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Žukauskaitė G, Domarkienė I, Rančelis T, Kavaliauskienė I, Baronas K, Kučinskas V, Ambrozaitytė L. Putative protective genomic variation in the Lithuanian population. Genet Mol Biol 2024; 47:e20230030. [PMID: 38626572 PMCID: PMC11021042 DOI: 10.1590/1678-4685-gmb-2023-0030] [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: 02/03/2023] [Accepted: 01/01/2024] [Indexed: 04/18/2024] Open
Abstract
Genomic effect variants associated with survival and protection against complex diseases vary between populations due to microevolutionary processes. The aim of this study was to analyse diversity and distribution of effect variants in a context of potential positive selection. In total, 475 individuals of Lithuanian origin were genotyped using high-throughput scanning and/or sequencing technologies. Allele frequency analysis for the pre-selected effect variants was performed using the catalogue of single nucleotide polymorphisms. Comparison of the pre-selected effect variants with variants in primate species was carried out to ascertain which allele was derived and potentially of protective nature. Recent positive selection analysis was performed to verify this protective effect. Four variants having significantly different frequencies compared to European populations were identified while two other variants reached borderline significance. Effect variant in SLC30A8 gene may potentially protect against type 2 diabetes. The existing paradox of high rates of type 2 diabetes in the Lithuanian population and the relatively high frequencies of potentially protective genome variants against it indicate a lack of knowledge about the interactions between environmental factors, regulatory regions, and other genome variation. Identification of effect variants is a step towards better understanding of the microevolutionary processes, etiopathogenetic mechanisms, and personalised medicine.
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Affiliation(s)
- Gabrielė Žukauskaitė
- Vilnius University, Faculty of Medicine, Institute of Biomedical Sciences, Department of Human and Medical Genetics, Vilnius, Lithuania
| | - Ingrida Domarkienė
- Vilnius University, Faculty of Medicine, Institute of Biomedical Sciences, Department of Human and Medical Genetics, Vilnius, Lithuania
| | - Tautvydas Rančelis
- Vilnius University, Faculty of Medicine, Institute of Biomedical Sciences, Department of Human and Medical Genetics, Vilnius, Lithuania
| | - Ingrida Kavaliauskienė
- Vilnius University, Faculty of Medicine, Institute of Biomedical Sciences, Department of Human and Medical Genetics, Vilnius, Lithuania
| | - Karolis Baronas
- Vilnius University, Faculty of Medicine, Institute of Biomedical Sciences, Department of Human and Medical Genetics, Vilnius, Lithuania
| | - Vaidutis Kučinskas
- Vilnius University, Faculty of Medicine, Institute of Biomedical Sciences, Department of Human and Medical Genetics, Vilnius, Lithuania
| | - Laima Ambrozaitytė
- Vilnius University, Faculty of Medicine, Institute of Biomedical Sciences, Department of Human and Medical Genetics, Vilnius, Lithuania
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2
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Wang P, Xu X, Li M, Lou XY, Xu S, Wu B, Gao G, Yin P, Liu N. Gene-based association tests in family samples using GWAS summary statistics. Genet Epidemiol 2024; 48:103-113. [PMID: 38317324 DOI: 10.1002/gepi.22548] [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: 07/12/2023] [Revised: 11/18/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024]
Abstract
Genome-wide association studies (GWAS) have led to rapid growth in detecting genetic variants associated with various phenotypes. Owing to a great number of publicly accessible GWAS summary statistics, and the difficulty in obtaining individual-level genotype data, many existing gene-based association tests have been adapted to require only GWAS summary statistics rather than individual-level data. However, these association tests are restricted to unrelated individuals and thus do not apply to family samples directly. Moreover, due to its flexibility and effectiveness, the linear mixed model has been increasingly utilized in GWAS to handle correlated data, such as family samples. However, it remains unknown how to perform gene-based association tests in family samples using the GWAS summary statistics estimated from the linear mixed model. In this study, we show that, when family size is negligible compared to the total sample size, the diagonal block structure of the kinship matrix makes it possible to approximate the correlation matrix of marginal Z scores by linkage disequilibrium matrix. Based on this result, current methods utilizing summary statistics for unrelated individuals can be directly applied to family data without any modifications. Our simulation results demonstrate that this proposed strategy controls the type 1 error rate well in various situations. Finally, we exemplify the usefulness of the proposed approach with a dental caries GWAS data set.
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Affiliation(s)
- Peng Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei, People's Republic of China
| | - Xiao Xu
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, Indiana, USA
| | - Ming Li
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, Indiana, USA
| | - Xiang-Yang Lou
- Department of Biostatistics, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Siqi Xu
- Department of Statistics and Actuarial Science, The University of Hong Kong, Hong Kong, Hong Kong
| | - Baolin Wu
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Guimin Gao
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, USA
| | - Ping Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei, People's Republic of China
| | - Nianjun Liu
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, Indiana, USA
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3
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da Silva Rosa SC, Barzegar Behrooz A, Guedes S, Vitorino R, Ghavami S. Prioritization of genes for translation: a computational approach. Expert Rev Proteomics 2024; 21:125-147. [PMID: 38563427 DOI: 10.1080/14789450.2024.2337004] [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: 05/26/2023] [Accepted: 02/21/2024] [Indexed: 04/04/2024]
Abstract
INTRODUCTION Gene identification for genetic diseases is critical for the development of new diagnostic approaches and personalized treatment options. Prioritization of gene translation is an important consideration in the molecular biology field, allowing researchers to focus on the most promising candidates for further investigation. AREAS COVERED In this paper, we discussed different approaches to prioritize genes for translation, including the use of computational tools and machine learning algorithms, as well as experimental techniques such as knockdown and overexpression studies. We also explored the potential biases and limitations of these approaches and proposed strategies to improve the accuracy and reliability of gene prioritization methods. Although numerous computational methods have been developed for this purpose, there is a need for computational methods that incorporate tissue-specific information to enable more accurate prioritization of candidate genes. Such methods should provide tissue-specific predictions, insights into underlying disease mechanisms, and more accurate prioritization of genes. EXPERT OPINION Using advanced computational tools and machine learning algorithms to prioritize genes, we can identify potential targets for therapeutic intervention of complex diseases. This represents an up-and-coming method for drug development and personalized medicine.
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Affiliation(s)
- Simone C da Silva Rosa
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Science, University of Manitoba, Winnipeg, Canada
| | - Amir Barzegar Behrooz
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Science, University of Manitoba, Winnipeg, Canada
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sofia Guedes
- LAQV/REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Rui Vitorino
- LAQV/REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal
- Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, Aveiro, Portugal
- UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Science, University of Manitoba, Winnipeg, Canada
- Faculty of Medicine in Zabrze, Academia of Silesia, Katowice, Poland
- Research Institute of Oncology and Hematology, Cancer Care Manitoba, University of Manitoba, Winnipeg, Canada
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Savić R, Yang J, Koplev S, An MC, Patel PL, O'Brien RN, Dubose BN, Dodatko T, Rogatsky E, Sukhavasi K, Ermel R, Ruusalepp A, Houten SM, Kovacic JC, Stewart AF, Yohn CB, Schadt EE, Laberge RM, Björkegren JLM, Tu Z, Argmann C. Integration of transcriptomes of senescent cell models with multi-tissue patient samples reveals reduced COL6A3 as an inducer of senescence. Cell Rep 2023; 42:113371. [PMID: 37938972 PMCID: PMC10955802 DOI: 10.1016/j.celrep.2023.113371] [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: 06/30/2021] [Revised: 05/23/2023] [Accepted: 10/17/2023] [Indexed: 11/10/2023] Open
Abstract
Senescent cells are a major contributor to age-dependent cardiovascular tissue dysfunction, but knowledge of their in vivo cell markers and tissue context is lacking. To reveal tissue-relevant senescence biology, we integrate the transcriptomes of 10 experimental senescence cell models with a 224 multi-tissue gene co-expression network based on RNA-seq data of seven tissues biopsies from ∼600 coronary artery disease (CAD) patients. We identify 56 senescence-associated modules, many enriched in CAD GWAS genes and correlated with cardiometabolic traits-which supports universality of senescence gene programs across tissues and in CAD. Cross-tissue network analyses reveal 86 candidate senescence-associated secretory phenotype (SASP) factors, including COL6A3. Experimental knockdown of COL6A3 induces transcriptional changes that overlap the majority of the experimental senescence models, with cell-cycle arrest linked to modulation of DREAM complex-targeted genes. We provide a transcriptomic resource for cellular senescence and identify candidate biomarkers, SASP factors, and potential drivers of senescence in human tissues.
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Affiliation(s)
- Radoslav Savić
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Jialiang Yang
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Simon Koplev
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Mahru C An
- UNITY Biotechnology, South San Francisco, CA 94080, USA
| | | | | | | | - Tetyana Dodatko
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Eduard Rogatsky
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Katyayani Sukhavasi
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia
| | - Raili Ermel
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia
| | - Arno Ruusalepp
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia; Clinical Gene Networks AB, Stockholm, Sweden
| | - Sander M Houten
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Jason C Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Andrew F Stewart
- Diabetes Obesity Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Eric E Schadt
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | | | - Johan L M Björkegren
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Clinical Gene Networks AB, Stockholm, Sweden; Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Zhidong Tu
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Carmen Argmann
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA.
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Xiong D, Yang J, Li D, Wang J. Exploration of Key Immune-Related Transcriptomes Associated with Doxorubicin-Induced Cardiotoxicity in Patients with Breast Cancer. Cardiovasc Toxicol 2023; 23:329-348. [PMID: 37684436 PMCID: PMC10514147 DOI: 10.1007/s12012-023-09806-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023]
Abstract
Based on a few studies, heart failure patients with breast cancer were assessed to find potential biomarkers for doxorubicin-induced cardiotoxicity. However, key immune-related transcriptional markers linked to doxorubicin-induced cardiotoxicity in breast cancer patients have not been thoroughly investigated. We used GSE40447, GSE76314, and TCGA BRCA cohorts to perform this study. Then, we performed various bioinformatics approaches to identify the key immune-related transcriptional markers and their association with doxorubicin-induced cardiotoxicity in patients with breast cancer. We found 255 upregulated genes and 286 downregulated genes in patients with doxorubicin-induced heart failure in breast cancer. We discovered that in patients with breast cancer comorbidity doxorubicin-induced cardiotoxicity, the 58 immunological genes are elevated (such as CPA3, VSIG4, GATA2, RFX2, IL3RA, and LRP1), and the 60 genes are significantly suppressed (such as MS4A1, FCRL1, CD200, FCRLA, FCRL2, and CD79A). Furthermore, we revealed that the immune-related differentially expressed genes (DEGs) are substantially associated with the enrichment of KEGG pathways, including B-cell receptor signaling pathway, primary immunodeficiency, chemokine signaling pathway, hematopoietic cell lineage, cytokine-cytokine receptor interaction, Toll-like receptor signaling pathway, MAPK signaling pathway, focal adhesion, dilated cardiomyopathy, cell adhesion molecule, etc. Moreover, we discovered that the doxorubicin-induced immune-related genes are crucially involved in the protein-protein interaction and gene clusters. The immune-related genes, including IFIT5, XCL1, SPIB, BTLA, MS4A1, CD19, TCL1A, CD83, CD200, FCRLA, CD79A, BIRC3, and IGF2R are significantly associated with a poor survival prognosis of breast cancer patients and showed diagnostic efficacy in patients with breast cancer and heart failure. Molecular docking revealed that the survival-associated genes interact with the doxorubicin with appreciable binding affinity. Finally, we validated the expression level of immune-related genes in breast cancer patients-derived cardiomyocytes with doxorubicin-induced cardiotoxicity and found that the level of RAD9A, HSPA1B, GATA2, IGF2R, CD200, ERCC8, and BCL11A genes are consistently dysregulated. Our findings offered a basis for understanding the mechanism and pathogenesis of the cardiotoxicity caused by doxorubicin in breast cancer patients and predicted the interaction of immune-related potential biomarkers with doxorubicin.
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Affiliation(s)
- Daiqin Xiong
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
| | - Jianhua Yang
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
| | - Dongfeng Li
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
| | - Jie Wang
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China.
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6
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van de Vegte YJ, Eppinga RN, van der Ende MY, Hagemeijer YP, Mahendran Y, Salfati E, Smith AV, Tan VY, Arking DE, Ntalla I, Appel EV, Schurmann C, Brody JA, Rueedi R, Polasek O, Sveinbjornsson G, Lecoeur C, Ladenvall C, Zhao JH, Isaacs A, Wang L, Luan J, Hwang SJ, Mononen N, Auro K, Jackson AU, Bielak LF, Zeng L, Shah N, Nethander M, Campbell A, Rankinen T, Pechlivanis S, Qi L, Zhao W, Rizzi F, Tanaka T, Robino A, Cocca M, Lange L, Müller-Nurasyid M, Roselli C, Zhang W, Kleber ME, Guo X, Lin HJ, Pavani F, Galesloot TE, Noordam R, Milaneschi Y, Schraut KE, den Hoed M, Degenhardt F, Trompet S, van den Berg ME, Pistis G, Tham YC, Weiss S, Sim XS, Li HL, van der Most PJ, Nolte IM, Lyytikäinen LP, Said MA, Witte DR, Iribarren C, Launer L, Ring SM, de Vries PS, Sever P, Linneberg A, Bottinger EP, Padmanabhan S, Psaty BM, Sotoodehnia N, Kolcic I, Arnar DO, Gudbjartsson DF, Holm H, Balkau B, Silva CT, Newton-Cheh CH, Nikus K, Salo P, Mohlke KL, Peyser PA, Schunkert H, Lorentzon M, Lahti J, Rao DC, Cornelis MC, Faul JD, Smith JA, Stolarz-Skrzypek K, Bandinelli S, Concas MP, Sinagra G, Meitinger T, Waldenberger M, Sinner MF, Strauch K, Delgado GE, Taylor KD, Yao J, Foco L, Melander O, de Graaf J, de Mutsert R, de Geus EJC, Johansson Å, Joshi PK, Lind L, Franke A, Macfarlane PW, Tarasov KV, Tan N, Felix SB, Tai ES, Quek DQ, Snieder H, Ormel J, Ingelsson M, Lindgren C, Morris AP, Raitakari OT, Hansen T, Assimes T, Gudnason V, Timpson NJ, Morrison AC, Munroe PB, Strachan DP, Grarup N, Loos RJF, Heckbert SR, Vollenweider P, Hayward C, Stefansson K, Froguel P, Groop L, Wareham NJ, van Duijn CM, Feitosa MF, O'Donnell CJ, Kähönen M, Perola M, Boehnke M, Kardia SLR, Erdmann J, Palmer CNA, Ohlsson C, Porteous DJ, Eriksson JG, Bouchard C, Moebus S, Kraft P, Weir DR, Cusi D, Ferrucci L, Ulivi S, Girotto G, Correa A, Kääb S, Peters A, Chambers JC, Kooner JS, März W, Rotter JI, Hicks AA, Smith JG, Kiemeney LALM, Mook-Kanamori DO, Penninx BWJH, Gyllensten U, Wilson JF, Burgess S, Sundström J, Lieb W, Jukema JW, Eijgelsheim M, Lakatta ELM, Cheng CY, Dörr M, Wong TY, Sabanayagam C, Oldehinkel AJ, Riese H, Lehtimäki T, Verweij N, van der Harst P. Genetic insights into resting heart rate and its role in cardiovascular disease. Nat Commun 2023; 14:4646. [PMID: 37532724 PMCID: PMC10397318 DOI: 10.1038/s41467-023-39521-2] [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: 06/06/2022] [Accepted: 06/16/2023] [Indexed: 08/04/2023] Open
Abstract
Resting heart rate is associated with cardiovascular diseases and mortality in observational and Mendelian randomization studies. The aims of this study are to extend the number of resting heart rate associated genetic variants and to obtain further insights in resting heart rate biology and its clinical consequences. A genome-wide meta-analysis of 100 studies in up to 835,465 individuals reveals 493 independent genetic variants in 352 loci, including 68 genetic variants outside previously identified resting heart rate associated loci. We prioritize 670 genes and in silico annotations point to their enrichment in cardiomyocytes and provide insights in their ECG signature. Two-sample Mendelian randomization analyses indicate that higher genetically predicted resting heart rate increases risk of dilated cardiomyopathy, but decreases risk of developing atrial fibrillation, ischemic stroke, and cardio-embolic stroke. We do not find evidence for a linear or non-linear genetic association between resting heart rate and all-cause mortality in contrast to our previous Mendelian randomization study. Systematic alteration of key differences between the current and previous Mendelian randomization study indicates that the most likely cause of the discrepancy between these studies arises from false positive findings in previous one-sample MR analyses caused by weak-instrument bias at lower P-value thresholds. The results extend our understanding of resting heart rate biology and give additional insights in its role in cardiovascular disease development.
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Affiliation(s)
- Yordi J van de Vegte
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, 9700RB, the Netherlands
| | - Ruben N Eppinga
- Department of Cardiology, Isala Zwolle ziekenhuis, Zwolle, 8025 AB, the Netherlands
| | - M Yldau van der Ende
- Department of Cardiology, University medical Center Utrecht, Utrecht, 3584 Cx, the Netherlands
| | - Yanick P Hagemeijer
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, 9700RB, the Netherlands
- Analytical Biochemistry, University of Groningen, Groningen, 9713 AV, the Netherlands
| | - Yuvaraj Mahendran
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medicine Science, University of Copenhagen, Copenhagen Ø, 2100, Denmark
| | - Elias Salfati
- Department of Medicine, Stanford University School of Medicine, Stanford, 94305, USA
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI48109, USA
| | - Vanessa Y Tan
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, BS82BN, UK
- MRC Integrative Epidemiology, University of Bristol, Bristol, BS82BN, UK
| | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, 21215, USA
| | - Ioanna Ntalla
- Clinical Pharmacology and Precision Medicine, William Harvey Research Institute, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Emil V Appel
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medicine Science, University of Copenhagen, Copenhagen Ø, 2100, Denmark
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, 10029, USA
| | | | - Rico Rueedi
- Department of Computational Biology, University of Lausanne, Lausanne, 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Ozren Polasek
- Department of Public Health, University of Split School of Medicine, Split, 21000, Croatia
- Algebra LAB, Algebra University College, Zagreb, 10000, Croatia
| | | | - Cecile Lecoeur
- UMR 8199, University of Lille Nord de France, Lille, 59000, France
| | - Claes Ladenvall
- Clinial Genomics Uppsala, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, 75185, Sweden
- Lund University Diabetes Center, Department of Clinical Sciences, Lund University, Malmö, 20502, Sweden
| | - Jing Hua Zhao
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, CB2 0BB, UK
| | - Aaron Isaacs
- CARIM School for Cardiovascular Diseases, Maastricht Centre for Systems Biology (MaCSBio), Department of Physiology, Maastricht University, Maastricht, 6229ER, Netherlands
| | - Lihua Wang
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63108-2212, Campus Box 8506, USA
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Shih-Jen Hwang
- Division of Intramural Research, National Heart Lung and Blood Institute, NIH, USA, Framingham, 1702, USA
| | - Nina Mononen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, FI-33014, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
| | - Kirsi Auro
- Department of Health, unit of genetics and biomarkers, , National Institute for Health and Welfare, Finland, Helsinki, FI-00290, Finland
- Department of molecular medicine, University of Helsinki, Helsinki, FI-00290, Finland
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Lawrence F Bielak
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Linyao Zeng
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, 80636, Germany
| | - Nabi Shah
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK
- Pharmacogenetics Research Lab, Department of Pharmacy, COMSATS University Islamabad, Abbottabad, 22060, Pakistan
| | - Maria Nethander
- Sahlgrenska Osteoporosis Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41345, Sweden
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Usher Institute for Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, EH16 4UX, UK
| | - Tuomo Rankinen
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, 70808, USA
| | - Sonali Pechlivanis
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, University Duisburg-Essen, Essen, 45122, Germany
| | - Lu Qi
- Department of Epidemiology, Tulane University, New Orleans, LA, 70112, USA
| | - Wei Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Federica Rizzi
- Unit of Biomedicine, Bio4Dreams-Business Nursery for Life Sciences, Milano, 20121, Italy
| | - Toshiko Tanaka
- Longitudinal Study Section, National Institute on Aging, Baltimore, 21224, USA
| | - Antonietta Robino
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, 34137, Italy
| | - Massimiliano Cocca
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, 34137, Italy
| | - Leslie Lange
- Medicine, University of Colorado Anschutz Medical Campus, Aurora, 80045, USA
| | - Martina Müller-Nurasyid
- IBE, Ludwig-Maximilians-University Munich, LMU Munich, Munich, 81377, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, 55101, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
| | - Carolina Roselli
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, 02142, USA
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
| | - Marcus E Kleber
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, 68167, Germany
- SYNLAB MVZ Humangenetik Mannheim, Mannheim, 68163, Germany
| | - Xiuqing Guo
- Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA, Torrance, 90502, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, 90502, USA
| | - Henry J Lin
- Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA, Torrance, 90502, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, 90502, USA
| | - Francesca Pavani
- Institute for Biomedicine, Eurac Research, Bolzano, 39100, Italy
| | | | - Raymond Noordam
- Department of Internal Medicine, section Gerontology and Geriatrics, Leiden University Medical Center, Leiden, 2300 RC, the Netherlands
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Public Health, Amsterdam UMC, Amsterdam UMC, Vrije Universiteit, Amsterdam, Amsterdam, 1081 HL, the Netherlands
| | - Katharina E Schraut
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, Scotland, UK
| | - Marcel den Hoed
- The Beijer laboratory and Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, 75237, Sweden
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, 24105, Germany
| | - Stella Trompet
- Department of Internal Medicine, section Gerontology and Geriatrics, Leiden University Medical Center, Leiden, 2300 RC, the Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden, ZA, 2333, the Netherlands
| | - Marten E van den Berg
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, 3015GD, the Netherlands
| | - Giorgio Pistis
- Institute of Genetics and Biomedic Research (IRGB), Italian National Research Council (CNR), Monserrato, (CA), 9042, Italy
- Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, USA
| | - Yih-Chung Tham
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, 17475, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, 17475, Germany
| | - Xueling S Sim
- Saw Swee Hock School of Public Health, National University Health System and National University of Singapore, Singapore, 117549, Singapore
| | - Hengtong L Li
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, 9700 RB, The Netherlands
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, 9700 RB, The Netherlands
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, FI-33014, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB2 0SL, UK
| | - M Abdullah Said
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, 9700RB, the Netherlands
| | - Daniel R Witte
- Department of Public Health, Aarhus University, Aarhus C, 8000, Denmark
| | - Carlos Iribarren
- Division of Research, Kaiser Permenente of Northern California, Oakland, 94612, USA
- The Scripps Research Institute, La Jolla, 10550, USA
| | | | - Susan M Ring
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, BS82BN, UK
- MRC Integrative Epidemiology, University of Bristol, Bristol, BS82BN, UK
| | - Paul S de Vries
- Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Science Center at Houston, School of Public Health, Houston, 77030, USA
| | - Peter Sever
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, 2400, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, 10029, USA
- Department of Preventive Medicine, The Icahn School of Medicine at Mount Sinai, New York, 10029, USA
| | - Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Bruce M Psaty
- Departments of Medicine, Epidemiology and Health Systems and Population Health, University of Washington, Seattle, 98195, USA
| | - Nona Sotoodehnia
- Medicine and Epidemiology, University of Washington, Seattle, 98195, USA
| | - Ivana Kolcic
- Department of Public Health, University of Split School of Medicine, Split, 21000, Croatia
- Algebra LAB, Algebra University College, Zagreb, 10000, Croatia
| | - David O Arnar
- deCODE genetics / Amgen Inc., Reykjavik, 102, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, 101, Iceland
- Department of Medicine, Landspitali-The National University Hospital of Iceland, Reykjavik, 101, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics / Amgen Inc., Reykjavik, 102, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Hilma Holm
- deCODE genetics / Amgen Inc., Reykjavik, 102, Iceland
| | - Beverley Balkau
- Centre for Research in Epidemiology and Population Health, Institut national de la santé et de la recherche médicale, Villejuif, 94800, France
- UMRS 1018, University Versailles Saint-Quentin-en-Yvelines, Versailles, 78035, France
- UMRS 1018, University Paris Sud, Villejuif, 94807, France
| | - Claudia T Silva
- Genetic Epidemiology Unit, Dept. of Epidemiology, Erasmus University Medical Center, Rotterdam, 3000CA, Netherlands
| | | | - Kjell Nikus
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere, FI-33521, Finland
- Department of Cardiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
| | - Perttu Salo
- Department of Health, unit of genetics and biomarkers, , National Institute for Health and Welfare, Finland, Helsinki, FI-00290, Finland
- Department of molecular medicine, University of Helsinki, Helsinki, FI-00290, Finland
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Heribert Schunkert
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, 80636, Germany
- Deutsches Zentrum für Herz- und Kreislauferkrankungen (DZHK), Partner Site Munich Heart Alliance, Munich, 80636, Germany
| | - Mattias Lorentzon
- Sahlgrenska Osteoporosis Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41345, Sweden
- Region Västra Götaland, Geriatric Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Mölndal, 43180, Sweden
- Mary McKillop Institute for Health Research, Australian Catholic University, Melbourne, 3000, Australia
| | - Jari Lahti
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, 00014, Finland
| | - Dabeeru C Rao
- Division of Biostatistics, Washington University, St. Louis, MO, 63110, USA
| | | | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Katarzyna Stolarz-Skrzypek
- Department of Cardiology, Interventional Electrocardiology and Hypertension, Jagiellonian University Medical College, Kraków, 31-008, Poland
| | - Stefania Bandinelli
- Geriatric Unit, Unità sanitaria locale Toscana Centro, Florence, 50142, Italy
| | - Maria Pina Concas
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, 34137, Italy
| | - Gianfranco Sinagra
- Cardiovascular Department, "Ospedali Riuniti and University of Trieste", Trieste, 34149, Italy
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, München, 81675, Germany
- Institute of Human Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, 80802, Germany
| | - Moritz F Sinner
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, 80802, Germany
- Department of Cardiology, University Hospital, LMU Munich, Munich, 81377, Germany
| | - Konstantin Strauch
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, 55101, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, 81377, Germany
| | - Graciela E Delgado
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, 68167, Germany
| | - Kent D Taylor
- Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA, Torrance, 90502, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, 90502, USA
| | - Jie Yao
- Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA, Torrance, 90502, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, 90502, USA
| | - Luisa Foco
- Institute for Biomedicine, Eurac Research, Bolzano, 39100, Italy
| | - Olle Melander
- Department of Internal Medicine, Clinical Sciences, Lund University and Skåne University Hospital, Malmo, 221 85, Sweden
- Lund University Diabetes Center, Lund University, Malmö, 221 85, Sweden
| | | | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2300 RC, the Netherlands
| | - Eco J C de Geus
- Biological Psychology, EMGO+ Institute for Health and Care Research and Neuroscience Campus Amsterdam, VU University, Amsterdam, 1081 BT, the Netherlands
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, 75108, Sweden
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, Scotland, UK
| | - Lars Lind
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University Hospital, Uppsala, 75237, Sweden
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, 24105, Germany
| | - Peter W Macfarlane
- Institute of Health and Wellbeing, Faculty of Medicine, University of Glasgow, Glasgow, G12 0XH, UK
| | - Kirill V Tarasov
- Laboratory of Cardiovascular Sciences, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Nicholas Tan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
| | - Stephan B Felix
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, 17475, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, 17475, Germany
| | - E-Shyong Tai
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Debra Q Quek
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, 9700 RB, The Netherlands
| | - Johan Ormel
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, 9700 RB, The Netherlands
| | - Martin Ingelsson
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Uppsala University, Uppsala, 75237, Sweden
| | - Cecilia Lindgren
- Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Andrew P Morris
- Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, FI-20521, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, FI-20521, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, FI-20521, Finland
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medicine Science, University of Copenhagen, Copenhagen Ø, 2100, Denmark
| | - Themistocles Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, 94305, USA
| | - Vilmundur Gudnason
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
- Icelandic Heart Association, Kopavogur, 201, Iceland
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School,, University of Bristol, Bristol, BS8 2BN, UK
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Science Center at Houston, School of Public Health, Houston, 77030, USA
| | - Patricia B Munroe
- Clinical Pharmacology and Precision Medicine, William Harvey Research Institute, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Biomedical Research Centre, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, SW17 0RE, UK
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medicine Science, University of Copenhagen, Copenhagen Ø, 2100, Denmark
| | - Ruth J F Loos
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medicine Science, University of Copenhagen, Copenhagen Ø, 2100, Denmark
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, 10029, USA
- The Mindich Child Health and Development Institute, The Icahn School of Medicine at Mount Sinai, New York, 10029, USA
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle, 98195, USA
| | - Peter Vollenweider
- Department of Medicine, Internal Medicine, Lausanne University hospital, Lausanne, 1015, Switzerland
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, Scotland, UK
| | - Kari Stefansson
- deCODE genetics / Amgen Inc., Reykjavik, 102, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Philippe Froguel
- Department of Metabolism, Imperial College London, London, W12 0HS, UK
- Inserm/CNRS UMR 1283/8199, Pasteur Institute of Lille, Lille University Hospital, EGID, Lille, 59000, France
- University of Lille, Lille, 59000, France
| | - Leif Groop
- Lund University Diabetes Center, Department of Clinical Sciences, Lund University, Malmö, 20502, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, 00290, Finland
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Cornelia M van Duijn
- Genetic Epidemiology Unit, Dept. of Epidemiology, Erasmus University Medical Center, Rotterdam, 3000CA, Netherlands
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63108-2212, Campus Box 8506, USA
| | - Christopher J O'Donnell
- Cardiology Section, VA Boston Healthcare System, Harvard Medical School, Boston, MA, 02132, USA
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, FI-33521, Finland
- Department of Clinical Physiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33521, Finland
| | - Markus Perola
- Department of Health, unit of genetics and biomarkers, , National Institute for Health and Welfare, Finland, Helsinki, FI-00290, Finland
- Department of molecular medicine, University of Helsinki, Helsinki, FI-00290, Finland
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jeanette Erdmann
- Institute for Cardiogenetics, University of Lübeck, Lübeck, 23562, Germany
| | - Colin N A Palmer
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK
| | - Claes Ohlsson
- Sahlgrenska Osteoporosis Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41345, Sweden
- Department of Drug Treatment, Sahlgrenska University Hospital, Gothenburg, 41345, Sweden
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Johan G Eriksson
- Department of General practice and primary care, University of Helsinki, Helsinki, 00014, Finland
- Department of Obstetrics and Gynecology, National University of Singapore, Singapore, 119228, Singapore
- Public health Research Program, Folkhalsan Research Center, Helsinki, 000250, Finland
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, 70808, USA
| | - Susanne Moebus
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, University Duisburg-Essen, Essen, 45122, Germany
- Centre for Urban Epidemiology, University Hospital of Essen, University Duisburg-Essen, Essen, 45122, Germany
| | - Peter Kraft
- Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02112, USA
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Daniele Cusi
- Unit of Biomedicine, Bio4Dreams-Business Nursery for Life Sciences, Milano, 20121, Italy
- Institute of Biomedical Technologies, National Research Council of Italy, Segrate, (MI), 20090, Italy
| | - Luigi Ferrucci
- Longitudinal Study Section, National Institute on Aging, Baltimore, 21224, USA
| | - Sheila Ulivi
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, 34137, Italy
| | - Giorgia Girotto
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, 34137, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, 34149, Italy
| | - Adolfo Correa
- Jackson Heart Study, University of Mississippi Medical Center, Jackson, 39216, USA
| | - Stefan Kääb
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, 80802, Germany
- Department of Cardiology, University Hospital, LMU Munich, Munich, 81377, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, 80802, Germany
- Chair of Epidemiology, Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, 81377, Germany
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, W12 0HS, UK
| | - Winfried März
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, 68167, Germany
- Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim, 68161, Germany
| | - Jerome I Rotter
- Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA, Torrance, 90502, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, 90502, USA
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Bolzano, 39100, Italy
| | - J Gustav Smith
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, 221 85, Sweden
- Wallenberg Center for Molecular Medicine and Lund University Diabetes Center, Lund University, Lund, 221 84, Sweden
- The Wallenberg Laboratory/Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University and the Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, 413 45, Sweden
| | | | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2300 RC, the Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2300 RC, the Netherlands
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Public Health, Amsterdam UMC, Amsterdam UMC, Vrije Universiteit, Amsterdam, Amsterdam, 1081 HL, the Netherlands
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, 75108, Sweden
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, Scotland, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, Scotland, UK
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Johan Sundström
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University Hospital, Uppsala, 75237, Sweden
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank PopGen, Kiel University, Kiel, 24105, Germany
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, ZA, 2333, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, ZA, 2333, the Netherlands
- Netherlands Heart Institute, Utrecht, 3511 EP, the Netherlands
| | - Mark Eijgelsheim
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, 3015GD, the Netherlands
- Department of Nephrology, University Medical Center Groningen, Groningen, 9700RB, the Netherlands
| | - Edward L M Lakatta
- Laboratory of Cardiovascular Sciences, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, 169857, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Marcus Dörr
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, 17475, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, 17475, Germany
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, 169857, Singapore
- Tsinghua Medicine, Tsinghua University, Beijing, 100084, China
| | - Charumathi Sabanayagam
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Albertine J Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation, University of Groningen, University Medical Center Groningen, Groningen, 9700 RB, The Netherlands
| | - Harriette Riese
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, 9700 RB, The Netherlands
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, FI-33014, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, 9700RB, the Netherlands
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, 9700RB, the Netherlands.
- Department of Cardiology, University medical Center Utrecht, Utrecht, 3584 Cx, the Netherlands.
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9700RB, the Netherlands.
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Rath S, Panda S, Sacchettini JC, Berthel SJ. DAIKON: A Data Acquisition, Integration, and Knowledge Capture Web Application for Target-Based Drug Discovery. ACS Pharmacol Transl Sci 2023; 6:1043-1051. [PMID: 37470023 PMCID: PMC10353056 DOI: 10.1021/acsptsci.3c00034] [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: 02/19/2023] [Indexed: 07/21/2023]
Abstract
Primitive data organization practices struggle to deliver at the scale and consistency required to meet multidisciplinary collaborations in drug discovery. For effective data sharing and coordination, a unified platform that can collect and analyze scientific information is essential. We present DAIKON, an open-source framework that integrates targets, screens, hits, and manages projects within a target-based drug discovery portfolio. Its knowledge capture components enable teams to record subsequent molecules as their properties improve, facilitate team collaboration through discussion threads, and include modules that visually illustrate the progress of each target as it advances through the pipeline. It serves as a repository for scientists sourcing data from Mycobrowser, UniProt, PDB. The goal is to globalize several variations of the drug-discovery program without compromising local aspects of specific workflows. DAIKON is modularized by abstracting the database and creating separate layers for entities, business logic, infrastructure, APIs, and frontend, with each tier allowing for extensions. Using Docker, the framework is packaged into two solutions: daikon-server-core and daikon-client. Organizations may deploy the project to on-premises servers or VPC. Active-Directory/SSO is supported for user administration. End users can access the application with a web browser. Currently, DAIKON is implemented in the TB Drug Accelerator program (TBDA).
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Affiliation(s)
- Siddhant Rath
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - Saswati Panda
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - James C. Sacchettini
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
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8
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Wang L, Western D, Timsina J, Repaci C, Song WM, Norton J, Kohlfeld P, Budde J, Climer S, Butt OH, Jacobson D, Garvin M, Templeton AR, Campagna S, O’Halloran J, Presti R, Goss CW, Mudd PA, Ances BM, Zhang B, Sung YJ, Cruchaga C. Plasma proteomics of SARS-CoV-2 infection and severity reveals impact on Alzheimer's and coronary disease pathways. iScience 2023; 26:106408. [PMID: 36974157 PMCID: PMC10010831 DOI: 10.1016/j.isci.2023.106408] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/21/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
Identification of proteins dysregulated by COVID-19 infection is critically important for better understanding of its pathophysiology, building prognostic models, and identifying new targets. Plasma proteomic profiling of 4,301 proteins was performed in two independent datasets and tested for the association for three COVID-19 outcomes (infection, ventilation, and death). We identified 1,449 proteins consistently associated in both datasets with any of these three outcomes. We subsequently created highly accurate models that distinctively predict infection, ventilation, and death. These proteins were enriched in specific biological processes including cytokine signaling, Alzheimer's disease, and coronary artery disease. Mendelian randomization and gene network analyses identified eight causal proteins and 141 highly connected hub proteins including 35 with known drug targets. Our findings provide distinctive prognostic biomarkers for two severe COVID-19 outcomes, reveal their relationship to Alzheimer's disease and coronary artery disease, and identify potential therapeutic targets for COVID-19 outcomes.
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Affiliation(s)
- Lihua Wang
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel Western
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Charlie Repaci
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Pat Kohlfeld
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Sharlee Climer
- Department of Computer Science, University of Missouri-St. Louis, St. Louis, MO, USA
| | - Omar H. Butt
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Michael Garvin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Alan R. Templeton
- Department of Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Shawn Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Jane O’Halloran
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Rachel Presti
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Charles W. Goss
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Philip A. Mudd
- Department of Emergency Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Beau M. Ances
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St Louis, MO, USA
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9
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Kentistou KA, Luan J, Wittemans LBL, Hambly C, Klaric L, Kutalik Z, Speakman JR, Wareham NJ, Kendall TJ, Langenberg C, Wilson JF, Joshi PK, Morton NM. Large scale phenotype imputation and in vivo functional validation implicate ADAMTS14 as an adiposity gene. Nat Commun 2023; 14:307. [PMID: 36658113 PMCID: PMC9852585 DOI: 10.1038/s41467-022-35563-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 12/09/2022] [Indexed: 01/20/2023] Open
Abstract
Obesity remains an unmet global health burden. Detrimental anatomical distribution of body fat is a major driver of obesity-mediated mortality risk and is demonstrably heritable. However, our understanding of the full genetic contribution to human adiposity is incomplete, as few studies measure adiposity directly. To address this, we impute whole-body imaging adiposity phenotypes in UK Biobank from the 4,366 directly measured participants onto the rest of the cohort, greatly increasing our discovery power. Using these imputed phenotypes in 392,535 participants yielded hundreds of genome-wide significant associations, six of which replicate in independent cohorts. The leading causal gene candidate, ADAMTS14, is further investigated in a mouse knockout model. Concordant with the human association data, the Adamts14-/- mice exhibit reduced adiposity and weight-gain under obesogenic conditions, alongside an improved metabolic rate and health. Thus, we show that phenotypic imputation at scale offers deeper biological insights into the genetics of human adiposity that could lead to therapeutic targets.
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Affiliation(s)
- Katherine A Kentistou
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, UK
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Laura B L Wittemans
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Catherine Hambly
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Zoltán Kutalik
- Centre for Primary Care and Public Health, University of Lausanne, Lausanne, 1010, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - John R Speakman
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
- Centre for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen Key Laboratory of Metabolic Health, CAS Centre of Excellence in Animal Evolution and Genetics, Kunming, China
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Timothy J Kendall
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
- Computational Medicine, Berlin Institute of Health (BIH) Charité University Medicine, Berlin, Germany
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Nicholas M Morton
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK.
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10
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Kurki MI, Karjalainen J, Palta P, Sipilä TP, Kristiansson K, Donner KM, Reeve MP, Laivuori H, Aavikko M, Kaunisto MA, Loukola A, Lahtela E, Mattsson H, Laiho P, Della Briotta Parolo P, Lehisto AA, Kanai M, Mars N, Rämö J, Kiiskinen T, Heyne HO, Veerapen K, Rüeger S, Lemmelä S, Zhou W, Ruotsalainen S, Pärn K, Hiekkalinna T, Koskelainen S, Paajanen T, Llorens V, Gracia-Tabuenca J, Siirtola H, Reis K, Elnahas AG, Sun B, Foley CN, Aalto-Setälä K, Alasoo K, Arvas M, Auro K, Biswas S, Bizaki-Vallaskangas A, Carpen O, Chen CY, Dada OA, Ding Z, Ehm MG, Eklund K, Färkkilä M, Finucane H, Ganna A, Ghazal A, Graham RR, Green EM, Hakanen A, Hautalahti M, Hedman ÅK, Hiltunen M, Hinttala R, Hovatta I, Hu X, Huertas-Vazquez A, Huilaja L, Hunkapiller J, Jacob H, Jensen JN, Joensuu H, John S, Julkunen V, Jung M, Junttila J, Kaarniranta K, Kähönen M, Kajanne R, Kallio L, Kälviäinen R, Kaprio J, Kerimov N, Kettunen J, Kilpeläinen E, Kilpi T, Klinger K, Kosma VM, Kuopio T, Kurra V, Laisk T, Laukkanen J, Lawless N, Liu A, Longerich S, Mägi R, Mäkelä J, Mäkitie A, Malarstig A, Mannermaa A, Maranville J, Matakidou A, Meretoja T, Mozaffari SV, Niemi MEK, Niemi M, Niiranen T, O Donnell CJ, Obeidat ME, Okafo G, Ollila HM, Palomäki A, Palotie T, Partanen J, Paul DS, Pelkonen M, Pendergrass RK, Petrovski S, Pitkäranta A, Platt A, Pulford D, Punkka E, Pussinen P, Raghavan N, Rahimov F, Rajpal D, Renaud NA, Riley-Gillis B, Rodosthenous R, Saarentaus E, Salminen A, Salminen E, Salomaa V, Schleutker J, Serpi R, Shen HY, Siegel R, Silander K, Siltanen S, Soini S, Soininen H, Sul JH, Tachmazidou I, Tasanen K, Tienari P, Toppila-Salmi S, Tukiainen T, Tuomi T, Turunen JA, Ulirsch JC, Vaura F, Virolainen P, Waring J, Waterworth D, Yang R, Nelis M, Reigo A, Metspalu A, Milani L, Esko T, Fox C, Havulinna AS, Perola M, Ripatti S, Jalanko A, Laitinen T, Mäkelä TP, Plenge R, McCarthy M, Runz H, Daly MJ, Palotie A. FinnGen provides genetic insights from a well-phenotyped isolated population. Nature 2023; 613:508-518. [PMID: 36653562 PMCID: PMC9849126 DOI: 10.1038/s41586-022-05473-8] [Citation(s) in RCA: 748] [Impact Index Per Article: 748.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 10/21/2022] [Indexed: 01/20/2023]
Abstract
Population isolates such as those in Finland benefit genetic research because deleterious alleles are often concentrated on a small number of low-frequency variants (0.1% ≤ minor allele frequency < 5%). These variants survived the founding bottleneck rather than being distributed over a large number of ultrarare variants. Although this effect is well established in Mendelian genetics, its value in common disease genetics is less explored1,2. FinnGen aims to study the genome and national health register data of 500,000 Finnish individuals. Given the relatively high median age of participants (63 years) and the substantial fraction of hospital-based recruitment, FinnGen is enriched for disease end points. Here we analyse data from 224,737 participants from FinnGen and study 15 diseases that have previously been investigated in large genome-wide association studies (GWASs). We also include meta-analyses of biobank data from Estonia and the United Kingdom. We identified 30 new associations, primarily low-frequency variants, enriched in the Finnish population. A GWAS of 1,932 diseases also identified 2,733 genome-wide significant associations (893 phenome-wide significant (PWS), P < 2.6 × 10-11) at 2,496 (771 PWS) independent loci with 807 (247 PWS) end points. Among these, fine-mapping implicated 148 (73 PWS) coding variants associated with 83 (42 PWS) end points. Moreover, 91 (47 PWS) had an allele frequency of <5% in non-Finnish European individuals, of which 62 (32 PWS) were enriched by more than twofold in Finland. These findings demonstrate the power of bottlenecked populations to find entry points into the biology of common diseases through low-frequency, high impact variants.
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Affiliation(s)
- Mitja I Kurki
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 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
| | - Juha Karjalainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 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
| | - Priit Palta
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Timo P Sipilä
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | - Kati M Donner
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Mary P Reeve
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Hannele Laivuori
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), 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, Tampere, Finland.,Faculty of Medicine and Health Technology, Center for Child, Adolescent and Maternal Health, University of Tampere, Tampere, Finland
| | - Mervi Aavikko
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Mari A Kaunisto
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Anu Loukola
- Helsinki Biobank, University of Helsinki and Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Elisa Lahtela
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Hannele Mattsson
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Päivi Laiho
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Pietro Della Briotta Parolo
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Arto A Lehisto
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Masahiro Kanai
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 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.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Nina Mars
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Joel Rämö
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tuomo Kiiskinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Henrike O Heyne
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Digital Health Center, Hasso Plattner Institute for Digital Engineering, University of Potsdam Potsdam, Potsdam, Germany.,Hasso Plattner Institute for Digital Health at Mount Sinai, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kumar Veerapen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 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
| | - Sina Rüeger
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Susanna Lemmelä
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Wei Zhou
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 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
| | - Sanni Ruotsalainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Kalle Pärn
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tero Hiekkalinna
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Sami Koskelainen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Teemu Paajanen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Vincent Llorens
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Javier Gracia-Tabuenca
- TAUCHI Research Center, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland
| | - Harri Siirtola
- TAUCHI Research Center, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland
| | - Kadri Reis
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Benjamin Sun
- Translational Biology, Research and Development, Biogen, Cambridge, MA, USA.,BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Christopher N Foley
- Optima Partners, Edinburgh, UK.,MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Mikko Arvas
- Finnish Red Cross Blood Service, Helsinki, Finland
| | | | | | | | - Olli Carpen
- Helsinki Biobank, University of Helsinki and Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | | | - Oluwaseun A Dada
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Zhihao Ding
- Boehringer Ingelheim, Ingelheim am Rhein, Germany
| | | | - Kari Eklund
- Division of Rheumatology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland.,Orton Orthopedic Hospital, Helsinki, Finland
| | - Martti Färkkilä
- Abdominal Center, Helsinki University Hospital, Helsinki University, Helsinki, Finland
| | - Hilary Finucane
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 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
| | - Andrea Ganna
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 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
| | - Awaisa Ghazal
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | | | - Antti Hakanen
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | | | - Åsa K Hedman
- Pfizer, New York, NY, USA.,Department of Medicine, Karolinska Institute, Solna, Sweden
| | - Mikko Hiltunen
- Clinical Biobank Tampere, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Reetta Hinttala
- Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Oulu University Hospital, Oulu, Finland
| | - Iiris Hovatta
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,SleepWell Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | | | - Laura Huilaja
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Department of Dermatology and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | | | | | | | - Heikki Joensuu
- Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | | | - Valtteri Julkunen
- Neuro Center, Neurology, Kuopio University Hospital, Kuopio, Finland.,Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland
| | - Marc Jung
- Boehringer Ingelheim, Ingelheim am Rhein, Germany
| | - Juhani Junttila
- Northern Finland Biobank Borealis, University of Oulu, Northern Ostrobothnia Hospital District, Oulu, Finland
| | - Kai Kaarniranta
- Department of Ophthalmology, Kuopio University Hospital, Kuopio, Finland.,Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Mika Kähönen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Risto Kajanne
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Lila Kallio
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | - Reetta Kälviäinen
- Epilepsy Center, Kuopio University Hospital, Kuopio, Finland.,Department of Neurology, University of Eastern Finland, Kuopio, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland
| | | | - Nurlan Kerimov
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Johannes Kettunen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Computational Medicine, Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Elina Kilpeläinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Terhi Kilpi
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | | | - Veli-Matti Kosma
- Biobank of Eastern Finland, University of Eastern Finland, Kuopio, Finland.,Kuopio University Hospital, Kuopio, Finland
| | - Teijo Kuopio
- Central Finland Biobank, Central Finland Health Care District, Jyväskylä, Finland
| | - Venla Kurra
- Department of Clinical Genetics, Tampere University Hospital, Tampere, Finland.,Department of Clinical Genetics, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Jari Laukkanen
- Central Finland Biobank, Central Finland Health Care District, Jyväskylä, Finland.,Department of Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | | | - Aoxing Liu
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Antti Mäkitie
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki, Helsinki, Finland.,Helsinki University Hospital, Helsinki, Finland
| | - Anders Malarstig
- Pfizer, Cambridge, MA, USA.,Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Solna, Sweden
| | - Arto Mannermaa
- Biobank of Eastern Finland, University of Eastern Finland, Kuopio, Finland.,Kuopio University Hospital, Kuopio, Finland
| | | | - Athena Matakidou
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Tuomo Meretoja
- Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | | | - Mari E K Niemi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Marianna Niemi
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,TAUCHI Research Center & Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Teemu Niiranen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland.,Turku University Hospital and University of Turku, Turku, Finland
| | | | - Ma En Obeidat
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - George Okafo
- Boehringer Ingelheim, Ingelheim am Rhein, Germany
| | - Hanna M Ollila
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Antti Palomäki
- Turku University Hospital and University of Turku, Turku, Finland
| | - Tuula Palotie
- Department of Oral and Maxillofacial Diseases, Helsinki University Hospital, Helsinki, Finland.,Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | - Jukka Partanen
- Finnish Red Cross Blood Service, Helsinki, Finland.,Finnish Hematological Biobank, Helsinki, Finland
| | - Dirk S Paul
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Margit Pelkonen
- Department of Pulmonary Diseases, Kuopio University Hospital, Kuopio, Finland
| | | | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Anne Pitkäranta
- Department of Otorhinolaryngology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Adam Platt
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Eero Punkka
- Helsinki Biobank, University of Helsinki and Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Pirkko Pussinen
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | | | | | - Deepak Rajpal
- Translational Sciences, Sanofi R&D, Framingham, MA, USA
| | - Nicole A Renaud
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Rodosthenis Rodosthenous
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Elmo Saarentaus
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Aino Salminen
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | - Eveliina Salminen
- Helsinki University Hospital, Helsinki, Finland.,Department of Clinical Genetics, HUSLAB, HUS Diagnostic Center, University of Helsinki, Helsinki, Finland
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Johanna Schleutker
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | - Raisa Serpi
- Northern Finland Biobank Borealis, University of Oulu, Northern Ostrobothnia Hospital District, Oulu, Finland
| | - Huei-Yi Shen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Richard Siegel
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Kaisa Silander
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Sanna Siltanen
- Finnish Clinical Biobank Tampere, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Sirpa Soini
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Hilkka Soininen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | | | - Ioanna Tachmazidou
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Kaisa Tasanen
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Department of Dermatology and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Pentti Tienari
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland.,Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Sanna Toppila-Salmi
- Department of Allergy, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Taru Tukiainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Abdominal Center, Endocrinology, Helsinki University Hospital, Helsinki, Finland.,Folkhalsan Research Center, Helsinki, Finland.,Research Program of Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
| | - Joni A Turunen
- Helsinki University Hospital and University of Helsinki, Helsinki, Finland.,Eye Genetics Group, Folkhälsan Research Center, Helsinki, Finland
| | - Jacob C Ulirsch
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Felix Vaura
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland.,University of Turku, Turku, Finland
| | - Petri Virolainen
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | | | | | | | - Mari Nelis
- Genomics Core Facility, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anu Reigo
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Markus Perola
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Anu Jalanko
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tarja Laitinen
- Finnish Clinical Biobank Tampere, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Tomi P Mäkelä
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | | | | | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 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
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland. .,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 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.
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11
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Angelidis G, Valotassiou V, Satra M, Psimadas D, Koutsikos J, Skoularigis J, Kollia P, Georgoulias P. Investigating the genetic characteristics of CAD: Is there a role for myocardial perfusion imaging techniques? J Nucl Cardiol 2022; 29:2909-2916. [PMID: 33141407 DOI: 10.1007/s12350-020-02403-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/02/2020] [Indexed: 01/18/2023]
Abstract
Several environmental and genetic factors have been found to influence the development and progression of coronary artery disease (CAD). Although the effects of the environmental hazards on CAD pathophysiology are well documented, the genetic architecture of the disease remains quite unclear. A number of single-nucleotide polymorphisms have been identified based on the results of the genome-wide association studies. However, there is a lack of strong evidence regarding molecular causality. The minority of the reported predisposing variants can be related to the conventional risk factors of CAD, while most of the polymorphisms occur in non-protein-coding regions of the DNA. However, independently of the specific underlying mechanisms, genetic information could lead to the identification of a population at higher genetic risk for the long-term development of CAD. Myocardial single-photon emission computed tomography (SPECT) and positron emission tomography (PET) are functional imaging techniques that can evaluate directly myocardial perfusion, and detect vascular and/or endothelial dysfunction. Therefore, these techniques could have a role in the investigation of the underlying mechanisms associated with the identified predisposing variants, advancing our understanding regarding molecular causality. In the population at higher genetic risk, myocardial SPECT or PET could provide important evidence through the early depiction of sub-clinical dysfunctions, well before any atherosclerosis marker could be identified. Notably, SPECT and PET techniques have been already used for the investigation of the functional consequences of several CAD-related polymorphisms, as well as the response to certain treatments (statins). Furthermore, therefore, in the clinical setting, the combination of genetic evidence with the findings of myocardial SPECT, or PET, functional imaging techniques could lead to more efficient screening methods and may improve decision making with regard to the diagnostic investigation and patients' management.
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Affiliation(s)
- G Angelidis
- Nuclear Medicine Laboratory, University Hospital of Larissa, University of Thessaly, Larissa, Greece.
| | - V Valotassiou
- Nuclear Medicine Laboratory, University Hospital of Larissa, University of Thessaly, Larissa, Greece
| | - M Satra
- Biology & Genetics Laboratory, University of Thessaly, Larissa, Greece
| | - D Psimadas
- Nuclear Medicine Laboratory, University Hospital of Larissa, University of Thessaly, Larissa, Greece
| | - J Koutsikos
- Department of Nuclear Medicine, 401 General Military Hospital, Athens, Greece
| | - J Skoularigis
- Department of Cardiology, University of Thessaly, Larissa, Greece
| | - P Kollia
- Department of Genetics & Biotechnology, Faculty of Biology, National & Kapodistrian University of Athens, Athens, Greece
| | - P Georgoulias
- Nuclear Medicine Laboratory, University Hospital of Larissa, University of Thessaly, Larissa, Greece
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12
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Identifying interpretable gene-biomarker associations with functionally informed kernel-based tests in 190,000 exomes. Nat Commun 2022; 13:5332. [PMID: 36088354 PMCID: PMC9464252 DOI: 10.1038/s41467-022-32864-2] [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: 01/20/2022] [Accepted: 08/22/2022] [Indexed: 12/05/2022] Open
Abstract
Here we present an exome-wide rare genetic variant association study for 30 blood biomarkers in 191,971 individuals in the UK Biobank. We compare gene-based association tests for separate functional variant categories to increase interpretability and identify 193 significant gene-biomarker associations. Genes associated with biomarkers were ~ 4.5-fold enriched for conferring Mendelian disorders. In addition to performing weighted gene-based variant collapsing tests, we design and apply variant-category-specific kernel-based tests that integrate quantitative functional variant effect predictions for missense variants, splicing and the binding of RNA-binding proteins. For these tests, we present a computationally efficient combination of the likelihood-ratio and score tests that found 36% more associations than the score test alone while also controlling the type-1 error. Kernel-based tests identified 13% more associations than their gene-based collapsing counterparts and had advantages in the presence of gain of function missense variants. We introduce local collapsing by amino acid position for missense variants and use it to interpret associations and identify potential novel gain of function variants in PIEZO1. Our results show the benefits of investigating different functional mechanisms when performing rare-variant association tests, and demonstrate pervasive rare-variant contribution to biomarker variability.
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13
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Roa-Díaz ZM, Teuscher J, Gamba M, Bundo M, Grisotto G, Wehrli F, Gamboa E, Rojas LZ, Gómez-Ochoa SA, Verhoog S, Vargas MF, Minder B, Franco OH, Dehghan A, Pazoki R, Marques-Vidal P, Muka T. Gene-diet interactions and cardiovascular diseases: a systematic review of observational and clinical trials. BMC Cardiovasc Disord 2022; 22:377. [PMID: 35987633 PMCID: PMC9392936 DOI: 10.1186/s12872-022-02808-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Both genetic background and diet are important determinants of cardiovascular diseases (CVD). Understanding gene-diet interactions could help improve CVD prevention and prognosis. We aimed to summarise the evidence on gene-diet interactions and CVD outcomes systematically. METHODS We searched MEDLINE® via Ovid, Embase, PubMed®, and The Cochrane Library for relevant studies published until June 6th 2022. We considered for inclusion cross-sectional, case-control, prospective cohort, nested case-control, and case-cohort studies as well as randomised controlled trials that evaluated the interaction between genetic variants and/or genetic risk scores and food or diet intake on the risk of related outcomes, including myocardial infarction, coronary heart disease (CHD), stroke and CVD as a composite outcome. The PROSPERO protocol registration code is CRD42019147031. RESULTS AND DISCUSSION We included 59 articles based on data from 29 studies; six articles involved multiple studies, and seven did not report details of their source population. The median sample size of the articles was 2562 participants. Of the 59 articles, 21 (35.6%) were qualified as high quality, while the rest were intermediate or poor. Eleven (18.6%) articles adjusted for multiple comparisons, four (7.0%) attempted to replicate the findings, 18 (30.5%) were based on Han-Chinese ethnicity, and 29 (49.2%) did not present Minor Allele Frequency. Fifty different dietary exposures and 52 different genetic factors were investigated, with alcohol intake and ADH1C variants being the most examined. Of 266 investigated diet-gene interaction tests, 50 (18.8%) were statistically significant, including CETP-TaqIB and ADH1C variants, which interacted with alcohol intake on CHD risk. However, interactions effects were significant only in some articles and did not agree on the direction of effects. Moreover, most of the studies that reported significant interactions lacked replication. Overall, the evidence on gene-diet interactions on CVD is limited, and lack correction for multiple testing, replication and sample size consideration.
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Affiliation(s)
- Zayne M Roa-Díaz
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland. .,Graduate School for Health Sciences, University of Bern, Bern, Switzerland.
| | - Julian Teuscher
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland
| | - Magda Gamba
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland.,Graduate School for Health Sciences, University of Bern, Bern, Switzerland
| | - Marvin Bundo
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland.,Graduate School for Health Sciences, University of Bern, Bern, Switzerland.,Oeschger Center for Climate Change Research, University of Bern, Bern, Switzerland
| | - Giorgia Grisotto
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland.,Graduate School for Health Sciences, University of Bern, Bern, Switzerland.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Faina Wehrli
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland
| | - Edna Gamboa
- School of Nutrition and Dietetics, Health Faculty, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Lyda Z Rojas
- Nursing Research and Knowledge Development Group GIDCEN, Fundación Cardiovascular de Colombia, Floridablanca, Colombia
| | - Sergio A Gómez-Ochoa
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland
| | - Sanne Verhoog
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland.,Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Beatrice Minder
- Public Health & Primary Care Library, University Library of Bern, University of Bern, Bern, Switzerland
| | - Oscar H Franco
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands.,Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Raha Pazoki
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK.,Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.,CIRTM Centre for Inflammation Research and Translational Medicine, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Pedro Marques-Vidal
- Department of Medicine, Internal Medicine, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Taulant Muka
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland
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14
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Butnariu LI, Florea L, Badescu MC, Țarcă E, Costache II, Gorduza EV. Etiologic Puzzle of Coronary Artery Disease: How Important Is Genetic Component? LIFE (BASEL, SWITZERLAND) 2022; 12:life12060865. [PMID: 35743896 PMCID: PMC9225091 DOI: 10.3390/life12060865] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 12/11/2022]
Abstract
In the modern era, coronary artery disease (CAD) has become the most common form of heart disease and, due to the severity of its clinical manifestations and its acute complications, is a major cause of morbidity and mortality worldwide. The phenotypic variability of CAD is correlated with the complex etiology, multifactorial (caused by the interaction of genetic and environmental factors) but also monogenic. The purpose of this review is to present the genetic factors involved in the etiology of CAD and their relationship to the pathogenic mechanisms of the disease. Method: we analyzed data from the literature, starting with candidate gene-based association studies, then continuing with extensive association studies such as Genome-Wide Association Studies (GWAS) and Whole Exome Sequencing (WES). The results of these studies revealed that the number of genetic factors involved in CAD etiology is impressive. The identification of new genetic factors through GWASs offers new perspectives on understanding the complex pathophysiological mechanisms that determine CAD. In conclusion, deciphering the genetic architecture of CAD by extended genomic analysis (GWAS/WES) will establish new therapeutic targets and lead to the development of new treatments. The identification of individuals at high risk for CAD using polygenic risk scores (PRS) will allow early prophylactic measures and personalized therapy to improve their prognosis.
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Affiliation(s)
- Lăcrămioara Ionela Butnariu
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iași, Romania; (L.I.B.); (E.V.G.)
| | - Laura Florea
- Department of Nefrology—Internal Medicine, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iași, Romania;
| | - Minerva Codruta Badescu
- Department of Internal Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iași, Romania
- III Internal Medicine Clinic, “St. Spiridon” County Emergency Clinical Hospital, 1 Independence Boulevard, 700111 Iași, Romania
- Correspondence: (M.C.B.); (E.Ț.)
| | - Elena Țarcă
- Department of Surgery II—Pediatric Surgery, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iași, Romania
- Correspondence: (M.C.B.); (E.Ț.)
| | - Irina-Iuliana Costache
- Department of Internal Medicine (Cardiology), “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iași, Romania;
| | - Eusebiu Vlad Gorduza
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iași, Romania; (L.I.B.); (E.V.G.)
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15
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He Y, Chen Y, Yao L, Wang J, Sha X, Wang Y. The Inflamm-Aging Model Identifies Key Risk Factors in Atherosclerosis. Front Genet 2022; 13:865827. [PMID: 35706446 PMCID: PMC9191626 DOI: 10.3389/fgene.2022.865827] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Atherosclerosis, one of the main threats to human life and health, is driven by abnormal inflammation (i.e., chronic inflammation or oxidative stress) during accelerated aging. Many studies have shown that inflamm-aging exerts a significant impact on the occurrence of atherosclerosis, particularly by inducing an immune homeostasis imbalance. However, the potential mechanism by which inflamm-aging induces atherosclerosis needs to be studied more thoroughly, and there is currently a lack of powerful prediction models.Methods: First, an improved inflamm-aging prediction model was constructed by integrating aging, inflammation, and disease markers with the help of machine learning methods; then, inflamm-aging scores were calculated. In addition, the causal relationship between aging and disease was identified using Mendelian randomization. A series of risk factors were also identified by causal analysis, sensitivity analysis, and network analysis.Results: Our results revealed an accelerated inflamm-aging pattern in atherosclerosis and suggested a causal relationship between inflamm-aging and atherosclerosis. Mechanisms involving inflammation, nutritional balance, vascular homeostasis, and oxidative stress were found to be driving factors of atherosclerosis in the context of inflamm-aging.Conclusion: In summary, we developed a model integrating crucial risk factors in inflamm-aging and atherosclerosis. Our computation pipeline could be used to explore potential mechanisms of related diseases.
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Affiliation(s)
- Yudan He
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Yao Chen
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Lilin Yao
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Junyi Wang
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Xianzheng Sha
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Yin Wang
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
- *Correspondence: Yin Wang,
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16
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Manduchi E, Le TT, Fu W, Moore JH. Genetic Analysis of Coronary Artery Disease Using Tree-Based Automated Machine Learning Informed By Biology-Based Feature Selection. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1379-1386. [PMID: 34310318 PMCID: PMC9291719 DOI: 10.1109/tcbb.2021.3099068] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Machine Learning (ML) approaches are increasingly being used in biomedical applications. Important challenges of ML include choosing the right algorithm and tuning the parameters for optimal performance. Automated ML (AutoML) methods, such as Tree-based Pipeline Optimization Tool (TPOT), have been developed to take some of the guesswork out of ML thus making this technology available to users from more diverse backgrounds. The goals of this study were to assess applicability of TPOT to genomics and to identify combinations of single nucleotide polymorphisms (SNPs) associated with coronary artery disease (CAD), with a focus on genes with high likelihood of being good CAD drug targets. We leveraged public functional genomic resources to group SNPs into biologically meaningful sets to be selected by TPOT. We applied this strategy to data from the U.K. Biobank, detecting a strikingly recurrent signal stemming from a group of 28 SNPs. Importance analysis of these SNPs uncovered functional relevance of the top SNPs to genes whose association with CAD is supported in the literature and other resources. Furthermore, we employed game-theory based metrics to study SNP contributions to individual-level TPOT predictions and discover distinct clusters of well-predicted CAD cases. The latter indicates a promising approach towards precision medicine.
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17
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Hao K, Ermel R, Sukhavasi K, Cheng H, Ma L, Li L, Amadori L, Koplev S, Franzén O, d’Escamard V, Chandel N, Wolhuter K, Bryce NS, Venkata VRM, Miller CL, Ruusalepp A, Schunkert H, Björkegren JL, Kovacic JC. Integrative Prioritization of Causal Genes for Coronary Artery Disease. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2022; 15:e003365. [PMID: 34961328 PMCID: PMC8847335 DOI: 10.1161/circgen.121.003365] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND Hundreds of candidate genes have been associated with coronary artery disease (CAD) through genome-wide association studies. However, a systematic way to understand the causal mechanism(s) of these genes, and a means to prioritize them for further study, has been lacking. This represents a major roadblock for developing novel disease- and gene-specific therapies for patients with CAD. Recently, powerful integrative genomics analyses pipelines have emerged to identify and prioritize candidate causal genes by integrating tissue/cell-specific gene expression data with genome-wide association study data sets. METHODS We aimed to develop a comprehensive integrative genomics analyses pipeline for CAD and to provide a prioritized list of causal CAD genes. To this end, we leveraged several complimentary informatics approaches to integrate summary statistics from CAD genome-wide association studies (from UK Biobank and CARDIoGRAMplusC4D) with transcriptomic and expression quantitative trait loci data from 9 cardiometabolic tissue/cell types in the STARNET study (Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task). RESULTS We identified 162 unique candidate causal CAD genes, which exerted their effect from between one and up to 7 disease-relevant tissues/cell types, including the arterial wall, blood, liver, skeletal muscle, adipose, foam cells, and macrophages. When their causal effect was ranked, the top candidate causal CAD genes were CDKN2B (associated with the 9p21.3 risk locus) and PHACTR1; both exerting their causal effect in the arterial wall. A majority of candidate causal genes were represented in cross-tissue gene regulatory co-expression networks that are involved with CAD, with 22/162 being key drivers in those networks. CONCLUSIONS We identified and prioritized candidate causal CAD genes, also localizing their tissue(s) of causal effect. These results should serve as a resource and facilitate targeted studies to identify the functional impact of top causal CAD genes.
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Affiliation(s)
- Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY,Sema4, Stamford, CT
| | - Raili Ermel
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia
| | - Katyayani Sukhavasi
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia
| | - Haoxiang Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Lijiang Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY,Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ling Li
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany,Center for Doctoral Studies in Informatics and its Applications, Dept of Informatics, Technische Universität München, Munich, Germany,Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Munich Heart Alliance, Munich, Germany
| | - Letizia Amadori
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY,Current affiliation: New York University Cardiovascular Research Center, Department of Medicine, Leon H. Charney Division of Cardiology, New York University Grossman School of Medicine, New York University Langone Health, New York, NY
| | - Simon Koplev
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Oscar Franzén
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Valentina d’Escamard
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nirupama Chandel
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kathryn Wolhuter
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia,University of New South Wales, Faculty of Medicine and Health, Sydney, Australia
| | - Nicole S. Bryce
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia,University of New South Wales, Faculty of Medicine and Health, Sydney, Australia
| | | | - Clint L. Miller
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA
| | - Arno Ruusalepp
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia,Department of Cardiology, Institute of Clinical Medicine, Tartu University
| | - Heribert Schunkert
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany,Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Munich Heart Alliance, Munich, Germany
| | - Johan L.M. Björkegren
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY,Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Jason C. Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY,Victor Chang Cardiac Research Institute, Darlinghurst, Australia,St Vincent's Clinical School, University of New South Wales, Sydney, Australia
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18
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Slenders L, Landsmeer LPL, Cui K, Depuydt MAC, Verwer M, Mekke J, Timmerman N, van den Dungen NAM, Kuiper J, de Winther MPJ, Prange KHM, Ma WF, Miller CL, Aherrahrou R, Civelek M, de Borst GJ, de Kleijn DPV, Asselbergs FW, den Ruijter HM, Boltjes A, Pasterkamp G, van der Laan SW, Mokry M. Intersecting single-cell transcriptomics and genome-wide association studies identifies crucial cell populations and candidate genes for atherosclerosis. EUROPEAN HEART JOURNAL OPEN 2022; 2:oeab043. [PMID: 35174364 PMCID: PMC8841481 DOI: 10.1093/ehjopen/oeab043] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/15/2021] [Indexed: 12/14/2022]
Abstract
Aims Genome-wide association studies (GWASs) have discovered hundreds of common genetic variants for atherosclerotic disease and cardiovascular risk factors. The translation of susceptibility loci into biological mechanisms and targets for drug discovery remains challenging. Intersecting genetic and gene expression data has led to the identification of candidate genes. However, previously studied tissues are often non-diseased and heterogeneous in cell composition, hindering accurate candidate prioritization. Therefore, we analysed single-cell transcriptomics from atherosclerotic plaques for cell-type-specific expression to identify atherosclerosis-associated candidate gene–cell pairs. Methods and results We applied gene-based analyses using GWAS summary statistics from 46 atherosclerotic and cardiovascular disease, risk factors, and other traits. We then intersected these candidates with single-cell RNA sequencing (scRNA-seq) data to identify genes specific for individual cell (sub)populations in atherosclerotic plaques. The coronary artery disease (CAD) loci demonstrated a prominent signal in plaque smooth muscle cells (SMCs) (SKI, KANK2, and SORT1) P-adj. = 0.0012, and endothelial cells (ECs) (SLC44A1, ATP2B1) P-adj. = 0.0011. Finally, we used liver-derived scRNA-seq data and showed hepatocyte-specific enrichment of genes involved in serum lipid levels. Conclusion We discovered novel and known gene–cell pairs pointing to new biological mechanisms of atherosclerotic disease. We highlight that loci associated with CAD reveal prominent association levels in mainly plaque SMC and EC populations. We present an intuitive single-cell transcriptomics-driven workflow rooted in human large-scale genetic studies to identify putative candidate genes and affected cells associated with cardiovascular traits. Collectively, our workflow allows for the identification of cell-specific targets relevant for atherosclerosis and can be universally applied to other complex genetic diseases and traits.
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Affiliation(s)
- Lotte Slenders
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Lennart P L Landsmeer
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Kai Cui
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Marie A C Depuydt
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Maarten Verwer
- Department of Vascular Surgery, University Medical Centre Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Joost Mekke
- Department of Vascular Surgery, University Medical Centre Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Nathalie Timmerman
- Department of Vascular Surgery, University Medical Centre Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Noortje A M van den Dungen
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Johan Kuiper
- Department of Medical Biochemistry, Amsterdam University Medical Centers-Location AMC, University of Amsterdam, Experimental Vascular Biology, Amsterdam Cardiovascular Sciences, Meibergdreef 9, Amsterdam, The Netherlands
| | - Menno P J de Winther
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Koen H M Prange
- Department of Medical Biochemistry, Amsterdam University Medical Centers-Location AMC, University of Amsterdam, Experimental Vascular Biology, Amsterdam Cardiovascular Sciences, Meibergdreef 9, Amsterdam, The Netherlands
| | - Wei Feng Ma
- Medical Scientist Training Program, University of Virginia, 200 Jeanette Lancaster Way, Charlottesville, VA 22908, USA.,Center for Public Health Genomics, University of Virginia, West Complex, 1335 Lee St, Charlottesville, VA 22908, USA
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, West Complex, 1335 Lee St, Charlottesville, VA 22908, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Rark Avenue, Charlottesville, VA 22908, USA.,Department of Public Health Sciences, University of Virginia, West Complex Rm 3181, Charlottesville, VA 22908, USA
| | - Redouane Aherrahrou
- Center for Public Health Genomics, University of Virginia, West Complex, 1335 Lee St, Charlottesville, VA 22908, USA
| | - Mete Civelek
- Center for Public Health Genomics, University of Virginia, West Complex, 1335 Lee St, Charlottesville, VA 22908, USA.,Department of Biomedical Engineering, University of Virginia, 415 Lane Road, Charlottesville, VA 22908, USA
| | - Gert J de Borst
- Department of Vascular Surgery, University Medical Centre Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Dominique P V de Kleijn
- Department of Vascular Surgery, University Medical Centre Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Folkert W Asselbergs
- Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, Utrecht 3508 GA, The Netherlands
| | - Hester M den Ruijter
- Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, Utrecht 3508 GA, The Netherlands
| | - Arjan Boltjes
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Gerard Pasterkamp
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands
| | - Michal Mokry
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, 3508 GA Utrecht, The Netherlands.,Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, University Utrecht, Heidelberglaan 100, Utrecht 3508 GA, The Netherlands
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19
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Wai Yeung M, Wang S, van de Vegte YJ, Borisov O, van Setten J, Snieder H, Verweij N, Said MA, van der Harst P. Twenty-Five Novel Loci for Carotid Intima-Media Thickness: A Genome-Wide Association Study in >45 000 Individuals and Meta-Analysis of >100 000 Individuals. Arterioscler Thromb Vasc Biol 2021; 42:484-501. [PMID: 34852643 PMCID: PMC8939707 DOI: 10.1161/atvbaha.121.317007] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
OBJECTIVE Carotid artery intima-media thickness (cIMT) is a widely accepted marker of subclinical atherosclerosis. Twenty susceptibility loci for cIMT were previously identified and the identification of additional susceptibility loci furthers our knowledge on the genetic architecture underlying atherosclerosis. Approach and Results: We performed 3 genome-wide association studies in 45 185 participants from the UK Biobank study who underwent cIMT measurements and had data on minimum, mean, and maximum thickness. We replicated 15 known loci and identified 20 novel loci associated with cIMT at P<5×10-8. Seven novel loci (ZNF385D, ADAMTS9, EDNRA, HAND2, MYOCD, ITCH/EDEM2/matrix metalloproteinase [MMP]24, and MRTFA) were identified in all 3 phenotypes. An additional new locus (LOXL1) was identified in the meta-analysis of the 3 phenotypes. Sex interaction analysis revealed sex differences in 7 loci including a novel locus (SYNE3) in males. Meta-analysis of UK Biobank data with a previous meta-analysis led to identification of three novel loci (APOB, FIP1L1, and LOXL4). Transcriptome-wide association analyses implicated additional genes ARHGAP42, NDRG4, and KANK2. Gene set analysis showed an enrichment in extracellular organization and the PDGF (platelet-derived growth factor) signaling pathway. We found positive genetic correlations of cIMT with coronary artery disease rg=0.21 (P=1.4×10-7), peripheral artery disease rg=0.45 (P=5.3×10-5), and systolic blood pressure rg=0.30 (P=4.0×10-18). A negative genetic correlation between average of maximum cIMT and high-density lipoprotein was found rg=-0.12 (P=7.0×10-4). CONCLUSIONS Genome-wide association meta-analyses in >100 000 individuals identified 25 novel loci associated with cIMT providing insights into genes and tissue-specific regulatory mechanisms of proatherosclerotic processes. We found evidence for shared biological mechanisms with cardiovascular diseases.
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Affiliation(s)
- Ming Wai Yeung
- Department of Cardiology, University of Groningen, University Medical Center Groningen, the Netherlands. (M.W.Y., S.W., Y.J.v.d.V., N.V., M.A.S., P.v.d.H.)
| | - Siqi Wang
- Department of Cardiology, University of Groningen, University Medical Center Groningen, the Netherlands. (M.W.Y., S.W., Y.J.v.d.V., N.V., M.A.S., P.v.d.H.).,Department of Epidemiology, University of Groningen, University Medical Center Groningen, the Netherlands. (S.W., H.S.)
| | - Yordi J van de Vegte
- Department of Cardiology, University of Groningen, University Medical Center Groningen, the Netherlands. (M.W.Y., S.W., Y.J.v.d.V., N.V., M.A.S., P.v.d.H.)
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Germany (O.B.)
| | - Jessica van Setten
- Division of Heart & Lungs, Department of Cardiology, University Medical Center Utrecht, University of Utrecht, the Netherlands (M.W.Y., J.v.S., P.v.d.H.)
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, the Netherlands. (S.W., H.S.)
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, the Netherlands. (M.W.Y., S.W., Y.J.v.d.V., N.V., M.A.S., P.v.d.H.)
| | - M Abdullah Said
- Department of Cardiology, University of Groningen, University Medical Center Groningen, the Netherlands. (M.W.Y., S.W., Y.J.v.d.V., N.V., M.A.S., P.v.d.H.).,Division of Heart & Lungs, Department of Cardiology, University Medical Center Utrecht, University of Utrecht, the Netherlands (M.W.Y., J.v.S., P.v.d.H.)
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, the Netherlands. (M.W.Y., S.W., Y.J.v.d.V., N.V., M.A.S., P.v.d.H.).,Division of Heart & Lungs, Department of Cardiology, University Medical Center Utrecht, University of Utrecht, the Netherlands (M.W.Y., J.v.S., P.v.d.H.)
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20
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Zorkoltseva I, Shadrina A, Belonogova N, Kirichenko A, Tsepilov Y, Axenovich T. In silico genome-wide gene-based association analysis reveals new genes predisposing to coronary artery disease. Clin Genet 2021; 101:78-86. [PMID: 34687547 DOI: 10.1111/cge.14073] [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: 07/19/2021] [Revised: 09/29/2021] [Accepted: 10/13/2021] [Indexed: 11/30/2022]
Abstract
Genome-wide association study (GWAS) have identified more than 300 single nucleotide polymorphisms at 163 independent loci associated with coronary artery disease (CAD). However, there is no full understanding about the causal genes for CAD and the mechanisms of their action. We aimed to perform a post GWAS analysis to identify genes whose polymorphism may influence the risk of CAD. Using the UK Biobank GWAS summary statistics, we performed a gene-based association analysis. We found 63 genes significantly associated with CAD due to their within-gene polymorphisms. Many of these genes are well known. Some known CAD genes such as FURIN and SORT1 did not show the gene-based association because their variants had low GWAS signals or gene-based association was inflated by the strong GWAS signal outside the gene. For several known CAD genes, we demonstrated that their effects could be explained not only or not at all by their own variants but by the variants within the neighboring genes controlling their expression. Using several bioinformatics techniques, we suggested potential mechanisms underlying gene-CAD associations. Three genes, CDK19, NCALD, and ARHGEF12 were not previously associated with CAD. The role of these genes should be clarified in further studies.
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Affiliation(s)
- Irina Zorkoltseva
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Alexandra Shadrina
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Nadezhda Belonogova
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Anatoly Kirichenko
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Yakov Tsepilov
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Tatiana Axenovich
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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21
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Mapping gene and gene pathways associated with coronary artery disease: a CARDIoGRAM exome and multi-ancestry UK biobank analysis. Sci Rep 2021; 11:16461. [PMID: 34385509 PMCID: PMC8361107 DOI: 10.1038/s41598-021-95637-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 07/28/2021] [Indexed: 02/07/2023] Open
Abstract
Coronary artery disease (CAD) genome-wide association studies typically focus on single nucleotide variants (SNVs), and many potentially associated SNVs fail to reach the GWAS significance threshold. We performed gene and pathway-based association (GBA) tests on publicly available Coronary ARtery DIsease Genome wide Replication and Meta-analysis consortium Exome (n = 120,575) and multi ancestry pan UK Biobank study (n = 442,574) summary data using versatile gene-based association study (VEGAS2) and Multi-marker analysis of genomic annotation (MAGMA) to identify novel genes and pathways associated with CAD. We included only exonic SNVs and excluded regulatory regions. VEGAS2 and MAGMA ranked genes and pathways based on aggregated SNV test statistics. We used Bonferroni corrected gene and pathway significance threshold at 3.0 × 10-6 and 1.0 × 10-5, respectively. We also report the top one percent of ranked genes and pathways. We identified 17 top enriched genes with four genes (PCSK9, FAM177, LPL, ARGEF26), reaching statistical significance (p ≤ 3.0 × 10-6) using both GBA tests in two GWAS studies. In addition, our analyses identified ten genes (DUSP13, KCNJ11, CD300LF/RAB37, SLCO1B1, LRRFIP1, QSER1, UBR2, MOB3C, MST1R, and ABCC8) with previously unreported associations with CAD, although none of the single SNV associations within the genes were genome-wide significant. Among the top 1% non-lipid pathways, we detected pathways regulating coagulation, inflammation, neuronal aging, and wound healing.
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22
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Shashkova TI, Gorev DD, Pakhomov ED, Shadrina AS, Sharapov SZ, Tsepilov YA, Karssen LC, Aulchenko YS. The GWAS-MAP platform for aggregation of results of genome-wide association studies and the GWAS-MAP|homo database of 70 billion genetic associations of human traits. Vavilovskii Zhurnal Genet Selektsii 2020; 24:876-884. [PMID: 35088001 PMCID: PMC8763720 DOI: 10.18699/vj20.686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 11/23/2022] Open
Abstract
Hundreds of genome-wide association studies (GWAS) of human traits are performed each year. The
results of GWAS are often published in the form of summary statistics. Information from summary statistics can
be used for multiple purposes – from fundamental research in biology and genetics to the search for potential
biomarkers and therapeutic targets. While the amount of GWAS summary statistics collected by the scientific community is rapidly increasing, the use of this data is limited by the lack of generally accepted standards. In particular,
the researchers who would like to use GWAS summary statistics in their studies have to become aware that the data
are scattered across multiple websites, are presented in a variety of formats, and, often, were not quality controlled.
Moreover, each available summary statistics analysis tools will ask for data to be presented in their own internal
format. To address these issues, we developed GWAS-MAP, a high-throughput platform for aggregating, storing,
analyzing, visualizing and providing access to a database of big data that result from region- and genome-wide
association studies. The database currently contains information on more than 70 billion associations between
genetic variants and human diseases, quantitative traits, and “omics” traits. The GWAS-MAP platform and database
can be used for studying the etiology of human diseases, building predictive risk models and finding potential biomarkers and therapeutic interventions. In order to demonstrate a typical application of the platform as an approach
for extracting new biological knowledge and establishing mechanistic hypotheses, we analyzed varicose veins, a
disease affecting on average every third adult in Russia. The results of analysis confirmed known epidemiologic associations for this disease and led us to propose a hypothesis that increased levels of MICB and CD209 proteins in
human plasma may increase susceptibility to varicose veins.
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Affiliation(s)
- T. I. Shashkova
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University
| | - D. D. Gorev
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University
| | - E. D. Pakhomov
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University;
PolyKnomics BV
| | - A. S. Shadrina
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University
| | - S. Zh. Sharapov
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University
| | - Y. A. Tsepilov
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University
| | | | - Y. S. Aulchenko
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University
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