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1. 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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2. The DNA sequence of the human X chromosome

Author

Ross, Mark T., Grafham, Darren V., Coffey, Alison J., Scherer, Steven, McLay, Kirsten, Muzny, Donna, Platzer, Matthias, Howell, Gareth R., Burrows, Christine, Bird, Christine P., Frankish, Adam, Lovell, Frances L., Howe, Kevin L., Ashurst, Jennifer L., Fulton, Robert S., Sudbrak, Ralf, Wen, Gaiping, Jones, Matthew C., Hurles, Matthew E., Andrews, T. Daniel, Scott, Carol E., Searle, Stephen, Ramser, Juliane, Whittaker, Adam, Deadman, Rebecca, Carter, Nigel P., Hunt, Sarah E., Chen, Rui, Cree, Andrew, Gunaratne, Preethi, Havlak, Paul, Hodgson, Anne, Metzker, Michael L., Richards, Stephen, Scott, Graham, Steffen, David, Sodergren, Erica, Wheeler, David A., Worley, Kim C., Ainscough, Rachael, Ambrose, Kerrie D., Ansari-Lari, M. Ali, Aradhya, Swaroop, Ashwell, Robert I. S., Babbage, Anne K., Bagguley, Claire L., Ballabio, Andrea, Banerjee, Ruby, Barker, Gary E., Barlow, Karen F., Barrett, Ian P., Bates, Karen N., Beare, David M., Beasley, Helen, Beasley, Oliver, Beck, Alfred, Bethel, Graeme, Blechschmidt, Karin, Brady, Nicola, Bray-Allen, Sarah, Bridgeman, Anne M., Brown, Andrew J., Brown, Mary J., Bonnin, David, Bruford, Elspeth A., Buhay, Christian, Burch, Paula, Burford, Deborah, Burgess, Joanne, Burrill, Wayne, Burton, John, Bye, Jackie M., Carder, Carol, Carrel, Laura, Chako, Joseph, Chapman, Joanne C., Chavez, Dean, Chen, Ellson, Chen, Guan, Chen, Yuan, Chen, Zhijian, Chinault, Craig, Ciccodicola, Alfredo, Clark, Sue Y., Clarke, Graham, Clee, Chris M., Clegg, Sheila, Clerc-Blankenburg, Kerstin, Clifford, Karen, Cobley, Vicky, Cole, Charlotte G., Conquer, Jen S., Corby, Nicole, Connor, Richard E., David, Robert, Davies, Joy, Davis, Clay, Davis, John, Delgado, Oliver, DeShazo, Denise, Dhami, Pawandeep, Ding, Yan, Dinh, Huyen, Dodsworth, Steve, Draper, Heather, Dugan-Rocha, Shannon, Dunham, Andrew, Dunn, Matthew, Durbin, K. James, Dutta, Ireena, Eades, Tamsin, Ellwood, Matthew, Emery-Cohen, Alexandra, Errington, Helen, Evans, Kathryn L., Faulkner, Louisa, Francis, Fiona, Frankland, John, Fraser, Audrey E., Galgoczy, Petra, Gilbert, James, Gill, Rachel, Glockner, Gernot, Gregory, Simon G., Gribble, Susan, Griffiths, Coline, Grocock, Russell, Gu, Yanghong, Gwilliam, Rhian, Hamilton, Cerissa, Hart, Elizabeth A., Hawes, Alicia, Heath, Paul D., Heitmann, Katja, Hennig, Steffen, Hernandez, Judith, Hinzmann, Bernd, Ho, Sarah, Hoffs, Michael, Howden, Phillip J., Huckle, Elizabeth J., Hume, Jennifer, Hunt, Paul J., Hunt, Adrienne R., Isherwood, Judith, Jacob, Leni, Johnson, David, Jones, Sally, de Jong, Pieter J., Joseph, Shirin S., Keenan, Stephen, Kelly, Susan, Kershaw, Joanne K., Khan, Ziad, Kioschis, Petra, Klages, Sven, Knights, Andrew J., Kosiura, Anna, Kovar-Smith, Christie, Laird, Gavin K., Langford, Cordelia, Lawlor, Stephanie, Leversha, Margaret, Lewis, Lora, Liu, Wen, Lloyd, Christine, Lloyd, David M., Loulseged, Hermela, Loveland, Jane E., Lovell, Jamieson D., Lozado, Ryan, Lu, Jing, Lyne, Rachael, Ma, Jie, Maheshwari, Manjula, Matthews, Lucy H., McDowall, Jennifer, McLaren, Stuart, McMurray, Amanda, Meidl, Patrick, Meitinger, Thomas, Milne, Sarah, Miner, George, Mistry, Shailesh L., Morgan, Margaret, Morris, Sidney, Muller, Ines, Mullikin, James C., Nguyen, Ngoc, Nordsiek, Gabriele, Nyakatura, Gerald, O'Dell, Christopher N., Okwuonu, Geoffery, Palmer, Sophie, Pandian, Richard, Parker, David, Parrish, Julia, Pasternak, Shiran, Patel, Dina, Pearce, Alex V., Pearson, Danita M., Pelan, Sarah E., Perez, Lesette, Porter, Keith M., Ramsey, Yvonne, Reichwald, Kathrin, Rhodes, Susan, Ridler, Kerry A., Schlessinger, David, Schueler, Mary G., Sehra, Harminder K., Shaw-Smith, Charles, Shen, Hua, Sheridan, Elizabeth M., Shownkeen, Ratna, Skuce, Carl D., Smith, Michelle L., Sotheran, Elizabeth C., Steingruber, Helen E., Steward, Charles A., Storey, Roy, Swann, R. Mark, Swarbreck, David, Tabor, Paul E., Taudien, Stefan, Taylor, Tineace, Teague, Brian, Thomas, Karen, Thorpe, Andrea, Timms, Kirsten, Tracey, Alan, Trevanion, Steve, Tromans, Anthony C., d'Urso, Michele, Verduzco, Daniel, Villasana, Donna, Waldron, Lenee, Wall, Melanie, Wang, Qiaoyan, Warren, James, Warry, Georgina L., Wei, Xuehong, West, Anthony, Whitehead, Siobhan L., Whiteley, Mathew N., Wilkinson, Jane E., Willey, David L., Williams, Gabrielle, Williams, Leanne, Williamson, Angela, Williamson, Helen, Wilming, Laurens, Woodmansey, Rebecca L., Wray, Paul W., Yen, Jennifer, Zhang, Jingkun, Zhou, Jianling, Zoghbi, Huda, Zorilla, Sara, Buck, David, Reinhardt, Richard, Poustka, Annemarie, Rosenthal, Andre, Lehrach, Hans, Meindl, Alfons, Minx, Patrick J., Hillier, LaDeana W., Willard, Huntington F., Wilson, Richard K., Waterston, Robert H., Rice, Catherine M., Vaudin, Mark, Coulson, Alan, Nelson, David L., Weinstock, George, Sulston, John E., Durbin, Richard, Hubbard, Tim, Gibbs, Richard A., Beck, Stephan, Rogers, Jane, and Bentley, David R.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Mark T. Ross (corresponding author) [1]; Darren V. Grafham [1]; Alison J. Coffey [1]; Steven Scherer [2]; Kirsten McLay [1]; Donna Muzny [2]; Matthias Platzer [3]; Gareth R. Howell [...]

Published
2005
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3. A physical map of the mouse genome

Author

Gregory, Simon G., Sekhon, Mandeep, Schein, Jacqueline, Zhao, Shaying, Osoegawa, Kazutoyo, Scott, Carol E., Evans, Richard S., Burridge, Paul W., Cox, Tony V., Fox, Christopher A., Hutton, Richard D., Mullenger, Ian R., Phillips, Kimbly J., Smith, James, Stalker, Jim, Threadgold, Glen J., Birney, Ewan, Wylie, Kristine, Chinwalla, Asif, Wallis, John, Hillier, LaDeana, Carter, Jason, Gaige, Tony, Jaeger, Sara, Kremitzki, Colin, Layman, Dan, Maas, Jason, McGrane, Rebecca, Mead, Kelly, Walker, Rebecca, Jones, Steven, Smith, Michael, Asano, Jennifer, Bosdet, Ian, Chan, Susanna, Chittaranjan, Suganthi, Chiu, Readman, Fjell, Chris, Fuhrmann, Dan, Girn, Noreen, Gray, Catharine, Guin, Ran, Hsiao, Letticia, Krzywinski, Martin, Kutsche, Reta, Lee, Soo Sen, Mathewson, Carrie, McLeavy, Candice, Messervier, Steve, Ness, Steven, Pandoh, Pawan, Prabhu, Anna-Liisa, Saeedi, Parvaneh, Smailus, Duane, Spence, Lorraine, Stott, Jeff, Taylor, Sheryl, Terpstra, Wesley, Tsai, Miranda, Vardy, Jill, Wye, Natasja, Yang, George, Shatsman, Sofiya, Ayodeji, Bola, Geer, Keita, Tsegaye, Getahun, Shvartsbeyn, Alla, Gebregeorgis, Elizabeth, Krol, Margaret, Russell, Daniel, Overton, Larry, Malek, Joel A., Holmes, Mike, Heaney, Michael, Shetty, Jyoti, Feldblyum, Tamara, Nierman, William C., Catanese, Joseph J., Hubbard, Tim, Waterston, Robert H., Rogers, Jane, de Jong, Pieter J., Fraser, Claire M., Marra, Marco, McPherson, John D., and Bentley, David R.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

A physical map of a genome is an essential guide for navigation, allowing the location of any gene or other landmark in the chromosomal DNA. We have constructed a physical map of the mouse genome that contains 296 contigs of overlapping bacterial clones and 16,992 unique markers. The mouse contigs were aligned to the human genome sequence on the basis of 51,486 homology matches, thus enabling use of the conserved synteny (correspondence between chromosome blocks) of the two genomes to accelerate construction of the mouse map. The map provides a framework for assembly of whole-genome shotgun sequence data, and a tile path of clones for generation of the reference sequence. Definition of the human-mouse alignment at this level of resolution enables identification of a mouse clone that corresponds to almost any position in the human genome. The human sequence may be used to facilitate construction of other mammalian genome maps using the same strategy., Author(s): Simon G. Gregory [1]; Mandeep Sekhon [2]; Jacqueline Schein [3]; Shaying Zhao [4]; Kazutoyo Osoegawa [5]; Carol E. Scott [1]; Richard S. Evans [1]; Paul W. Burridge [1]; Tony [...]

Published
2002

4. A physical map of the human genome

Author

McPherson, John D., Marra, Marco, Hillier, LaDeana, Waterston, Robert H., Chinwalla, Asif, Wallis, John, Sekhon, Mandeep, Wylie, Kristine, Mardis, Elaine R., Wilson, Richard K., Fulton, Robert, Kucaba, Tamara A., Wagner-McPherson, Caryn, Barbazuk, William B., Gregory, Simon G., Humphray, Sean J., French, Lisa, Evans, Richard S., Bethel, Graeme, Whittaker, Adam, Holden, Jane L., McCann, Owen T., Dunham, Andrew, Soderlund, Carol, Scott, Carol E., Bentley, David R., Schuler, Gregory, Chen, Hsiu-Chuan, Jang, Wonhee, Green, Eric D., Idol, Jacquelyn R., Maduro, Valerie V. Braden, Montgomery, Kate T., Lee, Eunice, Miller, Ashley, Emerling, Suzanne, Kucherlapati, Raju, Gibbs, Richard, Scherer, Steve, Gorrell, J. Harley, Sodergren, Erica, Clerc-Blankenburg, Kerstin, Tabor, Paul, Naylor, Susan, Garcia, Dawn, de Jong, Pieter J., Catanese, Joseph J., Nowak, Norma, Osoegawa, Kazutoyo, Qin, Shizhen, Rowen, Lee, Madan, Anuradha, Dors, Monica, Hood, Leroy, Trask, Barbara, Friedman, Cynthia, Massa, Hillary, Cheung, Vivian G., Kirsch, Ilan R., Reid, Thomas, Yonescu, Raluca, Weissenbach, Jean, Bruls, Thomas, Heilig, Roland, Branscomb, Elbert, Olsen, Anne, Doggett, Norman, Cheng, Jan-Fang, Hawkins, Trevor, Myers, Richard M., Shang, Jin, Ramirez, Lucia, Schmutz, Jeremy, Velasquez, Olivia, Dixon, Kami, Stone, Nancy E., Cox, David R., Haussler, David, Kent, W. James, Furey, Terrence, Rogic, Sanja, Kennedy, Scot, Jones, Steven, Rosenthal, Andre, Wen, Gaiping, Schilhabel, Markus, Gloeckner, Gernot, Nyakatura, Gerald, Siebert, Reiner, Schlegelberger, Brigitte, Korenberg, Julie, Chen, Xiao-Ning, Fujiyama, Asao, Hattori, Masahira, Toyoda, Atsushi, Yada, Tetsushi, Park, Hong-Seok, Sakaki, Yoshiyuki, Shimizu, Nobuyoshi, Asakawa, Shuichi, Kawasaki, Kazuhiko, Sasaki, Takashi, Shintani, Ai, Shimizu, Atsushi, Shibuya, Kazunori, Kudoh, Jun, Minoshima, Shinsei, Ramser, Juliane, Seranski, Peter, Hoff, Celine, Poustka, Annemarie, Reinhardt, Richard, and Lehrach, Hans

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): The International Human Genome Mapping Consortium ; Washington University School of Medicine, Genome Sequencing Center: ; John D. McPherson (corresponding author) [1]; Marco Marra [1]; LaDeana Hillier [1]; Robert [...]

Published
2001
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5. 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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6. Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags

Author

Hubbard, Simon J., Beattie, Kevin J., Grafham, Darren V., Overton, Ian M., McLaren, Stuart R., Croning, Michael D.R., Bonfield, James K., Boardman, Paul E., Burnside, Joan, Davies, Robert M., Farrell, Elizabeth R., Griffiths-Jones, Sam, Francis, Matthew D., Humphray, Sean J., Hyland, Christopher, Scott, Carol E., Haizhou Tang, Taylor, Ruth G., Tickle, Cheryll, Brown, William R.A., Birney, Ewan, Rogers, Jane, and Wilson, Stuart A.

Subjects
Nucleotide sequence -- Analysis, RNA -- Analysis, DNA -- Analysis, Chickens -- Genetic aspects, Health
Abstract

An analysis of the chicken transcriptome based on the full insert sequences for 19,626 cDNA, combined with 485,337 expressed sequence tag (EST) sequences is presented. Analysis of the ncRNAs reveals a set that is highly conserved in chickens and mammals, including sequences for 14 pri-miRNAs encoding 23 different miRNAs.

Published
2005

7. Definition of the zebrafish genome using flow cytometry and cytogenetic mapping

Author

Zhou Yi, Rogers Jane, Humphray Sean, Scott Carol E, Zepeda Cinthya, Ng Bee, Chi Jianxiang, Maguire Sean F, Dallaire Stephanie, Banerjee Ruby, Adeniyi Adeola, Freeman Jennifer L, Zon Leonard I, Carter Nigel P, Yang Fengtang, and Lee Charles

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The zebrafish (Danio rerio) is an important vertebrate model organism system for biomedical research. The syntenic conservation between the zebrafish and human genome allows one to investigate the function of human genes using the zebrafish model. To facilitate analysis of the zebrafish genome, genetic maps have been constructed and sequence annotation of a reference zebrafish genome is ongoing. However, the duplicative nature of teleost genomes, including the zebrafish, complicates accurate assembly and annotation of a representative genome sequence. Cytogenetic approaches provide "anchors" that can be integrated with accumulating genomic data. Results Here, we cytogenetically define the zebrafish genome by first estimating the size of each linkage group (LG) chromosome using flow cytometry, followed by the cytogenetic mapping of 575 bacterial artificial chromosome (BAC) clones onto metaphase chromosomes. Of the 575 BAC clones, 544 clones localized to apparently unique chromosomal locations. 93.8% of these clones were assigned to a specific LG chromosome location using fluorescence in situ hybridization (FISH) and compared to the LG chromosome assignment reported in the zebrafish genome databases. Thirty-one BAC clones localized to multiple chromosomal locations in several different hybridization patterns. From these data, a refined second generation probe panel for each LG chromosome was also constructed. Conclusion The chromosomal mapping of the 575 large-insert DNA clones allows for these clones to be integrated into existing zebrafish mapping data. An accurately annotated zebrafish reference genome serves as a valuable resource for investigating the molecular basis of human diseases using zebrafish mutant models.

Published
2007
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8. 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
Full Text
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9. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Author

Hillier, LaDeana W, Miller, Webb, Birney, Ewan, Warren, Wesley, Hardison, Ross C, Ponting, Chris P, Bork, Peer, Burt, Peer, Groenen, Martien A M, Delany, Mary E, Dodgson, Jerry B, Chinwalla, Asif, Cliften, Paul F, Clifton, Sandra W, Delehaunty, Kimberly D, Fronick, Catrina, Fulton, Robert S, Graves, Tina A, Kremitzki, Colin, Layman, Dan, Magrini, Vincent, McPherson, John D, Miner, Tracie L, Minx, Patrick, Nash, William E, Nhan, Michael N, Nelson, Joanne O, Oddy, Lachlan G, Pohl, Craig S, Randall-Maher, Jennifer, Smith, Scott M, Wallis, John W, Yang, Shiaw-Pyng, Romanov, Michael N, Rondelli, Catherine M, Paton, Bob, Smith, Jacqueline, Morrice, David, Daniels, Laura, Tempest, Helen G, Robertson, Lindsay, Masabanda, Julio S, Griffin, Darren K., Vignal, Alain, Fillon, Valerie, Jacobbson, Lina, Kerje, Susanne, Andersson, Leif, Crooijmans, Richard P M A, Aerts, Jan, van der Poel, Jan J, Ellegren, Hans, Caldwell, Randolph B, Hubbard, Simon J, Grafham, Darren V, Kierzek, Andrzej M, McLaren, Stuart R, Overton, Ian M, Arakawa, Hiroshi, Beattie, Kevin J, Bezzubov, Yuri, Boardman, Paul E, Bonfield, James K, Croning, Michael D R, Davies, Robert M, Francis, Matthew D, Humphray, Sean J, Scott, Carol E, Taylor, Ruth G, Tickle, Cheryll, Brown, William R A, Rogers, Jane, Buerstedde, Jean-Marie, Wilson, Stuart A, Stubbs, Lisa, Ovcharenko, Ivan, Gordon, Laurie, Lucas, Susan, Miller, Marcia M, Inoko, Hidetoshi, Shiina, Takashi, Kaufman, Jim, Salomonsen, Jan, Skjoedt, Karsten, Wong, Gane Ka-Shu, Wang, Jun, Liu, Bin, Wang, Jian, Yu, Jun, Yang, Huanming, Nefedov, Mikhail, Koriabine, Maxim, de Jong, Pieter J, Goodstadt, Leo, Webber, Caleb, Dickens, Nicholas J, Letunic, Ivica, Suyama, Mikita, Torrents, David, von Mering, Christian, Zdobnov, Evgeny M, Makova, Kateryna, Nekrutenko, Anton, Elnitski, Laura, Eswara, Pallavi, King, David C, Yang, Shan, Tyekucheva, Svitlana, Radakrishnan, Anusha, Harris, Robert S, Chiaromonte, Francesca, Taylor, James, He, Jianbin, Rijnkels, Monique, Griffiths-Jones, Sam, Ureta-Vidal, Abe, Hoffman, Michael M, Severin, Jessica, Searle, Stephen M J, Law, Andy S, Speed, David, Waddington, David, Cheng, Ze, Tuzun, Eray, Eichler, Evan, Bao, Zhirong, Flicek, Paul, Shteynberg, David D, Brent, Michael R, Bye, Jacqueline M, Huckle, Elizabeth J, Chatterjee, Sourav, Dewey, Colin, Pachter, Lior, Kouranov, Andrei, Mourelatos, Zissimos, Hatzigeorgiou, Artemis G, Paterson, Andrew H, Ivarie, Robert, Brandstrom, Mikael, Axelsson, Erik, Backström, Niclas, Berlin, Sofia, Webster, Matthew T, Pourquie, Olivier, Reymond, Alexandre, Ucla, Catherine, Antonarakis, Stylianos E, Long, Manyuan, Emerson, J J, Betran, Esther, Dupanloup, Isabelle, Kaessmann, Henrik, Hinrichs, Angie S, Bejerano, Gill, Furey, Terrence S, Harte, Rachel A, Raney, Brian, Siepel, Adam, Kent, W James, Haussler, David, Eyras, Eduardo, Castelo, Robert, Abril, Josep F, Castellano, Sergi, Camara, Francisco, Parra, Genis, Guigo, Roderic, Bourque, Guillaume, Tesler, Glenn, Pevzner, Pavel A., Smit, Arian F. A., Fulton, Lucinda A., Mardis, Elaine R., Wilson, Richard K., International Chicken Genome Sequencing Consortium, ProdInra, Migration, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Zdobnov, Evgeny

Subjects
RNA, Untranslated, olfactory receptor, [SDV]Life Sciences [q-bio], mouse genome, QH75, Genome, 0302 clinical medicine, Gene Duplication, Coding region, ddc:576.5, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, Short Interspersed Nucleotide Elements, Genetics, 0303 health sciences, Multidisciplinary, CHICKENS, recent segmental duplications, Untranslated, GENOME SEQUENCE, International Chicken Genome Sequencing Consortium, Genomics, Physical Chromosome Mapping, major histocompatibility complex, mammalian evolution, [SDV] Life Sciences [q-bio], Multigene Family, Vertebrates, SEQUENCE DU GENOME, Sequence Analysis, Pseudogenes, Biotechnology, brown-norway rat, animal structures, Evolution, General Science & Technology, Sequence analysis, Biology, Animal Breeding and Genomics, Synteny, Evolution, Molecular, Avian Proteins, 03 medical and health sciences, non-ltr retrotransposons, Animals, Humans, alcohol-dehydrogenase, Fokkerij en Genomica, SF, QP506, Gene, QH426, 030304 developmental biology, Whole genome sequencing, QL, phylogenetic analysis, QH, Human Genome, Molecular, Sequence Analysis, DNA, DNA, tissue-specific genes, EVOLUTION, Retroviridae, Long Interspersed Nucleotide Elements, Genes, Mutagenesis, Evolutionary biology, DNA Transposable Elements, Microchromosome, WIAS, RNA, Chickens, 030217 neurology & neurosurgery
Abstract

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.

Published
2004

10. Erratum: Corrigendum: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Author

Hillier, LaDeana W, Miller, Webb, Birney, Ewan, Warren, Wesley, Hardison, Ross C, Ponting, Chris P, Bork, Peer, Burt, Peer, Groenen, Martien A M, Delany, Mary E, Dodgson, Jerry B, Chinwalla, Asif, Cliften, Paul F, Clifton, Sandra W, Delehaunty, Kimberly D, Fronick, Catrina, Fulton, Robert S, Graves, Tina A, Kremitzki, Colin, Layman, Dan, Magrini, Vincent, McPherson, John D, Miner, Tracie L, Minx, Patrick, Nash, William E, Nhan, Michael N, Nelson, Joanne O, Oddy, Lachlan G, Pohl, Craig S, Randall-Maher, Jennifer, Smith, Scott M, Wallis, John W, Yang, Shiaw-Pyng, Romanov, Michael N, Rondelli, Catherine M, Paton, Bob, Smith, Jacqueline, Morrice, David, Daniels, Laura, Tempest, Helen G, Robertson, Lindsay, Masabanda, Julio S, Griffin, Darren K., Vignal, Alain, Fillon, Valerie, Jacobbson, Lina, Kerje, Susanne, Andersson, Leif, Crooijmans, Richard P M A, Aerts, Jan, van der Poel, Jan J, Ellegren, Hans, Caldwell, Randolph B, Hubbard, Simon J, Grafham, Darren V, Kierzek, Andrzej M, McLaren, Stuart R, Overton, Ian M, Arakawa, Hiroshi, Beattie, Kevin J, Bezzubov, Yuri, Boardman, Paul E, Bonfield, James K, Croning, Michael D R, Davies, Robert M, Francis, Matthew D, Humphray, Sean J, Scott, Carol E, Taylor, Ruth G, Tickle, Cheryll, Brown, William R A, Rogers, Jane, Buerstedde, Jean-Marie, Wilson, Stuart A, Stubbs, Lisa, Ovcharenko, Ivan, Gordon, Laurie, Lucas, Susan, Miller, Marcia M, Inoko, Hidetoshi, Shiina, Takashi, Kaufman, Jim, Salomonsen, Jan, Skjoedt, Karsten, Wong, Gane Ka-Shu, Wang, Jun, Liu, Bin, Wang, Jian, Yu, Jun, Yang, Huanming, Nefedov, Mikhail, Koriabine, Maxim, de Jong, Pieter J, Goodstadt, Leo, Webber, Caleb, Dickens, Nicholas J, Letunic, Ivica, Suyama, Mikita, Torrents, David, von Mering, Christian, Zdobnov, Evgeny M, Makova, Kateryna, Nekrutenko, Anton, Elnitski, Laura, Eswara, Pallavi, King, David C, Yang, Shan, Tyekucheva, Svitlana, Radakrishnan, Anusha, Harris, Robert S, Chiaromonte, Francesca, Taylor, James, He, Jianbin, Rijnkels, Monique, Griffiths-Jones, Sam, Ureta-Vidal, Abe, Hoffman, Michael M, Severin, Jessica, Searle, Stephen M J, Law, Andy S, Speed, David, Waddington, David, Cheng, Ze, Tuzun, Eray, Eichler, Evan, Bao, Zhirong, Flicek, Paul, Shteynberg, David D, Brent, Michael R, Bye, Jacqueline M, Huckle, Elizabeth J, Chatterjee, Sourav, Dewey, Colin, Pachter, Lior, Kouranov, Andrei, Mourelatos, Zissimos, Hatzigeorgiou, Artemis G, Paterson, Andrew H, Ivarie, Robert, Brandstrom, Mikael, Axelsson, Erik, Backström, Niclas, Berlin, Sofia, Webster, Matthew T, Pourquie, Olivier, Reymond, Alexandre, Ucla, Catherine, Antonarakis, Stylianos E, Long, Manyuan, Emerson, J J, Betran, Esther, Dupanloup, Isabelle, Kaessmann, Henrik, Hinrichs, Angie S, Bejerano, Gill, Furey, Terrence S, Harte, Rachel A, Raney, Brian, Siepel, Adam, Kent, W James, Haussler, David, Eyras, Eduardo, Castelo, Robert, Abril, Josep F, Castellano, Sergi, Camara, Francisco, Parra, Genis, Guigo, Roderic, Bourque, Guillaume, Tesler, Glenn, Pevzner, Pavel A., Smit, Arian F. A., Fulton, Lucinda A., Mardis, Elaine R., Wilson, Richard K., Hillier, LaDeana W, Miller, Webb, Birney, Ewan, Warren, Wesley, Hardison, Ross C, Ponting, Chris P, Bork, Peer, Burt, Peer, Groenen, Martien A M, Delany, Mary E, Dodgson, Jerry B, Chinwalla, Asif, Cliften, Paul F, Clifton, Sandra W, Delehaunty, Kimberly D, Fronick, Catrina, Fulton, Robert S, Graves, Tina A, Kremitzki, Colin, Layman, Dan, Magrini, Vincent, McPherson, John D, Miner, Tracie L, Minx, Patrick, Nash, William E, Nhan, Michael N, Nelson, Joanne O, Oddy, Lachlan G, Pohl, Craig S, Randall-Maher, Jennifer, Smith, Scott M, Wallis, John W, Yang, Shiaw-Pyng, Romanov, Michael N, Rondelli, Catherine M, Paton, Bob, Smith, Jacqueline, Morrice, David, Daniels, Laura, Tempest, Helen G, Robertson, Lindsay, Masabanda, Julio S, Griffin, Darren K., Vignal, Alain, Fillon, Valerie, Jacobbson, Lina, Kerje, Susanne, Andersson, Leif, Crooijmans, Richard P M A, Aerts, Jan, van der Poel, Jan J, Ellegren, Hans, Caldwell, Randolph B, Hubbard, Simon J, Grafham, Darren V, Kierzek, Andrzej M, McLaren, Stuart R, Overton, Ian M, Arakawa, Hiroshi, Beattie, Kevin J, Bezzubov, Yuri, Boardman, Paul E, Bonfield, James K, Croning, Michael D R, Davies, Robert M, Francis, Matthew D, Humphray, Sean J, Scott, Carol E, Taylor, Ruth G, Tickle, Cheryll, Brown, William R A, Rogers, Jane, Buerstedde, Jean-Marie, Wilson, Stuart A, Stubbs, Lisa, Ovcharenko, Ivan, Gordon, Laurie, Lucas, Susan, Miller, Marcia M, Inoko, Hidetoshi, Shiina, Takashi, Kaufman, Jim, Salomonsen, Jan, Skjoedt, Karsten, Wong, Gane Ka-Shu, Wang, Jun, Liu, Bin, Wang, Jian, Yu, Jun, Yang, Huanming, Nefedov, Mikhail, Koriabine, Maxim, de Jong, Pieter J, Goodstadt, Leo, Webber, Caleb, Dickens, Nicholas J, Letunic, Ivica, Suyama, Mikita, Torrents, David, von Mering, Christian, Zdobnov, Evgeny M, Makova, Kateryna, Nekrutenko, Anton, Elnitski, Laura, Eswara, Pallavi, King, David C, Yang, Shan, Tyekucheva, Svitlana, Radakrishnan, Anusha, Harris, Robert S, Chiaromonte, Francesca, Taylor, James, He, Jianbin, Rijnkels, Monique, Griffiths-Jones, Sam, Ureta-Vidal, Abe, Hoffman, Michael M, Severin, Jessica, Searle, Stephen M J, Law, Andy S, Speed, David, Waddington, David, Cheng, Ze, Tuzun, Eray, Eichler, Evan, Bao, Zhirong, Flicek, Paul, Shteynberg, David D, Brent, Michael R, Bye, Jacqueline M, Huckle, Elizabeth J, Chatterjee, Sourav, Dewey, Colin, Pachter, Lior, Kouranov, Andrei, Mourelatos, Zissimos, Hatzigeorgiou, Artemis G, Paterson, Andrew H, Ivarie, Robert, Brandstrom, Mikael, Axelsson, Erik, Backström, Niclas, Berlin, Sofia, Webster, Matthew T, Pourquie, Olivier, Reymond, Alexandre, Ucla, Catherine, Antonarakis, Stylianos E, Long, Manyuan, Emerson, J J, Betran, Esther, Dupanloup, Isabelle, Kaessmann, Henrik, Hinrichs, Angie S, Bejerano, Gill, Furey, Terrence S, Harte, Rachel A, Raney, Brian, Siepel, Adam, Kent, W James, Haussler, David, Eyras, Eduardo, Castelo, Robert, Abril, Josep F, Castellano, Sergi, Camara, Francisco, Parra, Genis, Guigo, Roderic, Bourque, Guillaume, Tesler, Glenn, Pevzner, Pavel A., Smit, Arian F. A., Fulton, Lucinda A., Mardis, Elaine R., and Wilson, Richard K.

Abstract

International Chicken Genome Sequencing Consortium. The Original Article was published on 09 December 2004. Nature432, 695–716 (2004). In Table 5 of this Article, the last four values listed in the ‘Copy number’ column were incorrect. These should be: LTR elements, 30,000; DNA transposons, 20,000; simple repeats, 140,000; and satellites, 4,000. These errors do not affect any of the conclusions in our paper. Additional information. The online version of the original article can be found at 10.1038/nature03154

Published
2005

11. Mosaic overgrowth with fibroadipose hyperplasia is caused by somatic activating mutations in PIK3CA

Author

Lindhurst, Marjorie J, primary, Parker, Victoria E R, additional, Payne, Felicity, additional, Sapp, Julie C, additional, Rudge, Simon, additional, Harris, Julie, additional, Witkowski, Alison M, additional, Zhang, Qifeng, additional, Groeneveld, Matthijs P, additional, Scott, Carol E, additional, Daly, Allan, additional, Huson, Susan M, additional, Tosi, Laura L, additional, Cunningham, Michael L, additional, Darling, Thomas N, additional, Geer, Joseph, additional, Gucev, Zoran, additional, Sutton, V Reid, additional, Tziotzios, Christos, additional, Dixon, Adrian K, additional, Helliwell, Timothy, additional, O'Rahilly, Stephen, additional, Savage, David B, additional, Wakelam, Michael J O, additional, Barroso, Inês, additional, Biesecker, Leslie G, additional, and Semple, Robert K, additional

Published
2012
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12. The GENCODE exome: sequencing the complete human exome

Author

Coffey, Alison J, primary, Kokocinski, Felix, additional, Calafato, Maria S, additional, Scott, Carol E, additional, Palta, Priit, additional, Drury, Eleanor, additional, Joyce, Christopher J, additional, LeProust, Emily M, additional, Harrow, Jen, additional, Hunt, Sarah, additional, Lehesjoki, Anna-Elina, additional, Turner, Daniel J, additional, Hubbard, Tim J, additional, and Palotie, Aarno, additional

Published
2011
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15. Definition of the zebrafish genome using flow cytometry and cytogenetic mapping

Author

Freeman, Jennifer L, primary, Adeniyi, Adeola, additional, Banerjee, Ruby, additional, Dallaire, Stephanie, additional, Maguire, Sean F, additional, Chi, Jianxiang, additional, Ng, Bee Ling, additional, Zepeda, Cinthya, additional, Scott, Carol E, additional, Humphray, Sean, additional, Rogers, Jane, additional, Zhou, Yi, additional, Zon, Leonard I, additional, Carter, Nigel P, additional, Yang, Fengtang, additional, and Lee, Charles, additional

Published
2007
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16. A high utility integrated map of the pig genome

Author

Humphray, Sean J, primary, Scott, Carol E, additional, Clark, Richard, additional, Marron, Brandy, additional, Bender, Clare, additional, Camm, Nick, additional, Davis, Jayne, additional, Jenks, Andrew, additional, Noon, Angela, additional, Patel, Manish, additional, Sehra, Harminder, additional, Yang, Fengtang, additional, Rogatcheva, Margarita B, additional, Milan, Denis, additional, Chardon, Patrick, additional, Rohrer, Gary, additional, Nonneman, Dan, additional, de Jong, Pieter, additional, Meyers, Stacey N, additional, Archibald, Alan, additional, Beever, Jonathan E, additional, Schook, Lawrence B, additional, and Rogers, Jane, additional

Published
2007
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17. Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags

Author

Hubbard, Simon J., primary, Grafham, Darren V., additional, Beattie, Kevin J., additional, Overton, Ian M., additional, McLaren, Stuart R., additional, Croning, Michael D.R., additional, Boardman, Paul E., additional, Bonfield, James K., additional, Burnside, Joan, additional, Davies, Robert M., additional, Farrell, Elizabeth R., additional, Francis, Matthew D., additional, Griffiths-Jones, Sam, additional, Humphray, Sean J., additional, Hyland, Christopher, additional, Scott, Carol E., additional, Tang, Haizhou, additional, Taylor, Ruth G., additional, Tickle, Cheryll, additional, Brown, William R.A., additional, Birney, Ewan, additional, Rogers, Jane, additional, and Wilson, Stuart A., additional

Published
2004
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18. High-Resolution Landmark Framework for the Sequence-Ready Mapping of Xq23–q26.1

Author

Steingruber, Helen E., primary, Dunham, Andrew, additional, Coffey, Alison J., additional, Clegg, Sheila M., additional, Howell, Gareth R., additional, Maslen, Gareth L., additional, Scott, Carol E., additional, Gwilliam, Rhian, additional, Hunt, Paul J., additional, Sotheran, Elizabeth C., additional, Huckle, Elizabeth J., additional, Hunt, Sarah E., additional, Dhami, Pawandeep, additional, Soderlund, Cari, additional, Leversha, Margaret A., additional, Bentley, David R., additional, and Ross, Mark T., additional

Published
1999
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19. 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.

20. 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.

21. DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones.

Author

Fiegler H, Carr P, Douglas EJ, Burford DC, Hunt S, Scott CE, Smith J, Vetrie D, Gorman P, Tomlinson IP, and Carter NP

Subjects
Animals, Carcinoma, Renal Cell genetics, Cell Line, Chromosome Aberrations, DNA, Bacterial genetics, Drosophila melanogaster genetics, Escherichia coli genetics, Female, Humans, Kidney Neoplasms genetics, Lymphocytes chemistry, Lymphocytes cytology, Lymphocytes metabolism, Male, Nucleic Acid Hybridization, Polymerase Chain Reaction standards, Tumor Cells, Cultured, Chromosomes, Artificial, Bacterial genetics, Chromosomes, Artificial, P1 Bacteriophage genetics, DNA genetics, DNA Primers genetics, Nucleic Acid Amplification Techniques methods, Oligonucleotide Array Sequence Analysis methods, Polymerase Chain Reaction methods
Abstract

We have designed DOP-PCR primers specifically for the amplification of large insert clones for use in the construction of DNA microarrays. A bioinformatic approach was used to construct primers that were efficient in the general amplification of human DNA but were poor at amplifying E. coli DNA, a common contaminant of DNA preparations from large insert clones. We chose the three most selective primers for use in printing DNA microarrays. DNA combined from the amplification of large insert clones by use of these three primers and spotted onto glass slides showed more than a sixfold increase in the human to E. coli hybridization ratio when compared to the standard DOP-PCR primer, 6MW. The microarrays reproducibly delineated previously characterized gains and deletions in a cancer cell line and identified a small gain not detected by use of conventional CGH. We also describe a method for the bulk testing of the hybridization characteristics of chromosome-specific clones spotted on microarrays by use of DNA amplified from flow-sorted chromosomes. Finally, we describe a set of clones selected from the publicly available Golden Path of the human genome at 1-Mb intervals and a view in the Ensembl genome browser from which data required for the use of these clones in array CGH and other experiments can be downloaded across the Internet., (Copyright 2003 Wiley-Liss, Inc.)

Published
2003
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