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1.  New genetic loci link adipose and insulin biology to body fat distribution 
Shungin, Dmitry | Winkler, Thomas W | Croteau-Chonka, Damien C | Ferreira, Teresa | Locke, Adam E | Mägi, Reedik | Strawbridge, Rona J | Pers, Tune H | Fischer, Krista | Justice, Anne E | Workalemahu, Tsegaselassie | Wu, Joseph M.W. | Buchkovich, Martin L | Heard-Costa, Nancy L | Roman, Tamara S | Drong, Alexander W | Song, Ci | Gustafsson, Stefan | Day, Felix R | Esko, Tonu | Fall, Tove | Kutalik, Zoltán | Luan, Jian’an | Randall, Joshua C | Scherag, André | Vedantam, Sailaja | Wood, Andrew R | Chen, Jin | Fehrmann, Rudolf | Karjalainen, Juha | Kahali, Bratati | Liu, Ching-Ti | Schmidt, Ellen M | Absher, Devin | Amin, Najaf | Anderson, Denise | Beekman, Marian | Bragg-Gresham, Jennifer L | Buyske, Steven | Demirkan, Ayse | Ehret, Georg B | Feitosa, Mary F | Goel, Anuj | Jackson, Anne U | Johnson, Toby | Kleber, Marcus E | Kristiansson, Kati | Mangino, Massimo | Leach, Irene Mateo | Medina-Gomez, Carolina | Palmer, Cameron D | Pasko, Dorota | Pechlivanis, Sonali | Peters, Marjolein J | Prokopenko, Inga | Stančáková, Alena | Sung, Yun Ju | Tanaka, Toshiko | Teumer, Alexander | Van Vliet-Ostaptchouk, Jana V | Yengo, Loïc | Zhang, Weihua | Albrecht, Eva | Ärnlöv, Johan | Arscott, Gillian M | Bandinelli, Stefania | Barrett, Amy | Bellis, Claire | Bennett, Amanda J | Berne, Christian | Blüher, Matthias | Böhringer, Stefan | Bonnet, Fabrice | Böttcher, Yvonne | Bruinenberg, Marcel | Carba, Delia B | Caspersen, Ida H | Clarke, Robert | Daw, E Warwick | Deelen, Joris | Deelman, Ewa | Delgado, Graciela | Doney, Alex SF | Eklund, Niina | Erdos, Michael R | Estrada, Karol | Eury, Elodie | Friedrich, Nele | Garcia, Melissa E | Giedraitis, Vilmantas | Gigante, Bruna | Go, Alan S | Golay, Alain | Grallert, Harald | Grammer, Tanja B | Gräßler, Jürgen | Grewal, Jagvir | Groves, Christopher J | Haller, Toomas | Hallmans, Goran | Hartman, Catharina A | Hassinen, Maija | Hayward, Caroline | Heikkilä, Kauko | Herzig, Karl-Heinz | Helmer, Quinta | Hillege, Hans L | Holmen, Oddgeir | Hunt, Steven C | Isaacs, Aaron | Ittermann, Till | James, Alan L | Johansson, Ingegerd | Juliusdottir, Thorhildur | Kalafati, Ioanna-Panagiota | Kinnunen, Leena | Koenig, Wolfgang | Kooner, Ishminder K | Kratzer, Wolfgang | Lamina, Claudia | Leander, Karin | Lee, Nanette R | Lichtner, Peter | Lind, Lars | Lindström, Jaana | Lobbens, Stéphane | Lorentzon, Mattias | Mach, François | Magnusson, Patrik KE | Mahajan, Anubha | McArdle, Wendy L | Menni, Cristina | Merger, Sigrun | Mihailov, Evelin | Milani, Lili | Mills, Rebecca | Moayyeri, Alireza | Monda, Keri L | Mooijaart, Simon P | Mühleisen, Thomas W | Mulas, Antonella | Müller, Gabriele | Müller-Nurasyid, Martina | Nagaraja, Ramaiah | Nalls, Michael A | Narisu, Narisu | Glorioso, Nicola | Nolte, Ilja M | Olden, Matthias | Rayner, Nigel W | Renstrom, Frida | Ried, Janina S | Robertson, Neil R | Rose, Lynda M | Sanna, Serena | Scharnagl, Hubert | Scholtens, Salome | Sennblad, Bengt | Seufferlein, Thomas | Sitlani, Colleen M | Smith, Albert Vernon | Stirrups, Kathleen | Stringham, Heather M | Sundström, Johan | Swertz, Morris A | Swift, Amy J | Syvänen, Ann-Christine | Tayo, Bamidele O | Thorand, Barbara | Thorleifsson, Gudmar | Tomaschitz, Andreas | Troffa, Chiara | van Oort, Floor VA | Verweij, Niek | Vonk, Judith M | Waite, Lindsay L | Wennauer, Roman | Wilsgaard, Tom | Wojczynski, Mary K | Wong, Andrew | Zhang, Qunyuan | Zhao, Jing Hua | Brennan, Eoin P. | Choi, Murim | Eriksson, Per | Folkersen, Lasse | Franco-Cereceda, Anders | Gharavi, Ali G | Hedman, Åsa K | Hivert, Marie-France | Huang, Jinyan | Kanoni, Stavroula | Karpe, Fredrik | Keildson, Sarah | Kiryluk, Krzysztof | Liang, Liming | Lifton, Richard P | Ma, Baoshan | McKnight, Amy J | McPherson, Ruth | Metspalu, Andres | Min, Josine L | Moffatt, Miriam F | Montgomery, Grant W | Murabito, Joanne M | Nicholson, George | Nyholt, Dale R | Olsson, Christian | Perry, John RB | Reinmaa, Eva | Salem, Rany M | Sandholm, Niina | Schadt, Eric E | Scott, Robert A | Stolk, Lisette | Vallejo, Edgar E. | Westra, Harm-Jan | Zondervan, Krina T | Amouyel, Philippe | Arveiler, Dominique | Bakker, Stephan JL | Beilby, John | Bergman, Richard N | Blangero, John | Brown, Morris J | Burnier, Michel | Campbell, Harry | Chakravarti, Aravinda | Chines, Peter S | Claudi-Boehm, Simone | Collins, Francis S | Crawford, Dana C | Danesh, John | de Faire, Ulf | de Geus, Eco JC | Dörr, Marcus | Erbel, Raimund | Eriksson, Johan G | Farrall, Martin | Ferrannini, Ele | Ferrières, Jean | Forouhi, Nita G | Forrester, Terrence | Franco, Oscar H | Gansevoort, Ron T | Gieger, Christian | Gudnason, Vilmundur | Haiman, Christopher A | Harris, Tamara B | Hattersley, Andrew T | Heliövaara, Markku | Hicks, Andrew A | Hingorani, Aroon D | Hoffmann, Wolfgang | Hofman, Albert | Homuth, Georg | Humphries, Steve E | Hyppönen, Elina | Illig, Thomas | Jarvelin, Marjo-Riitta | Johansen, Berit | Jousilahti, Pekka | Jula, Antti M | Kaprio, Jaakko | Kee, Frank | Keinanen-Kiukaanniemi, Sirkka M | Kooner, Jaspal S | Kooperberg, Charles | Kovacs, Peter | Kraja, Aldi T | Kumari, Meena | Kuulasmaa, Kari | Kuusisto, Johanna | Lakka, Timo A | Langenberg, Claudia | Le Marchand, Loic | Lehtimäki, Terho | Lyssenko, Valeriya | Männistö, Satu | Marette, André | Matise, Tara C | McKenzie, Colin A | McKnight, Barbara | Musk, Arthur W | Möhlenkamp, Stefan | Morris, Andrew D | Nelis, Mari | Ohlsson, Claes | Oldehinkel, Albertine J | Ong, Ken K | Palmer, Lyle J | Penninx, Brenda W | Peters, Annette | Pramstaller, Peter P | Raitakari, Olli T | Rankinen, Tuomo | Rao, DC | Rice, Treva K | Ridker, Paul M | Ritchie, Marylyn D. | Rudan, Igor | Salomaa, Veikko | Samani, Nilesh J | Saramies, Jouko | Sarzynski, Mark A | Schwarz, Peter EH | Shuldiner, Alan R | Staessen, Jan A | Steinthorsdottir, Valgerdur | Stolk, Ronald P | Strauch, Konstantin | Tönjes, Anke | Tremblay, Angelo | Tremoli, Elena | Vohl, Marie-Claude | Völker, Uwe | Vollenweider, Peter | Wilson, James F | Witteman, Jacqueline C | Adair, Linda S | Bochud, Murielle | Boehm, Bernhard O | Bornstein, Stefan R | Bouchard, Claude | Cauchi, Stéphane | Caulfield, Mark J | Chambers, John C | Chasman, Daniel I | Cooper, Richard S | Dedoussis, George | Ferrucci, Luigi | Froguel, Philippe | Grabe, Hans-Jörgen | Hamsten, Anders | Hui, Jennie | Hveem, Kristian | Jöckel, Karl-Heinz | Kivimaki, Mika | Kuh, Diana | Laakso, Markku | Liu, Yongmei | März, Winfried | Munroe, Patricia B | Njølstad, Inger | Oostra, Ben A | Palmer, Colin NA | Pedersen, Nancy L | Perola, Markus | Pérusse, Louis | Peters, Ulrike | Power, Chris | Quertermous, Thomas | Rauramaa, Rainer | Rivadeneira, Fernando | Saaristo, Timo E | Saleheen, Danish | Sinisalo, Juha | Slagboom, P Eline | Snieder, Harold | Spector, Tim D | Stefansson, Kari | Stumvoll, Michael | Tuomilehto, Jaakko | Uitterlinden, André G | Uusitupa, Matti | van der Harst, Pim | Veronesi, Giovanni | Walker, Mark | Wareham, Nicholas J | Watkins, Hugh | Wichmann, H-Erich | Abecasis, Goncalo R | Assimes, Themistocles L | Berndt, Sonja I | Boehnke, Michael | Borecki, Ingrid B | Deloukas, Panos | Franke, Lude | Frayling, Timothy M | Groop, Leif C | Hunter, David J. | Kaplan, Robert C | O’Connell, Jeffrey R | Qi, Lu | Schlessinger, David | Strachan, David P | Thorsteinsdottir, Unnur | van Duijn, Cornelia M | Willer, Cristen J | Visscher, Peter M | Yang, Jian | Hirschhorn, Joel N | Zillikens, M Carola | McCarthy, Mark I | Speliotes, Elizabeth K | North, Kari E | Fox, Caroline S | Barroso, Inês | Franks, Paul W | Ingelsson, Erik | Heid, Iris M | Loos, Ruth JF | Cupples, L Adrienne | Morris, Andrew P | Lindgren, Cecilia M | Mohlke, Karen L
Nature  2015;518(7538):187-196.
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.
doi:10.1038/nature14132
PMCID: PMC4338562  PMID: 25673412
2.  Parent-of-origin specific allelic associations among 106 genomic loci for age at menarche 
Perry, John RB | Day, Felix | Elks, Cathy E | Sulem, Patrick | Thompson, Deborah J | Ferreira, Teresa | He, Chunyan | Chasman, Daniel I | Esko, Tõnu | Thorleifsson, Gudmar | Albrecht, Eva | Ang, Wei Q | Corre, Tanguy | Cousminer, Diana L | Feenstra, Bjarke | Franceschini, Nora | Ganna, Andrea | Johnson, Andrew D | Kjellqvist, Sanela | Lunetta, Kathryn L | McMahon, George | Nolte, Ilja M | Paternoster, Lavinia | Porcu, Eleonora | Smith, Albert V | Stolk, Lisette | Teumer, Alexander | Tšernikova, Natalia | Tikkanen, Emmi | Ulivi, Sheila | Wagner, Erin K | Amin, Najaf | Bierut, Laura J | Byrne, Enda M | Hottenga, Jouke-Jan | Koller, Daniel L | Mangino, Massimo | Pers, Tune H | Yerges-Armstrong, Laura M | Zhao, Jing Hua | Andrulis, Irene L | Anton-Culver, Hoda | Atsma, Femke | Bandinelli, Stefania | Beckmann, Matthias W | Benitez, Javier | Blomqvist, Carl | Bojesen, Stig E | Bolla, Manjeet K | Bonanni, Bernardo | Brauch, Hiltrud | Brenner, Hermann | Buring, Julie E | Chang-Claude, Jenny | Chanock, Stephen | Chen, Jinhui | Chenevix-Trench, Georgia | Collée, J. Margriet | Couch, Fergus J | Couper, David | Coveillo, Andrea D | Cox, Angela | Czene, Kamila | D’adamo, Adamo Pio | Smith, George Davey | De Vivo, Immaculata | Demerath, Ellen W | Dennis, Joe | Devilee, Peter | Dieffenbach, Aida K | Dunning, Alison M | Eiriksdottir, Gudny | Eriksson, Johan G | Fasching, Peter A | Ferrucci, Luigi | Flesch-Janys, Dieter | Flyger, Henrik | Foroud, Tatiana | Franke, Lude | Garcia, Melissa E | García-Closas, Montserrat | Geller, Frank | de Geus, Eco EJ | Giles, Graham G | Gudbjartsson, Daniel F | Gudnason, Vilmundur | Guénel, Pascal | Guo, Suiqun | Hall, Per | Hamann, Ute | Haring, Robin | Hartman, Catharina A | Heath, Andrew C | Hofman, Albert | Hooning, Maartje J | Hopper, John L | Hu, Frank B | Hunter, David J | Karasik, David | Kiel, Douglas P | Knight, Julia A | Kosma, Veli-Matti | Kutalik, Zoltan | Lai, Sandra | Lambrechts, Diether | Lindblom, Annika | Mägi, Reedik | Magnusson, Patrik K | Mannermaa, Arto | Martin, Nicholas G | Masson, Gisli | McArdle, Patrick F | McArdle, Wendy L | Melbye, Mads | Michailidou, Kyriaki | Mihailov, Evelin | Milani, Lili | Milne, Roger L | Nevanlinna, Heli | Neven, Patrick | Nohr, Ellen A | Oldehinkel, Albertine J | Oostra, Ben A | Palotie, Aarno | Peacock, Munro | Pedersen, Nancy L | Peterlongo, Paolo | Peto, Julian | Pharoah, Paul DP | Postma, Dirkje S | Pouta, Anneli | Pylkäs, Katri | Radice, Paolo | Ring, Susan | Rivadeneira, Fernando | Robino, Antonietta | Rose, Lynda M | Rudolph, Anja | Salomaa, Veikko | Sanna, Serena | Schlessinger, David | Schmidt, Marjanka K | Southey, Mellissa C | Sovio, Ulla | Stampfer, Meir J | Stöckl, Doris | Storniolo, Anna M | Timpson, Nicholas J | Tyrer, Jonathan | Visser, Jenny A | Vollenweider, Peter | Völzke, Henry | Waeber, Gerard | Waldenberger, Melanie | Wallaschofski, Henri | Wang, Qin | Willemsen, Gonneke | Winqvist, Robert | Wolffenbuttel, Bruce HR | Wright, Margaret J | Boomsma, Dorret I | Econs, Michael J | Khaw, Kay-Tee | Loos, Ruth JF | McCarthy, Mark I | Montgomery, Grant W | Rice, John P | Streeten, Elizabeth A | Thorsteinsdottir, Unnur | van Duijn, Cornelia M | Alizadeh, Behrooz Z | Bergmann, Sven | Boerwinkle, Eric | Boyd, Heather A | Crisponi, Laura | Gasparini, Paolo | Gieger, Christian | Harris, Tamara B | Ingelsson, Erik | Järvelin, Marjo-Riitta | Kraft, Peter | Lawlor, Debbie | Metspalu, Andres | Pennell, Craig E | Ridker, Paul M | Snieder, Harold | Sørensen, Thorkild IA | Spector, Tim D | Strachan, David P | Uitterlinden, André G | Wareham, Nicholas J | Widen, Elisabeth | Zygmunt, Marek | Murray, Anna | Easton, Douglas F | Stefansson, Kari | Murabito, Joanne M | Ong, Ken K
Nature  2014;514(7520):92-97.
Age at menarche is a marker of timing of puberty in females. It varies widely between individuals, is a heritable trait and is associated with risks for obesity, type 2 diabetes, cardiovascular disease, breast cancer and all-cause mortality1. Studies of rare human disorders of puberty and animal models point to a complex hypothalamic-pituitary-hormonal regulation2,3, but the mechanisms that determine pubertal timing and underlie its links to disease risk remain unclear. Here, using genome-wide and custom-genotyping arrays in up to 182,416 women of European descent from 57 studies, we found robust evidence (P<5×10−8) for 123 signals at 106 genomic loci associated with age at menarche. Many loci were associated with other pubertal traits in both sexes, and there was substantial overlap with genes implicated in body mass index and various diseases, including rare disorders of puberty. Menarche signals were enriched in imprinted regions, with three loci (DLK1/WDR25, MKRN3/MAGEL2 and KCNK9) demonstrating parent-of-origin specific associations concordant with known parental expression patterns. Pathway analyses implicated nuclear hormone receptors, particularly retinoic acid and gamma-aminobutyric acid-B2 receptor signaling, among novel mechanisms that regulate pubertal timing in humans. Our findings suggest a genetic architecture involving at least hundreds of common variants in the coordinated timing of the pubertal transition.
doi:10.1038/nature13545
PMCID: PMC4185210  PMID: 25231870
3.  Genetic studies of body mass index yield new insights for obesity biology 
Locke, Adam E. | Kahali, Bratati | Berndt, Sonja I. | Justice, Anne E. | Pers, Tune H. | Day, Felix R. | Powell, Corey | Vedantam, Sailaja | Buchkovich, Martin L. | Yang, Jian | Croteau-Chonka, Damien C. | Esko, Tonu | Fall, Tove | Ferreira, Teresa | Gustafsson, Stefan | Kutalik, Zoltán | Luan, Jian’an | Mägi, Reedik | Randall, Joshua C. | Winkler, Thomas W. | Wood, Andrew R. | Workalemahu, Tsegaselassie | Faul, Jessica D. | Smith, Jennifer A. | Zhao, Jing Hua | Zhao, Wei | Chen, Jin | Fehrmann, Rudolf | Hedman, Åsa K. | Karjalainen, Juha | Schmidt, Ellen M. | Absher, Devin | Amin, Najaf | Anderson, Denise | Beekman, Marian | Bolton, Jennifer L. | Bragg-Gresham, Jennifer L. | Buyske, Steven | Demirkan, Ayse | Deng, Guohong | Ehret, Georg B. | Feenstra, Bjarke | Feitosa, Mary F. | Fischer, Krista | Goel, Anuj | Gong, Jian | Jackson, Anne U. | Kanoni, Stavroula | Kleber, Marcus E. | Kristiansson, Kati | Lim, Unhee | Lotay, Vaneet | Mangino, Massimo | Leach, Irene Mateo | Medina-Gomez, Carolina | Medland, Sarah E. | Nalls, Michael A. | Palmer, Cameron D. | Pasko, Dorota | Pechlivanis, Sonali | Peters, Marjolein J. | Prokopenko, Inga | Shungin, Dmitry | Stančáková, Alena | Strawbridge, Rona J. | Sung, Yun Ju | Tanaka, Toshiko | Teumer, Alexander | Trompet, Stella | van der Laan, Sander W. | van Setten, Jessica | Van Vliet-Ostaptchouk, Jana V. | Wang, Zhaoming | Yengo, Loïc | Zhang, Weihua | Isaacs, Aaron | Albrecht, Eva | Ärnlöv, Johan | Arscott, Gillian M. | Attwood, Antony P. | Bandinelli, Stefania | Barrett, Amy | Bas, Isabelita N. | Bellis, Claire | Bennett, Amanda J. | Berne, Christian | Blagieva, Roza | Blüher, Matthias | Böhringer, Stefan | Bonnycastle, Lori L. | Böttcher, Yvonne | Boyd, Heather A. | Bruinenberg, Marcel | Caspersen, Ida H. | Chen, Yii-Der Ida | Clarke, Robert | Daw, E. Warwick | de Craen, Anton J. M. | Delgado, Graciela | Dimitriou, Maria | Doney, Alex S. F. | Eklund, Niina | Estrada, Karol | Eury, Elodie | Folkersen, Lasse | Fraser, Ross M. | Garcia, Melissa E. | Geller, Frank | Giedraitis, Vilmantas | Gigante, Bruna | Go, Alan S. | Golay, Alain | Goodall, Alison H. | Gordon, Scott D. | Gorski, Mathias | Grabe, Hans-Jörgen | Grallert, Harald | Grammer, Tanja B. | Gräßler, Jürgen | Grönberg, Henrik | Groves, Christopher J. | Gusto, Gaëlle | Haessler, Jeffrey | Hall, Per | Haller, Toomas | Hallmans, Goran | Hartman, Catharina A. | Hassinen, Maija | Hayward, Caroline | Heard-Costa, Nancy L. | Helmer, Quinta | Hengstenberg, Christian | Holmen, Oddgeir | Hottenga, Jouke-Jan | James, Alan L. | Jeff, Janina M. | Johansson, Åsa | Jolley, Jennifer | Juliusdottir, Thorhildur | Kinnunen, Leena | Koenig, Wolfgang | Koskenvuo, Markku | Kratzer, Wolfgang | Laitinen, Jaana | Lamina, Claudia | Leander, Karin | Lee, Nanette R. | Lichtner, Peter | Lind, Lars | Lindström, Jaana | Lo, Ken Sin | Lobbens, Stéphane | Lorbeer, Roberto | Lu, Yingchang | Mach, François | Magnusson, Patrik K. E. | Mahajan, Anubha | McArdle, Wendy L. | McLachlan, Stela | Menni, Cristina | Merger, Sigrun | Mihailov, Evelin | Milani, Lili | Moayyeri, Alireza | Monda, Keri L. | Morken, Mario A. | Mulas, Antonella | Müller, Gabriele | Müller-Nurasyid, Martina | Musk, Arthur W. | Nagaraja, Ramaiah | Nöthen, Markus M. | Nolte, Ilja M. | Pilz, Stefan | Rayner, Nigel W. | Renstrom, Frida | Rettig, Rainer | Ried, Janina S. | Ripke, Stephan | Robertson, Neil R. | Rose, Lynda M. | Sanna, Serena | Scharnagl, Hubert | Scholtens, Salome | Schumacher, Fredrick R. | Scott, William R. | Seufferlein, Thomas | Shi, Jianxin | Smith, Albert Vernon | Smolonska, Joanna | Stanton, Alice V. | Steinthorsdottir, Valgerdur | Stirrups, Kathleen | Stringham, Heather M. | Sundström, Johan | Swertz, Morris A. | Swift, Amy J. | Syvänen, Ann-Christine | Tan, Sian-Tsung | Tayo, Bamidele O. | Thorand, Barbara | Thorleifsson, Gudmar | Tyrer, Jonathan P. | Uh, Hae-Won | Vandenput, Liesbeth | Verhulst, Frank C. | Vermeulen, Sita H. | Verweij, Niek | Vonk, Judith M. | Waite, Lindsay L. | Warren, Helen R. | Waterworth, Dawn | Weedon, Michael N. | Wilkens, Lynne R. | Willenborg, Christina | Wilsgaard, Tom | Wojczynski, Mary K. | Wong, Andrew | Wright, Alan F. | Zhang, Qunyuan | Brennan, Eoin P. | Choi, Murim | Dastani, Zari | Drong, Alexander W. | Eriksson, Per | Franco-Cereceda, Anders | Gådin, Jesper R. | Gharavi, Ali G. | Goddard, Michael E. | Handsaker, Robert E. | Huang, Jinyan | Karpe, Fredrik | Kathiresan, Sekar | Keildson, Sarah | Kiryluk, Krzysztof | Kubo, Michiaki | Lee, Jong-Young | Liang, Liming | Lifton, Richard P. | Ma, Baoshan | McCarroll, Steven A. | McKnight, Amy J. | Min, Josine L. | Moffatt, Miriam F. | Montgomery, Grant W. | Murabito, Joanne M. | Nicholson, George | Nyholt, Dale R. | Okada, Yukinori | Perry, John R. B. | Dorajoo, Rajkumar | Reinmaa, Eva | Salem, Rany M. | Sandholm, Niina | Scott, Robert A. | Stolk, Lisette | Takahashi, Atsushi | Tanaka, Toshihiro | van ’t Hooft, Ferdinand M. | Vinkhuyzen, Anna A. E. | Westra, Harm-Jan | Zheng, Wei | Zondervan, Krina T. | Heath, Andrew C. | Arveiler, Dominique | Bakker, Stephan J. L. | Beilby, John | Bergman, Richard N. | Blangero, John | Bovet, Pascal | Campbell, Harry | Caulfield, Mark J. | Cesana, Giancarlo | Chakravarti, Aravinda | Chasman, Daniel I. | Chines, Peter S. | Collins, Francis S. | Crawford, Dana C. | Cupples, L. Adrienne | Cusi, Daniele | Danesh, John | de Faire, Ulf | den Ruijter, Hester M. | Dominiczak, Anna F. | Erbel, Raimund | Erdmann, Jeanette | Eriksson, Johan G. | Farrall, Martin | Felix, Stephan B. | Ferrannini, Ele | Ferrières, Jean | Ford, Ian | Forouhi, Nita G. | Forrester, Terrence | Franco, Oscar H. | Gansevoort, Ron T. | Gejman, Pablo V. | Gieger, Christian | Gottesman, Omri | Gudnason, Vilmundur | Gyllensten, Ulf | Hall, Alistair S. | Harris, Tamara B. | Hattersley, Andrew T. | Hicks, Andrew A. | Hindorff, Lucia A. | Hingorani, Aroon D. | Hofman, Albert | Homuth, Georg | Hovingh, G. Kees | Humphries, Steve E. | Hunt, Steven C. | Hyppönen, Elina | Illig, Thomas | Jacobs, Kevin B. | Jarvelin, Marjo-Riitta | Jöckel, Karl-Heinz | Johansen, Berit | Jousilahti, Pekka | Jukema, J. Wouter | Jula, Antti M. | Kaprio, Jaakko | Kastelein, John J. P. | Keinanen-Kiukaanniemi, Sirkka M. | Kiemeney, Lambertus A. | Knekt, Paul | Kooner, Jaspal S. | Kooperberg, Charles | Kovacs, Peter | Kraja, Aldi T. | Kumari, Meena | Kuusisto, Johanna | Lakka, Timo A. | Langenberg, Claudia | Marchand, Loic Le | Lehtimäki, Terho | Lyssenko, Valeriya | Männistö, Satu | Marette, André | Matise, Tara C. | McKenzie, Colin A. | McKnight, Barbara | Moll, Frans L. | Morris, Andrew D. | Morris, Andrew P. | Murray, Jeffrey C. | Nelis, Mari | Ohlsson, Claes | Oldehinkel, Albertine J. | Ong, Ken K. | Madden, Pamela A. F. | Pasterkamp, Gerard | Peden, John F. | Peters, Annette | Postma, Dirkje S. | Pramstaller, Peter P. | Price, Jackie F. | Qi, Lu | Raitakari, Olli T. | Rankinen, Tuomo | Rao, D. C. | Rice, Treva K. | Ridker, Paul M. | Rioux, John D. | Ritchie, Marylyn D. | Rudan, Igor | Salomaa, Veikko | Samani, Nilesh J. | Saramies, Jouko | Sarzynski, Mark A. | Schunkert, Heribert | Schwarz, Peter E. H. | Sever, Peter | Shuldiner, Alan R. | Sinisalo, Juha | Stolk, Ronald P. | Strauch, Konstantin | Tönjes, Anke | Trégouët, David-Alexandre | Tremblay, Angelo | Tremoli, Elena | Virtamo, Jarmo | Vohl, Marie-Claude | Völker, Uwe | Waeber, Gérard | Willemsen, Gonneke | Witteman, Jacqueline C. | Zillikens, M. Carola | Adair, Linda S. | Amouyel, Philippe | Asselbergs, Folkert W. | Assimes, Themistocles L. | Bochud, Murielle | Boehm, Bernhard O. | Boerwinkle, Eric | Bornstein, Stefan R. | Bottinger, Erwin P. | Bouchard, Claude | Cauchi, Stéphane | Chambers, John C. | Chanock, Stephen J. | Cooper, Richard S. | de Bakker, Paul I. W. | Dedoussis, George | Ferrucci, Luigi | Franks, Paul W. | Froguel, Philippe | Groop, Leif C. | Haiman, Christopher A. | Hamsten, Anders | Hui, Jennie | Hunter, David J. | Hveem, Kristian | Kaplan, Robert C. | Kivimaki, Mika | Kuh, Diana | Laakso, Markku | Liu, Yongmei | Martin, Nicholas G. | März, Winfried | Melbye, Mads | Metspalu, Andres | Moebus, Susanne | Munroe, Patricia B. | Njølstad, Inger | Oostra, Ben A. | Palmer, Colin N. A. | Pedersen, Nancy L. | Perola, Markus | Pérusse, Louis | Peters, Ulrike | Power, Chris | Quertermous, Thomas | Rauramaa, Rainer | Rivadeneira, Fernando | Saaristo, Timo E. | Saleheen, Danish | Sattar, Naveed | Schadt, Eric E. | Schlessinger, David | Slagboom, P. Eline | Snieder, Harold | Spector, Tim D. | Thorsteinsdottir, Unnur | Stumvoll, Michael | Tuomilehto, Jaakko | Uitterlinden, André G. | Uusitupa, Matti | van der Harst, Pim | Walker, Mark | Wallaschofski, Henri | Wareham, Nicholas J. | Watkins, Hugh | Weir, David R. | Wichmann, H-Erich | Wilson, James F. | Zanen, Pieter | Borecki, Ingrid B. | Deloukas, Panos | Fox, Caroline S. | Heid, Iris M. | O’Connell, Jeffrey R. | Strachan, David P. | Stefansson, Kari | van Duijn, Cornelia M. | Abecasis, Gonçalo R. | Franke, Lude | Frayling, Timothy M. | McCarthy, Mark I. | Visscher, Peter M. | Scherag, André | Willer, Cristen J. | Boehnke, Michael | Mohlke, Karen L. | Lindgren, Cecilia M. | Beckmann, Jacques S. | Barroso, Inês | North, Kari E. | Ingelsson, Erik | Hirschhorn, Joel N. | Loos, Ruth J. F. | Speliotes, Elizabeth K.
Nature  2015;518(7538):197-206.
Obesity is heritable and predisposes to many diseases. To understand the genetic basis of obesity better, here we conduct a genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals. This analysis identifies 97 BMI-associated loci (P < 5 × 10−8), 56 of which are novel. Five loci demonstrate clear evidence of several independent association signals, and many loci have significant effects on other metabolic phenotypes. The 97 loci account for ~2.7% of BMI variation, and genome-wide estimates suggest that common variation accounts for >20% of BMI variation. Pathway analyses provide strong support for a role of the central nervous system in obesity susceptibility and implicate new genes and pathways, including those related to synaptic function, glutamate signalling, insulin secretion/action, energy metabolism, lipid biology and adipogenesis.
doi:10.1038/nature14177
PMCID: PMC4382211  PMID: 25673413
4.  Transcriptome and genome sequencing uncovers functional variation in humans 
Nature  2013;501(7468):506-511.
Summary
Genome sequencing projects are discovering millions of genetic variants in humans, and interpretation of their functional effects is essential for understanding the genetic basis of variation in human traits. Here we report sequencing and deep analysis of mRNA and miRNA from lymphoblastoid cell lines of 462 individuals from the 1000 Genomes Project – the first uniformly processed RNA-seq data from multiple human populations with high-quality genome sequences. We discovered extremely widespread genetic variation affecting regulation of the majority of genes, with transcript structure and expression level variation being equally common but genetically largely independent. Our characterization of causal regulatory variation sheds light on cellular mechanisms of regulatory and loss-of-function variation, and allowed us to infer putative causal variants for dozens of disease-associated loci. Altogether, this study provides a deep understanding of the cellular mechanisms of transcriptome variation and of the landscape of functional variants in the human genome.
doi:10.1038/nature12531
PMCID: PMC3918453  PMID: 24037378
5.  Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer 
Nature  2012;493(7432):406-410.
Improved sequencing technologies offer unprecedented opportunities for investigating the role of rare genetic variation in common disease. However, there are considerable challenges with respect to study design, data analysis and replication1. Here, using pooled next-generation sequencing of 507 genes implicated in the repair of DNA in 1,150 samples, an analytical strategy focussed on protein truncating variants (PTVs) and a large-scale sequencing case-control replication experiment in 13,642 individuals, we show that rare PTVs in the p53 inducible protein phosphatase PPM1D are associated with predisposition to breast cancer and to ovarian cancer. PPM1D PTV mutations were present in 25/7781 cases vs 1/5861 controls; P=1.12×10−5, which included 18 mutations in 6,912 individuals with breast cancer; P = 2.42×10−4 and 12 mutations in 1,121 individuals with ovarian cancer; P = 3.10×10−9. Notably, all the identified PPM1D PTVs were mosaic in lymphocyte DNA and clustered within a 370 bp region in the final exon of the gene, C-terminal to the phosphatase catalytic domain. Functional studies demonstrated that the mutations result in enhanced suppression of p53 in response to ionising radiation exposure, suggesting the mutant alleles encode hyperactive PPM1D isoforms. Thus, although the mutations cause premature protein truncation, they do not result in the simple loss-of-function typically associated with this class of variant, but instead likely have a gain-of-function effect. Our results have implications for the detection and management of breast and ovarian cancer risk. More generally, these data provide new insights into the role of rare and of mosaic genetic variants in common conditions, and the utility of sequencing in their identification.
doi:10.1038/nature11725
PMCID: PMC3759028  PMID: 23242139
6.  FTO genotype is associated with phenotypic variability of body mass index 
Yang, Jian | Loos, Ruth J. F. | Powell, Joseph E. | Medland, Sarah E. | Speliotes, Elizabeth K. | Chasman, Daniel I. | Rose, Lynda M. | Thorleifsson, Gudmar | Steinthorsdottir, Valgerdur | Mägi, Reedik | Waite, Lindsay | Smith, Albert Vernon | Yerges-Armstrong, Laura M. | Monda, Keri L. | Hadley, David | Mahajan, Anubha | Li, Guo | Kapur, Karen | Vitart, Veronique | Huffman, Jennifer E. | Wang, Sophie R. | Palmer, Cameron | Esko, Tõnu | Fischer, Krista | Zhao, Jing Hua | Demirkan, Ayşe | Isaacs, Aaron | Feitosa, Mary F. | Luan, Jian’an | Heard-Costa, Nancy L. | White, Charles | Jackson, Anne U. | Preuss, Michael | Ziegler, Andreas | Eriksson, Joel | Kutalik, Zoltán | Frau, Francesca | Nolte, Ilja M. | Van Vliet-Ostaptchouk, Jana V. | Hottenga, Jouke-Jan | Jacobs, Kevin B. | Verweij, Niek | Goel, Anuj | Medina-Gomez, Carolina | Estrada, Karol | Bragg-Gresham, Jennifer Lynn | Sanna, Serena | Sidore, Carlo | Tyrer, Jonathan | Teumer, Alexander | Prokopenko, Inga | Mangino, Massimo | Lindgren, Cecilia M. | Assimes, Themistocles L. | Shuldiner, Alan R. | Hui, Jennie | Beilby, John P. | McArdle, Wendy L. | Hall, Per | Haritunians, Talin | Zgaga, Lina | Kolcic, Ivana | Polasek, Ozren | Zemunik, Tatijana | Oostra, Ben A. | Junttila, M. Juhani | Grönberg, Henrik | Schreiber, Stefan | Peters, Annette | Hicks, Andrew A. | Stephens, Jonathan | Foad, Nicola S. | Laitinen, Jaana | Pouta, Anneli | Kaakinen, Marika | Willemsen, Gonneke | Vink, Jacqueline M. | Wild, Sarah H. | Navis, Gerjan | Asselbergs, Folkert W. | Homuth, Georg | John, Ulrich | Iribarren, Carlos | Harris, Tamara | Launer, Lenore | Gudnason, Vilmundur | O’Connell, Jeffrey R. | Boerwinkle, Eric | Cadby, Gemma | Palmer, Lyle J. | James, Alan L. | Musk, Arthur W. | Ingelsson, Erik | Psaty, Bruce M. | Beckmann, Jacques S. | Waeber, Gerard | Vollenweider, Peter | Hayward, Caroline | Wright, Alan F. | Rudan, Igor | Groop, Leif C. | Metspalu, Andres | Khaw, Kay Tee | van Duijn, Cornelia M. | Borecki, Ingrid B. | Province, Michael A. | Wareham, Nicholas J. | Tardif, Jean-Claude | Huikuri, Heikki V. | Cupples, L. Adrienne | Atwood, Larry D. | Fox, Caroline S. | Boehnke, Michael | Collins, Francis S. | Mohlke, Karen L. | Erdmann, Jeanette | Schunkert, Heribert | Hengstenberg, Christian | Stark, Klaus | Lorentzon, Mattias | Ohlsson, Claes | Cusi, Daniele | Staessen, Jan A. | Van der Klauw, Melanie M. | Pramstaller, Peter P. | Kathiresan, Sekar | Jolley, Jennifer D. | Ripatti, Samuli | Jarvelin, Marjo-Riitta | de Geus, Eco J. C. | Boomsma, Dorret I. | Penninx, Brenda | Wilson, James F. | Campbell, Harry | Chanock, Stephen J. | van der Harst, Pim | Hamsten, Anders | Watkins, Hugh | Hofman, Albert | Witteman, Jacqueline C. | Zillikens, M. Carola | Uitterlinden, André G. | Rivadeneira, Fernando | Zillikens, M. Carola | Kiemeney, Lambertus A. | Vermeulen, Sita H. | Abecasis, Goncalo R. | Schlessinger, David | Schipf, Sabine | Stumvoll, Michael | Tönjes, Anke | Spector, Tim D. | North, Kari E. | Lettre, Guillaume | McCarthy, Mark I. | Berndt, Sonja I. | Heath, Andrew C. | Madden, Pamela A. F. | Nyholt, Dale R. | Montgomery, Grant W. | Martin, Nicholas G. | McKnight, Barbara | Strachan, David P. | Hill, William G. | Snieder, Harold | Ridker, Paul M. | Thorsteinsdottir, Unnur | Stefansson, Kari | Frayling, Timothy M. | Hirschhorn, Joel N. | Goddard, Michael E. | Visscher, Peter M.
Nature  2012;490(7419):267-272.
There is evidence across several species for genetic control of phenotypic variation of complex traits1–4, such that the variance among phenotypes is genotype dependent. Understanding genetic control of variability is important in evolutionary biology, agricultural selection programmes and human medicine, yet for complex traits, no individual genetic variants associated with variance, as opposed to the mean, have been identified. Here we perform a meta-analysis of genome-wide association studies of phenotypic variation using 170,000 samples on height and body mass index (BMI) in human populations. We report evidence that the single nucleotide polymorphism (SNP) rs7202116 at the FTO gene locus, which is known to be associated with obesity (as measured by mean BMI for each rs7202116 genotype)5–7, is also associated with phenotypic variability. We show that the results are not due to scale effects or other artefacts, and find no other experiment-wise significant evidence for effects on variability, either at loci other than FTO for BMI or at any locus for height. The difference in variance for BMI among individuals with opposite homozygous genotypes at the FTO locus is approximately 7%, corresponding to a difference of 0.5 kilograms in the standard deviation of weight. Our results indicate that genetic variants can be discovered that are associated with variability, and that between-person variability in obesity can partly be explained by the genotype at the FTO locus. The results are consistent with reported FTO by environment interactions for BMI8, possibly mediated by DNA methylation9,10. Our BMI results for other SNPs and our height results for all SNPs suggest that most genetic variants, including those that influence mean height or mean BMI, are not associated with phenotypic variance, or that their effects on variability are too small to detect even with samples sizes greater than 100,000.
doi:10.1038/nature11401
PMCID: PMC3564953  PMID: 22982992
7.  Hundreds of variants clustered in genomic loci and biological pathways affect human height 
Lango Allen, Hana | Estrada, Karol | Lettre, Guillaume | Berndt, Sonja I. | Weedon, Michael N. | Rivadeneira, Fernando | Willer, Cristen J. | Jackson, Anne U. | Vedantam, Sailaja | Raychaudhuri, Soumya | Ferreira, Teresa | Wood, Andrew R. | Weyant, Robert J. | Segrè, Ayellet V. | Speliotes, Elizabeth K. | Wheeler, Eleanor | Soranzo, Nicole | Park, Ju-Hyun | Yang, Jian | Gudbjartsson, Daniel | Heard-Costa, Nancy L. | Randall, Joshua C. | Qi, Lu | Smith, Albert Vernon | Mägi, Reedik | Pastinen, Tomi | Liang, Liming | Heid, Iris M. | Luan, Jian'an | Thorleifsson, Gudmar | Winkler, Thomas W. | Goddard, Michael E. | Lo, Ken Sin | Palmer, Cameron | Workalemahu, Tsegaselassie | Aulchenko, Yurii S. | Johansson, Åsa | Zillikens, M.Carola | Feitosa, Mary F. | Esko, Tõnu | Johnson, Toby | Ketkar, Shamika | Kraft, Peter | Mangino, Massimo | Prokopenko, Inga | Absher, Devin | Albrecht, Eva | Ernst, Florian | Glazer, Nicole L. | Hayward, Caroline | Hottenga, Jouke-Jan | Jacobs, Kevin B. | Knowles, Joshua W. | Kutalik, Zoltán | Monda, Keri L. | Polasek, Ozren | Preuss, Michael | Rayner, Nigel W. | Robertson, Neil R. | Steinthorsdottir, Valgerdur | Tyrer, Jonathan P. | Voight, Benjamin F. | Wiklund, Fredrik | Xu, Jianfeng | Zhao, Jing Hua | Nyholt, Dale R. | Pellikka, Niina | Perola, Markus | Perry, John R.B. | Surakka, Ida | Tammesoo, Mari-Liis | Altmaier, Elizabeth L. | Amin, Najaf | Aspelund, Thor | Bhangale, Tushar | Boucher, Gabrielle | Chasman, Daniel I. | Chen, Constance | Coin, Lachlan | Cooper, Matthew N. | Dixon, Anna L. | Gibson, Quince | Grundberg, Elin | Hao, Ke | Junttila, M. Juhani | Kaplan, Lee M. | Kettunen, Johannes | König, Inke R. | Kwan, Tony | Lawrence, Robert W. | Levinson, Douglas F. | Lorentzon, Mattias | McKnight, Barbara | Morris, Andrew P. | Müller, Martina | Ngwa, Julius Suh | Purcell, Shaun | Rafelt, Suzanne | Salem, Rany M. | Salvi, Erika | Sanna, Serena | Shi, Jianxin | Sovio, Ulla | Thompson, John R. | Turchin, Michael C. | Vandenput, Liesbeth | Verlaan, Dominique J. | Vitart, Veronique | White, Charles C. | Ziegler, Andreas | Almgren, Peter | Balmforth, Anthony J. | Campbell, Harry | Citterio, Lorena | De Grandi, Alessandro | Dominiczak, Anna | Duan, Jubao | Elliott, Paul | Elosua, Roberto | Eriksson, Johan G. | Freimer, Nelson B. | Geus, Eco J.C. | Glorioso, Nicola | Haiqing, Shen | Hartikainen, Anna-Liisa | Havulinna, Aki S. | Hicks, Andrew A. | Hui, Jennie | Igl, Wilmar | Illig, Thomas | Jula, Antti | Kajantie, Eero | Kilpeläinen, Tuomas O. | Koiranen, Markku | Kolcic, Ivana | Koskinen, Seppo | Kovacs, Peter | Laitinen, Jaana | Liu, Jianjun | Lokki, Marja-Liisa | Marusic, Ana | Maschio, Andrea | Meitinger, Thomas | Mulas, Antonella | Paré, Guillaume | Parker, Alex N. | Peden, John F. | Petersmann, Astrid | Pichler, Irene | Pietiläinen, Kirsi H. | Pouta, Anneli | Ridderstråle, Martin | Rotter, Jerome I. | Sambrook, Jennifer G. | Sanders, Alan R. | Schmidt, Carsten Oliver | Sinisalo, Juha | Smit, Jan H. | Stringham, Heather M. | Walters, G.Bragi | Widen, Elisabeth | Wild, Sarah H. | Willemsen, Gonneke | Zagato, Laura | Zgaga, Lina | Zitting, Paavo | Alavere, Helene | Farrall, Martin | McArdle, Wendy L. | Nelis, Mari | Peters, Marjolein J. | Ripatti, Samuli | van Meurs, Joyce B.J. | Aben, Katja K. | Ardlie, Kristin G | Beckmann, Jacques S. | Beilby, John P. | Bergman, Richard N. | Bergmann, Sven | Collins, Francis S. | Cusi, Daniele | den Heijer, Martin | Eiriksdottir, Gudny | Gejman, Pablo V. | Hall, Alistair S. | Hamsten, Anders | Huikuri, Heikki V. | Iribarren, Carlos | Kähönen, Mika | Kaprio, Jaakko | Kathiresan, Sekar | Kiemeney, Lambertus | Kocher, Thomas | Launer, Lenore J. | Lehtimäki, Terho | Melander, Olle | Mosley, Tom H. | Musk, Arthur W. | Nieminen, Markku S. | O'Donnell, Christopher J. | Ohlsson, Claes | Oostra, Ben | Palmer, Lyle J. | Raitakari, Olli | Ridker, Paul M. | Rioux, John D. | Rissanen, Aila | Rivolta, Carlo | Schunkert, Heribert | Shuldiner, Alan R. | Siscovick, David S. | Stumvoll, Michael | Tönjes, Anke | Tuomilehto, Jaakko | van Ommen, Gert-Jan | Viikari, Jorma | Heath, Andrew C. | Martin, Nicholas G. | Montgomery, Grant W. | Province, Michael A. | Kayser, Manfred | Arnold, Alice M. | Atwood, Larry D. | Boerwinkle, Eric | Chanock, Stephen J. | Deloukas, Panos | Gieger, Christian | Grönberg, Henrik | Hall, Per | Hattersley, Andrew T. | Hengstenberg, Christian | Hoffman, Wolfgang | Lathrop, G.Mark | Salomaa, Veikko | Schreiber, Stefan | Uda, Manuela | Waterworth, Dawn | Wright, Alan F. | Assimes, Themistocles L. | Barroso, Inês | Hofman, Albert | Mohlke, Karen L. | Boomsma, Dorret I. | Caulfield, Mark J. | Cupples, L.Adrienne | Erdmann, Jeanette | Fox, Caroline S. | Gudnason, Vilmundur | Gyllensten, Ulf | Harris, Tamara B. | Hayes, Richard B. | Jarvelin, Marjo-Riitta | Mooser, Vincent | Munroe, Patricia B. | Ouwehand, Willem H. | Penninx, Brenda W. | Pramstaller, Peter P. | Quertermous, Thomas | Rudan, Igor | Samani, Nilesh J. | Spector, Timothy D. | Völzke, Henry | Watkins, Hugh | Wilson, James F. | Groop, Leif C. | Haritunians, Talin | Hu, Frank B. | Kaplan, Robert C. | Metspalu, Andres | North, Kari E. | Schlessinger, David | Wareham, Nicholas J. | Hunter, David J. | O'Connell, Jeffrey R. | Strachan, David P. | Wichmann, H.-Erich | Borecki, Ingrid B. | van Duijn, Cornelia M. | Schadt, Eric E. | Thorsteinsdottir, Unnur | Peltonen, Leena | Uitterlinden, André | Visscher, Peter M. | Chatterjee, Nilanjan | Loos, Ruth J.F. | Boehnke, Michael | McCarthy, Mark I. | Ingelsson, Erik | Lindgren, Cecilia M. | Abecasis, Gonçalo R. | Stefansson, Kari | Frayling, Timothy M. | Hirschhorn, Joel N
Nature  2010;467(7317):832-838.
Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence phenotype. Genome-wide association (GWA) studies have identified >600 variants associated with human traits1, but these typically explain small fractions of phenotypic variation, raising questions about the utility of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait2,3. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P=0.016), and that underlie skeletal growth defects (P<0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants, and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented amongst variants that alter amino acid structure of proteins and expression levels of nearby genes. Our data explain ∼10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to ∼16% of phenotypic variation (∼20% of heritable variation). Although additional approaches are needed to fully dissect the genetic architecture of polygenic human traits, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.
doi:10.1038/nature09410
PMCID: PMC2955183  PMID: 20881960
8.  Biological, Clinical, and Population Relevance of 95 Loci for Blood Lipids 
Teslovich, Tanya M. | Musunuru, Kiran | Smith, Albert V. | Edmondson, Andrew C. | Stylianou, Ioannis M. | Koseki, Masahiro | Pirruccello, James P. | Ripatti, Samuli | Chasman, Daniel I. | Willer, Cristen J. | Johansen, Christopher T. | Fouchier, Sigrid W. | Isaacs, Aaron | Peloso, Gina M. | Barbalic, Maja | Ricketts, Sally L. | Bis, Joshua C. | Aulchenko, Yurii S. | Thorleifsson, Gudmar | Feitosa, Mary F. | Chambers, John | Orho-Melander, Marju | Melander, Olle | Johnson, Toby | Li, Xiaohui | Guo, Xiuqing | Li, Mingyao | Cho, Yoon Shin | Go, Min Jin | Kim, Young Jin | Lee, Jong-Young | Park, Taesung | Kim, Kyunga | Sim, Xueling | Ong, Rick Twee-Hee | Croteau-Chonka, Damien C. | Lange, Leslie A. | Smith, Joshua D. | Song, Kijoung | Zhao, Jing Hua | Yuan, Xin | Luan, Jian'an | Lamina, Claudia | Ziegler, Andreas | Zhang, Weihua | Zee, Robert Y.L. | Wright, Alan F. | Witteman, Jacqueline C.M. | Wilson, James F. | Willemsen, Gonneke | Wichmann, H-Erich | Whitfield, John B. | Waterworth, Dawn M. | Wareham, Nicholas J. | Waeber, Gérard | Vollenweider, Peter | Voight, Benjamin F. | Vitart, Veronique | Uitterlinden, Andre G. | Uda, Manuela | Tuomilehto, Jaakko | Thompson, John R. | Tanaka, Toshiko | Surakka, Ida | Stringham, Heather M. | Spector, Tim D. | Soranzo, Nicole | Smit, Johannes H. | Sinisalo, Juha | Silander, Kaisa | Sijbrands, Eric J.G. | Scuteri, Angelo | Scott, James | Schlessinger, David | Sanna, Serena | Salomaa, Veikko | Saharinen, Juha | Sabatti, Chiara | Ruokonen, Aimo | Rudan, Igor | Rose, Lynda M. | Roberts, Robert | Rieder, Mark | Psaty, Bruce M. | Pramstaller, Peter P. | Pichler, Irene | Perola, Markus | Penninx, Brenda W.J.H. | Pedersen, Nancy L. | Pattaro, Cristian | Parker, Alex N. | Pare, Guillaume | Oostra, Ben A. | O'Donnell, Christopher J. | Nieminen, Markku S. | Nickerson, Deborah A. | Montgomery, Grant W. | Meitinger, Thomas | McPherson, Ruth | McCarthy, Mark I. | McArdle, Wendy | Masson, David | Martin, Nicholas G. | Marroni, Fabio | Mangino, Massimo | Magnusson, Patrik K.E. | Lucas, Gavin | Luben, Robert | Loos, Ruth J. F. | Lokki, Maisa | Lettre, Guillaume | Langenberg, Claudia | Launer, Lenore J. | Lakatta, Edward G. | Laaksonen, Reijo | Kyvik, Kirsten O. | Kronenberg, Florian | König, Inke R. | Khaw, Kay-Tee | Kaprio, Jaakko | Kaplan, Lee M. | Johansson, Åsa | Jarvelin, Marjo-Riitta | Janssens, A. Cecile J.W. | Ingelsson, Erik | Igl, Wilmar | Hovingh, G. Kees | Hottenga, Jouke-Jan | Hofman, Albert | Hicks, Andrew A. | Hengstenberg, Christian | Heid, Iris M. | Hayward, Caroline | Havulinna, Aki S. | Hastie, Nicholas D. | Harris, Tamara B. | Haritunians, Talin | Hall, Alistair S. | Gyllensten, Ulf | Guiducci, Candace | Groop, Leif C. | Gonzalez, Elena | Gieger, Christian | Freimer, Nelson B. | Ferrucci, Luigi | Erdmann, Jeanette | Elliott, Paul | Ejebe, Kenechi G. | Döring, Angela | Dominiczak, Anna F. | Demissie, Serkalem | Deloukas, Panagiotis | de Geus, Eco J.C. | de Faire, Ulf | Crawford, Gabriel | Collins, Francis S. | Chen, Yii-der I. | Caulfield, Mark J. | Campbell, Harry | Burtt, Noel P. | Bonnycastle, Lori L. | Boomsma, Dorret I. | Boekholdt, S. Matthijs | Bergman, Richard N. | Barroso, Inês | Bandinelli, Stefania | Ballantyne, Christie M. | Assimes, Themistocles L. | Quertermous, Thomas | Altshuler, David | Seielstad, Mark | Wong, Tien Y. | Tai, E-Shyong | Feranil, Alan B. | Kuzawa, Christopher W. | Adair, Linda S. | Taylor, Herman A. | Borecki, Ingrid B. | Gabriel, Stacey B. | Wilson, James G. | Stefansson, Kari | Thorsteinsdottir, Unnur | Gudnason, Vilmundur | Krauss, Ronald M. | Mohlke, Karen L. | Ordovas, Jose M. | Munroe, Patricia B. | Kooner, Jaspal S. | Tall, Alan R. | Hegele, Robert A. | Kastelein, John J.P. | Schadt, Eric E. | Rotter, Jerome I. | Boerwinkle, Eric | Strachan, David P. | Mooser, Vincent | Holm, Hilma | Reilly, Muredach P. | Samani, Nilesh J | Schunkert, Heribert | Cupples, L. Adrienne | Sandhu, Manjinder S. | Ridker, Paul M | Rader, Daniel J. | van Duijn, Cornelia M. | Peltonen, Leena | Abecasis, Gonçalo R. | Boehnke, Michael | Kathiresan, Sekar
Nature  2010;466(7307):707-713.
Serum concentrations of total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglycerides (TG) are among the most important risk factors for coronary artery disease (CAD) and are targets for therapeutic intervention. We screened the genome for common variants associated with serum lipids in >100,000 individuals of European ancestry. Here we report 95 significantly associated loci (P < 5 × 10-8), with 59 showing genome-wide significant association with lipid traits for the first time. The newly reported associations include single nucleotide polymorphisms (SNPs) near known lipid regulators (e.g., CYP7A1, NPC1L1, and SCARB1) as well as in scores of loci not previously implicated in lipoprotein metabolism. The 95 loci contribute not only to normal variation in lipid traits but also to extreme lipid phenotypes and impact lipid traits in three non-European populations (East Asians, South Asians, and African Americans). Our results identify several novel loci associated with serum lipids that are also associated with CAD. Finally, we validated three of the novel genes—GALNT2, PPP1R3B, and TTC39B—with experiments in mouse models. Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD.
doi:10.1038/nature09270
PMCID: PMC3039276  PMID: 20686565
9.  Finding the missing heritability of complex diseases 
Nature  2009;461(7265):747-753.
Genome-wide association studies have identified hundreds of genetic variants associated with complex human diseases and traits, and have provided valuable insights into their genetic architecture. Most variants identified so far confer relatively small increments in risk, and explain only a small proportion of familial clustering, leading many to question how the remaining, ‘missing’ heritability can be explained. Here we examine potential sources of missing heritability and propose research strategies, including and extending beyond current genome-wide association approaches, to illuminate the genetics of complex diseases and enhance its potential to enable effective disease prevention or treatment.
doi:10.1038/nature08494
PMCID: PMC2831613  PMID: 19812666

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