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1. Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis

Author

Nabais, M.F., Lin, T., Benyamin, B., Williams, K.L., Garton, F.C., Vinkhuyzen, A.A.E., Zhang, F., Vallerga, C.L., Restuadi, R., Freydenzon, A., Zwamborn, R.A.J., Hop, P.J., Robinson, M.R., Gratten, J., Visscher, P.M., Hannon, E., Mill, J., Brown, M.A., Laing, N.G., Mather, K.A., Sachdev, P.S., Ngoh, S.T., Steyn, F.J., Wallace, L., Henders, A.K., Needham, M., Veldink, J.H., Mathers, S., Nicholson, G., Rowe, D.B., Henderson, R.D., McCombe, P.A., Pamphlett, R., Yang, J., Blair, I.P., McRae, A.F., Wray, N.R., Nabais, M.F., Lin, T., Benyamin, B., Williams, K.L., Garton, F.C., Vinkhuyzen, A.A.E., Zhang, F., Vallerga, C.L., Restuadi, R., Freydenzon, A., Zwamborn, R.A.J., Hop, P.J., Robinson, M.R., Gratten, J., Visscher, P.M., Hannon, E., Mill, J., Brown, M.A., Laing, N.G., Mather, K.A., Sachdev, P.S., Ngoh, S.T., Steyn, F.J., Wallace, L., Henders, A.K., Needham, M., Veldink, J.H., Mathers, S., Nicholson, G., Rowe, D.B., Henderson, R.D., McCombe, P.A., Pamphlett, R., Yang, J., Blair, I.P., McRae, A.F., and Wray, N.R.

Abstract

We conducted DNA methylation association analyses using Illumina 450K data from whole blood for an Australian amyotrophic lateral sclerosis (ALS) case–control cohort (782 cases and 613 controls). Analyses used mixed linear models as implemented in the OSCA software. We found a significantly higher proportion of neutrophils in cases compared to controls which replicated in an independent cohort from the Netherlands (1159 cases and 637 controls). The OSCA MOMENT linear mixed model has been shown in simulations to best account for confounders. When combined in a methylation profile score, the 25 most-associated probes identified by MOMENT significantly classified case–control status in the Netherlands sample (area under the curve, AUC = 0.65, CI95% = [0.62–0.68], p = 8.3 × 10−22). The maximum AUC achieved was 0.69 (CI95% = [0.66–0.71], p = 4.3 × 10−34) when cell-type proportion was included in the predictor.

Published
2020

3. Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals

Author

23Andme Research Team, Abdellaoui, A., Peyrot, Wouter J, Hottenga, J.J., Vinkhuyzen, A.A.E., Willemsen, Gonneke, Boomsma, D.I., van Duijn, Cornelia M, Penninx, Brenda, Posthuma, Danielle, Uitterlinden, André G, 23Andme Research Team, Abdellaoui, A., Peyrot, Wouter J, Hottenga, J.J., Vinkhuyzen, A.A.E., Willemsen, Gonneke, Boomsma, D.I., van Duijn, Cornelia M, Penninx, Brenda, Posthuma, Danielle, and Uitterlinden, André G

Abstract

Here we conducted a large-scale genetic association analysis of educational attainment in a sample of approximately 1.1 million individuals and identify 1,271 independent genome-wide-significant SNPs. For the SNPs taken together, we found evidence of heterogeneous effects across environments. The SNPs implicate genes involved in brain-development processes and neuron-to-neuron communication. In a separate analysis of the X chromosome, we identify 10 independent genome-wide-significant SNPs and estimate a SNP heritability of around 0.3% in both men and women, consistent with partial dosage compensation. A joint (multi-phenotype) analysis of educational attainment and three related cognitive phenotypes generates polygenic scores that explain 11–13% of the variance in educational attainment and 7–10% of the variance in cognitive performance. This prediction accuracy substantially increases the utility of polygenic scores as tools in research.

Published
2018
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4. Gestational vitamin D deficiency and autism spectrum disorder

Author

Vinkhuyzen, A.A.E. (Anna A.), Eyles, D.W. (Darryl W.), Burne, T.H. (Thomas H.), Blanken, L.M.E. (Laura), Kruithof, C.J. (Claudia), Verhulst, F.C. (Frank), White, T.J.H. (Tonya), Jaddoe, V.W.V. (Vincent), Tiemeier, H.W. (Henning), Mcgrath, J.J. (John J.), Vinkhuyzen, A.A.E. (Anna A.), Eyles, D.W. (Darryl W.), Burne, T.H. (Thomas H.), Blanken, L.M.E. (Laura), Kruithof, C.J. (Claudia), Verhulst, F.C. (Frank), White, T.J.H. (Tonya), Jaddoe, V.W.V. (Vincent), Tiemeier, H.W. (Henning), and Mcgrath, J.J. (John J.)

Abstract

Background: There is growing interest in linking vitamin D deficiency with autism spectrum disorders (ASDs). The association between vitamin D deficiency during gestation, a critical period in neurodevelopment, and ASD is not well understood. Aims: To determine the association between gestational vitamin D status and ASD. Method: Based on a birth cohort (n=4334), we examined the association between 25-hydroxyvitamin D (25OHD), assessed from both maternal mid-gestation sera and neonatal sera, and ASD (defined by clinical records; n=68 cases). Results: Individuals in the 25OHD-deficient group at mid-gestation had more than twofold increased risk of ASD (odds ratio (OR)=2.42, 95% confidence interval (CI) 1.09 to 5.07, P=0.03) compared with the sufficient group. The findings persisted in analyses including children of European ethnicity only. Conclusions: Mid-gestational vitamin D deficiency was associated with an increased risk of ASD. Because gestational vitamin D deficiency is readily preventable with safe, inexpensive and readily available supplementation, this risk factor warrants closer scrutiny.

Published
2017
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5. Genome-wide association study identifies 74 loci associated with educational attainment

Author

Okbay, A. (Aysu), Beauchamp, J.P. (Jonathan), Fontana, M.A. (Mark Alan), Lee, J.J. (James J.), Pers, T.H. (Tune), Rietveld, C.A. (Cornelius A.), Turley, P. (Patrick), Chen, G.-B. (Guo-Bo), Emilsson, V. (Valur), Meddens, S.F.W. (S. Fleur W.), Oskarsson, S. (Sven), Pickrell, J.K. (Joseph K.), Thom, K. (Kevin), Timshel, P. (Pascal), Vlaming, R. (Ronald) de, Abdellaoui, A. (Abdel), Ahluwalia, T.S. (Tarunveer Singh), Bacelis, J. (Jonas), Baumbach, C. (Clemens), Bjornsdottir, G. (Gyda), Brandsma, J.H. (Johan), Pina Concas, M. (Maria), Derringer, J., Furlotte, N.A. (Nicholas A.), Galesloot, T.E. (Tessel), Girotto, S., Gupta, R. (Richa), Hall, L.M. (Leanne M.), Harris, S.E. (Sarah), Hofer, E., Horikoshi, M. (Momoko), Huffman, J.E. (Jennifer E.), Kaasik, K. (Kadri), Kalafati, I.-P. (Ioanna-Panagiota), Karlsson, R. (Robert), Kong, A. (Augustine), Lahti, J. (Jari), Lee, S.J. (Sven) van der, Deleeuw, C. (Christiaan), Lind, P.A. (Penelope), Lindgren, K.-O. (Karl-Oskar), Liu, T. (Tian), Mangino, M. (Massimo), Marten, J. (Jonathan), Mihailov, E. (Evelin), Miller, M. (Mike), Most, P.J. (Peter) van der, Oldmeadow, C. (Christopher), Payton, A. (Antony), Pervjakova, N. (Natalia), Peyrot, W.J. (Wouter ), Qian, Y. (Yong), Raitakari, O. (Olli), Rueedi, R. (Rico), Salvi, E. (Erika), Schmidt, B. (Börge), Schraut, K.E. (Katharina E.), Shi, J. (Jianxin), Smith, A.V. (Albert Vernon), Poot, R.A. (Raymond), St Pourcain, B. (Beate), Teumer, A. (Alexander), Thorleifsson, G. (Gudmar), Verweij, N. (Niek), Vuckovic, D. (Dragana), Wellmann, J. (Juergen), Westra, H.J. (Harm-Jan), Yang, J. (Jingyun), Zhao, W. (Wei), Zhu, Z. (Zhihong), Alizadeh, B.Z. (Behrooz), Amin, N. (Najaf), Bakshi, A. (Andrew), Baumeister, S.E. (Sebastian), Biino, G. (Ginevra), Bønnelykke, K. (Klaus), Boyle, P.A. (Patricia), Campbell, H. (Harry), Cappuccio, F.P. (Francesco P.), Davies, G. (Gail), Neve, J.E. (Jan-Emmanuel) de, Deloukas, P. (Panagiotis), Demuth, I. (Ilja), Ding, J. (Jun), Eibich, P. (Peter), Eisele, L. (Lewin), Eklund, N. (Niina), Evans, D.M. (David), Faul, J.D. (Jessica D.), Feitosa, M.F. (Mary Furlan), Forstner, A.J. (Andreas), Gandin, I. (Ilaria), Gunnarsson, B. (Bjarni), Halldorsson, B.V. (Bjarni), Harris, T.B. (Tamara), Holliday, E.G. (Elizabeth), Heath, A.C. (Andrew C.), Hocking, L.J., Homuth, G. (Georg), Horan, M. (Mike), Hottenga, J.J. (Jouke Jan), Jager, P.L. (Philip) de, Joshi, P.K. (Peter), Juqessur, A. (Astanand), Kaakinen, M. (Marika), Kähönen, M. (Mika), Kanoni, S. (Stavroula), Keltigangas-Järvinen, L. (Liisa), Kiemeney, L.A.L.M. (Bart), Kolcic, I. (Ivana), Koskinen, S. (Seppo), Kraja, A. (Aldi), Kroh, M. (Martin), Kutalik, Z. (Zoltán), Latvala, A. (Antti), Launer, L.J. (Lenore), Lebreton, M.P. (Maël P.), Levinson, D.F. (Douglas F.), Lichtenstein, P. (Paul), Lichtner, P. (Peter), Liewald, D.C.M. (David), Loukola, A. (Anu), Madden, P.A. (Pamela), Mägi, R. (Reedik), Mäki-Opas, T. (Tomi), Marioni, R.E. (Riccardo), Marques-Vidal, P. (Pedro), Meddens, G.A. (Gerardus A.), Mcmahon, G. (George), Meisinger, C. (Christa), Meitinger, T. (Thomas), Milaneschi, Y. (Yusplitri), Milani, L. (Lili), Montgomery, G.W. (Grant), Myhre, R. (Ronny), Nelson, C.P. (Christopher P.), Nyholt, D.R. (Dale), Ollier, W.E.R. (William), Palotie, A. (Aarno), Paternoster, L. (Lavinia), Pedersen, N.L. (Nancy), Petrovic, K. (Katja), Porteous, D.J. (David J.), Räikkönen, K. (Katri), Ring, S.M. (Susan M.), Robino, A. (Antonietta), Rostapshova, O. (Olga), Rudan, I. (Igor), Rustichini, A. (Aldo), Salomaa, V. (Veikko), Sanders, A.R. (Alan R.), Sarin, A.-P., Schmidt, R. (Reinhold), Scott, R.J. (Rodney), Smith, B.H. (Blair), Smith, J.A. (Jennifer A), Staessen, J.A. (Jan), Steinhagen-Thiessen, E. (Elisabeth), Strauch, K. (Konstantin), Terracciano, A., Tobin, M.D. (Martin), Ulivi, S. (Shelia), Vaccargiu, S. (Simona), Quaye, L. (Lydia), Rooij, F.J.A. (Frank) van, Venturini, C. (Cristina), Vinkhuyzen, A.A.E. (Anna A.), Völker, U. (Uwe), Völzke, H. (Henry), Vonk, J.M. (Judith), Vozzi, D. (Diego), Waage, J. (Johannes), Ware, E.B. (Erin B.), Willemsen, G.A.H.M. (Gonneke), Attia, J. (John), Bennett, D.A. (David A.), Berger, K. (Klaus), Bertram, L. (Lars), Bisgaard, H. (Hans), Boomsma, D.I. (Dorret), Borecki, I.B. (Ingrid), Bültmann, U. (Ute), Chabris, C.F. (Christopher F.), Cucca, F. (Francesco), Cusi, D. (Daniele), Deary, I.J. (Ian), Dedoussis, G.V. (George), Duijn, C.M. (Cornelia) van, Hagen, K. (Knut), Franke, B. (Barbara), Franke, L. (Lude), Gasparini, P. (Paolo), Gejman, P.V. (Pablo), Gieger, C. (Christian), Grabe, H.J. (Hans Jörgen), Gratten, J. (Jacob), Groenen, P.J.F. (Patrick), Gudnason, V. (Vilmundur), Harst, P. (Pim) van der, Hayward, C. (Caroline), Hinds, D.A. (David A.), Hoffmann, W. (Wolfgang), Hypponen, E. (Elina), Iacono, W.G. (William), Jacobsson, B. (Bo), Jarvelin, M.-R. (Marjo-Riitta), JöCkel, K.-H. (Karl-Heinz), Kaprio, J. (Jaakko), Kardia, S.L.R. (Sharon), Lehtimäki, T. (Terho), Lehrer, S.F. (Steven F.), Magnusson, P.K. (Patrik), Martin, N.G. (Nicholas), McGue, M. (Matt), Metspalu, A. (Andres), Pendleton, N. (Neil), Penninx, B.W.J.H. (Brenda), Perola, M. (Markus), Pirastu, N. (Nicola), Pirastu, M. (Mario), Polasek, O. (Ozren), Posthuma, D. (Danielle), Power, C. (Christopher), Province, M.A. (Mike), Samani, N.J. (Nilesh), Schlessinger, D. (David), Sørensen, T.I.A. (Thorkild), Spector, T.D. (Timothy), Zwart, J-A. (John-Anker), Thorsteinsdottir, U. (Unnur), Thurik, A.R. (Roy), Timpson, N.J. (Nicholas J.), Tiemeier, H.W. (Henning), Tung, J.Y. (Joyce Y.), Uitterlinden, A.G. (André), Vitart, V. (Veronique), Vollenweider, P. (Peter), Weir, D.R. (David), Wilson, J.F. (James F.), Wright, A.F. (Alan), Conley, D.C. (Dalton C.), Krueger, R.F., Smith, A.V. (Davey), Hofman, A. (Albert), Laibson, D. (David), Medland, S.E. (Sarah), Meyer, M.N. (Michelle N.), Yang, J. (Joanna), Johannesson, M. (Magnus), Visscher, P.M. (Peter), Esko, T. (Tõnu), Koellinger, Ph.D. (Philipp), Cesarini, D. (David), Benjamin, D.J. (Daniel J.), Okbay, A. (Aysu), Beauchamp, J.P. (Jonathan), Fontana, M.A. (Mark Alan), Lee, J.J. (James J.), Pers, T.H. (Tune), Rietveld, C.A. (Cornelius A.), Turley, P. (Patrick), Chen, G.-B. (Guo-Bo), Emilsson, V. (Valur), Meddens, S.F.W. (S. Fleur W.), Oskarsson, S. (Sven), Pickrell, J.K. (Joseph K.), Thom, K. (Kevin), Timshel, P. (Pascal), Vlaming, R. (Ronald) de, Abdellaoui, A. (Abdel), Ahluwalia, T.S. (Tarunveer Singh), Bacelis, J. (Jonas), Baumbach, C. (Clemens), Bjornsdottir, G. (Gyda), Brandsma, J.H. (Johan), Pina Concas, M. (Maria), Derringer, J., Furlotte, N.A. (Nicholas A.), Galesloot, T.E. (Tessel), Girotto, S., Gupta, R. (Richa), Hall, L.M. (Leanne M.), Harris, S.E. (Sarah), Hofer, E., Horikoshi, M. (Momoko), Huffman, J.E. (Jennifer E.), Kaasik, K. (Kadri), Kalafati, I.-P. (Ioanna-Panagiota), Karlsson, R. (Robert), Kong, A. (Augustine), Lahti, J. (Jari), Lee, S.J. (Sven) van der, Deleeuw, C. (Christiaan), Lind, P.A. (Penelope), Lindgren, K.-O. (Karl-Oskar), Liu, T. (Tian), Mangino, M. (Massimo), Marten, J. (Jonathan), Mihailov, E. (Evelin), Miller, M. (Mike), Most, P.J. (Peter) van der, Oldmeadow, C. (Christopher), Payton, A. (Antony), Pervjakova, N. (Natalia), Peyrot, W.J. (Wouter ), Qian, Y. (Yong), Raitakari, O. (Olli), Rueedi, R. (Rico), Salvi, E. (Erika), Schmidt, B. (Börge), Schraut, K.E. (Katharina E.), Shi, J. (Jianxin), Smith, A.V. (Albert Vernon), Poot, R.A. (Raymond), St Pourcain, B. (Beate), Teumer, A. (Alexander), Thorleifsson, G. (Gudmar), Verweij, N. (Niek), Vuckovic, D. (Dragana), Wellmann, J. (Juergen), Westra, H.J. (Harm-Jan), Yang, J. (Jingyun), Zhao, W. (Wei), Zhu, Z. (Zhihong), Alizadeh, B.Z. (Behrooz), Amin, N. (Najaf), Bakshi, A. (Andrew), Baumeister, S.E. (Sebastian), Biino, G. (Ginevra), Bønnelykke, K. (Klaus), Boyle, P.A. (Patricia), Campbell, H. (Harry), Cappuccio, F.P. (Francesco P.), Davies, G. (Gail), Neve, J.E. (Jan-Emmanuel) de, Deloukas, P. (Panagiotis), Demuth, I. (Ilja), Ding, J. (Jun), Eibich, P. (Peter), Eisele, L. (Lewin), Eklund, N. (Niina), Evans, D.M. (David), Faul, J.D. (Jessica D.), Feitosa, M.F. (Mary Furlan), Forstner, A.J. (Andreas), Gandin, I. (Ilaria), Gunnarsson, B. (Bjarni), Halldorsson, B.V. (Bjarni), Harris, T.B. (Tamara), Holliday, E.G. (Elizabeth), Heath, A.C. (Andrew C.), Hocking, L.J., Homuth, G. (Georg), Horan, M. (Mike), Hottenga, J.J. (Jouke Jan), Jager, P.L. (Philip) de, Joshi, P.K. (Peter), Juqessur, A. (Astanand), Kaakinen, M. (Marika), Kähönen, M. (Mika), Kanoni, S. (Stavroula), Keltigangas-Järvinen, L. (Liisa), Kiemeney, L.A.L.M. (Bart), Kolcic, I. (Ivana), Koskinen, S. (Seppo), Kraja, A. (Aldi), Kroh, M. (Martin), Kutalik, Z. (Zoltán), Latvala, A. (Antti), Launer, L.J. (Lenore), Lebreton, M.P. (Maël P.), Levinson, D.F. (Douglas F.), Lichtenstein, P. (Paul), Lichtner, P. (Peter), Liewald, D.C.M. (David), Loukola, A. (Anu), Madden, P.A. (Pamela), Mägi, R. (Reedik), Mäki-Opas, T. (Tomi), Marioni, R.E. (Riccardo), Marques-Vidal, P. (Pedro), Meddens, G.A. (Gerardus A.), Mcmahon, G. (George), Meisinger, C. (Christa), Meitinger, T. (Thomas), Milaneschi, Y. (Yusplitri), Milani, L. (Lili), Montgomery, G.W. (Grant), Myhre, R. (Ronny), Nelson, C.P. (Christopher P.), Nyholt, D.R. (Dale), Ollier, W.E.R. (William), Palotie, A. (Aarno), Paternoster, L. (Lavinia), Pedersen, N.L. (Nancy), Petrovic, K. (Katja), Porteous, D.J. (David J.), Räikkönen, K. (Katri), Ring, S.M. (Susan M.), Robino, A. (Antonietta), Rostapshova, O. (Olga), Rudan, I. (Igor), Rustichini, A. (Aldo), Salomaa, V. (Veikko), Sanders, A.R. (Alan R.), Sarin, A.-P., Schmidt, R. (Reinhold), Scott, R.J. (Rodney), Smith, B.H. (Blair), Smith, J.A. (Jennifer A), Staessen, J.A. (Jan), Steinhagen-Thiessen, E. (Elisabeth), Strauch, K. (Konstantin), Terracciano, A., Tobin, M.D. (Martin), Ulivi, S. (Shelia), Vaccargiu, S. (Simona), Quaye, L. (Lydia), Rooij, F.J.A. (Frank) van, Venturini, C. (Cristina), Vinkhuyzen, A.A.E. (Anna A.), Völker, U. (Uwe), Völzke, H. (Henry), Vonk, J.M. (Judith), Vozzi, D. (Diego), Waage, J. (Johannes), Ware, E.B. (Erin B.), Willemsen, G.A.H.M. (Gonneke), Attia, J. (John), Bennett, D.A. (David A.), Berger, K. (Klaus), Bertram, L. (Lars), Bisgaard, H. (Hans), Boomsma, D.I. (Dorret), Borecki, I.B. (Ingrid), Bültmann, U. (Ute), Chabris, C.F. (Christopher F.), Cucca, F. (Francesco), Cusi, D. (Daniele), Deary, I.J. (Ian), Dedoussis, G.V. (George), Duijn, C.M. (Cornelia) van, Hagen, K. (Knut), Franke, B. (Barbara), Franke, L. (Lude), Gasparini, P. (Paolo), Gejman, P.V. (Pablo), Gieger, C. (Christian), Grabe, H.J. (Hans Jörgen), Gratten, J. (Jacob), Groenen, P.J.F. (Patrick), Gudnason, V. (Vilmundur), Harst, P. (Pim) van der, Hayward, C. (Caroline), Hinds, D.A. (David A.), Hoffmann, W. (Wolfgang), Hypponen, E. (Elina), Iacono, W.G. (William), Jacobsson, B. (Bo), Jarvelin, M.-R. (Marjo-Riitta), JöCkel, K.-H. (Karl-Heinz), Kaprio, J. (Jaakko), Kardia, S.L.R. (Sharon), Lehtimäki, T. (Terho), Lehrer, S.F. (Steven F.), Magnusson, P.K. (Patrik), Martin, N.G. (Nicholas), McGue, M. (Matt), Metspalu, A. (Andres), Pendleton, N. (Neil), Penninx, B.W.J.H. (Brenda), Perola, M. (Markus), Pirastu, N. (Nicola), Pirastu, M. (Mario), Polasek, O. (Ozren), Posthuma, D. (Danielle), Power, C. (Christopher), Province, M.A. (Mike), Samani, N.J. (Nilesh), Schlessinger, D. (David), Sørensen, T.I.A. (Thorkild), Spector, T.D. (Timothy), Zwart, J-A. (John-Anker), Thorsteinsdottir, U. (Unnur), Thurik, A.R. (Roy), Timpson, N.J. (Nicholas J.), Tiemeier, H.W. (Henning), Tung, J.Y. (Joyce Y.), Uitterlinden, A.G. (André), Vitart, V. (Veronique), Vollenweider, P. (Peter), Weir, D.R. (David), Wilson, J.F. (James F.), Wright, A.F. (Alan), Conley, D.C. (Dalton C.), Krueger, R.F., Smith, A.V. (Davey), Hofman, A. (Albert), Laibson, D. (David), Medland, S.E. (Sarah), Meyer, M.N. (Michelle N.), Yang, J. (Joanna), Johannesson, M. (Magnus), Visscher, P.M. (Peter), Esko, T. (Tõnu), Koellinger, Ph.D. (Philipp), Cesarini, D. (David), and Benjamin, D.J. (Daniel J.)

Abstract

Educational attainment is strongly influenced by social and other environmental factors, but genetic factors are estimated to account for at least 20% of the variation across individuals. Here we report the results of a genome-wide association study (GWAS) for educational attainment that extends our earlier discovery sample of 101,069 individuals to 293,723 individuals, and a replication study in an independent sample of 111,349 individuals from the UK Biobank. We identify 74 genome-wide significant loci associated with the number of years of schooling completed. Single-nucleotide polymorphisms associated with educational attainment are disproportionately found in genomic regions regulating gene expression in the fetal brain. Candidate genes are preferentially expressed in neural tissue, especially during the prenatal period, and enriched for biological pathways involved in neural development. Our findings demonstrate that, even for a behavioural phenotype that is mostly environmentally determined, a well-powered GWAS identifies replicable associated genetic variants that suggest biologically relevant pathways. Because educational attainment is measured in large numbers of individuals, it will continue to be useful as a proxy phenotype in efforts to characterize the genetic influences of related phenotypes, including cognition and neuropsychiatric diseases.

Published
2016
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6. The genetic etiology of cannabis use initiation: a meta-analysis of genome-wide association studies, and a SNP-based heritability estimation

Author

Verweij, K.J.H., Vinkhuyzen, A.A.E., Benyamin, B., Lynskey, M.T., Quaye, L., Agrawal, A., Gordon, S.D., Montgomery, G.W., Madden, P.A.F., Heath, A.C., Spector, T.D., Martin, N.G., Medland, S.E., Clinical Developmental Psychology, and EMGO+ - Mental Health

Subjects
SDG 3 - Good Health and Well-being
Abstract

While initiation of cannabis use is around 40% heritable, not much is known about the underlying genetic aetiology. Here, we meta-analysed two genome-wide association studies of initiation of cannabis use with > 10 000 individuals. None of the genetic variants reached genome-wide significance. We also performed a gene-based association test, which also revealed no significant effects of individual genes. Finally, we estimated that only approximately 6% of the variation in cannabis initiation is due to common genetic variants. Future genetic studies using larger sample sizes and different methodologies (including sequencing) might provide more insight in the complex genetic aetiology of cannabis use. © 2012 The Authors, Addiction Biology © 2012 Society for the Study of Addiction.

Published
2013
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7. Behavior Genetics

Author

Vinkhuyzen, A.A.E., van der Sluis, S., Posthuma, D., Carlstedt, Roland A., Functional Genomics, and Neuroscience Campus Amsterdam - integrative Analysis & Modeling

Published
2010

12. Defining the role of common variation in the genomic and biological architecture of adult human height

Author

Wood, A.R., Esko, T., Yang, J., Vedantam, S., Pers, T.H., Gustafsson, S., Chu, A.Y., Estrada, K., Luan, J., Kutalik, Z., Amin, N., Buchkovich, M.L., Croteau-Chonka, D.C., Day, F.R., Duan, Y., Fall, T., Fehrmann, R., Ferreira, T., Jackson, A.U., Karjalainen, J., Lo, K.S., Locke, A.E., Magi, R., Mihailov, E., Porcu, E., Randall, J.C., Scherag, A., Vinkhuyzen, A.A.E., Westra, H.J., Winkler, T.W., Workalemahu, T., Zhao, J.H., Absher, D., Albrecht, E., Anderson, D., Baron, J., Beekman, M., Demirkan, A., Ehret, G.B., Feenstra, B., Feitosa, M.F., Fischer, K., Fraser, R.M., Goel, A., Gong, J., Justice, A.E., Kanoni, S., Kleber, M.E., Kristiansson, K., Lim, U., Lotay, V., Lui, J.C., Mangino, M., Leach, I.M., Medina-Gomez, C., Nalls, M.A., Nyholt, D.R., Palmer, C.D., Pasko, D., Pechlivanis, S., Prokopenko, I., Ried, J.S., Ripke, S., Shungin, D., Stancakova, A., Strawbridge, R.J., Sung, Y.J., Tanaka, T., Teumer, A., Trompet, S., Laan, S.W. van der, Setten, J. van, Vliet-Ostaptchouk, J.V. Van, Wang, Z., Yengo, L., Zhang, W., Afzal, U., Arnlov, J., Arscott, G.M., Bandinelli, S., Barrett, A., Bellis, C., Bennett, A.J., Berne, C., Bluher, M., Bolton, J.L., Bottcher, Y., Boyd, H.A., Bruinenberg, M., Buckley, B.M., Buyske, S., Caspersen, I.H., Chines, P.S., Clarke, R., Claudi-Boehm, S., Cooper, M., Daw, E.W., Jong, P.A. de, Deelen, J., Delgado, G., Vermeulen, S., Kiemeney, L.A., et al., Wood, A.R., Esko, T., Yang, J., Vedantam, S., Pers, T.H., Gustafsson, S., Chu, A.Y., Estrada, K., Luan, J., Kutalik, Z., Amin, N., Buchkovich, M.L., Croteau-Chonka, D.C., Day, F.R., Duan, Y., Fall, T., Fehrmann, R., Ferreira, T., Jackson, A.U., Karjalainen, J., Lo, K.S., Locke, A.E., Magi, R., Mihailov, E., Porcu, E., Randall, J.C., Scherag, A., Vinkhuyzen, A.A.E., Westra, H.J., Winkler, T.W., Workalemahu, T., Zhao, J.H., Absher, D., Albrecht, E., Anderson, D., Baron, J., Beekman, M., Demirkan, A., Ehret, G.B., Feenstra, B., Feitosa, M.F., Fischer, K., Fraser, R.M., Goel, A., Gong, J., Justice, A.E., Kanoni, S., Kleber, M.E., Kristiansson, K., Lim, U., Lotay, V., Lui, J.C., Mangino, M., Leach, I.M., Medina-Gomez, C., Nalls, M.A., Nyholt, D.R., Palmer, C.D., Pasko, D., Pechlivanis, S., Prokopenko, I., Ried, J.S., Ripke, S., Shungin, D., Stancakova, A., Strawbridge, R.J., Sung, Y.J., Tanaka, T., Teumer, A., Trompet, S., Laan, S.W. van der, Setten, J. van, Vliet-Ostaptchouk, J.V. Van, Wang, Z., Yengo, L., Zhang, W., Afzal, U., Arnlov, J., Arscott, G.M., Bandinelli, S., Barrett, A., Bellis, C., Bennett, A.J., Berne, C., Bluher, M., Bolton, J.L., Bottcher, Y., Boyd, H.A., Bruinenberg, M., Buckley, B.M., Buyske, S., Caspersen, I.H., Chines, P.S., Clarke, R., Claudi-Boehm, S., Cooper, M., Daw, E.W., Jong, P.A. de, Deelen, J., Delgado, G., Vermeulen, S., Kiemeney, L.A., and et al.

Abstract

Item does not contain fulltext, 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 approximately 2,000, approximately 3,700 and approximately 9,500 SNPs explained approximately 21%, approximately 24% and approximately 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/beta-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.

Published
2014

13. Replicability and Robustness of Genome-Wide-Association Studies for Behavioral Traits

Author

Rietveld, C.A. (Niels), Conley, D. (Dalton), Eriksson, N. (Nicholas), Esko, T. (Tõnu), Medland, S.E. (Sarah), Vinkhuyzen, A.A.E. (Anna A.), Yang, J. (Joanna), Boardman, J.D. (Jason D.), Chabris, C.F. (Christopher F.), Dawes, C.T. (Christopher T.), Domingue, B.W. (Benjamin W.), Hinds, D.A. (David A.), Johannesson, M. (Magnus), Kiefer, A.K. (Amy K.), Laibson, D. (David), Magnusson, P.K. (Patrik), Mountain, J.L. (Joanna L.), Oskarsson, S. (Sven), Rostapshova, O. (Olga), Teumer, A. (Alexander), Tung, J.Y. (Joyce Y.), Visscher, P.M. (Peter), Benjamin, D.J. (Daniel J.), Cesarini, D. (David), Koellinger, Ph.D. (Philipp), Rietveld, C.A. (Niels), Conley, D. (Dalton), Eriksson, N. (Nicholas), Esko, T. (Tõnu), Medland, S.E. (Sarah), Vinkhuyzen, A.A.E. (Anna A.), Yang, J. (Joanna), Boardman, J.D. (Jason D.), Chabris, C.F. (Christopher F.), Dawes, C.T. (Christopher T.), Domingue, B.W. (Benjamin W.), Hinds, D.A. (David A.), Johannesson, M. (Magnus), Kiefer, A.K. (Amy K.), Laibson, D. (David), Magnusson, P.K. (Patrik), Mountain, J.L. (Joanna L.), Oskarsson, S. (Sven), Rostapshova, O. (Olga), Teumer, A. (Alexander), Tung, J.Y. (Joyce Y.), Visscher, P.M. (Peter), Benjamin, D.J. (Daniel J.), Cesarini, D. (David), and Koellinger, Ph.D. (Philipp)

Abstract

A recent genome-wide-association study of educational attainment identified three single-nucleotide polymorphisms (SNPs) whose associations, despite their small effect sizes (each R2 ≈ 0.02%), reached genome-wide significance (p < 5 × 10−8) in a large discovery sample and were replicated in an independent sample (p <.05). The study also reported associations between educational attainment and indices of SNPs called “polygenic scores.” In three studies, we evaluated the robustness of these findings. Study 1 showed that the associations with all three SNPs were replicated in another large (N = 34,428) independent sample. We also found that the scores remained predictive (R2 ≈ 2%) in regressions with stringent controls for stratification (Study 2) and in new within-family analyses (Study 3). Our results show that large and therefore well-powered genome-wide-association studies can identify replicable genetic associations with behavioral traits. The small effect sizes of individual SNPs are likely to be a major contributing factor explaining the striking contrast between our results and the disappointing replication record of most candidate-gene studies.

Published
2014
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14. Common genetic variants associated with cognitive performance identified using the proxy-phenotype method

Author

Rietveld, C.A. (Niels), Esko, T. (Tõnu), Davies, G. (Gail), Pers, T.H. (Tune), Turley, P. (Patrick), Benyamin, B. (Beben), Chabris, C.F. (Christopher F.), Emilsson, V. (Valur), Johnson, A.D. (Andrew), Lee, J.J. (James J.), Leeuw, C. (Christiaan) de, Marioni, R.E. (Riccardo), Medland, S.E. (Sarah), Miller, M. (Mike), Rostapshova, O. (Olga), Lee, S.J. (Sven) van der, Vinkhuyzen, A.A.E. (Anna A.), Amin, N. (Najaf), Conley, D. (Dalton), Derringer, J., Duijn, C.M. (Cornelia) van, Fehrmann, R.S.N. (Rudolf), Franke, L. (Lude), Glaeser, E.L. (Edward L.), Hansell, N.K. (Narelle), Hayward, C. (Caroline), Iacono, W.G. (William), Ibrahim-Verbaas, C.A. (Carla), Jaddoe, V.W.V. (Vincent), Karjalainen, J. (Juha), Laibson, D. (David), Lichtenstein, P. (Paul), Liewald, D.C.M. (David), Magnusson, P.K. (Patrik), Martin, N.G. (Nicholas), McGue, M. (Matt), Mcmahon, G. (George), Pedersen, N.L. (Nancy), Pinker, S. (Steven), Porteous, D.J. (David J.), Posthuma, D. (Danielle), Rivadeneira Ramirez, F. (Fernando), Smithk, B.H. (Blair H.), Starr, J.M. (John), Tiemeier, H.W. (Henning), Timpsonm, N.J. (Nicholas J.), Trzaskowskin, M. (Maciej), Uitterlinden, A.G. (André), Verhulst, F.C. (Frank), Ward, M.E. (Mary), Wright, M.J. (Margaret), Smith, A.V. (Davey), Deary, I.J. (Ian), Johannesson, M. (Magnus), Plomin, R. (Robert), Visscher, P.M. (Peter), Benjamin, D.J. (Daniel J.), Cesarini, D. (David), Koellinger, Ph.D. (Philipp), Rietveld, C.A. (Niels), Esko, T. (Tõnu), Davies, G. (Gail), Pers, T.H. (Tune), Turley, P. (Patrick), Benyamin, B. (Beben), Chabris, C.F. (Christopher F.), Emilsson, V. (Valur), Johnson, A.D. (Andrew), Lee, J.J. (James J.), Leeuw, C. (Christiaan) de, Marioni, R.E. (Riccardo), Medland, S.E. (Sarah), Miller, M. (Mike), Rostapshova, O. (Olga), Lee, S.J. (Sven) van der, Vinkhuyzen, A.A.E. (Anna A.), Amin, N. (Najaf), Conley, D. (Dalton), Derringer, J., Duijn, C.M. (Cornelia) van, Fehrmann, R.S.N. (Rudolf), Franke, L. (Lude), Glaeser, E.L. (Edward L.), Hansell, N.K. (Narelle), Hayward, C. (Caroline), Iacono, W.G. (William), Ibrahim-Verbaas, C.A. (Carla), Jaddoe, V.W.V. (Vincent), Karjalainen, J. (Juha), Laibson, D. (David), Lichtenstein, P. (Paul), Liewald, D.C.M. (David), Magnusson, P.K. (Patrik), Martin, N.G. (Nicholas), McGue, M. (Matt), Mcmahon, G. (George), Pedersen, N.L. (Nancy), Pinker, S. (Steven), Porteous, D.J. (David J.), Posthuma, D. (Danielle), Rivadeneira Ramirez, F. (Fernando), Smithk, B.H. (Blair H.), Starr, J.M. (John), Tiemeier, H.W. (Henning), Timpsonm, N.J. (Nicholas J.), Trzaskowskin, M. (Maciej), Uitterlinden, A.G. (André), Verhulst, F.C. (Frank), Ward, M.E. (Mary), Wright, M.J. (Margaret), Smith, A.V. (Davey), Deary, I.J. (Ian), Johannesson, M. (Magnus), Plomin, R. (Robert), Visscher, P.M. (Peter), Benjamin, D.J. (Daniel J.), Cesarini, D. (David), and Koellinger, Ph.D. (Philipp)

Abstract

We identify common genetic variants associated with cognitive performance using a two-stage approach, which we call the proxyphenotype method. First, we conduct a genome-wide association study of educational attainment in a large sample (n = 106,736), which produces a set of 69 education-associated SNPs. Second, using independent samples (n = 24,189), we measure the association of these education-associated SNPs with cognitive performance. Three SNPs (rs1487441, rs7923609, and rs2721173) are significantly associated with cognitive performance after correction for multiple hypothesis testing. In an independent sample of older Americans (n = 8,652), we also show that a polygenic score derived from the education-associated SNPs is associated with memory and absence of dementia. Convergent evidence from a set of bioinformatics analyses implicates four specific genes (KNCMA1, NRXN1, POU2F3, and SCRT). All of these genes are associated with a particular neurotransmitter pathway involved in synaptic plasticity, the main cellular mechanism for learning and memory.

Published
2014
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15. Genetic influences are virtually absent for trust

Author

Lange, P.A.M. (Paul) van, Vinkhuyzen, A.A.E. (Anna A.), Posthuma, D. (Danielle), Lange, P.A.M. (Paul) van, Vinkhuyzen, A.A.E. (Anna A.), and Posthuma, D. (Danielle)

Abstract

Over the past decades, numerous twin studies have revealed moderate to high heritability estimates for individual differences in a wide range of human traits, including cognitive ability, psychiatric disorders, and personality traits. Even factors that are generally believed to be environmental in nature have been shown to be under genetic control, albeit modest. Is such heritability also present in social traits that are conceptualized as causes and consequences of social interactions or in other ways strongly shaped by behavior of other people? Here we examine a population-based sample of 1,012 twins and relatives. We show that the genetic influence on generalized trust in other people (trust-in-others: h2 = 5%, ns), and beliefs regarding other people's trust in the self (trust-in-self: h2 = 13%, ns), is virtually absent. As test-retest reliability for both scales were found to be moderate or high (r = .76 and r = .53, respectively) in an independent sample, we conclude that all variance in trust is likely to be accounted for by non-shared environmental influences. We show that, relative to cognitive abilities, psychiatric disorders, and classic personality variables, genetic influences are smaller for trust, and propose that experiences with or observations of the behavior of other people shape trust more strongly than other traits.

Published
2014
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16. The genetic aetiology of cannabis use initiation: A meta-analysis of genome-wide association studies and a SNP-based heritability estimation

Author

Verweij, K.J.H., Vinkhuyzen, A.A.E., Benyamin, B., Lynskey, M.T., Quaye, L., Agrawal, A., Gordon, S.D., Montgomery, G.W., Madden, P.A.F., Heath, A.C., Spector, T.D., Martin, N.G., Medland, S.E., Verweij, K.J.H., Vinkhuyzen, A.A.E., Benyamin, B., Lynskey, M.T., Quaye, L., Agrawal, A., Gordon, S.D., Montgomery, G.W., Madden, P.A.F., Heath, A.C., Spector, T.D., Martin, N.G., and Medland, S.E.

Abstract

Item does not contain fulltext, While initiation of cannabis use is around 40% heritable, not much is known about the underlying genetic aetiology. Here, we meta-analysed two genome-wide association studies of initiation of cannabis use with >10000 individuals. None of the genetic variants reached genome-wide significance. We also performed a gene-based association test, which also revealed no significant effects of individual genes. Finally, we estimated that only approximately 6% of the variation in cannabis initiation is due to common genetic variants. Future genetic studies using larger sample sizes and different methodologies (including sequencing) might provide more insight in the complex genetic aetiology of cannabis use.

Published
2013

17. Genome-wide association uncovers shared genetic effects among personality traits and mood states.

Author

Luciano, M., Huffman, J.E., Arias Vasquez, A., Vinkhuyzen, A.A.E., Middeldorp, C.M., Giegling, I., Payton, A., Davies, G., Zgaga, L., Janzing, J.G.E., Ke, X., Galesloot, T.E., Hartmann, A.M., Ollier, W., Tenesa, A., Hayward, C., Verhagen, M., Montgomery, G.W., Hottenga, J.J., Konte, B., Starr, J.M., Vitart, V., Vos, P.E., Madden, P.A.F., Willemsen, G., Konnerth, H., Horan, M.A., Porteous, D.J., Campbell, H., Vermeulen, S., Heath, A.C., Wright, A., Polasek, O., Kovacevic, S.B., Hastie, N.D., Franke, B., Boomsma, D.I., Martin, N.G., Rujescu, D., Wilson, J.F., Buitelaar, J.K., Pendleton, N., Rudan, I., Deary, I.J., Luciano, M., Huffman, J.E., Arias Vasquez, A., Vinkhuyzen, A.A.E., Middeldorp, C.M., Giegling, I., Payton, A., Davies, G., Zgaga, L., Janzing, J.G.E., Ke, X., Galesloot, T.E., Hartmann, A.M., Ollier, W., Tenesa, A., Hayward, C., Verhagen, M., Montgomery, G.W., Hottenga, J.J., Konte, B., Starr, J.M., Vitart, V., Vos, P.E., Madden, P.A.F., Willemsen, G., Konnerth, H., Horan, M.A., Porteous, D.J., Campbell, H., Vermeulen, S., Heath, A.C., Wright, A., Polasek, O., Kovacevic, S.B., Hastie, N.D., Franke, B., Boomsma, D.I., Martin, N.G., Rujescu, D., Wilson, J.F., Buitelaar, J.K., Pendleton, N., Rudan, I., and Deary, I.J.

Abstract

1 september 2012, Item does not contain fulltext, Measures of personality and psychological distress are correlated and exhibit genetic covariance. We conducted univariate genome-wide SNP ( approximately 2.5 million) and gene-based association analyses of these traits and examined the overlap in results across traits, including a prediction analysis of mood states using genetic polygenic scores for personality. Measures of neuroticism, extraversion, and symptoms of anxiety, depression, and general psychological distress were collected in eight European cohorts (n ranged 546-1,338; maximum total n = 6,268) whose mean age ranged from 55 to 79 years. Meta-analysis of the cohort results was performed, with follow-up associations of the top SNPs and genes investigated in independent cohorts (n = 527-6,032). Suggestive association (P = 8 x 10(-8) ) of rs1079196 in the FHIT gene was observed with symptoms of anxiety. Other notable associations (P < 6.09 x 10(-6) ) included SNPs in five genes for neuroticism (LCE3C, POLR3A, LMAN1L, ULK3, SCAMP2), KIAA0802 for extraversion, and NOS1 for general psychological distress. An association between symptoms of depression and rs7582472 (near to MGAT5 and NCKAP5) was replicated in two independent samples, but other replication findings were less consistent. Gene-based tests identified a significant locus on chromosome 15 (spanning five genes) associated with neuroticism which replicated (P < 0.05) in an independent cohort. Support for common genetic effects among personality and mood (particularly neuroticism and depressive symptoms) was found in terms of SNP association overlap and polygenic score prediction. The variance explained by individual SNPs was very small (up to 1%) confirming that there are no moderate/large effects of common SNPs on personality and related traits. (c) 2012 Wiley Periodicals, Inc.

Published
2012

18. The Construction and Validation of an Abridged Version of the Autism-Spectrum Quotient (AQ-Short)

Author

Hoekstra, R.A., Vinkhuyzen, A.A.E., Wheelwright, S., Bartels, M., Boomsma, D.I., Baron-Cohen, S., Posthuma, D., van der Sluis, S., Hoekstra, R.A., Vinkhuyzen, A.A.E., Wheelwright, S., Bartels, M., Boomsma, D.I., Baron-Cohen, S., Posthuma, D., and van der Sluis, S.

Abstract

This study reports on the development and validation of an abridged version of the 50-item Autism-Spectrum Quotient (AQ), a self-report measure of autistic traits. We aimed to reduce the number of items whilst retaining high validity and a meaningful factor structure. The item reduction procedure was performed on data from 1,263 Dutch students and general population adults. The resulting 28-item AQ-Short was subsequently validated in 3 independent samples, both clinical and controls, from the Netherlands and the UK. The AQ-Short comprises two higher-order factors assessing 'social behavioral difficulties' and 'a fascination for numbers/patterns'. The clear factor structure of the AQ-Short and its high sensitivity and specificity make the AQ-Short a useful alternative to the full 50-item version. © 2010 The Author(s).

Published
2011
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19. The heritability of aptitude and exceptional talent across different domains in adolescents and young adults

Author

Vinkhuyzen, A.A.E., van der Sluis, S., Posthuma, D., Boomsma, D.I., Vinkhuyzen, A.A.E., van der Sluis, S., Posthuma, D., and Boomsma, D.I.

Abstract

The origin of individual differences in aptitude, defined as a domain-specific skill within the normal ability range, and talent, defined as a domain specific skill of exceptional quality, is under debate. The nature of the variation in aptitudes and exceptional talents across different domains was investigated in a population based twin sample. Self-report data from 1,685 twin pairs (12-24 years) were analyzed for Music, Arts, Writing, Language, Chess, Mathematics, Sports, Memory, and Knowledge. The influence of shared environment was small for both aptitude and talent. Additive and non-additive genetic effects explained the major part of the substantial familial clustering in the aptitude measures with heritability estimates ranging between .32 and .71. Heritability estimates for talents were higher and ranged between .50 and .92. In general, the genetic architecture for aptitude and talent was similar in men and women. Genetic factors contribute to a large extent to variation in aptitude and talent across different domains of intellectual, creative, and sports abilities.

Published
2009
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20. Defining the role of common variation in the genomic and biological architecture of adult human height

Author

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, Aa, 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, As, 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 LC, 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, Pk, 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 FV, 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, Sj, 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, 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Price A.L., Lettre G., Loos R.J.F., Weedon M.N., Ingelsson E., O'Connell J.R., Abecasis G.R., Chasman D.I., Goddard M.E., Visscher P.M., Hirschhorn J.N., and Frayling T.M.

Subjects
Netherlands Twin Register (NTR), BIO/12 - BIOCHIMICA CLINICA E BIOLOGIA MOLECOLARE CLINICA, Electronic Medical Records and Genomics (eMEMERGEGE) Consortium, Medizin, Genome-wide association study, Adult, Analysis of Variance, Body Height/genetics, European Continental Ancestry Group/genetics, Genetic Variation/genetics, Genetics, Population, Genome-Wide Association Study/methods, Humans, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide/genetics, heritability, 0302 clinical medicine, Genome-wide, SNPS, snps, Genetics & Heredity, ddc:616, Genetics, Medical And Health Sciences, 0303 health sciences, education.field_of_study, variants, GENETIC-VARIATION, Biological Sciences, Urological cancers Radboud Institute for Health Sciences [Radboudumc 15], body height, genetic-variation, Life Sciences & Biomedicine, Single Nucleotide/genetics, Human, European Continental Ancestry Group, Population, Single-nucleotide polymorphism, Biology, Polymorphism, Single Nucleotide, Article, White People, NO, complex traits, 03 medical and health sciences, Genetic variation, heritability, adult, height, Polymorphism, Human height, PAGEGE Consortium, education, Gene, VLAG, 030304 developmental biology, Global Nutrition, Wereldvoeding, genome-wide association study, Science & Technology, Whites, Oligonucleotide Array Sequence Analysi, MUTATIONS, COMPLEX TRAITS, ta1184, Klinisk medicin, population genetics, Genetic Variation, Heritability, ta3121, mutations, Genetic architecture, Body Height, genetic variation, MIGen Consortium, Inflammatory diseases Radboud Institute for Health Sciences [Radboudumc 5], Clinical Medicine, 030217 neurology & neurosurgery, height, LifeLines Cohort Study, Developmental Biology, Genome-Wide Association Study
Abstract

Item does not contain fulltext 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 approximately 2,000, approximately 3,700 and approximately 9,500 SNPs explained approximately 21%, approximately 24% and approximately 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/beta-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.

Published
2014
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