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4 results on '"Sim, Kar Seng"'

1. Genome-Wide Analysis of Protein-Coding Variants in Leprosy

Author

Liu, Hong, Wang, Zhenzhen, Li, Yi, Yu, Gongqi, Fu, Xi’an, Wang, Chuan, Liu, Wenting, Yu, Yongxiang, Bao, Fangfang, Irwanto, Astrid, Liu, Jian, Chu, Tongsheng, Andiappan, Anand Kumar, Maurer-Stroh, Sebastian, Limviphuvadh, Vachiranee, Wang, Honglei, Mi, Zihao, Sun, Yonghu, Sun, Lele, Wang, Ling, Wang, Chaolong, You, Jiabao, Li, Jinghui, Foo, Jia Nee, Liany, Herty, Meah, Wee Yang, Niu, Guiye, Yue, Zhenhua, Zhao, Qing, Wang, Na, Yu, Meiwen, Yu, Wenjun, Cheng, Xiujun, Khor, Chiea Chuen, Sim, Kar Seng, Aung, Tin, Wang, Ningli, Wang, Deyun, Shi, Li, Ning, Yong, Zheng, Zhongyi, Yang, Rongde, Li, Jinlan, Yang, Jun, Yan, Liangbin, Shen, Jianping, Zhang, Guocheng, Chen, Shumin, Liu, Jianjun, and Zhang, Furen

Abstract

Although genome-wide association studies have greatly advanced our understanding of the contribution of common noncoding variants to leprosy susceptibility, protein-coding variants have not been systematically investigated. We carried out a three-stage genome-wide association study of protein-coding variants in Han Chinese, of whom were 7,048 leprosy patients and 14,398 were healthy control subjects. Seven coding variants of exome-wide significance were discovered, including two rare variants: rs145562243 in NCKIPSD(P = 1.71 × 10–9, odds ratio [OR] = 4.35) and rs149308743 in CARD9(P = 2.09 × 10–8, OR = 4.75); three low-frequency variants: rs76418789 in IL23R(P = 1.03 × 10–10, OR = 1.36), rs146466242 in FLG(P = 3.39 × 10–12, OR = 1.45), and rs55882956 in TYK2(P = 1.04 × 10–6, OR = 1.30); and two common variants: rs780668 in SLC29A3(P = 2.17 × 10–9, OR = 1.14) and rs181206 in IL27(P = 1.08 × 10–7, OR = 0.83). Discovered protein-coding variants, particularly low-frequency and rare ones, showed involvement of skin barrier and endocytosis/phagocytosis/autophagy, in addition to known innate and adaptive immunity, in the pathogenesis of leprosy, highlighting the merits of protein-coding variant studies for complex diseases.

Published
2017
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2. Genetic association study of exfoliation syndrome identifies a protective rare variant at LOXL1 and five new susceptibility loci

Author

Aung, Tin, Ozaki, Mineo, Lee, Mei Chin, Schlötzer-Schrehardt, Ursula, Thorleifsson, Gudmar, Mizoguchi, Takanori, Igo, Robert P, Haripriya, Aravind, Williams, Susan E, Astakhov, Yury S, Orr, Andrew C, Burdon, Kathryn P, Nakano, Satoko, Mori, Kazuhiko, Abu-Amero, Khaled, Hauser, Michael, Li, Zheng, Prakadeeswari, Gopalakrishnan, Bailey, Jessica N Cooke, Cherecheanu, Alina Popa, Kang, Jae H, Nelson, Sarah, Hayashi, Ken, Manabe, Shin-ichi, Kazama, Shigeyasu, Zarnowski, Tomasz, Inoue, Kenji, Irkec, Murat, Coca-Prados, Miguel, Sugiyama, Kazuhisa, Järvelä, Irma, Schlottmann, Patricio, Lerner, S Fabian, Lamari, Hasnaa, Nilgün, Yildirim, Bikbov, Mukharram, Park, Ki Ho, Cha, Soon Cheol, Yamashiro, Kenji, Zenteno, Juan C, Jonas, Jost B, Kumar, Rajesh S, Perera, Shamira A, Chan, Anita S Y, Kobakhidze, Nino, George, Ronnie, Vijaya, Lingam, Do, Tan, Edward, Deepak P, de Juan Marcos, Lourdes, Pakravan, Mohammad, Moghimi, Sasan, Ideta, Ryuichi, Bach-Holm, Daniella, Kappelgaard, Per, Wirostko, Barbara, Thomas, Samuel, Gaston, Daniel, Bedard, Karen, Greer, Wenda L, Yang, Zhenglin, Chen, Xueyi, Huang, Lulin, Sang, Jinghong, Jia, Hongyan, Jia, Liyun, Qiao, Chunyan, Zhang, Hui, Liu, Xuyang, Zhao, Bowen, Wang, Ya-Xing, Xu, Liang, Leruez, Stéphanie, Reynier, Pascal, Chichua, George, Tabagari, Sergo, Uebe, Steffen, Zenkel, Matthias, Berner, Daniel, Mossböck, Georg, Weisschuh, Nicole, Hoja, Ursula, Welge-Luessen, Ulrich-Christoph, Mardin, Christian, Founti, Panayiota, Chatzikyriakidou, Anthi, Pappas, Theofanis, Anastasopoulos, Eleftherios, Lambropoulos, Alexandros, Ghosh, Arkasubhra, Shetty, Rohit, Porporato, Natalia, Saravanan, Vijayan, Venkatesh, Rengaraj, Shivkumar, Chandrashekaran, Kalpana, Narendran, Sarangapani, Sripriya, Kanavi, Mozhgan R, Beni, Afsaneh Naderi, Yazdani, Shahin, lashay, Alireza, Naderifar, Homa, Khatibi, Nassim, Fea, Antonio, Lavia, Carlo, Dallorto, Laura, Rolle, Teresa, Frezzotti, Paolo, Paoli, Daniela, Salvi, Erika, Manunta, Paolo, Mori, Yosai, Miyata, Kazunori, Higashide, Tomomi, Chihara, Etsuo, Ishiko, Satoshi, Yoshida, Akitoshi, Yanagi, Masahide, Kiuchi, Yoshiaki, Ohashi, Tsutomu, Sakurai, Toshiya, Sugimoto, Takako, Chuman, Hideki, Aihara, Makoto, Inatani, Masaru, Miyake, Masahiro, Gotoh, Norimoto, Matsuda, Fumihiko, Yoshimura, Nagahisa, Ikeda, Yoko, Ueno, Morio, Sotozono, Chie, Jeoung, Jin Wook, Sagong, Min, Park, Kyu Hyung, Ahn, Jeeyun, Cruz-Aguilar, Marisa, Ezzouhairi, Sidi M, Rafei, Abderrahman, Chong, Yaan Fun, Ng, Xiao Yu, Goh, Shuang Ru, Chen, Yueming, Yong, Victor H K, Khan, Muhammad Imran, Olawoye, Olusola O, Ashaye, Adeyinka O, Ugbede, Idakwo, Onakoya, Adeola, Kizor-Akaraiwe, Nkiru, Teekhasaenee, Chaiwat, Suwan, Yanin, Supakontanasan, Wasu, Okeke, Suhanya, Uche, Nkechi J, Asimadu, Ifeoma, Ayub, Humaira, Akhtar, Farah, Kosior-Jarecka, Ewa, Lukasik, Urszula, Lischinsky, Ignacio, Castro, Vania, Grossmann, Rodolfo Perez, Megevand, Gordana Sunaric, Roy, Sylvain, Dervan, Edward, Silke, Eoin, Rao, Aparna, Sahay, Priti, Fornero, Pablo, Cuello, Osvaldo, Sivori, Delia, Zompa, Tamara, Mills, Richard A, Souzeau, Emmanuelle, Mitchell, Paul, Wang, Jie Jin, Hewitt, Alex W, Coote, Michael, Crowston, Jonathan G, Astakhov, Sergei Y, Akopov, Eugeny L, Emelyanov, Anton, Vysochinskaya, Vera, Kazakbaeva, Gyulli, Fayzrakhmanov, Rinat, Al-Obeidan, Saleh A, Owaidhah, Ohoud, Aljasim, Leyla Ali, Chowbay, Balram, Foo, Jia Nee, Soh, Raphael Q, Sim, Kar Seng, Xie, Zhicheng, Cheong, Augustine W O, Mok, Shi Qi, Soo, Hui Meng, Chen, Xiao Yin, Peh, Su Qin, Heng, Khai Koon, Husain, Rahat, Ho, Su-Ling, Hillmer, Axel M, Cheng, Ching-Yu, Escudero-Domínguez, Francisco A, González-Sarmiento, Rogelio, Martinon-Torres, Frederico, Salas, Antonio, Pathanapitoon, Kessara, Hansapinyo, Linda, Wanichwecharugruang, Boonsong, Kitnarong, Naris, Sakuntabhai, Anavaj, Nguyn, Hip X, Nguyn, Giang T T, Nguyn, Trình V, Zenz, Werner, Binder, Alexander, Klobassa, Daniela S, Hibberd, Martin L, Davila, Sonia, Herms, Stefan, Nöthen, Markus M, Moebus, Susanne, Rautenbach, Robyn M, Ziskind, Ari, Carmichael, Trevor R, Ramsay, Michele, Álvarez, Lydia, García, Montserrat, González-Iglesias, Héctor, Rodríguez-Calvo, Pedro P, Cueto, Luis Fernández-Vega, Oguz, Çilingir, Tamcelik, Nevbahar, Atalay, Eray, Batu, Bilge, Aktas, Dilek, Kasım, Burcu, Wilson, M Roy, Coleman, Anne L, Liu, Yutao, Challa, Pratap, Herndon, Leon, Kuchtey, Rachel W, Kuchtey, John, Curtin, Karen, Chaya, Craig J, Crandall, Alan, Zangwill, Linda M, Wong, Tien Yin, Nakano, Masakazu, Kinoshita, Shigeru, den Hollander, Anneke I, Vesti, Eija, Fingert, John H, Lee, Richard K, Sit, Arthur J, Shingleton, Bradford J, Wang, Ningli, Cusi, Daniele, Qamar, Raheel, Kraft, Peter, Pericak-Vance, Margaret A, Raychaudhuri, Soumya, Heegaard, Steffen, Kivelä, Tero, Reis, André, Kruse, Friedrich E, Weinreb, Robert N, Pasquale, Louis R, Haines, Jonathan L, Thorsteinsdottir, Unnur, Jonasson, Fridbert, Allingham, R Rand, Milea, Dan, Ritch, Robert, Kubota, Toshiaki, Tashiro, Kei, Vithana, Eranga N, Micheal, Shazia, Topouzis, Fotis, Craig, Jamie E, Dubina, Michael, Sundaresan, Periasamy, Stefansson, Kari, Wiggs, Janey L, Pasutto, Francesca, and Khor, Chiea Chuen

Abstract

Exfoliation syndrome (XFS) is the most common known risk factor for secondary glaucoma and a major cause of blindness worldwide. Variants in two genes, LOXL1 and CACNA1A, have previously been associated with XFS. To further elucidate the genetic basis of XFS, we collected a global sample of XFS cases to refine the association at LOXL1, which previously showed inconsistent results across populations, and to identify new variants associated with XFS. We identified a rare protective allele at LOXL1 (p.Phe407, odds ratio (OR) = 25, P = 2.9 × 10−14) through deep resequencing of XFS cases and controls from nine countries. A genome-wide association study (GWAS) of XFS cases and controls from 24 countries followed by replication in 18 countries identified seven genome-wide significant loci (P < 5 × 10−8). We identified association signals at 13q12 (POMP), 11q23.3 (TMEM136), 6p21 (AGPAT1), 3p24 (RBMS3) and 5q23 (near SEMA6A). These findings provide biological insights into the pathology of XFS and highlight a potential role for naturally occurring rare LOXL1 variants in disease biology.

Published
2017
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3. A missense variant in FGD6 confers increased risk of polypoidal choroidal vasculopathy

Author

Huang, Lulin, Zhang, Houbin, Cheng, Ching-Yu, Wen, Feng, Tam, Pancy O S, Zhao, Peiquan, Chen, Haoyu, Li, Zheng, Chen, Lijia, Tai, Zhengfu, Yamashiro, Kenji, Deng, Shaoping, Zhu, Xianjun, Chen, Weiqi, Cai, Li, Lu, Fang, Li, Yuanfeng, Cheung, Chui-Ming G, Shi, Yi, Miyake, Masahiro, Lin, Yin, Gong, Bo, Liu, Xiaoqi, Sim, Kar-Seng, Yang, Jiyun, Mori, Keisuke, Zhang, Xiongzhe, Cackett, Peter D, Tsujikawa, Motokazu, Nishida, Kohji, Hao, Fang, Ma, Shi, Lin, He, Cheng, Jing, Fei, Ping, Lai, Timothy Y Y, Tang, Sibo, Laude, Augustinus, Inoue, Satoshi, Yeo, Ian Y, Sakurada, Yoichi, Zhou, Yu, Iijima, Hiroyuki, Honda, Shigeru, Lei, Chuntao, Zhang, Lin, Zheng, Hong, Jiang, Dan, Zhu, Xiong, Wong, Tien-Ying, Khor, Chiea-Chuen, Pang, Chi-Pui, Yoshimura, Nagahisa, and Yang, Zhenglin

Abstract

Polypoidal choroidal vasculopathy (PCV), a subtype of 'wet' age-related macular degeneration (AMD), constitutes up to 55% of cases of wet AMD in Asian patients. In contrast to the choroidal neovascularization (CNV) subtype, the genetic risk factors for PCV are relatively unknown. Exome sequencing analysis of a Han Chinese cohort followed by replication in four independent cohorts identified a rare c.986A>G (p.Lys329Arg) variant in the FGD6 gene as significantly associated with PCV (P = 2.19 × 10−16, odds ratio (OR) = 2.12) but not with CNV (P = 0.26, OR = 1.13). The intracellular localization of FGD6-Arg329 is distinct from that of FGD6-Lys329. In vitro, FGD6 could regulate proangiogenic activity, and oxidized phospholipids increased expression of FGD6. FGD6-Arg329 promoted more abnormal vessel development in the mouse retina than FGD6-Lys329. Collectively, our data suggest that oxidized phospholipids and FGD6-Arg329 might act synergistically to increase susceptibility to PCV.

Published
2016
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4. Genome-wide association study identifies five new susceptibility loci for primary angle closure glaucoma

Author

Khor, Chiea Chuen, Do, Tan, Jia, Hongyan, Nakano, Masakazu, George, Ronnie, Abu-Amero, Khaled, Duvesh, Roopam, Chen, Li Jia, Li, Zheng, Nongpiur, Monisha E, Perera, Shamira A, Qiao, Chunyan, Wong, Hon-Tym, Sakai, Hiroshi, Barbosa de Melo, Mônica, Lee, Mei-Chin, Chan, Anita S, Azhany, Yaakub, Dao, Thi Lam Huong, Ikeda, Yoko, Perez-Grossmann, Rodolfo A, Zarnowski, Tomasz, Day, Alexander C, Jonas, Jost B, Tam, Pancy O S, Tran, Tuan Anh, Ayub, Humaira, Akhtar, Farah, Micheal, Shazia, Chew, Paul T K, Aljasim, Leyla A, Dada, Tanuj, Luu, Tam Thi, Awadalla, Mona S, Kitnarong, Naris, Wanichwecharungruang, Boonsong, Aung, Yee Yee, Mohamed-Noor, Jelinar, Vijayan, Saravanan, Sarangapani, Sripriya, Husain, Rahat, Jap, Aliza, Baskaran, Mani, Goh, David, Su, Daniel H, Wang, Huaizhou, Yong, Vernon K, Yip, Leonard W, Trinh, Tuyet Bach, Makornwattana, Manchima, Nguyen, Thanh Thu, Leuenberger, Edgar U, Park, Ki-Ho, Wiyogo, Widya Artini, Kumar, Rajesh S, Tello, Celso, Kurimoto, Yasuo, Thapa, Suman S, Pathanapitoon, Kessara, Salmon, John F, Sohn, Yong Ho, Fea, Antonio, Ozaki, Mineo, Lai, Jimmy S M, Tantisevi, Visanee, Khaing, Chaw Chaw, Mizoguchi, Takanori, Nakano, Satoko, Kim, Chan-Yun, Tang, Guangxian, Fan, Sujie, Wu, Renyi, Meng, Hailin, Nguyen, Thi Thuy Giang, Tran, Tien Dat, Ueno, Morio, Martinez, Jose Maria, Ramli, Norlina, Aung, Yin Mon, Reyes, Rigo Daniel, Vernon, Stephen A, Fang, Seng Kheong, Xie, Zhicheng, Chen, Xiao Yin, Foo, Jia Nee, Sim, Kar Seng, Wong, Tina T, Quek, Desmond T, Venkatesh, Rengaraj, Kavitha, Srinivasan, Krishnadas, Subbiah R, Soumittra, Nagaswamy, Shantha, Balekudaru, Lim, Boon-Ang, Ogle, Jeanne, de Vasconcellos, José P C, Costa, Vital P, Abe, Ricardo Y, de Souza, Bruno B, Sng, Chelvin C, Aquino, Maria C, Kosior-Jarecka, Ewa, Fong, Guillermo Barreto, Tamanaja, Vania Castro, Fujita, Ricardo, Jiang, Yuzhen, Waseem, Naushin, Low, Sancy, Pham, Huan Nguyen, Al-Shahwan, Sami, Craven, E Randy, Khan, Muhammad Imran, Dada, Rrima, Mohanty, Kuldeep, Faiq, Muneeb A, Hewitt, Alex W, Burdon, Kathryn P, Gan, Eng Hui, Prutthipongsit, Anuwat, Patthanathamrongkasem, Thipnapa, Catacutan, Mary Ann T, Felarca, Irene R, Liao, Chona S, Rusmayani, Emma, Istiantoro, Vira Wardhana, Consolandi, Giulia, Pignata, Giulia, Lavia, Carlo, Rojanapongpun, Prin, Mangkornkanokpong, Lerprat, Chansangpetch, Sunee, Chan, Jonathan C H, Choy, Bonnie N K, Shum, Jennifer W H, Than, Hlaing May, Oo, Khin Thida, Han, Aye Thi, Yong, Victor H, Ng, Xiao-Yu, Goh, Shuang Ru, Chong, Yaan Fun, Hibberd, Martin L, Seielstad, Mark, Png, Eileen, Dunstan, Sarah J, Chau, Nguyen Van Vinh, Bei, Jinxin, Zeng, Yi Xin, Karkey, Abhilasha, Basnyat, Buddha, Pasutto, Francesca, Paoli, Daniela, Frezzotti, Paolo, Wang, Jie Jin, Mitchell, Paul, Fingert, John H, Allingham, R Rand, Hauser, Michael A, Lim, Soon Thye, Chew, Soo Hong, Ebstein, Richard P, Sakuntabhai, Anavaj, Park, Kyu Hyung, Ahn, Jeeyun, Boland, Greet, Snippe, Harm, Stead, Richard, Quino, Raquel, Zaw, Su Nyunt, Lukasik, Urszula, Shetty, Rohit, Zahari, Mimiwati, Bae, Hyoung Won, Oo, Nay Lin, Kubota, Toshiaki, Manassakorn, Anita, Ho, Wing Lau, Dallorto, Laura, Hwang, Young Hoon, Kiire, Christine A, Kuroda, Masako, Djamal, Zeiras Eka, Peregrino, Jovell Ian M, Ghosh, Arkasubhra, Jeoung, Jin Wook, Hoan, Tung S, Srisamran, Nuttamon, Sandragasu, Thayanithi, Set, Saw Htoo, Doan, Vi Huyen, Bhattacharya, Shomi S, Ho, Ching-Lin, Tan, Donald T, Sihota, Ramanjit, Loon, Seng-Chee, Mori, Kazuhiko, Kinoshita, Shigeru, Hollander, Anneke I den, Qamar, Raheel, Wang, Ya-Xing, Teo, Yik Y, Tai, E-Shyong, Hartleben-Matkin, Curt, Lozano-Giral, David, Saw, Seang Mei, Cheng, Ching-Yu, Zenteno, Juan C, Pang, Chi Pui, Bui, Huong T T, Hee, Owen, Craig, Jamie E, Edward, Deepak P, Yonahara, Michiko, Neto, Jamil Miguel, Guevara-Fujita, Maria L, Xu, Liang, Ritch, Robert, Liza-Sharmini, Ahmad Tajudin, Wong, Tien Y, Al-Obeidan, Saleh, Do, Nhu Hon, Sundaresan, Periasamy, Tham, Clement C, Foster, Paul J, Vijaya, Lingam, Tashiro, Kei, Vithana, Eranga N, Wang, Ningli, and Aung, Tin

Abstract

Primary angle closure glaucoma (PACG) is a major cause of blindness worldwide. We conducted a genome-wide association study (GWAS) followed by replication in a combined total of 10,503 PACG cases and 29,567 controls drawn from 24 countries across Asia, Australia, Europe, North America, and South America. We observed significant evidence of disease association at five new genetic loci upon meta-analysis of all patient collections. These loci are at EPDR1 rs3816415 (odds ratio (OR) = 1.24, P = 5.94 × 10−15), CHAT rs1258267 (OR = 1.22, P = 2.85 × 10−16), GLIS3 rs736893 (OR = 1.18, P = 1.43 × 10−14), FERMT2 rs7494379 (OR = 1.14, P = 3.43 × 10−11), and DPM2–FAM102A rs3739821 (OR = 1.15, P = 8.32 × 10−12). We also confirmed significant association at three previously described loci (P < 5 × 10−8for each sentinel SNP at PLEKHA7, COL11A1, and PCMTD1–ST18), providing new insights into the biology of PACG.

Published
2016
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