1
|
Núñez E, Gómez-Serrano M, Calvo E, Bonzon-Kulichenko E, Trevisan-Herraz M, Rodríguez JM, García-Marqués F, Magni R, Lara-Pezzi E, Martín-Ventura JL, Camafeita E, Vázquez J. A Multiplexed Quantitative Proteomics Approach to the Human Plasma Protein Signature. Biomedicines 2024; 12:2118. [PMID: 39335631 PMCID: PMC11428418 DOI: 10.3390/biomedicines12092118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 08/30/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
Despite the plasma proteome being able to provide a unique insight into the health and disease status of individuals, holding singular promise as a source of protein biomarkers that could be pivotal in the context of personalized medicine, only around 100 proteins covering a few human conditions have been approved as biomarkers by the US Food and Drug Administration (FDA) so far. Mass spectrometry (MS) currently has enormous potential for high-throughput analysis in clinical research; however, plasma proteomics remains challenging mainly due to the wide dynamic range of plasma protein abundances and the time-consuming procedures required. We applied a new MS-based multiplexed proteomics workflow to quantitate proteins, encompassing 67 FDA-approved biomarkers, in >1300 human plasma samples from a clinical cohort. Our results indicate that this workflow is suitable for large-scale clinical studies, showing good accuracy and reproducibility (coefficient of variation (CV) < 20 for 90% of the proteins). Furthermore, we identified plasma signature proteins (stable in time on an individual basis), stable proteins (exhibiting low biological variability and high temporal stability), and highly variable proteins (with low temporal stability) that can be used for personalized health monitoring and medicine.
Collapse
Affiliation(s)
- Estefanía Núñez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain; (E.N.); (E.C.); (E.B.-K.); (J.M.R.); (R.M.); (E.L.-P.)
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain;
| | - María Gómez-Serrano
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology (ZTI), Philipps University, 35043 Marburg, Germany;
| | - Enrique Calvo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain; (E.N.); (E.C.); (E.B.-K.); (J.M.R.); (R.M.); (E.L.-P.)
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain;
| | - Elena Bonzon-Kulichenko
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain; (E.N.); (E.C.); (E.B.-K.); (J.M.R.); (R.M.); (E.L.-P.)
| | - Marco Trevisan-Herraz
- International Center for Life, Newcastle University, Newcastle upon Tyne NE1 4EP, UK;
| | - José Manuel Rodríguez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain; (E.N.); (E.C.); (E.B.-K.); (J.M.R.); (R.M.); (E.L.-P.)
| | | | - Ricardo Magni
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain; (E.N.); (E.C.); (E.B.-K.); (J.M.R.); (R.M.); (E.L.-P.)
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain;
| | - Enrique Lara-Pezzi
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain; (E.N.); (E.C.); (E.B.-K.); (J.M.R.); (R.M.); (E.L.-P.)
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain;
| | - José Luis Martín-Ventura
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain;
- IIS-Fundación Jiménez-Díaz, 28015 Madrid, Spain
| | - Emilio Camafeita
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain; (E.N.); (E.C.); (E.B.-K.); (J.M.R.); (R.M.); (E.L.-P.)
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain;
| | - Jesús Vázquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain; (E.N.); (E.C.); (E.B.-K.); (J.M.R.); (R.M.); (E.L.-P.)
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain;
| |
Collapse
|
2
|
Ashrafi V, Yazdi A, Farhadian M. Evaluation of the Relationship between Family History and Occurrence, Anatomical Location, and Extent of Coronary Artery Disease among Patients Undergoing Coronary Angiography. Med J Islam Repub Iran 2023; 37:69. [PMID: 37575688 PMCID: PMC10423060 DOI: 10.47176/mjiri.37.69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Indexed: 08/15/2023] Open
Abstract
Background A positive family history (FH) of coronary artery disease (CAD) is considered an independent risk factor for developing CAD. However, the relationship between the occurrence, angiographic anatomical location of the stenosis, and extent of CAD and the risk factors in the patients and their relatives is not well defined. Evaluation of this relationship is our main goal in this study. Methods In this descriptive cross-sectional study, the FH data for CAD and premature death in first-and second-degree relatives, angiographic anatomical location of the stenosis, the extent of CAD in the patients and their relatives, as well as the relationship between other risk factors and the extent of CAD, were collected from 300 adult patients undergoing coronary angiography at Farshchian cardiovascular hospital in Hamadan (Iran) between March 2020 and 2021. SPSS 24 and the chi-square, Fisher exact, and student t tests were used to analyze data. The significance level was considered P < 0.05. Results Out of 300 patients, 185 (61.7%) were men and 115 (38.3%) were women. A total of 177 patients (59%) in maternal and 82 patients (27.3%) in paternal relatives had an FH of CAD. There was a significant relationship between the severity of coronary artery involvement and risk factors (P < 0.001). Moreover, there was no significant relationship between the location of coronary artery involvement of the right coronary artery, left coronary artery, and left anterior descending artery and the severity of involvement of patients undergoing coronary angiography and their first- and second-degree relatives (P = 0.480). Conclusion Our findings suggest that there was no significant relationship between the anatomical location of the stenosis and the number of vessels involved and the FH of the patients. In patients with an FH, the extent of CAD significantly increased according to their risk factors for heart disease.
Collapse
Affiliation(s)
- Vahid Ashrafi
- Cardiovascular Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
- Department of Cardiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Amirhossein Yazdi
- Cardiovascular Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
- Department of Cardiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Maryam Farhadian
- Research Center for Health Sciences, Department of Biostatistics, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran
| |
Collapse
|
3
|
Liu S, Li Y, Wei X, Adi D, Wang YT, Han M, Liu F, Chen BD, Li XM, Yang YN, Fu ZY, Ma YT. Genetic analysis of DNA methylation in dyslipidemia: a case-control study. PeerJ 2022; 10:e14590. [PMID: 36570009 PMCID: PMC9774006 DOI: 10.7717/peerj.14590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Background Coronary heart disease has become the leading cause of death in developed countries, and dyslipidemia is closely associated with the risk of cardiovascular disease. Dyslipidemia is caused by the abnormal regulation of several genes and signaling pathways, and dyslipidemia is influenced mainly by genetic variation. AMFR, FBXW7, INSIG1, INSIG2, and MBTPS1 genes are associated with lipid metabolism. In a recent GWAS study, the GRINA gene has been reported to be associated with dyslipidemia, but its molecular mechanism has not been thoroughly investigated. The correlation between the DNA methylation of these genes and lipid metabolism has not been studied. This study aimed to examine the relationship between the DNA methylation of these genes and the risk of dyslipidemia by comparing the methylation levels of dyslipidemia and control samples. Methods A case-control research method was used in this study. The patient's blood samples were collected at the Heart Center of the First Affiliated Hospital of Xinjiang Medical University. In the Xinjiang Han population, 100 cases of hyperlipidemia and 80 cases of the control group were selected. The two groups were age and gender-matched. Quantitative methylation analysis of CpG sites in the gene promoter regions of six genes was performed by Solexa high-throughput sequencing. Results The DNA methylation levels of 23 CpG sites in six genes were shown to be associated with hyperlipidemia, and a total of 20 DNA methylation haplotypes showed statistically significant differences between the two groups. When compared with the control group, the dyslipidemia group had significantly higher levels of methylation in the GRINA gene (2.68 vs 2.36, P = 0.04). Additionally, we also discovered a significant methylation haplotype of GRINA (P = 0.017). Conclusion The findings of this study reveal that the DNA methylation of GRINA increases the risk for dyslipidemia in humans.
Collapse
Affiliation(s)
- Shuai Liu
- First Affiliated Hospital of Xinjiang Medical University, Urumqi, China,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, China
| | - Yang Li
- First Affiliated Hospital of Xinjiang Medical University, Urumqi, China,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, China
| | - Xian Wei
- First Affiliated Hospital of Xinjiang Medical University, Urumqi, China,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, China
| | - Dilare Adi
- First Affiliated Hospital of Xinjiang Medical University, Urumqi, China,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, China
| | - Yong-Tao Wang
- First Affiliated Hospital of Xinjiang Medical University, Urumqi, China,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, China
| | - Min Han
- First Affiliated Hospital of Xinjiang Medical University, Urumqi, China,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, China
| | - Fen Liu
- First Affiliated Hospital of Xinjiang Medical University, Urumqi, China,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, China
| | - Bang-Dang Chen
- First Affiliated Hospital of Xinjiang Medical University, Urumqi, China,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, China
| | - Xiao-Mei Li
- First Affiliated Hospital of Xinjiang Medical University, Urumqi, China,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, China
| | - Yi-Ning Yang
- First Affiliated Hospital of Xinjiang Medical University, Urumqi, China,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, China
| | - Zhen-Yan Fu
- First Affiliated Hospital of Xinjiang Medical University, Urumqi, China,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, China
| | - Yi-Tong Ma
- First Affiliated Hospital of Xinjiang Medical University, Urumqi, China,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, China
| |
Collapse
|
4
|
Hartmann K, Seweryn M, Sadee W. Interpreting coronary artery disease GWAS results: A functional genomics approach assessing biological significance. PLoS One 2022; 17:e0244904. [PMID: 35192625 PMCID: PMC8863290 DOI: 10.1371/journal.pone.0244904] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/01/2022] [Indexed: 01/09/2023] Open
Abstract
Genome-wide association studies (GWAS) have implicated 58 loci in coronary artery disease (CAD). However, the biological basis for these associations, the relevant genes, and causative variants often remain uncertain. Since the vast majority of GWAS loci reside outside coding regions, most exert regulatory functions. Here we explore the complexity of each of these loci, using tissue specific RNA sequencing data from GTEx to identify genes that exhibit altered expression patterns in the context of GWAS-significant loci, expanding the list of candidate genes from the 75 currently annotated by GWAS to 245, with almost half of these transcripts being non-coding. Tissue specific allelic expression imbalance data, also from GTEx, allows us to uncover GWAS variants that mark functional variation in a locus, e.g., rs7528419 residing in the SORT1 locus, in liver specifically, and rs72689147 in the GUYC1A1 locus, across a variety of tissues. We consider the GWAS variant rs1412444 in the LIPA locus in more detail as an example, probing tissue and transcript specific effects of genetic variation in the region. By evaluating linkage disequilibrium (LD) between tissue specific eQTLs, we reveal evidence for multiple functional variants within loci. We identify 3 variants (rs1412444, rs1051338, rs2250781) that when considered together, each improve the ability to account for LIPA gene expression, suggesting multiple interacting factors. These results refine the assignment of 58 GWAS loci to likely causative variants in a handful of cases and for the remainder help to re-prioritize associated genes and RNA isoforms, suggesting that ncRNAs maybe a relevant transcript in almost half of CAD GWAS results. Our findings support a multi-factorial system where a single variant can influence multiple genes and each genes is regulated by multiple variants.
Collapse
Affiliation(s)
- Katherine Hartmann
- Department of Cancer Biology and Genetics, Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus, OH, United States of America
- * E-mail:
| | - Michał Seweryn
- Biobank Lab, Department of Molecular Biophysics, University of Lodz, Lodz, Poland
| | - Wolfgang Sadee
- Department of Cancer Biology and Genetics, Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus, OH, United States of America
| |
Collapse
|
5
|
Jones AC, Irvin MR, Claas SA, Arnett DK. Lipid Phenotypes and DNA Methylation: a Review of the Literature. Curr Atheroscler Rep 2021; 23:71. [PMID: 34468868 DOI: 10.1007/s11883-021-00965-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2021] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW Epigenetic modifications via DNA methylation have previously been linked to blood lipid levels, dyslipidemias, and atherosclerosis. The purpose of this review is to discuss current literature on the role of DNA methylation on lipid traits and their associated pathologies. RECENT FINDINGS Candidate gene and epigenome-wide approaches have identified differential methylation of genes associated with lipid traits (particularly CPT1A, ABCG1, SREBF1), and novel approaches are being implemented to further characterize these relationships. Moreover, studies on environmental factors have shown that methylation variations at lipid-related genes are associated with diet and pollution exposure. Further investigation is needed to elucidate the directionality of the associations between the environment, lipid traits, and epigenome. Future studies should also seek to increase the diversity of cohorts, as European and Asian ancestry populations are the predominant study populations in the current literature.
Collapse
Affiliation(s)
- Alana C Jones
- Medical Scientist Training Program, University of Alabama-Birmingham, Birmingham, AL, USA.,Department of Epidemiology, School of Public Health, University of Alabama-Birmingham, Birmingham, AL, USA
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama-Birmingham, Birmingham, AL, USA
| | - Steven A Claas
- Department of Epidemiology, College of Public Health, University of Kentucky, 111 Washington Ave, Lexington, KY, 40508, USA
| | - Donna K Arnett
- Department of Epidemiology, College of Public Health, University of Kentucky, 111 Washington Ave, Lexington, KY, 40508, USA.
| |
Collapse
|
6
|
Abstract
With regard to heritability of phenotypes, the serum triglyceride level is considered to be highly heritable, with approximately 50% of its variability estimated to derive from parents. Thus, approximately 50% could be modifiable via environmental factors, including lifestyle and medications. Lipoproteins are definitive risk factors for atherosclerotic cardiovascular disease (ASCVD); among these, low-density lipoprotein (LDL) particles have been established as a causal factor for the development of ASCVD. Recently, triglyceride-rich lipoproteins have emerged as additional lipoproteins, which should be considered as residual targets for ASCVD risk reduction by LDL-lowering therapies. Compared with LDL particles, triglyceride-rich lipoproteins are significantly increased in the postprandial state, making it difficult to assess their clinical relevance. However, numerous pieces of evidence suggest that fasting and non-fasting triglycerides are associated with ASCVD. In addition, a recent meta-analysis of a Mendelian randomization study suggests that consideration of apolipoprotein B (APOB) might be better than considering LDL and triglyceride-rich lipoproteins separately. In this review, we examine (1) how triglyceride levels are determined by genetics, (2) lessons from extreme cases exhibiting severe hypertriglyceridemia, and (3) why triglycerides are important, by highlighting clinical and genetic evidence of their associations with ASCVD risk.
Collapse
Affiliation(s)
- Hayato Tada
- Department of Cardiology, Kanazawa University, Graduate School of Medical Sciences, Kanazawa, Japan.
| | - Masayuki Takamura
- Department of Cardiology, Kanazawa University, Graduate School of Medical Sciences, Kanazawa, Japan
| | - Masa-Aki Kawashiri
- Department of Cardiology, Kanazawa University, Graduate School of Medical Sciences, Kanazawa, Japan
| |
Collapse
|
7
|
Nurnberg ST, Guerraty MA, Wirka RC, Rao HS, Pjanic M, Norton S, Serrano F, Perisic L, Elwyn S, Pluta J, Zhao W, Testa S, Park Y, Nguyen T, Ko YA, Wang T, Hedin U, Sinha S, Barash Y, Brown CD, Quertermous T, Rader DJ. Genomic profiling of human vascular cells identifies TWIST1 as a causal gene for common vascular diseases. PLoS Genet 2020; 16:e1008538. [PMID: 31917787 PMCID: PMC6975560 DOI: 10.1371/journal.pgen.1008538] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 01/22/2020] [Accepted: 11/25/2019] [Indexed: 02/02/2023] Open
Abstract
Genome-wide association studies have identified multiple novel genomic loci associated with vascular diseases. Many of these loci are common non-coding variants that affect the expression of disease-relevant genes within coronary vascular cells. To identify such genes on a genome-wide level, we performed deep transcriptomic analysis of genotyped primary human coronary artery smooth muscle cells (HCASMCs) and coronary endothelial cells (HCAECs) from the same subjects, including splicing Quantitative Trait Loci (sQTL), allele-specific expression (ASE), and colocalization analyses. We identified sQTLs for TARS2, YAP1, CFDP1, and STAT6 in HCASMCs and HCAECs, and 233 ASE genes, a subset of which are also GTEx eGenes in arterial tissues. Colocalization of GWAS association signals for coronary artery disease (CAD), migraine, stroke and abdominal aortic aneurysm with GTEx eGenes in aorta, coronary artery and tibial artery discovered novel candidate risk genes for these diseases. At the CAD and stroke locus tagged by rs2107595 we demonstrate colocalization with expression of the proximal gene TWIST1. We show that disrupting the rs2107595 locus alters TWIST1 expression and that the risk allele has increased binding of the NOTCH signaling protein RBPJ. Finally, we provide data that TWIST1 expression influences vascular SMC phenotypes, including proliferation and calcification, as a potential mechanism supporting a role for TWIST1 in CAD.
Collapse
Affiliation(s)
- Sylvia T. Nurnberg
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marie A. Guerraty
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Robert C. Wirka
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - H. Shanker Rao
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Milos Pjanic
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Scott Norton
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Felipe Serrano
- Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Ljubica Perisic
- Department of Molecular Medicine and Surgery, Karolinska Institute, Solna, Sweden
| | - Susannah Elwyn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - John Pluta
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Wei Zhao
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Stephanie Testa
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - YoSon Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Trieu Nguyen
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Yi-An Ko
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ting Wang
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Ulf Hedin
- Department of Molecular Medicine and Surgery, Karolinska Institute, Solna, Sweden
| | - Sanjay Sinha
- Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Christopher D. Brown
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Thomas Quertermous
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Daniel J. Rader
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
8
|
Petty LE, Highland HM, Gamazon ER, Hu H, Karhade M, Chen HH, de Vries PS, Grove ML, Aguilar D, Bell GI, Huff CD, Hanis CL, Doddapaneni H, Munzy DM, Gibbs RA, Ma J, Parra EJ, Cruz M, Valladares-Salgado A, Arking DE, Barbeira A, Im HK, Morrison AC, Boerwinkle E, Below JE. Functionally oriented analysis of cardiometabolic traits in a trans-ethnic sample. Hum Mol Genet 2019; 28:1212-1224. [PMID: 30624610 PMCID: PMC6423424 DOI: 10.1093/hmg/ddy435] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 11/13/2018] [Accepted: 11/20/2018] [Indexed: 01/02/2023] Open
Abstract
Interpretation of genetic association results is difficult because signals often lack biological context. To generate hypotheses of the functional genetic etiology of complex cardiometabolic traits, we estimated the genetically determined component of gene expression from common variants using PrediXcan (1) and determined genes with differential predicted expression by trait. PrediXcan imputes tissue-specific expression levels from genetic variation using variant-level effect on gene expression in transcriptome data. To explore the value of imputed genetically regulated gene expression (GReX) models across different ancestral populations, we evaluated imputed expression levels for predictive accuracy genome-wide in RNA sequence data in samples drawn from European-ancestry and African-ancestry populations and identified substantial predictive power using European-derived models in a non-European target population. We then tested the association of GReX on 15 cardiometabolic traits including blood lipid levels, body mass index, height, blood pressure, fasting glucose and insulin, RR interval, fibrinogen level, factor VII level and white blood cell and platelet counts in 15 755 individuals across three ancestry groups, resulting in 20 novel gene-phenotype associations reaching experiment-wide significance across ancestries. In addition, we identified 18 significant novel gene-phenotype associations in our ancestry-specific analyses. Top associations were assessed for additional support via query of S-PrediXcan (2) results derived from publicly available genome-wide association studies summary data. Collectively, these findings illustrate the utility of transcriptome-based imputation models for discovery of cardiometabolic effect genes in a diverse dataset.
Collapse
Affiliation(s)
- Lauren E Petty
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Heather M Highland
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Eric R Gamazon
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Clare Hall, University of Cambridge, Cambridge, UK
| | - Hao Hu
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | - Mandar Karhade
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hung-Hsin Chen
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Paul S de Vries
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Megan L Grove
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - David Aguilar
- Department of Cardiology, Baylor College of Medicine Houston, TX, USA
| | - Graeme I Bell
- Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Chad D Huff
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | - Craig L Hanis
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - Donna M Munzy
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jianzhong Ma
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Miguel Cruz
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, IMSS, Mexico City, Mexico
| | - Adan Valladares-Salgado
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, IMSS, Mexico City, Mexico
| | - Dan E Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alvaro Barbeira
- Section of Genetic Medicine, Department of Medicine, University of Chicago, IL, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, IL, USA
| | - Alanna C Morrison
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| |
Collapse
|
9
|
López-Cortegano E, Caballero A. Inferring the Nature of Missing Heritability in Human Traits Using Data from the GWAS Catalog. Genetics 2019; 212:891-904. [PMID: 31123044 PMCID: PMC6614893 DOI: 10.1534/genetics.119.302077] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/11/2019] [Indexed: 02/07/2023] Open
Abstract
Thousands of genes responsible for many diseases and other common traits in humans have been detected by Genome Wide Association Studies (GWAS) in the last decade. However, candidate causal variants found so far usually explain only a small fraction of the heritability estimated by family data. The most common explanation for this observation is that the missing heritability corresponds to variants, either rare or common, with very small effect, which pass undetected due to a lack of statistical power. We carried out a meta-analysis using data from the NHGRI-EBI GWAS Catalog in order to explore the observed distribution of locus effects for a set of 42 complex traits and to quantify their contribution to narrow-sense heritability. With the data at hand, we were able to predict the expected distribution of locus effects for 16 traits and diseases, their expected contribution to heritability, and the missing number of loci yet to be discovered to fully explain the familial heritability estimates. Our results indicate that, for 6 out of the 16 traits, the additive contribution of a great number of loci is unable to explain the familial (broad-sense) heritability, suggesting that the gap between GWAS and familial estimates of heritability may not ever be closed for these traits. In contrast, for the other 10 traits, the additive contribution of hundreds or thousands of loci yet to be found could potentially explain the familial heritability estimates, if this were the case. Computer simulations are used to illustrate the possible contribution from nonadditive genetic effects to the gap between GWAS and familial estimates of heritability.
Collapse
Affiliation(s)
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310, Spain
| |
Collapse
|
10
|
Khlebus E, Kutsenko V, Meshkov A, Ershova A, Kiseleva A, Shevtsov A, Shcherbakova N, Zharikova A, Lankin V, Tikhaze A, Chazova I, Yarovaya E, Drapkina O, Boytsov S. Multiple rare and common variants in APOB gene locus associated with oxidatively modified low-density lipoprotein levels. PLoS One 2019; 14:e0217620. [PMID: 31150472 PMCID: PMC6544350 DOI: 10.1371/journal.pone.0217620] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 05/15/2019] [Indexed: 01/17/2023] Open
Abstract
Oxidatively modified low-density lipoproteins (oxLDL) play an important role in the occurrence and progression of atherosclerosis. To identify the genetic factors influencing the oxLDL levels, we have genotyped 776 DNA samples of Russian individuals for 196,725 single-nucleotide polymorphisms (SNPs) using the Cardio-MetaboChip (Illumina, USA) and conducted genome-wide association study (GWAS). Fourteen common variants in the locus including APOB gene were significantly associated with the oxLDL levels (P < 2.18 × 10−7). These variants explained only 6% of the variation in the oxLDL levels. Then, we assessed the contribution of rare coding variants of APOB gene to the oxLDL levels. Individuals with the extreme oxLDL levels (48 with the lowest and 48 with the highest values) were selected for targeted sequencing of the region including APOB gene. To evaluate the contribution of the SNPs to the oxLDL levels we used various statistical methods for the association analysis of rare variants: WST, SKAT, and SKAT-O. We revealed that both synonymous and nonsynonymous SNPs affected the oxLDL levels. For the joint analysis of the rare and common variants, we conducted the SKAT-C testing and found a group of 15 SNPs significantly associated with the oxLDL levels (P = 2.14 × 10−9). Our results indicate that the oxLDL levels depend on both common and rare variants of the APOB gene.
Collapse
Affiliation(s)
- Eleonora Khlebus
- Federal State Institution National Medical Research Center for Preventive Medicine of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
- Moscow Institute of Physics and Technology (State University), Moscow, Russia
- * E-mail:
| | - Vladimir Kutsenko
- Federal State Institution National Medical Research Center for Preventive Medicine of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
| | - Alexey Meshkov
- Federal State Institution National Medical Research Center for Preventive Medicine of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Alexandra Ershova
- Federal State Institution National Medical Research Center for Preventive Medicine of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Anna Kiseleva
- Federal State Institution National Medical Research Center for Preventive Medicine of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | | | - Natalia Shcherbakova
- Federal State Institution National Medical Research Center for Preventive Medicine of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Anastasiia Zharikova
- Federal State Institution National Medical Research Center for Preventive Medicine of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Vadim Lankin
- Federal State Budget Organization National Medical Research Center of Cardiology of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Alla Tikhaze
- Federal State Budget Organization National Medical Research Center of Cardiology of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Irina Chazova
- Federal State Budget Organization National Medical Research Center of Cardiology of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | | | - Oksana Drapkina
- Federal State Institution National Medical Research Center for Preventive Medicine of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Sergey Boytsov
- Federal State Budget Organization National Medical Research Center of Cardiology of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| |
Collapse
|
11
|
My Cousin Also Has Atrial Fibrillation: Family Relationships in a Genomic Era. JACC Clin Electrophysiol 2019; 5:501-503. [PMID: 31000105 DOI: 10.1016/j.jacep.2019.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 01/24/2023]
|
12
|
Hou TT, Lin F, Bai S, Cleves MA, Xu HM, Lou XY. Generalized multifactor dimensionality reduction approaches to identification of genetic interactions underlying ordinal traits. Genet Epidemiol 2018; 43:24-36. [PMID: 30387901 DOI: 10.1002/gepi.22169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/31/2018] [Accepted: 09/21/2018] [Indexed: 12/11/2022]
Abstract
The manifestation of complex traits is influenced by gene-gene and gene-environment interactions, and the identification of multifactor interactions is an important but challenging undertaking for genetic studies. Many complex phenotypes such as disease severity are measured on an ordinal scale with more than two categories. A proportional odds model can improve statistical power for these outcomes, when compared to a logit model either collapsing the categories into two mutually exclusive groups or limiting the analysis to pairs of categories. In this study, we propose a proportional odds model-based generalized multifactor dimensionality reduction (GMDR) method for detection of interactions underlying polytomous ordinal phenotypes. Computer simulations demonstrated that this new GMDR method has a higher power and more accurate predictive ability than the GMDR methods based on a logit model and a multinomial logit model. We applied this new method to the genetic analysis of low-density lipoprotein (LDL) cholesterol, a causal risk factor for coronary artery disease, in the Multi-Ethnic Study of Atherosclerosis, and identified a significant joint action of the CELSR2, SERPINA12, HPGD, and APOB genes. This finding provides new information to advance the limited knowledge about genetic regulation and gene interactions in metabolic pathways of LDL cholesterol. In conclusion, the proportional odds model-based GMDR is a useful tool that can boost statistical power and prediction accuracy in studying multifactor interactions underlying ordinal traits.
Collapse
Affiliation(s)
- Ting-Ting Hou
- Biostatistics Program, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas.,Arkansas Children's Research Institute, Little Rock, Arkansas.,Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Feng Lin
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shasha Bai
- Biostatistics Program, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas.,Arkansas Children's Research Institute, Little Rock, Arkansas
| | - Mario A Cleves
- Biostatistics Program, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas.,Arkansas Children's Research Institute, Little Rock, Arkansas
| | - Hai-Ming Xu
- Biostatistics Program, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas.,Arkansas Children's Research Institute, Little Rock, Arkansas.,Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiang-Yang Lou
- Biostatistics Program, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas.,Arkansas Children's Research Institute, Little Rock, Arkansas.,Arkansas Children's Nutrition Center, Little Rock, Arkansas
| |
Collapse
|
13
|
Zhou Y, Mägi R, Milani L, Lauschke VM. Global genetic diversity of human apolipoproteins and effects on cardiovascular disease risk. J Lipid Res 2018; 59:1987-2000. [PMID: 30076208 PMCID: PMC6168301 DOI: 10.1194/jlr.p086710] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/16/2018] [Indexed: 12/13/2022] Open
Abstract
Abnormal plasma apolipoprotein levels are consistently implicated in CVD risk. Although 30% to 60% of their interindividual variability is genetic, common genetic variants explain only 10% to 20% of these differences. Rare genetic variants may be major sources of the missing heritability, yet quantitative evaluations of their contribution to phenotypic variability are lacking. Here, we analyzed whole-genome and whole-exome sequencing data from 138,632 individuals across seven major human populations to present a systematic overview of genetic apolipoprotein variability. We provide population-specific frequencies of 38 clinically important apolipoprotein alleles and identify further 6,875 genetic variants, 33% of which are novel and 98.7% of which are rare with minor allele frequencies <1%. We predicted the functional impact of rare variants and found that their relative importance differed drastically between genes and among ethnicities. Importantly, we validated the clinical relevance of multiple variants with predicted effects by leveraging association data from the CARDIoGRAM (Coronary Artery Disease Genomewide Replication and Meta-analysis) and Global Lipids Genetics consortia. Overall, we provide a consolidated overview of population-specific apolipoprotein genetics as a valuable data resource for scientists and clinicians, estimate the importance of rare genetic variants for the missing heritability of apolipoprotein-associated disease traits, and pinpoint multiple novel apolipoprotein variants with putative population-specific impacts on serum lipid levels.
Collapse
Affiliation(s)
- Yitian Zhou
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
14
|
Hoffmann TJ, Theusch E, Haldar T, Ranatunga DK, Jorgenson E, Medina MW, Kvale MN, Kwok PY, Schaefer C, Krauss RM, Iribarren C, Risch N. A large electronic-health-record-based genome-wide study of serum lipids. Nat Genet 2018; 50:401-413. [PMID: 29507422 PMCID: PMC5942247 DOI: 10.1038/s41588-018-0064-5] [Citation(s) in RCA: 191] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 01/19/2018] [Indexed: 12/16/2022]
Abstract
A genome-wide association study of 94,674 multi-ethnic Kaiser Permanente members utilizing 478,866 longitudinal untreated serum lipid electronic-health-record-derived measurements (EHRs) empowered multiple novel findings: 121 new SNP associations (46 primary, 15 conditional, 60 in meta-analysis with Global Lipids Genetic Consortium); increase of 33-42% in variance explained with multiple measurements; sex differences in genetic impact (greater in females for LDL, HDL, TC, the opposite for TG); differences in variance explained amongst non-Hispanic whites, Latinos, African Americans, and East Asians; genetic dominance and epistasis, with strong evidence for both at ABOxFUT2 for LDL; and eQTL tissue-enrichment implicating the liver, adipose, and pancreas. Utilizing EHR pharmacy data, both LDL and TG genetic risk scores (477 SNPs) were strongly predictive of age-at-initiation of lipid-lowering treatment. These findings highlight the value of longitudinal EHRs for identifying novel genetic features of cholesterol and lipoprotein metabolism with implications for lipid treatment and risk of coronary heart disease.
Collapse
Affiliation(s)
- Thomas J Hoffmann
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA. .,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
| | | | - Tanushree Haldar
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Dilrini K Ranatunga
- Division of Research, Kaiser Permanente, Northern California, Oakland, CA, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente, Northern California, Oakland, CA, USA
| | - Marisa W Medina
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Mark N Kvale
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Catherine Schaefer
- Division of Research, Kaiser Permanente, Northern California, Oakland, CA, USA
| | - Ronald M Krauss
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Carlos Iribarren
- Division of Research, Kaiser Permanente, Northern California, Oakland, CA, USA
| | - Neil Risch
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA. .,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA. .,Division of Research, Kaiser Permanente, Northern California, Oakland, CA, USA.
| |
Collapse
|
15
|
Mishra A, Ferrari R, Heutink P, Hardy J, Pijnenburg Y, Posthuma D. Gene-based association studies report genetic links for clinical subtypes of frontotemporal dementia. Brain 2017; 140:1437-1446. [PMID: 28387812 DOI: 10.1093/brain/awx066] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/23/2017] [Indexed: 01/02/2023] Open
Abstract
Genome-wide association studies in frontotemporal dementia showed limited success in identifying associated loci. This is possibly due to small sample size, allelic heterogeneity, small effect sizes of single genetic variants, and the necessity to statistically correct for testing millions of genetic variants. To overcome these issues, we performed gene-based association studies on 3348 clinically identified frontotemporal dementia cases and 9390 controls (discovery, replication and joint-cohort analyses). We report association of APOE and TOMM40 with behavioural variant frontotemporal dementia, and ARHGAP35 and SERPINA1 with progressive non-fluent aphasia. Further, we found the ɛ2 and ɛ4 alleles of APOE harbouring protective and risk increasing effects, respectively, in clinical subtypes of frontotemporal dementia against neurologically normal controls. The APOE-locus association with behavioural variant frontotemporal dementia indicates its potential risk-increasing role across different neurodegenerative diseases, whereas the novel genetic associations of ARHGAP35 and SERPINA1 with progressive non-fluent aphasia point towards a potential role of the stress-signalling pathway in its pathophysiology.
Collapse
Affiliation(s)
- Aniket Mishra
- Department of Complex Trait Genetics, VU University, Center for Neurogenomics and Cognitive Research, Amsterdam, 1081 HV, The Netherlands
| | - Raffaele Ferrari
- Department of Molecular Neuroscience, UCL, Russell Square House, 9-12 Russell Square House London, WC1B 5EH, UK
| | - Peter Heutink
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE)-Tübingen, 72076, Tübingen, Germany
| | - John Hardy
- Department of Molecular Neuroscience, UCL, Russell Square House, 9-12 Russell Square House London, WC1B 5EH, UK
| | - Yolande Pijnenburg
- Alzheimer Center and Department of Neurology, VU University Medical Center (VUMC), Neuroscience Campus Amsterdam, Amsterdam, 1081 HV, The Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, VU University, Center for Neurogenomics and Cognitive Research, Amsterdam, 1081 HV, The Netherlands.,Department of Clinical Genetics, VU University Medical Center (VUMC), Neuroscience Campus Amsterdam, Amsterdam, 1081 HV, The Netherlands
| | | |
Collapse
|
16
|
Graff M, Emery LS, Justice AE, Parra E, Below JE, Palmer ND, Gao C, Duan Q, Valladares-Salgado A, Cruz M, Morrison AC, Boerwinkle E, Whitsel EA, Kooperberg C, Reiner A, Li Y, Rodriguez CJ, Talavera GA, Langefeld CD, Wagenknecht LE, Norris JM, Taylor KD, Papanicolaou G, Kenny E, Loos RJF, Chen YDI, Laurie C, Sofer T, North KE. Genetic architecture of lipid traits in the Hispanic community health study/study of Latinos. Lipids Health Dis 2017; 16:200. [PMID: 29025430 PMCID: PMC5639746 DOI: 10.1186/s12944-017-0591-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/04/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Despite ethnic disparities in lipid profiles, there are few genome-wide association studies investigating genetic variation of lipids in non-European ancestry populations. In this study, we present findings from genetic association analyses for total cholesterol, low density lipoprotein cholesterol (LDL), high density lipoprotein cholesterol (HDL), and triglycerides in a large Hispanic/Latino cohort in the U.S., the Hispanic Community Health Study / Study of Latinos (HCHS/SOL). METHODS We estimated a heritability of approximately 20% for each lipid trait, similar to previous estimates in Europeans. To search for novel lipid loci, we performed conditional association analysis in which the statistical model was adjusted for previously reported SNPs associated with any of the four lipid traits. SNPs that remained genome-wide significant (P < 5 × 10-8) after conditioning on known loci were evaluated for replication. RESULTS We identified eight potentially novel lipid signals with minor allele frequencies <1%, none of which replicated. We tested previously reported SNP-trait associations for generalization to Hispanics/Latinos via a statistical framework. The generalization analysis revealed that approximately 50% of previously established lipid variants generalize to HCHS/SOL based on directional FDR r-value < 0.05. Some failures to generalize were due to lack of power. CONCLUSIONS These results demonstrate that many loci associated with lipid levels are shared across populations.
Collapse
Affiliation(s)
- Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Leslie S Emery
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Anne E Justice
- Biomedical and Translational Informatics, Geisinger Health, Danville, PA, USA
| | - Esteban Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON, Canada
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Vanderbuilt University, Nashville, TN, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Chuan Gao
- Molecular Genetics and Genomics Program, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Qing Duan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adan Valladares-Salgado
- Unidad de Investigacion Medica en Bioquimica, Hospital de Especialidades, CMNSXX1-IMSS, Mexico City, Mexico
| | - Miguel Cruz
- Unidad de Investigacion Medica en Bioquimica, Hospital de Especialidades, CMNSXX1-IMSS, Mexico City, Mexico
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Charles Kooperberg
- Fred Hutchinson Cancer Research Center, Public Health Sciences, Seattle, WA, USA
| | - Alex Reiner
- Fred Hutchinson Cancer Research Center, Public Health Sciences, Seattle, WA, USA
| | - Yun Li
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Carlos Jose Rodriguez
- Department of Medicine and Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Gregory A Talavera
- Graduate School of Public Health, San Diego State University, San Diego, CA, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Lynne E Wagenknecht
- Department of Medicine and Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jill M Norris
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | - Eimear Kenny
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Cathy Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| |
Collapse
|
17
|
Tada H, Kawashiri MA, Yamagishi M. Clinical Perspectives of Genetic Analyses on Dyslipidemia and Coronary Artery Disease. J Atheroscler Thromb 2017; 24:452-461. [PMID: 28250266 PMCID: PMC5429159 DOI: 10.5551/jat.rv17002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We have learned that low-density lipoprotein (LDL) cholesterol is the cause of atherosclerosis from various aspects, including a single case with familial hypercholesterolemia, other cases with different types of Mendelian dyslipidemias, large-scale randomized controlled trials using LDL cholesterol lowering therapies, and Mendelian randomization studies using common as well as rare variants associated with LDL cholesterol levels. There is no doubt that determinations of genotypes in lipid-associated genes have contributed not only to the genetic diagnosis for Mendelian dyslipidemias but also to the discoveries of novel therapeutic targets. Furthermore, recent studies have shown that such genetic information could provide useful clues for the risk prediction as well as risk stratification in general and in particular population. We provide the current understanding of genetic analyses relating to plasma lipids and coronary artery disease.
Collapse
Affiliation(s)
- Hayato Tada
- Department of Cardiovascular and Internal Medicine, Kanazawa University Graduate School of Medicine
| | - Masa-Aki Kawashiri
- Department of Cardiovascular and Internal Medicine, Kanazawa University Graduate School of Medicine
| | - Masakazu Yamagishi
- Department of Cardiovascular and Internal Medicine, Kanazawa University Graduate School of Medicine
| |
Collapse
|
18
|
Ryder JR, Pankratz ND, Dengel DR, Pankow JS, Jacobs DR, Sinaiko AR, Gooty V, Steinberger J. Heritability of Vascular Structure and Function: A Parent-Child Study. J Am Heart Assoc 2017; 6:JAHA.116.004757. [PMID: 28154165 PMCID: PMC5523771 DOI: 10.1161/jaha.116.004757] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background Understanding the heritable contribution of vascular measures, from parent to offspring, may aid in risk stratification and atherosclerosis prevention efforts. We hypothesized that measures of vascular structure and function would be heritable in this cohort of parents and their adolescent offspring. Methods and Results High‐resolution ultrasound scans of the brachial and carotid arteries were obtained in parents (n=558) and their offspring (n=369). Lumen diameter and flow‐mediated dilation were measured in the brachial artery. Intima‐media thickness, lumen diameter, incremental elastic modulus, diameter distensibility, and cross‐sectional distensibility were measured, and carotid cross‐sectional compliance was measured in the carotid artery. Carotid–radial pulse wave velocity was obtained using SphygmoCor®. Heritability analysis (h2, expressed as %) using Sequential Oligogenic Linkage Analysis Routines was performed on the entire cohort and adjusted for age, sex, race, body–mass index, smoking, and mean arterial pressure. Data are presented as mean±SE. Measures of brachial artery diameter (h2=25±9%, P=0.001), lumen diameter (h2=55±9%, P<0.001), intima‐media thickness (h2=29±13%, P=0.014), diameter distensibility (h2=28±7%, P<0.001), cross‐sectional distensibility (h2=27±7%, P<0.001), and pulse wave velocity (h2=26±9%, P<0.001) were significantly heritable. Flow‐mediated dilation and incremental elastic modulus were not significantly heritable. Similar associations were observed in analysis restricted to siblings and complete Trios (mother, father, and child). Conclusions These data show that the majority of noninvasive measures of vascular structure and function are heritable, suggesting that measurement of these subclinical risk factors in parents may be helpful in assessing childhood risk for future cardiovascular disease.
Collapse
Affiliation(s)
- Justin R Ryder
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN
| | - Nathan D Pankratz
- Department of Lab Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Donald R Dengel
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN.,School of Kinesiology, University of Minnesota, Minneapolis, MN
| | - James S Pankow
- Division of Epidemiology & Community Health, University of Minnesota School of Public Health, Minneapolis, MN
| | - David R Jacobs
- Division of Epidemiology & Community Health, University of Minnesota School of Public Health, Minneapolis, MN
| | - Alan R Sinaiko
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN
| | - Vasu Gooty
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN
| | - Julia Steinberger
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN
| |
Collapse
|
19
|
A 45-SNP genetic risk score is increased in early-onset coronary artery disease but independent of familial disease clustering. Atherosclerosis 2017; 257:172-178. [DOI: 10.1016/j.atherosclerosis.2017.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/16/2016] [Accepted: 01/12/2017] [Indexed: 12/28/2022]
|
20
|
Abul-Husn NS, Manickam K, Jones LK, Wright EA, Hartzel DN, Gonzaga-Jauregui C, O’Dushlaine C, Leader JB, Lester Kirchner H, Lindbuchler DM, Barr ML, Giovanni MA, Ritchie MD, Overton JD, Reid JG, Metpally RPR, Wardeh AH, Borecki IB, Yancopoulos GD, Baras A, Shuldiner AR, Gottesman O, Ledbetter DH, Carey DJ, Dewey FE, Murray MF. Genetic identification of familial hypercholesterolemia within a single U.S. health care system. Science 2016; 354:354/6319/aaf7000. [DOI: 10.1126/science.aaf7000] [Citation(s) in RCA: 264] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 11/16/2016] [Indexed: 12/12/2022]
|
21
|
Genome-wide association analyses using electronic health records identify new loci influencing blood pressure variation. Nat Genet 2016; 49:54-64. [PMID: 27841878 PMCID: PMC5370207 DOI: 10.1038/ng.3715] [Citation(s) in RCA: 227] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 10/11/2016] [Indexed: 11/17/2022]
Abstract
Longitudinal electronic health records on 99,785 Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort individuals provided 1,342,814 systolic and diastolic blood pressure measurements for a genome-wide association study on long-term average systolic, diastolic, and pulse pressure. We identified 39 novel among 75 significant loci (P≤5×10−8), most replicating in the combined International Consortium for Blood Pressure (ICBP, n=69,396) and UK Biobank (UKB, n=152,081) studies. Combining GERA with ICBP yielded 36 additional novel loci, most replicating in UKB. Combining all three studies (n=321,262) yielded 241 additional genome-wide significant loci, although for these no replication sample was available. All associated loci explained 2.9%/2.5%/3.1% of systolic/diastolic/pulse pressure variation in GERA non-Hispanic whites. Using multiple BP measurements in GERA doubled the variance explained. A normalized risk score was associated with time-to-onset of hypertension (hazards ratio=1.18, P=10−44). Expression quantitative trait locus analysis of BP loci showed enrichment in aorta and tibial artery.
Collapse
|
22
|
Anderson CD, Falcone GJ, Phuah CL, Radmanesh F, Brouwers HB, Battey TWK, Biffi A, Peloso GM, Liu DJ, Ayres AM, Goldstein JN, Viswanathan A, Greenberg SM, Selim M, Meschia JF, Brown DL, Worrall BB, Silliman SL, Tirschwell DL, Flaherty ML, Kraft P, Jagiella JM, Schmidt H, Hansen BM, Jimenez-Conde J, Giralt-Steinhauer E, Elosua R, Cuadrado-Godia E, Soriano C, van Nieuwenhuizen KM, Klijn CJM, Rannikmae K, Samarasekera N, Al-Shahi Salman R, Sudlow CL, Deary IJ, Morotti A, Pezzini A, Pera J, Urbanik A, Pichler A, Enzinger C, Norrving B, Montaner J, Fernandez-Cadenas I, Delgado P, Roquer J, Lindgren A, Slowik A, Schmidt R, Kidwell CS, Kittner SJ, Waddy SP, Langefeld CD, Abecasis G, Willer CJ, Kathiresan S, Woo D, Rosand J. Genetic variants in CETP increase risk of intracerebral hemorrhage. Ann Neurol 2016; 80:730-740. [PMID: 27717122 PMCID: PMC5115931 DOI: 10.1002/ana.24780] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 09/13/2016] [Accepted: 09/13/2016] [Indexed: 12/26/2022]
Abstract
Objective In observational epidemiologic studies, higher plasma high‐density lipoprotein cholesterol (HDL‐C) has been associated with increased risk of intracerebral hemorrhage (ICH). DNA sequence variants that decrease cholesteryl ester transfer protein (CETP) gene activity increase plasma HDL‐C; as such, medicines that inhibit CETP and raise HDL‐C are in clinical development. Here, we test the hypothesis that CETP DNA sequence variants associated with higher HDL‐C also increase risk for ICH. Methods We performed 2 candidate‐gene analyses of CETP. First, we tested individual CETP variants in a discovery cohort of 1,149 ICH cases and 1,238 controls from 3 studies, followed by replication in 1,625 cases and 1,845 controls from 5 studies. Second, we constructed a genetic risk score comprised of 7 independent variants at the CETP locus and tested this score for association with HDL‐C as well as ICH risk. Results Twelve variants within CETP demonstrated nominal association with ICH, with the strongest association at the rs173539 locus (odds ratio [OR] = 1.25, standard error [SE] = 0.06, p = 6.0 × 10−4) with no heterogeneity across studies (I2 = 0%). This association was replicated in patients of European ancestry (p = 0.03). A genetic score of CETP variants found to increase HDL‐C by ∼2.85mg/dl in the Global Lipids Genetics Consortium was strongly associated with ICH risk (OR = 1.86, SE = 0.13, p = 1.39 × 10−6). Interpretation Genetic variants in CETP associated with increased HDL‐C raise the risk of ICH. Given ongoing therapeutic development in CETP inhibition and other HDL‐raising strategies, further exploration of potential adverse cerebrovascular outcomes may be warranted. Ann Neurol 2016;80:730–740
Collapse
Affiliation(s)
- Christopher D Anderson
- Center for Human Genetic Research, Massachusetts General Hospital (MGH), Boston, MA.,J. Philip Kistler Stroke Research Center, Department of Neurology, MGH, Boston, MA.,Division of Neurocritical Care and Emergency Neurology, Department of Neurology, MGH, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Guido J Falcone
- Center for Human Genetic Research, Massachusetts General Hospital (MGH), Boston, MA.,J. Philip Kistler Stroke Research Center, Department of Neurology, MGH, Boston, MA.,Division of Neurocritical Care and Emergency Neurology, Department of Neurology, MGH, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA.,Departments of Epidemiology and Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Chia-Ling Phuah
- Center for Human Genetic Research, Massachusetts General Hospital (MGH), Boston, MA.,J. Philip Kistler Stroke Research Center, Department of Neurology, MGH, Boston, MA.,Division of Neurocritical Care and Emergency Neurology, Department of Neurology, MGH, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Farid Radmanesh
- Center for Human Genetic Research, Massachusetts General Hospital (MGH), Boston, MA.,J. Philip Kistler Stroke Research Center, Department of Neurology, MGH, Boston, MA.,Division of Neurocritical Care and Emergency Neurology, Department of Neurology, MGH, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - H Bart Brouwers
- Center for Human Genetic Research, Massachusetts General Hospital (MGH), Boston, MA.,J. Philip Kistler Stroke Research Center, Department of Neurology, MGH, Boston, MA.,Division of Neurocritical Care and Emergency Neurology, Department of Neurology, MGH, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Thomas W K Battey
- Center for Human Genetic Research, Massachusetts General Hospital (MGH), Boston, MA.,J. Philip Kistler Stroke Research Center, Department of Neurology, MGH, Boston, MA.,Division of Neurocritical Care and Emergency Neurology, Department of Neurology, MGH, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Alessandro Biffi
- Center for Human Genetic Research, Massachusetts General Hospital (MGH), Boston, MA.,J. Philip Kistler Stroke Research Center, Department of Neurology, MGH, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA.,Division of Behavioral Neurology, Department of Neurology, MGH, Boston, MA.,Division of Psychiatry, Department of Psychiatry, MGH, Boston, MA
| | - Gina M Peloso
- Center for Human Genetic Research, Massachusetts General Hospital (MGH), Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Dajiang J Liu
- Department of Public Health Sciences, Institute of Personalized Medicine, Penn State College of Medicine, Hershey, PA
| | - Alison M Ayres
- Center for Human Genetic Research, Massachusetts General Hospital (MGH), Boston, MA.,J. Philip Kistler Stroke Research Center, Department of Neurology, MGH, Boston, MA
| | | | - Anand Viswanathan
- J. Philip Kistler Stroke Research Center, Department of Neurology, MGH, Boston, MA
| | - Steven M Greenberg
- J. Philip Kistler Stroke Research Center, Department of Neurology, MGH, Boston, MA
| | - Magdy Selim
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA
| | | | - Devin L Brown
- Stroke Program, Department of Neurology, University of Michigan Health System, Ann Arbor, MI
| | - Bradford B Worrall
- Departments of Neurology and Public Health Sciences, University of Virginia Health System, Charlottesville, VA
| | - Scott L Silliman
- Department of Neurology, University of Florida College of Medicine, Jacksonville, FL
| | - David L Tirschwell
- Stroke Center, Harborview Medical Center, University of Washington, Seattle, WA
| | - Matthew L Flaherty
- Department of Neurology, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Peter Kraft
- Departments of Epidemiology and Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Jeremiasz M Jagiella
- Department of Neurology, Jagiellonian University Medical College, Krakow, Poland
| | - Helena Schmidt
- Institute of Molecular Biology and Biochemistry, Medical University Graz, Graz, Austria
| | - Björn M Hansen
- Division of Neurology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Division of Neurology, Department of Neurology and Rehabilitation Medicine, Skåne University Hospital, Lund, Sweden
| | - Jordi Jimenez-Conde
- Neurovascular Research Unit, Department of Neurology, Municipal Institute of Medical Investigation-Hospital of the Sea, Autonomous University of Barcelona, Barcelona, Spain.,Program in Inflammation and Cardiovascular Disorders, Municipal Institute of Medical Investigation-Hospital of the Sea, Autonomous University of Barcelona, Barcelona, Spain
| | - Eva Giralt-Steinhauer
- Neurovascular Research Unit, Department of Neurology, Municipal Institute of Medical Investigation-Hospital of the Sea, Autonomous University of Barcelona, Barcelona, Spain.,Program in Inflammation and Cardiovascular Disorders, Municipal Institute of Medical Investigation-Hospital of the Sea, Autonomous University of Barcelona, Barcelona, Spain
| | - Roberto Elosua
- Neurovascular Research Unit, Department of Neurology, Municipal Institute of Medical Investigation-Hospital of the Sea, Autonomous University of Barcelona, Barcelona, Spain.,Program in Inflammation and Cardiovascular Disorders, Municipal Institute of Medical Investigation-Hospital of the Sea, Autonomous University of Barcelona, Barcelona, Spain
| | - Elisa Cuadrado-Godia
- Neurovascular Research Unit, Department of Neurology, Municipal Institute of Medical Investigation-Hospital of the Sea, Autonomous University of Barcelona, Barcelona, Spain.,Program in Inflammation and Cardiovascular Disorders, Municipal Institute of Medical Investigation-Hospital of the Sea, Autonomous University of Barcelona, Barcelona, Spain
| | - Carolina Soriano
- Neurovascular Research Unit, Department of Neurology, Municipal Institute of Medical Investigation-Hospital of the Sea, Autonomous University of Barcelona, Barcelona, Spain.,Program in Inflammation and Cardiovascular Disorders, Municipal Institute of Medical Investigation-Hospital of the Sea, Autonomous University of Barcelona, Barcelona, Spain
| | - Koen M van Nieuwenhuizen
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Catharina J M Klijn
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands.,Department of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Kristiina Rannikmae
- Division of Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Neshika Samarasekera
- Division of Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Catherine L Sudlow
- Division of Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrea Morotti
- Department of Clinical and Experimental Sciences, Neurology Clinic, University of Brescia, Brescia, Italy
| | - Alessandro Pezzini
- Department of Clinical and Experimental Sciences, Neurology Clinic, University of Brescia, Brescia, Italy
| | - Joanna Pera
- Department of Neurology, Jagiellonian University Medical College, Krakow, Poland
| | - Andrzej Urbanik
- Department of Neurology, Jagiellonian University Medical College, Krakow, Poland
| | | | - Christian Enzinger
- Department of Neurology, Medical University of Graz, Graz, Austria.,Division of Neuroradiology, Department of Radiology, Medical University of Graz, Graz, Austria
| | - Bo Norrving
- Division of Neurology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Division of Neurology, Department of Neurology and Rehabilitation Medicine, Skåne University Hospital, Lund, Sweden
| | - Joan Montaner
- Neurovascular Research Laboratory and Neurovascular Unit, Research Institute, Vall d'Hebron Hospital, Autonomous University of Barcelona, Barcelona, Spain
| | - Israel Fernandez-Cadenas
- Neurovascular Research Laboratory and Neurovascular Unit, Research Institute, Vall d'Hebron Hospital, Autonomous University of Barcelona, Barcelona, Spain.,Stroke Pharmacogenomics and Genetics, Terrassa Mutual Teaching and Research Foundation, Terrassa Mutual Hospital, Terrassa, Spain
| | - Pilar Delgado
- Neurovascular Research Laboratory and Neurovascular Unit, Research Institute, Vall d'Hebron Hospital, Autonomous University of Barcelona, Barcelona, Spain
| | - Jaume Roquer
- Neurovascular Research Unit, Department of Neurology, Municipal Institute of Medical Investigation-Hospital of the Sea, Autonomous University of Barcelona, Barcelona, Spain.,Program in Inflammation and Cardiovascular Disorders, Municipal Institute of Medical Investigation-Hospital of the Sea, Autonomous University of Barcelona, Barcelona, Spain
| | - Arne Lindgren
- Division of Neurology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Division of Neurology, Department of Neurology and Rehabilitation Medicine, Skåne University Hospital, Lund, Sweden
| | - Agnieszka Slowik
- Department of Neurology, Jagiellonian University Medical College, Krakow, Poland
| | - Reinhold Schmidt
- Department of Neurology, Medical University of Graz, Graz, Austria
| | | | - Steven J Kittner
- Department of Neurology, Baltimore Veterans Administration Medical Center and University of Maryland School of Medicine, Baltimore, MD
| | - Salina P Waddy
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Carl D Langefeld
- Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest University, Winston-Salem, NC
| | - Goncalo Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI
| | - Cristen J Willer
- Division of Cardiology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI.,Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI
| | - Sekar Kathiresan
- Center for Human Genetic Research, Massachusetts General Hospital (MGH), Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA.,Cardiovascular Disease Prevention Center, MGH, Boston, MA
| | - Daniel Woo
- Department of Neurology, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Jonathan Rosand
- Center for Human Genetic Research, Massachusetts General Hospital (MGH), Boston, MA.,J. Philip Kistler Stroke Research Center, Department of Neurology, MGH, Boston, MA.,Division of Neurocritical Care and Emergency Neurology, Department of Neurology, MGH, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | | |
Collapse
|
23
|
Kanoni S, Masca NGD, Stirrups KE, Varga TV, Warren HR, Scott RA, Southam L, Zhang W, Yaghootkar H, Müller-Nurasyid M, Couto Alves A, Strawbridge RJ, Lataniotis L, An Hashim N, Besse C, Boland A, Braund PS, Connell JM, Dominiczak A, Farmaki AE, Franks S, Grallert H, Jansson JH, Karaleftheri M, Keinänen-Kiukaanniemi S, Matchan A, Pasko D, Peters A, Poulter N, Rayner NW, Renström F, Rolandsson O, Sabater-Lleal M, Sennblad B, Sever P, Shields D, Silveira A, Stanton AV, Strauch K, Tomaszewski M, Tsafantakis E, Waldenberger M, Blakemore AIF, Dedoussis G, Escher SA, Kooner JS, McCarthy MI, Palmer CNA, Hamsten A, Caulfield MJ, Frayling TM, Tobin MD, Jarvelin MR, Zeggini E, Gieger C, Chambers JC, Wareham NJ, Munroe PB, Franks PW, Samani NJ, Deloukas P. Analysis with the exome array identifies multiple new independent variants in lipid loci. Hum Mol Genet 2016; 25:4094-4106. [PMID: 27466198 DOI: 10.1093/hmg/ddw227] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 05/06/2016] [Accepted: 07/08/2016] [Indexed: 12/25/2022] Open
Abstract
It has been hypothesized that low frequency (1-5% minor allele frequency (MAF)) and rare (<1% MAF) variants with large effect sizes may contribute to the missing heritability in complex traits. Here, we report an association analysis of lipid traits (total cholesterol, LDL-cholesterol, HDL-cholesterol triglycerides) in up to 27 312 individuals with a comprehensive set of low frequency coding variants (ExomeChip), combined with conditional analysis in the known lipid loci. No new locus reached genome-wide significance. However, we found a new lead variant in 26 known lipid association regions of which 16 were >1000-fold more significant than the previous sentinel variant and not in close LD (six had MAF <5%). Furthermore, conditional analysis revealed multiple independent signals (ranging from 1 to 5) in a third of the 98 lipid loci tested, including rare variants. Addition of our novel associations resulted in between 1.5- and 2.5-fold increase in the proportion of heritability explained for the different lipid traits. Our findings suggest that rare coding variants contribute to the genetic architecture of lipid traits.
Collapse
Affiliation(s)
- Stavroula Kanoni
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Nicholas G D Masca
- Department of Cardiovascular Sciences, University of Leicester, BHF Cardiovascular Research Centre, Glenfield Hospital, Leicester, UK.,NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Kathleen E Stirrups
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Tibor V Varga
- The Broad Institute of MIT and Harvard, Boston, MA 02142, USA.,Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA.,Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | - Helen R Warren
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,NIHR Barts Cardiovascular Biomedical Research Unit, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Robert A Scott
- Medical Research Council (MRC) Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Lorraine Southam
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK.,Ealing Hospital NHS Trust, Middlesex, UK
| | - Hanieh Yaghootkar
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Martina Müller-Nurasyid
- Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, Munich, Germany.,Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Alexessander Couto Alves
- Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPE) Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Rona J Strawbridge
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Lazaros Lataniotis
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Nikman An Hashim
- Section of Investigative Medicine, Imperial College London, London, UK
| | - Céline Besse
- CEA, Institut de Génomique, Centre National de Génotypage, Evry, France
| | - Anne Boland
- CEA, Institut de Génomique, Centre National de Génotypage, Evry, France
| | - Peter S Braund
- Department of Cardiovascular Sciences, University of Leicester, BHF Cardiovascular Research Centre, Glenfield Hospital, Leicester, UK.,NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - John M Connell
- Medical Research Institute, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Anna Dominiczak
- Division of Cardiovascular and Medical Sciences, BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Western Infirmary, Glasgow, UK
| | - Aliki-Eleni Farmaki
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University Athens, Athens, Greece
| | - Stephen Franks
- Department of Surgery and Cancer, Imperial College London, Institute of Reproductive and Developmental Biology, London, UK
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Diabetes Research, Neuherberg, Germany
| | - Jan-Håkan Jansson
- Department of Public Health and Clinical Medicine, Skellefteå Research Unit, Umeå University, Umeå, Sweden
| | | | | | - Angela Matchan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Dorota Pasko
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Annette Peters
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Neil Poulter
- International Centre for Circulatory Health, Imperial College London, London, UK
| | - Nigel W Rayner
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK.,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Frida Renström
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Skåne University Hospital Malmö, Malmö, Sweden.,Department of Biobank Research, Umeå University, Umeå, Sweden
| | - Olov Rolandsson
- Department of Public Health & Clinical Medicine, Section for Family Medicine, Umeå University, Umeå, Sweden
| | - Maria Sabater-Lleal
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Bengt Sennblad
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Peter Sever
- International Centre for Circulatory Health, Imperial College London, London, UK
| | - Denis Shields
- Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Angela Silveira
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Alice V Stanton
- Molecular & Cellular Therapeutics, Royal College of Surgeons in Ireland, Stephens Green, Dublin, Ireland
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Maciej Tomaszewski
- Department of Cardiovascular Sciences, University of Leicester, BHF Cardiovascular Research Centre, Glenfield Hospital, Leicester, UK.,NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, LE3 9QP, UK
| | | | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Alexandra I F Blakemore
- Section of Investigative Medicine, Imperial College London, London, UK.,Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University Athens, Athens, Greece
| | - Stefan A Escher
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | - Jaspal S Kooner
- Ealing Hospital NHS Trust, Middlesex, UK.,Imperial College Healthcare NHS Trust, London, UK.,National Heart and Lung Institute, Imperial College London, London, UK
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK.,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK.,Oxford National Institute for Health Research (NIHR) Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Colin N A Palmer
- Medical Research Institute, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | | | - Anders Hamsten
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Mark J Caulfield
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK.,NIHR Barts Cardiovascular Biomedical Research Unit, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPE) Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.,Institute of Health Sciences, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Unit of Primary Care, Oulu University Hospital, Oulu, Finland.,Department of Children and Young People and Families, National Institute for Health and Welfare, Oulu, Finland
| | | | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Diabetes Research, Neuherberg, Germany
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK.,Ealing Hospital NHS Trust, Middlesex, UK.,Imperial College Healthcare NHS Trust, London, UK
| | - Nick J Wareham
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Patricia B Munroe
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK.,NIHR Barts Cardiovascular Biomedical Research Unit, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Paul W Franks
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Skåne University Hospital Malmö, Malmö, Sweden.,Department of Nutrition, Harvard School of Public Health, Boston, MA, USA.,Department of Public Health & Clinical Medicine, Umeå University Hospital, Umeå, Sweden
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, BHF Cardiovascular Research Centre, Glenfield Hospital, Leicester, UK .,NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Panos Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK .,Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
24
|
Artigas MS, Wain LV, Miller S, Kheirallah AK, Huffman JE, Ntalla I, Shrine N, Obeidat M, Trochet H, McArdle WL, Alves AC, Hui J, Zhao JH, Joshi PK, Teumer A, Albrecht E, Imboden M, Rawal R, Lopez LM, Marten J, Enroth S, Surakka I, Polasek O, Lyytikäinen LP, Granell R, Hysi PG, Flexeder C, Mahajan A, Beilby J, Bossé Y, Brandsma CA, Campbell H, Gieger C, Gläser S, González JR, Grallert H, Hammond CJ, Harris SE, Hartikainen AL, Heliövaara M, Henderson J, Hocking L, Horikoshi M, Hutri-Kähönen N, Ingelsson E, Johansson Å, Kemp JP, Kolcic I, Kumar A, Lind L, Melén E, Musk AW, Navarro P, Nickle DC, Padmanabhan S, Raitakari OT, Ried JS, Ripatti S, Schulz H, Scott RA, Sin DD, Starr JM, Viñuela A, Völzke H, Wild SH, Wright AF, Zemunik T, Jarvis DL, Spector TD, Evans DM, Lehtimäki T, Vitart V, Kähönen M, Gyllensten U, Rudan I, Deary IJ, Karrasch S, Probst-Hensch NM, Heinrich J, Stubbe B, Wilson JF, Wareham NJ, James AL, Morris AP, Jarvelin MR, Hayward C, Sayers I, Strachan DP, Hall IP, Tobin MD. Sixteen new lung function signals identified through 1000 Genomes Project reference panel imputation. Nat Commun 2015; 6:8658. [PMID: 26635082 PMCID: PMC4686825 DOI: 10.1038/ncomms9658] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 09/17/2015] [Indexed: 01/11/2023] Open
Abstract
Lung function measures are used in the diagnosis of chronic obstructive pulmonary disease. In 38,199 European ancestry individuals, we studied genome-wide association of forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC with 1000 Genomes Project (phase 1)-imputed genotypes and followed up top associations in 54,550 Europeans. We identify 14 novel loci (P<5 × 10(-8)) in or near ENSA, RNU5F-1, KCNS3, AK097794, ASTN2, LHX3, CCDC91, TBX3, TRIP11, RIN3, TEKT5, LTBP4, MN1 and AP1S2, and two novel signals at known loci NPNT and GPR126, providing a basis for new understanding of the genetic determinants of these traits and pulmonary diseases in which they are altered.
Collapse
Affiliation(s)
- María Soler Artigas
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Louise V. Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Suzanne Miller
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2RD, UK
| | - Abdul Kader Kheirallah
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2RD, UK
| | - Jennifer E. Huffman
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH8 9AD, UK
| | - Ioanna Ntalla
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Nick Shrine
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Ma'en Obeidat
- University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada V6Z 1Y6
| | - Holly Trochet
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH8 9AD, UK
- Generation Scotland, A Collaboration between the University Medical Schools and NHS, Aberdeen, Dundee, Edinburgh, Glasgow EH4 2XU, UK
| | - Wendy L. McArdle
- School of Social and Community Medicine, University of Bristol, Bristol BS8 1TH, UK
| | - Alexessander Couto Alves
- Department of Epidemiology and Biostatistics, MRC -PHE Centre for Environment & Health, School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Jennie Hui
- Busselton Population Medical Research Institute, Busselton, Western Australia 6280, Australia
- PathWest Laboratory Medicine WA, Sir Charles Gairdner Hospital, Western Australia 6009, Australia
- School of Population Health, The University of Western Australia, Western Australia 6009, Australia
- School of Pathology and Laboratory Medicine, The University of Western Australia, Western Australia 6009, Australia
| | - Jing Hua Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0SL, UK
| | - Peter K. Joshi
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AD, Scotland, UK
| | - Alexander Teumer
- University Medicine Greifswald, Community Medicine, SHIP—Clinical Epidemiological Research, Greifswald 17489, Germany
- Department for Genetics and Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald 17489, Germany
| | - Eva Albrecht
- Institute of Genetic Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg D-85764, Germany
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel 4051, Switzerland
- University of Basel, Basel 4001, Switzerland
| | - Rajesh Rawal
- Institute of Genetic Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg D-85764, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg D-85764, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg D-85764, Germany
| | - Lorna M. Lopez
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9AD, UK
- Department of Psychology, University of Edinburgh, Edinburgh EH8 9AD, UK
| | - Jonathan Marten
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH8 9AD, UK
| | - Stefan Enroth
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, Uppsala 751 23, Sweden
| | - Ida Surakka
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FI-00014, Finland
- The National Institute for Health and Welfare (THL), Helsinki FI-00271, Finland
| | - Ozren Polasek
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AD, Scotland, UK
- Department of Public Health, Faculty of Medicine, University of Split, Split 21000, Croatia
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere FI-33101, Finland
- Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere FI-33520, Finland
| | - Raquel Granell
- School of Social and Community Medicine, University of Bristol, Bristol BS8 1TH, UK
| | - Pirro G. Hysi
- KCL Department of Twins Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - Claudia Flexeder
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg D-85764, Germany
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - John Beilby
- Busselton Population Medical Research Institute, Busselton, Western Australia 6280, Australia
- PathWest Laboratory Medicine WA, Sir Charles Gairdner Hospital, Western Australia 6009, Australia
- School of Pathology and Laboratory Medicine, The University of Western Australia, Western Australia 6009, Australia
| | - Yohan Bossé
- Department of Molecular Medicine, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, Canada G1V 0A6
| | - Corry-Anke Brandsma
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen 9700, The Netherlands
| | - Harry Campbell
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AD, Scotland, UK
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg D-85764, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg D-85764, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg D-85764, Germany
| | - Sven Gläser
- Department of Internal Medicine B, Pneumology, Cardiology, Intensive Care, Weaning, Field of Research: Pneumological Epidemiology, University Medicine Greifswald, Greifswald 17489, Germany
| | - Juan R. González
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona E-08003, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid 28029, Spain
- Pompeu Fabra University (UPF), Barcelona 08002, Catalonia, Spain
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg D-85764, Germany
| | - Chris J. Hammond
- KCL Department of Twins Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9AD, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh EH8 9AD, UK
| | - Anna-Liisa Hartikainen
- Department of Obstetrics and Gynecology of Oulu University Hospital ,MRC of Oulu University, Oulu 90220, Finland
| | - Markku Heliövaara
- The National Institute for Health and Welfare (THL), Helsinki FI-00271, Finland
| | - John Henderson
- School of Social and Community Medicine, University of Bristol, Bristol BS8 1TH, UK
| | - Lynne Hocking
- Generation Scotland, A Collaboration between the University Medical Schools and NHS, Aberdeen, Dundee, Edinburgh, Glasgow EH4 2XU, UK
- Division of Applied Health Sciences, University of Aberdeen, Aberdeen, Scotland AB24 3FX, UK
| | - Momoko Horikoshi
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX1 2JD, UK
| | - Nina Hutri-Kähönen
- Department of Pediatrics, Tampere University Hospital, Tampere 33521, Finland
- Department of Pediatrics, University of Tampere School of Medicine, Tampere FI-33520, Finland
| | - Erik Ingelsson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala 751 23, Sweden
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Åsa Johansson
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, Uppsala 751 23, Sweden
- Uppsala Clinical Research Centre, Uppsala University, Uppsala 751 23, Sweden
| | - John P. Kemp
- School of Social and Community Medicine, University of Bristol, Bristol BS8 1TH, UK
- Diamantina Institute, Translational Research Institute, University of Queensland, Brisbane, Queensland QLD 4072, Australia
- MRC Integrative Epidemiology Unit, Bristol BS8 1TH, UK
| | - Ivana Kolcic
- Department of Public Health, Faculty of Medicine, University of Split, Split 21000, Croatia
| | - Ashish Kumar
- Swiss Tropical and Public Health Institute, Basel 4051, Switzerland
- University of Basel, Basel 4001, Switzerland
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm SE-171 7, Sweden
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala 751 23, Sweden
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet and Sachs' Children's Hospital, Stockholm SE-171 7, Sweden
| | - Arthur W. Musk
- Busselton Population Medical Research Institute, Busselton, Western Australia 6280, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Western Australia 6009, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Western Australia 6009, Australia
| | - Pau Navarro
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH8 9AD, UK
| | - David C. Nickle
- Genetics and Pharmacogenomics, Merck Research Labs, Boston, Massachusetts 02115, USA
| | - Sandosh Padmanabhan
- Generation Scotland, A Collaboration between the University Medical Schools and NHS, Aberdeen, Dundee, Edinburgh, Glasgow EH4 2XU, UK
- Division of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8TA, Scotland, UK
| | - Olli T. Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku 20520, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku 20014, Finland
| | - Janina S. Ried
- Institute of Genetic Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg D-85764, Germany
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FI-00014, Finland
- Department of Public Health, University of Helsinki, Helsinki FI-00014, Finland
- Department of Human Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg D-85764, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich 85764, Germany
| | - Robert A. Scott
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0SL, UK
| | - Don D. Sin
- University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada V6Z 1Y6
- Respiratory Division, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9AD, UK
- Alzheimer Scotland Research Centre, University of Edinburgh, Edinburgh EH8 9AD, UK
| | - Ana Viñuela
- KCL Department of Twins Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - Henry Völzke
- University Medicine Greifswald, Community Medicine, SHIP—Clinical Epidemiological Research, Greifswald 17489, Germany
| | - Sarah H. Wild
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AD, Scotland, UK
| | - Alan F. Wright
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH8 9AD, UK
| | - Tatijana Zemunik
- Department of Medical Biology, Faculty of Medicine, University of Split, Split 21000, Croatia
| | - Deborah L. Jarvis
- Respiratory Epidemiology and Public Health, Imperial College London, London SW7 2AZ, UK
- MRC Health Protection Agency (HPA) Centre for Environment and Health, Imperial College London, London SW7 2AZ, UK
| | - Tim D. Spector
- KCL Department of Twins Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - David M. Evans
- School of Social and Community Medicine, University of Bristol, Bristol BS8 1TH, UK
- Diamantina Institute, Translational Research Institute, University of Queensland, Brisbane, Queensland QLD 4072, Australia
- MRC Integrative Epidemiology Unit, Bristol BS8 1TH, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere FI-33101, Finland
- Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere FI-33520, Finland
| | - Veronique Vitart
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH8 9AD, UK
| | - Mika Kähönen
- Department of Clinical Physiology, University of Tampere and Tampere University Hospital, Tampere 33521, Finland
| | - Ulf Gyllensten
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, Uppsala 751 23, Sweden
| | - Igor Rudan
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AD, Scotland, UK
- Centre for Population Health Sciences, Medical School, University of Edinburgh, Edinburgh EH8 9AD, Scotland, UK
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9AD, UK
- Department of Psychology, University of Edinburgh, Edinburgh EH8 9AD, UK
| | - Stefan Karrasch
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg D-85764, Germany
- Institute of General Practice, University Hospital Klinikum rechts der Isar, Technische Universität München, Munich D - 81675, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich 80539, Germany
| | - Nicole M. Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel 4051, Switzerland
- University of Basel, Basel 4001, Switzerland
| | - Joachim Heinrich
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg D-85764, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich 85764, Germany
- University Hospital Munich, Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilian University Munich, Munich 80539, Germany
| | - Beate Stubbe
- Department of Internal Medicine B, Pneumology, Cardiology, Intensive Care, Weaning, Field of Research: Pneumological Epidemiology, University Medicine Greifswald, Greifswald 17489, Germany
| | - James F. Wilson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH8 9AD, UK
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AD, Scotland, UK
| | - Nicholas J. Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0SL, UK
| | - Alan L. James
- Busselton Population Medical Research Institute, Busselton, Western Australia 6280, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Western Australia 6009, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Western Australia 6009, Australia
| | - Andrew P. Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Department of Biostatistics, University of Liverpool, Liverpool L69 7ZX, UK
- Estonian Genome Centre, University of Tartu, Tartu 50090, Estonia
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC -PHE Centre for Environment & Health, School of Public Health, Imperial College London, London SW7 2AZ, UK
- Center for Life Course Epidemiology, Faculty of Medicine, P.O.Box 5000, FI-90014 University of Oulu, Oulu FI-01051, Finland
- Biocenter Oulu, P.O.Box 5000, Aapistie 5A, FI-90014 University of Oulu, Oulu FI-01051, Finland
- Unit of Primary Care, Oulu University Hospital, Kajaanintie 50, P.O.Box 20, FI-90220 Oulu, 90029 OYS, Finland
| | - Caroline Hayward
- Generation Scotland, A Collaboration between the University Medical Schools and NHS, Aberdeen, Dundee, Edinburgh, Glasgow EH4 2XU, UK
| | - Ian Sayers
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2RD, UK
| | - David P. Strachan
- Population Health Research Institute, St George's, University of London, Cranmer Terrace, London WC1B 5DN, UK
| | - Ian P. Hall
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2RD, UK
| | - Martin D. Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester LE3 9QP, UK
| |
Collapse
|
25
|
Role of Tribbles Pseudokinase 1 (TRIB1) in human hepatocyte metabolism. Biochim Biophys Acta Mol Basis Dis 2015; 1862:223-32. [PMID: 26657055 DOI: 10.1016/j.bbadis.2015.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 11/18/2015] [Accepted: 12/01/2015] [Indexed: 01/23/2023]
Abstract
Genome-wide association studies for plasma triglycerides and hepatic steatosis identified a risk locus on chromosome 8q24 close to the TRIB1 gene, encoding Tribbles Pseudokinase 1 (TRIB1). In previous studies conducted in murine models, hepatic over-expression of Trib1 was shown to increase fatty acid oxidation and decrease triglyceride synthesis whereas Trib1 knockdown mice exhibited hypertriglyceridemia. Here we have examined the impact of TRIB1 suppression in human and mouse hepatocytes. Examination of a panel of lipid regulator transcripts revealed species-specific effects, prompting us to focus on human models for the remainder of the study. Acute knockdown of TRIB1 in human primary hepatocytes resulted in decreased expression of MTTP and APOB, required for very low density lipoprotein (VLDL) assembly although particle secretion was not significantly affected. A parallel analysis performed in HepG2 revealed reduced MTTP, but not APOB, protein as a result of TRIB1 suppression. Global gene expression changes of human primary hepatocytes upon TRIB1 suppression were analyzed by clustering algorithms and found to be consistent with dysregulation of several pathways fundamental to liver function, including altered CEBPA and B transcript levels and impaired glucose handling. Indeed, TRIB1 expression in HepG2 cells was found to be inversely proportional to glucose concentration. Lastly TRIB1 downregulation in primary hepatocytes was associated with suppression of the HNF4A axis. In HepG2 cells, TRIB1 suppression resulted in reduced HNF4A protein levels while HNF4A suppression increased TRIB1 expression. Taken together these studies reveal an important role for TRIB1 in human hepatocyte biology.
Collapse
|
26
|
Schmidt EM, Willer CJ. Insights into blood lipids from rare variant discovery. Curr Opin Genet Dev 2015; 33:25-31. [PMID: 26241468 DOI: 10.1016/j.gde.2015.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 06/19/2015] [Accepted: 06/22/2015] [Indexed: 12/18/2022]
Abstract
Large-scale genome wide screens have discovered over 160 common variants associated with plasma lipids, which are risk factors often linked to heart disease. A large fraction of lipid heritability remains unexplained, and it is hypothesized that rare variants of functional consequence may account for some of the missing heritability. Finding lipid-associated variants that occur less frequently in the human population poses a challenge, primarily due to lack of power and difficulties to identify and test them. Interrogation of the protein-coding regions of the genome using array and sequencing techniques has led to important discoveries of rare variants that affect lipid levels and related disease risk. Here, we summarize the latest methods and findings that contribute to our current understanding of rare variant lipid genetics.
Collapse
Affiliation(s)
- Ellen M Schmidt
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Cristen J Willer
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
27
|
Rosenberg S. Transcriptional Signatures, Imaging, and Coronary Artery Disease Diagnosis. J Cardiovasc Transl Res 2015; 8:279-80. [PMID: 25968136 DOI: 10.1007/s12265-015-9634-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 05/04/2015] [Indexed: 11/24/2022]
|
28
|
Vatta M, Spoonamore KG. Use of genetic testing to identify sudden cardiac death syndromes. Trends Cardiovasc Med 2015; 25:738-48. [PMID: 25864170 DOI: 10.1016/j.tcm.2015.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 03/06/2015] [Accepted: 03/07/2015] [Indexed: 01/25/2023]
Abstract
Sudden cardiac death (SCD) is a leading cause of mortality worldwide. Although coronary artery disease remains the most common substrate for SCD, primary cardiac genetic diseases, presenting with or without structural heart abnormalities, play a significant role. In the last 30 years, the study of large family pedigrees allowed the discovery of causative genes unveiling the genetic basis of diseases such as primary cardiomyopathies and arrhythmia syndromes, which are known to increase the risk of SCD. However, recent technological advancement with the ability to perform massive parallel sequencing and analyze the entire genome has uncovered a higher level of complexity in the genetic predisposition for cardiac diseases, which are usually characterized by Mendelian inheritance patterns. Clinical genetic testing, historically shaped around a monogenic Mendelian disorder paradigm, is now facing the challenge to adopt and adapt to a more complex model in which a significant portion of subjects may present with multi-allelic inheritance involving additional genes that could modulate the severity and type of disease-related phenotypes. Here, we will try to provide a viewpoint that will hopefully foster further debate in the field.
Collapse
Affiliation(s)
- Matteo Vatta
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN; Department of Medicine, Krannert Institute of Cardiology, Indiana University School of Medicine, Indianapolis, IN.
| | - Katherine G Spoonamore
- Department of Medicine, Krannert Institute of Cardiology, Indiana University School of Medicine, Indianapolis, IN
| |
Collapse
|