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51. De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders.

Author

Guo, Yicheng, Qi, Hongjian, Zhou, Xueya, Zhu, Na, Zhao, Haoquan, Kitaygorodsky, Alexander, Shen, Yufeng, Warner, Brad W., Mychaliska, George B., Potoka, Douglas, Wagner, Amy J., ElFiky, Mahmoud, Wilson, Jay M., High, Frances A., Longoni, Mauro, Donahoe, Patricia K., Nickerson, Debbie, Bamshad, Michael, Yu, Lan, and Wynn, Julia

Subjects
CONGENITAL disorders, DIAPHRAGMATIC hernia, PHENOTYPES, MYELIN regulatory factor, TRANSCRIPTOMES, FIBROBLASTS
Abstract

Congenital diaphragmatic hernia (CDH) is a severe birth defect that is often accompanied by other congenital anomalies. Previous exome sequencing studies for CDH have supported a role of de novo damaging variants but did not identify any recurrently mutated genes. To investigate further the genetics of CDH, we analyzed de novo coding variants in 362 proband-parent trios including 271 new trios reported in this study. We identified four unrelated individuals with damaging de novo variants in MYRF (P = 5.3x10-8), including one likely gene-disrupting (LGD) and three deleterious missense (D-mis) variants. Eight additional individuals with de novo LGD or missense variants were identified from our other genetic studies or from the literature. Common phenotypes of MYRF de novo variant carriers include CDH, congenital heart disease and genitourinary abnormalities, suggesting that it represents a novel syndrome. MYRF is a membrane associated transcriptional factor highly expressed in developing diaphragm and is depleted of LGD variants in the general population. All de novo missense variants aggregated in two functional protein domains. Analyzing the transcriptome of patient-derived diaphragm fibroblast cells suggest that disease associated variants abolish the transcription factor activity. Furthermore, we showed that the remaining genes with damaging variants in CDH significantly overlap with genes implicated in other developmental disorders. Gene expression patterns and patient phenotypes support pleiotropic effects of damaging variants in these genes on CDH and other developmental disorders. Finally, functional enrichment analysis implicates the disruption of regulation of gene expression, kinase activities, intra-cellular signaling, and cytoskeleton organization as pathogenic mechanisms in CDH. [ABSTRACT FROM AUTHOR]

Published
2018
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52. Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation

Author

Kato, Norihiro, Loh, Marie, Takeuchi, Fumihiko, Verweij, Niek, Wang, Xu, Zhang, Weihua, Kelly, Tanika N., Saleheen, Danish, Lehne, Benjamin, Leach, Irene Mateo, Drong, Alexander W., Abbott, James, Wahl, Simone, Tan, Sian-Tsung, Scott, William R., Campanella, Gianluca, Chadeau-Hyam, Marc, Afzal, Uzma, Ahluwalia, Tarunveer S., Bonder, Marc Jan, Chen, Peng, Dehghan, Abbas, Edwards, Todd L., Esko, Tonu, Go, Min Jin, Harris, Sarah E., Hartiala, Jaana, Kasela, Silva, Kasturiratne, Anuradhani, Khor, Chiea-Chuen, Kleber, Marcus E., Li, Huaixing, Mok, Zuan Yu, Nakatochi, Masahiro, Sapari, Nur Sabrina, Saxena, Richa, Stewart, Alexandre F. R., Stolk, Lisette, Tabara, Yasuharu, Teh, Ai Ling, Wu, Ying, Wu, Jer-Yuarn, Zhang, Yi, Aits, Imke, Alves, Alexessander Da Silva Couto, Das, Shikta, Dorajoo, Rajkumar, Hopewell, Jemma C., Kim, Yun Kyoung, Koivula, Robert W., Luan, Jian'an, Lyytikainen, Leo-Pekka, Nguyen, Quang N., Pereira, Mark A., Postmus, Iris, Raitakari, Olli T., Bryan, Molly Scannell, Scott, Robert A., Sorice, Rossella, Tragante, Vinicius, Traglia, Michela, White, Jon, Yamamoto, Ken, Zhang, Yonghong, Adair, Linda S., Ahmed, Alauddin, Akiyama, Koichi, Asif, Rasheed, Aung, Tin, Barroso, Ines, Bjonnes, Andrew, Braun, Timothy R., Cai, Hui, Chang, Li-Ching, Chen, Chien-Hsiun, Cheng, Ching-Yu, Chong, Yap-Seng, Collins, Rory, Courtney, Regina, Davies, Gail, Delgado, Graciela, Do, Loi D., Doevendans, Pieter A., Gansevoort, Ron T., Gao, Yu-Tang, Grammer, Tanja B., Grarup, Niels, Grewal, Jagvir, Gu, Dongfeng, Wander, Gurpreet S., Hartikainen, Anna-Liisa, Hazen, Stanley L., He, Jing, Heng, Chew-Kiat, Hixson, James E., Hofman, Albert, Hsu, Chris, Huang, Wei, Husemoen, Lise L. N., Hwang, Joo-Yeon, Ichihara, Sahoko, Igase, Michiya, Isono, Masato, Justesen, Johanne M., Katsuy, Tomohiro, Kibriya, Muhammad G., Kim, Young Jin, Kishimoto, Miyako, Koh, Woon-Puay, Kohara, Katsuhiko, Kumari, Meena, Kwek, Kenneth, Lee, Nanette R., Lee, Jeannette, Liao, Jiemin, Lieb, Wolfgang, Liewald, David C. M., Matsubara, Tatsuaki, Matsushita, Yumi, Meitinger, Thomas, Mihailov, Evelin, Milani, Lili, Mills, Rebecca, Mononen, Nina, Mueller-Nurasyid, Martina, Nabika, Toru, Nakashima, Eitaro, Ng, Hong Kiat, Nikus, Kjell, Nutile, Teresa, Ohkubo, Takayoshi, Ohnaka, Keizo, Parish, Sarah, Paternoster, Lavinia, Peng, Hao, Peters, Annette, Pham, Son T., Pinidiyapathirage, Mohitha J., Rahman, Mahfuzar, Rakugi, Hiromi, Rolandsson, Olov, Rozario, Michelle Ann, Ruggiero, Daniela, Sala, Cinzia F., Sarju, Ralhan, Shimokawa, Kazuro, Snieder, Harold, Sparso, Thomas, Spiering, Wilko, Starr, John M., Stott, David J., Stram, Daniel O., Sugiyama, Takao, Szymczak, Silke, Tang, W. H. Wilson, Tong, Lin, Trompet, Stella, Turjanmaa, Vaino, Ueshima, Hirotsugu, Uitterlinden, Andre G., Umemura, Satoshi, Vaarasmaki, Marja, van Dam, Rob M., van Gilst, Wiek H., van Veldhuisen, Dirk J., Viikari, Jorma S., Waldenberger, Melanie, Wang, Yiqin, Wang, Aili, Wilson, Rory, Wong, Tien-Yin, Xiang, Yong-Bing, Yamaguchi, Shuhei, Ye, Xingwang, Young, Robin D., Young, Terri L., Yuan, Jian-Min, Zhou, Xueya, Asselbergs, Folkert W., Ciullo, Marina, Clarke, Robert, Deloukas, Panos, Franke, Andre, Franks, Paul W, Franks, Steve, Friedlander, Yechiel, Gross, Myron D., Guo, Zhirong, Hansen, Torben, Jarvelin, Marjo-Riitta, Jorgensen, Torben, Jukema, J. Wouter, Kahonen, Mika, Kajio, Hiroshi, Kivimaki, Mika, Lee, Jong-Young, Lehtimaki, Terho, Linneberg, Allan, Miki, Tetsuro, Pedersen, Oluf, Samani, Nilesh J., Sorensen, Thorkild I. A., Takayanagi, Ryoichi, Toniolo, Daniela, Ahsan, Habibul, Allayee, Hooman, Chen, Yuan-Tsong, Danesh, John, Deary, Ian J., Franco, Oscar H., Franke, Lude, Heijman, Bastiaan T., Holbrook, Joanna D., Isaacs, Aaron, Kim, Bong-Jo, Lin, Xu, Liu, Jianjun, Maerz, Winfried, Metspalu, Andres, Mohlke, Karen L., Sanghera, Dharambir K., Shu, Xiao-Ou, van Meurs, Joyce B. J., Vithana, Eranga, Wickremasinghe, Ananda R., Wijmenga, Cisca, Wolffenbuttel, Bruce H. W., Yokota, Mitsuhiro, Zheng, Wei, Zhu, Dingliang, Vineis, Paolo, Kyrtopoulos, Soterios A., Kleinjans, Jos C. S., McCarthy, Mark I., Soong, Richie, Gieger, Christian, Scott, James, Teo, Yik-Ying, He, Jiang, Elliott, Paul, Tai, E. Shyong, van der Harst, Pim, Kooner, Jaspal S., Chambers, John C., Kato, Norihiro, Loh, Marie, Takeuchi, Fumihiko, Verweij, Niek, Wang, Xu, Zhang, Weihua, Kelly, Tanika N., Saleheen, Danish, Lehne, Benjamin, Leach, Irene Mateo, Drong, Alexander W., Abbott, James, Wahl, Simone, Tan, Sian-Tsung, Scott, William R., Campanella, Gianluca, Chadeau-Hyam, Marc, Afzal, Uzma, Ahluwalia, Tarunveer S., Bonder, Marc Jan, Chen, Peng, Dehghan, Abbas, Edwards, Todd L., Esko, Tonu, Go, Min Jin, Harris, Sarah E., Hartiala, Jaana, Kasela, Silva, Kasturiratne, Anuradhani, Khor, Chiea-Chuen, Kleber, Marcus E., Li, Huaixing, Mok, Zuan Yu, Nakatochi, Masahiro, Sapari, Nur Sabrina, Saxena, Richa, Stewart, Alexandre F. R., Stolk, Lisette, Tabara, Yasuharu, Teh, Ai Ling, Wu, Ying, Wu, Jer-Yuarn, Zhang, Yi, Aits, Imke, Alves, Alexessander Da Silva Couto, Das, Shikta, Dorajoo, Rajkumar, Hopewell, Jemma C., Kim, Yun Kyoung, Koivula, Robert W., Luan, Jian'an, Lyytikainen, Leo-Pekka, Nguyen, Quang N., Pereira, Mark A., Postmus, Iris, Raitakari, Olli T., Bryan, Molly Scannell, Scott, Robert A., Sorice, Rossella, Tragante, Vinicius, Traglia, Michela, White, Jon, Yamamoto, Ken, Zhang, Yonghong, Adair, Linda S., Ahmed, Alauddin, Akiyama, Koichi, Asif, Rasheed, Aung, Tin, Barroso, Ines, Bjonnes, Andrew, Braun, Timothy R., Cai, Hui, Chang, Li-Ching, Chen, Chien-Hsiun, Cheng, Ching-Yu, Chong, Yap-Seng, Collins, Rory, Courtney, Regina, Davies, Gail, Delgado, Graciela, Do, Loi D., Doevendans, Pieter A., Gansevoort, Ron T., Gao, Yu-Tang, Grammer, Tanja B., Grarup, Niels, Grewal, Jagvir, Gu, Dongfeng, Wander, Gurpreet S., Hartikainen, Anna-Liisa, Hazen, Stanley L., He, Jing, Heng, Chew-Kiat, Hixson, James E., Hofman, Albert, Hsu, Chris, Huang, Wei, Husemoen, Lise L. N., Hwang, Joo-Yeon, Ichihara, Sahoko, Igase, Michiya, Isono, Masato, Justesen, Johanne M., Katsuy, Tomohiro, Kibriya, Muhammad G., Kim, Young Jin, Kishimoto, Miyako, Koh, Woon-Puay, Kohara, Katsuhiko, Kumari, Meena, Kwek, Kenneth, Lee, Nanette R., Lee, Jeannette, Liao, Jiemin, Lieb, Wolfgang, Liewald, David C. M., Matsubara, Tatsuaki, Matsushita, Yumi, Meitinger, Thomas, Mihailov, Evelin, Milani, Lili, Mills, Rebecca, Mononen, Nina, Mueller-Nurasyid, Martina, Nabika, Toru, Nakashima, Eitaro, Ng, Hong Kiat, Nikus, Kjell, Nutile, Teresa, Ohkubo, Takayoshi, Ohnaka, Keizo, Parish, Sarah, Paternoster, Lavinia, Peng, Hao, Peters, Annette, Pham, Son T., Pinidiyapathirage, Mohitha J., Rahman, Mahfuzar, Rakugi, Hiromi, Rolandsson, Olov, Rozario, Michelle Ann, Ruggiero, Daniela, Sala, Cinzia F., Sarju, Ralhan, Shimokawa, Kazuro, Snieder, Harold, Sparso, Thomas, Spiering, Wilko, Starr, John M., Stott, David J., Stram, Daniel O., Sugiyama, Takao, Szymczak, Silke, Tang, W. H. Wilson, Tong, Lin, Trompet, Stella, Turjanmaa, Vaino, Ueshima, Hirotsugu, Uitterlinden, Andre G., Umemura, Satoshi, Vaarasmaki, Marja, van Dam, Rob M., van Gilst, Wiek H., van Veldhuisen, Dirk J., Viikari, Jorma S., Waldenberger, Melanie, Wang, Yiqin, Wang, Aili, Wilson, Rory, Wong, Tien-Yin, Xiang, Yong-Bing, Yamaguchi, Shuhei, Ye, Xingwang, Young, Robin D., Young, Terri L., Yuan, Jian-Min, Zhou, Xueya, Asselbergs, Folkert W., Ciullo, Marina, Clarke, Robert, Deloukas, Panos, Franke, Andre, Franks, Paul W, Franks, Steve, Friedlander, Yechiel, Gross, Myron D., Guo, Zhirong, Hansen, Torben, Jarvelin, Marjo-Riitta, Jorgensen, Torben, Jukema, J. Wouter, Kahonen, Mika, Kajio, Hiroshi, Kivimaki, Mika, Lee, Jong-Young, Lehtimaki, Terho, Linneberg, Allan, Miki, Tetsuro, Pedersen, Oluf, Samani, Nilesh J., Sorensen, Thorkild I. A., Takayanagi, Ryoichi, Toniolo, Daniela, Ahsan, Habibul, Allayee, Hooman, Chen, Yuan-Tsong, Danesh, John, Deary, Ian J., Franco, Oscar H., Franke, Lude, Heijman, Bastiaan T., Holbrook, Joanna D., Isaacs, Aaron, Kim, Bong-Jo, Lin, Xu, Liu, Jianjun, Maerz, Winfried, Metspalu, Andres, Mohlke, Karen L., Sanghera, Dharambir K., Shu, Xiao-Ou, van Meurs, Joyce B. J., Vithana, Eranga, Wickremasinghe, Ananda R., Wijmenga, Cisca, Wolffenbuttel, Bruce H. W., Yokota, Mitsuhiro, Zheng, Wei, Zhu, Dingliang, Vineis, Paolo, Kyrtopoulos, Soterios A., Kleinjans, Jos C. S., McCarthy, Mark I., Soong, Richie, Gieger, Christian, Scott, James, Teo, Yik-Ying, He, Jiang, Elliott, Paul, Tai, E. Shyong, van der Harst, Pim, Kooner, Jaspal S., and Chambers, John C.

Abstract

We carried out a trans-ancestry genome-wide association and replication study of blood pressure phenotypes among up to 320,251 individuals of East Asian, European and South Asian ancestry. We find genetic variants at 12 new loci to be associated with blood pressure (P = 3.9 × 10−11 to 5.0 × 10−21). The sentinel blood pressure SNPs are enriched for association with DNA methylation at multiple nearby CpG sites, suggesting that, at some of the loci identified, DNA methylation may lie on the regulatory pathway linking sequence variation to blood pressure. The sentinel SNPs at the 12 new loci point to genes involved in vascular smooth muscle (IGFBP3, KCNK3, PDE3A and PRDM6) and renal (ARHGAP24, OSR1, SLC22A7 and TBX2) function. The new and known genetic variants predict increased left ventricular mass, circulating levels of NT-proBNP, and cardiovascular and all-cause mortality (P = 0.04 to 8.6 × 10−6). Our results provide new evidence for the role of DNA methylation in blood pressure regulation.

Published
2015
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53. 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

54. Resolving the genetic heterogeneity of prelingual hearing loss within one family: Performance comparison and application of two targeted next generation sequencing approaches

Author

Lu, Yu, primary, Zhou, Xueya, additional, Jin, Zhanguo, additional, Cheng, Jing, additional, Shen, Weidong, additional, Ji, Fei, additional, Liu, Liyang, additional, Zhang, Xuegong, additional, Zhang, Michael, additional, Cao, Ye, additional, Han, Dongyi, additional, Choy, KwongWai, additional, and Yuan, Huijun, additional

Published
2014
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55. Exome Sequencing Identifies a Novel Frameshift Mutation ofMYO6as the Cause of Autosomal Dominant Nonsyndromic Hearing Loss in a Chinese Family

Author

Cheng, Jing, primary, Zhou, Xueya, additional, Lu, Yu, additional, Chen, Jing, additional, Han, Bing, additional, Zhu, Yuhua, additional, Liu, Liyang, additional, Choy, Kwong-Wai, additional, Han, Dongyi, additional, Sham, Pak C., additional, Zhang, Michael Q., additional, Zhang, Xuegong, additional, and Yuan, Huijun, additional

Published
2014
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57. Genome-wide Association Analysis of Blood-Pressure Traits in African-Ancestry Individuals Reveals Common Associated Genes in African and Non-African Populations

Author

Franceschini, Nora, primary, Fox, Ervin, additional, Zhang, Zhaogong, additional, Edwards, Todd L., additional, Nalls, Michael A., additional, Sung, Yun Ju, additional, Tayo, Bamidele O., additional, Sun, Yan V., additional, Gottesman, Omri, additional, Adeyemo, Adebawole, additional, Johnson, Andrew D., additional, Young, J. Hunter, additional, Rice, Ken, additional, Duan, Qing, additional, Chen, Fang, additional, Li, Yun, additional, Tang, Hua, additional, Fornage, Myriam, additional, Keene, Keith L., additional, Andrews, Jeanette S., additional, Smith, Jennifer A., additional, Faul, Jessica D., additional, Guangfa, Zhang, additional, Guo, Wei, additional, Liu, Yu, additional, Murray, Sarah S., additional, Musani, Solomon K., additional, Srinivasan, Sathanur, additional, Velez Edwards, Digna R., additional, Wang, Heming, additional, Becker, Lewis C., additional, Bovet, Pascal, additional, Bochud, Murielle, additional, Broeckel, Ulrich, additional, Burnier, Michel, additional, Carty, Cara, additional, Chasman, Daniel I., additional, Ehret, Georg, additional, Chen, Wei-Min, additional, Chen, Guanjie, additional, Chen, Wei, additional, Ding, Jingzhong, additional, Dreisbach, Albert W., additional, Evans, Michele K., additional, Guo, Xiuqing, additional, Garcia, Melissa E., additional, Jensen, Rich, additional, Keller, Margaux F., additional, Lettre, Guillaume, additional, Lotay, Vaneet, additional, Martin, Lisa W., additional, Moore, Jason H., additional, Morrison, Alanna C., additional, Mosley, Thomas H., additional, Ogunniyi, Adesola, additional, Palmas, Walter, additional, Papanicolaou, George, additional, Penman, Alan, additional, Polak, Joseph F., additional, Ridker, Paul M., additional, Salako, Babatunde, additional, Singleton, Andrew B., additional, Shriner, Daniel, additional, Taylor, Kent D., additional, Vasan, Ramachandran, additional, Wiggins, Kerri, additional, Williams, Scott M., additional, Yanek, Lisa R., additional, Zhao, Wei, additional, Zonderman, Alan B., additional, Becker, Diane M., additional, Berenson, Gerald, additional, Boerwinkle, Eric, additional, Bottinger, Erwin, additional, Cushman, Mary, additional, Eaton, Charles, additional, Nyberg, Fredrik, additional, Heiss, Gerardo, additional, Hirschhron, Joel N., additional, Howard, Virginia J., additional, Karczewsk, Konrad J., additional, Lanktree, Matthew B., additional, Liu, Kiang, additional, Liu, Yongmei, additional, Loos, Ruth, additional, Margolis, Karen, additional, Snyder, Michael, additional, Psaty, Bruce M., additional, Schork, Nicholas J., additional, Weir, David R., additional, Rotimi, Charles N., additional, Sale, Michele M., additional, Harris, Tamara, additional, Kardia, Sharon L.R., additional, Hunt, Steven C., additional, Arnett, Donna, additional, Redline, Susan, additional, Cooper, Richard S., additional, Risch, Neil J., additional, Rao, D.C., additional, Rotter, Jerome I., additional, Chakravarti, Aravinda, additional, Reiner, Alex P., additional, Levy, Daniel, additional, Keating, Brendan J., additional, Zhu, Xiaofeng, additional, Go, Min Jin, additional, Kim, Young Jin, additional, Lee, Jong-Young, additional, Jeon, Jae-Pil, additional, Kim, Sung Soo, additional, Han, Bok-Ghee, additional, Cho, Yoon Shin, additional, Sim, Xueling, additional, Tay, Wan Ting, additional, Ong, Rick Twee Hee, additional, Seielstad, Mark, additional, Liu, Jian Jun, additional, Aung, Tin, additional, Wong, Tien Yin, additional, Teo, Yik Ying, additional, Tai, E. Shyong, additional, Chen, Chien-Hsiun, additional, Chang, Li-ching, additional, Chen, Yuan-Tsong, additional, Wu, Jer-Yuarn, additional, Kelly, Tanika N., additional, Gu, Dongfeng, additional, Hixson, James E., additional, He, Jiang, additional, Tabara, Yasuharu, additional, Kokubo, Yoshihiro, additional, Miki, Tetsuro, additional, Iwai, Naoharu, additional, Kato, Norihiro, additional, Takeuchi, Fumihiko, additional, Katsuya, Tomohiro, additional, Nabika, Toru, additional, Sugiyama, Takao, additional, Zhang, Yi, additional, Huang, Wei, additional, Zhang, Xuegong, additional, Zhou, Xueya, additional, Jin, Li, additional, and Zhu, Dingliang, additional

Published
2013
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60. Meta-analysis of genome-wide association studies identifies common variants associated with blood pressure variation in east Asians

Author

Kato, Norihiro, primary, Takeuchi, Fumihiko, additional, Tabara, Yasuharu, additional, Kelly, Tanika N, additional, Go, Min Jin, additional, Sim, Xueling, additional, Tay, Wan Ting, additional, Chen, Chien-Hsiun, additional, Zhang, Yi, additional, Yamamoto, Ken, additional, Katsuya, Tomohiro, additional, Yokota, Mitsuhiro, additional, Kim, Young Jin, additional, Ong, Rick Twee Hee, additional, Nabika, Toru, additional, Gu, Dongfeng, additional, Chang, Li-ching, additional, Kokubo, Yoshihiro, additional, Huang, Wei, additional, Ohnaka, Keizo, additional, Yamori, Yukio, additional, Nakashima, Eitaro, additional, Jaquish, Cashell E, additional, Lee, Jong-Young, additional, Seielstad, Mark, additional, Isono, Masato, additional, Hixson, James E, additional, Chen, Yuan-Tsong, additional, Miki, Tetsuro, additional, Zhou, Xueya, additional, Sugiyama, Takao, additional, Jeon, Jae-Pil, additional, Liu, Jian Jun, additional, Takayanagi, Ryoichi, additional, Kim, Sung Soo, additional, Aung, Tin, additional, Sung, Yun Ju, additional, Zhang, Xuegong, additional, Wong, Tien Yin, additional, Han, Bok-Ghee, additional, Kobayashi, Shotai, additional, Ogihara, Toshio, additional, Zhu, Dingliang, additional, Iwai, Naoharu, additional, Wu, Jer-Yuarn, additional, Teo, Yik Ying, additional, Tai, E Shyong, additional, Cho, Yoon Shin, additional, and He, Jiang, additional

Published
2011
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62. A Rare Variant at the KYNUGene Is Associated With Kynureninase Activity and Essential Hypertension in the Han Chinese Population

Author

Zhang, Yi, Shen, Jie, He, Xin, Zhang, Kuixing, Wu, Shengnan, Xiao, Bing, Zhou, Xueya, Phillips, Robert S., Gao, Pingjin, Jeunemaitre, Xavier, and Zhu, Dingliang

Abstract

Genetic studies in mouse and human suggest that kynureninase activity may influence blood pressure and renal function. The gene coding kynureninase (KYNU) is also located on chromosome band 2q14-q23, where a linkage peak for essential hypertension was previously detected in the Chinese Han population.

Published
2011
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63. Correction to: Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH.

Author

Zhu, Na, Swietlik, Emilia M., Welch, Carrie L., Pauciulo, Michael W., Hagen, Jacob J., Zhou, Xueya, Guo, Yicheng, Karten, Johannes, Pandya, Divya, Tilly, Tobias, Lutz, Katie A., Martin, Jennifer M., Treacy, Carmen M., Rosenzweig, Erika B., Krishnan, Usha, Coleman, Anna W., Gonzaga-Jauregui, Claudia, Lawrie, Allan, Trembath, Richard C., and Wilkins, Martin R.

Subjects
PULMONARY hypertension, PROSTACYCLIN
Abstract

Na Zhu, Emilia M. Swietlik, Carrie L. Welch, Michael W. Pauciulo contributed equally to this work. Reference 1 Zhu N. Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH. [Extracted from the article]

Published
2021
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64. De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders

Author

Qi, Hongjian, Yu, Lan, Zhou, Xueya, Wynn, Julia, Zhao, Haoquan, Guo, Yicheng, Zhu, Na, Kitaygorodsky, Alexander, Hernan, Rebecca Rose, Aspelund, Gudrun, Lim, Foong-Yen, Crombleholme, Timothy, Cusick, Robert, Azarow, Kenneth, Danko, Melissa E., Chung, Dai, Warner, Brad W., Mychaliska, George B., Potoka, Douglas, Wagner, Amy J., ElFiky, Mahmoud, Wilson, Jay M., Nickerson, Debbie, Bamshad, Michael, High, Frances A., Longoni, Mauro, Donahoe, Patricia K., Chung, Wendy K., and Shen, Yufeng

Subjects
Diaphragmatic hernia, Myelin genes--Expression, Genetic disorders, 3. Good health
Abstract

Congenital diaphragmatic hernia (CDH) is a severe birth defect that is often accompanied by other congenital anomalies. Previous exome sequencing studies for CDH have supported a role of de novo damaging variants but did not identify any recurrently mutated genes. To investigate further the genetics of CDH, we analyzed de novo coding variants in 362 proband-parent trios including 271 new trios reported in this study. We identified four unrelated individuals with damaging de novo variants in MYRF (P = 5.3x10-8), including one likely gene-disrupting (LGD) and three deleterious missense (D-mis) variants. Eight additional individuals with de novo LGD or missense variants were identified from our other genetic studies or from the literature. Common phenotypes of MYRF de novo variant carriers include CDH, congenital heart disease and genitourinary abnormalities, suggesting that it represents a novel syndrome. MYRF is a membrane associated transcriptional factor highly expressed in developing diaphragm and is depleted of LGD variants in the general population. All de novo missense variants aggregated in two functional protein domains. Analyzing the transcriptome of patient-derived diaphragm fibroblast cells suggest that disease associated variants abolish the transcription factor activity. Furthermore, we showed that the remaining genes with damaging variants in CDH significantly overlap with genes implicated in other developmental disorders. Gene expression patterns and patient phenotypes support pleiotropic effects of damaging variants in these genes on CDH and other developmental disorders. Finally, functional enrichment analysis implicates the disruption of regulation of gene expression, kinase activities, intra-cellular signaling, and cytoskeleton organization as pathogenic mechanisms in CDH.

65. A dominant negative mutation at the ATP binding domain of AMHR2 is associated with a defective anti-Müllerian hormone signaling pathway.

Author

Li L, Zhou X, Wang X, Wang J, Zhang W, Wang B, Cao Y, and Kee K

Subjects
Anti-Mullerian Hormone genetics, Blotting, Western, Cell Line, Exome genetics, Female, Humans, Primary Ovarian Insufficiency genetics, Primary Ovarian Insufficiency metabolism, Protein Binding, Protein Domains, Receptors, Peptide genetics, Receptors, Peptide metabolism, Signal Transduction genetics, Signal Transduction physiology, Anti-Mullerian Hormone metabolism, Mutation genetics, Receptors, Transforming Growth Factor beta genetics, Receptors, Transforming Growth Factor beta metabolism
Abstract

Study Question: Does a heterozygous mutation in AMHR2, identified in whole-exome sequencings (WES) of patients with primary ovarian insufficiency (POI), cause a defect in anti-Müllerian hormone (AMH) signaling?, Summary Answer: The I209N mutation at the adenosine triphosphate binding domain of AMHR2 exerts dominant negative defects in the AMH signaling pathway., What Is Known Already: Previous studies have demonstrated the associations of several sequence variants in AMH or AMHR2 with POI, but no functional assay has been performed to verify whether there was any defect on AMH signaling., Study Design, Samples/materials, Methods: Ninety-six unrelated female Chinese Han patients were diagnosed with idiopathic POI and subjected to WES. In silico analysis was done for the sequence variants followed by molecular assays to examine the functional effects of the sequence variants in human granulosa cells. In silico analysis, immunostaining, Western analysis, genome-wide expression analysis, quantitatively polymerase chain reaction were applied to the characterization of the sequence variants., Main Results and the Role of Chance: We identified one novel heterozygous missense variant, p.Ala17Glu (A17E), in AMHR2. Subsequently, A17E and two independently reported missense variants, p.Ile209Asn (I209N) and p.Leu354Phe (L354F), were evaluated for effects on the AMH signaling pathway. In silico analysis predicted that all three variants may be deleterious. However, only one variant, I209N, showed severe defects in transducing the AMH signal as well as impaired SMAD1/5/8 phosphorylation. Furthermore, using genome-wide gene expression analysis, we identified genes whose expression was affected by the mutation, these included genes previously reported to participate in AMH signaling as well as newly identified genes. They are EMILIN2, FAM155A, GATA2, HES5, ID1, ID2, RLTPR, SMAD7, CBL, MALAT1 and SMARCA2., Large Scale Data: None., Limitations, Reasons for Caution: Although the in vitro assays demonstrated the causative effect of I209N on AMH signaling, further studies need to validate its long-term effects on folliculogenesis and POI., Wider Implications of the Findings: These results will aid both researchers and clinicians in understanding the molecular pathology of AMH signaling and POI to develop diagnostic assays or therapeutics approaches., Study Funding and Competing Interests: Research funding is provided by the Ministry of Science and Technology of China [2012CB944704; 2012CB966702], and the National Natural Science Foundation of China [Grant number: 31171429]. The authors declare no conflict of interest., (© The Author 2016. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Published
2016
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66. Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation.

Author

Kato N, Loh M, Takeuchi F, Verweij N, Wang X, Zhang W, Kelly TN, Saleheen D, Lehne B, Leach IM, Drong AW, Abbott J, Wahl S, Tan ST, Scott WR, Campanella G, Chadeau-Hyam M, Afzal U, Ahluwalia TS, Bonder MJ, Chen P, Dehghan A, Edwards TL, Esko T, Go MJ, Harris SE, Hartiala J, Kasela S, Kasturiratne A, Khor CC, Kleber ME, Li H, Yu Mok Z, Nakatochi M, Sapari NS, Saxena R, Stewart AFR, Stolk L, Tabara Y, Teh AL, Wu Y, Wu JY, Zhang Y, Aits I, Da Silva Couto Alves A, Das S, Dorajoo R, Hopewell JC, Kim YK, Koivula RW, Luan J, Lyytikäinen LP, Nguyen QN, Pereira MA, Postmus I, Raitakari OT, Scannell Bryan M, Scott RA, Sorice R, Tragante V, Traglia M, White J, Yamamoto K, Zhang Y, Adair LS, Ahmed A, Akiyama K, Asif R, Aung T, Barroso I, Bjonnes A, Braun TR, Cai H, Chang LC, Chen CH, Cheng CY, Chong YS, Collins R, Courtney R, Davies G, Delgado G, Do LD, Doevendans PA, Gansevoort RT, Gao YT, Grammer TB, Grarup N, Grewal J, Gu D, Wander GS, Hartikainen AL, Hazen SL, He J, Heng CK, Hixson JE, Hofman A, Hsu C, Huang W, Husemoen LLN, Hwang JY, Ichihara S, Igase M, Isono M, Justesen JM, Katsuya T, Kibriya MG, Kim YJ, Kishimoto M, Koh WP, Kohara K, Kumari M, Kwek K, Lee NR, Lee J, Liao J, Lieb W, Liewald DCM, Matsubara T, Matsushita Y, Meitinger T, Mihailov E, Milani L, Mills R, Mononen N, Müller-Nurasyid M, Nabika T, Nakashima E, Ng HK, Nikus K, Nutile T, Ohkubo T, Ohnaka K, Parish S, Paternoster L, Peng H, Peters A, Pham ST, Pinidiyapathirage MJ, Rahman M, Rakugi H, Rolandsson O, Ann Rozario M, Ruggiero D, Sala CF, Sarju R, Shimokawa K, Snieder H, Sparsø T, Spiering W, Starr JM, Stott DJ, Stram DO, Sugiyama T, Szymczak S, Tang WHW, Tong L, Trompet S, Turjanmaa V, Ueshima H, Uitterlinden AG, Umemura S, Vaarasmaki M, van Dam RM, van Gilst WH, van Veldhuisen DJ, Viikari JS, Waldenberger M, Wang Y, Wang A, Wilson R, Wong TY, Xiang YB, Yamaguchi S, Ye X, Young RD, Young TL, Yuan JM, Zhou X, Asselbergs FW, Ciullo M, Clarke R, Deloukas P, Franke A, Franks PW, Franks S, Friedlander Y, Gross MD, Guo Z, Hansen T, Jarvelin MR, Jørgensen T, Jukema JW, Kähönen M, Kajio H, Kivimaki M, Lee JY, Lehtimäki T, Linneberg A, Miki T, Pedersen O, Samani NJ, Sørensen TIA, Takayanagi R, Toniolo D, Ahsan H, Allayee H, Chen YT, Danesh J, Deary IJ, Franco OH, Franke L, Heijman BT, Holbrook JD, Isaacs A, Kim BJ, Lin X, Liu J, März W, Metspalu A, Mohlke KL, Sanghera DK, Shu XO, van Meurs JBJ, Vithana E, Wickremasinghe AR, Wijmenga C, Wolffenbuttel BHW, Yokota M, Zheng W, Zhu D, Vineis P, Kyrtopoulos SA, Kleinjans JCS, McCarthy MI, Soong R, Gieger C, Scott J, Teo YY, He J, Elliott P, Tai ES, van der Harst P, Kooner JS, and Chambers JC

Subjects
Adult, Aged, Aged, 80 and over, Asian People genetics, Cardiovascular Diseases blood, Cardiovascular Diseases ethnology, Cardiovascular Diseases genetics, Female, Genetic Predisposition to Disease ethnology, Genetic Predisposition to Disease genetics, Genetic Variation, Genotype, Humans, Male, Middle Aged, Natriuretic Peptide, Brain blood, Peptide Fragments blood, Polymorphism, Single Nucleotide, Regression Analysis, Risk Factors, White People genetics, Blood Pressure genetics, DNA Methylation, Genetic Loci genetics, Genome-Wide Association Study methods
Abstract

We carried out a trans-ancestry genome-wide association and replication study of blood pressure phenotypes among up to 320,251 individuals of East Asian, European and South Asian ancestry. We find genetic variants at 12 new loci to be associated with blood pressure (P = 3.9 × 10(-11) to 5.0 × 10(-21)). The sentinel blood pressure SNPs are enriched for association with DNA methylation at multiple nearby CpG sites, suggesting that, at some of the loci identified, DNA methylation may lie on the regulatory pathway linking sequence variation to blood pressure. The sentinel SNPs at the 12 new loci point to genes involved in vascular smooth muscle (IGFBP3, KCNK3, PDE3A and PRDM6) and renal (ARHGAP24, OSR1, SLC22A7 and TBX2) function. The new and known genetic variants predict increased left ventricular mass, circulating levels of NT-proBNP, and cardiovascular and all-cause mortality (P = 0.04 to 8.6 × 10(-6)). Our results provide new evidence for the role of DNA methylation in blood pressure regulation.

Published
2015
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67. Short read mapping for exome sequencing.

Author

Zhou X, Bao S, Wang B, Zhang X, and Song YQ

Subjects
Animals, Humans, Sequence Alignment methods, Software, Exome, High-Throughput Nucleotide Sequencing methods
Abstract

Mapping short reads to the reference genome is very often the prerequisite for applications utilizing the next-generation sequencing technologies. A dozen of software tools developed for this purpose have been widely used. But many practical issues remained when utilizing them to build a computational pipeline for downstream analyses. In this chapter, we describe the read mapping procedures adopted in our lab for the exome sequencing studies as an example to illustrate those practical details.

Published
2013
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