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Best LG, Erdei E, Haack K, Kent JW, Malloy KM, Newman DE, O’Leary M, O’Leary RA, Sun Q, Navas-Acien A, Franceschini N, Cole SA. Genetic variant rs1205 is associated with COVID-19 outcomes: The Strong Heart Study and Strong Heart Family Study. PLoS One 2024; 19:e0302464. [PMID: 38662664 PMCID: PMC11045144 DOI: 10.1371/journal.pone.0302464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Although COVID-19 infection has been associated with a number of clinical and environmental risk factors, host genetic variation has also been associated with the incidence and morbidity of infection. The CRP gene codes for a critical component of the innate immune system and CRP variants have been reported associated with infectious disease and vaccination outcomes. We investigated possible associations between COVID-19 outcome and a limited number of candidate gene variants including rs1205. METHODOLOGY/PRINCIPAL FINDINGS The Strong Heart and Strong Heart Family studies have accumulated detailed genetic, cardiovascular risk and event data in geographically dispersed American Indian communities since 1988. Genotypic data and 91 COVID-19 adjudicated deaths or hospitalizations from 2/1/20 through 3/1/23 were identified among 3,780 participants in two subsets. Among 21 candidate variants including genes in the interferon response pathway, APOE, TMPRSS2, TLR3, the HLA complex and the ABO blood group, only rs1205, a 3' untranslated region variant in the CRP gene, showed nominally significant association in T-dominant model analyses (odds ratio 1.859, 95%CI 1.001-3.453, p = 0.049) after adjustment for age, sex, center, body mass index, and a history of cardiovascular disease. Within the younger subset, association with the rs1205 T-Dom genotype was stronger, both in the same adjusted logistic model and in the SOLAR analysis also adjusting for other genetic relatedness. CONCLUSION A T-dominant genotype of rs1205 in the CRP gene is associated with COVID-19 death or hospitalization, even after adjustment for relevant clinical factors and potential participant relatedness. Additional study of other populations and genetic variants of this gene are warranted.
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Affiliation(s)
- Lyle G. Best
- Epidemiology Division, Missouri Breaks Industries Research, Inc. Eagle Butte, SD, United States of America
- Pathology Department, University of North Dakota, Grand Forks, ND, United States of America
| | - Esther Erdei
- Pharmaceutical Sciences, University of New Mexico—Albuquerque, Albuquerque, New Mexico, United States of America
| | - Karin Haack
- Texas Biomedical Research Institute, Population Health Program, San Antonio, TX, United States of America
| | - Jack W. Kent
- Texas Biomedical Research Institute, Population Health Program, San Antonio, TX, United States of America
| | - Kimberly M. Malloy
- Department of Biostatistics and Epidemiology, Center for American Indian Health Research, Hudson College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States of America
| | - Deborah E. Newman
- Texas Biomedical Research Institute, Population Health Program, San Antonio, TX, United States of America
| | - Marcia O’Leary
- Epidemiology Division, Missouri Breaks Industries Research, Inc. Eagle Butte, SD, United States of America
| | - Rae A. O’Leary
- Epidemiology Division, Missouri Breaks Industries Research, Inc. Eagle Butte, SD, United States of America
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Ana Navas-Acien
- Department of Environmental Health Science, Mailman School of Public Health, Columbia University, New York, NY, United States of America
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Shelley A. Cole
- Texas Biomedical Research Institute, Population Health Program, San Antonio, TX, United States of America
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Li X, Ploner A, Wang Y, Mak JKL, Lu Y, Magnusson PKE, Jylhävä J, Hägg S. Rare functional variants in the CRP and G6PC genes modify the relationship between obesity and serum C-reactive protein in white British population. Mol Genet Genomic Med 2023; 11:e2255. [PMID: 37493001 PMCID: PMC10724514 DOI: 10.1002/mgg3.2255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/03/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND C-reactive protein (CRP) is a sensitive biomarker of inflammation with moderate heritability. The role of rare functional genetic variants in relation to serum CRP is understudied. We aimed to examine gene mutation burden of protein-altering (PA) and loss-of-function (LOF) variants in association with serum CRP, and to further explore the clinical relevance. METHODS We included 161,430 unrelated participants of European ancestry from the UK Biobank. Of the rare (minor allele frequency <0.1%) and functional variants, 1,776,249 PA and 266,226 LOF variants were identified. Gene-based burden tests, linear regressions, and logistic regressions were performed to identify the candidate mutations at the gene and variant levels, to estimate the potential interaction effect between the identified PA mutation and obesity, and to evaluate the relative risk of 16 CRP-associated diseases. RESULTS At the gene level, PA mutation burdens of the CRP (β = -0.685, p = 2.87e-28) and G6PC genes (β = 0.203, p = 1.50e-06) were associated with reduced and increased serum CRP concentration, respectively. At the variant level, seven PA alleles in the CRP gene decreased serum CRP, of which the per-allele effects were approximately three to seven times greater than that of a common variant in the same locus. The effects of obesity and central obesity on serum CRP concentration were smaller among the PA mutation carriers in the CRP (pinteraction = 0.008) and G6PC gene (pinteraction = 0.034) compared to the corresponding non-carriers. CONCLUSION PA mutation burdens in the CRP and G6PC genes are strongly associated with decreased serum CRP concentrations. As serum CRP and obesity are important predictors of cardiovascular risks in clinics, our observations suggest taking rare genetic factors into consideration might improve the delivery of precision medicine.
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Affiliation(s)
- Xia Li
- School of Public Health and Emergency ManagementSouthern University of Science and TechnologyShenzhenChina
- Shenzhen Key Laboratory of Cardiovascular Health and Precision MedicineSouthern University of Science and TechnologyShenzhenChina
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Alexander Ploner
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Yunzhang Wang
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Jonathan K. L. Mak
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Yi Lu
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Patrik K. E. Magnusson
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Juulia Jylhävä
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
- Social Sciences (Health Sciences) and Gerontology Research Center (GEREC)University of TampereTampereFinland
| | - Sara Hägg
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
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3
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Jiang MZ, Gaynor SM, Li X, Van Buren E, Stilp A, Buth E, Wang FF, Manansala R, Gogarten SM, Li Z, Polfus LM, Salimi S, Bis JC, Pankratz N, Yanek LR, Durda P, Tracy RP, Rich SS, Rotter JI, Mitchell BD, Lewis JP, Psaty BM, Pratte KA, Silverman EK, Kaplan RC, Avery C, North K, Mathias RA, Faraday N, Lin H, Wang B, Carson AP, Norwood AF, Gibbs RA, Kooperberg C, Lundin J, Peters U, Dupuis J, Hou L, Fornage M, Benjamin EJ, Reiner AP, Bowler RP, Lin X, Auer PL, Raffield LM. Whole Genome Sequencing Based Analysis of Inflammation Biomarkers in the Trans-Omics for Precision Medicine (TOPMed) Consortium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.10.555215. [PMID: 37745480 PMCID: PMC10515765 DOI: 10.1101/2023.09.10.555215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Inflammation biomarkers can provide valuable insight into the role of inflammatory processes in many diseases and conditions. Sequencing based analyses of such biomarkers can also serve as an exemplar of the genetic architecture of quantitative traits. To evaluate the biological insight, which can be provided by a multi-ancestry, whole-genome based association study, we performed a comprehensive analysis of 21 inflammation biomarkers from up to 38,465 individuals with whole-genome sequencing from the Trans-Omics for Precision Medicine (TOPMed) program. We identified 22 distinct single-variant associations across 6 traits - E-selectin, intercellular adhesion molecule 1, interleukin-6, lipoprotein-associated phospholipase A2 activity and mass, and P-selectin - that remained significant after conditioning on previously identified associations for these inflammatory biomarkers. We further expanded upon known biomarker associations by pairing the single-variant analysis with a rare variant set-based analysis that further identified 19 significant rare variant set-based associations with 5 traits. These signals were distinct from both significant single variant association signals within TOPMed and genetic signals observed in prior studies, demonstrating the complementary value of performing both single and rare variant analyses when analyzing quantitative traits. We also confirm several previously reported signals from semi-quantitative proteomics platforms. Many of these signals demonstrate the extensive allelic heterogeneity and ancestry-differentiated variant-trait associations common for inflammation biomarkers, a characteristic we hypothesize will be increasingly observed with well-powered, large-scale analyses of complex traits.
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Affiliation(s)
- Min-Zhi Jiang
- Department of Genetics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Sheila M. Gaynor
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA, 02115, USA
- Regeneron Genetics Center, Tarrytown, NY, 10591, USA
| | - Xihao Li
- Department of Genetics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Eric Van Buren
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA, 02115, USA
| | - Adrienne Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, 98105, USA
| | - Erin Buth
- Department of Biostatistics, University of Washington, Seattle, WA, 98105, USA
| | - Fei Fei Wang
- Department of Biostatistics, University of Washington, Seattle, WA, 98105, USA
| | - Regina Manansala
- Centre for Health Economics Research & Modelling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO) WHO Collaborating Centre, University of Antwerp, Antwerp, BE
| | | | - Zilin Li
- School of Mathematics and Statistics, Northeast Normal University, Changchun, Jilin, 130024, China
| | - Linda M. Polfus
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Shabnam Salimi
- Department of Epidemiology and Public Health, Division of Gerontology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, 4333 Brooklyn Ave NE, Box 359458, Seattle, WA, 98195, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Lisa R. Yanek
- Department of Medicine, General Internal Medicine, Johns Hopkins University School of Medicine, 1830 E Monument St Rm 8024, Baltimore, MD, 21287, USA
| | - Peter Durda
- Department of Pathology & Laboratory Medicine, University of Vermont Larner College of Medicine, 360 South Park Drive, Colchester, VT, 05446, USA
| | - Russell P. Tracy
- Department of Pathology & Laboratory Medicine, University of Vermont Larner College of Medicine, 360 South Park Drive, Colchester, VT, 05446, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, 200 Jeanette Lancaster Way, Charlottesville, VA, 22903, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, 1124 W. Carson Street, Torrance, CA, 90502, USA
| | - Braxton D. Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, 670 W. Baltimore St., Baltimore, MD, 21201, USA
| | - Joshua P. Lewis
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, 670 W. Baltimore St., Baltimore, MD, 21201, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, 4333 Brooklyn Ave NE, Box 359458, Seattle, WA, 98195, USA
- Departments of Epidemiology and Health Systems and Population Health, University of Washington, 4333 Brooklyn Ave NE, Seattle, WA, 98101, USA
| | - Katherine A. Pratte
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Edwin K. Silverman
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Robert C. Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Christy Avery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kari North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Rasika A. Mathias
- Department of Medicine, Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, 5501 Hopkins Bayview Cir JHAAC Room 3B53, Baltimore, MD, 21287, USA
| | - Nauder Faraday
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, 600 N Wolfe St, Baltimore, MD, 21287, USA
| | - Honghuang Lin
- Department of Medicine, University of Massachusetts Chan Medical School, 55 Lake Ave North, Worcester, MA, 01655, USA
| | - Biqi Wang
- Department of Medicine, University of Massachusetts Chan Medical School, 55 Lake Ave North, Worcester, MA, 01655, USA
| | - April P. Carson
- Department of Medicine, University of Mississippi Medical Center, 350 W. Woodrow Wilson Avenue, Suite 701, Jackson, MS, 39213, USA
| | - Arnita F. Norwood
- Department of Medicine, University of Mississippi Medical Center, 350 W. Woodrow Wilson Avenue, Suite 701, Jackson, MS, 39213, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Jessica Lundin
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Josée Dupuis
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Québec, H3A 1G1, Canada
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Emelia J. Benjamin
- Department of Medicine, Cardiovascular Medicine, Boston Medical Center, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, 02118, USA
- Boston University and National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, 01702, USA
| | - Alexander P. Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, 98105, USA
| | - Russell P. Bowler
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA, 02115, USA
| | - Paul L. Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA
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4
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Young KL, Fisher V, Deng X, Brody JA, Graff M, Lim E, Lin BM, Xu H, Amin N, An P, Aslibekyan S, Fohner AE, Hidalgo B, Lenzini P, Kraaij R, Medina-Gomez C, Prokić I, Rivadeneira F, Sitlani C, Tao R, van Rooij J, Zhang D, Broome JG, Buth EJ, Heavner BD, Jain D, Smith AV, Barnes K, Boorgula MP, Chavan S, Darbar D, De Andrade M, Guo X, Haessler J, Irvin MR, Kalyani RR, Kardia SLR, Kooperberg C, Kim W, Mathias RA, McDonald ML, Mitchell BD, Peyser PA, Regan EA, Redline S, Reiner AP, Rich SS, Rotter JI, Smith JA, Weiss S, Wiggins KL, Yanek LR, Arnett D, Heard-Costa NL, Leal S, Lin D, McKnight B, Province M, van Duijn CM, North KE, Cupples LA, Liu CT. Whole-exome sequence analysis of anthropometric traits illustrates challenges in identifying effects of rare genetic variants. HGG ADVANCES 2023; 4:100163. [PMID: 36568030 PMCID: PMC9772568 DOI: 10.1016/j.xhgg.2022.100163] [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: 08/01/2022] [Accepted: 11/22/2022] [Indexed: 11/26/2022] Open
Abstract
Anthropometric traits, measuring body size and shape, are highly heritable and significant clinical risk factors for cardiometabolic disorders. These traits have been extensively studied in genome-wide association studies (GWASs), with hundreds of genome-wide significant loci identified. We performed a whole-exome sequence analysis of the genetics of height, body mass index (BMI) and waist/hip ratio (WHR). We meta-analyzed single-variant and gene-based associations of whole-exome sequence variation with height, BMI, and WHR in up to 22,004 individuals, and we assessed replication of our findings in up to 16,418 individuals from 10 independent cohorts from Trans-Omics for Precision Medicine (TOPMed). We identified four trait associations with single-nucleotide variants (SNVs; two for height and two for BMI) and replicated the LECT2 gene association with height. Our expression quantitative trait locus (eQTL) analysis within previously reported GWAS loci implicated CEP63 and RFT1 as potential functional genes for known height loci. We further assessed enrichment of SNVs, which were monogenic or syndromic variants within loci associated with our three traits. This led to the significant enrichment results for height, whereas we observed no Bonferroni-corrected significance for all SNVs. With a sample size of ∼20,000 whole-exome sequences in our discovery dataset, our findings demonstrate the importance of genomic sequencing in genetic association studies, yet they also illustrate the challenges in identifying effects of rare genetic variants.
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Affiliation(s)
- Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Virginia Fisher
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Xuan Deng
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Misa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Elise Lim
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Bridget M Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Hanfei Xu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Ping An
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Alison E Fohner
- Department of Epidemiology, University of Washington, Seattle, WA 98101, USA.,Institute for Public Health Genetics, University of Washington, Seattle, WA 98101, USA
| | - Bertha Hidalgo
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Petra Lenzini
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Ivana Prokić
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Colleen Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Di Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jai G Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA.,Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Erin J Buth
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Benjamin D Heavner
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Kathleen Barnes
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.,Tempus Labs, Chicago, IL 60654, USA
| | - Meher Preethi Boorgula
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sameer Chavan
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Dawood Darbar
- Division of Cardiology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Mariza De Andrade
- Health Quantitative Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rita R Kalyani
- Division of Endocrinology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wonji Kim
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Merry-Lynn McDonald
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Patricia A Peyser
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | | | - Susan Redline
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98101, USA.,Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Scott Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kerri L Wiggins
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Donna Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
| | | | - Suzanne Leal
- Department of Neurology, Columbia University, New York City, NY, USA
| | - Danyu Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Michael Province
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - L Adrienne Cupples
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Ching-Ti Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
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5
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Molecular Biology Networks and Key Gene Regulators for Inflammatory Biomarkers Shared by Breast Cancer Development: Multi-Omics Systems Analysis. Biomolecules 2021; 11:biom11091379. [PMID: 34572592 PMCID: PMC8469138 DOI: 10.3390/biom11091379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 11/17/2022] Open
Abstract
As key inflammatory biomarkers C-reactive protein (CRP) and interleukin-6 (IL6) play an important role in the pathogenesis of non-inflammatory diseases, including specific cancers, such as breast cancer (BC). Previous genome-wide association studies (GWASs) have neither explained the large proportion of genetic heritability nor provided comprehensive understanding of the underlying regulatory mechanisms. We adopted an integrative genomic network approach by incorporating our previous GWAS data for CRP and IL6 with multi-omics datasets, such as whole-blood expression quantitative loci, molecular biologic pathways, and gene regulatory networks to capture the full range of genetic functionalities associated with CRP/IL6 and tissue-specific key drivers (KDs) in gene subnetworks. We applied another systematic genomics approach for BC development to detect shared gene sets in enriched subnetworks across BC and CRP/IL6. We detected the topmost significant common pathways across CRP/IL6 (e.g., immune regulatory; chemokines and their receptors; interferon γ, JAK-STAT, and ERBB4 signaling), several of which overlapped with BC pathways. Further, in gene–gene interaction networks enriched by those topmost pathways, we identified KDs—both well-established (e.g., JAK1/2/3, STAT3) and novel (e.g., CXCR3, CD3D, CD3G, STAT6)—in a tissue-specific manner, for mechanisms shared in regulating CRP/IL6 and BC risk. Our study may provide robust, comprehensive insights into the mechanisms of CRP/IL6 regulation and highlight potential novel genetic targets as preventive and therapeutic strategies for associated disorders, such as BC.
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Jung SY, Yu H, Pellegrini M, Papp JC, Sobel EM, Zhang ZF. Genetically determined elevated C-reactive protein associated with primary colorectal cancer risk: Mendelian randomization with lifestyle interactions. Am J Cancer Res 2021; 11:1733-1753. [PMID: 33948386 PMCID: PMC8085861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/11/2021] [Indexed: 06/12/2023] Open
Abstract
Systemic inflammation-related etiologic pathways via inflammatory cytokines in the development of colorectal cancer (CRC) have not been convincingly determined and may be confounded by lifestyle factors or reverse causality. We investigated the genetically predicted C-reactive protein (CRP) phenotype in the potential causal pathway of primary CRC risk in postmenopausal women in a Mendelian randomization (MR) framework. We employed individual-level data of the Women's Health Initiative Database for Genotypes and Phenotypes Study, which consists of 5 genome-wide association (GWA) studies, including 10,142 women, 737 of whom developed primary CRC. We examined 61 GWA single-nucleotide polymorphisms (SNPs) associated with CRP by using weighted/penalized MR weighted-medians and MR gene-environment interactions that allow some relaxation of the strict variable requirements and attenuate the heterogeneous estimates of outlying SNPs. In lifestyle-stratification analyses, genetically determined CRP exhibited its effects on the decreased CRC risk in non-viscerally obese and high-fat diet subgroups. In contrast, genetically driven CRP was associated with an increased risk for CRC in women who smoked ≥ 15 cigarettes/day, with significant interaction of the gene-smoking relationship. Further, a substantially increased risk of CRC induced by CRP was observed in relatively short-term users (< 5 years) of estrogen (E)-only and also longer-term users (5 to > 10 years) of E plus progestin. Our findings may provide novel evidence on immune-related etiologic pathways connected to CRC risk and suggest the possible use of CRP as a CRC-predictive biomarker in women with particular behaviors and CRP marker-informed interventions to reduce CRC risk.
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Affiliation(s)
- Su Yon Jung
- Translational Sciences Section, Jonsson Comprehensive Cancer Center, School of Nursing, University of CaliforniaLos Angeles, CA 90095, USA
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer CenterHonolulu, HI 96813, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, Life Sciences Division, University of CaliforniaLos Angeles, CA 90095, USA
| | - Jeanette C Papp
- Department of Human Genetics, David Geffen School of Medicine, University of CaliforniaLos Angeles, CA 90095, USA
| | - Eric M Sobel
- Department of Human Genetics, David Geffen School of Medicine, University of CaliforniaLos Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of CaliforniaLos Angeles, CA 90095, USA
| | - Zuo-Feng Zhang
- Department of Epidemiology, Fielding School of Public Health, University of CaliforniaLos Angeles, CA 90095, USA
- Center for Human Nutrition, David Geffen School of Medicine, University of CaliforniaLos Angeles, CA 90095, USA
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7
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Jung SY, Papp JC, Sobel EM, Pellegrini M, Yu H, Zhang ZF. Genetically Predicted C-Reactive Protein Associated With Postmenopausal Breast Cancer Risk: Interrelation With Estrogen and Cancer Molecular Subtypes Using Mendelian Randomization. Front Oncol 2021; 10:630994. [PMID: 33614510 PMCID: PMC7888276 DOI: 10.3389/fonc.2020.630994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 12/21/2020] [Indexed: 12/14/2022] Open
Abstract
Background Immune-related etiologic pathways that influence breast cancer risk are incompletely understood and may be confounded by lifestyles or reverse causality. Using a Mendelian randomization (MR) approach, we investigated the potential causal relationship between genetically elevated C-reactive protein (CRP) concentrations and primary invasive breast cancer risk in postmenopausal women. Methods We used individual-level data obtained from 10,179 women, including 537 who developed breast cancer, from the Women’s Health Initiative Database for Genotypes and Phenotypes Study, which consists of five genome-wide association (GWA) studies. We examined 61 GWA single-nucleotide polymorphisms (SNPs) previously associated with CRP. We employed weighted/penalized weighted–medians and MR gene–environment interactions that allow instruments’ invalidity to some extent and attenuate the heterogeneous estimates of outlying SNPs. Results In lifestyle-stratification analyses, genetically elevated CRP decreased risk for breast cancer in exogenous estrogen-only, estrogen + progestin, and past oral contraceptive (OC) users, but only among relatively short-term users (<5 years). Estrogen-only users for ≥5 years had more profound CRP-decreased breast cancer risk in dose–response fashion, whereas past OC users for ≥5 years had CRP-increased cancer risk. Also, genetically predicted CRP was strongly associated with increased risk for hormone-receptor positive or human epidermal growth factor receptor-2 negative breast cancer. Conclusions Our findings may provide novel evidence on the immune-related molecular pathways linking to breast cancer risk and suggest potential clinical use of CRP to predict the specific cancer subtypes. Our findings suggest potential interventions targeting CRP–inflammatory markers to reduce breast cancer risk.
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Affiliation(s)
- Su Yon Jung
- Translational Sciences Section, Jonsson Comprehensive Cancer Center, School of Nursing, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jeanette C Papp
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Eric M Sobel
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, Life Sciences Division, University of California, Los Angeles, Los Angeles, CA, United States
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, United States
| | - Zuo-Feng Zhang
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, United States.,Center for Human Nutrition, David Geffen School of Medicine, University of California, Los Angeles, CA, United States
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8
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Jung SY, Papp JC, Sobel EM, Pellegrini M, Yu H, Zhang ZF. Pro-inflammatory cytokine polymorphisms and interactions with dietary alcohol and estrogen, risk factors for invasive breast cancer using a post genome-wide analysis for gene-gene and gene-lifestyle interaction. Sci Rep 2021; 11:1058. [PMID: 33441805 PMCID: PMC7807068 DOI: 10.1038/s41598-020-80197-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/17/2020] [Indexed: 11/13/2022] Open
Abstract
Molecular and genetic immune-related pathways connected to breast cancer and lifestyles in postmenopausal women are not fully characterized. In this study, we explored the role of pro-inflammatory cytokines such as C-reactive protein (CRP) and interleukin-6 (IL-6) in those pathways at the genome-wide level. With single-nucleotide polymorphisms (SNPs) in the biomarkers and lifestyles together, we further constructed risk profiles to improve predictability for breast cancer. Our earlier genome-wide association gene-environment interaction study used large cohort data from the Women's Health Initiative Database for Genotypes and Phenotypes Study and identified 88 SNPs associated with CRP and IL-6. For this study, we added an additional 68 SNPs from previous GWA studies, and together with 48 selected lifestyles, evaluated for the association with breast cancer risk via a 2-stage multimodal random survival forest and generalized multifactor dimensionality reduction methods. Overall and in obesity strata (by body mass index, waist, waist-to-hip ratio, exercise, and dietary fat intake), we identified the most predictive genetic and lifestyle variables. Two SNPs (SALL1 rs10521222 and HLA-DQA1 rs9271608) and lifestyles, including alcohol intake, lifetime cumulative exposure to estrogen, and overall and visceral obesity, are the most common and strongest predictive markers for breast cancer across the analyses. The risk profile that combined those variables presented their synergistic effect on the increased breast cancer risk in a gene-lifestyle dose-dependent manner. Our study may contribute to improved predictability for breast cancer and suggest potential interventions for the women with the risk genotypes and lifestyles to reduce their breast cancer risk.
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Affiliation(s)
- Su Yon Jung
- Translational Sciences Section, Jonsson Comprehensive Cancer Center, School of Nursing, University of California, Los Angeles, 700 Tiverton Ave, 3-264 Factor Building, Los Angeles, CA, 90095, USA.
| | - Jeanette C Papp
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Eric M Sobel
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, Life Sciences Division, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Zuo-Feng Zhang
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Center for Human Nutrition, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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Alfaddagh A, Martin SS, Leucker TM, Michos ED, Blaha MJ, Lowenstein CJ, Jones SR, Toth PP. Inflammation and cardiovascular disease: From mechanisms to therapeutics. Am J Prev Cardiol 2020; 4:100130. [PMID: 34327481 PMCID: PMC8315628 DOI: 10.1016/j.ajpc.2020.100130] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/14/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
Inflammation constitutes a complex, highly conserved cascade of molecular and cellular events. Inflammation has been labeled as “the fire within,” is highly regulated, and is critical to host defense and tissue repair. In general, inflammation is beneficial and has evolved to promote survival. However, inflammation can also be maladaptive when chronically activated and sustained, leading to progressive tissue injury and reduced survival. Examples of a maladaptive response include rheumatologic disease and atherosclerosis. Despite evidence gathered by Virchow over 100 years ago showing that inflammatory white cells play a role in atherogenesis, atherosclerosis was until recently viewed as a disease of passive cholesterol accumulation in the subendothelial space. This view has been supplanted by considerable basic scientific and clinical evidence demonstrating that every step of atherogenesis, from the development of endothelial cell dysfunction to foam cell formation, plaque formation and progression, and ultimately plaque rupture stemming from architectural instability, is driven by the cytokines, interleukins, and cellular constituents of the inflammatory response. Herein we provide an overview of the role of inflammation in atherosclerotic cardiovascular disease, discuss the predictive value of various biomarkers involved in inflammation, and summarize recent clinical trials that evaluated the capacity of various pharmacologic interventions to attenuate the intensity of inflammation and impact risk for acute cardiovascular events.
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Affiliation(s)
- Abdulhamied Alfaddagh
- Ciccarone Center for the Prevention of Cardiovascular Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Seth S Martin
- Ciccarone Center for the Prevention of Cardiovascular Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thorsten M Leucker
- Ciccarone Center for the Prevention of Cardiovascular Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Erin D Michos
- Ciccarone Center for the Prevention of Cardiovascular Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael J Blaha
- Ciccarone Center for the Prevention of Cardiovascular Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Charles J Lowenstein
- Ciccarone Center for the Prevention of Cardiovascular Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steven R Jones
- Ciccarone Center for the Prevention of Cardiovascular Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter P Toth
- Ciccarone Center for the Prevention of Cardiovascular Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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10
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Jung SY, Papp JC, Sobel EM, Pellegrini M, Yu H, Zhang ZF. Pro-inflammatory cytokine polymorphisms in ONECUT2 and HNF4A and primary colorectal carcinoma: a post genome-wide gene-lifestyle interaction study. Am J Cancer Res 2020; 10:2955-2976. [PMID: 33042629 PMCID: PMC7539781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023] Open
Abstract
Immune-related molecular and genetic pathways that are connected to colorectal cancer (CRC) and lifestyles in postmenopausal women are incompletely characterized. In this study, we examined the role of pro-inflammatory biomarkers such as C-reactive protein (CRP) and interleukin-6 (IL-6) in those pathways. Through selection of the best predictive single-nucleotide polymorphisms (SNPs) and lifestyles, our goal was to improve the prediction accuracy and ability for CRC risk. Using large cohort data of postmenopausal women from the Women's Health Initiative Database for Genotypes and Phenotypes Study, we previously conducted a genome-wide association (GWA) for a CRP and IL-6 gene-behavioral interaction study. For the present study, we added GWA-SNPs from outside GWA studies, resulting in a total of 152 SNPs. Together with 41 selected lifestyles, we performed a 2-stage multimodal random survival forest analysis with generalized multifactor dimensionality reduction approach to construct CRC risk profiles. Overall and in obesity strata (by body mass index, waist circumference, waist-to-hip ratio, exercise, and dietary fat intake), we identified the best predictive genetic markers in inflammatory cytokines and lifestyles. Across the strata, 2 SNPs (ONECUT2 rs4092465 and HNF4A rs1800961) and 1 lifestyle factor (relatively short-term past use of oral contraceptives) were the most common and strongest predictive markers for CRC risk. The risk profile that combined those variables exhibited synergistically increased risk for CRC; this pattern appeared more strongly in obese and inactive subgroups. Our results may contribute to improved predictability for CRC and suggest genetically targeted lifestyle interventions for women carrying the inflammatory-risk genotypes, reducing CRC risk.
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Affiliation(s)
- Su Yon Jung
- Translational Sciences Section, Jonsson Comprehensive Cancer Center, School of Nursing, University of CaliforniaLos Angeles, CA 90095, USA
| | - Jeanette C Papp
- Department of Human Genetics, David Geffen School of Medicine, University of CaliforniaLos Angeles, CA 90095, USA
| | - Eric M Sobel
- Department of Human Genetics, David Geffen School of Medicine, University of CaliforniaLos Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of CaliforniaLos Angeles, CA 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, Life Sciences Division, University of CaliforniaLos Angeles, CA 90095, USA
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer CenterHonolulu, HI 96813, USA
| | - Zuo-Feng Zhang
- Department of Epidemiology, Fielding School of Public Health, University of CaliforniaLos Angeles, CA 90095, USA
- Center for Human Nutrition, David Geffen School of Medicine, University of CaliforniaLos Angeles, CA 90095, USA
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11
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Tang W, Stimson MR, Basu S, Heckbert SR, Cushman M, Pankow JS, Folsom AR, Pankratz N. Burden of rare exome sequence variants in PROC gene is associated with venous thromboembolism: a population-based study. J Thromb Haemost 2020; 18:445-453. [PMID: 31680443 PMCID: PMC7787541 DOI: 10.1111/jth.14676] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/13/2019] [Accepted: 10/30/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Rare coding mutations underlying deficiencies of antithrombin and proteins C and S contribute to familial venous thromboembolism (VTE). It is uncertain whether rare variants play a role in the etiology of VTE in the general population. OBJECTIVES We conducted a deep whole-exome sequencing (WES) study to investigate the associations between rare coding variants and the risk of VTE in two population-based prospective cohorts. PATIENTS/METHODS Whole-exome sequencing was performed in the Longitudinal Investigation of Thromboembolism Etiology (LITE), which combines the Atherosclerosis Risk in Communities (ARIC) study (316 incident VTE events among 3159 African Americans [AAs] and 458 incident VTEs among 7772 European Americans [EAs]) and the Cardiovascular Healthy Study (CHS; 60 incident VTEs among 1751 EAs). We performed gene-based tests of rare variants (allele frequency < 1%, exome-wide significance P < 1.47 × 10-6 ) separately in each study and ancestry group, and meta-analyzed the results for the EAs in ARIC and CHS. RESULTS In the meta-analysis of EAs, we identified one gene, PROC, in which the burden of rare, coding variants was significantly associated with increased risk of VTE (HR = 5.42 [3.11, 9.42] for carriers versus non-carriers, P = 2.27 × 10-9 ). In ARIC EAs, carriers of the PROC rare variants had on average 0.75 standard deviation (SD) lower concentrations of plasma protein C and 0.28 SD higher D-dimer (P < .05) than non-carriers. Adjustment for low protein C status did not eliminate the association of PROC burden with VTE. In AAs, rare coding PROC variants were not associated with VTE. CONCLUSIONS Rare coding variants in PROC contribute to increased VTE risk in EAs in this general population sample.
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Affiliation(s)
- Weihong Tang
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States
| | - Mary Rachel Stimson
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis, Minnesota, United States
| | - Saonli Basu
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States
| | - Susan R. Heckbert
- Department of Epidemiology, University of Washington, Seattle, Washington, United States
| | - Mary Cushman
- Department of Pathology, University of Vermont, Burlington, Vermont, United States
| | - James S. Pankow
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States
| | - Aaron R. Folsom
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis, Minnesota, United States
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12
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Raffield LM, Iyengar AK, Wang B, Gaynor SM, Spracklen CN, Zhong X, Kowalski MH, Salimi S, Polfus LM, Benjamin EJ, Bis JC, Bowler R, Cade BE, Choi WJ, Comellas AP, Correa A, Cruz P, Doddapaneni H, Durda P, Gogarten SM, Jain D, Kim RW, Kral BG, Lange LA, Larson MG, Laurie C, Lee J, Lee S, Lewis JP, Metcalf GA, Mitchell BD, Momin Z, Muzny DM, Pankratz N, Park CJ, Rich SS, Rotter JI, Ryan K, Seo D, Tracy RP, Viaud-Martinez KA, Yanek LR, Zhao LP, Lin X, Li B, Li Y, Dupuis J, Reiner AP, Mohlke KL, Auer PL. Allelic Heterogeneity at the CRP Locus Identified by Whole-Genome Sequencing in Multi-ancestry Cohorts. Am J Hum Genet 2020; 106:112-120. [PMID: 31883642 PMCID: PMC7042494 DOI: 10.1016/j.ajhg.2019.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/02/2019] [Indexed: 12/19/2022] Open
Abstract
Whole-genome sequencing (WGS) can improve assessment of low-frequency and rare variants, particularly in non-European populations that have been underrepresented in existing genomic studies. The genetic determinants of C-reactive protein (CRP), a biomarker of chronic inflammation, have been extensively studied, with existing genome-wide association studies (GWASs) conducted in >200,000 individuals of European ancestry. In order to discover novel loci associated with CRP levels, we examined a multi-ancestry population (n = 23,279) with WGS (∼38× coverage) from the Trans-Omics for Precision Medicine (TOPMed) program. We found evidence for eight distinct associations at the CRP locus, including two variants that have not been identified previously (rs11265259 and rs181704186), both of which are non-coding and more common in individuals of African ancestry (∼10% and ∼1% minor allele frequency, respectively, and rare or monomorphic in 1000 Genomes populations of East Asian, South Asian, and European ancestry). We show that the minor (G) allele of rs181704186 is associated with lower CRP levels and decreased transcriptional activity and protein binding in vitro, providing a plausible molecular mechanism for this African ancestry-specific signal. The individuals homozygous for rs181704186-G have a mean CRP level of 0.23 mg/L, in contrast to individuals heterozygous for rs181704186 with mean CRP of 2.97 mg/L and major allele homozygotes with mean CRP of 4.11 mg/L. This study demonstrates the utility of WGS in multi-ethnic populations to drive discovery of complex trait associations of large effect and to identify functional alleles in noncoding regulatory regions.
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Affiliation(s)
- Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Apoorva K Iyengar
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Biqi Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Sheila M Gaynor
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Xue Zhong
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Madeline H Kowalski
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Shabnam Salimi
- Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Linda M Polfus
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Emelia J Benjamin
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA; Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA; National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Joshua C Bis
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA 98101, USA
| | - Russell Bowler
- Department of Medicine, Division of Pulmonary, Critical Care & Sleep Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Brian E Cade
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | - Alejandro P Comellas
- Department of Medicine, Division of Pulmonary and Critical Care, University of Iowa, Iowa City, IA 52242, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Pedro Cruz
- Illumina Laboratory Services, Illumina Inc., San Diego, CA 92122, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter Durda
- Department of Pathology & Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05446, USA
| | | | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | | | - Brian G Kral
- GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Leslie A Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Martin G Larson
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA; National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Jiwon Lee
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | - Joshua P Lewis
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD 21201, USA
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Kathleen Ryan
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | - Russell P Tracy
- Department of Pathology & Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05446, USA; Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, VT 05446, USA
| | | | - Lisa R Yanek
- GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lue Ping Zhao
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Statistics, Harvard University, Cambridge, MA 02138, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA; National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Paul L Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin Milwaukee, Milwaukee, WI 53205, USA.
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13
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Genetic analysis of hsCRP in American Indians: The Strong Heart Family Study. PLoS One 2019; 14:e0223574. [PMID: 31622379 PMCID: PMC6797125 DOI: 10.1371/journal.pone.0223574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023] Open
Abstract
Background Increased serum levels of C-reactive protein (CRP), an important component of the innate immune response, are associated with increased risk of cardiovascular disease (CVD). Multiple single nucleotide polymorphisms (SNP) have been identified which are associated with CRP levels, and Mendelian randomization studies have shown a positive association between SNPs increasing CRP expression and risk of colon cancer (but thus far not CVD). The effects of individual genetic variants often interact with the genetic background of a population and hence we sought to resolve the genetic determinants of serum CRP in a number of American Indian populations. Methods The Strong Heart Family Study (SHFS) has serum CRP measurements from 2428 tribal members, recruited as large families from three regions of the United States. Microsatellite markers and MetaboChip defined SNP genotypes were incorporated into variance components, decomposition-based linkage and association analyses. Results CRP levels exhibited significant heritability (h2 = 0.33 ± 0.05, p<1.3 X 10−20). A locus on chromosome (chr) 6, near marker D6S281 (approximately at 169.6 Mb, GRCh38/hg38) showed suggestive linkage (LOD = 1.9) to CRP levels. No individual SNPs were found associated with CRP levels after Bonferroni adjustment for multiple testing (threshold <7.77 x 10−7), however, we found nominal associations, many of which replicate previous findings at the CRP, HNF1A and 7 other loci. In addition, we report association of 46 SNPs located at 7 novel loci on chromosomes 2, 5, 6(2 loci), 9, 10 and 17, with an average of 15.3 Kb between SNPs and all with p-values less than 7.2 X 10−4. Conclusion In agreement with evidence from other populations, these data show CRP serum levels are under considerable genetic influence; and include loci, such as near CRP and other genes, that replicate results from other ethnic groups. These findings also suggest possible novel loci on chr 6 and other chromosomes that warrant further investigation.
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14
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Zhao L, He Z, Zhang D, Wang GT, Renton AE, Vardarajan BN, Nothnagel M, Goate AM, Mayeux R, Leal SM. A Rare Variant Nonparametric Linkage Method for Nuclear and Extended Pedigrees with Application to Late-Onset Alzheimer Disease via WGS Data. Am J Hum Genet 2019; 105:822-835. [PMID: 31585107 DOI: 10.1016/j.ajhg.2019.09.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 09/05/2019] [Indexed: 10/25/2022] Open
Abstract
To analyze family-based whole-genome sequence (WGS) data for complex traits, we developed a rare variant (RV) non-parametric linkage (NPL) analysis method, which has advantages over association methods. The RV-NPL differs from the NPL in that RVs are analyzed, and allele sharing among affected relative-pairs is estimated only for minor alleles. Analyzing families can increase power because causal variants with familial aggregation usually have larger effect sizes than those underlying sporadic diseases. Differing from association analysis, for NPL only affected individuals are analyzed, which can increase power, since unaffected family members can be susceptibility variant carriers. RV-NPL is robust to population substructure and admixture, inclusion of nonpathogenic variants, as well as allelic and locus heterogeneity and can readily be applied outside of coding regions. In contrast to analyzing common variants using NPL, where loci localize to large genomic regions (e.g., >50 Mb), mapped regions are well defined for RV-NPL. Using simulation studies, we demonstrate that RV-NPL is substantially more powerful than applying traditional NPL methods to analyze RVs. The RV-NPL was applied to analyze 107 late-onset Alzheimer disease (LOAD) pedigrees of Caribbean Hispanic and European ancestry with WGS data, and statistically significant linkage (LOD ≥ 3.8) was found with RVs in PSMF1 and PTPN21 which have been shown to be involved in LOAD etiology. Additionally, nominally significant linkage was observed with RVs in ABCA7, ACE, EPHA1, and SORL1, genes that were previously reported to be associated with LOAD. RV-NPL is an ideal method to elucidate the genetic etiology of complex familial diseases.
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15
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C-reactive protein gene 1846C>T polymorphism is associated with increased risk and clinical features of lung cancer: a case-control study. Biosci Rep 2019; 39:BSR20181936. [PMID: 31142628 PMCID: PMC6616045 DOI: 10.1042/bsr20181936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/18/2019] [Accepted: 05/23/2019] [Indexed: 12/13/2022] Open
Abstract
Chronic inflammation plays an important role in lung carcinogenesis. Recently, several studies investigated the association of C-reactive protein (CRP) gene 1846C>T polymorphism and lung cancer (LC) risk, but with conflicting findings. In the present study, we conducted this case-control study with 408 LC patients and 472 healthy controls in a Chinese Han population. Genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLR) method. Our data found that CRP gene 1846C>T polymorphism increased the risk of LC. Subgroup analyses obtained significant associations among the groups of males, ≥50 years old, smoking, and non-drinkers. Bioinformatics analysis showed that the expression levels of CRP in LC tissues were significantly increased compared with normal tissues. Additionally, the present study found CRP mRNA high expression was associated with worse survival in LC patients. Furthermore, our data indicated that TT genotype of 1846C>T polymorphism was associated with a larger size of tumor and was related with lymphatic metastasis in LC patients. In conclusion, the present study suggests that CRP gene 1846C>T polymorphism is associated with increased risk of LC. CRP gene 1846C>T polymorphism may be a potential marker for the diagnosis of LC.
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16
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Ducat A, Vargas A, Doridot L, Bagattin A, Lerner J, Vilotte JL, Buffat C, Pontoglio M, Miralles F, Vaiman D. Low-dose aspirin protective effects are correlated with deregulation of HNF factor expression in the preeclamptic placentas from mice and humans. Cell Death Discov 2019; 5:94. [PMID: 31098302 PMCID: PMC6510804 DOI: 10.1038/s41420-019-0170-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/21/2019] [Accepted: 03/28/2019] [Indexed: 01/07/2023] Open
Abstract
Aspirin (acetyl-salicylic acid) is one of the most ancient drugs of the human pharmacopeia. Nonetheless, its action at low doses is not well understood at the molecular level. One of the applications of low-dose aspirin treatment is the prevention of preeclampsia (PE) in patients at risk. Foeto-placental overexpression of the STOX1A transcription factor in mice triggers PE symptoms. Transcriptomic analysis of the placentas, showed that aspirin massively down-regulates genes of the coagulation and complement cascade, as well as genes involved in lipid transport. The genes modified by aspirin treatment are not the ones that are modified by STOX1 overexpression, suggesting that aspirin could act downstream, symptomatically on the preeclamptic disease. Bioinformatics analysis of the promoters of the deregulated genes showed that they are strongly enriched in HNF transcription factors-binding sites, in accordance with existing literature showing their roles as regulators of coagulation. Two of these transcription factors, Hnf1β and Hnf4α are found down-regulated by aspirin treatment. In parallel, we show that in human patient placentas, aspirin-induced deregulations of genes of the coagulation cascade are also observed. Finally, the expression of Hnf1β target sequences (Kif12, F2, Hnf4α promoters and a synthetic concatemer of the Hnf1β-binding site) were investigated by transfection in trophoblast cell models, with or without aspirin treatment and with or without STOX1A overexpression. In this model we observed that STOX1A and aspirin tended to synergize in the down-regulation of Hnf1β target genes in trophoblasts.
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Affiliation(s)
- Aurélien Ducat
- Institut Cochin, INSERM U1016, UMR 8104 CNRS, Faculté René Descartes, 24 rue du Faubourg St Jacques, 75014 Paris, France
| | - Alexandra Vargas
- Institut Cochin, INSERM U1016, UMR 8104 CNRS, Faculté René Descartes, 24 rue du Faubourg St Jacques, 75014 Paris, France.,2Epigenetics and Cell Signaling, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
| | - Ludivine Doridot
- Institut Cochin, INSERM U1016, UMR 8104 CNRS, Faculté René Descartes, 24 rue du Faubourg St Jacques, 75014 Paris, France
| | - Alessia Bagattin
- Institut Cochin, INSERM U1016, UMR 8104 CNRS, Faculté René Descartes, 24 rue du Faubourg St Jacques, 75014 Paris, France
| | - Jonathan Lerner
- Institut Cochin, INSERM U1016, UMR 8104 CNRS, Faculté René Descartes, 24 rue du Faubourg St Jacques, 75014 Paris, France
| | - Jean-Luc Vilotte
- 3GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352 Jouy-en-Josas, France
| | - Christophe Buffat
- 4Department of Neonatology, Hôpital La Conception, 147 Boulevard Baille, 13005 Marseille, France
| | - Marco Pontoglio
- Institut Cochin, INSERM U1016, UMR 8104 CNRS, Faculté René Descartes, 24 rue du Faubourg St Jacques, 75014 Paris, France
| | - Francisco Miralles
- Institut Cochin, INSERM U1016, UMR 8104 CNRS, Faculté René Descartes, 24 rue du Faubourg St Jacques, 75014 Paris, France
| | - Daniel Vaiman
- Institut Cochin, INSERM U1016, UMR 8104 CNRS, Faculté René Descartes, 24 rue du Faubourg St Jacques, 75014 Paris, France
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17
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Martiskainen H, Takalo M, Solomon A, Stančáková A, Marttinen M, Natunen T, Haapasalo A, Herukka SK, Kuusisto J, Soininen H, Kivipelto M, Laakso M, Hiltunen M. Decreased plasma C-reactive protein levels in APOE ε4 allele carriers. Ann Clin Transl Neurol 2018; 5:1229-1240. [PMID: 30349858 PMCID: PMC6186931 DOI: 10.1002/acn3.639] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 02/06/2023] Open
Abstract
Objective Apolipoprotein E (APOE) ε4 allele is a well‐established risk factor in Alzheimer's disease (AD). Here, we assessed the effects of APOE polymorphism on cardiovascular, metabolic, and inflammation‐related parameters in population‐based cohorts. Methods Association of cardiovascular, metabolic, and inflammation‐related parameters with the APOE polymorphism in a large Finnish Metabolic Syndrome in Men (METSIM) cohort and Finnish Geriatric Intervention study to prevent cognitive impairment and disability (FINGER) were investigated. Brain‐specific effects were addressed in postmortem brain samples. Results Individuals carrying the APOE ε4 allele displayed significantly elevated serum/plasma LDL cholesterol and apolipoprotein B levels. APOE ε3ε4 and ε4ε4 significantly associated with lower levels of plasma high‐sensitivity C‐reactive protein (hs‐CRP). Plasma amyloid‐β 42 (Aβ42) and reduced hs‐CRP levels showed an association independently of the APOE status. Interpretation These data suggest that the APOE ε4 allele associates with lower levels of hs‐CRP in individuals without dementia. Moreover, Aβ42 may encompass anti‐inflammatory effects reflected by reduced hs‐CRP levels.
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Affiliation(s)
- Henna Martiskainen
- Institute of Clinical Medicine Internal Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland
| | - Mari Takalo
- Institute of Biomedicine University of Eastern Finland Yliopistonranta 1 E, P.O. Box 1627 Kuopio 70211 Finland
| | - Alina Solomon
- Department of Neurology Institute of Clinical Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland.,Division of Clinical Geriatrics Center for Alzheimer Research NVS, Karolinska Institutet Novum 5th floor Huddinge 14157 Sweden
| | - Alena Stančáková
- Institute of Clinical Medicine Internal Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland
| | - Mikael Marttinen
- Institute of Biomedicine University of Eastern Finland Yliopistonranta 1 E, P.O. Box 1627 Kuopio 70211 Finland
| | - Teemu Natunen
- Institute of Biomedicine University of Eastern Finland Yliopistonranta 1 E, P.O. Box 1627 Kuopio 70211 Finland
| | - Annakaisa Haapasalo
- A.I Virtanen Institute for Molecular Sciences University of Eastern Finland Neulaniementie 2 Kuopio 70211 Finland
| | - Sanna-Kaisa Herukka
- Department of Neurology Institute of Clinical Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland.,Neurocenter Neurology Kuopio University Hospital Kuopio Finland
| | - Johanna Kuusisto
- Institute of Clinical Medicine Internal Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland.,Kuopio University Hospital Kuopio Finland
| | - Hilkka Soininen
- Department of Neurology Institute of Clinical Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland.,Neurocenter Neurology Kuopio University Hospital Kuopio Finland
| | - Miia Kivipelto
- Department of Neurology Institute of Clinical Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland.,Division of Clinical Geriatrics Center for Alzheimer Research NVS, Karolinska Institutet Novum 5th floor Huddinge 14157 Sweden.,Department of Public Health Solutions Public Health Promotion Unit National Institute for Health and Welfare PO Box 30 Helsinki 00271 Finland
| | - Markku Laakso
- Institute of Clinical Medicine Internal Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland.,Kuopio University Hospital Kuopio Finland
| | - Mikko Hiltunen
- Institute of Biomedicine University of Eastern Finland Yliopistonranta 1 E, P.O. Box 1627 Kuopio 70211 Finland
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18
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Kocarnik JM, Richard M, Graff M, Haessler J, Bien S, Carlson C, Carty CL, Reiner AP, Avery CL, Ballantyne CM, LaCroix AZ, Assimes TL, Barbalic M, Pankratz N, Tang W, Tao R, Chen D, Talavera GA, Daviglus ML, Chirinos-Medina DA, Pereira R, Nishimura K, Bůžková P, Best LG, Ambite JL, Cheng I, Crawford DC, Hindorff LA, Fornage M, Heiss G, North KE, Haiman CA, Peters U, Le Marchand L, Kooperberg C. Discovery, fine-mapping, and conditional analyses of genetic variants associated with C-reactive protein in multiethnic populations using the Metabochip in the Population Architecture using Genomics and Epidemiology (PAGE) study. Hum Mol Genet 2018; 27:2940-2953. [PMID: 29878111 PMCID: PMC6077792 DOI: 10.1093/hmg/ddy211] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/02/2018] [Accepted: 05/28/2018] [Indexed: 12/11/2022] Open
Abstract
C-reactive protein (CRP) is a circulating biomarker indicative of systemic inflammation. We aimed to evaluate genetic associations with CRP levels among non-European-ancestry populations through discovery, fine-mapping and conditional analyses. A total of 30 503 non-European-ancestry participants from 6 studies participating in the Population Architecture using Genomics and Epidemiology study had serum high-sensitivity CRP measurements and ∼200 000 single nucleotide polymorphisms (SNPs) genotyped on the Metabochip. We evaluated the association between each SNP and log-transformed CRP levels using multivariate linear regression, with additive genetic models adjusted for age, sex, the first four principal components of genetic ancestry, and study-specific factors. Differential linkage disequilibrium patterns between race/ethnicity groups were used to fine-map regions associated with CRP levels. Conditional analyses evaluated for multiple independent signals within genetic regions. One hundred and sixty-three unique variants in 12 loci in overall or race/ethnicity-stratified Metabochip-wide scans reached a Bonferroni-corrected P-value <2.5E-7. Three loci have no (HACL1, OLFML2B) or only limited (PLA2G6) previous associations with CRP levels. Six loci had different top hits in race/ethnicity-specific versus overall analyses. Fine-mapping refined the signal in six loci, particularly in HNF1A. Conditional analyses provided evidence for secondary signals in LEPR, IL1RN and HNF1A, and for multiple independent signals in CRP and APOE. We identified novel variants and loci associated with CRP levels, generalized known CRP associations to a multiethnic study population, refined association signals at several loci and found evidence for multiple independent signals at several well-known loci. This study demonstrates the benefit of conducting inclusive genetic association studies in large multiethnic populations.
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Affiliation(s)
- Jonathan M Kocarnik
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Institute of Translational Health Sciences, University of Washington, Seattle, WA, USA
| | - Melissa Richard
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Misa Graff
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Jeffrey Haessler
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephanie Bien
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chris Carlson
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Alexander P Reiner
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christy L Avery
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Christie M Ballantyne
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Andrea Z LaCroix
- Department of Epidemiology, University of San Diego, San Diego, CA, USA
| | | | - Maja Barbalic
- Division of Epidemiology, Human Genetics & Environmental Sciences, The University of Texas, Houston, TX, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Weihong Tang
- Division of Epidemiology & Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dongquan Chen
- Division of Preventive Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gregory A Talavera
- Division of Health Promotion and Behavioral Science, San Diego State University, San Diego, CA, USA
| | - Martha L Daviglus
- Institute for Minority Health Research, University of Illinois College of Medicine, Chicago, IL, USA
| | - Diana A Chirinos-Medina
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Rocio Pereira
- Division of Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katie Nishimura
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Petra Bůžková
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Lyle G Best
- Missouri Breaks Industries Research, Inc., Eagle Butte, SD, USA
| | - José Luis Ambite
- Information Sciences Institute, University of Southern California, Marina del Rey, CA, USA
| | - Iona Cheng
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Dana C Crawford
- Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, TX, USA
| | - Gerardo Heiss
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ulrike Peters
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Charles Kooperberg
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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19
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Nesic MJ, Maric NP. Population-based differences in immune system response contribute to an increased risk of schizophrenia in African migrants? Rev Neurosci 2018; 29:347-353. [PMID: 29150991 DOI: 10.1515/revneuro-2017-0037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/05/2017] [Indexed: 11/15/2022]
Abstract
Among the highest incidences of schizophrenia is the one documented in second-generation migrants of African descent in the Western countries. Interestingly, people of African and European ancestry demonstrate significant genetic-based differences in immune system regulation and response. As a result, the pro-inflammatory phenotype is more pronounced in people of African descent than it is in Europeans. At the same time, the role of the immune system in the etiology of schizophrenia is gaining increased recognition. Here, we propose that the population-specific genetic variation within the immune system interacts with unfavourable environments to contribute to a higher risk of schizophrenia in people of African ancestry. Our hypothesis is supported by recent findings from two separate fields of research-population genetics and psychoneuroimmunology. Moreover, we highlight the need to include African populations in genetic studies of schizophrenia.
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Affiliation(s)
- Milica J Nesic
- Clinic for Psychiatry, Clinical Centre of Serbia, Pasterova 2, 11000 Belgrade, Serbia
| | - Nadja P Maric
- Clinic for Psychiatry, Clinical Centre of Serbia, Pasterova 2, 11000 Belgrade, Serbia
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20
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Carnethon MR, Pu J, Howard G, Albert MA, Anderson CAM, Bertoni AG, Mujahid MS, Palaniappan L, Taylor HA, Willis M, Yancy CW. Cardiovascular Health in African Americans: A Scientific Statement From the American Heart Association. Circulation 2017; 136:e393-e423. [PMID: 29061565 DOI: 10.1161/cir.0000000000000534] [Citation(s) in RCA: 645] [Impact Index Per Article: 92.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND PURPOSE Population-wide reductions in cardiovascular disease incidence and mortality have not been shared equally by African Americans. The burden of cardiovascular disease in the African American community remains high and is a primary cause of disparities in life expectancy between African Americans and whites. The objectives of the present scientific statement are to describe cardiovascular health in African Americans and to highlight unique considerations for disease prevention and management. METHOD The primary sources of information were identified with PubMed/Medline and online sources from the Centers for Disease Control and Prevention. RESULTS The higher prevalence of traditional cardiovascular risk factors (eg, hypertension, diabetes mellitus, obesity, and atherosclerotic cardiovascular risk) underlies the relatively earlier age of onset of cardiovascular diseases among African Americans. Hypertension in particular is highly prevalent among African Americans and contributes directly to the notable disparities in stroke, heart failure, and peripheral artery disease among African Americans. Despite the availability of effective pharmacotherapies and indications for some tailored pharmacotherapies for African Americans (eg, heart failure medications), disease management is less effective among African Americans, yielding higher mortality. Explanations for these persistent disparities in cardiovascular disease are multifactorial and span from the individual level to the social environment. CONCLUSIONS The strategies needed to promote equity in the cardiovascular health of African Americans require input from a broad set of stakeholders, including clinicians and researchers from across multiple disciplines.
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21
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Mahlman M, Karjalainen MK, Huusko JM, Andersson S, Kari MA, Tammela OKT, Sankilampi U, Lehtonen L, Marttila RH, Bassler D, Poets CF, Lacaze-Masmonteil T, Danan C, Delacourt C, Palotie A, Muglia LJ, Lavoie PM, Hadchouel A, Rämet M, Hallman M. Genome-wide association study of bronchopulmonary dysplasia: a potential role for variants near the CRP gene. Sci Rep 2017; 7:9271. [PMID: 28839172 PMCID: PMC5571168 DOI: 10.1038/s41598-017-08977-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/20/2017] [Indexed: 11/28/2022] Open
Abstract
Bronchopulmonary dysplasia (BPD), the main consequence of prematurity, has a significant heritability, but little is known about predisposing genes. The aim of this study was to identify gene loci predisposing infants to BPD. The initial genome-wide association study (GWAS) included 174 Finnish preterm infants of gestational age 24–30 weeks. Thereafter, the most promising single-nucleotide polymorphisms (SNPs) associated with BPD were genotyped in both Finnish (n = 555) and non-Finnish (n = 388) replication cohorts. Finally, plasma CRP levels from the first week of life and the risk of BPD were assessed. SNP rs11265269, flanking the CRP gene, showed the strongest signal in GWAS (odds ratio [OR] 3.2, p = 3.4 × 10−6). This association was nominally replicated in Finnish and French African populations. A number of other SNPs in the CRP region, including rs3093059, had nominal associations with BPD. During the first week of life the elevated plasma levels of CRP predicted the risk of BPD (OR 3.4, p = 2.9 × 10–4) and the SNP rs3093059 associated nominally with plasma CRP levels. Finally, SNP rs11265269 was identified as a risk factor of BPD (OR 1.8, p = 5.3 × 10−5), independently of the robust antenatal risk factors. As such, in BPD, a potential role for variants near CRP gene is proposed.
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Affiliation(s)
- Mari Mahlman
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, Oulu, Finland. .,Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland.
| | - Minna K Karjalainen
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Johanna M Huusko
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland.,Perinatal Institute, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Sture Andersson
- Children's Hospital, University of Helsinki, and Helsinki University Hospital, Helsinki, Finland
| | - M Anneli Kari
- Children's Hospital, University of Helsinki, and Helsinki University Hospital, Helsinki, Finland
| | - Outi K T Tammela
- Tampere University Hospital, Tampere University, and Center of Pediatric Child Health, Tampere, Finland
| | - Ulla Sankilampi
- Department of Pediatrics, Kuopio University Hospital, Kuopio, Finland
| | - Liisa Lehtonen
- Turku University Hospital, and the University of Turku, Turku, Finland
| | - Riitta H Marttila
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Dirk Bassler
- Department of Neonatology, University Hospital Zurich, and University of Zurich, Zurich, Switzerland
| | - Christian F Poets
- Department of Neonatology, Tuebingen University Hospital, Tuebingen, Germany
| | | | - Claude Danan
- Inserm, U955, Créteil, France.,CRB, CHI-Creteil, France.,Department of neonatology, CHI-Creteil, Creteil, France
| | - Christophe Delacourt
- Inserm, U955, Créteil, France.,AP-HP, Hôpital Necker-Enfants Malades, Service de Pneumologie Pédiatrique, Paris, France.,Université Paris-Descartes, Paris, France
| | - Aarno Palotie
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.,Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Louis J Muglia
- Perinatal Institute, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Pascal M Lavoie
- BC Children's Hospital Research Institute, Vancouver Canada, Vancouver, Canada
| | - Alice Hadchouel
- Inserm, U955, Créteil, France.,AP-HP, Hôpital Necker-Enfants Malades, Service de Pneumologie Pédiatrique, Paris, France.,Université Paris-Descartes, Paris, France
| | - Mika Rämet
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland.,BioMediTech Institute and Faculty of Medical and Life Sciences, University of Tampere, Tampere, Finland
| | - Mikko Hallman
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
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Zhang D, Zhao L, Li B, He Z, Wang GT, Liu DJ, Leal SM. SEQSpark: A Complete Analysis Tool for Large-Scale Rare Variant Association Studies Using Whole-Genome and Exome Sequence Data. Am J Hum Genet 2017; 101:115-122. [PMID: 28669402 DOI: 10.1016/j.ajhg.2017.05.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/23/2017] [Indexed: 01/25/2023] Open
Abstract
Massively parallel sequencing technologies provide great opportunities for discovering rare susceptibility variants involved in complex disease etiology via large-scale imputation and exome and whole-genome sequence-based association studies. Due to modest effect sizes, large sample sizes of tens to hundreds of thousands of individuals are required for adequately powered studies. Current analytical tools are obsolete when it comes to handling these large datasets. To facilitate the analysis of large-scale sequence-based studies, we developed SEQSpark which implements parallel processing based on Spark to increase the speed and efficiency of performing data quality control, annotation, and association analysis. To demonstrate the versatility and speed of SEQSpark, we analyzed whole-genome sequence data from the UK10K, testing for associations with waist-to-hip ratios. The analysis, which was completed in 1.5 hr, included loading data, annotation, principal component analysis, and single variant and rare variant aggregate association analysis of >9 million variants. For rare variant aggregate analysis, an exome-wide significant association (p < 2.5 × 10-6) was observed with CCDC62 (SKAT-O [p = 6.89 × 10-7], combined multivariate collapsing [p = 1.48 × 10-6], and burden of rare variants [p = 1.48 × 10-6]). SEQSpark was also used to analyze 50,000 simulated exomes and it required 1.75 hr for the analysis of a quantitative trait using several rare variant aggregate association methods. Additionally, the performance of SEQSpark was compared to Variant Association Tools and PLINK/SEQ. SEQSpark was always faster and in some situations computation was reduced to a hundredth of the time. SEQSpark will empower large sequence-based epidemiological studies to quickly elucidate genetic variation involved in the etiology of complex traits.
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Morrison AC, Huang Z, Yu B, Metcalf G, Liu X, Ballantyne C, Coresh J, Yu F, Muzny D, Feofanova E, Rustagi N, Gibbs R, Boerwinkle E. Practical Approaches for Whole-Genome Sequence Analysis of Heart- and Blood-Related Traits. Am J Hum Genet 2017; 100:205-215. [PMID: 28089252 DOI: 10.1016/j.ajhg.2016.12.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/14/2016] [Indexed: 01/11/2023] Open
Abstract
Whole-genome sequencing (WGS) allows for a comprehensive view of the sequence of the human genome. We present and apply integrated methodologic steps for interrogating WGS data to characterize the genetic architecture of 10 heart- and blood-related traits in a sample of 1,860 African Americans. In order to evaluate the contribution of regulatory and non-protein coding regions of the genome, we conducted aggregate tests of rare variation across the entire genomic landscape using a sliding window, complemented by an annotation-based assessment of the genome using predefined regulatory elements and within the first intron of all genes. These tests were performed treating all variants equally as well as with individual variants weighted by a measure of predicted functional consequence. Significant findings were assessed in 1,705 individuals of European ancestry. After these steps, we identified and replicated components of the genomic landscape significantly associated with heart- and blood-related traits. For two traits, lipoprotein(a) levels and neutrophil count, aggregate tests of low-frequency and rare variation were significantly associated across multiple motifs. For a third trait, cardiac troponin T, investigation of regulatory domains identified a locus on chromosome 9. These practical approaches for WGS analysis led to the identification of informative genomic regions and also showed that defined non-coding regions, such as first introns of genes and regulatory domains, are associated with important risk factor phenotypes. This study illustrates the tractable nature of WGS data and outlines an approach for characterizing the genetic architecture of complex traits.
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Affiliation(s)
- Alanna C Morrison
- Human Genetics Center, University of Texas School of Public Health, Houston, TX 77030, USA.
| | - Zhuoyi Huang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bing Yu
- Human Genetics Center, University of Texas School of Public Health, Houston, TX 77030, USA
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiaoming Liu
- Human Genetics Center, University of Texas School of Public Health, Houston, TX 77030, USA
| | - Christie Ballantyne
- Section of Cardiovascular Research, Baylor College of Medicine, Houston, TX 77030, USA; Houston Methodist Debakey Heart and Vascular Center, Houston, TX 77030, USA
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21287, USA
| | - Fuli Yu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elena Feofanova
- Human Genetics Center, University of Texas School of Public Health, Houston, TX 77030, USA
| | - Navin Rustagi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas School of Public Health, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
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Abstract
Genetic factors contribute importantly to the risk of coronary artery disease (CAD), and in the past decade, there has been major progress in this area. The tools applied include genome-wide association studies encompassing >200,000 individuals complemented by bioinformatic approaches, including 1000 Genomes imputation, expression quantitative trait locus analyses, and interrogation of Encyclopedia of DNA Elements, Roadmap, and other data sets. close to 60 common SNPs (minor allele frequency>0.05) associated with CAD risk and reaching genome-wide significance (P<5 × 10(-8)) have been identified. Furthermore, a total of 202 independent signals in 109 loci have achieved a false discovery rate (q<0.05) and together explain 28% of the estimated heritability of CAD. These data have been used successfully to create genetic risk scores that can improve risk prediction beyond conventional risk factors and identify those individuals who will benefit most from statin therapy. Such information also has important applications in clinical medicine and drug discovery by using a Mendelian randomization approach to interrogate the causal nature of many factors found to associate with CAD risk in epidemiological studies. In contrast to genome-wide association studies, whole-exome sequencing has provided valuable information directly relevant to genes with known roles in plasma lipoprotein metabolism but has, thus far, failed to identify other rare coding variants linked to CAD. Overall, recent studies have led to a broader understanding of the genetic architecture of CAD and demonstrate that it largely derives from the cumulative effect of multiple common risk alleles individually of small effect size rather than rare variants with large effects on CAD risk. Despite this success, there has been limited progress in understanding the function of the novel loci; the majority of which are in noncoding regions of the genome.
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Affiliation(s)
- Ruth McPherson
- From the Department of Medicine, Atherogenomics Laboratory, Division of Cardiology, Ruddy Canadian Cardiovascular Genetics Center, University of Ottawa Heart Institute, Ottawa, Ontario, Canada (R.M.); and Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (A.T.-H.).
| | - Anne Tybjaerg-Hansen
- From the Department of Medicine, Atherogenomics Laboratory, Division of Cardiology, Ruddy Canadian Cardiovascular Genetics Center, University of Ottawa Heart Institute, Ottawa, Ontario, Canada (R.M.); and Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (A.T.-H.)
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25
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The effect of phenotypic outliers and non-normality on rare-variant association testing. Eur J Hum Genet 2016; 24:1188-94. [PMID: 26733287 DOI: 10.1038/ejhg.2015.270] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/03/2015] [Accepted: 11/15/2015] [Indexed: 02/07/2023] Open
Abstract
Rare-variant association studies (RVAS) have made important contributions to human complex trait genetics. These studies rely on specialized statistical methods for analyzing rare-variant associations, both individually and in aggregate. We investigated the impact that phenotypic outliers and non-normality have on the performance of rare-variant association testing procedures. Ignoring outliers or non-normality can significantly inflate Type I error rates. We found that rank-based inverse normal transformation (INT) and trait winsorisation were both effective at maintaining Type I error control without sacrificing power in the presence of outliers. INT was the optimal method for non-normally distributed traits. For RVAS of quantitative traits with outliers or non-normality, we recommend using INT to transform phenotypic values before association testing.
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26
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Yu B, Pulit SL, Hwang SJ, Brody JA, Amin N, Auer PL, Bis JC, Boerwinkle E, Burke GL, Chakravarti A, Correa A, Dreisbach AW, Franco OH, Ehret GB, Franceschini N, Hofman A, Lin DY, Metcalf GA, Musani SK, Muzny D, Palmas W, Raffel L, Reiner A, Rice K, Rotter JI, Veeraraghavan N, Fox E, Guo X, North KE, Gibbs RA, van Duijn CM, Psaty BM, Levy D, Newton-Cheh C, Morrison AC. Rare Exome Sequence Variants in CLCN6 Reduce Blood Pressure Levels and Hypertension Risk. ACTA ACUST UNITED AC 2015; 9:64-70. [PMID: 26658788 DOI: 10.1161/circgenetics.115.001215] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 12/10/2015] [Indexed: 11/16/2022]
Abstract
BACKGROUND Rare genetic variants influence blood pressure (BP). METHODS AND RESULTS Whole-exome sequencing was performed on DNA samples from 17 956 individuals of European ancestry and African ancestry (14 497, first-stage discovery and 3459, second-stage discovery) to examine the effect of rare variants on hypertension and 4 BP traits: systolic BP, diastolic BP, pulse pressure, and mean arterial pressure. Tests of ≈170 000 common variants (minor allele frequency, ≥1%; statistical significance, P≤2.9×10(-7)) and gene-based tests of rare variants (minor allele frequency, <1%; ≈17 000 genes; statistical significance, P≤1.5×10(-6)) were evaluated for each trait and ancestry, followed by multiethnic meta-analyses. In the first-stage discovery, rare coding variants (splicing, stop-gain, stop-loss, nonsynonymous variants, or indels) in CLCN6 were associated with lower diastolic BP (cumulative minor allele frequency, 1.3%; β=-3.20; P=4.1×10(-6)) and were independent of a nearby common variant (rs17367504) previously associated with BP. CLCN6 rare variants were also associated with lower systolic BP (β=-4.11; P=2.8×10(-4)), mean arterial pressure (β=-3.50; P=8.9×10(-6)), and reduced hypertension risk (odds ratio, 0.72; P=0.017). Meta-analysis of the 2-stage discovery samples showed that CLCN6 was associated with lower diastolic BP at exome-wide significance (cumulative minor allele frequency, 1.1%; β=-3.30; P=5.0×10(-7)). CONCLUSIONS These findings implicate the effect of rare coding variants in CLCN6 in BP variation and offer new insights into BP regulation.
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Johnson SC, Dong X, Vijg J, Suh Y. Genetic evidence for common pathways in human age-related diseases. Aging Cell 2015; 14:809-17. [PMID: 26077337 PMCID: PMC4568968 DOI: 10.1111/acel.12362] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2015] [Indexed: 12/23/2022] Open
Abstract
Aging is the single largest risk factor for chronic disease. Studies in model organisms have identified conserved pathways that modulate aging rate and the onset and progression of multiple age-related diseases, suggesting that common pathways of aging may influence age-related diseases in humans as well. To determine whether there is genetic evidence supporting the notion of common pathways underlying age-related diseases, we analyzed the genes and pathways found to be associated with five major categories of age-related disease using a total of 410 genomewide association studies (GWAS). While only a small number of genes are shared among all five disease categories, those found in at least three of the five major age-related disease categories are highly enriched for apoliprotein metabolism genes. We found that a more substantial number of gene ontology (GO) terms are shared among the 5 age-related disease categories and shared GO terms include canonical aging pathways identified in model organisms, such as nutrient-sensing signaling, translation, proteostasis, stress responses, and genome maintenance. Taking advantage of the vast amount of genetic data from the GWAS, our findings provide the first direct evidence that conserved pathways of aging simultaneously influence multiple age-related diseases in humans as has been demonstrated in model organisms.
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Affiliation(s)
- Simon C. Johnson
- Department of Genetics Albert Einstein College of Medicine Bronx NY USA
| | - Xiao Dong
- Department of Genetics Albert Einstein College of Medicine Bronx NY USA
| | - Jan Vijg
- Department of Genetics Albert Einstein College of Medicine Bronx NY USA
- Department of Ophthalmology and Visual Sciences Albert Einstein College of Medicine Bronx NY USA
| | - Yousin Suh
- Department of Genetics Albert Einstein College of Medicine Bronx NY USA
- Department of Medicine Endocrinology Albert Einstein College of Medicine Bronx NY USA
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28
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Sidore C, Busonero F, Maschio A, Porcu E, Naitza S, Zoledziewska M, Mulas A, Pistis G, Steri M, Danjou F, Kwong A, Ortega Del Vecchyo VD, Chiang CWK, Bragg-Gresham J, Pitzalis M, Nagaraja R, Tarrier B, Brennan C, Uzzau S, Fuchsberger C, Atzeni R, Reinier F, Berutti R, Huang J, Timpson NJ, Toniolo D, Gasparini P, Malerba G, Dedoussis G, Zeggini E, Soranzo N, Jones C, Lyons R, Angius A, Kang HM, Novembre J, Sanna S, Schlessinger D, Cucca F, Abecasis GR. Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers. Nat Genet 2015; 47:1272-1281. [PMID: 26366554 PMCID: PMC4627508 DOI: 10.1038/ng.3368] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 07/06/2015] [Indexed: 12/31/2022]
Abstract
We report ∼17.6 million genetic variants from whole-genome sequencing of 2,120 Sardinians; 22% are absent from previous sequencing-based compilations and are enriched for predicted functional consequences. Furthermore, ∼76,000 variants common in our sample (frequency >5%) are rare elsewhere (<0.5% in the 1000 Genomes Project). We assessed the impact of these variants on circulating lipid levels and five inflammatory biomarkers. We observe 14 signals, including 2 major new loci, for lipid levels and 19 signals, including 2 new loci, for inflammatory markers. The new associations would have been missed in analyses based on 1000 Genomes Project data, underlining the advantages of large-scale sequencing in this founder population.
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Affiliation(s)
- Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Cagliari, Italy.,Center for Statistical Genetics, Ann Arbor, University of Michigan, MI, USA.,Università degli Studi di Sassari, Sassari, Italy
| | - Fabio Busonero
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Cagliari, Italy.,Center for Statistical Genetics, Ann Arbor, University of Michigan, MI, USA.,University of Michigan, DNA Sequencing Core, Ann Arbor, MI, USA
| | - Andrea Maschio
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Cagliari, Italy.,Center for Statistical Genetics, Ann Arbor, University of Michigan, MI, USA.,University of Michigan, DNA Sequencing Core, Ann Arbor, MI, USA
| | - Eleonora Porcu
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Cagliari, Italy.,Center for Statistical Genetics, Ann Arbor, University of Michigan, MI, USA.,Università degli Studi di Sassari, Sassari, Italy
| | - Silvia Naitza
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Cagliari, Italy
| | | | - Antonella Mulas
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Cagliari, Italy.,Università degli Studi di Sassari, Sassari, Italy
| | - Giorgio Pistis
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Cagliari, Italy.,Center for Statistical Genetics, Ann Arbor, University of Michigan, MI, USA.,Università degli Studi di Sassari, Sassari, Italy
| | - Maristella Steri
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Cagliari, Italy
| | - Fabrice Danjou
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Cagliari, Italy
| | - Alan Kwong
- Center for Statistical Genetics, Ann Arbor, University of Michigan, MI, USA
| | | | - Charleston W K Chiang
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | | | | | - Ramaiah Nagaraja
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Brendan Tarrier
- University of Michigan, DNA Sequencing Core, Ann Arbor, MI, USA
| | | | - Sergio Uzzau
- Porto Conte Ricerche srl, Tramariglio, Alghero, 07041 Italy
| | | | - Rossano Atzeni
- Center for Advanced Studies, Research, and Development in Sardinia (CRS4), AGCT Program, Parco Scientifico e tecnologico della Sardegna, Pula, Italy
| | - Frederic Reinier
- Center for Advanced Studies, Research, and Development in Sardinia (CRS4), AGCT Program, Parco Scientifico e tecnologico della Sardegna, Pula, Italy
| | - Riccardo Berutti
- Università degli Studi di Sassari, Sassari, Italy.,Center for Advanced Studies, Research, and Development in Sardinia (CRS4), AGCT Program, Parco Scientifico e tecnologico della Sardegna, Pula, Italy
| | - Jie Huang
- Human Genetics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1HH
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, United Kingdom
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy
| | - Paolo Gasparini
- DSM-University of Trieste and IRCCS-Burlo Garofolo Children Hospital (Trieste, Italy).,Experimental Genetics Division, Sidra, (Doha, Qatar)
| | - Giovanni Malerba
- Department of Life and Reproduction Sciences, University of Verona, Verona, Italy
| | | | - Eleftheria Zeggini
- Human Genetics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1HH
| | - Nicole Soranzo
- Human Genetics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1HH.,Department of Haematology, University of Cambridge, Hills Rd, Cambridge CB2 0AH
| | - Chris Jones
- Center for Advanced Studies, Research, and Development in Sardinia (CRS4), AGCT Program, Parco Scientifico e tecnologico della Sardegna, Pula, Italy
| | - Robert Lyons
- University of Michigan, DNA Sequencing Core, Ann Arbor, MI, USA
| | - Andrea Angius
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Cagliari, Italy.,Center for Advanced Studies, Research, and Development in Sardinia (CRS4), AGCT Program, Parco Scientifico e tecnologico della Sardegna, Pula, Italy
| | - Hyun M Kang
- Center for Statistical Genetics, Ann Arbor, University of Michigan, MI, USA
| | - John Novembre
- Department of Human Genetics, University of Chicago, IL, USA
| | - Serena Sanna
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Cagliari, Italy
| | - David Schlessinger
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Cagliari, Italy.,Università degli Studi di Sassari, Sassari, Italy
| | - Gonçalo R Abecasis
- Center for Statistical Genetics, Ann Arbor, University of Michigan, MI, USA
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Hart SN, Maxwell KN, Thomas T, Ravichandran V, Wubberhorst B, Klein RJ, Schrader K, Szabo C, Weitzel JN, Neuhausen SL, Nathanson K, Offit K, Couch FJ, Vijai J. Collaborative science in the next-generation sequencing era: a viewpoint on how to combine exome sequencing data across sites to identify novel disease susceptibility genes. Brief Bioinform 2015; 17:672-7. [PMID: 26358132 DOI: 10.1093/bib/bbv075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Indexed: 11/14/2022] Open
Abstract
The purpose of this article is to inform readers about technical challenges that we encountered when assembling exome sequencing data from the 'Simplifying Complex Exomes' (SIMPLEXO) consortium-whose mandate is the discovery of novel genes predisposing to breast and ovarian cancers. Our motivation is to share these obstacles-and our solutions to them-as a means of communicating important technical details that should be discussed early in projects involving massively parallel sequencing.
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Ahluwalia TS, Allin KH, Sandholt CH, Sparsø TH, Jørgensen ME, Rowe M, Christensen C, Brandslund I, Lauritzen T, Linneberg A, Husemoen LL, Jørgensen T, Hansen T, Grarup N, Pedersen O. Discovery of coding genetic variants influencing diabetes-related serum biomarkers and their impact on risk of type 2 diabetes. J Clin Endocrinol Metab 2015; 100:E664-71. [PMID: 25599387 DOI: 10.1210/jc.2014-3677] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Type 2 diabetes (T2D) prevalence is spiraling globally, and knowledge of its pathophysiological signatures is crucial for a better understanding and treatment of the disease. OBJECTIVE We aimed to discover underlying coding genetic variants influencing fasting serum levels of nine biomarkers associated with T2D: adiponectin, C-reactive protein, ferritin, heat shock 70-kDa protein 1B, IGF binding protein 1 and IGF binding protein 2, IL-18, IL-2 receptor-α, and leptin. DESIGN AND PARTICIPANTS A population-based sample of 6215 adult Danes was genotyped for 16 340 coding single-nucleotide polymorphisms and were tested for association with each biomarker. Identified loci were tested for association with T2D through a large-scale meta-analysis involving up to 17 024 T2D cases and up to 64 186 controls. RESULTS We discovered 11 associations between single-nucleotide polymorphisms and five distinct biomarkers at a study-wide P < 3.4 × 10(-7). Nine associations were novel: IL18: BIRC6, RAD17, MARVELD2; ferritin: F5; IGF binding protein 1: SERPING1, KLKB, GCKR, CELSR2, and heat shock 70-kDa protein 1B: CFH. Three of the identified loci (CELSR2, HNF1A, and GCKR) were significantly associated with T2D, of which the association with the CELSR2 locus has not been shown previously. CONCLUSION The identified loci influence processes related to insulin signaling, cell communication, immune function, apoptosis, DNA repair, and oxidative stress, all of which could provide a rationale for novel diabetes therapeutic strategies.
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Affiliation(s)
- Tarunveer Singh Ahluwalia
- Novo Nordisk Foundation Center for Basic Metabolic Research (T.S.A., K.H.A., C.H.S., T.H.A., T.H., N.G., O.P.), Section of Metabolic Genetics, Faculty of Health and Medical Sciences, Department of Clinical Medicine (A.L.), Faculty of Health and Medical Sciences, and Institute of Public Health (T.J.), University of Copenhagen, 2100 Copenhagen, Denmark; Copenhagen Prospective Studies on Asthma in Childhood (T.S.A.), Faculty of Health and Medical Sciences, University of Copenhagen, 2820 Copenhagen, Denmark; The Danish Paediatric Asthma Center (T.S.A.), Gentofte Hospital, The Capital Region, 2820 Copenhagen, Denmark; Steno Diabetes Center (E.J.), 2820 Gentofte, Denmark; Tethys Bioscience Inc (M.R.), Emeryville, California 94608; Departments of Internal Medicine and Endocrinology (C.C.) and Clinical Biochemistry (I.B.), Vejle Hospital, 7100 Vejle, Denmark; Institute of Regional Health Research (I.B.), and Faculty of Health Sciences (T.H.), University of Southern Denmark, 5230 Odense, Denmark; Department of General Practice (T.L.), Aarhus University, 8000 C Aarhus, Denmark; Research Centre for Prevention and Health (A.L., L.L.H., T.J.), The Capital Region of Denmark, Copenhagen, Denmark; Department of Clinical Experimental Research (A.L.), Glostrup University Hospital, 2600 Glostrup, Denmark; and Faculty of Medicine (T.J.), University of Aalborg, 9220 Aalborg, Denmark
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