Whole-genome sequencing coupled to imputation discovers genetic signals for anthropometric traits

Autor:	Graham R. S. Ritchie, Massimiliano Cocca, Anette Varbo, Nicholas J. Timpson, George Dedoussis, Michael Boehnke, Marjolein N. Kooijman, Beate St Pourcain, Yasin Memari, André G. Uitterlinden, Andrew A Crawford, Eleftheria Zeggini, Fernando Rivadeneira, Satu Männistö, Caroline L Relton, Yali Xue, Petr Danecek, Kalliope Panoutsopoulou, Albert Hofman, George Davey Smith, María Soler Artigas, Michela Traglia, Josine L. Min, Weihua Zhang, Janine F. Felix, Christopher J Hammond, Claudia Langenberg, Jie Huang, Brian R. Walker, Narinder Bansal, Nigel W. Rayner, Emanuele Di Angelantonio, Kerrin S. Small, Konstantinos Hatzikotoulas, Cecilia M. Lindgren, Alisa K. Manning, Shane A. McCarthy, Susan M. Ring, Marcus E. Kleber, Abhishek Nag, Oliver Stegle, Paul Burton, Oscar H. Franco, William R. Scott, Carolina Medina-Gomez, Valentina Iotchkova, John R. B. Perry, Alireza Moayyeri, Lavinia Paternoster, Marianne Benn, Markus Perola, Katerina Trajanoska, Inês Barroso, Audrey E. Hendricks, Cinzia Sala, Carlo Sidore, Celia M. T. Greenwood, Jeremy Schwartzentruber, Richard Durbin, Cristina Bombieri, Klaudia Walter, Wei-Yu Lin, Hashem A. Shihab, Gialuigi Zaza, Jaspal S. Kooner, Magdalena Zoledziewska, Angela Matchan, Adam S. Butterworth, Pekka Jousilahti, Julia Steinberg, Anne Tybjærg-Hansen, John P. Kemp, Daniel Suveges, Nicole Soranzo, Chris Finan, Veikko Salomaa, Ioanna Ntalla, Nicholas J. Wareham, Adam E. Locke, Vincent W. V. Jaddoe, Ioanna Tachmazidou, Daniela Toniolo, Scott Wilson, Antonella Mulas, Aliki-Eleni Farmaki, Lorraine Southam, Martin D. Tobin, Tom R. Gaunt, Zhongsheng Chen, Paolo Gasparini, Andrew P. Morris, Giovanni Gambaro, John C. Chambers, Børge G. Nordestgaard, Sarah Metrustry, Benjamin Lehne, Jian'an Luan, Giovanni Malerba, Robert A. Scott, Mark I. McCarthy, Michal Szpak, Francesco Cucca, Tim D. Spector
Přispěvatelé:	Epidemiology, Erasmus MC other, Pediatrics, Internal Medicine, University of Helsinki, Institute for Molecular Medicine Finland, Quantitative Genetics, Tachmazidou, Ioanna, Süveges, Dániel, Min, Josine L., Ritchie, Graham R. S., Steinberg, Julia, Walter, Klaudia, Iotchkova, Valentina, Schwartzentruber, Jeremy, Huang, Jie, Memari, Yasin, Mccarthy, Shane, Crawford, Andrew A., Bombieri, Cristina, Cocca, Massimiliano, Farmaki, Aliki-Eleni, Gaunt, Tom R., Jousilahti, Pekka, Kooijman, Marjolein N., Lehne, Benjamin, Malerba, Giovanni, Männistö, Satu, Matchan, Angela, Medina-Gomez, Carolina, Metrustry, Sarah J., Nag, Abhishek, Ntalla, Ioanna, Paternoster, Lavinia, Rayner, Nigel W., Sala, Cinzia, Scott, William R., Shihab, Hashem A., Southam, Lorraine, St Pourcain, Beate, Traglia, Michela, Trajanoska, Katerina, Zaza, Gialuigi, Zhang, Weihua, Artigas, María S., Bansal, Narinder, Benn, Marianne, Chen, Zhongsheng, Danecek, Petr, Lin, Wei-Yu, Locke, Adam, Luan, Jian'An, Manning, Alisa K., Mulas, Antonella, Sidore, Carlo, Tybjaerg-Hansen, Anne, Varbo, Anette, Zoledziewska, Magdalena, Finan, Chri, Hatzikotoulas, Konstantino, Hendricks, Audrey E., Kemp, John P., Moayyeri, Alireza, Panoutsopoulou, Kalliope, Szpak, Michal, Wilson, Scott G., Boehnke, Michael, Cucca, Francesco, Di Angelantonio, Emanuele, Langenberg, Claudia, Lindgren, Cecilia, Mccarthy, Mark I., Morris, Andrew P., Nordestgaard, Børge G., Scott, Robert A., Tobin, Martin D., Wareham, Nicholas J., Burton, Paul, Chambers, John C., Smith, George Davey, Dedoussis, George, Felix, Janine F., Franco, Oscar H., Gambaro, Giovanni, Gasparini, Paolo, Hammond, Christopher J., Hofman, Albert, Jaddoe, Vincent W. V., Kleber, Marcu, Kooner, Jaspal S., Perola, Marku, Relton, Caroline, Ring, Susan M., Rivadeneira, Fernando, Salomaa, Veikko, Spector, Timothy D., Stegle, Oliver, Toniolo, Daniela, Uitterlinden, André G., Barroso, Inê, Greenwood, Celia M. T., Perry, John R. B., Walker, Brian R., Butterworth, Adam S., Xue, Yali, Durbin, Richard, Small, Kerrin S., Soranzo, Nicole, Timpson, Nicholas J., Zeggini, Eleftheria, McCarthy, Shane [0000-0002-2715-4187], Bansal, Narinder [0000-0002-6925-1719], Luan, Jian'an [0000-0003-3137-6337], Di Angelantonio, Emanuele [0000-0001-8776-6719], Langenberg, Claudia [0000-0002-5017-7344], Wareham, Nicholas [0000-0003-1422-2993], Barroso, Ines [0000-0001-5800-4520], Perry, John [0000-0001-6483-3771], Butterworth, Adam [0000-0002-6915-9015], Soranzo, Nicole [0000-0003-1095-3852], Apollo - University of Cambridge Repository
Jazyk:	angličtina
Rok vydání:	2017
Předmět:	Male 0301 basic medicine DXA trait Lipodystrophy next-generation whole-genome sequencing GoT2D Consortium LOCI Genome-wide association study imputation anthropometry DXA traits genetic association study UK Biobank UK10K Body Height Cohort Studies DNA Methylation Databases Genetic Female Genetic Variation Humans Meta-Analysis as Topic Obesity Physical Chromosome Mapping Quantitative Trait Loci Sequence Analysis DNA Sex Characteristics Syndrome United Kingdom Anthropometry Genome Human Genome-Wide Association Study Genetics Genetics (clinical) Settore MED/03 - GENETICA MEDICA DISEASE HOMEOBOX GENE WIDE ASSOCIATION Genetics & Heredity Genome 1184 Genetics developmental biology physiology 11 Medical And Health Sciences RARE VARIANTS OBESITY LOW-FREQUENCY Life Sciences & Biomedicine Sequence Analysis arcOGEN Consortium Human ADULT HUMAN HEIGHT Understanding Society Scientific Group Computational biology TARGETED DISRUPTION Quantitative trait locus Biology Article Databases 03 medical and health sciences Genetic Genetic variation Journal Article UK10K Consortium Allele Genetic association Whole genome sequencing Science & Technology SpiroMeta Consortium DNA 06 Biological Sciences Sex Characteristic 030104 developmental biology Human genome 3111 Biomedicine Cohort Studie KNOCKOUT MICE Imputation (genetics)
Zdroj:	American Journal of Human Genetics, 100(6), 865-884. Cell Press Tachmazidou, I, Süveges, D, Min, J L, Ritchie, G R S, Steinberg, J, Walter, K, Iotchkova, V, Schwartzentruber, J, Huang, J, Memari, Y, McCarthy, S, Crawford, A A, Bombieri, C, Cocca, M, Farmaki, A-E, Gaunt, T R, Jousilahti, P, Kooijman, M N, Lehne, B, Malerba, G, Männistö, S, Matchan, A, Medina-Gomez, C, Metrustry, S J, Nag, A, Ntalla, I, Paternoster, L, Rayner, N W, Sala, C, Scott, W R, Shihab, H A, Southam, L, St Pourcain, B, Traglia, M, Trajanoska, K, Zaza, G, Zhang, W, Artigas, M S, Bansal, N, Benn, M, Chen, Z, Danecek, P, Lin, W-Y, Locke, A, Luan, J, Manning, A K, Mulas, A, Sidore, C, Tybjaerg-Hansen, A, Varbo, A, Zoledziewska, M, Finan, C, Hatzikotoulas, K, Hendricks, A E, Kemp, J P, Moayyeri, A, Panoutsopoulou, K, Szpak, M, Wilson, S G, Boehnke, M, Cucca, F, Di Angelantonio, E, Langenberg, C, Lindgren, C, McCarthy, M I, Morris, A P, Nordestgaard, B G, Scott, R A, Tobin, M D, Wareham, N J, Burton, P, Chambers, J C, Smith, G D, Dedoussis, G, Felix, J F, Franco, O H, Gambaro, G, Gasparini, P, Hammond, C J, Hofman, A, Jaddoe, V W V, Kleber, M, Kooner, J S, Perola, M, Relton, C, Ring, S M, Rivadeneira, F, Salomaa, V, Spector, T D, Stegle, O, Toniolo, D, Uitterlinden, A G, Barroso, I, Greenwood, C M T, Perry, J R B, Walker, B R, Butterworth, A S, Xue, Y, Durbin, R, Small, K S, Soranzo, N, Timpson, N J, Zeggini, E & Bansal, N 2017, ' Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits ', American Journal of Human Genetics, vol. 100, no. 6, pp. 865-884 . https://doi.org/10.1016/j.ajhg.2017.04.014 The American Journal of Human Genetics Tachmazidou, I, Süveges, D, Min, J L, Ritchie, G R S, Steinberg, J, Walter, K, Iotchkova, V, Schwartzentruber, J, Huang, J, Memari, Y, McCarthy, S, Crawford, A J, Bombieri, C, Cocca, M, Farmaki, A-E, Gaunt, T R, Jousilahti, P, Kooijman, M N, Lehne, B, Malerba, G, Männistö, S, Matchan, A, Medina-Gomez, C, Metrustry, S J, Nag, A, Ntalla, I, Paternoster, L, Rayner, N W, Sala, C, Scott, W R, Shihab, H A, Southam, L, St Pourcain, B, Traglia, M, Trajanoska, K, Zaza, G, Zhang, W, Artigas, M S, Bansal, N, Benn, M, Chen, Z, Danecek, P, Lin, W-Y, Locke, A E, Luan, J, Manning, A K, Mulas, A, Sidore, C, Tybjaerg-Hansen, A, Nordestgaard, B G & SpiroMeta Consortium 2017, ' Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits ', American Journal of Human Genetics, vol. 100, no. 6, pp. 865-884 . https://doi.org/10.1016/j.ajhg.2017.04.014 AMERICAN JOURNAL OF HUMAN GENETICS Tachmazidou, I, Süveges, D, Min, J L, Ritchie, G R S, Steinberg, J, Walter, K, Iotchkova, V, Schwartzentruber, J, Huang, J, Memari, Y, Mccarthy, S, Crawford, A A, Bombieri, C, Cocca, M, Farmaki, A, Gaunt, T R, Jousilahti, P, Kooijman, M N, Lehne, B, Malerba, G, Männistö, S, Matchan, A, Medina-gomez, C, Metrustry, S J, Nag, A, Ntalla, I, Paternoster, L, Rayner, N W, Sala, C, Scott, W R, Shihab, H A, Southam, L, St Pourcain, B, Traglia, M, Trajanoska, K, Zaza, G, Zhang, W, Artigas, M S, Bansal, N, Benn, M, Chen, Z, Danecek, P, Lin, W, Locke, A, Luan, J, Manning, A K, Mulas, A, Sidore, C, Tybjaerg-hansen, A, Varbo, A, Zoledziewska, M, Finan, C, Hatzikotoulas, K, Hendricks, A E, Kemp, J P, Moayyeri, A, Panoutsopoulou, K, Szpak, M, Wilson, S G, Boehnke, M, Cucca, F, Di Angelantonio, E, Langenberg, C, Lindgren, C, Mccarthy, M I, Morris, A P, Nordestgaard, B G, Scott, R A, Tobin, M D, Wareham, N J, Burton, P, Chambers, J C, Smith, G D, Dedoussis, G, Felix, J F, Franco, O H, Gambaro, G, Gasparini, P, Hammond, C J, Hofman, A, Jaddoe, V W V, Kleber, M, Kooner, J S, Perola, M, Relton, C, Ring, S M, Rivadeneira, F, Salomaa, V, Spector, T D, Stegle, O, Toniolo, D, Uitterlinden, A G, Barroso, I, Greenwood, C M T, Perry, J R B, Walker, B R, Butterworth, A S, Xue, Y, Durbin, R, Small, K S, Soranzo, N, Timpson, N J & Zeggini, E 2017, ' Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits ', American Journal of Human Genetics, vol. 100, no. 6, pp. 865-884 . https://doi.org/10.1016/j.ajhg.2017.04.014 Tachmazidou, I, Süveges, D, Min, J L, Ritchie, G R S, Steinberg, J, Walter, K, Iotchkova, V, Schwartzentruber, J, Huang, J, Memari, Y, McCarthy, S, Crawford, A A, Bombieri, C, Cocca, M, Farmaki, A-E, Gaunt, T R, Jousilahti, P, Kooijman, M N, Lehne, B, Malerba, G, Männistö, S, Matchan, A, Medina-Gomez, C, Metrustry, S J, Nag, A, Ntalla, I, Paternoster, L, Rayner, N W, Sala, C, Scott, W R, Shihab, H A, Southam, L, St Pourcain, B, Traglia, M, Trajanoska, K, Zaza, G, Zhang, W, Artigas, M S, Bansal, N, Benn, M, Chen, Z, Danecek, P, Lin, W-Y, Locke, A, Luan, J, Manning, A K, Mulas, A, Sidore, C, Tybjaerg-Hansen, A, Varbo, A, Zoledziewska, M, Finan, C, Hatzikotoulas, K, Hendricks, A E, Kemp, J P, Moayyeri, A, Panoutsopoulou, K, Szpak, M, Wilson, S G, Boehnke, M, Cucca, F, Di Angelantonio, E, Langenberg, C, Lindgren, C, McCarthy, M I, Morris, A P, Nordestgaard, B G, Scott, R A, Tobin, M D, Wareham, N J, Burton, P, Chambers, J C, Smith, G D, Dedoussis, G, Felix, J F, Franco, O H, Gambaro, G, Gasparini, P, Hammond, C J, Hofman, A, Jaddoe, V W V, Kleber, M, Kooner, J S, Perola, M, Relton, C, Ring, S M, Rivadeneira, F, Salomaa, V, Spector, T D, Stegle, O, Toniolo, D, Uitterlinden, A G, Barroso, I, Greenwood, C M T, Perry, J R B, Walker, B R, Butterworth, A S, Xue, Y, Durbin, R, Small, K S, Soranzo, N, Timpson, N J & Zeggini, E 2017, ' Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits ', American Journal of Human Genetics, vol. 100, no. 6, pp. 865–884 . https://doi.org/10.1016/j.ajhg.2017.04.014
ISSN:	0002-9297
DOI:	10.1016/j.ajhg.2017.04.014
Popis:	Deep sequence-based imputation can enhance the discovery power of genome-wide association studies by assessing previously unexplored variation across the common- and low-frequency spectra. We applied a hybrid whole genome sequencing (WGS) and deep imputation approach to examine the broader allelic architecture of twelve anthropometric traits associated with height, body mass and fat distribution in up to 267,616 individuals. We report 106 genome-wide significant signals that have not been previously identified, including 9 low-frequency variants pointing to functional candidates. Of the 106 signals, 6 are in genomic regions that have not been implicated with related traits before, 28 are independent signals at previously reported regions, and 72 represent previously reported signals for a different anthropometric trait. Seventy-one percent of signals reside within genes and fine-mapping resolves 23 signals to one or two likely causal variants. We confirm genetic overlap between human monogenic and polygenic anthropometric traits, and find signal enrichment in cis expression QTLs in relevant tissues. Our results highlight the potential of WGS strategies to enhance biologically-relevant discoveries across the frequency spectrum.
Databáze:	OpenAIRE
Externí odkaz:	https://explore.openaire.eu/search/publication?articleId=doi_dedup___::204f2ad0000de30434091d05a9fc3854 http://hdl.handle.net/11562/965145 Zobrazit plný text záznamu