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14. A Method to Exploit the Structure of Genetic Ancestry Space to Enhance Case-Control Studies

Author

Barclay, Murray, Peyrin-Biroulet, Laurent, Chamaillard, Mathias, Colombel, Jean-Frederick, Cottone, Mario, Croft, Anthony, D’Incà, Renata, Halfvarson, Jonas, Hanigan, Katherine, Henderson, Paul, Hugot, Jean-Pierre, Karban, Amir, Kennedy, Nicholas A., Khan, Mohammed Azam, Lémann, Marc, Levine, Arie, Massey, Dunecan, Milla, Monica, Montgomery, Grant W., Ng, Sok Meng Evelyn, Oikonomou, Ioannis, Peeters, Harald, Proctor, Deborah D., Rahier, Jean-Francois, Roberts, Rebecca, Rutgeerts, Paul, Seibold, Frank, Stronati, Laura, Taylor, Kirstin M., Törkvist, Leif, Ublick, Kullak, Van Limbergen, Johan, Van Gossum, Andre, Vatn, Morten H., Zhang, Hu, Zhang, Wei, Andrews, Jane M., Bampton, Peter A., Florin, Timothy H., Gearry, Richard, Krishnaprasad, Krupa, Lawrance, Ian C., Mahy, Gillian, Radford-Smith, Graham, Roberts, Rebecca L., Simms, Lisa A., Amininijad, Leila, Cleynen, Isabelle, Dewit, Olivier, Franchimont, Denis, Georges, Michel, Laukens, Debby, Theatre, Emilie, Van Gossum, André, Vermeire, Severine, Aumais, Guy, Baidoo, Leonard, Barrie, Arthur M., III, Beck, Karen, Bernard, Edmond-Jean, Binion, David G., Bitton, Alain, Brant, Steve R., Cho, Judy H., Cohen, Albert, Croitoru, Kenneth, Daly, Mark J., Datta, Lisa W., Deslandres, Colette, Duerr, Richard H., Dutridge, Debra, Ferguson, John, Fultz, Joann, Goyette, Philippe, Greenberg, Gordon R., Haritunians, Talin, Jobin, Gilles, Katz, Seymour, Lahaie, Raymond G., McGovern, Dermot P., Nelson, Linda, Ng, Sok Meng, Ning, Kaida, Paré, Pierre, Regueiro, Miguel D., Rioux, John D., Ruggiero, Elizabeth, Schumm, L. Philip, Schwartz, Marc, Scott, Regan, Sharma, Yashoda, Silverberg, Mark S., Spears, Denise, Steinhart, A. Hillary, Stempak, Joanne M., Swoger, Jason M., Tsagarelis, Constantina, Zhang, Clarence, Zhao, Hongyu, Aerts, Jan, Ahmad, Tariq, Arbury, Hazel, Attwood, Anthony, Auton, Adam, Ball, Stephen G., Balmforth, Anthony J., Barnes, Chris, Barrett, Jeffrey C., Barroso, Inês, Barton, Anne, Bennett, Amanda J., Bhaskar, Sanjeev, Blaszczyk, Katarzyna, Bowes, John, Brand, Oliver J., Braund, Peter S., Bredin, Francesca, Breen, Gerome, Brown, Morris J., Bruce, Ian N., Bull, Jaswinder, Burren, Oliver S., Burton, John, Byrnes, Jake, Caesar, Sian, Cardin, Niall, Clee, Chris M., Coffey, Alison J., Connell, John M.C., Conrad, Donald F., Cooper, Jason D., Dominiczak, Anna F., Downes, Kate, Drummond, Hazel E., Dudakia, Darshna, Dunham, Andrew, Ebbs, Bernadette, Eccles, Diana, Edkins, Sarah, Edwards, Cathryn, Elliot, Anna, Emery, Paul, Evans, David M., Evans, Gareth, Eyre, Steve, Farmer, Anne, I, Ferrier, Nicol, Flynn, Edward, Forbes, Alistair, Forty, Liz, Franklyn, Jayne A., Frayling, Timothy M., Freathy, Rachel M., Giannoulatou, Eleni, Gibbs, Polly, Gilbert, Paul, Gordon-Smith, Katherine, Gray, Emma, Green, Elaine, Groves, Chris J., Grozeva, Detelina, Gwilliam, Rhian, Hall, Anita, Hammond, Naomi, Hardy, Matt, Harrison, Pile, Hassanali, Neelam, Hebaishi, Husam, Hines, Sarah, Hinks, Anne, Hitman, Graham A., Hocking, Lynne, Holmes, Chris, Howard, Eleanor, Howard, Philip, Howson, Joanna M.M., Hughes, Debbie, Hunt, Sarah, Isaacs, John D., Jain, Mahim, Jewell, Derek P., Johnson, Toby, Jolley, Jennifer D., Jones, Ian R., Jones, Lisa A., Kirov, George, Langford, Cordelia F., Lango-Allen, Hana, Lathrop, G. Mark, Lee, James, Lee, Kate L., Lees, Charlie, Lewis, Kevin, Lindgren, Cecilia M., Maisuria-Armer, Meeta, Maller, Julian, Mansfield, John, Marchini, Jonathan L., Martin, Paul, Massey, Dunecan C.O., McArdle, Wendy L., McGuffin, Peter, McLay, Kirsten E., McVean, Gil, Mentzer, Alex, Mimmack, Michael L., Morgan, Ann E., Morris, Andrew P., Mowat, Craig, Munroe, Patricia B., Myers, Simon, Newman, William, Nimmo, Elaine R., O’Donovan, Michael C., Onipinla, Abiodun, Ovington, Nigel R., Owen, Michael J., Palin, Kimmo, Palotie, Aarno, Parnell, Kirstie, Pearson, Richard, Pernet, David, Perry, John R.B., Phillips, Anne, Plagnol, Vincent, Prescott, Natalie J., Prokopenko, Inga, Quail, Michael A., Rafelt, Suzanne, Rayner, Nigel W., Reid, David M., Renwick, Anthony, Ring, Susan M., Robertson, Neil, Robson, Samuel, Russell, Ellie, St Clair, David, Sambrook, Jennifer G., Sanderson, Jeremy D., Sawcer, Stephen J., Schuilenburg, Helen, Scott, Carol E., Scott, Richard, Seal, Sheila, Shaw-Hawkins, Sue, Shields, Beverley M., Simmonds, Matthew J., Smyth, Debbie J., Somaskantharajah, Elilan, Spanova, Katarina, Steer, Sophia, Stephens, Jonathan, Stevens, Helen E., Stirrups, Kathy, Stone, Millicent A., Strachan, David P., Su, Zhan, Symmons, Deborah P.M., Thompson, John R., Thomson, Wendy, Tobin, Martin D., Travers, Mary E., Turnbull, Clare, Vukcevic, Damjan, Wain, Louise V., Walker, Mark, Walker, Neil M., Wallace, Chris, Warren-Perry, Margaret, Watkins, Nicholas A., Webster, John, Weedon, Michael N., Wilson, Anthony G., Woodburn, Matthew, Wordsworth, B. Paul, Yau, Chris, Young, Allan H., Zeggini, Eleftheria, Brown, Matthew A., Burton, Paul R., Caulfield, Mark J., Compston, Alastair, Farrall, Martin, Gough, Stephen C.L., Hall, Alistair S., Hattersley, Andrew T., Hill, Adrian V.S., Mathew, Christopher G., Pembrey, Marcus, Satsangi, Jack, Stratton, Michael R., Worthington, Jane, Hurles, Matthew E., Duncanson, Audrey, Ouwehand, Willem H., Parkes, Miles, Rahman, Nazneen, Todd, John A., Samani, Nilesh J., Kwiatkowski, Dominic P., McCarthy, Mark I., Craddock, Nick, Deloukas, Panos, Donnelly, Peter, Blackwell, Jenefer M., Bramon, Elvira, Casas, Juan P., Corvin, Aiden, Jankowski, Janusz, Markus, Hugh S., Palmer, Colin N.A., Plomin, Robert, Rautanen, Anna, Trembath, Richard C., Viswanathan, Ananth C., Wood, Nicholas W., Spencer, Chris C.A., Band, Gavin, Bellenguez, Céline, Freeman, Colin, Hellenthal, Garrett, Pirinen, Matti, Strange, Amy, Blackburn, Hannah, Bumpstead, Suzannah J., Dronov, Serge, Gillman, Matthew, Jayakumar, Alagurevathi, McCann, Owen T., Liddle, Jennifer, Potter, Simon C., Ravindrarajah, Radhi, Ricketts, Michelle, Waller, Matthew, Weston, Paul, Widaa, Sara, Whittaker, Pamela, Bodea, Corneliu A., Neale, Benjamin M., Ripke, Stephan, Devlin, Bernie, and Roeder, Kathryn

Published
2016
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16. SARS-CoV-2 infects an in vitro model of the human developing pancreas through endocytosis

Author

Szlachcic, Wojciech J., primary, Dabrowska, Agnieszka, additional, Milewska, Aleksandra, additional, Ziojla, Natalia, additional, Blaszczyk, Katarzyna, additional, Barreto-Duran, Emilia, additional, Sanak, Marek, additional, Surmiak, Marcin, additional, Owczarek, Katarzyna, additional, Grzanka, Dariusz, additional, Durzynska, Julia, additional, Pyrc, Krzysztof, additional, and Borowiak, Malgorzata, additional

Published
2022
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19. Investigation of Crohn's Disease Risk Loci in Ulcerative Colitis Further Defines Their Molecular Relationship

Author

Anderson, Carl A., Massey, Dunecan C.O., Barrett, Jeffrey C., Prescott, Natalie J., Tremelling, Mark, Fisher, Sheila A., Gwilliam, Rhian, Jacob, Jemima, Nimmo, Elaine R., Drummond, Hazel, Lees, Charlie W., Onnie, Clive M., Hanson, Catherine, Blaszczyk, Katarzyna, Ravindrarajah, Radhi, Hunt, Sarah, Varma, Dhiraj, Hammond, Naomi, Lewis, Gregory, Attlesey, Heather, Watkins, Nick, Ouwehand, Willem, Strachan, David, McArdle, Wendy, Lewis, Cathryn M., Lobo, Alan, Sanderson, Jeremy, Jewell, Derek P., Deloukas, Panos, Mansfield, John C., Mathew, Christopher G., Satsangi, Jack, and Parkes, Miles

Published
2009
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20. Independent and population-specific association of risk variants at the IRGM locus with Crohnʼs disease

Author

Prescott, Natalie J., Dominy, Katherine M., Kubo, Michiaki, Lewis, Cathryn M., Fisher, Sheila A., Redon, Richard, Huang, Ni, Stranger, Barbara E., Blaszczyk, Katarzyna, Hudspith, Barry, Parkes, Gareth, Hosono, Naoya, Yamazaki, Keiko, Onnie, Clive M., Forbes, Alastair, Dermitzakis, Emmanouil T., Nakamura, Yusuke, Mansfield, John C., Sanderson, Jeremy, Hurles, Matthew E., Roberts, Roland G., and Mathew, Christopher G.

Published
2010
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21. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls

Author

Craddock, Nick, Hurles, Matthew E., Cardin, Niall, Pearson, Richard D., Plagnol, Vincent, Robson, Samuel, Vukcevic, Damjan, Barnes, Chris, Conrad, Donald F., Giannoulatou, Eleni, Holmes, Chris, Marchini, Jonathan L., Stirrups, Kathy, Tobin, Martin D., Wain, Louise V., Yau, Chris, Aerts, Jan, Ahmad, Tariq, Daniel Andrews, T., Arbury, Hazel, Attwood, Anthony, Auton, Adam, Ball, Stephen G., Balmforth, Anthony J., Barrett, Jeffrey C., Barroso, Inês, Barton, Anne, Bennett, Amanda J., Bhaskar, Sanjeev, Blaszczyk, Katarzyna, Bowes, John, Brand, Oliver J., Braund, Peter S., Bredin, Francesca, Breen, Gerome, Brown, Morris J., Bruce, Ian N., Bull, Jaswinder, Burren, Oliver S., Burton, John, Byrnes, Jake, Caesar, Sian, Clee, Chris M., Coffey, Alison J., Connell, John M. C., Cooper, Jason D., Dominiczak, Anna F., Downes, Kate, Drummond, Hazel E., Dudakia, Darshna, Dunham, Andrew, Ebbs, Bernadette, Eccles, Diana, Edkins, Sarah, Edwards, Cathryn, Elliot, Anna, Emery, Paul, Evans, David M., Evans, Gareth, Eyre, Steve, Farmer, Anne, Nicol Ferrier, I., Feuk, Lars, Fitzgerald, Tomas, Flynn, Edward, Forbes, Alistair, Forty, Liz, Franklyn, Jayne A., Freathy, Rachel M., Gibbs, Polly, Gilbert, Paul, Gokumen, Omer, Gordon-Smith, Katherine, Gray, Emma, Green, Elaine, Groves, Chris J., Grozeva, Detelina, Gwilliam, Rhian, Hall, Anita, Hammond, Naomi, Hardy, Matt, Harrison, Pile, Hassanali, Neelam, Hebaishi, Husam, Hines, Sarah, Hinks, Anne, Hitman, Graham A, Hocking, Lynne, Howard, Eleanor, Howard, Philip, Howson, Joanna M. M., Hughes, Debbie, Hunt, Sarah, Isaacs, John D., Jain, Mahim, Jewell, Derek P., Johnson, Toby, Jolley, Jennifer D., Jones, Ian R., Jones, Lisa A., Kirov, George, Langford, Cordelia F., Lango-Allen, Hana, Mark Lathrop, G., Lee, James, Lee, Kate L., Lees, Charlie, Lewis, Kevin, Lindgren, Cecilia M., Maisuria-Armer, Meeta, Maller, Julian, Mansfield, John, Martin, Paul, Massey, Dunecan C. O., McArdle, Wendy L., McGuffin, Peter, McLay, Kirsten E., Mentzer, Alex, Mimmack, Michael L., Morgan, Ann E., Morris, Andrew P., Mowat, Craig, Myers, Simon, Newman, William, Nimmo, Elaine R., O’Donovan, Michael C., Onipinla, Abiodun, Onyiah, Ifejinelo, Ovington, Nigel R., Owen, Michael J., Palin, Kimmo, Parnell, Kirstie, Pernet, David, Perry, John R. B., Phillips, Anne, Pinto, Dalila, Prescott, Natalie J., Prokopenko, Inga, Quail, Michael A., Rafelt, Suzanne, Rayner, Nigel W., Redon, Richard, Reid, David M., Renwick, Anthony, Ring, Susan M., Robertson, Neil, Russell, Ellie, St Clair, David, Sambrook, Jennifer G., Sanderson, Jeremy D., Schuilenburg, Helen, Scott, Carol E., Scott, Richard, Seal, Sheila, Shaw-Hawkins, Sue, Shields, Beverley M., Simmonds, Matthew J., Smyth, Debbie J., Somaskantharajah, Elilan, Spanova, Katarina, Steer, Sophia, Stephens, Jonathan, Stevens, Helen E., Stone, Millicent A., Su, Zhan, Symmons, Deborah P. M., Thompson, John R., Thomson, Wendy, Travers, Mary E., Turnbull, Clare, Valsesia, Armand, Walker, Mark, Walker, Neil M., Wallace, Chris, Warren-Perry, Margaret, Watkins, Nicholas A., Webster, John, Weedon, Michael N., Wilson, Anthony G., Woodburn, Matthew, Wordsworth, Paul B., Young, Allan H., Zeggini, Eleftheria, Carter, Nigel P., Frayling, Timothy M., Lee, Charles, McVean, Gil, Munroe, Patricia B., Palotie, Aarno, Sawcer, Stephen J., Scherer, Stephen W., Strachan, David P., Tyler-Smith, Chris, Brown, Matthew A., Burton, Paul R., Caulfield, Mark J., Compston, Alastair, Farrall, Martin, Gough, Stephen C. L., Hall, Alistair S., Hattersley, Andrew T., Hill, Adrian V. S., Mathew, Christopher G., Pembrey, Marcus, Satsangi, Jack, Stratton, Michael R., Worthington, Jane, Deloukas, Panos, Duncanson, Audrey, Kwiatkowski, Dominic P., McCarthy, Mark I., Ouwehand, Willem H., Parkes, Miles, Rahman, Nazneen, Todd, John A., Samani, Nilesh J., and Donnelly, Peter

Published
2010
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23. Independent and population-specific association of risk variants at the IRGM locus with Crohn's disease

Author

Prescott, Natalie J., Dominy, Katherine M., Kubo, Michiaki, Lewis, Cathryn M., Fisher, Sheila A., Redon, Richard, Huang, Ni, Stranger, Barbara E., Blaszczyk, Katarzyna, Hudspith, Barry, Parkes, Gareth, Hosono, Naoya, Yamazaki, Keiko, Onnie, Clive M., Forbes, Alastair, Dermitzakis, Emmanouil T., Nakamura, Yusuke, Mansfield, John C., Sanderson, Jeremy, Hurles, Matthew E., Roberts, Roland G., Mathew, Christopher G., Prescott, Natalie J., Dominy, Katherine M., Kubo, Michiaki, Lewis, Cathryn M., Fisher, Sheila A., Redon, Richard, Huang, Ni, Stranger, Barbara E., Blaszczyk, Katarzyna, Hudspith, Barry, Parkes, Gareth, Hosono, Naoya, Yamazaki, Keiko, Onnie, Clive M., Forbes, Alastair, Dermitzakis, Emmanouil T., Nakamura, Yusuke, Mansfield, John C., Sanderson, Jeremy, Hurles, Matthew E., Roberts, Roland G., and Mathew, Christopher G.

Abstract

DNA polymorphisms in a region on chromosome 5q33.1 which contains two genes, immunity related GTPase related family, M (IRGM) and zinc finger protein 300 (ZNF300), are associated with Crohn's disease (CD). The deleted allele of a 20 kb copy number variation (CNV) upstream of IRGM was recently shown to be in strong linkage disequilibrium (LD) with the CD-associated single nucleotide polymorphisms and is itself associated with CD (P < 0.01). The deletion was correlated with increased or reduced expression of IRGM in transformed cells in a cell line-dependent manner, and has been proposed as a likely causal variant. We report here that small insertion/deletion polymorphisms in the promoter and 5′ untranslated region of IRGM are, together with the CNV, strongly associated with CD (P = 1.37 × 10−5 to 1.40 × 10−9), and that the CNV and the 5′-untranslated region variant −308(GTTT)5 contribute independently to CD susceptibility (P = 2.6 × 10−7 and P = 2 × 10−5, respectively). We also show that the CD risk haplotype is associated with a significant decrease in IRGM expression (P < 10−12) in untransformed lymphocytes from CD patients. Further analysis of these variants in a Japanese CD case-control sample and of IRGM expression in HapMap populations revealed that neither the IRGM insertion/deletion polymorphisms nor the CNV was associated with CD or with altered IRGM expression in the Asian population. This suggests that the involvement of the IRGM risk haplotype in the pathogenesis of CD requires gene-gene or gene-environment interactions which are absent in Asian populations, or that none of the variants analysed are causal, and that the true causal variants arose after the European-Asian split

Published
2017

24. A Method to Exploit the Structure of Genetic Ancestry Space to Enhance Case-Control Studies

Author

Bodea, Corneliu A., primary, Neale, Benjamin M., additional, Ripke, Stephan, additional, Daly, Mark J., additional, Devlin, Bernie, additional, Roeder, Kathryn, additional, Barclay, Murray, additional, Peyrin-Biroulet, Laurent, additional, Chamaillard, Mathias, additional, Colombel, Jean-Frederick, additional, Cottone, Mario, additional, Croft, Anthony, additional, D’Incà, Renata, additional, Halfvarson, Jonas, additional, Hanigan, Katherine, additional, Henderson, Paul, additional, Hugot, Jean-Pierre, additional, Karban, Amir, additional, Kennedy, Nicholas A., additional, Khan, Mohammed Azam, additional, Lémann, Marc, additional, Levine, Arie, additional, Massey, Dunecan, additional, Milla, Monica, additional, Montgomery, Grant W., additional, Ng, Sok Meng Evelyn, additional, Oikonomou, Ioannis, additional, Peeters, Harald, additional, Proctor, Deborah D., additional, Rahier, Jean-Francois, additional, Roberts, Rebecca, additional, Rutgeerts, Paul, additional, Seibold, Frank, additional, Stronati, Laura, additional, Taylor, Kirstin M., additional, Törkvist, Leif, additional, Ublick, Kullak, additional, Van Limbergen, Johan, additional, Van Gossum, Andre, additional, Vatn, Morten H., additional, Zhang, Hu, additional, Zhang, Wei, additional, Andrews, Jane M., additional, Bampton, Peter A., additional, Florin, Timothy H., additional, Gearry, Richard, additional, Krishnaprasad, Krupa, additional, Lawrance, Ian C., additional, Mahy, Gillian, additional, Radford-Smith, Graham, additional, Roberts, Rebecca L., additional, Simms, Lisa A., additional, Amininijad, Leila, additional, Cleynen, Isabelle, additional, Dewit, Olivier, additional, Franchimont, Denis, additional, Georges, Michel, additional, Laukens, Debby, additional, Theatre, Emilie, additional, Van Gossum, André, additional, Vermeire, Severine, additional, Aumais, Guy, additional, Baidoo, Leonard, additional, Barrie, Arthur M., additional, Beck, Karen, additional, Bernard, Edmond-Jean, additional, Binion, David G., additional, Bitton, Alain, additional, Brant, Steve R., additional, Cho, Judy H., additional, Cohen, Albert, additional, Croitoru, Kenneth, additional, Datta, Lisa W., additional, Deslandres, Colette, additional, Duerr, Richard H., additional, Dutridge, Debra, additional, Ferguson, John, additional, Fultz, Joann, additional, Goyette, Philippe, additional, Greenberg, Gordon R., additional, Haritunians, Talin, additional, Jobin, Gilles, additional, Katz, Seymour, additional, Lahaie, Raymond G., additional, McGovern, Dermot P., additional, Nelson, Linda, additional, Ng, Sok Meng, additional, Ning, Kaida, additional, Paré, Pierre, additional, Regueiro, Miguel D., additional, Rioux, John D., additional, Ruggiero, Elizabeth, additional, Schumm, L. Philip, additional, Schwartz, Marc, additional, Scott, Regan, additional, Sharma, Yashoda, additional, Silverberg, Mark S., additional, Spears, Denise, additional, Steinhart, A. Hillary, additional, Stempak, Joanne M., additional, Swoger, Jason M., additional, Tsagarelis, Constantina, additional, Zhang, Clarence, additional, Zhao, Hongyu, additional, Aerts, Jan, additional, Ahmad, Tariq, additional, Arbury, Hazel, additional, Attwood, Anthony, additional, Auton, Adam, additional, Ball, Stephen G., additional, Balmforth, Anthony J., additional, Barnes, Chris, additional, Barrett, Jeffrey C., additional, Barroso, Inês, additional, Barton, Anne, additional, Bennett, Amanda J., additional, Bhaskar, Sanjeev, additional, Blaszczyk, Katarzyna, additional, Bowes, John, additional, Brand, Oliver J., additional, Braund, Peter S., additional, Bredin, Francesca, additional, Breen, Gerome, additional, Brown, Morris J., additional, Bruce, Ian N., additional, Bull, Jaswinder, additional, Burren, Oliver S., additional, Burton, John, additional, Byrnes, Jake, additional, Caesar, Sian, additional, Cardin, Niall, additional, Clee, Chris M., additional, Coffey, Alison J., additional, Connell, John M.C., additional, Conrad, Donald F., additional, Cooper, Jason D., additional, Dominiczak, Anna F., additional, Downes, Kate, additional, Drummond, Hazel E., additional, Dudakia, Darshna, additional, Dunham, Andrew, additional, Ebbs, Bernadette, additional, Eccles, Diana, additional, Edkins, Sarah, additional, Edwards, Cathryn, additional, Elliot, Anna, additional, Emery, Paul, additional, Evans, David M., additional, Evans, Gareth, additional, Eyre, Steve, additional, Farmer, Anne, additional, Ferrier, Nicol, additional, Flynn, Edward, additional, Forbes, Alistair, additional, Forty, Liz, additional, Franklyn, Jayne A., additional, Frayling, Timothy M., additional, Freathy, Rachel M., additional, Giannoulatou, Eleni, additional, Gibbs, Polly, additional, Gilbert, Paul, additional, Gordon-Smith, Katherine, additional, Gray, Emma, additional, Green, Elaine, additional, Groves, Chris J., additional, Grozeva, Detelina, additional, Gwilliam, Rhian, additional, Hall, Anita, additional, Hammond, Naomi, additional, Hardy, Matt, additional, Harrison, Pile, additional, Hassanali, Neelam, additional, Hebaishi, Husam, additional, Hines, Sarah, additional, Hinks, Anne, additional, Hitman, Graham A., additional, Hocking, Lynne, additional, Holmes, Chris, additional, Howard, Eleanor, additional, Howard, Philip, additional, Howson, Joanna M.M., additional, Hughes, Debbie, additional, Hunt, Sarah, additional, Isaacs, John D., additional, Jain, Mahim, additional, Jewell, Derek P., additional, Johnson, Toby, additional, Jolley, Jennifer D., additional, Jones, Ian R., additional, Jones, Lisa A., additional, Kirov, George, additional, Langford, Cordelia F., additional, Lango-Allen, Hana, additional, Lathrop, G. Mark, additional, Lee, James, additional, Lee, Kate L., additional, Lees, Charlie, additional, Lewis, Kevin, additional, Lindgren, Cecilia M., additional, Maisuria-Armer, Meeta, additional, Maller, Julian, additional, Mansfield, John, additional, Marchini, Jonathan L., additional, Martin, Paul, additional, Massey, Dunecan C.O., additional, McArdle, Wendy L., additional, McGuffin, Peter, additional, McLay, Kirsten E., additional, McVean, Gil, additional, Mentzer, Alex, additional, Mimmack, Michael L., additional, Morgan, Ann E., additional, Morris, Andrew P., additional, Mowat, Craig, additional, Munroe, Patricia B., additional, Myers, Simon, additional, Newman, William, additional, Nimmo, Elaine R., additional, O’Donovan, Michael C., additional, Onipinla, Abiodun, additional, Ovington, Nigel R., additional, Owen, Michael J., additional, Palin, Kimmo, additional, Palotie, Aarno, additional, Parnell, Kirstie, additional, Pearson, Richard, additional, Pernet, David, additional, Perry, John R.B., additional, Phillips, Anne, additional, Plagnol, Vincent, additional, Prescott, Natalie J., additional, Prokopenko, Inga, additional, Quail, Michael A., additional, Rafelt, Suzanne, additional, Rayner, Nigel W., additional, Reid, David M., additional, Renwick, Anthony, additional, Ring, Susan M., additional, Robertson, Neil, additional, Robson, Samuel, additional, Russell, Ellie, additional, St Clair, David, additional, Sambrook, Jennifer G., additional, Sanderson, Jeremy D., additional, Sawcer, Stephen J., additional, Schuilenburg, Helen, additional, Scott, Carol E., additional, Scott, Richard, additional, Seal, Sheila, additional, Shaw-Hawkins, Sue, additional, Shields, Beverley M., additional, Simmonds, Matthew J., additional, Smyth, Debbie J., additional, Somaskantharajah, Elilan, additional, Spanova, Katarina, additional, Steer, Sophia, additional, Stephens, Jonathan, additional, Stevens, Helen E., additional, Stirrups, Kathy, additional, Stone, Millicent A., additional, Strachan, David P., additional, Su, Zhan, additional, Symmons, Deborah P.M., additional, Thompson, John R., additional, Thomson, Wendy, additional, Tobin, Martin D., additional, Travers, Mary E., additional, Turnbull, Clare, additional, Vukcevic, Damjan, additional, Wain, Louise V., additional, Walker, Mark, additional, Walker, Neil M., additional, Wallace, Chris, additional, Warren-Perry, Margaret, additional, Watkins, Nicholas A., additional, Webster, John, additional, Weedon, Michael N., additional, Wilson, Anthony G., additional, Woodburn, Matthew, additional, Wordsworth, B. Paul, additional, Yau, Chris, additional, Young, Allan H., additional, Zeggini, Eleftheria, additional, Brown, Matthew A., additional, Burton, Paul R., additional, Caulfield, Mark J., additional, Compston, Alastair, additional, Farrall, Martin, additional, Gough, Stephen C.L., additional, Hall, Alistair S., additional, Hattersley, Andrew T., additional, Hill, Adrian V.S., additional, Mathew, Christopher G., additional, Pembrey, Marcus, additional, Satsangi, Jack, additional, Stratton, Michael R., additional, Worthington, Jane, additional, Hurles, Matthew E., additional, Duncanson, Audrey, additional, Ouwehand, Willem H., additional, Parkes, Miles, additional, Rahman, Nazneen, additional, Todd, John A., additional, Samani, Nilesh J., additional, Kwiatkowski, Dominic P., additional, McCarthy, Mark I., additional, Craddock, Nick, additional, Deloukas, Panos, additional, Donnelly, Peter, additional, Blackwell, Jenefer M., additional, Bramon, Elvira, additional, Casas, Juan P., additional, Corvin, Aiden, additional, Jankowski, Janusz, additional, Markus, Hugh S., additional, Palmer, Colin N.A., additional, Plomin, Robert, additional, Rautanen, Anna, additional, Trembath, Richard C., additional, Viswanathan, Ananth C., additional, Wood, Nicholas W., additional, Spencer, Chris C.A., additional, Band, Gavin, additional, Bellenguez, Céline, additional, Freeman, Colin, additional, Hellenthal, Garrett, additional, Pirinen, Matti, additional, Strange, Amy, additional, Blackburn, Hannah, additional, Bumpstead, Suzannah J., additional, Dronov, Serge, additional, Gillman, Matthew, additional, Jayakumar, Alagurevathi, additional, McCann, Owen T., additional, Liddle, Jennifer, additional, Potter, Simon C., additional, Ravindrarajah, Radhi, additional, Ricketts, Michelle, additional, Waller, Matthew, additional, Weston, Paul, additional, Widaa, Sara, additional, and Whittaker, Pamela, additional

Published
2016
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25. ID: 242

Author

Blaszczyk, Katarzyna, primary, Nowicka, Hanna, additional, Michalska, Agata, additional, Wesoly, Joanna, additional, and Bluyssen, Johannes, additional

Published
2015
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29. Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease.

Author

Fisher, Sheila A., Tremelling, Mark, Anderson, Carl A, Gwilliam, Rhian, Bumpstead, Suzannah, Prescott, Natalie J., Nimmo, Elaine R., Massey, Dunecan, Berzuini, Carlo, Johnson, Christopher, Barrett, Jeffrey C., Cummings, Fraser R., Drummond, Hazel, Lees, Charlie W., Onnie, Clive M., Hanson, Catherine E., Blaszczyk, Katarzyna, Inouye, Mike, Ewels, Philip, and Ravindrarajah, Radhi

Subjects
HUMAN genetics, ULCERATIVE colitis, CROHN'S disease, INFLAMMATORY bowel diseases, INTESTINAL diseases
Abstract

We report results of a nonsynonymous SNP scan for ulcerative colitis and identify a previously unknown susceptibility locus at ECM1. We also show that several risk loci are common to ulcerative colitis and Crohn's disease (IL23R, IL12B, HLA, NKX2-3 and MST1), whereas autophagy genes ATG16L1 and IRGM, along with NOD2 (also known as CARD15), are specific for Crohn's disease. These data provide the first detailed illustration of the genetic relationship between these common inflammatory bowel diseases. [ABSTRACT FROM AUTHOR]

Published
2008
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30. Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data

Author

Romagnoni, Alberto, Jégou, Simon, Van Steen, Kristel, Wainrib, Gilles, Hugot, Jean-Pierre, Peyrin-Biroulet, Laurent, Chamaillard, Mathias, Colombel, Jean-Frederick, Cottone, Mario, D’Amato, Mauro, D’Incà, Renata, Halfvarson, Jonas, Henderson, Paul, Karban, Amir, Kennedy, Nicholas A., Khan, Mohammed Azam, Lémann, Marc, Levine, Arie, Massey, Dunecan, Milla, Monica, Ng, Sok Meng Evelyn, Oikonomou, Ioannis, Peeters, Harald, Proctor, Deborah D., Rahier, Jean-Francois, Rutgeerts, Paul, Seibold, Frank, Stronati, Laura, Taylor, Kirstin M., Törkvist, Leif, Ublick, Kullak, Van Limbergen, Johan, Van Gossum, Andre, Vatn, Morten H., Zhang, Hu, Zhang, Wei, Andrews, Jane M., Bampton, Peter A., Barclay, Murray, Florin, Timothy H., Gearry, Richard, Krishnaprasad, Krupa, Lawrance, Ian C., Mahy, Gillian, Montgomery, Grant W., Radford-Smith, Graham, Roberts, Rebecca L., Simms, Lisa A., Hanigan, Katherine, Croft, Anthony, Amininijad, Leila, Cleynen, Isabelle, Dewit, Olivier, Franchimont, Denis, Georges, Michel, Laukens, Debby, Theatre, Emilie, Van Gossum, André, Vermeire, Severine, Aumais, Guy, Baidoo, Leonard, Barrie, Arthur M., Beck, Karen, Bernard, Edmond-Jean, Binion, David G., Bitton, Alain, Brant, Steve R., Cho, Judy H., Cohen, Albert, Croitoru, Kenneth, Daly, Mark J., Datta, Lisa W., Deslandres, Colette, Duerr, Richard H., Dutridge, Debra, Ferguson, John, Fultz, Joann, Goyette, Philippe, Greenberg, Gordon R., Haritunians, Talin, Jobin, Gilles, Katz, Seymour, Lahaie, Raymond G., McGovern, Dermot P., Nelson, Linda, Ng, Sok Meng, Ning, Kaida, Paré, Pierre, Regueiro, Miguel D., Rioux, John D., Ruggiero, Elizabeth, Schumm, L. Philip, Schwartz, Marc, Scott, Regan, Sharma, Yashoda, Silverberg, Mark S., Spears, Denise, Steinhart, A. Hillary, Stempak, Joanne M., Swoger, Jason M., Tsagarelis, Constantina, Zhang, Clarence, Zhao, Hongyu, Aerts, Jan, Ahmad, Tariq, Arbury, Hazel, Attwood, Anthony, Auton, Adam, Ball, Stephen G., Balmforth, Anthony J., Barnes, Chris, Barrett, Jeffrey C., Barroso, Inês, Barton, Anne, Bennett, Amanda J., Bhaskar, Sanjeev, Blaszczyk, Katarzyna, Bowes, John, Brand, Oliver J., Braund, Peter S., Bredin, Francesca, Breen, Gerome, Brown, Morris J., Bruce, Ian N., Bull, Jaswinder, Burren, Oliver S., Burton, John, Byrnes, Jake, Caesar, Sian, Cardin, Niall, Clee, Chris M., Coffey, Alison J., MC Connell, John, Conrad, Donald F., Cooper, Jason D., Dominiczak, Anna F., Downes, Kate, Drummond, Hazel E., Dudakia, Darshna, Dunham, Andrew, Ebbs, Bernadette, Eccles, Diana, Edkins, Sarah, Edwards, Cathryn, Elliot, Anna, Emery, Paul, Evans, David M., Evans, Gareth, Eyre, Steve, Farmer, Anne, Ferrier, I. Nicol, Flynn, Edward, Forbes, Alistair, Forty, Liz, Franklyn, Jayne A., Frayling, Timothy M., Freathy, Rachel M., Giannoulatou, Eleni, Gibbs, Polly, Gilbert, Paul, Gordon-Smith, Katherine, Gray, Emma, Green, Elaine, Groves, Chris J., Grozeva, Detelina, Gwilliam, Rhian, Hall, Anita, Hammond, Naomi, Hardy, Matt, Harrison, Pile, Hassanali, Neelam, Hebaishi, Husam, Hines, Sarah, Hinks, Anne, Hitman, Graham A., Hocking, Lynne, Holmes, Chris, Howard, Eleanor, Howard, Philip, Howson, Joanna M. M., Hughes, Debbie, Hunt, Sarah, Isaacs, John D., Jain, Mahim, Jewell, Derek P., Johnson, Toby, Jolley, Jennifer D., Jones, Ian R., Jones, Lisa A., Kirov, George, Langford, Cordelia F., Lango-Allen, Hana, Lathrop, G. Mark, Lee, James, Lee, Kate L., Lees, Charlie, Lewis, Kevin, Lindgren, Cecilia M., Maisuria-Armer, Meeta, Maller, Julian, Mansfield, John, Marchini, Jonathan L., Martin, Paul, Massey, Dunecan CO, McArdle, Wendy L., McGuffin, Peter, McLay, Kirsten E., McVean, Gil, Mentzer, Alex, Mimmack, Michael L., Morgan, Ann E., Morris, Andrew P., Mowat, Craig, Munroe, Patricia B., Myers, Simon, Newman, William, Nimmo, Elaine R., O’Donovan, Michael C., Onipinla, Abiodun, Ovington, Nigel R., Owen, Michael J., Palin, Kimmo, Palotie, Aarno, Parnell, Kirstie, Pearson, Richard, Pernet, David, Perry, John RB, Phillips, Anne, Plagnol, Vincent, Prescott, Natalie J., Prokopenko, Inga, Quail, Michael A., Rafelt, Suzanne, Rayner, Nigel W., Reid, David M., Renwick, Anthony, Ring, Susan M., Robertson, Neil, Robson, Samuel, Russell, Ellie, Clair, David St, Sambrook, Jennifer G., Sanderson, Jeremy D., Sawcer, Stephen J., Schuilenburg, Helen, Scott, Carol E., Scott, Richard, Seal, Sheila, Shaw-Hawkins, Sue, Shields, Beverley M., Simmonds, Matthew J., Smyth, Debbie J., Somaskantharajah, Elilan, Spanova, Katarina, Steer, Sophia, Stephens, Jonathan, Stevens, Helen E., Stirrups, Kathy, Stone, Millicent A., Strachan, David P., Su, Zhan, Symmons, Deborah P. M., Thompson, John R., Thomson, Wendy, Tobin, Martin D., Travers, Mary E., Turnbull, Clare, Vukcevic, Damjan, Wain, Louise V., Walker, Mark, Walker, Neil M., Wallace, Chris, Warren-Perry, Margaret, Watkins, Nicholas A., Webster, John, Weedon, Michael N., Wilson, Anthony G., Woodburn, Matthew, Wordsworth, B. Paul, Yau, Chris, Young, Allan H., Zeggini, Eleftheria, Brown, Matthew A., Burton, Paul R., Caulfield, Mark J., Compston, Alastair, Farrall, Martin, Gough, Stephen C. L., Hall, Alistair S., Hattersley, Andrew T., Hill, Adrian V. S., Mathew, Christopher G., Pembrey, Marcus, Satsangi, Jack, Stratton, Michael R., Worthington, Jane, Hurles, Matthew E., Duncanson, Audrey, Ouwehand, Willem H., Parkes, Miles, Rahman, Nazneen, Todd, John A., Samani, Nilesh J., Kwiatkowski, Dominic P., McCarthy, Mark I., Craddock, Nick, Deloukas, Panos, Donnelly, Peter, Blackwell, Jenefer M., Bramon, Elvira, Casas, Juan P., Corvin, Aiden, Jankowski, Janusz, Markus, Hugh S., Palmer, Colin NA, Plomin, Robert, Rautanen, Anna, Trembath, Richard C., Viswanathan, Ananth C., Wood, Nicholas W., Spencer, Chris C. A., Band, Gavin, Bellenguez, Céline, Freeman, Colin, Hellenthal, Garrett, Pirinen, Matti, Strange, Amy, Blackburn, Hannah, Bumpstead, Suzannah J., Dronov, Serge, Gillman, Matthew, Jayakumar, Alagurevathi, McCann, Owen T., Liddle, Jennifer, Potter, Simon C., Ravindrarajah, Radhi, Ricketts, Michelle, Waller, Matthew, Weston, Paul, Widaa, Sara, and Whittaker, Pamela

Subjects
692/4020/1503/257/1402, 45, 692/308/2056, 45/43, article, 129, 3. Good health
Abstract

Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers.

31. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls

Author

Craddock, Nick, Hurles, Matthew E., Cardin, Niall, Pearson, Richard D., Plagnol, Vincent, Robson, Samuel, Vukcevic, Damjan, Barnes, Chris, Conrad, Donald F., Giannoulatou, Eleni, Holmes, Chris, Marchini, Jonathan L., Stirrups, Kathy, Tobin, Martin D., Wain, Louise V., Yau, Chris, Aerts, Jan, Ahmad, Tariq, Daniel Andrews, T., Arbury, Hazel, Attwood, Anthony, Auton, Adam, Ball, Stephen G., Balmforth, Anthony J., Barrett, Jeffrey C., Barroso, Inês, Barton, Anne, Bennett, Amanda J., Bhaskar, Sanjeev, Blaszczyk, Katarzyna, Bowes, John, Brand, Oliver J., Braund, Peter S., Bredin, Francesca, Breen, Gerome, Brown, Morris J., Bruce, Ian N., Bull, Jaswinder, Burren, Oliver S., Burton, John, Byrnes, Jake, Caesar, Sian, Clee, Chris M., Coffey, Alison J., Connell, John M. C., Cooper, Jason D., Dominiczak, Anna F., Downes, Kate, Drummond, Hazel E., Dudakia, Darshna, Dunham, Andrew, Ebbs, Bernadette, Eccles, Diana, Edkins, Sarah, Edwards, Cathryn, Elliot, Anna, Emery, Paul, Evans, David M., Evans, Gareth, Eyre, Steve, Farmer, Anne, Nicol Ferrier, I., Feuk, Lars, Fitzgerald, Tomas, Flynn, Edward, Forbes, Alistair, Forty, Liz, Franklyn, Jayne A., Freathy, Rachel M., Gibbs, Polly, Gilbert, Paul, Gokumen, Omer, Gordon-Smith, Katherine, Gray, Emma, Green, Elaine, Groves, Chris J., Grozeva, Detelina, Gwilliam, Rhian, Hall, Anita, Hammond, Naomi, Hardy, Matt, Harrison, Pile, Hassanali, Neelam, Hebaishi, Husam, Hines, Sarah, Hinks, Anne, Hitman, Graham A, Hocking, Lynne, Howard, Eleanor, Howard, Philip, Howson, Joanna M. M., Hughes, Debbie, Hunt, Sarah, Isaacs, John D., Jain, Mahim, Jewell, Derek P., Johnson, Toby, Jolley, Jennifer D., Jones, Ian R., Jones, Lisa A., Kirov, George, Langford, Cordelia F., Lango-Allen, Hana, Mark Lathrop, G., Lee, James, Lee, Kate L., Lees, Charlie, Lewis, Kevin, Lindgren, Cecilia M., Maisuria-Armer, Meeta, Maller, Julian, Mansfield, John, Martin, Paul, Massey, Dunecan C. O., McArdle, Wendy L., McGuffin, Peter, McLay, Kirsten E., Mentzer, Alex, Mimmack, Michael L., Morgan, Ann E., Morris, Andrew P., Mowat, Craig, Myers, Simon, Newman, William, Nimmo, Elaine R., O’Donovan, Michael C., Onipinla, Abiodun, Onyiah, Ifejinelo, Ovington, Nigel R., Owen, Michael J., Palin, Kimmo, Parnell, Kirstie, Pernet, David, Perry, John R. B., Phillips, Anne, Pinto, Dalila, Prescott, Natalie J., Prokopenko, Inga, Quail, Michael A., Rafelt, Suzanne, Rayner, Nigel W., Redon, Richard, Reid, David M., Renwick, Anthony, Ring, Susan M., Robertson, Neil, Russell, Ellie, St Clair, David, Sambrook, Jennifer G., Sanderson, Jeremy D., Schuilenburg, Helen, Scott, Carol E., Scott, Richard, Seal, Sheila, Shaw-Hawkins, Sue, Shields, Beverley M., Simmonds, Matthew J., Smyth, Debbie J., Somaskantharajah, Elilan, Spanova, Katarina, Steer, Sophia, Stephens, Jonathan, Stevens, Helen E., Stone, Millicent A., Su, Zhan, Symmons, Deborah P. M., Thompson, John R., Thomson, Wendy, Travers, Mary E., Turnbull, Clare, Valsesia, Armand, Walker, Mark, Walker, Neil M., Wallace, Chris, Warren-Perry, Margaret, Watkins, Nicholas A., Webster, John, Weedon, Michael N., Wilson, Anthony G., Woodburn, Matthew, Wordsworth, B. Paul, Young, Allan H., Zeggini, Eleftheria, Carter, Nigel P., Frayling, Timothy M., Lee, Charles, McVean, Gil, Munroe, Patricia B., Palotie, Aarno, Sawcer, Stephen J., Scherer, Stephen W., Strachan, David P., Tyler-Smith, Chris, Brown, Matthew A., Burton, Paul R., Caulfield, Mark J., Compston, Alastair, Farrall, Martin, Gough, Stephen C. L., Hall, Alistair S., Hattersley, Andrew T., Hill, Adrian V. S., Mathew, Christopher G., Pembrey, Marcus, Satsangi, Jack, Stratton, Michael R., Worthington, Jane, Deloukas, Panos, Duncanson, Audrey, Kwiatkowski, Dominic P., McCarthy, Mark I., Ouwehand, Willem H., Parkes, Miles, Rahman, Nazneen, Todd, John A., Samani, Nilesh J., Donnelly, Peter, Craddock, Nick, Hurles, Matthew E., Cardin, Niall, Pearson, Richard D., Plagnol, Vincent, Robson, Samuel, Vukcevic, Damjan, Barnes, Chris, Conrad, Donald F., Giannoulatou, Eleni, Holmes, Chris, Marchini, Jonathan L., Stirrups, Kathy, Tobin, Martin D., Wain, Louise V., Yau, Chris, Aerts, Jan, Ahmad, Tariq, Daniel Andrews, T., Arbury, Hazel, Attwood, Anthony, Auton, Adam, Ball, Stephen G., Balmforth, Anthony J., Barrett, Jeffrey C., Barroso, Inês, Barton, Anne, Bennett, Amanda J., Bhaskar, Sanjeev, Blaszczyk, Katarzyna, Bowes, John, Brand, Oliver J., Braund, Peter S., Bredin, Francesca, Breen, Gerome, Brown, Morris J., Bruce, Ian N., Bull, Jaswinder, Burren, Oliver S., Burton, John, Byrnes, Jake, Caesar, Sian, Clee, Chris M., Coffey, Alison J., Connell, John M. C., Cooper, Jason D., Dominiczak, Anna F., Downes, Kate, Drummond, Hazel E., Dudakia, Darshna, Dunham, Andrew, Ebbs, Bernadette, Eccles, Diana, Edkins, Sarah, Edwards, Cathryn, Elliot, Anna, Emery, Paul, Evans, David M., Evans, Gareth, Eyre, Steve, Farmer, Anne, Nicol Ferrier, I., Feuk, Lars, Fitzgerald, Tomas, Flynn, Edward, Forbes, Alistair, Forty, Liz, Franklyn, Jayne A., Freathy, Rachel M., Gibbs, Polly, Gilbert, Paul, Gokumen, Omer, Gordon-Smith, Katherine, Gray, Emma, Green, Elaine, Groves, Chris J., Grozeva, Detelina, Gwilliam, Rhian, Hall, Anita, Hammond, Naomi, Hardy, Matt, Harrison, Pile, Hassanali, Neelam, Hebaishi, Husam, Hines, Sarah, Hinks, Anne, Hitman, Graham A, Hocking, Lynne, Howard, Eleanor, Howard, Philip, Howson, Joanna M. M., Hughes, Debbie, Hunt, Sarah, Isaacs, John D., Jain, Mahim, Jewell, Derek P., Johnson, Toby, Jolley, Jennifer D., Jones, Ian R., Jones, Lisa A., Kirov, George, Langford, Cordelia F., Lango-Allen, Hana, Mark Lathrop, G., Lee, James, Lee, Kate L., Lees, Charlie, Lewis, Kevin, Lindgren, Cecilia M., Maisuria-Armer, Meeta, Maller, Julian, Mansfield, John, Martin, Paul, Massey, Dunecan C. O., McArdle, Wendy L., McGuffin, Peter, McLay, Kirsten E., Mentzer, Alex, Mimmack, Michael L., Morgan, Ann E., Morris, Andrew P., Mowat, Craig, Myers, Simon, Newman, William, Nimmo, Elaine R., O’Donovan, Michael C., Onipinla, Abiodun, Onyiah, Ifejinelo, Ovington, Nigel R., Owen, Michael J., Palin, Kimmo, Parnell, Kirstie, Pernet, David, Perry, John R. B., Phillips, Anne, Pinto, Dalila, Prescott, Natalie J., Prokopenko, Inga, Quail, Michael A., Rafelt, Suzanne, Rayner, Nigel W., Redon, Richard, Reid, David M., Renwick, Anthony, Ring, Susan M., Robertson, Neil, Russell, Ellie, St Clair, David, Sambrook, Jennifer G., Sanderson, Jeremy D., Schuilenburg, Helen, Scott, Carol E., Scott, Richard, Seal, Sheila, Shaw-Hawkins, Sue, Shields, Beverley M., Simmonds, Matthew J., Smyth, Debbie J., Somaskantharajah, Elilan, Spanova, Katarina, Steer, Sophia, Stephens, Jonathan, Stevens, Helen E., Stone, Millicent A., Su, Zhan, Symmons, Deborah P. M., Thompson, John R., Thomson, Wendy, Travers, Mary E., Turnbull, Clare, Valsesia, Armand, Walker, Mark, Walker, Neil M., Wallace, Chris, Warren-Perry, Margaret, Watkins, Nicholas A., Webster, John, Weedon, Michael N., Wilson, Anthony G., Woodburn, Matthew, Wordsworth, B. Paul, Young, Allan H., Zeggini, Eleftheria, Carter, Nigel P., Frayling, Timothy M., Lee, Charles, McVean, Gil, Munroe, Patricia B., Palotie, Aarno, Sawcer, Stephen J., Scherer, Stephen W., Strachan, David P., Tyler-Smith, Chris, Brown, Matthew A., Burton, Paul R., Caulfield, Mark J., Compston, Alastair, Farrall, Martin, Gough, Stephen C. L., Hall, Alistair S., Hattersley, Andrew T., Hill, Adrian V. S., Mathew, Christopher G., Pembrey, Marcus, Satsangi, Jack, Stratton, Michael R., Worthington, Jane, Deloukas, Panos, Duncanson, Audrey, Kwiatkowski, Dominic P., McCarthy, Mark I., Ouwehand, Willem H., Parkes, Miles, Rahman, Nazneen, Todd, John A., Samani, Nilesh J., and Donnelly, Peter

Abstract

Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed 19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with diseaseIRGM for Crohns disease, HLA for Crohns disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetesalthough in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases. © 2010 Macmillan Publishers Limited. All rights reserved.

32. Independent and population-specific association of risk variants at the IRGM locus with Crohn's disease

Author

Prescott, Natalie J., Dominy, Katherine M., Kubo, Michiaki, Lewis, Cathryn M., Fisher, Sheila A., Redon, Richard, Huang, Ni, Stranger, Barbara E., Blaszczyk, Katarzyna, Hudspith, Barry, Parkes, Gareth, Hosono, Naoya, Yamazaki, Keiko, Onnie, Clive M., Forbes, Alastair, Dermitzakis, Emmanouil T., Nakamura, Yusuke, Mansfield, John C., Sanderson, Jeremy, Hurles, Matthew E., Roberts, Roland G., Mathew, Christopher G., Prescott, Natalie J., Dominy, Katherine M., Kubo, Michiaki, Lewis, Cathryn M., Fisher, Sheila A., Redon, Richard, Huang, Ni, Stranger, Barbara E., Blaszczyk, Katarzyna, Hudspith, Barry, Parkes, Gareth, Hosono, Naoya, Yamazaki, Keiko, Onnie, Clive M., Forbes, Alastair, Dermitzakis, Emmanouil T., Nakamura, Yusuke, Mansfield, John C., Sanderson, Jeremy, Hurles, Matthew E., Roberts, Roland G., and Mathew, Christopher G.

Abstract

DNA polymorphisms in a region on chromosome 5q33.1 which contains two genes, immunity related GTPase related family, M (IRGM) and zinc finger protein 300 (ZNF300), are associated with Crohn's disease (CD). The deleted allele of a 20 kb copy number variation (CNV) upstream of IRGM was recently shown to be in strong linkage disequilibrium (LD) with the CD-associated single nucleotide polymorphisms and is itself associated with CD (P < 0.01). The deletion was correlated with increased or reduced expression of IRGM in transformed cells in a cell line-dependent manner, and has been proposed as a likely causal variant. We report here that small insertion/deletion polymorphisms in the promoter and 5′ untranslated region of IRGM are, together with the CNV, strongly associated with CD (P = 1.37 × 10−5 to 1.40 × 10−9), and that the CNV and the 5′-untranslated region variant −308(GTTT)5 contribute independently to CD susceptibility (P = 2.6 × 10−7 and P = 2 × 10−5, respectively). We also show that the CD risk haplotype is associated with a significant decrease in IRGM expression (P < 10−12) in untransformed lymphocytes from CD patients. Further analysis of these variants in a Japanese CD case-control sample and of IRGM expression in HapMap populations revealed that neither the IRGM insertion/deletion polymorphisms nor the CNV was associated with CD or with altered IRGM expression in the Asian population. This suggests that the involvement of the IRGM risk haplotype in the pathogenesis of CD requires gene-gene or gene-environment interactions which are absent in Asian populations, or that none of the variants analysed are causal, and that the true causal variants arose after the European-Asian split

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