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5 results on '"GENERATION SCOTLAND, Consortium"'

1. Novel approach identifies SNPs in SLC2A10 and KCNK9 with evidence for parent-of-origin effect on body mass index.

Author

Clive J Hoggart, Giulia Venturini, Massimo Mangino, Felicia Gomez, Giulia Ascari, Jing Hua Zhao, Alexander Teumer, Thomas W Winkler, Natalia Tšernikova, Jian'an Luan, Evelin Mihailov, Georg B Ehret, Weihua Zhang, David Lamparter, Tõnu Esko, Aurelien Macé, Sina Rüeger, Pierre-Yves Bochud, Matteo Barcella, Yves Dauvilliers, Beben Benyamin, David M Evans, Caroline Hayward, Mary F Lopez, Lude Franke, Alessia Russo, Iris M Heid, Erika Salvi, Sailaja Vendantam, Dan E Arking, Eric Boerwinkle, John C Chambers, Giovanni Fiorito, Harald Grallert, Simonetta Guarrera, Georg Homuth, Jennifer E Huffman, David Porteous, Generation Scotland Consortium, LifeLines Cohort study, GIANT Consortium, Darius Moradpour, Alex Iranzo, Johannes Hebebrand, John P Kemp, Gert J Lammers, Vincent Aubert, Markus H Heim, Nicholas G Martin, Grant W Montgomery, Rosa Peraita-Adrados, Joan Santamaria, Francesco Negro, Carsten O Schmidt, Robert A Scott, Tim D Spector, Konstantin Strauch, Henry Völzke, Nicholas J Wareham, Wei Yuan, Jordana T Bell, Aravinda Chakravarti, Jaspal S Kooner, Annette Peters, Giuseppe Matullo, Henri Wallaschofski, John B Whitfield, Fred Paccaud, Peter Vollenweider, Sven Bergmann, Jacques S Beckmann, Mehdi Tafti, Nicholas D Hastie, Daniele Cusi, Murielle Bochud, Timothy M Frayling, Andres Metspalu, Marjo-Riitta Jarvelin, André Scherag, George Davey Smith, Ingrid B Borecki, Valentin Rousson, Joel N Hirschhorn, Carlo Rivolta, Ruth J F Loos, and Zoltán Kutalik

Subjects
Genetics, QH426-470
Abstract

The phenotypic effect of some single nucleotide polymorphisms (SNPs) depends on their parental origin. We present a novel approach to detect parent-of-origin effects (POEs) in genome-wide genotype data of unrelated individuals. The method exploits increased phenotypic variance in the heterozygous genotype group relative to the homozygous groups. We applied the method to >56,000 unrelated individuals to search for POEs influencing body mass index (BMI). Six lead SNPs were carried forward for replication in five family-based studies (of ∼4,000 trios). Two SNPs replicated: the paternal rs2471083-C allele (located near the imprinted KCNK9 gene) and the paternal rs3091869-T allele (located near the SLC2A10 gene) increased BMI equally (beta = 0.11 (SD), P

Published
2014
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2. Corrigendum: Rare coding variants and X-linked loci associated with age at menarche

Author

Lunetta, K.L., Day, F.R., Sulem, P., Ruth, K.S., Tung, J.Y., Hinds, D.A., Esko, T., Elks, C.E., Altmaier, E., He, C., Huffman, J.E., Mihailov, E., Porcu, E., Robino, A., Rose, L.M., Schick, U.M., Stolk, L., Teumer, A., Thompson, D.J., Traglia, M., Wang, C.A., Yerges-Armstrong, L.M., Antoniou, A.C., Barbieri, C., Coviello, A.D., Cucca, F., Demerath, E.W., Dunning, A.M., Gandin, I., Grove, M.L., Gudbjartsson, D.F., Hocking, L.J., Hofman, A., Huang, J., Jackson, R.D., Karasik, D., Kriebel, J., Lange, E.M., Lange, L.A., Langenberg, C., Li, X., Luan, J., Mägi, R., Morrison, A.C., Padmanabhan, S., Pirie, A., Polasek, O., Porteous, D.J., Reiner, A.P., Rivadeneira, F., Rudan, I., Sala, C.F., Schlessinger, D., Scott, R.A., Stöckl, D., Visser, J.A., Völker, U., Vozzi, D., Wilson, J.G., Zygmunt, M., EPIC-Interact Consortium (), Generation Scotland Consortium (), Boerwinkle, E., Buring, J.E., Crisponi, L., Easton, D.F., Hayward, C., Hu, F.B., Liu, S., Metspalu, A., Pennell, C.E., Ridker, P.M., Strauch, K., Streeten, E.A., Toniolo, D., Uitterlinden, A.G., Ulivi, S., Völzke, H., Wareham, N.J., Wellons, M., Franceschini, N., Chasman, D.I., Thorsteinsdottir, U., Murray, A., Stefansson, K., Murabito, J.M., Ong, K.K., and Perry, J.R.

Subjects
Adult, Adolescent, Genotype, Mutation, Missense, Immunoglobulins, Cell Cycle Proteins, Penetrance, AMP-Activated Protein Kinases, Autoantigens, White People, Young Adult, Gene Frequency, Genes, X-Linked, Humans, Aged, Menarche, Chromosomes, Human, X, Hypogonadism, Fatty Acids, Age Factors, Genetic Variation, Membrane Proteins, Proteins, RNA-Binding Proteins, Receptors, Neurokinin-3, Middle Aged, Corrigenda, Amides, Phenotype, Codon, Nonsense, Female, RNA Interference, Laminin, Energy Metabolism, Signal Transduction
Abstract

More than 100 loci have been identified for age at menarche by genome-wide association studies; however, collectively these explain only ∼3% of the trait variance. Here we test two overlooked sources of variation in 192,974 European ancestry women: low-frequency protein-coding variants and X-chromosome variants. Five missense/nonsense variants (in ALMS1/LAMB2/TNRC6A/TACR3/PRKAG1) are associated with age at menarche (minor allele frequencies 0.08-4.6%; effect sizes 0.08-1.25 years per allele; P5 × 10(-8)). In addition, we identify common X-chromosome loci at IGSF1 (rs762080, P=9.4 × 10(-13)) and FAAH2 (rs5914101, P=4.9 × 10(-10)). Highlighted genes implicate cellular energy homeostasis, post-transcriptional gene silencing and fatty-acid amide signalling. A frequently reported mutation in TACR3 for idiopathic hypogonatrophic hypogonadism (p.W275X) is associated with 1.25-year-later menarche (P=2.8 × 10(-11)), illustrating the utility of population studies to estimate the penetrance of reportedly pathogenic mutations. Collectively, these novel variants explain ∼0.5% variance, indicating that these overlooked sources of variation do not substantially explain the 'missing heritability' of this complex trait.

Published
2015

3. Novel Approach Identifies SNPs in SLC2A10 and KCNK9 with Evidence for Parent-of-Origin Effect on Body Mass Index.

Author

Generation Scotland Consortium, LifeLines Cohort study, GIANT Consortium, Hoggart, C.J., Venturini, G., Mangino, M., Gomez, F., Ascari, G., Zhao, J.H., Teumer, A., Winkler, T.W., Ternikova, N., Luan, J., Mihailov, E., Ehret, G.B., Zhang, W., Lamparter, D., Esko, T., Macé, A., Rüeger, S., Bochud, P.Y., Barcella, M., Dauvilliers, Y., Benyamin, B., Evans, D.M., Hayward, C., Lopez, M.F., Franke, L., Russo, A., Heid, I.M., Salvi, E., Vendantam, S., Arking, D.E., Boerwinkle, E., Chambers, J.C., Fiorito, G., Grallert, H., Guarrera, S., Homuth, G., Huffman, J.E., Porteous, D., Moradpour, D., Iranzo, A., Hebebrand, J., Kemp, J.P., Lammers, G.J., Aubert, V., Heim, M.H., Martin, N.G., Montgomery, G.W., Peraita-Adrados, R., Santamaria, J., Negro, F., Schmidt, C.O., Scott, R.A., Spector, T.D., Strauch, K., Völzke, H., Wareham, N.J., Yuan, W., Bell, J.T., Chakravarti, A., Kooner, J.S., Peters, A., Matullo, G., Wallaschofski, H., Whitfield, J.B., Paccaud, F., Vollenweider, P., Bergmann, S., Beckmann, J.S., Tafti, M., Hastie, N.D., Cusi, D., Bochud, M., Frayling, T.M., Metspalu, A., Jarvelin, M.R., Scherag, A., Smith, G.D., Borecki, I.B., Rousson, V., Hirschhorn, J.N., Rivolta, C., Loos, R.J., Kutalik, Z., Generation Scotland Consortium, LifeLines Cohort study, GIANT Consortium, Hoggart, C.J., Venturini, G., Mangino, M., Gomez, F., Ascari, G., Zhao, J.H., Teumer, A., Winkler, T.W., Ternikova, N., Luan, J., Mihailov, E., Ehret, G.B., Zhang, W., Lamparter, D., Esko, T., Macé, A., Rüeger, S., Bochud, P.Y., Barcella, M., Dauvilliers, Y., Benyamin, B., Evans, D.M., Hayward, C., Lopez, M.F., Franke, L., Russo, A., Heid, I.M., Salvi, E., Vendantam, S., Arking, D.E., Boerwinkle, E., Chambers, J.C., Fiorito, G., Grallert, H., Guarrera, S., Homuth, G., Huffman, J.E., Porteous, D., Moradpour, D., Iranzo, A., Hebebrand, J., Kemp, J.P., Lammers, G.J., Aubert, V., Heim, M.H., Martin, N.G., Montgomery, G.W., Peraita-Adrados, R., Santamaria, J., Negro, F., Schmidt, C.O., Scott, R.A., Spector, T.D., Strauch, K., Völzke, H., Wareham, N.J., Yuan, W., Bell, J.T., Chakravarti, A., Kooner, J.S., Peters, A., Matullo, G., Wallaschofski, H., Whitfield, J.B., Paccaud, F., Vollenweider, P., Bergmann, S., Beckmann, J.S., Tafti, M., Hastie, N.D., Cusi, D., Bochud, M., Frayling, T.M., Metspalu, A., Jarvelin, M.R., Scherag, A., Smith, G.D., Borecki, I.B., Rousson, V., Hirschhorn, J.N., Rivolta, C., Loos, R.J., and Kutalik, Z.

Abstract

The phenotypic effect of some single nucleotide polymorphisms (SNPs) depends on their parental origin. We present a novel approach to detect parent-of-origin effects (POEs) in genome-wide genotype data of unrelated individuals. The method exploits increased phenotypic variance in the heterozygous genotype group relative to the homozygous groups. We applied the method to >56,000 unrelated individuals to search for POEs influencing body mass index (BMI). Six lead SNPs were carried forward for replication in five family-based studies (of ∼4,000 trios). Two SNPs replicated: the paternal rs2471083-C allele (located near the imprinted KCNK9 gene) and the paternal rs3091869-T allele (located near the SLC2A10 gene) increased BMI equally (beta = 0.11 (SD), P<0.0027) compared to the respective maternal alleles. Real-time PCR experiments of lymphoblastoid cell lines from the CEPH families showed that expression of both genes was dependent on parental origin of the SNPs alleles (P<0.01). Our scheme opens new opportunities to exploit GWAS data of unrelated individuals to identify POEs and demonstrates that they play an important role in adult obesity.

Published
2014

4. Novel Approach Identifies SNPs in SLC2A10 and KCNK9 with Evidence for Parent-of-Origin Effect on Body Mass Index

Author

University of Helsinki, Haartman Institute, Hoggart, Clive J., Venturini, Giulia, Mangino, Massimo, Gomez, Felicia, Ascari, Giulia, Zhao, Jing Hua, Teumer, Alexander, Winkler, Thomas W., Tsernikova, Natalia, Luan, Jian'an, Mihailov, Evelin, Ehret, Georg B., Zhang, Weihua, Lamparter, David, Esko, Tonu, Mace, Aurelien, Rueeger, Sina, Bochud, Pierre-Yves, Barcella, Matteo, Dauvilliers, Yves, Benyamin, Beben, Evans, David M., Hayward, Caroline, Lopez, Mary F., Franke, Lude, Russo, Alessia, Heid, Iris M., Salvi, Erika, Vendantam, Sailaja, Arking, Dan E., Boerwinkle, Eric, Chambers, John C., Fiorito, Giovanni, Grallert, Harald, Guarrera, Simonetta, Homuth, Georg, Huffman, Jennifer E., Porteous, David, Moradpour, Darius, Iranzo, Alex, Hebebrand, Johannes, Kemp, John P., Lammers, Gert J., Aubert, Vincent, Heim, Markus H., Martin, Nicholas G., Montgomery, Grant W., Peraita-Adrados, Rosa, Santamaria, Joan, Negro, Francesco, Schmidt, Carsten O., Scott, Robert A., Spector, Tim D., Strauch, Konstantin, Voelzke, Henry, Wareham, Nicholas J., Yuan, Wei, Bell, Jordana T., Chakravarti, Aravinda, Kooner, Jaspal S., Peters, Annette, Matullo, Giuseppe, Wallaschofski, Henri, Whitfield, John B., Paccaud, Fred, Vollenweider, Peter, Bergmann, Sven, Beckmann, Jacques S., Tafti, Mehdi, Hastie, Nicholas D., Cusi, Daniele, Bochud, Murielle, Frayling, Timothy M., Metspalu, Andres, Jarvelin, Marjo-Riitta, Scherag, Andre, Smith, George Davey, Borecki, Ingrid B., Rousson, Valentin, Hirschhorn, Joel N., Rivolta, Carlo, Loos, Ruth J. F., Kutalik, Zoltan, Generation Scotland Consortium, LifeLines Cohort Study, GIANT Consortium, Lokki, Marja-Liisa, University of Helsinki, Haartman Institute, Hoggart, Clive J., Venturini, Giulia, Mangino, Massimo, Gomez, Felicia, Ascari, Giulia, Zhao, Jing Hua, Teumer, Alexander, Winkler, Thomas W., Tsernikova, Natalia, Luan, Jian'an, Mihailov, Evelin, Ehret, Georg B., Zhang, Weihua, Lamparter, David, Esko, Tonu, Mace, Aurelien, Rueeger, Sina, Bochud, Pierre-Yves, Barcella, Matteo, Dauvilliers, Yves, Benyamin, Beben, Evans, David M., Hayward, Caroline, Lopez, Mary F., Franke, Lude, Russo, Alessia, Heid, Iris M., Salvi, Erika, Vendantam, Sailaja, Arking, Dan E., Boerwinkle, Eric, Chambers, John C., Fiorito, Giovanni, Grallert, Harald, Guarrera, Simonetta, Homuth, Georg, Huffman, Jennifer E., Porteous, David, Moradpour, Darius, Iranzo, Alex, Hebebrand, Johannes, Kemp, John P., Lammers, Gert J., Aubert, Vincent, Heim, Markus H., Martin, Nicholas G., Montgomery, Grant W., Peraita-Adrados, Rosa, Santamaria, Joan, Negro, Francesco, Schmidt, Carsten O., Scott, Robert A., Spector, Tim D., Strauch, Konstantin, Voelzke, Henry, Wareham, Nicholas J., Yuan, Wei, Bell, Jordana T., Chakravarti, Aravinda, Kooner, Jaspal S., Peters, Annette, Matullo, Giuseppe, Wallaschofski, Henri, Whitfield, John B., Paccaud, Fred, Vollenweider, Peter, Bergmann, Sven, Beckmann, Jacques S., Tafti, Mehdi, Hastie, Nicholas D., Cusi, Daniele, Bochud, Murielle, Frayling, Timothy M., Metspalu, Andres, Jarvelin, Marjo-Riitta, Scherag, Andre, Smith, George Davey, Borecki, Ingrid B., Rousson, Valentin, Hirschhorn, Joel N., Rivolta, Carlo, Loos, Ruth J. F., Kutalik, Zoltan, Generation Scotland Consortium, LifeLines Cohort Study, GIANT Consortium, and Lokki, Marja-Liisa

Published
2014

5. Novel approach identifies SNPs in SLC2A10 and KCNK9 with evidence for parent-of-origin effect on body mass index.

Author

Visscher, PM, Hoggart, CJ, Venturini, G, Mangino, M, Gomez, F, Ascari, G, Zhao, JH, Teumer, A, Winkler, TW, Tšernikova, N, Luan, J, Mihailov, E, Ehret, GB, Zhang, W, Lamparter, D, Esko, T, Macé, A, Rüeger, S, Bochud, P-Y, Barcella, M, Dauvilliers, Y, Benyamin, B, Evans, DM, Hayward, C, Lopez, MF, Franke, L, Russo, A, Heid, IM, Salvi, E, Vendantam, S, Arking, DE, Boerwinkle, E, Chambers, JC, Fiorito, G, Grallert, H, Guarrera, S, Homuth, G, Huffman, JE, Porteous, D, Generation Scotland Consortium, LifeLines Cohort study, GIANT Consortium, Moradpour, D, Iranzo, A, Hebebrand, J, Kemp, JP, Lammers, GJ, Aubert, V, Heim, MH, Martin, NG, Montgomery, GW, Peraita-Adrados, R, Santamaria, J, Negro, F, Schmidt, CO, Scott, RA, Spector, TD, Strauch, K, Völzke, H, Wareham, NJ, Yuan, W, Bell, JT, Chakravarti, A, Kooner, JS, Peters, A, Matullo, G, Wallaschofski, H, Whitfield, JB, Paccaud, F, Vollenweider, P, Bergmann, S, Beckmann, JS, Tafti, M, Hastie, ND, Cusi, D, Bochud, M, Frayling, TM, Metspalu, A, Jarvelin, M-R, Scherag, A, Smith, GD, Borecki, IB, Rousson, V, Hirschhorn, JN, Rivolta, C, Loos, RJF, Kutalik, Z, Visscher, PM, Hoggart, CJ, Venturini, G, Mangino, M, Gomez, F, Ascari, G, Zhao, JH, Teumer, A, Winkler, TW, Tšernikova, N, Luan, J, Mihailov, E, Ehret, GB, Zhang, W, Lamparter, D, Esko, T, Macé, A, Rüeger, S, Bochud, P-Y, Barcella, M, Dauvilliers, Y, Benyamin, B, Evans, DM, Hayward, C, Lopez, MF, Franke, L, Russo, A, Heid, IM, Salvi, E, Vendantam, S, Arking, DE, Boerwinkle, E, Chambers, JC, Fiorito, G, Grallert, H, Guarrera, S, Homuth, G, Huffman, JE, Porteous, D, Generation Scotland Consortium, LifeLines Cohort study, GIANT Consortium, Moradpour, D, Iranzo, A, Hebebrand, J, Kemp, JP, Lammers, GJ, Aubert, V, Heim, MH, Martin, NG, Montgomery, GW, Peraita-Adrados, R, Santamaria, J, Negro, F, Schmidt, CO, Scott, RA, Spector, TD, Strauch, K, Völzke, H, Wareham, NJ, Yuan, W, Bell, JT, Chakravarti, A, Kooner, JS, Peters, A, Matullo, G, Wallaschofski, H, Whitfield, JB, Paccaud, F, Vollenweider, P, Bergmann, S, Beckmann, JS, Tafti, M, Hastie, ND, Cusi, D, Bochud, M, Frayling, TM, Metspalu, A, Jarvelin, M-R, Scherag, A, Smith, GD, Borecki, IB, Rousson, V, Hirschhorn, JN, Rivolta, C, Loos, RJF, and Kutalik, Z

Abstract

The phenotypic effect of some single nucleotide polymorphisms (SNPs) depends on their parental origin. We present a novel approach to detect parent-of-origin effects (POEs) in genome-wide genotype data of unrelated individuals. The method exploits increased phenotypic variance in the heterozygous genotype group relative to the homozygous groups. We applied the method to >56,000 unrelated individuals to search for POEs influencing body mass index (BMI). Six lead SNPs were carried forward for replication in five family-based studies (of ∼4,000 trios). Two SNPs replicated: the paternal rs2471083-C allele (located near the imprinted KCNK9 gene) and the paternal rs3091869-T allele (located near the SLC2A10 gene) increased BMI equally (beta = 0.11 (SD), P<0.0027) compared to the respective maternal alleles. Real-time PCR experiments of lymphoblastoid cell lines from the CEPH families showed that expression of both genes was dependent on parental origin of the SNPs alleles (P<0.01). Our scheme opens new opportunities to exploit GWAS data of unrelated individuals to identify POEs and demonstrates that they play an important role in adult obesity.

Published
2014

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