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3. TRAF1-C5 as a risk locus for rheumatoid arthritis- a genomewide study

Author

Plenge, Robert M., Seielstad, Mark, Padyukov, Leonid, Lee, Annette, T., Remmers, Elaine F., Seldin, Michael F., Bo Ding, Liew, Anthony, Khalili, Houman, Chandrasekaran, Alamelu, Davies, Leela R. L., Kastner, Daniel L., Wentian Li, Tan, Andrian K. S., Bonnard, Carine, Ong, Rick T. H., Thalamuthu, Anbupalam, Klareskog, Lars, Pettersson, Sven, Chunyu Liu, Chao Tian, Wei V. Chen, Carulli, John P., Gregerson, Peter K., Beckman, Evan M., Evan M., Altshuler, David, Alfredsson, Lars, Criswell, Lindsey A., and Amos, Christopher I.

Subjects
Tumor necrosis factor -- Research, Tumor necrosis factor -- Physiological aspects, Rheumatoid arthritis -- Risk factors, Rheumatoid arthritis -- Research, Rheumatoid arthritis -- Genetic aspects, Quantitative trait loci -- Research, Quantitative trait loci -- Physiological aspects
Abstract

The article discusses a study that helps in the identification of several genetic loci, including TRAF1 (encoding tumor necrosis factor-receptor associated factor 1) and C5 (encoding complement component 5) that increase the risk for rheumatoid arthritis considerably.

Published
2007

6. Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.

Author

CRyPTIC Consortium and the 100,000 Genomes Project, CRyPTIC Consortium and the 100,000 Genomes Project, Allix-Béguec, Caroline, Arandjelovic, Irena, Bi, Lijun, Beckert, Patrick, Bonnet, Maryline, Bradley, Phelim, Cabibbe, Andrea M, Cancino-Muñoz, Irving, Caulfield, Mark J, Chaiprasert, Angkana, Cirillo, Daniela M, Clifton, David A, Comas, Iñaki, Crook, Derrick W, De Filippo, Maria R, de Neeling, Han, Diel, Roland, Drobniewski, Francis A, Faksri, Kiatichai, Farhat, Maha R, Fleming, Joy, Fowler, Philip, Fowler, Tom A, Gao, Qian, Gardy, Jennifer, Gascoyne-Binzi, Deborah, Gibertoni-Cruz, Ana-Luiza, Gil-Brusola, Ana, Golubchik, Tanya, Gonzalo, Ximena, Grandjean, Louis, He, Guangxue, Guthrie, Jennifer L, Hoosdally, Sarah, Hunt, Martin, Iqbal, Zamin, Ismail, Nazir, Johnston, James, Khanzada, Faisal M, Khor, Chiea C, Kohl, Thomas A, Kong, Clare, Lipworth, Sam, Liu, Qingyun, Maphalala, Gugu, Martinez, Elena, Mathys, Vanessa, Merker, Matthias, Miotto, Paolo, Mistry, Nerges, Moore, David AJ, Murray, Megan, Niemann, Stefan, Omar, Shaheed V, Ong, Rick T-H, Peto, Tim EA, Posey, James E, Prammananan, Therdsak, Pym, Alexander, Rodrigues, Camilla, Rodrigues, Mabel, Rodwell, Timothy, Rossolini, Gian M, Sánchez Padilla, Elisabeth, Schito, Marco, Shen, Xin, Shendure, Jay, Sintchenko, Vitali, Sloutsky, Alex, Smith, E Grace, Snyder, Matthew, Soetaert, Karine, Starks, Angela M, Supply, Philip, Suriyapol, Prapat, Tahseen, Sabira, Tang, Patrick, Teo, Yik-Ying, Thuong, Thuong NT, Thwaites, Guy, Tortoli, Enrico, van Soolingen, Dick, Walker, A Sarah, Walker, Timothy M, Wilcox, Mark, Wilson, Daniel J, Wyllie, David, Yang, Yang, Zhang, Hongtai, Zhao, Yanlin, Zhu, Baoli, CRyPTIC Consortium and the 100,000 Genomes Project, CRyPTIC Consortium and the 100,000 Genomes Project, Allix-Béguec, Caroline, Arandjelovic, Irena, Bi, Lijun, Beckert, Patrick, Bonnet, Maryline, Bradley, Phelim, Cabibbe, Andrea M, Cancino-Muñoz, Irving, Caulfield, Mark J, Chaiprasert, Angkana, Cirillo, Daniela M, Clifton, David A, Comas, Iñaki, Crook, Derrick W, De Filippo, Maria R, de Neeling, Han, Diel, Roland, Drobniewski, Francis A, Faksri, Kiatichai, Farhat, Maha R, Fleming, Joy, Fowler, Philip, Fowler, Tom A, Gao, Qian, Gardy, Jennifer, Gascoyne-Binzi, Deborah, Gibertoni-Cruz, Ana-Luiza, Gil-Brusola, Ana, Golubchik, Tanya, Gonzalo, Ximena, Grandjean, Louis, He, Guangxue, Guthrie, Jennifer L, Hoosdally, Sarah, Hunt, Martin, Iqbal, Zamin, Ismail, Nazir, Johnston, James, Khanzada, Faisal M, Khor, Chiea C, Kohl, Thomas A, Kong, Clare, Lipworth, Sam, Liu, Qingyun, Maphalala, Gugu, Martinez, Elena, Mathys, Vanessa, Merker, Matthias, Miotto, Paolo, Mistry, Nerges, Moore, David AJ, Murray, Megan, Niemann, Stefan, Omar, Shaheed V, Ong, Rick T-H, Peto, Tim EA, Posey, James E, Prammananan, Therdsak, Pym, Alexander, Rodrigues, Camilla, Rodrigues, Mabel, Rodwell, Timothy, Rossolini, Gian M, Sánchez Padilla, Elisabeth, Schito, Marco, Shen, Xin, Shendure, Jay, Sintchenko, Vitali, Sloutsky, Alex, Smith, E Grace, Snyder, Matthew, Soetaert, Karine, Starks, Angela M, Supply, Philip, Suriyapol, Prapat, Tahseen, Sabira, Tang, Patrick, Teo, Yik-Ying, Thuong, Thuong NT, Thwaites, Guy, Tortoli, Enrico, van Soolingen, Dick, Walker, A Sarah, Walker, Timothy M, Wilcox, Mark, Wilson, Daniel J, Wyllie, David, Yang, Yang, Zhang, Hongtai, Zhao, Yanlin, and Zhu, Baoli

Abstract

BackgroundThe World Health Organization recommends drug-susceptibility testing of Mycobacterium tuberculosis complex for all patients with tuberculosis to guide treatment decisions and improve outcomes. Whether DNA sequencing can be used to accurately predict profiles of susceptibility to first-line antituberculosis drugs has not been clear.MethodsWe obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis drugs isoniazid, rifampin, ethambutol, and pyrazinamide for isolates from 16 countries across six continents. For each isolate, mutations associated with drug resistance and drug susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These profiles were predicted to be susceptible to all four drugs (i.e., pansusceptible) if they were predicted to be susceptible to isoniazid and to the other drugs or if they contained mutations of unknown association in genes that affect susceptibility to the other drugs. We simulated the way in which the negative predictive value changed with the prevalence of drug resistance.ResultsA total of 10,209 isolates were analyzed. The largest proportion of phenotypes was predicted for rifampin (9660 [95.4%] of 10,130) and the smallest was predicted for ethambutol (8794 [89.8%] of 9794). Resistance to isoniazid, rifampin, ethambutol, and pyrazinamide was correctly predicted with 97.1%, 97.5%, 94.6%, and 91.3% sensitivity, respectively, and susceptibility to these drugs was correctly predicted with 99.0%, 98.8%, 93.6%, and 96.8% specificity. Of the 7516 isolates with complete phenotypic drug-susceptibility profiles, 5865 (78.0%) had complete genotypic predictions, among which 5250 profiles (89.5%) were correctly predicted. Among the 4037 phenotypic profil

Published
2018

7. Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing

Author

Ministerio de Economía y Competitividad (España), European Research Council, Comas, Iñaki [0000-0001-5504-9408], CRyPTIC Consortium and the 100,000 Genomes Project, Allix-Beguec, Caroline, Arandjelovic, Irena, Bi, Lijun, Beckert, Patrick, Bonnet, Maryline, Bradley, Phelim, Cabibbe, Andrea M., Cancino-Muñoz, Irving, Caulfield, Mark J., Chaiprasert, Angkana, Cirillo, Daniela M., Clifton, David A., Comas, Iñaki, Crook, Derrick W., De Filippo, Maria R., de Neeling, Han, Diel, Roland, Drobniewski, Francis A, Faksri, Kiatichai, Farhat, Maha R., Fleming, Joy, Fowler, Philip, Fowler, Tom A, Gao, Qian, Gardy, Jennifer, Gascoyne-Binzi, Deborah, Gibertoni-Cruz, Ana-Luiza, Gil-Brusola, Ana, Golubchik, Tanya, Gonzalo, Ximena, Grandjean, Louis, He, Guangxue, Guthrie, Jennifer L., Hoosdally, Sarah, Hunt, Martin, Iqbal, Zamin, Ismail, Nazir, Johnston, James, Khanzada, Faisal M., Khor, Chiea C., Kohl, Thomas A, Kong, Clare, Lipworth, Sam, Liu, Qingyun, Maphalala, Gugu, Martínez, Elena, Mathys, Vanessa, Merker, Matthias, Miotto, Paolo, Mistry, Nerges, Moore, David A. J., Murray, Megan, Niemann, Stefan, Omar, Shaheed V., Ong, Rick T-H., Peto, Tim E.A., Posey, James E., Prammananan, Therdsak, Pym, Alexander, Rodrigues, Camilla, Rodrigues, Mabel, Rodwell, Timothy, Rossolini, Gian M., Sanchez Padilla, Elisabeth, Schito, Marco, Shen, Xin, Shendure, Jay, Sintchenko, Vitali, Sloutsky, Alex, Smith, E. Grace, Snyder, Matthew, Soetaert, Karine, Starks, Angela M., Supply, Philip, Suriyapol, Prapat, Tahseen, Sabira, Tang, Patrick, Teo, Yik-Ying, Thuong, Thuong N. T., Thwaites, Guy, Tortoli, Enrico, van Soolingen, Dick, Walker, A. Sarah, Walker, Timothy M., Wilcox, Mark, Wilson, Daniel J., Wyllie, David, Yang, Yang, Zhang, Hongtai, Zhao, Yanlin, Zhu, Baoli, Ministerio de Economía y Competitividad (España), European Research Council, Comas, Iñaki [0000-0001-5504-9408], CRyPTIC Consortium and the 100,000 Genomes Project, Allix-Beguec, Caroline, Arandjelovic, Irena, Bi, Lijun, Beckert, Patrick, Bonnet, Maryline, Bradley, Phelim, Cabibbe, Andrea M., Cancino-Muñoz, Irving, Caulfield, Mark J., Chaiprasert, Angkana, Cirillo, Daniela M., Clifton, David A., Comas, Iñaki, Crook, Derrick W., De Filippo, Maria R., de Neeling, Han, Diel, Roland, Drobniewski, Francis A, Faksri, Kiatichai, Farhat, Maha R., Fleming, Joy, Fowler, Philip, Fowler, Tom A, Gao, Qian, Gardy, Jennifer, Gascoyne-Binzi, Deborah, Gibertoni-Cruz, Ana-Luiza, Gil-Brusola, Ana, Golubchik, Tanya, Gonzalo, Ximena, Grandjean, Louis, He, Guangxue, Guthrie, Jennifer L., Hoosdally, Sarah, Hunt, Martin, Iqbal, Zamin, Ismail, Nazir, Johnston, James, Khanzada, Faisal M., Khor, Chiea C., Kohl, Thomas A, Kong, Clare, Lipworth, Sam, Liu, Qingyun, Maphalala, Gugu, Martínez, Elena, Mathys, Vanessa, Merker, Matthias, Miotto, Paolo, Mistry, Nerges, Moore, David A. J., Murray, Megan, Niemann, Stefan, Omar, Shaheed V., Ong, Rick T-H., Peto, Tim E.A., Posey, James E., Prammananan, Therdsak, Pym, Alexander, Rodrigues, Camilla, Rodrigues, Mabel, Rodwell, Timothy, Rossolini, Gian M., Sanchez Padilla, Elisabeth, Schito, Marco, Shen, Xin, Shendure, Jay, Sintchenko, Vitali, Sloutsky, Alex, Smith, E. Grace, Snyder, Matthew, Soetaert, Karine, Starks, Angela M., Supply, Philip, Suriyapol, Prapat, Tahseen, Sabira, Tang, Patrick, Teo, Yik-Ying, Thuong, Thuong N. T., Thwaites, Guy, Tortoli, Enrico, van Soolingen, Dick, Walker, A. Sarah, Walker, Timothy M., Wilcox, Mark, Wilson, Daniel J., Wyllie, David, Yang, Yang, Zhang, Hongtai, Zhao, Yanlin, and Zhu, Baoli

Abstract

BACKGROUND: The World Health Organization recommends drug-susceptibility testing of Mycobacterium tuberculosis complex for all patients with tuberculosis to guide treatment decisions and improve outcomes. Whether DNA sequencing can be used to accurately predict profiles of susceptibility to first-line antituberculosis drugs has not been clear. METHODS: We obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis drugs isoniazid, rifampin, ethambutol, and pyrazinamide for isolates from 16 countries across six continents. For each isolate, mutations associated with drug resistance and drug susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These profiles were predicted to be susceptible to all four drugs (i.e., pansusceptible) if they were predicted to be susceptible to isoniazid and to the other drugs or if they contained mutations of unknown association in genes that affect susceptibility to the other drugs. We simulated the way in which the negative predictive value changed with the prevalence of drug resistance. RESULTS: A total of 10,209 isolates were analyzed. The largest proportion of phenotypes was predicted for rifampin (9660 [95.4%] of 10,130) and the smallest was predicted for ethambutol (8794 [89.8%] of 9794). Resistance to isoniazid, rifampin, ethambutol, and pyrazinamide was correctly predicted with 97.1%, 97.5%, 94.6%, and 91.3% sensitivity, respectively, and susceptibility to these drugs was correctly predicted with 99.0%, 98.8%, 93.6%, and 96.8% specificity. Of the 7516 isolates with complete phenotypic drug-susceptibility profiles, 5865 (78.0%) had complete genotypic predictions, among which 5250 profiles (89.5%) were correctly predicted. Among the 4037 phenotypi

Published
2018

8. Meta-analysis of genome-wide association studies in East Asian-ancestry populations identifies four new loci for body mass index

Author

Wen Wanqing, Zheng Wei, Okada Yukinori, Takeuchi Fumihiko, Tabara Yasuharu, Hwang Joo-Yeon, Dorajoo Rajkumar, Li Huaixing, Tsai Fuu-Jen, Yang Xiaobo, He Jiang, Wu Ying, He Meian, Zhang Yi, Liang Jun, Guo Xiuqing, Sheu Wayne Huey-Herng, Delahanty Ryan, Guo Xingyi, Kubo Michiaki, Yamamoto Ken, Ohkubo Takayoshi, Go Min Jin, Liu Jian Jun, Gan Wei, Chen Ching-Chu, Gao Yong, Li Shengxu, Lee Nanette R., Wu Chen, Zhou Xueya, Song Huaidong, Yao Jie, Lee I-Te, Long Jirong, Tsunoda Tatsuhiko, Akiyama Koichi, Takashima Naoyuki, Cho Yoon Shin, Ong Rick T. H., Lu Ling, Chen Chien-Hsiun, Tan Aihua, Rice Treva K., Adair Linda S., Gui Lixuan, Allison Matthew, Lee Wen-Jane, Cai Qiuyin, ISOMURA, Minoru, Umemura Satoshi, Kim Young Jin, Seielstad Mark, Hixson James, Xiang Yong-Bing, Isono Masato, Kim Bong-Jo, Sim Xueling, Lu Wei, Nabika, Toru, Lee Juyoung, Lim Wei-Yen, Gao Yu-Tang, Takayanagi Ryoichi, Kang Dae-Hee, Wong Tien Yin, Hsiung ChaoAgnes, Wu I-Chien, Juang Jyh-Ming Jimmy, Shi Jiajun, Choi Bo Youl, Aung Tin, Hu Frank, Kim Mi Kyung, Lim WeiYen, Wang Tzung-Dao, Shin Min-Ho, Lee Jeannette, Ji Bu-Tian, Lee Young-Hoon, Young Terri L., Shin Dong Hoon, Chun Byung-Yeol, Cho Myeong-Chan, Han Bok-Ghee, Hwu Chii-Min, Assimes Themistocles L., Absher Devin, Yan Xiaofei, Kim Eric, Kuo Jane Z., Kwon Soonil, Taylor Kent D., Chen Yii-Der I., Rotter Jerome I., Qi Lu, Zhu Dingliang, Wu Tangchun, Mohlke Karen L., Gu Dongfeng, Mo Zengnan, Wu Jer-Yuarn, Lin Xu, Miki Tetsuro, Tai E. Shyong, Lee Jong-Young, Kato Norihiro, Shu Xiao-Ou, Tanaka Toshihiro, Wen Wanqing, Zheng Wei, Okada Yukinori, Takeuchi Fumihiko, Tabara Yasuharu, Hwang Joo-Yeon, Dorajoo Rajkumar, Li Huaixing, Tsai Fuu-Jen, Yang Xiaobo, He Jiang, Wu Ying, He Meian, Zhang Yi, Liang Jun, Guo Xiuqing, Sheu Wayne Huey-Herng, Delahanty Ryan, Guo Xingyi, Kubo Michiaki, Yamamoto Ken, Ohkubo Takayoshi, Go Min Jin, Liu Jian Jun, Gan Wei, Chen Ching-Chu, Gao Yong, Li Shengxu, Lee Nanette R., Wu Chen, Zhou Xueya, Song Huaidong, Yao Jie, Lee I-Te, Long Jirong, Tsunoda Tatsuhiko, Akiyama Koichi, Takashima Naoyuki, Cho Yoon Shin, Ong Rick T. H., Lu Ling, Chen Chien-Hsiun, Tan Aihua, Rice Treva K., Adair Linda S., Gui Lixuan, Allison Matthew, Lee Wen-Jane, Cai Qiuyin, ISOMURA, Minoru, Umemura Satoshi, Kim Young Jin, Seielstad Mark, Hixson James, Xiang Yong-Bing, Isono Masato, Kim Bong-Jo, Sim Xueling, Lu Wei, Nabika, Toru, Lee Juyoung, Lim Wei-Yen, Gao Yu-Tang, Takayanagi Ryoichi, Kang Dae-Hee, Wong Tien Yin, Hsiung ChaoAgnes, Wu I-Chien, Juang Jyh-Ming Jimmy, Shi Jiajun, Choi Bo Youl, Aung Tin, Hu Frank, Kim Mi Kyung, Lim WeiYen, Wang Tzung-Dao, Shin Min-Ho, Lee Jeannette, Ji Bu-Tian, Lee Young-Hoon, Young Terri L., Shin Dong Hoon, Chun Byung-Yeol, Cho Myeong-Chan, Han Bok-Ghee, Hwu Chii-Min, Assimes Themistocles L., Absher Devin, Yan Xiaofei, Kim Eric, Kuo Jane Z., Kwon Soonil, Taylor Kent D., Chen Yii-Der I., Rotter Jerome I., Qi Lu, Zhu Dingliang, Wu Tangchun, Mohlke Karen L., Gu Dongfeng, Mo Zengnan, Wu Jer-Yuarn, Lin Xu, Miki Tetsuro, Tai E. Shyong, Lee Jong-Young, Kato Norihiro, Shu Xiao-Ou, and Tanaka Toshihiro

Published
2014

9. Genome-wide association identifies multiple ulcerative colitis susceptibility loci (vol 42, pg 332, 2010)

Author

McGovern, Dermot P. B., Gardet, Agnes, Törkvist, Leif, Goyette, Philippe, Essers, Jonah, Taylor, Kent D., Neale, Benjamin M., Ong, Rick T. H., Lagace, Caroline, Li, Chun, Green, Todd, Stevens, Christine R., Beauchamp, Claudine, Fleshner, Phillip R., Carlson, Marie, D'Amato, Mauro, Halfvarson, Jonas, Hibberd, Martin L., Loerdal, Mikael, Padyukov, Leonid, Andriulli, Angelo, Colombo, Elisabetta, Latiano, Anna, Palmieri, Orazio, Bernard, Edmond-Jean, Deslandres, Colette, Hommes, Daan W., de Jong, Dirk J., Stokkers, Pieter C., Weersma, Rinse K., Sharma, Yashoda, Silverberg, Mark S., Cho, Judy H., Wu, Jing, Roeder, Kathryn, Brant, Steven R., Schumm, L. Phillip, Duerr, Richard H., Dubinsky, Marla C., Glazer, Nicole L., Haritunians, Talin, Ippoliti, Andy, Melmed, Gil Y., Siscovick, David S., Vasiliauskas, Eric A., Targan, Stephan R., Annese, Vito, Wijmenga, Cisca, Pettersson, Sven, Rotter, Jerome I., Xavier, Ramnik J., Daly, Mark J., Rioux, John D., Seielstad, Mark, McGovern, Dermot P. B., Gardet, Agnes, Törkvist, Leif, Goyette, Philippe, Essers, Jonah, Taylor, Kent D., Neale, Benjamin M., Ong, Rick T. H., Lagace, Caroline, Li, Chun, Green, Todd, Stevens, Christine R., Beauchamp, Claudine, Fleshner, Phillip R., Carlson, Marie, D'Amato, Mauro, Halfvarson, Jonas, Hibberd, Martin L., Loerdal, Mikael, Padyukov, Leonid, Andriulli, Angelo, Colombo, Elisabetta, Latiano, Anna, Palmieri, Orazio, Bernard, Edmond-Jean, Deslandres, Colette, Hommes, Daan W., de Jong, Dirk J., Stokkers, Pieter C., Weersma, Rinse K., Sharma, Yashoda, Silverberg, Mark S., Cho, Judy H., Wu, Jing, Roeder, Kathryn, Brant, Steven R., Schumm, L. Phillip, Duerr, Richard H., Dubinsky, Marla C., Glazer, Nicole L., Haritunians, Talin, Ippoliti, Andy, Melmed, Gil Y., Siscovick, David S., Vasiliauskas, Eric A., Targan, Stephan R., Annese, Vito, Wijmenga, Cisca, Pettersson, Sven, Rotter, Jerome I., Xavier, Ramnik J., Daly, Mark J., Rioux, John D., and Seielstad, Mark

Published
2011
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10. Analysis of 39 Crohn's Disease Risk Loci in Swedish Inflammatory Bowel Disease Patients

Author

Torkvist, Leif, Halfvarson, Jonas, Ong, Rick T. H., Lordal, Mikael, Sjoqvist, Urban, Bresso, Francesca, Bjork, Jan, Befrits, Ragnar, Lofberg, Robert, Blom, Johannes, Carlson, Marie, Padyukov, Leonid, D'Amato, Mauro, Seielstad, Mark, Pettersson, Sven, Torkvist, Leif, Halfvarson, Jonas, Ong, Rick T. H., Lordal, Mikael, Sjoqvist, Urban, Bresso, Francesca, Bjork, Jan, Befrits, Ragnar, Lofberg, Robert, Blom, Johannes, Carlson, Marie, Padyukov, Leonid, D'Amato, Mauro, Seielstad, Mark, and Pettersson, Sven

Published
2010
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11. Genome-wide association identifies multiple ulcerative colitis susceptibility loci

Author

McGovern, Dermot P. B., Gardet, Agnes, Torkvist, Leif, Goyette, Philippe, Essers, Jonah, Taylor, Kent D., Neale, Benjamin M., Ong, Rick T. H., Lagace, Caroline, Li, Chun, Green, Todd, Stevens, Christine R., Beauchamp, Claudine, Fleshner, Phillip R., Carlson, Marie, D'Amato, Mauro, Halfvarson, Jonas, Hibberd, Martin L., Lordal, Mikael, Padyukov, Leonid, Andriulli, Angelo, Colombo, Elisabetta, Latiano, Anna, Palmieri, Orazio, Bernard, Edmond-Jean, Deslandres, Colette, Hommes, Daan W., de Jong, Dirk J., Stokkers, Pieter C., Weersma, Rinse K., Sharma, Yashoda, Silverberg, Mark S., Cho, Judy H., Wu, Jing, Roeder, Kathryn, Brant, Steven R., Schumm, L. Phillip, Duerr, Richard H., Dubinsky, Marla C., Glazer, Nicole L., Haritunians, Talin, Ippoliti, Andy, Melmed, Gil Y., Siscovick, David S., Vasiliauskas, Eric A., Targan, Stephan R., Annese, Vito, Wijmenga, Cisca, Pettersson, Sven, Rotter, Jerome I., Xavier, Ramnik J., Daly, Mark J., Rioux, John D., Seielstad, Mark, McGovern, Dermot P. B., Gardet, Agnes, Torkvist, Leif, Goyette, Philippe, Essers, Jonah, Taylor, Kent D., Neale, Benjamin M., Ong, Rick T. H., Lagace, Caroline, Li, Chun, Green, Todd, Stevens, Christine R., Beauchamp, Claudine, Fleshner, Phillip R., Carlson, Marie, D'Amato, Mauro, Halfvarson, Jonas, Hibberd, Martin L., Lordal, Mikael, Padyukov, Leonid, Andriulli, Angelo, Colombo, Elisabetta, Latiano, Anna, Palmieri, Orazio, Bernard, Edmond-Jean, Deslandres, Colette, Hommes, Daan W., de Jong, Dirk J., Stokkers, Pieter C., Weersma, Rinse K., Sharma, Yashoda, Silverberg, Mark S., Cho, Judy H., Wu, Jing, Roeder, Kathryn, Brant, Steven R., Schumm, L. Phillip, Duerr, Richard H., Dubinsky, Marla C., Glazer, Nicole L., Haritunians, Talin, Ippoliti, Andy, Melmed, Gil Y., Siscovick, David S., Vasiliauskas, Eric A., Targan, Stephan R., Annese, Vito, Wijmenga, Cisca, Pettersson, Sven, Rotter, Jerome I., Xavier, Ramnik J., Daly, Mark J., Rioux, John D., and Seielstad, Mark

Abstract

Ulcerative colitis is a chronic, relapsing inflammatory condition of the gastrointestinal tract with a complex genetic and environmental etiology. In an effort to identify genetic variation underlying ulcerative colitis risk, we present two distinct genome-wide association studies of ulcerative colitis and their joint analysis with a previously published scan(1), comprising, in aggregate, 2,693 individuals with ulcerative colitis and 6,791 control subjects. Fifty-nine SNPs from 14 independent loci attained an association significance of P < 10(-5). Seven of these loci exceeded genome-wide significance (P < 5 x 10(-8)). After testing an independent cohort of 2,009 cases of ulcerative colitis and 1,580 controls, we identified 13 loci that were significantly associated with ulcerative colitis (P < 5 x 10(-8)), including the immunoglobulin receptor gene FCGR2A, 5p15, 2p16 and ORMDL3 (orosomucoid1-like 3). We confirmed association with 14 previously identified ulcerative colitis susceptibility loci, and an analysis of acknowledged Crohn's disease loci showed that roughly half of the known Crohn's disease associations are shared with ulcerative colitis. These data implicate approximately 30 loci in ulcerative colitis, thereby providing insight into disease pathogenesis.

Published
2010
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12. Genome-wide association study identifies susceptibility loci for dengue shock syndrome at MICB and PLCE1

Author

Khor, Chiea Chuen, primary, Chau, Tran Nguyen Bich, additional, Pang, Junxiong, additional, Davila, Sonia, additional, Long, Hoang Truong, additional, Ong, Rick T H, additional, Dunstan, Sarah J, additional, Wills, Bridget, additional, Farrar, Jeremy, additional, Van Tram, Ta, additional, Gan, Tran Thi, additional, Binh, Nguyen Thi Nguyet, additional, Tri, Le Trung, additional, Lien, Le Bich, additional, Tuan, Nguyen Minh, additional, Tham, Nguyen Thi Hong, additional, Lanh, Mai Ngoc, additional, Nguyet, Nguyen Minh, additional, Hieu, Nguyen Trong, additional, Van N Vinh Chau, Nguyen, additional, Thuy, Tran Thi, additional, Tan, Dennis E K, additional, Sakuntabhai, Anavaj, additional, Teo, Yik-Ying, additional, Hibberd, Martin L, additional, and Simmons, Cameron P, additional

Published
2011
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15. Erratum: Genome-wide association identifies multiple ulcerative colitis susceptibility loci.

Author

McGovern, Dermot P. B., Gardet, Agnès, Törkvist, Leif, Goyette, Philippe, Essers, Jonah, Taylor, Kent D., Neale, Benjamin M., Ong, Rick T. H., Lagacé, Caroline, Li, Chun, Green, Todd, Stevens, Christine R., Beauchamp, Claudine, Fleshner, Phillip R., Carlson, Marie, D'Amato, Mauro, Halfvarson, Jonas, Hibberd, Martin L., Lördal, Mikael, and Padyukov, Leonid

Subjects
SPELLING errors
Abstract

A correction to the article "Genome-wide association study identifies new HLA class II haplotypes strongly protective against narcolepsy," by Hyun Hor and colleagues that was published in the 2010 issue is presented.

Published
2011
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16. Genetic determinants of hepatitis B vaccine response.

Author

Png, Eileen, Thalamuthu, Anbupalam, Ong, Rick T. H., Snippe, Harm, Sudoyo, Herawati, Muljono, David H., Marzuki, Sangkot, Boland, Greet J., and Seielstad, Mark

Subjects
HEPATITIS B vaccines
Abstract

An abstract of the paper "Genetic determinants of hepatitis B vaccine response," by Eileen Png and colleagues presented during the Institut Pasteur International Network Annual Scientific Meeting at Hong Kong, China, from November 22-23, 2010 is presented.

Published
2011
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17. Association of Skin Barrier Genes within the PSORS4 Locus Is Enriched in Singaporean Chinese with Early-Onset Psoriasis.

Author

Chen, Huijia, Toh, Terry K L, Szeverenyi, Ildiko, Ong, Rick T H, Theng, Colin T S, McLean, W H Irwin, Seielstad, Mark, and Lane, E Birgitte

Subjects
*PSORIASIS, *GENETIC disorders, *SKIN disease genetics, *INFLAMMATION, *ETIOLOGY of diseases, *GENETICS
Abstract

Psoriasis (OMIM#177900) is a common polygenic skin disorder affecting approximately 2% of the northern European population and 0.1% of the Han Chinese. Psoriasis patients suffer from chronic skin inflammation, manifested by erythematous scaly lesions. PSORS1–PSORS9 have been confirmed as psoriasis susceptibility loci in independent genetic studies on predominantly Caucasian populations, with psoriasis susceptibility loci (PSORS1, PSORS9) and additional loci at 9q33-34 and 2p22.3-11.2 reported in Han Chinese patients. In this study, we show the association of PSORS4 with psoriasis in Singaporean Chinese. Dense genotyping of single-nucleotide polymorphism-tagging candidate genes within the epidermal differentiation complex revealed significant association in the proximity of the involucrin gene (IVL); the strongest association was seen in early-onset psoriasis patients (P=0.0014). A follow-up genome-wide association screen localized the psoriasis susceptibility region to ∼360 kb along chromosome 1 in the vicinity of IVL, small proline-rich region (SPRR) and proline-rich region 9 (PRR9) genes. The study of interactions between the causative variant(s) in this locus will provide insights into a possible role for epidermal barrier formation in the pathogenesis of psoriasis.Journal of Investigative Dermatology (2009) 129, 606–614; doi:10.1038/jid.2008.273; published online 11 September 2008 [ABSTRACT FROM AUTHOR]

Published
2009
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18. Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.

Author

Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, Golubchik T, Gonzalo X, Grandjean L, He G, Guthrie JL, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Johnston J, Khanzada FM, Khor CC, Kohl TA, Kong C, Lipworth S, Liu Q, Maphalala G, Martinez E, Mathys V, Merker M, Miotto P, Mistry N, Moore DAJ, Murray M, Niemann S, Omar SV, Ong RT, Peto TEA, Posey JE, Prammananan T, Pym A, Rodrigues C, Rodrigues M, Rodwell T, Rossolini GM, Sánchez Padilla E, Schito M, Shen X, Shendure J, Sintchenko V, Sloutsky A, Smith EG, Snyder M, Soetaert K, Starks AM, Supply P, Suriyapol P, Tahseen S, Tang P, Teo YY, Thuong TNT, Thwaites G, Tortoli E, van Soolingen D, Walker AS, Walker TM, Wilcox M, Wilson DJ, Wyllie D, Yang Y, Zhang H, Zhao Y, and Zhu B

Subjects
Antitubercular Agents therapeutic use, Ethambutol pharmacology, Genotype, Humans, Isoniazid pharmacology, Microbial Sensitivity Tests, Mutation, Mycobacterium tuberculosis drug effects, Mycobacterium tuberculosis isolation & purification, Phenotype, Pyrazinamide pharmacology, Rifampin pharmacology, Tuberculosis microbiology, Antitubercular Agents pharmacology, Drug Resistance, Bacterial genetics, Genome, Bacterial, Mycobacterium tuberculosis genetics, Tuberculosis drug therapy, Whole Genome Sequencing
Abstract

Background: The World Health Organization recommends drug-susceptibility testing of Mycobacterium tuberculosis complex for all patients with tuberculosis to guide treatment decisions and improve outcomes. Whether DNA sequencing can be used to accurately predict profiles of susceptibility to first-line antituberculosis drugs has not been clear., Methods: We obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis drugs isoniazid, rifampin, ethambutol, and pyrazinamide for isolates from 16 countries across six continents. For each isolate, mutations associated with drug resistance and drug susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These profiles were predicted to be susceptible to all four drugs (i.e., pansusceptible) if they were predicted to be susceptible to isoniazid and to the other drugs or if they contained mutations of unknown association in genes that affect susceptibility to the other drugs. We simulated the way in which the negative predictive value changed with the prevalence of drug resistance., Results: A total of 10,209 isolates were analyzed. The largest proportion of phenotypes was predicted for rifampin (9660 [95.4%] of 10,130) and the smallest was predicted for ethambutol (8794 [89.8%] of 9794). Resistance to isoniazid, rifampin, ethambutol, and pyrazinamide was correctly predicted with 97.1%, 97.5%, 94.6%, and 91.3% sensitivity, respectively, and susceptibility to these drugs was correctly predicted with 99.0%, 98.8%, 93.6%, and 96.8% specificity. Of the 7516 isolates with complete phenotypic drug-susceptibility profiles, 5865 (78.0%) had complete genotypic predictions, among which 5250 profiles (89.5%) were correctly predicted. Among the 4037 phenotypic profiles that were predicted to be pansusceptible, 3952 (97.9%) were correctly predicted., Conclusions: Genotypic predictions of the susceptibility of M. tuberculosis to first-line drugs were found to be correlated with phenotypic susceptibility to these drugs. (Funded by the Bill and Melinda Gates Foundation and others.).

Published
2018
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19. Meta-analysis identifies common variants associated with body mass index in east Asians.

Author

Wen W, Cho YS, Zheng W, Dorajoo R, Kato N, Qi L, Chen CH, Delahanty RJ, Okada Y, Tabara Y, Gu D, Zhu D, Haiman CA, Mo Z, Gao YT, Saw SM, Go MJ, Takeuchi F, Chang LC, Kokubo Y, Liang J, Hao M, Le Marchand L, Zhang Y, Hu Y, Wong TY, Long J, Han BG, Kubo M, Yamamoto K, Su MH, Miki T, Henderson BE, Song H, Tan A, He J, Ng DP, Cai Q, Tsunoda T, Tsai FJ, Iwai N, Chen GK, Shi J, Xu J, Sim X, Xiang YB, Maeda S, Ong RT, Li C, Nakamura Y, Aung T, Kamatani N, Liu JJ, Lu W, Yokota M, Seielstad M, Fann CS, Wu JY, Lee JY, Hu FB, Tanaka T, Tai ES, and Shu XO

Subjects
Asia, Eastern, Genome-Wide Association Study, Genotype, Humans, Polymorphism, Single Nucleotide genetics, Asian People genetics, Body Mass Index, Genetic Predisposition to Disease genetics, Obesity genetics, Quantitative Trait Loci genetics
Abstract

Multiple genetic loci associated with obesity or body mass index (BMI) have been identified through genome-wide association studies conducted predominantly in populations of European ancestry. We performed a meta-analysis of associations between BMI and approximately 2.4 million SNPs in 27,715 east Asians, which was followed by in silico and de novo replication studies in 37,691 and 17,642 additional east Asians, respectively. We identified ten BMI-associated loci at genome-wide significance (P < 5.0 × 10(-8)), including seven previously identified loci (FTO, SEC16B, MC4R, GIPR-QPCTL, ADCY3-DNAJC27, BDNF and MAP2K5) and three novel loci in or near the CDKAL1, PCSK1 and GP2 genes. Three additional loci nearly reached the genome-wide significance threshold, including two previously identified loci in the GNPDA2 and TFAP2B genes and a newly identified signal near PAX6, all of which were associated with BMI with P < 5.0 × 10(-7). Findings from this study may shed light on new pathways involved in obesity and demonstrate the value of conducting genetic studies in non-European populations.

Published
2012
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20. A genome-wide association study of hepatitis B vaccine response in an Indonesian population reveals multiple independent risk variants in the HLA region.

Author

Png E, Thalamuthu A, Ong RT, Snippe H, Boland GJ, and Seielstad M

Subjects
Case-Control Studies, HLA Antigens immunology, Hepatitis B Vaccines genetics, Hepatitis B, Chronic prevention & control, Humans, Indonesia, Polymorphism, Single Nucleotide, Asian People genetics, Genome-Wide Association Study, HLA Antigens genetics, Hepatitis Antibodies immunology, Hepatitis B Vaccines immunology, Hepatitis B, Chronic genetics, Hepatitis B, Chronic immunology
Abstract

We performed a two-stage genome-wide association study (GWAS) of antibody titer in 3614 hepatitis B vaccine recipients from Indonesia's Riau Archipelago, leading to the identification of at least three independent signals within the human leukocyte antigen (HLA) complex. These appear to implicate HLA-DR [rs3135363; P= 6.53 × 10(-22); odds ratio (OR) = 1.53, 95% confidence interval (CI) = 1.35-1.74]; HLA-DP, previously associated with the risk of chronic hepatitis B infection (rs9277535; P= 2.91 × 10(-12); OR = 0.72, 95% CI = 0.63-0.81); and a gene rich HLA Class III interval (rs9267665; P = 1.24 × 10(-17); OR = 2.05, CI = 1.64-2.57). The substantial overlap of these variants and those identified by GWAS of chronic hepatitis B infection confirms vaccine response as a model for infection, while suggesting that the vaccine is least effective in those most at risk of lifelong infection, following exposure to the virus.

Published
2011
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21. Identifying candidate causal variants via trans-population fine-mapping.

Author

Teo YY, Ong RT, Sim X, Tai ES, and Chia KS

Subjects
Alleles, Case-Control Studies, Computer Simulation, Cyclin-Dependent Kinase 5 genetics, Gene Frequency, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Models, Genetic, Molecular Epidemiology, Polymorphism, Single Nucleotide, tRNA Methyltransferases, Chromosome Mapping methods, Genetic Variation, Linkage Disequilibrium
Abstract

Genome-wide association studies have discovered and confirmed a large number of loci that are implicated with disease susceptibility and severity. Polymorphisms that emerged from these studies are mostly indirectly associated to the phenotype, and the natural progression is to identify the causal variants that are functionally responsible for these association signals. Long stretches of high linkage disequilibrium (LD) benefitted the initial discovery phase in a genome-wide scan, allowing commercial genotyping products with imperfect coverage to detect genomic regions genuinely associated with the phenotype. However, regions of high LD confound the fine-mapping phase, as markers that are perfectly correlated to the causal variants display similar evidence of phenotypic association, hampering the process of differentiating the functional polymorphisms from neighboring surrogates. Here, we explore the potential of integrating information across different populations for narrowing the candidate region that a causal variant resides in, and compare the efficacy of this process of trans-population fine-mapping with the extent of variation in patterns of LD between the populations. In addition, we explore two different strategies for pooling data across multiple populations for the purpose of prioritizing the rankings of the causal variants. Our results clearly establish the benefits of trans-population analysis in reducing the number of possible candidates for the causal variants, particularly in genomic regions displaying strong evidence of inter-population LD variation. Directly integrating the statistical evidence by summing the test statistics outperforms the standard meta-analytic procedure. These findings have direct relevance to the design and analysis of ongoing fine-mapping studies., (© 2010 Wiley-Liss, Inc.)

Published
2010
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22. Genomic copy number variations in three Southeast Asian populations.

Author

Ku CS, Pawitan Y, Sim X, Ong RT, Seielstad M, Lee EJ, Teo YY, Chia KS, and Salim A

Subjects
Aryl Hydrocarbon Hydroxylases genetics, Asian People ethnology, Chromosome Mapping, Cytochrome P-450 CYP2A6, Gene Deletion, Gene Duplication, Genetic Predisposition to Disease ethnology, Genetics, Population, Humans, India ethnology, Lung Neoplasms genetics, Malaysia ethnology, Principal Component Analysis, Singapore, Asian People genetics, Gene Dosage genetics, Genetic Predisposition to Disease genetics, Genetic Variation
Abstract

Research on the role of copy number variations (CNVs) in the genetic risk of diseases in Asian populations has been hampered by a relative lack of reference CNV maps for Asian populations outside the East Asians. In this article, we report the population characteristics of CNVs in Chinese, Malay, and Asian Indian populations in Singapore. Using the Illumina Human 1M Beadchip array, we identify 1,174 CNV loci in these populations that corroborated with findings when the same samples were typed on the Affymetrix 6.0 platform. We identify 441 novel loci not previously reported in the Database of Genomic Variations (DGV). We observe a considerable number of loci that span all three populations and were previously unreported, as well as population-specific loci that are quite common in the respective populations. From this we observe the distribution of CNVs in the Asian Indian population to be considerably different from the Chinese and Malay populations. About half of the deletion loci and three-quarters of duplication loci overlap UCSC genes. Tens of loci show population differentiation and overlap with genes previously known to be associated with genetic risk of diseases. One of these loci is the CYP2A6 deletion, previously linked to reduced susceptibility to lung cancer., ((c) 2010 Wiley-Liss, Inc.)

Published
2010
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23. Analysis of 39 Crohn's disease risk loci in Swedish inflammatory bowel disease patients.

Author

Törkvist L, Halfvarson J, Ong RT, Lördal M, Sjöqvist U, Bresso F, Björk J, Befrits R, Löfberg R, Blom J, Carlson M, Padyukov L, D'Amato M, Seielstad M, and Pettersson S

Subjects
Adult, Aged, Crohn Disease epidemiology, DNA-Binding Proteins genetics, Female, GTP-Binding Proteins genetics, Humans, Inflammatory Bowel Diseases epidemiology, Inflammatory Bowel Diseases genetics, Leucine-Rich Repeat Serine-Threonine Protein Kinase-2, Male, Middle Aged, Polymorphism, Single Nucleotide, Protein Serine-Threonine Kinases genetics, Receptors, Interleukin genetics, Risk Factors, Sweden epidemiology, Transcription Factors genetics, Crohn Disease genetics, Genetic Loci
Published
2010
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24. Singapore Genome Variation Project: a haplotype map of three Southeast Asian populations.

Author

Teo YY, Sim X, Ong RT, Tan AK, Chen J, Tantoso E, Small KS, Ku CS, Lee EJ, Seielstad M, and Chia KS

Subjects
China, Chromosome Mapping, Gene Frequency, Genetics, Population methods, Genome-Wide Association Study methods, Genomics methods, Genotype, Humans, India, Linkage Disequilibrium, Malaysia, Polymorphism, Single Nucleotide, Principal Component Analysis, Selection, Genetic, Singapore, Databases, Genetic, Genetic Variation genetics, Genome, Human genetics, Haplotypes genetics
Abstract

The Singapore Genome Variation Project (SGVP) provides a publicly available resource of 1.6 million single nucleotide polymorphisms (SNPs) genotyped in 268 individuals from the Chinese, Malay, and Indian population groups in Southeast Asia. This online database catalogs information and summaries on genotype and phased haplotype data, including allele frequencies, assessment of linkage disequilibrium (LD), and recombination rates in a format similar to the International HapMap Project. Here, we introduce this resource and describe the analysis of human genomic variation upon agglomerating data from the HapMap and the Human Genome Diversity Project, providing useful insights into the population structure of the three major population groups in Asia. In addition, this resource also surveyed across the genome for variation in regional patterns of LD between the HapMap and SGVP populations, and for signatures of positive natural selection using two well-established metrics: iHS and XP-EHH. The raw and processed genetic data, together with all population genetic summaries, are publicly available for download and browsing through a web browser modeled with the Generic Genome Browser.

Published
2009
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