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Singh H, Shyamveer, Jori C, Mahajan SD, Aalinkeel R, Kaliyappan K, Bhattacharya M, Parvez MK, Al-Dosari MS. Role of APOC3 3238C/G, APOB 12669G/A and SCARB1 1050C/T polymorphisms, their expression in patients of HIV-associated lipodystrophy. Heliyon 2024; 10:e30519. [PMID: 38742060 PMCID: PMC11089352 DOI: 10.1016/j.heliyon.2024.e30519] [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: 03/13/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
Apolipoproteins and Scavenger Receptor Class B1 (SCARB1) proteins are involved in the etiology of HIV-associated lipodystrophy (HIVLD). APOC3 3238C/G, APOB 12669G/A and SCARB1 1050C/T polymorphisms were linked with increased level of APOB, TG, HDL-C and risk of cardiovascular diseases (CVDs). Hence, we evaluated the genetic variations of APOC3 3238C/G, APOB 12669G/A and SCARB1 1050C/T in 187 patients of HIV (64 with HIVLD, 123 without HIVLD) and 139 healthy controls using PCR-RFLP and expression by qPCR. The genotypes of SCARB1 1050 TT and APOB 12669AA showed a risk to severe HIVLD (P = 0.23, OR = 4.95; P = 0.16, OR = 2.02). The APOC3 3238 GG genotype was associated with a lesser risk of severe HIVLD (P = 0.07, OR = 0.22). The APOB 12669 GA genotype was associated with a greater risk of HIVLD severity in patients with impaired LDL, triglyceride (TG), and cholesterol levels (P = 0.34, OR = 4.13; P = 0.25, OR = 3.64; P = 0.26, OR = 5.47). Similarly, APOB 12669AA genotypes in the presence of impaired triglyceride levels displayed the susceptibility to severity of HIVLD (P = 0.77, OR = 2.91). APOB 12669 GA genotype along with impaired HDL and cholesterol levels indicated an increased risk for HIVLD acquisition among patients without HIVLD (P = 0.42, OR = 2.42; P = 0.26, OR = 2.27). In patients with and without HIVLD, APOC3 3238CG genotypes having impaired cholesterol and glucose levels had higher risk for severity and development of HIVLD (P = 0.13, OR = 2.84, P = 0.34, OR = 1.58; P = 0.71, OR = 1.86; P = 0.14, OR = 2.30). An increased expression of APOB and SCARB1 genes were observed in patients with HIVLD (+0.51 vs. -0.93; +4.78 vs. +3.29), and decreased expression of APOC3 gene was observed in patients with HIVLD (-0.35 vs. -1.65). In conclusion, the polymorphisms mentioned above were not associated with the modulation of HIVLD. However, in the presence of impaired triglyceride, HDL, cholesterol and glucose levels, APOB 12669AA and 12669 GA, APOC3 3238CG genotypes indicated a risk for the development and severity of HIVLD.
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Affiliation(s)
- HariOm Singh
- Department of Molecular Biology, National AIDS Research Institute, Pune, 411026, India
| | - Shyamveer
- Department of Molecular Biology, National AIDS Research Institute, Pune, 411026, India
| | - Chandrashekhar Jori
- Department of Molecular Biology, National AIDS Research Institute, Pune, 411026, India
| | - Supriya D. Mahajan
- Department of Medicine, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo's Clinical Translational Research Center, 875 Ellicott Street, Buffalo, NY14203, USA
| | - Ravikumar Aalinkeel
- Department of Medicine, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo's Clinical Translational Research Center, 875 Ellicott Street, Buffalo, NY14203, USA
| | - Kathiravan Kaliyappan
- Department of Medicine, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo's Clinical Translational Research Center, 875 Ellicott Street, Buffalo, NY14203, USA
| | - Meenakshi Bhattacharya
- Department of Medicine, ART PLUS CENTRE, OPD-136, Government Medical College & Hospital, University Road, Aurangabad, 431004, India
| | - Mohammad Khalid Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mohammed S. Al-Dosari
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
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Landfors F, Henneman P, Chorell E, Nilsson SK, Kersten S. Drug-target Mendelian randomization analysis supports lowering plasma ANGPTL3, ANGPTL4, and APOC3 levels as strategies for reducing cardiovascular disease risk. EUROPEAN HEART JOURNAL OPEN 2024; 4:oeae035. [PMID: 38895109 PMCID: PMC11182694 DOI: 10.1093/ehjopen/oeae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/30/2024] [Accepted: 04/26/2024] [Indexed: 06/21/2024]
Abstract
Aims APOC3, ANGPTL3, and ANGPTL4 are circulating proteins that are actively pursued as pharmacological targets to treat dyslipidaemia and reduce the risk of atherosclerotic cardiovascular disease. Here, we used human genetic data to compare the predicted therapeutic and adverse effects of APOC3, ANGPTL3, and ANGPTL4 inactivation. Methods and results We conducted drug-target Mendelian randomization analyses using variants in proximity to the genes associated with circulating protein levels to compare APOC3, ANGPTL3, and ANGPTL4 as drug targets. We obtained exposure and outcome data from large-scale genome-wide association studies and used generalized least squares to correct for linkage disequilibrium-related correlation. We evaluated five primary cardiometabolic endpoints and screened for potential side effects across 694 disease-related endpoints, 43 clinical laboratory tests, and 11 internal organ MRI measurements. Genetically lowering circulating ANGPTL4 levels reduced the odds of coronary artery disease (CAD) [odds ratio, 0.57 per s.d. protein (95% CI 0.47-0.70)] and Type 2 diabetes (T2D) [odds ratio, 0.73 per s.d. protein (95% CI 0.57-0.94)]. Genetically lowering circulating APOC3 levels also reduced the odds of CAD [odds ratio, 0.90 per s.d. protein (95% CI 0.82-0.99)]. Genetically lowered ANGPTL3 levels via common variants were not associated with CAD. However, meta-analysis of protein-truncating variants revealed that ANGPTL3 inactivation protected against CAD (odds ratio, 0.71 per allele [95%CI, 0.58-0.85]). Analysis of lowered ANGPTL3, ANGPTL4, and APOC3 levels did not identify important safety concerns. Conclusion Human genetic evidence suggests that therapies aimed at reducing circulating levels of ANGPTL3, ANGPTL4, and APOC3 reduce the risk of CAD. ANGPTL4 lowering may also reduce the risk of T2D.
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Affiliation(s)
- Fredrik Landfors
- Department of Public Health and Clinical Medicine, Section of Medicine, Umeå University, B41, Norrlands universitetssjukhus, S-901 87 Umeå, Sweden
- Lipigon Pharmaceuticals AB, Tvistevägen 48C, S-907 36 Umeå, Sweden
| | - Peter Henneman
- Department of Human Genetics, Amsterdam University Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Elin Chorell
- Department of Public Health and Clinical Medicine, Section of Medicine, Umeå University, B41, Norrlands universitetssjukhus, S-901 87 Umeå, Sweden
| | - Stefan K Nilsson
- Lipigon Pharmaceuticals AB, Tvistevägen 48C, S-907 36 Umeå, Sweden
- Department of Medical Biosciences, Umeå University, B41, Norrlands universitetssjukhus, S-901 87 Umeå, Sweden
| | - Sander Kersten
- Nutrition, Metabolism, and Genomics group, Division of Human Nutrition and Health, Wageningen University, 6708WE Wageningen, the Netherlands
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
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Snaebjarnarson AS, Helgadottir A, Arnadottir GA, Ivarsdottir EV, Thorleifsson G, Ferkingstad E, Einarsson G, Sveinbjornsson G, Thorgeirsson TE, Ulfarsson MO, Halldorsson BV, Olafsson I, Erikstrup C, Pedersen OB, Nyegaard M, Bruun MT, Ullum H, Brunak S, Iversen KK, Christensen AH, Olesen MS, Ghouse J, Banasik K, Knowlton KU, Arnar DO, Thorgeirsson G, Nadauld L, Ostrowski SR, Bundgaard H, Holm H, Sulem P, Stefansson K, Gudbjartsson DF. Complex effects of sequence variants on lipid levels and coronary artery disease. Cell 2023; 186:4085-4099.e15. [PMID: 37714134 DOI: 10.1016/j.cell.2023.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/06/2023] [Accepted: 08/10/2023] [Indexed: 09/17/2023]
Abstract
Many sequence variants have additive effects on blood lipid levels and, through that, on the risk of coronary artery disease (CAD). We show that variants also have non-additive effects and interact to affect lipid levels as well as affecting variance and correlations. Variance and correlation effects are often signatures of epistasis or gene-environmental interactions. These complex effects can translate into CAD risk. For example, Trp154Ter in FUT2 protects against CAD among subjects with the A1 blood group, whereas it associates with greater risk of CAD in others. His48Arg in ADH1B interacts with alcohol consumption to affect lipid levels and CAD. The effect of variants in TM6SF2 on blood lipids is greatest among those who never eat oily fish but absent from those who often do. This work demonstrates that variants that affect variance of quantitative traits can allow for the discovery of epistasis and interactions of variants with the environment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Magnus O Ulfarsson
- deCODE genetics/Amgen, Inc., Reykjavik 102, Iceland; Faculty of Electrical and Computer Engineering, University of Iceland, Reykjavik 102, Iceland
| | | | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali - National University Hospital of Iceland, Hringbraut, Reykjavik 101, Iceland
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus 8200, Denmark; Department of Clinical Medicine, Health, Aarhus University, Aarhus 8200, Denmark
| | - Ole B Pedersen
- Department of Clinical Immunology, Zealand University Hospital, Køge 4600, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen 1165, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Faculty of Medicine, Aalborg University, Aalborg 9220, Denmark
| | - Mie T Bruun
- Department of Clinical Immunology, Odense University Hospital, Odense 5000, Denmark
| | - Henrik Ullum
- Statens Serum Institut, Copenhagen 2300, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Kasper Karmark Iversen
- Department of Clinical Medicine, University of Copenhagen, Copenhagen 1165, Denmark; Department of Emergency Medicine, Copenhagen University Hospital Herlev and Gentofte, Herlev 2900, Denmark; Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte Hospital, Herlev 2900, Denmark
| | - Alex Hoerby Christensen
- Department of Clinical Medicine, University of Copenhagen, Copenhagen 1165, Denmark; Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte Hospital, Herlev 2900, Denmark
| | - Morten S Olesen
- Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen 2100, Denmark; Laboratory for Molecular Cardiology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Jonas Ghouse
- Laboratory for Molecular Cardiology, Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen 2100, Denmark; Laboratory for Molecular Cardiology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Kirk U Knowlton
- Intermountain Medical Center, Intermountain Heart Institute, Salt Lake City, UT 84143, USA
| | - David O Arnar
- deCODE genetics/Amgen, Inc., Reykjavik 102, Iceland; Faculty of Medicine, University of Iceland, Vatnsmyrarvegur, Reykjavik 101, Iceland; Division of Cardiology, Department of Internal Medicine, Landspitali - National University Hospital of Iceland, Hringbraut, Reykjavik 101, Iceland
| | - Gudmundur Thorgeirsson
- deCODE genetics/Amgen, Inc., Reykjavik 102, Iceland; Faculty of Medicine, University of Iceland, Vatnsmyrarvegur, Reykjavik 101, Iceland; Division of Cardiology, Department of Internal Medicine, Landspitali - National University Hospital of Iceland, Hringbraut, Reykjavik 101, Iceland
| | - Lincoln Nadauld
- Precision Genomics, Intermountain Healthcare, Saint George, UT 84790, USA
| | - Sisse Rye Ostrowski
- Department of Clinical Medicine, University of Copenhagen, Copenhagen 1165, Denmark; Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen 2100, Denmark
| | - Henning Bundgaard
- Department of Clinical Medicine, University of Copenhagen, Copenhagen 1165, Denmark; Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | - Hilma Holm
- deCODE genetics/Amgen, Inc., Reykjavik 102, Iceland
| | | | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Reykjavik 102, Iceland; Faculty of Medicine, University of Iceland, Vatnsmyrarvegur, Reykjavik 101, Iceland.
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Reykjavik 102, Iceland; School of Engineering and Natural Sciences, University of Iceland, Reykjavik 102, Iceland.
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Butnariu LI, Gorduza EV, Țarcă E, Pânzaru MC, Popa S, Stoleriu S, Lupu VV, Lupu A, Cojocaru E, Trandafir LM, Moisă ȘM, Florea A, Stătescu L, Bădescu MC. Current Data and New Insights into the Genetic Factors of Atherogenic Dyslipidemia Associated with Metabolic Syndrome. Diagnostics (Basel) 2023; 13:2348. [PMID: 37510094 PMCID: PMC10378477 DOI: 10.3390/diagnostics13142348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Atherogenic dyslipidemia plays a critical role in the development of metabolic syndrome (MetS), being one of its major components, along with central obesity, insulin resistance, and hypertension. In recent years, the development of molecular genetics techniques and extended analysis at the genome or exome level has led to important progress in the identification of genetic factors (heritability) involved in lipid metabolism disorders associated with MetS. In this review, we have proposed to present the current knowledge related to the genetic etiology of atherogenic dyslipidemia, but also possible challenges for future studies. Data from the literature provided by candidate gene-based association studies or extended studies, such as genome-wide association studies (GWAS) and whole exome sequencing (WES,) have revealed that atherogenic dyslipidemia presents a marked genetic heterogeneity (monogenic or complex, multifactorial). Despite sustained efforts, many of the genetic factors still remain unidentified (missing heritability). In the future, the identification of new genes and the molecular mechanisms by which they intervene in lipid disorders will allow the development of innovative therapies that act on specific targets. In addition, the use of polygenic risk scores (PRS) or specific biomarkers to identify individuals at increased risk of atherogenic dyslipidemia and/or other components of MetS will allow effective preventive measures and personalized therapy.
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Affiliation(s)
- Lăcramioara Ionela Butnariu
- Department of Medical Genetics, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Eusebiu Vlad Gorduza
- Department of Medical Genetics, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Elena Țarcă
- Department of Surgery II-Pediatric Surgery, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Monica-Cristina Pânzaru
- Department of Medical Genetics, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Setalia Popa
- Department of Medical Genetics, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Simona Stoleriu
- Odontology-Periodontology, Fixed Prosthesis Department, Faculty of Dental Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Vasile Valeriu Lupu
- Department of Pediatrics, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Ancuta Lupu
- Department of Pediatrics, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Elena Cojocaru
- Department of Morphofunctional Sciences I, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Laura Mihaela Trandafir
- Department of Pediatrics, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Ștefana Maria Moisă
- Department of Pediatrics, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Andreea Florea
- Department of Medical Genetics, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Laura Stătescu
- Medical III Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Minerva Codruța Bădescu
- III Internal Medicine Clinic, "St. Spiridon" County Emergency Clinical Hospital, 1 Independence Boulevard, 700111 Iasi, Romania
- Department of Internal Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
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Walker-Smith T, Joyce K, Maishman R, Smartt H, Hopkins E, Brierley R, Reeves BC, Rogers CA, Angelini GD, Culliford L. Outcome Monitoring After Cardiac Surgery (OMACS): a single-centre prospective cohort study of cardiac surgery patients. BMJ Open 2022; 12:e063268. [PMID: 36535713 PMCID: PMC9764648 DOI: 10.1136/bmjopen-2022-063268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION More than 30 000 cardiac surgery procedures are performed in the UK each year, however, postoperative complications and long-term failure of interventions are common, leading to repeated surgeries. This represents a significant burden on the patient and health service.Routinely, patients are discharged to their general practitioner 6 weeks postoperatively and research studies typically only report short-term outcomes up to 1 year after surgery, together this makes long-term outcomes of cardiac surgery difficult to monitor. Further, traditional research methods have yet to advance understanding of what causes early complications and why surgical interventions fail. METHODS AND ANALYSIS This prospective cohort study will characterise participants undergoing cardiac surgery at baseline, describe short-term, medium-term and long-term health outcomes postoperatively and collect tissue samples.All eligible adult patients undergoing cardiac surgery at the Bristol Heart Institute, UK will be approached for consent. Recruitment is expected to continue for up to 10 years resulting in the largest cohort of cardiac patients reported to date. Blood, urine and waste tissue samples will be collected during admission. Samples, along with anonymised data, will be used to investigate outcomes and inform predictive models of complications associated with cardiac surgery.Data about the surgical admission will be obtained from hospital databases and medical notes. Participants may be monitored up to 5 years postoperatively using data obtained from NHS digital. Participants will complete health questionnaires 3 months and 12 months postoperatively.The analysis of data and tissue samples to address specific research questions will require separate research protocols and ethical approval. ETHICS AND DISSEMINATION This study was approved by the East Midlands Nottingham 2 Research Ethics Committee.Findings will be disseminated through peer-reviewed publications and presentation at national and international meetings. Participants will be informed of results in annual newsletters. TRIAL REGISTRATION NUMBER ISRCTN90204321.
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Affiliation(s)
- Terrie Walker-Smith
- Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, UK, University of Bristol, Bristol, UK
| | - Katherine Joyce
- Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, UK, University of Bristol, Bristol, UK
| | - Rachel Maishman
- Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, UK, University of Bristol, Bristol, UK
| | - Helena Smartt
- Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, UK, University of Bristol, Bristol, UK
| | - Emma Hopkins
- Bristol Heart Institute, Univerisity of Bristol, Bristol, UK
| | - Rachel Brierley
- Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, UK, University of Bristol, Bristol, UK
| | - Barnaby C Reeves
- Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, UK, University of Bristol, Bristol, UK
| | - Chris A Rogers
- Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, UK, University of Bristol, Bristol, UK
| | | | - Lucy Culliford
- Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, UK, University of Bristol, Bristol, UK
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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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Peng L, Jing J, He S, Wang J, Gao X, Wang T. The role of lipid traits in mediating the effect of body mass index on serum urate. Front Endocrinol (Lausanne) 2022; 13:938891. [PMID: 36213277 PMCID: PMC9539818 DOI: 10.3389/fendo.2022.938891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/05/2022] [Indexed: 12/05/2022] Open
Abstract
OBJECTIVE To explore whether total cholesterol (TC), high-density lipoprotein (HDL), low-density lipoprotein (LDL), and triglyceride (TG) are mediators in the pathway of body mass index (BMI) on serum urate and determine the proportion of the mediation effect. METHODS This study used observational and two-sample Mendelian randomization (MR) analyses to explore the mediation effects of TC, HDL, LDL, and TG in the pathway of BMI on serum urate. We determined the size and the extent to which these lipids mediate any effect of BMI on serum urate. RESULTS Observational analysis results showed that HDL and TG can partially explain the association of BMI on serum urate, and the proportion of mediation effect was 10.2% and 8.9%, respectively. MR results demonstrated that TG has a causal effect on serum urate (β = 0.22, 95% CI: 0.15, 0.29; p = 2.28×10-10.) and its proportion of mediation effect was 14.1%. TC, HDL, and LDL are not the mediators in the pathway of BMI on serum urate in MR estimates. CONCLUSION To a certain extent, TG mediates the effect of BMI on serum urate, and the risk of gout may be reduced by controlling both BMI and TG.
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CRISPR/Cas9-mediated knockout of APOC3 stabilizes plasma lipids and inhibits atherosclerosis in rabbits. Lipids Health Dis 2021; 20:180. [PMID: 34922545 PMCID: PMC8684289 DOI: 10.1186/s12944-021-01605-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/26/2021] [Indexed: 01/14/2023] Open
Abstract
Background High levels of apolipoprotein C3 (APOC3) can lead to hypertriglyceridemia, which increases the risk of cardiovascular disease. We aim to create APOC3-knockout (KO) rabbits and explore the effects of APOC3 deletion on the occurrence and development of atherosclerosis. Methods An sgRNA anchored to exon 2 of APOC3 was designed to edit embryo genomes using the CRISPR/Cas9 system. The founder rabbits were sequenced, and their lipid profile, inflammatory cytokines, and atherosclerotic plaques were analyzed. Results When given a normal chow (NC) diet, all APOC3-KO rabbits had 50% lower triglyceride (TG) levels than those of the matched age control group. Additionally, their plasma lipoprotein lipase increased. When fed a high-fat diet, APOC3 deficiency was observed to be more conducive to the maintenance of plasma TG, total cholesterol, and low-density lipoprotein cholesterol levels, and the inhibition of the inflammatory response and the protection against atherosclerosis in rabbits. Conclusion APOC3 deficiency can delay the formation of atherosclerosis-induced HFD in rabbits, indicating this is a novel therapeutic target to treat atherosclerosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12944-021-01605-7.
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Liu G, Lai P, Guo J, Wang Y, Xian X. Genetically-engineered hamster models: applications and perspective in dyslipidemia and atherosclerosis-related cardiovascular disease. MEDICAL REVIEW (BERLIN, GERMANY) 2021; 1:92-110. [PMID: 37724074 PMCID: PMC10388752 DOI: 10.1515/mr-2021-0004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/03/2021] [Indexed: 09/20/2023]
Abstract
Cardiovascular disease is the leading cause of morbidity and mortality in both developed and developing countries, in which atherosclerosis triggered by dyslipidemia is the major pathological basis. Over the past 40 years, small rodent animals, such as mice, have been widely used for understanding of human atherosclerosis-related cardiovascular disease (ASCVD) with the advantages of low cost and ease of maintenance and manipulation. However, based on the concept of precision medicine and high demand of translational research, the applications of mouse models for human ASCVD study would be limited due to the natural differences in metabolic features between mice and humans even though they are still the most powerful tools in this research field, indicating that other species with biological similarity to humans need to be considered for studying ASCVD in future. With the development and breakthrough of novel gene editing technology, Syrian golden hamster, a small rodent animal replicating the metabolic characteristics of humans, has been genetically modified, suggesting that gene-targeted hamster models will provide new insights into the precision medicine and translational research of ASCVD. The purpose of this review was to summarize the genetically-modified hamster models with dyslipidemia to date, and their potential applications and perspective for ASCVD.
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Affiliation(s)
- George Liu
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, School of Basic Medical Sciences, Peking University 38 Xueyuan Road, Beijing 100191, China
| | - Pingping Lai
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, School of Basic Medical Sciences, Peking University 38 Xueyuan Road, Beijing 100191, China
| | - Jiabao Guo
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, School of Basic Medical Sciences, Peking University 38 Xueyuan Road, Beijing 100191, China
| | - Yuhui Wang
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, School of Basic Medical Sciences, Peking University 38 Xueyuan Road, Beijing 100191, China
| | - Xunde Xian
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, School of Basic Medical Sciences, Peking University 38 Xueyuan Road, Beijing 100191, China
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10
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Wang H, Huang X, Xu P, Liu X, Zhou Z, Wang F, Li J, Wang Y, Xian X, Liu G, Huang W. Apolipoprotein C3 aggravates diabetic nephropathy in type 1 diabetes by activating the renal TLR2/NF-κB pathway. Metabolism 2021; 119:154740. [PMID: 33639183 DOI: 10.1016/j.metabol.2021.154740] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 01/09/2023]
Abstract
OBJECTIVE Apolipoprotein C3 (ApoC3) is a regulator of triglyceride metabolism and inflammation, and its plasma levels are positively correlated with the progression of diabetic nephropathy (DN) in patients. However, the role and underlying mechanism of ApoC3 in DN remain unclear. METHODS Diabetes was induced in ApoC3 transgenic (Tg) and knockout (KO) mice by injection of streptozotocin. We studied the effect of ApoC3 on type 1 DN after 4 months of diabetes. Plasma glucose and lipid levels, renal function parameters and inflammation- and fibrogenesis-related gene and protein expression levels were studied. In vitro, human mesangial cells (HMCs) were incubated with high levels of glucose or/and triglyceride-rich lipoproteins (TRLs) with a high or low ApoC3 content isolated from Tg or wild-type (WT) mice, respectively, to explore the mechanisms of ApoC3 on development of DN. RESULTS We found that compared to WT mice, Tg mice exhibited hypertriglyceridemia (HTG), aggravated early renal function injury and inflammation, enlarged glomerular and mesangial surface areas, renal lipid deposition and elevated fibrogenesis-related gene expression levels after 4 months of diabetes. ApoC3 overexpression activated the renal Toll-like receptor 2 (TLR2) and nuclear factor-κB (NF-κB) signaling pathways and increased the renal gene and protein expression levels of the downstream inflammatory factors TNF-α, VCAM-1 and MCP-1. Unfortunately, we did not find that ApoC3 deficiency had an obvious protective effect against DN. In vitro, we found that TRLs with a high ApoC3 content increased the gene and protein expression levels of inflammation- and fibrogenesis-related factors in HMCs compared to those following administration of the same concentration of TRLs with a low ApoC3 content. These effects of ApoC3 were inhibited by blockade of TLR2 or NF-κB. CONCLUSIONS These findings suggest that ApoC3 aggravates early-stage DN by activating the renal TLR2/NF-κB pathway which is partially independent of HTG.
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MESH Headings
- Animals
- Apolipoprotein C-III/genetics
- Apolipoprotein C-III/physiology
- Cells, Cultured
- Diabetes Mellitus, Experimental/chemically induced
- Diabetes Mellitus, Experimental/genetics
- Diabetes Mellitus, Experimental/metabolism
- Diabetes Mellitus, Type 1/complications
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 1/metabolism
- Diabetic Nephropathies/genetics
- Diabetic Nephropathies/metabolism
- Diabetic Nephropathies/pathology
- Disease Progression
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Transgenic
- NF-kappa B/metabolism
- Signal Transduction/genetics
- Streptozocin
- Toll-Like Receptor 2/metabolism
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Affiliation(s)
- Huan Wang
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; Experimental and Translational Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Xiaomin Huang
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Pengfei Xu
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xuejing Liu
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Zihao Zhou
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Fuhua Wang
- Department of Critical Care Medicine, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Jingyi Li
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yuhui Wang
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xunde Xian
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - George Liu
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Wei Huang
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
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11
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Shou W, Zhang C, Shi J, Wu H, Huang W. Fine genetic mapping of the chromosome 11q23.3 region in a Han Chinese population: insights into the apolipoprotein genes underlying the blood lipid-lipoprotein variances. J Genet Genomics 2020; 47:756-769. [PMID: 33753020 DOI: 10.1016/j.jgg.2020.11.010] [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: 07/03/2020] [Revised: 11/09/2020] [Accepted: 11/20/2020] [Indexed: 12/01/2022]
Abstract
The unusual chromosome 11q23.3 harboring the apolipoprotein (APO) gene cluster has been well documented for its essential roles in plasma lipid-related traits and atherosclerotic cardiovascular diseases. However, its genetic architecture and the potential biological mechanisms underlying complex phenotypes have not been well assessed. We conducted a study for this target region in a Han Chinese population through a stepwise forward framework based on massive parallel sequencing, association analyses, genetic fine mapping, and functional interpretation. The present study identified new meaningful genetic associations that were not simply determined by statistical significance. In addition to the APOA5 gene, we found robust evidence of the genetic commitments of APOC3 and APOA1 to blood lipids. Several variants with high confidence were prioritized along with the potential biological mechanism interpretations in the wake of adaptive fine-mapping analyses. rs2849174 in the APOC3 enhancer was discovered with an unrivaled posterior probability of causality for triglyceride levels and could mediate APOC3 expression through enhancer activity modulated by a combination of histone modifications and transcription factor accessibility. Similarly, multiple lines of evidence converged in favor of rs3741297 as a causal variant influencing high-density lipoprotein cholesterol. Our findings provided novel insights into this genomic locus in the Chinese population.
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Affiliation(s)
- Weihua Shou
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and Shanghai Academy of Science and Technology, Shanghai 200025, China.
| | - Chenhui Zhang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and Shanghai Academy of Science and Technology, Shanghai 200025, China
| | - Jinxiu Shi
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and Shanghai Academy of Science and Technology, Shanghai 200025, China
| | - Hong Wu
- Department of Cardiology, Changhai Hospital, The Second Military Medical University, Shanghai 200433, China
| | - Wei Huang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and Shanghai Academy of Science and Technology, Shanghai 200025, China.
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12
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D'Erasmo L, Di Costanzo A, Gallo A, Bruckert E, Arca M. ApoCIII: A multifaceted protein in cardiometabolic disease. Metabolism 2020; 113:154395. [PMID: 33058850 DOI: 10.1016/j.metabol.2020.154395] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 09/20/2020] [Accepted: 09/26/2020] [Indexed: 01/15/2023]
Abstract
ApoCIII has a well-recognized role in triglyceride-rich lipoproteins metabolism. A considerable amount of data has clearly highlighted that high levels of ApoCIII lead to hypertriglyceridemia and, thereby, may influence the risk of cardiovascular disease. However, recent findings indicate that ApoCIII might also act beyond lipid metabolism. Indeed, ApoCIII has been implicated in other physiological processes such as glucose homeostasis, monocyte adhesion, activation of inflammatory pathways, and modulation of the coagulation cascade. As the inhibition of ApoCIII is emerging as a new promising therapeutic strategy, the complete understanding of multifaceted pathophysiological role of this apoprotein may be relevant. Therefore, the purpose of this work is to review available evidences not only related to genetics and biochemistry of ApoCIII, but also highlighting the role of this apoprotein in triglyceride and glucose metabolism, in the inflammatory process and coagulation cascade as well as in cardiovascular disease.
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Affiliation(s)
- Laura D'Erasmo
- Department of Translational and Precision Medicine, Sapienza University of Rome, Italy; Department of Endocrinology and Cardiovascular Disease Prevention, Assistance Publique-Hôpitaux de Paris, La Pitié-Salpêtrière Hospital, Sorbonne University Paris, France.
| | - Alessia Di Costanzo
- Department of Translational and Precision Medicine, Sapienza University of Rome, Italy.
| | - Antonio Gallo
- Department of Endocrinology and Cardiovascular Disease Prevention, Assistance Publique-Hôpitaux de Paris, La Pitié-Salpêtrière Hospital, Sorbonne University Paris, France
| | - Eric Bruckert
- Department of Endocrinology and Cardiovascular Disease Prevention, Assistance Publique-Hôpitaux de Paris, La Pitié-Salpêtrière Hospital, Sorbonne University Paris, France
| | - Marcello Arca
- Department of Translational and Precision Medicine, Sapienza University of Rome, Italy
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13
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Corbin LJ, Hughes DA, Chetwynd AJ, Taylor AE, Southam AD, Jankevics A, Weber RJM, Groom A, Dunn WB, Timpson NJ. Metabolic characterisation of disturbances in the APOC3/triglyceride-rich lipoprotein pathway through sample-based recall by genotype. Metabolomics 2020; 16:69. [PMID: 32494907 PMCID: PMC7270992 DOI: 10.1007/s11306-020-01689-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 05/15/2020] [Indexed: 12/11/2022]
Abstract
INTRODUCTION High plasma triacylglyceride levels are known to be associated with increased risk of atherosclerotic cardiovascular disease. Apolipoprotein C-III (apoC-III) is a key regulator of plasma triacylglyceride levels and is associated with hypertriglyceridemia via a number of pathways. There is consistent evidence for an association of cardiovascular events with blood apoC-III level, with support from human genetic studies of APOC3 variants. As such, apoC-III has been recognised as a potential therapeutic target for patients with severe hypertriglyceridaemia with one of the most promising apoC-III-targeting drugs, volanesorsen, having recently progressed through Phase III trials. OBJECTIVES To exploit a rare loss of function variant in APOC3 (rs138326449) to characterise the potential long-term treatment effects of apoC-III targeting interventions on the metabolome. METHODS In a recall-by-genotype study, 115 plasma samples were analysed by UHPLC-MS to acquire non-targeted metabolomics data. The study included samples from 57 adolescents and 33 adults. Overall, 12 985 metabolic features were tested for an association with APOC3 genotype. RESULTS 161 uniquely annotated metabolites were found to be associated with rs138326449(APOC3). The highest proportion of associated metabolites belonged to the acyl-acyl glycerophospholipid and triacylglyceride metabolite classes. In addition to the anticipated (on-target) reduction of metabolites in the triacylglyceride and related classes, carriers of the rare variant exhibited previously unreported increases in levels of a number of metabolites from the acyl-alkyl glycerophospholipid class. CONCLUSION Overall, our results suggest that therapies targeting apoC-III may potentially achieve a broad shift in lipid profile that favours better metabolic health.
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Affiliation(s)
- Laura J Corbin
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - David A Hughes
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Andrew J Chetwynd
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Amy E Taylor
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- NIHR Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol, Bristol, BS8 2BN, UK
| | - Andrew D Southam
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Andris Jankevics
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ralf J M Weber
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Alix Groom
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Warwick B Dunn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, BS8 2BN, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK.
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14
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Yang T, Wu C, Wei P, Pan W. Integrating DNA sequencing and transcriptomic data for association analyses of low-frequency variants and lipid traits. Hum Mol Genet 2020; 29:515-526. [PMID: 31919517 PMCID: PMC7015848 DOI: 10.1093/hmg/ddz314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 12/13/2022] Open
Abstract
Transcriptome-wide association studies (TWAS) integrate genome-wide association studies (GWAS) and transcriptomic data to showcase their improved statistical power of identifying gene-trait associations while, importantly, offering further biological insights. TWAS have thus far focused on common variants as available from GWAS. Compared with common variants, the findings for or even applications to low-frequency variants are limited and their underlying role in regulating gene expression is less clear. To fill this gap, we extend TWAS to integrating whole genome sequencing data with transcriptomic data for low-frequency variants. Using the data from the Framingham Heart Study, we demonstrate that low-frequency variants play an important and universal role in predicting gene expression, which is not completely due to linkage disequilibrium with the nearby common variants. By including low-frequency variants, in addition to common variants, we increase the predictivity of gene expression for 79% of the examined genes. Incorporating this piece of functional genomic information, we perform association testing for five lipid traits in two UK10K whole genome sequencing cohorts, hypothesizing that cis-expression quantitative trait loci, including low-frequency variants, are more likely to be trait-associated. We discover that two genes, LDLR and TTC22, are genome-wide significantly associated with low-density lipoprotein cholesterol based on 3203 subjects and that the association signals are largely independent of common variants. We further demonstrate that a joint analysis of both common and low-frequency variants identifies association signals that would be missed by testing on either common variants or low-frequency variants alone.
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Affiliation(s)
- Tianzhong Yang
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Chong Wu
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wei Pan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
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15
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Yang T, Kim J, Wu C, Ma Y, Wei P, Pan W. An adaptive test for meta-analysis of rare variant association studies. Genet Epidemiol 2020; 44:104-116. [PMID: 31830326 PMCID: PMC6980317 DOI: 10.1002/gepi.22273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/12/2019] [Accepted: 11/25/2019] [Indexed: 01/02/2023]
Abstract
Single genome-wide studies may be underpowered to detect trait-associated rare variants with moderate or weak effect sizes. As a viable alternative, meta-analysis is widely used to increase power by combining different studies. The power of meta-analysis critically depends on the underlying association patterns and heterogeneity levels, which are unknown and vary from locus to locus. However, existing methods mainly focus on one or only a few combinations of the association pattern and heterogeneity level, thus may lose power in many situations. To address this issue, we propose a general and unified framework by combining a class of tests including and beyond some existing ones, leading to high power across a wide range of scenarios. We demonstrate that the proposed test is more powerful than some existing methods in simulation studies, then show their performance with the NHLBI Exome-Sequencing Project (ESP) data. One gene (B4GALNT2) was found by our proposed test, but not by others, to be statistically significantly associated with plasma triglyceride. The signal was driven by African-ancestry subjects but it was previously reported to be associated with coronary artery disease among European-ancestry subjects. We implemented our method in an R package aSPUmeta, publicly available at https://github.com/ytzhong/metaRV and will be on CRAN soon.
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Affiliation(s)
- Tianzhong Yang
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Junghi Kim
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Chong Wu
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Yiding Ma
- Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wei Pan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
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16
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Baiyisaiti A, Wang Y, Zhang X, Chen W, Qi R. Rosa rugosa flavonoids exhibited PPARα agonist-like effects on genetic severe hypertriglyceridemia of mice. JOURNAL OF ETHNOPHARMACOLOGY 2019; 240:111952. [PMID: 31100436 DOI: 10.1016/j.jep.2019.111952] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 04/22/2019] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Rosa rugosa Thunb. is a traditional Chinese medicine that was used in the treatment of cardiovascular diseases and relative risk factors such as diabetes, hyperlipidemia, hypertension, and inflammation. Rosa rugosa flavonoids (RRFs) are the main components in Rosa rugosa Thunb. Several studies have demonstrated that RRFs can regulate plasma lipid contents, but the related mechanism of which has not yet been elucidated clearly. AIM OF THE STUDY The goal of this study was to clarify the effects of RRFs on triglyceride metabolism and its related mechanisms. MATERIALS AND METHODS RRFs were obtained by ethanol extraction from Rosa rugosa Thunb.. Transgenic mice expressing human Apolipoprotein C3 (ApoC3) were used as a mouse model of hypertriglyceridemia. Fenofibrate (FNB), a PPARα agonist, was used as a positive control drug of decreasing high triglyceride. FNB (100 mg/kg) or RRFs (300 mg/kg) were given to the mice by gavage daily. Two weeks later, the changes of plasma lipid levels in the mice were measured by commercial kits, the clearance of triglyceride was evaluated by oral fat load test, and expression of the genes related to lipid β-oxidation and synthesis was detected in the mice livers by real time PCR. RESULTS RRFs, as well as FNB, were found to significantly reduce plasma triglyceride (TG) levels in ApoC3 transgenic mice after administration of the drug for two weeks. Plasma lipid clearance rate was increased and lipid content in the mice livers was reduced after administration of RRF. Treatment with RRFs up-regulated mRNA expression of PPARα and its downstream gene of ACOX, while down-regulated mRNA expression of the genes related to fatty acid synthesis (FASN, SREBP-1c, and ACC1). The expression of LPL was raised, while the expression of ApoC3 was decreased, and Foxo1 was inhibited by RRFs in the mice livers. CONCLUSION RRFs can reduce plasma TG levels by repressing the expression of ApoC3 and inducing the expression of LPL in liver. RRFs could also reduce triglyceride in hepatocytes through increasing β-oxidation and decreasing synthesis of the lipids. These findings show the potency of further clinical application of RRFs as a hypolipidemic drug for treatment of cardiovascular diseases.
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Affiliation(s)
- Asiya Baiyisaiti
- School of Pharmacy, Shihezi University, 832000, Xinjiang, China; Peking University Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Peking University Health Science Center, Peking University, Beijing, 100191, China; Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, Beijing, 100191, China.
| | - Yuhui Wang
- Peking University Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Peking University Health Science Center, Peking University, Beijing, 100191, China.
| | - Xuehui Zhang
- School of Pharmacy, Shihezi University, 832000, Xinjiang, China; Peking University Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Peking University Health Science Center, Peking University, Beijing, 100191, China; Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, Beijing, 100191, China.
| | - Wen Chen
- School of Pharmacy, Shihezi University, 832000, Xinjiang, China.
| | - Rong Qi
- School of Pharmacy, Shihezi University, 832000, Xinjiang, China; Peking University Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Peking University Health Science Center, Peking University, Beijing, 100191, China; Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, Beijing, 100191, China.
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17
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Dunn J, Ferluga S, Sharma V, Futschik M, Hilton DA, Adams CL, Lasonder E, Hanemann CO. Proteomic analysis discovers the differential expression of novel proteins and phosphoproteins in meningioma including NEK9, HK2 and SET and deregulation of RNA metabolism. EBioMedicine 2018; 40:77-91. [PMID: 30594554 PMCID: PMC6412084 DOI: 10.1016/j.ebiom.2018.12.048] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/20/2018] [Accepted: 12/20/2018] [Indexed: 12/26/2022] Open
Abstract
Background Meningioma is the most frequent primary intracranial tumour. Surgical resection remains the main therapeutic option as pharmacological intervention is hampered by poor knowledge of their proteomic signature. There is an urgent need to identify new therapeutic targets and biomarkers of meningioma. Methods We performed proteomic profiling of grade I, II and III frozen meningioma specimens and three normal healthy human meninges using LC-MS/MS to analyse global proteins, enriched phosphoproteins and phosphopeptides. Differential expression and functional annotation of proteins was completed using Perseus, IPA® and DAVID. We validated differential expression of proteins and phosphoproteins by Western blot on a meningioma validation set and by immunohistochemistry. Findings We quantified 3888 proteins and 3074 phosphoproteins across all meningioma grades and normal meninges. Bioinformatics analysis revealed commonly upregulated proteins and phosphoproteins to be enriched in Gene Ontology terms associated with RNA metabolism. Validation studies confirmed significant overexpression of proteins such as EGFR and CKAP4 across all grades, as well as the aberrant activation of the downstream PI3K/AKT pathway, which seems differential between grades. Further, we validated upregulation of the total and activated phosphorylated form of the NIMA-related kinase, NEK9, involved in mitotic progression. Novel proteins identified and validated in meningioma included the nuclear proto-oncogene SET, the splicing factor SF2/ASF and the higher-grade specific protein, HK2, involved in cellular metabolism. Interpretation Overall, we generated a proteomic thesaurus of meningiomas for the identification of potential biomarkers and therapeutic targets. Fund This study was supported by Brain Tumour Research.
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Affiliation(s)
- Jemma Dunn
- Institute of Translational and Stratified Medicine, Plymouth University Peninsula Schools of Medicine and Dentistry, John Bull Building, Plymouth Science Park, Research Way, Derriford, Plymouth PL6 8BU, UK
| | - Sara Ferluga
- Institute of Translational and Stratified Medicine, Plymouth University Peninsula Schools of Medicine and Dentistry, John Bull Building, Plymouth Science Park, Research Way, Derriford, Plymouth PL6 8BU, UK
| | - Vikram Sharma
- School of Biomedical Science, Faculty of Medicine and Dentistry, University of Plymouth, Derriford Research Facility, Research Way, Derriford, Plymouth PL6 8BU, UK
| | - Matthias Futschik
- School of Biomedical Science, Faculty of Medicine and Dentistry, University of Plymouth, Derriford Research Facility, Research Way, Derriford, Plymouth PL6 8BU, UK
| | - David A Hilton
- Cellular and Anatomical Pathology, Plymouth Hospitals NHS Trust, Derriford Road, Plymouth PL6 8DH, UK
| | - Claire L Adams
- Institute of Translational and Stratified Medicine, Plymouth University Peninsula Schools of Medicine and Dentistry, John Bull Building, Plymouth Science Park, Research Way, Derriford, Plymouth PL6 8BU, UK
| | - Edwin Lasonder
- School of Biomedical Science, Faculty of Medicine and Dentistry, University of Plymouth, Derriford Research Facility, Research Way, Derriford, Plymouth PL6 8BU, UK
| | - C Oliver Hanemann
- Institute of Translational and Stratified Medicine, Plymouth University Peninsula Schools of Medicine and Dentistry, John Bull Building, Plymouth Science Park, Research Way, Derriford, Plymouth PL6 8BU, UK.
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18
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Zhou Y, Mägi R, Milani L, Lauschke VM. Global genetic diversity of human apolipoproteins and effects on cardiovascular disease risk. J Lipid Res 2018; 59:1987-2000. [PMID: 30076208 PMCID: PMC6168301 DOI: 10.1194/jlr.p086710] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/16/2018] [Indexed: 12/13/2022] Open
Abstract
Abnormal plasma apolipoprotein levels are consistently implicated in CVD risk. Although 30% to 60% of their interindividual variability is genetic, common genetic variants explain only 10% to 20% of these differences. Rare genetic variants may be major sources of the missing heritability, yet quantitative evaluations of their contribution to phenotypic variability are lacking. Here, we analyzed whole-genome and whole-exome sequencing data from 138,632 individuals across seven major human populations to present a systematic overview of genetic apolipoprotein variability. We provide population-specific frequencies of 38 clinically important apolipoprotein alleles and identify further 6,875 genetic variants, 33% of which are novel and 98.7% of which are rare with minor allele frequencies <1%. We predicted the functional impact of rare variants and found that their relative importance differed drastically between genes and among ethnicities. Importantly, we validated the clinical relevance of multiple variants with predicted effects by leveraging association data from the CARDIoGRAM (Coronary Artery Disease Genomewide Replication and Meta-analysis) and Global Lipids Genetics consortia. Overall, we provide a consolidated overview of population-specific apolipoprotein genetics as a valuable data resource for scientists and clinicians, estimate the importance of rare genetic variants for the missing heritability of apolipoprotein-associated disease traits, and pinpoint multiple novel apolipoprotein variants with putative population-specific impacts on serum lipid levels.
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Affiliation(s)
- Yitian Zhou
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden
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19
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Crawford DC, Restrepo NA, Diggins KE, Farber-Eger E, Wells QS. Frequency and phenotype consequence of APOC3 rare variants in patients with very low triglyceride levels. BMC Med Genomics 2018; 11:66. [PMID: 30255797 PMCID: PMC6156840 DOI: 10.1186/s12920-018-0387-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Background High levels of triglycerides (TG ≥200 mg/dL) are an emerging risk factor for cardiovascular disease. Conversely, very low levels of TG are associated with decreased risk for cardiovascular disease. Precision medicine aims to capitalize on recent findings that rare variants such as APOC3 R19X (rs76353203) are associated with risk of disease, but it is unclear how population-based associations can be best translated in clinical settings at the individual-patient level. Methods To explore the potential usefulness of screening for genetic predictors of cardiovascular disease, we surveyed BioVU, the Vanderbilt University Medical Center’s biorepository linked to de-identified electronic health records (EHRs), for APOC3 19X mutations among adult European American patients (> 45 and > 55 years of age for men and women, respectively) with the lowest percentile of TG levels. The initial search identified 262 patients with the lowest TG levels in the biorepository; among these, 184 patients with sufficient DNA and the lowest TG levels were chosen for Illumina ExomeChip genotyping. Results A total of two patients were identified as heterozygotes of APOC3 R19X for a minor allele frequency (MAF) of 0.55% in this patient population. Both heterozygous patients had only a single mention of TG in the EHR (31 and 35 mg/dL, respectively), and one patient had evidence of previous cardiovascular disease. Conclusions In this patient population, we identified two patients who were carriers of the APOC3 19X null variant, but only one lacked evidence of disease in the EHR highlighting the challenges of inclusion of functional or previously associated genetic variation in clinical risk assessment. Electronic supplementary material The online version of this article (10.1186/s12920-018-0387-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dana C Crawford
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University, 2103 Cornell Road, Wolstein Research Building, Suite 2-527, Cleveland, OH, 44106, USA.
| | - Nicole A Restrepo
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University, 2103 Cornell Road, Wolstein Research Building, Suite 2-527, Cleveland, OH, 44106, USA
| | - Kirsten E Diggins
- Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Eric Farber-Eger
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Quinn S Wells
- Departments of Medicine and Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
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20
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Hsueh WC, Nair AK, Kobes S, Chen P, Göring HHH, Pollin TI, Malhotra A, Knowler WC, Baier LJ, Hanson RL. Identity-by-Descent Mapping Identifies Major Locus for Serum Triglycerides in Amerindians Largely Explained by an APOC3 Founder Mutation. ACTA ACUST UNITED AC 2018; 10:CIRCGENETICS.117.001809. [PMID: 29237685 DOI: 10.1161/circgenetics.117.001809] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 10/03/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Identity-by-descent mapping using empirical estimates of identity-by-descent allele sharing may be useful for studies of complex traits in founder populations, where hidden relationships may augment the inherent genetic information that can be used for localization. METHODS AND RESULTS Through identity-by-descent mapping, using ≈400 000 single-nucleotide polymorphisms (SNPs), of serum lipid profiles, we identified a major linkage signal for triglycerides in 1007 Pima Indians (LOD=9.23; P=3.5×10-11 on chromosome 11q). In subsequent fine-mapping and replication association studies in ≈7500 Amerindians, we determined that this signal reflects effects of a loss-of-function Ala43Thr substitution in APOC3 (rs147210663) and 3 established functional SNPs in APOA5. The association with rs147210663 was particularly strong; each copy of the Thr allele conferred 42% lower triglycerides (β=-0.92±0.059 SD unit; P=9.6×10-55 in 4668 Pimas and 2793 Southwest Amerindians combined). The Thr allele is extremely rare in most global populations but has a frequency of 2.5% in Pimas. We further demonstrated that 3 APOA5 SNPs with established functional impact could explain the association with the most well-replicated SNP (rs964184) for triglycerides identified by genome-wide association studies. Collectively, these 4 SNPs account for 6.9% of variation in triglycerides in Pimas (and 4.1% in Southwest Amerindians), and their inclusion in the original linkage model reduced the linkage signal to virtually null. CONCLUSIONS APOC3/APOA5 constitutes a major locus for serum triglycerides in Amerindians, especially the Pimas, and these results provide an empirical example for the concept that population-based linkage analysis is a useful strategy to identify complex trait variants.
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Affiliation(s)
- Wen-Chi Hsueh
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.).
| | - Anup K Nair
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.)
| | - Sayuko Kobes
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.)
| | - Peng Chen
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.)
| | - Harald H H Göring
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.)
| | - Toni I Pollin
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.)
| | - Alka Malhotra
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.)
| | - William C Knowler
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.)
| | - Leslie J Baier
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.)
| | - Robert L Hanson
- From the Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, AZ (W.-C.H., A.K.N., S.K., P.C., A.M., W.C.K., L.J.B., R.L.H.); South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, San Antonio (H.H.H.G.); Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore (T.I.P.); and Illumina Inc, San Diego, CA (A.M.)
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21
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Abstract
PURPOSE OF REVIEW Apolipoprotein (apo) C-III is a key player in triglyceride-rich lipoprotein metabolism and strongly associated with elevated plasma triglyceride levels. Several new studies added important insights on apoC-III and its physiological function confirming its promise as a valid therapeutic target. RECENT FINDINGS APOC3 is expressed in liver and intestine and regulates triglyceride-rich lipoprotein (TRL) catabolism and anabolism. The transcriptional regulation in both organs requires different regulatory elements. Clinical and preclinical studies established that apoC-III raises plasma triglyceride levels predominantly by inhibiting hepatic TRL clearance. Mechanistic insights into missense variants indicate accelerated renal clearance of apoC-III variants resulting in enhanced TRL catabolism. In contrast, an APOC3 gain-of-function variant enhances de novo lipogenesis and hepatic TRL production. Multiple studies confirmed the correlation between increased apoC-III levels and cardiovascular disease. This has opened up new therapeutic avenues allowing targeting of specific apoC-III properties in triglyceride metabolism. SUMMARY Novel in vivo models and APOC3 missense variants revealed unique mechanisms by which apoC-III inhibits TRL catabolism. Clinical trials with Volanesorsen, an APOC3 antisense oligonucleotide, report very promising lipid-lowering outcomes. However, future studies will need to address if acute apoC-III lowering will have the same clinical benefits as a life-long reduction.
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Affiliation(s)
- Bastian Ramms
- Department of Cellular and Molecular Medicine
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, San Diego, California, USA
- Department of Chemistry, Biochemistry I, Bielefeld University, Bielefeld, Germany
| | - Philip L S M Gordts
- Department of Cellular and Molecular Medicine
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, San Diego, California, USA
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22
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Wulff AB, Nordestgaard BG, Tybjærg-Hansen A. APOC3
Loss-of-Function Mutations, Remnant Cholesterol, Low-Density Lipoprotein Cholesterol, and Cardiovascular Risk. Arterioscler Thromb Vasc Biol 2018; 38:660-668. [DOI: 10.1161/atvbaha.117.310473] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/02/2018] [Indexed: 11/16/2022]
Affiliation(s)
- Anders B. Wulff
- From the Department of Clinical Biochemistry, Rigshospitalet (A.B.W., A.T.-H.), Department of Clinical Biochemistry, Herlev and Gentofte Hospital (B.G.N.), and Copenhagen City Heart Study, Frederiksberg Hospital (B.G.N., A.T.-H.), Copenhagen University Hospital, University of Copenhagen, Denmark; Department of Clinical Biochemistry, Zealand University Hospital, Denmark (A.B.W.); and Copenhagen General Population Study, Herlev and Gentofte Hospital, Denmark (B.G.N., A.T.-H.)
| | - Børge G. Nordestgaard
- From the Department of Clinical Biochemistry, Rigshospitalet (A.B.W., A.T.-H.), Department of Clinical Biochemistry, Herlev and Gentofte Hospital (B.G.N.), and Copenhagen City Heart Study, Frederiksberg Hospital (B.G.N., A.T.-H.), Copenhagen University Hospital, University of Copenhagen, Denmark; Department of Clinical Biochemistry, Zealand University Hospital, Denmark (A.B.W.); and Copenhagen General Population Study, Herlev and Gentofte Hospital, Denmark (B.G.N., A.T.-H.)
| | - Anne Tybjærg-Hansen
- From the Department of Clinical Biochemistry, Rigshospitalet (A.B.W., A.T.-H.), Department of Clinical Biochemistry, Herlev and Gentofte Hospital (B.G.N.), and Copenhagen City Heart Study, Frederiksberg Hospital (B.G.N., A.T.-H.), Copenhagen University Hospital, University of Copenhagen, Denmark; Department of Clinical Biochemistry, Zealand University Hospital, Denmark (A.B.W.); and Copenhagen General Population Study, Herlev and Gentofte Hospital, Denmark (B.G.N., A.T.-H.)
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23
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Timpson NJ, Greenwood CMT, Soranzo N, Lawson DJ, Richards JB. Genetic architecture: the shape of the genetic contribution to human traits and disease. Nat Rev Genet 2018; 19:110-124. [PMID: 29225335 DOI: 10.1038/nrg.2017.101] [Citation(s) in RCA: 236] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Genetic architecture describes the characteristics of genetic variation that are responsible for heritable phenotypic variability. It depends on the number of genetic variants affecting a trait, their frequencies in the population, the magnitude of their effects and their interactions with each other and the environment. Defining the genetic architecture of a complex trait or disease is central to the scientific and clinical goals of human genetics, which are to understand disease aetiology and aid in disease screening, diagnosis, prognosis and therapy. Recent technological advances have enabled genome-wide association studies and emerging next-generation sequencing studies to begin to decipher the nature of the heritable contribution to traits and disease. Here, we describe the types of genetic architecture that have been observed, how architecture can be measured and why an improved understanding of genetic architecture is central to future advances in the field.
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Affiliation(s)
- Nicholas J Timpson
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Clifton, Bristol BS8 2BN, UK
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Montréal, Québec H3T 1E2, Canada.,Department of Oncology, McGill University, 3755 Cote Ste Catherine, Montréal, Québec H3T 1E2, Canada.,Departments of Human Genetics and Epidemiology, Biostatistics and Occupational Health, McGill University, 3755 Cote Ste Catherine, Montréal, Québec H3T 1E2, Canada
| | - Nicole Soranzo
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK.,Department of Haematology, University of Cambridge, Long Road, Cambridge CB2 0PT, UK
| | - Daniel J Lawson
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Clifton, Bristol BS8 2BN, UK
| | - J Brent Richards
- Departments of Human Genetics and Epidemiology, Biostatistics and Occupational Health, McGill University, 3755 Cote Ste Catherine, Montréal, Québec H3T 1E2, Canada.,Department of Medicine, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Montréal, Québec H3T 1E2, Canada.,Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Campus, Lambeth Palace Road, London SE1 7EH, UK
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24
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Espino Guarch M, Font-Llitjós M, Murillo-Cuesta S, Errasti-Murugarren E, Celaya AM, Girotto G, Vuckovic D, Mezzavilla M, Vilches C, Bodoy S, Sahún I, González L, Prat E, Zorzano A, Dierssen M, Varela-Nieto I, Gasparini P, Palacín M, Nunes V. Mutations in L-type amino acid transporter-2 support SLC7A8 as a novel gene involved in age-related hearing loss. eLife 2018; 7:31511. [PMID: 29355479 PMCID: PMC5811215 DOI: 10.7554/elife.31511] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/18/2018] [Indexed: 12/19/2022] Open
Abstract
Age-related hearing loss (ARHL) is the most common sensory deficit in the elderly. The disease has a multifactorial etiology with both environmental and genetic factors involved being largely unknown. SLC7A8/SLC3A2 heterodimer is a neutral amino acid exchanger. Here, we demonstrated that SLC7A8 is expressed in the mouse inner ear and that its ablation resulted in ARHL, due to the damage of different cochlear structures. These findings make SLC7A8 transporter a strong candidate for ARHL in humans. Thus, a screening of a cohort of ARHL patients and controls was carried out revealing several variants in SLC7A8, whose role was further investigated by in vitro functional studies. Significant decreases in SLC7A8 transport activity was detected for patient’s variants (p.Val302Ile, p.Arg418His, p.Thr402Met and p.Val460Glu) further supporting a causative role for SLC7A8 in ARHL. Moreover, our preliminary data suggest that a relevant proportion of ARHL cases could be explained by SLC7A8 mutations. Age-related hearing loss affects about one in three individuals between the ages of 65 and 74. The first symptom is difficulty hearing high-pitched sounds like children’s voices. The disease starts gradually and worsens over time. Changes in the ear, the nerve that connects it to the brain, or the brain itself can cause hearing loss. Sometimes all three play a role. Genetics, exposure to noise, disease, and aging may all contribute. The condition is so complex it is difficult for scientists to pinpoint a primary suspect or develop treatments. Now, Guarch, Font-Llitjós et al. show that errors in a protein called SLC7A8 cause age-related hearing loss in mice and humans. The SLC7A8 protein acts like a door that allows amino acids – the building blocks of proteins – to enter or leave a cell. This door is blocked in mice lacking SLC7A8 and damage occurs in the part of their inner ear responsible for hearing. As a result, the animals lose their hearing. Next, Guarch, Font-Llitjós et al. scanned the genomes of 147 people from isolated villages in Italy for mutations in the gene for SLC7A8. The people also underwent hearing tests. Mutations in the gene for SLC7A8 that partially block the door and prevent the flow of amino acids were found in people with hearing loss. Some mutations in SLC7A8 that allow the door to stay open where found in people who could hear. The experiments suggest that certain mutations in the gene for SLC7A8 are likely an inherited cause of age-related hearing loss. It is possible that other proteins that control the flow of amino acids into or out of cells also may play a role in hearing. More studies are needed to see if it is possible to fix errors in the SLC7A8 protein to delay or restore the hearing loss.
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Affiliation(s)
- Meritxell Espino Guarch
- Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar.,Genes, Disease and Therapy Program, Molecular Genetics Laboratory - IDIBELL, Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mariona Font-Llitjós
- Genes, Disease and Therapy Program, Molecular Genetics Laboratory - IDIBELL, Barcelona, Spain.,Biomedical Research Networking Centre on Rare Diseases (CIBERER), Institute of Health Carlos III, Barcelona, Spain
| | - Silvia Murillo-Cuesta
- Biomedical Research Networking Centre on Rare Diseases (CIBERER), Institute of Health Carlos III, Barcelona, Spain.,Alberto Sols Biomedical Research Institute (CSIC/UAM), Madrid, Spain.,Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Ekaitz Errasti-Murugarren
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Biomedical Research Networking Centre on Rare Diseases (CIBERER), Institute of Health Carlos III, Barcelona, Spain
| | - Adelaida M Celaya
- Biomedical Research Networking Centre on Rare Diseases (CIBERER), Institute of Health Carlos III, Barcelona, Spain.,Alberto Sols Biomedical Research Institute (CSIC/UAM), Madrid, Spain
| | - Giorgia Girotto
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Medical Genetics, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Dragana Vuckovic
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Medical Genetics, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | | | - Clara Vilches
- Genes, Disease and Therapy Program, Molecular Genetics Laboratory - IDIBELL, Barcelona, Spain
| | - Susanna Bodoy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Biomedical Research Networking Centre on Rare Diseases (CIBERER), Institute of Health Carlos III, Barcelona, Spain
| | - Ignasi Sahún
- Biomedical Research Networking Centre on Rare Diseases (CIBERER), Institute of Health Carlos III, Barcelona, Spain.,Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Laura González
- Genes, Disease and Therapy Program, Molecular Genetics Laboratory - IDIBELL, Barcelona, Spain.,Biomedical Research Networking Centre on Rare Diseases (CIBERER), Institute of Health Carlos III, Barcelona, Spain
| | - Esther Prat
- Genes, Disease and Therapy Program, Molecular Genetics Laboratory - IDIBELL, Barcelona, Spain.,Biomedical Research Networking Centre on Rare Diseases (CIBERER), Institute of Health Carlos III, Barcelona, Spain.,Genetics Section, Physiological Sciences Department, Health Sciences and Medicine Faculty, University of Barcelona, Barcelona, Spain
| | - Antonio Zorzano
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Biochemistry and Molecular Biomedicine Department, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Biomedical Research Networking Centre on Diabetes and Associated Metabolic Diseases (CIBERDEM), Barcelona, Spain
| | - Mara Dierssen
- Biomedical Research Networking Centre on Rare Diseases (CIBERER), Institute of Health Carlos III, Barcelona, Spain.,Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Isabel Varela-Nieto
- Biomedical Research Networking Centre on Rare Diseases (CIBERER), Institute of Health Carlos III, Barcelona, Spain.,Alberto Sols Biomedical Research Institute (CSIC/UAM), Madrid, Spain.,Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Paolo Gasparini
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Medical Genetics, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Manuel Palacín
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Biomedical Research Networking Centre on Rare Diseases (CIBERER), Institute of Health Carlos III, Barcelona, Spain.,Biochemistry and Molecular Biomedicine Department, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Virginia Nunes
- Genes, Disease and Therapy Program, Molecular Genetics Laboratory - IDIBELL, Barcelona, Spain.,Biomedical Research Networking Centre on Rare Diseases (CIBERER), Institute of Health Carlos III, Barcelona, Spain.,Genetics Section, Physiological Sciences Department, Health Sciences and Medicine Faculty, University of Barcelona, Barcelona, Spain
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25
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Abstract
While genome-wide association studies have been very successful in identifying associations of common genetic variants with many different traits, the rarer frequency spectrum of the genome has not yet been comprehensively explored. Technological developments increasingly lift restrictions to access rare genetic variation. Dense reference panels enable improved genotype imputation for rarer variants in studies using DNA microarrays. Moreover, the decreasing cost of next generation sequencing makes whole exome and genome sequencing increasingly affordable for large samples. Large-scale efforts based on sequencing, such as ExAC, 100,000 Genomes, and TopMed, are likely to significantly advance this field.The main challenge in evaluating complex trait associations of rare variants is statistical power. The choice of population should be considered carefully because allele frequencies and linkage disequilibrium structure differ between populations. Genetically isolated populations can have favorable genomic characteristics for the study of rare variants.One strategy to increase power is to assess the combined effect of multiple rare variants within a region, known as aggregate testing. A range of methods have been developed for this. Model performance depends on the genetic architecture of the region of interest.
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Affiliation(s)
- Karoline Kuchenbaecker
- Wellcome Trust Sanger Institute, Cambridge, UK. .,University College London, London, UK.
| | - Emil Vincent Rosenbaum Appel
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Genetics, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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26
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Igartua C, Mozaffari SV, Nicolae DL, Ober C. Rare non-coding variants are associated with plasma lipid traits in a founder population. Sci Rep 2017; 7:16415. [PMID: 29180722 PMCID: PMC5704019 DOI: 10.1038/s41598-017-16550-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/14/2017] [Indexed: 12/31/2022] Open
Abstract
Founder populations are ideally suited for studies on the clinical effects of alleles that are rare in general populations but occur at higher frequencies in these isolated populations. Whole genome sequencing in 98 Hutterites, a founder population of European descent, and subsequent imputation revealed 660,238 single nucleotide polymorphisms that are rare (<1%) or absent in European populations, but occur at frequencies >1% in the Hutterites. We examined the effects of these rare in European variants on plasma lipid levels in 828 Hutterites and applied a Bayesian hierarchical framework to prioritize potentially causal variants based on functional annotations. We identified two novel non-coding rare variants associated with LDL cholesterol (rs17242388 in LDLR) and HDL cholesterol (rs189679427 between GOT2 and APOOP5), and replicated previous associations of a splice variant in APOC3 (rs138326449) with triglycerides and HDL-C. All three variants are at well-replicated loci in GWAS but are independent from and have larger effect sizes than the known common variation in these regions. Candidate eQTL analyses in in LCLs in the Hutterites suggest that these rare non-coding variants are likely to mediate their effects on lipid traits by regulating gene expression.
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Affiliation(s)
- Catherine Igartua
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
| | - Sahar V Mozaffari
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.,Committee of Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Dan L Nicolae
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.,Department of Statistics, University of Chicago, Chicago, IL, 60637, USA.,Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.,Committee of Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
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Zhu C, Zhu H, Song H, Xu L, Li L, Liu F, Liu X. Hepatitis B virus inhibits the in vivo and in vitro synthesis and secretion of apolipoprotein C3. Lipids Health Dis 2017; 16:213. [PMID: 29132372 PMCID: PMC5683573 DOI: 10.1186/s12944-017-0607-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/05/2017] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) infection in the body can damage liver cells and cause disorders in blood lipid metabolism. Apolipoprotein C3 (ApoC3) plays an important role in the regulation of lipid metabolism, but no study on the HBV regulation of ApoC3 has been reported. This purpose of this study was to investigate the effect of HBV on ApoC3 expression and its regulatory mechanism. METHODS The expression levels of ApoC3 mRNA and protein in the human hepatoma cell lines HepG2 and HepG2.2.15 were determined using real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) and Western blot. The HepG2 cells were co-transfected with the ApoC3 gene promoter and either HBV-infected clone pHBV1.3 or its individual genes. The changes in luciferase activity were assayed. The expression levels of ApoC3 mRNA and protein were determined using RT-qPCR and Western blot. The content of ApoC3 in the supernatant of the cultured cells was determined using an enzyme-linked immunosorbent assay (ELISA). The sera were collected from 149 patients with HBV infection and 102 healthy subjects at physical examination as the normal controls. The serological levels of ApoC3 in the HBV group and the normal control group were determined using ELISA. The contents of serum triglyceride (TG) and very-low-density lipoprotein (VLDL) in the HBV patients and the normal control were determined using an automatic biochemical analyser. RESULTS The expression levels of ApoC3 mRNA and protein were lower in the HepG2.2.15 cells than in the HepG2 cells. pHBV1.3 and its X gene could inhibit the activity of the ApoC3 promoter and its mRNA and protein expression. The serum levels of ApoC3, VLDL and TG were 65.39 ± 7.48 μg/ml, 1.24 ± 0.49 mmol/L, and 0.46 ± 0.10 mmol/L in the HBV patients and 41.02 ± 6.88 μg/ml, 0.76 ± 0.21 mmol/L, 0.29 ± 0.05 mmol/L in the normal controls, respectively, statistical analysis revealed significantly lower serum levels of ApoC3, VLDL and TG in HBV patients than in the normal controls (P < 0.05). CONCLUSION HBV can inhibit the in vivo and in vitro synthesis and secretion of ApoC3.
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Affiliation(s)
- Chengliang Zhu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, People's Republic of China
| | - Hengcheng Zhu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, People's Republic of China
| | - Hui Song
- Department of Clinical Laboratory, Shanghai Gongli Hospital, the Second Military Medical University, Pudong New Area, Shanghai, 200135, China
| | - Limin Xu
- Department of Clinical Laboratory, Shanghai Gongli Hospital, the Second Military Medical University, Pudong New Area, Shanghai, 200135, China
| | - Longxuan Li
- Department of Neurology, Shanghai Gongli Hospital, the Second Military Medical University, Pudong New Area, Shanghai, 200135, China
| | - Fang Liu
- The State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, People's Republic of China
| | - Xinghui Liu
- Department of Clinical Laboratory, Shanghai Gongli Hospital, the Second Military Medical University, Pudong New Area, Shanghai, 200135, China.
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28
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Xu L, Borges MC, Hemani G, Lawlor DA. The role of glycaemic and lipid risk factors in mediating the effect of BMI on coronary heart disease: a two-step, two-sample Mendelian randomisation study. Diabetologia 2017; 60:2210-2220. [PMID: 28889241 PMCID: PMC6342872 DOI: 10.1007/s00125-017-4396-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/29/2017] [Indexed: 02/06/2023]
Abstract
AIMS/HYPOTHESIS The extent to which effects of BMI on CHD are mediated by glycaemic and lipid risk factors is unclear. In this study we examined the effects of these traits using genetic evidence. METHODS We used two-sample Mendelian randomisation to determine: (1) the causal effect of BMI on CHD (60,801 case vs 123,504 control participants), type 2 diabetes (34,840 case vs 114,981 control participants), fasting glucose (n = 46,186), insulin (n = 38,238), HbA1c (n = 46,368) and LDL-cholesterol, HDL-cholesterol and triacylglycerols (n = 188,577); (2) the causal effects of glycaemic and lipids traits on CHD; and (3) the extent to which these traits mediate any effect of BMI on CHD. RESULTS One SD higher BMI (~ 4.5 kg/m2) was associated with higher risk of CHD (OR 1.45 [95% CI 1.27, 1.66]) and type 2 diabetes (1.96 [95% CI 1.35, 2.83]), higher levels of fasting glucose (0.07 mmol/l [95% CI 0.03, 0.11]), HbA1c (0.05% [95% CI 0.01, 0.08]), fasting insulin (0.18 log pmol/l [95% CI 0.14, 0.22]) and triacylglycerols (0.20 SD [95% CI 0.14, 0.26]) and lower levels of HDL-cholesterol (-0.23 SD [95% CI -0.32, -0.15]). There was no evidence for a causal relation between BMI and LDL-cholesterol. The causal associations of higher triacylglycerols, HbA1c and diabetes risk with CHD risk remained after performing sensitivity analyses that considered different models of horizontal pleiotropy. The BMI-CHD effect reduced from 1.45 to 1.16 (95% CI 0.99, 1.36) and to 1.36 (95% CI 1.19, 1.57) with genetic adjustment for triacylglycerols or HbA1c, respectively, and to 1.09 (95% CI 0.94, 1.27) with adjustment for both. CONCLUSIONS/INTERPRETATION Increased triacylglycerol levels and poor glycaemic control appear to mediate much of the effect of BMI on CHD.
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Affiliation(s)
- Lin Xu
- School of Public Health, Sun Yat-sen University, Guangzhou, 510080, Guangdong, People's Republic of China
- MRC Integrative Epidemiology Unit, University of Bristol, Rm OS11, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- School of Public Health, University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Maria Carolina Borges
- MRC Integrative Epidemiology Unit, University of Bristol, Rm OS11, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, Rm OS11, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Rm OS11, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
- School of Social and Community Medicine, University of Bristol, Bristol, UK.
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29
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Brown AA, Viñuela A, Delaneau O, Spector TD, Small KS, Dermitzakis ET. Predicting causal variants affecting expression by using whole-genome sequencing and RNA-seq from multiple human tissues. Nat Genet 2017; 49:1747-1751. [PMID: 29058714 DOI: 10.1038/ng.3979] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 09/27/2017] [Indexed: 12/16/2022]
Abstract
Genetic association mapping produces statistical links between phenotypes and genomic regions, but identifying causal variants remains difficult. Whole-genome sequencing (WGS) can help by providing complete knowledge of all genetic variants, but it is financially prohibitive for well-powered GWAS studies. We performed mapping of expression quantitative trait loci (eQTLs) with WGS and RNA-seq, and found that lead eQTL variants called with WGS were more likely to be causal. Through simulations, we derived properties of causal variants and used them to develop a method for identifying likely causal SNPs. We estimated that 25-70% of causal variants were located in open-chromatin regions, depending on the tissue and experiment. Finally, we identified a set of high-confidence causal variants and showed that these were more enriched in GWAS associations than other eQTLs. Of those, we found 65 associations with GWAS traits and provide examples in which genes implicated by expression are functionally validated as being relevant for complex traits.
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Affiliation(s)
- Andrew Anand Brown
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland.,NORMENT, KG Jebsen Centre for Psychosis Research, Oslo University Hospital, Oslo, Norway
| | - Ana Viñuela
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Olivier Delaneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
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30
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Genome-wide analysis of health-related biomarkers in the UK Household Longitudinal Study reveals novel associations. Sci Rep 2017; 7:11008. [PMID: 28887542 PMCID: PMC5591265 DOI: 10.1038/s41598-017-10812-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/08/2017] [Indexed: 11/24/2022] Open
Abstract
Serum biomarker levels are associated with the risk of complex diseases. Here, we aimed to gain insights into the genetic architecture of biomarker traits which can reflect health status. We performed genome-wide association analyses for twenty serum biomarkers involved in organ function and reproductive health. 9,961 individuals from the UK Household Longitudinal Study were genotyped using the Illumina HumanCoreExome array and variants imputed to the 1000 Genomes Project and UK10K haplotypes. We establish a polygenic heritability for all biomarkers, confirm associations of fifty-four established loci, and identify five novel, replicating associations at genome-wide significance. A low-frequency variant, rs28929474, (beta = 0.04, P = 2 × 10−10) was associated with levels of alanine transaminase, an indicator of liver damage. The variant is located in the gene encoding serine protease inhibitor, low levels of which are associated with alpha-1 antitrypsin deficiency which leads to liver disease. We identified novel associations (rs78900934, beta = 0.05, P = 6 × 10−12; rs2911280, beta = 0.09, P = 6 × 10−10) for dihydroepiandrosterone sulphate, a precursor to major sex-hormones, and for glycated haemoglobin (rs12819124, beta = −0.03, P = 4 × 10−9; rs761772, beta = 0.05, P = 5 × 10−9). rs12819124 is nominally associated with risk of type 2 diabetes. Our study offers insights into the genetic architecture of well-known and less well-studied biomarkers.
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31
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Taskinen MR, Borén J. Why Is Apolipoprotein CIII Emerging as a Novel Therapeutic Target to Reduce the Burden of Cardiovascular Disease? Curr Atheroscler Rep 2017; 18:59. [PMID: 27613744 PMCID: PMC5018018 DOI: 10.1007/s11883-016-0614-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
ApoC-III was discovered almost 50 years ago, but for many years, it did not attract much attention. However, as epidemiological and Mendelian randomization studies have associated apoC-III with low levels of triglycerides and decreased incidence of cardiovascular disease (CVD), it has emerged as a novel and potentially powerful therapeutic approach to managing dyslipidemia and CVD risk. The atherogenicity of apoC-III has been attributed to both direct lipoprotein lipase-mediated mechanisms and indirect mechanisms, such as promoting secretion of triglyceride-rich lipoproteins (TRLs), provoking proinflammatory responses in vascular cells and impairing LPL-independent hepatic clearance of TRL remnants. Encouraging results from clinical trials using antisense oligonucleotide, which selectively inhibits apoC-III, indicate that modulating apoC-III may be a potent therapeutic approach to managing dyslipidemia and cardiovascular disease risk.
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Affiliation(s)
- Marja-Riitta Taskinen
- Heart and Lung Centre, Helsinki University Central Hospital and Research Programs' Unit, Diabetes & Obesity, University of Helsinki, Helsinki, Finland
| | - Jan Borén
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden. .,Wallenberg Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden.
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32
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Dewey FE, Murray MF, Overton JD, Habegger L, Leader JB, Fetterolf SN, O'Dushlaine C, Van Hout CV, Staples J, Gonzaga-Jauregui C, Metpally R, Pendergrass SA, Giovanni MA, Kirchner HL, Balasubramanian S, Abul-Husn NS, Hartzel DN, Lavage DR, Kost KA, Packer JS, Lopez AE, Penn J, Mukherjee S, Gosalia N, Kanagaraj M, Li AH, Mitnaul LJ, Adams LJ, Person TN, Praveen K, Marcketta A, Lebo MS, Austin-Tse CA, Mason-Suares HM, Bruse S, Mellis S, Phillips R, Stahl N, Murphy A, Economides A, Skelding KA, Still CD, Elmore JR, Borecki IB, Yancopoulos GD, Davis FD, Faucett WA, Gottesman O, Ritchie MD, Shuldiner AR, Reid JG, Ledbetter DH, Baras A, Carey DJ. Distribution and clinical impact of functional variants in 50,726 whole-exome sequences from the DiscovEHR study. Science 2017; 354:354/6319/aaf6814. [PMID: 28008009 DOI: 10.1126/science.aaf6814] [Citation(s) in RCA: 368] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 11/16/2016] [Indexed: 11/02/2022]
Abstract
The DiscovEHR collaboration between the Regeneron Genetics Center and Geisinger Health System couples high-throughput sequencing to an integrated health care system using longitudinal electronic health records (EHRs). We sequenced the exomes of 50,726 adult participants in the DiscovEHR study to identify ~4.2 million rare single-nucleotide variants and insertion/deletion events, of which ~176,000 are predicted to result in a loss of gene function. Linking these data to EHR-derived clinical phenotypes, we find clinical associations supporting therapeutic targets, including genes encoding drug targets for lipid lowering, and identify previously unidentified rare alleles associated with lipid levels and other blood level traits. About 3.5% of individuals harbor deleterious variants in 76 clinically actionable genes. The DiscovEHR data set provides a blueprint for large-scale precision medicine initiatives and genomics-guided therapeutic discovery.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Korey A Kost
- Geisinger Health System, Danville, PA 17822, USA
| | | | | | - John Penn
- Regeneron Genetics Center, Tarrytown, NY 10591, USA
| | | | | | | | | | | | | | | | | | | | - Matthew S Lebo
- Laboratory for Molecular Medicine, Cambridge, MA 02139, USA
| | | | | | | | - Scott Mellis
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | - Neil Stahl
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY 10591, USA
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33
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Baig F, Mayr M. What are the prospects of apolipoprotein profiling for cardiovascular disease? Expert Rev Mol Diagn 2017; 17:805-807. [DOI: 10.1080/14737159.2017.1352472] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ferheen Baig
- King’s British Heart Foundation Centre, King’s College London, London, UK
| | - Manuel Mayr
- King’s British Heart Foundation Centre, King’s College London, London, UK
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34
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Abstract
Despite thousands of genetic loci identified to date, a large proportion of genetic variation predisposing to complex disease and traits remains unaccounted for. Advances in sequencing technology enable focused explorations on the contribution of low-frequency and rare variants to human traits. Here we review experimental approaches and current knowledge on the contribution of these genetic variants in complex disease and discuss challenges and opportunities for personalised medicine.
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Affiliation(s)
- Lorenzo Bomba
- Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, CB10 1HH, UK
| | - Klaudia Walter
- Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, CB10 1HH, UK
| | - Nicole Soranzo
- Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, CB10 1HH, UK. .,Department of Haematology, University of Cambridge, Hills Rd, Cambridge, CB2 0AH, UK. .,The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK.
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35
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Mitt M, Kals M, Pärn K, Gabriel SB, Lander ES, Palotie A, Ripatti S, Morris AP, Metspalu A, Esko T, Mägi R, Palta P. Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel. Eur J Hum Genet 2017; 25:869-876. [PMID: 28401899 PMCID: PMC5520064 DOI: 10.1038/ejhg.2017.51] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 02/14/2017] [Accepted: 02/25/2017] [Indexed: 02/08/2023] Open
Abstract
Genetic imputation is a cost-efficient way to improve the power and resolution of genome-wide association (GWA) studies. Current publicly accessible imputation reference panels accurately predict genotypes for common variants with minor allele frequency (MAF)≥5% and low-frequency variants (0.5≤MAF<5%) across diverse populations, but the imputation of rare variation (MAF<0.5%) is still rather limited. In the current study, we evaluate imputation accuracy achieved with reference panels from diverse populations with a population-specific high-coverage (30 ×) whole-genome sequencing (WGS) based reference panel, comprising of 2244 Estonian individuals (0.25% of adult Estonians). Although the Estonian-specific panel contains fewer haplotypes and variants, the imputation confidence and accuracy of imputed low-frequency and rare variants was significantly higher. The results indicate the utility of population-specific reference panels for human genetic studies.
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Affiliation(s)
- Mario Mitt
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Mart Kals
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia
| | - Kalle Pärn
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Stacey B Gabriel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Andrew P Morris
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Priit Palta
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
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36
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Abstract
PURPOSE OF REVIEW Metabolomics directly measure substrates and products of biological processes and pathways. Based on instrumentation and throughput advances, the use of metabolomics has only recently become feasible at the population level. This has led to an intense interest in using the new information in combination with genomics, and other omics technologies, to give biological context to the rapidly accumulating associations between genes and diseases or their risk factors. RECENT FINDINGS The use of metabolomics-genomic associations for the metabolic characterization of genes of interest has confirmed known pathways and permitted the identification of new ones. These include the unknown metabolite X12063 linking statins to myopathies, the role of glycerophospholipids in cholesterol metabolism, the structure of lipoprotein (a), the lipoprotein lipase-independent effect of Apolipoprotein C-III coding and the role of branched chain amino acids in the antagonistic coregulation of levels of HDLs and triglyceride. SUMMARY The findings reviewed illustrate the importance of integrating metabolomics and genomics for the greater understanding of biological mechanisms. The limitations of the current approaches are also discussed together with approaches that will be required to make the most of the current multiomics data available.
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Affiliation(s)
- Fotios Drenos
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Oakfield House, Bristol, UK
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37
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Nagy R, Boutin TS, Marten J, Huffman JE, Kerr SM, Campbell A, Evenden L, Gibson J, Amador C, Howard DM, Navarro P, Morris A, Deary IJ, Hocking LJ, Padmanabhan S, Smith BH, Joshi P, Wilson JF, Hastie ND, Wright AF, McIntosh AM, Porteous DJ, Haley CS, Vitart V, Hayward C. Exploration of haplotype research consortium imputation for genome-wide association studies in 20,032 Generation Scotland participants. Genome Med 2017; 9:23. [PMID: 28270201 PMCID: PMC5339960 DOI: 10.1186/s13073-017-0414-4] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 02/09/2017] [Indexed: 01/31/2023] Open
Abstract
Background The Generation Scotland: Scottish Family Health Study (GS:SFHS) is a family-based population cohort with DNA, biological samples, socio-demographic, psychological and clinical data from approximately 24,000 adult volunteers across Scotland. Although data collection was cross-sectional, GS:SFHS became a prospective cohort due to of the ability to link to routine Electronic Health Record (EHR) data. Over 20,000 participants were selected for genotyping using a large genome-wide array. Methods GS:SFHS was analysed using genome-wide association studies (GWAS) to test the effects of a large spectrum of variants, imputed using the Haplotype Research Consortium (HRC) dataset, on medically relevant traits measured directly or obtained from EHRs. The HRC dataset is the largest available haplotype reference panel for imputation of variants in populations of European ancestry and allows investigation of variants with low minor allele frequencies within the entire GS:SFHS genotyped cohort. Results Genome-wide associations were run on 20,032 individuals using both genotyped and HRC imputed data. We present results for a range of well-studied quantitative traits obtained from clinic visits and for serum urate measures obtained from data linkage to EHRs collected by the Scottish National Health Service. Results replicated known associations and additionally reveal novel findings, mainly with rare variants, validating the use of the HRC imputation panel. For example, we identified two new associations with fasting glucose at variants near to Y_RNA and WDR4 and four new associations with heart rate at SNPs within CSMD1 and ASPH, upstream of HTR1F and between PROKR2 and GPCPD1. All were driven by rare variants (minor allele frequencies in the range of 0.08–1%). Proof of principle for use of EHRs was verification of the highly significant association of urate levels with the well-established urate transporter SLC2A9. Conclusions GS:SFHS provides genetic data on over 20,000 participants alongside a range of phenotypes as well as linkage to National Health Service laboratory and clinical records. We have shown that the combination of deeper genotype imputation and extended phenotype availability make GS:SFHS an attractive resource to carry out association studies to gain insight into the genetic architecture of complex traits. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0414-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Reka Nagy
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Thibaud S Boutin
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Jonathan Marten
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Jennifer E Huffman
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Shona M Kerr
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - Louise Evenden
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - Jude Gibson
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - Carmen Amador
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - David M Howard
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Pau Navarro
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Andrew Morris
- Farr Institute of Health Informatics Research, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Lynne J Hocking
- Division of Applied Health Sciences, University of Aberdeen, Aberdeen, UK
| | - Sandosh Padmanabhan
- Division of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Blair H Smith
- Medical Research Institute, University of Dundee, Dundee, UK
| | - Peter Joshi
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - James F Wilson
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Nicholas D Hastie
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Alan F Wright
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK.,Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK.,Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Chris S Haley
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
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Erion DM, Park HJ, Lee HY. The role of lipids in the pathogenesis and treatment of type 2 diabetes and associated co-morbidities. BMB Rep 2017; 49:139-48. [PMID: 26728273 PMCID: PMC4915228 DOI: 10.5483/bmbrep.2016.49.3.268] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Indexed: 12/25/2022] Open
Abstract
In the past decade, the incidence of type 2 diabetes (T2D) has rapidly increased, along with the associated cardiovascular complications. Therefore, understanding the pathophysiology underlying T2D, the associated complications and the impact of therapeutics on the T2D development has critical importance for current and future therapeutics. The prevailing feature of T2D is hyperglycemia due to excessive hepatic glucose production, insulin resistance, and insufficient secretion of insulin by the pancreas. These contribute to increased fatty acid influx into the liver and muscle causing accumulation of lipid metabolites. These lipid metabolites cause dyslipidemia and non-alcoholic fatty liver disease, which ultimately contributes to the increased cardiovascular risk in T2D. Therefore, understanding the mechanisms of hepatic insulin resistance and the specific role of liver lipids is critical in selecting and designing the most effective therapeutics for T2D and the associated co-morbidities, including dyslipidemia and cardiovascular disease. Herein, we review the effects and molecular mechanisms of conventional anti-hyperglycemic and lipid-lowering drugs on glucose and lipid metabolism. [BMB Reports 2016; 49(3): 139-148].
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Affiliation(s)
- Derek M Erion
- Takeda Pharmaceuticals 350 Massachusetts Ave. Cambridge, MA, 02139, USA
| | - Hyun-Jun Park
- Department of Molecular Medicine, Lee Gil Ya Cancer and Diabetes Institute, School of Medicine, Gachon University, Incheon 21999, Korea
| | - Hui-Young Lee
- Department of Molecular Medicine and Korea Mouse Metabolic Phenotyping Center, Lee Gil Ya Cancer and Diabetes Institute, School of Medicine, Gachon University, Incheon 21999, Korea
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39
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Testosterone Deficiency Induces Changes of the Transcriptomes of Visceral Adipose Tissue in Miniature Pigs Fed a High-Fat and High-Cholesterol Diet. Int J Mol Sci 2016; 17:ijms17122125. [PMID: 27999286 PMCID: PMC5187925 DOI: 10.3390/ijms17122125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/08/2016] [Accepted: 12/12/2016] [Indexed: 12/14/2022] Open
Abstract
Testosterone deficiency causes fat deposition, particularly in visceral fat, and its replacement might reverse fat accumulation, however, the underlying mechanisms of such processes under diet-induced adiposity are largely unknown. To gain insights into the genome-wide role of androgen on visceral adipose tissue (VAT), RNA-Seq was used to investigate testosterone deficiency induced changes of VAT in miniature pigs fed a high-fat and high-cholesterol (HFC) diet among intact male pigs (IM), castrated male pigs (CM), and castrated male pigs with testosterone replacement (CMT) treatments. The results showed that testosterone deficiency significantly increased VAT deposition and serum leptin concentrations. Moreover, a total of 1732 differentially expressed genes (DEGs) were identified between any two groups. Compared with gene expression profiles in IM and CMT pigs, upregulated genes in CM pigs, i.e., LOC100520753 (CD68), LCN2, EMR1, S100A9, NCF1 (p47phox), and LEP, were mainly involved in inflammatory response, oxidation-reduction process, and lipid metabolic process, while downregulated genes in CM pigs, i.e., ABHD5, SPP1, and GAS6, were focused on cell differentiation and cell adhesion. Taken together, our study demonstrates that testosterone deficiency alters the expression of numerous genes involved in key biological processes of VAT accumulation under HFC diet and provides a novel genome-wide view on the role of androgen on VAT deposition under HFC diet, thus improving our understanding of the molecular mechanisms involved in VAT changes induced by testosterone deficiency.
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40
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Iotchkova V, Huang J, Morris JA, Jain D, Barbieri C, Walter K, Min JL, Chen L, Astle W, Cocca M, Deelen P, Elding H, Farmaki AE, Franklin CS, Franberg M, Gaunt TR, Hofman A, Jiang T, Kleber ME, Lachance G, Luan J, Malerba G, Matchan A, Mead D, Memari Y, Ntalla I, Panoutsopoulou K, Pazoki R, Perry JR, Rivadeneira F, Sabater-Lleal M, Sennblad B, Shin SY, Southam L, Traglia M, van Dijk F, van Leeuwen EM, Zaza G, Zhang W, Amin N, Butterworth A, Chambers JC, Dedoussis G, Dehghan A, Franco OH, Franke L, Frontini M, Gambaro G, Gasparini P, Hamsten A, Issacs A, Kooner JS, Kooperberg C, Langenberg C, Marz W, Scott RA, Swertz MA, Toniolo D, Uitterlinden AG, van Duijn CM, Watkins H, Zeggini E, Maurano MT, Timpson NJ, Reiner AP, Auer PL, Soranzo N. Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps. Nat Genet 2016; 48:1303-1312. [PMID: 27668658 PMCID: PMC5279872 DOI: 10.1038/ng.3668] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 08/15/2016] [Indexed: 12/21/2022]
Abstract
Large-scale whole-genome sequence data sets offer novel opportunities to identify genetic variation underlying human traits. Here we apply genotype imputation based on whole-genome sequence data from the UK10K and 1000 Genomes Project into 35,981 study participants of European ancestry, followed by association analysis with 20 quantitative cardiometabolic and hematological traits. We describe 17 new associations, including 6 rare (minor allele frequency (MAF) < 1%) or low-frequency (1% < MAF < 5%) variants with platelet count (PLT), red blood cell indices (MCH and MCV) and HDL cholesterol. Applying fine-mapping analysis to 233 known and new loci associated with the 20 traits, we resolve the associations of 59 loci to credible sets of 20 or fewer variants and describe trait enrichments within regions of predicted regulatory function. These findings improve understanding of the allelic architecture of risk factors for cardiometabolic and hematological diseases and provide additional functional insights with the identification of potentially novel biological targets.
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Affiliation(s)
- Valentina Iotchkova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Jie Huang
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Boston VA Research Institute, Boston, Massachusetts, USA
| | - John A. Morris
- Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Caterina Barbieri
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Klaudia Walter
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Josine L. Min
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Lu Chen
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Department of Hematology, University of Cambridge, Cambridge, UK
| | - William Astle
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Massimilian Cocca
- Medical Genetics, Institute for Maternal and Child Health IRCCS “Burlo Garofolo”, Trieste, Italy
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Patrick Deelen
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Heather Elding
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Aliki-Eleni Farmaki
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | | | - Mattias Franberg
- Cardiovascular Medicine Unit, Dep. Medicine, Karolinska Institute, Stockholm, Sweden
| | - Tom R. Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Albert Hofman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Tao Jiang
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Genevieve Lachance
- Department of Twin Research & Genetic Epidemiology, King's College London, Londo, UK
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Giovanni Malerba
- Biology and Genetics, Department Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Angela Matchan
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Daniel Mead
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Yasin Memari
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Ioanna Ntalla
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | | | - Raha Pazoki
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - John R.B. Perry
- Department of Twin Research & Genetic Epidemiology, King's College London, Londo, UK
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Maria Sabater-Lleal
- Cardiovascular Medicine Unit, Dep. Medicine, Karolinska Institute, Stockholm, Sweden
| | - Bengt Sennblad
- Cardiovascular Medicine Unit, Dep. Medicine, Karolinska Institute, Stockholm, Sweden
| | - So-Youn Shin
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Lorraine Southam
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, UK
| | - Michela Traglia
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Freerk van Dijk
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | | | - Gianluigi Zaza
- Renal Unit, Department of Medicine, University of Verona, Verona, Italy
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, St Mary’s campus, London, UK
| | | | - Najaf Amin
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Adam Butterworth
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge, UK
| | - John C. Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, St Mary’s campus, London, UK
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Oscar H. Franco
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | | | - Giovanni Gambaro
- Division of Nephrology and Dialysis, Institute of Internal Medicine, Renal Program, Columbus-Gemelli University Hospital, Catholic University, Rome, Italy
| | - Paolo Gasparini
- Medical Genetics, Institute for Maternal and Child Health IRCCS “Burlo Garofolo”, Trieste, Italy
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
- Experimental Genetics Division, Sidra, Doha, Qatar
| | - Anders Hamsten
- Cardiovascular Medicine Unit, Dep. Medicine, Karolinska Institute, Stockholm, Sweden
| | - Aaron Issacs
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jaspal S. Kooner
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Winfried Marz
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
- Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim, Germany
- Medical Clinic V (Nephrology, Hypertensiology, Rheumatology, Endocrinolgy, Diabetology), Mannheim Medical Faculty, Heidelberg University, Mannheim, Germany
| | - Robert A. Scott
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Morris A. Swertz
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
- LifeLines Cohort Study, University Medical Center Groningen, Groningen, Netherlands
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Andre G. Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Cornelia M. van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Hugh Watkins
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | - Mathew T. Maurano
- Institute for Systems Genetics, New York University Langone Medical Center, New York, USA
| | - Nicholas J. Timpson
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Paul L. Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Nicole Soranzo
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Department of Hematology, University of Cambridge, Cambridge, UK
- The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge, UK
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41
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Drenos F, Davey Smith G, Ala-Korpela M, Kettunen J, Würtz P, Soininen P, Kangas AJ, Dale C, Lawlor DA, Gaunt TR, Casas JP, Timpson NJ. Metabolic Characterization of a Rare Genetic Variation Within APOC3 and Its Lipoprotein Lipase-Independent Effects. CIRCULATION. CARDIOVASCULAR GENETICS 2016; 9:231-9. [PMID: 27114411 PMCID: PMC4920206 DOI: 10.1161/circgenetics.115.001302] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 04/21/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND Plasma triglyceride levels have been implicated in atherosclerosis and coronary heart disease. Apolipoprotein C-III (APOC3) plays a key role in the hydrolysis of triglyceride-rich lipoproteins to remnant particles by lipoprotein lipase (LPL) and their uptake by the liver. A rare variant in APOC3(rs138326449) has been associated with triglyceride, very low-density lipoprotein, and high-density lipoprotein levels, as well as risk of coronary heart disease. We aimed to characterize the impact of this locus across a broad set of mainly lipids-focused metabolic measures. METHODS AND RESULTS A high-throughput serum nuclear magnetic resonance metabolomics platform was used to quantify 225 metabolic measures in 13 285 participants from 2 European population cohorts. We analyzed the effect of the APOC3 variant on the metabolic measures and used the common LPL(rs12678919) polymorphism to test for LPL-independent effects. Eighty-one metabolic measures showed evidence of association with APOC3(rs138326449). In addition to previously reported triglyceride and high-density lipoprotein associations, the variant was also associated with very low-density lipoprotein and high-density lipoprotein composition measures, other cholesterol measures, and fatty acids. Comparison of the APOC3 and LPL associations revealed that APOC3 association results for medium and very large very low-density lipoprotein composition are unlikely to be solely predictable by the action of APOC3 through LPL. CONCLUSIONS We characterized the effects of the rare APOC3(rs138326449) loss of function mutation in lipoprotein metabolism, as well as the effects of LPL(rs12678919). Our results improve our understanding of the role of APOC3 in triglyceride metabolism, its LPL independent action, and the complex and correlated nature of human metabolites.
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Affiliation(s)
- Fotios Drenos
- From the MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol (F.D., G.D.S., M.A.-K., D.A.L., T.R.G., N.J.T.); Institute of Cardiovascular Science, University College London, London, United Kingdom (F.D., C.D., J.-P.C.); Computational Medicine, Faculty of Medicine, University of Oulu & Biocenter Oulu, Oulu (M.A.-K., J.K., P.W., P.S., A.J.K.); NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio (M.A.-K., J.K., P.S.); Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland (J.K.); and Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom (C.D., J.-P.C.).
| | - George Davey Smith
- From the MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol (F.D., G.D.S., M.A.-K., D.A.L., T.R.G., N.J.T.); Institute of Cardiovascular Science, University College London, London, United Kingdom (F.D., C.D., J.-P.C.); Computational Medicine, Faculty of Medicine, University of Oulu & Biocenter Oulu, Oulu (M.A.-K., J.K., P.W., P.S., A.J.K.); NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio (M.A.-K., J.K., P.S.); Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland (J.K.); and Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom (C.D., J.-P.C.)
| | - Mika Ala-Korpela
- From the MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol (F.D., G.D.S., M.A.-K., D.A.L., T.R.G., N.J.T.); Institute of Cardiovascular Science, University College London, London, United Kingdom (F.D., C.D., J.-P.C.); Computational Medicine, Faculty of Medicine, University of Oulu & Biocenter Oulu, Oulu (M.A.-K., J.K., P.W., P.S., A.J.K.); NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio (M.A.-K., J.K., P.S.); Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland (J.K.); and Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom (C.D., J.-P.C.)
| | - Johannes Kettunen
- From the MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol (F.D., G.D.S., M.A.-K., D.A.L., T.R.G., N.J.T.); Institute of Cardiovascular Science, University College London, London, United Kingdom (F.D., C.D., J.-P.C.); Computational Medicine, Faculty of Medicine, University of Oulu & Biocenter Oulu, Oulu (M.A.-K., J.K., P.W., P.S., A.J.K.); NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio (M.A.-K., J.K., P.S.); Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland (J.K.); and Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom (C.D., J.-P.C.)
| | - Peter Würtz
- From the MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol (F.D., G.D.S., M.A.-K., D.A.L., T.R.G., N.J.T.); Institute of Cardiovascular Science, University College London, London, United Kingdom (F.D., C.D., J.-P.C.); Computational Medicine, Faculty of Medicine, University of Oulu & Biocenter Oulu, Oulu (M.A.-K., J.K., P.W., P.S., A.J.K.); NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio (M.A.-K., J.K., P.S.); Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland (J.K.); and Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom (C.D., J.-P.C.)
| | - Pasi Soininen
- From the MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol (F.D., G.D.S., M.A.-K., D.A.L., T.R.G., N.J.T.); Institute of Cardiovascular Science, University College London, London, United Kingdom (F.D., C.D., J.-P.C.); Computational Medicine, Faculty of Medicine, University of Oulu & Biocenter Oulu, Oulu (M.A.-K., J.K., P.W., P.S., A.J.K.); NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio (M.A.-K., J.K., P.S.); Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland (J.K.); and Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom (C.D., J.-P.C.)
| | - Antti J Kangas
- From the MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol (F.D., G.D.S., M.A.-K., D.A.L., T.R.G., N.J.T.); Institute of Cardiovascular Science, University College London, London, United Kingdom (F.D., C.D., J.-P.C.); Computational Medicine, Faculty of Medicine, University of Oulu & Biocenter Oulu, Oulu (M.A.-K., J.K., P.W., P.S., A.J.K.); NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio (M.A.-K., J.K., P.S.); Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland (J.K.); and Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom (C.D., J.-P.C.)
| | - Caroline Dale
- From the MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol (F.D., G.D.S., M.A.-K., D.A.L., T.R.G., N.J.T.); Institute of Cardiovascular Science, University College London, London, United Kingdom (F.D., C.D., J.-P.C.); Computational Medicine, Faculty of Medicine, University of Oulu & Biocenter Oulu, Oulu (M.A.-K., J.K., P.W., P.S., A.J.K.); NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio (M.A.-K., J.K., P.S.); Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland (J.K.); and Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom (C.D., J.-P.C.)
| | - Debbie A Lawlor
- From the MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol (F.D., G.D.S., M.A.-K., D.A.L., T.R.G., N.J.T.); Institute of Cardiovascular Science, University College London, London, United Kingdom (F.D., C.D., J.-P.C.); Computational Medicine, Faculty of Medicine, University of Oulu & Biocenter Oulu, Oulu (M.A.-K., J.K., P.W., P.S., A.J.K.); NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio (M.A.-K., J.K., P.S.); Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland (J.K.); and Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom (C.D., J.-P.C.)
| | - Tom R Gaunt
- From the MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol (F.D., G.D.S., M.A.-K., D.A.L., T.R.G., N.J.T.); Institute of Cardiovascular Science, University College London, London, United Kingdom (F.D., C.D., J.-P.C.); Computational Medicine, Faculty of Medicine, University of Oulu & Biocenter Oulu, Oulu (M.A.-K., J.K., P.W., P.S., A.J.K.); NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio (M.A.-K., J.K., P.S.); Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland (J.K.); and Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom (C.D., J.-P.C.)
| | - Juan-Pablo Casas
- From the MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol (F.D., G.D.S., M.A.-K., D.A.L., T.R.G., N.J.T.); Institute of Cardiovascular Science, University College London, London, United Kingdom (F.D., C.D., J.-P.C.); Computational Medicine, Faculty of Medicine, University of Oulu & Biocenter Oulu, Oulu (M.A.-K., J.K., P.W., P.S., A.J.K.); NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio (M.A.-K., J.K., P.S.); Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland (J.K.); and Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom (C.D., J.-P.C.)
| | - Nicholas J Timpson
- From the MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol (F.D., G.D.S., M.A.-K., D.A.L., T.R.G., N.J.T.); Institute of Cardiovascular Science, University College London, London, United Kingdom (F.D., C.D., J.-P.C.); Computational Medicine, Faculty of Medicine, University of Oulu & Biocenter Oulu, Oulu (M.A.-K., J.K., P.W., P.S., A.J.K.); NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio (M.A.-K., J.K., P.S.); Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland (J.K.); and Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom (C.D., J.-P.C.).
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Cheng TH, Thompson DJ, O'Mara TA, Painter JN, Glubb DM, Flach S, Lewis A, French JD, Freeman-Mills L, Church D, Gorman M, Martin L, Hodgson S, Webb PM, Attia J, Holliday EG, McEvoy M, Scott RJ, Henders AK, Martin NG, Montgomery GW, Nyholt DR, Ahmed S, Healey CS, Shah M, Dennis J, Fasching PA, Beckmann MW, Hein A, Ekici AB, Hall P, Czene K, Darabi H, Li J, Dörk T, Dürst M, Hillemanns P, Runnebaum I, Amant F, Schrauwen S, Zhao H, Lambrechts D, Depreeuw J, Dowdy SC, Goode EL, Fridley BL, Winham SJ, Njølstad TS, Salvesen HB, Trovik J, Werner HM, Ashton K, Otton G, Proietto T, Liu T, Mints M, Tham E, Consortium C, Jun Li M, Yip SH, Wang J, Bolla MK, Michailidou K, Wang Q, Tyrer JP, Dunlop M, Houlston R, Palles C, Hopper JL, Peto J, Swerdlow AJ, Burwinkel B, Brenner H, Meindl A, Brauch H, Lindblom A, Chang-Claude J, Couch FJ, Giles GG, Kristensen VN, Cox A, Cunningham JM, Pharoah PDP, Dunning AM, Edwards SL, Easton DF, Tomlinson I, Spurdle AB. Five endometrial cancer risk loci identified through genome-wide association analysis. Nat Genet 2016; 48:667-674. [PMID: 27135401 PMCID: PMC4907351 DOI: 10.1038/ng.3562] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 04/08/2016] [Indexed: 12/18/2022]
Abstract
We conducted a meta-analysis of three endometrial cancer genome-wide association studies (GWAS) and two follow-up phases totaling 7,737 endometrial cancer cases and 37,144 controls of European ancestry. Genome-wide imputation and meta-analysis identified five new risk loci of genome-wide significance at likely regulatory regions on chromosomes 13q22.1 (rs11841589, near KLF5), 6q22.31 (rs13328298, in LOC643623 and near HEY2 and NCOA7), 8q24.21 (rs4733613, telomeric to MYC), 15q15.1 (rs937213, in EIF2AK4, near BMF) and 14q32.33 (rs2498796, in AKT1, near SIVA1). We also found a second independent 8q24.21 signal (rs17232730). Functional studies of the 13q22.1 locus showed that rs9600103 (pairwise r(2) = 0.98 with rs11841589) is located in a region of active chromatin that interacts with the KLF5 promoter region. The rs9600103[T] allele that is protective in endometrial cancer suppressed gene expression in vitro, suggesting that regulation of the expression of KLF5, a gene linked to uterine development, is implicated in tumorigenesis. These findings provide enhanced insight into the genetic and biological basis of endometrial cancer.
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Affiliation(s)
- Timothy Ht Cheng
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Tracy A O'Mara
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Jodie N Painter
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Dylan M Glubb
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Susanne Flach
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Annabelle Lewis
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Juliet D French
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Luke Freeman-Mills
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Church
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Maggie Gorman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lynn Martin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Shirley Hodgson
- Department of Clinical Genetics, St George's, University of London, London, UK
| | - Penelope M Webb
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - John Attia
- Hunter Medical Research Institute, John Hunter Hospital, Newcastle, NSW, Australia
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, NSW, Australia
| | - Elizabeth G Holliday
- Hunter Medical Research Institute, John Hunter Hospital, Newcastle, NSW, Australia
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, NSW, Australia
| | - Mark McEvoy
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, NSW, Australia
| | - Rodney J Scott
- Hunter Medical Research Institute, John Hunter Hospital, Newcastle, NSW, Australia
- Hunter Area Pathology Service, John Hunter Hospital, Newcastle, NSW, Australia
- Centre for Information Based Medicine, University of Newcastle, NSW, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW, Australia
| | - Anjali K Henders
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Nicholas G Martin
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Grant W Montgomery
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Dale R Nyholt
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - Shahana Ahmed
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Catherine S Healey
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Peter A Fasching
- University of California at Los Angeles, Department of Medicine, Division of Hematology/Oncology, David Geffen School of Medicine, Los Angeles, CA, USA
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Alexander Hein
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jingmei Li
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Thilo Dörk
- Hannover Medical School, Gynaecology Research Unit, Hannover, Germany
| | - Matthias Dürst
- Department of Gynaecology, Jena University Hospital - Friedrich Schiller University, Jena, Germany
| | - Peter Hillemanns
- Hannover Medical School, Clinics of Gynaecology and Obstetrics, Hannover, Germany
| | - Ingo Runnebaum
- Department of Gynaecology, Jena University Hospital - Friedrich Schiller University, Jena, Germany
| | - Frederic Amant
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University Hospitals, KU Leuven - University of Leuven, Belgium
| | - Stefanie Schrauwen
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University Hospitals, KU Leuven - University of Leuven, Belgium
| | - Hui Zhao
- Vesalius Research Center, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Jeroen Depreeuw
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University Hospitals, KU Leuven - University of Leuven, Belgium
- Vesalius Research Center, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Sean C Dowdy
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Mayo Clinic, Rochester, MN, USA
| | - Ellen L Goode
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Brooke L Fridley
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, USA
| | - Stacey J Winham
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Tormund S Njølstad
- Centre for Cancerbiomarkers, Department of Clinical Science, The University of Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Helga B Salvesen
- Centre for Cancerbiomarkers, Department of Clinical Science, The University of Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Jone Trovik
- Centre for Cancerbiomarkers, Department of Clinical Science, The University of Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Henrica Mj Werner
- Centre for Cancerbiomarkers, Department of Clinical Science, The University of Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Katie Ashton
- Hunter Medical Research Institute, John Hunter Hospital, Newcastle, NSW, Australia
- Centre for Information Based Medicine, University of Newcastle, NSW, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW, Australia
| | - Geoffrey Otton
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, Australia
| | - Tony Proietto
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, Australia
| | - Tao Liu
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Miriam Mints
- Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Chibcha Consortium
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- A list of members and affiliations appears in the Supplementary Note
| | - Mulin Jun Li
- Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Shun H Yip
- Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Junwen Wang
- Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jonathan P Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Malcolm Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Western General Hospital Edinburgh, Edinburgh, UK
| | - Richard Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Claire Palles
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Vic, Australia
| | - Julian Peto
- London School of Hygiene and Tropical Medicine, London, UK
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, Institute of Cancer Research, London, UK
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany
- Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alfons Meindl
- Department of Obstetrics and Gynecology, Division of Tumor Genetics, Technical University of Munich, Munich, Germany
| | - Hiltrud Brauch
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fergus J Couch
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Vic, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Vic, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Vic, Australia
| | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
- Department of Clinical Molecular Oncology, Division of Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Angela Cox
- Sheffield Cancer Research, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Stacey L Edwards
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
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Gilly A, Ritchie GR, Southam L, Farmaki AE, Tsafantakis E, Dedoussis G, Zeggini E. Very low-depth sequencing in a founder population identifies a cardioprotective APOC3 signal missed by genome-wide imputation. Hum Mol Genet 2016; 25:2360-2365. [PMID: 27146844 PMCID: PMC5081052 DOI: 10.1093/hmg/ddw088] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/14/2016] [Indexed: 11/13/2022] Open
Abstract
Cohort-wide very low-depth whole-genome sequencing (WGS) can comprehensively capture low-frequency sequence variation for the cost of a dense genome-wide genotyping array. Here, we analyse 1x sequence data across the APOC3 gene in a founder population from the island of Crete in Greece (n = 1239) and find significant evidence for association with blood triglyceride levels with the previously reported R19X cardioprotective null mutation (β = -1.09,σ = 0.163, P = 8.2 × 10-11) and a second loss of function mutation, rs138326449 (β = -1.17,σ = 0.188, P = 1.14 × 10-9). The signal cannot be recapitulated by imputing genome-wide genotype data on a large reference panel of 5122 individuals including 249 with 4x WGS data from the same population. Gene-level meta-analysis with other studies reporting burden signals at APOC3 provides robust evidence for a replicable cardioprotective rare variant aggregation (P = 3.2 × 10-31, n = 13 480).
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Affiliation(s)
- Arthur Gilly
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Graham Rs Ritchie
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lorraine Southam
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Aliki-Eleni Farmaki
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens 17671, Greece
| | | | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens 17671, Greece
| | - Eleftheria Zeggini
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
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Abstract
Empirical studies and evolutionary theory support a role for rare variants in the etiology of complex traits. Given this motivation and increasing affordability of whole-exome and whole-genome sequencing, methods for rare variant association have been an active area of research for the past decade. Here, we provide a survey of the current literature and developments from the Genetics Analysis Workshop 19 (GAW19) Collapsing Rare Variants working group. In particular, we present the generalized linear regression framework and associated score statistic for the 2 major types of methods: burden and variance components methods. We further show that by simply modifying weights within these frameworks we arrive at many of the popular existing methods, for example, the cohort allelic sums test and sequence kernel association test. Meta-analysis techniques are also described. Next, we describe the 6 contributions from the GAW19 Collapsing Rare Variants working group. These included development of new methods, such as a retrospective likelihood for family data, a method using genomic structure to compare cases and controls, a haplotype-based meta-analysis, and a permutation-based method for combining different statistical tests. In addition, one contribution compared a mega-analysis of family-based and population-based data to meta-analysis. Finally, the power of existing family-based methods for binary traits was compared. We conclude with suggestions for open research questions.
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Affiliation(s)
- Stephanie A Santorico
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO, 80217-3364, USA.
| | - Audrey E Hendricks
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO, 80217-3364, USA.
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Update on the molecular biology of dyslipidemias. Clin Chim Acta 2016; 454:143-85. [DOI: 10.1016/j.cca.2015.10.033] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/24/2015] [Accepted: 10/30/2015] [Indexed: 12/20/2022]
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Richardson TG, Shihab HA, Rivas MA, McCarthy MI, Campbell C, Timpson NJ, Gaunt TR. A Protein Domain and Family Based Approach to Rare Variant Association Analysis. PLoS One 2016; 11:e0153803. [PMID: 27128313 PMCID: PMC4851355 DOI: 10.1371/journal.pone.0153803] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 04/04/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND It has become common practice to analyse large scale sequencing data with statistical approaches based around the aggregation of rare variants within the same gene. We applied a novel approach to rare variant analysis by collapsing variants together using protein domain and family coordinates, regarded to be a more discrete definition of a biologically functional unit. METHODS Using Pfam definitions, we collapsed rare variants (Minor Allele Frequency ≤ 1%) together in three different ways 1) variants within single genomic regions which map to individual protein domains 2) variants within two individual protein domain regions which are predicted to be responsible for a protein-protein interaction 3) all variants within combined regions from multiple genes responsible for coding the same protein domain (i.e. protein families). A conventional collapsing analysis using gene coordinates was also undertaken for comparison. We used UK10K sequence data and investigated associations between regions of variants and lipid traits using the sequence kernel association test (SKAT). RESULTS We observed no strong evidence of association between regions of variants based on Pfam domain definitions and lipid traits. Quantile-Quantile plots illustrated that the overall distributions of p-values from the protein domain analyses were comparable to that of a conventional gene-based approach. Deviations from this distribution suggested that collapsing by either protein domain or gene definitions may be favourable depending on the trait analysed. CONCLUSION We have collapsed rare variants together using protein domain and family coordinates to present an alternative approach over collapsing across conventionally used gene-based regions. Although no strong evidence of association was detected in these analyses, future studies may still find value in adopting these approaches to detect previously unidentified association signals.
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Affiliation(s)
- Tom G. Richardson
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Hashem A. Shihab
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Manuel A. Rivas
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom
| | - Colin Campbell
- Intelligent Systems Laboratory, University of Bristol, Bristol, United Kingdom
| | - Nicholas J. Timpson
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Tom R. Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
- * E-mail:
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Incorporating Non-Coding Annotations into Rare Variant Analysis. PLoS One 2016; 11:e0154181. [PMID: 27128317 PMCID: PMC4851421 DOI: 10.1371/journal.pone.0154181] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/11/2016] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The success of collapsing methods which investigate the combined effect of rare variants on complex traits has so far been limited. The manner in which variants within a gene are selected prior to analysis has a crucial impact on this success, which has resulted in analyses conventionally filtering variants according to their consequence. This study investigates whether an alternative approach to filtering, using annotations from recently developed bioinformatics tools, can aid these types of analyses in comparison to conventional approaches. METHODS & RESULTS We conducted a candidate gene analysis using the UK10K sequence and lipids data, filtering according to functional annotations using the resource CADD (Combined Annotation-Dependent Depletion) and contrasting results with 'nonsynonymous' and 'loss of function' consequence analyses. Using CADD allowed the inclusion of potentially deleterious intronic variants, which was not possible when filtering by consequence. Overall, different filtering approaches provided similar evidence of association, although filtering according to CADD identified evidence of association between ANGPTL4 and High Density Lipoproteins (P = 0.02, N = 3,210) which was not observed in the other analyses. We also undertook genome-wide analyses to determine how filtering in this manner compared to conventional approaches for gene regions. Results suggested that filtering by annotations according to CADD, as well as other tools known as FATHMM-MKL and DANN, identified association signals not detected when filtering by variant consequence and vice versa. CONCLUSION Incorporating variant annotations from non-coding bioinformatics tools should prove to be a valuable asset for rare variant analyses in the future. Filtering by variant consequence is only possible in coding regions of the genome, whereas utilising non-coding bioinformatics annotations provides an opportunity to discover unknown causal variants in non-coding regions as well. This should allow studies to uncover a greater number of causal variants for complex traits and help elucidate their functional role in disease.
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48
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Richardson TG, Timpson NJ, Campbell C, Gaunt TR. A pathway-centric approach to rare variant association analysis. Eur J Hum Genet 2016; 25:123-129. [PMID: 27577545 PMCID: PMC5136291 DOI: 10.1038/ejhg.2016.113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 05/18/2016] [Accepted: 07/19/2016] [Indexed: 01/01/2023] Open
Abstract
Current endeavours in rare variant analysis are typically underpowered when investigating association signals from individual genes. We undertook an approach to rare variant analysis which utilises biological pathway information to analyse functionally relevant genes together. Conventional filtering approaches for rare variant analysis are based on variant consequence and are therefore confined to coding regions of the genome. Therefore, we undertook a novel approach to this process by obtaining functional annotations from the Combined Annotation Dependent Depletion (CADD) tool, which allowed potentially deleterious variants from intronic regions of genes to be incorporated into analyses. This work was undertaken using whole-genome sequencing data from the UK10K project. Rare variants from the KEGG pathway for arginine and proline metabolism were collectively associated with systolic blood pressure (P=3.32x10-5) based on analyses using the optimal sequence kernel association test. Variants along this pathway also showed evidence of replication using imputed data from the Avon Longitudinal Study of Parents and Children cohort (P=0.02). Subsequent analyses found that the strength of evidence diminished when analysing genes in this pathway individually, suggesting that they would have been overlooked in a conventional gene-based analysis. Future studies that adopt similar approaches to investigate polygenic effects should yield value in better understanding the genetic architecture of complex disease.
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Affiliation(s)
- Tom G Richardson
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Colin Campbell
- Intelligent Systems Laboratory, University of Bristol, Bristol, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK.
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Strength in numbers in the low-frequency spectrum. Nat Rev Genet 2015; 16:623. [DOI: 10.1038/nrg4024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Norata GD, Tsimikas S, Pirillo A, Catapano AL. Apolipoprotein C-III: From Pathophysiology to Pharmacology. Trends Pharmacol Sci 2015; 36:675-687. [DOI: 10.1016/j.tips.2015.07.001] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/07/2015] [Accepted: 07/10/2015] [Indexed: 01/14/2023]
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