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. © 2014 Hoggart et al.

Novel Approach Identifies SNPs in SLC2A10 and KCNK9 with Evidence for Parent-of-Origin Effect on Body Mass Index / C.J. Hoggart, G. Venturini, M. Mangino, F. Gomez, G. Ascari, J.H. Zhao, A. Teumer, T.W. Winkler, N. Tšernikova, J. Luan, E. Mihailov, G.B. Ehret, W. Zhang, D. Lamparter, T. Esko, A. Macé, S. Rüeger, P. Bochud, M. Barcella, Y. Dauvilliers, B. Benyamin, D.M. Evans, C. Hayward, M.F. Lopez, L. Franke, A. Russo, I.M. Heid, E. Salvi, S. Vendantam, D.E. Arking, E. Boerwinkle, J.C. Chambers, G. Fiorito, H. Grallert, S. Guarrera, G. Homuth, J.E. Huffman, D. Porteous, J. Berg, D. Blackwood, H. Campbell, J. Cavanagh, J. Connell, M. Connor, S. Cunningham-Burley, I. Deary, A. Dominiczak, P. Ellis, B. FitzPatrick, I. Ford, R. Gertz, A. Grau, G. Haddow, C. Jackson, S. Kerr, R. Lindsay, M. McGilchrist, D. McIntyre, A. Morris, R. Morton, W. Muir, G. Murray, C. Palmer, J. Pell, A. Philp, D. Porteous, M. Porteous, R. Procter, S. Ralston, D. Reid, R. Sinnott, B. Smith, D. St Clair, F. Sullivan, M. Sweetland, J. Ure, G. Watt, R. Wolf, A. Wright, P. de Bakker, U. Bültmann, M. Geleijnse, P.V.D. Harst, G. Koppelman, J.G.M. Rosmalen, L. van Rossum, H. Smidt, M.A. Swertz, R.P. Stolk, B. Alizadeh, R. de Boer, H.M. Boezen, M. Bruinenberg, L. Franke, P. van der Harst, H. Hillege, M. van der Klauw, G. Navis, J. Ormel, D. Postma, J. Rosmalen, J. Slaets, H. Snieder, R. Stolk, B. Wolffenbuttel, C. Wijmenga, S.I. Berndt, S. Gustafsson, R. Mägi, A. Ganna, E. Wheeler, M.F. Feitosa, A.E. Justice, K.L. Monda, D.C. Croteau- Chonka, F.R. Day, T. Esko, T. Fall, T. Ferreira, D. Gentilini, A.U. Jackson, J. Luan, J.C. Randall, S. Vedantam, C.J. Willer, T.W. Winkler, A.R. Wood, T. Workalemahu, Y. Hu, S.H. Lee, L. Liang, D. Lin, J.L. Min, B.M. Neale, G. Thorleifsson, J. Yang, E. Albrecht, N. Amin, J.L. Bragg-Gresham, G. Cadby, M. den Heijer, N. Eklund, K. Fischer, A. Goel, J. Hottenga, J.E. Huffman, I. Jarick, A. Johansson, T. Johnson, S. Kanoni, M.E. Kleber, I.R. König, K. Kristiansson, Z. Kutalik, C. Lamina, C. Lecoeur, G. Li, M. Mangino, W.L. McArdle, C. Medina-Gomez, M. Müller-Nurasyid, J.S. Ngwa, I.M. Nolte, L. Paternoster, S. Pechlivanis, M. Perola, M.J. Peters, M. Preuss, L.M. Rose, J. Shi, D. Shungin, A.V. Smith, R.J. Strawbridge, I. Surakka, A. Teumer, M.D. Trip, J. Tyrer, J.V. Van Vliet-Ostaptchouk, L. Vandenput, L.L. Waite, J.H. Zhao, D. Absher, F.W. Asselbergs, M. Atalay, A.P. Attwood, A.J. Balmforth, H. Basart, J. Beilby, L.L. Bonnycastle, P. Brambilla, M. Bruinenberg, H. Campbell, D.I. Chasman, P.S. Chines, F.S. Collins, J.M. Connell, W. Cookson, U. de Faire, F. de Vegt, M. Dei, M. Dimitriou, S. Edkins, K. Estrada, D.M. Evans, M. Farrall, M.M. Ferrario, J. Ferrières, L. Franke, F. Frau, P.V. Gejman, H. Grallert, H. Grönberg, V. Gudnason, A.S. Hall, P. Hall, A. Hartikainen, C. Hayward, N.L. Heard-Costa, A.C. Heath, J. Hebebrand, G. Homuth, F.B. Hu, S.E. Hunt, E. Hyppönen, C. Iribarren, K.B. Jacobs, J. Jansson, A. Jula, M. Kähönen, S. Kathiresan, F. Kee, K. Khaw, M. Kivimaki, W. Koenig, A.T. Kraja, M. Kumari, n. KariKuulasmaa, J. Kuusisto, J.H. Laitinen, T.A. Lakka, C. Langenberg, L.J. Launer, L. Lind, J. Lindström, J. Liu, A. Liuzzi, M. Lokki, M. Lorentzon, P.A. Madden, P.K. Magnusson, P. Manunta, D. Marek, W. März, I.M. Leach, B. McKnight, S.E. Medland, E. Mihailov, L. Milani, G.W. Montgomery, V. Mooser, T.W. Mühleisen, P.B. Munroe, A.W. Musk, N. Narisu, G. Navis, G. Nicholson, E.A. Nohr, K.K. Ong, B.A. Oostra, C.N..A. Palmer, A. Palotie, J.F. Peden, N. Pedersen, A. Peters, O. Polasek, A. Pouta, P.P. Pramstaller, I. Prokopenko, C. Pütter, A. Radhakrishnan, O. Raitakari, A. Rendon, F. Rivadeneira, I. Rudan, T.E. Saaristo, J.G. Sambrook, A.R. Sanders, S. Sanna, J. Saramies, S. Schipf, S. Schreiber, H. Schunkert, S. Shin, S. Signorini, J. Sinisalo, B. Skrobek, N. Soranzo, A. Stancakova, K. Stark, J.C. Stephens, K. Stirrups, R.P. Stolk, M. Stumvoll, A.J. Swift, E.V. Theodoraki, B. Thorand, D. Tregouet, E. Tremoli, M.M. Van der Klauw, J.B..J. van Meurs, S.H. Vermeulen, J. Viikari, J. Virtamo, V. Vitart, G. Waeber, Z. Wang, E. Widen, S.H. Wild, G. Willemsen, B.R. Winkelmann, J.C..M. Witteman, B.H..R. Wolffenbuttel, A. Wong, A.F. Wright, M..C. Zillikens, P. Amouyel, B.O. Boehm, E. Boerwinkle, D.I. Boomsma, M.J. Caulfield, S.J. Chanock, L..A. Cupples, D. Cusi, G.V. Dedoussis, J. Erdmann, J.G. Eriksson, P.W. Franks, P. Froguel, C. Gieger, U. Gyllensten, A. Hamsten, T.B. Harris, C. Hengstenberg, A.A. Hicks, A. Hingorani, A. Hinney, A. Hofman, K.G. Hovingh, K. Hveem, T. Illig, M. Jarvelin, K. Jöckel, S.M. Keinanen-Kiukaanniemi, L.A. Kiemeney, D. Kuh, M. Laakso, T. Lehtimäki, D.F. Levinson, N.G. Martin, A. Metspalu, A.D. Morris, M.S. Nieminen, I. Njølstad, C. Ohlsson, A.J. Oldehinkel, W.H. Ouwehand, L.J. Palmer, B. Penninx, C. Power, M.A. Province, B.M. Psaty, L. Qi, R. Rauramaa, P.M. Ridker, S. Ripatti, V. Salomaa, N.J. Samani, H. Snieder, T.I..A. Sørensen, T.D. Spector, K. Stefansson, A. Tönjes, J. Tuomilehto, A.G. Uitterlinden, M. Uusitupa, P. van der Harst, P. Vollenweider, H. Wallaschofski, N.J. Wareham, H. Watkins, H.-. Wichmann, J.F. Wilson, G.R. Abecasis, T.L. Assimes, I. Barroso, M. Boehnke, I.B. Borecki, P. Deloukas, C.S. Fox, T. Frayling, L.C. Groop, T. Haritunian, I.M. Heid, D. Hunter, R.C. Kaplan, F. Karpe, n. MiriamMoffatt, K.L. Mohlke, J.R. O'Connell, Y. Pawitan, E.E. Schadt, D. Schlessinger, V. Steinthorsdottir, D.P. Strachan, U. Thorsteinsdottir, C.M. van Duijn, P.M. Visscher, A.M. Di Blasio, J.N. Hirschhorn, C.M. Lindgren, A.P. Morris, D. Meyre, A. Scherag, M.I. McCarthy, E.K. Speliotes, K.E. North, R.J..F. Loos, E. Ingelsson, D. Moradpour, A. Iranzo, J. Hebebrand, J.P. Kemp, G.J. Lammers, V. Aubert, M.H. Heim, N.G. Martin, G.W. Montgomery, R. Peraita-Adrados, J. Santamaria, F. Negro, C.O. Schmidt, R.A. Scott, T.D. Spector, K. Strauch, H. Völzke, N.J. Wareham, W. Yuan, J.T. Bell, A. Chakravarti, J.S. Kooner, A. Peters, G. Matullo, H. Wallaschofski, J.B. Whitfield, F. Paccaud, P. Vollenweider, S. Bergmann, J.S. Beckmann, M. Tafti, N.D. Hastie, D. Cusi, M. Bochud, T.M. Frayling, A. Metspalu, M. Jarvelin, A. Scherag, G. Da Smith, I.B. Borecki, V. Rousson, J.N. Hirschhorn, C. Rivolta, R.J..F. Loos, Z. Kutalik. - In: PLOS GENETICS. - ISSN 1553-7390. - 10:7(2014 Jul), pp. e1004508.1-e1004508.12. [10.1371/journal.pgen.1004508]

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

M. Barcella;E. Salvi;E. Tremoli;D. Cusi;
2014

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. © 2014 Hoggart et al.
Genetics ; Molecular Biology ; Ecology, Evolution, Behavior and Systematics ; Cancer Research; Genetics (clinical)
Settore BIO/14 - Farmacologia
lug-2014
Article (author)
File in questo prodotto:
File Dimensione Formato  
fetchObject.pdf

accesso aperto

Descrizione: ArticoloNovel Approach Identifies SNPs
Tipologia: Publisher's version/PDF
Dimensione 536.55 kB
Formato Adobe PDF
536.55 kB Adobe PDF Visualizza/Apri
Pubblicazioni consigliate

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/239643
Citazioni
  • ???jsp.display-item.citation.pmc??? 29
  • Scopus 48
  • ???jsp.display-item.citation.isi??? 46
social impact