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1. Mitochondrial DNA variants modulate N-formylmethionine, proteostasis and risk of late-onset human diseases

Author

Medical Research Council (UK), Engineering and Physical Sciences Research Council (UK), Economic and Social Research Council (UK), Department of Health & Social Care (UK), Wellcome Trust, University of Cambridge, European Commission, NIHR Biomedical Research Centre (UK), Cai, Na [0000-0001-7496-2075], Gómez-Durán, Aurora [0000-0002-5895-6860], Kundu, Kousik [0000-0002-1019-8351], Burgess, Annette I. [0000-0003-3442-8083], Calabrese, Claudia [0000-0002-8941-2620], Camacho, Marta [0000-0002-1490-5703], Lawson, Rachael A. [0000-0003-2608-8285], Williams-Gray, Caroline H. [0000-0002-2648-9743], Di Angelantonio, Emanuele [0000-0001-8776-6719], Butterworth, Adam S. [0000-0002-6915-9015], Pietzner, Maik [0000-0003-3437-9963], Wareham, Nicholas J. [0000-0003-1422-2993], Langenberg, Claudia [0000-0002-5017-7344], Danesh, John [0000-0003-1158-6791], Walter, Klaudia [0000-0003-4448-0301], Rothwell, Peter M. [0000-0001-9739-9211], Howson, Joanna M. M. [0000-0001-7618-0050], Stegle, Oliver [0000-0002-8818-7193], Chinnery, Patrick F. [0000-0002-7065-6617], Soranzo, Nicole [0000-0003-1095-3852], Cai, Na, Gómez-Durán, Aurora, Yonova-Doing, Ekaterina, Kundu, Kousik, Burgess, Annette I., Golder, Zoe J., Calabrese, Claudia, Bonder, Marc J., Camacho, Marta, Lawson, Rachael A., Li, Lixin, Williams-Gray, Caroline H., ICICLE-PD Study Group, Di Angelantonio, Emanuele, Roberts, David J., Watkins, Nick A., Ouwehand, Willem H., Butterworth, Adam S., Stewart, Isobel D., Pietzner, Maik, Wareham, Nicholas J., Langenberg, Claudia, Danesh, John, Walter, Klaudia, Rothwell, Peter M., Howson, Joanna M. M., Stegle, Oliver, Chinnery, Patrick F., Soranzo, Nicole, Medical Research Council (UK), Engineering and Physical Sciences Research Council (UK), Economic and Social Research Council (UK), Department of Health & Social Care (UK), Wellcome Trust, University of Cambridge, European Commission, NIHR Biomedical Research Centre (UK), Cai, Na [0000-0001-7496-2075], Gómez-Durán, Aurora [0000-0002-5895-6860], Kundu, Kousik [0000-0002-1019-8351], Burgess, Annette I. [0000-0003-3442-8083], Calabrese, Claudia [0000-0002-8941-2620], Camacho, Marta [0000-0002-1490-5703], Lawson, Rachael A. [0000-0003-2608-8285], Williams-Gray, Caroline H. [0000-0002-2648-9743], Di Angelantonio, Emanuele [0000-0001-8776-6719], Butterworth, Adam S. [0000-0002-6915-9015], Pietzner, Maik [0000-0003-3437-9963], Wareham, Nicholas J. [0000-0003-1422-2993], Langenberg, Claudia [0000-0002-5017-7344], Danesh, John [0000-0003-1158-6791], Walter, Klaudia [0000-0003-4448-0301], Rothwell, Peter M. [0000-0001-9739-9211], Howson, Joanna M. M. [0000-0001-7618-0050], Stegle, Oliver [0000-0002-8818-7193], Chinnery, Patrick F. [0000-0002-7065-6617], Soranzo, Nicole [0000-0003-1095-3852], Cai, Na, Gómez-Durán, Aurora, Yonova-Doing, Ekaterina, Kundu, Kousik, Burgess, Annette I., Golder, Zoe J., Calabrese, Claudia, Bonder, Marc J., Camacho, Marta, Lawson, Rachael A., Li, Lixin, Williams-Gray, Caroline H., ICICLE-PD Study Group, Di Angelantonio, Emanuele, Roberts, David J., Watkins, Nick A., Ouwehand, Willem H., Butterworth, Adam S., Stewart, Isobel D., Pietzner, Maik, Wareham, Nicholas J., Langenberg, Claudia, Danesh, John, Walter, Klaudia, Rothwell, Peter M., Howson, Joanna M. M., Stegle, Oliver, Chinnery, Patrick F., and Soranzo, Nicole

Abstract

Mitochondrial DNA (mtDNA) variants influence the risk of late-onset human diseases, but the reasons for this are poorly understood. Undertaking a hypothesis-free analysis of 5,689 blood-derived biomarkers with mtDNA variants in 16,220 healthy donors, here we show that variants defining mtDNA haplogroups Uk and H4 modulate the level of circulating N-formylmethionine (fMet), which initiates mitochondrial protein translation. In human cytoplasmic hybrid (cybrid) lines, fMet modulated both mitochondrial and cytosolic proteins on multiple levels, through transcription, post-translational modification and proteolysis by an N-degron pathway, abolishing known differences between mtDNA haplogroups. In a further 11,966 individuals, fMet levels contributed to all-cause mortality and the disease risk of several common cardiovascular disorders. Together, these findings indicate that fMet plays a key role in common age-related disease through pleiotropic effects on cell proteostasis.

Published
2021

2. Genetically personalised organ-specific metabolic models in health and disease

Author

Carles Foguet, Yu Xu, Scott C. Ritchie, Samuel A. Lambert, Elodie Persyn, Artika P. Nath, Emma E. Davenport, David J. Roberts, Dirk S. Paul, Emanuele Di Angelantonio, John Danesh, Adam S. Butterworth, Christopher Yau, Michael Inouye, Foguet, Carles [0000-0001-8494-9595], Xu, Yu [0000-0002-7304-5045], Ritchie, Scott C [0000-0002-8454-9548], Lambert, Samuel A [0000-0001-8222-008X], Paul, Dirk S [0000-0002-8230-0116], Butterworth, Adam S [0000-0002-6915-9015], Inouye, Michael [0000-0001-9413-6520], Apollo - University of Cambridge Repository, Ritchie, Scott C. [0000-0002-8454-9548], Lambert, Samuel A. [0000-0001-8222-008X], Paul, Dirk S. [0000-0002-8230-0116], and Butterworth, Adam S. [0000-0002-6915-9015]

Subjects
141, Multidisciplinary, Genome, Human, 45/43, article, Brain, General Physics and Astronomy, Heart, Coronary Artery Disease, General Chemistry, 631/45/320, 119/118, 140/58, 692/699/75, General Biochemistry, Genetics and Molecular Biology, 631/553/2710, Adipose Tissue, 140/131, Humans
Abstract

Funder: RCUK | Science and Technology Facilities Council (STFC); doi: https://doi.org/10.13039/501100000271, Funder: Scottish Government Health and Social Care Directorate (SGHSC); doi: https://doi.org/10.13039/100011529, Funder: Wellcome Trust (Wellcome); doi: https://doi.org/10.13039/100010269, Funder: NHS Blood and Transplant; doi: https://doi.org/10.13039/100009033, Funder: Health Data Research UK Department of Health and Social Care (England) Health and Social Care Research and Development Division (Welsh Government) Public Health Agency (Northern Ireland), Understanding how genetic variants influence disease risk and complex traits (variant-to-function) is one of the major challenges in human genetics. Here we present a model-driven framework to leverage human genome-scale metabolic networks to define how genetic variants affect biochemical reaction fluxes across major human tissues, including skeletal muscle, adipose, liver, brain and heart. As proof of concept, we build personalised organ-specific metabolic flux models for 524,615 individuals of the INTERVAL and UK Biobank cohorts and perform a fluxome-wide association study (FWAS) to identify 4,312 associations between personalised flux values and the concentration of metabolites in blood. Furthermore, we apply FWAS to identify 92 metabolic fluxes associated with the risk of developing coronary artery disease, many of which are linked to processes previously described to play in role in the disease. Our work demonstrates that genetically personalised metabolic models can elucidate the downstream effects of genetic variants on biochemical reactions involved in common human diseases., Participants in the INTERVAL trial were recruited with the active collaboration of NHS Blood and Transplant (www.nhsbt.nhs.uk), which has supported fieldwork and other elements of the trial. DNA extraction and genotyping were co-funded by the National Institute for Health and Care Research (NIHR), the NIHR BioResource (http://bioresource.nihr.ac.uk) and the NIHR Cambridge Biomedical Research Centre (BRC) (no. BRC-1215-20014)*. Nightingale Health NMR assays were funded by the European Commission Framework Programme 7 (HEALTH-F2-2012-279233). Metabolon Metabolomics assays were funded by the NIHR BioResource and the NIHR Cambridge Biomedical Research Centre (BRC-1215-20014)*. The academic coordinating centre for INTERVAL was supported by core funding from the NIHR Blood and Transplant Research Unit in Donor Health and Genomics (no. NIHR BTRU-2014-10024), NIHR BTRU in Donor Health and Behaviour (NIHR203337), UK Medical Research Council (MRC) (no. MR/L003120/1), British Heart Foundation (nos SP/09/002, RG/13/13/30194 and RG/18/13/33946) and the NIHR Cambridge BRC (no. BRC-1215-20014)*. *The views expressed are those of the author(s) and not necessarily those of the NIHR, NHSBT or the Department of Health and Social Care. A complete list of the investigators and contributors to the INTERVAL trial is provided in ref. 36. The academic coordinating centre would like to thank blood donor centre staff and blood donors for participating in the INTERVAL trial. This work was supported by Health Data Research UK, which is funded by the UK MRC, Engineering and Physical Sciences Research Council (EPSRC), Economic and Social Research Council, Department of Health and Social Care (England), Chief Scientist Office of the Scottish Government Health and Social Care Directorates, Health and Social Care Research and Development Division (Welsh Government), Public Health Agency (Northern Ireland), British Heart Foundation and Wellcome. The authors are grateful to UK Biobank for access to data to undertake this study (Projects #7439). This work was performed using resources provided by the Cambridge Service for Data Driven Discovery (CSD3) operated by the University of Cambridge Research Computing Service (www.csd3.cam.ac.uk), provided by Dell EMC and Intel using Tier-2 funding from the Engineering and Physical Sciences Research Council (capital grant EP/P020259/1), and DiRAC funding from the Science and Technology Facilities Council (www.dirac.ac.uk). S.R. is funded by the NIHR Cambridge Biomedical Research Centre (BRC-1215-20014). S.L. is supported by a Canadian Institutes of Health Research postdoctoral fellowship (MFE-171279). E.P. was funded by the EU/EFPIA Innovative Medicines Initiative Joint Undertaking BigData@Heart grant 116074 and the NIHR BTRU in Donor Health and Genomics (NIHR BTRU-2014-10024) and is funded by the NIHR BTRU in Donor Health and Behaviour (NIHR203337). J.D. holds a British Heart Foundation Professorship and a NIHR Senior Investigator Award. M.I. is supported by the Munz Chair of Cardiovascular Prediction and Prevention and the NIHR Cambridge Biomedical Research Centre (BRC-1215-20014). M.I. was also supported by the UK Economic and Social Research 878 Council (ES/T013192/1).

Published
2022
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3. Polygenic basis and biomedical consequences of telomere length variation

Author

Christopher P. Nelson, Veryan Codd, John R Thompson, Crispin Musicha, Tao Jiang, Angela M. Wood, Shilpi Sheth, Charley A. Budgeon, Willem H. Ouwehand, Emanuele Di Angelantonio, Svetlana Stoma, Vasiliki Bountziouka, Matthew Denniff, Peter S. Braund, James Eales, Stephen E. Hamby, Sophie C Warner, Dominika E Nanus, Qingning Wang, Stephen Kaptoge, Chloe Swinfield, Amit Khera, Manolo Papakonstantinou, Nilesh J. Samani, Adam S. Butterworth, John Danesh, Minxian Wang, Elias Allara, Codd, Veryan [0000-0002-9430-8254], Allara, Elias [0000-0002-1634-8330], Braund, Peter S. [0000-0001-8540-5709], Papakonstantinou, Manolo [0000-0003-2664-9046], Wang, Minxian [0000-0002-3753-508X], Khera, Amit V. [0000-0001-6535-5839], Eales, James [0000-0001-6238-5952], Ouwehand, Willem H. [0000-0002-7744-1790], Thompson, John R. [0000-0003-4819-1611], Butterworth, Adam S. [0000-0002-6915-9015], Samani, Nilesh J. [0000-0002-3286-8133], Apollo - University of Cambridge Repository, Braund, Peter S [0000-0001-8540-5709], Khera, Amit V [0000-0001-6535-5839], Ouwehand, Willem H [0000-0002-7744-1790], Thompson, John R [0000-0003-4819-1611], Butterworth, Adam S [0000-0002-6915-9015], Samani, Nilesh J [0000-0002-3286-8133], Kaptoge, Stephen [0000-0002-1155-4872], Ouwehand, Willem [0000-0002-7744-1790], Di Angelantonio, Emanuele [0000-0001-8776-6719], Wood, Angela [0000-0002-7937-304X], Butterworth, Adam [0000-0002-6915-9015], and Danesh, John [0000-0003-1158-6791]

Subjects
Senescence, Multifactorial Inheritance, media_common.quotation_subject, Quantitative Trait Loci, 631/208/205/2138, 45/43, Computational biology, Biology, Genome-wide association studies, Health data, Length variation, Genetics research, Genetics, Humans, media_common, Basis (linear algebra), Genome, Human, Longevity, 692/308/2056, article, Telomere Homeostasis, Mendelian Randomization Analysis, Biobank, Phenotype, Genetic architecture, Telomere, Evolutionary biology, Function (biology), Genome-Wide Association Study
Abstract

Funder: Health Data Research UK EU/EFPIA Innovative Medicines Initiative Joint Undertaking BigData@Heart (11607)., Funder: Health Data Research UK, Telomeres, the end fragments of chromosomes, play key roles in cellular proliferation and senescence. Here we characterize the genetic architecture of naturally occurring variation in leukocyte telomere length (LTL) and identify causal links between LTL and biomedical phenotypes in 472,174 well-characterized UK Biobank participants. We identified 197 independent sentinel variants associated with LTL at 138 genomic loci (108 new). Genetically determined differences in LTL were associated with multiple biological traits, ranging from height to bone marrow function, as well as several diseases spanning neoplastic, vascular and inflammatory pathologies. Finally, we estimated that, at the age of 40 years, people with an LTL >1 s.d. shorter than the population mean had a 2.5-year-lower life expectancy compared with the group with ≥1 s.d. longer LDL. Overall, we furnish new insights into the genetic regulation of LTL, reveal wide-ranging influences of LTL on physiological traits, diseases and longevity, and provide a powerful resource available to the global research community.

Published
2021

4. Large genome-wide association study identifies three novel risk variants for restless legs syndrome

Author

Thordur Sigmundsson, Erik Sørensen, David B. Rye, Katja van den Hurk, Franke A. Quee, Poul Jennum, Muhammad Nawaz, Willem H. Ouwehand, Michael W.T. Tanck, Steven Bell, Sigurdur H. Magnusson, Hreinn Stefansson, Gudmar Thorleifsson, Nicole Soranzo, Prabhjyot Saini, Maria Didriksen, Joseph Dowsett, Emanuele Di Angelantonio, Lynn Marie Trotti, Henrik Ullum, Eric J. Earley, Alan E. Mast, Michael P. Busch, David J. Roberts, Christian Erikstrup, Kari Stefansson, Kristoffer Sølvsten Burgdorf, Albert P. Sigurdsson, Ole Birger Pedersen, John Danesh, Grier P. Page, Lilja Stefansdottir, Brendan Burchell, Adam S. Butterworth, Didriksen, Maria [0000-0002-4856-496X], Nawaz, Muhammad Sulaman [0000-0002-5576-9007], Dowsett, Joseph [0000-0001-5381-2633], Bell, Steven [0000-0001-6774-3149], Erikstrup, Christian [0000-0001-6551-6647], Pedersen, Ole B [0000-0003-2312-5976], Burchell, Brendan [0000-0002-8243-937X], Butterworth, Adam S [0000-0002-6915-9015], Tanck, Michael WT [0000-0001-9828-4459], Ouwehand, Willem H [0000-0002-7744-1790], Earley, Eric J [0000-0001-6576-1319], Busch, Michael P [0000-0002-1446-125X], Page, Grier P [0000-0003-2582-3786], Stefansson, Hreinn [0000-0002-9331-6666], Stefansson, Kari [0000-0003-1676-864X], Apollo - University of Cambridge Repository, Pedersen, Ole B. [0000-0003-2312-5976], Butterworth, Adam S. [0000-0002-6915-9015], Tanck, Michael W. T. [0000-0001-9828-4459], Ouwehand, Willem H. [0000-0002-7744-1790], Earley, Eric J. [0000-0001-6576-1319], Busch, Michael P. [0000-0002-1446-125X], Page, Grier P. [0000-0003-2582-3786], Epidemiology and Data Science, APH - Methodology, and Public and occupational health

Subjects
0301 basic medicine, Adult, medicine.medical_specialty, Linkage disequilibrium, QH301-705.5, 692/617/375/1816, 631/208/205/2138, Medicine (miscellaneous), Genome-wide association study, Disease, Bioinformatics, Genome-wide association studies, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Linkage Disequilibrium, 38, 38/43, 03 medical and health sciences, 0302 clinical medicine, Restless Legs Syndrome, Epidemiology, 38/23, mental disorders, medicine, Humans, Genetic Predisposition to Disease, Restless legs syndrome, Biology (General), health care economics and organizations, Genetic association, Aged, business.industry, article, Sleep disorders, Middle Aged, medicine.disease, Obesity, 631/208/199, 030104 developmental biology, Meta-analysis, 38/39, Gene expression, General Agricultural and Biological Sciences, business, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

Funder: Scottish Government; doi: https://doi.org/10.13039/100012095, Funder: Cancer Research UK (CRUK); doi: https://doi.org/10.13039/501100000289, Restless legs syndrome (RLS) is a common neurological sensorimotor disorder often described as an unpleasant sensation associated with an urge to move the legs. Here we report findings from a meta-analysis of genome-wide association studies of RLS including 480,982 Caucasians (cases = 10,257) and a follow up sample of 24,977 (cases = 6,651). We confirm 19 of the 20 previously reported RLS sequence variants at 19 loci and report three novel RLS associations; rs112716420-G (OR = 1.25, P = 1.5 × 10−18), rs10068599-T (OR = 1.09, P = 6.9 × 10−10) and rs10769894-A (OR = 0.90, P = 9.4 × 10−14). At four of the 22 RLS loci, cis-eQTL analysis indicates a causal impact on gene expression. Through polygenic risk score for RLS we extended prior epidemiological findings implicating obesity, smoking and high alcohol intake as risk factors for RLS. To improve our understanding, with the purpose of seeking better treatments, more genetics studies yielding deeper insights into the disease biology are needed.

Published
2020

5. Mitochondrial DNA variants modulate N-formylmethionine, proteostasis and risk of late-onset human diseases

Author

Rachael A Lawson, Adam S. Butterworth, Emanuele Di Angelantonio, Klaudia Walter, Joanna M M Howson, Lixin Li, Caroline H. Williams-Gray, Ekaterina Yonova-Doing, Zoe J. Golder, Marta Camacho, Aurora Gomez-Duran, Peter M. Rothwell, Kousik Kundu, Na Cai, Maik Pietzner, Nicholas J. Wareham, John Danesh, Annette I. Burgess, Willem H. Ouwehand, Oliver Stegle, Marc Jan Bonder, Claudia Calabrese, Claudia Langenberg, Nicole Soranzo, Nicholas A. Watkins, Patrick F. Chinnery, David J. Roberts, Isobel D. Stewart, Medical Research Council (UK), Engineering and Physical Sciences Research Council (UK), Economic and Social Research Council (UK), Department of Health & Social Care (UK), Wellcome Trust, University of Cambridge, European Commission, NIHR Biomedical Research Centre (UK), Cai, Na, Gómez-Durán, Aurora, Kundu, Kousik, Burgess, Annette I., Calabrese, Claudia, Camacho, Marta, Lawson, Rachael A., Williams-Gray, Caroline H., Di Angelantonio, Emanuele, Butterworth, Adam S., Pietzner, Maik, Wareham, Nicholas J., Langenberg, Claudia, Danesh, John, Walter, Klaudia, Rothwell, Peter M., Howson, Joanna M. M., Stegle, Oliver, Chinnery, Patrick F., Soranzo, Nicole, Cai, Na [0000-0001-7496-2075], Gómez-Durán, Aurora [0000-0002-5895-6860], Kundu, Kousik [0000-0002-1019-8351], Burgess, Annette I. [0000-0003-3442-8083], Calabrese, Claudia [0000-0002-8941-2620], Camacho, Marta [0000-0002-1490-5703], Lawson, Rachael A. [0000-0003-2608-8285], Williams-Gray, Caroline H. [0000-0002-2648-9743], Di Angelantonio, Emanuele [0000-0001-8776-6719], Butterworth, Adam S. [0000-0002-6915-9015], Pietzner, Maik [0000-0003-3437-9963], Wareham, Nicholas J. [0000-0003-1422-2993], Langenberg, Claudia [0000-0002-5017-7344], Danesh, John [0000-0003-1158-6791], Walter, Klaudia [0000-0003-4448-0301], Rothwell, Peter M. [0000-0001-9739-9211], Howson, Joanna M. M. [0000-0001-7618-0050], Stegle, Oliver [0000-0002-8818-7193], Chinnery, Patrick F. [0000-0002-7065-6617], Soranzo, Nicole [0000-0003-1095-3852], Burgess, Annette I [0000-0003-3442-8083], Lawson, Rachael A [0000-0003-2608-8285], Butterworth, Adam S [0000-0002-6915-9015], Wareham, Nick J [0000-0003-1422-2993], Howson, Joanna MM [0000-0001-7618-0050], Chinnery, Patrick F [0000-0002-7065-6617], and Apollo - University of Cambridge Repository

Subjects
Male, Mitochondrial DNA, education, Cell, Blood Donors, Disease, Biology, Cytoplasmic hybrid, DNA, Mitochondrial, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Transcription (biology), Risk Factors, medicine, Humans, Age of Onset, health care economics and organizations, 030304 developmental biology, Genetics, 0303 health sciences, N-Formylmethionine, General Medicine, Middle Aged, United Kingdom, 3. Good health, Mitochondria, Cytosol, Proteostasis, medicine.anatomical_structure, Haplotypes, Cardiovascular Diseases, Female, 030217 neurology & neurosurgery, Biomarkers, Human mitochondrial DNA haplogroup, Follow-Up Studies
Abstract

47 p.-11 fig., Mitochondrial DNA (mtDNA) variants influence the risk of late-onset human diseases, but the reasons for this are poorly understood. Undertaking a hypothesis-free analysis of 5,689 blood-derived biomarkers with mtDNA variants in 16,220 healthy donors, here we show that variants defining mtDNA haplogroups Uk and H4 modulate the level of circulating N-formylmethionine (fMet), which initiates mitochondrial protein translation. In human cytoplasmic hybrid (cybrid) lines, fMet modulated both mitochondrial and cytosolic proteins on multiple levels, through transcription, post-translational modification and proteolysis by an N-degron pathway, abolishing known differences between mtDNA haplogroups. In a further 11,966 individuals, fMet levels contributed to all-cause mortality and the disease risk of several common cardiovascular disorders. Together, these findings indicate that fMet plays a key role in common age-related disease through pleiotropic effects on cell proteostasis., This work was supported by Health Data Research UK, which is funded by the UK Medical Research Council, the Engineering and Physical Sciences Research Council, the Economic and Social Research Council, the Department of Health and Social Care (England), the Chief Scientist Office of the Scottish Government Health and Social Care Directorates, the Health and Social Care Research and Development Division (Welsh Government), the Public Health Agency (Northern Ireland), the British Heart Foundation and Wellcome. N.C. is supported by an EBI–Sanger Postdoctoral Fellowship. A.G.-D. receives funding from the NIHR Biomedical Research Centre based at Cambridge University Hospitals NHS Foundation Trust. E.Y.-D. was funded by the Isaac Newton Trust/Wellcome Trust ISSF/University of Cambridge Joint Research Grants Scheme. J.M.M.H. was funded by the NIHR Cambridge BRC (BRC-1215-20014)*. P.F.C.is a Wellcome Trust Principal Research Fellow (212219/Z/18/Z) and a UK NIHR Senior Investigator, who receives support from the Medical Research Council Mitochondrial Biology Unit (MC_UU_00015/9), the Evelyn Trust and the NIHR Biomedical Research Centre based at Cambridge University Hospitals NHS Foundation Trust and the University of Cambridge. C.H.W.-G. is supported by a RCUK/UKRI Research Innovation Fellowship awarded by the Medical Research Council (MR/R007446/1) and by the Cambridge Centre for Parkinson-Plus. N.S. is supported by the Wellcome Trust(grant number 098051 until 30 September 2016 and 206194 from 1 October 2016),the Cambridge BHF Centre of Research Excellence (RE/18/1/34212) and the NIHR Cambridge Biomedical Research Centre Biomedical Resources Grant, University of Cambridge, Cardiovascular Theme (RG64226). J.D. holds a British Heart Foundation Professorship and an NIHR Senior Investigator Award*. R.A.L. is supported by grants from Parkinson’s UK. Sequencing of INTERVAL samples was supported by the Wellcome Trust (grant number 206194). Metabolon metabolomics assays were funded by the NIHR BioResource, the Wellcome Trust (grant number 206194) and the NIHR Cambridge BRC (BRC-1215-20014)*. Nightingale Health NMR assays were funded by the European Commission Framework Programme 7 (HEALTH-F2-2012-279233). SomaLogic assays were funded by Merck and the NIHR Cambridge BRC (BRC-1215-20014)*. ICICLE-PD was funded by Parkinson’s UK (J-0802, G-1301, G-1507) and the Lockhart Parkinson’s Disease Research Fund and supported by the NIHR Newcastle Biomedical Research Unit and the NIHR Cambridge Biomedical Research Centre (146281). The EPIC-Norfolk study (https://doi.org/10.22025/2019.10.105.00004) has received funding from the Medical Research Council (MR/N003284/1 and MC-UU_12015/1) and Cancer Research UK (C864/A14136). Genetic work in the EPIC-Norfolk study was funded by the Medical Research Council (MC_PC_13048). Metabolite measurements in the EPIC-Norfolk study were supported by the MRC Cambridge Initiative in Metabolic Science (MR/L00002/1) and the Innovative Medicines Initiative Joint Undertaking under EMIF grant agreement no. 115372.

Published
2020

6. Lipoprotein signatures of cholesteryl ester transfer protein and HMG-CoA reductase inhibition

Author

Qin Wang, Marjo-Riitta Järvelin, Terho Lehtimäki, Veikko Salomaa, Michael V. Holmes, Mika Ala-Korpela, Clare Oliver-Williams, Emanuele Di Angelantonio, Therese Tillin, Adam S. Butterworth, Elias Allara, Mika Kähönen, Johannes Kettunen, Nish Chaturvedi, George Davey Smith, Pauli Ohukainen, Markus Perola, John Danesh, Olli T. Raitakari, Jorma Viikari, Alun D. Hughes, Olga Anufrieva, Research Programs Unit, CAMM - Research Program for Clinical and Molecular Metabolism, University of Helsinki, Lääketieteen ja terveysteknologian tiedekunta - Faculty of Medicine and Health Technology, Tampere University, Holmes, Michael V [0000-0001-6617-0879], Allara, Elias [0000-0002-1634-8330], Ohukainen, Pauli [0000-0002-0919-7204], Oliver-Williams, Clare [0000-0002-3573-2426], Hughes, Alun D [0000-0001-5432-5271], Salomaa, Veikko [0000-0001-7563-5324], Järvelin, Marjo-Riitta [0000-0002-2149-0630], Davey Smith, George [0000-0002-1407-8314], Butterworth, Adam S [0000-0002-6915-9015], Ala-Korpela, Mika [0000-0001-5905-1206], Apollo - University of Cambridge Repository, UNIVERSITY OF OULU, Holmes, Michael V. [0000-0001-6617-0879], Hughes, Alun D. [0000-0001-5432-5271], and Butterworth, Adam S. [0000-0002-6915-9015]

Subjects
Life Sciences & Biomedicine - Other Topics, Male, 0301 basic medicine, Very low-density lipoprotein, Apolipoprotein B, LOCI, Coronary Disease, Biochemistry, Vascular Medicine, DISEASE, Cohort Studies, chemistry.chemical_compound, 0302 clinical medicine, Medicine and Health Sciences, Coronary Heart Disease, EPIDEMIOLOGY, Biology (General), Genetics of disease, 11 Medical and Health Sciences, education.field_of_study, biology, PLASMA, General Neuroscience, CARDIOVASCULAR RISK, Middle Aged, Lipids, Coronary heart disease, Cholesterol, HMG-CoA reductase, Female, lipids (amino acids, peptides, and proteins), General Agricultural and Biological Sciences, Life Sciences & Biomedicine, Research Article, Adult, Biochemistry & Molecular Biology, medicine.medical_specialty, Adolescent, Biolääketieteet - Biomedicine, QH301-705.5, Lipoproteins, Population, Cardiology, General Biochemistry, Genetics and Molecular Biology, LDL, Young Adult, 03 medical and health sciences, MAGNETIC-RESONANCE METABOLOMICS, 07 Agricultural and Veterinary Sciences, Internal medicine, Cholesterylester transfer protein, REVEALS, medicine, Genetics, Humans, GENOME-WIDE ASSOCIATION, education, Biology, Triglycerides, Alleles, Apolipoproteins B, Science & Technology, General Immunology and Microbiology, Triglyceride, Genetic Variation, Biology and Life Sciences, Proteins, Cholesterol, LDL, 06 Biological Sciences, Cholesterol Ester Transfer Proteins, Medical risk factors, 030104 developmental biology, Endocrinology, Apolipoproteins, chemistry, Genetic Loci, Medical Risk Factors, Genetics of Disease, biology.protein, COHORT PROFILE, 1182 Biochemistry, cell and molecular biology, Hydroxymethylglutaryl CoA Reductases, 3111 Biomedicine, Hydroxymethylglutaryl-CoA Reductase Inhibitors, 030217 neurology & neurosurgery, Follow-Up Studies, Developmental Biology, Lipoprotein
Abstract

Cholesteryl ester transfer protein (CETP) inhibition reduces vascular event risk, but confusion surrounds its effects on low-density lipoprotein (LDL) cholesterol. Here, we clarify associations of genetic inhibition of CETP on detailed lipoprotein measures and compare those to genetic inhibition of 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR). We used an allele associated with lower CETP expression (rs247617) to mimic CETP inhibition and an allele associated with lower HMGCR expression (rs12916) to mimic the well-known effects of statins for comparison. The study consists of 65,427 participants of European ancestries with detailed lipoprotein subclass profiling from nuclear magnetic resonance spectroscopy. Genetic associations were scaled to 10% reduction in relative risk of coronary heart disease (CHD). We also examined observational associations of the lipoprotein subclass measures with risk of incident CHD in 3 population-based cohorts totalling 616 incident cases and 13,564 controls during 8-year follow-up. Genetic inhibition of CETP and HMGCR resulted in near-identical associations with LDL cholesterol concentration estimated by the Friedewald equation. Inhibition of HMGCR had relatively consistent associations on lower cholesterol concentrations across all apolipoprotein B-containing lipoproteins. In contrast, the associations of the inhibition of CETP were stronger on lower remnant and very-low-density lipoprotein (VLDL) cholesterol, but there were no associations on cholesterol concentrations in LDL defined by particle size (diameter 18–26 nm) (−0.02 SD LDL defined by particle size; 95% CI: −0.10 to 0.05 for CETP versus −0.24 SD, 95% CI −0.30 to −0.18 for HMGCR). Inhibition of CETP was strongly associated with lower proportion of triglycerides in all high-density lipoprotein (HDL) particles. In observational analyses, a higher triglyceride composition within HDL subclasses was associated with higher risk of CHD, independently of total cholesterol and triglycerides (strongest hazard ratio per 1 SD higher triglyceride composition in very large HDL 1.35; 95% CI: 1.18–1.54). In conclusion, CETP inhibition does not appear to affect size-specific LDL cholesterol but is likely to lower CHD risk by lowering concentrations of other atherogenic, apolipoprotein B-containing lipoproteins (such as remnant and VLDLs). Inhibition of CETP also lowers triglyceride composition in HDL particles, a phenomenon reflecting combined effects of circulating HDL, triglycerides, and apolipoprotein B-containing particles and is associated with a lower CHD risk in observational analyses. Our results reveal that conventional composite lipid assays may mask heterogeneous effects of emerging lipid-altering therapies., Inhibition of cholesteryl ester transfer protein does not affect size-specific low-density lipoprotein cholesterol, but may lower coronary heart disease risk by lowering cholesterol concentrations in other apolipoprotein-B containing atherogenic lipoproteins, and by lowering triglyceride content of high-density lipoprotein particles.

Published
2020
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7. Genome-wide analysis identifies molecular systems and 149 genetic loci associated with income

Author

Shen Xueyi, David J. Porteous, Neil M Davies, Andrew M. McIntosh, Emanuele Di Angelantonio, Catharine R. Gale, Ian J. Deary, W. David Hill, David J. Roberts, Julien Bryois, Gail Davies, David C. Liewald, Nathan G. Skene, Steven Bell, Stuart J. Ritchie, Adam S. Butterworth, Caroline Hayward, Davies, Neil M. [0000-0002-2460-0508], Skene, Nathan G. [0000-0002-6807-3180], Bryois, Julien [0000-0002-4747-2166], Bell, Steven [0000-0001-6774-3149], Xueyi, Shen [0000-0002-0538-4774], Liewald, David C. M. [0000-0002-0544-7368], Porteous, David J. [0000-0003-1249-6106], Hayward, Caroline [0000-0002-9405-9550], Butterworth, Adam S. [0000-0002-6915-9015], McIntosh, Andrew M. [0000-0002-0198-4588], Gale, Catharine R. [0000-0002-3361-8638], Apollo - University of Cambridge Repository, Davies, Neil M [0000-0002-2460-0508], Skene, Nathan G [0000-0002-6807-3180], Liewald, David C M [0000-0002-0544-7368], Porteous, David J [0000-0003-1249-6106], Butterworth, Adam S [0000-0002-6915-9015], McIntosh, Andrew M [0000-0002-0198-4588], Gale, Catharine R [0000-0002-3361-8638], and Liewald, David CM [0000-0002-0544-7368]

Subjects
0301 basic medicine, Adult, Male, Genotype, Economics, Science, Intelligence, Quantitative Trait Loci, 631/208/205/2138, 45/43, General Physics and Astronomy, Genome-wide association study, Biology, Quantitative trait locus, Social class, Polymorphism, Single Nucleotide, Genome-wide association studies, General Biochemistry, Genetics and Molecular Biology, 38, 38/43, 03 medical and health sciences, 0302 clinical medicine, 706/689/159, Mendelian randomization, Human behaviour, Humans, Society, health care economics and organizations, Aged, Multidisciplinary, 706/689/477/2811, article, General Chemistry, Middle Aged, Biobank, United Kingdom, 3. Good health, 030104 developmental biology, 706/689/522, Social Class, Evolutionary biology, Expression quantitative trait loci, Trait, Income, Household income, Female, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

Socioeconomic position (SEP) is a multi-dimensional construct reflecting (and influencing) multiple socio-cultural, physical, and environmental factors. In a sample of 286,301 participants from UK Biobank, we identify 30 (29 previously unreported) independent-loci associated with income. Using a method to meta-analyze data from genetically-correlated traits, we identify an additional 120 income-associated loci. These loci show clear evidence of functionality, with transcriptional differences identified across multiple cortical tissues, and links to GABAergic and serotonergic neurotransmission. By combining our genome wide association study on income with data from eQTL studies and chromatin interactions, 24 genes are prioritized for follow up, 18 of which were previously associated with intelligence. We identify intelligence as one of the likely causal, partly-heritable phenotypes that might bridge the gap between molecular genetic inheritance and phenotypic consequence in terms of income differences. These results indicate that, in modern era Great Britain, genetic effects contribute towards some of the observed socioeconomic inequalities., Household income is used as a marker of socioeconomic position, a trait that is associated with better physical and mental health. Here, Hill et al. report a genome-wide association study for household income in the UK and explore its relationship with intelligence in post-GWAS analyses including Mendelian randomization.

Published
2019

8. Genomic risk score offers predictive performance comparable to clinical risk factors for ischaemic stroke

Author

Tingting Wang, Agus Salim, Gad Abraham, Joanna M. M. Howson, John Danesh, Adam S. Butterworth, Michael Inouye, Rainer Malik, Martin Dichgans, Ekaterina Yonova-Doing, Butterworth, Adam S [0000-0002-6915-9015], Howson, Joanna MM [0000-0001-7618-0050], Dichgans, Martin [0000-0002-0654-387X], Apollo - University of Cambridge Repository, Butterworth, Adam S. [0000-0002-6915-9015], Howson, Joanna M. M. [0000-0001-7618-0050], and Howson, Joanna M M [0000-0001-7618-0050]

Subjects
0301 basic medicine, Male, General Physics and Astronomy, Datasets as Topic, Blood Pressure, Disease, Comorbidity, epidemiology [United Kingdom], Genome-wide association studies, Body Mass Index, Brain Ischemia, 692/617/375/534, 0302 clinical medicine, epidemiology [Smoking], Family history, lcsh:Science, Medical History Taking, Stroke, 2. Zero hunger, 0303 health sciences, Multidisciplinary, Framingham Risk Score, methods [Genomics], Hazard ratio, Smoking, Genomics, Middle Aged, 3. Good health, Predictive value of tests, Female, ddc:500, Risk assessment, 692/499, medicine.medical_specialty, Science, 631/208/205/2138, 631/208/212/2166, genetics [Brain Ischemia], Polymorphism, Single Nucleotide, Risk Assessment, General Biochemistry, Genetics and Molecular Biology, Article, 38/43, 03 medical and health sciences, Predictive Value of Tests, Internal medicine, medicine, epidemiology [Brain Ischemia], Humans, Genetic Predisposition to Disease, cardiovascular diseases, Risk factor, Author Correction, 030304 developmental biology, Aged, business.industry, fungi, General Chemistry, Guideline, medicine.disease, Personalized medicine, United Kingdom, methods [Risk Assessment], 030104 developmental biology, Blood pressure, Risk factors, lcsh:Q, business, Body mass index, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

Recent genome-wide association studies in stroke have enabled the generation of genomic risk scores (GRS) but their predictive power has been modest compared to established stroke risk factors. Here, using a meta-scoring approach, we develop a metaGRS for ischaemic stroke (IS) and analyse this score in the UK Biobank (n = 395,393; 3075 IS events by age 75). The metaGRS hazard ratio for IS (1.26, 95% CI 1.22–1.31 per metaGRS standard deviation) doubles that of a previous GRS, identifying a subset of individuals at monogenic levels of risk: the top 0.25% of metaGRS have three-fold risk of IS. The metaGRS is similarly or more predictive compared to several risk factors, such as family history, blood pressure, body mass index, and smoking. We estimate the reductions needed in modifiable risk factors for individuals with different levels of genomic risk and suggest that, for individuals with high metaGRS, achieving risk factor levels recommended by current guidelines may be insufficient to mitigate risk., Stroke risk is influenced by genetic and lifestyle factors and previously a genomic risk score (GRS) for stroke was proposed, albeit with limited predictive power. Here, Abraham et al. develop a metaGRS that is composed of several stroke-related GRSs and demonstrate improved predictive power compared with individual GRS or classic risk factors.

Published
2019

9. Genome-wide association meta-analyses and fine-mapping elucidate pathways influencing albuminuria

Author

Tobias Hermle, Holger Kirsten, Karsten B. Sieber, Aiko P. J. de Vries, Su Chi Lim, Peter Kovacs, Charumathi Sabanayagam, Carl D. Langefeld, Bernhard K. Krämer, Kent D. Taylor, Janine F. Felix, Belen Ponte, Markus Loeffler, Mary F. Feitosa, Kai-Uwe Eckardt, Jianjun Liu, Katalin Dittrich, Charlene A. Wong, Uwe Völker, Adriana M. Hung, Thomas Meitinger, Anubha Mahajan, Anselm Hoppmann, Erik Ingelsson, Martin H. de Borst, Oscar H. Franco, Niek Verweij, Kai-Uwe Saum, Vilmundur Gudnason, Bram P. Prins, Carsten A. Böger, Terho Lehtimäki, Andrew A. Hicks, Todd L. Edwards, Olivier Devuyst, Peter P. Pramstaller, Katrin Horn, Leslie A. Lange, Johanne Tremblay, Jin-Fang Chai, Sahar Ghasemi, Kjell Nikus, Tanja Poulain, Massimiliano Cocca, Anna Köttgen, Eric Boerwinkle, Barry I. Freedman, Miao-Ling Chee, Man Li, Stephan J. L. Bakker, Tamara B. Harris, Albert V. Smith, Ton J. Rabelink, Dennis O. Mook-Kanamori, Iris M. Heid, Jasmin Divers, Chaolong Wang, Kathleen A. Ryan, Pavel Hamet, Silke Szymczak, Shih-Jen Hwang, Hauke Thomsen, Rainer Rettig, Ayush Giri, Fernando Rivadeneira, Leo-Pekka Lyytikäinen, Cristian Pattaro, Andrej Teren, Valencia Hui Xian Foo, Myriam Rheinberger, Audrey Y. Chu, Barbara McMullen, Franziska Grundner-Culemann, Masayuki Yasuda, Murielle Bochud, Martin Gögele, Anke Tönjes, Jeannette Lee, Adrienne Tin, Kevin Ho, Konstantin Strauch, Josef Coresh, Renée de Mutsert, Sandra Freitag-Wolf, Gardar Sveinbjornsson, Yizhe Xu, Katalin Susztak, Tien Yin Wong, Mary L. Biggs, Isleifur Olafsson, Qiong Yang, Antje Körner, Chengxiang Qiu, E-Shyong Tai, Martina Müller-Nurasyid, Ben Schöttker, Jeffrey O' Connell, Mengmeng Chen, Daniel F. Gudbjartsson, Dermot F. Reilly, Vincent W. V. Jaddoe, Damia Noce, Pim van der Harst, Sanaz Sedaghat, Chiea Chuen Khor, Adam S. Butterworth, Mathias Gorski, Robert J. Carroll, James G. Wilson, Johan Ärnlöv, Christa Meisinger, Kenneth Rice, Bettina Jung, Christian M. Shaffer, Unnur Thorsteinsdottir, Matthias Nauck, Shreeram Akilesh, Mika Kähönen, Johanna Jakobsdottir, Melanie Waldenberger, Ralph Burkhardt, Daniela Baptista, John Danesh, Benjamin B. Sun, Karlhans Endlich, Holly Kramer, Frauke Degenhardt, Wolfgang Lieb, Kari Stefansson, Joachim Thiery, Lars Lind, Nicholette D. Palmer, Sarah A. Pendergrass, Suzanne Vogelezang, Peter J. van der Most, Afshin Parsa, Markus Scholz, Florian Kronenberg, Joseph C. Maranville, Laura M. Raffield, Hermann Brenner, Wieland Kiess, Anna I. Podgornaia, Yuan Shi, Tanguy Corre, Miao-Li Chee, Deborah Mascalzoni, Bamidele O. Tayo, Navya Shilpa Josyula, Ching-Yu Cheng, Lea Gerstner, Nisha Bansal, Jerome I. Rotter, Alexander Teumer, Vilmantas Giedraitis, Raymond Noordam, Ron T. Gansevoort, Lihua Wang, Andrew P. Morris, Bruce M. Psaty, Boting Ning, Zhi Yu, Christian Fuchsberger, Matthias Wuttke, Heiko Runz, Annette Peters, Yih Chung Tham, James P. Cook, Yong Li, Chris H. L. Thio, Hilma Holm, Alessandro De Grandi, Jonathan Marten, André G. Uitterlinden, Andre Franke, Nicholas Y. Q. Tan, Otis D. Wilson, Georg Ehret, Cecilia M. Lindgren, Josyf C. Mychaleckyj, Wolfgang Koenig, Harold Snieder, Michael Stumvoll, Kozeta Miliku, M. Arfan Ikram, Teresa Nutile, Læknadeild (HÍ), Faculty of Medicine (UI), School of Health Sciences (UI), Heilbrigðisvísindasvið (HÍ), Háskóli Íslands, University of Iceland, Teumer, Alexander [0000-0002-8309-094X], Li, Yong [0000-0003-2651-8791], Wuttke, Matthias [0000-0003-3420-5082], Giri, Ayush [0000-0002-7786-4670], Qiu, Chengxiang [0000-0002-6346-8669], Kirsten, Holger [0000-0002-3126-7950], Tin, Adrienne [0000-0002-4207-5866], Feitosa, Mary F. [0000-0002-0933-2410], Chai, Jin-Fang [0000-0003-3770-1137], Cocca, Massimiliano [0000-0002-1127-7596], Gorski, Mathias [0000-0002-9103-5860], Horn, Katrin [0000-0002-5307-6936], Li, Man [0000-0002-3839-0281], Marten, Jonathan [0000-0001-6916-2014], van der Most, Peter J. [0000-0001-8450-3518], Burkhardt, Ralph [0000-0003-1924-1202], Coresh, Josef [0000-0002-4598-0669], de Borst, Martin H. [0000-0002-4127-8733], Ehret, Georg [0000-0002-5730-0675], Endlich, Karlhans [0000-0001-6052-6061], Felix, Janine F. [0000-0002-9801-5774], Franke, Andre [0000-0003-1530-5811], Freedman, Barry I. [0000-0003-0275-5530], Freitag-Wolf, Sandra [0000-0002-1069-7740], Giedraitis, Vilmantas [0000-0003-3423-2021], Grundner-Culemann, Franziska [0000-0001-9649-281X], Gudnason, Vilmundur [0000-0001-5696-0084], Hicks, Andrew A. [0000-0001-6320-0411], Ikram, M. Arfan [0000-0003-0372-8585], Ingelsson, Erik [0000-0003-2256-6972], Jaddoe, Vincent W. V. [0000-0003-2939-0041], Josyula, Navya Shilpa [0000-0003-2782-8812], Khor, Chiea-Chuen [0000-0002-1128-4729], Koenig, Wolfgang [0000-0002-2064-9603], Kovacs, Peter [0000-0002-0290-5423], Kronenberg, Florian [0000-0003-2229-1120], Lindgren, Cecilia M. [0000-0002-4903-9374], Liu, Jianjun [0000-0002-3255-3019], Lyytikäinen, Leo-Pekka [0000-0002-7200-5455], Mahajan, Anubha [0000-0001-5585-3420], Mascalzoni, Deborah [0000-0003-4156-1464], Miliku, Kozeta [0000-0002-9614-7191], Müller-Nurasyid, Martina [0000-0003-3793-5910], Mychaleckyj, Josyf C. [0000-0003-2595-0005], Palmer, Nicholette D. [0000-0001-8883-2511], Poulain, Tanja [0000-0003-3825-5829], Raffield, Laura M. [0000-0002-7892-193X], Rice, Kenneth M. [0000-0002-3071-7278], Rivadeneira, Fernando [0000-0001-9435-9441], Sabanayagam, Charumathi [0000-0002-4042-4719], Smith, Albert V. [0000-0003-1942-5845], Sun, Benjamin B. [0000-0001-6347-2281], Szymczak, Silke [0000-0002-8897-9035], Taylor, Kent D. [0000-0002-2756-4370], Thio, Chris H. L. [0000-0003-2623-7172], Uitterlinden, André G. [0000-0002-7276-3387], van der Harst, Pim [0000-0002-2713-686X], Verweij, Niek [0000-0002-4303-7685], Völker, Uwe [0000-0002-5689-3448], Wang, Chaolong [0000-0003-3945-1012], Yang, Qiong [0000-0002-3658-1375], Devuyst, Olivier [0000-0003-3744-4767], Edwards, Todd L. [0000-0003-4318-6119], Ho, Kevin [0000-0002-3054-8697], Morris, Andrew P. [0000-0002-6805-6014], Pendergrass, Sarah A. [0000-0002-0565-6522], Rotter, Jerome I. [0000-0001-7191-1723], Stefansson, Kari [0000-0003-1676-864X], Susztak, Katalin [0000-0002-1005-3726], Scholz, Markus [0000-0002-4059-1779], Butterworth, Adam S. [0000-0002-6915-9015], Hung, Adriana M. [0000-0002-3203-1608], Pattaro, Cristian [0000-0002-4119-0109], Köttgen, Anna [0000-0002-4671-3714], Apollo - University of Cambridge Repository, Groningen Institute for Organ Transplantation (GIOT), Lifestyle Medicine (LM), Groningen Kidney Center (GKC), Cardiovascular Centre (CVC), Life Course Epidemiology (LCE), Epidemiology, Erasmus MC other, Pediatrics, Internal Medicine, Feitosa, Mary F [0000-0002-0933-2410], van der Most, Peter J [0000-0001-8450-3518], de Borst, Martin H [0000-0002-4127-8733], Felix, Janine F [0000-0002-9801-5774], Freedman, Barry I [0000-0003-0275-5530], Hicks, Andrew A [0000-0001-6320-0411], Ikram, M Arfan [0000-0003-0372-8585], Jaddoe, Vincent WV [0000-0003-2939-0041], Lindgren, Cecilia M [0000-0002-4903-9374], Mychaleckyj, Josyf C [0000-0003-2595-0005], Palmer, Nicholette D [0000-0001-8883-2511], Raffield, Laura M [0000-0002-7892-193X], Rice, Kenneth M [0000-0002-3071-7278], Smith, Albert V [0000-0003-1942-5845], Sun, Benjamin B [0000-0001-6347-2281], Taylor, Kent D [0000-0002-2756-4370], Thio, Chris HL [0000-0003-2623-7172], Uitterlinden, André G [0000-0002-7276-3387], Edwards, Todd L [0000-0003-4318-6119], Morris, Andrew P [0000-0002-6805-6014], Pendergrass, Sarah A [0000-0002-0565-6522], Rotter, Jerome I [0000-0001-7191-1723], Butterworth, Adam S [0000-0002-6915-9015], and Hung, Adriana M [0000-0002-3203-1608]

Subjects
0301 basic medicine, Drosophila melanogaster/genetics, Diabetes Mellitus/genetics, LD SCORE REGRESSION, 030232 urology & nephrology, 45/43, General Physics and Astronomy, Genome-wide association study, BLOOD-PRESSURE, Bioinformatics, GLOMERULAR-FILTRATION-RATE, Genome-wide association studies, Diabetes mellitus genetics, 0302 clinical medicine, Creatinine/urine, Risk Factors, Genome-wide, Phenomics, lcsh:Science, ddc:616, Regulation of gene expression, RISK, Gene knockdown, Kidney diseases, Multidisciplinary, HERITABILITY, Albuminuria/genetics, article, Chromosome Mapping, Kidney disease, ddc, 3. Good health, Drosophila melanogaster, Creatinine, Nýrnasjúkdómar, 692/4022/1585, Slit diaphragm, Medical genetics, medicine.symptom, Erfðarannsóknir, Medical Genetics, medicine.medical_specialty, Science, 631/208/205/2138, 610 Medicine & health, Biology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Meta-Analysis as Topic, 360 Social problems & social services, Diabetes Mellitus, medicine, Animals, Humans, Albuminuria, Genetic Predisposition to Disease, ddc:610, EXCRETION RATE, CARDIOVASCULAR EVENTS, Genetic association, Medicinsk genetik, TRANS-EQTLS, KIDNEY-DISEASE, General Chemistry, 030104 developmental biology, Gene Expression Regulation, Genetic Loci, COLLABORATIVE METAANALYSIS, lcsh:Q, Genome-Wide Association Study
Abstract

Publisher's version (útgefin grein)., Increased levels of the urinary albumin-to-creatinine ratio (UACR) are associated with higher risk of kidney disease progression and cardiovascular events, but underlying mechanisms are incompletely understood. Here, we conduct trans-ethnic (n = 564,257) and European-ancestry specific meta-analyses of genome-wide association studies of UACR, including ancestry- and diabetes-specific analyses, and identify 68 UACR-associated loci. Genetic correlation analyses and risk score associations in an independent electronic medical records database (n = 192,868) reveal connections with proteinuria, hyperlipidemia, gout, and hypertension. Fine-mapping and trans-Omics analyses with gene expression in 47 tissues and plasma protein levels implicate genes potentially operating through differential expression in kidney (including TGFB1, MUC1, PRKCI, and OAF), and allow coupling of UACR associations to altered plasma OAF concentrations. Knockdown of OAF and PRKCI orthologs in Drosophila nephrocytes reduces albumin endocytosis. Silencing fly PRKCI further impairs slit diaphragm formation. These results generate a priority list of genes and pathways for translational research to reduce albuminuria., Competing interests: Karsten B. Sieber is full-time employee of GlaxoSmithKline. Gardar Sveinbjornsson, Daniel F. Gudbjartsson, Hilma Holm, Unnur Thorsteinsdottir and Kari Stefansson are full-time employees of deCODE genetics, Amgen Inc. John Danesh is member of the Novartis Cardiovascular and Metabolic Advisory Board, received grant support from Novartis. Oscar H. Franco works in ErasmusAGE, a center for aging research across the life course funded by Nestlé Nutrition (Nestec Ltd.), Metagenics Inc., and AXA. Wolfgang Koenig received modest consultation fees for advisory board meetings from Amgen, DalCor, Kowa, Novartis, Pfizer and Sanofi, and modest personal fees for lectures from Amgen, AstraZeneca, Novartis, Pfizer and Sanofi. Anna I. Podgornaia and Dermot F. Reilly are employees of Merck Sharp Dohme Corp., Whitehouse Station, NJ, USA. Kevin Ho disclosed a research and financial relationship with Sanofi-Genzyme. Bruce M. Psaty serves on the DSMB of a clinical trial funded by the manufacturer (Zoll LifeCor) and on the Steering Committee of the Yale Open Data Access Project funded by Johnson & Johnson. Markus Scholz: Consultancy of and grant support from Merck Serono not related to this project. Adam S. Butterworth received grants from MSD, Pfizer, Novartis, Biogen and Bioverativ and personal fees from Novartis. Anna Köttgen received grant support from Gruenenthal not related to this project. The other authors declare no competing interests.

Published
2019
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10. Genome-wide association meta-analysis of spontaneous coronary artery dissection identifies risk variants and genes related to artery integrity and tissue-mediated coagulation

Author

Adlam, David, Berrandou, Takiy-Eddine, Georges, Adrien, Nelson, Christopher P, Giannoulatou, Eleni, Henry, Joséphine, Ma, Lijiang, Blencowe, Montgomery, Turley, Tamiel N, Yang, Min-Lee, Chopade, Sandesh, Finan, Chris, Braund, Peter S, Sadeg-Sayoud, Ines, Iismaa, Siiri E, Kosel, Matthew L, Zhou, Xiang, Hamby, Stephen E, Cheng, Jenny, Liu, Lu, Tarr, Ingrid, Muller, David WM, D'Escamard, Valentina, King, Annette, Brunham, Liam R, Baranowska-Clarke, Ania A, Debette, Stéphanie, Amouyel, Philippe, Olin, Jeffrey W, Patil, Snehal, Hesselson, Stephanie E, Junday, Keerat, Kanoni, Stavroula, Aragam, Krishna G, Butterworth, Adam S, CARDIoGRAMPlusC4D, MEGASTROKE, International Stroke Genetics Consortium (ISGC) Intracranial Aneurysm Working Group, Tweet, Marysia S, Gulati, Rajiv, Combaret, Nicolas, DISCO Register, Kadian-Dodov, Daniella, Kalman, Jonathan M, Fatkin, Diane, Hingorani, Aroon D, Saw, Jacqueline, Webb, Tom R, Hayes, Sharonne N, Yang, Xia, Ganesh, Santhi K, Olson, Timothy M, Kovacic, Jason C, Graham, Robert M, Samani, Nilesh J, Bouatia-Naji, Nabila, Adlam, David [0000-0002-0080-9884], Berrandou, Takiy-Eddine [0000-0002-0525-3002], Georges, Adrien [0000-0003-4208-2393], Nelson, Christopher P [0000-0001-8025-2897], Finan, Chris [0000-0002-3319-1937], Braund, Peter S [0000-0001-8540-5709], Iismaa, Siiri E [0000-0003-2409-7356], Zhou, Xiang [0000-0002-4331-7599], Hamby, Stephen E [0000-0002-6215-5791], Muller, David WM [0000-0002-5281-0166], Brunham, Liam R [0000-0002-3686-3807], Debette, Stéphanie [0000-0001-8675-7968], Amouyel, Philippe [0000-0001-9088-234X], Olin, Jeffrey W [0000-0003-3374-616X], Hesselson, Stephanie E [0000-0002-4521-5086], Kanoni, Stavroula [0000-0002-1691-9615], Aragam, Krishna G [0000-0003-3223-9131], Butterworth, Adam S [0000-0002-6915-9015], Combaret, Nicolas [0000-0003-4905-0765], Fatkin, Diane [0000-0002-9010-9856], Hingorani, Aroon D [0000-0001-8365-0081], Saw, Jacqueline [0000-0002-7027-984X], Webb, Tom R [0000-0001-5998-8226], Hayes, Sharonne N [0000-0003-3129-362X], Yang, Xia [0000-0002-3971-038X], Olson, Timothy M [0000-0003-2716-9423], Kovacic, Jason C [0000-0003-4555-769X], Graham, Robert M [0000-0002-1042-2587], Bouatia-Naji, Nabila [0000-0001-5424-2134], and Apollo - University of Cambridge Repository

Subjects
Myocardial Infarction, Humans, Female, Vascular Diseases, Coronary Artery Disease, Genome-Wide Association Study
Abstract

Spontaneous coronary artery dissection (SCAD) is an understudied cause of myocardial infarction primarily affecting women. It is not known to what extent SCAD is genetically distinct from other cardiovascular diseases, including atherosclerotic coronary artery disease (CAD). Here we present a genome-wide association meta-analysis (1,917 cases and 9,292 controls) identifying 16 risk loci for SCAD. Integrative functional annotations prioritized genes that are likely to be regulated in vascular smooth muscle cells and artery fibroblasts and implicated in extracellular matrix biology. One locus containing the tissue factor gene F3, which is involved in blood coagulation cascade initiation, appears to be specific for SCAD risk. Several associated variants have diametrically opposite associations with CAD, suggesting that shared biological processes contribute to both diseases, but through different mechanisms. We also infer a causal role for high blood pressure in SCAD. Our findings provide novel pathophysiological insights involving arterial integrity and tissue-mediated coagulation in SCAD and set the stage for future specific therapeutics and preventions.

Published
2023

11. South Asian medical cohorts reveal strong founder effects and high rates of homozygosity

Author

Wall, Jeffrey D, Sathirapongsasuti, J Fah, Gupta, Ravi, Rasheed, Asif, Venkatesan, Radha, Belsare, Saurabh, Menon, Ramesh, Phalke, Sameer, Mittal, Anuradha, Fang, John, Tanneeru, Deepak, Deshmukh, Manjari, Bassi, Akshi, Robinson, Jacqueline, Chaudhary, Ruchi, Murugan, Sakthivel, Ul-Asar, Zameer, Saleem, Imran, Ishtiaq, Unzila, Fatima, Areej, Sheikh, Saqib Shafi, Hameed, Shahid, Ishaq, Mohammad, Rasheed, Syed Zahed, Memon, Fazal-Ur-Rehman, Jalal, Anjum, Abbas, Shahid, Frossard, Philippe, Fuchsberger, Christian, Forer, Lukas, Schoenherr, Sebastian, Bei, Qixin, Bhangale, Tushar, Tom, Jennifer, Gadde, Santosh Gopi Krishna, B V, Priya, Naik, Naveen Kumar, Wang, Minxian, Kwok, Pui-Yan, Khera, Amit V, Lakshmi, BR, Butterworth, Adam S, Chowdhury, Rajiv, Danesh, John, di Angelantonio, Emanuele, Naheed, Aliya, Goyal, Vinay, Kandadai, Rukmini M, Kumar, Hrishikesh, Borgohain, Rupam, Mukherjee, Adreesh, Wadia, Pettarusp M, Yadav, Ravi, Desai, Soaham, Kumar, Niraj, Biswas, Atanu, Pal, Pramod Kumar, Muthane, Uday B, Das, Shymal K, Ramprasad, Vedam L, Kukkle, Prashanth L, Seshagiri, Somasekar, Kathiresan, Sekar, Ghosh, Arkasubhra, Mohan, V, Saleheen, Danish, Stawiski, Eric W, Peterson, Andrew S, Wall, Jeffrey D [0000-0001-5066-1235], Venkatesan, Radha [0000-0002-4281-0250], Belsare, Saurabh [0000-0002-8148-1867], Fang, John [0000-0003-2372-0839], Bassi, Akshi [0000-0002-4443-1430], Robinson, Jacqueline [0000-0002-5556-815X], Forer, Lukas [0000-0003-2139-7329], Wang, Minxian [0000-0002-3753-508X], Kwok, Pui-Yan [0000-0002-5087-3059], Khera, Amit V [0000-0001-6535-5839], Butterworth, Adam S [0000-0002-6915-9015], Desai, Soaham [0000-0003-0378-1888], Kumar, Niraj [0000-0002-5863-2532], Kukkle, Prashanth L [0000-0002-4610-947X], Mohan, V [0000-0001-5038-6210], Saleheen, Danish [0000-0001-6193-020X], Stawiski, Eric W [0000-0002-9387-6719], and Apollo - University of Cambridge Repository

Subjects
Bangladesh, Homozygote, Human Genome, India, Founder Effect, Good Health and Well Being, Asian People, South Asian People, Clinical Research, Genetics, Humans, Pakistan, Generic health relevance, Biotechnology
Abstract

The benefits of large-scale genetic studies for healthcare of the populations studied are well documented, but these genetic studies have traditionally ignored people from some parts of the world, such as South Asia. Here we describe whole genome sequence (WGS) data from 4806 individuals recruited from the healthcare delivery systems of Pakistan, India and Bangladesh, combined with WGS from 927 individuals from isolated South Asian populations. We characterize population structure in South Asia and describe a genotyping array (SARGAM) and imputation reference panel that are optimized for South Asian genomes. We find evidence for high rates of reproductive isolation, endogamy and consanguinity that vary across the subcontinent and that lead to levels of rare homozygotes that reach 100 times that seen in outbred populations. Founder effects increase the power to associate functional variants with disease processes and make South Asia a uniquely powerful place for population-scale genetic studies.

Published
2023

12. A nutritional biomarker score of the Mediterranean diet and incident type 2 diabetes: Integrated analysis of data from the MedLey randomised controlled trial and the EPIC-InterAct case-cohort study

Author

Jakub G. Sobiecki, Fumiaki Imamura, Courtney R. Davis, Stephen J. Sharp, Albert Koulman, Jonathan M. Hodgson, Marcela Guevara, Matthias B. Schulze, Ju-Sheng Zheng, Claudia Agnoli, Catalina Bonet, Sandra M. Colorado-Yohar, Guy Fagherazzi, Paul W. Franks, Thomas E. Gundersen, Franziska Jannasch, Rudolf Kaaks, Verena Katzke, Esther Molina-Montes, Peter M. Nilsson, Domenico Palli, Salvatore Panico, Keren Papier, Olov Rolandsson, Carlotta Sacerdote, Anne Tjønneland, Tammy Y. N. Tong, Yvonne T. van der Schouw, John Danesh, Adam S. Butterworth, Elio Riboli, Karen J. Murphy, Nicholas J. Wareham, Nita G. Forouhi, Sobiecki, Jakub G [0000-0003-2641-2313], Imamura, Fumiaki [0000-0002-6841-8396], Davis, Courtney R [0000-0002-3866-2603], Sharp, Stephen J [0000-0003-2375-1440], Koulman, Albert [0000-0001-9998-051X], Hodgson, Jonathan M [0000-0001-6184-7764], Guevara, Marcela [0000-0001-9242-6364], Schulze, Matthias B [0000-0002-0830-5277], Zheng, Ju-Sheng [0000-0001-6560-4890], Agnoli, Claudia [0000-0003-4472-1179], Colorado-Yohar, Sandra M [0000-0002-6700-0780], Fagherazzi, Guy [0000-0001-5033-5966], Franks, Paul W [0000-0002-0520-7604], Jannasch, Franziska [0000-0003-3478-4758], Katzke, Verena [0000-0002-6509-6555], Molina-Montes, Esther [0000-0002-0428-2426], Nilsson, Peter M [0000-0002-5652-8459], Papier, Keren [0000-0002-4102-6835], Sacerdote, Carlotta [0000-0002-8008-5096], Tjønneland, Anne [0000-0003-4385-2097], Tong, Tammy YN [0000-0002-0284-8959], van der Schouw, Yvonne T [0000-0002-4605-435X], Butterworth, Adam S [0000-0002-6915-9015], Riboli, Elio [0000-0001-6795-6080], Wareham, Nicholas J [0000-0003-1422-2993], Forouhi, Nita G [0000-0002-5041-248X], Apollo - University of Cambridge Repository, Sobiecki, Jakub G, Imamura, Fumiaki, Davis, Courtney R, Sharp, Stephen J, and Forouhi, Nita G

Subjects
Adult, Clinical Trials and Supportive Activities, 32 Biomedical and Clinical Sciences, Endocrinology and Diabetes, Diet, Mediterranean, Cohort Studies, Diabetes Mellitus, Type 2/diagnosis, Risk Factors, Clinical Research, Mediterranean diet, Neoplasms, Humans, Neoplasms/complications, Obesity, nutritional biomarker score, Metabolic and endocrine, Nutrition, Cancer, Nutrition and Dietetics, Prevention, Diabetes, Australia, 42 Health Sciences, General Medicine, Näringslära, Diabetes Mellitus, Type 2, Endokrinologi och diabetes, 3210 Nutrition and Dietetics, type 2 diabetes, Biomarkers
Abstract

The MedLey trial was funded by a National Health and Medical Research Council Grant (#APP1050949 to KJM). The InterAct project was funded by the EU FP6 programme (grant number LSHM_CT_2006_037197 to NJW). Biomarker measurements for carotenoids were funded jointly by the InterAct project, the EPIC-CVD project, and the MRC Cambridge Initiative (RG71466 and SJAH/004 to NJW, NGF, JD, AB). EPIC-CVD has been supported by the UK Medical Research Council (MR/L003120/1 to ASB and JD), the British Heart Foundation (RG/13/13/30194 and RG/18/13/33946 to ASB and JD), the European Commission Framework Programme 7 (HEALTH -F2-2012-279233 to ASB and JD), the European Research Council (268834 to ASB and JD), and the National Institute for Health Research (NIHR; Cambridge Biomedical Research Centre at the Cambridge University Hospitals NHS Foundation Trust, BRC-1215-20014 to ASB and JD). This work was also supported by Health Data Research UK (to ASB and JD), which is funded by the UK Medical Research Council, Engineering and Physical Sciences Research Council, Economic and Social Research Council, Department of Health and Social Care (England), Chief Scientist Office of the Scottish Government Health and Social Care Directorates, Health and Social Care Research and Development Division (Welsh Government), Public Health Agency (Northern Ireland), and Wellcome. The coordination of EPIC is financially supported by the International Agency for Research on Cancer (IARC) and also by the Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London which has additional infrastructure support provided by the NIHR Imperial Biomedical Research Centre (BRC). The national cohorts are supported by: Danish Cancer Society (Denmark); Ligue Contre le Cancer, Institut Gustave Roussy, Mutuelle Ge'ne'rale de l'Education Nationale, Institut National de la Sante' et de la Recherche Me'dicale (INSERM) (France); German Cancer Aid, German Cancer Research Center (DKFZ), German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Federal Ministry of Education and Research (BMBF) (Germany); Associazione Iblea Ricerca Epidemiologica (A.I.R.E. - ONLUS) Ragusa, Associazione Italiana per la Ricerca sul Cancro-AIRC-Italy, Compagnia di San Paolo, National Research Council and Sicilian Regional Government (Italy); Dutch Ministry of Public Health, Welfare and Sports (VWS), Netherlands~Cancer Registry (NKR), LK Research Funds, Dutch Prevention Funds, Dutch ZON (Zorg Onderzoek Nederland), World Cancer Research Fund (WCRF), Statistics Netherlands (The Netherlands); Health Research Fund (FIS) -Instituto de Salud Carlos III (ISCIII), Regional Governments of Andaluci'a, Asturias, Basque Country, Murcia and Navarra, and the Catalan Institute of Oncology -ICO (Spain); Swedish Cancer Society, Swedish Research Council and County Councils of Skane and Vasterbotten (Sweden); Cancer Research UK (14136 to NJW; C8221/A29017), Medical Research Council (1000143 to NJW; MR/M012190/1) (United Kingdom). JGS was supported by the MRC PhD studentship. NJW, NGF, and FI acknowledge funding from the Medical Research Council Epidemiology Unit (MC_UU_00006/1, MC_UU_00006/3); and NJW, NGF and AK from the NIHR Cambridge Biomedical Research Centre (IS-BRC-1215-20014; NIHR203312). NGF and JD are NIHR Senior Investigators. JD holds a British Heart Foundation Professorship. MBS acknowledges funding from the Federal Ministry of Education and Research and the State of Brandenburg (DZD grant 82DZD03D03). JSZ has received funding from Westlake University (No YSYY0209) and European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 701708. PWF has received funding from Novo Nordisk, Swedish Diabetes Association, Swedish Heart-Lung Foundation, European Research Council. ER has received funding from Imperial College Biomedical Research Centre. The funders of the studies had no role in the study design, data collection, data analysis, data interpretation, or report preparation. Trial Australian., Background Self-reported adherence to the Mediterranean diet has been modestly inversely associated with incidence of type 2 diabetes (T2D) in cohort studies. There is uncertainty about the validity and magnitude of this association due to subjective reporting of diet. The association has not been evaluated using an objectively measured biomarker of the Mediterranean diet. Methods and findings We derived a biomarker score based on 5 circulating carotenoids and 24 fatty acids that discriminated between the Mediterranean or habitual diet arms of a parallel design, 6-month partial-feeding randomised controlled trial (RCT) conducted between 2013 and 2014, the MedLey trial (128 participants out of 166 randomised). We applied this biomarker score in an observational study, the European Prospective Investigation into Cancer and Nutrition (EPIC)-InterAct case-cohort study, to assess the association of the score with T2D incidence over an average of 9.7 years of follow-up since the baseline (1991 to 1998). We included 22,202 participants, of whom 9,453 were T2D cases, with relevant biomarkers from an original case-cohort of 27,779 participants sampled from a cohort of 340,234 people. As a secondary measure of the Mediterranean diet, we used a score estimated from dietary-self report. Within the trial, the biomarker score discriminated well between the 2 arms; the cross-validated C-statistic was 0.88 (95% confidence interval (CI) 0.82 to 0.94). The score was inversely associated with incident T2D in EPIC-InterAct: the hazard ratio (HR) per standard deviation of the score was 0.71 (95% CI: 0.65 to 0.77) following adjustment for sociodemographic, lifestyle and medical factors, and adiposity. In comparison, the HR per standard deviation of the self-reported Mediterranean diet was 0.90 (95% CI: 0.86 to 0.95). Assuming the score was causally associated with T2D, higher adherence to the Mediterranean diet in Western European adults by 10 percentiles of the score was estimated to reduce the incidence of T2D by 11% (95% CI: 7% to 14%). The study limitations included potential measurement error in nutritional biomarkers, unclear specificity of the biomarker score to the Mediterranean diet, and possible residual confounding. Conclusions These findings suggest that objectively assessed adherence to the Mediterranean diet is associated with lower risk of T2D and that even modestly higher adherence may have the potential to reduce the population burden of T2D meaningfully., EU FP6 programme LSHM_CT_2006_037197, European Commission Framework Programme 7 HEALTH-F2-2012-279233, European Research Council (ERC), World Health Organization, Health Research Fund (FIS) - Instituto de Salud Carlos III (ISCIII), Catalan Institute of Oncology - ICO (Spain), Spanish Government 701708, Marie Curie Actions 701708, European Union's Horizon 2020, Marie Sklodowska-Curie 701708

Published
2023

13. An atlas of genetic scores to predict multi-omic traits

Author

Yu Xu, Scott C. Ritchie, Yujian Liang, Paul R. H. J. Timmers, Maik Pietzner, Loïc Lannelongue, Samuel A. Lambert, Usman A. Tahir, Sebastian May-Wilson, Carles Foguet, Åsa Johansson, Praveen Surendran, Artika P. Nath, Elodie Persyn, James E. Peters, Clare Oliver-Williams, Shuliang Deng, Bram Prins, Jian’an Luan, Lorenzo Bomba, Nicole Soranzo, Emanuele Di Angelantonio, Nicola Pirastu, E. Shyong Tai, Rob M. van Dam, Helen Parkinson, Emma E. Davenport, Dirk S. Paul, Christopher Yau, Robert E. Gerszten, Anders Mälarstig, John Danesh, Xueling Sim, Claudia Langenberg, James F. Wilson, Adam S. Butterworth, Michael Inouye, Xu, Yu [0000-0002-7304-5045], Ritchie, Scott C [0000-0002-8454-9548], Timmers, Paul RHJ [0000-0002-5197-1267], Pietzner, Maik [0000-0003-3437-9963], Lannelongue, Loïc [0000-0002-9135-1345], Lambert, Samuel A [0000-0001-8222-008X], May-Wilson, Sebastian [0000-0003-2668-5717], Foguet, Carles [0000-0001-8494-9595], Johansson, Åsa [0000-0002-2915-4498], Persyn, Elodie [0000-0001-9104-1972], Peters, James E [0000-0002-9415-3440], Prins, Bram [0000-0001-5774-034X], Luan, Jian'an [0000-0003-3137-6337], Soranzo, Nicole [0000-0003-1095-3852], Tai, E Shyong [0000-0003-2929-8966], Paul, Dirk S [0000-0002-8230-0116], Yau, Christopher [0000-0001-7615-8523], Gerszten, Robert E [0000-0002-6767-7687], Mälarstig, Anders [0000-0003-2608-1358], Sim, Xueling [0000-0002-1233-7642], Langenberg, Claudia [0000-0002-5017-7344], Wilson, James F [0000-0001-5751-9178], Butterworth, Adam S [0000-0002-6915-9015], Inouye, Michael [0000-0001-9413-6520], and Apollo - University of Cambridge Repository

Subjects
Proteomics, European People, Internet, Multidisciplinary, Asian, Proteome, Databases, Factual, Datasets as Topic, Reproducibility of Results, Coronary Artery Disease, Multiomics, United Kingdom, Machine Learning, Black or African American, Cohort Studies, Plasma, Phenotype, Metabolome, Humans, Metabolomics
Abstract

The use of omic modalities to dissect the molecular underpinnings of common diseases and traits is becoming increasingly common. But multi-omic traits can be genetically predicted, which enables highly cost-effective and powerful analyses for studies that do not have multi-omics1. Here we examine a large cohort (the INTERVAL study2; n = 50,000 participants) with extensive multi-omic data for plasma proteomics (SomaScan, n = 3,175; Olink, n = 4,822), plasma metabolomics (Metabolon HD4, n = 8,153), serum metabolomics (Nightingale, n = 37,359) and whole-blood Illumina RNA sequencing (n = 4,136), and use machine learning to train genetic scores for 17,227 molecular traits, including 10,521 that reach Bonferroni-adjusted significance. We evaluate the performance of genetic scores through external validation across cohorts of individuals of European, Asian and African American ancestries. In addition, we show the utility of these multi-omic genetic scores by quantifying the genetic control of biological pathways and by generating a synthetic multi-omic dataset of the UK Biobank3 to identify disease associations using a phenome-wide scan. We highlight a series of biological insights with regard to genetic mechanisms in metabolism and canonical pathway associations with disease; for example, JAK-STAT signalling and coronary atherosclerosis. Finally, we develop a portal ( https://www.omicspred.org/ ) to facilitate public access to all genetic scores and validation results, as well as to serve as a platform for future extensions and enhancements of multi-omic genetic scores.

Published
2023

14. Quality control and removal of technical variation of NMR metabolic biomarker data in ~120,000 UK Biobank participants

Author

Scott C. Ritchie, Praveen Surendran, Savita Karthikeyan, Samuel A. Lambert, Thomas Bolton, Lisa Pennells, John Danesh, Emanuele Di Angelantonio, Adam S. Butterworth, Michael Inouye, Ritchie, Scott C [0000-0002-8454-9548], Butterworth, Adam S [0000-0002-6915-9015], and Apollo - University of Cambridge Repository

Subjects
Statistics and Probability, Quality Control, Magnetic Resonance Spectroscopy, Humans, Library and Information Sciences, Statistics, Probability and Uncertainty, Magnetic Resonance Imaging, United Kingdom, Computer Science Applications, Education, Information Systems, Biological Specimen Banks
Abstract

Funder: S.C.R was funded by the National Institute for Health and Care Research (NIHR) Cambridge Biomedical Research Centre (BRC) (BRC-1215-20014) and by the British Heart Foundation (BHF) programme grant (RG/18/13/33946)., Funder: Praveen Surendran was supported by a Rutherford Fund Fellowship from the Medical Research Council grant MR/S003746/1, Funder: Savita Karthikeyan was funded by a British Heart Foundation Programme Grant (RG/18/13/33946), Funder: Samuel A. Lambert was supported by a Canadian Institutes of Health Research postdoctoral fellowship (MFE-171279), Funder: Thomas Bolton was funded by the NIHR Blood and Transplant Research Unit in Donor Health and Genomics (NIHR BTRU-2014-10024), Funder: Lisa Pennells was funded by a British Heart Foundation Programme Grant (RG/18/13/33946), Funder: John Danesh holds a British Heart Foundation Professorship and a NIHR Senior Investigator Award., Funder: Michael Inouye is supported by the Munz Chair of Cardiovascular Prediction and Prevention and the NIHR Cambridge Biomedical Research Centre (BRC-1215-20014), and was also supported by the UK Economic and Social Research 878 Council (ES/T013192/1)., Metabolic biomarker data quantified by nuclear magnetic resonance (NMR) spectroscopy in approximately 121,000 UK Biobank participants has recently been released as a community resource, comprising absolute concentrations and ratios of 249 circulating metabolites, lipids, and lipoprotein sub-fractions. Here we identify and characterise additional sources of unwanted technical variation influencing individual biomarkers in the data available to download from UK Biobank. These included sample preparation time, shipping plate well, spectrometer batch effects, drift over time within spectrometer, and outlier shipping plates. We developed a procedure for removing this unwanted technical variation, and demonstrate that it increases signal for genetic and epidemiological studies of the NMR metabolic biomarker data in UK Biobank. We subsequently developed an R package, ukbnmr, which we make available to the wider research community to enhance the utility of the UK Biobank NMR metabolic biomarker data and to facilitate rapid analysis.

Published
2023

15. Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants

Author

Aragam, Krishna G, Jiang, Tao, Goel, Anuj, Kanoni, Stavroula, Wolford, Brooke N, Atri, Deepak S, Weeks, Elle M, Wang, Minxian, Hindy, George, Zhou, Wei, Grace, Christopher, Roselli, Carolina, Marston, Nicholas A, Kamanu, Frederick K, Surakka, Ida, Venegas, Loreto Muñoz, Sherliker, Paul, Koyama, Satoshi, Ishigaki, Kazuyoshi, Åsvold, Bjørn O, Brown, Michael R, Brumpton, Ben, De Vries, Paul S, Giannakopoulou, Olga, Giardoglou, Panagiota, Gudbjartsson, Daniel F, Güldener, Ulrich, Haider, Syed M Ijlal, Helgadottir, Anna, Ibrahim, Maysson, Kastrati, Adnan, Kessler, Thorsten, Kyriakou, Theodosios, Konopka, Tomasz, Li, Ling, Ma, Lijiang, Meitinger, Thomas, Mucha, Sören, Munz, Matthias, Murgia, Federico, Nielsen, Jonas B, Nöthen, Markus M, Pang, Shichao, Reinberger, Tobias, Schnitzler, Gavin, Smedley, Damian, Thorleifsson, Gudmar, Von Scheidt, Moritz, Ulirsch, Jacob C, Danesh, John, Arnar, David O, Burtt, Noël P, Costanzo, Maria C, Flannick, Jason, Ito, Kaoru, Jang, Dong-Keun, Kamatani, Yoichiro, Khera, Amit V, Komuro, Issei, Kullo, Iftikhar J, Lotta, Luca A, Nelson, Christopher P, Roberts, Robert, Thorgeirsson, Gudmundur, Thorsteinsdottir, Unnur, Webb, Thomas R, Baras, Aris, Björkegren, Johan LM, Boerwinkle, Eric, Dedoussis, George, Holm, Hilma, Hveem, Kristian, Melander, Olle, Morrison, Alanna C, Orho-Melander, Marju, Rallidis, Loukianos S, Ruusalepp, Arno, Sabatine, Marc S, Stefansson, Kari, Zalloua, Pierre, Ellinor, Patrick T, Farrall, Martin, Ruff, Christian T, Finucane, Hilary K, Hopewell, Jemma C, Clarke, Robert, Gupta, Rajat M, Erdmann, Jeanette, Samani, Nilesh J, Schunkert, Heribert, Watkins, Hugh, Willer, Cristen J, Deloukas, Panos, Kathiresan, Sekar, Butterworth, Adam S, Aragam, Krishna G [0000-0003-3223-9131], Goel, Anuj [0000-0003-2307-4021], Kanoni, Stavroula [0000-0002-1691-9615], Wolford, Brooke N [0000-0003-3153-1552], Atri, Deepak S [0000-0001-8139-5419], Weeks, Elle M [0000-0002-4317-4444], Wang, Minxian [0000-0002-3753-508X], Zhou, Wei [0000-0001-7719-0859], Roselli, Carolina [0000-0001-5267-6756], Kamanu, Frederick K [0000-0001-7208-1047], Koyama, Satoshi [0000-0002-9286-0360], Ishigaki, Kazuyoshi [0000-0003-2881-0657], Åsvold, Bjørn O [0000-0003-3837-2101], Brumpton, Ben [0000-0002-3058-1059], Gudbjartsson, Daniel F [0000-0002-5222-9857], Güldener, Ulrich [0000-0001-5052-8610], Helgadottir, Anna [0000-0002-1806-2467], Kessler, Thorsten [0000-0003-3326-1621], Li, Ling [0000-0002-3280-9475], Mucha, Sören [0000-0002-1647-2526], Munz, Matthias [0000-0002-4728-3357], Murgia, Federico [0000-0002-3608-845X], Pang, Shichao [0000-0002-4111-2864], Smedley, Damian [0000-0002-5836-9850], Thorleifsson, Gudmar [0000-0003-4623-9087], von Scheidt, Moritz [0000-0001-7159-8271], Ulirsch, Jacob C [0000-0002-7947-0827], Costanzo, Maria C [0000-0001-9043-693X], Flannick, Jason [0000-0002-3618-795X], Ito, Kaoru [0000-0003-1843-773X], Khera, Amit V [0000-0001-6535-5839], Komuro, Issei [0000-0002-0714-7182], Kullo, Iftikhar J [0000-0002-6524-3471], Roberts, Robert [0000-0002-6792-4633], Webb, Thomas R [0000-0001-5998-8226], Baras, Aris [0000-0002-6830-3396], Björkegren, Johan LM [0000-0003-1945-7425], Holm, Hilma [0000-0002-9517-6636], Morrison, Alanna C [0000-0001-6381-4296], Orho-Melander, Marju [0000-0002-3578-2503], Stefansson, Kari [0000-0003-1676-864X], Farrall, Martin [0000-0003-4564-2165], Finucane, Hilary K [0000-0003-3864-9828], Clarke, Robert [0000-0002-9802-8241], Erdmann, Jeanette [0000-0002-4486-6231], Samani, Nilesh J [0000-0002-3286-8133], Schunkert, Heribert [0000-0001-6428-3001], Watkins, Hugh [0000-0002-5287-9016], Willer, Cristen J [0000-0001-5645-4966], Kathiresan, Sekar [0000-0002-3711-7101], Butterworth, Adam S [0000-0002-6915-9015], and Apollo - University of Cambridge Repository

Subjects
692/699/75/2, 631/208/205/2138, article, Humans, Coronary Artery Disease, Genome-Wide Association Study
Abstract

Funder: K.G.A. has received support from the American Heart Association Institute for Precision Cardiovascular Medicine (17IFUNP3384001), a KL2/Catalyst Medical Research Investigator Training (CMeRIT) award from the Harvard Catalyst (KL2 TR002542), and the NIH (1K08HL153937)., Funder: B.N.W is supported by the National Science Foundation Graduate Research Program (DGE 1256260)., Funder: I.S. is supported by a Precision Health Scholars Award from the University of Michigan Medical School., Funder: I.K., S.Ko., and K.It. are funded by the Japan Agency for Medical Research and Development, AMED, under Grant Numbers JP16ek0109070h0003, JP18kk0205008h0003, JP18kk0205001s0703, JP20km0405209, and JP20ek0109487. The BioBank Japan is supported by AMED under Grant Number JP20km0605001., Funder: J.L.M.B. acknowledges research support from NIH R01HL125863, American Heart Association (A14SFRN20840000), the Swedish Research Council (2018-02529) and Heart Lung Foundation (20170265) and the Foundation Leducq (PlaqueOmics: Novel Roles of Smooth Muscle and Other Matrix Producing Cells in Atherosclerotic Plaque Stability and Rupture, 18CVD02., Funder: P.S.dV was supported by American Heart Association grant number 18CDA34110116 and National Heart, Lung, and Blood Institute grant R01HL146860. The Atherosclerosis Risk in Communities study has been funded in whole or in part with Federal funds from the National Heart, Lung, and Blood Institute, National Institutes of Health, Department of Health and Human Services (contract numbers HHSN268201700001I, HHSN268201700002I, HHSN268201700003I, HHSN268201700004I and HHSN268201700005I), R01HL087641, R01HL059367 and R01HL086694; National Human Genome Research Institute contract U01HG004402; and National Institutes of Health contract HHSN268200625226C. The authors thank the staff and participants of the ARIC study for their important contributions. Infrastructure was partly supported by Grant Number UL1RR025005, a component of the National Institutes of Health and NIH Roadmap for Medical Research., Funder: O.G. has received funding from the British Heart Foundation (BHF) (FS/14/66/3129)., Funder: T.K. is supported by the Corona-Foundation (Junior Research Group Translational Cardiovascular Genomics) and the German Research Foundation (DFG) as part of the Sonderforschungsbereich SFB 1123 (B02)., Funder: D.S.A. has received support from a training grant from the NIH (T32HL007604)., Funder: N.P.B., M.C.C., J.F., and D.-K.J. have been funded by the National Institute of Diabetes and Digestive and Kidney Diseases (2UM1DK105554)., Funder: A.V.K. has been funded by 1K08HG010155 from the National Human Genome Research Institute., Funder: C.P.N. and T.R.W received funding from the British Heart Foundation (SP/16/4/32697)., Funder: The Trøndelag Health Study (The HUNT Study) is a collaboration between HUNT Research Centre (Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology), Trøndelag County Council, Central Norway Regional Health Authority, and the Norwegian Institute of Public Health. The K.G. Jebsen Center for Genetic Epidemiology is financed by Stiftelsen Kristian Gerhard Jebsen; Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology; and Central Norway Regional Health Authority. Whole genome sequencing for the HUNT study was funded by HL109946., Funder: O.M. was funded by the Swedish Heart- and Lung Foundation, the Swedish Research Council, the European Research Council ERC-AdG-2019-885003 and Lund University Infrastructure grant ”Malmö population-based cohorts” (STYR 2019/2046)., Funder: This work was supported by the European Commission (HEALTH-F2–2013-601456) and the TriPartite Immunometabolism Consortium [TrIC]- NovoNordisk Foundation (NNF15CC0018486), VIAgenomics (SP/19/2/344612), the British Heart Foundation, a Wellcome Trust core award (M.F., H.W., 203141/Z/16/Z) and support from the NIHR Oxford Biomedical Research Centre. M.F. and H.W. are members of the Oxford BHF Centre of Research Excellence (RE/13/1/30181). The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health., Funder: J.D. is a British Heart Foundation Professor, European Research Council Senior Investigator, and National Institute for Health Research (NIHR) Senior Investigator., Funder: J.C.H. acknowledges personal funding from the British Heart Foundation (FS/14/55/30806) and is a member of the Oxford BHF Centre of Research Excellence (RE/13/1/30181)., Funder: R.C. has received funding from the British Heart Foundation and British Heart Foundation Centre of Research Excellence., Funder: This research was supported by BHF (SP/13/2/30111) and conducted using the UK Biobank Resource (application number 9922)., Funder: The GerMIFs gratefully acknowledge the support of the Bavarian State Ministry of Health and Care, furthermore founded this work within its framework of DigiMed Bayern (grant No: DMB-1805-0001), the German Federal Ministry of Education and Research (BMBF) within the framework of ERA-NET on Cardiovascular Disease (Druggable-MI-genes: 01KL1802), within the scheme of target validation (BlockCAD: 16GW0198K), within the framework of the e:Med research and funding concept (AbCD-Net: 01ZX1706C), the British Heart Foundation (BHF)/German Centre of Cardiovascular Research (DZHK)-collaboration (VIAgenomics) and the German Research Foundation (DFG) as part of the Sonderforschungsbereich SFB 1123 (B02) and the Sonderforschungsbereich SFB TRR 267 (B05)., Funder: C.J.W. is funded by NIH grant R35-HL135824., Funder: This work was supported by the British Heart Foundation (BHF) grant RG/14/5/30893 (P.D.) and forms part of the research themes contributing to the translational research portfolios of the Barts Biomedical Research Centre funded by the UK National Institute for Health Research (NIHR)., The discovery of genetic loci associated with complex diseases has outpaced the elucidation of mechanisms of disease pathogenesis. Here we conducted a genome-wide association study (GWAS) for coronary artery disease (CAD) comprising 181,522 cases among 1,165,690 participants of predominantly European ancestry. We detected 241 associations, including 30 new loci. Cross-ancestry meta-analysis with a Japanese GWAS yielded 38 additional new loci. We prioritized likely causal variants using functionally informed fine-mapping, yielding 42 associations with less than five variants in the 95% credible set. Similarity-based clustering suggested roles for early developmental processes, cell cycle signaling and vascular cell migration and proliferation in the pathogenesis of CAD. We prioritized 220 candidate causal genes, combining eight complementary approaches, including 123 supported by three or more approaches. Using CRISPR–Cas9, we experimentally validated the effect of an enhancer in MYO9B, which appears to mediate CAD risk by regulating vascular cell motility. Our analysis identifies and systematically characterizes >250 risk loci for CAD to inform experimental interrogation of putative causal mechanisms for CAD.

Published
2022
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16. Mild-to-Moderate Kidney Dysfunction and Cardiovascular Disease: Observational and Mendelian Randomization Analyses

Author

Liam Gaziano, Luanluan Sun, Matthew Arnold, Steven Bell, Kelly Cho, Stephen K. Kaptoge, Rebecca J. Song, Stephen Burgess, Daniel C. Posner, Katja Mosconi, Cassianne Robinson-Cohen, Amy M. Mason, Thomas R. Bolton, Ran Tao, Elias Allara, Petra Schubert, Lingyan Chen, James R. Staley, Natalie Staplin, Servet Altay, Pilar Amiano, Volker Arndt, Johan Ärnlöv, Elizabeth L.M. Barr, Cecilia Björkelund, Jolanda M.A. Boer, Hermann Brenner, Edoardo Casiglia, Paolo Chiodini, Jackie A. Cooper, Josef Coresh, Mary Cushman, Rachel Dankner, Karina W. Davidson, Renate T. de Jongh, Chiara Donfrancesco, Gunnar Engström, Heinz Freisling, Agustín Gómez de la Cámara, Vilmundur Gudnason, Graeme J. Hankey, Per-Olof Hansson, Alicia K. Heath, Ewout J. Hoorn, Hironori Imano, Simerjot K. Jassal, Rudolf Kaaks, Verena Katzke, Jussi Kauhanen, Stefan Kiechl, Wolfgang Koenig, Richard A. Kronmal, Cecilie Kyrø, Deborah A. Lawlor, Börje Ljungberg, Conor MacDonald, Giovanna Masala, Christa Meisinger, Olle Melander, Conchi Moreno Iribas, Toshiharu Ninomiya, Dorothea Nitsch, Børge G. Nordestgaard, Charlotte Onland-Moret, Luigi Palmieri, Dafina Petrova, Jose Ramón Quirós Garcia, Annika Rosengren, Carlotta Sacerdote, Masaru Sakurai, Carmen Santiuste, Matthias B. Schulze, Sabina Sieri, Johan Sundström, Valérie Tikhonoff, Anne Tjønneland, Tammy Tong, Rosario Tumino, Ioanna Tzoulaki, Yvonne T. van der Schouw, W.M. Monique Verschuren, Henry Völzke, Robert B. Wallace, S. Goya Wannamethee, Elisabete Weiderpass, Peter Willeit, Mark Woodward, Kazumasa Yamagishi, Raul Zamora-Ros, Elvis A. Akwo, Saiju Pyarajan, David R. Gagnon, Philip S. Tsao, Sumitra Muralidhar, Todd L. Edwards, Scott M. Damrauer, Jacob Joseph, Lisa Pennells, Peter W.F. Wilson, Seamus Harrison, Thomas A. Gaziano, Michael Inouye, Colin Baigent, Juan P. Casas, Claudia Langenberg, Nick Wareham, Elio Riboli, J.Michael Gaziano, John Danesh, Adriana M. Hung, Adam S. Butterworth, Angela M. Wood, Emanuele Di Angelantonio, Anna Koettgen, Jonathan Shaw, Robert Atkins, Paul Zimmet, Peter Whincup, Johann Willeit, Christoph Leitner, Anne Tybjaerg-Hansen, Peter Schnohr, Shoaib Afzal, David Lora Pablos, Cristina Martin Arriscado, Carmen Romero Ferreiro, Hannah Stocker, Ben Schöttker, Bernd Holleczek, Angela Chetrit, Lennart Welin, Kurt Svärdsudd, Lauren Lissner, Dominique Hange, Kirsten Mehlig, Dorothea Nagel, Paul E. Norman, Osvaldo Almeida, Leon Flicker, Jun Hata, Takanori Honda, Yoshihiko Furuta, Hiroyasu Iso, Akihiko Kitamura, Isao Muraki, Jukka T. Salonen, Tomi-Pekka Tuomainen, E. M. van Zutphen, N. M. van Schoor, Cinzia Lo Noce, Richard Kronmal, Georg Lappas, Peter M. Nilsson, Bo Hedblad, Jonathan Shaffer, Joseph Schwartz, Daichi Shimbo, Shinichi Sato, Mina Hayama-Terada, Simerjot Jassal, Thor Aspelund, Bolli Thorsson, Gunnar Sigurdsson, Layal Chaker, Kamran M. Ikram, Maryam Kavousi, Hugh Tunstall-Pedoe, Günay Can, Hüsniye Yüksel, Uğur Özkan, Hideaki Nakagawa, Yuko Morikawa, Masao Ishizaki, Edith Feskens, Johanna M Geleijnse, Daan Kromhout, Internal Medicine, Neurology, Epidemiology, Bell, Steven [0000-0001-6774-3149], Posner, Daniel C [0000-0002-3056-6924], Mason, Amy M [0000-0002-8019-0777], Allara, Elias [0000-0002-1634-8330], Staplin, Natalie [0000-0003-4482-4418], Arndt, Volker [0000-0001-9320-8684], Ärnlöv, Johan [0000-0002-6933-4637], Barr, Elizabeth LM [0000-0003-4284-1716], Boer, Jolanda MA [0000-0002-9714-4304], Brenner, Hermann [0000-0002-6129-1572], Casiglia, Edoardo [0000-0002-0003-3289], Chiodini, Paolo [0000-0003-0139-2264], Coresh, Josef [0000-0002-4598-0669], Cushman, Mary [0000-0002-7871-6143], Davidson, Karina W [0000-0002-9162-477X], de Jongh, Renate T [0000-0001-8414-3938], Engström, Gunnar [0000-0002-8618-9152], de la Cámara, Agustín Gómez [0000-0001-6827-6319], Gudnason, Vilmundur [0000-0001-5696-0084], Hankey, Graeme J [0000-0002-6044-7328], Hansson, Per-Olof [0000-0001-6323-0506], Heath, Alicia K [0000-0001-6517-1300], Hoorn, Ewout J [0000-0002-8738-3571], Imano, Hironori [0000-0002-6661-4254], Katzke, Verena [0000-0002-6509-6555], Kiechl, Stefan [0000-0002-9836-2514], Koenig, Wolfgang [0000-0002-2064-9603], Kronmal, Richard A [0000-0002-9897-7076], Kyrø, Cecilie [0000-0002-9083-8960], Ljungberg, Börje [0000-0002-4121-3753], MacDonald, Conor [0000-0002-4989-803X], Masala, Giovanna [0000-0002-5758-9069], Ninomiya, Toshiharu [0000-0003-1345-9032], Nordestgaard, Børge G [0000-0002-1954-7220], Onland-Moret, Charlotte [0000-0002-2360-913X], Palmieri, Luigi [0000-0002-4298-2642], Rosengren, Annika [0000-0002-5409-6605], Schulze, Matthias B [0000-0002-0830-5277], Sieri, Sabina [0000-0001-5201-172X], Sundström, Johan [0000-0003-2247-8454], Tikhonoff, Valérie [0000-0001-7846-0101], Tong, Tammy [0000-0002-0284-8959], Tzoulaki, Ioanna [0000-0002-4275-9328], van der Schouw, Yvonne T [0000-0002-4605-435X], Wannamethee, S Goya [0000-0001-9484-9977], Weiderpass, Elisabete [0000-0003-2237-0128], Willeit, Peter [0000-0002-1866-7159], Woodward, Mark [0000-0001-9800-5296], Yamagishi, Kazumasa [0000-0003-3301-5519], Zamora-Ros, Raul [0000-0002-6236-6804], Gagnon, David R [0000-0002-6367-3179], Tsao, Philip S [0000-0001-7274-9318], Edwards, Todd L [0000-0003-4318-6119], Damrauer, Scott M [0000-0001-8009-1632], Joseph, Jacob [0000-0002-7279-4896], Pennells, Lisa [0000-0002-8594-3061], Gaziano, Thomas A [0000-0002-5985-345X], Langenberg, Claudia [0000-0002-5017-7344], Wareham, Nick [0000-0003-1422-2993], Hung, Adriana M [0000-0002-3203-1608], Butterworth, Adam S [0000-0002-6915-9015], Di Angelantonio, Emanuele [0000-0001-8776-6719], Apollo - University of Cambridge Repository, Gaziano, Liam, Sun, Luanluan, Arnold, Matthew, Bell, Steven, Cho, Kelly, Kaptoge, Stephen K, Song, Rebecca J, Burgess, Stephen, Posner, Daniel C, Mosconi, Katja, Robinson-Cohen, Cassianne, Mason, Amy M, Bolton, Thomas R, Tao, Ran, Allara, Elia, Schubert, Petra, Chen, Lingyan, Staley, James R, Staplin, Natalie, Altay, Servet, Amiano, Pilar, Arndt, Volker, Ärnlöv, Johan, Barr, Elizabeth L M, Björkelund, Cecilia, Boer, Jolanda M A, Brenner, Hermann, Casiglia, Edoardo, Chiodini, Paolo, Cooper, Jackie A, Coresh, Josef, Cushman, Mary, Dankner, Rachel, Davidson, Karina W, de Jongh, Renate T, Donfrancesco, Chiara, Engström, Gunnar, Freisling, Heinz, de la Cámara, Agustín Gómez, Gudnason, Vilmundur, Hankey, Graeme J, Hansson, Per-Olof, Heath, Alicia K, Hoorn, Ewout J, Imano, Hironori, Jassal, Simerjot K, Kaaks, Rudolf, Katzke, Verena, Kauhanen, Jussi, Kiechl, Stefan, Koenig, Wolfgang, Kronmal, Richard A, Kyrø, Cecilie, Lawlor, Deborah A, Ljungberg, Börje, Macdonald, Conor, Masala, Giovanna, Meisinger, Christa, Melander, Olle, Moreno Iribas, Conchi, Ninomiya, Toshiharu, Nitsch, Dorothea, Nordestgaard, Børge G, Onland-Moret, Charlotte, Palmieri, Luigi, Petrova, Dafina, Garcia, Jose Ramón Quiró, Rosengren, Annika, Sacerdote, Carlotta, Sakurai, Masaru, Santiuste, Carmen, Schulze, Matthias B, Sieri, Sabina, Sundström, Johan, Tikhonoff, Valérie, Tjønneland, Anne, Tong, Tammy, Tumino, Rosario, Tzoulaki, Ioanna, van der Schouw, Yvonne T, Monique Verschuren, W M, Völzke, Henry, Wallace, Robert B, Wannamethee, S Goya, Weiderpass, Elisabete, Willeit, Peter, Woodward, Mark, Yamagishi, Kazumasa, Zamora-Ros, Raul, Akwo, Elvis A, Pyarajan, Saiju, Gagnon, David R, Tsao, Philip S, Muralidhar, Sumitra, Edwards, Todd L, Damrauer, Scott M, Joseph, Jacob, Pennells, Lisa, Wilson, Peter W F, Harrison, Seamu, Gaziano, Thomas A, Inouye, Michael, Baigent, Colin, Casas, Juan P, Langenberg, Claudia, Wareham, Nick, Riboli, Elio, Gaziano, J Michael, Danesh, John, Hung, Adriana M, Butterworth, Adam S, Wood, Angela M, Di Angelantonio, Emanuele, Internal medicine, AMS - Ageing & Vitality, AMS - Musculoskeletal Health, Amsterdam Gastroenterology Endocrinology Metabolism, Epidemiology and Data Science, APH - Aging & Later Life, and APH - Personalized Medicine

Subjects
kidney disease, General Practice, Emerging Risk Factors Collaboration/EPIC-CVD/Million Veteran Program, Coronary Disease, coronary disease, Kidney, Malalties coronàries, 1117 Public Health and Health Services, Coronary diseases, SDG 3 - Good Health and Well-being, cardiovascular disease, Risk Factors, Physiology (medical), Diabetes Mellitus, Humans, Cardiac and Cardiovascular Systems, Prospective Studies, 1102 Cardiorespiratory Medicine and Haematology, Kardiologi, Kidney diseases, Malalties cardiovasculars, Cardiovascular Diseases, Kidney Diseases, Stroke, 1103 Clinical Sciences, Mendelian Randomization Analysis, kidney diseases, stroke, Allmänmedicin, Cardiovascular diseases, Cardiovascular System & Hematology, Malalties del ronyó, Cardiology and Cardiovascular Medicine, cardiovascular diseases
Abstract

Background: End-stage renal disease is associated with a high risk of cardiovascular events. It is unknown, however, whether mild-to-moderate kidney dysfunction is causally related to coronary heart disease (CHD) and stroke. Methods: Observational analyses were conducted using individual-level data from 4 population data sources (Emerging Risk Factors Collaboration, EPIC-CVD [European Prospective Investigation into Cancer and Nutrition–Cardiovascular Disease Study], Million Veteran Program, and UK Biobank), comprising 648 135 participants with no history of cardiovascular disease or diabetes at baseline, yielding 42 858 and 15 693 incident CHD and stroke events, respectively, during 6.8 million person-years of follow-up. Using a genetic risk score of 218 variants for estimated glomerular filtration rate (eGFR), we conducted Mendelian randomization analyses involving 413 718 participants (25 917 CHD and 8622 strokes) in EPIC-CVD, Million Veteran Program, and UK Biobank. Results: There were U-shaped observational associations of creatinine-based eGFR with CHD and stroke, with higher risk in participants with eGFR values 105 mL·min –1 ·1.73 m –2 , compared with those with eGFR between 60 and 105 mL·min –1 ·1.73 m –2 . Mendelian randomization analyses for CHD showed an association among participants with eGFR –1 ·1.73 m –2 , with a 14% (95% CI, 3%–27%) higher CHD risk per 5 mL·min –1 ·1.73 m –2 lower genetically predicted eGFR, but not for those with eGFR >105 mL·min –1 ·1.73 m –2 . Results were not materially different after adjustment for factors associated with the eGFR genetic risk score, such as lipoprotein(a), triglycerides, hemoglobin A1c, and blood pressure. Mendelian randomization results for stroke were nonsignificant but broadly similar to those for CHD. Conclusions: In people without manifest cardiovascular disease or diabetes, mild-to-moderate kidney dysfunction is causally related to risk of CHD, highlighting the potential value of preventive approaches that preserve and modulate kidney function.

Published
2022

17. Rare and common genetic determinants of metabolic individuality and their effects on human health

Author

Surendran, Praveen, Stewart, Isobel, AuYeung, Victoria PW, Pietzner, Mark, Li, Chen, Smith, Rebecca F, Wittemans, Laura BL, Watkins, Nicholas A, Di Angelantonio, Emanuele, Soranzo, Nicole, Lotta, Luca A, Howson, Joanna MM, Wood, Angela M, Danesh, John, Wareham, Nicholas J, Butterworth, Adam S, Langenberg, Claudia, Pietzner, Maik [0000-0003-3437-9963], Wörheide, Maria A [0000-0002-9326-7227], Menni, Cristina [0000-0001-9790-0571], Zierer, Jonas [0000-0002-9693-1859], Mangino, Massimo [0000-0002-2167-7470], Falchi, Mario [0000-0002-5646-1004], Spector, Tim D [0000-0002-9795-0365], Soranzo, Nicole [0000-0003-1095-3852], Michelotti, Gregory A [0000-0002-3936-4675], Arlt, Wiebke [0000-0001-5106-9719], Howson, Joanna MM [0000-0001-7618-0050], Wareham, Nicholas J [0000-0003-1422-2993], Kastenmüller, Gabi [0000-0002-2368-7322], Fauman, Eric B [0000-0002-9739-0249], Butterworth, Adam S [0000-0002-6915-9015], Langenberg, Claudia [0000-0002-5017-7344], and Apollo - University of Cambridge Repository

Subjects
Plasma, Phenotype, 3-Oxo-5-alpha-Steroid 4-Dehydrogenase, Metabolome, Humans, Metabolomics, Membrane Proteins, Metabolism, Inborn Errors
Abstract

Garrod’s concept of “chemical individuality” has contributed to comprehension of molecular origins of human diseases. Untargeted high throughput metabolomic technologies provide an in-depth snapshot of human metabolism at scale. Here we studied the genetic architecture of the human plasma metabolome using 913 metabolites assayed in 19,994 individuals. We identified 2,599 variant-metabolite associations (P

Published
2022

18. Higher body mass index raises immature platelet count: potential contribution to obesity-related thrombosis

Author

Lucy J. Goudswaard, Laura J. Corbin, Kate L. Burley, Andrew Mumford, Parsa Akbari, Nicole Soranzo, Adam S. Butterworth, Nicholas A. Watkins, Dimitri J. Pournaras, Jessica Harris, Nicholas J. Timpson, Ingeborg Hers, Goudswaard, Lucy J [0000-0003-1481-6871], Corbin, Laura J [0000-0002-4032-9500], Burley, Kate L [0000-0002-1569-5007], Mumford, Andrew [0000-0002-5523-511X], Soranzo, Nicole [0000-0003-1095-3852], Butterworth, Adam S [0000-0002-6915-9015], Hers, Ingeborg [0000-0002-6467-5715], and Apollo - University of Cambridge Repository

Subjects
Blood Platelets, Aggregation, obesity, Platelet Count, parasitic diseases, Mendelian randomization, Humans, epidemiology, Thrombosis, Hematology, General Medicine, immature platelets, Body Mass Index
Abstract

Higher body mass index (BMI) is a risk factor for thrombosis. Platelets are essential for hemostasis but contribute to thrombosis when activated pathologically. We hypothesized that higher BMI leads to changes in platelet characteristics, thereby increasing thrombotic risk. The effect of BMI on platelet traits (measured by Sysmex) was explored in 33 388 UK blood donors (INTERVAL study). Linear regression showed that higher BMI was positively associated with greater plateletcrit (PCT), platelet count (PLT), immature platelet count (IPC), and side fluorescence (SFL, a measure of mRNA content used to derive IPC). Mendelian randomization (MR), applied to estimate a causal effect with BMI proxied by a genetic risk score, provided causal estimates for a positive effect of BMI on both SFL and IPC, but there was little evidence for a causal effect of BMI on PCT or PLT. Follow-up analyses explored the functional relevance of platelet characteristics in a pre-operative cardiac cohort (COPTIC). Linear regression provided observational evidence for a positive association between IPC and agonist-induced whole blood platelet aggregation. Results indicate that higher BMI raises the number of immature platelets, which is associated with greater whole blood platelet aggregation in a cardiac cohort. Higher IPC could therefore contribute to obesity-related thrombosis.

Published
2022

19. Actionable druggable genome-wide Mendelian randomization identifies repurposing opportunities for COVID-19

Author

Gaziano, Liam, Giambartolomei, Claudia, Pereira, Alexandre C, Gaulton, Anna, Posner, Daniel C, Swanson, Sonja A, Ho, Yuk-Lam, Iyengar, Sudha K, Kosik, Nicole M, Vujkovic, Marijana, Gagnon, David R, Bento, A Patrícia, Barrio-Hernandez, Inigo, Rönnblom, Lars, Hagberg, Niklas, Lundtoft, Christian, Langenberg, Claudia, Pietzner, Maik, Valentine, Dennis, Gustincich, Stefano, Tartaglia, Gian Gaetano, Allara, Elias, Surendran, Praveen, Burgess, Stephen, Zhao, Jing Hua, Peters, James E, Prins, Bram P, Angelantonio, Emanuele Di, Devineni, Poornima, Shi, Yunling, Lynch, Kristine E, DuVall, Scott L, Garcon, Helene, Thomann, Lauren O, Zhou, Jin J, Gorman, Bryan R, Huffman, Jennifer E, O'Donnell, Christopher J, Tsao, Philip S, Beckham, Jean C, Pyarajan, Saiju, Muralidhar, Sumitra, Huang, Grant D, Ramoni, Rachel, Beltrao, Pedro, Danesh, John, Hung, Adriana M, Chang, Kyong-Mi, Sun, Yan V, Joseph, Jacob, Leach, Andrew R, Edwards, Todd L, Cho, Kelly, Gaziano, J Michael, Butterworth, Adam S, Casas, Juan P, VA Million Veteran Program COVID-19 Science Initiative, Epidemiology, Medical Research Council (MRC), Giambartolomei, Claudia [0000-0003-2786-1225], Gaulton, Anna [0000-0003-2634-7400], Posner, Daniel C [0000-0002-3056-6924], Kosik, Nicole M [0000-0003-1384-7035], Vujkovic, Marijana [0000-0003-4924-5714], Gagnon, David R [0000-0002-6367-3179], Bento, A Patrícia [0000-0003-1424-480X], Rönnblom, Lars [0000-0001-9403-6503], Hagberg, Niklas [0000-0003-2064-2716], Lundtoft, Christian [0000-0001-5872-4253], Langenberg, Claudia [0000-0002-5017-7344], Pietzner, Maik [0000-0003-3437-9963], Gustincich, Stefano [0000-0002-2749-2514], Tartaglia, Gian Gaetano [0000-0001-7524-6310], Allara, Elias [0000-0002-1634-8330], Burgess, Stephen [0000-0001-5365-8760], Peters, James E [0000-0002-9415-3440], Prins, Bram P [0000-0001-5774-034X], Huffman, Jennifer E [0000-0002-9672-2491], O'Donnell, Christopher J [0000-0002-2667-8624], Beltrao, Pedro [0000-0002-2724-7703], Chang, Kyong-Mi [0000-0001-6811-9364], Sun, Yan V [0000-0002-2838-1824], Butterworth, Adam S [0000-0002-6915-9015], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Biochemistry & Molecular Biology, Immunology, Quantitative Trait Loci, Druggability, Genome-wide association study, Receptor, Interferon alpha-beta, Computational biology, Research & Experimental Medicine, Quantitative trait locus, Biology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Mendelian randomization, Humans, VA Million Veteran Program COVID-19 Science Initiative, health care economics and organizations, 11 Medical and Health Sciences, Repurposing, Science & Technology, RECEPTOR, SARS-CoV-2, Drug Repositioning, COVID-19, Cell Biology, IN-VITRO, General Medicine, Mendelian Randomization Analysis, Interleukin-10 Receptor beta Subunit, COVID-19 Drug Treatment, Drug repositioning, 030104 developmental biology, Medicine, Research & Experimental, Drug development, 030220 oncology & carcinogenesis, Expression quantitative trait loci, Angiotensin-Converting Enzyme 2, INTERFERON-ALPHA, Life Sciences & Biomedicine, Genome-Wide Association Study
Abstract

Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2, P = 1.6 × 10−6; IFNAR2, P = 9.8 × 10−11 and IL-10RB, P = 2.3 × 10−14) using cis-expression quantitative trait loci genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared expression quantitative trait loci signal for IL10RB and IFNAR2, we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.

Published
2021

20. Phenome-wide Mendelian randomization mapping the influence of the plasma proteome on complex diseases

Author

Hannah M. Martin, Yi Liu, Tom R. Gaunt, Michael V. Holmes, Matthew R. Nelson, Jie Zheng, Benjamin B. Sun, Stephen Burgess, George Davey Smith, Jamie Robinson, John Danesh, James R Staley, Shan Luo, Robert A. Scott, Pau Erola, Karol Estrada, Dawn M. Waterworth, Gibran Hemani, Benjamin Elsworth, Alex Gutteridge, Valeriia Haberland, Charles Laurin, Heiko Runz, Denis Baird, Venexia M Walker, Tom G. Richardson, Mark R. Hurle, Jimmy Z. Liu, Joseph C. Maranville, Adam S. Butterworth, Philip C Haycock, James Yarmolinsky, Rita Santos, Linda McCarthy, Zheng, Jie [0000-0002-6623-6839], Haberland, Valeriia [0000-0002-3874-0683], Robinson, Jamie [0000-0001-8721-6514], Richardson, Tom G [0000-0002-7918-2040], Elsworth, Benjamin [0000-0001-7328-4233], Sun, Benjamin B [0000-0001-6347-2281], Smith, George Davey [0000-0002-1407-8314], Butterworth, Adam S [0000-0002-6915-9015], Hemani, Gibran [0000-0003-0920-1055], Scott, Robert A [0000-0003-3634-3016], Gaunt, Tom R [0000-0003-0924-3247], and Apollo - University of Cambridge Repository

Subjects
Proteomics, Linkage disequilibrium, Proteome, Genome-wide association study, Computational biology, 030204 cardiovascular system & hematology, Phenome, Biology, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, 0302 clinical medicine, Mendelian randomization, Human proteome project, Genetics, Humans, Genetic Predisposition to Disease, health care economics and organizations, Genetic association, 030304 developmental biology, 0303 health sciences, Drug discovery, High-throughput screening, Colocalization, Mendelian Randomization Analysis, Blood Proteins, Phenotype, 3. Good health, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

The human proteome is a major source of therapeutic targets. Recent genetic association analyses of the plasma proteome enable systematic evaluation of the causal consequences of variation in plasma protein levels. Here, we estimated the effects of 1002 proteins on 225 phenotypes using two-sample Mendelian randomization (MR) and colocalization. Of 413 associations supported by evidence from MR, 130 (31.5%) were not supported by results of colocalization analyses, suggesting that genetic confounding due to linkage disequilibrium (LD) is widespread in naive phenome-wide association studies of proteins. Combining MR and colocalization evidence in cis-only analyses, we identified 111 putatively causal effects between 65 proteins and 52 disease-related phenotypes (www.epigraphdb.org/pqtl/). Evaluation of data from historic drug development programmes showed that target-indication pairs with MR and colocalization support were more likely to be approved, evidencing the value of our approach in identifying and prioritising potential therapeutic targets.

Published
2020

21. Integrative analysis of the plasma proteome and polygenic risk of cardiometabolic diseases

Author

Petar Scepanovic, Jonathan Marten, Shu Mei Teo, Michael Inouye, Nicholas A. Watkins, David J. Roberts, Scott C. Ritchie, Brian G. Drew, Nicole Soranzo, Adam S. Butterworth, Matthew Arnold, Sol Lim, Samuel A. Lambert, Michael A Chapman, Yingying Liu, Amit Khera, Emanuele Di Angelantonio, Sohail Zahid, Stephen Burgess, Mark Chaffin, John Danesh, Anna C. Calkin, Willem H. Ouwehand, Sekar Kathiresan, Gad Abraham, Ritchie, Scott C [0000-0002-8454-9548], Lambert, Samuel A [0000-0001-8222-008X], Arnold, Matthew [0000-0001-6339-1115], Lim, Sol [0000-0001-7786-3355], Chaffin, Mark [0000-0002-1234-5562], Ouwehand, Willem H [0000-0002-7744-1790], Drew, Brian G [0000-0002-7839-9467], Calkin, Anna C [0000-0002-9861-0602], Soranzo, Nicole [0000-0003-1095-3852], Burgess, Stephen [0000-0001-5365-8760], Chapman, Michael [0000-0002-4582-6303], Kathiresan, Sekar [0000-0002-3711-7101], Butterworth, Adam S [0000-0002-6915-9015], Inouye, Michael [0000-0001-9413-6520], and Apollo - University of Cambridge Repository

Subjects
Adult, Male, Multifactorial Inheritance, Letter, Heart Diseases, Proteome, Population genetics, Endocrinology, Diabetes and Metabolism, Disease, Type 2 diabetes, Quantitative trait locus, Bioinformatics, Coronary artery disease, Pathogenesis, Young Adult, Metabolic Diseases, Physiology (medical), Internal Medicine, Genetic predisposition, Medicine, Humans, Genetic Predisposition to Disease, Public Health Surveillance, Vascular diseases, business.industry, Disease Management, Functional genomics, Cell Biology, Blood Proteins, Middle Aged, medicine.disease, Metabolism, England, Female, Disease Susceptibility, business, Biomarkers, Kidney disease
Abstract

Cardiometabolic diseases are frequently polygenic in architecture, comprising a large number of risk alleles with small effects spread across the genome1–3. Polygenic scores (PGS) aggregate these into a metric representing an individual’s genetic predisposition to disease. PGS have shown promise for early risk prediction4–7 and there is an open question as to whether PGS can also be used to understand disease biology8. Here, we demonstrate that cardiometabolic disease PGS can be used to elucidate the proteins underlying disease pathogenesis. In 3,087 healthy individuals, we found that PGS for coronary artery disease, type 2 diabetes, chronic kidney disease and ischaemic stroke are associated with the levels of 49 plasma proteins. Associations were polygenic in architecture, largely independent of cis and trans protein quantitative trait loci and present for proteins without quantitative trait loci. Over a follow-up of 7.7 years, 28 of these proteins associated with future myocardial infarction or type 2 diabetes events, 16 of which were mediators between polygenic risk and incident disease. Twelve of these were druggable targets with therapeutic potential. Our results demonstrate the potential for PGS to uncover causal disease biology and targets with therapeutic potential, including those that may be missed by approaches utilizing information at a single locus., Ritchie et al. use polygenic scores to identify plasma proteins with causal roles in cardiometabolic disease.

Published
2021

22. Systematic Mendelian randomization using the human plasma proteome to discover potential therapeutic targets for stroke

Author

Chen, Lingyan, Peters, James E, Prins, Bram, Persyn, Elodie, Traylor, Matthew, Surendran, Praveen, Karthikeyan, Savita, Yonova-Doing, Ekaterina, Di Angelantonio, Emanuele, Roberts, David J, Watkins, Nicholas A, Ouwehand, Willem H, Danesh, John, Lewis, Cathryn M, Bronson, Paola G, Markus, Hugh S, Burgess, Stephen, Butterworth, Adam S, Howson, Joanna MM, Chen, Lingyan [0000-0003-3750-6761], Peters, James E [0000-0002-9415-3440], Prins, Bram [0000-0001-5774-034X], Persyn, Elodie [0000-0001-9104-1972], Ouwehand, Willem H [0000-0002-7744-1790], Lewis, Cathryn M [0000-0002-8249-8476], Bronson, Paola G [0000-0001-9996-9812], Burgess, Stephen [0000-0001-5365-8760], Butterworth, Adam S [0000-0002-6915-9015], Howson, Joanna MM [0000-0001-7618-0050], and Apollo - University of Cambridge Repository

Subjects
Multidisciplinary, 631/208/2489/144, 45, Proteome, 45/43, article, General Physics and Astronomy, General Chemistry, Blood Proteins, Mendelian Randomization Analysis, 692/699/75, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Stroke, Diabetes Mellitus, Type 2, Risk Factors, Atrial Fibrillation, Humans, Genetic Predisposition to Disease, 692/499, Genome-Wide Association Study
Abstract

Funder: NIHR Cambridge Biomedical Research Centre (BRC-1215-20014), Stroke is the second leading cause of death with substantial unmet therapeutic needs. To identify potential stroke therapeutic targets, we estimate the causal effects of 308 plasma proteins on stroke outcomes in a two-sample Mendelian randomization framework and assess mediation effects by stroke risk factors. We find associations between genetically predicted plasma levels of six proteins and stroke (P ≤ 1.62 × 10-4). The genetic associations with stroke colocalize (Posterior Probability >0.7) with the genetic associations of four proteins (TFPI, TMPRSS5, CD6, CD40). Mendelian randomization supports atrial fibrillation, body mass index, smoking, blood pressure, white matter hyperintensities and type 2 diabetes as stroke risk factors (P ≤ 0.0071). Body mass index, white matter hyperintensity and atrial fibrillation appear to mediate the TFPI, IL6RA, TMPRSS5 associations with stroke. Furthermore, thirty-six proteins are associated with one or more of these risk factors using Mendelian randomization. Our results highlight causal pathways and potential therapeutic targets for stroke.

Published
2021

23. New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries

Author

Phuwanat Sakornsakolpat, James F. Wilson, María Soler Artigas, Beate Stubbe, Nicholas J. Wareham, James D. Crapo, Victoria E. Jackson, Eleftheria Zeggini, Olga G. Troyanskaya, Medea Imboden, A. Mesut Erzurumluoglu, Adam S. Butterworth, Carl A. Melbourne, Ian Sayers, Lars Lind, Stefan Weiss, Margaret M. Parker, Timmers Prhj, Edwin K. Silverman, John C. Whittaker, Ian P. Hall, Ozren Polasek, Mika Kähönen, Katherine A. Fawcett, Anna Hansell, Liming Li, David J. Porteous, Louise V. Wain, Robert A. Scott, Richard Packer, Richard J. Allen, Robin G Walters, Anna L. Guyatt, Terho Lehtimäki, Nicole Probst-Hensch, Shona M. Kerr, Christian Gieger, Matthias Wielscher, Rajesh Rawal, Jing Hua Zhao, John E. Hokanson, Holger Schulz, Nicola F. Reeve, Claudia Langenberg, Ke Hao, Corry-Anke Brandsma, Megan L. Paynton, Vitart, Dmitry Prokopenko, Jennie Hui, Eugene R. Bleecker, Ma'en Obeidat, John Danesh, Ralf Ewert, Benjamin B. Sun, Frank Dudbridge, Jian Zhou, Brian D. Hobbs, Blair H. Smith, Don D. Sin, Dawn L. DeMeo, Joseph C. Maranville, Ida Surakka, Alison Catherine Murray, Nicholas Locantore, Katherine A. Kentistou, Terri H. Beaty, Igor Rudan, Kuang Lin, Amund Gulsvik, Ian J. Deary, Ruth Tal-Singer, Kijoung Song, David C. Nickle, Michael H. Cho, Jian'an Luan, Joshua D. Hoffman, Georg Homuth, Zhengming Chen, Dandi Qiao, Heiko Runz, Per Bakke, Chiara Batini, Caroline Hayward, Stefan Karrasch, Alan James, Andrew P. Morris, Prescott G. Woodruff, Laura M Yerges Armstrong, David Sparrow, Ulf Gyllensten, James P. Cook, Jonathan Marten, Olli T. Raitakari, Nick Shrine, Deborah A. Meyers, Tobin, Ruth Boxall, Marjo-Riitta Järvelin, David P. Strachan, Sarah E. Harris, Philippe Joubert, Stefan Enroth, Xingnan Li, van den Berge M, Anubha Mahajan, Yohan Bossé, Peter K. Joshi, Shrine, Nick [0000-0003-3641-4371], Guyatt, Anna L [0000-0003-1860-6337], Hobbs, Brian D [0000-0001-9564-0745], Sakornsakolpat, Phuwanat [0000-0002-4308-0974], Obeidat, Ma'en [0000-0002-5443-2752], Weiss, Stefan [0000-0002-3553-4315], Kentistou, Katherine A [0000-0002-5816-664X], Sun, Benjamin B [0000-0001-6347-2281], Enroth, Stefan [0000-0002-5056-9137], Vitart, Veronique [0000-0002-4991-3797], Allen, Richard J [0000-0002-8450-3056], Beaty, Terri H [0000-0002-7644-1705], Bossé, Yohan [0000-0002-3067-3711], Joshi, Peter K [0000-0002-6361-5059], Mahajan, Anubha [0000-0001-5585-3420], Murray, Alison [0000-0003-4915-4847], Porteous, David J [0000-0003-1249-6106], Sayers, Ian [0000-0001-5601-5410], Smith, Blair H [0000-0002-5362-9430], Tal-Singer, Ruth [0000-0002-5275-8062], Timmers, Paul RHJ [0000-0002-5197-1267], Troyanskaya, Olga G [0000-0002-5676-5737], Rudan, Igor [0000-0001-6993-6884], Wilson, James F [0000-0001-5751-9178], Zeggini, Eleftheria [0000-0003-4238-659X], Hayward, Caroline [0000-0002-9405-9550], Morris, Andrew P [0000-0002-6805-6014], Butterworth, Adam S [0000-0002-6915-9015], Walters, Robin G [0000-0002-9179-0321], Cho, Michael H [0000-0002-4907-1657], Strachan, David P [0000-0001-7854-1366], Tobin, Martin D [0000-0002-3596-7874], Wain, Louise V [0000-0003-4951-1867], Apollo - University of Cambridge Repository, Institute for Molecular Medicine Finland, Groningen Research Institute for Asthma and COPD (GRIAC), UNIVERSITY OF OULU, and Commission of the European Communities

Subjects
Male, Smoking/genetics, LOCI, Genome-wide association study, VARIANTS, Bioinformatics, Genome-wide association studies, Pulmonary Disease, Chronic Obstructive, 0302 clinical medicine, Polymorphism (computer science), Risk Factors, GWAS, GENOME-WIDE ASSOCIATION, HERITABILITY, COPD, Lung, 11 Medical and Health Sciences, Genetics & Heredity, Aged, 80 and over, 0303 health sciences, Genetic Predisposition to Disease/genetics, Smoking, 1184 Genetics, developmental biology, physiology, Middle Aged, Polymorphism, Single Nucleotide/genetics, 3. Good health, medicine.anatomical_structure, Meta-analysis, Genome-Wide Association Study/methods, Medical genetics, Female, Life Sciences & Biomedicine, medicine.medical_specialty, Understanding Society Scientific Group, Biology, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Genetics, medicine, Humans, Genetic Predisposition to Disease, 030304 developmental biology, Genetic association, Aged, Respiratory tract diseases, Science & Technology, Case-control study, Lung/physiopathology, 06 Biological Sciences, medicine.disease, Pulmonary Disease, Chronic Obstructive/genetics, respiratory tract diseases, Case-Control Studies, 3111 Biomedicine, 030217 neurology & neurosurgery, Developmental Biology, Genome-Wide Association Study
Abstract

Reduced lung function predicts mortality and is key to the diagnosis of chronic obstructive pulmonary disease (COPD). In a genome-wide association study in 400,102 individuals of European ancestry, we define 279 lung function signals, 139 of which are new. In combination, these variants strongly predict COPD in independent patient populations. Furthermore, the combined effect of these variants showed generalizability across smokers and never-smokers, and across ancestral groups. We highlight biological pathways, known and potential drug targets for COPD and, in phenome-wide association studies, autoimmune-related and other pleiotropic effects of lung function associated variants. This new genetic evidence has potential to improve future preventive and therapeutic strategies for COPD., Editorial summary: A genome-wide association study in over 400,000 individuals identifies 139 new signals for lung function. These variants can predict chronic obstructive pulmonary disease in independent, trans-ethnic cohorts.

Published
2019

24. A genome-wide meta-analysis yields 46 new loci associating with biomarkers of iron homeostasis

Author

Bell, Steven, Rigas, Andreas S., Magnusson, Magnus K., Ferkingstad, Egil, Allara, Elias, Bjornsdottir, Gyda, Ramond, Anna, Sørensen, Erik, Halldorsson, Gisli H., Paul, Dirk S., Burgdorf, Kristoffer S., Eggertsson, Hannes P., Howson, Joanna M. M., Thørner, Lise W., Kristmundsdottir, Snaedis, Astle, William J., Erikstrup, Christian, Sigurdsson, Jon K., Vuckovic, Dragana, Dinh, Khoa M., Tragante, Vinicius, Surendran, Praveen, Pedersen, Ole B., Vidarsson, Brynjar, Jiang, Tao, Paarup, Helene M., Onundarson, Pall T., Akbari, Parsa, Nielsen, Kaspar R., Lund, Sigrun H., Juliusson, Kristinn, Magnusson, Magnus I., Frigge, Michael L., Oddsson, Asmundur, Olafsson, Isleifur, Kaptoge, Stephen, Hjalgrim, Henrik, Runarsson, Gudmundur, Wood, Angela M., Jonsdottir, Ingileif, Hansen, Thomas F., Sigurdardottir, Olof, Stefansson, Hreinn, Rye, David, Peters, James E., Westergaard, David, Holm, Hilma, Soranzo, Nicole, Banasik, Karina, Thorleifsson, Gudmar, Ouwehand, Willem H., Thorsteinsdottir, Unnur, Roberts, David J., Sulem, Patrick, Butterworth, Adam S., Gudbjartsson, Daniel F., Danesh, John, Brunak, Søren, Di Angelantonio, Emanuele, Ullum, Henrik, Stefansson, Kari, Andersen, Steffen, Burgdorf, Kristoffer, Jemec, Gregor, Jennum, Poul, Johansson, Pär, Nielsen, Kasper R., Nyegaard, Mette, Petersen, Mikkel, Werge, Thomas, Stefánsson, Hreinn, Thorsteinsdóttir, Unnur, Bell, Steven [0000-0001-6774-3149], Magnusson, Magnus K. [0000-0001-8593-4934], Ferkingstad, Egil [0000-0001-8090-7988], Allara, Elias [0000-0002-1634-8330], Halldorsson, Gisli H. [0000-0001-7067-9862], Paul, Dirk S. [0000-0002-8230-0116], Eggertsson, Hannes P. [0000-0002-1674-9978], Howson, Joanna M. M. [0000-0001-7618-0050], Erikstrup, Christian [0000-0001-6551-6647], Tragante, Vinicius [0000-0002-8223-8957], Pedersen, Ole B. [0000-0003-2312-5976], Paarup, Helene M. [0000-0003-1281-1567], Akbari, Parsa [0000-0001-9210-4760], Lund, Sigrun H. [0000-0002-3806-2296], Frigge, Michael L. [0000-0003-2984-535X], Oddsson, Asmundur [0000-0002-4606-5163], Jonsdottir, Ingileif [0000-0001-8339-150X], Hansen, Thomas F. [0000-0001-6703-7762], Stefansson, Hreinn [0000-0002-9331-6666], Westergaard, David [0000-0003-0128-8432], Holm, Hilma [0000-0002-9517-6636], Soranzo, Nicole [0000-0003-1095-3852], Banasik, Karina [0000-0003-2489-2499], Ouwehand, Willem H. [0000-0002-7744-1790], Sulem, Patrick [0000-0001-7123-6123], Butterworth, Adam S. [0000-0002-6915-9015], Gudbjartsson, Daniel F. [0000-0002-5222-9857], Brunak, Søren [0000-0003-0316-5866], Stefansson, Kari [0000-0003-1676-864X], and Apollo - University of Cambridge Repository

Subjects
45, 631/208/457/649, 692/308/2056, 45/43, article
Abstract

Iron is essential for many biological functions and iron deficiency and overload have major health implications. We performed a meta-analysis of three genome-wide association studies from Iceland, the UK and Denmark of blood levels of ferritin (N = 246,139), total iron binding capacity (N = 135,430), iron (N = 163,511) and transferrin saturation (N = 131,471). We found 62 independent sequence variants associating with iron homeostasis parameters at 56 loci, including 46 novel loci. Variants at DUOX2, F5, SLC11A2 and TMPRSS6 associate with iron deficiency anemia, while variants at TF, HFE, TFR2 and TMPRSS6 associate with iron overload. A HBS1L-MYB intergenic region variant associates both with increased risk of iron overload and reduced risk of iron deficiency anemia. The DUOX2 missense variant is present in 14% of the population, associates with all iron homeostasis biomarkers, and increases the risk of iron deficiency anemia by 29%. The associations implicate proteins contributing to the main physiological processes involved in iron homeostasis: iron sensing and storage, inflammation, absorption of iron from the gut, iron recycling, erythropoiesis and bleeding/menstruation.

Published
2021
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25. Effects of adiposity on the human plasma proteome: Observational and Mendelian randomization estimates

Author

Laura J Corbin, Nicholas J. Timpson, Emanuele Di Angelantonio, Nicole Soranzo, Joshua A. Bell, David A. Hughes, George Davey Smith, Willem H. Ouwehand, Lucy J Goudswaard, Nicholas A. Watkins, Klaudia Walter, Ingeborg Hers, Adam S. Butterworth, David J. Roberts, John Danesh, Goudswaard, Lucy J [0000-0003-1481-6871], Hughes, David A [0000-0002-9644-8998], Corbin, Laura J [0000-0002-4032-9500], Walter, Klaudia [0000-0003-4448-0301], Ouwehand, Willem H [0000-0002-7744-1790], Butterworth, Adam S [0000-0002-6915-9015], Timpson, Nicholas J [0000-0002-7141-9189], and Apollo - University of Cambridge Repository

Subjects
Adult, Male, Proteome, Genome-wide association study, Disease, Bioinformatics, Body Mass Index, Cohort Studies, symbols.namesake, Surveys and Questionnaires, Mendelian randomization, Human proteome project, Humans, Medicine, Prospective Studies, Adiposity, business.industry, nutritional and metabolic diseases, Mendelian Randomization Analysis, Middle Aged, Bonferroni correction, symbols, Female, Observational study, business, Body mass index
Abstract

BACKGROUND: Variation in adiposity is associated with cardiometabolic disease outcomes, but mechanisms leading from this exposure to disease are unclear. This study aimed to estimate effects of body mass index (BMI) on an extensive set of circulating proteins. METHODS: We used SomaLogic proteomic data from up to 2737 healthy participants from the INTERVAL study. Associations between self-reported BMI and 3622 unique plasma proteins were explored using linear regression. These were complemented by Mendelian randomisation (MR) analyses using a genetic risk score (GRS) comprised of 654 BMI-associated polymorphisms from a recent genome-wide association study (GWAS) of adult BMI. A disease enrichment analysis was performed using DAVID Bioinformatics 6.8 for proteins which were altered by BMI. RESULTS: Observationally, BMI was associated with 1576 proteins (P < 1.4 × 10-5), with particularly strong evidence for a positive association with leptin and fatty acid-binding protein-4 (FABP4), and a negative association with sex hormone-binding globulin (SHBG). Observational estimates were likely confounded, but the GRS for BMI did not associate with measured confounders. MR analyses provided evidence for a causal relationship between BMI and eight proteins including leptin (0.63 standard deviation (SD) per SD BMI, 95% CI 0.48-0.79, P = 1.6 × 10-15), FABP4 (0.64 SD per SD BMI, 95% CI 0.46-0.83, P = 6.7 × 10-12) and SHBG (-0.45 SD per SD BMI, 95% CI -0.65 to -0.25, P = 1.4 × 10-5). There was agreement in the magnitude of observational and MR estimates (R2 = 0.33) and evidence that proteins most strongly altered by BMI were enriched for genes involved in cardiovascular disease. CONCLUSIONS: This study provides evidence for a broad impact of adiposity on the human proteome. Proteins strongly altered by BMI include those involved in regulating appetite, sex hormones and inflammation; such proteins are also enriched for cardiovascular disease-related genes. Altogether, results help focus attention onto new proteomic signatures of obesity-related disease.

Published
2020

26. Genomic and drug target evaluation of 90 cardiovascular proteins in 30,931 individuals

Author

Tom Palmer, Lars Lind, George Davey Smith, Ting Qi, Michael W. Nagle, Paul W. Franks, Bram P. Prins, Julie Lee, Jingyuan Fu, Niclas Eriksson, Peter K. Joshi, Chris Haley, Ljubica Perisic Matic, Jeremy D. Gale, Mika Ala-Korpela, Michael V. Holmes, Urmo Võsa, Adam S. Butterworth, Eric B. Fauman, Anette Kalnapenkis, Reedik Mägi, Åsa Johansson, James F. Wilson, Mikael Landén, Gunnar Engström, Johan Ärnlöv, Anders Hamsten, Ozren Polasek, Andres Ingason, Andrew J. Schork, Agneta Siegbahn, Lasse Folkersen, Qin Wang, Andrew P. Morris, Johan Sundström, Daria V. Zhernakova, Olle Melander, Erik Ingelsson, Federico De Masi, Lude Franke, James E. Peters, Alexandra Zhernakova, Seung Hoan Choi, Rasmus Wernersson, Thibaud Boutin, Karl Michaëlsson, Stefan Gustafsson, Bianca E. Suur, Karen Page, Yang Wu, Caroline Hayward, Marketa Sjögren, Cecilia M. Lindgren, Stefan Enroth, Tõnu Esko, Amira Quazi, John Danesh, Anders Mälarstig, Daniel Hvidberg Hansen, Åsa K Hedman, Jan Nilsson, Ulf Gyllensten, Vilmantas Giedraitis, J. Gustav Smith, Martin Magnusson, Marju Orho-Melander, Steven A. Lubitz, Erin Macdonald-Dunlop, Thomas Werge, Praveen Surendran, Yan Chen, Céline Fernandez, Weidong Zhang, Lars Wallentin, Andrew D. Bretherick, Jian Yang, Peter M. Nilsson, Jesper R. Gådin, Annique Claringbould, Sölve Elmståhl, Sarah E Bergen, Harm-Jan Westra, Erik Pålsson, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Translational Immunology Groningen (TRIGR), Center for Liver, Digestive and Metabolic Diseases (CLDM), Stem Cell Aging Leukemia and Lymphoma (SALL), United Kingdom Research and Innovation, Folkersen, Lasse [0000-0003-0708-9530], Hansen, Daniel Hvidberg [0000-0003-3285-605X], Wu, Yang [0000-0002-0128-7280], Eriksson, Niclas [0000-0002-2152-4343], Bretherick, Andrew D [0000-0001-9258-3140], Enroth, Stefan [0000-0002-5056-9137], Lee, Julie [0000-0001-6090-6718], Ala-Korpela, Mika [0000-0001-5905-1206], Claringbould, Annique [0000-0002-9201-6557], Davey Smith, George [0000-0002-1407-8314], Fauman, Eric [0000-0002-9739-0249], Fernandez, Celine [0000-0003-1290-4982], Franke, Lude [0000-0002-5159-8802], Franks, Paul W [0000-0002-0520-7604], Giedraitis, Vilmantas [0000-0003-3423-2021], Haley, Chris [0000-0002-9811-0210], Johansson, Åsa [0000-0002-2915-4498], Lubitz, Steven [0000-0002-9599-4866], Palmer, Tom [0000-0003-4655-4511], Macdonald-Dunlop, Erin [0000-0001-6569-6086], Magnusson, Martin [0000-0003-1710-5936], Michaelsson, Karl [0000-0003-2815-1217], Nagle, Michael W [0000-0002-4677-7582], Nilsson, Peter M [0000-0002-5652-8459], Nilsson, Jan [0000-0002-9752-7479], Prins, Bram [0000-0001-5774-034X], Sundström, Johan [0000-0003-2247-8454], Werge, Thomas [0000-0003-1829-0766], Westra, Harm-Jan [0000-0001-7038-567X], Fu, Jingyuan [0000-0001-5578-1236], Esko, Tõnu [0000-0003-1982-6569], Hayward, Caroline [0000-0002-9405-9550], Landen, Mikael [0000-0002-4496-6451], Butterworth, Adam S [0000-0002-6915-9015], Holmes, Michael V [0000-0001-6617-0879], Ingelsson, Erik [0000-0003-2256-6972], Mälarstig, Anders [0000-0003-2608-1358], Apollo - University of Cambridge Repository, and 30387078 - Magnusson, P. Martin

Subjects
Proteomics, Proteome, Endocrinology, Diabetes and Metabolism, Asthma, ATP Binding Cassette Transporter 1, Cardiovascular System, Chromosome Mapping, Drug Delivery Systems, Gene Knockdown Techniques, Genome-Wide Association Study, Genomics, Humans, Inflammatory Bowel Diseases, Interleukin-1 Receptor-Like 1 Protein, Intracellular Signaling Peptides and Proteins, Linkage Disequilibrium, Mendelian Randomization Analysis, Protein-Serine-Threonine Kinases, Quantitative Trait Loci, Receptors, CCR2, Receptors, CCR5, Genome-wide association study, 030204 cardiovascular system & hematology, Chemokine receptor, 0302 clinical medicine, RECEPTOR ANTAGONIST, GWAS, Cardiac and Cardiovascular Systems, 0303 health sciences, Molecular medicine, 3. Good health, Medical genetics, Medical Genetics, Life Sciences & Biomedicine, medicine.medical_specialty, Computational biology, Biology, Protein Serine-Threonine Kinases, Article, 03 medical and health sciences, Endocrinology & Metabolism, Physiology (medical), Mendelian randomization, Internal Medicine, medicine, 030304 developmental biology, Science & Technology, Cell Biology, GENE, ANTIBODY
Abstract

Circulating proteins are vital in human health and disease and are frequently used as biomarkers for clinical decision-making or as targets for pharmacological intervention. Here, we map and replicate protein quantitative trait loci (pQTL) for 90 cardiovascular proteins in over 30,000 individuals, resulting in 451 pQTLs for 85 proteins. For each protein, we further perform pathway mapping to obtain trans-pQTL gene and regulatory designations. We substantiate these regulatory findings with orthogonal evidence for trans-pQTLs using mouse knockdown experiments (ABCA1 and TRIB1) and clinical trial results (chemokine receptors CCR2 and CCR5), with consistent regulation. Finally, we evaluate known drug targets, and suggest new target candidates or repositioning opportunities using Mendelian randomization. This identifies 11 proteins with causal evidence of involvement in human disease that have not previously been targeted, including EGF, IL-16, PAPPA, SPON1, F3, ADM, CASP-8, CHI3L1, CXCL16, GDF15 and MMP-12. Taken together, these findings demonstrate the utility of large-scale mapping of the genetics of the proteome and provide a resource for future precision studies of circulating proteins in human health.

Published
2020
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27. Assessing the causal association of glycine with risk of cardio-metabolic diseases

Author

Heribert Schunkert, Stephen Burgess, Adam S. Butterworth, Nita G. Forouhi, Julian L. Griffin, Claudia Langenberg, Savita Karthikeyan, Clare Oliver-Williams, Lingyao Zeng, Laura B. L. Wittemans, Felix R. Day, Albert Koulman, Isobel D. Stewart, Angela M. Wood, Kay-Tee Khaw, Luca A. Lotta, Nicholas J. Wareham, John Danesh, Praveen Surendran, Jeanette Erdmann, Joanna M. M. Howson, Robert A. Scott, Fumiaki Imamura, Day, Felix R [0000-0003-3789-7651], Koulman, Albert [0000-0001-9998-051X], Imamura, Fumiaki [0000-0002-6841-8396], Forouhi, Nita G [0000-0002-5041-248X], Burgess, Stephen [0000-0001-5365-8760], Howson, Joanna MM [0000-0001-7618-0050], Butterworth, Adam S [0000-0002-6915-9015], Langenberg, Claudia [0000-0002-5017-7344], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Science, Glycine, General Physics and Astronomy, Genome-wide association study, Coronary Disease, 02 engineering and technology, Type 2 diabetes, Bioinformatics, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Insulin resistance, Polymorphism (computer science), Diabetes mellitus, Hyperinsulinism, medicine, Humans, Genetic Predisposition to Disease, lcsh:Science, Genetic association, Multidisciplinary, business.industry, Incidence, General Chemistry, 021001 nanoscience & nanotechnology, medicine.disease, 3. Good health, ddc, 030104 developmental biology, Diabetes Mellitus, Type 2, Genetic Loci, Meta-analysis, lcsh:Q, 0210 nano-technology, business, Metabolic Networks and Pathways, Genome-Wide Association Study
Abstract

Circulating levels of glycine have previously been associated with lower incidence of coronary heart disease (CHD) and type 2 diabetes (T2D) but it remains uncertain if glycine plays an aetiological role. We present a meta-analysis of genome-wide association studies for glycine in 80,003 participants and investigate the causality and potential mechanisms of the association between glycine and cardio-metabolic diseases using genetic approaches. We identify 27 genetic loci, of which 22 have not previously been reported for glycine. We show that glycine is genetically associated with lower CHD risk and find that this may be partly driven by blood pressure. Evidence for a genetic association of glycine with T2D is weaker, but we find a strong inverse genetic effect of hyperinsulinaemia on glycine. Our findings strengthen evidence for a protective effect of glycine on CHD and show that the glycine-T2D association may be driven by a glycine-lowering effect of insulin resistance., Epidemiological studies have associated circulating levels of the amino acid glycine with cardiometabolic outcomes. Here, in a genome-wide meta-analysis of 80,003 individuals, Wittemans et al. identify 22 novel genetic loci for glycine and find a causal relationship with coronary heart disease using MR.

Published
2019

28. Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution

Author

Justice, Anne E, Karaderi, Tugce, Highland, Heather M, Young, Kristin L, Graff, Mariaelisa, Lu, Yingchang, Turcot, Valérie, Auer, Paul L, Fine, Rebecca S, Guo, Xiuqing, Schurmann, Claudia, Lempradl, Adelheid, Marouli, Eirini, Mahajan, Anubha, Winkler, Thomas W, Locke, Adam E, Medina-Gomez, Carolina, Esko, Tõnu, Vedantam, Sailaja, Giri, Ayush, Lo, Ken Sin, Alfred, Tamuno, Mudgal, Poorva, Ng, Maggie CY, Heard-Costa, Nancy L, Feitosa, Mary F, Manning, Alisa K, Willems, Sara M, Sivapalaratnam, Suthesh, Abecasis, Goncalo, Alam, Dewan S, Allison, Matthew, Amouyel, Philippe, Arzumanyan, Zorayr, Balkau, Beverley, Bastarache, Lisa, Bergmann, Sven, Bielak, Lawrence F, Blüher, Matthias, Boehnke, Michael, Boeing, Heiner, Boerwinkle, Eric, Böger, Carsten A, Bork-Jensen, Jette, Bottinger, Erwin P, Bowden, Donald W, Brandslund, Ivan, Broer, Linda, Burt, Amber A, Butterworth, Adam S, Caulfield, Mark J, Cesana, Giancarlo, Chambers, John C, Chasman, Daniel I, Chen, Yii-Der Ida, Chowdhury, Rajiv, Christensen, Cramer, Chu, Audrey Y, Collins, Francis S, Cook, James P, Cox, Amanda J, Crosslin, David S, Danesh, John, de Bakker, Paul IW, Denus, Simon de, Mutsert, Renée de, Dedoussis, George, Demerath, Ellen W, Dennis, Joe G, Denny, Josh C, Angelantonio, Emanuele Di, Dörr, Marcus, Drenos, Fotios, Dubé, Marie-Pierre, Dunning, Alison M, Easton, Douglas F, Elliott, Paul, Evangelou, Evangelos, Farmaki, Aliki-Eleni, Feng, Shuang, Ferrannini, Ele, Ferrieres, Jean, Florez, Jose C, Fornage, Myriam, Fox, Caroline S, Franks, Paul W, Friedrich, Nele, Gan, Wei, Gandin, Ilaria, Gasparini, Paolo, Giedraitis, Vilmantas, Girotto, Giorgia, Gorski, Mathias, Grallert, Harald, Grarup, Niels, Grove, Megan L, Gustafsson, Stefan, Haessler, Jeff, Hansen, Torben, Hattersley, Andrew T, Hayward, Caroline, Heid, Iris M, Holmen, Oddgeir L, Hovingh, G Kees, Howson, Joanna MM, Hu, Yao, Hung, Yi-Jen, Hveem, Kristian, Ikram, M Arfan, Ingelsson, Erik, Jackson, Anne U, Jarvik, Gail P, Jia, Yucheng, Jørgensen, Torben, Jousilahti, Pekka, Justesen, Johanne M, Kahali, Bratati, Karaleftheri, Maria, Kardia, Sharon LR, Karpe, Fredrik, Kee, Frank, Kitajima, Hidetoshi, Komulainen, Pirjo, Kooner, Jaspal S, Kovacs, Peter, Krämer, Bernhard K, Kuulasmaa, Kari, Kuusisto, Johanna, Laakso, Markku, Lakka, Timo A, Lamparter, David, Lange, Leslie A, Langenberg, Claudia, Larson, Eric B, Lee, Nanette R, Lee, Wen-Jane, Lehtimäki, Terho, Lewis, Cora E, Li, Huaixing, Li, Jin, Li-Gao, Ruifang, Lin, Li-An, Lin, Xu, Lind, Lars, Lindström, Jaana, Linneberg, Allan, Liu, Ching-Ti, Liu, Dajiang J, Luan, Jian'an, Lyytikäinen, Leo-Pekka, MacGregor, Stuart, Mägi, Reedik, Männistö, Satu, Marenne, Gaëlle, Marten, Jonathan, Masca, Nicholas GD, McCarthy, Mark I, Meidtner, Karina, Mihailov, Evelin, Moilanen, Leena, Moitry, Marie, Mook-Kanamori, Dennis O, Morgan, Anna, Morris, Andrew P, Müller-Nurasyid, Martina, Munroe, Patricia B, Narisu, Narisu, Nelson, Christopher P, Neville, Matt, Ntalla, Ioanna, O'Connell, Jeffrey R, Owen, Katharine R, Pedersen, Oluf, Peloso, Gina M, Pennell, Craig E, Perola, Markus, Perry, James A, Perry, John RB, Pers, Tune H, Ewing, Ailith, Polasek, Ozren, Raitakari, Olli T, Rasheed, Asif, Raulerson, Chelsea K, Rauramaa, Rainer, Reilly, Dermot F, Reiner, Alex P, Ridker, Paul M, Rivas, Manuel A, Robertson, Neil R, Robino, Antonietta, Rudan, Igor, Ruth, Katherine S, Saleheen, Danish, Salomaa, Veikko, Samani, Nilesh J, Schreiner, Pamela J, Schulze, Matthias B, Scott, Robert A, Segura-Lepe, Marcelo, Sim, Xueling, Slater, Andrew J, Small, Kerrin S, Smith, Blair H, Smith, Jennifer A, Southam, Lorraine, Spector, Timothy D, Speliotes, Elizabeth K, Stefansson, Kari, Steinthorsdottir, Valgerdur, Stirrups, Kathleen E, Strauch, Konstantin, Stringham, Heather M, Stumvoll, Michael, Sun, Liang, Surendran, Praveen, Swart, Karin MA, Tardif, Jean-Claude, Taylor, Kent D, Teumer, Alexander, Thompson, Deborah J, Thorleifsson, Gudmar, Thorsteinsdottir, Unnur, Thuesen, Betina H, Tönjes, Anke, Torres, Mina, Tsafantakis, Emmanouil, Tuomilehto, Jaakko, Uitterlinden, André G, Uusitupa, Matti, van Duijn, Cornelia M, Vanhala, Mauno, Varma, Rohit, Vermeulen, Sita H, Vestergaard, Henrik, Vitart, Veronique, Vogt, Thomas F, Vuckovic, Dragana, Wagenknecht, Lynne E, Walker, Mark, Wallentin, Lars, Wang, Feijie, Wang, Carol A, Wang, Shuai, Wareham, Nicholas J, Warren, Helen R, Waterworth, Dawn M, Wessel, Jennifer, White, Harvey D, Willer, Cristen J, Wilson, James G, Wood, Andrew R, Wu, Ying, Yaghootkar, Hanieh, Yao, Jie, Yerges-Armstrong, Laura M, Young, Robin, Zeggini, Eleftheria, Zhan, Xiaowei, Zhang, Weihua, Zhao, Jing Hua, Zhao, Wei, Zheng, He, Zhou, Wei, Zillikens, M Carola, CHD Exome+ Consortium, Cohorts for Heart and Aging Research in Genomic Epidemiology (CH, EPIC-CVD Consortium, ExomeBP Consortium, Global Lipids Genetic Consortium, GoT2D Genes Consortium, InterAct, ReproGen Consortium, T2D-Genes Consortium, MAGIC Investigators, Rivadeneira, Fernando, Borecki, Ingrid B, Pospisilik, J Andrew, Deloukas, Panos, Frayling, Timothy M, Lettre, Guillaume, Mohlke, Karen L, Rotter, Jerome I, Kutalik, Zoltán, Hirschhorn, Joel N, Cupples, L Adrienne, Loos, Ruth JF, North, Kari E, Lindgren, Cecilia M, Vascular Medicine, ACS - Atherosclerosis & ischemic syndromes, Internal Medicine, Epidemiology, Obstetrics & Gynecology, Radiology & Nuclear Medicine, CHD Exome+ Consortium, Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium, EPIC-CVD Consortium, ExomeBP Consortium, Global Lipids Genetic Consortium, GoT2D Genes Consortium, InterAct, ReproGen Consortium, T2D-Genes Consortium, MAGIC Investigators, Institute for Molecular Medicine Finland, Research Programs Unit, Diabetes and Obesity Research Program, University of Helsinki, Young, Kristin L [0000-0003-0070-6145], Mahajan, Anubha [0000-0001-5585-3420], Winkler, Thomas W [0000-0003-0292-5421], Locke, Adam E [0000-0001-6227-198X], Medina-Gomez, Carolina [0000-0001-7999-5538], Giri, Ayush [0000-0002-7786-4670], Ng, Maggie CY [0000-0002-4133-2007], Heard-Costa, Nancy L [0000-0001-9730-0306], Manning, Alisa K [0000-0003-0247-902X], Alam, Dewan S [0000-0002-2051-3837], Amouyel, Philippe [0000-0001-9088-234X], Bergmann, Sven [0000-0002-6785-9034], Boehnke, Michael [0000-0002-6442-7754], Butterworth, Adam S [0000-0002-6915-9015], Caulfield, Mark J [0000-0001-9295-3594], Collins, Francis S [0000-0002-1023-7410], de Bakker, Paul IW [0000-0001-7735-7858], Dennis, Joe G [0000-0003-4591-1214], Easton, Douglas F [0000-0003-2444-3247], Elliott, Paul [0000-0002-7511-5684], Evangelou, Evangelos [0000-0002-5488-2999], Giedraitis, Vilmantas [0000-0003-3423-2021], Girotto, Giorgia [0000-0003-4507-6589], Grarup, Niels [0000-0001-5526-1070], Gustafsson, Stefan [0000-0001-5894-0351], Hansen, Torben [0000-0001-8748-3831], Hayward, Caroline [0000-0002-9405-9550], Howson, Joanna MM [0000-0001-7618-0050], Ikram, M Arfan [0000-0003-0372-8585], Jackson, Anne U [0000-0002-9672-2547], Justesen, Johanne M [0000-0002-0484-8522], Kovacs, Peter [0000-0002-0290-5423], Kuulasmaa, Kari [0000-0003-2165-1411], Langenberg, Claudia [0000-0002-5017-7344], Lin, Li-An [0000-0003-2731-1346], Linneberg, Allan [0000-0002-0994-0184], Liu, Ching-Ti [0000-0002-0703-0742], Lyytikäinen, Leo-Pekka [0000-0002-7200-5455], MacGregor, Stuart [0000-0001-6731-8142], McCarthy, Mark I [0000-0002-4393-0510], Morgan, Anna [0000-0001-6290-445X], Müller-Nurasyid, Martina [0000-0003-3793-5910], Munroe, Patricia B [0000-0002-4176-2947], Narisu, Narisu [0000-0002-8483-1156], Neville, Matt [0000-0002-6004-5433], Reilly, Dermot F [0000-0002-9456-1364], Rudan, Igor [0000-0001-6993-6884], Saleheen, Danish [0000-0001-6193-020X], Salomaa, Veikko [0000-0001-7563-5324], Sim, Xueling [0000-0002-1233-7642], Small, Kerrin S [0000-0003-4566-0005], Smith, Blair H [0000-0002-5362-9430], Smith, Jennifer A [0000-0002-3575-5468], Southam, Lorraine [0000-0002-7546-9650], Stefansson, Kari [0000-0003-1676-864X], Stirrups, Kathleen E [0000-0002-6823-3252], Stringham, Heather M [0000-0002-2991-6392], Teumer, Alexander [0000-0002-8309-094X], Thompson, Deborah J [0000-0003-1465-5799], Vestergaard, Henrik [0000-0003-3090-269X], Vitart, Veronique [0000-0002-4991-3797], Wang, Carol A [0000-0002-4301-3974], Wessel, Jennifer [0000-0002-7031-0085], Willer, Cristen J [0000-0001-5645-4966], Zeggini, Eleftheria [0000-0003-4238-659X], Rivadeneira, Fernando [0000-0001-9435-9441], Pospisilik, J Andrew [0000-0002-9745-0977], Deloukas, Panos [0000-0001-9251-070X], Mohlke, Karen L [0000-0001-6721-153X], Kutalik, Zoltán [0000-0001-8285-7523], Loos, Ruth JF [0000-0002-8532-5087], Lindgren, Cecilia M [0000-0002-4903-9374], Apollo - University of Cambridge Repository, Home Office, Medical Research Council (MRC), National Institute for Health Research, Imperial College Healthcare NHS Trust- BRC Funding, UK DRI Ltd, Medical and Clinical Psychology, Justice, Anne E., Karaderi, Tugce, Highland, Heather M., Young, Kristin L., Graff, Mariaelisa, Lu, Yingchang, Turcot, Valérie, Auer, Paul L., Fine, Rebecca S., Guo, Xiuqing, Schurmann, Claudia, Lempradl, Adelheid, Marouli, Eirini, Mahajan, Anubha, Winkler, Thomas W., Locke, Adam E., Medina-Gomez, Carolina, Esko, Tõnu, Vedantam, Sailaja, Giri, Ayush, Lo, Ken Sin, Alfred, Tamuno, Mudgal, Poorva, Ng, Maggie C. Y., Heard-Costa, Nancy L., Feitosa, Mary F., Manning, Alisa K., Willems, Sara M., Sivapalaratnam, Suthesh, Abecasis, Goncalo, Alam, Dewan S., Allison, Matthew, Amouyel, Philippe, Arzumanyan, Zorayr, Balkau, Beverley, Bastarache, Lisa, Bergmann, Sven, Bielak, Lawrence F., Blüher, Matthia, Boehnke, Michael, Boeing, Heiner, Boerwinkle, Eric, Böger, Carsten A., Bork-Jensen, Jette, Bottinger, Erwin P., Bowden, Donald W., Brandslund, Ivan, Broer, Linda, Burt, Amber A., Butterworth, Adam S., Caulfield, Mark J., Cesana, Giancarlo, Chambers, John C., Chasman, Daniel I., Chen, Yii-Der Ida, Chowdhury, Rajiv, Christensen, Cramer, Chu, Audrey Y., Collins, Francis S., Cook, James P., Cox, Amanda J., Crosslin, David S., Danesh, John, de Bakker, Paul I. W., Denus, Simon de, Mutsert, Renée de, Dedoussis, George, Demerath, Ellen W., Dennis, Joe G., Denny, Josh C., Angelantonio, Emanuele Di, Dörr, Marcu, Drenos, Fotio, Dubé, Marie-Pierre, Dunning, Alison M., Easton, Douglas F., Elliott, Paul, Evangelou, Evangelo, Farmaki, Aliki-Eleni, Feng, Shuang, Ferrannini, Ele, Ferrieres, Jean, Florez, Jose C., Fornage, Myriam, Fox, Caroline S., Franks, Paul W., Friedrich, Nele, Gan, Wei, Gandin, Ilaria, Gasparini, Paolo, Giedraitis, Vilmanta, Girotto, Giorgia, Gorski, Mathia, Grallert, Harald, Grarup, Niel, Grove, Megan L., Gustafsson, Stefan, Haessler, Jeff, Hansen, Torben, Hattersley, Andrew T., Hayward, Caroline, Heid, Iris M., Holmen, Oddgeir L., Hovingh, G. Kee, Howson, Joanna M. M., Hu, Yao, Hung, Yi-Jen, Hveem, Kristian, Ikram, M. Arfan, Ingelsson, Erik, Jackson, Anne U., Jarvik, Gail P., Jia, Yucheng, Jørgensen, Torben, Jousilahti, Pekka, Justesen, Johanne M., Kahali, Bratati, Karaleftheri, Maria, Kardia, Sharon L. R., Karpe, Fredrik, Kee, Frank, Kitajima, Hidetoshi, Komulainen, Pirjo, Kooner, Jaspal S., Kovacs, Peter, Krämer, Bernhard K., Kuulasmaa, Kari, Kuusisto, Johanna, Laakso, Markku, Lakka, Timo A., Lamparter, David, Lange, Leslie A., Langenberg, Claudia, Larson, Eric B., Lee, Nanette R., Lee, Wen-Jane, Lehtimäki, Terho, Lewis, Cora E., Li, Huaixing, Li, Jin, Li-Gao, Ruifang, Lin, Li-An, Lin, Xu, Lind, Lar, Lindström, Jaana, Linneberg, Allan, Liu, Ching-Ti, Liu, Dajiang J., Luan, Jian’An, Lyytikäinen, Leo-Pekka, Macgregor, Stuart, Mägi, Reedik, Männistö, Satu, Marenne, Gaëlle, Marten, Jonathan, Masca, Nicholas G. D., Mccarthy, Mark I., Meidtner, Karina, Mihailov, Evelin, Moilanen, Leena, Moitry, Marie, Mook-Kanamori, Dennis O., Morgan, Anna, Morris, Andrew P., Müller-Nurasyid, Martina, Munroe, Patricia B., Narisu, Narisu, Nelson, Christopher P., Neville, Matt, Ntalla, Ioanna, O’Connell, Jeffrey R., Owen, Katharine R., Pedersen, Oluf, Peloso, Gina M., Pennell, Craig E., Perola, Marku, Perry, James A., Perry, John R. B., Pers, Tune H., Ewing, Ailith, Polasek, Ozren, Raitakari, Olli T., Rasheed, Asif, Raulerson, Chelsea K., Rauramaa, Rainer, Reilly, Dermot F., Reiner, Alex P., Ridker, Paul M., Rivas, Manuel A., Robertson, Neil R., Robino, Antonietta, Rudan, Igor, Ruth, Katherine S., Saleheen, Danish, Salomaa, Veikko, Samani, Nilesh J., Schreiner, Pamela J., Schulze, Matthias B., Scott, Robert A., Segura-Lepe, Marcelo, Sim, Xueling, Slater, Andrew J., Small, Kerrin S., Smith, Blair H., Smith, Jennifer A., Southam, Lorraine, Spector, Timothy D., Speliotes, Elizabeth K., Stefansson, Kari, Steinthorsdottir, Valgerdur, Stirrups, Kathleen E., Strauch, Konstantin, Stringham, Heather M., Stumvoll, Michael, Sun, Liang, Surendran, Praveen, Swart, Karin M. A., Tardif, Jean-Claude, Taylor, Kent D., Teumer, Alexander, Thompson, Deborah J., Thorleifsson, Gudmar, Thorsteinsdottir, Unnur, Thuesen, Betina H., Tönjes, Anke, Torres, Mina, Tsafantakis, Emmanouil, Tuomilehto, Jaakko, Uitterlinden, André G., Uusitupa, Matti, van Duijn, Cornelia M., Vanhala, Mauno, Varma, Rohit, Vermeulen, Sita H., Vestergaard, Henrik, Vitart, Veronique, Vogt, Thomas F., Vuckovic, Dragana, Wagenknecht, Lynne E., Walker, Mark, Wallentin, Lar, Wang, Feijie, Wang, Carol A., Wang, Shuai, Wareham, Nicholas J., Warren, Helen R., Waterworth, Dawn M., Wessel, Jennifer, White, Harvey D., Willer, Cristen J., Wilson, James G., Wood, Andrew R., Wu, Ying, Yaghootkar, Hanieh, Yao, Jie, Yerges-Armstrong, Laura M., Young, Robin, Zeggini, Eleftheria, Zhan, Xiaowei, Zhang, Weihua, Zhao, Jing Hua, Zhao, Wei, Zheng, He, Zhou, Wei, Zillikens, M. Carola, Rivadeneira, Fernando, Borecki, Ingrid B., Pospisilik, J. Andrew, Deloukas, Pano, Frayling, Timothy M., Lettre, Guillaume, Mohlke, Karen L., Rotter, Jerome I., Kutalik, Zoltán, Hirschhorn, Joel N., Cupples, L. Adrienne, Loos, Ruth J. F., North, Kari E., Lindgren, Cecilia M., APH - Societal Participation & Health, APH - Health Behaviors & Chronic Diseases, APH - Aging & Later Life, Epidemiology and Data Science, and VU University medical center

Subjects
Exome/genetics, Male, ReproGen Consortium, Adipose tissue, Genome-wide association study, Type 2 diabetes, White adipose tissue, Body Mass Index, Animals, Body Fat Distribution, Case-Control Studies, Drosophila, Exome, Female, Gene Frequency, Genetic Predisposition to Disease, Genetic Variation, Genome-Wide Association Study, Homeostasis, Humans, Lipids, Proteins, Risk Factors, Waist-Hip Ratio, 0302 clinical medicine, Hyperlipidemia, Body fat distribution, 2. Zero hunger, Genetics, 0303 health sciences, INSULIN-RESISTANCE, ADIPOCYTE DIFFERENTIATION, CHD Exome+ Consortium, Genetic Predisposition to Disease/genetics, Drosophila/genetics, RS11209026 POLYMORPHISM, KINASE 7, 1184 Genetics, developmental biology, physiology, T2D-Genes Consortium, 11 Medical And Health Sciences, Body Fat Distribution/methods, RECEPTOR ALK7, ADIPOSE-TISSUE, Gene Frequency/genetics, Genetic Variation/genetics, InterAct, Urological cancers Radboud Institute for Health Sciences [Radboudumc 15], genetic association study, RNA splicing, Proteins/genetics, Genome-Wide Association Study/methods, Lipid particle, ExomeBP Consortium, WAIST CIRCUMFERENCE, Waist-Hip Ratio/methods, Biology, EPIC-CVD Consortium, Article, MAGIC Investigators, 03 medical and health sciences, Homeostasis/genetics, Lipids/genetics, All institutes and research themes of the Radboud University Medical Center, medicine, Global Lipids Genetic Consortium, Risk factor, GENOME-WIDE ASSOCIATION, ABDOMINAL ADIPOSITY, Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium, Gene, 030304 developmental biology, 06 Biological Sciences, medicine.disease, Minor allele frequency, GoT2D Genes Consortium, genetics research, TYPE-2 DIABETES SUSCEPTIBILITY, 3111 Biomedicine, Body mass index, 030217 neurology & neurosurgery, Developmental Biology
Abstract

Body fat distribution is a risk factor for adverse cardiovascular health consequences. We analyzed the association of body fat distribution, assessed by waist-to-hip ratio adjusted for body mass index, with 228,985 predicted coding and splice site variants available on exome arrays in up to 344,369 individuals from five major ancestries (discovery) and 132,177 European-ancestry individuals (validation). We identified 15 common (minor allele frequency, MAF ≥ 5%) and 9 low frequency or rare (MAF < 5%) coding novel variants. Pathway/gene set enrichment analyses identified lipid particle, adiponectin, abnormal white adipose tissue physiology, and bone development and morphology as important contributors to fat distribution, while cross-trait associations highlight cardiometabolic traits. In functional follow-up analyses, specifically in Drosophila RNAi-knockdowns, we observed a significant increase in the total body triglyceride levels for two genes (DNAH10 and PLXND1). We implicate novel genes in fat distribution, stressing the importance of interrogating low-frequency and protein-coding variants., Editorial summary: A trans-ethnic exome-wide association study for body fat distribution identifies protein-coding variants that are significantly associated with waist-to-hip ratio adjusted for body mass index.

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