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Tada H, Kawashiri MA, Nohara A, Sekiya T, Watanabe A, Takamura M. Genetic Counseling and Genetic Testing for Familial Hypercholesterolemia. Genes (Basel) 2024; 15:297. [PMID: 38540356 PMCID: PMC10970256 DOI: 10.3390/genes15030297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 06/14/2024] Open
Abstract
Familial hypercholesterolemia (FH) is one of the most common autosomal codominant Mendelian diseases. The major complications of FH include tendon and cutaneous xanthomas and coronary artery disease (CAD) associated with a substantial elevation of serum low-density lipoprotein levels (LDL). Genetic counseling and genetic testing for FH is useful for its diagnosis, risk stratification, and motivation for further LDL-lowering treatments. In this study, we summarize the epidemiology of FH based on numerous genetic studies, including its pathogenic variants, genotype-phenotype correlation, prognostic factors, screening, and usefulness of genetic counseling and genetic testing. Due to the variety of treatments available for this common Mendelian disease, genetic counseling and genetic testing for FH should be implemented in daily clinical practice.
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Affiliation(s)
- Hayato Tada
- Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medicine, Kanazawa 920-8640, Japan;
| | - Masa-aki Kawashiri
- Department of Internal Medicine, Kaga Medical Center, Kaga 922-8522, Japan;
| | - Atsushi Nohara
- Department of Clinical Genetics, Ishikawa Prefectural Central Hospital, Kanazawa 920-8530, Japan;
| | - Tomoko Sekiya
- Division of Clinical Genetics, Kanazawa University Hospital, Kanazawa 920-8641, Japan; (T.S.); (A.W.)
| | - Atsushi Watanabe
- Division of Clinical Genetics, Kanazawa University Hospital, Kanazawa 920-8641, Japan; (T.S.); (A.W.)
| | - Masayuki Takamura
- Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medicine, Kanazawa 920-8640, Japan;
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Wan J, Vadaq N, Konings J, Jaeger M, Kumar V, de Laat B, Joosten L, Netea MG, van der Ven AJ, de Groot PG, de Mast Q, Roest M. Kallikrein augments the anticoagulant function of the protein C system in thrombin generation. J Thromb Haemost 2022; 20:48-57. [PMID: 34532976 PMCID: PMC9293419 DOI: 10.1111/jth.15530] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/13/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Genetics play a significant role in coagulation phenotype and venous thromboembolism risk. Resistance to the anticoagulant activated protein C (APC) is an established risk for thrombosis. Herein, we explored the genetic determinants of thrombin generation (TG) and thrombomodulin (TM)-modulated TG using plasma from the Human Functional Genomics Project. METHODS Calibrated TG was measured both in absence and presence of TM using tissue factor as trigger. Genetic determinants of TG parameters and protein C pathway function were assessed using genome-wide single-nucleotide polymorphism (SNP) genotyping. Plasma samples were supplemented with purified apolipoprotein A-IV, prekallikrein, or kallikrein to test their influence on the anticoagulant function of TM and APC in TG. RESULTS Thrombin generation data from 392 individuals were analyzed. Genotyping showed that the KLKB1 gene (top SNP: rs4241819) on chromosome 4 was associated with the normalized sensitivity ratio of endogenous thrombin potential to TM at genome-wide level (nETP-TMsr, P = 4.27 × 10-8 ). In vitro supplementation of kallikrein, but not prekallikrein or apolipoprotein A-IV, into plasma dose-dependently augmented the anticoagulant effect of TM and APC in TG. Variations of rs4241819 was not associated with the plasma concentration of prekallikrein. Association between rs4241819 and nETP-TMsr was absent when TG was measured in presence of a contact pathway inhibitor corn trypsin inhibitor. CONCLUSIONS Our results suggest that kallikrein plays a role in the regulation of the anticoagulant protein C pathway in TG, which may provide a novel mechanism for the previously observed association between the KLKB1 gene and venous thrombosis.
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Affiliation(s)
- Jun Wan
- Synapse Research InstituteCardiovascular Research Institute MaastrichtMaastricht University Medical CenterMaastrichtthe Netherlands
| | - Nadira Vadaq
- Department of Internal MedicineRadboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenthe Netherlands
- Dr. Kariadi Hospital; Center for Tropical and Infectious Diseases (CENTRID)Faculty of MedicineDiponegoro UniversitySemarangIndonesia
| | - Joke Konings
- Synapse Research InstituteCardiovascular Research Institute MaastrichtMaastricht University Medical CenterMaastrichtthe Netherlands
| | - Martin Jaeger
- Department of Internal MedicineRadboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenthe Netherlands
| | - Vinod Kumar
- Department of Internal MedicineRadboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenthe Netherlands
- Department of GeneticsUniversity Medical Centre GroningenGroningenthe Netherlands
- Nitte (Deemed to be University)Nitte University Centre for Science Education and Research (NUCSER)Medical Sciences ComplexDeralakatte, MangaloreIndia
| | - Bas de Laat
- Synapse Research InstituteCardiovascular Research Institute MaastrichtMaastricht University Medical CenterMaastrichtthe Netherlands
| | - Leo Joosten
- Department of Internal MedicineRadboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenthe Netherlands
| | - Mihai G. Netea
- Department of Internal MedicineRadboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenthe Netherlands
- Department for Immunology and Metabolism, Life and Medical Sciences Institute (LIMES)University of BonnBonnGermany
| | - Andre J. van der Ven
- Department of Internal MedicineRadboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenthe Netherlands
| | - Philip G. de Groot
- Synapse Research InstituteCardiovascular Research Institute MaastrichtMaastricht University Medical CenterMaastrichtthe Netherlands
| | - Quirijn de Mast
- Department of Internal MedicineRadboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenthe Netherlands
| | - Mark Roest
- Synapse Research InstituteCardiovascular Research Institute MaastrichtMaastricht University Medical CenterMaastrichtthe Netherlands
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Soremekun O, Soremekun C, Machipisa T, Soliman M, Nashiru O, Chikowore T, Fatumo S. Genome-Wide Association and Mendelian Randomization Analysis Reveal the Causal Relationship Between White Blood Cell Subtypes and Asthma in Africans. Front Genet 2021; 12:749415. [PMID: 34925446 PMCID: PMC8674726 DOI: 10.3389/fgene.2021.749415] [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: 07/29/2021] [Accepted: 11/01/2021] [Indexed: 12/03/2022] Open
Abstract
Background: White blood cell (WBC) traits and their subtypes such as basophil count (Bas), eosinophil count (Eos), lymphocyte count (Lym), monocyte count (Mon), and neutrophil counts (Neu) are known to be associated with diseases such as stroke, peripheral arterial disease, and coronary heart disease. Methods: We meta-analyze summary statistics from genome-wide association studies in 17,802 participants from the African Partnership for Chronic Disease Research (APCDR) and African ancestry individuals from the Blood Cell Consortium (BCX2) using GWAMA. We further carried out a Bayesian fine mapping to identify causal variants driving the association with WBC subtypes. To access the causal relationship between WBC subtypes and asthma, we conducted a two-sample Mendelian randomization (MR) analysis using summary statistics of the Consortium on Asthma among African Ancestry Populations (CAAPA: n cases = 7,009, n control = 7,645) as our outcome phenotype. Results: Our metanalysis identified 269 loci at a genome-wide significant value of (p = 5 × 10-9) in a composite of the WBC subtypes while the Bayesian fine-mapping analysis identified genetic variants that are more causal than the sentinel single-nucleotide polymorphism (SNP). We found for the first time five novel genes (LOC126987/MTCO3P14, LINC01525, GAPDHP32/HSD3BP3, FLG-AS1/HMGN3P1, and TRK-CTT13-1/MGST3) not previously reported to be associated with any WBC subtype. Our MR analysis showed that Mon (IVW estimate = 0.38, CI: 0.221, 0.539, p < 0.001), Neu (IVW estimate = 0.189, CI: 0.133, 0.245, p < 0.001), and WBCc (IVW estimate = 0.185, CI: 0.108, 0.262, p < 0.001) are associated with increased risk of asthma. However, there was no evidence of causal relationship between Lym and asthma risk. Conclusion: This study provides insight into the relationship between some WBC subtypes and asthma and potential route in the treatment of asthma and may further inform a new therapeutic approach.
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Affiliation(s)
- Opeyemi Soremekun
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe, Uganda
| | - Chisom Soremekun
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe, Uganda
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
| | - Tafadzwa Machipisa
- Department of Medicine, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
- The Department of Pathology and Molecular Medicine, Population Health Research Institute (PHRI), Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada
| | - Mahmoud Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - Oyekanmi Nashiru
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
| | - Tinashe Chikowore
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- MRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Segun Fatumo
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe, Uganda
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Irvin MR, Jones AC, Claas SA, Arnett DK. DNA Methylation and Blood Pressure Phenotypes: A Review of the Literature. Am J Hypertens 2021; 34:267-273. [PMID: 33821945 DOI: 10.1093/ajh/hpab026] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 12/20/2022] Open
Abstract
Genetic studies of DNA have been unable to explain a significant portion of the variance of the estimated heritability of blood pressure (BP). Epigenetic mechanisms, particularly DNA methylation, have helped explain additional biological processes linked to BP phenotypes and diseases. Candidate gene methylation studies and genome-wide methylation studies of BP have highlighted impactful cytosine-phosphate-guanine (CpG) markers across different ethnicities. Furthermore, many of these BP-related CpG sites are also linked to metabolism-related phenotypes. Integrating epigenome-wide association study data with other layers of molecular data such as genotype data (from single nucleotide polymorphism arrays or sequencing), other epigenetic data, and/or transcriptome data can provide additional information about the significance and complexity of these relationships. Recent data suggest that epigenetic changes can be consequences rather than causes of BP variation. Finally, these data can give insight into downstream effects of long-standing high BP (due to target organ damage (TOD)). The current review provides a literature overview of epigenetic modifications in BP and TOD. Recent studies strongly support the importance of epigenetic modifications, such as DNA methylation, in BP and TOD for relevant biological insights, reliable biomarkers, and possible future therapeutics.
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Affiliation(s)
- Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Alana C Jones
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Steven A Claas
- Department of Epidemiology, College of Public Health, University of Kentucky, Lexington, Kentucky, USA
| | - Donna K Arnett
- Department of Epidemiology, College of Public Health, University of Kentucky, Lexington, Kentucky, USA
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Single-Cell Transcriptome Analysis Maps the Developmental Track of the Human Heart. Cell Rep 2020; 26:1934-1950.e5. [PMID: 30759401 DOI: 10.1016/j.celrep.2019.01.079] [Citation(s) in RCA: 287] [Impact Index Per Article: 71.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/14/2018] [Accepted: 01/22/2019] [Indexed: 02/06/2023] Open
Abstract
The heart is the central organ of the circulatory system, and its proper development is vital for maintaining human life. Here, we used single-cell RNA sequencing to profile the gene expression landscapes of ∼4,000 cardiac cells from human embryos and identified four major types of cells: cardiomyocytes (CMs), cardiac fibroblasts, endothelial cells (ECs), and valvar interstitial cells (VICs). Atrial and ventricular CMs acquired distinct features early in heart development. Furthermore, both CMs and fibroblasts show stepwise changes in gene expression. As development proceeds, VICs may be involved in the remodeling phase, and ECs display location-specific characteristics. Finally, we compared gene expression profiles between humans and mice and identified a series of unique features of human heart development. Our study lays the groundwork for elucidating the mechanisms of in vivo human cardiac development and provides potential clues to understand cardiac regeneration.
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6
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Hodonsky CJ, Baldassari AR, Bien SA, Raffield LM, Highland HM, Sitlani CM, Wojcik GL, Tao R, Graff M, Tang W, Thyagarajan B, Buyske S, Fornage M, Hindorff LA, Li Y, Lin D, Reiner AP, North KE, Loos RJF, Kooperberg C, Avery CL. Ancestry-specific associations identified in genome-wide combined-phenotype study of red blood cell traits emphasize benefits of diversity in genomics. BMC Genomics 2020; 21:228. [PMID: 32171239 PMCID: PMC7071748 DOI: 10.1186/s12864-020-6626-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/26/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Quantitative red blood cell (RBC) traits are highly polygenic clinically relevant traits, with approximately 500 reported GWAS loci. The majority of RBC trait GWAS have been performed in European- or East Asian-ancestry populations, despite evidence that rare or ancestry-specific variation contributes substantially to RBC trait heritability. Recently developed combined-phenotype methods which leverage genetic trait correlation to improve statistical power have not yet been applied to these traits. Here we leveraged correlation of seven quantitative RBC traits in performing a combined-phenotype analysis in a multi-ethnic study population. RESULTS We used the adaptive sum of powered scores (aSPU) test to assess combined-phenotype associations between ~ 21 million SNPs and seven RBC traits in a multi-ethnic population (maximum n = 67,885 participants; 24% African American, 30% Hispanic/Latino, and 43% European American; 76% female). Thirty-nine loci in our multi-ethnic population contained at least one significant association signal (p < 5E-9), with lead SNPs at nine loci significantly associated with three or more RBC traits. A majority of the lead SNPs were common (MAF > 5%) across all ancestral populations. Nineteen additional independent association signals were identified at seven known loci (HFE, KIT, HBS1L/MYB, CITED2/FILNC1, ABO, HBA1/2, and PLIN4/5). For example, the HBA1/2 locus contained 14 conditionally independent association signals, 11 of which were previously unreported and are specific to African and Amerindian ancestries. One variant in this region was common in all ancestries, but exhibited a narrower LD block in African Americans than European Americans or Hispanics/Latinos. GTEx eQTL analysis of all independent lead SNPs yielded 31 significant associations in relevant tissues, over half of which were not at the gene immediately proximal to the lead SNP. CONCLUSION This work identified seven loci containing multiple independent association signals for RBC traits using a combined-phenotype approach, which may improve discovery in genetically correlated traits. Highly complex genetic architecture at the HBA1/2 locus was only revealed by the inclusion of African Americans and Hispanics/Latinos, underscoring the continued importance of expanding large GWAS to include ancestrally diverse populations.
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Affiliation(s)
- Chani J. Hodonsky
- University of North Carolina Gillings School of Public Health, 135 Dauer Dr, Chapel Hill, NC 27599 USA
- University of Virginia Center for Public Health Genomics, 1355 Lee St, Charlottesville, VA 22908 USA
| | - Antoine R. Baldassari
- University of North Carolina Gillings School of Public Health, 135 Dauer Dr, Chapel Hill, NC 27599 USA
| | - Stephanie A. Bien
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109 USA
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599 USA
| | - Heather M. Highland
- University of North Carolina Gillings School of Public Health, 135 Dauer Dr, Chapel Hill, NC 27599 USA
| | - Colleen M. Sitlani
- University of Washington, 1730 Minor Ave, Ste 1360, Seattle, WA 98101 USA
| | - Genevieve L. Wojcik
- Stanford University School of Medicine, 291 Campus Dr, Stanford, CA 94305 USA
| | - Ran Tao
- Vanderbilt University, 2525 West End Ave #1100, Nashville, TN 37203 USA
| | - Marielisa Graff
- University of North Carolina Gillings School of Public Health, 135 Dauer Dr, Chapel Hill, NC 27599 USA
| | - Weihong Tang
- University of Minnesota, 420 Delaware St SE, Minneapolis, MN 55455 USA
| | | | - Steve Buyske
- Rutgers University, 683 Hoes Ln W, Piscataway, NJ 08854 USA
| | - Myriam Fornage
- University of Texas Houston, 7000 Fannin Street, Houston, TX 77030 USA
| | - Lucia A. Hindorff
- National Human Genome Research Institute, 31 Center Dr, Bethesda, MD 20894 USA
| | - Yun Li
- University of North Carolina Gillings School of Public Health, 135 Dauer Dr, Chapel Hill, NC 27599 USA
| | - Danyu Lin
- University of North Carolina Gillings School of Public Health, 135 Dauer Dr, Chapel Hill, NC 27599 USA
| | - Alex P. Reiner
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109 USA
- University of Washington, 1705 NE Pacific St, Seattle, WA 98195 USA
| | - Kari E. North
- University of North Carolina Gillings School of Public Health, 135 Dauer Dr, Chapel Hill, NC 27599 USA
- Department of Genetics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599 USA
| | - Ruth J. F. Loos
- Icahn School of Medicine at Mount Sinai, 1468 Madison Ave, New York, NY 10029 USA
| | | | - Christy L. Avery
- University of North Carolina Gillings School of Public Health, 135 Dauer Dr, Chapel Hill, NC 27599 USA
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Lin SH, Loftfield E, Sampson JN, Zhou W, Yeager M, Freedman ND, Chanock SJ, Machiela MJ. Mosaic chromosome Y loss is associated with alterations in blood cell counts in UK Biobank men. Sci Rep 2020; 10:3655. [PMID: 32108144 PMCID: PMC7046668 DOI: 10.1038/s41598-020-59963-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/04/2020] [Indexed: 12/31/2022] Open
Abstract
Mosaic loss of Y chromosome (mLOY) is the most frequently detected somatic copy number alteration in leukocytes of men. In this study, we investigate blood cell counts as a potential mechanism linking mLOY to disease risk in 206,353 UK males. Associations between mLOY, detected by genotyping arrays, and blood cell counts were assessed by multivariable linear models adjusted for relevant risk factors. Among the participants, mLOY was detected in 39,809 men. We observed associations between mLOY and reduced erythrocyte count (−0.009 [−0.014, −0.005] × 1012 cells/L, p = 2.75 × 10−5) and elevated thrombocyte count (5.523 [4.862, 6.183] × 109 cells/L, p = 2.32 × 10−60) and leukocyte count (0.218 [0.198, 0.239] × 109 cells/L, p = 9.22 × 10−95), particularly for neutrophil count (0.174 × [0.158, 0.190]109 cells/L, p = 1.24 × 10−99) and monocyte count (0.021 [0.018 to 0.024] × 109 cells/L, p = 6.93 × 10−57), but lymphocyte count was less consistent (0.016 [0.007, 0.025] × 109 cells/L, p = 8.52 × 10−4). Stratified analyses indicate these associations are independent of the effects of aging and smoking. Our findings provide population-based evidence for associations between mLOY and blood cell counts that should stimulate investigation of the underlying biological mechanisms linking mLOY to cancer and chronic disease risk.
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Affiliation(s)
- Shu-Hong Lin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Erikka Loftfield
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Josh N Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, 8717 Grovemont Circle, Gaithersburg, MD, 20877, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, 8717 Grovemont Circle, Gaithersburg, MD, 20877, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA.
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Kazmi N, Elliott HR, Burrows K, Tillin T, Hughes AD, Chaturvedi N, Gaunt TR, Relton CL. Associations between high blood pressure and DNA methylation. PLoS One 2020; 15:e0227728. [PMID: 31999706 PMCID: PMC6991984 DOI: 10.1371/journal.pone.0227728] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/29/2019] [Indexed: 12/14/2022] Open
Abstract
Background High blood pressure is a major risk factor for cardiovascular disease and is influenced by both environmental and genetic factors. Epigenetic processes including DNA methylation potentially mediate the relationship between genetic factors, the environment and cardiovascular disease. Despite an increased risk of hypertension and cardiovascular disease in individuals of South Asians compared to Europeans, it is not clear whether associations between blood pressure and DNA methylation differ between these groups. Methods We performed an epigenome-wide association study and differentially methylated region (DMR) analysis to identify DNA methylation sites and regions that were associated with systolic blood pressure, diastolic blood pressure and hypertension. We analyzed samples from 364 European and 348 South Asian men (first generation migrants to the UK) from the Southall And Brent REvisited cohort, measuring DNA methylation from blood using the Illumina Infinium® HumanMethylation450 BeadChip. Results One CpG site was found to be associated with DBP in trans-ancestry analyses (i.e. both ethnic groups combined), while in Europeans alone seven CpG sites were associated with DBP. No associations were identified between DNA methylation and either SBP or hypertension. Comparison of effect sizes between South Asian and European EWAS for DBP, SBP and hypertension revealed little concordance between analyses. DMR analysis identified several regions with known relationships with CVD and its risk factors. Conclusion This study identified differentially methylated sites and regions associated with blood pressure and revealed ethnic differences in these associations. These findings may point to molecular pathways which may explain the elevated cardiovascular disease risk experienced by those of South Asian ancestry when compared to Europeans.
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Affiliation(s)
- Nabila Kazmi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- * E-mail:
| | - Hannah R. Elliott
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Kim Burrows
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Therese Tillin
- Department of Population Science & Experimental Medicine, Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Alun D. Hughes
- Department of Population Science & Experimental Medicine, Institute of Cardiovascular Science, University College London, London, United Kingdom
- MRC Lifelong Health & Aging Unit at UCL, London, United Kingdom
| | - Nish Chaturvedi
- Department of Population Science & Experimental Medicine, Institute of Cardiovascular Science, University College London, London, United Kingdom
- MRC Lifelong Health & Aging Unit at UCL, London, United Kingdom
| | - Tom R. Gaunt
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- NIHR Bristol Biomedical Research Centre, Bristol, United Kingdom
| | - Caroline L. Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- NIHR Bristol Biomedical Research Centre, Bristol, United Kingdom
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9
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Jo Hodonsky C, Schurmann C, Schick UM, Kocarnik J, Tao R, van Rooij FJ, Wassel C, Buyske S, Fornage M, Hindorff LA, Floyd JS, Ganesh SK, Lin DY, North KE, Reiner AP, Loos RJ, Kooperberg C, Avery CL. Generalization and fine mapping of red blood cell trait genetic associations to multi-ethnic populations: The PAGE Study. Am J Hematol 2018; 93:10.1002/ajh.25161. [PMID: 29905378 PMCID: PMC6300146 DOI: 10.1002/ajh.25161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/29/2018] [Accepted: 05/29/2018] [Indexed: 12/17/2022]
Abstract
Red blood cell (RBC) traits provide insight into a wide range of physiological states and exhibit moderate to high heritability, making them excellent candidates for genetic studies to inform underlying biologic mechanisms. Previous RBC trait genome-wide association studies were performed primarily in European- or Asian-ancestry populations, missing opportunities to inform understanding of RBC genetic architecture in diverse populations and reduce intervals surrounding putative functional SNPs through fine-mapping. Here, we report the first fine-mapping of six correlated (Pearson's r range: |0.04 - 0.92|) RBC traits in up to 19,036 African Americans and 19,562 Hispanic/Latinos participants of the Population Architecture using Genomics and Epidemiology (PAGE) consortium. Trans-ethnic meta-analysis of race/ethnic- and study-specific estimates for approximately 11,000 SNPs flanking 13 previously identified association signals as well as 150,000 additional array-wide SNPs was performed using inverse-variance meta-analysis after adjusting for study and clinical covariates. Approximately half of previously reported index SNP-RBC trait associations generalized to the trans-ethnic study population (p<1.7x10-4 ); previously unreported independent association signals within the ABO region reinforce the potential for multiple functional variants affecting the same locus. Trans-ethnic fine-mapping did not reveal additional signals at the HFE locus independent of the known functional variants. Finally, we identified a potential novel association in the Hispanic/Latino study population at the HECTD4/RPL6 locus for RBC count (p=1.9x10-7 ). The identification of a previously unknown association, generalization of a large proportion of known association signals, and refinement of known association signals all exemplify the benefits of genetic studies in diverse populations. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Chani Jo Hodonsky
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, NC
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ursula M Schick
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Jonathan Kocarnik
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - Frank Ja van Rooij
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3000, the Netherlands
| | - Christina Wassel
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, VT
| | - Steve Buyske
- Department of Statistics and Biostatistics, Hill Center, Rutgers, The State University of New Jersey, 110 Frelinghuysen Rd. Piscataway, NY
| | - Myriam Fornage
- Institute of Molecular Medicine and Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National institutes of Health, Bethesda, MD
| | - James S Floyd
- Departments of Medicine, University of Washington, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Santhi K Ganesh
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI
| | - Dan-Yu Lin
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC
| | - Kari E North
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, NC
| | - Alex P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Ruth Jf Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Christy L Avery
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, NC
- Carolina Population Center, University of North Carolina, Chapel Hill, NC
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10
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Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions. Cell Stem Cell 2017; 20:858-873.e4. [DOI: 10.1016/j.stem.2017.03.007] [Citation(s) in RCA: 237] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/30/2016] [Accepted: 03/15/2017] [Indexed: 11/15/2022]
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11
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Pirastu N, Kooyman M, Traglia M, Robino A, Willems SM, Pistis G, Amin N, Sala C, Karssen LC, Van Duijn C, Toniolo D, Gasparini P. A Genome-Wide Association Study in isolated populations reveals new genes associated to common food likings. Rev Endocr Metab Disord 2016; 17:209-19. [PMID: 27129595 DOI: 10.1007/s11154-016-9354-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Food preferences are the first factor driving food choice and thus nutrition. They involve numerous different senses such as taste and olfaction as well as various other factors such as personal experiences and hedonistic aspects. Although it is clear that several of these have a genetic basis, up to now studies have focused mostly on the effects of polymorphisms of taste receptor genes. Therefore, we have carried out one of the first large scale (4611 individuals) GWAS on food likings assessed for 20 specific food likings belonging to 4 different categories (vegetables, fatty, dairy and bitter). A two-step meta-analysis using three different isolated populations from Italy for the discovery step and two populations from The Netherlands and Central Asia for replication, revealed 15 independent genome-wide significant loci (p < 5 × 10(-8)) for 12 different foods. None of the identified genes coded for either taste or olfactory receptors suggesting that genetics impacts in determining food likings in a much broader way than simple differences in taste perception. These results represent a further step in uncovering the genes that underlie liking of common foods that in the end will greatly help understanding the genetics of human nutrition in general.
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Affiliation(s)
- Nicola Pirastu
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy.
- University of Trieste, Trieste, Italy.
| | - Maarten Kooyman
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Michela Traglia
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy
| | - Antonietta Robino
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Sara M Willems
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Giorgio Pistis
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy
| | - Najaf Amin
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Cinzia Sala
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy
| | - Lennart C Karssen
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- PolyOmica, Groningen, The Netherlands
| | - Cornelia Van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Centre for Medical Systems Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy
| | - Paolo Gasparini
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
- University of Trieste, Trieste, Italy
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12
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Sobota RS, Stein CM, Kodaman N, Scheinfeldt LB, Maro I, Wieland-Alter W, Igo RP, Magohe A, Malone LL, Chervenak K, Hall NB, Modongo C, Zetola N, Matee M, Joloba M, Froment A, Nyambo TB, Moore JH, Scott WK, Lahey T, Boom WH, von Reyn CF, Tishkoff SA, Sirugo G, Williams SM. A Locus at 5q33.3 Confers Resistance to Tuberculosis in Highly Susceptible Individuals. Am J Hum Genet 2016; 98:514-524. [PMID: 26942285 PMCID: PMC4800052 DOI: 10.1016/j.ajhg.2016.01.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/26/2016] [Indexed: 12/22/2022] Open
Abstract
Immunosuppression resulting from HIV infection increases the risk of progression to active tuberculosis (TB) both in individuals newly exposed to Mycobacterium tuberculosis (MTB) and in those with latent infections. We hypothesized that HIV-positive individuals who do not develop TB, despite living in areas where it is hyperendemic, provide a model of natural resistance. We performed a genome-wide association study of TB resistance by using 581 HIV-positive Ugandans and Tanzanians enrolled in prospective cohort studies of TB; 267 of these individuals developed active TB, and 314 did not. A common variant, rs4921437 at 5q33.3, was significantly associated with TB (odds ratio = 0.37, p = 2.11 × 10(-8)). This variant lies within a genomic region that includes IL12B and is embedded in an H3K27Ac histone mark. The locus also displays consistent patterns of linkage disequilibrium across African populations and has signals of strong selection in populations from equatorial Africa. Along with prior studies demonstrating that therapy with IL-12 (the cytokine encoded in part by IL12B, associated with longer survival following MTB infection in mice deficient in CD4 T cells), our results suggest that this pathway might be an excellent target for the development of new modalities for treating TB, especially for HIV-positive individuals. Our results also indicate that studying extreme disease resistance in the face of extensive exposure can increase the power to detect associations in complex infectious disease.
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Affiliation(s)
- Rafal S Sobota
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37232, USA; Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Catherine M Stein
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA; Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Nuri Kodaman
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37232, USA; Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA; Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Laura B Scheinfeldt
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Coriell Institute for Medical Research, Camden, NJ 08103, USA
| | - Isaac Maro
- Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | | | - Robert P Igo
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Albert Magohe
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - LaShaunda L Malone
- Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Keith Chervenak
- Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Noemi B Hall
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Chawangwa Modongo
- Division of Infectious Diseases, University of Pennsylvania, Philadelphia, PA 19104, USA; Botswana-UPenn Partnership, 214 Independence Avenue, Gaborone, Botswana; Department of Medicine, University of Botswana, Gaborone, Botswana
| | - Nicola Zetola
- Division of Infectious Diseases, University of Pennsylvania, Philadelphia, PA 19104, USA; Botswana-UPenn Partnership, 214 Independence Avenue, Gaborone, Botswana; Department of Medicine, University of Botswana, Gaborone, Botswana
| | - Mecky Matee
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Moses Joloba
- Uganda-CWRU Research Collaboration, Kampala, Uganda; College of Health Sciences Makerere University and Mulago Hospital, Kampala, Uganda
| | - Alain Froment
- UMR 208, Institut de Recherche pour le Développement and Musée de l'Homme, Muséum National d'Histoire Naturelle, 75116 Paris, France
| | - Thomas B Nyambo
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Jason H Moore
- Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William K Scott
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL 33136, USA
| | - Timothy Lahey
- Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - W Henry Boom
- Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH 44106, USA; Uganda-CWRU Research Collaboration, Kampala, Uganda
| | | | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Giorgio Sirugo
- Centro di Ricerca, Ospedale San Pietro Fatebenefratelli, 00189 Rome, Italy
| | - Scott M Williams
- Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA; Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA.
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13
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Deming Y, Xia J, Cai Y, Lord J, Del-Aguila JL, Fernandez MV, Carrell D, Black K, Budde J, Ma S, Saef B, Howells B, Bertelsen S, Bailey M, Ridge PG, Holtzman D, Morris JC, Bales K, Pickering EH, Lee JM, Heitsch L, Kauwe J, Goate A, Piccio L, Cruchaga C. Genetic studies of plasma analytes identify novel potential biomarkers for several complex traits. Sci Rep 2016; 6:18092. [PMID: 36647296 PMCID: PMC4698720 DOI: 10.1038/srep18092] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/11/2015] [Indexed: 01/23/2023] Open
Abstract
Genome-wide association studies of 146 plasma protein levels in 818 individuals revealed 56 genome-wide significant associations (28 novel) with 47 analytes. Loci associated with plasma levels of 39 proteins tested have been previously associated with various complex traits such as heart disease, inflammatory bowel disease, Type 2 diabetes and multiple sclerosis. These data suggest that these plasma protein levels may constitute informative endophenotypes for these complex traits. We found three potential pleiotropic genes: ABO for plasma SELE and ACE levels, FUT2 for CA19-9 and CEA plasma levels and APOE for ApoE and CRP levels. We also found multiple independent signals in loci associated with plasma levels of ApoH, CA19-9, FetuinA, IL6r and LPa. Our study highlights the power of biological traits for genetic studies to identify genetic variants influencing clinically relevant traits, potential pleiotropic effects and complex disease associations in the same locus.
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Affiliation(s)
- Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Jian Xia
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Yefei Cai
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Jenny Lord
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
- Human Genetics Programme, Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | - Jorge L. Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - David Carrell
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Kathleen Black
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - ShengMei Ma
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Benjamin Saef
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Bill Howells
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Sarah Bertelsen
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Matthew Bailey
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Perry G. Ridge
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - David Holtzman
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, 4488 Forest Park Ave., St Louis, MO 63108, USA
- Hope Center for Neurological Disorders. Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO 63110, USA
| | - John C. Morris
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, 4488 Forest Park Ave., St Louis, MO 63108, USA
- Hope Center for Neurological Disorders. Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO 63110, USA
| | - Kelly Bales
- Neuroscience Research Unit, Worldwide Research and Development, Pfizer, Inc., Groton, CT, USA
| | - Eve H. Pickering
- Neuroscience Research Unit, Worldwide Research and Development, Pfizer, Inc., Groton, CT, USA
| | - Jin-Moo Lee
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Laura Heitsch
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - John Kauwe
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Alison Goate
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, 4488 Forest Park Ave., St Louis, MO 63108, USA
- Hope Center for Neurological Disorders. Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO 63110, USA
| | - Laura Piccio
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders. Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO 63110, USA
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14
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Genome-wide association studies identify genetic loci for low von Willebrand factor levels. Eur J Hum Genet 2015; 24:1035-40. [PMID: 26486471 DOI: 10.1038/ejhg.2015.222] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 08/23/2015] [Accepted: 09/11/2015] [Indexed: 01/14/2023] Open
Abstract
Low von Willebrand factor (VWF) levels are associated with bleeding symptoms and are a diagnostic criterion for von Willebrand disease, the most common inherited bleeding disorder. To date, it is unclear which genetic loci are associated with reduced VWF levels. Therefore, we conducted a meta-analysis of genome-wide association studies to identify genetic loci associated with low VWF levels. For this meta-analysis, we included 31 149 participants of European ancestry from 11 community-based studies. From all participants, VWF antigen (VWF:Ag) measurements and genome-wide single-nucleotide polymorphism (SNP) scans were available. Each study conducted analyses using logistic regression of SNPs on dichotomized VWF:Ag measures (lowest 5% for blood group O and non-O) with an additive genetic model adjusted for age and sex. An inverse-variance weighted meta-analysis was performed for VWF:Ag levels. A total of 97 SNPs exceeded the genome-wide significance threshold of 5 × 10(-8) and comprised five loci on four different chromosomes: 6q24 (smallest P-value 5.8 × 10(-10)), 9q34 (2.4 × 10(-64)), 12p13 (5.3 × 10(-22)), 12q23 (1.2 × 10(-8)) and 13q13 (2.6 × 10(-8)). All loci were within or close to genes, including STXBP5 (Syntaxin Binding Protein 5) (6q24), STAB5 (stabilin-5) (12q23), ABO (9q34), VWF (12p13) and UFM1 (ubiquitin-fold modifier 1) (13q13). Of these, UFM1 has not been previously associated with VWF:Ag levels. Four genes that were previously associated with VWF levels (VWF, ABO, STXBP5 and STAB2) were also associated with low VWF levels, and, in addition, we identified a new gene, UFM1, that is associated with low VWF levels. These findings point to novel mechanisms for the occurrence of low VWF levels.
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15
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Mannhalter C. Biomarkers for arterial and venous thrombotic disorders. Hamostaseologie 2015; 34:115-20, 122-6, 128-30, passim. [PMID: 24819458 DOI: 10.5482/hamo-13-08-0041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 03/21/2014] [Indexed: 02/06/2023] Open
Abstract
The haemostatic system maintains the blood in a fluid state, but allows rapid clot formation at sites of vascular injury to prevent excessive bleeding. Unbalances within the haemostatic system can lead to thrombosis. Inspite of successful research our understanding of the disease pathogenesis is still incomplete. There is great hope that genetic, genomic, and epigenetic discoveries will enhance the diagnostic capability, and improve the treatment options. During the preceding 20 years, the identification of polymorphisms and the elucidation of their role in arterial and venous thromboses became an important area of research. Today, a large body of data is available regarding associations of single nucleotide polymorphisms (SNPs) in candidate genes with plasma concentrations and e. g. the risk of ischaemic stroke or myocardial infarction. However, the results for individual polymorphisms and genes are often controversial. It is now well established that besides acquired also hereditary risk factors influence the occurrence of thrombotic events, and environmental factors may add to this risk. Currently available statistical methods are only able to identify combined risk genotypes if very large patient collectives (>10,000 cases) are tested, and appropriate algorithms to evaluate the data have yet to be developed. Further research is needed to understand the functional effects of genetic variants in genes of blood coagulation proteins that are critical to the pathogenesis of arterial and venous thrombotic disorders. In this review genetic variants in selected genes of the haemostatic system and their relevance for arterial and venous thrombosis will be discussed.
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Affiliation(s)
- C Mannhalter
- Univ.-Prof. Dr. Christine Mannhalter Dept. Laboratory Medicine, Medical University Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria, Tel. +43/1/404 00 20 85, Fax +43/1/404 00 20 97, E-mail:
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16
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Freyburger G, Labrouche S, Hubert C, Bauduer F. Haemostaseome-associated SNPs: has the thrombotic phenotype a greater influence than ethnicity? GMT study from Aquitaine including Basque individuals. Thromb Haemost 2014; 113:66-76. [PMID: 25374097 DOI: 10.1160/th14-02-0189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 08/15/2014] [Indexed: 11/05/2022]
Abstract
The Genetic Markers for Thrombosis (GMT) study compared the relative influence of ethnicity and thrombotic phenotype regarding the distribution of SNPs implicated in haemostasis pathophysiology ("haemostaseome"). We assessed 384 SNPs in three groups, each of 480 subjects: 1) general population of Aquitaine region (Southwestern France) used as control; 2) patients with venous thromboembolism from the same area; and 3) autochthonous Basques, a genetic isolate, who demonstrate unusual characteristics regarding the coagulation system. This study sought to evaluate i) the value of looking for a large number of genes in order to identify new genetic markers of thrombosis, ii) the value of investigating low risk factors and potential preferential associations, iii) the impact of ethnicity on the characterisation of markers for thrombosis. We did not detect any previously unrecognised SNP significantly associated with thrombosis risk or any preferential associations of low-risk factors in patients with thrombosis. The sum of ϰ² values for our 110 significant SNPs demonstrated a smaller genetic distance between patients and controls (321 cumulated ϰ² value) than between Basques and controls (1,570 cumulated ϰ² value). Hence, our study confirms the genetic particularity of Basques especially regarding a significantly lower expression of the non-O blood group (p< 0.0004). This is mitigated by a higher prevalence of factor II Leiden (p< 0.02) while factor V Leiden prevalence does not differ. Numerous other differences covering a wide range of proteins of the haemostaseome may result in an overall different genetic risk for venous thromboembolism.
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Affiliation(s)
- Geneviève Freyburger
- Geneviève Freyburger, Laboratory for Hematology, CHU Pellegrin, 33076 Bordeaux cedex, France, Tel.: +335 57 820 206, Fax: +335 56 79 60 20, E-mail:
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17
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Li J, Lange LA, Duan Q, Lu Y, Singleton AB, Zonderman AB, Evans MK, Li Y, Taylor HA, Willis MS, Nalls M, Wilson JG, Lange EM. Genome-wide admixture and association study of serum iron, ferritin, transferrin saturation and total iron binding capacity in African Americans. Hum Mol Genet 2014; 24:572-81. [PMID: 25224454 DOI: 10.1093/hmg/ddu454] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Iron is an essential component of many important proteins and enzymes, including hemoglobin, which is responsible for carrying oxygen to the cells. African Americans (AAs) have a greater prevalence of iron deficiency compared with European Americans. We conducted genome-wide admixture-mapping and association studies for serum iron, serum ferritin, transferrin saturation (SAT) and total iron binding capacity (TIBC) in 2347 AAs participating in the Jackson Heart Study (JHS). Follow-up replication analyses for JHS iron-trait associated SNPs were conducted in 329 AA participants in the Healthy Aging in Neighborhoods of Diversity across the Life Span study (HANDLS). Higher estimated proportions of global African ancestry were significantly associated with lower levels of iron (P = 2.4 × 10(-5)), SAT (P = 0.0019) and TIBC (P = 0.042). We observed significant associations (P < 5 × 10(-8)) between serum TIBC levels and two independent SNPs around TF on chromosome 3, the first report of a genome-wide significant second independent signal in this region, and SNPs near two novel genes: HDGFL1 on chromosome 6 and MAF on chromosome 16. We also observed significant associations between ferritin levels and SNPs near GAB3 on chromosome X. We replicated our two independent associations at TF and our association at GAB3 in HANDLS. Our study provides evidence for both shared and unique genetic risk factors that are associated with iron-related measures in AAs. The top two variants in TF explain 11.2% of the total variation in TIBC levels in AAs after accounting for age, gender, body mass index and background ancestry.
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Affiliation(s)
| | | | | | | | | | | | - Michele K Evans
- Health Disparities Unit, National Institute on Aging, National Institutes of Health, Bethesda, MD 21225, USA
| | - Yun Li
- Department of Genetics Department of Biostatistics and
| | - Herman A Taylor
- Department of Medicine and School of Health Sciences, Jackson State University, Jackson, MS 39217, USA and Division of Natural Science, Tougaloo College, Tougaloo, MS 39174, USA
| | - Monte S Willis
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Ethan M Lange
- Department of Genetics Department of Biostatistics and
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Kraja AT, Chasman DI, North KE, Reiner AP, Yanek LR, Kilpeläinen TO, Smith JA, Dehghan A, Dupuis J, Johnson AD, Feitosa MF, Tekola-Ayele F, Chu AY, Nolte IM, Dastani Z, Morris A, Pendergrass SA, Sun YV, Ritchie MD, Vaez A, Lin H, Ligthart S, Marullo L, Rohde R, Shao Y, Ziegler MA, Im HK, Schnabel RB, Jørgensen T, Jørgensen ME, Hansen T, Pedersen O, Stolk RP, Snieder H, Hofman A, Uitterlinden AG, Franco OH, Ikram MA, Richards JB, Rotimi C, Wilson JG, Lange L, Ganesh SK, Nalls M, Rasmussen-Torvik LJ, Pankow JS, Coresh J, Tang W, Linda Kao WH, Boerwinkle E, Morrison AC, Ridker PM, Becker DM, Rotter JI, Kardia SLR, Loos RJF, Larson MG, Hsu YH, Province MA, Tracy R, Voight BF, Vaidya D, O'Donnell CJ, Benjamin EJ, Alizadeh BZ, Prokopenko I, Meigs JB, Borecki IB. Pleiotropic genes for metabolic syndrome and inflammation. Mol Genet Metab 2014; 112:317-38. [PMID: 24981077 PMCID: PMC4122618 DOI: 10.1016/j.ymgme.2014.04.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 04/26/2014] [Accepted: 04/26/2014] [Indexed: 01/11/2023]
Abstract
Metabolic syndrome (MetS) has become a health and financial burden worldwide. The MetS definition captures clustering of risk factors that predict higher risk for diabetes mellitus and cardiovascular disease. Our study hypothesis is that additional to genes influencing individual MetS risk factors, genetic variants exist that influence MetS and inflammatory markers forming a predisposing MetS genetic network. To test this hypothesis a staged approach was undertaken. (a) We analyzed 17 metabolic and inflammatory traits in more than 85,500 participants from 14 large epidemiological studies within the Cross Consortia Pleiotropy Group. Individuals classified with MetS (NCEP definition), versus those without, showed on average significantly different levels for most inflammatory markers studied. (b) Paired average correlations between 8 metabolic traits and 9 inflammatory markers from the same studies as above, estimated with two methods, and factor analyses on large simulated data, helped in identifying 8 combinations of traits for follow-up in meta-analyses, out of 130,305 possible combinations between metabolic traits and inflammatory markers studied. (c) We performed correlated meta-analyses for 8 metabolic traits and 6 inflammatory markers by using existing GWAS published genetic summary results, with about 2.5 million SNPs from twelve predominantly largest GWAS consortia. These analyses yielded 130 unique SNPs/genes with pleiotropic associations (a SNP/gene associating at least one metabolic trait and one inflammatory marker). Of them twenty-five variants (seven loci newly reported) are proposed as MetS candidates. They map to genes MACF1, KIAA0754, GCKR, GRB14, COBLL1, LOC646736-IRS1, SLC39A8, NELFE, SKIV2L, STK19, TFAP2B, BAZ1B, BCL7B, TBL2, MLXIPL, LPL, TRIB1, ATXN2, HECTD4, PTPN11, ZNF664, PDXDC1, FTO, MC4R and TOMM40. Based on large data evidence, we conclude that inflammation is a feature of MetS and several gene variants show pleiotropic genetic associations across phenotypes and might explain a part of MetS correlated genetic architecture. These findings warrant further functional investigation.
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Affiliation(s)
- Aldi T Kraja
- Division of Statistical Genomics, Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Kari E North
- Department of Epidemiology and Carolina Center for Genome Sciences, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC, USA.
| | | | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Tuomas O Kilpeläinen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA.
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA; National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, USA.
| | - Andrew D Johnson
- National Heart, Lung and Blood Institute (NHLBI) Division of Intramural Research and NHLBI's Framingham Heart Study, Framingham, MA, USA.
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Fasil Tekola-Ayele
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Audrey Y Chu
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Zari Dastani
- Department of Epidemiology, Biostatistics and Occupational Health, Jewish General Hospital, Lady Davis Institute, McGill University Montreal, Quebec, Canada.
| | - Andrew Morris
- The Welcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Sarah A Pendergrass
- Department of Biochemistry and Molecular Biology, Eberly College of Science and The Huck Institutes of the Life Sciences, The Pennsylvania State University, PA, USA.
| | - Yan V Sun
- Department of Epidemiology, Rollins School of Public Health, and Department of Biomedical Informatics, School of Medicine, Emory University, Atlanta, GA, USA.
| | - Marylyn D Ritchie
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
| | - Ahmad Vaez
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Honghuang Lin
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
| | - Symen Ligthart
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Letizia Marullo
- The Welcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
| | - Rebecca Rohde
- Department of Epidemiology and Carolina Center for Genome Sciences, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC, USA.
| | - Yaming Shao
- Department of Epidemiology and Carolina Center for Genome Sciences, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC, USA.
| | - Mark A Ziegler
- Division of Biostatistics, MSIBS Program, Washington University School of Medicine, St. Louis, MO, USA.
| | - Hae Kyung Im
- Department of Health Studies, University of Chicago, IL, USA.
| | - Renate B Schnabel
- Department of General and Interventional Cardiology University Heart Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Torben Jørgensen
- Research Centre for Prevention and Health, Glostrup Hospital, Glostrup, Denmark; Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark.
| | | | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Ronald P Stolk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Oscar H Franco
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - J Brent Richards
- Department of Epidemiology, Biostatistics and Occupational Health, Jewish General Hospital, Lady Davis Institute, McGill University Montreal, Quebec, Canada; Department of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Canada; Department of Twin Research, King's College, London, UK.
| | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | | | - Leslie Lange
- Department of Genetics, University of North Carolina, NC, USA.
| | - Santhi K Ganesh
- Department of Internal Medicine, University of Michigan, MI, USA.
| | - Mike Nalls
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD, USA.
| | | | - James S Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA.
| | - Josef Coresh
- Department of Medicine, Epidemiology, Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Weihong Tang
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA.
| | - W H Linda Kao
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas - Houston Health Science Center at Houston, Houston, TX, USA.
| | - Alanna C Morrison
- Human Genetics Center, University of Texas - Houston Health Science Center at Houston, Houston, TX, USA.
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Diane M Becker
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute (LA BioMed), Harbor-UCLA Medical Center, Torrance, CA, USA.
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA.
| | - Ruth J F Loos
- The Genetics of Obesity and Related Metabolic Traits Program, The Charles Bronfman Institute for Personalized Medicine, The Mindich Child Health and Development Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Martin G Larson
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA; National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, USA; Department of Mathematics and Statistics, Boston University, Boston, MA, USA.
| | - Yi-Hsiang Hsu
- Hebrew Senior Life Institute for Aging Research, Harvard Medical School and Molecular and Integrative Physiological Sciences, Harvard School of Public Health, Boston, MA, USA.
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Russell Tracy
- University of Vermont College of Medicine, Burlington, VT, USA.
| | - Benjamin F Voight
- Department of Pharmacology, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, USA.
| | - Dhananjay Vaidya
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Christopher J O'Donnell
- National Heart, Lung and Blood Institute (NHLBI) Division of Intramural Research and NHLBI's Framingham Heart Study, Framingham, MA, USA.
| | - Emelia J Benjamin
- National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, USA; Cardiology and Preventive Medicine Sections, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
| | - Behrooz Z Alizadeh
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Inga Prokopenko
- Department of Genomics of Common Diseases, School of Public Health, Imperial College London, London W12 0NN, UK.
| | - James B Meigs
- General Medicine Division, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Ingrid B Borecki
- Division of Statistical Genomics, Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
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19
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Weng LC, Tang W, Rich SS, Smith NL, Redline S, O'Donnell CJ, Basu S, Reiner AP, Delaney JA, Tracy RP, Palmer CD, Young T, Yang Q, Folsom AR, Cushman M. A genetic association study of D-dimer levels with 50K SNPs from a candidate gene chip in four ethnic groups. Thromb Res 2014; 134:462-7. [PMID: 24908450 PMCID: PMC4111961 DOI: 10.1016/j.thromres.2014.05.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/19/2014] [Accepted: 05/13/2014] [Indexed: 11/15/2022]
Abstract
INTRODUCTION D-dimer, a fibrin degradation product, is related to risk of cardiovascular disease and venous thromboembolism. Genetic determinants of D-dimer are not well characterized; notably, few data have been reported for African American (AA), Asian, and Hispanic populations. MATERIALS AND METHODS We conducted a large-scale candidate gene association study to identify variants in genes associated with D-dimer levels in multi-ethnic populations. Four cohorts, comprising 6,848 European Americans (EAs), 2,192 AAs, 670 Asians, and 1,286 Hispanics in the National Heart, Lung, and Blood Institute Candidate Gene Association Resource consortium, were assembled. Approximately 50,000 genotyped single nucleotide polymorphisms (SNPs) in 2,000 cardiovascular disease gene loci were analyzed by linear regression, adjusting for age, sex, study site, and principal components in each cohort and ethnic group. Results across studies were combined within each ethnic group by meta-analysis. RESULTS Twelve SNPs in coagulation factor V (F5) and 3 SNPs in the fibrinogen alpha chain (FGA) were significantly associated with D-dimer level in EAs with p<2.0×10(-6). The signal for the most associated SNP in F5 (rs6025, factor V Leiden) was replicated in Hispanics (p=0.023), while that for the top functional SNP in FGA (rs6050) was replicated in AAs (p=0.006). No additional SNPs were significantly associated with D-dimer. CONCLUSIONS Our study replicated previously reported associations of D-dimer with SNPs in F5 and FGA in EAs; we demonstrated replication of the association of D-dimer with FGA rs6050 in AAs and the factor V Leiden variant in Hispanics.
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Affiliation(s)
- Lu-Chen Weng
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Weihong Tang
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA.
| | - Stephen S Rich
- Department of Public Health Sciences and the Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Nicholas L Smith
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA; Group Health Research Institute, Group Health Cooperative, Seattle, WA, USA; Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, USA
| | - Susan Redline
- Division of Sleep Medicine, Department of Medicine, Brigham and Women's Hospital and Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | - Saonli Basu
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Alexander P Reiner
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Joseph A Delaney
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Russell P Tracy
- Departments of Pathology and Biochemistry, University of Vermont, Burlington, VT, USA
| | - Cameron D Palmer
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Taylor Young
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Qiong Yang
- The NHLBI's Framingham Heart Study, Framingham, MA, USA; Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Aaron R Folsom
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Mary Cushman
- Departments of Medicine and Pathology, University of Vermont, Burlington, VT, USA
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20
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Golub MS, Hogrefe CE, Malka R, Higgins JM. Developmental plasticity of red blood cell homeostasis. Am J Hematol 2014; 89:459-66. [PMID: 24415575 DOI: 10.1002/ajh.23666] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 01/08/2014] [Indexed: 02/03/2023]
Abstract
Most human physiologic set points like body temperature are tightly regulated and show little variation between healthy individuals. Red blood cell (RBC) characteristics such as hematocrit and mean cell volume are stable within individuals but can vary by 20% from one healthy person to the next. The mechanisms for the majority of this inter-individual variation are unknown and do not appear to involve common genetic variation. Here, we show that environmental conditions present during development, namely in utero iron availability, can exert long-term influence on a set point related to the RBC life cycle. In a controlled study of rhesus monkeys and a retrospective study of humans, we use a mathematical model of in vivo RBC population dynamics to show that in utero iron deficiency is associated with a lowered threshold for RBC clearance and turnover. This in utero effect is plastic, persisting at least 2 years after birth and after the cessation of iron deficiency. Our study reports a rare instance of developmental plasticity in the human hematologic system and also shows how mathematical modeling can be used to identify cellular mechanisms involved in the adaptive control of homeostatic set points.
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Affiliation(s)
- Mari S. Golub
- Department of Environmental Toxicology; University of California Davis; Davis California
- California National Primate Research Center; University of California Davis; Davis California
| | - Casey E. Hogrefe
- California National Primate Research Center; University of California Davis; Davis California
| | - Roy Malka
- Center for Systems Biology and Department of Pathology; Massachusetts General Hospital; Boston Massachusetts
- Department of Systems Biology; Harvard Medical School; Boston Massachusetts
| | - John M. Higgins
- Center for Systems Biology and Department of Pathology; Massachusetts General Hospital; Boston Massachusetts
- Department of Systems Biology; Harvard Medical School; Boston Massachusetts
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21
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Genome-wide association studies identified novel loci for non-high-density lipoprotein cholesterol and its postprandial lipemic response. Hum Genet 2014; 133:919-30. [PMID: 24604477 DOI: 10.1007/s00439-014-1435-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 02/24/2014] [Indexed: 12/27/2022]
Abstract
Non-high-density lipoprotein cholesterol(NHDL) is an independent and superior predictor of CVD risk as compared to low-density lipoprotein alone. It represents a spectrum of atherogenic lipid fractions with possibly a distinct genomic signature. We performed genome-wide association studies (GWAS) to identify loci influencing baseline NHDL and its postprandial lipemic (PPL) response. We carried out GWAS in 4,241 participants of European descent. Our discovery cohort included 928 subjects from the Genetics of Lipid-Lowering Drugs and Diet Network Study. Our replication cohorts included 3,313 subjects from the Heredity and Phenotype Intervention Heart Study and Family Heart Study. A linear mixed model using the kinship matrix was used for association tests. The best association signal was found in a tri-genic region at RHOQ-PIGF-CRIPT for baseline NHDL (lead SNP rs6544903, discovery p = 7e-7, MAF = 2 %; validation p = 6e-4 at 0.1 kb upstream neighboring SNP rs3768725, and 5e-4 at 0.7 kb downstream neighboring SNP rs6733143, MAF = 10 %). The lead and neighboring SNPs were not perfect surrogate proxies to each other (D' = 1, r (2) = 0.003) but they seemed to be partially dependent (likelihood ration test p = 0.04). Other suggestive loci (discovery p < 1e-6) included LOC100419812 and LOC100288337 for baseline NHDL, and LOC100420502 and CDH13 for NHDL PPL response that were not replicated (p > 0.01). The current and first GWAS of NHDL yielded an interesting common variant in RHOQ-PIGF-CRIPT influencing baseline NHDL levels. Another common variant in CDH13 for NHDL response to dietary high-fat intake challenge was also suggested. Further validations for both loci from large independent studies, especially interventional studies, are warranted.
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22
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23
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Gaunt TR, Zabaneh D, Shah S, Guyatt A, Ladroue C, Kumari M, Drenos F, Shah T, Talmud PJ, Casas JP, Lowe G, Rumley A, Lawlor DA, Kivimaki M, Whittaker J, Hingorani AD, Humphries SE, Day IN. Gene-centric association signals for haemostasis and thrombosis traits identified with the HumanCVD BeadChip. Thromb Haemost 2013; 110:995-1003. [PMID: 24178511 DOI: 10.1160/th13-02-0087] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 08/05/2013] [Indexed: 01/08/2023]
Abstract
Coagulation phenotypes show strong intercorrelations, affect cardiovascular disease risk and are influenced by genetic variants. The objective of this study was to search for novel genetic variants influencing the following coagulation phenotypes: factor VII levels, fibrinogen levels, plasma viscosity and platelet count. We genotyped the British Women's Heart and Health Study (n=3,445) and the Whitehall II study (n=5,059) using the Illumina HumanCVD BeadArray to investigate genetic associations and pleiotropy. In addition to previously reported associations (SH2B3, F7/F10, PROCR, GCKR, FGA/FGB/FGG, IL5), we identified novel associations at GRK5 (rs10128498, p=1.30x10(-6)), GCKR (rs1260326, p=1.63x10(-6)), ZNF259-APOA5 (rs651821, p=7.17x10(-6)) with plasma viscosity; and at CSF1 (rs333948, p=8.88x10(-6)) with platelet count. A pleiotropic effect was identified in GCKR which associated with factor VII (p=2.16x10(-7)) and plasma viscosity (p=1.63x10(-6)), and, to a lesser extent, ZNF259-APOA5 which also associated with factor VII and fibrinogen (p<1.00x10-²) and plasma viscosity (p<1.00x10(-5)). Triglyceride associated variants were overrepresented in factor VII and plasma viscosity associations. Adjusting for triglyceride levels resulted in attenuation of associations at the GCKR and ZNF259-APOA5 loci. In addition to confirming previously reported associations, we identified four single nucleotide polymorphisms (SNPs) associated with plasma viscosity and platelet count and found evidence of pleiotropic effects with SNPs in GCKR and ZNF259-APOA5. These triglyceride-associated, pleiotropic SNPs suggest a possible causal role for triglycerides in coagulation.
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Affiliation(s)
- Tom R Gaunt
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Delilah Zabaneh
- University College London Genetics Institute, Department of Genetics, Environment and Evolution, Gower St, London WC1E 6BT, UK
| | - Sonia Shah
- University College London Genetics Institute, Department of Genetics, Environment and Evolution, Gower St, London WC1E 6BT, UK
| | - Anna Guyatt
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Christophe Ladroue
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Meena Kumari
- Genetic Epidemiology Group, Department of Epidemiology and Public Health, University College London, 1-19 Torrington Street, London WC1E 6BT, UK
| | - Fotios Drenos
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, 5 University St, London WC1E 6JF, UK
| | - Tina Shah
- Genetic Epidemiology Group, Department of Epidemiology and Public Health, University College London, 1-19 Torrington Street, London WC1E 6BT, UK
| | - Philippa J Talmud
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, 5 University St, London WC1E 6JF, UK
| | - Juan Pablo Casas
- Department of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.,Institute of Cardiovascular Science, University College London, Gower Street, London, WC1E 6BT, UK
| | - Gordon Lowe
- Institute of Cardiovascular & Medical Sciences, Room 335, BHF Glasgow Cardiovascular Research Centre, University of Glasgow, 126 University Place, Glasgow, G12 8TA, UK
| | - Ann Rumley
- Institute of Cardiovascular & Medical Sciences, Room 335, BHF Glasgow Cardiovascular Research Centre, University of Glasgow, 126 University Place, Glasgow, G12 8TA, UK
| | - Debbie A Lawlor
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Mika Kivimaki
- Genetic Epidemiology Group, Department of Epidemiology and Public Health, University College London, 1-19 Torrington Street, London WC1E 6BT, UK
| | - John Whittaker
- Department of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.,Quantitative Sciences, GlaxoSmithKline, Stevenage, UK
| | - Aroon D Hingorani
- Genetic Epidemiology Group, Department of Epidemiology and Public Health, University College London, 1-19 Torrington Street, London WC1E 6BT, UK
| | - Steve E Humphries
- University College London Genetics Institute, Department of Genetics, Environment and Evolution, Gower St, London WC1E 6BT, UK.,Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, 5 University St, London WC1E 6JF, UK
| | - Ian N Day
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
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24
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Rodríguez JM, Wolfrum S, Robblee M, Chen KY, Gilbert ZN, Choi JH, Teupser D, Breslow JL. Altered expression of Raet1e, a major histocompatibility complex class 1-like molecule, underlies the atherosclerosis modifier locus Ath11 10b. Circ Res 2013; 113:1054-64. [PMID: 23948654 DOI: 10.1161/circresaha.113.302052] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
RATIONALE Quantitative trait locus mapping of an intercross between C57.Apoe⁻/⁻ and FVB.Apoe⁻/⁻ mice revealed an atherosclerosis locus controlling aortic root lesion area on proximal chromosome 10, Ath11. In a previous work, subcongenic analysis showed Ath11 to be complex with proximal (10a) and distal (10b) regions. OBJECTIVE To identify the causative genetic variation underlying the atherosclerosis modifier locus Ath11 10b. METHODS AND RESULTS We now report subcongenic J, which narrows the 10b region to 5 genes, Myb, Hbs1L, Aldh8a1, Sgk1, and Raet1e. Sequence analysis of these genes revealed no amino acid coding differences between the parental strains. However, comparing aortic expression of these genes between F1.Apoe⁻/⁻ Chr10SubJ((B/F)) and F1.Apoe⁻/⁻ Chr10SubJ((F/F)) uncovered a consistent difference only for Raet1e, with decreased, virtually background, expression associated with increased atherosclerosis in the latter. The key role of Raet1e was confirmed by showing that transgene-induced aortic overexpression of Raet1e in F1.Apoe⁻/⁻ Chr10SubJ((F/F)) mice decreased atherosclerosis. Promoter reporter constructs comparing C57 and FVB sequences identified an FVB mutation in the core of the major aortic transcription start site abrogating activity. CONCLUSIONS This nonbiased approach has revealed Raet1e, a major histocompatibility complex class 1-like molecule expressed in lesional aortic endothelial cells and macrophage-rich regions, as a novel atherosclerosis gene and represents one of the few successes of the quantitative trait locus strategy in complex diseases.
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Golub MS, Hogrefe CE. Predictors of hemoglobin variability in a population of weaning age (3- to 4-month old) rhesus monkeys. Am J Primatol 2013; 75:1139-46. [PMID: 23824639 DOI: 10.1002/ajp.22176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Revised: 05/04/2013] [Accepted: 06/05/2013] [Indexed: 11/07/2022]
Abstract
Sources of variability in hemoglobin concentration in blood were examined in over 600 rhesus infants at the California National Primate Research Center who had complete blood counts (CBCs) conducted at 3-4 months of age. These infants were born and raised in outdoor social housing. Hemoglobin values ranged from 8.5 to 15.3 µg/dl with a mean and standard deviation of 12.2±0.8 µg/dl. As expected, hemoglobin was strongly associated with the number of red blood cells (RBCs). Plasma protein concentration, an indicator of blood volume, was not a predictor. Associations with infant age, weight and sex, infant serum cortisol, dam's reproductive history, and birth year, month and location were evaluated in regression analyses. Cage of origin, maternal age at delivery and infant weight were associated with hemoglobin concentrations. Unexpectedly, serum cortisol, determined at the same time as CBC samples were taken, was the strongest predictor of hemoglobin concentration. The basis, as well as the functional significance, of the variation in infant hemoglobin and its association with serum cortisol in this population of rhesus fed a nutritionally optimized diet and housed under standard conditions is relevant to the development of both nonhuman and human primate infants.
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Affiliation(s)
- Mari S Golub
- Department of Environmental Toxicology, University of California, Davis, California
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26
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Gianfagna F, Tamburrelli C, Vohnout B, Crescente M, Izzi B, Pampuch A, De Curtis A, Di Castelnuovo A, Cutrone A, Napoleone E, Tayo B, Lorenzet R, Nanni L, Arca M, Donati MB, de Gaetano G, Cerletti C, Iacoviello L. Heritability, genetic correlation and linkage to the 9p21.3 region of mixed platelet-leukocyte conjugates in families with and without early myocardial infarction. Nutr Metab Cardiovasc Dis 2013; 23:684-692. [PMID: 22633792 DOI: 10.1016/j.numecd.2012.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 02/02/2012] [Accepted: 02/27/2012] [Indexed: 11/25/2022]
Abstract
BACKGROUND AND AIMS Variations in mixed platelet-leukocyte conjugate formation in human whole blood could be genetically determined. We quantified platelet and leukocyte activation and interaction in families with or without early myocardial infarction and evaluated their heritability, genetic correlation and linkage to the 9p21.3 region. METHODS AND RESULTS The study population included 739 subjects (≥ 15 years old) from 54 large pedigrees, 23 with and 31 without familial myocardial infarction. Mixed platelet-leukocyte conjugates and markers of platelet or leukocyte activation (P-selectin, CD11b and L-selectin surface expression) were measured both before and after in vitro blood stimulation with collagen-ADP. All traits had significant genetic components (17.5-65.3% of the phenotypic variability), while shared household effects (0-39.6%) and environmental covariates (0-10.2%) tended to be smaller. Stimulated platelet-polymorphonuclear leukocyte (PMN) and platelet-monocyte conjugates showed the highest linkage to the 9p21.3 region (LOD = 0.94 and 1.33, respectively; empirical p value = 0.017 and 0.009). PMN markers resulted strongly genetically correlated between them in bivariate analysis among pairs of quantitative traits. CONCLUSION This study supports a genetic regulation of human mixed platelet-leukocyte conjugates.
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Affiliation(s)
- F Gianfagna
- Laboratory of Genetic and Environmental Epidemiology, Fondazione di Ricerca e Cura Giovanni Paolo II, Università Cattolica, Campobasso, Italy
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Hinckley JD, Abbott D, Burns TL, Heiman M, Shapiro AD, Wang K, Di Paola J. Quantitative trait locus linkage analysis in a large Amish pedigree identifies novel candidate loci for erythrocyte traits. Mol Genet Genomic Med 2013; 1:131-141. [PMID: 24058921 PMCID: PMC3775389 DOI: 10.1002/mgg3.16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We characterized a large Amish pedigree and, in 384 pedigree members, analyzed the genetic variance components with covariate screen as well as genome-wide quantitative trait locus (QTL) linkage analysis of red blood cell count (RBC), hemoglobin (HB), hematocrit (HCT), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), red cell distribution width (RDW), platelet count (PLT), and white blood cell count (WBC) using SOLAR. Age and gender were found to be significant covariates in many CBC traits. We obtained significant heritability estimates for RBC, MCV, MCH, MCHC, RDW, PLT, and WBC. We report four candidate loci with Logarithm of the odds (LOD) scores above 2.0: 6q25 (MCH), 9q33 (WBC), 10p12 (RDW), and 20q13 (MCV). We also report eleven candidate loci with LOD scores between 1.5 and <2.0. Bivariate linkage analysis of MCV and MCH on chromosome 20 resulted in a higher maximum LOD score of 3.14. Linkage signals on chromosomes 4q28, 6p22, 6q25, and 20q13 are concomitant with previously reported QTL. All other linkage signals reported herein represent novel evidence of candidate QTL. Interestingly rs1800562, the most common causal variant of hereditary hemochromatosis in HFE (6p22) was associated with MCH and MCHC in this family. Linkage studies like the one presented here will allow investigators to focus the search for rare variants amidst the noise encountered in the large amounts of data generated by whole-genome sequencing.
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Affiliation(s)
- Jesse D Hinckley
- Department of Pediatrics and Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO
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Cakmak G, Alkan FA, Korkmaz K, Saglam ZA, Karis D, Yenigun M, Ercan M. Blood viscosity as a forgotten factor and its effect on pulmonary flow. TRANSLATIONAL RESPIRATORY MEDICINE 2013; 1:3. [PMID: 27234385 PMCID: PMC6733503 DOI: 10.1186/2213-0802-1-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 01/09/2013] [Indexed: 11/15/2022]
Abstract
Background The effect of smoking on blood viscosity is widely known. There are, however, few studies on the effect of blood viscosity on pulmonary circulation. Methods We aimed to observe the relationship between blood viscosity and pulmonary circulation among smokers and non-smokers. The study comprised 114 subjects in three groups: group 1, ex-smokers; group 2, smoked at least 10 packs/year and still smoking; group 3, never smoked. Blood viscosity (BV), pulmonary blood flow (PBF), and right ventricular systolic pressure (RVSP) were measured in all subjects. Results PBF was significantly lower in group 1 compared with group 3 (p < 0.05). BV in group 1 was significantly higher than group 3 (p < 0.05) while BV in group 2 was significantly higher than group 3 (p < 0.05). PBF in group 2 was significantly lower than group 3 (p = 0.01). Conclusions We believe that BV is a significant and forgotten factor that plays an important role in pulmonary and cardiovascular diseases. BV may affect PF even during the course of smoking, and before the clinical onset of chronic obstructive pulmonary disease (COPD). Therefore, individuals at risk of pulmonary hypertension could be detected earlier with a simple blood test.
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Affiliation(s)
- Gulfidan Cakmak
- Department of Chest Disease, Haseki Training and Research Hospital, Millet St Fatih, Istanbul, 34096, Turkey.
| | - Fatma Ates Alkan
- Department of Biophysics, Istanbul University Cerrahpasa Medical Faculty, Fatih, Istanbul, 34098, Turkey
| | - Kazim Korkmaz
- Department of Cardiology Disease, Haseki Training and Research Hospital, Millet St Fatih, Istanbul, 34096, Turkey
| | - Zuhal Aydan Saglam
- Department of Family Practitioners, Haseki Training and Research Hospital, Millet St Fatih, Istanbul, 34096, Turkey
| | - Denizhan Karis
- Department of Biophysics, Istanbul University Cerrahpasa Medical Faculty, Fatih, Istanbul, 34098, Turkey
| | - Mustafa Yenigun
- Department of Internal Disease, Haseki Training and Research Hospital, Millet St Fatih, Istanbul, 34096, Turkey
| | - Meltem Ercan
- Department of Biophysics, Istanbul University Cerrahpasa Medical Faculty, Fatih, Istanbul, 34098, Turkey
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Verdugo RA, Zeller T, Rotival M, Wild PS, Münzel T, Lackner KJ, Weidmann H, Ninio E, Trégouët DA, Cambien F, Blankenberg S, Tiret L. Graphical modeling of gene expression in monocytes suggests molecular mechanisms explaining increased atherosclerosis in smokers. PLoS One 2013; 8:e50888. [PMID: 23372645 PMCID: PMC3553098 DOI: 10.1371/journal.pone.0050888] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 10/24/2012] [Indexed: 01/07/2023] Open
Abstract
Smoking is a risk factor for atherosclerosis with reported widespread effects on gene expression in circulating blood cells. We hypothesized that a molecular signature mediating the relation between smoking and atherosclerosis may be found in the transcriptome of circulating monocytes. Genome-wide expression profiles and counts of atherosclerotic plaques in carotid arteries were collected in 248 smokers and 688 non-smokers from the general population. Patterns of co-expressed genes were identified by Independent Component Analysis (ICA) and network structure of the pattern-specific gene modules was inferred by the PC-algorithm. A likelihood-based causality test was implemented to select patterns that fit models containing a path “smoking→gene expression→plaques”. Robustness of the causal inference was assessed by bootstrapping. At a FDR ≤0.10, 3,368 genes were associated to smoking or plaques, of which 93% were associated to smoking only. SASH1 showed the strongest association to smoking and PPARG the strongest association to plaques. Twenty-nine gene patterns were identified by ICA. Modules containing SASH1 and PPARG did not show evidence for the “smoking→gene expression→plaques” causality model. Conversely, three modules had good support for causal effects and exhibited a network topology consistent with gene expression mediating the relation between smoking and plaques. The network with the strongest support for causal effects was connected to plaques through SLC39A8, a gene with known association to HDL-cholesterol and cellular uptake of cadmium from tobacco, while smoking was directly connected to GAS6, a gene reported to have anti-inflammatory effects in atherosclerosis and to be up-regulated in the placenta of women smoking during pregnancy. Our analysis of the transcriptome of monocytes recovered genes relevant for association to smoking and atherosclerosis, and connected genes that before, were only studied in separate contexts. Inspection of correlation structure revealed candidates that would be missed by expression-phenotype association analysis alone.
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Affiliation(s)
| | - Tanja Zeller
- University Heart Center Hamburg, Department of General and Interventional Cardiology, Hamburg, Germany
| | - Maxime Rotival
- INSERM UMR_S 937, Pierre and Marie Curie University, Paris, France
| | - Philipp S. Wild
- Department of Medicine II, University Medical Center Mainz, Mainz, Germany
- Clinical Epidemiology, Center for Thrombosis and Haemostasis, University Medical Center Mainz, Mainz, Germany
| | - Thomas Münzel
- Department of Medicine II, University Medical Center Mainz, Mainz, Germany
| | - Karl J. Lackner
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Mainz, Germany
| | - Henri Weidmann
- INSERM UMR_S 937, Pierre and Marie Curie University, Paris, France
| | - Ewa Ninio
- INSERM UMR_S 937, Pierre and Marie Curie University, Paris, France
| | | | - François Cambien
- INSERM UMR_S 937, Pierre and Marie Curie University, Paris, France
| | - Stefan Blankenberg
- University Heart Center Hamburg, Department of General and Interventional Cardiology, Hamburg, Germany
| | - Laurence Tiret
- INSERM UMR_S 937, Pierre and Marie Curie University, Paris, France
- * E-mail:
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Huang J, Sabater-Lleal M, Asselbergs FW, Tregouet D, Shin SY, Ding J, Baumert J, Oudot-Mellakh T, Folkersen L, Johnson AD, Smith NL, Williams SM, Ikram MA, Kleber ME, Becker DM, Truong V, Mychaleckyj JC, Tang W, Yang Q, Sennblad B, Moore JH, Williams FMK, Dehghan A, Silbernagel G, Schrijvers EMC, Smith S, Karakas M, Tofler GH, Silveira A, Navis GJ, Lohman K, Chen MH, Peters A, Goel A, Hopewell JC, Chambers JC, Saleheen D, Lundmark P, Psaty BM, Strawbridge RJ, Boehm BO, Carter AM, Meisinger C, Peden JF, Bis JC, McKnight B, Öhrvik J, Taylor K, Franzosi MG, Seedorf U, Collins R, Franco-Cereceda A, Syvänen AC, Goodall AH, Yanek LR, Cushman M, Müller-Nurasyid M, Folsom AR, Basu S, Matijevic N, van Gilst WH, Kooner JS, Hofman A, Danesh J, Clarke R, Meigs JB, Kathiresan S, Reilly MP, Klopp N, Harris TB, Winkelmann BR, Grant PJ, Hillege HL, Watkins H, Spector TD, Becker LC, Tracy RP, März W, Uitterlinden AG, Eriksson P, Cambien F, Morange PE, Koenig W, Soranzo N, van der Harst P, Liu Y, O'Donnell CJ, Hamsten A. Genome-wide association study for circulating levels of PAI-1 provides novel insights into its regulation. Blood 2012; 120:4873-81. [PMID: 22990020 PMCID: PMC3520624 DOI: 10.1182/blood-2012-06-436188] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 08/14/2012] [Indexed: 11/20/2022] Open
Abstract
We conducted a genome-wide association study to identify novel associations between genetic variants and circulating plasminogen activator inhibitor-1 (PAI-1) concentration, and examined functional implications of variants and genes that were discovered. A discovery meta-analysis was performed in 19 599 subjects, followed by replication analysis of genome-wide significant (P < 5 × 10(-8)) single nucleotide polymorphisms (SNPs) in 10 796 independent samples. We further examined associations with type 2 diabetes and coronary artery disease, assessed the functional significance of the SNPs for gene expression in human tissues, and conducted RNA-silencing experiments for one novel association. We confirmed the association of the 4G/5G proxy SNP rs2227631 in the promoter region of SERPINE1 (7q22.1) and discovered genome-wide significant associations at 3 additional loci: chromosome 7q22.1 close to SERPINE1 (rs6976053, discovery P = 3.4 × 10(-10)); chromosome 11p15.2 within ARNTL (rs6486122, discovery P = 3.0 × 10(-8)); and chromosome 3p25.2 within PPARG (rs11128603, discovery P = 2.9 × 10(-8)). Replication was achieved for the 7q22.1 and 11p15.2 loci. There was nominal association with type 2 diabetes and coronary artery disease at ARNTL (P < .05). Functional studies identified MUC3 as a candidate gene for the second association signal on 7q22.1. In summary, SNPs in SERPINE1 and ARNTL and an SNP associated with the expression of MUC3 were robustly associated with circulating levels of PAI-1.
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Affiliation(s)
- Jie Huang
- National Heart, Lung, and Blood Institute (NHBLI) Framingham Heart Study, Framingham, MA 01702, USA
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Lourdusamy A, Newhouse S, Lunnon K, Proitsi P, Powell J, Hodges A, Nelson SK, Stewart A, Williams S, Kloszewska I, Mecocci P, Soininen H, Tsolaki M, Vellas B, Lovestone S, Dobson R. Identification of cis-regulatory variation influencing protein abundance levels in human plasma. Hum Mol Genet 2012; 21:3719-26. [PMID: 22595970 PMCID: PMC6446535 DOI: 10.1093/hmg/dds186] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 05/01/2012] [Accepted: 05/11/2012] [Indexed: 12/30/2022] Open
Abstract
Proteins are central to almost all cellular processes, and dysregulation of expression and function is associated with a range of disorders. A number of studies in human have recently shown that genetic factors significantly contribute gene expression variation. In contrast, very little is known about the genetic basis of variation in protein abundance in man. Here, we assayed the abundance levels of proteins in plasma from 96 elderly Europeans using a new aptamer-based proteomic technology and performed genome-wide local (cis-) regulatory association analysis to identify protein quantitative trait loci (pQTL). We detected robust cis-associations for 60 proteins at a false discovery rate of 5%. The most highly significant single nucleotide polymorphism detected was rs7021589 (false discovery rate, 2.5 × 10(-12)), mapped within the gene coding sequence of Tenascin C (TNC). Importantly, we identified evidence of cis-regulatory variation for 20 previously disease-associated genes encoding protein, including variants with strong evidence of disease association show significant association with protein abundance levels. These results demonstrate that common genetic variants contribute to the differences in protein abundance levels in human plasma. Identification of pQTLs will significantly enhance our ability to discover and comprehend the biological and functional consequences of loci identified from genome-wide association study of complex traits. This is the first large-scale genetic association study of proteins in plasma measured using a novel, highly multiplexed slow off-rate modified aptamer (SOMAmer) proteomic platform.
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Panagiotou OA, Ioannidis JPA. What should the genome-wide significance threshold be? Empirical replication of borderline genetic associations. Int J Epidemiol 2011; 41:273-86. [PMID: 22253303 DOI: 10.1093/ije/dyr178] [Citation(s) in RCA: 187] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Robust replication is a sine qua non for the rigorous documentation of proposed associations in the genome-wide association (GWA) setting. Currently, associations of common variants reaching P ≤ 5 × 10(-8) are considered replicated. However, there is some ambiguity about the most suitable threshold for claiming genome-wide significance. METHODS We defined as 'borderline' associations those with P > 5 × 10(-8) and P ≤ 1 × 10(-7). The eligible associations were retrieved using the 'Catalog of Published Genome-Wide Association Studies'. For each association we assessed whether it reached P ≤ 5 × 10(-8) with inclusion of additional data from subsequent GWA studies. RESULTS Thirty-four eligible genotype-phenotype associations were evaluated with data and clarifications contributed from diverse investigators. Replication data from subsequent GWA studies could be obtained for 26 of them. Of those, 19 associations (73%) reached P ≤ 5 × 10(-8) for the same or a related trait implicating either the exact same allele or one in very high linkage disequilibrium and 17 reached P < 10(-8). If the seven associations that did not reach P ≤ 5 × 10(-8) when additional data were considered are assumed to have been false-positives, the false-discovery rate for borderline associations is estimated to be 27% [95% confidence interval (CI) 12-48%]. For five associations, the current P-value is > 10(-6) [corresponding false-discovery rate 19% (95% CI 7-39%)]. CONCLUSION A substantial proportion, but not all, of the associations with borderline genome-wide significance represent replicable, possibly genuine associations. Our empirical evaluation suggests a possible relaxation in the current GWS threshold.
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Affiliation(s)
- Orestis A Panagiotou
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
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Zhang X, He H, Ding L, Baye TM, Kurowski BG, Martin LJ. Family- and population-based designs identify different rare causal variants. BMC Proc 2011; 5 Suppl 9:S36. [PMID: 22373077 PMCID: PMC3287872 DOI: 10.1186/1753-6561-5-s9-s36] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Both family- and population-based samples are used to identify genetic variants associated with phenotypes. Each strategy has demonstrated advantages, but their ability to identify rare variants and genes containing rare variants is unclear. To compare these two study designs in the identification of rare causal variants, we applied various methods to the population- and family-based data simulated by the Genetic Analysis Workshop 17 with knowledge of the simulated model. Our results suggest that different variants can be identified by different study designs. Family-based and population-based study designs can be complementary in the identification of rare causal variants and should be considered in future studies.
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Affiliation(s)
- Xue Zhang
- Divisions of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.
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Vohnout B, Gianfagna F, Lorenzet R, Cerletti C, de Gaetano G, Donati MB, Iacoviello L. Genetic regulation of inflammation-mediated activation of haemostasis: family-based approaches in population studies. Nutr Metab Cardiovasc Dis 2011; 21:857-861. [PMID: 20692137 DOI: 10.1016/j.numecd.2010.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 02/02/2010] [Accepted: 03/08/2010] [Indexed: 11/25/2022]
Abstract
Blood coagulation and inflammation play a key role in atherosclerosis and thrombosis. Candidate gene and genome wide association studies have identified potential specific genes that might have a causal role in these pathogenic processes. The analysis of quantitative traits is more powerful as they are closer to direct gene action than disease phenotypes. Thus linkage-based studies on extended families might be useful both to estimate the heritability and to map the genetic loci responsible for the regulation of the trait. Family-based studies may estimate high heritability for thrombosis and quantitative traits regarding both platelet aggregation and blood coagulation. Some specific loci relevant to thrombosis have been identified, with some of them showing a direct pleiotropic effect on the risk of thrombosis. Haemostasis factors can be activated by inflammatory stimuli. Fibrinogen level is genetically correlated with C-reactive protein levels with a link for both traits on chromosomes 12 and 21. Genes related to prostanoid biosynthesis, involved both in inflammation and thrombosis, show high heritability levels in both enzyme expression and prostanoid production. Considering that few large family-based linkage studies have as yet been performed on haemostasis and inflammation-related traits, additional studies are highly needed. We are performing a family-based linkage study on large pedigrees (750 subjects from 23 families with juvenile myocardial infarction and 31 control families), to identify genes responsible for quantitative traits involved in the pathway progressively going from inflammation to haemostasis, cell activation, thrombus formation and cardiovascular events.
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Affiliation(s)
- B Vohnout
- Laboratory of Genetic and Environmental Epidemiology, Italy
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35
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Johnson AD. The genetics of common variation affecting platelet development, function and pharmaceutical targeting. J Thromb Haemost 2011; 9 Suppl 1:246-57. [PMID: 21781261 PMCID: PMC3151008 DOI: 10.1111/j.1538-7836.2011.04359.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Common variant effects on human platelet function and response to anti-platelet treatment have traditionally been studied using candidate gene approaches involving a limited number of variants and genes. These studies have often been undertaken in clinically defined cohorts. More recently, studies have applied genome-wide scans in larger population samples than prior candidate studies, in some cases scanning relatively healthy individuals. These studies demonstrate synergy with some prior candidate gene findings (e.g., GP6, ADRA2A) but also uncover novel loci involved in platelet function. Here, I summarise findings on common genetic variation influencing platelet development, function and therapeutics. Taken together, candidate gene and genome-wide studies begin to account for common variation in platelet function and provide information that may ultimately be useful in pharmacogenetic applications in the clinic. More than 50 loci have been identified with consistent associations with platelet phenotypes in ≥ 2 populations. Several variants are under further study in clinical trials relating to anti-platelet therapies. In order to have useful clinical applications, variants must have large effects on a modifiable outcome. Regardless of clinical applications, studies of common genetic influences, even of small effect, offer additional insights into platelet biology including the importance of intracellular signalling and novel receptors. Understanding of common platelet-related genetics remains behind parallel fields (e.g., lipids, blood pressure) due to challenges in phenotype ascertainment. Further work is necessary to discover and characterise loci for platelet function, and to assess whether these loci contribute to disease aetiologies or response to therapeutics.
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Affiliation(s)
- A D Johnson
- National Heart, Lung and Blood Institute's The Framingham Heart Study, Framingham, MA 01702, USA.
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Guerrero JA, Rivera J, Quiroga T, Martinez-Perez A, Antón AI, Martínez C, Panes O, Vicente V, Mezzano D, Soria JM, Corral J. Novel loci involved in platelet function and platelet count identified by a genome-wide study performed in children. Haematologica 2011; 96:1335-43. [PMID: 21546496 DOI: 10.3324/haematol.2011.042077] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Genome-wide association studies are currently identifying new loci with potential roles in thrombosis and hemostasis: these loci include novel polymorphisms associated with platelet function traits and count. However, no genome-wide study performed on children has been reported to date, in spite of the potential that these subjects have in genetic studies, when compared to adults, given the minimal degree of confounders, i.e., acquired and environmental factors, such as smoking, physical activity, diet, and drug or hormone intake, which are particularly important in platelet function. DESIGN AND METHODS To identify new genetic variants involved in platelet reactivity and count, we performed a genome-wide association study on 75 children (8.5±1.8 years) using the Illumina Sentrix Human CNV370-Quad BeadChip containing 320,610 single nucleotide polymorphisms. Functional analyses included assessment of platelet aggregation and granule secretion triggered by different agonists (arachidonic acid, collagen, epinephrine, ADP), as well as platelet count. Associations were selected based on statistical significance and physiological relevance for a subsequent replication study in a similar sample of 286 children. RESULTS We confirmed previously established associations with plasma levels of factors XII, VII and VIII as well as associations with platelet responses to ADP. Additionally, we identified 82 associations with platelet reactivity and count with a P value less than 10(-5). From the associations selected for further replication, we validated two single nucleotide polymorphisms with mildly increased platelet reactivity (rs4366150 and rs1787566) on the LPAR1 and MYO5B genes, encoding lisophosphatidic acid receptor-1 and myosin VB, respectively; and rs1937970, located on the NRG3 gene coding neuroregulin-3, associated with platelet count. CONCLUSIONS Our genome-wide association study performed in children, followed by a validation analysis, led us to the identification of new genes potentially relevant in platelet function and biogenesis.
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Affiliation(s)
- José A Guerrero
- University of Murcia, Centro Regional de Hemodonación, Murcia, Spain
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Fechtel K, Osterbur ML, Kehrer-Sawatzki H, Stenson PD, Cooper DN. Delineating the Hemostaseome as an aid to individualize the analysis of the hereditary basis of thrombotic and bleeding disorders. Hum Genet 2011; 130:149-66. [PMID: 21537949 DOI: 10.1007/s00439-011-0984-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2011] [Accepted: 04/05/2011] [Indexed: 01/22/2023]
Abstract
Next-generation sequencing and genome-wide association studies represent powerful tools to identify genetic variants that confer disease risk within populations. On their own, however, they cannot provide insight into how these variants contribute to individual risk for diseases that exhibit complex inheritance, or alternatively confer health in a given individual. Even in the case of well-characterized variants that confer a significant disease risk, more healthy individuals carry the variant, with no apparent ill effect, than those who manifest disease. Access to low-cost genome sequence data promises to provide an unprecedentedly detailed view of the nature of the hereditary component of complex diseases, but requires the large-scale comparison of sequence data from individuals with and without disease to deliver a clinical calibration. The provision of informatics support remains problematic as there are currently no means to interpret the data generated. Here, we initiate this process, a prerequisite for such a study, by narrowing the focus from an entire genome to that of a single biological system. To this end, we examine the 'Hemostaseome,' and more specifically focus on DNA sequence changes pertaining to those human genes known to impact upon hemostasis and thrombosis that can be analyzed coordinately, and on an individual basis, to interrogate how specific combinations of variants act to confer disease predisposition. As a first step, we delineate known members of the Hemostaseome and explore the nature of the genetic variants that may cause disease in individuals whose hemostatic balance has become shifted toward either a prothrombotic or anticoagulant phenotype.
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Affiliation(s)
- Kim Fechtel
- 3rd Millennium Inc., Waltham, MA 02451, USA.
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van Schie MC, van Loon JE, de Maat MPM, Leebeek FWG. Genetic determinants of von Willebrand factor levels and activity in relation to the risk of cardiovascular disease: a review. J Thromb Haemost 2011; 9:899-908. [PMID: 21342431 DOI: 10.1111/j.1538-7836.2011.04243.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
It is well established that high plasma von Willebrand factor (VWF) levels are associated with an increased risk of arterial thrombosis, including myocardial infarction and ischemic stroke. As plasma VWF levels are, to a large extent, genetically determined, numerous association studies have been performed to assess the effect of genetic variability in the VWF gene (VWF) on VWF antigen and activity levels, and on the risk of arterial thrombosis. Genetic variations in other regulators of VWF, including the ABO blood group, ADAMTS-13, thrombospondin-1 and the recently identified SNARE protein genes, have also been investigated. In this article, we review the current literature as exploring the associations between genetic variations and the risk of arterial thrombosis may help elucidate the role of VWF in the pathogenesis of arterial thrombosis. However, as studies frequently differ in design, population and endpoint, and are often underpowered, it remains unclear whether VWF is causally related to the occurrence of arterial thrombosis or primarily mirrors endothelial dysfunction, which predisposes to atherosclerosis and subsequent arterial thrombosis. Nevertheless, current studies provide interesting results that do not exclude the possibility of VWF as causal mediator and justify further research into the relationship between VWF and arterial thrombosis. Large prospective studies are required to further establish the role of VWF in the occurrence of arterial thrombosis.
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Affiliation(s)
- M C van Schie
- Department of Haematology, Erasmus University Medical Centre, Rotterdam, The Netherlands
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Smith NL, Huffman JE, Strachan DP, Huang J, Dehghan A, Trompet S, Lopez LM, Shin SY, Baumert J, Vitart V, Bis JC, Wild SH, Rumley A, Yang Q, Uitterlinden AG, Stott DJ, Davies G, Carter AM, Thorand B, Polašek O, McKnight B, Campbell H, Rudnicka AR, Chen MH, Buckley BM, Harris SE, Peters A, Pulanic D, Lumley T, de Craen AJM, Liewald DC, Gieger C, Campbell S, Ford I, Gow AJ, Luciano M, Porteous DJ, Guo X, Sattar N, Tenesa A, Cushman M, Slagboom PE, Visscher PM, Spector TD, Illig T, Rudan I, Bovill EG, Wright AF, McArdle WL, Tofler G, Hofman A, Westendorp RGJ, Starr JM, Grant PJ, Karakas M, Hastie ND, Psaty BM, Wilson JF, Lowe GDO, O'Donnell CJ, Witteman JCM, Jukema JW, Deary IJ, Soranzo N, Koenig W, Hayward C. Genetic predictors of fibrin D-dimer levels in healthy adults. Circulation 2011; 123:1864-72. [PMID: 21502573 DOI: 10.1161/circulationaha.110.009480] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND Fibrin fragment D-dimer, one of several peptides produced when crosslinked fibrin is degraded by plasmin, is the most widely used clinical marker of activated blood coagulation. To identity genetic loci influencing D-dimer levels, we performed the first large-scale, genome-wide association search. METHODS AND RESULTS A genome-wide investigation of the genomic correlates of plasma D-dimer levels was conducted among 21 052 European-ancestry adults. Plasma levels of D-dimer were measured independently in each of 13 cohorts. Each study analyzed the association between ≈2.6 million genotyped and imputed variants across the 22 autosomal chromosomes and natural-log–transformed D-dimer levels using linear regression in additive genetic models adjusted for age and sex. Among all variants, 74 exceeded the genome-wide significance threshold and marked 3 regions. At 1p22, rs12029080 (P=6.4×10(-52)) was 46.0 kb upstream from F3, coagulation factor III (tissue factor). At 1q24, rs6687813 (P=2.4×10(-14)) was 79.7 kb downstream of F5, coagulation factor V. At 4q32, rs13109457 (P=2.9×10(-18)) was located between 2 fibrinogen genes: 10.4 kb downstream from FGG and 3.0 kb upstream from FGA. Variants were associated with a 0.099-, 0.096-, and 0.061-unit difference, respectively, in natural-log–transformed D-dimer and together accounted for 1.8% of the total variance. When adjusted for nonsynonymous substitutions in F5 and FGA loci known to be associated with D-dimer levels, there was no evidence of an additional association at either locus. CONCLUSIONS Three genes were associated with fibrin D-dimer levels. Of these 3, the F3 association was the strongest, and has not been previously reported.
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Affiliation(s)
- Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle 98101, USA.
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Mick E, McGough JJ, Middleton FA, Neale B, Faraone SV. Genome-wide association study of blood pressure response to methylphenidate treatment of attention-deficit/hyperactivity disorder. Prog Neuropsychopharmacol Biol Psychiatry 2011; 35:466-72. [PMID: 21130132 DOI: 10.1016/j.pnpbp.2010.11.037] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 11/23/2010] [Accepted: 11/23/2010] [Indexed: 12/31/2022]
Abstract
OBJECTIVE We conducted a genome-wide association study of blood pressure in an open-label study of the methylphenidate transdermal system (MTS) for the treatment of attention-deficit/hyperactivity disorder (ADHD). METHOD Genotyping was conducted with the Affymetrix Genome-Wide Human SNP Array 6.0. Multivariate association analyses were conducted using the software package PLINK. After data cleaning and quality control we tested 316,934 SNPs in 140 children with ADHD. RESULTS We observed no genome-wide statistically significant findings, but a SNP in a K(+)-dependent Na(+)/Ca(2+) exchanger expressed in vascular smooth muscle (SLC24A3) was included in our top associations at p<1E-04. Genetic enrichment analyses of genes with ≥1 SNP significant at p<0.01, implicated several functional categories (FERM domain, p=5.0E-07; immunoglobulin domain, p=8.1E-06; the transmembrane region, p=4.4E-05; channel activity, p=2.0E-04; and type-III fibronectins, p=2.7E-05) harboring genes previously associated with related cardiovascular phenotypes. CONCLUSIONS The hypothesis generating results from this study suggests that polymorphisms in several genes consistently associated with cardiovascular diseases may impact changes in blood pressure observed with methylphenidate pharmacotherapy in children with ADHD.
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Affiliation(s)
- Eric Mick
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, United States.
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Williams MS, Weiss EJ, Sabatine MS, Simon DI, Bahou WF, Becker LC, Parise LV, Dauerman HL, French PA, Smyth SS, Becker RC. Genetic regulation of platelet receptor expression and function: application in clinical practice and drug development. Arterioscler Thromb Vasc Biol 2010; 30:2372-84. [PMID: 21084706 DOI: 10.1161/atvbaha.110.218131] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Understanding genetic contributions to platelet function could have profound clinical ramifications for personalizing platelet-directed pharmacotherapy, by providing insight into the risks and possible benefits associated with specific genotypes. This article represents an integrated summary of presentations related to genetic regulation of platelet receptor expression and function given at the Fifth Annual Platelet Colloquium in January 2010. It is supplemented with additional highlights from the literature covering (1) approaches to determining and evidence for the associations of genetic variants with platelet hypo- and hyperresponsive phenotypes, (2) the ramifications of these polymorphisms with regard to clinical responses to antiplatelet therapies, and (3) the role of platelet function/genetic testing in guiding antiplatelet therapy.
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Affiliation(s)
- Marlene S Williams
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, Md 21224, USA.
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Johnson AD, Yanek LR, Chen MH, Faraday N, Larson MG, Tofler G, Lin SJ, Kraja AT, Province MA, Yang Q, Becker DM, O'Donnell CJ, Becker LC. Genome-wide meta-analyses identifies seven loci associated with platelet aggregation in response to agonists. Nat Genet 2010; 42:608-13. [PMID: 20526338 PMCID: PMC3057573 DOI: 10.1038/ng.604] [Citation(s) in RCA: 211] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 05/12/2010] [Indexed: 12/26/2022]
Abstract
Platelet function mediates both beneficial and harmful effects on human health, but few genes are known to contribute to variability in this process. We tested association of 2.5 million SNPs with platelet aggregation responses to three agonists (ADP, epinephrine and collagen) in two cohorts of European ancestry (N
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Affiliation(s)
- Andrew D Johnson
- National Heart, Lung, and Blood Institute's The Framingham Heart Study, Framingham, Massachusetts, USA.
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Brunel H, Gallardo-Chacón JJ, Buil A, Vallverdú M, Soria JM, Caminal P, Perera A. MISS: a non-linear methodology based on mutual information for genetic association studies in both population and sib-pairs analysis. ACTA ACUST UNITED AC 2010; 26:1811-8. [PMID: 20562420 DOI: 10.1093/bioinformatics/btq273] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Finding association between genetic variants and phenotypes related to disease has become an important vehicle for the study of complex disorders. In this context, multi-loci genetic association might unravel additional information when compared with single loci search. The main goal of this work is to propose a non-linear methodology based on information theory for finding combinatorial association between multi-SNPs and a given phenotype. RESULTS The proposed methodology, called MISS (mutual information statistical significance), has been integrated jointly with a feature selection algorithm and has been tested on a synthetic dataset with a controlled phenotype and in the particular case of the F7 gene. The MISS methodology has been contrasted with a multiple linear regression (MLR) method used for genetic association in both, a population-based study and a sib-pairs analysis and with the maximum entropy conditional probability modelling (MECPM) method, which searches for predictive multi-locus interactions. Several sets of SNPs within the F7 gene region have been found to show a significant correlation with the FVII levels in blood. The proposed multi-site approach unveils combinations of SNPs that explain more significant information of the phenotype than their individual polymorphisms. MISS is able to find more correlations between SNPs and the phenotype than MLR and MECPM. Most of the marked SNPs appear in the literature as functional variants with real effect on the protein FVII levels in blood. AVAILABILITY The code is available at http://sisbio.recerca.upc.edu/R/MISS_0.2.tar.gz
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Affiliation(s)
- Helena Brunel
- Institut de Bioenginyeria de Catalunya, Departament d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, Pau Gargallo 5, 08028 Barcelona, Spain.
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Sherva R, Sripichai O, Abel K, Ma Q, Whitacre J, Angkachatchai V, Makarasara W, Winichagoon P, Svasti S, Fucharoen S, Braun A, Farrer LA. Genetic modifiers of Hb E/beta0 thalassemia identified by a two-stage genome-wide association study. BMC MEDICAL GENETICS 2010; 11:51. [PMID: 20353593 PMCID: PMC2853425 DOI: 10.1186/1471-2350-11-51] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Accepted: 03/30/2010] [Indexed: 11/18/2022]
Abstract
Background Patients with Hb E/β0 thalassemia display remarkable variability in disease severity. To identify genetic modifiers influencing disease severity, we conducted a two-stage genome scan in groups of 207 mild and 305 severe unrelated patients from Thailand with Hb E/β0 thalassemia and normal α-globin genes. Methods First, we estimated and compared the allele frequencies of approximately 110,000 gene-based single nucleotide polymorphisms (SNPs) in pooled DNAs from different severity groups. The 756 SNPs that showed reproducible allelic differences at P < 0.02 by pooling were selected for individual genotyping. Results After adjustment for age, gender and geographic region, logistic regression models showed 50 SNPs significantly associated with disease severity (P < 0.05) after Bonferroni adjustment for multiple testing. Forty-one SNPs in a large LD block within the β-globin gene cluster had major alleles associated with severe disease. The most significant was bthal_bg200 (odds ratio (OR) = 5.56, P = 2.6 × 10-13). Seven SNPs in two distinct LD blocks within a region centromeric to the β-globin gene cluster that contains many olfactory receptor genes were also associated with disease severity; rs3886223 had the strongest association (OR = 3.03, P = 3.7 × 10-11). Several previously unreported SNPs were also significantly associated with disease severity. Conclusions These results suggest that there may be an additional regulatory region centromeric to the β-globin gene cluster that affects disease severity by modulating fetal hemoglobin expression.
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Affiliation(s)
- Richard Sherva
- Department of Medicine, Genetics Program, Boston University School of Medicine, Boston 02118, USA
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Morange PE, Tregouet DA. Deciphering the molecular basis of venous thromboembolism: where are we and where should we go? Br J Haematol 2009; 148:495-506. [PMID: 19912223 DOI: 10.1111/j.1365-2141.2009.07975.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Venous thromboembolism (VTE) is a frequent disease that has a major genetic component of risk. However, known identified genetic risk factors account for <30% of idiopathic (without any environmental origin) VTE cases. This article aims to review the lessons learnt during recent decades in the field of the genetics of VTE, describe the present state-of-art methods and discuss promising themes for finding new susceptibility loci.
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Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium. Nat Genet 2009; 41:1191-8. [PMID: 19862010 PMCID: PMC2778265 DOI: 10.1038/ng.466] [Citation(s) in RCA: 280] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 09/01/2009] [Indexed: 12/13/2022]
Abstract
Measurements of erythrocytes within the blood are important clinical traits and can indicate various hematological disorders. We report here genome-wide association studies (GWAS) for six erythrocyte traits, including hemoglobin concentration (Hb), hematocrit (Hct), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC) and red blood cell count (RBC). We performed an initial GWAS in cohorts of the CHARGE Consortium totaling 24,167 individuals of European ancestry and replication in additional independent cohorts of the HaemGen Consortium totaling 9,456 individuals. We identified 23 loci significantly associated with these traits in a meta-analysis of the discovery and replication cohorts (combined P values ranging from 5 x 10(-8) to 7 x 10(-86)). Our findings include loci previously associated with these traits (HBS1L-MYB, HFE, TMPRSS6, TFR2, SPTA1) as well as new associations (EPO, TFRC, SH2B3 and 15 other loci). This study has identified new determinants of erythrocyte traits, offering insight into common variants underlying variation in erythrocyte measures.
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Influence of genetic polymorphisms of glutathione S-transferase T1 (GSTT1) and M1 (GSTM1) on hematological parameters. Mol Biol Rep 2009; 37:249-53. [DOI: 10.1007/s11033-009-9662-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2009] [Accepted: 07/24/2009] [Indexed: 12/11/2022]
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Sebastiani P, Timofeev N, Dworkis DA, Perls TT, Steinberg MH. Genome-wide association studies and the genetic dissection of complex traits. Am J Hematol 2009; 84:504-15. [PMID: 19569043 PMCID: PMC2895326 DOI: 10.1002/ajh.21440] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The availability of affordable high throughput technology for parallel genotyping has opened the field of genetics to genome-wide association studies (GWAS), and in the last few years hundreds of articles reporting results of GWAS for a variety of heritable traits have been published. What do these results tell us? Although GWAS have discovered a few hundred reproducible associations, this number is underwhelming in relation to the huge amount of data produced, and challenges the conjecture that common variants may be the genetic causes of common diseases. We argue that the massive amount of genetic data that result from these studies remains largely unexplored and unexploited because of the challenge of mining and modeling enormous data sets, the difficulty of using nontraditional computational techniques and the focus of accepted statistical analyses on controlling the false positive rate rather than limiting the false negative rate. In this article, we will review the common approach to analysis of GWAS data and then discuss options to learn more from these data. We will use examples from our ongoing studies of sickle cell anemia and also GWAS in multigenic traits.
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Affiliation(s)
- Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts 02118, USA.
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Zemunik T, Boban M, Lauc G, Janković S, Rotim K, Vatavuk Z, Bencić G, Dogas Z, Boraska V, Torlak V, Susac J, Zobić I, Rudan D, Pulanić D, Modun D, Mudnić I, Gunjaca G, Budimir D, Hayward C, Vitart V, Wright AF, Campbell H, Rudan I. Genome-wide association study of biochemical traits in Korcula Island, Croatia. Croat Med J 2009; 50:23-33. [PMID: 19260141 DOI: 10.3325/cmj.2009.50.23] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AIM To identify genetic variants underlying biochemical traits--total cholesterol, low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, triglycerides, uric acid, albumin, and fibrinogen, in a genome-wide association study in an isolated population where rare variants of larger effect may be more easily identified. METHODS The study included 944 adult inhabitants of the island of Korcula, as a part of larger DNA-based genetic epidemiological study in 2007. Biochemical measurements were performed in a single laboratory with stringent internal and external quality control procedures. Examinees were genotyped using Human Hap370CNV chip by Illumina, with a genome-wide scan containing 346027 single nucleotide polymorphisms (SNP). RESULTS A total of 31 SNPs were associated with 7 investigated traits at the level of P<1.00 x 10(-5). Nine of SNPs implicated the role of SLC2A9 in uric acid regulation (P=4.10 x 10(-6)-2.58 x 10(-12)), as previously found in other populations. All 22 remaining associations fell into the P=1.00 x 10(-5)-1.00 x 10(-6) significance range. One of them replicated the association between cholesteryl ester transfer protein (CETP) and HDL, and 7 associations were more than 100 kilobases away from the closest known gene. Nearby SNPs, rs4767631 and rs10444502, in gene kinase suppressor of ras 2 (KSR2) on chromosome 12 were associated with LDL cholesterol levels, and rs10444502 in the same gene with total cholesterol levels. Similarly, rs2839619 in gene PBX/knotted 1 homeobox 1 (PKNOX1) on chromosome 21 was associated with total and LDL cholesterol levels. The remaining 9 findings implied possible associations between phosphatidylethanolamine N-methyltransferase (PEMT) gene and total cholesterol; USP46, RAP1GDS1, and ZCCHC16 genes and triglycerides; BCAT1 and SLC14A2 genes and albumin; and NR3C2, GRIK2, and PCSK2 genes and fibrinogen. CONCLUSION Although this study was underpowered for most of the reported associations to reach formal threshold of genome-wide significance under the assumption of independent multiple testing, replications of previous findings and consistency of association between the identified variants and more than one studied trait make such findings interesting for further functional follow-up studies. Changed allele frequencies in isolate population may contribute to identifying variants that would not be easily identified in much larger samples in outbred populations.
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Affiliation(s)
- Tatijana Zemunik
- University of Split School of Medicine, Soltanska 2, 21000 Split, Croatia
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Duan X, Yue W, Liu L, Li Z, Li Y, He F, Zhu D, Zhou G, Wang S. Single-nucleotide polymorphism (SNP) genotyping using cationic conjugated polymers in homogeneous solution. Nat Protoc 2009; 4:984-91. [DOI: 10.1038/nprot.2009.70] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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