A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects (original) (raw)
References
Alcina A, Vandenbroeck K, Otaegui D, Saiz A, Gonzalez JR, Fernandez O, Cavanillas ML, Cenit MC, Arroyo R, Alloza I et al (2010) The autoimmune disease-associated KIF5A, CD226 and SH2B3 gene variants confer susceptibility for multiple sclerosis. Genes Immun 11:439–445 ArticleCASPubMed Google Scholar
Blattmann P, Schuberth C, Pepperkok R, Runz H (2013) RNAi-based functional profiling of loci from blood lipid genome-wide association studies identifies genes with cholesterol-regulatory function. PLoS Genet 9:e1003338 ArticleCASPubMed CentralPubMed Google Scholar
Cameron HA, Phillips R, Ibbotson RM, Carson PH (1983) Platelet size in myocardial infarction. Br Med J (Clin Res Ed) 287:449–451 ArticleCAS Google Scholar
Denny JC, Ritchie MD, Basford MA, Pulley JM, Bastarache L, Brown-Gentry K, Wang D, Masys DR, Roden DM, Crawford DC (2010) PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. Bioinformatics 26:1205–1210 ArticleCASPubMed Google Scholar
Denny JC, Crawford DC, Ritchie MD, Bielinski SJ, Basford MA, Bradford Y, Chai HS, Bastarache L, Zuvich R, Peissig P et al (2011) Variants near FOXE1 are associated with hypothyroidism and other thyroid conditions: using electronic medical records for genome- and phenome-wide studies. Am J Hum Genet 89:529–542 ArticleCASPubMed CentralPubMed Google Scholar
Denzer K, Kleijmeer MJ, Heijnen HF, Stoorvogel W, Geuze HJ (2000) Exosome: from internal vesicle of the multivesicular body to intercellular signaling device. J Cell Sci 113(Pt 19):3365–3374 CASPubMed Google Scholar
Du P, Feng G, Flatow J, Song J, Holko M, Kibbe WA, Lin SM (2009) From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. Bioinformatics 25:i63–i68 ArticleCASPubMed Google Scholar
Ehret GB, Munroe PB, Rice KM, Bochud M, Johnson AD, Chasman DI, Smith AV, Tobin MD, Verwoert GC, Hwang SJ et al (2011) Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk. Nature 478:103–109 ArticleCASPubMed Google Scholar
Eriksson N, Tung JY, Kiefer AK, Hinds DA, Francke U, Mountain JL, Do CB (2012) Novel associations for hypothyroidism include known autoimmune risk Loci. PLoS One 7:e34442 ArticleCASPubMed CentralPubMed Google Scholar
Evans DM, Spencer CC, Pointon JJ, Su Z, Harvey D, Kochan G, Oppermann U, Dilthey A, Pirinen M, Stone MA et al (2011) Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility. Nat Genet 43:761–767 ArticleCASPubMed CentralPubMed Google Scholar
Ferreira MA, Hottenga JJ, Warrington NM, Medland SE, Willemsen G, Lawrence RW, Gordon S, de Geus EJ, Henders AK, Smit JH et al (2009) Sequence variants in three loci influence monocyte counts and erythrocyte volume. Am J Hum Genet 85:745–749 ArticleCASPubMed CentralPubMed Google Scholar
Fitzgerald DJ (1999) Fibrinogen receptor and platelet signalling. Blood Coagul Fibrinolysis 10(Suppl 1):S77–S79 CASPubMed Google Scholar
Flaumenhaft R (2003) Molecular basis of platelet granule secretion. Arterioscler Thromb Vasc Biol 23:1152–1160 ArticleCASPubMed Google Scholar
Gay LJ, Felding-Habermann B (2011a) Contribution of platelets to tumour metastasis. Nat Rev Cancer 11:123–134 ArticleCASPubMed Google Scholar
Gay LJ, Felding-Habermann B (2011b) Platelets alter tumor cell attributes to propel metastasis: programming in transit. Cancer Cell 20:553–554 ArticleCASPubMed Google Scholar
Gibbins JM (2004) Platelet adhesion signalling and the regulation of thrombus formation. J Cell Sci 117:3415–3425 ArticleCASPubMed Google Scholar
Gieger C, Radhakrishnan A, Cvejic A, Tang W, Porcu E, Pistis G, Serbanovic-Canic J, Elling U, Goodall AH, Labrune Y et al (2011) New gene functions in megakaryopoiesis and platelet formation. Nature 480(7376):201–208. doi:10.1038/nature10659 Google Scholar
Gudbjartsson DF, Bjornsdottir US, Halapi E, Helgadottir A, Sulem P, Jonsdottir GM, Thorleifsson G, Helgadottir H, Steinthorsdottir V, Stefansson H et al (2009) Sequence variants affecting eosinophil numbers associate with asthma and myocardial infarction. Nat Genet 41:342–347 ArticleCASPubMed Google Scholar
Hebbring SJ, Schrodi SJ, Ye Z, Zhou Z, Page D, Brilliant MH (2013) A PheWAS approach in studying HLA-DRB1*1501. Genes Immun 14:187–191 ArticleCASPubMed CentralPubMed Google Scholar
Hinks A, Martin P, Flynn E, Eyre S, Packham J, Barton A, Worthington J, Thomson W (2010) Investigation of type 1 diabetes and coeliac disease susceptibility loci for association with juvenile idiopathic arthritis. Ann Rheum Dis 69:2169–2172 ArticlePubMed CentralPubMed Google Scholar
Honn KV, Tang DG, Crissman JD (1992) Platelets and cancer metastasis: a causal relationship? Cancer Metastasis Rev 11:325–351 ArticleCASPubMed Google Scholar
Hunt KA, Zhernakova A, Turner G, Heap GA, Franke L, Bruinenberg M, Romanos J, Dinesen LC, Ryan AW, Panesar D et al (2008) Newly identified genetic risk variants for celiac disease related to the immune response. Nat Genet 40:395–402 ArticleCASPubMed CentralPubMed Google Scholar
Huo Y, Ley KF (2004) Role of platelets in the development of atherosclerosis. Trends Cardiovasc Med 14:18–22 ArticleCASPubMed Google Scholar
Italiano JE Jr, Lecine P, Shivdasani RA, Hartwig JH (1999) Blood platelets are assembled principally at the ends of proplatelet processes produced by differentiated megakaryocytes. J Cell Biol 147:1299–1312 ArticleCASPubMed Google Scholar
Johnson AD (2011) The genetics of common variation affecting platelet development, function and pharmaceutical targeting. J Thromb Haemost 9(Suppl 1):246–257 ArticleCASPubMed CentralPubMed Google Scholar
Kamatani Y, Matsuda K, Okada Y, Kubo M, Hosono N, Daigo Y, Nakamura Y, Kamatani N (2010) Genome-wide association study of hematological and biochemical traits in a Japanese population. Nat Genet 42:210–215 ArticleCASPubMed Google Scholar
Kang HM, Sul JH, Service SK, Zaitlen NA, Kong SY, Freimer NB, Sabatti C, Eskin E (2010) Variance component model to account for sample structure in genome-wide association studies. Nat Genet 42:348–354 ArticleCASPubMed CentralPubMed Google Scholar
Kaplan JE, Saba TM (1978) Platelet removal from the circulation by the liver and spleen. Am J Physiol 235:H314–H320 CASPubMed Google Scholar
Kisacik B, Tufan A, Kalyoncu U, Karadag O, Akdogan A, Ozturk MA, Kiraz S, Ertenli I, Calguneri M (2008) Mean platelet volume (MPV) as an inflammatory marker in ankylosing spondylitis and rheumatoid arthritis. Jt Bone Spine 75:291–294 Article Google Scholar
Kottke-Marchant K (2009) Importance of platelets and platelet response in acute coronary syndromes. Cleve Clin J Med 76(Suppl 1):S2–S7 ArticlePubMed Google Scholar
Kullo IJ, Ding K, Jouni H, Smith CY, Chute CG (2010) A genome-wide association study of red blood cell traits using the electronic medical record. PLoS One 5(9). pii:e13011. doi:10.1371/journal.pone.0013011
Kunicki TJ, Nugent DJ (2010) The genetics of normal platelet reactivity. Blood 116:2627–2634 ArticleCASPubMed Google Scholar
Kunicki TJ, Williams SA, Salomon DR, Harrison P, Crisler P, Nakagawa P, Mondala TS, Head SR, Nugent DJ (2009) Genetics of platelet reactivity in normal, healthy individuals. J Thromb Haemost 7:2116–2122 ArticleCASPubMed Google Scholar
Labelle M, Begum S, Hynes RO (2011) Direct signaling between platelets and cancer cells induces an epithelial-mesenchymal-like transition and promotes metastasis. Cancer Cell 20:576–590 ArticleCASPubMed CentralPubMed Google Scholar
Levy D, Ehret GB, Rice K, Verwoert GC, Launer LJ, Dehghan A, Glazer NL, Morrison AC, Johnson AD, Aspelund T et al (2009) Genome-wide association study of blood pressure and hypertension. Nat Genet 41:677–687 ArticleCASPubMed CentralPubMed Google Scholar
Levy-Toledano S (1999) Platelet signal transduction pathways: could we organize them into a ‘hierarchy’? Haemostasis 29:4–15 CASPubMed Google Scholar
Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR (2010a) MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 34:816–834 ArticlePubMed CentralPubMed Google Scholar
Li Z, Delaney MK, O’Brien KA, Du X (2010b) Signaling during platelet adhesion and activation. Arterioscler Thromb Vasc Biol 30:2341–2349 ArticleCASPubMed CentralPubMed Google Scholar
Mahaney MC, Brugnara C, Lease LR, Platt OS (2005) Genetic influences on peripheral blood cell counts: a study in baboons. Blood 106:1210–1214 ArticleCASPubMed Google Scholar
Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B et al (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 37:D619–D622 ArticleCASPubMed CentralPubMed Google Scholar
McBane RD 2nd, Karnicki K, Miller RS, Owen WG (2004) The impact of peripheral arterial disease on circulating platelets. Thromb Res 113:137–145 ArticleCASPubMed Google Scholar
McCarty CA, Chisholm RL, Chute CG, Kullo IJ, Jarvik GP, Larson EB, Li R, Masys DR, Ritchie MD, Roden DM et al (2011) The eMERGE Network: a consortium of biorepositories linked to electronic medical records data for conducting genomic studies. BMC Med Genomics 4:13 ArticlePubMed CentralPubMed Google Scholar
Meisinger C, Prokisch H, Gieger C, Soranzo N, Mehta D, Rosskopf D, Lichtner P, Klopp N, Stephens J, Watkins NA et al (2009) A genome-wide association study identifies three loci associated with mean platelet volume. Am J Hum Genet 84:66–71 ArticleCASPubMed CentralPubMed Google Scholar
Menzel S, Jiang J, Silver N, Gallagher J, Cunningham J, Surdulescu G, Lathrop M, Farrall M, Spector TD, Thein SL (2007) The HBS1L-MYB intergenic region on chromosome 6q23.3 influences erythrocyte, platelet, and monocyte counts in humans. Blood 110:3624–3626 ArticleCASPubMed Google Scholar
Movat HZ, Weiser WJ, Glynn MF, Mustard JF (1965) Platelet phagocytosis and aggregation. J Cell Biol 27:531–543 ArticleCASPubMed Google Scholar
Newton-Cheh C, Johnson T, Gateva V, Tobin MD, Bochud M, Coin L, Najjar SS, Zhao JH, Heath SC, Eyheramendy S et al (2009) Genome-wide association study identifies eight loci associated with blood pressure. Nat Genet 41:666–676 ArticleCASPubMed CentralPubMed Google Scholar
O’Donnell CJ, Larson MG, Feng D, Sutherland PA, Lindpaintner K, Myers RH, D’Agostino RA, Levy D, Tofler GH (2001) Genetic and environmental contributions to platelet aggregation: the Framingham heart study. Circulation 103:3051–3056 ArticlePubMed Google Scholar
Pain A, Ferguson DJ, Kai O, Urban BC, Lowe B, Marsh K, Roberts DJ (2001) Platelet-mediated clumping of Plasmodium falciparum-infected erythrocytes is a common adhesive phenotype and is associated with severe malaria. Proc Natl Acad Sci USA 98:1805–1810 ArticleCASPubMed Google Scholar
Paul DS, Nisbet JP, Yang TP, Meacham S, Rendon A, Hautaviita K, Tallila J, White J, Tijssen MR, Sivapalaratnam S et al (2011) Maps of open chromatin guide the functional follow-up of genome-wide association signals: application to hematological traits. PLoS Genet 7:e1002139 ArticleCASPubMed CentralPubMed Google Scholar
Pendergrass SA, Brown-Gentry K, Dudek SM, Torstenson ES, Ambite JL, Avery CL, Buyske S, Cai C, Fesinmeyer MD, Haiman C et al (2011) The use of phenome-wide association studies (PheWAS) for exploration of novel genotype-phenotype relationships and pleiotropy discovery. Genet Epidemiol 35:410–422 ArticlePubMed CentralPubMed Google Scholar
Pruim RJ, Welch RP, Sanna S, Teslovich TM, Chines PS, Gliedt TP, Boehnke M, Abecasis GR, Willer CJ (2010) LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics 26:2336–2337 ArticleCASPubMed Google Scholar
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ et al (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559–575 ArticleCASPubMed CentralPubMed Google Scholar
Qayyum R, Snively BM, Ziv E, Nalls MA, Liu Y, Tang W, Yanek LR, Lange L, Evans MK, Ganesh S et al (2012) A meta-analysis and genome-wide association study of platelet count and mean platelet volume in African Americans. PLoS Genet 8:e1002491 ArticleCASPubMed CentralPubMed Google Scholar
Qiao JL, Shen Y, Gardiner EE, Andrews RK (2010) Proteolysis of platelet receptors in humans and other species. Biol Chem 391:893–900 ArticleCASPubMed Google Scholar
Richardson JL, Shivdasani RA, Boers C, Hartwig JH, Italiano JE Jr (2005) Mechanisms of organelle transport and capture along proplatelets during platelet production. Blood 106:4066–4075 ArticleCASPubMed Google Scholar
Ripatti S, Tikkanen E, Orho-Melander M, Havulinna AS, Silander K, Sharma A, Guiducci C, Perola M, Jula A, Sinisalo J et al (2010) A multilocus genetic risk score for coronary heart disease: case-control and prospective cohort analyses. Lancet 376:1393–1400 ArticlePubMed CentralPubMed Google Scholar
Ritchie MD, Denny JC, Zuvich RL, Crawford DC, Schildcrout JS, Bastarache L, Ramirez AH, Mosley JD, Pulley JM, Basford MA et al (2013) Genome- and phenome-wide analyses of cardiac conduction identifies markers of arrhythmia risk. Circulation 127:1377–1385 ArticleCASPubMed Google Scholar
Saade S, Cazier JB, Ghassibe-Sabbagh M, Youhanna S, Badro DA, Kamatani Y, Hager J, Yeretzian JS, El-Khazen G, Haber M et al (2011) Large scale association analysis identifies three susceptibility loci for coronary artery disease. PLoS One 6:e29427 ArticleCASPubMed CentralPubMed Google Scholar
Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M (2012) Linking disease associations with regulatory information in the human genome. Genome Res 22:1748–1759 ArticleCASPubMed Google Scholar
Schulze H, Korpal M, Bergmeier W, Italiano JE Jr, Wahl SM, Shivdasani RA (2004) Interactions between the megakaryocyte/platelet-specific beta1 tubulin and the secretory leukocyte protease inhibitor SLPI suggest a role for regulated proteolysis in platelet functions. Blood 104:3949–3957 ArticleCASPubMed Google Scholar
Soranzo N, Spector TD, Mangino M, Kuhnel B, Rendon A, Teumer A, Willenborg C, Wright B, Chen L, Li M et al (2009a) A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium. Nat Genet 41:1182–1190 ArticleCASPubMed CentralPubMed Google Scholar
Soranzo N, Rendon A, Gieger C, Jones CI, Watkins NA, Menzel S, Doring A, Stephens J, Prokisch H, Erber W et al (2009b) A novel variant on chromosome 7q22.3 associated with mean platelet volume, counts, and function. Blood 113:3831–3837 ArticleCASPubMed CentralPubMed Google Scholar
Suehiro Y, Veljkovic DK, Fuller N, Motomura Y, Masse JM, Cramer EM, Hayward CP (2005) Endocytosis and storage of plasma factor V by human megakaryocytes. Thromb Haemost 94:585–592 CASPubMed Google Scholar
Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A (2003) PANTHER: a library of protein families and subfamilies indexed by function. Genome Res 13:2129–2141 ArticleCASPubMed Google Scholar
Thon JN, Montalvo A, Patel-Hett S, Devine MT, Richardson JL, Ehrlicher A, Larson MK, Hoffmeister K, Hartwig JH, Italiano JE Jr (2010) Cytoskeletal mechanics of proplatelet maturation and platelet release. J Cell Biol 191:861–874 ArticleCASPubMed Google Scholar
Todd JA, Walker NM, Cooper JD, Smyth DJ, Downes K, Plagnol V, Bailey R, Nejentsev S, Field SF, Payne F et al (2007) Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. Nat Genet 39:857–864 ArticleCASPubMed CentralPubMed Google Scholar
Tong W, Zhang J, Lodish HF (2005) Lnk inhibits erythropoiesis and Epo-dependent JAK2 activation and downstream signaling pathways. Blood 105:4604–4612 ArticleCASPubMed Google Scholar
Trynka G, Sandor C, Han B, Xu H, Stranger BE, Liu XS, Raychaudhuri S (2013) Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat Genet 45:124–130 ArticleCASPubMed Google Scholar
Turner S, Armstrong LL, Bradford Y, Carlson CS, Crawford DC, Crenshaw AT, de Andrade M, Doheny KF, Haines JL, Hayes G et al (2011) Quality control procedures for genome-wide association studies. Current protocols in human genetics/editorial board, Jonathan L. Haines… [et al.], Chapter 1, Unit1 19
Wahlberg K, Jiang J, Rooks H, Jawaid K, Matsuda F, Yamaguchi M, Lathrop M, Thein SL, Best S (2009) The HBS1L-MYB intergenic interval associated with elevated HbF levels shows characteristics of a distal regulatory region in erythroid cells. Blood 114:1254–1262 ArticleCASPubMed Google Scholar
Wang DS, Shaw G (1995) The association of the C-terminal region of beta I sigma II spectrin to brain membranes is mediated by a PH domain, does not require membrane proteins, and coincides with a inositol-1,4,5 triphosphate binding site. Biochem Biophys Res Commun 217:608–615 ArticleCASPubMed Google Scholar
Watkins NA, Gusnanto A, de Bono B, De S, Miranda-Saavedra D, Hardie DL, Angenent WG, Attwood AP, Ellis PD, Erber W et al (2009) A HaemAtlas: characterizing gene expression in differentiated human blood cells. Blood 113:e1–e9 ArticleCASPubMed Google Scholar
Weber C (2005) Platelets and chemokines in atherosclerosis: partners in crime. Circ Res 96:612–616 ArticleCASPubMed Google Scholar
Willoughby S, Holmes A, Loscalzo J (2002) Platelets and cardiovascular disease. Eur J Cardiovasc Nurs 1:273–288 ArticlePubMed Google Scholar