Author: "Scheet, Paul A." - Searchworks@Jio Institute Digital Library Search Results

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201. Intelligence : shared genetic basis between Mendelian disorders and a polygenic trait

Author: Franić, Sanja, Groen-Blokhuis, Maria M, Dolan, Conor V, Kattenberg, Mathijs V, Pool, René, Xiao, Xiangjun, Scheet, Paul A, Ehli, Erik A, Davies, Gareth E, van der Sluis, Sophie, Abdellaoui, Abdel, Hansell, Narelle K, Martin, Nicholas G, Hudziak, James J, van Beijsterveldt, Catherina E M, Swagerman, Suzanne C, Hulshoff Pol, Hilleke E, de Geus, Eco J C, Bartels, Meike, Ropers, H Hilger, Hottenga, Jouke-Jan, Boomsma, Dorret I, Franić, Sanja, Groen-Blokhuis, Maria M, Dolan, Conor V, Kattenberg, Mathijs V, Pool, René, Xiao, Xiangjun, Scheet, Paul A, Ehli, Erik A, Davies, Gareth E, van der Sluis, Sophie, Abdellaoui, Abdel, Hansell, Narelle K, Martin, Nicholas G, Hudziak, James J, van Beijsterveldt, Catherina E M, Swagerman, Suzanne C, Hulshoff Pol, Hilleke E, de Geus, Eco J C, Bartels, Meike, Ropers, H Hilger, Hottenga, Jouke-Jan, and Boomsma, Dorret I
Published: 2015

202. Intelligence: shared genetic basis between Mendelian disorders and a polygenic trait

Author: Onderzoeksgroep 1, Brain, Franić, Sanja, Groen-Blokhuis, Maria M, Dolan, Conor V, Kattenberg, Mathijs V, Pool, René, Xiao, Xiangjun, Scheet, Paul A, Ehli, Erik A, Davies, Gareth E, van der Sluis, Sophie, Abdellaoui, Abdel, Hansell, Narelle K, Martin, Nicholas G, Hudziak, James J, van Beijsterveldt, Catherina E M, Swagerman, Suzanne C, Hulshoff Pol, Hilleke E, de Geus, Eco J C, Bartels, Meike, Ropers, H Hilger, Hottenga, Jouke-Jan, Boomsma, Dorret I, Onderzoeksgroep 1, Brain, Franić, Sanja, Groen-Blokhuis, Maria M, Dolan, Conor V, Kattenberg, Mathijs V, Pool, René, Xiao, Xiangjun, Scheet, Paul A, Ehli, Erik A, Davies, Gareth E, van der Sluis, Sophie, Abdellaoui, Abdel, Hansell, Narelle K, Martin, Nicholas G, Hudziak, James J, van Beijsterveldt, Catherina E M, Swagerman, Suzanne C, Hulshoff Pol, Hilleke E, de Geus, Eco J C, Bartels, Meike, Ropers, H Hilger, Hottenga, Jouke-Jan, and Boomsma, Dorret I
Published: 2015

203. Genetic Risk Factors for the Development of Osteonecrosis in Children Under Age 10 Treated for Acute Lymphoblastic Leukemia

Author: Karol, Seth E., primary, Yang, Wenjian, additional, Mattano, Leonard A., additional, Maloney, Kelly W., additional, Smith, Colton, additional, Liu, Chengcheng, additional, Ramsey, Laura B., additional, Fernandez, Christian A., additional, Chang, Tamara Y., additional, Neale, Geoffrey A., additional, Cheng, Cheng, additional, Mardis, Elaine R, additional, Fulton, Robert S., additional, Scheet, Paul, additional, Larsen, Eric C., additional, Loh, Mignon L., additional, Raetz, Elizabeth, additional, Hunger, Stephen P, additional, Devidas, Meenakshi, additional, and Relling, Mary V., additional
Published: 2015
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204. Association Between Autozygosity and Major Depression: Stratification Due to Religious Assortment

Author: Davies, Gareth, Hudziak, James, Brooks, Andrew, Sullivan, Patrick, de Geus, Eco, Penninx, Brenda, Smit, Johannes, Bartels, Meike, Hottenga, Jouke-Jan, Ehli, Erik, Boomsma, Dorret, Xiao, Xiangjun, Abdellaoui, Abdel, Willemsen, Gonneke, Smit, Dirk, and Scheet, Paul
Abstract: The effects of inbreeding on the health of offspring can be studied by measuring genome-wide autozygosity as the proportion of the genome in runs of homozygosity (Froh) and relate Froh to outcomes such as psychiatric phenotypes. To successfully conduct these studies, the main patterns of variation for genome-wide autozygosity between and within populations should be well understood and accounted for. Within population variation was investigated in the Dutch population by comparing autozygosity between religious and non-religious groups. The Netherlands have a history of societal segregation and assortment based on religious affiliation, which may have increased parental relatedness within religious groups. Religion has been associated with several psychiatric phenotypes, such as major depressive disorder (MDD). We investigated whether there is an association between autozygosity and MDD, and the extent to which this association can be explained by religious affiliation. All Froh analyses included adjustment for ancestry-informative principal components (PCs) and geographic factors.
Published: 2013
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205. XPAT: a toolkit to conduct cross-platform association studies with heterogeneous sequencing datasets.

Author: Yu, Yao, Hu, Hao, Bohlender, Ryan J, Hu, Fulan, Chen, Jiun-Sheng, Holt, Carson, Fowler, Jerry, Guthery, Stephen L, Scheet, Paul, and Hildebrandt, Michelle A T
Published: 2018
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206. A Genome-Wide Association Search for Type 2 Diabetes Genes in African Americans

Author: Palmer, Nicholette D, McDonough, Caitrin W, Hicks, Pamela J, Roh, Bong H, Wing, Maria R, An, S Sandy, Hester, Jessica M, Cooke, Jessica N, Bostrom, Meredith A, Rudock, Megan E, Talbert, Matthew E, Lewis, Joshua P, DIAGRAM Consortium, MAGIC Investigators, Ferrara, Assiamira, Lu, Lingyi, Ziegler, Julie T, Sale, Michele M, Divers, Jasmin, Shriner, Daniel, Adeyemo, Adebowale, Rotimi, Charles N, Ng, Maggie CY, Langefeld, Carl D, Freedman, Barry I, Bowden, Donald W, Voight, Benjamin F, Scott, Laura J, Steinthorsdottir, Valgerdur, Morris, Andrew P, Dina, Christian, Welch, Ryan P, Zeggini, Eleftheria, Huth, Cornelia, Aulchenko, Yurii S, Thorleifsson, Gudmar, McCulloch, Laura J, Ferreira, Teresa, Grallert, Harald, Amin, Najaf, Wu, Guanming, Willer, Cristen J, Raychaudhuri, Soumya, McCarroll, Steve A, Langenberg, Claudia, Hofmann, Oliver M, Dupuis, Josée, Qi, Lu, Segrè, Ayellet V, Van Hoek, Mandy, Navarro, Pau, Ardlie, Kristin, Balkau, Beverley, Benediktsson, Rafn, Bennett, Amanda J, Blagieva, Roza, Boerwinkle, Eric, Bonnycastle, Lori L, Boström, Kristina Bengtsson, Bravenboer, Bert, Bumpstead, Suzannah, Burtt, Noël P, Charpentier, Guillaume, Chines, Peter S, Cornelis, Marilyn, Couper, David J, Crawford, Gabe, Doney, Alex SF, Elliott, Katherine S, Elliott, Amanda L, Erdos, Michael R, Fox, Caroline S, Franklin, Christopher S, Ganser, Martha, Gieger, Christian, Grarup, Niels, Green, Todd, Griffin, Simon, Groves, Christopher J, Guiducci, Candace, Hadjadj, Samy, Hassanali, Neelam, Herder, Christian, Isomaa, Bo, Jackson, Anne U, Johnson, Paul RV, Jørgensen, Torben, Kao, Wen HL, Klopp, Norman, Kong, Augustine, Kraft, Peter, Kuusisto, Johanna, Lauritzen, Torsten, Li, Man, Lieverse, Aloysius, Lindgren, Cecilia M, Lyssenko, Valeriya, Marre, Michel, Meitinger, Thomas, Midthjell, Kristian, Morken, Mario A, Narisu, Narisu, Nilsson, Peter, Owen, Katharine R, Payne, Felicity, Perry, John RB, Petersen, Ann-Kristin, Platou, Carl, Proença, Christine, Prokopenko, Inga, Rathmann, Wolfgang, Rayner, N William, Robertson, Neil R, Rocheleau, Ghislain, Roden, Michael, Sampson, Michael J, Saxena, Richa, Shields, Beverley M, Shrader, Peter, Sigurdsson, Gunnar, Sparsø, Thomas, Strassburger, Klaus, Stringham, Heather M, Sun, Qi, Swift, Amy J, Thorand, Barbara, Tichet, Jean, Tuomi, Tiinamaija, Van Dam, Rob M, Van Haeften, Timon W, Van Herpt, Thijs, Van Vliet-Ostaptchouk, Jana V, Walters, G Bragi, Weedon, Michael N, Wijmenga, Cisca, Witteman, Jacqueline, Bergman, Richard N, Cauchi, Stephane, Collins, Francis S, Gloyn, Anna L, Gyllensten, Ulf, Hansen, Torben, Hide, Winston A, Hitman, Graham A, Hofman, Albert, Hunter, David J, Hveem, Kristian, Laakso, Markku, Mohlke, Karen L, Morris, Andrew D, Palmer, Colin NA, Pramstaller, Peter P, Rudan, Igor, Sijbrands, Eric, Stein, Lincoln D, Tuomilehto, Jaakko, Uitterlinden, Andre, Walker, Mark, Wareham, Nicholas J, Watanabe, Richard M, Abecasis, Goncalo R, Boehm, Bernhard O, Campbell, Harry, Daly, Mark J, Hattersley, Andrew T, Hu, Frank B, Meigs, James B, Pankow, James S, Pedersen, Oluf, Wichmann, H-Erich, Barroso, Inês, Florez, Jose C, Frayling, Timothy M, Groop, Leif, Sladek, Rob, Thorsteinsdottir, Unnur, Wilson, James F, Illig, Thomas, Froguel, Philippe, Van Duijn, Cornelia M, Stefansson, Kari, Altshuler, David, Boehnke, Michael, McCarthy, Mark I, Soranzo, Nicole, Wheeler, Eleanor, Glazer, Nicole L, Bouatia-Naji, Nabila, Mägi, Reedik, Randall, Joshua, Johnson, Toby, Elliott, Paul, Rybin, Denis, Henneman, Peter, Dehghan, Abbas, Hottenga, Jouke Jan, Song, Kijoung, Goel, Anuj, Egan, Josephine M, Lajunen, Taina, Doney, Alex, Kanoni, Stavroula, Cavalcanti-Proença, Christine, Kumari, Meena, Timpson, Nicholas J, Zabena, Carina, Ingelsson, Erik, An, Ping, O'Connell, Jeffrey, Luan, Jian'an, Elliott, Amanda, McCarroll, Steven A, Roccasecca, Rosa Maria, Pattou, François, Sethupathy, Praveen, Ariyurek, Yavuz, Barter, Philip, Beilby, John P, Ben-Shlomo, Yoav, Bergmann, Sven, Bochud, Murielle, Bonnefond, Amélie, Borch-Johnsen, Knut, Böttcher, Yvonne, Brunner, Eric, Bumpstead, Suzannah J, Chen, Yii-Der Ida, Chines, Peter, Clarke, Robert, Coin, Lachlan JM, Cooper, Matthew N, Crisponi, Laura, Day, Ian NM, De Geus, Eco JC, Delplanque, Jerome, Fedson, Annette C, Fischer-Rosinsky, Antje, Forouhi, Nita G, Frants, Rune, Franzosi, Maria Grazia, Galan, Pilar, Goodarzi, Mark O, Graessler, Jürgen, Grundy, Scott, Gwilliam, Rhian, Hallmans, Göran, Hammond, Naomi, Han, Xijing, Hartikainen, Anna-Liisa, Hayward, Caroline, Heath, Simon C, Hercberg, Serge, Hicks, Andrew A, Hillman, David R, Hingorani, Aroon D, Hui, Jennie, Hung, Joe, Jula, Antti, Kaakinen, Marika, Kaprio, Jaakko, Kesaniemi, Y Antero, Kivimaki, Mika, Knight, Beatrice, Koskinen, Seppo, Kovacs, Peter, Kyvik, Kirsten Ohm, Lathrop, G Mark, Lawlor, Debbie A, Le Bacquer, Olivier, Lecoeur, Cécile, Li, Yun, Mahley, Robert, Mangino, Massimo, Manning, Alisa K, Martínez-Larrad, María Teresa, McAteer, Jarred B, McPherson, Ruth, Meisinger, Christa, Melzer, David, Meyre, David, Mitchell, Braxton D, Mukherjee, Sutapa, Naitza, Silvia, Neville, Matthew J, Oostra, Ben A, Orrù, Marco, Pakyz, Ruth, Paolisso, Giuseppe, Pattaro, Cristian, Pearson, Daniel, Peden, John F, Pedersen, Nancy L, Perola, Markus, Pfeiffer, Andreas FH, Pichler, Irene, Polasek, Ozren, Posthuma, Danielle, Potter, Simon C, Pouta, Anneli, Province, Michael A, Psaty, Bruce M, Rayner, Nigel W, Rice, Kenneth, Ripatti, Samuli, Rivadeneira, Fernando, Rolandsson, Olov, Sandbaek, Annelli, Sandhu, Manjinder, Sanna, Serena, Sayer, Avan Aihie, Scheet, Paul, Seedorf, Udo, Sharp, Stephen J, Shields, Beverley, Sijbrands, Eric JG, Silveira, Angela, Simpson, Laila, Singleton, Andrew, Smith, Nicholas L, Sovio, Ulla, Swift, Amy, Syddall, Holly, Syvänen, Ann-Christine, Tanaka, Toshiko, Tönjes, Anke, Uitterlinden, André G, Van Dijk, Ko Willems, Varma, Dhiraj, Visvikis-Siest, Sophie, Vitart, Veronique, Vogelzangs, Nicole, Waeber, Gérard, Wagner, Peter J, Walley, Andrew, Ward, Kim L, Watkins, Hugh, Wild, Sarah H, Willemsen, Gonneke, Witteman, Jaqueline CM, Yarnell, John WG, Zelenika, Diana, Zethelius, Björn, Zhai, Guangju, Zhao, Jing Hua, Zillikens, M Carola, Borecki, Ingrid B, Loos, Ruth JF, Meneton, Pierre, Magnusson, Patrik KE, Nathan, David M, Williams, Gordon H, Silander, Kaisa, Salomaa, Veikko, Smith, George Davey, Bornstein, Stefan R, Schwarz, Peter, Spranger, Joachim, Karpe, Fredrik, Shuldiner, Alan R, Cooper, Cyrus, Dedoussis, George V, Serrano-Ríos, Manuel, Lind, Lars, Palmer, Lyle J, Franks, Paul W, Ebrahim, Shah, Marmot, Michael, Kao, WH Linda, Pramstaller, Peter Paul, Wright, Alan F, Stumvoll, Michael, Hamsten, Anders, Buchanan, Thomas A, Valle, Timo T, Rotter, Jerome I, Siscovick, David S, Penninx, Brenda WJH, Boomsma, Dorret I, Deloukas, Panos, Spector, Timothy D, Ferrucci, Luigi, Cao, Antonio, Scuteri, Angelo, Schlessinger, David, Uda, Manuela, Ruokonen, Aimo, Jarvelin, Marjo-Riitta, Waterworth, Dawn M, Vollenweider, Peter, Peltonen, Leena, Mooser, Vincent, Sladek, Robert, Center for Liver, Digestive and Metabolic Diseases (CLDM), Palmer, Nd, Mcdonough, Cw, Hicks, Pj, Roh, Bh, Wing, Mr, An, S, Hester, Jm, Cooke, Jn, Bostrom, Ma, Rudock, Me, Talbert, Me, Lewis, Jp, Diagram, Consortium, Magic, Investigator, Ferrara, A, Lu, L, Ziegler, Jt, Sale, Mm, Divers, J, Shriner, D, Adeyemo, A, Rotimi, Cn, Ng, Mc, Langefeld, Cd, Freedman, Bi, Bowden, Dw, Voight, Bf, Scott, Lj, Steinthorsdottir, V, Morris, Ap, Dina, C, Welch, Rp, Zeggini, E, Huth, C, Aulchenko, Y, Thorleifsson, G, Mcculloch, Lj, Ferreira, T, Grallert, H, Amin, N, Wu, G, Willer, Cj, Raychaudhuri, S, Mccarroll, Sa, Langenberg, C, Hofmann, Om, Dupuis, J, Qi, L, Segrè, Av, van Hoek, M, Navarro, P, Ardlie, K, Balkau, B, Benediktsson, R, Bennett, Aj, Blagieva, R, Boerwinkle, E, Bonnycastle, Ll, Boström, Kb, Bravenboer, B, Bumpstead, S, Burtt, Np, Charpentier, G, Chines, P, Cornelis, M, Couper, Dj, Crawford, G, Doney, A, Elliott, K, Elliott, Al, Erdos, Mr, Fox, C, Franklin, C, Ganser, M, Gieger, C, Grarup, N, Green, T, Griffin, S, Groves, Cj, Guiducci, C, Hadjadj, S, Hassanali, N, Herder, C, Isomaa, B, Jackson, Au, Johnson, Pr, Jørgensen, T, Kao, Wh, Klopp, N, Kong, A, Kraft, P, Kuusisto, J, Lauritzen, T, Li, M, Lieverse, A, Lindgren, Cm, Lyssenko, V, Marre, M, Meitinger, T, Midthjell, K, Morken, Ma, Narisu, N, Nilsson, P, Owen, Kr, Payne, F, Perry, Jr, Petersen, Ak, Platou, C, Proença, C, Prokopenko, I, Rathmann, W, Rayner, Nw, Robertson, Nr, Rocheleau, G, Roden, M, Sampson, Mj, Saxena, R, Shields, Bm, Shrader, P, Sigurdsson, G, Sparsø, T, Strassburger, K, Stringham, Hm, Sun, Q, Swift, Aj, Thorand, B, Tichet, J, Tuomi, T, van Dam, Rm, van Haeften, Tw, van Herpt, T, van Vliet Ostaptchouk, Jv, Walters, Gb, Weedon, Mn, Wijmenga, C, Witteman, J, Bergman, Rn, Cauchi, S, Collins, F, Gloyn, Al, Gyllensten, U, Hansen, T, Hide, Wa, Hitman, Ga, Hofman, A, Hunter, Dj, Hveem, K, Laakso, M, Mohlke, Kl, Morris, Ad, Palmer, Cn, Pramstaller, Pp, Rudan, I, Sijbrands, E, Stein, Ld, Tuomilehto, J, Uitterlinden, A, Walker, M, Wareham, Nj, Watanabe, Rm, Abecasis, Gr, Boehm, Bo, Campbell, H, Daly, Mj, Hattersley, At, Hu, Fb, Meigs, Jb, Pankow, J, Pedersen, O, Wichmann, He, Barroso, I, Florez, Jc, Frayling, Tm, Groop, L, Sladek, R, Thorsteinsdottir, U, Wilson, Jf, Illig, T, Froguel, P, van Duijn, Cm, Stefansson, K, Altshuler, D, Boehnke, M, Mccarthy, Mi, Soranzo, N, Wheeler, E, Glazer, Nl, Bouatia Naji, N, Mägi, R, Randall, J, Johnson, T, Elliott, P, Rybin, D, Henneman, P, Dehghan, A, Hottenga, Jj, Song, K, Goel, A, Egan, Jm, Lajunen, T, Kanoni, S, Cavalcanti Proença, C, Kumari, M, Timpson, Nj, Zabena, C, Ingelsson, E, An, P, O'Connell, J, Luan, J, Elliott, A, Roccasecca, Rm, Pattou, F, Sethupathy, P, Ariyurek, Y, Barter, P, Beilby, Jp, Ben Shlomo, Y, Bergmann, S, Bochud, M, Bonnefond, A, Borch Johnsen, K, Böttcher, Y, Brunner, E, Bumpstead, Sj, Chen, Yd, Clarke, R, Coin, Lj, Cooper, Mn, Crisponi, L, Day, In, de Geus, Ej, Delplanque, J, Fedson, Ac, Fischer Rosinsky, A, Forouhi, Ng, Frants, R, Franzosi, Mg, Galan, P, Goodarzi, Mo, Graessler, J, Grundy, S, Gwilliam, R, Hallmans, G, Hammond, N, Han, X, Hartikainen, Al, Hayward, C, Heath, Sc, Hercberg, S, Hicks, Aa, Hillman, Dr, Hingorani, Ad, Hui, J, Hung, J, Jula, A, Kaakinen, M, Kaprio, J, Kesaniemi, Ya, Kivimaki, M, Knight, B, Koskinen, S, Kovacs, P, Kyvik, Ko, Lathrop, Gm, Lawlor, Da, Le Bacquer, O, Lecoeur, C, Li, Y, Mahley, R, Mangino, M, Manning, Ak, Martínez Larrad, Mt, Mcateer, Jb, Mcpherson, R, Meisinger, C, Melzer, D, Meyre, D, Mitchell, Bd, Mukherjee, S, Naitza, S, Neville, Mj, Oostra, Ba, Orrù, M, Pakyz, R, Paolisso, Giuseppe, Pattaro, C, Pearson, D, Peden, Jf, Pedersen, Nl, Perola, M, Pfeiffer, Af, Pichler, I, Polasek, O, Posthuma, D, Potter, Sc, Pouta, A, Province, Ma, Psaty, Bm, Rice, K, Ripatti, S, Rivadeneira, F, Rolandsson, O, Sandbaek, A, Sandhu, M, Sanna, S, Sayer, Aa, Scheet, P, Seedorf, U, Sharp, Sj, Shields, B, Sijbrands, Ej, Silveira, A, Simpson, L, Singleton, A, Smith, Nl, Sovio, U, Swift, A, Syddall, H, Syvänen, Ac, Tanaka, T, Tönjes, A, Uitterlinden, Ag, van Dijk, Kw, Varma, D, Visvikis Siest, S, Vitart, V, Vogelzangs, N, Waeber, G, Wagner, Pj, Walley, A, Ward, Kl, Watkins, H, Wild, Sh, Willemsen, G, Witteman, Jc, Yarnell, Jw, Zelenika, D, Zethelius, B, Zhai, G, Zhao, Jh, Zillikens, Mc, Borecki, Ib, Loos, Rj, Meneton, P, Magnusson, Pk, Nathan, Dm, Williams, Gh, Silander, K, Salomaa, V, Smith, Gd, Bornstein, Sr, Schwarz, P, Spranger, J, Karpe, F, Shuldiner, Ar, Cooper, C, Dedoussis, Gv, Serrano Ríos, M, Lind, L, Palmer, Lj, Franks, Pw, Ebrahim, S, Marmot, M, Wright, Af, Stumvoll, M, Hamsten, A, Buchanan, Ta, Valle, Tt, Rotter, Ji, Siscovick, D, Penninx, Bw, Boomsma, Di, Deloukas, P, Spector, Td, Ferrucci, L, Cao, A, Scuteri, A, Schlessinger, D, Uda, M, Ruokonen, A, Jarvelin, Mr, Waterworth, Dm, Vollenweider, P, Peltonen, L, Mooser, V, Sladek, R., Medical Research Council (MRC), Human genetics, Psychiatry, NCA - Attention & Cognition, EMGO - Lifestyle, overweight and diabetes, Biological Psychology, Functional Genomics, Neuroscience Campus Amsterdam - Attention & Cognition, EMGO+ - Lifestyle, Overweight and Diabetes, Langenberg, Claudia [0000-0002-5017-7344], Griffin, Simon [0000-0002-2157-4797], Wareham, Nicholas [0000-0003-1422-2993], Soranzo, Nicole [0000-0003-1095-3852], Wheeler, Eleanor [0000-0002-8616-6444], Luan, Jian'an [0000-0003-3137-6337], Forouhi, Nita [0000-0002-5041-248X], Sharp, Stephen [0000-0003-2375-1440], Sovio, Ulla [0000-0002-0799-1105], Apollo - University of Cambridge Repository, DIAGRAM Consortium, MAGIC Investigators, Johnson, T., Bergman, S., Bochud, M., Waeber, G., and Vollenweider, P.
Subjects: Netherlands Twin Register (NTR), Male, Adult, African Americans/genetics, Aged, Case-Control Studies, Cohort Studies, Diabetes Mellitus, Type 2/ethnology, Diabetes Mellitus, Type 2/genetics, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Meta-Analysis as Topic, Middle Aged, Polymorphism, Single Nucleotide, Validation Studies as Topic, Medicin och hälsovetenskap, Linkage disequilibrium, Genetic Screens, endocrine system diseases, lcsh:Medicine, Genome-wide association study, Medical and Health Sciences, 0302 clinical medicine, Endocrinology, Genome Sequencing, lcsh:Science, Medicine(all), Genetics, African Americans, 0303 health sciences, education.field_of_study, INSULIN-RESISTANCE, Multidisciplinary, Agricultural and Biological Sciences(all), LARGE-SCALE ASSOCIATION, STAGE RENAL-DISEASE, COMMON VARIANTS, Genomics, Medicine, Research Article, SUSCEPTIBILITY LOCI, General Science & Technology, Population, Single-nucleotide polymorphism, Biology, DIAGRAM Consortium, 03 medical and health sciences, MAGIC Investigators, SDG 3 - Good Health and Well-being, Genetic linkage, MD Multidisciplinary, Genome-Wide Association Studies, SNP, ddc:610, education, Genotyping, 030304 developmental biology, Diabetic Endocrinology, LINKAGE ANALYSIS, Biochemistry, Genetics and Molecular Biology(all), lcsh:R, TCF7L2 GENE, Case-control study, Computational Biology, nutritional and metabolic diseases, Human Genetics, Diabetes Mellitus Type 2, Stage renal-disease, large-scale association, Susceptibility loci, Insulin-resistance, Fasting glucose, Tissue factor, Homeodomain protein, Linkage analysis, Common variants, TCF7L2 gene, Black or African American, Diabetes Mellitus, Type 2, TISSUE FACTOR, Genetics of Disease, HOMEODOMAIN PROTEIN, Genetic Polymorphism, lcsh:Q, Genome Expression Analysis, 030217 neurology & neurosurgery, Population Genetics, FASTING GLUCOSE
Abstract: African Americans are disproportionately affected by type 2 diabetes (T2DM) yet few studies have examined T2DM using genome-wide association approaches in this ethnicity. The aim of this study was to identify genes associated with T2DM in the African American population. We performed a Genome Wide Association Study (GWAS) using the Affymetrix 6.0 array in 965 African-American cases with T2DM and end-stage renal disease (T2DM-ESRD) and 1029 population-based controls. The most significant SNPs (n = 550 independent loci) were genotyped in a replication cohort and 122 SNPs (n = 98 independent loci) were further tested through genotyping three additional validation cohorts followed by meta-analysis in all five cohorts totaling 3,132 cases and 3,317 controls. Twelve SNPs had evidence of association in the GWAS (P
Published: 2012

207. Increased Genetic Vulnerability to Smoking at CHRNA5 in Early-Onset Smokers

Author: Gubjartsson, Daniel, Ducci, Francesca, Hansel, Nadia N., Jiang, Chenhui, Short, Susan E., Rosenberger, Albert, Scheet, Paul, Lyytikäinen, Leo-Pekka, Culverhouse, Robert, Vogelzangs, Nicole, Shaffer, John R., Stephens, Sarah H., Rawal, Rajesh, Saccone, Nancy L., Sun, Juzhong, Teumer, Alexander, Han, Younghun, Hartz, Sarah M., Franceschini, Nora, Keskitalo-Vuokko, Kaisu, Liu, Zhen, Coon, Hilary, Schwantes-An, Tae-Hwi, Vink, Jacqueline M., Michel, Martha, Wenzlaff, Angela S., Chen, LiShiun, Dueker, Nicole, Thompson, John R., Frank, Josef, Chen, Xiangning, and Geller, Frank
Subjects: education, mental disorders
Abstract: Recent studies have shown an association between cigarettes per day (CPD) and a nonsynonymous single-nucleotide polymorphism in CHRNA5, rs16969968.
Published: 2012
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208. Genetics of glucocorticoid-associated osteonecrosis in children with acute lymphoblastic leukemia

Author: Karol, Seth E., primary, Yang, Wenjian, additional, Van Driest, Sara L., additional, Chang, Tamara Y., additional, Kaste, Sue, additional, Bowton, Erica, additional, Basford, Melissa, additional, Bastarache, Lisa, additional, Roden, Dan M., additional, Denny, Joshua C., additional, Larsen, Eric, additional, Winick, Naomi, additional, Carroll, William L., additional, Cheng, Cheng, additional, Pei, Deqing, additional, Fernandez, Christian A., additional, Liu, Chengcheng, additional, Smith, Colton, additional, Loh, Mignon L., additional, Raetz, Elizabeth A., additional, Hunger, Stephen P., additional, Scheet, Paul, additional, Jeha, Sima, additional, Pui, Ching-Hon, additional, Evans, William E., additional, Devidas, Meenakshi, additional, Mattano, Leonard A., additional, and Relling, Mary V., additional
Published: 2015
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209. Abstract 4806: Characterizing the genomic landscape of premalignant colorectal polyps using next-generation sequencing

Author: Borras, Ester, primary, San Lucas, Anthony, additional, Chang, Kyle, additional, Bhatia, Gita, additional, Wu, Hong, additional, Fowler, Jerry, additional, You, Y. Nancy, additional, Lynch, Patrick M., additional, Taggart, Melissa W., additional, Hawk, Ernest T., additional, Capella, Gabriel, additional, Scheet, Paul, additional, and Vilar, Eduardo, additional
Published: 2015
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210. Abstract 1087: Genomic analysis reveals evidence of clonality in premalignant colonic polyps

Author: Chang, Kyle, primary, Borras, Ester, additional, San Lucas, Anthony, additional, Fowler, Jerry, additional, Hawk, Ernest T., additional, Capella, Gabriel, additional, Scheet, Paul, additional, and Vilar, Eduardo, additional
Published: 2015
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211. Abstract 2993: The landscape of DNA allelic imbalance in the normal-appearing airway field of cancerization

Author: Jakubek, Yasminka, primary, Lang, Wenhua, additional, Vattathil, Selina, additional, Garcia, Melinda, additional, Huang, Lili, additional, Lu, Wei, additional, Chow, Chi-Wan, additional, Weber, Zachary, additional, Davies, Gareth E., additional, Behrens, Carmen, additional, Kalhor, Neda, additional, Moran, Cesar, additional, Fujimoto, Junya, additional, Mehran, Reza J., additional, Fowler, Jerry, additional, Ehli, Erik A., additional, Wistuba, Ignacio I., additional, Scheet, Paul, additional, and Kadara, Humam, additional
Published: 2015
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212. A genome-wide approach to children's aggressive behavior:The EAGLE consortium

Author: Pappa, Irene, primary, St Pourcain, Beate, additional, Benke, Kelly, additional, Cavadino, Alana, additional, Hakulinen, Christian, additional, Nivard, Michel G., additional, Nolte, Ilja M., additional, Tiesler, Carla M. T., additional, Bakermans-Kranenburg, Marian J., additional, Davies, Gareth E., additional, Evans, David M., additional, Geoffroy, Marie-Claude, additional, Grallert, Harald, additional, Groen-Blokhuis, Maria M., additional, Hudziak, James J., additional, Kemp, John P., additional, Keltikangas-Järvinen, Liisa, additional, McMahon, George, additional, Mileva-Seitz, Viara R., additional, Motazedi, Ehsan, additional, Power, Christine, additional, Raitakari, Olli T., additional, Ring, Susan M., additional, Rivadeneira, Fernando, additional, Rodriguez, Alina, additional, Scheet, Paul A., additional, Seppälä, Ilkka, additional, Snieder, Harold, additional, Standl, Marie, additional, Thiering, Elisabeth, additional, Timpson, Nicholas J., additional, Veenstra, René, additional, Velders, Fleur P., additional, Whitehouse, Andrew J. O., additional, Smith, George Davey, additional, Heinrich, Joachim, additional, Hypponen, Elina, additional, Lehtimäki, Terho, additional, Middeldorp, Christel M., additional, Oldehinkel, Albertine J., additional, Pennell, Craig E., additional, Boomsma, Dorret I., additional, and Tiemeier, Henning, additional
Published: 2015
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213. Intelligence: shared genetic basis between Mendelian disorders and a polygenic trait

Author: Franić, Sanja, primary, Groen-Blokhuis, Maria M, additional, Dolan, Conor V, additional, Kattenberg, Mathijs V, additional, Pool, René, additional, Xiao, Xiangjun, additional, Scheet, Paul A, additional, Ehli, Erik A, additional, Davies, Gareth E, additional, van der Sluis, Sophie, additional, Abdellaoui, Abdel, additional, Hansell, Narelle K, additional, Martin, Nicholas G, additional, Hudziak, James J, additional, van Beijsterveldt, Catherina E M, additional, Swagerman, Suzanne C, additional, Hulshoff Pol, Hilleke E, additional, de Geus, Eco J C, additional, Bartels, Meike, additional, Ropers, H Hilger, additional, Hottenga, Jouke-Jan, additional, and Boomsma, Dorret I, additional
Published: 2015
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214. Somatic mutation load of estrogen receptor-positive breast tumors predicts overall survival: an analysis of genome sequence data.

Author: Haricharan, Svasti, Haricharan, Svasti, Bainbridge, Matthew N, Scheet, Paul, Brown, Powel H, Haricharan, Svasti, Haricharan, Svasti, Bainbridge, Matthew N, Scheet, Paul, and Brown, Powel H
Abstract: Breast cancer is one of the most commonly diagnosed cancers in women. While there are several effective therapies for breast cancer and important single gene prognostic/predictive markers, more than 40,000 women die from this disease every year. The increasing availability of large-scale genomic datasets provides opportunities for identifying factors that influence breast cancer survival in smaller, well-defined subsets. The purpose of this study was to investigate the genomic landscape of various breast cancer subtypes and its potential associations with clinical outcomes. We used statistical analysis of sequence data generated by the Cancer Genome Atlas initiative including somatic mutation load (SML) analysis, Kaplan-Meier survival curves, gene mutational frequency, and mutational enrichment evaluation to study the genomic landscape of breast cancer. We show that ER(+), but not ER(-), tumors with high SML associate with poor overall survival (HR = 2.02). Further, these high mutation load tumors are enriched for coincident mutations in both DNA damage repair and ER signature genes. While it is known that somatic mutations in specific genes affect breast cancer survival, this study is the first to identify that SML may constitute an important global signature for a subset of ER(+) tumors prone to high mortality. Moreover, although somatic mutations in individual DNA damage genes affect clinical outcome, our results indicate that coincident mutations in DNA damage response and signature ER genes may prove more informative for ER(+) breast cancer survival. Next generation sequencing may prove an essential tool for identifying pathways underlying poor outcomes and for tailoring therapeutic strategies.
Published: 2014

215. A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data.

Author: Hu, Hao, Hu, Hao, Roach, Jared C, Coon, Hilary, Guthery, Stephen L, Voelkerding, Karl V, Margraf, Rebecca L, Durtschi, Jacob D, Tavtigian, Sean V, Shankaracharya, Wu, Wilfred, Scheet, Paul, Wang, Shuoguo, Xing, Jinchuan, Glusman, Gustavo, Hubley, Robert, Li, Hong, Garg, Vidu, Moore, Barry, Hood, Leroy, Galas, David J, Srivastava, Deepak, Reese, Martin G, Jorde, Lynn B, Yandell, Mark, Huff, Chad D, Hu, Hao, Hu, Hao, Roach, Jared C, Coon, Hilary, Guthery, Stephen L, Voelkerding, Karl V, Margraf, Rebecca L, Durtschi, Jacob D, Tavtigian, Sean V, Shankaracharya, Wu, Wilfred, Scheet, Paul, Wang, Shuoguo, Xing, Jinchuan, Glusman, Gustavo, Hubley, Robert, Li, Hong, Garg, Vidu, Moore, Barry, Hood, Leroy, Galas, David J, Srivastava, Deepak, Reese, Martin G, Jorde, Lynn B, Yandell, Mark, and Huff, Chad D
Abstract: High-throughput sequencing of related individuals has become an important tool for studying human disease. However, owing to technical complexity and lack of available tools, most pedigree-based sequencing studies rely on an ad hoc combination of suboptimal analyses. Here we present pedigree-VAAST (pVAAST), a disease-gene identification tool designed for high-throughput sequence data in pedigrees. pVAAST uses a sequence-based model to perform variant and gene-based linkage analysis. Linkage information is then combined with functional prediction and rare variant case-control association information in a unified statistical framework. pVAAST outperformed linkage and rare-variant association tests in simulations and identified disease-causing genes from whole-genome sequence data in three human pedigrees with dominant, recessive and de novo inheritance patterns. The approach is robust to incomplete penetrance and locus heterogeneity and is applicable to a wide variety of genetic traits. pVAAST maintains high power across studies of monogenic, high-penetrance phenotypes in a single pedigree to highly polygenic, common phenotypes involving hundreds of pedigrees.
Published: 2014

216. A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data.

Author: Luxembourg Centre for Systems Biomedicine (LCSB): Experimental Neurobiology (Balling Group) [research center], Hu, Hao, Roach, Jared C., Coon, Hilary, Guthery, Stephen L., Voelkerding, Karl V., Margraf, Rebecca L., Durtschi, Jacob D., Tavtigian, Sean V., Shankaracharya, Wu, Wilfred, Scheet, Paul, Wang, Shuoguo, Xing, Jinchuan, Glusman, Gustavo, Hubley, Robert, Li, Hong, Garg, Vidu, Moore, Barry, Hood, Leroy, Galas, David J., Srivastava, Deepak, Reese, Martin G., Jorde, Lynn B., Yandell, Mark, Huff, Chad D., Luxembourg Centre for Systems Biomedicine (LCSB): Experimental Neurobiology (Balling Group) [research center], Hu, Hao, Roach, Jared C., Coon, Hilary, Guthery, Stephen L., Voelkerding, Karl V., Margraf, Rebecca L., Durtschi, Jacob D., Tavtigian, Sean V., Shankaracharya, Wu, Wilfred, Scheet, Paul, Wang, Shuoguo, Xing, Jinchuan, Glusman, Gustavo, Hubley, Robert, Li, Hong, Garg, Vidu, Moore, Barry, Hood, Leroy, Galas, David J., Srivastava, Deepak, Reese, Martin G., Jorde, Lynn B., Yandell, Mark, and Huff, Chad D.
Abstract: High-throughput sequencing of related individuals has become an important tool for studying human disease. However, owing to technical complexity and lack of available tools, most pedigree-based sequencing studies rely on an ad hoc combination of suboptimal analyses. Here we present pedigree-VAAST (pVAAST), a disease-gene identification tool designed for high-throughput sequence data in pedigrees. pVAAST uses a sequence-based model to perform variant and gene-based linkage analysis. Linkage information is then combined with functional prediction and rare variant case-control association information in a unified statistical framework. pVAAST outperformed linkage and rare-variant association tests in simulations and identified disease-causing genes from whole-genome sequence data in three human pedigrees with dominant, recessive and de novo inheritance patterns. The approach is robust to incomplete penetrance and locus heterogeneity and is applicable to a wide variety of genetic traits. pVAAST maintains high power across studies of monogenic, high-penetrance phenotypes in a single pedigree to highly polygenic, common phenotypes involving hundreds of pedigrees.
Published: 2014

217. Glutamate Receptor Polymorphisms Contribute to Glucocorticoid-Associated Osteonecrosis

Author: Chang, Tamara, primary, Yang, Wenjian, additional, Sara, Van Driest L, additional, Kaste, Sue C., additional, Bowten, Erica A, additional, Basford, Melissa, additional, Bastarache, Lisa, additional, Roden, Dan M, additional, Denny, Joshua C, additional, Mattano, Leonard A., additional, Larsen, Eric C., additional, Winick, Naomi J., additional, Carroll, William L., additional, Cheng, Cheng, additional, Pei, Deqing, additional, Fernandez, Christian A., additional, Liu, Chengcheng, additional, Smith, Colton, additional, Loh, Mignon, additional, Raetz, Elizabeth A, additional, Hunger, Stephen, additional, Scheet, Paul, additional, Jeha, Sima, additional, Pui, Ching-Hon, additional, Evans, William E., additional, Devidas, Meenakshi, additional, and Relling, Mary V., additional
Published: 2014
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218. Preliminary whole-exome sequencing reveals mutations that imply common tumorigenicity pathways in multiple endocrine neoplasia type 1 patients

Author: Romero Arenas, Minerva Angélica, primary, Fowler, Richard G., additional, San Lucas, F. Anthony, additional, Shen, Jie, additional, Rich, Thereasa A., additional, Grubbs, Elizabeth G., additional, Lee, Jeffrey E., additional, Scheet, Paul, additional, Perrier, Nancy D., additional, and Zhao, Hua, additional
Published: 2014
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219. Cancer In Silico Drug Discovery: A Systems Biology Tool for Identifying Candidate Drugs to Target Specific Molecular Tumor Subtypes

Author: San Lucas, F. Anthony, primary, Fowler, Jerry, additional, Chang, Kyle, additional, Kopetz, Scott, additional, Vilar, Eduardo, additional, and Scheet, Paul, additional
Published: 2014
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220. Common variants at 30 loci contribute to polygenic dyslipidemia

Author: Tanaka, Toshiko, Galan, Pilar, Demissie, Serkalem, Schadt, Eric E, Surti, Aarti, Ferrucci, Luigi, Bennett, Derrick, Kubalanza, Kari A, Peloso, Gina M, Parish, Sarah, Zelenika, Diana, Voight, Benjamin F, Scott, Laura J, Kaplan, Lee, Clarke, Robert, Jackson, Anne U, Musunuru, Kiran, Laakso, Markku, Bonnycastle, Lori L, Bergman, Richard N, Kuusisto, Johanna, Swift, Amy J, Kathiresan, Sekar, Burtt, Noel P, Li, Yun, Crawford, Gabriel, Scheet, Paul, Willer, Cristen J, Sundvall, Jouko, Stringham, Heather M, Morken, Mario A, and Guiducci, Candace
Subjects: lipids (amino acids, peptides, and proteins)
Abstract: Blood low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol and triglyceride levels are risk factors for cardiovascular disease. To dissect the polygenic basis of these traits, we conducted genome-wide association screens in 19,840 individuals and replication in up to 20,623 individuals. We identified 30 distinct loci associated with lipoprotein concentrations (each with P < 5 × 10-8), including 11 loci that reached genome-wide significance for the first time. The 11 newly defined loci include common variants associated with LDL cholesterol near ABCG8, MAFB, HNF1A and TIMD4; with HDL cholesterol near ANGPTL4, FADS1-FADS2-FADS3, HNF4A, LCAT, PLTP and TTC39B; and with triglycerides near AMAC1L2, FADS1-FADS2-FADS3 and PLTP. The proportion of individuals exceeding clinical cut points for high LDL cholesterol, low HDL cholesterol and high triglycerides varied according to an allelic dosage score (P < 10-15 for each trend). These results suggest that the cumulative effect of multiple common variants contributes to polygenic dyslipidemia.
Published: 2009
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221. Correction: Genome-Wide Association Scan Meta-Analysis Identifies Three Loci Influencing Adiposity and Fat Distribution

Author: Timpson, Nicholas J., Scheet, Paul, Thorleifsson, Gudmar, Speliotes, Elizabeth K., Lim, Noha, Almgren, Peter, Lamina, Claudia, Randall, Joshua C., Bergman, Richard N., Qi, Lu, Zhao, Jing Hua, Drong, Alexander, Bandinelli, Stefania, Lyon, Helen N., Bonnycastle, Lori L., Heid, Iris M., Bennett, Amanda J., Willer, Cristen J., Soranzo, Nicole, Amin, Najaf, Aulchenko, Yurii S., Zillikens, M. Carola, Luan, Jian'an, Rivadeneira, Fernando, Sanna, Serena, Chanock, Stephen J., Bumpstead, Suzannah J., Jackson, Anne U., Steinthorsdottir, Valgerdur, Herrera, Blanca M., Chambers, John C., and Lindgren, Cecilia M.
Abstract: To identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580) informative for adult waist circumference (WC) and waist–hip ratio (WHR). We selected 26 SNPs for follow-up, for which the evidence of association with measures of central adiposity (WC and/or WHR) was strong and disproportionate to that for overall adiposity or height. Follow-up studies in a maximum of 70,689 individuals identified two loci strongly associated with measures of central adiposity; these map near TFAP2B (WC, P = 1.9×10−11) and MSRA (WC, P = 8.9×10−9). A third locus, near LYPLAL1, was associated with WHR in women only (P = 2.6×10−8). The variants near TFAP2B appear to influence central adiposity through an effect on overall obesity/fat-mass, whereas LYPLAL1 displays a strong female-only association with fat distribution. By focusing on anthropometric measures of central obesity and fat distribution, we have identified three loci implicated in the regulation of human adiposity.
Published: 2009
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222. Six new loci associated with body mass index highlight a neuronal influence on body weight regulation

Author: Willer, Cristen J, Scheet, Paul, Prokopenko, Inga, McCarroll, Steven A, Soranzo, Nicole, Weedon, Michael N, Lim, Noha, Speliotes, Elizabeth K, Bingham, Sheila A, Bergman, Richard N, Li, Shengxu, Heid, Iris M, Bennett, Amanda, Wheeler, Eleanor, Jackson, Anne U, Berndt, Sonja I, Sanna, Serena, Qi, Lu, Lindgren, Cecilia M, Papadakis, Konstantinos, Elliott, Amanda L, Tanaka, Toshiko, Zhao, Jing Hua, Almgren, Peter, Roccasecca, Rosa Maria, Lettre, Guillaume, Timpson, Nicholas J, Jacobs, Leonie C, Randall, Joshua C, Lamina, Claudia, Loos, Ruth J F, and Lyon, Helen N
Abstract: Common variants at only two loci, FTO and MC4R, have been reproducibly associated with body mass index (BMI) in humans. To identify additional loci, we conducted meta-analysis of 15 genome-wide association studies for BMI (n > 32,000) and followed up top signals in 14 additional cohorts (n > 59,000). We strongly confirm FTO and MC4R and identify six additional loci (P < 5 × 10−8): TMEM18, KCTD15, GNPDA2, SH2B1, MTCH2 and NEGR1 (where a 45-kb deletion polymorphism is a candidate causal variant). Several of the likely causal genes are highly expressed or known to act in the central nervous system (CNS), emphasizing, as in rare monogenic forms of obesity, the role of the CNS in predisposition to obesity.
Published: 2009
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223. Variants in the melatonin receptor 1B gene (MTNR1B) influence fasting glucose levels

Author: Prokopenko, Inga, Langenberg, Claudia, Florez, Jose C., Saxena, Richa, Soranzo, Nicole, Thorleifsson, Gudmar, Loos, Ruth J.F., Manning, Alisa K., Jackson, Anne U., Aulchenko, Yurii, Potter, Simon C., Erdos, Michael R., Sanna, Serena, Hottenga, Jouke-Jan, Wheeler, Eleanor, Kaakinen, Marika, Lyssenko, Valeriya, Chen, Wei-Min, Ahmadi, Kourosh, Beckmann, Jacques S., Bergman, Richard N., Bochud, Murielle, Bonnycastle, Lori L., Buchanan, Thomas A., Cao, Antonio, Cervino, Alessandra, Coin, Lachlan, Collins, Francis S., Crisponi, Laura, de Geus, Eco JC, Dehghan, Abbas, Deloukas, Panos, Doney, Alex S F, Elliott, Paul, Freimer, Nelson, Gateva, Vesela, Herder, Christian, Hofman, Albert, Hughes, Thomas E., Hunt, Sarah, Illig, Thomas, Inouye, Michael, Isomaa, Bo, Johnson, Toby, Kong, Augustine, Krestyaninova, Maria, Kuusisto, Johanna, Laakso, Markku, Lim, Noha, Lindblad, Ulf, Lindgren, Cecilia M., McCann, Owen T., Mohlke, Karen L., Morris, Andrew D, Naitza, Silvia, Orrù, Marco, Palmer, Colin N A, Pouta, Anneli, Randall, Joshua, Rathmann, Wolfgang, Saramies, Jouko, Scheet, Paul, Scott, Laura J., Scuteri, Angelo, Sharp, Stephen, Sijbrands, Eric, Smit, Jan H., Song, Kijoung, Steinthorsdottir, Valgerdur, Stringham, Heather M., Tuomi, Tiinamaija, Tuomilehto, Jaakko, Uitterlinden, André G., Voight, Benjamin F., Waterworth, Dawn, Wichmann, H.-Erich, Willemsen, Gonneke, Witteman, Jacqueline CM, Yuan, Xin, Zhao, Jing Hua, Zeggini, Eleftheria, Schlessinger, David, Sandhu, Manjinder, Boomsma, Dorret I, Uda, Manuela, Spector, Tim D., Penninx, Brenda WJH, Altshuler, David, Vollenweider, Peter, Jarvelin, Marjo Riitta, Lakatta, Edward, Waeber, Gerard, Fox, Caroline S., Peltonen, Leena, Groop, Leif C., Mooser, Vincent, Cupples, L. Adrienne, Thorsteinsdottir, Unnur, Boehnke, Michael, Barroso, Inês, Van Duijn, Cornelia, Dupuis, Josée, Watanabe, Richard M., Stefansson, Kari, McCarthy, Mark I., Wareham, Nicholas J., Meigs, James B., and Abecasis, Goncalo R.
Subjects: Blood Glucose, Diabetes Mellitus, Type 2, Meta-Analysis as Topic, Receptor, Melatonin, MT2, Case-Control Studies, Quantitative Trait Loci, Receptors, Melatonin, Humans, Genetic Predisposition to Disease, Fasting, Polymorphism, Single Nucleotide, Article, Genome-Wide Association Study
Abstract: To identify previously unknown genetic loci associated with fasting glucose concentrations, we examined the leading association signals in ten genome-wide association scans involving a total of 36,610 individuals of European descent. Variants in the gene encoding melatonin receptor 1B (MTNR1B) were consistently associated with fasting glucose across all ten studies. The strongest signal was observed at rs10830963, where each G allele (frequency 0.30 in HapMap CEU) was associated with an increase of 0.07 (95% CI = 0.06-0.08) mmol/l in fasting glucose levels (P = 3.2 x 10(-50)) and reduced beta-cell function as measured by homeostasis model assessment (HOMA-B, P = 1.1 x 10(-15)). The same allele was associated with an increased risk of type 2 diabetes (odds ratio = 1.09 (1.05-1.12), per G allele P = 3.3 x 10(-7)) in a meta-analysis of 13 case-control studies totaling 18,236 cases and 64,453 controls. Our analyses also confirm previous associations of fasting glucose with variants at the G6PC2 (rs560887, P = 1.1 x 10(-57)) and GCK (rs4607517, P = 1.0 x 10(-25)) loci.
Published: 2008

224. Newly identified loci that influence lipid concentrations and risk of coronary artery disease

Author: Meneton, Pierre, Duren, William L, Scheet, Paul A, Heath, Simon C, Jackson, Anne U, Narisu, Narisu, Timpson, Nicholas J, Bonnycastle, Lori L, Maschio, Andrea, Busonero, Fabio, Shen, Haiqing, Clarke, Robert, Albai, Giuseppe, Chen, Wei-Min, Stringham, Heather M, Hercberg, Serge, Zelenika, Diana, Scuteri, Angelo, Strait, James, Scott, Laura J, Parish, Sarah, Bennett, Derrick, Morken, Mario A, Galan, Pilar, Watanabe, Richard M, Sundvall, Jouko, Najjar, Samer S, Li, Yun, Swift, Amy J, Sanna, Serena, Willer, Cristen J, and Mulas, Antonella
Subjects: lipids (amino acids, peptides, and proteins)
Abstract: To identify genetic variants influencing plasma lipid concentrations, we first used genotype imputation and meta-analysis to combine three genome-wide scans totaling 8,816 individuals and comprising 6,068 individuals specific to our study (1,874 individuals from the FUSION study of type 2 diabetes and 4,184 individuals from the SardiNIA study of aging-associated variables) and 2,758 individuals from the Diabetes Genetics Initiative, reported in a companion study in this issue. We subsequently examined promising signals in 11,569 additional individuals. Overall, we identify strongly associated variants in eleven loci previously implicated in lipid metabolism (ABCA1, the APOA5-APOA4-APOC3-APOA1 and APOE-APOC clusters, APOB, CETP, GCKR, LDLR, LPL, LIPC, LIPG and PCSK9) and also in several newly identified loci (near MVK-MMAB and GALNT2, with variants primarily associated with high-density lipoprotein (HDL) cholesterol; near SORT1, with variants primarily associated with low-density lipoprotein (LDL) cholesterol; near TRIB1, MLXIPL and ANGPTL3, with variants primarily associated with triglycerides; and a locus encompassing several genes near NCAN, with variants strongly associated with both triglycerides and LDL cholesterol). Notably, the 11 independent variants associated with increased LDL cholesterol concentrations in our study also showed increased frequency in a sample of coronary artery disease cases versus controls.
Published: 2008
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225. Covid-19 Vaccine Efficacy: Accuracy Assessment, Comparison, and Caveats.

Author: WENJIANG FU, JIENI LI, and SCHEET, PAUL A.
Subjects: *VACCINE effectiveness, *COVID-19 vaccines, *VACCINE trials, *VACCINE development
Abstract: Vaccine efficacy is a key index to evaluate vaccines in initial clinical trials during the development of vaccines. In particular, it plays a crucial role in authorizing Covid-19 vaccines. It has been reported that Covid-19 vaccine efficacy varies with a number of factors, including demographics of population, time after vaccine administration, and virus strains. By examining clinical trial data of three Covid-19 vaccine studies, we find that current approach to evaluating vaccines with an overall efficacy does not provide desired accuracy. It requires no time frame during which a candidate vaccine is evaluated, and is subject to misuse, resulting in potential misleading information and interpretation. In particular, we illustrate with clinical trial data that the variability of vaccine efficacy is underestimated. We demonstrate that a new method may help to address these caveats. It leads to accurate estimation of the variation of efficacy, provides useful information to define a reasonable time frame to evaluate vaccines, and avoids misuse of vaccine efficacy and misleading information. [ABSTRACT FROM AUTHOR]
Published: 2024
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226. Development of Kras mutant lung adenocarcinoma in mice with knockout of the airway lineage-specific gene G prc5a.

Author: Fujimoto, Junya, Nunomura‐Nakamura, Sayuri, Liu, Yihua, Lang, Wenhua, McDowell, Tina, Jakubek, Yasminka, Ezzeddine, Dalia, Kapere Ochieng, Joshua, Petersen, Jason, Davies, Gareth, Fukuoka, Junya, Wistuba, Ignacio I., Ehli, Erik, Fowler, Jerry, Scheet, Paul, and Kadara, Humam
Abstract: Despite the urgency for prevention and treatment of lung adenocarcinoma (LUAD), we still do not know drivers in pathogenesis of the disease. Earlier work revealed that mice with knockout of the G-protein coupled receptor Gprc5a develop late onset lung tumors including LUADs. Here, we sought to further probe the impact of Gprc5a expression on LUAD pathogenesis. We first surveyed GPRC5A expression in human tissues and found that GPRC5A was markedly elevated in human normal lung relative to other normal tissues and was consistently downregulated in LUADs. In sharp contrast to wild-type littermates, Gprc5a-/- mice treated chronically with the nicotine-specific carcinogen NNK developed LUADs by 6 months following NNK exposure. Immunofluorescence analysis revealed that the LUADs exhibited abundant expression of surfactant protein C and lacked the clara cell marker Ccsp, suggesting that these LUADs originated from alveolar type II cells. Next, we sought to survey genome-wide alterations in the pathogenesis of Gprc5a-/- LUADs. Using whole exome sequencing, we found that carcinogen-induced LUADs exhibited markedly higher somatic mutation burdens relative to spontaneous tumors. All LUADs were found to harbor somatic mutations in the Kras oncogene (p. G12D or p. Q61R). In contrast to spontaneous lesions, carcinogen-induced Gprc5a-/- LUADs exhibited mutations (variants and copy number gains) in additional drivers ( Atm, Kmt2d, Nf1, Trp53, Met, Ezh2). Our study underscores genomic alterations that represent early events in the development of Kras mutant LUAD following Gprc5a loss and tobacco carcinogen exposure and that may constitute targets for prevention and early treatment of this disease. [ABSTRACT FROM AUTHOR]
Published: 2017
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227. Directional allelic imbalance profiling and visualization from multi-sample data with RECUR.

Author: Jakubek, Yasminka A, Lucas, F Anthony San, and Scheet, Paul
Subjects: VISUALIZATION, ETIOLOGY of cancer, HAPLOTYPES, SOURCE code, EXPECTED returns, CANCER invasiveness
Abstract: Motivation Genetic analysis of cancer regularly includes two or more samples from the same patient. Somatic copy number alterations leading to allelic imbalance (AI) play a critical role in cancer initiation and progression. Directional analysis and visualization of the alleles in imbalance in multi-sample settings allow for inference of recurrent mutations, providing insights into mutation rates, clonality and the genomic architecture and etiology of cancer. Results The REpeat Chromosomal changes Uncovered by Reflection (RECUR) is an R application for the comparative analysis of AI profiles derived from SNP array and next-generation sequencing data. The algorithm accepts genotype calls and 'B allele' frequencies (BAFs) from at least two samples derived from the same individual. For a predefined set of genomic regions with AI, RECUR compares BAF values among samples. In the presence of AI, the expected value of a BAF can shift in two possible directions, reflecting an increased or decreased abundance of the maternal haplotype, relative to the paternal. The phenomenon of opposite haplotype shifts, or 'mirrored subclonal allelic imbalance', is a form of heterogeneity, and has been linked to clinico-pathological features of cancer. RECUR detects such genomic segments of opposite haplotypes in imbalance and plots BAF values for all samples, using a two-color scheme for intuitive visualization. Availability and implementation RECUR is available as an R application. Source code and documentation are available at scheet.org. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]
Published: 2019
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228. Attention-Deficit/Hyperactivity Disorder Polygenic Risk Scores Predict Attention Problems in a Population-Based Sample of Children

Author: Groen-Blokhuis, Maria M., primary, Middeldorp, Christel M., additional, Kan, Kees-Jan, additional, Abdellaoui, Abdel, additional, van Beijsterveldt, Catharina E.M., additional, Ehli, Erik A., additional, Davies, Gareth E., additional, Scheet, Paul A., additional, Xiao, Xiangjun, additional, Hudziak, James J., additional, Hottenga, Jouke-Jan, additional, Neale, Ben M., additional, and Boomsma, Dorret I., additional
Published: 2014
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229. Abstract LB-310: Single cell genome sequencing reveals clonal stability and diversity in breast cancer

Author: Wang, Yong, primary, Navin, Nicholas, additional, Waters, Jill, additional, Leung, Marco, additional, Unruh, Anna, additional, Shi, Xiuqing, additional, Roh, Whijae, additional, Chen, Ken, additional, Scheet, Paul, additional, Vattathil, Selina, additional, Liang, Han, additional, Multani, Asha, additional, Zhang, Hong, additional, Meric-Bernstam, Funda, additional, Michor, Franziska, additional, and Zhao, Rui, additional
Published: 2014
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230. Abstract 5320: Novel computational methods reveal subtle clonal mosaicism

Author: Scheet, Paul, primary, Xia, Rui, additional, Lucas, F. Anthony San, additional, Hahn, Christina, additional, Fowler, Jerry, additional, and Vattathil, Selina, additional
Published: 2014
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231. Abstract 5371: Drug repositioning with a bioinformatics platform that integrates the TCGA, cMap and CCLE

Author: Lucas, Francis A. San, primary, Fowler, Jerry, additional, Kopetz, Scott, additional, Vilar, Eduardo, additional, and Scheet, Paul, additional
Published: 2014
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232. Identification of Allelic Imbalance with a Statistical Model for Subtle Genomic Mosaicism

Author: Xia, Rui, primary, Vattathil, Selina, additional, and Scheet, Paul, additional
Published: 2014
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233. HLA-DRB1*07:01 is associated with a higher risk of asparaginase allergies

Author: Fernandez, Christian A., primary, Smith, Colton, additional, Yang, Wenjian, additional, Daté, Mihir, additional, Bashford, Donald, additional, Larsen, Eric, additional, Bowman, W. Paul, additional, Liu, Chengcheng, additional, Ramsey, Laura B., additional, Chang, Tamara, additional, Turner, Victoria, additional, Loh, Mignon L., additional, Raetz, Elizabeth A., additional, Winick, Naomi J., additional, Hunger, Stephen P., additional, Carroll, William L., additional, Onengut-Gumuscu, Suna, additional, Chen, Wei-Min, additional, Concannon, Patrick, additional, Rich, Stephen S., additional, Scheet, Paul, additional, Jeha, Sima, additional, Pui, Ching-Hon, additional, Evans, William E., additional, Devidas, Meenakshi, additional, and Relling, Mary V., additional
Published: 2014
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234. Clonal evolution in breast cancer revealed by single nucleus genome sequencing

Author: Wang, Yong, primary, Waters, Jill, additional, Leung, Marco L., additional, Unruh, Anna, additional, Roh, Whijae, additional, Shi, Xiuqing, additional, Chen, Ken, additional, Scheet, Paul, additional, Vattathil, Selina, additional, Liang, Han, additional, Multani, Asha, additional, Zhang, Hong, additional, Zhao, Rui, additional, Michor, Franziska, additional, Meric-Bernstam, Funda, additional, and Navin, Nicholas E., additional
Published: 2014
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235. Effects of Long-Term Averaging of Quantitative Blood Pressure Traits on the Detection of Genetic Associations

Author: Ganesh, Santhi K., primary, Chasman, Daniel I., additional, Larson, Martin G., additional, Guo, Xiuqing, additional, Verwoert, Germain, additional, Bis, Joshua C., additional, Gu, Xiangjun, additional, Smith, Albert V., additional, Yang, Min-Lee, additional, Zhang, Yan, additional, Ehret, Georg, additional, Rose, Lynda M., additional, Hwang, Shih-Jen, additional, Papanicolau, George J., additional, Sijbrands, Eric J., additional, Rice, Kenneth, additional, Eiriksdottir, Gudny, additional, Pihur, Vasyl, additional, Ridker, Paul M., additional, Vasan, Ramachandran S., additional, Newton-Cheh, Christopher, additional, Raffel, Leslie J., additional, Amin, Najaf, additional, Rotter, Jerome I., additional, Liu, Kiang, additional, Launer, Lenore J., additional, Xu, Ming, additional, Caulfield, Mark, additional, Morrison, Alanna C., additional, Johnson, Andrew D., additional, Vaidya, Dhananjay, additional, Dehghan, Abbas, additional, Li, Guo, additional, Bouchard, Claude, additional, Harris, Tamara B., additional, Zhang, He, additional, Boerwinkle, Eric, additional, Siscovick, David S., additional, Gao, Wei, additional, Uitterlinden, Andre G., additional, Rivadeneira, Fernando, additional, Hofman, Albert, additional, Willer, Cristen J., additional, Franco, Oscar H., additional, Huo, Yong, additional, Witteman, Jacqueline C.M., additional, Munroe, Patricia B., additional, Gudnason, Vilmundur, additional, Palmas, Walter, additional, van Duijn, Cornelia, additional, Fornage, Myriam, additional, Levy, Daniel, additional, Psaty, Bruce M., additional, Chakravarti, Aravinda, additional, Johnson, Toby, additional, Gateva, Vesela, additional, Tobin, Martin D., additional, Bochud, Murielle, additional, Coin, Lachlan, additional, Najjar, Samer S., additional, Zhao, Jing Hua, additional, Heath, Simon C., additional, Eyheramendy, Susana, additional, Papadakis, Konstantinos, additional, Voight, Benjamin F., additional, Scott, Laura J., additional, Zhang, Feng, additional, Farrall, Martin, additional, Tanaka, Toshiko, additional, Wallace, Chris, additional, Chambers, John C., additional, Khaw, Kay-Tee, additional, Nilsson, Peter, additional, van der Harst, Pim, additional, Polidoro, Silvia, additional, Grobbee, Diederick E., additional, Onland-Moret, N. Charlotte, additional, Bots, Michiel L., additional, Wain, Louise V., additional, Elliott, Katherine S., additional, Teumer, Alexander, additional, Luan, Jian’an, additional, Lucas, Gavin, additional, Kuusisto, Johanna, additional, Burton, Paul R., additional, Hadley, David, additional, McArdle, Wendy L., additional, Brown, Morris, additional, Dominiczak, Anna, additional, Newhouse, Stephen J., additional, Samani, Nilesh J., additional, Webster, John, additional, Zeggini, Eleftheria, additional, Beckmann, Jacques S., additional, Bergmann, Sven, additional, Lim, Noha, additional, Song, Kijoung, additional, Vollenweider, Peter, additional, Waeber, Gerard, additional, Waterworth, Dawn M., additional, Yuan, Xin, additional, Groop, Leif, additional, Orho-Melander, Marju, additional, Allione, Alessandra, additional, Di Gregorio, Alessandra, additional, Guarrera, Simonetta, additional, Panico, Salvatore, additional, Ricceri, Fulvio, additional, Romanazzi, Valeria, additional, Sacerdote, Carlotta, additional, Vineis, Paolo, additional, Barroso, Inês, additional, Sandhu, Manjinder S., additional, Luben, Robert N., additional, Crawford, Gabriel J., additional, Jousilahti, Pekka, additional, Perola, Markus, additional, Boehnke, Michael, additional, Bonnycastle, Lori L., additional, Collins, Francis S., additional, Jackson, Anne U., additional, Mohlke, Karen L., additional, Stringham, Heather M., additional, Valle, Timo T., additional, Willer, Cristen J., additional, Bergman, Richard N., additional, Morken, Mario A., additional, Döring, Angela, additional, Gieger, Christian, additional, Illig, Thomas, additional, Meitinger, Thomas, additional, Org, Elin, additional, Pfeufer, Arne, additional, Wichmann, H. Erich, additional, Kathiresan, Sekar, additional, Marrugat, Jaume, additional, O’Donnell, Christopher J., additional, Schwartz, Stephen M., additional, Siscovick, David S., additional, Subirana, Isaac, additional, Freimer, Nelson B., additional, Hartikainen, Anna-Liisa, additional, McCarthy, Mark I., additional, O’Reilly, Paul F., additional, Peltonen, Leena, additional, Pouta, Anneli, additional, de Jong, Paul E., additional, Snieder, Harold, additional, van Gilst, Wiek H., additional, Clarke, Robert, additional, Goel, Anuj, additional, Hamsten, Anders, additional, Peden, John F., additional, Seedorf, Udo, additional, Syvänen, Ann-Christine, additional, Tognoni, Giovanni, additional, Lakatta, Edward G., additional, Sanna, Serena, additional, Scheet, Paul, additional, Schlessinger, David, additional, Scuteri, Angelo, additional, Dörr, Marcus, additional, Ernst, Florian, additional, Felix, Stephan B., additional, Homuth, Georg, additional, Lorbeer, Roberto, additional, Reffelmann, Thorsten, additional, Rettig, Rainer, additional, Völker, Uwe, additional, Galan, Pilar, additional, Gut, Ivo G., additional, Hercberg, Serge, additional, Lathrop, G. Mark, additional, Zeleneka, Diana, additional, Deloukas, Panos, additional, Soranzo, Nicole, additional, Williams, Frances M., additional, Zhai, Guangju, additional, Salomaa, Veikko, additional, Laakso, Markku, additional, Elosua, Roberto, additional, Forouhi, Nita G., additional, Völzke, Henry, additional, Uiterwaal, Cuno S., additional, van der Schouw, Yvonne T, additional, Numans, Mattijs E., additional, Matullo, Giuseppe, additional, Navis, Gerjan, additional, Berglund, Göran, additional, Bingham, Sheila A., additional, Kooner, Jaspal S., additional, Paterson, Andrew D., additional, Connell, John M., additional, Bandinelli, Stefania, additional, Ferrucci, Luigi, additional, Watkins, Hugh, additional, Spector, Tim D., additional, Tuomilehto, Jaakko, additional, Altshuler, David, additional, Strachan, David P., additional, Laan, Maris, additional, Meneton, Pierre, additional, Wareham, Nicholas J., additional, Uda, Manuela, additional, Jarvelin, Marjo-Riitta, additional, Mooser, Vincent, additional, Melander, Olle, additional, Loos, Ruth J.F., additional, Elliott, Paul, additional, Abecasis, Gonçalo R., additional, and Munroe, Patricia B., additional
Published: 2014
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236. A Genome-wide Association Meta-analysis of Preschool Internalizing Problems

Author: Benke, Kelly S., primary, Nivard, Michel G., additional, Velders, Fleur P., additional, Walters, Raymond K., additional, Pappa, Irene, additional, Scheet, Paul A., additional, Xiao, Xiangjun, additional, Ehli, Erik A., additional, Palmer, Lyle J., additional, Whitehouse, Andrew J.O., additional, Verhulst, Frank C., additional, Jaddoe, Vincent W., additional, Rivadeneira, Fernando, additional, Groen-Blokhuis, Maria M., additional, van Beijsterveldt, Catharina E.M., additional, Davies, Gareth E., additional, Hudziak, James J., additional, Lubke, Gitta H., additional, Boomsma, Dorret I., additional, Pennell, Craig E., additional, Tiemeier, Henning, additional, and Middeldorp, Christel M., additional
Published: 2014
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237. Somatic mutation load of estrogen receptor-positive breast tumors predicts overall survival: an analysis of genome sequence data

Author: Haricharan, Svasti, primary, Bainbridge, Matthew N., additional, Scheet, Paul, additional, and Brown, Powel H., additional
Published: 2014
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238. The Dopaminergic Reward System And Leisure Time Exercise Behavior

Author: Huppertz, Charlotte, primary, Bartels, Meike, additional, Groen-Blokhuis, Maria, additional, de Moor, Marleen, additional, van der Aa, Niels, additional, Abdellaoui, Abdel, additional, van Beijsterveldt, Catharina, additional, Ehli, Erik, additional, Hottenga, Jouke-Jan, additional, Willemsen, Gonneke, additional, Xiao, Xiangjun, additional, Scheet, Paul, additional, Davies, Gareth, additional, Boomsma, Dorret, additional, Hudziak, James, additional, and de Geus, Eco, additional
Published: 2014
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239. The Dopaminergic Reward System and Leisure Time Exercise Behavior: A Candidate Allele Study

Author: Huppertz, Charlotte, primary, Bartels, Meike, additional, Groen-Blokhuis, Maria M., additional, Dolan, Conor V., additional, de Moor, Marleen H. M., additional, Abdellaoui, Abdel, additional, van Beijsterveldt, Catharina E. M., additional, Ehli, Erik A., additional, Hottenga, Jouke-Jan, additional, Willemsen, Gonneke, additional, Xiao, Xiangjun, additional, Scheet, Paul, additional, Davies, Gareth E., additional, Boomsma, Dorret I., additional, Hudziak, James J., additional, and Geus, Eco J. C. de, additional
Published: 2014
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240. The Molecular Genetic Architecture of Self-Employment

Author: University of Helsinki, Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Clinicum, University of Helsinki, Institute of Behavioural Sciences, University of Helsinki, Hjelt Institute, van der Loos, Matthijs J. H. M., Rietveld, Cornelius A., Eklund, Niina, Koellinger, Philipp D., Rivadeneira, Fernando, Abecasis, Goncalo R., Ankra-Badu, Georgina A., Baumeister, Sebastian E., Benjamin, Daniel J., Biffar, Reiner, Blankenberg, Stefan, Boomsma, Dorret I., Cesarini, David, Cucca, Francesco, de Geus, Eco J. C., Dedoussis, George, Deloukas, Panos, Dimitriou, Maria, Eiriksdottir, Guony, Eriksson, Johan, Gieger, Christian, Gudnason, Vilmundur, Hoehne, Birgit, Holle, Rolf, Hottenga, Jouke-Jan, Isaacs, Aaron, Jarvelin, Marjo-Riitta, Johannesson, Magnus, Kaakinen, Marika, Kahonen, Mika, Kanoni, Stavroula, Laaksonen, Maarit A., Lahti, Jari, Launer, Lenore J., Lehtimaki, Terho, Loitfelder, Marisa, Magnusson, Patrik K. E., Naitza, Silvia, Oostra, Ben A., Perola, Markus, Petrovic, Katja, Quaye, Lydia, Raitakari, Olli, Ripatti, Samuli, Scheet, Paul, Schlessinger, David, Schmidt, Carsten O., Schmidt, Helena, Schmidt, Reinhold, Senft, Andrea, Smith, Albert V., Spector, Timothy D., Surakka, Ida, Svento, Rauli, Terracciano, Antonio, Tikkanen, Emmi, van Duijn, Cornelia M., Viikari, Jorma, Voelzke, Henry, Wichmann, H. -Erich, Wild, Philipp S., Willems, Sara M., Willemsen, Gonneke, van Rooij, Frank J. A., Groenen, Patrick J. F., Uitterlinden, Andre G., Hofman, Albert, Thurik, A. Roy, University of Helsinki, Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Clinicum, University of Helsinki, Institute of Behavioural Sciences, University of Helsinki, Hjelt Institute, van der Loos, Matthijs J. H. M., Rietveld, Cornelius A., Eklund, Niina, Koellinger, Philipp D., Rivadeneira, Fernando, Abecasis, Goncalo R., Ankra-Badu, Georgina A., Baumeister, Sebastian E., Benjamin, Daniel J., Biffar, Reiner, Blankenberg, Stefan, Boomsma, Dorret I., Cesarini, David, Cucca, Francesco, de Geus, Eco J. C., Dedoussis, George, Deloukas, Panos, Dimitriou, Maria, Eiriksdottir, Guony, Eriksson, Johan, Gieger, Christian, Gudnason, Vilmundur, Hoehne, Birgit, Holle, Rolf, Hottenga, Jouke-Jan, Isaacs, Aaron, Jarvelin, Marjo-Riitta, Johannesson, Magnus, Kaakinen, Marika, Kahonen, Mika, Kanoni, Stavroula, Laaksonen, Maarit A., Lahti, Jari, Launer, Lenore J., Lehtimaki, Terho, Loitfelder, Marisa, Magnusson, Patrik K. E., Naitza, Silvia, Oostra, Ben A., Perola, Markus, Petrovic, Katja, Quaye, Lydia, Raitakari, Olli, Ripatti, Samuli, Scheet, Paul, Schlessinger, David, Schmidt, Carsten O., Schmidt, Helena, Schmidt, Reinhold, Senft, Andrea, Smith, Albert V., Spector, Timothy D., Surakka, Ida, Svento, Rauli, Terracciano, Antonio, Tikkanen, Emmi, van Duijn, Cornelia M., Viikari, Jorma, Voelzke, Henry, Wichmann, H. -Erich, Wild, Philipp S., Willems, Sara M., Willemsen, Gonneke, van Rooij, Frank J. A., Groenen, Patrick J. F., Uitterlinden, Andre G., Hofman, Albert, and Thurik, A. Roy
Published: 2013

241. Novel susceptibility variants at 10p12.31-12.2 for childhood acute lymphoblastic leukemia in ethnically diverse populations.

Author: Xu, Heng, Xu, Heng, Yang, Wenjian, Perez-Andreu, Virginia, Devidas, Meenakshi, Fan, Yiping, Cheng, Cheng, Pei, Deqing, Scheet, Paul, Burchard, Esteban González, Eng, Celeste, Huntsman, Scott, Torgerson, Dara G, Dean, Michael, Winick, Naomi J, Martin, Paul L, Camitta, Bruce M, Bowman, W Paul, Willman, Cheryl L, Carroll, William L, Mullighan, Charles G, Bhojwani, Deepa, Hunger, Stephen P, Pui, Ching-Hon, Evans, William E, Relling, Mary V, Loh, Mignon L, Yang, Jun J, Xu, Heng, Xu, Heng, Yang, Wenjian, Perez-Andreu, Virginia, Devidas, Meenakshi, Fan, Yiping, Cheng, Cheng, Pei, Deqing, Scheet, Paul, Burchard, Esteban González, Eng, Celeste, Huntsman, Scott, Torgerson, Dara G, Dean, Michael, Winick, Naomi J, Martin, Paul L, Camitta, Bruce M, Bowman, W Paul, Willman, Cheryl L, Carroll, William L, Mullighan, Charles G, Bhojwani, Deepa, Hunger, Stephen P, Pui, Ching-Hon, Evans, William E, Relling, Mary V, Loh, Mignon L, and Yang, Jun J
Abstract: BackgroundAcute lymphoblastic leukemia (ALL) is the most common cancer in children and the incidence of ALL varies by ethnicity. Although accumulating evidence indicates inherited predisposition to ALL, the genetic basis of ALL susceptibility in diverse ancestry has not been comprehensively examined.MethodsWe performed a multiethnic genome-wide association study in 1605 children with ALL and 6661 control subjects after adjusting for population structure, with validation in three replication series of 845 case subjects and 4316 control subjects. Association was tested by two-sided logistic regression.ResultsA novel ALL susceptibility locus at 10p12.31-12.2 (BMI1-PIP4K2A, rs7088318, P = 1.1 × 10(-11)) was identified in the genome-wide association study, with independent replication in European Americans, African Americans, and Hispanic Americans (P = .001, .009, and .04, respectively). Association was also validated at four known ALL susceptibility loci: ARID5B, IKZF1, CEBPE, and CDKN2A/2B. Associations at ARID5B, IKZF1, and BMI1-PIP4K2A variants were consistent across ethnicity, with multiple independent signals at IKZF1 and BMI1-PIP4K2A loci. The frequency of ARID5B and BMI1-PIP4K2A variants differed by ethnicity, in parallel with ethnic differences in ALL incidence. Suggestive evidence for modifying effects of age on genetic predisposition to ALL was also observed. ARID5B, IKZF1, CEBPE, and BMI1-PIP4K2A variants cumulatively conferred strong predisposition to ALL, with children carrying six to eight copies of risk alleles at a ninefold (95% confidence interval = 6.9 to 11.8) higher ALL risk relative to those carrying zero to one risk allele at these four single nucleotide polymorphisms.ConclusionsThese findings indicate strong associations between inherited genetic variation and ALL susceptibility in children and shed new light on ALL molecular etiology in diverse ancestry.
Published: 2013

242. HLA-DRB1*07:01 Is Associated With Asparaginase Allergies In Children With Acute Lymphoblastic Leukemia

Author: Fernandez, Christian A, primary, Relling, Mary V., additional, Smith, Colton, additional, Yang, Wenjian, additional, Larsen, Eric C., additional, Bowman, W. Paul, additional, Liu, Chengcheng, additional, Ramsey, Laura B., additional, Chang, Tamara, additional, Turner, Victoria, additional, Loh, Mignon L., additional, Raetz, Elizabeth A., additional, Winick, Naomi J., additional, Hunger, Stephen P., additional, Carroll, William L., additional, Onengut-Gumuscu, Suna, additional, Chen, Wei-Min, additional, Concannon, Patrick, additional, Rich, Stephen S, additional, Scheet, Paul, additional, Jeha, Sima, additional, Pui, Ching-Hon, additional, Evans, William E., additional, and Devidas, Meenakshi, additional
Published: 2013
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243. New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk

Author: Dupuis, Josée, Langenberg, Claudia, Prokopenko, Inga, Saxena, Richa, Soranzo, Nicole, Jackson, Anne U, Wheeler, Eleanor, Glazer, Nicole L, Bouatia-Naji, Nabila, Gloyn, Anna L, Lindgren, Cecilia M, Mägi, Reedik, Morris, Andrew P, Randall, Joshua, Johnson, Toby, Elliott, Paul, Rybin, Denis, Thorleifsson, Gudmar, Steinthorsdottir, Valgerdur, Henneman, Peter, Grallert, Harald, Dehghan, Abbas, Hottenga, Jouke Jan, Franklin, Christopher S, Navarro, Pau, Song, Kijoung, Goel, Anuj, Perry, John R B, Egan, Josephine M, Lajunen, Taina, Grarup, Niels, Sparsø, Thomas, Doney, Alex, Voight, Benjamin F, Stringham, Heather M, Li, Man, Kanoni, Stavroula, Shrader, Peter, Cavalcanti-Proença, Christine, Kumari, Meena, Qi, Lu, Timpson, Nicholas J, Gieger, Christian, Zabena, Carina, Rocheleau, Ghislain, Ingelsson, Erik, An, Ping, O'Connell, Jeffrey, Luan, Jian'an, Elliott, Amanda, McCarroll, Steven A, Payne, Felicity, Roccasecca, Rosa Maria, Pattou, François, Sethupathy, Praveen, Ardlie, Kristin, Ariyurek, Yavuz, Balkau, Beverley, Barter, Philip, Beilby, John P, Ben-Shlomo, Yoav, Benediktsson, Rafn, Bennett, Amanda J, Bergmann, Sven, Bochud, Murielle, Boerwinkle, Eric, Bonnefond, Amélie, Bonnycastle, Lori L, Borch-Johnsen, Knut, Böttcher, Yvonne, Brunner, Eric, Bumpstead, Suzannah J, Charpentier, Guillaume, Chen, Yii-Der Ida, Chines, Peter, Clarke, Robert, Coin, Lachlan J M, Cooper, Matthew N, Cornelis, Marilyn, Crawford, Gabe, Crisponi, Laura, Day, Ian N M, de Geus, Eco J C, Delplanque, Jerome, Dina, Christian, Erdos, Michael R, Fedson, Annette C, Fischer-Rosinsky, Antje, Forouhi, Nita G, Fox, Caroline S, Frants, Rune, Franzosi, Maria Grazia, Galan, Pilar, Goodarzi, Mark O, Graessler, Jürgen, Groves, Christopher J, Grundy, Scott, Gwilliam, Rhian, Gyllensten, Ulf, Hadjadj, Samy, Hallmans, Göran, Hammond, Naomi, Han, Xijing, Hartikainen, Anna-Liisa, Hassanali, Neelam, Hayward, Caroline, Heath, Simon C, Hercberg, Serge, Herder, Christian, Hicks, Andrew A, Hillman, David R, Hingorani, Aroon D, Hofman, Albert, Hui, Jennie, Hung, Joe, Isomaa, Bo, Johnson, Paul R V, Jørgensen, Torben, Jula, Antti, Kaakinen, Marika, Kaprio, Jaakko, Kesaniemi, Y Antero, Kivimaki, Mika, Knight, Beatrice, Koskinen, Seppo, Kovacs, Peter, Kyvik, Kirsten Ohm, Lathrop, G Mark, Lawlor, Debbie A, Le Bacquer, Olivier, Lecoeur, Cécile, Li, Yun, Lyssenko, Valeriya, Mahley, Robert, Mangino, Massimo, Manning, Alisa K, Martínez-Larrad, María Teresa, McAteer, Jarred B, McCulloch, Laura J, McPherson, Ruth, Meisinger, Christa, Melzer, David, Meyre, David, Mitchell, Braxton D, Morken, Mario A, Mukherjee, Sutapa, Naitza, Silvia, Narisu, Narisu, Neville, Matthew J, Oostra, Ben A, Orrù, Marco, Pakyz, Ruth, Palmer, Colin N A, Paolisso, Giuseppe, Pattaro, Cristian, Pearson, Daniel, Peden, John F, Pedersen, Nancy L, Perola, Markus, Pfeiffer, Andreas F H, Pichler, Irene, Polasek, Ozren, Posthuma, Danielle, Potter, Simon C, Pouta, Anneli, Province, Michael A, Psaty, Bruce M, Rathmann, Wolfgang, Rayner, Nigel W, Rice, Kenneth, Ripatti, Samuli, Rivadeneira, Fernando, Roden, Michael, Rolandsson, Olov, Sandbaek, Annelli, Sandhu, Manjinder, Sanna, Serena, Sayer, Avan Aihie, Scheet, Paul, Scott, Laura J, Seedorf, Udo, Sharp, Stephen J, Shields, Beverley, Sigurethsson, Gunnar, Sijbrands, Eric J G, Silveira, Angela, Simpson, Laila, Singleton, Andrew, Smith, Nicholas L, Sovio, Ulla, Swift, Amy, Syddall, Holly, Syvänen, Ann-Christine, Tanaka, Toshiko, Thorand, Barbara, Tichet, Jean, Tönjes, Anke, Tuomi, Tiinamaija, Uitterlinden, André G, van Dijk, Ko Willems, van Hoek, Mandy, Varma, Dhiraj, Visvikis-Siest, Sophie, Vitart, Veronique, Vogelzangs, Nicole, Waeber, Gérard, Wagner, Peter J, Walley, Andrew, Walters, G Bragi, Ward, Kim L, Watkins, Hugh, Weedon, Michael N, Wild, Sarah H, Willemsen, Gonneke, Witteman, Jaqueline C M, Yarnell, John W G, Zeggini, Eleftheria, Zelenika, Diana, Zethelius, Björn, Zhai, Guangju, Zhao, Jing Hua, Zillikens, M Carola, Borecki, Ingrid B, Loos, Ruth J F, Meneton, Pierre, Magnusson, Patrik K E, Nathan, David M, Williams, Gordon H, Hattersley, Andrew T, Silander, Kaisa, Salomaa, Veikko, Smith, George Davey, Bornstein, Stefan R, Schwarz, Peter, Spranger, Joachim, Karpe, Fredrik, Shuldiner, Alan R, Cooper, Cyrus, Dedoussis, George V, Serrano-Ríos, Manuel, Morris, Andrew D, Lind, Lars, Palmer, Lyle J, Hu, Frank B, Franks, Paul W, Ebrahim, Shah, Marmot, Michael, Kao, W H Linda, Pankow, James S, Sampson, Michael J, Kuusisto, Johanna, Laakso, Markku, Hansen, Torben, Pedersen, Oluf, Pramstaller, Peter Paul, Wichmann, H Erich, Illig, Thomas, Rudan, Igor, Wright, Alan F, Stumvoll, Michael, Campbell, Harry, Wilson, James F, Bergman, Richard N, Buchanan, Thomas A, Collins, Francis S, Mohlke, Karen L, Tuomilehto, Jaakko, Valle, Timo T, Altshuler, David, Rotter, Jerome I, Siscovick, David S, Penninx, Brenda W J H, Boomsma, Dorret I, Deloukas, Panos, Spector, Timothy D, Frayling, Timothy M, Ferrucci, Luigi, Kong, Augustine, Thorsteinsdottir, Unnur, Stefansson, Kari, van Duijn, Cornelia M, Aulchenko, Yurii S, Cao, Antonio, Scuteri, Angelo, Schlessinger, David, Uda, Manuela, Ruokonen, Aimo, Jarvelin, Marjo-Riitta, Waterworth, Dawn M, Vollenweider, Peter, Peltonen, Leena, Mooser, Vincent, Abecasis, Goncalo R, Wareham, Nicholas J, Sladek, Robert, Froguel, Philippe, Watanabe, Richard M, Meigs, James B, Groop, Leif, Boehnke, Michael, McCarthy, Mark I, Florez, Jose C, Barroso, Inês, Dupuis, Josée, Langenberg, Claudia, Prokopenko, Inga, Saxena, Richa, Soranzo, Nicole, Jackson, Anne U, Wheeler, Eleanor, Glazer, Nicole L, Bouatia-Naji, Nabila, Gloyn, Anna L, Lindgren, Cecilia M, Mägi, Reedik, Morris, Andrew P, Randall, Joshua, Johnson, Toby, Elliott, Paul, Rybin, Denis, Thorleifsson, Gudmar, Steinthorsdottir, Valgerdur, Henneman, Peter, Grallert, Harald, Dehghan, Abbas, Hottenga, Jouke Jan, Franklin, Christopher S, Navarro, Pau, Song, Kijoung, Goel, Anuj, Perry, John R B, Egan, Josephine M, Lajunen, Taina, Grarup, Niels, Sparsø, Thomas, Doney, Alex, Voight, Benjamin F, Stringham, Heather M, Li, Man, Kanoni, Stavroula, Shrader, Peter, Cavalcanti-Proença, Christine, Kumari, Meena, Qi, Lu, Timpson, Nicholas J, Gieger, Christian, Zabena, Carina, Rocheleau, Ghislain, Ingelsson, Erik, An, Ping, O'Connell, Jeffrey, Luan, Jian'an, Elliott, Amanda, McCarroll, Steven A, Payne, Felicity, Roccasecca, Rosa Maria, Pattou, François, Sethupathy, Praveen, Ardlie, Kristin, Ariyurek, Yavuz, Balkau, Beverley, Barter, Philip, Beilby, John P, Ben-Shlomo, Yoav, Benediktsson, Rafn, Bennett, Amanda J, Bergmann, Sven, Bochud, Murielle, Boerwinkle, Eric, Bonnefond, Amélie, Bonnycastle, Lori L, Borch-Johnsen, Knut, Böttcher, Yvonne, Brunner, Eric, Bumpstead, Suzannah J, Charpentier, Guillaume, Chen, Yii-Der Ida, Chines, Peter, Clarke, Robert, Coin, Lachlan J M, Cooper, Matthew N, Cornelis, Marilyn, Crawford, Gabe, Crisponi, Laura, Day, Ian N M, de Geus, Eco J C, Delplanque, Jerome, Dina, Christian, Erdos, Michael R, Fedson, Annette C, Fischer-Rosinsky, Antje, Forouhi, Nita G, Fox, Caroline S, Frants, Rune, Franzosi, Maria Grazia, Galan, Pilar, Goodarzi, Mark O, Graessler, Jürgen, Groves, Christopher J, Grundy, Scott, Gwilliam, Rhian, Gyllensten, Ulf, Hadjadj, Samy, Hallmans, Göran, Hammond, Naomi, Han, Xijing, Hartikainen, Anna-Liisa, Hassanali, Neelam, Hayward, Caroline, Heath, Simon C, Hercberg, Serge, Herder, Christian, Hicks, Andrew A, Hillman, David R, Hingorani, Aroon D, Hofman, Albert, Hui, Jennie, Hung, Joe, Isomaa, Bo, Johnson, Paul R V, Jørgensen, Torben, Jula, Antti, Kaakinen, Marika, Kaprio, Jaakko, Kesaniemi, Y Antero, Kivimaki, Mika, Knight, Beatrice, Koskinen, Seppo, Kovacs, Peter, Kyvik, Kirsten Ohm, Lathrop, G Mark, Lawlor, Debbie A, Le Bacquer, Olivier, Lecoeur, Cécile, Li, Yun, Lyssenko, Valeriya, Mahley, Robert, Mangino, Massimo, Manning, Alisa K, Martínez-Larrad, María Teresa, McAteer, Jarred B, McCulloch, Laura J, McPherson, Ruth, Meisinger, Christa, Melzer, David, Meyre, David, Mitchell, Braxton D, Morken, Mario A, Mukherjee, Sutapa, Naitza, Silvia, Narisu, Narisu, Neville, Matthew J, Oostra, Ben A, Orrù, Marco, Pakyz, Ruth, Palmer, Colin N A, Paolisso, Giuseppe, Pattaro, Cristian, Pearson, Daniel, Peden, John F, Pedersen, Nancy L, Perola, Markus, Pfeiffer, Andreas F H, Pichler, Irene, Polasek, Ozren, Posthuma, Danielle, Potter, Simon C, Pouta, Anneli, Province, Michael A, Psaty, Bruce M, Rathmann, Wolfgang, Rayner, Nigel W, Rice, Kenneth, Ripatti, Samuli, Rivadeneira, Fernando, Roden, Michael, Rolandsson, Olov, Sandbaek, Annelli, Sandhu, Manjinder, Sanna, Serena, Sayer, Avan Aihie, Scheet, Paul, Scott, Laura J, Seedorf, Udo, Sharp, Stephen J, Shields, Beverley, Sigurethsson, Gunnar, Sijbrands, Eric J G, Silveira, Angela, Simpson, Laila, Singleton, Andrew, Smith, Nicholas L, Sovio, Ulla, Swift, Amy, Syddall, Holly, Syvänen, Ann-Christine, Tanaka, Toshiko, Thorand, Barbara, Tichet, Jean, Tönjes, Anke, Tuomi, Tiinamaija, Uitterlinden, André G, van Dijk, Ko Willems, van Hoek, Mandy, Varma, Dhiraj, Visvikis-Siest, Sophie, Vitart, Veronique, Vogelzangs, Nicole, Waeber, Gérard, Wagner, Peter J, Walley, Andrew, Walters, G Bragi, Ward, Kim L, Watkins, Hugh, Weedon, Michael N, Wild, Sarah H, Willemsen, Gonneke, Witteman, Jaqueline C M, Yarnell, John W G, Zeggini, Eleftheria, Zelenika, Diana, Zethelius, Björn, Zhai, Guangju, Zhao, Jing Hua, Zillikens, M Carola, Borecki, Ingrid B, Loos, Ruth J F, Meneton, Pierre, Magnusson, Patrik K E, Nathan, David M, Williams, Gordon H, Hattersley, Andrew T, Silander, Kaisa, Salomaa, Veikko, Smith, George Davey, Bornstein, Stefan R, Schwarz, Peter, Spranger, Joachim, Karpe, Fredrik, Shuldiner, Alan R, Cooper, Cyrus, Dedoussis, George V, Serrano-Ríos, Manuel, Morris, Andrew D, Lind, Lars, Palmer, Lyle J, Hu, Frank B, Franks, Paul W, Ebrahim, Shah, Marmot, Michael, Kao, W H Linda, Pankow, James S, Sampson, Michael J, Kuusisto, Johanna, Laakso, Markku, Hansen, Torben, Pedersen, Oluf, Pramstaller, Peter Paul, Wichmann, H Erich, Illig, Thomas, Rudan, Igor, Wright, Alan F, Stumvoll, Michael, Campbell, Harry, Wilson, James F, Bergman, Richard N, Buchanan, Thomas A, Collins, Francis S, Mohlke, Karen L, Tuomilehto, Jaakko, Valle, Timo T, Altshuler, David, Rotter, Jerome I, Siscovick, David S, Penninx, Brenda W J H, Boomsma, Dorret I, Deloukas, Panos, Spector, Timothy D, Frayling, Timothy M, Ferrucci, Luigi, Kong, Augustine, Thorsteinsdottir, Unnur, Stefansson, Kari, van Duijn, Cornelia M, Aulchenko, Yurii S, Cao, Antonio, Scuteri, Angelo, Schlessinger, David, Uda, Manuela, Ruokonen, Aimo, Jarvelin, Marjo-Riitta, Waterworth, Dawn M, Vollenweider, Peter, Peltonen, Leena, Mooser, Vincent, Abecasis, Goncalo R, Wareham, Nicholas J, Sladek, Robert, Froguel, Philippe, Watanabe, Richard M, Meigs, James B, Groop, Leif, Boehnke, Michael, McCarthy, Mark I, Florez, Jose C, and Barroso, Inês
Abstract: Levels of circulating glucose are tightly regulated. To identify new loci influencing glycemic traits, we performed meta-analyses of 21 genome-wide association studies informative for fasting glucose, fasting insulin and indices of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR) in up to 46,186 nondiabetic participants. Follow-up of 25 loci in up to 76,558 additional subjects identified 16 loci associated with fasting glucose and HOMA-B and two loci associated with fasting insulin and HOMA-IR. These include nine loci newly associated with fasting glucose (in or near ADCY5, MADD, ADRA2A, CRY2, FADS1, GLIS3, SLC2A2, PROX1 and C2CD4B) and one influencing fasting insulin and HOMA-IR (near IGF1). We also demonstrated association of ADCY5, PROX1, GCK, GCKR and DGKB-TMEM195 with type 2 diabetes. Within these loci, likely biological candidate genes influence signal transduction, cell proliferation, development, glucose-sensing and circadian regulation. Our results demonstrate that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes.
Published: 2010
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244. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes

Author: Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan ; Department of Biostatistics, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, Department of Genetics, Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, Texas, Li, Yun, Willer, Cristen J., Ding, Jun, Scheet, Paul, Abecasis, Gon??alo R., Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan ; Department of Biostatistics, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, Department of Genetics, Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, Texas, Li, Yun, Willer, Cristen J., Ding, Jun, Scheet, Paul, and Abecasis, Gon??alo R.
Abstract: Genome-wide association studies (GWAS) can identify common alleles that contribute to complex disease susceptibility. Despite the large number of SNPs assessed in each study, the effects of most common SNPs must be evaluated indirectly using either genotyped markers or haplotypes thereof as proxies. We have previously implemented a computationally efficient Markov Chain framework for genotype imputation and haplotyping in the freely available MaCH software package. The approach describes sampled chromosomes as mosaics of each other and uses available genotype and shotgun sequence data to estimate unobserved genotypes and haplotypes, together with useful measures of the quality of these estimates. Our approach is already widely used to facilitate comparison of results across studies as well as meta-analyses of GWAS. Here, we use simulations and experimental genotypes to evaluate its accuracy and utility, considering choices of genotyping panels, reference panel configurations, and designs where genotyping is replaced with shotgun sequencing. Importantly, we show that genotype imputation not only facilitates cross study analyses but also increases power of genetic association studies. We show that genotype imputation of common variants using HapMap haplotypes as a reference is very accurate using either genome-wide SNP data or smaller amounts of data typical in fine-mapping studies. Furthermore, we show the approach is applicable in a variety of populations. Finally, we illustrate how association analyses of unobserved variants will benefit from ongoing advances such as larger HapMap reference panels and whole genome shotgun sequencing technologies. Genet. Epidemiol . 34: 816-834, 2010. ?? 2010 Wiley-Liss, Inc.
Published: 2010

245. Genome-wide association scan meta-analysis identifies three Loci influencing adiposity and fat distribution.

Author: Lindgren, Cecilia M, Heid, Iris M, Randall, Joshua C, Lamina, Claudia, Steinthorsdottir, Valgerdur, Qi, Lu, Speliotes, Elizabeth K, Thorleifsson, Gudmar, Willer, Cristen J, Herrera, Blanca M, Jackson, Anne U, Lim, Noha, Scheet, Paul, Soranzo, Nicole, Amin, Najaf, Aulchenko, Yurii S, Chambers, John C, Drong, Alexander, Luan, Jian'an, Lyon, Helen N, Rivadeneira, Fernando, Sanna, Serena, Timpson, Nicholas J, Zillikens, M Carola, Zhao, Jing Hua, Almgren, Peter, Bandinelli, Stefania, Bennett, Amanda J, Bergman, Richard N, Bonnycastle, Lori L, Bumpstead, Suzannah J, Chanock, Stephen J, Cherkas, Lynn, Chines, Peter, Coin, Lachlan, Cooper, Cyrus, Crawford, Gabriel, Doering, Angela, Dominiczak, Anna, Doney, Alex S F, Ebrahim, Shah, Elliott, Paul, Erdos, Michael R, Estrada, Karol, Ferrucci, Luigi, Fischer, Guido, Forouhi, Nita G, Gieger, Christian, Grallert, Harald, Groves, Christopher J, Grundy, Scott, Guiducci, Candace, Hadley, David, Hamsten, Anders, Havulinna, Aki S, Hofman, Albert, Holle, Rolf, Holloway, John W, Illig, Thomas, Isomaa, Bo, Jacobs, Leonie C, Jameson, Karen, Jousilahti, Pekka, Karpe, Fredrik, Kuusisto, Johanna, Laitinen, Jaana, Lathrop, G Mark, Lawlor, Debbie A, Mangino, Massimo, McArdle, Wendy L, Meitinger, Thomas, Morken, Mario A, Morris, Andrew P, Munroe, Patricia, Narisu, Narisu, Nordström, Anna, Nordström, Peter, Oostra, Ben A, Palmer, Colin N A, Payne, Felicity, Peden, John F, Prokopenko, Inga, Renström, Frida, Ruokonen, Aimo, Salomaa, Veikko, Sandhu, Manjinder S, Scott, Laura J, Scuteri, Angelo, Silander, Kaisa, Song, Kijoung, Yuan, Xin, Stringham, Heather M, Swift, Amy J, Tuomi, Tiinamaija, Uda, Manuela, Vollenweider, Peter, Waeber, Gerard, Wallace, Chris, Walters, G Bragi, Weedon, Michael N, Witteman, Jacqueline C M, Zhang, Cuilin, Zhang, Weihua, Caulfield, Mark J, Collins, Francis S, Davey Smith, George, Day, Ian N M, Franks, Paul W, Hattersley, Andrew T, Hu, Frank B, Jarvelin, Marjo-Riitta, Kong, Augustine, Kooner, Jaspal S, Laakso, Markku, Lakatta, Edward, Mooser, Vincent, Morris, Andrew D, Peltonen, Leena, Samani, Nilesh J, Spector, Timothy D, Strachan, David P, Tanaka, Toshiko, Tuomilehto, Jaakko, Uitterlinden, André G, van Duijn, Cornelia M, Wareham, Nicholas J, Hugh Watkins, Waterworth, Dawn M, Boehnke, Michael, Deloukas, Panos, Groop, Leif, Hunter, David J, Thorsteinsdottir, Unnur, Schlessinger, David, Wichmann, H-Erich, Frayling, Timothy M, Abecasis, Gonçalo R, Hirschhorn, Joel N, Loos, Ruth J F, Stefansson, Kari, Mohlke, Karen L, Barroso, Inês, McCarthy, Mark I, Lindgren, Cecilia M, Heid, Iris M, Randall, Joshua C, Lamina, Claudia, Steinthorsdottir, Valgerdur, Qi, Lu, Speliotes, Elizabeth K, Thorleifsson, Gudmar, Willer, Cristen J, Herrera, Blanca M, Jackson, Anne U, Lim, Noha, Scheet, Paul, Soranzo, Nicole, Amin, Najaf, Aulchenko, Yurii S, Chambers, John C, Drong, Alexander, Luan, Jian'an, Lyon, Helen N, Rivadeneira, Fernando, Sanna, Serena, Timpson, Nicholas J, Zillikens, M Carola, Zhao, Jing Hua, Almgren, Peter, Bandinelli, Stefania, Bennett, Amanda J, Bergman, Richard N, Bonnycastle, Lori L, Bumpstead, Suzannah J, Chanock, Stephen J, Cherkas, Lynn, Chines, Peter, Coin, Lachlan, Cooper, Cyrus, Crawford, Gabriel, Doering, Angela, Dominiczak, Anna, Doney, Alex S F, Ebrahim, Shah, Elliott, Paul, Erdos, Michael R, Estrada, Karol, Ferrucci, Luigi, Fischer, Guido, Forouhi, Nita G, Gieger, Christian, Grallert, Harald, Groves, Christopher J, Grundy, Scott, Guiducci, Candace, Hadley, David, Hamsten, Anders, Havulinna, Aki S, Hofman, Albert, Holle, Rolf, Holloway, John W, Illig, Thomas, Isomaa, Bo, Jacobs, Leonie C, Jameson, Karen, Jousilahti, Pekka, Karpe, Fredrik, Kuusisto, Johanna, Laitinen, Jaana, Lathrop, G Mark, Lawlor, Debbie A, Mangino, Massimo, McArdle, Wendy L, Meitinger, Thomas, Morken, Mario A, Morris, Andrew P, Munroe, Patricia, Narisu, Narisu, Nordström, Anna, Nordström, Peter, Oostra, Ben A, Palmer, Colin N A, Payne, Felicity, Peden, John F, Prokopenko, Inga, Renström, Frida, Ruokonen, Aimo, Salomaa, Veikko, Sandhu, Manjinder S, Scott, Laura J, Scuteri, Angelo, Silander, Kaisa, Song, Kijoung, Yuan, Xin, Stringham, Heather M, Swift, Amy J, Tuomi, Tiinamaija, Uda, Manuela, Vollenweider, Peter, Waeber, Gerard, Wallace, Chris, Walters, G Bragi, Weedon, Michael N, Witteman, Jacqueline C M, Zhang, Cuilin, Zhang, Weihua, Caulfield, Mark J, Collins, Francis S, Davey Smith, George, Day, Ian N M, Franks, Paul W, Hattersley, Andrew T, Hu, Frank B, Jarvelin, Marjo-Riitta, Kong, Augustine, Kooner, Jaspal S, Laakso, Markku, Lakatta, Edward, Mooser, Vincent, Morris, Andrew D, Peltonen, Leena, Samani, Nilesh J, Spector, Timothy D, Strachan, David P, Tanaka, Toshiko, Tuomilehto, Jaakko, Uitterlinden, André G, van Duijn, Cornelia M, Wareham, Nicholas J, Hugh Watkins, Waterworth, Dawn M, Boehnke, Michael, Deloukas, Panos, Groop, Leif, Hunter, David J, Thorsteinsdottir, Unnur, Schlessinger, David, Wichmann, H-Erich, Frayling, Timothy M, Abecasis, Gonçalo R, Hirschhorn, Joel N, Loos, Ruth J F, Stefansson, Kari, Mohlke, Karen L, Barroso, Inês, and McCarthy, Mark I
Abstract: To identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580) informative for adult waist circumference (WC) and waist-hip ratio (WHR). We selected 26 SNPs for follow-up, for which the evidence of association with measures of central adiposity (WC and/or WHR) was strong and disproportionate to that for overall adiposity or height. Follow-up studies in a maximum of 70,689 individuals identified two loci strongly associated with measures of central adiposity; these map near TFAP2B (WC, P = 1.9x10(-11)) and MSRA (WC, P = 8.9x10(-9)). A third locus, near LYPLAL1, was associated with WHR in women only (P = 2.6x10(-8)). The variants near TFAP2B appear to influence central adiposity through an effect on overall obesity/fat-mass, whereas LYPLAL1 displays a strong female-only association with fat distribution. By focusing on anthropometric measures of central obesity and fat distribution, we have identified three loci implicated in the regulation of human adiposity.
Published: 2009
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246. Genome-wide association study identifies eight loci associated with blood pressure

Author: Newton-Cheh, Christopher, Johnson, Toby, Gateva, Vesela, Tobin, D, Bochud, Murielle, Coin, Lachlan, Najjar, S, Zhao, Hua, Heath, C, Eyheramendy, Susana, Papadakis, Konstantinos, Voight, F, Scott, J, Zhang, Feng, Farrall, Martin, Tanaka, Toshiko, Wallace, Chris, Chambers, C, Khaw, Kay-Tee, Nilsson, Peter, van der Harst, Pim, Polidoro, Silvia, Grobbee, E, Onland-Moret, Charlotte, Bots, L, Wain, V, Elliott, S, Teumer, Alexander, Luan, Jian'an, Lucas, Gavin, Kuusisto, Johanna, Burton, R, Hadley, David, McArdle, L, Brown, Morris, Dominiczak, Anna, Newhouse, J, Samani, J, Webster, John, Zeggini, Eleftheria, Beckmann, S, Bergmann, Sven, Lim, Noha, Song, Kijoung, Vollenweider, Peter, Waeber, Gerard, Waterworth, M, Yuan, Xin, Groop, Leif, Orho-Melander, Marju, Allione, Alessandra, Di Gregorio, Alessandra, Guarrera, Simonetta, Panico, Salvatore, Ricceri, Fulvio, Romanazzi, Valeria, Sacerdote, Carlotta, Vineis, Paolo, Barroso, Ines, Sandhu, S, Luben, N, Crawford, J, Jousilahti, Pekka, Perola, Markus, Boehnke, Michael, Bonnycastle, L, Collins, S, Jackson, U, Mohlke, L, Stringham, M, Valle, T, Willer, J, Bergman, N, Morken, A, Doering, Angela, Gieger, Christian, Illig, Thomas, Meitinger, Thomas, Org, Elin, Pfeufer, Arne, Wichmann, Erich, Kathiresan, Sekar, Marrugat, Jaume, O'Donnell, J, Schwartz, M, Siscovick, S, Subirana, Isaac, Freimer, B, Hartikainen, Anna-Liisa, McCarthy, I, O'Reilly, F, Peltonen, Leena, Pouta, Anneli, de Jong, E, Snieder, Harold, van Gilst, H, Clarke, Robert, Goel, Anuj, Hamsten, Anders, Peden, F, Seedorf, Udo, Syvänen, Ann-Christine, Tognoni, Giovanni, Lakatta, G, Sanna, Serena, Scheet, Paul, Schlessinger, David, Scuteri, Angelo, Doerr, Marcus, Ernst, Florian, Felix, B, Homuth, Georg, Lorbeer, Roberto, Reffelmann, Thorsten, Rettig, Rainer, Voelker, Uwe, Galan, Pilar, Gut, G, Hercberg, Serge, Lathrop, Mark, Zelenika, Diana, Deloukas, Panos, Soranzo, Nicole, Williams, M, Zhai, Guangju, Salomaa, Veikko, Laakso, Markku, Elosua, Roberto, Forouhi, G, Volzke, Henry, Uiterwaal, S, van der Schouw, T, Numans, E, Matullo, Giuseppe, Navis, Gerjan, Berglund, Goran, Bingham, A, Kooner, S, Connell, M, Bandinelli, Stefania, Ferrucci, Luigi, Watkins, Hugh, Spector, D, Tuomilehto, Jaakko, Altshuler, David, Strachan, P, Laan, Maris, Meneton, Pierre, Wareham, J, Uda, Manuela, Jarvelin, Marjo-Riitta, Mooser, Vincent, Melander, Olle, Loos, F, Elliott, Paul, Abecasis, R, Caulfield, Mark, Munroe, Patricia B., Newton-Cheh, Christopher, Johnson, Toby, Gateva, Vesela, Tobin, D, Bochud, Murielle, Coin, Lachlan, Najjar, S, Zhao, Hua, Heath, C, Eyheramendy, Susana, Papadakis, Konstantinos, Voight, F, Scott, J, Zhang, Feng, Farrall, Martin, Tanaka, Toshiko, Wallace, Chris, Chambers, C, Khaw, Kay-Tee, Nilsson, Peter, van der Harst, Pim, Polidoro, Silvia, Grobbee, E, Onland-Moret, Charlotte, Bots, L, Wain, V, Elliott, S, Teumer, Alexander, Luan, Jian'an, Lucas, Gavin, Kuusisto, Johanna, Burton, R, Hadley, David, McArdle, L, Brown, Morris, Dominiczak, Anna, Newhouse, J, Samani, J, Webster, John, Zeggini, Eleftheria, Beckmann, S, Bergmann, Sven, Lim, Noha, Song, Kijoung, Vollenweider, Peter, Waeber, Gerard, Waterworth, M, Yuan, Xin, Groop, Leif, Orho-Melander, Marju, Allione, Alessandra, Di Gregorio, Alessandra, Guarrera, Simonetta, Panico, Salvatore, Ricceri, Fulvio, Romanazzi, Valeria, Sacerdote, Carlotta, Vineis, Paolo, Barroso, Ines, Sandhu, S, Luben, N, Crawford, J, Jousilahti, Pekka, Perola, Markus, Boehnke, Michael, Bonnycastle, L, Collins, S, Jackson, U, Mohlke, L, Stringham, M, Valle, T, Willer, J, Bergman, N, Morken, A, Doering, Angela, Gieger, Christian, Illig, Thomas, Meitinger, Thomas, Org, Elin, Pfeufer, Arne, Wichmann, Erich, Kathiresan, Sekar, Marrugat, Jaume, O'Donnell, J, Schwartz, M, Siscovick, S, Subirana, Isaac, Freimer, B, Hartikainen, Anna-Liisa, McCarthy, I, O'Reilly, F, Peltonen, Leena, Pouta, Anneli, de Jong, E, Snieder, Harold, van Gilst, H, Clarke, Robert, Goel, Anuj, Hamsten, Anders, Peden, F, Seedorf, Udo, Syvänen, Ann-Christine, Tognoni, Giovanni, Lakatta, G, Sanna, Serena, Scheet, Paul, Schlessinger, David, Scuteri, Angelo, Doerr, Marcus, Ernst, Florian, Felix, B, Homuth, Georg, Lorbeer, Roberto, Reffelmann, Thorsten, Rettig, Rainer, Voelker, Uwe, Galan, Pilar, Gut, G, Hercberg, Serge, Lathrop, Mark, Zelenika, Diana, Deloukas, Panos, Soranzo, Nicole, Williams, M, Zhai, Guangju, Salomaa, Veikko, Laakso, Markku, Elosua, Roberto, Forouhi, G, Volzke, Henry, Uiterwaal, S, van der Schouw, T, Numans, E, Matullo, Giuseppe, Navis, Gerjan, Berglund, Goran, Bingham, A, Kooner, S, Connell, M, Bandinelli, Stefania, Ferrucci, Luigi, Watkins, Hugh, Spector, D, Tuomilehto, Jaakko, Altshuler, David, Strachan, P, Laan, Maris, Meneton, Pierre, Wareham, J, Uda, Manuela, Jarvelin, Marjo-Riitta, Mooser, Vincent, Melander, Olle, Loos, F, Elliott, Paul, Abecasis, R, Caulfield, Mark, and Munroe, Patricia B.
Abstract: Elevated blood pressure is a common, heritable cause of cardiovascular disease worldwide. To date, identification of common genetic variants influencing blood pressure has proven challenging. We tested 2.5 million genotyped and imputed SNPs for association with systolic and diastolic blood pressure in 34,433 subjects of European ancestry from the Global BPgen consortium and followed up findings with direct genotyping (N ≤ 71,225 European ancestry, N ≤ 12,889 Indian Asian ancestry) and in silico comparison (CHARGE consortium, N = 29,136). We identified association between systolic or diastolic blood pressure and common variants in eight regions near the CYP17A1 (P = 7 × 10−24), CYP1A2 (P = 1 × 10−23), FGF5 (P = 1 × 10−21), SH2B3 (P = 3 × 10−18), MTHFR (P = 2 × 10−13), c10orf107 (P = 1 × 10−9), ZNF652 (P = 5 × 10−9) and PLCD3 (P = 1 × 10−8) genes. All variants associated with continuous blood pressure were associated with dichotomous hypertension. These associations between common variants and blood pressure and hypertension offer mechanistic insights into the regulation of blood pressure and may point to novel targets for interventions to prevent cardiovascular disease.
Published: 2009
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247. Genome-wide association scan meta-analysis identifies three loci influencing adiposity and fat distribution

Author: Lindgren, Cecilia M., Heid, Iris M., Randall, Joshua C., Lamina, Claudia, Steinthorsdottir, Valgerdur, Qi, Lu, Speliotes, Elizabeth K., Thorleifsson, Gudmar, Willer, Cristen J., Herrera, Blanca M., Jackson, Anne U., Lim, Noha, Scheet, Paul, Soranzo, Nicole, Amin, Najaf, Aulchenko, Yurii S., Chambers, John C., Drong, Alexander, Luan, Jia N.an, Lyon, Helen N., Rivadeneira, Fernando, Sanna, Serena, Timpson, Nicholas J., Zillikens, M. Carola, Jing, Hua Zhao, Almgren, Peter, Bandinelli, Stefania, Bennett, Amanda J., Bergman, Richard N., Bonnycastle, Lori L., Bumpstead, Suzannah J., Chanock, Stephen J., Cherkas, Lynn, Chines, Peter, Coin, Lachlan, Cooper, Cyrus, Crawford, Gabriel, Doering, Angela, Dominiczak, Anna, Doney, Alex S.F., Ebrahim, Shah, Elliott, Paul, Erdos, Michael R., Estrada, Karol, Ferrucci, Luigi, Hofman, Albert, Jacobs, Leonie C., Oostra, Ben A., Uitterlinden, André G., Van Duijn, Cornelia M., Lindgren, Cecilia M., Heid, Iris M., Randall, Joshua C., Lamina, Claudia, Steinthorsdottir, Valgerdur, Qi, Lu, Speliotes, Elizabeth K., Thorleifsson, Gudmar, Willer, Cristen J., Herrera, Blanca M., Jackson, Anne U., Lim, Noha, Scheet, Paul, Soranzo, Nicole, Amin, Najaf, Aulchenko, Yurii S., Chambers, John C., Drong, Alexander, Luan, Jia N.an, Lyon, Helen N., Rivadeneira, Fernando, Sanna, Serena, Timpson, Nicholas J., Zillikens, M. Carola, Jing, Hua Zhao, Almgren, Peter, Bandinelli, Stefania, Bennett, Amanda J., Bergman, Richard N., Bonnycastle, Lori L., Bumpstead, Suzannah J., Chanock, Stephen J., Cherkas, Lynn, Chines, Peter, Coin, Lachlan, Cooper, Cyrus, Crawford, Gabriel, Doering, Angela, Dominiczak, Anna, Doney, Alex S.F., Ebrahim, Shah, Elliott, Paul, Erdos, Michael R., Estrada, Karol, Ferrucci, Luigi, Hofman, Albert, Jacobs, Leonie C., Oostra, Ben A., Uitterlinden, André G., and Van Duijn, Cornelia M.
Abstract: To identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580) informative for adult waist circumference (WC) and waist-hip ratio (WHR). We selected 26 SNPs for follow-up, for which the evidence of association with measures of central adiposity (WC and/or WHR) was strong and disproportionate to that for overall adiposity or height. Follow-up studies in a maximum of 70,689 individuals identified two loci strongly associated with measures of central adiposity; these map near TFAP2B (WC, P = 1.9×102 -11) and MSRA (WC, P = 8.9×10-9). A third locus, near LYPLAL1, was associated with WHR in women only (P = 2.6×10 -8). The variants near TFAP2B appear to influence central adiposity through an effect on overall obesity/fat-mass, whereas LYPLAL1 displays a strong female-only association with fat distribution. By focusing on anthropometric measures of central obesity and fat distribution, we have identified three loci implicated in the regulation of human adiposity.
Published: 2009

248. Association Between Autozygosity and Major Depression: Stratification Due to Religious Assortment

Author: Abdellaoui, Abdel, primary, Hottenga, Jouke-Jan, additional, Xiao, Xiangjun, additional, Scheet, Paul, additional, Ehli, Erik A., additional, Davies, Gareth E., additional, Hudziak, James J., additional, Smit, Dirk J. A., additional, Bartels, Meike, additional, Willemsen, Gonneke, additional, Brooks, Andrew, additional, Sullivan, Patrick F., additional, Smit, Johannes H., additional, de Geus, Eco J., additional, Penninx, Brenda W. J. H., additional, and Boomsma, Dorret I., additional
Published: 2013
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249. MICA, a gene contributing strong susceptibility to ankylosing spondylitis

Author: Zhou, Xiaodong, primary, Wang, Jiucun, additional, Zou, Hejian, additional, Ward, Michael M, additional, Weisman, Michael H, additional, Espitia, Maribel G, additional, Xiao, Xiangjun, additional, Petersdorf, Effie, additional, Mignot, Emmanuel, additional, Martin, Javier, additional, Gensler, Lianne S, additional, Scheet, Paul, additional, and Reveille, John D, additional
Published: 2013
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250. Discovering new targeted therapies for BRAF mutant-like colorectal cancers.

Author: San Lucas, F. Anthony, primary, Kopetz, Scott, additional, Scheet, Paul A., additional, and Vilar Sanchez, Eduardo, additional
Published: 2013
Full Text: View/download PDF

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