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Wain LV, Vaez A, Jansen R, Joehanes R, van der Most PJ, Erzurumluoglu AM, O’Reilly PF, Cabrera CP, Warren HR, Rose LM, Verwoert GC, Hottenga JJ, Strawbridge RJ, Esko T, Arking DE, Hwang SJ, Guo X, Kutalik Z, Trompet S, Shrine N, Teumer A, Ried JS, Bis JC, Smith AV, Amin N, Nolte IM, Lyytikäinen LP, Mahajan A, Wareham NJ, Hofer E, Joshi PK, Kristiansson K, Traglia M, Havulinna AS, Goel A, Nalls MA, Sõber S, Vuckovic D, Luan J, Fabiola Del Greco M, Ayers KL, Marrugat J, Ruggiero D, Lopez LM, Niiranen T, Enroth S, Jackson AU, Nelson CP, Huffman JE, Zhang W, Marten J, Gandin I, Harris SE, Zemunik T, Lu Y, Evangelou E, Shah N, de Borst MH, Mangino M, Prins BP, Campbell A, Li-Gao R, Chauhan G, Oldmeadow C, Abecasis G, Abedi M, Barbieri CM, Barnes MR, Batini C, Beilby J, Blake T, Boehnke M, Bottinger EP, Braund PS, Brown M, Brumat M, Campbell H, Chambers JC, Cocca M, Collins F, Connell J, Cordell HJ, Damman JJ, Davies G, de Geus EJ, de Mutsert R, Deelen J, Demirkale Y, Doney AS, Dörr M, Farrall M, Ferreira T, Frånberg M, Gao H, Giedraitis V, Gieger C, Giulianini F, Gow AJ, Hamsten A, Harris TB, Hofman A, Holliday EG, Hui J, Jarvelin MR, Johansson Å, Johnson AD, Jousilahti P, Jula A, Kähönen M, Kathiresan S, Khaw KT, Kolcic I, Koskinen S, Langenberg C, Larson M, Launer LJ, Lehne B, Liewald DC, Lin L, Lind L, Mach F, Mamasoula C, Menni C, Mifsud B, Milaneschi Y, Morgan A, Morris AD, Morrison AC, Munson PJ, Nandakumar P, Nguyen QT, Nutile T, Oldehinkel AJ, Oostra BA, Org E, Padmanabhan S, Palotie A, Paré G, Pattie A, Penninx BW, Poulter N, Pramstaller PP, Raitakari OT, Ren M, Rice K, Ridker PM, Riese H, Ripatti S, Robino A, Rotter JI, Rudan I, Saba Y, Pierre AS, Sala CF, Sarin AP, Schmidt R, Scott R, Seelen MA, Shields DC, Siscovick D, Sorice R, Stanton A, Stott DJ, Sundström J, Swertz M, Taylor KD, Thom S, Tzoulaki I, Tzourio C, Uitterlinden AG, Völker U, Vollenweider P, Wild S, Willemsen G, Wright AF, Yao J, Thériault S, Conen D, Attia J, Sever P, Debette S, Mook-Kanamori DO, Zeggini E, Spector TD, van der Harst P, Palmer CN, Vergnaud AC, Loos RJ, Polasek O, Starr JM, Girotto G, Hayward C, Kooner JS, Lindgren CM, Vitart V, Samani NJ, Tuomilehto J, Gyllensten U, Knekt P, Deary IJ, Ciullo M, Elosua R, Keavney BD, Hicks AA, Scott RA, Gasparini P, Laan M, Liu Y, Watkins H, Hartman CA, Salomaa V, Toniolo D, Perola M, Wilson JF, Schmidt H, Zhao JH, Lehtimäki T, van Duijn CM, Gudnason V, Psaty BM, Peters A, Rettig R, James A, Jukema JW, Strachan DP, Palmas W, Metspalu A, Ingelsson E, Boomsma DI, Franco OH, Bochud M, Newton-Cheh C, Munroe PB, Elliott P, Chasman DI, Chakravarti A, Knight J, Morris AP, Levy D, Tobin MD, Snieder H, Caulfield MJ, Ehret GB. Novel Blood Pressure Locus and Gene Discovery Using Genome-Wide Association Study and Expression Data Sets From Blood and the Kidney. Hypertension 2017; 70:e4-e19. [PMID: 28739976 PMCID: PMC5783787 DOI: 10.1161/hypertensionaha.117.09438] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Elevated blood pressure is a major risk factor for cardiovascular disease and has a substantial genetic contribution. Genetic variation influencing blood pressure has the potential to identify new pharmacological targets for the treatment of hypertension. To discover additional novel blood pressure loci, we used 1000 Genomes Project-based imputation in 150 134 European ancestry individuals and sought significant evidence for independent replication in a further 228 245 individuals. We report 6 new signals of association in or near HSPB7, TNXB, LRP12, LOC283335, SEPT9, and AKT2, and provide new replication evidence for a further 2 signals in EBF2 and NFKBIA. Combining large whole-blood gene expression resources totaling 12 607 individuals, we investigated all novel and previously reported signals and identified 48 genes with evidence for involvement in blood pressure regulation that are significant in multiple resources. Three novel kidney-specific signals were also detected. These robustly implicated genes may provide new leads for therapeutic innovation.
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Saleheen D, Zhao W, Young R, Nelson CP, Ho W, Ferguson JF, Rasheed A, Ou K, Nurnberg ST, Bauer RC, Goel A, Do R, Stewart AF, Hartiala J, Zhang W, Thorleifsson G, Strawbridge RJ, Sinisalo J, Kanoni S, Sedaghat S, Marouli E, Kristiansson K, Zhao JH, Scott R, Gauguier D, Shah SH, Smith AV, van Zuydam N, Cox AJ, Willenborg C, Kessler T, Zeng L, Province MA, Ganna A, Lind L, Pedersen NL, White CC, Joensuu A, Kleber ME, Hall AS, März W, Salomaa V, O’Donnell C, Ingelsson E, Feitosa MF, Erdmann J, Bowden DW, Palmer CN, Gudnason V, De Faire U, Zalloua P, Wareham N, Thompson JR, Kuulasmaa K, Dedoussis G, Perola M, Dehghan A, Chambers JC, Kooner J, Allayee H, Deloukas P, McPherson R, Stefansson K, Schunkert H, Kathiresan S, Farrall M, Frossard PM, Rader DJ, Samani NJ, Reilly MP. Loss of Cardioprotective Effects at the ADAMTS7 Locus as a Result of Gene-Smoking Interactions. Circulation 2017; 135:2336-2353. [PMID: 28461624 PMCID: PMC5612779 DOI: 10.1161/circulationaha.116.022069] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 03/21/2017] [Indexed: 01/14/2023]
Abstract
BACKGROUND Common diseases such as coronary heart disease (CHD) are complex in etiology. The interaction of genetic susceptibility with lifestyle factors may play a prominent role. However, gene-lifestyle interactions for CHD have been difficult to identify. Here, we investigate interaction of smoking behavior, a potent lifestyle factor, with genotypes that have been shown to associate with CHD risk. METHODS We analyzed data on 60 919 CHD cases and 80 243 controls from 29 studies for gene-smoking interactions for genetic variants at 45 loci previously reported to be associated with CHD risk. We also studied 5 loci associated with smoking behavior. Study-specific gene-smoking interaction effects were calculated and pooled using fixed-effects meta-analyses. Interaction analyses were declared to be significant at a P value of <1.0×10-3 (Bonferroni correction for 50 tests). RESULTS We identified novel gene-smoking interaction for a variant upstream of the ADAMTS7 gene. Every T allele of rs7178051 was associated with lower CHD risk by 12% in never-smokers (P=1.3×10-16) in comparison with 5% in ever-smokers (P=2.5×10-4), translating to a 60% loss of CHD protection conferred by this allelic variation in people who smoked tobacco (interaction P value=8.7×10-5). The protective T allele at rs7178051 was also associated with reduced ADAMTS7 expression in human aortic endothelial cells and lymphoblastoid cell lines. Exposure of human coronary artery smooth muscle cells to cigarette smoke extract led to induction of ADAMTS7. CONCLUSIONS: Allelic variation at rs7178051 that associates with reduced ADAMTS7 expression confers stronger CHD protection in never-smokers than in ever-smokers. Increased vascular ADAMTS7 expression may contribute to the loss of CHD protection in smokers.
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Graff M, Scott RA, Justice AE, Young KL, Feitosa MF, Barata L, Winkler TW, Chu AY, Mahajan A, Hadley D, Xue L, Workalemahu T, Heard-Costa NL, den Hoed M, Ahluwalia TS, Qi Q, Ngwa JS, Renström F, Quaye L, Eicher JD, Hayes JE, Cornelis M, Kutalik Z, Lim E, Luan J, Huffman JE, Zhang W, Zhao W, Griffin PJ, Haller T, Ahmad S, Marques-Vidal PM, Bien S, Yengo L, Teumer A, Smith AV, Kumari M, Harder MN, Justesen JM, Kleber ME, Hollensted M, Lohman K, Rivera NV, Whitfield JB, Zhao JH, Stringham HM, Lyytikäinen LP, Huppertz C, Willemsen G, Peyrot WJ, Wu Y, Kristiansson K, Demirkan A, Fornage M, Hassinen M, Bielak LF, Cadby G, Tanaka T, Mägi R, van der Most PJ, Jackson AU, Bragg-Gresham JL, Vitart V, Marten J, Navarro P, Bellis C, Pasko D, Johansson Å, Snitker S, Cheng YC, Eriksson J, Lim U, Aadahl M, Adair LS, Amin N, Balkau B, Auvinen J, Beilby J, Bergman RN, Bergmann S, Bertoni AG, Blangero J, Bonnefond A, Bonnycastle LL, Borja JB, Brage S, Busonero F, Buyske S, Campbell H, Chines PS, Collins FS, Corre T, Smith GD, Delgado GE, Dueker N, Dörr M, Ebeling T, Eiriksdottir G, Esko T, Faul JD, Fu M, Færch K, Gieger C, Gläser S, Gong J, Gordon-Larsen P, Grallert H, Grammer TB, Grarup N, van Grootheest G, Harald K, Hastie ND, Havulinna AS, Hernandez D, Hindorff L, Hocking LJ, Holmens OL, Holzapfel C, Hottenga JJ, Huang J, Huang T, Hui J, Huth C, Hutri-Kähönen N, James AL, Jansson JO, Jhun MA, Juonala M, Kinnunen L, Koistinen HA, Kolcic I, Komulainen P, Kuusisto J, Kvaløy K, Kähönen M, Lakka TA, Launer LJ, Lehne B, Lindgren CM, Lorentzon M, Luben R, Marre M, Milaneschi Y, Monda KL, Montgomery GW, De Moor MHM, Mulas A, Müller-Nurasyid M, Musk AW, Männikkö R, Männistö S, Narisu N, Nauck M, Nettleton JA, Nolte IM, Oldehinkel AJ, Olden M, Ong KK, Padmanabhan S, Paternoster L, Perez J, Perola M, Peters A, Peters U, Peyser PA, Prokopenko I, Puolijoki H, Raitakari OT, Rankinen T, Rasmussen-Torvik LJ, Rawal R, Ridker PM, Rose LM, Rudan I, Sarti C, Sarzynski MA, Savonen K, Scott WR, Sanna S, Shuldiner AR, Sidney S, Silbernagel G, Smith BH, Smith JA, Snieder H, Stančáková A, Sternfeld B, Swift AJ, Tammelin T, Tan ST, Thorand B, Thuillier D, Vandenput L, Vestergaard H, van Vliet-Ostaptchouk JV, Vohl MC, Völker U, Waeber G, Walker M, Wild S, Wong A, Wright AF, Zillikens MC, Zubair N, Haiman CA, Lemarchand L, Gyllensten U, Ohlsson C, Hofman A, Rivadeneira F, Uitterlinden AG, Pérusse L, Wilson JF, Hayward C, Polasek O, Cucca F, Hveem K, Hartman CA, Tönjes A, Bandinelli S, Palmer LJ, Kardia SLR, Rauramaa R, Sørensen TIA, Tuomilehto J, Salomaa V, Penninx BWJH, de Geus EJC, Boomsma DI, Lehtimäki T, Mangino M, Laakso M, Bouchard C, Martin NG, Kuh D, Liu Y, Linneberg A, März W, Strauch K, Kivimäki M, Harris TB, Gudnason V, Völzke H, Qi L, Järvelin MR, Chambers JC, Kooner JS, Froguel P, Kooperberg C, Vollenweider P, Hallmans G, Hansen T, Pedersen O, Metspalu A, Wareham NJ, Langenberg C, Weir DR, Porteous DJ, Boerwinkle E, Chasman DI, Abecasis GR, Barroso I, McCarthy MI, Frayling TM, O’Connell JR, van Duijn CM, Boehnke M, Heid IM, Mohlke KL, Strachan DP, Fox CS, Liu CT, Hirschhorn JN, Klein RJ, Johnson AD, Borecki IB, Franks PW, North KE, Cupples LA, Loos RJF, Kilpeläinen TO. Genome-wide physical activity interactions in adiposity - A meta-analysis of 200,452 adults. PLoS Genet 2017; 13:e1006528. [PMID: 28448500 PMCID: PMC5407576 DOI: 10.1371/journal.pgen.1006528] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/07/2016] [Indexed: 11/23/2022] Open
Abstract
Physical activity (PA) may modify the genetic effects that give rise to increased risk of obesity. To identify adiposity loci whose effects are modified by PA, we performed genome-wide interaction meta-analyses of BMI and BMI-adjusted waist circumference and waist-hip ratio from up to 200,452 adults of European (n = 180,423) or other ancestry (n = 20,029). We standardized PA by categorizing it into a dichotomous variable where, on average, 23% of participants were categorized as inactive and 77% as physically active. While we replicate the interaction with PA for the strongest known obesity-risk locus in the FTO gene, of which the effect is attenuated by ~30% in physically active individuals compared to inactive individuals, we do not identify additional loci that are sensitive to PA. In additional genome-wide meta-analyses adjusting for PA and interaction with PA, we identify 11 novel adiposity loci, suggesting that accounting for PA or other environmental factors that contribute to variation in adiposity may facilitate gene discovery.
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Ried JS, Jeff M. J, Chu AY, Bragg-Gresham JL, van Dongen J, Huffman JE, Ahluwalia TS, Cadby G, Eklund N, Eriksson J, Esko T, Feitosa MF, Goel A, Gorski M, Hayward C, Heard-Costa NL, Jackson AU, Jokinen E, Kanoni S, Kristiansson K, Kutalik Z, Lahti J, Luan J, Mägi R, Mahajan A, Mangino M, Medina-Gomez C, Monda KL, Nolte IM, Pérusse L, Prokopenko I, Qi L, Rose LM, Salvi E, Smith MT, Snieder H, Stančáková A, Ju Sung Y, Tachmazidou I, Teumer A, Thorleifsson G, van der Harst P, Walker RW, Wang SR, Wild SH, Willems SM, Wong A, Zhang W, Albrecht E, Couto Alves A, Bakker SJL, Barlassina C, Bartz TM, Beilby J, Bellis C, Bergman RN, Bergmann S, Blangero J, Blüher M, Boerwinkle E, Bonnycastle LL, Bornstein SR, Bruinenberg M, Campbell H, Chen YDI, Chiang CWK, Chines PS, Collins FS, Cucca F, Cupples LA, D'Avila F, de Geus EJ.C, Dedoussis G, Dimitriou M, Döring A, Eriksson JG, Farmaki AE, Farrall M, Ferreira T, Fischer K, Forouhi NG, Friedrich N, Gjesing AP, Glorioso N, Graff M, Grallert H, Grarup N, Gräßler J, Grewal J, Hamsten A, Harder MN, Hartman CA, Hassinen M, Hastie N, Hattersley AT, Havulinna AS, Heliövaara M, Hillege H, Hofman A, Holmen O, Homuth G, Hottenga JJ, Hui J, Husemoen LL, Hysi PG, Isaacs A, Ittermann T, Jalilzadeh S, James AL, Jørgensen T, Jousilahti P, Jula A, Marie Justesen J, Justice AE, Kähönen M, Karaleftheri M, Tee Khaw K, Keinanen-Kiukaanniemi SM, Kinnunen L, Knekt PB, Koistinen HA, Kolcic I, Kooner IK, Koskinen S, Kovacs P, Kyriakou T, Laitinen T, Langenberg C, Lewin AM, Lichtner P, Lindgren CM, Lindström J, Linneberg A, Lorbeer R, Lorentzon M, Luben R, Lyssenko V, Männistö S, Manunta P, Leach IM, McArdle WL, Mcknight B, Mohlke KL, Mihailov E, Milani L, Mills R, Montasser ME, Morris AP, Müller G, Musk AW, Narisu N, Ong KK, Oostra BA, Osmond C, Palotie A, Pankow JS, Paternoster L, Penninx BW, Pichler I, Pilia MG, Polašek O, Pramstaller PP, Raitakari OT, Rankinen T, Rao DC, Rayner NW, Ribel-Madsen R, Rice TK, Richards M, Ridker PM, Rivadeneira F, Ryan KA, Sanna S, Sarzynski MA, Scholtens S, Scott RA, Sebert S, Southam L, Sparsø TH, Steinthorsdottir V, Stirrups K, Stolk RP, Strauch K, Stringham HM, Swertz MA, Swift AJ, Tönjes A, Tsafantakis E, van der Most PJ, Van Vliet-Ostaptchouk JV, Vandenput L, Vartiainen E, Venturini C, Verweij N, Viikari JS, Vitart V, Vohl MC, Vonk JM, Waeber G, Widén E, Willemsen G, Wilsgaard T, Winkler TW, Wright AF, Yerges-Armstrong LM, Hua Zhao J, Carola Zillikens M, Boomsma DI, Bouchard C, Chambers JC, Chasman DI, Cusi D, Gansevoort RT, Gieger C, Hansen T, Hicks AA, Hu F, Hveem K, Jarvelin MR, Kajantie E, Kooner JS, Kuh D, Kuusisto J, Laakso M, Lakka TA, Lehtimäki T, Metspalu A, Njølstad I, Ohlsson C, Oldehinkel AJ, Palmer LJ, Pedersen O, Perola M, Peters A, Psaty BM, Puolijoki H, Rauramaa R, Rudan I, Salomaa V, Schwarz PEH, Shudiner AR, Smit JH, Sørensen TIA, Spector TD, Stefansson K, Stumvoll M, Tremblay A, Tuomilehto J, Uitterlinden AG, Uusitupa M, Völker U, Vollenweider P, Wareham NJ, Watkins H, Wilson JF, Zeggini E, Abecasis GR, Boehnke M, Borecki IB, Deloukas P, van Duijn CM, Fox C, Groop LC, Heid IM, Hunter DJ, Kaplan RC, McCarthy MI, North KE, O'Connell JR, Schlessinger D, Thorsteinsdottir U, Strachan DP, Frayling T, Hirschhorn JN, Müller-Nurasyid M, Loos RJF. A principal component meta-analysis on multiple anthropometric traits identifies novel loci for body shape. Nat Commun 2016; 7:13357. [PMID: 27876822 PMCID: PMC5114527 DOI: 10.1038/ncomms13357] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 09/21/2016] [Indexed: 01/15/2023] Open
Abstract
Large consortia have revealed hundreds of genetic loci associated with anthropometric traits, one trait at a time. We examined whether genetic variants affect body shape as a composite phenotype that is represented by a combination of anthropometric traits. We developed an approach that calculates averaged PCs (AvPCs) representing body shape derived from six anthropometric traits (body mass index, height, weight, waist and hip circumference, waist-to-hip ratio). The first four AvPCs explain >99% of the variability, are heritable, and associate with cardiometabolic outcomes. We performed genome-wide association analyses for each body shape composite phenotype across 65 studies and meta-analysed summary statistics. We identify six novel loci: LEMD2 and CD47 for AvPC1, RPS6KA5/C14orf159 and GANAB for AvPC3, and ARL15 and ANP32 for AvPC4. Our findings highlight the value of using multiple traits to define complex phenotypes for discovery, which are not captured by single-trait analyses, and may shed light onto new pathways.
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Ehret GB, Ferreira T, Chasman DI, Jackson AU, Schmidt EM, Johnson T, Thorleifsson G, Luan J, Donnelly LA, Kanoni S, Petersen AK, Pihur V, Strawbridge RJ, Shungin D, Hughes MF, Meirelles O, Kaakinen M, Bouatia-Naji N, Kristiansson K, Shah S, Kleber ME, Guo X, Lyytikäinen LP, Fava C, Eriksson N, Nolte IM, Magnusson PK, Salfati EL, Rallidis LS, Theusch E, Smith AJ, Folkersen L, Witkowska K, Pers TH, Joehanes R, Kim SK, Lataniotis L, Jansen R, Johnson AD, Warren H, Kim YJ, Zhao W, Wu Y, Tayo BO, Bochud M, Absher D, Adair LS, Amin N, Arking DE, Axelsson T, Baldassarre D, Balkau B, Bandinelli S, Barnes MR, Barroso I, Bevan S, Bis JC, Bjornsdottir G, Boehnke M, Boerwinkle E, Bonnycastle LL, Boomsma DI, Bornstein SR, Brown MJ, Burnier M, Cabrera CP, Chambers JC, Chang IS, Cheng CY, Chines PS, Chung RH, Collins FS, Connell JM, Döring A, Dallongeville J, Danesh J, de Faire U, Delgado G, Dominiczak AF, Doney AS, Drenos F, Edkins S, Eicher JD, Elosua R, Enroth S, Erdmann J, Eriksson P, Esko T, Evangelou E, Evans A, Fall T, Farrall M, Felix JF, Ferrières J, Ferrucci L, Fornage M, Forrester T, Franceschini N, Duran OHF, Franco-Cereceda A, Fraser RM, Ganesh SK, Gao H, Gertow K, Gianfagna F, Gigante B, Giulianini F, Goel A, Goodall AH, Goodarzi MO, Gorski M, Gräßler J, Groves C, Gudnason V, Gyllensten U, Hallmans G, Hartikainen AL, Hassinen M, Havulinna AS, Hayward C, Hercberg S, Herzig KH, Hicks AA, Hingorani AD, Hirschhorn JN, Hofman A, Holmen J, Holmen OL, Hottenga JJ, Howard P, Hsiung CA, Hunt SC, Ikram MA, Illig T, Iribarren C, Jensen RA, Kähönen M, Kang H, Kathiresan S, Keating BJ, Khaw KT, Kim YK, Kim E, Kivimaki M, Klopp N, Kolovou G, Komulainen P, Kooner JS, Kosova G, Krauss RM, Kuh D, Kutalik Z, Kuusisto J, Kvaløy K, Lakka TA, Lee NR, Lee IT, Lee WJ, Levy D, Li X, Liang KW, Lin H, Lin L, Lindström J, Lobbens S, Männistö S, Müller G, Müller-Nurasyid M, Mach F, Markus HS, Marouli E, McCarthy MI, McKenzie CA, Meneton P, Menni C, Metspalu A, Mijatovic V, Moilanen L, Montasser ME, Morris AD, Morrison AC, Mulas A, Nagaraja R, Narisu N, Nikus K, O'Donnell CJ, O'Reilly PF, Ong KK, Paccaud F, Palmer CD, Parsa A, Pedersen NL, Penninx BW, Perola M, Peters A, Poulter N, Pramstaller PP, Psaty BM, Quertermous T, Rao DC, Rasheed A, Rayner NWN, Renström F, Rettig R, Rice KM, Roberts R, Rose LM, Rossouw J, Samani NJ, Sanna S, Saramies J, Schunkert H, Sebert S, Sheu WHH, Shin YA, Sim X, Smit JH, Smith AV, Sosa MX, Spector TD, Stančáková A, Stanton A, Stirrups KE, Stringham HM, Sundstrom J, Swift AJ, Syvänen AC, Tai ES, Tanaka T, Tarasov KV, Teumer A, Thorsteinsdottir U, Tobin MD, Tremoli E, Uitterlinden AG, Uusitupa M, Vaez A, Vaidya D, van Duijn CM, van Iperen EP, Vasan RS, Verwoert GC, Virtamo J, Vitart V, Voight BF, Vollenweider P, Wagner A, Wain LV, Wareham NJ, Watkins H, Weder AB, Westra HJ, Wilks R, Wilsgaard T, Wilson JF, Wong TY, Yang TP, Yao J, Yengo L, Zhang W, Zhao JH, Zhu X, Bovet P, Cooper RS, Mohlke KL, Saleheen D, Lee JY, Elliott P, Gierman HJ, Willer CJ, Franke L, Hovingh GK, Taylor KD, Dedoussis G, Sever P, Wong A, Lind L, Assimes TL, Njølstad I, Schwarz PEH, Langenberg C, Snieder H, Caulfield MJ, Melander O, Laakso M, Saltevo J, Rauramaa R, Tuomilehto J, Ingelsson E, Lehtimäki T, Hveem K, Palmas W, März W, Kumari M, Salomaa V, Chen YDI, Rotter JI, Froguel P, Jarvelin MR, Lakatta EG, Kuulasmaa K, Franks PW, Hamsten A, Wichmann HE, Palmer CN, Stefansson K, Ridker PM, Loos RJ, Chakravarti A, Deloukas P, Morris AP, Newton-Cheh C, Munroe PB. The genetics of blood pressure regulation and its target organs from association studies in 342,415 individuals. Nat Genet 2016; 48:1171-1184. [PMID: 27618452 PMCID: PMC5042863 DOI: 10.1038/ng.3667] [Citation(s) in RCA: 287] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 08/15/2016] [Indexed: 02/02/2023]
Abstract
To dissect the genetic architecture of blood pressure and assess effects on target organ damage, we analyzed 128,272 SNPs from targeted and genome-wide arrays in 201,529 individuals of European ancestry, and genotypes from an additional 140,886 individuals were used for validation. We identified 66 blood pressure-associated loci, of which 17 were new; 15 harbored multiple distinct association signals. The 66 index SNPs were enriched for cis-regulatory elements, particularly in vascular endothelial cells, consistent with a primary role in blood pressure control through modulation of vascular tone across multiple tissues. The 66 index SNPs combined in a risk score showed comparable effects in 64,421 individuals of non-European descent. The 66-SNP blood pressure risk score was significantly associated with target organ damage in multiple tissues but with minor effects in the kidney. Our findings expand current knowledge of blood pressure-related pathways and highlight tissues beyond the classical renal system in blood pressure regulation.
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Lu Y, Day FR, Gustafsson S, Buchkovich ML, Na J, Bataille V, Cousminer DL, Dastani Z, Drong AW, Esko T, Evans DM, Falchi M, Feitosa MF, Ferreira T, Hedman ÅK, Haring R, Hysi PG, Iles MM, Justice AE, Kanoni S, Lagou V, Li R, Li X, Locke A, Lu C, Mägi R, Perry JRB, Pers TH, Qi Q, Sanna M, Schmidt EM, Scott WR, Shungin D, Teumer A, Vinkhuyzen AAE, Walker RW, Westra HJ, Zhang M, Zhang W, Zhao JH, Zhu Z, Afzal U, Ahluwalia TS, Bakker SJL, Bellis C, Bonnefond A, Borodulin K, Buchman AS, Cederholm T, Choh AC, Choi HJ, Curran JE, de Groot LCPGM, De Jager PL, Dhonukshe-Rutten RAM, Enneman AW, Eury E, Evans DS, Forsen T, Friedrich N, Fumeron F, Garcia ME, Gärtner S, Han BG, Havulinna AS, Hayward C, Hernandez D, Hillege H, Ittermann T, Kent JW, Kolcic I, Laatikainen T, Lahti J, Leach IM, Lee CG, Lee JY, Liu T, Liu Y, Lobbens S, Loh M, Lyytikäinen LP, Medina-Gomez C, Michaëlsson K, Nalls MA, Nielson CM, Oozageer L, Pascoe L, Paternoster L, Polašek O, Ripatti S, Sarzynski MA, Shin CS, Narančić NS, Spira D, Srikanth P, Steinhagen-Thiessen E, Sung YJ, Swart KMA, Taittonen L, Tanaka T, Tikkanen E, van der Velde N, van Schoor NM, Verweij N, Wright AF, Yu L, Zmuda JM, Eklund N, Forrester T, Grarup N, Jackson AU, Kristiansson K, Kuulasmaa T, Kuusisto J, Lichtner P, Luan J, Mahajan A, Männistö S, Palmer CD, Ried JS, Scott RA, Stancáková A, Wagner PJ, Demirkan A, Döring A, Gudnason V, Kiel DP, Kühnel B, Mangino M, Mcknight B, Menni C, O'Connell JR, Oostra BA, Shuldiner AR, Song K, Vandenput L, van Duijn CM, Vollenweider P, White CC, Boehnke M, Boettcher Y, Cooper RS, Forouhi NG, Gieger C, Grallert H, Hingorani A, Jørgensen T, Jousilahti P, Kivimaki M, Kumari M, Laakso M, Langenberg C, Linneberg A, Luke A, Mckenzie CA, Palotie A, Pedersen O, Peters A, Strauch K, Tayo BO, Wareham NJ, Bennett DA, Bertram L, Blangero J, Blüher M, Bouchard C, Campbell H, Cho NH, Cummings SR, Czerwinski SA, Demuth I, Eckardt R, Eriksson JG, Ferrucci L, Franco OH, Froguel P, Gansevoort RT, Hansen T, Harris TB, Hastie N, Heliövaara M, Hofman A, Jordan JM, Jula A, Kähönen M, Kajantie E, Knekt PB, Koskinen S, Kovacs P, Lehtimäki T, Lind L, Liu Y, Orwoll ES, Osmond C, Perola M, Pérusse L, Raitakari OT, Rankinen T, Rao DC, Rice TK, Rivadeneira F, Rudan I, Salomaa V, Sørensen TIA, Stumvoll M, Tönjes A, Towne B, Tranah GJ, Tremblay A, Uitterlinden AG, van der Harst P, Vartiainen E, Viikari JS, Vitart V, Vohl MC, Völzke H, Walker M, Wallaschofski H, Wild S, Wilson JF, Yengo L, Bishop DT, Borecki IB, Chambers JC, Cupples LA, Dehghan A, Deloukas P, Fatemifar G, Fox C, Furey TS, Franke L, Han J, Hunter DJ, Karjalainen J, Karpe F, Kaplan RC, Kooner JS, McCarthy MI, Murabito JM, Morris AP, Bishop JAN, North KE, Ohlsson C, Ong KK, Prokopenko I, Richards JB, Schadt EE, Spector TD, Widén E, Willer CJ, Yang J, Ingelsson E, Mohlke KL, Hirschhorn JN, Pospisilik JA, Zillikens MC, Lindgren C, Kilpeläinen TO, Loos RJF. New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk. Nat Commun 2016; 7:10495. [PMID: 26833246 PMCID: PMC4740398 DOI: 10.1038/ncomms10495] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 12/16/2015] [Indexed: 12/24/2022] Open
Abstract
To increase our understanding of the genetic basis of adiposity and its links to cardiometabolic disease risk, we conducted a genome-wide association meta-analysis of body fat percentage (BF%) in up to 100,716 individuals. Twelve loci reached genome-wide significance (P<5 × 10(-8)), of which eight were previously associated with increased overall adiposity (BMI, BF%) and four (in or near COBLL1/GRB14, IGF2BP1, PLA2G6, CRTC1) were novel associations with BF%. Seven loci showed a larger effect on BF% than on BMI, suggestive of a primary association with adiposity, while five loci showed larger effects on BMI than on BF%, suggesting association with both fat and lean mass. In particular, the loci more strongly associated with BF% showed distinct cross-phenotype association signatures with a range of cardiometabolic traits revealing new insights in the link between adiposity and disease risk.
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Kilpeläinen TO, Carli JFM, Skowronski AA, Sun Q, Kriebel J, Feitosa MF, Hedman ÅK, Drong AW, Hayes JE, Zhao J, Pers TH, Schick U, Grarup N, Kutalik Z, Trompet S, Mangino M, Kristiansson K, Beekman M, Lyytikäinen LP, Eriksson J, Henneman P, Lahti J, Tanaka T, Luan J, Del Greco M F, Pasko D, Renström F, Willems SM, Mahajan A, Rose LM, Guo X, Liu Y, Kleber ME, Pérusse L, Gaunt T, Ahluwalia TS, Ju Sung Y, Ramos YF, Amin N, Amuzu A, Barroso I, Bellis C, Blangero J, Buckley BM, Böhringer S, I Chen YD, de Craen AJN, Crosslin DR, Dale CE, Dastani Z, Day FR, Deelen J, Delgado GE, Demirkan A, Finucane FM, Ford I, Garcia ME, Gieger C, Gustafsson S, Hallmans G, Hankinson SE, Havulinna AS, Herder C, Hernandez D, Hicks AA, Hunter DJ, Illig T, Ingelsson E, Ioan-Facsinay A, Jansson JO, Jenny NS, Jørgensen ME, Jørgensen T, Karlsson M, Koenig W, Kraft P, Kwekkeboom J, Laatikainen T, Ladwig KH, LeDuc CA, Lowe G, Lu Y, Marques-Vidal P, Meisinger C, Menni C, Morris AP, Myers RH, Männistö S, Nalls MA, Paternoster L, Peters A, Pradhan AD, Rankinen T, Rasmussen-Torvik LJ, Rathmann W, Rice TK, Brent Richards J, Ridker PM, Sattar N, Savage DB, Söderberg S, Timpson NJ, Vandenput L, van Heemst D, Uh HW, Vohl MC, Walker M, Wichmann HE, Widén E, Wood AR, Yao J, Zeller T, Zhang Y, Meulenbelt I, Kloppenburg M, Astrup A, Sørensen TIA, Sarzynski MA, Rao DC, Jousilahti P, Vartiainen E, Hofman A, Rivadeneira F, Uitterlinden AG, Kajantie E, Osmond C, Palotie A, Eriksson JG, Heliövaara M, Knekt PB, Koskinen S, Jula A, Perola M, Huupponen RK, Viikari JS, Kähönen M, Lehtimäki T, Raitakari OT, Mellström D, Lorentzon M, Casas JP, Bandinelli S, März W, Isaacs A, van Dijk KW, van Duijn CM, Harris TB, Bouchard C, Allison MA, Chasman DI, Ohlsson C, Lind L, Scott RA, Langenberg C, Wareham NJ, Ferrucci L, Frayling TM, Pramstaller PP, Borecki IB, Waterworth DM, Bergmann S, Waeber G, Vollenweider P, Vestergaard H, Hansen T, Pedersen O, Hu FB, Eline Slagboom P, Grallert H, Spector TD, Jukema JW, Klein RJ, Schadt EE, Franks PW, Lindgren CM, Leibel RL, Loos RJF. Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels. Nat Commun 2016; 7:10494. [PMID: 26833098 PMCID: PMC4740377 DOI: 10.1038/ncomms10494] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 12/16/2015] [Indexed: 01/20/2023] Open
Abstract
Leptin is an adipocyte-secreted hormone, the circulating levels of which correlate closely with overall adiposity. Although rare mutations in the leptin (LEP) gene are well known to cause leptin deficiency and severe obesity, no common loci regulating circulating leptin levels have been uncovered. Therefore, we performed a genome-wide association study (GWAS) of circulating leptin levels from 32,161 individuals and followed up loci reaching P<10(-6) in 19,979 additional individuals. We identify five loci robustly associated (P<5 × 10(-8)) with leptin levels in/near LEP, SLC32A1, GCKR, CCNL1 and FTO. Although the association of the FTO obesity locus with leptin levels is abolished by adjustment for BMI, associations of the four other loci are independent of adiposity. The GCKR locus was found associated with multiple metabolic traits in previous GWAS and the CCNL1 locus with birth weight. Knockdown experiments in mouse adipose tissue explants show convincing evidence for adipogenin, a regulator of adipocyte differentiation, as the novel causal gene in the SLC32A1 locus influencing leptin levels. Our findings provide novel insights into the regulation of leptin production by adipose tissue and open new avenues for examining the influence of variation in leptin levels on adiposity and metabolic health.
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Hägg S, Fall T, Ploner A, Mägi R, Fischer K, Draisma HHM, Kals M, de Vries PS, Dehghan A, Willems SM, Sarin AP, Kristiansson K, Nuotio ML, Havulinna AS, de Bruijn RFAG, Ikram MA, Kuningas M, Stricker BH, Franco OH, Benyamin B, Gieger C, Hall AS, Huikari V, Jula A, Järvelin MR, Kaakinen M, Kaprio J, Kobl M, Mangino M, Nelson CP, Palotie A, Samani NJ, Spector TD, Strachan DP, Tobin MD, Whitfield JB, Uitterlinden AG, Salomaa V, Syvänen AC, Kuulasmaa K, Magnusson PK, Esko T, Hofman A, de Geus EJC, Lind L, Giedraitis V, Perola M, Evans A, Ferrières J, Virtamo J, Kee F, Tregouet DA, Arveiler D, Amouyel P, Gianfagna F, Brambilla P, Ripatti S, van Duijn CM, Metspalu A, Prokopenko I, McCarthy MI, Pedersen NL, Ingelsson E. Adiposity as a cause of cardiovascular disease: a Mendelian randomization study. Int J Epidemiol 2015; 44:578-86. [PMID: 26016847 DOI: 10.1093/ije/dyv094] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2015] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Adiposity, as indicated by body mass index (BMI), has been associated with risk of cardiovascular diseases in epidemiological studies. We aimed to investigate if these associations are causal, using Mendelian randomization (MR) methods. METHODS The associations of BMI with cardiovascular outcomes [coronary heart disease (CHD), heart failure and ischaemic stroke], and associations of a genetic score (32 BMI single nucleotide polymorphisms) with BMI and cardiovascular outcomes were examined in up to 22,193 individuals with 3062 incident cardiovascular events from nine prospective follow-up studies within the ENGAGE consortium. We used random-effects meta-analysis in an MR framework to provide causal estimates of the effect of adiposity on cardiovascular outcomes. RESULTS There was a strong association between BMI and incident CHD (HR = 1.20 per SD-increase of BMI, 95% CI, 1.12-1.28, P = 1.9.10(-7)), heart failure (HR = 1.47, 95% CI, 1.35-1.60, P = 9.10(-19)) and ischaemic stroke (HR = 1.15, 95% CI, 1.06-1.24, P = 0.0008) in observational analyses. The genetic score was robustly associated with BMI (β = 0.030 SD-increase of BMI per additional allele, 95% CI, 0.028-0.033, P = 3.10(-107)). Analyses indicated a causal effect of adiposity on development of heart failure (HR = 1.93 per SD-increase of BMI, 95% CI, 1.12-3.30, P = 0.017) and ischaemic stroke (HR = 1.83, 95% CI, 1.05-3.20, P = 0.034). Additional cross-sectional analyses using both ENGAGE and CARDIoGRAMplusC4D data showed a causal effect of adiposity on CHD. CONCLUSIONS Using MR methods, we provide support for the hypothesis that adiposity causes CHD, heart failure and, previously not demonstrated, ischaemic stroke.
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Nettleton JA, Follis JL, Ngwa JS, Smith CE, Ahmad S, Tanaka T, Wojczynski MK, Voortman T, Lemaitre RN, Kristiansson K, Nuotio ML, Houston DK, Perälä MM, Qi Q, Sonestedt E, Manichaikul A, Kanoni S, Ganna A, Mikkilä V, North KE, Siscovick DS, Harald K, Mckeown NM, Johansson I, Rissanen H, Liu Y, Lahti J, Hu FB, Bandinelli S, Rukh G, Rich S, Booij L, Dmitriou M, Ax E, Raitakari O, Mukamal K, Männistö S, Hallmans G, Jula A, Ericson U, Jacobs DR, Van Rooij FJA, Deloukas P, Sjögren P, Kähönen M, Djousse L, Perola M, Barroso I, Hofman A, Stirrups K, Viikari J, Uitterlinden AG, Kalafati IP, Franco OH, Mozaffarian D, Salomaa V, Borecki IB, Knekt P, Kritchevsky SB, Eriksson JG, Dedoussis GV, Qi L, Ferrucci L, Orho-Melander M, Zillikens MC, Ingelsson E, Lehtimäki T, Renström F, Cupples LA, Loos RJF, Franks PW. Gene × dietary pattern interactions in obesity: analysis of up to 68 317 adults of European ancestry. Hum Mol Genet 2015; 24:4728-38. [PMID: 25994509 PMCID: PMC4512626 DOI: 10.1093/hmg/ddv186] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/17/2015] [Indexed: 11/14/2022] Open
Abstract
Obesity is highly heritable. Genetic variants showing robust associations with obesity traits have been identified through genome-wide association studies. We investigated whether a composite score representing healthy diet modifies associations of these variants with obesity traits. Totally, 32 body mass index (BMI)- and 14 waist-hip ratio (WHR)-associated single nucleotide polymorphisms were genotyped, and genetic risk scores (GRS) were calculated in 18 cohorts of European ancestry (n = 68 317). Diet score was calculated based on self-reported intakes of whole grains, fish, fruits, vegetables, nuts/seeds (favorable) and red/processed meats, sweets, sugar-sweetened beverages and fried potatoes (unfavorable). Multivariable adjusted, linear regression within each cohort followed by inverse variance-weighted, fixed-effects meta-analysis was used to characterize: (a) associations of each GRS with BMI and BMI-adjusted WHR and (b) diet score modification of genetic associations with BMI and BMI-adjusted WHR. Nominally significant interactions (P = 0.006-0.04) were observed between the diet score and WHR-GRS (but not BMI-GRS), two WHR loci (GRB14 rs10195252; LYPLAL1 rs4846567) and two BMI loci (LRRN6C rs10968576; MTIF3 rs4771122), for the respective BMI-adjusted WHR or BMI outcomes. Although the magnitudes of these select interactions were small, our data indicated that associations between genetic predisposition and obesity traits were stronger with a healthier diet. Our findings generate interesting hypotheses; however, experimental and functional studies are needed to determine their clinical relevance.
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Fall T, Hägg S, Ploner A, Mägi R, Fischer K, Draisma HHM, Sarin AP, Benyamin B, Ladenvall C, Åkerlund M, Kals M, Esko T, Nelson CP, Kaakinen M, Huikari V, Mangino M, Meirhaeghe A, Kristiansson K, Nuotio ML, Kobl M, Grallert H, Dehghan A, Kuningas M, de Vries PS, de Bruijn RFAG, Willems SM, Heikkilä K, Silventoinen K, Pietiläinen KH, Legry V, Giedraitis V, Goumidi L, Syvänen AC, Strauch K, Koenig W, Lichtner P, Herder C, Palotie A, Menni C, Uitterlinden AG, Kuulasmaa K, Havulinna AS, Moreno LA, Gonzalez-Gross M, Evans A, Tregouet DA, Yarnell JWG, Virtamo J, Ferrières J, Veronesi G, Perola M, Arveiler D, Brambilla P, Lind L, Kaprio J, Hofman A, Stricker BH, van Duijn CM, Ikram MA, Franco OH, Cottel D, Dallongeville J, Hall AS, Jula A, Tobin MD, Penninx BW, Peters A, Gieger C, Samani NJ, Montgomery GW, Whitfield JB, Martin NG, Groop L, Spector TD, Magnusson PK, Amouyel P, Boomsma DI, Nilsson PM, Järvelin MR, Lyssenko V, Metspalu A, Strachan DP, Salomaa V, Ripatti S, Pedersen NL, Prokopenko I, McCarthy MI, Ingelsson E. Age- and sex-specific causal effects of adiposity on cardiovascular risk factors. Diabetes 2015; 64:1841-52. [PMID: 25712996 PMCID: PMC4407863 DOI: 10.2337/db14-0988] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 11/30/2014] [Indexed: 12/18/2022]
Abstract
Observational studies have reported different effects of adiposity on cardiovascular risk factors across age and sex. Since cardiovascular risk factors are enriched in obese individuals, it has not been easy to dissect the effects of adiposity from those of other risk factors. We used a Mendelian randomization approach, applying a set of 32 genetic markers to estimate the causal effect of adiposity on blood pressure, glycemic indices, circulating lipid levels, and markers of inflammation and liver disease in up to 67,553 individuals. All analyses were stratified by age (cutoff 55 years of age) and sex. The genetic score was associated with BMI in both nonstratified analysis (P = 2.8 × 10(-107)) and stratified analyses (all P < 3.3 × 10(-30)). We found evidence of a causal effect of adiposity on blood pressure, fasting levels of insulin, C-reactive protein, interleukin-6, HDL cholesterol, and triglycerides in a nonstratified analysis and in the <55-year stratum. Further, we found evidence of a smaller causal effect on total cholesterol (P for difference = 0.015) in the ≥55-year stratum than in the <55-year stratum, a finding that could be explained by biology, survival bias, or differential medication. In conclusion, this study extends previous knowledge of the effects of adiposity by providing sex- and age-specific causal estimates on cardiovascular risk factors.
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Shungin D, Winkler TW, Croteau-Chonka DC, Ferreira T, Locke AE, Mägi R, Strawbridge RJ, Pers TH, Fischer K, Justice AE, Workalemahu T, Wu JMW, Buchkovich ML, Heard-Costa NL, Roman TS, Drong AW, Song C, Gustafsson S, Day FR, Esko T, Fall T, Kutalik Z, Luan J, Randall JC, Scherag A, Vedantam S, Wood AR, Chen J, Fehrmann R, Karjalainen J, Kahali B, Liu CT, Schmidt EM, Absher D, Amin N, Anderson D, Beekman M, Bragg-Gresham JL, Buyske S, Demirkan A, Ehret GB, Feitosa MF, Goel A, Jackson AU, Johnson T, Kleber ME, Kristiansson K, Mangino M, Mateo Leach I, Medina-Gomez C, Palmer CD, Pasko D, Pechlivanis S, Peters MJ, Prokopenko I, Stančáková A, Ju Sung Y, Tanaka T, Teumer A, Van Vliet-Ostaptchouk JV, Yengo L, Zhang W, Albrecht E, Ärnlöv J, Arscott GM, Bandinelli S, Barrett A, Bellis C, Bennett AJ, Berne C, Blüher M, Böhringer S, Bonnet F, Böttcher Y, Bruinenberg M, Carba DB, Caspersen IH, Clarke R, Warwick Daw E, Deelen J, Deelman E, Delgado G, Doney ASF, Eklund N, Erdos MR, Estrada K, Eury E, Friedrich N, Garcia ME, Giedraitis V, Gigante B, Go AS, Golay A, Grallert H, Grammer TB, Gräßler J, Grewal J, Groves CJ, Haller T, Hallmans G, Hartman CA, Hassinen M, Hayward C, Heikkilä K, Herzig KH, Helmer Q, Hillege HL, Holmen O, Hunt SC, Isaacs A, Ittermann T, James AL, Johansson I, Juliusdottir T, Kalafati IP, Kinnunen L, Koenig W, Kooner IK, Kratzer W, Lamina C, Leander K, Lee NR, Lichtner P, Lind L, Lindström J, Lobbens S, Lorentzon M, Mach F, Magnusson PKE, Mahajan A, McArdle WL, Menni C, Merger S, Mihailov E, Milani L, Mills R, Moayyeri A, Monda KL, Mooijaart SP, Mühleisen TW, Mulas A, Müller G, Müller-Nurasyid M, Nagaraja R, Nalls MA, Narisu N, Glorioso N, Nolte IM, Olden M, Rayner NW, Renstrom F, Ried JS, Robertson NR, Rose LM, Sanna S, Scharnagl H, Scholtens S, Sennblad B, Seufferlein T, Sitlani CM, Vernon Smith A, Stirrups K, Stringham HM, Sundström J, Swertz MA, Swift AJ, Syvänen AC, Tayo BO, Thorand B, Thorleifsson G, Tomaschitz A, Troffa C, van Oort FVA, Verweij N, Vonk JM, Waite LL, Wennauer R, Wilsgaard T, Wojczynski MK, Wong A, Zhang Q, Hua Zhao J, Brennan EP, Choi M, Eriksson P, Folkersen L, Franco-Cereceda A, Gharavi AG, Hedman ÅK, Hivert MF, Huang J, Kanoni S, Karpe F, Keildson S, Kiryluk K, Liang L, Lifton RP, Ma B, McKnight AJ, McPherson R, Metspalu A, Min JL, Moffatt MF, Montgomery GW, Murabito JM, Nicholson G, Nyholt DR, Olsson C, Perry JRB, Reinmaa E, Salem RM, Sandholm N, Schadt EE, Scott RA, Stolk L, Vallejo EE, Westra HJ, Zondervan KT, Amouyel P, Arveiler D, Bakker SJL, Beilby J, Bergman RN, Blangero J, Brown MJ, Burnier M, Campbell H, Chakravarti A, Chines PS, Claudi-Boehm S, Collins FS, Crawford DC, Danesh J, de Faire U, de Geus EJC, Dörr M, Erbel R, Eriksson JG, Farrall M, Ferrannini E, Ferrières J, Forouhi NG, Forrester T, Franco OH, Gansevoort RT, Gieger C, Gudnason V, Haiman CA, Harris TB, Hattersley AT, Heliövaara M, Hicks AA, Hingorani AD, Hoffmann W, Hofman A, Homuth G, Humphries SE, Hyppönen E, Illig T, Jarvelin MR, Johansen B, Jousilahti P, Jula AM, Kaprio J, Kee F, Keinanen-Kiukaanniemi SM, Kooner JS, Kooperberg C, Kovacs P, Kraja AT, Kumari M, Kuulasmaa K, Kuusisto J, Lakka TA, Langenberg C, Le Marchand L, Lehtimäki T, Lyssenko V, Männistö S, Marette A, Matise TC, McKenzie CA, McKnight B, Musk AW, Möhlenkamp S, Morris AD, Nelis M, Ohlsson C, Oldehinkel AJ, Ong KK, Palmer LJ, Penninx BW, Peters A, Pramstaller PP, Raitakari OT, Rankinen T, Rao DC, Rice TK, Ridker PM, Ritchie MD, Rudan I, Salomaa V, Samani NJ, Saramies J, Sarzynski MA, Schwarz PEH, Shuldiner AR, Staessen JA, Steinthorsdottir V, Stolk RP, Strauch K, Tönjes A, Tremblay A, Tremoli E, Vohl MC, Völker U, Vollenweider P, Wilson JF, Witteman JC, Adair LS, Bochud M, Boehm BO, Bornstein SR, Bouchard C, Cauchi S, Caulfield MJ, Chambers JC, Chasman DI, Cooper RS, Dedoussis G, Ferrucci L, Froguel P, Grabe HJ, Hamsten A, Hui J, Hveem K, Jöckel KH, Kivimaki M, Kuh D, Laakso M, Liu Y, März W, Munroe PB, Njølstad I, Oostra BA, Palmer CNA, Pedersen NL, Perola M, Pérusse L, Peters U, Power C, Quertermous T, Rauramaa R, Rivadeneira F, Saaristo TE, Saleheen D, Sinisalo J, Eline Slagboom P, Snieder H, Spector TD, Thorsteinsdottir U, Stumvoll M, Tuomilehto J, Uitterlinden AG, Uusitupa M, van der Harst P, Veronesi G, Walker M, Wareham NJ, Watkins H, Wichmann HE, Abecasis GR, Assimes TL, Berndt SI, Boehnke M, Borecki IB, Deloukas P, Franke L, Frayling TM, Groop LC, Hunter DJ, Kaplan RC, O’Connell JR, Qi L, Schlessinger D, Strachan DP, Stefansson K, van Duijn CM, Willer CJ, Visscher PM, Yang J, Hirschhorn JN, Carola Zillikens M, McCarthy MI, Speliotes EK, North KE, Fox CS, Barroso I, Franks PW, Ingelsson E, Heid IM, Loos RJF, Cupples LA, Morris AP, Lindgren CM, Mohlke KL. New genetic loci link adipose and insulin biology to body fat distribution. Nature 2015; 518:187-196. [PMID: 25673412 PMCID: PMC4338562 DOI: 10.1038/nature14132] [Citation(s) in RCA: 1046] [Impact Index Per Article: 116.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 12/02/2014] [Indexed: 12/17/2022]
Abstract
Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, we conducted genome-wide association meta-analyses of waist and hip circumference-related traits in up to 224,459 individuals. We identified 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (WHRadjBMI) and an additional 19 loci newly associated with related waist and hip circumference measures (P<5×10−8). Twenty of the 49 WHRadjBMI loci showed significant sexual dimorphism, 19 of which displayed a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation, and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms.
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Herder C, Nuotio ML, Shah S, Blankenberg S, Brunner EJ, Carstensen M, Gieger C, Grallert H, Jula A, Kähönen M, Kettunen J, Kivimäki M, Koenig W, Kristiansson K, Langenberg C, Lehtimäki T, Luotola K, Marzi C, Müller C, Peters A, Prokisch H, Raitakari O, Rathmann W, Roden M, Salmi M, Schramm K, Swerdlow D, Tabak AG, Thorand B, Wareham N, Wild PS, Zeller T, Hingorani AD, Witte DR, Kumari M, Perola M, Salomaa V. Genetic determinants of circulating interleukin-1 receptor antagonist levels and their association with glycemic traits. Diabetes 2014; 63:4343-59. [PMID: 24969107 PMCID: PMC4237993 DOI: 10.2337/db14-0731] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The proinflammatory cytokine interleukin (IL)-1β is implicated in the development of insulin resistance and β-cell dysfunction, whereas higher circulating levels of IL-1 receptor antagonist (IL-1RA), an endogenous inhibitor of IL-1β, has been suggested to improve glycemia and β-cell function in patients with type 2 diabetes. To elucidate the protective role of IL-1RA, this study aimed to identify genetic determinants of circulating IL-1RA concentration and to investigate their associations with immunological and metabolic variables related to cardiometabolic risk. In the analysis of seven discovery and four replication cohort studies, two single nucleotide polymorphisms (SNPs) were independently associated with circulating IL-1RA concentration (rs4251961 at the IL1RN locus [n = 13,955, P = 2.76 × 10(-21)] and rs6759676, closest gene locus IL1F10 [n = 13,994, P = 1.73 × 10(-17)]). The proportion of the variance in IL-1RA explained by both SNPs combined was 2.0%. IL-1RA-raising alleles of both SNPs were associated with lower circulating C-reactive protein concentration. The IL-1RA-raising allele of rs6759676 was also associated with lower fasting insulin levels and lower HOMA insulin resistance. In conclusion, we show that circulating IL-1RA levels are predicted by two independent SNPs at the IL1RN and IL1F10 loci and that genetically raised IL-1RA may be protective against the development of insulin resistance.
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Siggberg L, Ala-Mello S, Linnankivi T, Avela K, Scheinin I, Kristiansson K, Lahermo P, Hietala M, Metsähonkala L, Kuusinen E, Laaksonen M, Saarela J, Knuutila S. Erratum to: High-resolution SNP array analysis of patients with developmental disorder and normal array CGH result. BMC MEDICAL GENETICS 2014; 15:124. [PMID: 25928284 PMCID: PMC4429685 DOI: 10.1186/s12881-014-0124-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Wood AR, Esko T, Yang J, Vedantam S, Pers TH, Gustafsson S, Chu AY, Estrada K, Luan J, Kutalik Z, Amin N, Buchkovich ML, Croteau-Chonka DC, Day FR, Duan Y, Fall T, Fehrmann R, Ferreira T, Jackson AU, Karjalainen J, Lo KS, Locke AE, Mägi R, Mihailov E, Porcu E, Randall JC, Scherag A, Vinkhuyzen AAE, Westra HJ, Winkler TW, Workalemahu T, Zhao JH, Absher D, Albrecht E, Anderson D, Baron J, Beekman M, Demirkan A, Ehret GB, Feenstra B, Feitosa MF, Fischer K, Fraser RM, Goel A, Gong J, Justice AE, Kanoni S, Kleber ME, Kristiansson K, Lim U, Lotay V, Lui JC, Mangino M, Mateo Leach I, Medina-Gomez C, Nalls MA, Nyholt DR, Palmer CD, Pasko D, Pechlivanis S, Prokopenko I, Ried JS, Ripke S, Shungin D, Stancáková A, Strawbridge RJ, Sung YJ, Tanaka T, Teumer A, Trompet S, van der Laan SW, van Setten J, Van Vliet-Ostaptchouk JV, Wang Z, Yengo L, Zhang W, Afzal U, Arnlöv J, Arscott GM, Bandinelli S, Barrett A, Bellis C, Bennett AJ, Berne C, Blüher M, Bolton JL, Böttcher Y, Boyd HA, Bruinenberg M, Buckley BM, Buyske S, Caspersen IH, Chines PS, Clarke R, Claudi-Boehm S, Cooper M, Daw EW, De Jong PA, Deelen J, Delgado G, Denny JC, Dhonukshe-Rutten R, Dimitriou M, Doney ASF, Dörr M, Eklund N, Eury E, Folkersen L, Garcia ME, Geller F, Giedraitis V, Go AS, Grallert H, Grammer TB, Gräßler J, Grönberg H, de Groot LCPGM, Groves CJ, Haessler J, Hall P, Haller T, Hallmans G, Hannemann A, Hartman CA, Hassinen M, Hayward C, Heard-Costa NL, Helmer Q, Hemani G, Henders AK, Hillege HL, Hlatky MA, Hoffmann W, Hoffmann P, Holmen O, Houwing-Duistermaat JJ, Illig T, Isaacs A, James AL, Jeff J, Johansen B, Johansson Å, Jolley J, Juliusdottir T, Junttila J, Kho AN, Kinnunen L, Klopp N, Kocher T, Kratzer W, Lichtner P, Lind L, Lindström J, Lobbens S, Lorentzon M, Lu Y, Lyssenko V, Magnusson PKE, Mahajan A, Maillard M, McArdle WL, McKenzie CA, McLachlan S, McLaren PJ, Menni C, Merger S, Milani L, Moayyeri A, Monda KL, Morken MA, Müller G, Müller-Nurasyid M, Musk AW, Narisu N, Nauck M, Nolte IM, Nöthen MM, Oozageer L, Pilz S, Rayner NW, Renstrom F, Robertson NR, Rose LM, Roussel R, Sanna S, Scharnagl H, Scholtens S, Schumacher FR, Schunkert H, Scott RA, Sehmi J, Seufferlein T, Shi J, Silventoinen K, Smit JH, Smith AV, Smolonska J, Stanton AV, Stirrups K, Stott DJ, Stringham HM, Sundström J, Swertz MA, Syvänen AC, Tayo BO, Thorleifsson G, Tyrer JP, van Dijk S, van Schoor NM, van der Velde N, van Heemst D, van Oort FVA, Vermeulen SH, Verweij N, Vonk JM, Waite LL, Waldenberger M, Wennauer R, Wilkens LR, Willenborg C, Wilsgaard T, Wojczynski MK, Wong A, Wright AF, Zhang Q, Arveiler D, Bakker SJL, Beilby J, Bergman RN, Bergmann S, Biffar R, Blangero J, Boomsma DI, Bornstein SR, Bovet P, Brambilla P, Brown MJ, Campbell H, Caulfield MJ, Chakravarti A, Collins R, Collins FS, Crawford DC, Cupples LA, Danesh J, de Faire U, den Ruijter HM, Erbel R, Erdmann J, Eriksson JG, Farrall M, Ferrannini E, Ferrières J, Ford I, Forouhi NG, Forrester T, Gansevoort RT, Gejman PV, Gieger C, Golay A, Gottesman O, Gudnason V, Gyllensten U, Haas DW, Hall AS, Harris TB, Hattersley AT, Heath AC, Hengstenberg C, Hicks AA, Hindorff LA, Hingorani AD, Hofman A, Hovingh GK, Humphries SE, Hunt SC, Hypponen E, Jacobs KB, Jarvelin MR, Jousilahti P, Jula AM, Kaprio J, Kastelein JJP, Kayser M, Kee F, Keinanen-Kiukaanniemi SM, Kiemeney LA, Kooner JS, Kooperberg C, Koskinen S, Kovacs P, Kraja AT, Kumari M, Kuusisto J, Lakka TA, Langenberg C, Le Marchand L, Lehtimäki T, Lupoli S, Madden PAF, Männistö S, Manunta P, Marette A, Matise TC, McKnight B, Meitinger T, Moll FL, Montgomery GW, Morris AD, Morris AP, Murray JC, Nelis M, Ohlsson C, Oldehinkel AJ, Ong KK, Ouwehand WH, Pasterkamp G, Peters A, Pramstaller PP, Price JF, Qi L, Raitakari OT, Rankinen T, Rao DC, Rice TK, Ritchie M, Rudan I, Salomaa V, Samani NJ, Saramies J, Sarzynski MA, Schwarz PEH, Sebert S, Sever P, Shuldiner AR, Sinisalo J, Steinthorsdottir V, Stolk RP, Tardif JC, Tönjes A, Tremblay A, Tremoli E, Virtamo J, Vohl MC, Amouyel P, Asselbergs FW, Assimes TL, Bochud M, Boehm BO, Boerwinkle E, Bottinger EP, Bouchard C, Cauchi S, Chambers JC, Chanock SJ, Cooper RS, de Bakker PIW, Dedoussis G, Ferrucci L, Franks PW, Froguel P, Groop LC, Haiman CA, Hamsten A, Hayes MG, Hui J, Hunter DJ, Hveem K, Jukema JW, Kaplan RC, Kivimaki M, Kuh D, Laakso M, Liu Y, Martin NG, März W, Melbye M, Moebus S, Munroe PB, Njølstad I, Oostra BA, Palmer CNA, Pedersen NL, Perola M, Pérusse L, Peters U, Powell JE, Power C, Quertermous T, Rauramaa R, Reinmaa E, Ridker PM, Rivadeneira F, Rotter JI, Saaristo TE, Saleheen D, Schlessinger D, Slagboom PE, Snieder H, Spector TD, Strauch K, Stumvoll M, Tuomilehto J, Uusitupa M, van der Harst P, Völzke H, Walker M, Wareham NJ, Watkins H, Wichmann HE, Wilson JF, Zanen P, Deloukas P, Heid IM, Lindgren CM, Mohlke KL, Speliotes EK, Thorsteinsdottir U, Barroso I, Fox CS, North KE, Strachan DP, Beckmann JS, Berndt SI, Boehnke M, Borecki IB, McCarthy MI, Metspalu A, Stefansson K, Uitterlinden AG, van Duijn CM, Franke L, Willer CJ, Price AL, Lettre G, Loos RJF, Weedon MN, Ingelsson E, O'Connell JR, Abecasis GR, Chasman DI, Goddard ME, Visscher PM, Hirschhorn JN, Frayling TM. Defining the role of common variation in the genomic and biological architecture of adult human height. Nat Genet 2014; 46:1173-86. [PMID: 25282103 PMCID: PMC4250049 DOI: 10.1038/ng.3097] [Citation(s) in RCA: 1192] [Impact Index Per Article: 119.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 08/29/2014] [Indexed: 12/17/2022]
Abstract
Using genome-wide data from 253,288 individuals, we identified 697 variants at genome-wide significance that together explained one-fifth of the heritability for adult height. By testing different numbers of variants in independent studies, we show that the most strongly associated ∼2,000, ∼3,700 and ∼9,500 SNPs explained ∼21%, ∼24% and ∼29% of phenotypic variance. Furthermore, all common variants together captured 60% of heritability. The 697 variants clustered in 423 loci were enriched for genes, pathways and tissue types known to be involved in growth and together implicated genes and pathways not highlighted in earlier efforts, such as signaling by fibroblast growth factors, WNT/β-catenin and chondroitin sulfate-related genes. We identified several genes and pathways not previously connected with human skeletal growth, including mTOR, osteoglycin and binding of hyaluronic acid. Our results indicate a genetic architecture for human height that is characterized by a very large but finite number (thousands) of causal variants.
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Qi Q, Kilpeläinen TO, Downer MK, Tanaka T, Smith CE, Sluijs I, Sonestedt E, Chu AY, Renström F, Lin X, Ängquist LH, Huang J, Liu Z, Li Y, Asif Ali M, Xu M, Ahluwalia TS, Boer JMA, Chen P, Daimon M, Eriksson J, Perola M, Friedlander Y, Gao YT, Heppe DHM, Holloway JW, Houston DK, Kanoni S, Kim YM, Laaksonen MA, Jääskeläinen T, Lee NR, Lehtimäki T, Lemaitre RN, Lu W, Luben RN, Manichaikul A, Männistö S, Marques-Vidal P, Monda KL, Ngwa JS, Perusse L, van Rooij FJA, Xiang YB, Wen W, Wojczynski MK, Zhu J, Borecki IB, Bouchard C, Cai Q, Cooper C, Dedoussis GV, Deloukas P, Ferrucci L, Forouhi NG, Hansen T, Christiansen L, Hofman A, Johansson I, Jørgensen T, Karasawa S, Khaw KT, Kim MK, Kristiansson K, Li H, Lin X, Liu Y, Lohman KK, Long J, Mikkilä V, Mozaffarian D, North K, Pedersen O, Raitakari O, Rissanen H, Tuomilehto J, van der Schouw YT, Uitterlinden AG, Zillikens MC, Franco OH, Shyong Tai E, Ou Shu X, Siscovick DS, Toft U, Verschuren WMM, Vollenweider P, Wareham NJ, Witteman JCM, Zheng W, Ridker PM, Kang JH, Liang L, Jensen MK, Curhan GC, Pasquale LR, Hunter DJ, Mohlke KL, Uusitupa M, Cupples LA, Rankinen T, Orho-Melander M, Wang T, Chasman DI, Franks PW, Sørensen TIA, Hu FB, Loos RJF, Nettleton JA, Qi L. FTO genetic variants, dietary intake and body mass index: insights from 177,330 individuals. Hum Mol Genet 2014; 23:6961-72. [PMID: 25104851 DOI: 10.1093/hmg/ddu411] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
FTO is the strongest known genetic susceptibility locus for obesity. Experimental studies in animals suggest the potential roles of FTO in regulating food intake. The interactive relation among FTO variants, dietary intake and body mass index (BMI) is complex and results from previous often small-scale studies in humans are highly inconsistent. We performed large-scale analyses based on data from 177,330 adults (154 439 Whites, 5776 African Americans and 17 115 Asians) from 40 studies to examine: (i) the association between the FTO-rs9939609 variant (or a proxy single-nucleotide polymorphism) and total energy and macronutrient intake and (ii) the interaction between the FTO variant and dietary intake on BMI. The minor allele (A-allele) of the FTO-rs9939609 variant was associated with higher BMI in Whites (effect per allele = 0.34 [0.31, 0.37] kg/m(2), P = 1.9 × 10(-105)), and all participants (0.30 [0.30, 0.35] kg/m(2), P = 3.6 × 10(-107)). The BMI-increasing allele of the FTO variant showed a significant association with higher dietary protein intake (effect per allele = 0.08 [0.06, 0.10] %, P = 2.4 × 10(-16)), and relative weak associations with lower total energy intake (-6.4 [-10.1, -2.6] kcal/day, P = 0.001) and lower dietary carbohydrate intake (-0.07 [-0.11, -0.02] %, P = 0.004). The associations with protein (P = 7.5 × 10(-9)) and total energy (P = 0.002) were attenuated but remained significant after adjustment for BMI. We did not find significant interactions between the FTO variant and dietary intake of total energy, protein, carbohydrate or fat on BMI. Our findings suggest a positive association between the BMI-increasing allele of FTO variant and higher dietary protein intake and offer insight into potential link between FTO, dietary protein intake and adiposity.
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Avery CL, Sitlani CM, Arking DE, Arnett DK, Bis JC, Boerwinkle E, Buckley BM, Ida Chen YD, de Craen AJM, Eijgelsheim M, Enquobahrie D, Evans DS, Ford I, Garcia ME, Gudnason V, Harris TB, Heckbert SR, Hochner H, Hofman A, Hsueh WC, Isaacs A, Jukema JW, Knekt P, Kors JA, Krijthe BP, Kristiansson K, Laaksonen M, Liu Y, Li X, Macfarlane PW, Newton-Cheh C, Nieminen MS, Oostra BA, Peloso GM, Porthan K, Rice K, Rivadeneira FF, Rotter JI, Salomaa V, Sattar N, Siscovick DS, Slagboom PE, Smith AV, Sotoodehnia N, Stott DJ, Stricker BH, Stürmer T, Trompet S, Uitterlinden AG, van Duijn C, Westendorp RGJ, Witteman JC, Whitsel EA, Psaty BM. Drug-gene interactions and the search for missing heritability: a cross-sectional pharmacogenomics study of the QT interval. THE PHARMACOGENOMICS JOURNAL 2014; 14:6-13. [PMID: 23459443 PMCID: PMC3766418 DOI: 10.1038/tpj.2013.4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 12/07/2012] [Accepted: 01/03/2013] [Indexed: 01/18/2023]
Abstract
Variability in response to drug use is common and heritable, suggesting that genome-wide pharmacogenomics studies may help explain the 'missing heritability' of complex traits. Here, we describe four independent analyses in 33 781 participants of European ancestry from 10 cohorts that were designed to identify genetic variants modifying the effects of drugs on QT interval duration (QT). Each analysis cross-sectionally examined four therapeutic classes: thiazide diuretics (prevalence of use=13.0%), tri/tetracyclic antidepressants (2.6%), sulfonylurea hypoglycemic agents (2.9%) and QT-prolonging drugs as classified by the University of Arizona Center for Education and Research on Therapeutics (4.4%). Drug-gene interactions were estimated using covariable-adjusted linear regression and results were combined with fixed-effects meta-analysis. Although drug-single-nucleotide polymorphism (SNP) interactions were biologically plausible and variables were well-measured, findings from the four cross-sectional meta-analyses were null (Pinteraction>5.0 × 10(-8)). Simulations suggested that additional efforts, including longitudinal modeling to increase statistical power, are likely needed to identify potentially important pharmacogenomic effects.
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Hu YJ, Berndt S, Gustafsson S, Ganna A, Hirschhorn J, North KE, Ingelsson E, Lin DY, Berndt S, Gustafsson S, Mägi R, Ganna A, Wheeler E, Feitosa M, Justice A, Monda K, Croteau-Chonka D, Day F, Esko T, Fall T, Ferreira T, Gentilini D, Jackson A, Luan J, Randall J, Vedantam S, Willer C, Winkler T, Wood A, Workalemahu T, Hu YJ, Lee S, Liang L, Lin DY, Min J, Neale B, Thorleifsson G, Yang J, Albrecht E, Amin N, Bragg-Gresham J, Cadby G, den Heijer M, Eklund N, Fischer K, Goel A, Hottenga JJ, Huffman J, Jarick I, Johansson Å, Johnson T, Kanoni S, Kleber M, König I, Kristiansson K, Kutalik Z, Lamina C, Lecoeur C, Li G, Mangino M, McArdle W, Medina-Gomez C, Müller-Nurasyid M, Ngwa J, Nolte I, Paternoster L, Pechlivanis S, Perola M, Peters M, Preuss M, Rose L, Shi J, Shungin D, Smith A, Strawbridge R, Surakka I, Teumer A, Trip M, Tyrer J, Van Vliet-Ostaptchouk J, Vandenput L, Waite L, Zhao J, Absher D, Asselbergs F, Atalay M, Attwood A, Balmforth A, Basart H, Beilby J, Bonnycastle L, Brambilla P, Bruinenberg M, Campbell H, Chasman D, Chines P, Collins F, Connell J, Cookson W, de Faire U, de Vegt F, Dei M, Dimitriou M, Edkins S, Estrada K, Evans D, Farrall M, Ferrario M, Ferrières J, Franke L, Frau F, Gejman P, Grallert H, Grönberg H, Gudnason V, Hall A, Hall P, Hartikainen AL, Hayward C, Heard-Costa N, Heath A, Hebebrand J, Homuth G, Hu F, Hunt S, Hyppönen E, Iribarren C, Jacobs K, Jansson JO, Jula A, Kähönen M, Kathiresan S, Kee F, Khaw KT, Kivimaki M, Koenig W, Kraja A, Kumari M, Kuulasmaa K, Kuusisto J, Laitinen J, Lakka T, Langenberg C, Launer L, Lind L, Lindström J, Liu J, Liuzzi A, Lokki ML, Lorentzon M, Madden P, Magnusson P, Manunta P, Marek D, März W, Leach I, McKnight B, Medland S, Mihailov E, Milani L, Montgomery G, Mooser V, Mühleisen T, Munroe P, Musk A, Narisu N, Navis G, Nicholson G, Nohr E, Ong K, Oostra B, Palmer C, Palotie A, Peden J, Pedersen N, Peters A, Polasek O, Pouta A, Pramstaller P, Prokopenko I, Pütter C, Radhakrishnan A, Raitakari O, Rendon A, Rivadeneira F, Rudan I, Saaristo T, Sambrook J, Sanders A, Sanna S, Saramies J, Schipf S, Schreiber S, Schunkert H, Shin SY, Signorini S, Sinisalo J, Skrobek B, Soranzo N, Stančáková A, Stark K, Stephens J, Stirrups K, Stolk R, Stumvoll M, Swift A, Theodoraki E, Thorand B, Tregouet DA, Tremoli E, Van der Klauw M, van Meurs J, Vermeulen S, Viikari J, Virtamo J, Vitart V, Waeber G, Wang Z, Widén E, Wild S, Willemsen G, Winkelmann B, Witteman J, Wolffenbuttel B, Wong A, Wright A, Zillikens M, Amouyel P, Boehm B, Boerwinkle E, Boomsma D, Caulfield M, Chanock S, Cupples L, Cusi D, Dedoussis G, Erdmann J, Eriksson J, Franks P, Froguel P, Gieger C, Gyllensten U, Hamsten A, Harris T, Hengstenberg C, Hicks A, Hingorani A, Hinney A, Hofman A, Hovingh K, Hveem K, Illig T, Jarvelin MR, Jöckel KH, Keinanen-Kiukaanniemi S, Kiemeney L, Kuh D, Laakso M, Lehtimäki T, Levinson D, Martin N, Metspalu A, Morris A, Nieminen M, Njølstad I, Ohlsson C, Oldehinkel A, Ouwehand W, Palmer L, Penninx B, Power C, Province M, Psaty B, Qi L, Rauramaa R, Ridker P, Ripatti S, Salomaa V, Samani N, Snieder H, Sørensen T, Spector T, Stefansson K, Tönjes A, Tuomilehto J, Uitterlinden A, Uusitupa M, van der Harst P, Vollenweider P, Wallaschofski H, Wareham N, Watkins H, Wichmann HE, Wilson J, Abecasis G, Assimes T, Barroso I, Boehnke M, Borecki I, Deloukas P, Fox C, Frayling T, Groop L, Haritunian T, Heid I, Hunter D, Kaplan R, Karpe F, Moffatt M, Mohlke K, O’Connell J, Pawitan Y, Schadt E, Schlessinger D, Steinthorsdottir V, Strachan D, Thorsteinsdottir U, van Duijn C, Visscher P, Di Blasio A, Hirschhorn J, Lindgren C, Morris A, Meyre D, Scherag A, McCarthy M, Speliotes E, North K, Loos R, Ingelsson E. Meta-analysis of gene-level associations for rare variants based on single-variant statistics. Am J Hum Genet 2013; 93:236-48. [PMID: 23891470 DOI: 10.1016/j.ajhg.2013.06.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/05/2013] [Accepted: 06/12/2013] [Indexed: 02/02/2023] Open
Abstract
Meta-analysis of genome-wide association studies (GWASs) has led to the discoveries of many common variants associated with complex human diseases. There is a growing recognition that identifying "causal" rare variants also requires large-scale meta-analysis. The fact that association tests with rare variants are performed at the gene level rather than at the variant level poses unprecedented challenges in the meta-analysis. First, different studies may adopt different gene-level tests, so the results are not compatible. Second, gene-level tests require multivariate statistics (i.e., components of the test statistic and their covariance matrix), which are difficult to obtain. To overcome these challenges, we propose to perform gene-level tests for rare variants by combining the results of single-variant analysis (i.e., p values of association tests and effect estimates) from participating studies. This simple strategy is possible because of an insight that multivariate statistics can be recovered from single-variant statistics, together with the correlation matrix of the single-variant test statistics, which can be estimated from one of the participating studies or from a publicly available database. We show both theoretically and numerically that the proposed meta-analysis approach provides accurate control of the type I error and is as powerful as joint analysis of individual participant data. This approach accommodates any disease phenotype and any study design and produces all commonly used gene-level tests. An application to the GWAS summary results of the Genetic Investigation of ANthropometric Traits (GIANT) consortium reveals rare and low-frequency variants associated with human height. The relevant software is freely available.
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Stoll G, Pietiläinen OPH, Linder B, Suvisaari J, Brosi C, Hennah W, Leppä V, Torniainen M, Ripatti S, Ala-Mello S, Plöttner O, Rehnström K, Tuulio-Henriksson A, Varilo T, Tallila J, Kristiansson K, Isohanni M, Kaprio J, Eriksson JG, Raitakari OT, Lehtimäki T, Jarvelin MR, Salomaa V, Hurles M, Stefansson H, Peltonen L, Sullivan PF, Paunio T, Lönnqvist J, Daly MJ, Fischer U, Freimer NB, Palotie A. Deletion of TOP3β, a component of FMRP-containing mRNPs, contributes to neurodevelopmental disorders. Nat Neurosci 2013; 16:1228-1237. [PMID: 23912948 DOI: 10.1038/nn.3484] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 07/01/2013] [Indexed: 02/08/2023]
Abstract
Implicating particular genes in the generation of complex brain and behavior phenotypes requires multiple lines of evidence. The rarity of most high-impact genetic variants typically precludes the possibility of accruing statistical evidence that they are associated with a given trait. We found that the enrichment of a rare chromosome 22q11.22 deletion in a recently expanded Northern Finnish sub-isolate enabled the detection of association between TOP3B and both schizophrenia and cognitive impairment. Biochemical analysis of TOP3β revealed that this topoisomerase was a component of cytosolic messenger ribonucleoproteins (mRNPs) and was catalytically active on RNA. The recruitment of TOP3β to mRNPs was independent of RNA cis-elements and was coupled to the co-recruitment of FMRP, the disease gene product in fragile X mental retardation syndrome. Our results indicate a previously unknown role for TOP3β in mRNA metabolism and suggest that it is involved in neurodevelopmental disorders.
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Rietveld CA, Medland SE, Derringer J, Yang J, Esko T, Martin NW, Westra HJ, Shakhbazov K, Abdellaoui A, Agrawal A, Albrecht E, Alizadeh BZ, Amin N, Barnard J, Baumeister SE, Benke KS, Bielak LF, Boatman JA, Boyle PA, Davies G, de Leeuw C, Eklund N, Evans DS, Ferhmann R, Fischer K, Gieger C, Gjessing HK, Hägg S, Harris JR, Hayward C, Holzapfel C, Ibrahim-Verbaas CA, Ingelsson E, Jacobsson B, Joshi PK, Jugessur A, Kaakinen M, Kanoni S, Karjalainen J, Kolcic I, Kristiansson K, Kutalik Z, Lahti J, Lee SH, Lin P, Lind PA, Liu Y, Lohman K, Loitfelder M, McMahon G, Vidal PM, Meirelles O, Milani L, Myhre R, Nuotio ML, Oldmeadow CJ, Petrovic KE, Peyrot WJ, Polašek O, Quaye L, Reinmaa E, Rice JP, Rizzi TS, Schmidt H, Schmidt R, Smith AV, Smith JA, Tanaka T, Terracciano A, van der Loos MJ, Vitart V, Völzke H, Wellmann J, Yu L, Zhao W, Allik J, Attia JR, Bandinelli S, Bastardot F, Beauchamp J, Bennett DA, Berger K, Bierut LJ, Boomsma DI, Bültmann U, Campbell H, Chabris CF, Cherkas L, Chung MK, Cucca F, de Andrade M, De Jager PL, De Neve JE, Deary IJ, Dedoussis GV, Deloukas P, Dimitriou M, Eiriksdottir G, Elderson MF, Eriksson JG, Evans DM, Faul JD, Ferrucci L, Garcia ME, Grönberg H, Gudnason V, Hall P, Harris JM, Harris TB, Hastie ND, Heath AC, Hernandez DG, Hoffmann W, Hofman A, Holle R, Holliday EG, Hottenga JJ, Iacono WG, Illig T, Järvelin MR, Kähönen M, Kaprio J, Kirkpatrick RM, Kowgier M, Latvala A, Launer LJ, Lawlor DA, Lehtimäki T, Li J, Lichtenstein P, Lichtner P, Liewald DC, Madden PA, Magnusson PKE, Mäkinen TE, Masala M, McGue M, Metspalu A, Mielck A, Miller MB, Montgomery GW, Mukherjee S, Nyholt DR, Oostra BA, Palmer LJ, Palotie A, Penninx B, Perola M, Peyser PA, Preisig M, Räikkönen K, Raitakari OT, Realo A, Ring SM, Ripatti S, Rivadeneira F, Rudan I, Rustichini A, Salomaa V, Sarin AP, Schlessinger D, Scott RJ, Snieder H, Pourcain BS, Starr JM, Sul JH, Surakka I, Svento R, Teumer A, Tiemeier H, Rooij FJA, Van Wagoner DR, Vartiainen E, Viikari J, Vollenweider P, Vonk JM, Waeber G, Weir DR, Wichmann HE, Widen E, Willemsen G, Wilson JF, Wright AF, Conley D, Davey-Smith G, Franke L, Groenen PJF, Hofman A, Johannesson M, Kardia SL, Krueger RF, Laibson D, Martin NG, Meyer MN, Posthuma D, Thurik AR, Timpson NJ, Uitterlinden AG, van Duijn CM, Visscher PM, Benjamin DJ, Cesarini D, Koellinger PD. GWAS of 126,559 individuals identifies genetic variants associated with educational attainment. Science 2013; 340:1467-71. [PMID: 23722424 PMCID: PMC3751588 DOI: 10.1126/science.1235488] [Citation(s) in RCA: 480] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A genome-wide association study (GWAS) of educational attainment was conducted in a discovery sample of 101,069 individuals and a replication sample of 25,490. Three independent single-nucleotide polymorphisms (SNPs) are genome-wide significant (rs9320913, rs11584700, rs4851266), and all three replicate. Estimated effects sizes are small (coefficient of determination R(2) ≈ 0.02%), approximately 1 month of schooling per allele. A linear polygenic score from all measured SNPs accounts for ≈2% of the variance in both educational attainment and cognitive function. Genes in the region of the loci have previously been associated with health, cognitive, and central nervous system phenotypes, and bioinformatics analyses suggest the involvement of the anterior caudate nucleus. These findings provide promising candidate SNPs for follow-up work, and our effect size estimates can anchor power analyses in social-science genetics.
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Randall JC, Winkler TW, Kutalik Z, Berndt SI, Jackson AU, Monda KL, Kilpeläinen TO, Esko T, Mägi R, Li S, Workalemahu T, Feitosa MF, Croteau-Chonka DC, Day FR, Fall T, Ferreira T, Gustafsson S, Locke AE, Mathieson I, Scherag A, Vedantam S, Wood AR, Liang L, Steinthorsdottir V, Thorleifsson G, Dermitzakis ET, Dimas AS, Karpe F, Min JL, Nicholson G, Clegg DJ, Person T, Krohn JP, Bauer S, Buechler C, Eisinger K, Bonnefond A, Froguel P, Hottenga JJ, Prokopenko I, Waite LL, Harris TB, Smith AV, Shuldiner AR, McArdle WL, Caulfield MJ, Munroe PB, Grönberg H, Chen YDI, Li G, Beckmann JS, Johnson T, Thorsteinsdottir U, Teder-Laving M, Khaw KT, Wareham NJ, Zhao JH, Amin N, Oostra BA, Kraja AT, Province MA, Cupples LA, Heard-Costa NL, Kaprio J, Ripatti S, Surakka I, Collins FS, Saramies J, Tuomilehto J, Jula A, Salomaa V, Erdmann J, Hengstenberg C, Loley C, Schunkert H, Lamina C, Wichmann HE, Albrecht E, Gieger C, Hicks AA, Johansson Å, Pramstaller PP, Kathiresan S, Speliotes EK, Penninx B, Hartikainen AL, Jarvelin MR, Gyllensten U, Boomsma DI, Campbell H, Wilson JF, Chanock SJ, Farrall M, Goel A, Medina-Gomez C, Rivadeneira F, Estrada K, Uitterlinden AG, Hofman A, Zillikens MC, den Heijer M, Kiemeney LA, Maschio A, Hall P, Tyrer J, Teumer A, Völzke H, Kovacs P, Tönjes A, Mangino M, Spector TD, Hayward C, Rudan I, Hall AS, Samani NJ, Attwood AP, Sambrook JG, Hung J, Palmer LJ, Lokki ML, Sinisalo J, Boucher G, Huikuri H, Lorentzon M, Ohlsson C, Eklund N, Eriksson JG, Barlassina C, Rivolta C, Nolte IM, Snieder H, Van der Klauw MM, Van Vliet-Ostaptchouk JV, Gejman PV, Shi J, Jacobs KB, Wang Z, Bakker SJL, Mateo Leach I, Navis G, van der Harst P, Martin NG, Medland SE, Montgomery GW, Yang J, Chasman DI, Ridker PM, Rose LM, Lehtimäki T, Raitakari O, Absher D, Iribarren C, Basart H, Hovingh KG, Hyppönen E, Power C, Anderson D, Beilby JP, Hui J, Jolley J, Sager H, Bornstein SR, Schwarz PEH, Kristiansson K, Perola M, Lindström J, Swift AJ, Uusitupa M, Atalay M, Lakka TA, Rauramaa R, Bolton JL, Fowkes G, Fraser RM, Price JF, Fischer K, KrjutÅ¡kov K, Metspalu A, Mihailov E, Langenberg C, Luan J, Ong KK, Chines PS, Keinanen-Kiukaanniemi SM, Saaristo TE, Edkins S, Franks PW, Hallmans G, Shungin D, Morris AD, Palmer CNA, Erbel R, Moebus S, Nöthen MM, Pechlivanis S, Hveem K, Narisu N, Hamsten A, Humphries SE, Strawbridge RJ, Tremoli E, Grallert H, Thorand B, Illig T, Koenig W, Müller-Nurasyid M, Peters A, Boehm BO, Kleber ME, März W, Winkelmann BR, Kuusisto J, Laakso M, Arveiler D, Cesana G, Kuulasmaa K, Virtamo J, Yarnell JWG, Kuh D, Wong A, Lind L, de Faire U, Gigante B, Magnusson PKE, Pedersen NL, Dedoussis G, Dimitriou M, Kolovou G, Kanoni S, Stirrups K, Bonnycastle LL, Njølstad I, Wilsgaard T, Ganna A, Rehnberg E, Hingorani A, Kivimaki M, Kumari M, Assimes TL, Barroso I, Boehnke M, Borecki IB, Deloukas P, Fox CS, Frayling T, Groop LC, Haritunians T, Hunter D, Ingelsson E, Kaplan R, Mohlke KL, O'Connell JR, Schlessinger D, Strachan DP, Stefansson K, van Duijn CM, Abecasis GR, McCarthy MI, Hirschhorn JN, Qi L, Loos RJF, Lindgren CM, North KE, Heid IM. Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits. PLoS Genet 2013; 9:e1003500. [PMID: 23754948 PMCID: PMC3674993 DOI: 10.1371/journal.pgen.1003500] [Citation(s) in RCA: 303] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 03/15/2013] [Indexed: 12/28/2022] Open
Abstract
Given the anthropometric differences between men and women and previous evidence of sex-difference in genetic effects, we conducted a genome-wide search for sexually dimorphic associations with height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip-ratio (133,723 individuals) and took forward 348 SNPs into follow-up (additional 137,052 individuals) in a total of 94 studies. Seven loci displayed significant sex-difference (FDR<5%), including four previously established (near GRB14/COBLL1, LYPLAL1/SLC30A10, VEGFA, ADAMTS9) and three novel anthropometric trait loci (near MAP3K1, HSD17B4, PPARG), all of which were genome-wide significant in women (P<5×10(-8)), but not in men. Sex-differences were apparent only for waist phenotypes, not for height, weight, BMI, or hip circumference. Moreover, we found no evidence for genetic effects with opposite directions in men versus women. The PPARG locus is of specific interest due to its role in diabetes genetics and therapy. Our results demonstrate the value of sex-specific GWAS to unravel the sexually dimorphic genetic underpinning of complex traits.
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Berndt SI, Gustafsson S, Mägi R, Ganna A, Wheeler E, Feitosa MF, Justice AE, Monda KL, Croteau-Chonka DC, Day FR, Esko T, Fall T, Ferreira T, Gentilini D, Jackson AU, Luan J, Randall JC, Vedantam S, Willer CJ, Winkler TW, Wood AR, Workalemahu T, Hu YJ, Lee SH, Liang L, Lin DY, Min JL, Neale BM, Thorleifsson G, Yang J, Albrecht E, Amin N, Bragg-Gresham JL, Cadby G, den Heijer M, Eklund N, Fischer K, Goel A, Hottenga JJ, Huffman JE, Jarick I, Johansson Å, Johnson T, Kanoni S, Kleber ME, König IR, Kristiansson K, Kutalik Z, Lamina C, Lecoeur C, Li G, Mangino M, McArdle WL, Medina-Gomez C, Müller-Nurasyid M, Ngwa JS, Nolte IM, Paternoster L, Pechlivanis S, Perola M, Peters MJ, Preuss M, Rose LM, Shi J, Shungin D, Smith AV, Strawbridge RJ, Surakka I, Teumer A, Trip MD, Tyrer J, Van Vliet-Ostaptchouk JV, Vandenput L, Waite LL, Zhao JH, Absher D, Asselbergs FW, Atalay M, Attwood AP, Balmforth AJ, Basart H, Beilby J, Bonnycastle LL, Brambilla P, Bruinenberg M, Campbell H, Chasman DI, Chines PS, Collins FS, Connell JM, Cookson W, de Faire U, de Vegt F, Dei M, Dimitriou M, Edkins S, Estrada K, Evans DM, Farrall M, Ferrario MM, Ferrières J, Franke L, Frau F, Gejman PV, Grallert H, Grönberg H, Gudnason V, Hall AS, Hall P, Hartikainen AL, Hayward C, Heard-Costa NL, Heath AC, Hebebrand J, Homuth G, Hu FB, Hunt SE, Hyppönen E, Iribarren C, Jacobs KB, Jansson JO, Jula A, Kähönen M, Kathiresan S, Kee F, Khaw KT, Kivimaki M, Koenig W, Kraja AT, Kumari M, Kuulasmaa K, Kuusisto J, Laitinen JH, Lakka TA, Langenberg C, Launer LJ, Lind L, Lindström J, Liu J, Liuzzi A, Lokki ML, Lorentzon M, Madden PA, Magnusson PK, Manunta P, Marek D, März W, Mateo Leach I, McKnight B, Medland SE, Mihailov E, Milani L, Montgomery GW, Mooser V, Mühleisen TW, Munroe PB, Musk AW, Narisu N, Navis G, Nicholson G, Nohr EA, Ong KK, Oostra BA, Palmer CN, Palotie A, Peden JF, Pedersen N, Peters A, Polasek O, Pouta A, Pramstaller PP, Prokopenko I, Pütter C, Radhakrishnan A, Raitakari O, Rendon A, Rivadeneira F, Rudan I, Saaristo TE, Sambrook JG, Sanders AR, Sanna S, Saramies J, Schipf S, Schreiber S, Schunkert H, Shin SY, Signorini S, Sinisalo J, Skrobek B, Soranzo N, Stančáková A, Stark K, Stephens JC, Stirrups K, Stolk RP, Stumvoll M, Swift AJ, Theodoraki EV, Thorand B, Tregouet DA, Tremoli E, Van der Klauw MM, van Meurs JB, Vermeulen SH, Viikari J, Virtamo J, Vitart V, Waeber G, Wang Z, Widén E, Wild SH, Willemsen G, Winkelmann BR, Witteman JC, Wolffenbuttel BH, Wong A, Wright AF, Zillikens MC, Amouyel P, Boehm BO, Boerwinkle E, Boomsma DI, Caulfield MJ, Chanock SJ, Cupples LA, Cusi D, Dedoussis GV, Erdmann J, Eriksson JG, Franks PW, Froguel P, Gieger C, Gyllensten U, Hamsten A, Harris TB, Hengstenberg C, Hicks AA, Hingorani A, Hinney A, Hofman A, Hovingh KG, Hveem K, Illig T, Jarvelin MR, Jöckel KH, Keinanen-Kiukaanniemi SM, Kiemeney LA, Kuh D, Laakso M, Lehtimäki T, Levinson DF, Martin NG, Metspalu A, Morris AD, Nieminen MS, Njølstad I, Ohlsson C, Oldehinkel AJ, Ouwehand WH, Palmer LJ, Penninx B, Power C, Province MA, Psaty BM, Qi L, Rauramaa R, Ridker PM, Ripatti S, Salomaa V, Samani NJ, Snieder H, Sørensen TI, Spector TD, Stefansson K, Tönjes A, Tuomilehto J, Uitterlinden AG, Uusitupa M, van der Harst P, Vollenweider P, Wallaschofski H, Wareham NJ, Watkins H, Wichmann HE, Wilson JF, Abecasis GR, Assimes TL, Barroso I, Boehnke M, Borecki IB, Deloukas P, Fox CS, Frayling T, Groop LC, Haritunian T, Heid IM, Hunter D, Kaplan RC, Karpe F, Moffatt M, Mohlke KL, O’Connell JR, Pawitan Y, Schadt EE, Schlessinger D, Steinthorsdottir V, Strachan DP, Thorsteinsdottir U, van Duijn CM, Visscher PM, Di Blasio AM, Hirschhorn JN, Lindgren CM, Morris AP, Meyre D, Scherag A, McCarthy MI, Speliotes EK, North KE, Loos RJ, Ingelsson E. Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. Nat Genet 2013; 45:501-12. [PMID: 23563607 PMCID: PMC3973018 DOI: 10.1038/ng.2606] [Citation(s) in RCA: 436] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 03/14/2013] [Indexed: 12/25/2022]
Abstract
Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.
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den Hoed M, Eijgelsheim M, Esko T, Brundel BJJM, Peal DS, Evans DM, Nolte IM, Segrè AV, Holm H, Handsaker RE, Westra HJ, Johnson T, Isaacs A, Yang J, Lundby A, Zhao JH, Kim YJ, Go MJ, Almgren P, Bochud M, Boucher G, Cornelis MC, Gudbjartsson D, Hadley D, van der Harst P, Hayward C, den Heijer M, Igl W, Jackson AU, Kutalik Z, Luan J, Kemp JP, Kristiansson K, Ladenvall C, Lorentzon M, Montasser ME, Njajou OT, O'Reilly PF, Padmanabhan S, St Pourcain B, Rankinen T, Salo P, Tanaka T, Timpson NJ, Vitart V, Waite L, Wheeler W, Zhang W, Draisma HHM, Feitosa MF, Kerr KF, Lind PA, Mihailov E, Onland-Moret NC, Song C, Weedon MN, Xie W, Yengo L, Absher D, Albert CM, Alonso A, Arking DE, de Bakker PIW, Balkau B, Barlassina C, Benaglio P, Bis JC, Bouatia-Naji N, Brage S, Chanock SJ, Chines PS, Chung M, Darbar D, Dina C, Dörr M, Elliott P, Felix SB, Fischer K, Fuchsberger C, de Geus EJC, Goyette P, Gudnason V, Harris TB, Hartikainen AL, Havulinna AS, Heckbert SR, Hicks AA, Hofman A, Holewijn S, Hoogstra-Berends F, Hottenga JJ, Jensen MK, Johansson A, Junttila J, Kääb S, Kanon B, Ketkar S, Khaw KT, Knowles JW, Kooner AS, Kors JA, Kumari M, Milani L, Laiho P, Lakatta EG, Langenberg C, Leusink M, Liu Y, Luben RN, Lunetta KL, Lynch SN, Markus MRP, Marques-Vidal P, Mateo Leach I, McArdle WL, McCarroll SA, Medland SE, Miller KA, Montgomery GW, Morrison AC, Müller-Nurasyid M, Navarro P, Nelis M, O'Connell JR, O'Donnell CJ, Ong KK, Newman AB, Peters A, Polasek O, Pouta A, Pramstaller PP, Psaty BM, Rao DC, Ring SM, Rossin EJ, Rudan D, Sanna S, Scott RA, Sehmi JS, Sharp S, Shin JT, Singleton AB, Smith AV, Soranzo N, Spector TD, Stewart C, Stringham HM, Tarasov KV, Uitterlinden AG, Vandenput L, Hwang SJ, Whitfield JB, Wijmenga C, Wild SH, Willemsen G, Wilson JF, Witteman JCM, Wong A, Wong Q, Jamshidi Y, Zitting P, Boer JMA, Boomsma DI, Borecki IB, van Duijn CM, Ekelund U, Forouhi NG, Froguel P, Hingorani A, Ingelsson E, Kivimaki M, Kronmal RA, Kuh D, Lind L, Martin NG, Oostra BA, Pedersen NL, Quertermous T, Rotter JI, van der Schouw YT, Verschuren WMM, Walker M, Albanes D, Arnar DO, Assimes TL, Bandinelli S, Boehnke M, de Boer RA, Bouchard C, Caulfield WLM, Chambers JC, Curhan G, Cusi D, Eriksson J, Ferrucci L, van Gilst WH, Glorioso N, de Graaf J, Groop L, Gyllensten U, Hsueh WC, Hu FB, Huikuri HV, Hunter DJ, Iribarren C, Isomaa B, Jarvelin MR, Jula A, Kähönen M, Kiemeney LA, van der Klauw MM, Kooner JS, Kraft P, Iacoviello L, Lehtimäki T, Lokki MLL, Mitchell BD, Navis G, Nieminen MS, Ohlsson C, Poulter NR, Qi L, Raitakari OT, Rimm EB, Rioux JD, Rizzi F, Rudan I, Salomaa V, Sever PS, Shields DC, Shuldiner AR, Sinisalo J, Stanton AV, Stolk RP, Strachan DP, Tardif JC, Thorsteinsdottir U, Tuomilehto J, van Veldhuisen DJ, Virtamo J, Viikari J, Vollenweider P, Waeber G, Widen E, Cho YS, Olsen JV, Visscher PM, Willer C, Franke L, Erdmann J, Thompson JR, Pfeufer A, Sotoodehnia N, Newton-Cheh C, Ellinor PT, Stricker BHC, Metspalu A, Perola M, Beckmann JS, Smith GD, Stefansson K, Wareham NJ, Munroe PB, Sibon OCM, Milan DJ, Snieder H, Samani NJ, Loos RJF. Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders. Nat Genet 2013; 45:621-31. [PMID: 23583979 DOI: 10.1038/ng.2610] [Citation(s) in RCA: 228] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 03/21/2013] [Indexed: 12/16/2022]
Abstract
Elevated resting heart rate is associated with greater risk of cardiovascular disease and mortality. In a 2-stage meta-analysis of genome-wide association studies in up to 181,171 individuals, we identified 14 new loci associated with heart rate and confirmed associations with all 7 previously established loci. Experimental downregulation of gene expression in Drosophila melanogaster and Danio rerio identified 20 genes at 11 loci that are relevant for heart rate regulation and highlight a role for genes involved in signal transmission, embryonic cardiac development and the pathophysiology of dilated cardiomyopathy, congenital heart failure and/or sudden cardiac death. In addition, genetic susceptibility to increased heart rate is associated with altered cardiac conduction and reduced risk of sick sinus syndrome, and both heart rate-increasing and heart rate-decreasing variants associate with risk of atrial fibrillation. Our findings provide fresh insights into the mechanisms regulating heart rate and identify new therapeutic targets.
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Deloukas P, Kanoni S, Willenborg C, Farrall M, Assimes TL, Thompson JR, Ingelsson E, Saleheen D, Erdmann J, Goldstein BA, Stirrups K, König IR, Cazier JB, Johansson A, Hall AS, Lee JY, Willer CJ, Chambers JC, Esko T, Folkersen L, Goel A, Grundberg E, Havulinna AS, Ho WK, Hopewell JC, Eriksson N, Kleber ME, Kristiansson K, Lundmark P, Lyytikäinen LP, Rafelt S, Shungin D, Strawbridge RJ, Thorleifsson G, Tikkanen E, Van Zuydam N, Voight BF, Waite LL, Zhang W, Ziegler A, Absher D, Altshuler D, Balmforth AJ, Barroso I, Braund PS, Burgdorf C, Claudi-Boehm S, Cox D, Dimitriou M, Do R, Doney ASF, El Mokhtari N, Eriksson P, Fischer K, Fontanillas P, Franco-Cereceda A, Gigante B, Groop L, Gustafsson S, Hager J, Hallmans G, Han BG, Hunt SE, Kang HM, Illig T, Kessler T, Knowles JW, Kolovou G, Kuusisto J, Langenberg C, Langford C, Leander K, Lokki ML, Lundmark A, McCarthy MI, Meisinger C, Melander O, Mihailov E, Maouche S, Morris AD, Müller-Nurasyid M, Nikus K, Peden JF, Rayner NW, Rasheed A, Rosinger S, Rubin D, Rumpf MP, Schäfer A, Sivananthan M, Song C, Stewart AFR, Tan ST, Thorgeirsson G, van der Schoot CE, Wagner PJ, Wells GA, Wild PS, Yang TP, Amouyel P, Arveiler D, Basart H, Boehnke M, Boerwinkle E, Brambilla P, Cambien F, Cupples AL, de Faire U, Dehghan A, Diemert P, Epstein SE, Evans A, Ferrario MM, Ferrières J, Gauguier D, Go AS, Goodall AH, Gudnason V, Hazen SL, Holm H, Iribarren C, Jang Y, Kähönen M, Kee F, Kim HS, Klopp N, Koenig W, Kratzer W, Kuulasmaa K, Laakso M, Laaksonen R, Lee JY, Lind L, Ouwehand WH, Parish S, Park JE, Pedersen NL, Peters A, Quertermous T, Rader DJ, Salomaa V, Schadt E, Shah SH, Sinisalo J, Stark K, Stefansson K, Trégouët DA, Virtamo J, Wallentin L, Wareham N, Zimmermann ME, Nieminen MS, Hengstenberg C, Sandhu MS, Pastinen T, Syvänen AC, Hovingh GK, Dedoussis G, Franks PW, Lehtimäki T, Metspalu A, Zalloua PA, Siegbahn A, Schreiber S, Ripatti S, Blankenberg SS, Perola M, Clarke R, Boehm BO, O'Donnell C, Reilly MP, März W, Collins R, Kathiresan S, Hamsten A, Kooner JS, Thorsteinsdottir U, Danesh J, Palmer CNA, Roberts R, Watkins H, Schunkert H, Samani NJ. Large-scale association analysis identifies new risk loci for coronary artery disease. Nat Genet 2012. [PMID: 23202125 DOI: 10.1038/ng.2480] [Citation(s) in RCA: 1227] [Impact Index Per Article: 102.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Coronary artery disease (CAD) is the commonest cause of death. Here, we report an association analysis in 63,746 CAD cases and 130,681 controls identifying 15 loci reaching genome-wide significance, taking the number of susceptibility loci for CAD to 46, and a further 104 independent variants (r(2) < 0.2) strongly associated with CAD at a 5% false discovery rate (FDR). Together, these variants explain approximately 10.6% of CAD heritability. Of the 46 genome-wide significant lead SNPs, 12 show a significant association with a lipid trait, and 5 show a significant association with blood pressure, but none is significantly associated with diabetes. Network analysis with 233 candidate genes (loci at 10% FDR) generated 5 interaction networks comprising 85% of these putative genes involved in CAD. The four most significant pathways mapping to these networks are linked to lipid metabolism and inflammation, underscoring the causal role of these activities in the genetic etiology of CAD. Our study provides insights into the genetic basis of CAD and identifies key biological pathways.
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Siggberg L, Ala-Mello S, Sirpa AM, Linnankivi T, Tarja L, Avela K, Kristiina A, Scheinin I, Ilari S, Kristiansson K, Kati K, Lahermo P, Päivi L, Hietala M, Marja H, Metsähonkala L, Liisa M, Kuusinen E, Esa K, Laaksonen M, Maarit L, Saarela J, Janna S, Khuutila S, Sakari K. High-resolution SNP array analysis of patients with developmental disorder and normal array CGH results. BMC MEDICAL GENETICS 2012; 13:84. [PMID: 22984989 PMCID: PMC3523000 DOI: 10.1186/1471-2350-13-84] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 09/05/2012] [Indexed: 12/02/2022]
Abstract
Background Diagnostic analysis of patients with developmental disorders has improved over recent years largely due to the use of microarray technology. Array methods that facilitate copy number analysis have enabled the diagnosis of up to 20% more patients with previously normal karyotyping results. A substantial number of patients remain undiagnosed, however. Methods and Results Using the Genome-Wide Human SNP array 6.0, we analyzed 35 patients with a developmental disorder of unknown cause and normal array comparative genomic hybridization (array CGH) results, in order to characterize previously undefined genomic aberrations. We detected no seemingly pathogenic copy number aberrations. Most of the vast amount of data produced by the array was polymorphic and non-informative. Filtering of this data, based on copy number variant (CNV) population frequencies as well as phenotypically relevant genes, enabled pinpointing regions of allelic homozygosity that included candidate genes correlating to the phenotypic features in four patients, but results could not be confirmed. Conclusions In this study, the use of an ultra high-resolution SNP array did not contribute to further diagnose patients with developmental disorders of unknown cause. The statistical power of these results is limited by the small size of the patient cohort, and interpretation of these negative results can only be applied to the patients studied here. We present the results of our study and the recurrence of clustered allelic homozygosity present in this material, as detected by the SNP 6.0 array.
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Kiryluk K, Li Y, Sanna-Cherchi S, Rohanizadegan M, Suzuki H, Eitner F, Snyder HJ, Choi M, Hou P, Scolari F, Izzi C, Gigante M, Gesualdo L, Savoldi S, Amoroso A, Cusi D, Zamboli P, Julian BA, Novak J, Wyatt RJ, Mucha K, Perola M, Kristiansson K, Viktorin A, Magnusson PK, Thorleifsson G, Thorsteinsdottir U, Stefansson K, Boland A, Metzger M, Thibaudin L, Wanner C, Jager KJ, Goto S, Maixnerova D, Karnib HH, Nagy J, Panzer U, Xie J, Chen N, Tesar V, Narita I, Berthoux F, Floege J, Stengel B, Zhang H, Lifton RP, Gharavi AG. Geographic differences in genetic susceptibility to IgA nephropathy: GWAS replication study and geospatial risk analysis. PLoS Genet 2012; 8:e1002765. [PMID: 22737082 PMCID: PMC3380840 DOI: 10.1371/journal.pgen.1002765] [Citation(s) in RCA: 256] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 04/30/2012] [Indexed: 12/31/2022] Open
Abstract
IgA nephropathy (IgAN), major cause of kidney failure worldwide, is common in Asians, moderately prevalent in Europeans, and rare in Africans. It is not known if these differences represent variation in genes, environment, or ascertainment. In a recent GWAS, we localized five IgAN susceptibility loci on Chr.6p21 (HLA-DQB1/DRB1, PSMB9/TAP1, and DPA1/DPB2 loci), Chr.1q32 (CFHR3/R1 locus), and Chr.22q12 (HORMAD2 locus). These IgAN loci are associated with risk of other immune-mediated disorders such as type I diabetes, multiple sclerosis, or inflammatory bowel disease. We tested association of these loci in eight new independent cohorts of Asian, European, and African-American ancestry (N = 4,789), followed by meta-analysis with risk-score modeling in 12 cohorts (N = 10,755) and geospatial analysis in 85 world populations. Four susceptibility loci robustly replicated and all five loci were genome-wide significant in the combined cohort (P = 5×10−32–3×10−10), with heterogeneity detected only at the PSMB9/TAP1 locus (I2 = 0.60). Conditional analyses identified two new independent risk alleles within the HLA-DQB1/DRB1 locus, defining multiple risk and protective haplotypes within this interval. We also detected a significant genetic interaction, whereby the odds ratio for the HORMAD2 protective allele was reversed in homozygotes for a CFHR3/R1 deletion (P = 2.5×10−4). A seven–SNP genetic risk score, which explained 4.7% of overall IgAN risk, increased sharply with Eastward and Northward distance from Africa (r = 0.30, P = 3×10−128). This model paralleled the known East–West gradient in disease risk. Moreover, the prediction of a South–North axis was confirmed by registry data showing that the prevalence of IgAN–attributable kidney failure is increased in Northern Europe, similar to multiple sclerosis and type I diabetes. Variation at IgAN susceptibility loci correlates with differences in disease prevalence among world populations. These findings inform genetic, biological, and epidemiological investigations of IgAN and permit cross-comparison with other complex traits that share genetic risk loci and geographic patterns with IgAN. IgA nephropathy (IgAN) is the most common cause of kidney failure in Asia, has lower prevalence in Europe, and is very infrequent among populations of African ancestry. A long-standing question in the field is whether these differences represent variation in genes, environment, or ascertainment. In a recent genome-wide association study of 5,966 individuals, we identified five susceptibility loci for this trait. In this paper, we study the largest IgAN case-control cohort reported to date, composed of 10,775 individuals of European, Asian, and African-American ancestry. We confirm that all five loci are significant contributors to disease risk across this multi-ethnic cohort. In addition, we identify two novel independent susceptibility alleles within the HLA-DQB1/DRB1 locus and a new genetic interaction between loci on Chr.1p36 and Chr.22q22. We develop a seven–SNP genetic risk score that explains nearly 5% of variation in disease risk. In geospatial analysis of 85 world populations, the genetic risk score closely parallels worldwide patterns of disease prevalence. The genetic risk score also predicts an unsuspected Northward risk gradient in Europe. This genetic prediction is verified by examination of registry data demonstrating, similarly to other immune-mediated diseases such as multiple sclerosis and type I diabetes, a previously unrecognized increase in IgAN–attributable kidney failure in Northern European countries.
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