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1. 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, Andrews, T. Daniel, Arbury, Hazel, Attwood, Anthony, Auton, Adam, Ball, Stephen G., Balmforth, Anthony J., Barrett, Jeffrey C., Barroso, Ines, 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, Ferrier, I. Nicol, 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, Lathrop, G. Mark, 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, Andrews, T. Daniel, Arbury, Hazel, Attwood, Anthony, Auton, Adam, Ball, Stephen G., Balmforth, Anthony J., Barrett, Jeffrey C., Barroso, Ines, 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, Ferrier, I. Nicol, 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, Lathrop, G. Mark, 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 similar to 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 disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although 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.

Published
2010
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2. Genome-Wide Association Study of Blood Pressure Extremes Identifies Variant near UMOD Associated with Hypertension

Author

Padmanabhan, Sandosh, Melander, Olle, Johnson, Toby, Di Blasio, Anna Maria, Lee, Wai K., Gentilini, Davide, Hastie, Claire E., Menni, Cristina, Monti, Maria Cristina, Delles, Christian, Laing, Stewart, Corso, Barbara, Navis, Gerjan, Kwakernaak, Arjan J., van der Harst, Pim, Bochud, Murielle, Maillard, Marc, Burnier, Michel, Hedner, Thomas, Kjeldsen, Sverre, Wahlstrand, Bjorn, Sjögren, Marketa, Fava, Cristiano, Montagnana, Martina, Danese, Elisa, Torffvit, Ole, Hedblad, Bo, Snieder, Harold, Connell, John M. C., Brown, Morris, Samani, Nilesh J., Farrall, Martin, Cesana, Giancarlo, Mancia, Giuseppe, Signorini, Stefano, Grassi, Guido, Eyheramendy, Susana, Wichmann, H. Erich, Laan, Maris, Strachan, David P., Sever, Peter, Shields, Denis Colm, Stanton, Alice, Vollenweider, Peter, Teumer, Alexander, Voelzke, Henry, Rettig, Rainer, Newton-Cheh, Christopher, Arora, Pankaj, Zhang, Feng, Soranzo, Nicole, Spector, Timothy D., Lucas, Gavin, Kathiresan, Sekar, Siscovick, David S., Luan, Jian'an, Loos, Ruth J. F., Wareham, Nicholas J., Penninx, Brenda W., Nolte, Ilja M., McBride, Martin, Miller, William H., Nicklin, Stuart A., Baker, Andrew H., Graham, Delyth, McDonald, Robert A., Pell, Jill P., Sattar, Naveed, Welsh, Paul, Munroe, Patricia, Caulfield, Mark J., Zanchetti, Alberto, Dominiczak, Anna F., Padmanabhan, Sandosh, Melander, Olle, Johnson, Toby, Di Blasio, Anna Maria, Lee, Wai K., Gentilini, Davide, Hastie, Claire E., Menni, Cristina, Monti, Maria Cristina, Delles, Christian, Laing, Stewart, Corso, Barbara, Navis, Gerjan, Kwakernaak, Arjan J., van der Harst, Pim, Bochud, Murielle, Maillard, Marc, Burnier, Michel, Hedner, Thomas, Kjeldsen, Sverre, Wahlstrand, Bjorn, Sjögren, Marketa, Fava, Cristiano, Montagnana, Martina, Danese, Elisa, Torffvit, Ole, Hedblad, Bo, Snieder, Harold, Connell, John M. C., Brown, Morris, Samani, Nilesh J., Farrall, Martin, Cesana, Giancarlo, Mancia, Giuseppe, Signorini, Stefano, Grassi, Guido, Eyheramendy, Susana, Wichmann, H. Erich, Laan, Maris, Strachan, David P., Sever, Peter, Shields, Denis Colm, Stanton, Alice, Vollenweider, Peter, Teumer, Alexander, Voelzke, Henry, Rettig, Rainer, Newton-Cheh, Christopher, Arora, Pankaj, Zhang, Feng, Soranzo, Nicole, Spector, Timothy D., Lucas, Gavin, Kathiresan, Sekar, Siscovick, David S., Luan, Jian'an, Loos, Ruth J. F., Wareham, Nicholas J., Penninx, Brenda W., Nolte, Ilja M., McBride, Martin, Miller, William H., Nicklin, Stuart A., Baker, Andrew H., Graham, Delyth, McDonald, Robert A., Pell, Jill P., Sattar, Naveed, Welsh, Paul, Munroe, Patricia, Caulfield, Mark J., Zanchetti, Alberto, and Dominiczak, Anna F.

Abstract

Hypertension is a heritable and major contributor to the global burden of disease. The sum of rare and common genetic variants robustly identified so far explain only 1%-2% of the population variation in BP and hypertension. This suggests the existence of more undiscovered common variants. We conducted a genome-wide association study in 1,621 hypertensive cases and 1,699 controls and follow-up validation analyses in 19,845 cases and 16,541 controls using an extreme case-control design. We identified a locus on chromosome 16 in the 59 region of Uromodulin (UMOD; rs13333226, combined P value of 3.6x10(-11)). The minor G allele is associated with a lower risk of hypertension (OR [95% CI]: 0.87 [0.84-0.91]), reduced urinary uromodulin excretion, better renal function; and each copy of the G allele is associated with a 7.7% reduction in risk of CVD events after adjusting for age, sex, BMI, and smoking status (H.R. = 0.923, 95% CI 0.860-0.991; p = 0.027). In a subset of 13,446 individuals with estimated glomerular filtration rate (eGFR) measurements, we show that rs13333226 is independently associated with hypertension (unadjusted for eGFR: 0.89 [0.83-0.96], p = 0.004; after eGFR adjustment: 0.89 [0.83-0.96], p = 0.003). In clinical functional studies, we also consistently show the minor G allele is associated with lower urinary uromodulin excretion. The exclusive expression of uromodulin in the thick portion of the ascending limb of Henle suggests a putative role of this variant in hypertension through an effect on sodium homeostasis. The newly discovered UMOD locus for hypertension has the potential to give new insights into the role of uromodulin in BP regulation and to identify novel drugable targets for reducing cardiovascular risk.

Published
2010

3. Genetic loci influencing kidney function and chronic kidney disease.

Author

Chambers, John C, Zhang, Weihua, Lord, Graham M, van der Harst, Pim, Lawlor, Debbie A, Sehmi, Joban S., Gale, Daniel P, Wass, Mark N., Ahmadi, Kourosh R, Bakker, Stephan J L, Beckmann, Jacqui, Bilo, Henk J G, Bochud, Murielle, Brown, Morris J, Caulfield, Mark J, Connell, John M C, Cook, H Terence, Cotlarciuc, Ioana, Davey Smith, George, de Silva, Ranil, Deng, Guohong, Devuyst, Olivier, Dikkeschei, Lambert D, Dimkovic, Nada, Dockrell, Mark, Dominiczak, Anna, Ebrahim, Shah, Eggermann, Thomas, Farrall, Martin, Ferrucci, Luigi, Floege, Jurgen, Forouhi, Nita G, Gansevoort, Ron T, Han, Xijin, Hedblad, Bo, Homan van der Heide, Jaap J, Hepkema, Bouke G, Hernandez-Fuentes, Maria, Hypponen, Elina, Johnson, Toby, de Jong, Paul E, Kleefstra, Nanne, Lagou, Vasiliki, Lapsley, Marta, Li, Yun, Loos, Ruth J F, Luan, Jian'an, Luttropp, Karin, Maréchal, Céline, Melander, Olle, Munroe, Patricia B, Nordfors, Louise, Parsa, Afshin, Peltonen, Leena, Penninx, Brenda W, Perucha, Esperanza, Pouta, Anneli, Prokopenko, Inga, Roderick, Paul J, Ruokonen, Aimo, Samani, Nilesh J, Sanna, Serena, Schalling, Martin, Schlessinger, David, Schlieper, Georg, Seelen, Marc A J, Shuldiner, Alan R, Sjögren, Marketa, Smit, Johannes H, Snieder, Harold, Soranzo, Nicole, Spector, Timothy D, Stenvinkel, Peter, Sternberg, Michael J.E., Swaminathan, Ramasamyiyer, Tanaka, Toshiko, Ubink-Veltmaat, Lielith J, Uda, Manuela, Vollenweider, Peter, Wallace, Chris, Waterworth, Dawn M, Zerres, Klaus, Waeber, Gerard, Wareham, Nicholas J, Maxwell, Patrick H, McCarthy, Mark I, Jarvelin, Marjo-Riitta, Mooser, Vincent, Abecasis, Goncalo R, Lightstone, Liz, Scott, James, Navis, Gerjan, Elliott, Paul, Kooner, Jaspal S, Chambers, John C, Zhang, Weihua, Lord, Graham M, van der Harst, Pim, Lawlor, Debbie A, Sehmi, Joban S., Gale, Daniel P, Wass, Mark N., Ahmadi, Kourosh R, Bakker, Stephan J L, Beckmann, Jacqui, Bilo, Henk J G, Bochud, Murielle, Brown, Morris J, Caulfield, Mark J, Connell, John M C, Cook, H Terence, Cotlarciuc, Ioana, Davey Smith, George, de Silva, Ranil, Deng, Guohong, Devuyst, Olivier, Dikkeschei, Lambert D, Dimkovic, Nada, Dockrell, Mark, Dominiczak, Anna, Ebrahim, Shah, Eggermann, Thomas, Farrall, Martin, Ferrucci, Luigi, Floege, Jurgen, Forouhi, Nita G, Gansevoort, Ron T, Han, Xijin, Hedblad, Bo, Homan van der Heide, Jaap J, Hepkema, Bouke G, Hernandez-Fuentes, Maria, Hypponen, Elina, Johnson, Toby, de Jong, Paul E, Kleefstra, Nanne, Lagou, Vasiliki, Lapsley, Marta, Li, Yun, Loos, Ruth J F, Luan, Jian'an, Luttropp, Karin, Maréchal, Céline, Melander, Olle, Munroe, Patricia B, Nordfors, Louise, Parsa, Afshin, Peltonen, Leena, Penninx, Brenda W, Perucha, Esperanza, Pouta, Anneli, Prokopenko, Inga, Roderick, Paul J, Ruokonen, Aimo, Samani, Nilesh J, Sanna, Serena, Schalling, Martin, Schlessinger, David, Schlieper, Georg, Seelen, Marc A J, Shuldiner, Alan R, Sjögren, Marketa, Smit, Johannes H, Snieder, Harold, Soranzo, Nicole, Spector, Timothy D, Stenvinkel, Peter, Sternberg, Michael J.E., Swaminathan, Ramasamyiyer, Tanaka, Toshiko, Ubink-Veltmaat, Lielith J, Uda, Manuela, Vollenweider, Peter, Wallace, Chris, Waterworth, Dawn M, Zerres, Klaus, Waeber, Gerard, Wareham, Nicholas J, Maxwell, Patrick H, McCarthy, Mark I, Jarvelin, Marjo-Riitta, Mooser, Vincent, Abecasis, Goncalo R, Lightstone, Liz, Scott, James, Navis, Gerjan, Elliott, Paul, and Kooner, Jaspal S

Abstract

Using genome-wide association, we identify common variants at 2p12-p13, 6q26, 17q23 and 19q13 associated with serum creatinine, a marker of kidney function (P = 10(-10) to 10(-15)). Of these, rs10206899 (near NAT8, 2p12-p13) and rs4805834 (near SLC7A9, 19q13) were also associated with chronic kidney disease (P = 5.0 x 10(-5) and P = 3.6 x 10(-4), respectively). Our findings provide insight into metabolic, solute and drug-transport pathways underlying susceptibility to chronic kidney disease.

Published
2010

4. Genetic loci influencing kidney function and chronic kidney disease.

Author

Chambers, John C, Zhang, Weihua, Lord, Graham M, van der Harst, Pim, Lawlor, Debbie A, Sehmi, Joban S., Gale, Daniel P, Wass, Mark N., Ahmadi, Kourosh R, Bakker, Stephan J L, Beckmann, Jacqui, Bilo, Henk J G, Bochud, Murielle, Brown, Morris J, Caulfield, Mark J, Connell, John M C, Cook, H Terence, Cotlarciuc, Ioana, Davey Smith, George, de Silva, Ranil, Deng, Guohong, Devuyst, Olivier, Dikkeschei, Lambert D, Dimkovic, Nada, Dockrell, Mark, Dominiczak, Anna, Ebrahim, Shah, Eggermann, Thomas, Farrall, Martin, Ferrucci, Luigi, Floege, Jurgen, Forouhi, Nita G, Gansevoort, Ron T, Han, Xijin, Hedblad, Bo, Homan van der Heide, Jaap J, Hepkema, Bouke G, Hernandez-Fuentes, Maria, Hypponen, Elina, Johnson, Toby, de Jong, Paul E, Kleefstra, Nanne, Lagou, Vasiliki, Lapsley, Marta, Li, Yun, Loos, Ruth J F, Luan, Jian'an, Luttropp, Karin, Maréchal, Céline, Melander, Olle, Munroe, Patricia B, Nordfors, Louise, Parsa, Afshin, Peltonen, Leena, Penninx, Brenda W, Perucha, Esperanza, Pouta, Anneli, Prokopenko, Inga, Roderick, Paul J, Ruokonen, Aimo, Samani, Nilesh J, Sanna, Serena, Schalling, Martin, Schlessinger, David, Schlieper, Georg, Seelen, Marc A J, Shuldiner, Alan R, Sjögren, Marketa, Smit, Johannes H, Snieder, Harold, Soranzo, Nicole, Spector, Timothy D, Stenvinkel, Peter, Sternberg, Michael J.E., Swaminathan, Ramasamyiyer, Tanaka, Toshiko, Ubink-Veltmaat, Lielith J, Uda, Manuela, Vollenweider, Peter, Wallace, Chris, Waterworth, Dawn M, Zerres, Klaus, Waeber, Gerard, Wareham, Nicholas J, Maxwell, Patrick H, McCarthy, Mark I, Jarvelin, Marjo-Riitta, Mooser, Vincent, Abecasis, Goncalo R, Lightstone, Liz, Scott, James, Navis, Gerjan, Elliott, Paul, Kooner, Jaspal S, Chambers, John C, Zhang, Weihua, Lord, Graham M, van der Harst, Pim, Lawlor, Debbie A, Sehmi, Joban S., Gale, Daniel P, Wass, Mark N., Ahmadi, Kourosh R, Bakker, Stephan J L, Beckmann, Jacqui, Bilo, Henk J G, Bochud, Murielle, Brown, Morris J, Caulfield, Mark J, Connell, John M C, Cook, H Terence, Cotlarciuc, Ioana, Davey Smith, George, de Silva, Ranil, Deng, Guohong, Devuyst, Olivier, Dikkeschei, Lambert D, Dimkovic, Nada, Dockrell, Mark, Dominiczak, Anna, Ebrahim, Shah, Eggermann, Thomas, Farrall, Martin, Ferrucci, Luigi, Floege, Jurgen, Forouhi, Nita G, Gansevoort, Ron T, Han, Xijin, Hedblad, Bo, Homan van der Heide, Jaap J, Hepkema, Bouke G, Hernandez-Fuentes, Maria, Hypponen, Elina, Johnson, Toby, de Jong, Paul E, Kleefstra, Nanne, Lagou, Vasiliki, Lapsley, Marta, Li, Yun, Loos, Ruth J F, Luan, Jian'an, Luttropp, Karin, Maréchal, Céline, Melander, Olle, Munroe, Patricia B, Nordfors, Louise, Parsa, Afshin, Peltonen, Leena, Penninx, Brenda W, Perucha, Esperanza, Pouta, Anneli, Prokopenko, Inga, Roderick, Paul J, Ruokonen, Aimo, Samani, Nilesh J, Sanna, Serena, Schalling, Martin, Schlessinger, David, Schlieper, Georg, Seelen, Marc A J, Shuldiner, Alan R, Sjögren, Marketa, Smit, Johannes H, Snieder, Harold, Soranzo, Nicole, Spector, Timothy D, Stenvinkel, Peter, Sternberg, Michael J.E., Swaminathan, Ramasamyiyer, Tanaka, Toshiko, Ubink-Veltmaat, Lielith J, Uda, Manuela, Vollenweider, Peter, Wallace, Chris, Waterworth, Dawn M, Zerres, Klaus, Waeber, Gerard, Wareham, Nicholas J, Maxwell, Patrick H, McCarthy, Mark I, Jarvelin, Marjo-Riitta, Mooser, Vincent, Abecasis, Goncalo R, Lightstone, Liz, Scott, James, Navis, Gerjan, Elliott, Paul, and Kooner, Jaspal S

Abstract

Using genome-wide association, we identify common variants at 2p12-p13, 6q26, 17q23 and 19q13 associated with serum creatinine, a marker of kidney function (P = 10(-10) to 10(-15)). Of these, rs10206899 (near NAT8, 2p12-p13) and rs4805834 (near SLC7A9, 19q13) were also associated with chronic kidney disease (P = 5.0 x 10(-5) and P = 3.6 x 10(-4), respectively). Our findings provide insight into metabolic, solute and drug-transport pathways underlying susceptibility to chronic kidney disease.

Published
2010

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, 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.

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