare Mendelian disorders and clinically relevant quantitative traits. We investigated associations between the fraction of the genome in runs of homozygosity (FROH) and common diseases in Genes & Health (n = 23,978 British South Asians), UK Biobank (n = 397,184), and 23andMe. We show that restricting analysis to offspring of first cousins is an effective way of reducing confounding due to social/environmental correlates of FROH. Within this group in G&H+UK Biobank, we found experiment-wide significant associations between FROH and twelve common diseases. We replicated associations with type 2 diabetes (T2D) and post-traumatic stress disorder via within-sibling analysis in 23andMe (median n = 480,282). We estimated that autozygosity due to consanguinity accounts for 5%-18% of T2D cases among British Pakistanis. Our work highlights the possibility of widespread non-additive genetic effects on common diseases and has important implications for global populations with high rates of consanguinity.
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Affiliation(s)
| | - Eva van Walree
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Complex Trait Genetics Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Amsterdam, Amsterdam, the Netherlands
| | - Benjamin M Jacobs
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK; Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Teng Hiang Heng
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Qin Qin Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ataf H Sabir
- West Midlands Regional Clinical Genetics Unit, Birmingham Women's and Children's NHS FT, Birmingham, UK; Institute of Cancer and Genomics, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Saadia Rahman
- Queen Square Institute of Neurology, University College London, London, UK
| | - Saghira Malik Sharif
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Ahsan Khan
- Waltham Forest Council, Waltham Forest Town Hall, Forest Road, Walthamstow E17 4JF, UK
| | - Maša Umićević Mirkov
- Congenica Limited, BioData Innovation Centre, Wellcome Genome Campus, Hinxton, UK
| | - Hiroyuki Kuwahara
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955, Saudi Arabia
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Danielle Posthuma
- Department of Complex Trait Genetics Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Amsterdam, Amsterdam, the Netherlands
| | - William G Newman
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Human Sciences, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK
| | - Christopher J Griffiths
- Wolfson Institute of Population Health, Queen Mary University of London, London, UK; MRC and Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, London, UK
| | - Rohini Mathur
- Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - David A van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Sarah Finer
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK; Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | | | - Hilary C Martin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
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18
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Hartmann S, Yasmeen S, Jacobs BM, Denaxas S, Pirmohamed M, Gamazon ER, Caulfield MJ, Hemingway H, Pietzner M, Langenberg C. ADRA2A and IRX1 are putative risk genes for Raynaud's phenomenon. Nat Commun 2023; 14:6156. [PMID: 37828025 PMCID: PMC10570309 DOI: 10.1038/s41467-023-41876-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 09/21/2023] [Indexed: 10/14/2023] Open
Abstract
Raynaud's phenomenon (RP) is a common vasospastic disorder that causes severe pain and ulcers, but despite its high reported heritability, no causal genes have been robustly identified. We conducted a genome-wide association study including 5,147 RP cases and 439,294 controls, based on diagnoses from electronic health records, and identified three unreported genomic regions associated with the risk of RP (p < 5 × 10-8). We prioritized ADRA2A (rs7090046, odds ratio (OR) per allele: 1.26; 95%-CI: 1.20-1.31; p < 9.6 × 10-27) and IRX1 (rs12653958, OR: 1.17; 95%-CI: 1.12-1.22, p < 4.8 × 10-13) as candidate causal genes through integration of gene expression in disease relevant tissues. We further identified a likely causal detrimental effect of low fasting glucose levels on RP risk (rG = -0.21; p-value = 2.3 × 10-3), and systematically highlighted drug repurposing opportunities, like the antidepressant mirtazapine. Our results provide the first robust evidence for a strong genetic contribution to RP and highlight a so far underrated role of α2A-adrenoreceptor signalling, encoded at ADRA2A, as a possible mechanism for hypersensitivity to catecholamine-induced vasospasms.
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Affiliation(s)
- Sylvia Hartmann
- Computational Medicine, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Summaira Yasmeen
- Computational Medicine, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Benjamin M Jacobs
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Spiros Denaxas
- Institute of Health Informatics, University College London, London, UK
- Health Data Research UK, London, UK
- British Heart Foundation Data Science Centre, London, UK
- National Institute of Health Research University College London Hospitals Biomedical Research Centre, London, UK
| | - Munir Pirmohamed
- Department of Pharmacology and Therapeutics, The Wolfson Centre for Personalised Medicine, University Liverpool, Liverpool, UK
| | - Eric R Gamazon
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Mark J Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Harry Hemingway
- Institute of Health Informatics, University College London, London, UK
- Health Data Research UK, London, UK
- National Institute of Health Research University College London Hospitals Biomedical Research Centre, London, UK
| | - Maik Pietzner
- Computational Medicine, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK.
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK.
| | - Claudia Langenberg
- Computational Medicine, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK.
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK.
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19
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Magavern EF, van Heel DA, Smedley D, Caulfield MJ. SLCO1B1*5 is protective against non-senile cataracts in cohort prescribed statins: analysis in a British-South Asian cohort. THE PHARMACOGENOMICS JOURNAL 2023; 23:134-139. [PMID: 37221222 PMCID: PMC10506906 DOI: 10.1038/s41397-023-00307-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/25/2023]
Abstract
BACKGROUND Reported association between statin use and cataract risk is controversial. The SLCO1B1 gene encodes a transport protein responsible for statin clearance. The aim of this study was to investigate a possible association between the SLCO1B1*5 reduced function variant and cataract risk in statin users of South Asian ethnicity. METHODS The Genes & Health cohort consists of British-Bangladeshi and British-Pakistani participants from East London, Manchester and Bradford, UK. SLCO1B1*5 genotype was assessed with the Illumina GSAMD-24v3-0-EA chip. Medication data from primary care health record linkage was used to compare those who had regularly used statins compared to those who had not. Multivariable logistic regression was used to test for association between statin use and cataracts, adjusting for population characteristics and potential confounders in 36,513 participants. Multivariable logistic regression was used to test association between SLCO1B1*5 heterozygotes or homozygotes and cataracts, in subgroups having been regularly prescribed statins versus not. RESULTS Statins were prescribed to 35% (12,704) of participants (average age 41 years old, 45% male). Non-senile cataract was diagnosed in 5% (1686) of participants. An apparent association between statins and non-senile cataract (12% in statin users and 0.8% in non-statin users) was negated by inclusion of confounders. In those prescribed a statin, presence of the SLCO1B1*5 genotype was independently associated with a decreased risk of non-senile cataract (OR 0.7 (CI 0.5-0.9, p 0.007)). CONCLUSIONS Our findings suggest that there is no independent association between statin use and non-senile cataract risk after adjusting for confounders. Among statin users, the SLCO1B1*5 genotype is associated with a 30% risk reduction of non-senile cataracts. Stratification of on-drug cohorts by validated pharmacogenomic variants is a useful tool to support or repudiate adverse drug events in observational cohorts.
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Grants
- Wellcome Trust
- Medical Research Council
- We acknowledge with thanks funding from Barts Biomedical Research Centre and funding from Barts Charity to support EFM.
- Genes & Health is core-funded by Wellcome (WT102627, WT210561), the Medical Research Council (UK) (M009017), Higher Education Funding Council for England Catalyst, Barts Charity (845/1796), Health Data Research UK (for London substantive site), and research delivery support from the NHS National Institute for Health Research Clinical Research Network (North Thames). Genes & Health is/has recently been funded by Alnylam Pharmaceuticals, Genomics PLC; and a Life Sciences Industry Consortium of Bristol-Myers Squibb Company, GlaxoSmithKline Research and Development Limited, Maze Therapeutics Inc, Merck Sharp & Dohme LLC, Novo Nordisk A/S, Pfizer Inc, Takeda Development Centre Americas Inc. We thank Social Action for Health, Centre of The Cell, members of our Community Advisory Group, and staff who have recruited and collected data from volunteers. We thank the NIHR National Biosample Centre (UK Biocentre), the Social Genetic & Developmental Psychiatry Centre (King’s College London), Wellcome Sanger Institute, and Broad Institute for sample processing, genotyping, sequencing and variant annotation. We thank: Barts Health NHS Trust, NHS Clinical Commissioning Groups (City and Hackney, Waltham Forest, Tower Hamlets, Newham, Redbridge, Havering, Barking and Dagenham), East London NHS Foundation Trust, Bradford Teaching Hospitals NHS Foundation Trust, Public Health England (especially David Wyllie), Discovery Data Service/Endeavour Health Charitable Trust (especially David Stables), NHS Digital - for GDPR-compliant data sharing backed by individual written informed consent.
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Affiliation(s)
- Emma F Magavern
- William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - David A van Heel
- Blizard Institute, Queen Mary University of London, London, E1 2AB, UK
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Mark J Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK.
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20
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Magavern EF, Jacobs B, Warren H, Finocchiaro G, Finer S, van Heel DA, Smedley D, Caulfield MJ. CYP2C19 Genotype Prevalence and Association With Recurrent Myocardial Infarction in British-South Asians Treated With Clopidogrel. JACC. ADVANCES 2023; 2:None. [PMID: 37808344 PMCID: PMC10550831 DOI: 10.1016/j.jacadv.2023.100573] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/04/2023] [Accepted: 07/17/2023] [Indexed: 10/10/2023]
Abstract
Background Cytochrome P450 family 2 subfamily C member 19 (CYP2C19) is a hepatic enzyme involved in the metabolism of clopidogrel from a prodrug to its active metabolite. Prior studies of genetic polymorphisms in CYP2C19 and their relationship with clinical efficacy have not included South Asian populations. Objectives The objective of this study was to assess prevalence of common CYP2C19 genotype polymorphisms in a British-South Asian population and correlate these with recurrent myocardial infarction risk in participants prescribed clopidogrel. Methods The Genes & Health cohort of British Bangladeshi and Pakistani ancestry participants were studied. CYP2C19 diplotypes were assessed using array data. Multivariable logistic regression was used to test for association between genetically inferred CYP2C19 metabolizer status and recurrent myocardial infarction, controlling for known cardiovascular disease risk factors, percutaneous coronary intervention, age, sex, and population stratification. Results Genes & Health cohort participants (N = 44,396) have a high prevalence (57%) of intermediate or poor CYP2C19 metabolizers, with at least 1 loss-of-function CYP2C19 allele. The prevalence of poor metabolizers carrying 2 CYP2C19 loss-of-function alleles is 13%, which is higher than that in previously studied European (2.4%) and Central/South Asian populations (8.2%). Sixty-nine percent of the cohort who were diagnosed with an acute myocardial infarction were prescribed clopidogrel. Poor metabolizers were significantly more likely to have a recurrent myocardial infarction (OR: 3.1; P = 0.019). Conclusions A pharmacogenomic-driven approach to clopidogrel prescribing has the potential to impact significantly on clinical management and outcomes in individuals of Bangladeshi and Pakistani ancestry.
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Affiliation(s)
- Emma F. Magavern
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - Benjamin Jacobs
- The Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom
| | - Helen Warren
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - Gherardo Finocchiaro
- Cardiovascular Sciences Research Centre, St George's, University of London, London, United Kingdom
| | - Sarah Finer
- The Blizard Institute, Queen Mary University of London, London, United Kingdom
| | - David A. van Heel
- The Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom
| | - Genes & Health Research Team
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
- The Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom
- Cardiovascular Sciences Research Centre, St George's, University of London, London, United Kingdom
- The Blizard Institute, Queen Mary University of London, London, United Kingdom
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - Mark J. Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
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21
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Patel AP, Wang M, Ruan Y, Koyama S, Clarke SL, Yang X, Tcheandjieu C, Agrawal S, Fahed AC, Ellinor PT, Tsao PS, Sun YV, Cho K, Wilson PWF, Assimes TL, van Heel DA, Butterworth AS, Aragam KG, Natarajan P, Khera AV. A multi-ancestry polygenic risk score improves risk prediction for coronary artery disease. Nat Med 2023; 29:1793-1803. [PMID: 37414900 PMCID: PMC10353935 DOI: 10.1038/s41591-023-02429-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 05/30/2023] [Indexed: 07/08/2023]
Abstract
Identification of individuals at highest risk of coronary artery disease (CAD)-ideally before onset-remains an important public health need. Prior studies have developed genome-wide polygenic scores to enable risk stratification, reflecting the substantial inherited component to CAD risk. Here we develop a new and significantly improved polygenic score for CAD, termed GPSMult, that incorporates genome-wide association data across five ancestries for CAD (>269,000 cases and >1,178,000 controls) and ten CAD risk factors. GPSMult strongly associated with prevalent CAD (odds ratio per standard deviation 2.14, 95% confidence interval 2.10-2.19, P < 0.001) in UK Biobank participants of European ancestry, identifying 20.0% of the population with 3-fold increased risk and conversely 13.9% with 3-fold decreased risk as compared with those in the middle quintile. GPSMult was also associated with incident CAD events (hazard ratio per standard deviation 1.73, 95% confidence interval 1.70-1.76, P < 0.001), identifying 3% of healthy individuals with risk of future CAD events equivalent to those with existing disease and significantly improving risk discrimination and reclassification. Across multiethnic, external validation datasets inclusive of 33,096, 124,467, 16,433 and 16,874 participants of African, European, Hispanic and South Asian ancestry, respectively, GPSMult demonstrated increased strength of associations across all ancestries and outperformed all available previously published CAD polygenic scores. These data contribute a new GPSMult for CAD to the field and provide a generalizable framework for how large-scale integration of genetic association data for CAD and related traits from diverse populations can meaningfully improve polygenic risk prediction.
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Affiliation(s)
- Aniruddh P Patel
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Minxian Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
| | - Yunfeng Ruan
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Satoshi Koyama
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Veteran Affairs Boston Healthcare System, Boston, MA, USA
| | - Shoa L Clarke
- Stanford University School of Medicine, Palo Alto, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Xiong Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | | | - Saaket Agrawal
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Akl C Fahed
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick T Ellinor
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Philip S Tsao
- Stanford University School of Medicine, Palo Alto, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Yan V Sun
- Veteran Affairs Atlanta Healthcare System, Decatur, GA, USA
| | - Kelly Cho
- Veteran Affairs Boston Healthcare System, Boston, MA, USA
| | | | - Themistocles L Assimes
- Stanford University School of Medicine, Palo Alto, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - David A van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, and Centre of Research Excellence, University of Cambridge, Cambridge, UK
| | - Krishna G Aragam
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Pradeep Natarajan
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Amit V Khera
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Verve Therapeutics, Boston, MA, USA.
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22
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Ghoussaini M, Nelson MR, Dunham I. Future prospects for human genetics and genomics in drug discovery. Curr Opin Struct Biol 2023; 80:102568. [PMID: 36963162 PMCID: PMC7614359 DOI: 10.1016/j.sbi.2023.102568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/27/2023] [Accepted: 02/13/2023] [Indexed: 03/26/2023]
Abstract
Evidence from human genetics supporting the therapeutic hypothesis increases the likelihood that a drug will succeed in clinical trials. Rare and common disease genetics yield a wide array of alleles with a range of effect sizes that can proxy for the effect of a drug in disease. Recent advances in large scale population collections and whole genome sequencing approaches have provided a rich resource of human genetic evidence to support drug target selection. As the range of phenotypes profiled increases and ever more alleles are discovered across world-wide populations, these approaches will increasingly influence multiple stages across the lifespan of a drug discovery programme.
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Affiliation(s)
- Maya Ghoussaini
- Wellcome Sanger Institute, Wellcome Genome Campus, United Kingdom; Open Targets, Wellcome Genome Campus, United Kingdom. https://twitter.com/MayaGhoussaini
| | | | - Ian Dunham
- Wellcome Sanger Institute, Wellcome Genome Campus, United Kingdom; Open Targets, Wellcome Genome Campus, United Kingdom; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, United Kingdom.
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23
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Honigberg MC, Truong B, Khan RR, Xiao B, Bhatta L, Vy HMT, Guerrero RF, Schuermans A, Selvaraj MS, Patel AP, Koyama S, Cho SMJ, Vellarikkal SK, Trinder M, Urbut SM, Gray KJ, Brumpton BM, Patil S, Zöllner S, Antopia MC, Saxena R, Nadkarni GN, Do R, Yan Q, Pe'er I, Verma SS, Gupta RM, Haas DM, Martin HC, van Heel DA, Laisk T, Natarajan P. Polygenic prediction of preeclampsia and gestational hypertension. Nat Med 2023; 29:1540-1549. [PMID: 37248299 PMCID: PMC10330886 DOI: 10.1038/s41591-023-02374-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/26/2023] [Indexed: 05/31/2023]
Abstract
Preeclampsia and gestational hypertension are common pregnancy complications associated with adverse maternal and child outcomes. Current tools for prediction, prevention and treatment are limited. Here we tested the association of maternal DNA sequence variants with preeclampsia in 20,064 cases and 703,117 control individuals and with gestational hypertension in 11,027 cases and 412,788 control individuals across discovery and follow-up cohorts using multi-ancestry meta-analysis. Altogether, we identified 18 independent loci associated with preeclampsia/eclampsia and/or gestational hypertension, 12 of which are new (for example, MTHFR-CLCN6, WNT3A, NPR3, PGR and RGL3), including two loci (PLCE1 and FURIN) identified in the multitrait analysis. Identified loci highlight the role of natriuretic peptide signaling, angiogenesis, renal glomerular function, trophoblast development and immune dysregulation. We derived genome-wide polygenic risk scores that predicted preeclampsia/eclampsia and gestational hypertension in external cohorts, independent of clinical risk factors, and reclassified eligibility for low-dose aspirin to prevent preeclampsia. Collectively, these findings provide mechanistic insights into the hypertensive disorders of pregnancy and have the potential to advance pregnancy risk stratification.
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Affiliation(s)
- Michael C Honigberg
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Buu Truong
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Raiyan R Khan
- Department of Computer Science, Columbia University, New York, NY, USA
| | - Brenda Xiao
- University of Pennsylvania, Philadelphia, PA, USA
| | - Laxmi Bhatta
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
| | - Ha My T Vy
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rafael F Guerrero
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Art Schuermans
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Margaret Sunitha Selvaraj
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aniruddh P Patel
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Satoshi Koyama
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - So Mi Jemma Cho
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Integrative Research Center for Cerebrovascular and Cardiovascular Diseases, Seoul, Republic of Korea
| | - Shamsudheen Karuthedath Vellarikkal
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Mark Trinder
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sarah M Urbut
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kathryn J Gray
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ben M Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
| | - Snehal Patil
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Sebastian Zöllner
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Mariah C Antopia
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Richa Saxena
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Girish N Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Qi Yan
- Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA
| | - Itsik Pe'er
- Department of Computer Science, Columbia University, New York, NY, USA
| | | | - Rajat M Gupta
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - David M Haas
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Hilary C Martin
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - David A van Heel
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Pradeep Natarajan
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
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24
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Braat S, Fielding K, Han J, Jackson VE, Zaloumis S, Xu JXH, Moir-Meyer G, Blaauwendraad SM, Jaddoe VWV, Gaillard R, Parkin PC, Borkhoff CM, Keown-Stoneman CDG, Birken CS, Maguire JL, Bahlo M, Davidson E, Pasricha SR. Statistical haemoglobin thresholds to define anaemia across the lifecycle. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.22.23290129. [PMID: 37292786 PMCID: PMC10246131 DOI: 10.1101/2023.05.22.23290129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Detection of anaemia is critical for clinical medicine and public health. Current WHO values that define anaemia are statistical thresholds (5 th centile) set over 50 years ago, and are presently <110g/L in children 6-59 months, <115g/L in children 5-11 years, <110g/L in pregnant women, <120g/L in children 12-14 years of age, <120g/L in non-pregnant women, and <130g/L in men. Haemoglobin is sensitive to iron and other nutrient deficiencies, medical illness and inflammation, and is impacted by genetic conditions; thus, careful exclusion of these conditions is crucial to obtain a healthy reference population. We identified data sources from which sufficient clinical and laboratory information was available to determine an apparently healthy reference sample. Individuals were excluded if they had any clinical or biochemical evidence of a condition that may diminish haemoglobin concentration. Discrete 5 th centiles were estimated along with two-sided 90% confidence intervals and estimates combined using a fixed-effect approach. Estimates for the 5 th centile of the healthy reference population in children were similar between sexes. Thresholds in children 6-23 months were 104.4g/L [90% CI 103.5, 105.3]; in children 24-59 months were 110.2g/L [109.5, 110.9]; and in children 5-11 years were 114.1g/L [113.2, 115.0]. Thresholds diverged by sex in adolescents and adults. In females and males 12-17 years, thresholds were 122.2g/L [121.3, 123.1] and 128.2 [126.4, 130.0], respectively. In adults 18-65 years, thresholds were 119.7g/L [119.1, 120.3] in non-pregnant females and 134.9g/L [134.2, 135.6] in males. Limited analyses indicated 5 th centiles in first-trimester pregnancy of 110.3g/L [109.5, 111.0] and 105.9g/L [104.0, 107.7] in the second trimester. All thresholds were robust to variations in definitions and analysis models. Using multiple datasets comprising Asian, African, and European ancestries, we did not identify novel high prevalence genetic variants that influence haemoglobin concentration, other than variants in genes known to cause important clinical disease, suggesting non-clinical genetic factors do not influence the 5 th centile between ancestries. Our results directly inform WHO guideline development and provide a platform for global harmonisation of laboratory, clinical and public health haemoglobin thresholds.
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25
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Zöllner J, Finer S, Linton KJ, van Heel DA, Williamson C, Dixon PH. Rare variant contribution to cholestatic liver disease in a South Asian population in the United Kingdom. Sci Rep 2023; 13:8120. [PMID: 37208429 PMCID: PMC10199085 DOI: 10.1038/s41598-023-33391-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/12/2023] [Indexed: 05/21/2023] Open
Abstract
This study assessed the contribution of five genes previously known to be involved in cholestatic liver disease in British Bangladeshi and Pakistani people. Five genes (ABCB4, ABCB11, ATP8B1, NR1H4, TJP2) were interrogated by exome sequencing data of 5236 volunteers. Included were non-synonymous or loss of function (LoF) variants with a minor allele frequency < 5%. Variants were filtered, and annotated to perform rare variant burden analysis, protein structure, and modelling analysis in-silico. Out of 314 non-synonymous variants, 180 fulfilled the inclusion criteria and were mostly heterozygous unless specified. 90 were novel and of those variants, 22 were considered likely pathogenic and 9 pathogenic. We identified variants in volunteers with gallstone disease (n = 31), intrahepatic cholestasis of pregnancy (ICP, n = 16), cholangiocarcinoma and cirrhosis (n = 2). Fourteen novel LoF variants were identified: 7 frameshift, 5 introduction of premature stop codon and 2 splice acceptor variants. The rare variant burden was significantly increased in ABCB11. Protein modelling demonstrated variants that appeared to likely cause significant structural alterations. This study highlights the significant genetic burden contributing to cholestatic liver disease. Novel likely pathogenic and pathogenic variants were identified addressing the underrepresentation of diverse ancestry groups in genomic research.
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Affiliation(s)
| | - Sarah Finer
- Institute for Population Health Sciences, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Kenneth J Linton
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - David A van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Catherine Williamson
- Department of Women and Children's Health, School of Life Course Sciences, FOLSM, King's College London, 2.30W Hodgkin Building, Guy's Campus, London, SE1 1UL, UK.
| | - Peter H Dixon
- Department of Women and Children's Health, School of Life Course Sciences, FOLSM, King's College London, 2.30W Hodgkin Building, Guy's Campus, London, SE1 1UL, UK
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26
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Jacobs BM, Schalk L, Dunne A, Scalfari A, Nandoskar A, Gran B, Mein CA, Sellers C, Spilker C, Rog D, Visentin E, Bezzina EL, Uzochukwu E, Tallantyre E, Wozniak E, Sacre E, Hassan-Smith G, Ford HL, Harris J, Bradley J, Breedon J, Brooke J, Kreft KL, Tuite Dalton K, George K, Papachatzaki M, O'Malley M, Peter M, Mattoscio M, Rhule N, Evangelou N, Vinod N, Quinn O, Shamji R, Kaimal R, Boulton R, Tanveer R, Middleton R, Murray R, Bellfield R, Hoque S, Patel S, Raj S, Gumus S, Mitchell S, Sawcer S, Arun T, Pogreban T, Brown TL, Begum T, Antoine V, Rashid W, Noyce AJ, Silber E, Morris H, Giovannoni G, Dobson R. ADAMS project: a genetic Association study in individuals from Diverse Ancestral backgrounds with Multiple Sclerosis based in the UK. BMJ Open 2023; 13:e071656. [PMID: 37197821 DOI: 10.1136/bmjopen-2023-071656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/19/2023] Open
Abstract
PURPOSE Genetic studies of multiple sclerosis (MS) susceptibility and severity have focused on populations of European ancestry. Studying MS genetics in other ancestral groups is necessary to determine the generalisability of these findings. The genetic Association study in individuals from Diverse Ancestral backgrounds with Multiple Sclerosis (ADAMS) project aims to gather genetic and phenotypic data on a large cohort of ancestrally-diverse individuals with MS living in the UK. PARTICIPANTS Adults with self-reported MS from diverse ancestral backgrounds. Recruitment is via clinical sites, online (https://app.mantal.co.uk/adams) or the UK MS Register. We are collecting demographic and phenotypic data using a baseline questionnaire and subsequent healthcare record linkage. We are collecting DNA from participants using saliva kits (Oragene-600) and genotyping using the Illumina Global Screening Array V.3. FINDINGS TO DATE As of 3 January 2023, we have recruited 682 participants (n=446 online, n=55 via sites, n=181 via the UK MS Register). Of this initial cohort, 71.2% of participants are female, with a median age of 44.9 years at recruitment. Over 60% of the cohort are non-white British, with 23.5% identifying as Asian or Asian British, 16.2% as Black, African, Caribbean or Black British and 20.9% identifying as having mixed or other backgrounds. The median age at first symptom is 28 years, and median age at diagnosis is 32 years. 76.8% have relapsing-remitting MS, and 13.5% have secondary progressive MS. FUTURE PLANS Recruitment will continue over the next 10 years. Genotyping and genetic data quality control are ongoing. Within the next 3 years, we aim to perform initial genetic analyses of susceptibility and severity with a view to replicating the findings from European-ancestry studies. In the long term, genetic data will be combined with other datasets to further cross-ancestry genetic discoveries.
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Affiliation(s)
- Benjamin M Jacobs
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Luisa Schalk
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Angie Dunne
- Leeds Centre for Neurosciences, Leeds teaching Hospitals NHS Trust, Leeds, UK
| | - Antonio Scalfari
- Centre of Neuroscience, Department of Medicine, Imperial College London, London, UK
| | | | - Bruno Gran
- Department of Neurology, Nottingham University Hospitals NHS Trust, Mental Health and Clinical Neuroscience Academic Unit, University of Nottingham School of Medicine, Nottingham, UK
| | - Charles A Mein
- Barts and the London Genome Centre, Queen Mary University of London, London, UK
| | - Charlotte Sellers
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Cord Spilker
- Bradford Teaching Hospital Foundation Trust, Bradford, UK
| | - David Rog
- Manchester Centre for Clinical Neurosciences, Northern Care Alliance NHS Trust, Manchester, UK
| | - Elisa Visentin
- Research and Innovation, Queen's Hospital, BHRUT, London, UK
| | | | - Emeka Uzochukwu
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Emma Tallantyre
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
- Department of Clinical Neurology, University Hospital of Wales, Cardiff, UK
| | - Eva Wozniak
- Barts and the London Genome Centre, Queen Mary University of London, London, UK
| | - Eve Sacre
- Leeds Centre for Neurosciences, Leeds teaching Hospitals NHS Trust, Leeds, UK
| | | | - Helen L Ford
- Leeds Centre for Neurosciences, Leeds teaching Hospitals NHS Trust, Leeds, UK
| | - Jade Harris
- Northern Care Alliance NHS Trust, Manchester, UK
| | | | - Joshua Breedon
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | | | - Karim L Kreft
- Department of Neurology, University Hospital of Wales, Cardiff, UK
| | | | - Katila George
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | | | - Martin O'Malley
- Leeds Centre for Neurosciences, Leeds teaching Hospitals NHS Trust, Leeds, UK
| | - Michelle Peter
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Miriam Mattoscio
- Department of neuroscience, Queen's Hospital, BHRUT NHS Trust, Romford, UK
| | - Neisha Rhule
- Queen Elizabeth Hospital (Lewisham and Greenwich NHS Trust), London, UK
| | - Nikos Evangelou
- Department of Neurology, Nottingham University Hospitals NHS Trust; Mental Health and Clinical Neuroscience Academic Unit, University of Nottingham School of Medicine, Nottingham, UK
| | | | - Outi Quinn
- Bradford Teaching Hospital Foundation Trust, Bradford, UK
| | - Ramya Shamji
- Research and Innovation, Queen's Hospital, BHRUT, London, UK
| | - Rashmi Kaimal
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Rebecca Boulton
- Department of Neurology, Nottingham University Hospitals NHS Trust; Mental Health and Clinical Neuroscience Academic Unit, University of Nottingham School of Medicine, Nottingham, UK
| | - Riffat Tanveer
- Lancashire Teaching Hospital NHS Foundation Trust, Preston, UK
| | - Rod Middleton
- Population Data Science, Swansea University Medical School, Swansea, UK
| | - Roxanne Murray
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Ruth Bellfield
- Bradford Teaching Hospital Foundation Trust, Bradford, UK
| | - Sadid Hoque
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Shakeelah Patel
- Lancashire Teaching Hospital NHS Foundation Trust, Preston, UK
| | - Sonia Raj
- Lancashire Teaching Hospital NHS Foundation Trust, Preston, UK
| | - Stephanie Gumus
- Mid and South Essex NHS Foundation Trust, Southend-on-Sea, UK
| | | | - Stephen Sawcer
- University of Cambridge, Department of Clinical Neuroscience, Addenbrookes Hospital, Hills Road, Cambridge, UK
| | - Tarunya Arun
- University Hospitals of Coventry and Warwickshire, Coventry, UK
| | | | - Terri-Louise Brown
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Thamanna Begum
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | | | - Waqar Rashid
- St George's University Hospitals NHS Foundation Trust, London, UK
| | - Alastair J Noyce
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Eli Silber
- Kings College Hospital and Lewisham and Greenwich NHS Trusts, London, UK
| | - Huw Morris
- Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London, UK
| | - Gavin Giovannoni
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Ruth Dobson
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
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27
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Burley K, Fitzgibbon L, van Heel D, Vuckovic D, Mumford AD. PIK3R3 is a candidate regulator of platelet count in people of Bangladeshi ancestry. Res Pract Thromb Haemost 2023; 7:100175. [PMID: 37538507 PMCID: PMC10394561 DOI: 10.1016/j.rpth.2023.100175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 04/27/2023] [Accepted: 05/05/2023] [Indexed: 08/05/2023] Open
Abstract
Background Blood platelets are mediators of atherothrombotic disease and are regulated by complex sets of genes. Association studies in European ancestry populations have already detected informative platelet regulatory loci. Studies in other ancestries can potentially reveal new associations because of different allele frequencies, linkage structures, and variant effects. Objectives To reveal new regulatory genes for platelet count (PLT). Methods Genome-wide association studies (GWAS) were performed in 20,218 Bangladeshi and 9198 Pakistani individuals from the Genes & Health study. Loci significantly associated with PLT underwent fine-mapping to identify candidate genes. Results Of 1588 significantly associated variants (P < 5 × 10-8) at 20 loci in the Bangladeshi analysis, most replicated findings in prior transancestry GWAS and in the Pakistani analysis. However, the Bangladeshi locus defined by rs946528 (chr1:46019890) did not associate with PLT in the Pakistani analysis but was in the same linkage disequilibrium block (r2 ≥ 0.5) as PLT-associated variants in prior East Asian GWAS. The single independent association signal was refined to a 95% credible set of 343 variants spanning 8 coding genes. Functional annotation, mapping to megakaryocyte regulatory regions, and colocalization with blood expression quantitative trait loci identified the likely mediator of the PLT phenotype to be PIK3R3 encoding a regulator of phosphoinositol 3-kinase (PI3K). Conclusion Abnormal PI3K activity in the vessel wall is already implicated in the pathogenesis of atherothrombosis. Our identification of a new association between PIK3R3 and PLT provides further mechanistic insights into the contribution of the PI3K pathway to platelet biology.
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Affiliation(s)
- Kate Burley
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Lucy Fitzgibbon
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - David van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | | | - Dragana Vuckovic
- Department of Epidemiology and Biostatistics, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
| | - Andrew D. Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
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28
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Gidziela A, Ahmadzadeh YI, Michelini G, Allegrini AG, Agnew-Blais J, Lau LY, Duret M, Procopio F, Daly E, Ronald A, Rimfeld K, Malanchini M. A meta-analysis of genetic effects associated with neurodevelopmental disorders and co-occurring conditions. Nat Hum Behav 2023; 7:642-656. [PMID: 36806400 PMCID: PMC10129867 DOI: 10.1038/s41562-023-01530-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 01/16/2023] [Indexed: 02/22/2023]
Abstract
A systematic understanding of the aetiology of neurodevelopmental disorders (NDDs) and their co-occurrence with other conditions during childhood and adolescence remains incomplete. In the current meta-analysis, we synthesized the literature on (1) the contribution of genetic and environmental factors to NDDs, (2) the genetic and environmental overlap between different NDDs, and (3) the co-occurrence between NDDs and disruptive, impulse control and conduct disorders (DICCs). Searches were conducted across three platforms: Web of Science, Ovid Medline and Ovid Embase. Studies were included only if 75% or more of the sample consisted of children and/or adolescents and the studies had measured the aetiology of NDDs and DICCs using single-generation family designs or genomic methods. Studies that had selected participants on the basis of unrelated diagnoses or injuries were excluded. We performed multilevel, random-effects meta-analyses on 296 independent studies, including over four million (partly overlapping) individuals. We further explored developmental trajectories and the moderating roles of gender, measurement, geography and ancestry. We found all NDDs to be substantially heritable (family-based heritability, 0.66 (s.e. = 0.03); SNP heritability, 0.19 (s.e. = 0.03)). Meta-analytic genetic correlations between NDDs were moderate (grand family-based genetic correlation, 0.36 (s.e. = 0.12); grand SNP-based genetic correlation, 0.39 (s.e. = 0.19)) but differed substantially between pairs of disorders. The genetic overlap between NDDs and DICCs was strong (grand family-based genetic correlation, 0.62 (s.e. = 0.20)). While our work provides evidence to inform and potentially guide clinical and educational diagnostic procedures and practice, it also highlights the imbalance in the research effort that has characterized developmental genetics research.
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Affiliation(s)
- Agnieszka Gidziela
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK.
| | - Yasmin I Ahmadzadeh
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Giorgia Michelini
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- UCLA Semel Institute for Neuroscience, Division of Child and Adolescent Psychiatry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Andrea G Allegrini
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
- Division of Psychology and Language Sciences, University College London, London, UK
| | - Jessica Agnew-Blais
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Lok Yan Lau
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Megan Duret
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Francesca Procopio
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Emily Daly
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Angelica Ronald
- Department of Psychological Sciences, Birkbeck University of London, London, UK
| | - Kaili Rimfeld
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
- Department of Psychology, Royal Holloway University of London, Egham, UK
| | - Margherita Malanchini
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK.
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29
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Truong B, Hull LE, Ruan Y, Huang QQ, Hornsby W, Martin H, van Heel DA, Wang Y, Martin AR, Lee SH, Natarajan P. Integrative polygenic risk score improves the prediction accuracy of complex traits and diseases. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.21.23286110. [PMID: 36865265 PMCID: PMC9980241 DOI: 10.1101/2023.02.21.23286110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Polygenic risk scores (PRS) are an emerging tool to predict the clinical phenotypes and outcomes of individuals. Validation and transferability of existing PRS across independent datasets and diverse ancestries are limited, which hinders the practical utility and exacerbates health disparities. We propose PRSmix, a framework that evaluates and leverages the PRS corpus of a target trait to improve prediction accuracy, and PRSmix+, which incorporates genetically correlated traits to better capture the human genetic architecture. We applied PRSmix to 47 and 32 diseases/traits in European and South Asian ancestries, respectively. PRSmix demonstrated a mean prediction accuracy improvement of 1.20-fold (95% CI: [1.10; 1.3]; P-value = 9.17 × 10-5) and 1.19-fold (95% CI: [1.11; 1.27]; P-value = 1.92 × 10-6), and PRSmix+ improved the prediction accuracy by 1.72-fold (95% CI: [1.40; 2.04]; P-value = 7.58 × 10-6) and 1.42-fold (95% CI: [1.25; 1.59]; P-value = 8.01 × 10-7) in European and South Asian ancestries, respectively. Compared to the previously established cross-trait-combination method with scores from pre-defined correlated traits, we demonstrated that our method can improve prediction accuracy for coronary artery disease up to 3.27-fold (95% CI: [2.1; 4.44]; P-value after FDR correction = 2.6 × 10-4). Our method provides a comprehensive framework to benchmark and leverage the combined power of PRS for maximal performance in a desired target population.
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Affiliation(s)
- Buu Truong
- Program in Medical and Population Genetics and the Cardiovascular
Disease Initiative, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA
02142
- Center for Genomic Medicine and Cardiovascular Research Center,
Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114
| | - Leland E. Hull
- Division of General Internal Medicine, 100 Cambridge Street,
Massachusetts General Hospital, Boston, MA, 02114
- Department of Medicine, Harvard Medical School, 25 Shattuck
Street, Boston, MA 02115
| | - Yunfeng Ruan
- Program in Medical and Population Genetics and the Cardiovascular
Disease Initiative, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA
02142
- Center for Genomic Medicine and Cardiovascular Research Center,
Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114
| | - Qin Qin Huang
- Department of Human Genetics, Wellcome Sanger Institute,
Cambridge, UK
| | - Whitney Hornsby
- Program in Medical and Population Genetics and the Cardiovascular
Disease Initiative, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA
02142
- Center for Genomic Medicine and Cardiovascular Research Center,
Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114
| | - Hilary Martin
- Department of Human Genetics, Wellcome Sanger Institute,
Cambridge, UK
| | - David A. van Heel
- Blizard Institute, Barts and the London School of Medicine and
Dentistry, Queen Mary University of London, London, UK
| | - Ying Wang
- Program in Medical and Population Genetics and the Cardiovascular
Disease Initiative, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA
02142
- Stanley Center for Psychiatric Research, Broad Institute of
Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General
Hospital, Boston, MA, USA
| | - Alicia R. Martin
- Stanley Center for Psychiatric Research, Broad Institute of
Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General
Hospital, Boston, MA, USA
| | - S. Hong Lee
- Australian Centre for Precision Health, University of South
Australia Cancer Research Institute, University of South Australia, Adelaide, SA, 5000,
Australia
| | - Pradeep Natarajan
- Program in Medical and Population Genetics and the Cardiovascular
Disease Initiative, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA
02142
- Center for Genomic Medicine and Cardiovascular Research Center,
Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114
- Department of Medicine, Harvard Medical School, 25 Shattuck
Street, Boston, MA 02115
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30
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Breedon JR, Marshall CR, Giovannoni G, van Heel DA, Dobson R, Jacobs BM. Polygenic risk score prediction of multiple sclerosis in individuals of South Asian ancestry. Brain Commun 2023; 5:fcad041. [PMID: 37006331 PMCID: PMC10053643 DOI: 10.1093/braincomms/fcad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/12/2022] [Accepted: 02/21/2023] [Indexed: 02/24/2023] Open
Abstract
Polygenic risk scores aggregate an individual's burden of risk alleles to estimate the overall genetic risk for a specific trait or disease. Polygenic risk scores derived from genome-wide association studies of European populations perform poorly for other ancestral groups. Given the potential for future clinical utility, underperformance of polygenic risk scores in South Asian populations has the potential to reinforce health inequalities. To determine whether European-derived polygenic risk scores underperform at multiple sclerosis prediction in a South Asian-ancestry population compared with a European-ancestry cohort, we used data from two longitudinal genetic cohort studies: Genes & Health (2015-present), a study of ∼50 000 British-Bangladeshi and British-Pakistani individuals, and UK Biobank (2006-present), which is comprised of ∼500 000 predominantly White British individuals. We compared individuals with and without multiple sclerosis in both studies (Genes & Health: N Cases = 42, N Control = 40 490; UK Biobank: N Cases = 2091, N Control = 374 866). Polygenic risk scores were calculated using clumping and thresholding with risk allele effect sizes obtained from the largest multiple sclerosis genome-wide association study to date. Scores were calculated with and without the major histocompatibility complex region, the most influential locus in determining multiple sclerosis risk. Polygenic risk score prediction was evaluated using Nagelkerke's pseudo-R 2 metric adjusted for case ascertainment, age, sex and the first four genetic principal components. We found that, as expected, European-derived polygenic risk scores perform poorly in the Genes & Health cohort, explaining 1.1% (including the major histocompatibility complex) and 1.5% (excluding the major histocompatibility complex) of disease risk. In contrast, multiple sclerosis polygenic risk scores explained 4.8% (including the major histocompatibility complex) and 2.8% (excluding the major histocompatibility complex) of disease risk in European-ancestry UK Biobank participants. These findings suggest that polygenic risk score prediction of multiple sclerosis based on European genome-wide association study results is less accurate in a South Asian population. Genetic studies of ancestrally diverse populations are required to ensure that polygenic risk scores can be useful across ancestries.
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Affiliation(s)
- Joshua R Breedon
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London EC1M 6BQ, UK
| | - Charles R Marshall
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London EC1M 6BQ, UK
- Department of Neurology, Royal London Hospital, London E1 1FR, UK
| | - Gavin Giovannoni
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London EC1M 6BQ, UK
- Department of Neurology, Royal London Hospital, London E1 1FR, UK
- Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - David A van Heel
- Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Ruth Dobson
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London EC1M 6BQ, UK
- Department of Neurology, Royal London Hospital, London E1 1FR, UK
| | - Benjamin M Jacobs
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London EC1M 6BQ, UK
- Department of Neurology, Royal London Hospital, London E1 1FR, UK
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31
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Carss KJ, Deaton AM, Del Rio-Espinola A, Diogo D, Fielden M, Kulkarni DA, Moggs J, Newham P, Nelson MR, Sistare FD, Ward LD, Yuan J. Using human genetics to improve safety assessment of therapeutics. Nat Rev Drug Discov 2023; 22:145-162. [PMID: 36261593 DOI: 10.1038/s41573-022-00561-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2022] [Indexed: 02/07/2023]
Abstract
Human genetics research has discovered thousands of proteins associated with complex and rare diseases. Genome-wide association studies (GWAS) and studies of Mendelian disease have resulted in an increased understanding of the role of gene function and regulation in human conditions. Although the application of human genetics has been explored primarily as a method to identify potential drug targets and support their relevance to disease in humans, there is increasing interest in using genetic data to identify potential safety liabilities of modulating a given target. Human genetic variants can be used as a model to anticipate the effect of lifelong modulation of therapeutic targets and identify the potential risk for on-target adverse events. This approach is particularly useful for non-clinical safety evaluation of novel therapeutics that lack pharmacologically relevant animal models and can contribute to the intrinsic safety profile of a drug target. This Review illustrates applications of human genetics to safety studies during drug discovery and development, including assessing the potential for on- and off-target associated adverse events, carcinogenicity risk assessment, and guiding translational safety study designs and monitoring strategies. A summary of available human genetic resources and recommended best practices is provided. The challenges and future perspectives of translating human genetic information to identify risks for potential drug effects in preclinical and clinical development are discussed.
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Affiliation(s)
| | - Aimee M Deaton
- Amgen, Cambridge, MA, USA.,Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Alberto Del Rio-Espinola
- Novartis Institutes for BioMedical Research, Basel, Switzerland.,GentiBio Inc., Cambridge, MA, USA
| | | | - Mark Fielden
- Amgen, Thousand Oaks, MA, USA.,Kate Therapeutics, San Diego, CA, USA
| | | | - Jonathan Moggs
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | - Frank D Sistare
- Merck & Co., West Point, PA, USA.,315 Meadowmont Ln, Chapel Hill, NC, USA
| | - Lucas D Ward
- Amgen, Cambridge, MA, USA. .,Alnylam Pharmaceuticals, Cambridge, MA, USA.
| | - Jing Yuan
- Amgen, Cambridge, MA, USA.,Pfizer, Cambridge, MA, USA
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32
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Nagirnaja L, Lopes AM, Charng WL, Miller B, Stakaitis R, Golubickaite I, Stendahl A, Luan T, Friedrich C, Mahyari E, Fadial E, Kasak L, Vigh-Conrad K, Oud MS, Xavier MJ, Cheers SR, James ER, Guo J, Jenkins TG, Riera-Escamilla A, Barros A, Carvalho F, Fernandes S, Gonçalves J, Gurnett CA, Jørgensen N, Jezek D, Jungheim ES, Kliesch S, McLachlan RI, Omurtag KR, Pilatz A, Sandlow JI, Smith J, Eisenberg ML, Hotaling JM, Jarvi KA, Punab M, Rajpert-De Meyts E, Carrell DT, Krausz C, Laan M, O'Bryan MK, Schlegel PN, Tüttelmann F, Veltman JA, Almstrup K, Aston KI, Conrad DF. Diverse monogenic subforms of human spermatogenic failure. Nat Commun 2022; 13:7953. [PMID: 36572685 PMCID: PMC9792524 DOI: 10.1038/s41467-022-35661-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 12/16/2022] [Indexed: 12/27/2022] Open
Abstract
Non-obstructive azoospermia (NOA) is the most severe form of male infertility and typically incurable. Defining the genetic basis of NOA has proven challenging, and the most advanced classification of NOA subforms is not based on genetics, but simple description of testis histology. In this study, we exome-sequenced over 1000 clinically diagnosed NOA cases and identified a plausible recessive Mendelian cause in 20%. We find further support for 21 genes in a 2-stage burden test with 2072 cases and 11,587 fertile controls. The disrupted genes are primarily on the autosomes, enriched for undescribed human "knockouts", and, for the most part, have yet to be linked to a Mendelian trait. Integration with single-cell RNA sequencing data shows that azoospermia genes can be grouped into molecular subforms with synchronized expression patterns, and analogs of these subforms exist in mice. This analysis framework identifies groups of genes with known roles in spermatogenesis but also reveals unrecognized subforms, such as a set of genes expressed across mitotic divisions of differentiating spermatogonia. Our findings highlight NOA as an understudied Mendelian disorder and provide a conceptual structure for organizing the complex genetics of male infertility, which may provide a rational basis for disease classification.
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Affiliation(s)
- Liina Nagirnaja
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Alexandra M Lopes
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Wu-Lin Charng
- Department of Neurology, Washington University, St. Louis, MO, USA
| | - Brian Miller
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Rytis Stakaitis
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Laboratory of Molecular Neurooncology, Neuroscience Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Ieva Golubickaite
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alexandra Stendahl
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Tianpengcheng Luan
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Corinna Friedrich
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Eisa Mahyari
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Eloise Fadial
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Laura Kasak
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Katinka Vigh-Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Manon S Oud
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Miguel J Xavier
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Samuel R Cheers
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Emma R James
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jingtao Guo
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Timothy G Jenkins
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Antoni Riera-Escamilla
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Catalonia, Spain
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB Sant Pau), Universitat Autònoma de Barcelona, Barcelona, Catalonia, 08025, Spain
| | - Alberto Barros
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Filipa Carvalho
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Susana Fernandes
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - João Gonçalves
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal
- Centre for Toxicogenomics and Human Health, Nova Medical School, Lisbon, Portugal
| | | | - Niels Jørgensen
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Davor Jezek
- Department of Histology and Embryology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Emily S Jungheim
- Department of Obstetrics and Gynecology at Northwestern University, Division of Reproductive Endocrinology, Chicago, IL, USA
| | - Sabine Kliesch
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - Robert I McLachlan
- Hudson Institute of Medical Research and the Department of Obstetrics and Gynecology, Monash University, Clayton, VIC, Australia
| | - Kenan R Omurtag
- Department of Obstetrics and Gynecology at Washington University, Division of Reproductive Endocrinology, St. Louis, MO, USA
| | - Adrian Pilatz
- Clinic for Urology, Pediatric Urology and Andrology, Justus Liebig University, Giessen, Germany
| | - Jay I Sandlow
- Department of Urology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - James Smith
- Department of Urology, University California San Francisco, San Francisco, CA, USA
| | - Michael L Eisenberg
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
| | - James M Hotaling
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Keith A Jarvi
- Division of Urology, Department of Surgery, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Margus Punab
- Andrology Center, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Ewa Rajpert-De Meyts
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Douglas T Carrell
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Csilla Krausz
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Maris Laan
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Moira K O'Bryan
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Peter N Schlegel
- Department of Urology, Weill Cornell Medicine, New York, NY, USA
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Joris A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Kristian Almstrup
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Kenneth I Aston
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Donald F Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA.
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Belkadi A, Thareja G, Abbaszadeh F, Badii R, Fauman E, Albagha OM, Suhre K. Identification of PCSK9-like human gene knockouts using metabolomics, proteomics, and whole-genome sequencing in a consanguineous population. CELL GENOMICS 2022; 3:100218. [PMID: 36777185 PMCID: PMC9903797 DOI: 10.1016/j.xgen.2022.100218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 07/16/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022]
Abstract
Natural human knockouts of genes associated with desirable outcomes, such as PCSK9 with low levels of LDL-cholesterol, can lead to the discovery of new drug targets and treatments. Rare loss-of-function variants are more likely to be found in the homozygous state in consanguineous populations, and deep molecular phenotyping of blood samples from homozygous carriers can help to discriminate between silent and functional variants. Here, we combined whole-genome sequencing with proteomics and metabolomics for 2,935 individuals from the Qatar Biobank (QBB) to evaluate the power of this approach for finding genes of clinical and pharmaceutical interest. As proof-of-concept, we identified a homozygous carrier of a very rare PCSK9 variant with extremely low circulating PCSK9 levels and low LDL. Our study demonstrates that the chances of finding such variants are about 168 times higher in QBB compared with GnomAD and emphasizes the potential of consanguineous populations for drug discovery.
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Affiliation(s)
- Aziz Belkadi
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha 24144, Qatar,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, NY, USA
| | - Gaurav Thareja
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha 24144, Qatar,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | - Omar M.E. Albagha
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar,Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha 24144, Qatar,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, NY, USA,Corresponding author
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Rodosthenous RS, Niemi MEK, Kallio L, Perala M, Terho P, Knopp T, Punkka E, Makkonen EM, Nurmi P, Makela J, Wihuri P, Hautalahti M, Moffatt C, Martini P, Germine L, Makela VA, Karhunen OA, Lahti J, Hiekkalinna TS, Jyrhama T, Shen HY, Runz H, Palotie A, Perola M, Ganna A. Recontacting biobank participants to collect lifestyle, behavioural and cognitive information via online questionnaires: lessons from a pilot study within FinnGen. BMJ Open 2022; 12:e064695. [PMID: 36198465 PMCID: PMC9535212 DOI: 10.1136/bmjopen-2022-064695] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVES To recontact biobank participants and collect cognitive, behavioural and lifestyle information via a secure online platform. DESIGN Biobank-based recontacting pilot study. SETTING Three Finnish biobanks (Helsinki, Auria, Tampere) recruiting participants from February 2021 to July 2021. PARTICIPANTS All eligible invitees were enrolled in FinnGen by their biobanks (Helsinki, Auria, Tampere), had available genetic data and were >18 years old. Individuals with severe neuropsychiatric disease or cognitive or physical disabilities were excluded. Lastly, 5995 participants were selected based on their polygenic score for cognitive abilities and invited to the study. Among invitees, 1115 had successfully participated and completed the study questionnaire(s). OUTCOME MEASURES The primary outcome was the participation rate among study invitees. Secondary outcomes included questionnaire completion rate, quality of data collected and comparison of participation rate boosting strategies. RESULTS The overall participation rate was 18.6% among all invitees and 23.1% among individuals aged 18-69. A second reminder letter yielded an additional 9.7% participation rate in those who did not respond to the first invitation. Recontacting participants via an online healthcare portal yielded lower participation than recontacting via physical letter. The completion rate of the questionnaire and cognitive tests was high (92% and 85%, respectively), and measurements were overall reliable among participants. For example, the correlation (r) between self-reported body mass index and that collected by the biobanks was 0.92. CONCLUSION In summary, this pilot suggests that recontacting FinnGen participants with the goal to collect a wide range of cognitive, behavioural and lifestyle information without additional engagement results in a low participation rate, but with reliable data. We suggest that such information be collected at enrolment, if possible, rather than via post hoc recontacting.
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Affiliation(s)
| | - Mari E K Niemi
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Lila Kallio
- Turku University Hospital (TYKS), Turku, Finland
| | - Merja Perala
- Turku University Hospital (TYKS), Turku, Finland
| | - Perttu Terho
- Turku University Hospital (TYKS), Turku, Finland
| | - Theresa Knopp
- Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Eero Punkka
- Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | | | - Paula Nurmi
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | | | | | | | | | | | - Viola A Makela
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Oona A Karhunen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine University of Helsinki, Helsinki, Finland
| | | | - Tero Jyrhama
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Huei-Yi Shen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Heiko Runz
- Translational Biology, Research and Development, Biogen Inc, Cambridge, Massachusetts, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Markus Perola
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Andrea Ganna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
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35
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Jacobs BM, Peter M, Giovannoni G, Noyce AJ, Morris HR, Dobson R. Towards a global view of multiple sclerosis genetics. Nat Rev Neurol 2022; 18:613-623. [PMID: 36075979 DOI: 10.1038/s41582-022-00704-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2022] [Indexed: 11/09/2022]
Abstract
Multiple sclerosis (MS) is a neuroimmunological disorder of the CNS with a strong heritable component. The genetic architecture of MS susceptibility is well understood in populations of European ancestry. However, the extent to which this architecture explains MS susceptibility in populations of non-European ancestry remains unclear. In this Perspective article, we outline the scientific arguments for studying MS genetics in ancestrally diverse populations. We argue that this approach is likely to yield insights that could benefit individuals with MS from all ancestral groups. We explore the logistical and theoretical challenges that have held back this field to date and conclude that, despite these challenges, inclusion of participants of non-European ancestry in MS genetics studies will ultimately be of value to all patients with MS worldwide.
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Affiliation(s)
- Benjamin Meir Jacobs
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University London, London, UK. .,Department of Neurology, Royal London Hospital, London, UK.
| | - Michelle Peter
- NHS North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Gavin Giovannoni
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University London, London, UK.,Department of Neurology, Royal London Hospital, London, UK.,Blizard Institute, Queen Mary University London, London, UK
| | - Alastair J Noyce
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University London, London, UK.,Department of Neurology, Royal London Hospital, London, UK.,Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Huw R Morris
- Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Ruth Dobson
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University London, London, UK.,Department of Neurology, Royal London Hospital, London, UK
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36
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O'Sullivan JW, Raghavan S, Marquez-Luna C, Luzum JA, Damrauer SM, Ashley EA, O'Donnell CJ, Willer CJ, Natarajan P. Polygenic Risk Scores for Cardiovascular Disease: A Scientific Statement From the American Heart Association. Circulation 2022; 146:e93-e118. [PMID: 35862132 PMCID: PMC9847481 DOI: 10.1161/cir.0000000000001077] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Cardiovascular disease is the leading contributor to years lost due to disability or premature death among adults. Current efforts focus on risk prediction and risk factor mitigation' which have been recognized for the past half-century. However, despite advances, risk prediction remains imprecise with persistently high rates of incident cardiovascular disease. Genetic characterization has been proposed as an approach to enable earlier and potentially tailored prevention. Rare mendelian pathogenic variants predisposing to cardiometabolic conditions have long been known to contribute to disease risk in some families. However, twin and familial aggregation studies imply that diverse cardiovascular conditions are heritable in the general population. Significant technological and methodological advances since the Human Genome Project are facilitating population-based comprehensive genetic profiling at decreasing costs. Genome-wide association studies from such endeavors continue to elucidate causal mechanisms for cardiovascular diseases. Systematic cataloging for cardiovascular risk alleles also enabled the development of polygenic risk scores. Genetic profiling is becoming widespread in large-scale research, including in health care-associated biobanks, randomized controlled trials, and direct-to-consumer profiling in tens of millions of people. Thus, individuals and their physicians are increasingly presented with polygenic risk scores for cardiovascular conditions in clinical encounters. In this scientific statement, we review the contemporary science, clinical considerations, and future challenges for polygenic risk scores for cardiovascular diseases. We selected 5 cardiometabolic diseases (coronary artery disease, hypercholesterolemia, type 2 diabetes, atrial fibrillation, and venous thromboembolic disease) and response to drug therapy and offer provisional guidance to health care professionals, researchers, policymakers, and patients.
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Huang QQ, Sallah N, Dunca D, Trivedi B, Hunt KA, Hodgson S, Lambert SA, Arciero E, Wright J, Griffiths C, Trembath RC, Hemingway H, Inouye M, Finer S, van Heel DA, Lumbers RT, Martin HC, Kuchenbaecker K. Transferability of genetic loci and polygenic scores for cardiometabolic traits in British Pakistani and Bangladeshi individuals. Nat Commun 2022; 13:4664. [PMID: 35945198 PMCID: PMC9363492 DOI: 10.1038/s41467-022-32095-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/15/2022] [Indexed: 12/30/2022] Open
Abstract
Individuals with South Asian ancestry have a higher risk of heart disease than other groups but have been largely excluded from genetic research. Using data from 22,000 British Pakistani and Bangladeshi individuals with linked electronic health records from the Genes & Health cohort, we conducted genome-wide association studies of coronary artery disease and its key risk factors. Using power-adjusted transferability ratios, we found evidence for transferability for the majority of cardiometabolic loci powered to replicate. The performance of polygenic scores was high for lipids and blood pressure, but lower for BMI and coronary artery disease. Adding a polygenic score for coronary artery disease to clinical risk factors showed significant improvement in reclassification. In Mendelian randomisation using transferable loci as instruments, our findings were consistent with results in European-ancestry individuals. Taken together, trait-specific transferability of trait loci between populations is an important consideration with implications for risk prediction and causal inference.
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Affiliation(s)
- Qin Qin Huang
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Neneh Sallah
- Institute of Health Informatics, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Diana Dunca
- Institute of Health Informatics, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Bhavi Trivedi
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Karen A Hunt
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Sam Hodgson
- Primary Care Research Centre, University of Southampton, Southampton, UK
| | - Samuel A Lambert
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Elena Arciero
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - John Wright
- Bradford Institute for Health Research, Bradford Teaching Hospitals National Health Service (NHS) Foundation Trust, Bradford, UK
| | - Chris Griffiths
- Institute of Population Health Sciences, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Richard C Trembath
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Harry Hemingway
- Institute of Health Informatics, University College London, London, UK
- Health Data Research UK, University College London, London, UK
- University College London Hospitals Biomedical Research Centre (UCLH BRC), London, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- British Heart Foundation Cambridge Centre of Research Excellence, Department of Clinical Medicine, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Sarah Finer
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - David A van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - R Thomas Lumbers
- Institute of Health Informatics, University College London, London, UK
- University College London Hospitals Biomedical Research Centre (UCLH BRC), London, UK
- British Heart Foundation Research Accelerator, University College London, London, UK
| | - Hilary C Martin
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Karoline Kuchenbaecker
- UCL Genetics Institute, University College London, London, UK.
- Division of Psychiatry, University College London, London, UK.
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Mann JP, Hoare M. A minority of somatically mutated genes in pre-existing fatty liver disease have prognostic importance in the development of NAFLD. Liver Int 2022; 42:1823-1835. [PMID: 35474605 PMCID: PMC9544140 DOI: 10.1111/liv.15283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Understanding the genetics of liver disease has the potential to facilitate clinical risk stratification. We recently identified acquired somatic mutations in six genes and one lncRNA in pre-existing fatty liver disease. We hypothesised that germline variation in these genes might be associated with the risk of developing steatosis and contribute to the prediction of disease severity. METHODS Genome-wide association study (GWAS) summary statistics were extracted from seven studies (>1.7 million participants) for variants near ACVR2A, ALB, CIDEB, FOXO1, GPAM, NEAT1 and TNRC6B for: aminotransferases, liver fat, HbA1c, diagnosis of NAFLD, ARLD and cirrhosis. Findings were replicated using GWAS data from multiple independent cohorts. A phenome-wide association study was performed to examine for related metabolic traits, using both common and rare variants, including gene-burden testing. RESULTS There was no evidence of association between rare germline variants or SNPs near five genes (ACVR2A, ALB, CIDEB, FOXO1 and TNRC6B) and risk or severity of liver disease. Variants in GPAM (proxies for p.Ile43Val) were associated with liver fat (p = 3.6 × 10-13 ), ALT (p = 2.8 × 10-39 ) and serum lipid concentrations. Variants in NEAT1 demonstrated borderline significant associations with ALT (p = 1.9 × 10-11 ) and HbA1c, but not with liver fat, as well as influencing waist-to-hip ratio, adjusted for BMI. CONCLUSIONS Despite the acquisition of somatic mutations at these loci during progressive fatty liver disease, we did not find associations between germline variation and markers of liver disease, except in GPAM. In the future, larger sample sizes may identify associations. Currently, germline polygenic risk scores will not capture data from genes affected by somatic mutations.
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Affiliation(s)
- Jake P. Mann
- Institute of Metabolic ScienceUniversity of CambridgeCambridgeUK
- School of Clinical MedicineUniversity of CambridgeCambridgeUK
| | - Matthew Hoare
- School of Clinical MedicineUniversity of CambridgeCambridgeUK
- CRUK Cambridge InstituteUniversity of CambridgeCambridgeUK
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Tschigg K, Consoli L, Biasiotto R, Mascalzoni D. Ethical, legal and social/societal implications (ELSI) of recall-by-genotype (RbG) and genotype-driven-research (GDR) approaches: a scoping review. Eur J Hum Genet 2022; 30:1000-1010. [PMID: 35705790 PMCID: PMC9437022 DOI: 10.1038/s41431-022-01120-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 03/17/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022] Open
Abstract
Recall by Genotype (RbG), Genotype-driven-recall (GDR), and Genotype-based-recall (GBR) strategies are increasingly used to conduct genomic or biobanking sub-studies that single out participants as eligible because of their specific individual genotypic information. However, existing regulatory and governance frameworks do not apply to all aspects of genotype-driven research approaches. The recall strategies disclose or withhold personal genotypic information with uncertain clinical utility. Accordingly, this scoping review aims to identify peculiar, explicit and implicit ethical, legal, and societal/social implications (ELSI) of RbG study designs. We conducted a systematic literature search of three electronic databases from November 2020 to February 2021. We investigated qualitative and quantitative research methods used to report ELSI aspects in RbG research. Congruent with other research findings, we identified a lack of qualitative research investigating the particular ELSI challenges with RbG. We included and analysed the content of twenty-five publications. We found a consensus on RbG posing significant ethical issues, dilemmas, barriers, concerns and societal challenges. However, we found that the approaches to disclosure and study-specific recall and communication strategies employed consent models and Return of Research Results (RoRR) policies varied considerably. Furthermore, we identified a high heterogeneity in perspectives of participants and experts about ELSI of study-specific RbG policies. Therefore, further fine-mapping through qualitative and empirical research is needed to draw conclusions and re-fine ELSI frameworks.
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Affiliation(s)
- Katharina Tschigg
- Department of Cellular, Computational, and Integrative Biology, University of Trento, Trento, Italy. .,Institute for Biomedicine & Affiliated Institute of the University of Lübeck, Eurac Research, Bolzano, Italy, Bozen, Italy.
| | - Luca Consoli
- Institute for Science in Society, Radboud University, Nijmegen, Netherlands
| | - Roberta Biasiotto
- Institute for Biomedicine & Affiliated Institute of the University of Lübeck, Eurac Research, Bolzano, Italy, Bozen, Italy.,Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Deborah Mascalzoni
- Institute for Biomedicine & Affiliated Institute of the University of Lübeck, Eurac Research, Bolzano, Italy, Bozen, Italy.,Department of Public Health and Caring Sciences, Center for Research Ethics and Bioethics, Uppsala University, Uppsala, Sweden
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40
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Hodgson S, Huang QQ, Sallah N, Griffiths CJ, Newman WG, Trembath RC, Wright J, Lumbers RT, Kuchenbaecker K, van Heel DA, Mathur R, Martin HC, Finer S. Integrating polygenic risk scores in the prediction of type 2 diabetes risk and subtypes in British Pakistanis and Bangladeshis: A population-based cohort study. PLoS Med 2022; 19:e1003981. [PMID: 35587468 PMCID: PMC9119501 DOI: 10.1371/journal.pmed.1003981] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 04/06/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Type 2 diabetes (T2D) is highly prevalent in British South Asians, yet they are underrepresented in research. Genes & Health (G&H) is a large, population study of British Pakistanis and Bangladeshis (BPB) comprising genomic and routine health data. We assessed the extent to which genetic risk for T2D is shared between BPB and European populations (EUR). We then investigated whether the integration of a polygenic risk score (PRS) for T2D with an existing risk tool (QDiabetes) could improve prediction of incident disease and the characterisation of disease subtypes. METHODS AND FINDINGS In this observational cohort study, we assessed whether common genetic loci associated with T2D in EUR individuals were replicated in 22,490 BPB individuals in G&H. We replicated fewer loci in G&H (n = 76/338, 22%) than would be expected given power if all EUR-ascertained loci were transferable (n = 101, 30%; p = 0.001). Of the 27 transferable loci that were powered to interrogate this, only 9 showed evidence of shared causal variants. We constructed a T2D PRS and combined it with a clinical risk instrument (QDiabetes) in a novel, integrated risk tool (IRT) to assess risk of incident diabetes. To assess model performance, we compared categorical net reclassification index (NRI) versus QDiabetes alone. In 13,648 patients free from T2D followed up for 10 years, NRI was 3.2% for IRT versus QDiabetes (95% confidence interval (CI): 2.0% to 4.4%). IRT performed best in reclassification of individuals aged less than 40 years deemed low risk by QDiabetes alone (NRI 5.6%, 95% CI 3.6% to 7.6%), who tended to be free from comorbidities and slim. After adjustment for QDiabetes score, PRS was independently associated with progression to T2D after gestational diabetes (hazard ratio (HR) per SD of PRS 1.23, 95% CI 1.05 to 1.42, p = 0.028). Using cluster analysis of clinical features at diabetes diagnosis, we replicated previously reported disease subgroups, including Mild Age-Related, Mild Obesity-related, and Insulin-Resistant Diabetes, and showed that PRS distribution differs between subgroups (p = 0.002). Integrating PRS in this cluster analysis revealed a Probable Severe Insulin Deficient Diabetes (pSIDD) subgroup, despite the absence of clinical measures of insulin secretion or resistance. We also observed differences in rates of progression to micro- and macrovascular complications between subgroups after adjustment for confounders. Study limitations include the absence of an external replication cohort and the potential biases arising from missing or incorrect routine health data. CONCLUSIONS Our analysis of the transferability of T2D loci between EUR and BPB indicates the need for larger, multiancestry studies to better characterise the genetic contribution to disease and its varied aetiology. We show that a T2D PRS optimised for this high-risk BPB population has potential clinical application in BPB, improving the identification of T2D risk (especially in the young) on top of an established clinical risk algorithm and aiding identification of subgroups at diagnosis, which may help future efforts to stratify care and treatment of the disease.
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Affiliation(s)
- Sam Hodgson
- Primary Care Research Centre, University of Southampton, Southampton, United Kingdom
| | - Qin Qin Huang
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Neneh Sallah
- Institute of Health Informatics, University College London, London, United Kingdom
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Genes & Health Research Team
- Wolfson Institute of Population Health, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Chris J. Griffiths
- Wolfson Institute of Population Health, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - William G. Newman
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Richard C. Trembath
- School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - John Wright
- Bradford Institute for Health Research, Bradford, United Kingdom
| | - R. Thomas Lumbers
- Institute of Health Informatics, University College London, London, United Kingdom
- British Heart Foundation Research Accelerator, University College London, London, United Kingdom
| | - Karoline Kuchenbaecker
- UCL Genetics Institute, University College London, London, United Kingdom
- Division of Psychiatry, University College London, London, United Kingdom
| | - David A. van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Rohini Mathur
- London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Hilary C. Martin
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Sarah Finer
- Wolfson Institute of Population Health, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
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Balick DJ, Jordan DM, Sunyaev S, Do R. Overcoming constraints on the detection of recessive selection in human genes from population frequency data. Am J Hum Genet 2022; 109:33-49. [PMID: 34951958 DOI: 10.1016/j.ajhg.2021.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/30/2021] [Indexed: 11/01/2022] Open
Abstract
The identification of genes that evolve under recessive natural selection is a long-standing goal of population genetics research that has important applications to the discovery of genes associated with disease. We found that commonly used methods to evaluate selective constraint at the gene level are highly sensitive to genes under heterozygous selection but ubiquitously fail to detect recessively evolving genes. Additionally, more sophisticated likelihood-based methods designed to detect recessivity similarly lack power for a human gene of realistic length from current population sample sizes. However, extensive simulations suggested that recessive genes may be detectable in aggregate. Here, we offer a method informed by population genetics simulations designed to detect recessive purifying selection in gene sets. Applying this to empirical gene sets produced significant enrichments for strong recessive selection in genes previously inferred to be under recessive selection in a consanguineous cohort and in genes involved in autosomal recessive monogenic disorders.
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42
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Darke P, Cassidy S, Catt M, Taylor R, Missier P, Bacardit J. Curating a longitudinal research resource using linked primary care EHR data-a UK Biobank case study. J Am Med Inform Assoc 2021; 29:546-552. [PMID: 34897458 PMCID: PMC8800530 DOI: 10.1093/jamia/ocab260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 11/03/2021] [Accepted: 11/23/2021] [Indexed: 11/30/2022] Open
Abstract
Primary care EHR data are often of clinical importance to cohort studies however they require careful handling. Challenges include determining the periods during which EHR data were collected. Participants are typically censored when they deregister from a medical practice, however, cohort studies wish to follow participants longitudinally including those that change practice. Using UK Biobank as an exemplar, we developed methodology to infer continuous periods of data collection and maximize follow-up in longitudinal studies. This resulted in longer follow-up for around 40% of participants with multiple registration records (mean increase of 3.8 years from the first study visit). The approach did not sacrifice phenotyping accuracy when comparing agreement between self-reported and EHR data. A diabetes mellitus case study illustrates how the algorithm supports longitudinal study design and provides further validation. We use UK Biobank data, however, the tools provided can be used for other conditions and studies with minimal alteration.
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Affiliation(s)
- Philip Darke
- School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Sophie Cassidy
- Central Clinical School, The University of Sydney, Sydney, Australia
| | - Michael Catt
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Roy Taylor
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Paolo Missier
- School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Jaume Bacardit
- School of Computing, Newcastle University, Newcastle upon Tyne, UK
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43
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Arciero E, Dogra SA, Malawsky DS, Mezzavilla M, Tsismentzoglou T, Huang QQ, Hunt KA, Mason D, Sharif SM, van Heel DA, Sheridan E, Wright J, Small N, Carmi S, Iles MM, Martin HC. Fine-scale population structure and demographic history of British Pakistanis. Nat Commun 2021; 12:7189. [PMID: 34893604 PMCID: PMC8664933 DOI: 10.1038/s41467-021-27394-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 11/09/2021] [Indexed: 02/08/2023] Open
Abstract
Previous genetic and public health research in the Pakistani population has focused on the role of consanguinity in increasing recessive disease risk, but little is known about its recent population history or the effects of endogamy. Here, we investigate fine-scale population structure, history and consanguinity patterns using genotype chip data from 2,200 British Pakistanis. We reveal strong recent population structure driven by the biraderi social stratification system. We find that all subgroups have had low recent effective population sizes (Ne), with some showing a decrease 15‒20 generations ago that has resulted in extensive identity-by-descent sharing and homozygosity, increasing the risk of recessive disorders. Our results from two orthogonal methods (one using machine learning and the other coalescent-based) suggest that the detailed reporting of parental relatedness for mothers in the cohort under-represents the true levels of consanguinity. These results demonstrate the impact of cultural practices on population structure and genomic diversity in Pakistanis, and have important implications for medical genetic studies.
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Affiliation(s)
- Elena Arciero
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Sufyan A Dogra
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | | | | | - Theofanis Tsismentzoglou
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Qin Qin Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Karen A Hunt
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Dan Mason
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Saghira Malik Sharif
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - David A van Heel
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Eamonn Sheridan
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - John Wright
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Neil Small
- Faculty of Health Studies, University of Bradford, Richmond Road, Bradford, UK
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mark M Iles
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Hilary C Martin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
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44
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Graham SE, Clarke SL, Wu KHH, Kanoni S, Zajac GJM, Ramdas S, Surakka I, Ntalla I, Vedantam S, Winkler TW, Locke AE, Marouli E, Hwang MY, Han S, Narita A, Choudhury A, Bentley AR, Ekoru K, Verma A, Trivedi B, Martin HC, Hunt KA, Hui Q, Klarin D, Zhu X, Thorleifsson G, Helgadottir A, Gudbjartsson DF, Holm H, Olafsson I, Akiyama M, Sakaue S, Terao C, Kanai M, Zhou W, Brumpton BM, Rasheed H, Ruotsalainen SE, Havulinna AS, Veturi Y, Feng Q, Rosenthal EA, Lingren T, Pacheco JA, Pendergrass SA, Haessler J, Giulianini F, Bradford Y, Miller JE, Campbell A, Lin K, Millwood IY, Hindy G, Rasheed A, Faul JD, Zhao W, Weir DR, Turman C, Huang H, Graff M, Mahajan A, Brown MR, Zhang W, Yu K, Schmidt EM, Pandit A, Gustafsson S, Yin X, Luan J, Zhao JH, Matsuda F, Jang HM, Yoon K, Medina-Gomez C, Pitsillides A, Hottenga JJ, Willemsen G, Wood AR, Ji Y, Gao Z, Haworth S, Mitchell RE, Chai JF, Aadahl M, Yao J, Manichaikul A, Warren HR, Ramirez J, Bork-Jensen J, Kårhus LL, Goel A, Sabater-Lleal M, Noordam R, Sidore C, Fiorillo E, McDaid AF, Marques-Vidal P, Wielscher M, Trompet S, Sattar N, Møllehave LT, Thuesen BH, Munz M, Zeng L, Huang J, Yang B, Poveda A, Kurbasic A, Lamina C, Forer L, Scholz M, Galesloot TE, Bradfield JP, Daw EW, Zmuda JM, Mitchell JS, Fuchsberger C, Christensen H, Brody JA, Feitosa MF, Wojczynski MK, Preuss M, Mangino M, Christofidou P, Verweij N, Benjamins JW, Engmann J, Kember RL, Slieker RC, Lo KS, Zilhao NR, Le P, Kleber ME, Delgado GE, Huo S, Ikeda DD, Iha H, Yang J, Liu J, Leonard HL, Marten J, Schmidt B, Arendt M, Smyth LJ, Cañadas-Garre M, Wang C, Nakatochi M, Wong A, Hutri-Kähönen N, Sim X, Xia R, Huerta-Chagoya A, Fernandez-Lopez JC, Lyssenko V, Ahmed M, Jackson AU, Yousri NA, Irvin MR, Oldmeadow C, Kim HN, Ryu S, Timmers PRHJ, Arbeeva L, Dorajoo R, Lange LA, Chai X, Prasad G, Lorés-Motta L, Pauper M, Long J, Li X, Theusch E, Takeuchi F, Spracklen CN, Loukola A, Bollepalli S, Warner SC, Wang YX, Wei WB, Nutile T, Ruggiero D, Sung YJ, Hung YJ, Chen S, Liu F, Yang J, Kentistou KA, Gorski M, Brumat M, Meidtner K, Bielak LF, Smith JA, Hebbar P, Farmaki AE, Hofer E, Lin M, Xue C, Zhang J, Concas MP, Vaccargiu S, van der Most PJ, Pitkänen N, Cade BE, Lee J, van der Laan SW, Chitrala KN, Weiss S, Zimmermann ME, Lee JY, Choi HS, Nethander M, Freitag-Wolf S, Southam L, Rayner NW, Wang CA, Lin SY, Wang JS, Couture C, Lyytikäinen LP, Nikus K, Cuellar-Partida G, Vestergaard H, Hildalgo B, Giannakopoulou O, Cai Q, Obura MO, van Setten J, Li X, Schwander K, Terzikhan N, Shin JH, Jackson RD, Reiner AP, Martin LW, Chen Z, Li L, Highland HM, Young KL, Kawaguchi T, Thiery J, Bis JC, Nadkarni GN, Launer LJ, Li H, Nalls MA, Raitakari OT, Ichihara S, Wild SH, Nelson CP, Campbell H, Jäger S, Nabika T, Al-Mulla F, Niinikoski H, Braund PS, Kolcic I, Kovacs P, Giardoglou T, Katsuya T, Bhatti KF, de Kleijn D, de Borst GJ, Kim EK, Adams HHH, Ikram MA, Zhu X, Asselbergs FW, Kraaijeveld AO, Beulens JWJ, Shu XO, Rallidis LS, Pedersen O, Hansen T, Mitchell P, Hewitt AW, Kähönen M, Pérusse L, Bouchard C, Tönjes A, Chen YDI, Pennell CE, Mori TA, Lieb W, Franke A, Ohlsson C, Mellström D, Cho YS, Lee H, Yuan JM, Koh WP, Rhee SY, Woo JT, Heid IM, Stark KJ, Völzke H, Homuth G, Evans MK, Zonderman AB, Polasek O, Pasterkamp G, Hoefer IE, Redline S, Pahkala K, Oldehinkel AJ, Snieder H, Biino G, Schmidt R, Schmidt H, Chen YE, Bandinelli S, Dedoussis G, Thanaraj TA, Kardia SLR, Kato N, Schulze MB, Girotto G, Jung B, Böger CA, Joshi PK, Bennett DA, De Jager PL, Lu X, Mamakou V, Brown M, Caulfield MJ, Munroe PB, Guo X, Ciullo M, Jonas JB, Samani NJ, Kaprio J, Pajukanta P, Adair LS, Bechayda SA, de Silva HJ, Wickremasinghe AR, Krauss RM, Wu JY, Zheng W, den Hollander AI, Bharadwaj D, Correa A, Wilson JG, Lind L, Heng CK, Nelson AE, Golightly YM, Wilson JF, Penninx B, Kim HL, Attia J, Scott RJ, Rao DC, Arnett DK, Hunt SC, Walker M, Koistinen HA, Chandak GR, Yajnik CS, Mercader JM, Tusié-Luna T, Aguilar-Salinas CA, Villalpando CG, Orozco L, Fornage M, Tai ES, van Dam RM, Lehtimäki T, Chaturvedi N, Yokota M, Liu J, Reilly DF, McKnight AJ, Kee F, Jöckel KH, McCarthy MI, Palmer CNA, Vitart V, Hayward C, Simonsick E, van Duijn CM, Lu F, Qu J, Hishigaki H, Lin X, März W, Parra EJ, Cruz M, Gudnason V, Tardif JC, Lettre G, 't Hart LM, Elders PJM, Damrauer SM, Kumari M, Kivimaki M, van der Harst P, Spector TD, Loos RJF, Province MA, Psaty BM, Brandslund I, Pramstaller PP, Christensen K, Ripatti S, Widén E, Hakonarson H, Grant SFA, Kiemeney LALM, de Graaf J, Loeffler M, Kronenberg F, Gu D, Erdmann J, Schunkert H, Franks PW, Linneberg A, Jukema JW, Khera AV, Männikkö M, Jarvelin MR, Kutalik Z, Cucca F, Mook-Kanamori DO, van Dijk KW, Watkins H, Strachan DP, Grarup N, Sever P, Poulter N, Rotter JI, Dantoft TM, Karpe F, Neville MJ, Timpson NJ, Cheng CY, Wong TY, Khor CC, Sabanayagam C, Peters A, Gieger C, Hattersley AT, Pedersen NL, Magnusson PKE, Boomsma DI, de Geus EJC, Cupples LA, van Meurs JBJ, Ghanbari M, Gordon-Larsen P, Huang W, Kim YJ, Tabara Y, Wareham NJ, Langenberg C, Zeggini E, Kuusisto J, Laakso M, Ingelsson E, Abecasis G, Chambers JC, Kooner JS, de Vries PS, Morrison AC, North KE, Daviglus M, Kraft P, Martin NG, Whitfield JB, Abbas S, Saleheen D, Walters RG, Holmes MV, Black C, Smith BH, Justice AE, Baras A, Buring JE, Ridker PM, Chasman DI, Kooperberg C, Wei WQ, Jarvik GP, Namjou B, Hayes MG, Ritchie MD, Jousilahti P, Salomaa V, Hveem K, Åsvold BO, Kubo M, Kamatani Y, Okada Y, Murakami Y, Thorsteinsdottir U, Stefansson K, Ho YL, Lynch JA, Rader DJ, Tsao PS, Chang KM, Cho K, O'Donnell CJ, Gaziano JM, Wilson P, Rotimi CN, Hazelhurst S, Ramsay M, Trembath RC, van Heel DA, Tamiya G, Yamamoto M, Kim BJ, Mohlke KL, Frayling TM, Hirschhorn JN, Kathiresan S, Boehnke M, Natarajan P, Peloso GM, Brown CD, Morris AP, Assimes TL, Deloukas P, Sun YV, Willer CJ. The power of genetic diversity in genome-wide association studies of lipids. Nature 2021; 600:675-679. [PMID: 34887591 PMCID: PMC8730582 DOI: 10.1038/s41586-021-04064-3] [Citation(s) in RCA: 349] [Impact Index Per Article: 116.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 09/27/2021] [Indexed: 01/14/2023]
Abstract
Increased blood lipid levels are heritable risk factors of cardiovascular disease with varied prevalence worldwide owing to different dietary patterns and medication use1. Despite advances in prevention and treatment, in particular through reducing low-density lipoprotein cholesterol levels2, heart disease remains the leading cause of death worldwide3. Genome-wideassociation studies (GWAS) of blood lipid levels have led to important biological and clinical insights, as well as new drug targets, for cardiovascular disease. However, most previous GWAS4-23 have been conducted in European ancestry populations and may have missed genetic variants that contribute to lipid-level variation in other ancestry groups. These include differences in allele frequencies, effect sizes and linkage-disequilibrium patterns24. Here we conduct a multi-ancestry, genome-wide genetic discovery meta-analysis of lipid levels in approximately 1.65 million individuals, including 350,000 of non-European ancestries. We quantify the gain in studying non-European ancestries and provide evidence to support the expansion of recruitment of additional ancestries, even with relatively small sample sizes. We find that increasing diversity rather than studying additional individuals of European ancestry results in substantial improvements in fine-mapping functional variants and portability of polygenic prediction (evaluated in approximately 295,000 individuals from 7 ancestry groupings). Modest gains in the number of discovered loci and ancestry-specific variants were also achieved. As GWAS expand emphasis beyond the identification of genes and fundamental biology towards the use of genetic variants for preventive and precision medicine25, we anticipate that increased diversity of participants will lead to more accurate and equitable26 application of polygenic scores in clinical practice.
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Affiliation(s)
- Sarah E Graham
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Shoa L Clarke
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Kuan-Han H Wu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Stavroula Kanoni
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Greg J M Zajac
- Department of Biostatistics and Center for Statistics Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Shweta Ramdas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ida Surakka
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Ioanna Ntalla
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Sailaja Vedantam
- Endocrinology, Boston Children's Hospital, Boston, MA, USA
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Adam E Locke
- McDonnell Genome Institute and Department of Medicine, Washington University, St Louis, MO, USA
| | - Eirini Marouli
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Mi Yeong Hwang
- Department of Precision Medicine, Division of Genome Science, National Institute of Health, Cheongju-si, South Korea
| | - Sohee Han
- Department of Precision Medicine, Division of Genome Science, National Institute of Health, Cheongju-si, South Korea
| | - Akira Narita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth Ekoru
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bhavi Trivedi
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | | | - Karen A Hunt
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Qin Hui
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
- Atlanta VA Health Care System, Decatur, GA, USA
| | - Derek Klarin
- Malcolm Randall VA Medical Center, Gainesville, FL, USA
- Division of Vascular Surgery and Endovascular Therapy, University of Florida College of Medicine, Gainesville, FL, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiang Zhu
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Statistics, The Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Statistics, Stanford University, Stanford, CA, USA
| | | | | | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Hilma Holm
- deCODE genetics/Amgen, Reykjavik, Iceland
| | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali-National University Hospital of Iceland, Reykjavik, Iceland
| | - 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
| | - 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
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masahiro Kanai
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Wei Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ben M Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Department of Thoracic Medicine, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Humaira Rasheed
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Sanni E Ruotsalainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Yogasudha Veturi
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - QiPing Feng
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elisabeth A Rosenthal
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA, USA
| | - Todd Lingren
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | | | - Jeffrey Haessler
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA, USA
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Yuki Bradford
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason E Miller
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Usher Institute for Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, UK
| | - Kuang Lin
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Iona Y Millwood
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - George Hindy
- Department of Population Medicine, Qatar University College of Medicine, QU Health, Doha, Qatar
| | - Asif Rasheed
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Constance Turman
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Hongyan Huang
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Michael R Brown
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Southall, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Ketian Yu
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Ellen M Schmidt
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Anita Pandit
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Stefan Gustafsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Xianyong Yin
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Jing-Hua Zhao
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge Strangeways Research Laboratory, Cambridge, UK
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hye-Mi Jang
- Department of Precision Medicine, Division of Genome Science, National Institute of Health, Cheongju-si, South Korea
| | - Kyungheon Yoon
- Department of Precision Medicine, Division of Genome Science, National Institute of Health, Cheongju-si, South Korea
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Achilleas Pitsillides
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Behavioral and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health, VU Medical Center Amsterdam, Amsterdam, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Behavioral and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, VU Medical Center Amsterdam, Amsterdam, The Netherlands
| | - Andrew R Wood
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Yingji Ji
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Zishan Gao
- Department of Clinical Acupuncture and Moxibustion, Nanjing University of Chinese Medicine, Nanjing, China
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Simon Haworth
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
| | - Ruth E Mitchell
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jin Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Mette Aadahl
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovations (Formerly LABioMed) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Helen R Warren
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, John Vane Science Centre, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Julia Ramirez
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, John Vane Science Centre, Queen Mary University of London, London, UK
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Line L Kårhus
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Anuj Goel
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Maria Sabater-Lleal
- Group of Genomics of Complex Diseases, Research Institute of Hospital de la Santa Creu i Sant Pau (IIB Sant Pau), Barcelona, Spain
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Raymond Noordam
- Department of Internal Medicine, Section Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Carlo Sidore
- Institute for Genetic and Biomedical Research, Italian National Council of Research (IRGB CNR), Cagliari,, Italy
| | - Edoardo Fiorillo
- Institute for Genetic and Biomedical Research, Italian National Council of Research (IRGB CNR), Lanusei, Italy
| | - Aaron F McDaid
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Pedro Marques-Vidal
- Department of Medicine, Internal Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Stella Trompet
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Naveed Sattar
- BHF Glasgow Cardiovascular Research Centre, Faculty of Medicine, Glasgow, UK
| | - Line T Møllehave
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Betina H Thuesen
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Matthias Munz
- Institute for Cardiogenetics, University of Lübeck, DZHK (German Research Centre for Cardiovascular Research), Partner site Hamburg/Lübeck/Kiel, University Heart Center Lübeck, Lübeck, Germany
- Charité-University Medicine Berlin, Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Periodontology and Synoptic Dentistry, Berlin Institute of Health, Institute for Dental and Craniofacial Sciences, Berlin, Germany
| | - Lingyao Zeng
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, Munich, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung (DZHK), Partner site Munich Heart Alliance, Munich, Germany
| | - Jianfeng Huang
- Key Laboratory of Cardiovascular Epidemiology and Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Yang
- Key Laboratory of Cardiovascular Epidemiology and Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | | | - Claudia Lamina
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
- German Chronic Kidney Disease Study, Innsbruck, Austria
| | - Lukas Forer
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
- German Chronic Kidney Disease Study, Innsbruck, Austria
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Tessel E Galesloot
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | | | - E Warwick Daw
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Joseph M Zmuda
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jonathan S Mitchell
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Christian Fuchsberger
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Henry Christensen
- Department of Clinical Biochemistry, Lillebaelt Hospital, Vejle, Denmark
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Mary K Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Michael Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, UK
| | | | - Niek Verweij
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jan W Benjamins
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jorgen Engmann
- Institute of Cardiovascular Sciences, University College London, London, UK
- Department of Epidemiology and Public Health, University College London, London, UK
| | - Rachel L Kember
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Roderick C Slieker
- Amsterdam UMC, Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ken Sin Lo
- Montreal Heart Institute, Montreal, Quebec, Canada
| | | | - Phuong Le
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Synlab MVZ Humangenetik Mannheim, Mannheim, Germany
| | - Graciela E Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Shaofeng Huo
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Daisuke D Ikeda
- Biomedical Technology Research Center, Tokushima Research Institute, Otsuka Pharmaceutical, Tokushima, Japan
| | - Hiroyuki Iha
- Biomedical Technology Research Center, Tokushima Research Institute, Otsuka Pharmaceutical, Tokushima, Japan
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Advanced Research, Wenzhou Medical University, Wenzhou, China
| | - Jun Liu
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Hampton L Leonard
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD, USA
- Data Tecnica International, Glen Echo, MD, USA
| | - Jonathan Marten
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Börge Schmidt
- Institute for Medical Informatics, Biometrie and Epidemiology, University of Duisburg-Essen, Essen, Germany
| | - Marina Arendt
- Institute for Medical Informatics, Biometrie and Epidemiology, University of Duisburg-Essen, Essen, Germany
- Department of Computer Science, University of Applied Sciences and Arts Dortmund, Dortmund, Germany
| | - Laura J Smyth
- Centre for Public Health, Queen's University of Belfast, Belfast, UK
| | | | - Chaolong Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing at UCL, London, UK
| | - Nina Hutri-Kähönen
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland
- Department of Pediatrics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Rui Xia
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Alicia Huerta-Chagoya
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, UNAM, Ciudad de Mexico, Mexico, Mexico
| | - Juan Carlos Fernandez-Lopez
- Departamento de Genómica Computacional, Instituto Nacional de Medicina Genómica, Ciudad de Mexico, Mexico, Mexico
| | - Valeriya Lyssenko
- Center for Diabetes Research, University of Bergen, Bergen, Norway
- Lund University Diabetes Center, Lund University, Malmo, Sweden
| | - Meraj Ahmed
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistics Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Noha A Yousri
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
- Department of Computer and Systems Engineering, Alexandria University, Alexandria, Egypt
| | - Marguerite R Irvin
- Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Han-Na Kim
- Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Clinical Research Design and Evaluation, SAIHST, Sungkyunkwan University, Seoul, Korea
| | - Seungho Ryu
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Occupational and Environmental Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Paul R H J Timmers
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Liubov Arbeeva
- Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC, USA
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, Anschutz Medical Campus, University of Colorado, Denver, Aurora, CO, USA
| | - Xiaoran Chai
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore, Singapore
| | - Gauri Prasad
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi, India
| | - Laura Lorés-Motta
- Departments of Ophthalmology and Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Marc Pauper
- Departments of Ophthalmology and Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Jirong Long
- Vanderbilt Epidemiology Center, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiaohui Li
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovations (Formerly LABioMed) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Elizabeth Theusch
- Department of Pediatrics, University of California, San Francisco, Oakland, CA,, USA
| | | | - Cassandra N Spracklen
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst, Amherst, MA,, USA
| | - Anu Loukola
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sailalitha Bollepalli
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sophie C Warner
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Ya Xing Wang
- Beijing Institute of Ophthalmology, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing, China
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Wen B Wei
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Teresa Nutile
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso"-CNR, Naples, Italy
| | - Daniela Ruggiero
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso"-CNR, Naples, Italy
- IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Yun Ju Sung
- Department of Psychiatry, Washington University, St Louis, MO, USA
| | - Yi-Jen Hung
- Division of Endocrinology and Metabolism, Tri-Service General Hospital Songshan Branch, Taipei, Taiwan
| | - Shufeng Chen
- Key Laboratory of Cardiovascular Epidemiology and Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fangchao Liu
- Key Laboratory of Cardiovascular Epidemiology and Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingyun Yang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Katherine A Kentistou
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Mathias Gorski
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Marco Brumat
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Karina Meidtner
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer A Smith
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Prashantha Hebbar
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait, Kuwait
| | - Aliki-Eleni Farmaki
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Athens, Greece
- Department of Population Science and Experimental Medicine, University College London, London, UK
| | - Edith Hofer
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University of Graz, Graz, Austria
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Maoxuan Lin
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Chao Xue
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Jifeng Zhang
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Maria Pina Concas
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Simona Vaccargiu
- Institute of Genetic and Biomedical Research, National Research Council of Italy, UOS of Sassari, Sassari, Italy
| | - Peter J van der Most
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Niina Pitkänen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Brian E Cade
- Sleep Medicine and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Jiwon Lee
- Sleep Medicine and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Kumaraswamy Naidu Chitrala
- Laboratory of Epidemiology and Population Science, National Institute on Aging Intramural Research Program, NIH Biomedical Research Center, NIA, Baltimore, MD, USA
| | - Stefan Weiss
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald and University Medicine Greifswald, Greifswald, Germany
| | - Martina E Zimmermann
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | | | - Hyeok Sun Choi
- Department of Biomedical Science, Hallym University, Chuncheon, Korea
| | - Maria Nethander
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sandra Freitag-Wolf
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
| | - Lorraine Southam
- Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Nigel W Rayner
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Oxford Centre for Diabetes Endocrinology and Metabolism, Oxford, UK
| | - Carol A Wang
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
| | - Shih-Yi Lin
- Center for Geriatrics and Gerontology, Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Jun-Sing Wang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | | | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kjell Nikus
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere, Finland
- Department of Cardiology, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Gabriel Cuellar-Partida
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Medicine, Bornholms Hospital, Ronne, Denmark
| | - Bertha Hildalgo
- School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Olga Giannakopoulou
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Qiuyin Cai
- Vanderbilt Epidemiology Center, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Morgan O Obura
- Amsterdam UMC, Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Jessica van Setten
- Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Xiaoyin Li
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Karen Schwander
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Natalie Terzikhan
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jae Hun Shin
- Department of Biomedical Science, Hallym University, Chuncheon, Korea
| | | | | | - Lisa Warsinger Martin
- School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Zhengming Chen
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Liming Li
- Department of Epidemiology, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Kristin L Young
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Takahisa Kawaguchi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Joachim Thiery
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute for Laboratory Medicine, University Hospital Leipzig, Leipzig, Germany
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Girish N Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Huaixing Li
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD, USA
- Data Tecnica International, Glen Echo, MD, USA
| | - Olli T Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Sahoko Ichihara
- Department of Environmental and Preventive Medicine, Jichi Medical University School of Medicine, Shimotsuke, Japan
| | - Sarah H Wild
- Centre for Population Health Sciences, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Susanne Jäger
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Toru Nabika
- Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait, Kuwait
| | - Harri Niinikoski
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
- Department of Physiology, University of Turku, Turku, Finland
| | - Peter S Braund
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Ivana Kolcic
- Faculty of Medicine, University of Split, Split, Croatia
| | - Peter Kovacs
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Tota Giardoglou
- Department of Nutrition-Dietetics, Harokopio University, Eleftheriou Venizelou, Athens, Greece
| | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Geriatric and General Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Konain Fatima Bhatti
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Dominique de Kleijn
- Department of Vascular Surgery, Division of Surgical Specialties, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Gert J de Borst
- Department of Vascular Surgery, Division of Surgical Specialties, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Eung Kweon Kim
- Corneal Dystrophy Research Institute, Department of Ophthalmology, Yonsei University College of Medicine, Seoul, Korea
| | - Hieab H H Adams
- Department of Radiology and Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Folkert W Asselbergs
- Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Adriaan O Kraaijeveld
- Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Joline W J Beulens
- Amsterdam UMC, Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Xiao-Ou Shu
- Vanderbilt Epidemiology Center, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Loukianos S Rallidis
- Second Department of Cardiology, Medical School, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Paul Mitchell
- Center for Vision Research, Department of Ophthalmology and The Westmead Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
- Centre for Eye Research Australia, University of Melbourne, Melbourne, Victoria, Australia
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
- Department of Clinical Physiology, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Louis Pérusse
- Department of Kinesiology, Université Laval, Quebec, Quebec, Canada
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec, Quebec, Canada
| | | | - Anke Tönjes
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovations (Formerly LABioMed) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Craig E Pennell
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
| | - Trevor A Mori
- Medical School, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Wolfgang Lieb
- Institute of Epidemiology, Kiel University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Claes Ohlsson
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Drug Treatment, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Dan Mellström
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Geriatric Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Chuncheon, Korea
| | - Hyejin Lee
- Department of Internal Medicine, Ewha Womans University School of Medicine, Seoul, Korea
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Woon-Puay Koh
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Sang Youl Rhee
- Department of Endocrinology and Metabolism, Kyung Hee University School of Medicine, Seoul, Korea
| | - Jeong-Taek Woo
- Department of Endocrinology and Metabolism, Kyung Hee University School of Medicine, Seoul, Korea
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Klaus J Stark
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald and University Medicine Greifswald, Greifswald, Germany
| | - Michele K Evans
- Laboratory of Epidemiology and Population Science, National Institute on Aging Intramural Research Program, NIH Biomedical Research Center, Baltimore, MD, USA
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Science, National Institute on Aging Intramural Research Program, NIH Biomedical Research Center, Baltimore, MD, USA
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Split, Croatia
| | - Gerard Pasterkamp
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Imo E Hoefer
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Susan Redline
- Sleep Medicine and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Katja Pahkala
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Paavo Nurmi Centre, Sports and Exercise Medicine Unit, Department of Physical Activity and Health, University of Turku, Turku, Finland
| | - Albertine J Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation (ICPE), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Harold Snieder
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ginevra Biino
- Institute of Molecular Genetics, National Research Council of Italy, Pavia, Italy
| | - Reinhold Schmidt
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University of Graz, Graz, Austria
| | - Helena Schmidt
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz, Austria
| | - Y Eugene Chen
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
| | | | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Athens, Greece
| | | | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Norihiro Kato
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Giorgia Girotto
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Bettina Jung
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Carsten A Böger
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
- Department of Nephrology, Diabetology, Rheumatology, Traunstein Hospital, Traunstein, Germany
- KfH Kidney Center Traunstein, Traunstein, Germany
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Center for Translational and Systems Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Xiangfeng Lu
- Key Laboratory of Cardiovascular Epidemiology and Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Vasiliki Mamakou
- Medical School, National and Kapodistrian University Athens, Athens, Greece
- Dromokaiteio Psychiatric Hospital, Athens, Greece
| | - Morris Brown
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Clinical Pharmacology, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Mark J Caulfield
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, John Vane Science Centre, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Patricia B Munroe
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, John Vane Science Centre, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovations (Formerly LABioMed) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marina Ciullo
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso"-CNR, Naples, Italy
- IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Jost B Jonas
- Department of Ophthalmology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Beijing Institute of Ophthalmology, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA
| | - Linda S Adair
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA
| | - Sonny Augustin Bechayda
- USC-Office of Population Studies Foundation, University of San Carlos, Cebu City, Philippines
- Department of Anthropology, Sociology, and History, University of San Carlos, Cebu City, Philippines
| | - H Janaka de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | | | - Ronald M Krauss
- Departments of Pediatrics and Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Wei Zheng
- Vanderbilt Epidemiology Center, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anneke I den Hollander
- Departments of Ophthalmology and Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Dwaipayan Bharadwaj
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi, India
- Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Chew-Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Amanda E Nelson
- Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Yvonne M Golightly
- Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Injury Prevention Research Center, University of North Carolina, Chapel Hill, NC, USA
- Division of Physical Therapy, University of North Carolina, Chapel Hill, NC, USA
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Brenda Penninx
- Department of Psychiatry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, VU Medical Center Amsterdam, Amsterdam, The Netherlands
| | - Hyung-Lae Kim
- Department of Biochemistry, College of Medicine, Ewha Womans University, Seoul, Korea
| | - John Attia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
- Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia
| | - Rodney J Scott
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
- Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia
| | - D C Rao
- Division of Biostatistics, Washington University School of Medicine, St Louis, MO, USA
| | - Donna K Arnett
- University of Kentucky, College of Public Health, Lexington, KY, USA
| | - Steven C Hunt
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Mark Walker
- Institute of Cellular Medicine (Diabetes), The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Heikki A Koistinen
- Department of Population Health, Finnish Institute for Health and Welfare, Helsinki, Finland
- University of Helsinki and Department of Medicine, Helsinki University Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | | | - Josep M Mercader
- Harvard Medical School, Boston, MA, USA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Teresa Tusié-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico, Mexico
- Instituto de Investigaciones Biomédicas, UNAM, Ciudad de México, Mexico, Mexico
- Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Bimédicas UNAM/ Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico, Mexico
| | - Carlos A Aguilar-Salinas
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico, Mexico
- Dirección de Nutrición and Unidad de Estudios de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico, Mexico
| | | | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Mexico, Mexico
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | | | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | | | | | - Frank Kee
- Centre for Public Health, Queen's University of Belfast, Belfast, UK
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometrie and Epidemiology, University of Duisburg-Essen, Essen, Germany
| | - Mark I McCarthy
- Genentech, South San Francisco, CA, USA
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Colin N A Palmer
- Population Health and Genomics, University of Dundee, Ninwells Hospital and Medical School, Dundee, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Eleanor Simonsick
- Intramural Research Program, National Institute on Aging, Baltimore, MD, USA
| | | | - Fan Lu
- The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
| | - Jia Qu
- The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
| | - Haretsugu Hishigaki
- Biomedical Technology Research Center, Tokushima Research Institute, Otsuka Pharmaceutical, Tokushima, Japan
| | - Xu Lin
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Synlab Academy, Synlab, Mannheim, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Miguel Cruz
- Unidad de Investigacion Medica en Bioquimica, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico, Mexico
| | - Vilmundur Gudnason
- Icelandic Heart Association, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Jean-Claude Tardif
- Montreal Heart Institute, Montreal, Quebec, Canada
- Department of Medicine, Faculty of Medecine, Université de Montréal, Quebec, Quebec, Canada
| | - Guillaume Lettre
- Montreal Heart Institute, Montreal, Quebec, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Leen M 't Hart
- Amsterdam UMC, Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Petra J M Elders
- Amsterdam UMC, Department of General Practice and Elderly Care, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Scott M Damrauer
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Meena Kumari
- Institute of Social and Economic Research, University of Essex, Essex, UK
| | - Mika Kivimaki
- Department of Epidemiology and Public Health, University College London, London, UK
| | - Pim van der Harst
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - 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
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA, USA
- Kaiser Permanent Washington Health Research Institute, Seattle, WA, USA
| | - Ivan Brandslund
- Department of Clinical Biochemistry, Lillebaelt Hospital, Vejle, Denmark
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Kaare Christensen
- Danish Aging Research Center, University of Southern Denmark, Odense, Denmark
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elisabeth Widén
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA
| | - Struan F A Grant
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lambertus A L M Kiemeney
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Jacqueline de Graaf
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Florian Kronenberg
- German Chronic Kidney Disease Study, Innsbruck, Austria
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Dongfeng Gu
- Key Laboratory of Cardiovascular Epidemiology and Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jeanette Erdmann
- Institute for Cardiogenetics, University of Lübeck, DZHK (German Research Centre for Cardiovascular Research), Partner site Hamburg/Lübeck/Kiel, and University Heart Center Lübeck, Lübeck, Germany
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, Munich, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung (DZHK) e.V., Partner site Munich Heart Alliance, Munich, Germany
| | | | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
| | - Amit V Khera
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program of Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Minna Männikkö
- Northern Finland Birth Cohorts, Infrastructure for Population Studies, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter of Oulu, University of Oulu, Oulu, Finland
| | - Zoltan Kutalik
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University Center for Primary Care and Public Health, Lausanne, Switzerland
| | - Francesco Cucca
- Institute for Genetic and Biomedical Research, Italian National Council of Research (IRGB CNR), Cagliari, Italy
- University of Sassari, Sassari, Italy
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Ko Willems van Dijk
- Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hugh Watkins
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - David P Strachan
- Population Health Research Institute, St George's University of London, London, UK
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Sever
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Neil Poulter
- School of Public Health, Imperial College London, London, UK
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovations (Formerly LABioMed) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Thomas M Dantoft
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Fredrik Karpe
- OCDEM, University of Oxford, Churchill Hospital, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Matt J Neville
- OCDEM, University of Oxford, Churchill Hospital, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ching-Yu Cheng
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Tien-Yin Wong
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Charumathi Sabanayagam
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance Partner Site, Munich, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | | | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Dorret I Boomsma
- Department of Biological Psychology, Behavioral and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health, VU Medical Center Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, VU Medical Center Amsterdam, Amsterdam, the Netherlands
| | - Eco J C de Geus
- Department of Biological Psychology, Behavioral and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, VU Medical Center Amsterdam, Amsterdam, The Netherlands
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD, USA
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Penny Gordon-Larsen
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA
| | - Wei Huang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Young Jin Kim
- Department of Precision Medicine, Division of Genome Science, National Institute of Health, Cheongju-si, South Korea
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Wellcome Trust Sanger Institute, Hinxton, UK
- TUM School of Medicine, Technical University of Munich (TUM) and Klinikum Rechts der Isar, Munich, Germany
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Erik Ingelsson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Goncalo Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Southall, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Southall, UK
- Imperial College Healthcare NHS Trust, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Martha Daviglus
- Institute for Minority Health Research, University of Illinois College of Medicine, Chicago, IL, USA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - John B Whitfield
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Shahid Abbas
- Center for Non-Communicable Diseases, Karachi, Pakistan
- Faisalabad Institute of Cardiology, Faislabad, Pakistan
| | - Danish Saleheen
- Center for Non-Communicable Diseases, Karachi, Pakistan
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Cardiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Robin G Walters
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Big Data Institute, University of Oxford, Oxford, UK
| | - Michael V Holmes
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals, Oxford, UK
| | - Corri Black
- Aberdeen Centre for Health Data Science, School of Medicine, Medical Science and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Anne E Justice
- Biomedical and Translational Informatics, Geisinger Health, Danville, PA, USA
| | - Aris Baras
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Julie E Buring
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Charles Kooperberg
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington Medical Center, Seattle, WA, USA
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Anthropology, Northwestern University, Evanston, IL, USA
- Center for Genetic Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Marylyn D Ritchie
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Pekka Jousilahti
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Department of Medicine, Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Bjørn Olav Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Department of Endocrinology, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - 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
| | - 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
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Yuk-Lam Ho
- VA Boston Healthcare System, Boston, MA, USA
| | - Julie A Lynch
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- University of Massachusetts, Boston, MA, USA
| | - Daniel J Rader
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Philip S Tsao
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Kyong-Mi Chang
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Kelly Cho
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham Women's Hospital, Boston, MA, USA
| | - Christopher J O'Donnell
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham Women's Hospital, Boston, MA, USA
| | - John M Gaziano
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham Women's Hospital, Boston, MA, USA
| | - Peter Wilson
- Atlanta VA Medical Center, Atlanta, GA, USA
- Division of Cardiology, Emory University School of Medicine, Atlanta, GA, USA
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Richard C Trembath
- School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - David A van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Bong-Jo Kim
- Department of Precision Medicine, Division of Genome Science, National Institute of Health, Cheongju-si, South Korea
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Joel N Hirschhorn
- Endocrinology, Boston Children's Hospital, Boston, MA, USA
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Departments of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA
| | - Sekar Kathiresan
- Program of Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistics Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Christopher D Brown
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Manchester, UK
| | - Themistocles L Assimes
- VA Palo Alto Health Care System, Palo Alto, CA, USA.
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA.
| | - Panos Deloukas
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yan V Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
- Atlanta VA Health Care System, Decatur, GA, USA
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
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Davitte JM, Stott-Miller M, Ehm MG, Cunnington MC, Reynolds RF. Integration of Real-World Data and Genetics to Support Target Identification and Validation. Clin Pharmacol Ther 2021; 111:63-76. [PMID: 34818443 DOI: 10.1002/cpt.2477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 10/06/2021] [Accepted: 10/27/2021] [Indexed: 01/01/2023]
Abstract
Even modest improvements in the probability of success of selecting drug targets which are ultimately approved can substantially reduce the costs of research and development. Drug targets with human genetic evidence of disease association are twice as likely to lead to approved drugs. A key enabler of identifying and validating these genetically validated targets is access to association results from genome-wide genotyping, whole-exome sequencing, and whole-genome sequencing studies with observable traits (often diseases) across large numbers of individuals. Today, linkage between genotype and real-world data (RWD) provides significant opportunities to not only increase the statistical power of genome-wide association studies by ascertaining additional cases for diseases of interest, but also to improve diversity and coverage of association studies across the disease phenome. As RWD-genetics linked resources continue to grow in diversity of participants, breadth of data captured, length of observation, and number of participants, there is a greater need to leverage the experience of RWD experts, clinicians, and highly experienced geneticists together to understand which lessons and frameworks from general research using RWD sources are relevant to improve genetics-driven drug discovery and development. This paper describes new challenges and opportunities for phenotypes enabled by diverse RWD sources, considerations in the use of RWD phenotypes for disease gene identification across the disease phenome, and challenges and opportunities in leveraging RWD phenotypes in target validation. The paper concludes with views on the future directions for phenotype development using RWD, and key questions requiring further research and development to advance this nascent field.
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Affiliation(s)
| | | | | | | | - Robert F Reynolds
- GlaxoSmithKline, New York, New York, USA.,Tulane School of Public Health and Tropical Medicine, New Orleans, Louisiana, USA
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Lam BYH, Williamson A, Finer S, Day FR, Tadross JA, Gonçalves Soares A, Wade K, Sweeney P, Bedenbaugh MN, Porter DT, Melvin A, Ellacott KLJ, Lippert RN, Buller S, Rosmaninho-Salgado J, Dowsett GKC, Ridley KE, Xu Z, Cimino I, Rimmington D, Rainbow K, Duckett K, Holmqvist S, Khan A, Dai X, Bochukova EG, Trembath RC, Martin HC, Coll AP, Rowitch DH, Wareham NJ, van Heel DA, Timpson N, Simerly RB, Ong KK, Cone RD, Langenberg C, Perry JRB, Yeo GS, O'Rahilly S. MC3R links nutritional state to childhood growth and the timing of puberty. Nature 2021; 599:436-441. [PMID: 34732894 PMCID: PMC8819628 DOI: 10.1038/s41586-021-04088-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 10/01/2021] [Indexed: 02/02/2023]
Abstract
The state of somatic energy stores in metazoans is communicated to the brain, which regulates key aspects of behaviour, growth, nutrient partitioning and development1. The central melanocortin system acts through melanocortin 4 receptor (MC4R) to control appetite, food intake and energy expenditure2. Here we present evidence that MC3R regulates the timing of sexual maturation, the rate of linear growth and the accrual of lean mass, which are all energy-sensitive processes. We found that humans who carry loss-of-function mutations in MC3R, including a rare homozygote individual, have a later onset of puberty. Consistent with previous findings in mice, they also had reduced linear growth, lean mass and circulating levels of IGF1. Mice lacking Mc3r had delayed sexual maturation and an insensitivity of reproductive cycle length to nutritional perturbation. The expression of Mc3r is enriched in hypothalamic neurons that control reproduction and growth, and expression increases during postnatal development in a manner that is consistent with a role in the regulation of sexual maturation. These findings suggest a bifurcating model of nutrient sensing by the central melanocortin pathway with signalling through MC4R controlling the acquisition and retention of calories, whereas signalling through MC3R primarily regulates the disposition of calories into growth, lean mass and the timing of sexual maturation.
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Affiliation(s)
- B Y H Lam
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - A Williamson
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - S Finer
- Wolfson Institute of Population Health, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - F R Day
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - J A Tadross
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - A Gonçalves Soares
- MRC Integrative Epidemiology Unit and Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - K Wade
- MRC Integrative Epidemiology Unit and Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - P Sweeney
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - M N Bedenbaugh
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - D T Porter
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - A Melvin
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - K L J Ellacott
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, UK
| | - R N Lippert
- Department of Neurocircuit Development and Function, German Institute of Human Nutrition, Potsdam, Germany
| | - S Buller
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - J Rosmaninho-Salgado
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - G K C Dowsett
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - K E Ridley
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Z Xu
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - I Cimino
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - D Rimmington
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - K Rainbow
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - K Duckett
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - S Holmqvist
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - A Khan
- Wolfson Institute of Population Health, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - X Dai
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - E G Bochukova
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - R C Trembath
- School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - H C Martin
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - A P Coll
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - D H Rowitch
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - N J Wareham
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - D A van Heel
- Wolfson Institute of Population Health, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - N Timpson
- MRC Integrative Epidemiology Unit and Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - R B Simerly
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - K K Ong
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - R D Cone
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology, School of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - C Langenberg
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - J R B Perry
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - G S Yeo
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - S O'Rahilly
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK.
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
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Agrawal N, Lawler K, Davidson CM, Keogh JM, Legg R, Barroso I, Farooqi IS, Brand AH. Predicting novel candidate human obesity genes and their site of action by systematic functional screening in Drosophila. PLoS Biol 2021; 19:e3001255. [PMID: 34748544 PMCID: PMC8575313 DOI: 10.1371/journal.pbio.3001255] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 09/29/2021] [Indexed: 11/18/2022] Open
Abstract
The discovery of human obesity-associated genes can reveal new mechanisms to target for weight loss therapy. Genetic studies of obese individuals and the analysis of rare genetic variants can identify novel obesity-associated genes. However, establishing a functional relationship between these candidate genes and adiposity remains a significant challenge. We uncovered a large number of rare homozygous gene variants by exome sequencing of severely obese children, including those from consanguineous families. By assessing the function of these genes in vivo in Drosophila, we identified 4 genes, not previously linked to human obesity, that regulate adiposity (itpr, dachsous, calpA, and sdk). Dachsous is a transmembrane protein upstream of the Hippo signalling pathway. We found that 3 further members of the Hippo pathway, fat, four-jointed, and hippo, also regulate adiposity and that they act in neurons, rather than in adipose tissue (fat body). Screening Hippo pathway genes in larger human cohorts revealed rare variants in TAOK2 associated with human obesity. Knockdown of Drosophila tao increased adiposity in vivo demonstrating the strength of our approach in predicting novel human obesity genes and signalling pathways and their site of action.
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Affiliation(s)
- Neha Agrawal
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Katherine Lawler
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Catherine M. Davidson
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Julia M. Keogh
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Robert Legg
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | | | - Inês Barroso
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - I. Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Andrea H. Brand
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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48
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Landsman D, Abdelbasit A, Wang C, Guerzhoy M, Joshi U, Mathew S, Pou-Prom C, Dai D, Pequegnat V, Murray J, Chokar K, Banning M, Mamdani M, Mishra S, Batt J. Cohort profile: St. Michael's Hospital Tuberculosis Database (SMH-TB), a retrospective cohort of electronic health record data and variables extracted using natural language processing. PLoS One 2021; 16:e0247872. [PMID: 33657184 PMCID: PMC7928444 DOI: 10.1371/journal.pone.0247872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 02/16/2021] [Indexed: 12/01/2022] Open
Abstract
Background Tuberculosis (TB) is a major cause of death worldwide. TB research draws heavily on clinical cohorts which can be generated using electronic health records (EHR), but granular information extracted from unstructured EHR data is limited. The St. Michael’s Hospital TB database (SMH-TB) was established to address gaps in EHR-derived TB clinical cohorts and provide researchers and clinicians with detailed, granular data related to TB management and treatment. Methods We collected and validated multiple layers of EHR data from the TB outpatient clinic at St. Michael’s Hospital, Toronto, Ontario, Canada to generate the SMH-TB database. SMH-TB contains structured data directly from the EHR, and variables generated using natural language processing (NLP) by extracting relevant information from free-text within clinic, radiology, and other notes. NLP performance was assessed using recall, precision and F1 score averaged across variable labels. We present characteristics of the cohort population using binomial proportions and 95% confidence intervals (CI), with and without adjusting for NLP misclassification errors. Results SMH-TB currently contains retrospective patient data spanning 2011 to 2018, for a total of 3298 patients (N = 3237 with at least 1 associated dictation). Performance of TB diagnosis and medication NLP rulesets surpasses 93% in recall, precision and F1 metrics, indicating good generalizability. We estimated 20% (95% CI: 18.4–21.2%) were diagnosed with active TB and 46% (95% CI: 43.8–47.2%) were diagnosed with latent TB. After adjusting for potential misclassification, the proportion of patients diagnosed with active and latent TB was 18% (95% CI: 16.8–19.7%) and 40% (95% CI: 37.8–41.6%) respectively Conclusion SMH-TB is a unique database that includes a breadth of structured data derived from structured and unstructured EHR data by using NLP rulesets. The data are available for a variety of research applications, such as clinical epidemiology, quality improvement and mathematical modeling studies.
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Affiliation(s)
- David Landsman
- MAP Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Ahmed Abdelbasit
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Christine Wang
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Michael Guerzhoy
- Princeton University, Princeton, New Jersey, United States of America
- University of Toronto, Toronto, Ontario, Canada
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Ujash Joshi
- University of Toronto, Toronto, Ontario, Canada
| | - Shaun Mathew
- Department of Computer Science, Ryerson University, Toronto, Ontario, Canada
| | | | - David Dai
- Unity Health Toronto, Toronto, Ontario, Canada
| | - Victoria Pequegnat
- Decision Support Services, St. Michael’s Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | | | - Kamalprit Chokar
- Division of Respirology, Department of Medicine, St. Michael’s Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | | | - Muhammad Mamdani
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Unity Health Toronto, Toronto, Ontario, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, Canada, Toronto, Ontario, Canada
- Institute of Health Policy, Management, and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Sharmistha Mishra
- MAP Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management, and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Jane Batt
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Keenan Research Center for Biomedical Science, St. Michael’s Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- * E-mail:
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Amin HA, Drenos F. No evidence that vitamin D is able to prevent or affect the severity of COVID-19 in individuals with European ancestry: a Mendelian randomisation study of open data. BMJ Nutr Prev Health 2021; 4:42-48. [PMID: 34308111 PMCID: PMC7798425 DOI: 10.1136/bmjnph-2020-000151] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/19/2020] [Accepted: 12/27/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Upper respiratory tract infections are reportedly more frequent and more severe in individuals with lower vitamin D levels. Based on these findings, it has been suggested that vitamin D can prevent or reduce the severity of COVID-19. METHODS We used two-sample Mendelian randomisation (MR) to assess the causal effect of vitamin D levels on SARS-CoV-2 infection risk and COVID-19 severity using publicly available data. We also carried out a genome-wide association analysis (GWA) of vitamin D deficiency in the UK Biobank (UKB) and used these results and two-sample MR to assess the causal effect of vitamin D deficiency on SARS-CoV-2 infection risk and COVID-19 severity. RESULTS We found no evidence that vitamin D levels causally affect the risk of SARS-CoV-2 infection (ln(OR)=0.17 (95% CI -0.22 to 0.57, p=0.39)) nor did we find evidence that vitamin D levels causally affect COVID-19 severity (ln(OR)=0.36 (95% CI -0.89 to 1.61, p=0.57)). Based on our GWA analysis, we found that 17 independent variants are associated with vitamin D deficiency in the UKB. Using these variants as instruments for our two-sample MR analyses, we found no evidence that vitamin D deficiency causally affects the risk of SARS-CoV-2 infection (ln(OR)=-0.04 (95% CI -0.1 to 0.03, p=0.25)) nor did we find evidence that vitamin D deficiency causally affects COVID-19 severity (ln(OR)=-0.24 (95% CI -0.55 to 0.08, p=0.14)). CONCLUSIONS In conclusion, we found no evidence that vitamin D is protective against SARS-CoV-2 infection or COVID-19 severity. Our data support the recent statement by the National Institute for Health and Care Excellence that the use of vitamin D supplementation to mitigate COVID-19 is not supported by the available data.
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Affiliation(s)
- Hasnat A Amin
- Department of Life Sciences, Brunel University London, Uxbridge, UK
| | - Fotios Drenos
- Department of Life Sciences, Brunel University London, Uxbridge, UK
- Institute of Cardiovascular Sciences, UCL, London, UK
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50
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Swietlik EM, Prapa M, Martin JM, Pandya D, Auckland K, Morrell NW, Gräf S. 'There and Back Again'-Forward Genetics and Reverse Phenotyping in Pulmonary Arterial Hypertension. Genes (Basel) 2020; 11:E1408. [PMID: 33256119 PMCID: PMC7760524 DOI: 10.3390/genes11121408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/17/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Although the invention of right heart catheterisation in the 1950s enabled accurate clinical diagnosis of pulmonary arterial hypertension (PAH), it was not until 2000 when the landmark discovery of the causative role of bone morphogenetic protein receptor type II (BMPR2) mutations shed new light on the pathogenesis of PAH. Since then several genes have been discovered, which now account for around 25% of cases with the clinical diagnosis of idiopathic PAH. Despite the ongoing efforts, in the majority of patients the cause of the disease remains elusive, a phenomenon often referred to as "missing heritability". In this review, we discuss research approaches to uncover the genetic architecture of PAH starting with forward phenotyping, which in a research setting should focus on stable intermediate phenotypes, forward and reverse genetics, and finally reverse phenotyping. We then discuss potential sources of "missing heritability" and how functional genomics and multi-omics methods are employed to tackle this problem.
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Affiliation(s)
- Emilia M. Swietlik
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Royal Papworth Hospital NHS Foundation Trust, Cambridge CB2 0AY, UK
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Matina Prapa
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Jennifer M. Martin
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Divya Pandya
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Kathryn Auckland
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Nicholas W. Morrell
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Royal Papworth Hospital NHS Foundation Trust, Cambridge CB2 0AY, UK
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
- NIHR BioResource for Translational Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- NIHR BioResource for Translational Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
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