Genome-wide analysis of blood lipid metabolites in over 5,000 South Asians reveals biological insights at cardiometabolic disease loci

Background Genetic, lifestyle, and environmental factors can lead to perturbations in circulating lipid levels and increase risk of cardiovascular and metabolic diseases. However, how changes in individual lipid species contribute to disease risk is often unclear. Moreover, little is known about the role of lipids on cardiovascular disease in Pakistan, a population historically underrepresented in cardiovascular studies. Methods We characterised the genetic architecture of the human blood lipidome in 5,662 hospital controls from the Pakistan Risk of Myocardial Infarction Study (PROMIS) and 13,814 healthy British blood donors from the INTERVAL study. We applied a candidate causal gene prioritisation tool to link the genetic variants associated with each lipid to the most likely causal genes, and Gaussian Graphical Modelling network analysis to identify and illustrate relationships between lipids and genetic loci. Results We identified 359 genetic associations with 255 lipids measured using direct infusion high-resolution mass spectrometry in PROMIS, and 616 genetic associations with 326 lipids in INTERVAL. Our analyses revealed new biological insights at genetic loci associated with cardiometabolic diseases, including novel lipid associations at the LPL, MBOAT7, LIPC, APOE-C1-C2-C4, SGPP1 , and SPTLC3 loci. Conclusions Our findings, generated using a distinctive lipidomics platform in an understudied South Asian population, strengthen and expand the knowledge base of the genetic determinants of lipids and their association with cardiometabolic disease-related loci. ### Competing Interest Statement E.B.F. and D.Z. are employees and shareholders of Pfizer, Inc. J.D. has received research funding from the British Heart Foundation, the National Institute for Health Research Cambridge Comprehensive Biomedical Research Centre, the Bupa Foundation, diaDexus, the European Research Council, the European Union, the Evelyn Trust, the Fogarty International Centre, GlaxoSmithKline, Merck, the National Heart, Lung, and Blood Institute, the National Institute for Health Research [Senior Investigator Award], the National Institute of Neurological Disorders and Stroke, NHS Blood and Transplant, Novartis, Pfizer, the UK Medical Research Council, and the Wellcome Trust [*]. J.L.G. has received funding from Agilent, Waters, GlaxoSmithKline, Medimmune, Unilever, AstraZeneca, the Medical Research Council, the Biotechnology and Biological Sciences Research Council, the National Institutes of Health, the British Heart Foundation, and the Wellcome Trust. D.Sa. has received funding from Pfizer, Regeneron Pharmaceuticals, Genentech, and Eli Lilly. All other authors declare no competing interests. [*] The views expressed are those of the authors and not necessarily those of the NHS, the NIHR, or the Department of Health and Social Care. ### Funding Statement PROMIS: Fieldwork, genotyping, and standard clinical chemistry assays in PROMIS were principally supported by grants awarded to the University of Cambridge from the British Heart Foundation (SP/09/002; RG/13/13/30194), the UK Medical Research Council (G0800270; MR/L003120/1), the Wellcome Trust, the EU Framework 6-funded Bloodomics Integrated Project, Pfizer, Novartis, and Merck. INTERVAL: Participants in the INTERVAL randomised controlled trial were recruited with the active collaboration of NHS Blood and Transplant England (http://www.nhsbt.nhs.uk), which has supported field work and other elements of the trial. DNA extraction and genotyping was co-funded by the National Institute for Health Research (NIHR), the NIHR BioResource (http://bioresource.nihr.ac.uk), and the NIHR \[Cambridge Biomedical Research Centre at the Cambridge University Hospitals NHS Foundation Trust\] \[*\]. The academic coordinating centre for INTERVAL was supported by core funding from: NIHR Blood and Transplant Research Unit in Donor Health and Genomics (NIHR BTRU-2014-10024), UK Medical Research Council (MR/L003120/1), British Heart Foundation (SP/09/002, RG/13/13/30194; RG/18/13/33946) and the NIHR \[Cambridge Biomedical Research Centre at the Cambridge University Hospitals NHS Foundation Trust\] \[*\]. A complete list of the investigators and contributors to the INTERVAL trial is provided in reference [46]. The academic coordinating centre would like to thank blood donor staff and blood donors for participating in the INTERVAL trial. [*] The views expressed are those of the authors and not necessarily those of the NHS, the NIHR, or the Department of Health and Social Care. This work was supported by Health Data Research UK, 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), British Heart Foundation, and Wellcome. J.L.G. and A.K. are funded by the UK Medical Research Council under the Lipid Dynamics and Regulation supplementary grant (MC\_PC\_13030) and Lipid Programming and Signalling program grant (MC\_UP\_A090_1006) and Cambridge Lipidomics Biomarker Research Initiative (G0800783). D.S.P. and D.St. are funded by the Wellcome Trust (105602/Z/14/Z). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: PROMIS: The institutional review board at the Center for Non-Communicable Diseases in Karachi, Pakistan approved the study (IRB: 00007048, IORG0005843, FWAS00014490) and all participants gave informed consent, including for use of samples in genetic, biochemical, and other analyses. INTERVAL: The National Research Ethics Service approved this study (11/EE/0538) and all participants gave electronic informed consent. All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request. * CHD : Coronary heart disease CVD : Cardiovascular disease DHA : Docosahexaenoic acid DIHRMS : Direct infusion high resolution mass spectrometry FDR : False discovery rate GGM : Gaussian Graphical Model HWE : Hardy-Weinberg Equilibrium MAF : Minor allele frequency MI : Myocardial infarction m/z : Mass-charge ratio NAFLD : Non-alcoholic fatty liver disease PROMIS : Pakistan Risk of Myocardial Infarction Study PUFA : Polyunsaturated fatty acid SD : Standard deviation SNP : Single nucleotide polymorphism T2D : Type 2 diabetes QC : Quality Control QTL : Quantitative trait loci