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1. Joint-Optimized Unsupervised Adversarial Domain Adaptation in Remote Sensing Segmentation with Prompted Foundation Model

Author

Lyu, Shuchang, Zhao, Qi, Cheng, Guangliang, He, Yiwei, Zhou, Zheng, Wang, Guangbiao, and Shi, Zhenwei

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Unsupervised Domain Adaptation for Remote Sensing Semantic Segmentation (UDA-RSSeg) addresses the challenge of adapting a model trained on source domain data to target domain samples, thereby minimizing the need for annotated data across diverse remote sensing scenes. This task presents two principal challenges: (1) severe inconsistencies in feature representation across different remote sensing domains, and (2) a domain gap that emerges due to the representation bias of source domain patterns when translating features to predictive logits. To tackle these issues, we propose a joint-optimized adversarial network incorporating the "Segment Anything Model (SAM) (SAM-JOANet)" for UDA-RSSeg. Our approach integrates SAM to leverage its robust generalized representation capabilities, thereby alleviating feature inconsistencies. We introduce a finetuning decoder designed to convert SAM-Encoder features into predictive logits. Additionally, a feature-level adversarial-based prompted segmentor is employed to generate class-agnostic maps, which guide the finetuning decoder's feature representations. The network is optimized end-to-end, combining the prompted segmentor and the finetuning decoder. Extensive evaluations on benchmark datasets, including ISPRS (Potsdam/Vaihingen) and CITY-OSM (Paris/Chicago), demonstrate the effectiveness of our method. The results, supported by visualization and analysis, confirm the method's interpretability and robustness. The code of this paper is available at https://github.com/CV-ShuchangLyu/SAM-JOANet., Comment: 12 pages,6 figures, 6 tables

Published
2024

5. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

Author

Aflitos, Saulo A., Schijlen, Elio, Finkers, Richard, Smit, Sandra, Wang, Jun, Zhang, Gengyun, Li, Ning, Mao, Likai, de Jong, Hans, Bakker, Freek, Gravendeel, Barbara, Breit, Timo, Dirks, Rob, Huits, Henk, Struss, Darush, Wagner, Ruth, van Leeuwen, Hans, van Ham, Roeland, Fito, Laia, Guigner, Laëtitia, Sevilla, Myrna, Ellul, Philippe, Ganko, Eric W., Kapur, Arvind, Reclus, Emmanuel, de Geus, Bernard, van de Geest, Henri, Hekkert, Bas te Lintel, Van Haarst, Jan C., Smits, Lars, Koops, Andries, Perez, Gabino Sanchez, de Ridder, Dick, van Heusden, Sjaak, Visser, Richard, Quan, Zhiwu, Min, Jiumeng, Liao, Li, Wang, Xiaoli, Wang, Guangbiao, Yue, Zhen, Yang, Xinhua, Xu, Na, Schranz, Eric, Smets, Eric F., Vos, Rutger A., Rauwerda, Han, Ursem, Remco, Schuit, Cees, Kerns, Mike, Berg, Jan van den, Vriezen, Wim H., Janssen, Antoine, Jahrman, Torben, Moquet, Frederic, Bonnet, Julien, and Peters, Sander A.

Subjects
Quantitative Biology - Genomics
Abstract

Genetic variation in the tomato clade was explored by sequencing a selection of 84 tomato accessions and related wild species representative for the Lycopersicon, Arcanum, Eriopersicon, and Neolycopersicon groups. We present a reconstruction of three new reference genomes in support of our comparative genome analyses. Sequence diversity in commercial breeding lines appears extremely low, indicating the dramatic genetic erosion of crop tomatoes. This is reflected by the SNP count in wild species which can exceed 10 million i.e. 20 fold higher than in crop accessions. Comparative sequence alignment reveals group, species, and accession specific polymorphisms, which explain characteristic fruit traits and growth habits in tomato accessions. Using gene models from the annotated Heinz reference genome, we observe a bias in dN/dS ratio in fruit and growth diversification genes compared to a random set of genes, which probably is the result of a positive selection. We detected highly divergent segments in wild S. lycopersicum species, and footprints of introgressions in crop accessions originating from a common donor accession. Phylogenetic relationships of fruit diversification and growth specific genes from crop accessions show incomplete resolution and are dependent on the introgression donor. In contrast, whole genome SNP information has sufficient power to resolve the phylogenetic placement of each accession in the four main groups in the Lycopersicon clade using Maximum Likelihood analyses. Phylogenetic relationships appear correlated with habitat and mating type and point to the occurrence of geographical races within these groups and thus are of practical importance for introgressive hybridization breeding. Our study illustrates the need for multiple reference genomes in support of tomato comparative genomics and Solanum genome evolution studies., Comment: 4 Figure, 10 Supplementary Figures, 2 Supplementary Figures This is the pre-peer reviewed version of the following article: The Plant Journal 80.1 (2014): 136-148, which has been published in final form at http://doi.org/10.1111/tpj.12616

Published
2015
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6. Molecular Signatures of Major Depression

Author

Cai, Na, Chang, Simon, Li, Yihan, Li, Qibin, Hu, Jingchu, Liang, Jieqin, Song, Li, Kretzschmar, Warren, Gan, Xiangchao, Nicod, Jerome, Rivera, Margarita, Deng, Hong, Du, Bo, Li, Keqing, Sang, Wenhu, Gao, Jingfang, Gao, Shugui, Ha, Baowei, Ho, Hung-Yao, Hu, Chunmei, Hu, Jian, Hu, Zhenfei, Huang, Guoping, Jiang, Guoqing, Jiang, Tao, Jin, Wei, Li, Gongying, Li, Kan, Li, Yi, Li, Yingrui, Li, Youhui, Lin, Yu-Ting, Liu, Lanfen, Liu, Tiebang, Liu, Ying, Liu, Yuan, Lu, Yao, Lv, Luxian, Meng, Huaqing, Qian, Puyi, Sang, Hong, Shen, Jianhua, Shi, Jianguo, Sun, Jing, Tao, Ming, Wang, Gang, Wang, Guangbiao, Wang, Jian, Wang, Linmao, Wang, Xueyi, Wang, Xumei, Yang, Huanming, Yang, Lijun, Yin, Ye, Zhang, Jinbei, Zhang, Kerang, Sun, Ning, Zhang, Wei, Zhang, Xiuqing, Zhang, Zhen, Zhong, Hui, Breen, Gerome, Wang, Jun, Marchini, Jonathan, Chen, Yiping, Xu, Qi, Xu, Xun, Mott, Richard, Huang, Guo-Jen, Kendler, Kenneth, and Flint, Jonathan

Subjects
Mental Health, Depression, Neurosciences, Genetics, Human Genome, Behavioral and Social Science, Brain Disorders, Aging, Animals, Biomarkers, Case-Control Studies, Child, Child Abuse, Sexual, DNA, Mitochondrial, Depressive Disorder, Major, Female, Glucocorticoids, Humans, Life Change Events, Male, Mice, Inbred C57BL, Stress, Psychological, Telomere Shortening, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology
Abstract

Adversity, particularly in early life, can cause illness. Clues to the responsible mechanisms may lie with the discovery of molecular signatures of stress, some of which include alterations to an individual's somatic genome. Here, using genome sequences from 11,670 women, we observed a highly significant association between a stress-related disease, major depression, and the amount of mtDNA (p = 9.00 × 10(-42), odds ratio 1.33 [95% confidence interval [CI] = 1.29-1.37]) and telomere length (p = 2.84 × 10(-14), odds ratio 0.85 [95% CI = 0.81-0.89]). While both telomere length and mtDNA amount were associated with adverse life events, conditional regression analyses showed the molecular changes were contingent on the depressed state. We tested this hypothesis with experiments in mice, demonstrating that stress causes both molecular changes, which are partly reversible and can be elicited by the administration of corticosterone. Together, these results demonstrate that changes in the amount of mtDNA and telomere length are consequences of stress and entering a depressed state. These findings identify increased amounts of mtDNA as a molecular marker of MD and have important implications for understanding how stress causes the disease.

Published
2015

8. Comparative genomics reveals insights into avian genome evolution and adaptation

Author

Zhang, Guojie, Li, Cai, Li, Qiye, Li, Bo, Larkin, Denis M, Lee, Chul, Storz, Jay F, Antunes, Agostinho, Greenwold, Matthew J, Meredith, Robert W, Ödeen, Anders, Cui, Jie, Zhou, Qi, Xu, Luohao, Pan, Hailin, Wang, Zongji, Jin, Lijun, Zhang, Pei, Hu, Haofu, Yang, Wei, Hu, Jiang, Xiao, Jin, Yang, Zhikai, Liu, Yang, Xie, Qiaolin, Yu, Hao, Lian, Jinmin, Wen, Ping, Zhang, Fang, Li, Hui, Zeng, Yongli, Xiong, Zijun, Liu, Shiping, Zhou, Long, Huang, Zhiyong, An, Na, Wang, Jie, Zheng, Qiumei, Xiong, Yingqi, Wang, Guangbiao, Wang, Bo, Wang, Jingjing, Fan, Yu, da Fonseca, Rute R, Alfaro-Núñez, Alonzo, Schubert, Mikkel, Orlando, Ludovic, Mourier, Tobias, Howard, Jason T, Ganapathy, Ganeshkumar, Pfenning, Andreas, Whitney, Osceola, Rivas, Miriam V, Hara, Erina, Smith, Julia, Farré, Marta, Narayan, Jitendra, Slavov, Gancho, Romanov, Michael N, Borges, Rui, Machado, João Paulo, Khan, Imran, Springer, Mark S, Gatesy, John, Hoffmann, Federico G, Opazo, Juan C, Håstad, Olle, Sawyer, Roger H, Kim, Heebal, Kim, Kyu-Won, Kim, Hyeon Jeong, Cho, Seoae, Li, Ning, Huang, Yinhua, Bruford, Michael W, Zhan, Xiangjiang, Dixon, Andrew, Bertelsen, Mads F, Derryberry, Elizabeth, Warren, Wesley, Wilson, Richard K, Li, Shengbin, Ray, David A, Green, Richard E, O’Brien, Stephen J, Griffin, Darren, Johnson, Warren E, Haussler, David, Ryder, Oliver A, Willerslev, Eske, Graves, Gary R, Alström, Per, Fjeldså, Jon, Mindell, David P, Edwards, Scott V, Braun, Edward L, Rahbek, Carsten, Burt, David W, Houde, Peter, and Zhang, Yong

Subjects
Human Genome, Biotechnology, Genetics, Adaptation, Physiological, Animals, Biodiversity, Biological Evolution, Birds, Conserved Sequence, Diet, Evolution, Molecular, Female, Flight, Animal, Genes, Genetic Variation, Genome, Genomics, Male, Molecular Sequence Annotation, Phylogeny, Reproduction, Selection, Genetic, Sequence Analysis, DNA, Synteny, Vision, Ocular, Vocalization, Animal, Avian Genome Consortium, General Science & Technology
Abstract

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

Published
2014

10. SWIN-TOD: Smooth Wasserstein Distance and Instance-Level Neighboring Enhancement for Remote Sensing Tiny Object Detection

Author

Wang, Guangbiao, Zhao, Hongbo, Lyu, Shuchang, Cheng, Guangliang, Chang, Qing, Feng, Wenquan, Zhao, Qi, and Shi, Zhenwei

Abstract

The advancement of deep neural network has propelled the widespread application of remote sensing target detection. However, compared to natural scenes, remote sensing targets possess inherent characteristics such as weak features and small scale, leading to a significant performance gap in traditional detection methods. To address these challenges, we undertake a systematic analysis of existing approaches, focusing on two key aspects: inadequate extraction of discriminative features and inappropriate regression measurement metrics. To tackle the first issue, an instance-level neighboring enhancement network (INEN) is proposed, enhancing the network’s feature extraction capability through inter-object feature aggregation. To address the second issue, a novel metric, smooth Wasserstein loss (SWL), is devised. Building upon these principles, a new tiny object detection (TOD) network for remote sensing images is developed. Extensive experiments on AI-TOD v1/v2 and DOTA v2 remote sensing tiny target detection datasets demonstrate that our approach achieves state-of-the-art (SOTA) performance. Codes are available at https://github.com/sevenwgb/SWIN-TOD.

Published
2024
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14. A global reference for human genetic variation

Author

Altshuler, David M., (Co-Chair), Durbin, Richard M., (Co-Chair, Principal Investigator), Donnelly, Peter, Green, Eric D., Nickerson, Deborah A., Boerwinkle, Eric, Doddapaneni, Harsha, Han, Yi, Korchina, Viktoriya, Kovar, Christie, Lee, Sandra, Muzny, Donna, Reid, Jeffrey G., Zhu, Yiming, Wang, Jun, (Principal Investigator), Chang, Yuqi, Feng, Qiang, Fang, Xiaodong, Guo, Xiaosen, Jian, Min, Jiang, Hui, Jin, Xin, Lan, Tianming, Li, Guoqing, Li, Jingxiang, Li, Yingrui, Liu, Shengmao, Liu, Xiao, Lu, Yao, Ma, Xuedi, Tang, Meifang, Wang, Bo, Wang, Guangbiao, Wu, Honglong, Wu, Renhua, Xu, Xun, Yin, Ye, Zhang, Dandan, Zhang, Wenwei, Zhao, Jiao, Zhao, Meiru, Zheng, Xiaole, Lander, Eric S., (Principal Investigator), Gabriel, Stacey B., (Co-Chair), Gupta, Namrata, Gharani, Neda, Toji, Lorraine H., Gerry, Norman P., Resch, Alissa M., Barker, Jonathan, Gil, Laurent, Hunt, Sarah E., Kelman, Gavin, Kulesha, Eugene, Leinonen, Rasko, McLaren, William M., Radhakrishnan, Rajesh, Roa, Asier, Smirnov, Dmitriy, Smith, Richard E., Streeter, Ian, Thormann, Anja, Toneva, Iliana, Vaughan, Brendan, Zheng-Bradley, Xiangqun, Bentley, David R., (Principal Investigator), Grocock, Russell, Humphray, Sean, James, Terena, Kingsbury, Zoya, Lehrach, Hans, (Principal Investigator), Sudbrak, Ralf, (Project Leader), Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Borodina, Tatiana A., Lienhard, Matthias, Mertes, Florian, Sultan, Marc, Timmermann, Bernd, Yaspo, Marie-Laure, Mardis, Elaine R., (Co-Principal Investigator) (Co-Chair), Wilson, Richard K., (Co-Principal Investigator), Fulton, Lucinda, Fulton, Robert, Ananiev, Victor, Belaia, Zinaida, Beloslyudtsev, Dimitriy, Bouk, Nathan, Chen, Chao, Church, Deanna, Cohen, Robert, Cook, Charles, Garner, John, Hefferon, Timothy, Kimelman, Mikhail, Liu, Chunlei, Lopez, John, Meric, Peter, O’Sullivan, Chris, Ostapchuk, Yuri, Phan, Lon, Ponomarov, Sergiy, Schneider, Valerie, Shekhtman, Eugene, Sirotkin, Karl, Slotta, Douglas, Zhang, Hua, Balasubramaniam, Senduran, Burton, John, Danecek, Petr, Keane, Thomas M., Kolb-Kokocinski, Anja, McCarthy, Shane, Stalker, James, Quail, Michael, Schmidt, Jeanette P., (Principal Investigator), Davies, Christopher J., Gollub, Jeremy, Webster, Teresa, Wong, Brant, Zhan, Yiping, Auton, Adam, (Principal Investigator), Campbell, Christopher L., Kong, Yu, Marcketta, Anthony, Yu, Fuli, (Project Leader), Antunes, Lilian, Bainbridge, Matthew, Sabo, Aniko, Huang, Zhuoyi, Coin, Lachlan J. M., Fang, Lin, Li, Qibin, Li, Zhenyu, Lin, Haoxiang, Liu, Binghang, Luo, Ruibang, Shao, Haojing, Xie, Yinlong, Ye, Chen, Yu, Chang, Zhang, Fan, Zheng, Hancheng, Zhu, Hongmei, Alkan, Can, Dal, Elif, Kahveci, Fatma, Garrison, Erik P., (Project Lead), Kural, Deniz, Lee, Wan-Ping, Leong, Wen Fung, Stromberg, Michael, Ward, Alistair N., Wu, Jiantao, Zhang, Mengyao, Daly, Mark J., (Principal Investigator), DePristo, Mark A., (Project Leader), Handsaker, Robert E., (Project Leader), Banks, Eric, Bhatia, Gaurav, del Angel, Guillermo, Genovese, Giulio, Li, Heng, Kashin, Seva, Nemesh, James C., Poplin, Ryan E., Yoon, Seungtai C., (Principal Investigator), Lihm, Jayon, Makarov, Vladimir, Clark, Andrew G., (Principal Investigator), Gottipati, Srikanth, Keinan, Alon, Rodriguez-Flores, Juan L., Rausch, Tobias, (Project Leader), Fritz, Markus H., Stütz, Adrian M., Beal, Kathryn, Datta, Avik, Herrero, Javier, Ritchie, Graham R. S., Zerbino, Daniel, Sabeti, Pardis C., (Principal Investigator), Shlyakhter, Ilya, Schaffner, Stephen F., Vitti, Joseph, Cooper, David N., (Principal Investigator), Ball, Edward V., Stenson, Peter D., Barnes, Bret, Bauer, Markus, Cheetham, Keira R., Cox, Anthony, Eberle, Michael, Kahn, Scott, Murray, Lisa, Peden, John, Shaw, Richard, Kenny, Eimear E., (Principal Investigator), Batzer, Mark A., (Principal Investigator), Konkel, Miriam K., Walker, Jerilyn A., MacArthur, Daniel G., (Principal Investigator), Lek, Monkol, Herwig, Ralf, Koboldt, Daniel C., Larson, David, Ye, Kai, Gravel, Simon, Swaroop, Anand, Chew, Emily, Lappalainen, Tuuli, (Principal Investigator), Erlich, Yaniv, (Principal Investigator), Gymrek, Melissa, Willems, Thomas Frederick, Simpson, Jared T., Shriver, Mark D., (Principal Investigator), Rosenfeld, Jeffrey A., (Principal Investigator), Montgomery, Stephen B., (Principal Investigator), De La Vega, Francisco M., (Principal Investigator), Byrnes, Jake K., Carroll, Andrew W., DeGorter, Marianne K., Lacroute, Phil, Maples, Brian K., Martin, Alicia R., Moreno-Estrada, Andres, Shringarpure, Suyash S., Zakharia, Fouad, Halperin, Eran, (Principal Investigator), Baran, Yael, Cerveira, Eliza, Hwang, Jaeho, Malhotra, Ankit, (Co-Project Lead), Plewczynski, Dariusz, Radew, Kamen, Romanovitch, Mallory, Zhang, Chengsheng, (Co-Project Lead), Hyland, Fiona C. L., Craig, David W., (Principal Investigator), Christoforides, Alexis, Homer, Nils, Izatt, Tyler, Kurdoglu, Ahmet A., Sinari, Shripad A., Squire, Kevin, Xiao, Chunlin, Sebat, Jonathan, (Principal Investigator), Antaki, Danny, Gujral, Madhusudan, Noor, Amina, Ye, Kenny, Burchard, Esteban G., (Principal Investigator), Hernandez, Ryan D., (Principal Investigator), Gignoux, Christopher R., Haussler, David, (Principal Investigator), Katzman, Sol J., Kent, James W., Howie, Bryan, Ruiz-Linares, Andres, (Principal Investigator), Dermitzakis, Emmanouil T., (Principal Investigator), Devine, Scott E., (Principal Investigator), Abecasis, Gonçalo R., (Principal Investigator) (Co-Chair), Kang, Hyun Min, (Project Leader), Kidd, Jeffrey M., (Principal Investigator), Blackwell, Tom, Caron, Sean, Chen, Wei, Emery, Sarah, Fritsche, Lars, Fuchsberger, Christian, Jun, Goo, Li, Bingshan, Lyons, Robert, Scheller, Chris, Sidore, Carlo, Song, Shiya, Sliwerska, Elzbieta, Taliun, Daniel, Tan, Adrian, Welch, Ryan, Wing, Mary Kate, Zhan, Xiaowei, Awadalla, Philip, (Principal Investigator), Hodgkinson, Alan, Li, Yun, Shi, Xinghua, (Principal Investigator), Quitadamo, Andrew, Lunter, Gerton, (Principal Investigator), McVean, Gil A., (Principal Investigator) (Co-Chair), Marchini, Jonathan L., (Principal Investigator), Myers, Simon, (Principal Investigator), Churchhouse, Claire, Delaneau, Olivier, Gupta-Hinch, Anjali, Kretzschmar, Warren, Iqbal, Zamin, Mathieson, Iain, Menelaou, Androniki, Rimmer, Andy, Xifara, Dionysia K., Oleksyk, Taras K., (Principal Investigator), Fu, Yunxin, (Principal Investigator), Liu, Xiaoming, Xiong, Momiao, Jorde, Lynn, (Principal Investigator), Witherspoon, David, Xing, Jinchuan, Browning, Brian L., (Principal Investigator), Browning, Sharon R., (Principal Investigator), Hormozdiari, Fereydoun, Sudmant, Peter H., Khurana, Ekta, (Principal Investigator), Hurles, Matthew E., (Principal Investigator), Albers, Cornelis A., Ayub, Qasim, Chen, Yuan, Colonna, Vincenza, Jostins, Luke, Walter, Klaudia, Xue, Yali, Abyzov, Alexej, Balasubramanian, Suganthi, Chen, Jieming, Clarke, Declan, Fu, Yao, Harmanci, Arif O., Jin, Mike, Lee, Donghoon, Liu, Jeremy, Mu, Xinmeng Jasmine, Zhang, Jing, Zhang, Yan, McCarroll, Steven A., (Principal Investigator), Hartl, Chris, Shakir, Khalid, Degenhardt, Jeremiah, Korbel, Jan O., (Principal Investigator) (Co-Chair), Meiers, Sascha, Raeder, Benjamin, Casale, Francesco Paolo, Stegle, Oliver, Lameijer, Eric-Wubbo, Ding, Li, (Principal Investigator), Hall, Ira, Lee, Charles, (Principal Investigator) (Co-Chair), Bafna, Vineet, Michaelson, Jacob, Gardner, Eugene J., (Project Leader), Mills, Ryan E., (Principal Investigator), Dayama, Gargi, Chen, Ken, (Principle Investigator), Fan, Xian, Chong, Zechen, Chen, Tenghui, Eichler, Evan E., (Principal Investigator) (Co-Chair), Chaisson, Mark J., Huddleston, John, Malig, Maika, Nelson, Bradley J., Parrish, Nicholas F., Blackburne, Ben, Lindsay, Sarah J., Ning, Zemin, Zhang, Yujun, Lam, Hugo, Sisu, Cristina, Gibbs, Richard A., (Principal Investigator) (Co-Chair), Challis, Danny, Evani, Uday S., Lu, James, Nagaswamy, Uma, Yu, Jin, Li, Wangshen, Marth, Gabor T., (Principal Investigator) (Co-Chair), Habegger, Lukas, Yu, Haiyuan, (Principal Investigator), Cunningham, Fiona, Dunham, Ian, Lage, Kasper, (Principal Investigator), Jespersen, Jakob Berg, Horn, Heiko, Tyler-Smith, Chris, (Principal Investigator) (Co-Chair), Gerstein, Mark B., (Principal Investigator) (Co-Chair), Kim, Donghoon, Desalle, Rob, Narechania, Apurva, Wilson Sayres, Melissa A., Bustamante, Carlos D., (Principal Investigator) (Co-Chair), Mendez, Fernando L., Poznik, David G., Underhill, Peter A., Coin, Lachlan, (Principal Investigator), Mittelman, David, Banerjee, Ruby, Cerezo, Maria, Fitzgerald, Thomas W., Louzada, Sandra, Massaia, Andrea, Ritchie, Graham R., Yang, Fengtang, Kalra, Divya, Hale, Walker, Dan, Xu, Flicek, Paul, (Principal Investigator) (Co-Chair), Clarke, Laura, (Project Lead), Sherry, Stephen T., (Principal Investigator) (Co-Chair), Chakravarti, Aravinda, (Co-Chair), Knoppers, Bartha M., (Co-Chair), Barnes, Kathleen C., Beiswanger, Christine, Cai, Hongyu, Cao, Hongzhi, Henn, Brenna, Jones, Danielle, Kaye, Jane S., Kent, Alastair, Kerasidou, Angeliki, Mathias, Rasika, Ossorio, Pilar N., Parker, Michael, Rotimi, Charles N., Royal, Charmaine D., Sandoval, Karla, Su, Yeyang, Tian, Zhongming, Tishkoff, Sarah, Via, Marc, Wang, Yuhong, Yang, Ling, Zhu, Jiayong, Bodmer, Walter, Bedoya, Gabriel, Cai, Zhiming, Gao, Yang, Chu, Jiayou, Peltonen, Leena, Garcia-Montero, Andres, Orfao, Alberto, Dutil, Julie, Martinez-Cruzado, Juan C., Mathias, Rasika A., Hennis, Anselm, Watson, Harold, McKenzie, Colin, Qadri, Firdausi, LaRocque, Regina, Deng, Xiaoyan, Asogun, Danny, Folarin, Onikepe, Happi, Christian, Omoniwa, Omonwunmi, Stremlau, Matt, Tariyal, Ridhi, Jallow, Muminatou, Joof, Fatoumatta Sisay, Corrah, Tumani, Rockett, Kirk, Kwiatkowski, Dominic, Kooner, Jaspal, Hiê`n, Trâ`n Tinh, Dunstan, Sarah J., Hang, Nguyen Thuy, Fonnie, Richard, Garry, Robert, Kanneh, Lansana, Moses, Lina, Schieffelin, John, Grant, Donald S., Gallo, Carla, Poletti, Giovanni, Saleheen, Danish, Rasheed, Asif, Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Vaydylevich, Yekaterina, Duncanson, Audrey, Dunn, Michael, Schloss, Jeffery A., and Yang, Huanming

Published
2015
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15. The UK10K project identifies rare variants in health and disease

Author

Walter, Klaudia, Min, Josine L., Huang, Jie, Crooks, Lucy, Memari, Yasin, Perry, John R. B., Xu, ChangJiang, Futema, Marta, Lawson, Daniel, Iotchkova, Valentina, Schiffels, Stephan, Hendricks, Audrey E., Danecek, Petr, Li, Rui, Floyd, James, Wain, Louise V., Humphries, Steve E., Barrett, Jeffrey C., Bala, Senduran, Clapham, Peter, Coates, Guy, Cox, Tony, Daly, Allan, Du, Yuanping, Edkins, Sarah, Ellis, Peter, Flicek, Paul, Guo, Xiaosen, Guo, Xueqin, Huang, Liren, Jackson, David K., Joyce, Chris, Keane, Thomas, Kolb-Kokocinski, Anja, Langford, Cordelia, Li, Yingrui, Liang, Jieqin, Lin, Hong, Liu, Ryan, Maslen, John, McCarthy, Shane, (co-chair), Muddyman, Dawn, Quail, Michael A., Stalker, Jim, (co-chair), Sun, Jianping, Tian, Jing, Wang, Guangbiao, Wang, Jun, Wang, Yu, Wong, Kim, Zhang, Pingbo, Birney, Ewan, Boustred, Chris, Chen, Lu, Clement, Gail, Cocca, Massimiliano, Smith, George Davey, Day, Ian N. M., Day-Williams, Aaron, Down, Thomas, Dunham, Ian, Evans, David M., Gaunt, Tom R., Geihs, Matthias, Hart, Deborah, Howie, Bryan, Hubbard, Tim, Hysi, Pirro, Jamshidi, Yalda, Karczewski, Konrad J., Kemp, John P., Lachance, Genevieve, Lek, Monkol, Lopes, Margarida, MacArthur, Daniel G., Marchini, Jonathan, Mangino, Massimo, Mathieson, Iain, Metrustry, Sarah, Moayyeri, Alireza, Northstone, Kate, Panoutsopoulou, Kalliope, Paternoster, Lavinia, Quaye, Lydia, Richards, Brent J., (co-chair), Ring, Susan, Ritchie, Graham R. S., Shihab, Hashem A., Shin, So-Youn, Small, Kerrin S., Artigas, María Soler, Soranzo, Nicole, (co-chair), Southam, Lorraine, Spector, Timothy D., St Pourcain, Beate, Surdulescu, Gabriela, Tachmazidou, Ioanna, Timpson, Nicholas J., (co-chair), Tobin, Martin D., Valdes, Ana M., Visscher, Peter M., Ward, Kirsten, Wilson, Scott G., Yang, Jian, Zhang, Feng, Zheng, Hou-Feng, Anney, Richard, Ayub, Muhammad, Blackwood, Douglas, Bolton, Patrick F., Breen, Gerome, Collier, David A., Craddock, Nick, Curran, Sarah, Curtis, David, Gallagher, Louise, Geschwind, Daniel, Gurling, Hugh, Holmans, Peter, Lee, Irene, Lönnqvist, Jouko, McGuffin, Peter, McIntosh, Andrew M., McKechanie, Andrew G., McQuillin, Andrew, Morris, James, OʼDonovan, Michael C., Owen, Michael J., (co-chair), Palotie, Aarno, (co-chair), Parr, Jeremy R., Paunio, Tiina, Pietilainen, Olli, Rehnström, Karola, Sharp, Sally I., Skuse, David, St Clair, David, Suvisaari, Jaana, Walters, James T. R., Williams, Hywel J., Barroso, Inês, (co-chair), Bochukova, Elena, Bounds, Rebecca, Dominiczak, Anna, Farooqi, Sadaf I., (co-chair), Keogh, Julia, Marenne, Gaëlle, Morris, Andrew, OʼRahilly, Stephen, Porteous, David J., Smith, Blair H., Wheeler, Eleanor, Al Turki, Saeed, Anderson, Carl A., Antony, Dinu, Beales, Phil, Bentham, Jamie, Bhattacharya, Shoumo, Calissano, Mattia, Carss, Keren, Chatterjee, Krishna, Cirak, Sebahattin, Cosgrove, Catherine, Fitzpatrick, David R., (co-chair), Foley, Reghan A., Franklin, Christopher S., Grozeva, Detelina, Hurles, Matthew E., (co-chair), Mitchison, Hannah M., Muntoni, Francesco, Onoufriadis, Alexandros, Parker, Victoria, Payne, Felicity, Raymond, Lucy F., Roberts, Nicola, Savage, David B., Scambler, Peter, Schmidts, Miriam, Schoenmakers, Nadia, Semple, Robert K., Serra, Eva, Spasic-Boskovic, Olivera, Stevens, Elizabeth, van Kogelenberg, Margriet, Vijayarangakannan, Parthiban, Williamson, Kathleen A., Wilson, Crispian, Whyte, Tamieka, Ciampi, Antonio, Greenwood, Celia M. T., (co-chair), Oualkacha, Karim, Zeggini, Eleftheria, (co-chair), Bobrow, Martin, Griffin, Heather, Kaye, Jane, (co-chair), Kennedy, Karen, Kent, Alastair, Smee, Carol, Charlton, Ruth, Ekong, Rosemary, Khawaja, Farrah, Lopes, Luis R., Migone, Nicola, Payne, Stewart J., Plagnol, Vincent, (chair), Pollitt, Rebecca C., Povey, Sue, Ridout, Cheryl K., Robinson, Rachel L., Scott, Richard H., Shaw, Adam, Syrris, Petros, Taylor, Rohan, Vandersteen, Anthony M., Durbin, Richard, (chair), Amuzu, Antoinette, Casas, Juan Pablo, Chambers, John C., Dedoussis, George, Gambaro, Giovanni, Gasparini, Paolo, Isaacs, Aaron, Johnson, Jon, Kleber, Marcus E., Kooner, Jaspal S., Langenberg, Claudia, Luan, Jianʼan, Malerba, Giovanni, März, Winfried, Matchan, Angela, Morris, Richard, Nordestgaard, Børge G., Benn, Marianne, Scott, Robert A., Toniolo, Daniela, Traglia, Michela, Tybjaerg-Hansen, Anne, van Duijn, Cornelia M., van Leeuwen, Elisabeth M., Varbo, Anette, Whincup, Peter, Zaza, Gianluigi, and Zhang, Weihua

Published
2015
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16. Sparse whole-genome sequencing identifies two loci for major depressive disorder

Author

Cai, Na, Bigdeli, Tim B., Kretzschmar, Warren, Li, Yihan, Liang, Jieqin, Song, Li, Hu, Jingchu, Li, Qibin, Jin, Wei, Hu, Zhenfei, Wang, Guangbiao, Wang, Linmao, Qian, Puyi, Liu, Yuan, Jiang, Tao, Lu, Yao, Zhang, Xiuqing, Yin, Ye, Li, Yingrui, Xu, Xun, Gao, Jingfang, Reimers, Mark, Webb, Todd, Riley, Brien, Bacanu, Silviu, Peterson, Roseann E., Chen, Yiping, Zhong, Hui, Liu, Zhengrong, Wang, Gang, Sun, Jing, Sang, Hong, Jiang, Guoqing, Zhou, Xiaoyan, Li, Yi, Zhang, Wei, Wang, Xueyi, Fang, Xiang, Pan, Runde, Miao, Guodong, Zhang, Qiwen, Hu, Jian, Yu, Fengyu, Du, Bo, Sang, Wenhua, Li, Keqing, Chen, Guibing, Cai, Min, Yang, Lijun, Yang, Donglin, Ha, Baowei, Hong, Xiaohong, Deng, Hong, Li, Gongying, Li, Kan, Song, Yan, Gao, Shugui, Zhang, Jinbei, Gan, Zhaoyu, Meng, Huaqing, Pan, Jiyang, Gao, Chengge, Zhang, Kerang, Sun, Ning, Li, Youhui, Niu, Qihui, Zhang, Yutang, Liu, Tieqiao, Hu, Chunmei, Zhang, Zhen, Lv, Luxian, Dong, Jicheng, Wang, Xiaoping, Tao, Ming, Wang, Xumei, Xia, Jing, Rong, Han, He, Qiang, Liu, Tiebang, Huang, Guoping, Mei, Qiyi, Shen, Zhenming, Liu, Ying, Shen, Jianhua, Tian, Tian, Liu, Xiaojuan, Wu, Wenyuan, Gu, Danhua, Fu, Guangyi, Shi, Jianguo, Chen, Yunchun, Gan, Xiangchao, Liu, Lanfen, Wang, Lina, Yang, Fuzhong, Cong, Enzhao, Marchini, Jonathan, Yang, Huanming, Wang, Jian, Shi, Shenxun, Mott, Richard, Xu, Qi, Wang, Jun, Kendler, Kenneth S., and Flint, Jonathan

Published
2015
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18. RESEARCH ARTICLE: Comparative genomics reveals insights into avian genome evolution and adaptation

Author

Zhang, Guojie, Li, Cai, Li, Qiye, Li, Bo, Larkin, Denis M., Lee, Chul, Storz, Jay F., Antunes, Agostinho, Greenwold, Matthew J., Meredith, Robert W., Ödeen, Anders, Cui, Jie, Zhou, Qi, Xu, Luohao, Pan, Hailin, Wang, Zongji, Jin, Lijun, Zhang, Pei, Hu, Haofu, Yang, Wei, Hu, Jiang, Xiao, Jin, Yang, Zhikai, Liu, Yang, Xie, Qiaolin, Yu, Hao, Lian, Jinmin, Wen, Ping, Zhang, Fang, Li, Hui, Zeng, Yongli, Xiong, Zijun, Liu, Shiping, Zhou, Long, Huang, Zhiyong, An, Na, Wang, Jie, Zheng, Qiumei, Xiong, Yingqi, Wang, Guangbiao, Wang, Bo, Wang, Jingjing, Fan, Yu, da Fonseca, Rute R., Alfaro-Núñez, Alonzo, Schubert, Mikkel, Orlando, Ludovic, Mourier, Tobias, Howard, Jason T., Ganapathy, Ganeshkumar, Pfenning, Andreas, Whitney, Osceola, Rivas, Miriam V., Hara, Erina, Smith, Julia, Farré, Marta, Narayan, Jitendra, Slavov, Gancho, Romanov, Michael N, Borges, Rui, Machado, João Paulo, Khan, Imran, Springer, Mark S., Gatesy, John, Hoffmann, Federico G., Opazo, Juan C., Håstad, Olle, Sawyer, Roger H., Kim, Heebal, Kim, Kyu-Won, Kim, Hyeon Jeong, Cho, Seoae, Li, Ning, Huang, Yinhua, Bruford, Michael W., Zhan, Xiangjiang, Dixon, Andrew, Bertelsen, Mads F., Derryberry, Elizabeth, Warren, Wesley, Wilson, Richard K, Li, Shengbin, Ray, David A., Green, Richard E., OʼBrien, Stephen J., Griffin, Darren, Johnson, Warren E., Haussler, David, Ryder, Oliver A., Willerslev, Eske, Graves, Gary R., Alström, Per, Fjeldså, Jon, Mindell, David P., Edwards, Scott V., Braun, Edward L., Rahbek, Carsten, Burt, David W., Houde, Peter, Zhang, Yong, Yang, Huanming, Wang, Jian, Consortium, Avian Genome, Jarvis, Erich D., Gilbert, M. Thomas P., and Wang, Jun

Published
2014
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19. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

Author

Aflitos, Saulo, Schijlen, Elio, de Jong, Hans, de Ridder, Dick, Smit, Sandra, Finkers, Richard, Wang, Jun, Zhang, Gengyun, Li, Ning, Mao, Likai, Bakker, Freek, Dirks, Rob, Breit, Timo, Gravendeel, Barbara, Huits, Henk, Struss, Darush, Swanson-Wagner, Ruth, van Leeuwen, Hans, van Ham, Roeland C.H.J., Fito, Laia, Guignier, Laëtitia, Sevilla, Myrna, Ellul, Philippe, Ganko, Eric, Kapur, Arvind, Reclus, Emannuel, de Geus, Bernard, van de Geest, Henri, te Lintel Hekkert, Bas, van Haarst, Jan, Smits, Lars, Koops, Andries, Sanchez-Perez, Gabino, van Heusden, Adriaan W., Visser, Richard, Quan, Zhiwu, Min, Jiumeng, Liao, Li, Wang, Xiaoli, Wang, Guangbiao, Yue, Zhen, Yang, Xinhua, Xu, Na, Schranz, Eric, Smets, Erik, Vos, Rutger, Rauwerda, Johan, Ursem, Remco, Schuit, Cees, Kerns, Mike, van den Berg, Jan, Vriezen, Wim, Janssen, Antoine, Datema, Erwin, Jahrman, Torben, Moquet, Frederic, Bonnet, Julien, and Peters, Sander

Published
2014
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21. Comparative Analysis of Sample Extraction and Library Construction for Shotgun Metagenomics

Author

Peng, Zonghui, Zhu, Xiaolong, Wang, Zhijiao, Yan, Xianting, Wang, Guangbiao, Tang, Meifang, Jiang, Awei, Kristiansen, Karsten, Peng, Zonghui, Zhu, Xiaolong, Wang, Zhijiao, Yan, Xianting, Wang, Guangbiao, Tang, Meifang, Jiang, Awei, and Kristiansen, Karsten

Abstract

Human fecal specimens, serve as important materials, are widely used in the field of microbiome research, in which inconsistent results have been a pressing issue. The possible attribute factors have been proposed including the specimen status after preservation, extracted DNA quality, library preparation protocol, and sample DNA input. In this study, quality comparisons for shotgun metagenomics sequencing were performed between 2 DNA extraction methods for fresh and freeze-thaw samples, 2 library preparation protocols, and various sample inputs. The results indicate that Mag-Bind® Universal Metagenomics Kit (OM) outperformed DNeasy PowerSoil Kit (QP) with a higher DNA quantity. Controlling on library preparation protocol, OM detected on-average more genes than QP. For library construction comparison by controlling on the same DNA sample, KAPA Hyper Prep Kit (KH) outperformed the TruePrep DNA Library Prep Kit V2 (TP) with the higher number of detected genes number and Shannon index. No significant differences were found in taxonomy between 2 library preparation protocols using the fresh, freeze-thaw and mock community samples. No significant difference was observed between 250 and 50 ng DNA inputs for library preparation on both fresh and freeze-thaw samples. Through the preliminary study, a combined protocol is recommended for performing metagenomics studies, by using OM method plus KH protocol as well as suitable DNA quantity on either fresh or freeze-thaw samples. Our findings provide clues for potential variations from various DNA extraction methods, library protocols, and sample DNA inputs, which are critical for consistent and comprehensive profiling of the human gut microbiome.

Published
2020

23. An integrated map of genetic variation from 1,092 human genomes

Author

McVean, Gil A., Altshuler, David M., Durbin, Richard M., Abecasis, Gonçalo R., Bentley, David R., Chakravarti, Aravinda, Clark, Andrew G., Donnelly, Peter, Eichler, Evan E., Flicek, Paul, Gabriel, Stacey B., Gibbs, Richard A., Green, Eric D., Hurles, Matthew E., Knoppers, Bartha M., Korbel, Jan O., Lander, Eric S., Lee, Charles, Lehrach, Hans, Mardis, Elaine R., Marth, Gabor T., Nickerson, Deborah A., Schmidt, Jeanette P., Sherry, Stephen T., Wang, Jun, Wilson, Richard K., Dinh, Huyen, Kovar, Christie, Lee, Sandra, Lewis, Lora, Muzny, Donna, Reid, Jeff, Wang, Min, Wang, Jun, Fang, Xiaodong, Guo, Xiaosen, Jian, Min, Jiang, Hui, Jin, Xin, Li, Guoqing, Li, Jingxiang, Li, Yingrui, Li, Zhuo, Liu, Xiao, Lu, Yao, Ma, Xuedi, Su, Zhe, Tai, Shuaishuai, Tang, Meifang, Wang, Bo, Wang, Guangbiao, Wu, Honglong, Wu, Renhua, Yin, Ye, Zhang, Wenwei, Zhao, Jiao, Zhao, Meiru, Zheng, Xiaole, Zhou, Yan, Lander, Eric S., Gabriel, Stacey B., Gupta, Namrata, Flicek, Paul, Clarke, Laura, Leinonen, Rasko, Smith, Richard E., Zheng-Bradley, Xiangqun, Bentley, David R., Grocock, Russell, Humphray, Sean, James, Terena, Kingsbury, Zoya, Lehrach, Hans, Sudbrak, Ralf, Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Borodina, Tatiana A., Lienhard, Matthias, Mertes, Florian, Sultan, Marc, Timmermann, Bernd, Yaspo, Marie-Laure, Sherry, Stephen T., McVean, Gil A., Mardis, Elaine R., Wilson, Richard K., Fulton, Lucinda, Fulton, Robert, Weinstock, George M., Durbin, Richard M., Balasubramaniam, Senduran, Burton, John, Danecek, Petr, Keane, Thomas M., Kolb-Kokocinski, Anja, McCarthy, Shane, Stalker, James, Quail, Michael, Schmidt, Jeanette P., Davies, Christopher J., Gollub, Jeremy, Webster, Teresa, Wong, Brant, Zhan, Yiping, Auton, Adam, Yu, Fuli, Bainbridge, Matthew, Challis, Danny, Evani, Uday S., Lu, James, Nagaswamy, Uma, Sabo, Aniko, Wang, Yi, Yu, Jin, Coin, Lachlan J. M., Fang, Lin, Li, Qibin, Li, Zhenyu, Lin, Haoxiang, Liu, Binghang, Luo, Ruibang, Qin, Nan, Shao, Haojing, Wang, Bingqiang, Xie, Yinlong, Ye, Chen, Yu, Chang, Zhang, Fan, Zheng, Hancheng, Zhu, Hongmei, Garrison, Erik P., Kural, Deniz, Lee, Wan-Ping, Fung Leong, Wen, Ward, Alistair N., Wu, Jiantao, Zhang, Mengyao, Lee, Charles, Griffin, Lauren, Hsieh, Chih-Heng, Mills, Ryan E., Shi, Xinghua, von Grotthuss, Marcin, Zhang, Chengsheng, Daly, Mark J., DePristo, Mark A., Banks, Eric, Bhatia, Gaurav, Carneiro, Mauricio O., del Angel, Guillermo, Genovese, Giulio, Handsaker, Robert E., Hartl, Chris, McCarroll, Steven A., Nemesh, James C., Poplin, Ryan E., Schaffner, Stephen F., Shakir, Khalid, Yoon, Seungtai C., Lihm, Jayon, Makarov, Vladimir, Jin, Hanjun, Kim, Wook, Cheol Kim, Ki, Korbel, Jan O., Rausch, Tobias, Beal, Kathryn, Cunningham, Fiona, Herrero, Javier, McLaren, William M., Ritchie, Graham R. S., Clark, Andrew G., Gottipati, Srikanth, Keinan, Alon, Rodriguez-Flores, Juan L., Sabeti, Pardis C., Grossman, Sharon R., Tabrizi, Shervin, Tariyal, Ridhi, Cooper, David N., Ball, Edward V., Stenson, Peter D., Barnes, Bret, Bauer, Markus, Keira Cheetham, R., Cox, Tony, Eberle, Michael, Kahn, Scott, Murray, Lisa, Peden, John, Shaw, Richard, Ye, Kai, Batzer, Mark A., Konkel, Miriam K., Walker, Jerilyn A., MacArthur, Daniel G., Lek, Monkol, Sudbrak, Herwig, Ralf, Shriver, Mark D., Bustamante, Carlos D., Byrnes, Jake K., De La Vega, Francisco M., Gravel, Simon, Kenny, Eimear E., Kidd, Jeffrey M., Lacroute, Phil, Maples, Brian K., Moreno-Estrada, Andres, Zakharia, Fouad, Halperin, Eran, Baran, Yael, Craig, David W., Christoforides, Alexis, Homer, Nils, Izatt, Tyler, Kurdoglu, Ahmet A., Sinari, Shripad A., Squire, Kevin, Xiao, Chunlin, Sebat, Jonathan, Bafna, Vineet, Ye, Kenny, Burchard, Esteban G., Hernandez, Ryan D., Gignoux, Christopher R., Haussler, David, Katzman, Sol J., James Kent, W., Howie, Bryan, Ruiz-Linares, Andres, Dermitzakis, Emmanouil T., Lappalainen, Tuuli, Devine, Scott E., Liu, Xinyue, Maroo, Ankit, Tallon, Luke J., Rosenfeld, Jeffrey A., Min Kang, Hyun, Anderson, Paul, Angius, Andrea, Bigham, Abigail, Blackwell, Tom, Busonero, Fabio, Cucca, Francesco, Fuchsberger, Christian, Jones, Chris, Jun, Goo, Li, Yun, Lyons, Robert, Maschio, Andrea, Porcu, Eleonora, Reinier, Fred, Sanna, Serena, Schlessinger, David, Sidore, Carlo, Tan, Adrian, Kate Trost, Mary, Awadalla, Philip, Hodgkinson, Alan, Lunter, Gerton, McVean, Gil A., Marchini, Jonathan L., Myers, Simon, Churchhouse, Claire, Delaneau, Olivier, Gupta-Hinch, Anjali, Iqbal, Zamin, Mathieson, Iain, Rimmer, Andy, Xifara, Dionysia K., Oleksyk, Taras K., Fu, Yunxin, Liu, Xiaoming, Xiong, Momiao, Jorde, Lynn, Witherspoon, David, Xing, Jinchuan, Eichler, Evan E., Browning, Brian L., Alkan, Can, Hajirasouliha, Iman, Hormozdiari, Fereydoun, Ko, Arthur, Sudmant, Peter H., Mardis, Elaine R., Chen, Ken, Chinwalla, Asif, Ding, Li, Dooling, David, Koboldt, Daniel C., McLellan, Michael D., Wallis, John W., Wendl, Michael C., Zhang, Qunyuan, Hurles, Matthew E., Tyler-Smith, Chris, Albers, Cornelis A., Ayub, Qasim, Chen, Yuan, Coffey, Alison J., Colonna, Vincenza, Huang, Ni, Jostins, Luke, Li, Heng, Scally, Aylwyn, Walter, Klaudia, Xue, Yali, Zhang, Yujun, Gerstein, Mark B., Abyzov, Alexej, Balasubramanian, Suganthi, Chen, Jieming, Clarke, Declan, Fu, Yao, Habegger, Lukas, Harmanci, Arif O., Jin, Mike, Khurana, Ekta, Jasmine Mu, Xinmeng, Sisu, Cristina, Lee, Charles, McCarroll, Steven A., Degenhardt, Jeremiah, Korbel, Jan O., Stütz, Adrian M., Church, Deanna, Michaelson, Jacob J., Eichler, Evan E., Hurles, Matthew E., Blackburne, Ben, Lindsay, Sarah J., Ning, Zemin, DePristo, Mark A., Min Kang, Hyun, Mardis, Elaine R., Yu, Fuli, Michelson, Leslie P., Tyler-Smith, Chris, Frankish, Adam, Harrow, Jennifer, Fowler, Gerald, Hale, Walker, Kalra, Divya, Flicek, Paul, Clarke, Laura, Barker, Jonathan, Kelman, Gavin, Kulesha, Eugene, Radhakrishnan, Rajesh, Roa, Asier, Smirnov, Dmitriy, Streeter, Ian, Toneva, Iliana, Vaughan, Brendan, Sherry, Stephen T., Ananiev, Victor, Belaia, Zinaida, Beloslyudtsev, Dimitriy, Bouk, Nathan, Chen, Chao, Cohen, Robert, Cook, Charles, Garner, John, Hefferon, Timothy, Kimelman, Mikhail, Liu, Chunlei, Lopez, John, Meric, Peter, OʼSullivan, Chris, Ostapchuk, Yuri, Phan, Lon, Ponomarov, Sergiy, Schneider, Valerie, Shekhtman, Eugene, Sirotkin, Karl, Slotta, Douglas, Zhang, Hua, Chakravarti, Aravinda, Knoppers, Bartha M., Barnes, Kathleen C., Beiswanger, Christine, Burchard, Esteban G., Bustamante, Carlos D., Cai, Hongyu, Cao, Hongzhi, Durbin, Richard M., Gharani, Neda, Henn, Brenna, Jones, Danielle, Jorde, Lynn, Kaye, Jane S., Kent, Alastair, Kerasidou, Angeliki, Mathias, Rasika, Ossorio, Pilar N., Parker, Michael, Reich, David, Rotimi, Charles N., Royal, Charmaine D., Sandoval, Karla, Su, Yeyang, Sudbrak, Ralf, Tian, Zhongming, Tishkoff, Sarah, Toji, Lorraine H., Tyler-Smith, Chris, Via, Marc, Wang, Yuhong, Yang, Huanming, Yang, Ling, Zhu, Jiayong, Bodmer, Walter, Bedoya, Gabriel, Ruiz-Linares, Andres, Zhi Ming, Cai, Yang, Gao, Jia You, Chu, Peltonen, Leena, Garcia-Montero, Andres, Orfao, Alberto, Dutil, Julie, Martinez-Cruzado, Juan C., Oleksyk, Taras K., Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Clemm, Nicholas C., Duncanson, Audrey, Dunn, Michael, Guyer, Mark S., Peterson, Jane L., Abecasis, Goncalo R., and Auton, Adam

Published
2012
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25. Steroid receptor coactivator-1 modulates the function of Pomc neurons and energy homeostasis

Author

Yang, Yongjie, van der Klaauw, Agatha A., Zhu, Liangru, Cacciottolo, Tessa M., He, Yanlin, Stadler, Lukas K. J., Wang, Chunmei, Xu, Pingwen, Saito, Kenji, Hinton, Antentor, Yan, Xiaofeng, Keogh, Julia M., Henning, Elana, Banton, Matthew C., Hendricks, Audrey E., Bochukova, Elena G., Mistry, Vanisha, Lawler, Katherine L., Liao, Lan, Xu, Jianming, O'Rahilly, Stephen, Tong, Qingchun, Barroso, Ines, O'Malley, Bert W., Farooqi, I. Sadaf, Xu, Yong, Balasubramanian, Senduran, Clapham, Peter, Coates, Guy, Cox, Tony, Daly, Allan, Danecek, Petr, Du, Yuanping, Durbin, Richard, Edkins, Sarah, Ellis, Peter, Flicek, Paul, Guo, Xiaosen, Guo, Xueqin, Huang, Liren, Jackson, David K., Joyce, Chris, Keane, Thomas, Kolb-Kokocinski, Anja, Langford, Cordelia, Li, Yingrui, Liang, Jieqin, Lin, Hong, Liu, Ryan, Maslen, John, McCarthy, Shane, Muddyman, Dawn, Quail, Michael A., Stalker, Jim, Sun, Jianping, Tian, Jing, Wang, Guangbiao, Wang, Jun, Wang, Yu, Wong, Kim, Zhang, Pingbo, Birney, Ewan, Boustred, Chris, Brion, Marie-Jo, Chen, Lu, Clement, Gail, Smith, George Davey, Day, Ian N. M., Day-Williams, Aaron, Down, Thomas, Dunham, Ian, Evans, David M., Fatemifar, Ghazaleh, Gaunt, Tom R., Geihs, Matthias, Greenwood, Celia M. T., Hart, Deborah, Howie, Bryan, Huang, Jie, Hubbard, Tim, Hysi, Pirro, Iotchkova, Valentina, Jamshidi, Yalda, Kemp, John P., Lachance, Genevieve, Lawson, Daniel, Lek, Monkol, Lopes, Margarida, MacArthur, Daniel G., Marchini, Jonathan, Massimo, Mangino, Mathieson, Iain, Memari, Yasin, Metrustry, Sarah, Min, Josine L., Moayyeri, Alireza, Northstone, Kate, Panoutsopoulou, Kalliope, Paternoster, Lavinia, Perry, John R. B., Quaye, Lydia, Richards, J. Brent, Ring, Susan, Ritchie, Graham R. S., Schiffels, Stephan, Shihab, Hashem A., Shin, So-Youn, Small, Kerrin S., Artigas, Maria Soler, Soranzo, Nicole, Southam, Lorraine, Spector, Timothy D., St Pourcain, Beate, Surdulescu, Gabriela, Tachmazidou, Ioanna, Timpson, Nicholas J., Tobin, Martin D., Valdes, Ana M., Visscher, Peter M., Wain, Louise V., Walter, Klaudia, Ward, Kirsten, Wilson, Scott G., Yang, Jian, Zeggini, Eleftheria, Zhang, Feng, Zheng, Hou-Feng, Anney, Richard, Ayub, Muhammad, Barrett, Jeffrey C., Blackwood, Douglas, Bolton, Patrick F., Breen, Gerome, Collier, David A., Craddock, Nick, Crooks, Lucy, Curran, Sarah, Curtis, David, Gallagher, Louise, Geschwind, Daniel, Gurling, Hugh, Holmans, Peter, Lee, Irene, Lonnqvist, Jouko, McGuffin, Peter, McIntosh, Andrew M., McKechanie, Andrew G., McQuillin, Andrew, Morris, James, O'Donovan, Michael C., Owen, Michael J., Palotie, Aarno, Parr, Jeremy R., Paunio, Tiina, Pietilainen, Olli, Rehnstrom, Karola, Sharp, Sally I., Skuse, David, St Clair, David, Suvisaari, Jaana, Walters, James T. R., Williams, Hywel J., Bochukova, Elena, Bounds, Rebecca, Dominiczak, Anna, Keogh, Julia, Marenne, Gaelle, Morris, Andrew, Porteous, David J., Smith, Blair H., Wheeler, Eleanor, Al Turki, Saeed, Anderson, Carl A., Antony, Dinu, Beales, Phil, Bentham, Jamie, Bhattacharya, Shoumo, Calissano, Mattia, Carss, Keren, Chatterjee, Krishna, Cirak, Sebahattin, Cosgrove, Catherine, Fitzpatrick, David R., Floyd, James, Foley, A. Reghan, Franklin, Christopher S., Futema, Marta, Grozeva, Detelina, Humphries, Steve E., Hurles, Matthew E., Mitchison, Hannah M., Muntoni, Francesco, Onoufriadis, Alexandros, Parker, Victoria, Payne, Felicity, Plagnol, Vincent, Raymond, F. Lucy, Roberts, Nicola, Savage, David B., Scambler, Peter, Schmidts, Miriam, Schoenmakers, Nadia, Semple, Robert K., Serra, Eva, Spasic-Boskovic, Olivera, Stevens, Elizabeth, van Kogelenberg, Margriet, Vijayarangakannan, Parthiban, Williamson, Kathleen A., Wilson, Crispian, Whyte, Tamieka, Ciampi, Antonio, Li, Rui, Oualkacha, Karim, Xu, ChangJiang, Bobrow, Martin, Griffin, Heather, Kaye, Jane, Kennedy, Karen, Kent, Alastair, Smee, Carol, Charlton, Ruth, Ekong, Rosemary, Khawaja, Farrah, Lopes, Luis R., Migone, Nicola, Payne, Stewart J., Pollitt, Rebecca C., Povey, Sue, Ridout, Cheryl K., Robinson, Rachel L., Scott, Richard H., Shaw, Adam, Syrris, Petros, Taylor, Rohan, Vandersteen, Anthony M., Amuzu, Antoinette, Casas, Juan Pablo, Chambers, John C., Cocca, Massimiliano, Dedoussis, George, Gambaro, Giovanni, Gasparini, Paolo, Isaacs, Aaron, Johnson, Jon, Kleber, Marcus E., Kooner, Jaspal S., Langenberg, Claudia, Luan, Jian'an, Malerba, Giovanni, Marz, Winfried, Matchan, Angela, Morris, Richard, Nordestgaard, Børge G., Benn, Marianne, Scott, Robert A., Toniolo, Daniela, Traglia, Michela, Tybjaerg-Hansen, Anne, van Duijn, Cornelia M., van Leeuwen, Elisabeth M., Varbo, Anette, Whincup, Peter, Zaza, Gianluigi, and Zhang, Weihua

Published
2019
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26. Low-frequency variation in TP53 has large effects on head circumference and intracranial volume

Author

Haworth, Simon, Shapland, Chin Yang, Hayward, Caroline, Prins, Bram P., Felix, Janine F., Medina-Gomez, Carolina, Rivadeneira, Fernando, Wang, Carol, Ahluwalia, Tarunveer S., Vrijheid, Martine, Guxens, Monica, Sunyer, Jordi, Tachmazidou, Ioanna, Walter, Klaudia, Iotchkova, Valentina, Jackson, Andrew, Cleal, Louise, Huffmann, Jennifer, Min, Josine L., Sass, Laerke, Timmers, Paul R. H. J., Al Turki, Saeed, Anderson, Carl A., Anney, Richard, Antony, Dinu, Artigas, Maria Soler, Ayub, Muhammad, Bala, Senduran, Barrett, Jeffrey C., Barroso, Ines, Beales, Phil, Bentham, Jamie, Bhattacharya, Shoumo, Birney, Ewan, Blackwood, Douglas, Bobrow, Martin, Bochukova, Elena, Bolton, Patrick F., Bounds, Rebecca, Boustred, Chris, Breen, Gerome, Calissano, Mattia, Carss, Keren, Charlton, Ruth, Chatterjee, Krishna, Chen, Lu, Ciampi, Antonio, Cirak, Sebahattin, Clapham, Peter, Clement, Gail, Coates, Guy, Cocca, Massimiliano, Collier, David A., Cosgrove, Catherine, Cox, Tony, Craddock, Nick, Crooks, Lucy, Curran, Sarah, Curtis, David, Daly, Allan, Danecek, Petr, Day, Ian N. M., Day-Williams, Aaron, Dominiczak, Anna, Down, Thomas, Du, Yuanping, Dunham, Ian, Durbin, Richard, Edkins, Sarah, Ekong, Rosemary, Ellis, Peter, Evans, David M., Farooqi, I. Sadaf, Fitzpatrick, David R., Flicek, Paul, Floyd, James, Foley, A. Reghan, Franklin, Christopher S., Futema, Marta, Gallagher, Louise, Gaunt, Tom R., Geihs, Matthias, Geschwind, Daniel, Greenwood, Celia M. T., Griffin, Heather, Grozeva, Detelina, Guo, Xiaosen, Guo, Xueqin, Gurling, Hugh, Hart, Deborah, Hendricks, Audrey E., Holmans, Peter, Howie, Bryan, Huang, Jie, Huang, Liren, Hubbard, Tim, Humphries, Steve E., Hurles, Matthew E., Hysi, Pirro, Jackson, David K., Jamshidi, Yalda, Joyce, Chris, Karczewski, Konrad J., Kaye, Jane, Keane, Thomas, Kemp, John P., Kennedy, Karen, Kent, Alastair, Keogh, Julia, Khawaja, Farrah, van Kogelenberg, Margriet, Kolb-Kokocinski, Anja, Lachance, Genevieve, Langford, Cordelia, Lawson, Daniel, Lee, Irene, Lek, Monkol, Li, Rui, Li, Yingrui, Liang, Jieqin, Lin, Hong, Liu, Ryan, Lonnqvist, Jouko, Lopes, Luis R., Lopes, Margarida, MacArthur, Daniel G., Mangino, Massimo, Marchini, Jonathan, Marenne, Gaelle, Maslen, John, Mathieson, Iain, McCarthy, Shane, McGuffin, Peter, McIntosh, Andrew M., McKechanie, Andrew G., McQuillin, Andrew, Memari, Yasin, Metrustry, Sarah, Migone, Nicola, Mitchison, Hannah M., Moayyeri, Alireza, Morris, Andrew, Morris, James, Muddyman, Dawn, Muntoni, Francesco, Northstone, Kate, O'Donovan, Michael C., O'Rahilly, Stephen, Onoufriadis, Alexandros, Oualkacha, Karim, Owen, Michael J., Palotie, Aarno, Panoutsopoulou, Kalliope, Parker, Victoria, Parr, Jeremy R., Paternoster, Lavinia, Paunio, Tiina, Payne, Felicity, Payne, Stewart J., Perry, John R. B., Pietilainen, Olli, Plagnol, Vincent, Pollitt, Rebecca C., Porteous, David J., Povey, Sue, Quail, Michael A., Quaye, Lydia, Raymond, F. Lucy, Rehnstrom, Karola, Richards, J. Brent, Ridout, Cheryl K., Ring, Susan, Ritchie, Graham R. S., Roberts, Nicola, Robinson, Rachel L., Savage, David B., Scambler, Peter, Schiffels, Stephan, Schmidts, Miriam, Schoenmakers, Nadia, Scott, Richard H., Semple, Robert K., Serra, Eva, Sharp, Sally I., Shaw, Adam, Shihab, Hashem A., Shin, So-Youn, Skuse, David, Small, Kerrin S., Smee, Carol, Smith, Blair H., Soranzo, Nicole, Southam, Lorraine, Spasic-Boskovic, Olivera, Spector, Timothy D., St Clair, David, Stalker, Jim, Stevens, Elizabeth, Sun, Jianping, Surdulescu, Gabriela, Suvisaari, Jaana, Syrris, Petros, Taylor, Rohan, Tian, Jing, Tobin, Martin D., Valdes, Ana M., Vandersteen, Anthony M., Vijayarangakannan, Parthiban, Visscher, Peter M., Wain, Louise V., Walters, James T. R., Wang, Guangbiao, Wang, Jun, Wang, Yu, Ward, Kirsten, Wheeler, Eleanor, Whyte, Tamieka, Williams, Hywel J., Williamson, Kathleen A., Wilson, Crispian, Wilson, Scott G., Wong, Kim, Xu, ChangJiang, Yang, Jian, Zhang, Feng, Zhang, Pingbo, Zheng, Hou-Feng, Smith, George Davey, Fisher, Simon E., Wilson, James F., Cole, Tim J., Fernandez-Orth, Dietmar, Bonnelykke, Klaus, Bisgaard, Hans, Pennell, Craig E., Jaddoe, Vincent W. V., Dedoussis, George, Timpson, Nicholas, Zeggini, Eleftheria, Vitart, Veronique, St Pourcain, Beate, Haworth, Simon, Shapland, Chin Yang, Hayward, Caroline, Prins, Bram P., Felix, Janine F., Medina-Gomez, Carolina, Rivadeneira, Fernando, Wang, Carol, Ahluwalia, Tarunveer S., Vrijheid, Martine, Guxens, Monica, Sunyer, Jordi, Tachmazidou, Ioanna, Walter, Klaudia, Iotchkova, Valentina, Jackson, Andrew, Cleal, Louise, Huffmann, Jennifer, Min, Josine L., Sass, Laerke, Timmers, Paul R. H. J., Al Turki, Saeed, Anderson, Carl A., Anney, Richard, Antony, Dinu, Artigas, Maria Soler, Ayub, Muhammad, Bala, Senduran, Barrett, Jeffrey C., Barroso, Ines, Beales, Phil, Bentham, Jamie, Bhattacharya, Shoumo, Birney, Ewan, Blackwood, Douglas, Bobrow, Martin, Bochukova, Elena, Bolton, Patrick F., Bounds, Rebecca, Boustred, Chris, Breen, Gerome, Calissano, Mattia, Carss, Keren, Charlton, Ruth, Chatterjee, Krishna, Chen, Lu, Ciampi, Antonio, Cirak, Sebahattin, Clapham, Peter, Clement, Gail, Coates, Guy, Cocca, Massimiliano, Collier, David A., Cosgrove, Catherine, Cox, Tony, Craddock, Nick, Crooks, Lucy, Curran, Sarah, Curtis, David, Daly, Allan, Danecek, Petr, Day, Ian N. M., Day-Williams, Aaron, Dominiczak, Anna, Down, Thomas, Du, Yuanping, Dunham, Ian, Durbin, Richard, Edkins, Sarah, Ekong, Rosemary, Ellis, Peter, Evans, David M., Farooqi, I. Sadaf, Fitzpatrick, David R., Flicek, Paul, Floyd, James, Foley, A. Reghan, Franklin, Christopher S., Futema, Marta, Gallagher, Louise, Gaunt, Tom R., Geihs, Matthias, Geschwind, Daniel, Greenwood, Celia M. T., Griffin, Heather, Grozeva, Detelina, Guo, Xiaosen, Guo, Xueqin, Gurling, Hugh, Hart, Deborah, Hendricks, Audrey E., Holmans, Peter, Howie, Bryan, Huang, Jie, Huang, Liren, Hubbard, Tim, Humphries, Steve E., Hurles, Matthew E., Hysi, Pirro, Jackson, David K., Jamshidi, Yalda, Joyce, Chris, Karczewski, Konrad J., Kaye, Jane, Keane, Thomas, Kemp, John P., Kennedy, Karen, Kent, Alastair, Keogh, Julia, Khawaja, Farrah, van Kogelenberg, Margriet, Kolb-Kokocinski, Anja, Lachance, Genevieve, Langford, Cordelia, Lawson, Daniel, Lee, Irene, Lek, Monkol, Li, Rui, Li, Yingrui, Liang, Jieqin, Lin, Hong, Liu, Ryan, Lonnqvist, Jouko, Lopes, Luis R., Lopes, Margarida, MacArthur, Daniel G., Mangino, Massimo, Marchini, Jonathan, Marenne, Gaelle, Maslen, John, Mathieson, Iain, McCarthy, Shane, McGuffin, Peter, McIntosh, Andrew M., McKechanie, Andrew G., McQuillin, Andrew, Memari, Yasin, Metrustry, Sarah, Migone, Nicola, Mitchison, Hannah M., Moayyeri, Alireza, Morris, Andrew, Morris, James, Muddyman, Dawn, Muntoni, Francesco, Northstone, Kate, O'Donovan, Michael C., O'Rahilly, Stephen, Onoufriadis, Alexandros, Oualkacha, Karim, Owen, Michael J., Palotie, Aarno, Panoutsopoulou, Kalliope, Parker, Victoria, Parr, Jeremy R., Paternoster, Lavinia, Paunio, Tiina, Payne, Felicity, Payne, Stewart J., Perry, John R. B., Pietilainen, Olli, Plagnol, Vincent, Pollitt, Rebecca C., Porteous, David J., Povey, Sue, Quail, Michael A., Quaye, Lydia, Raymond, F. Lucy, Rehnstrom, Karola, Richards, J. Brent, Ridout, Cheryl K., Ring, Susan, Ritchie, Graham R. S., Roberts, Nicola, Robinson, Rachel L., Savage, David B., Scambler, Peter, Schiffels, Stephan, Schmidts, Miriam, Schoenmakers, Nadia, Scott, Richard H., Semple, Robert K., Serra, Eva, Sharp, Sally I., Shaw, Adam, Shihab, Hashem A., Shin, So-Youn, Skuse, David, Small, Kerrin S., Smee, Carol, Smith, Blair H., Soranzo, Nicole, Southam, Lorraine, Spasic-Boskovic, Olivera, Spector, Timothy D., St Clair, David, Stalker, Jim, Stevens, Elizabeth, Sun, Jianping, Surdulescu, Gabriela, Suvisaari, Jaana, Syrris, Petros, Taylor, Rohan, Tian, Jing, Tobin, Martin D., Valdes, Ana M., Vandersteen, Anthony M., Vijayarangakannan, Parthiban, Visscher, Peter M., Wain, Louise V., Walters, James T. R., Wang, Guangbiao, Wang, Jun, Wang, Yu, Ward, Kirsten, Wheeler, Eleanor, Whyte, Tamieka, Williams, Hywel J., Williamson, Kathleen A., Wilson, Crispian, Wilson, Scott G., Wong, Kim, Xu, ChangJiang, Yang, Jian, Zhang, Feng, Zhang, Pingbo, Zheng, Hou-Feng, Smith, George Davey, Fisher, Simon E., Wilson, James F., Cole, Tim J., Fernandez-Orth, Dietmar, Bonnelykke, Klaus, Bisgaard, Hans, Pennell, Craig E., Jaddoe, Vincent W. V., Dedoussis, George, Timpson, Nicholas, Zeggini, Eleftheria, Vitart, Veronique, and St Pourcain, Beate

Abstract

Cranial growth and development is a complex process which affects the closely related traits of head circumference (HC) and intracranial volume (ICV). The underlying genetic influences shaping these traits during the transition from childhood to adulthood are little understood, but might include both age-specific genetic factors and low-frequency genetic variation. Here, we model the developmental genetic architecture of HC, showing this is genetically stable and correlated with genetic determinants of ICV. Investigating up to 46,000 children and adults of European descent, we identify association with final HC and/or final ICV + HC at 9 novel common and low-frequency loci, illustrating that genetic variation from a wide allele frequency spectrum contributes to cranial growth. The largest effects are reported for low-frequency variants within TP53, with 0.5 cm wider heads in increaser-allele carriers versus non-carriers during mid-childhood, suggesting a previously unrecognized role of TP53 transcripts in human cranial development.

Published
2019

27. Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity

Author

Hendricks, Audrey E., Bochukova, Elena G., Marenne, Gaëlle, Keogh, Julia M., Atanassova, Neli, Bounds, Rebecca, Wheeler, Eleanor, Mistry, Vanisha, Henning, Elana, Körner, Antje, Muddyman, Dawn, McCarthy, Shane, Hinney, Anke, Hebebrand, Johannes, Scott, Robert A., Langenberg, Claudia, Wareham, Nick J., Surendran, Praveen, Howson, Joanna M M, Butterworth, Adam S., Danesh, John, Nordestgaard, Børge G., Nielsen, Sune F., Afzal, Shoaib, Papadia, Sofia, Ashford, Sofie, Garg, Sumedha, Millhauser, Glenn L., Palomino, Rafael I., Kwasniewska, Alexandra, Tachmazidou, Ioanna, O'Rahilly, Stephen, Zeggini, Eleftheria, Barroso, Inês, Farooqi, I. Sadaf, Benzeval, Michaela, Burton, Jonathan, Buck, Nicholas, Jäckle, Annette, Kumari, Meena, Laurie, Heather, Lynn, Peter, Pudney, Stephen, Rabe, Birgitta, Wolke, Dieter, Overvad, Kim, Tjønneland, Anne, Clavel-Chapelon, Francoise, Kaaks, Rudolf, Boeing, Heiner, Trichopoulou, Antonia, Ferrari, Pietro, Palli, Domenico, Krogha, Vittorio, Panico, Salvatore, Tuminoa, Rosario, Matullo, Giuseppe, Boer, Jolanda Ma, Van Der Schouw, Yvonne, Weiderpass, Elisabete, Quiros, J. Ramon, Sánchez, María José, Navarro, Carmen, Moreno-Iribas, Conchi, Arriola, Larraitz, Melander, Olle, Wennberg, Patrik, Key, Timothy J., Riboli, Elio, Al-Turki, Saeed, Anderson, Carl A, Anney, Richard, Antony, Dinu, Soler Artigas, María, Ayub, Muhammad, Bala, Senduran, Barrett, Jeffrey C, Beales, Phil, Bentham, Jamie, Bhattacharyaa, Shoumo, Birney, Ewan, Blackwooda, Douglas, Bobrow, Martin, Bolton, Patrick F., Boustred, Chris, Breen, Gerome, Calissanoa, Mattia, Carss, Keren, Charlton, Ruth, Chatterjee, Krishna, Chen, Lu, Ciampia, Antonio, Cirak, Sebahattin, Clapham, Peter, Clement, Gail, Coates, Guy, Coccaa, Massimiliano, Collier, David A, Cosgrove, Catherine, Coxa, Tony, Craddock, Nick, Crooks, Lucy, Curran, Sarah, Curtis, David, Daly, Allan, Danecek, Petr, Day, Ian N M, Day-Williams, Aaron G, Dominiczak, Anna, Down, Thomas, Du, Yuanping, Dunham, Ian, Durbin, Richard, Edkins, Sarah, Ekong, Rosemary, Ellis, Peter, Evansa, David M., FitzPatrick, David R., Flicek, Paul, Floyd, James S., Foley, A. Reghan, Franklin, Christopher S., Futema, Marta, Gallagher, Louise, Gaunt, Tom R., Geihs, Matthias, Geschwind, Daniel H., Greenwood, Celia M.T., Griffin, Heather, Grozeva, Detelina, Guo, Xiaosen, Guo, Xueqin, Gurling, Hugh, Hart, Deborah J., Holmans, Peter A, Howie, Bryan, Huang, Jie, Huang, Liren, Hubbard, Tim, Humphries, Steve E., Hurles, Matthew E., Hysi, Pirro G., Iotchkova, Valentina, Jackson, David K., Jamshidi, Yalda, Joyce, Chris, Karczewski, Konrad J., Kaye, Jane, Keane, Thomas, Kemp, John P., Kennedy, Karen, Kent, Alastair, Khawaja, Farrah, Van Kogelenberg, Margriet, Kolb-Kokocinski, Anja, Lachance, Genevieve, Langford, Cordelia, Lawson, Daniel, Lee, Irene, Lek, Monkol, Li, Rui, Li, Yingrui, Liang, Jieqin, Lin, Hong, Liu, Ryan, Lönnqvist, Jouko, Lopes, Luis R., Lopes, Margarida, MacArthur, Daniel G., Mangino, Massimo, Marchini, Jonathan, Maslen, John, Mathieson, Iain, McGuffin, Peter, McIntosh, Andrew M., McKechanie, Andrew G., McQuillin, Andrew, Memari, Yasin, Metrustry, Sarah, Migone, Nicola, Min, Josine L., Mitchison, Hannah M, Moayyeri, Alireza, Morris, Andrew D., Morris, James, Muntoni, Francesco, Northstone, Kate, O'Donovan, Michael C., Onoufriadis, Alexandros, Oualkacha, Karim, Owen, Michael J, Palotie, Aarno, Panoutsopoulou, Kalliope, Parker, Victoria, Parr, Jeremy R., Paternoster, Lavinia, Paunio, Tiina, Payne, Felicity, Payne, Stewart J., Perry, John R. B., Pietilainen, Olli, Plagnol, Vincent, Pollitt, Rebecca C., Porteous, David J., Povey, Sue, Quail, Michael A., Quaye, Lydia, Raymond, F. Lucy, Rehnström, Karola, Richards, J Brent, Ridout, Cheryl K., Ring, Susan M., Ritchie, Graham R.S., Roberts, Nicola, Robinson, Rachel L., Savage, David B., Scambler, Peter, Schiffels, Stephan, Schmidts, Miriam, Schoenmakers, Nadia, Scott, Richard H., Semple, Robert K., Serra, Eva, Sharp, Sally I., Shaw, Adam, Shihab, Hashem A., Shin, So Youn, Skuse, David, Small, Kerrin S, Smee, Carol, Smith, Blair H., Davey Smith, George, Soranzo, Nicole, Southam, Lorraine, Spasic-Boskovic, Olivera, Spector, Timothy D, St Clair, David, St Pourcain, Beate, Stalker, Jim, Stevens, Elizabeth, Sun, Jianping, Surdulescu, Gabriela L, Suvisaari, Jaana, Syrris, Petros, Taylor, Rohan, Tian, Jing, Timpson, Nicholas J., Tobin, Martin D, Valdes, Ana M., Vandersteen, Anthony M., Vijayarangakannan, Parthiban, Visscher, Peter M., Wain, Louise V., Walter, Klaudia, Walters, James T.R., Wang, Guangbiao, Wang, Jun, Wang, Nai-Yu, Ward, Kirsten, Whyte, Tamieka, Williams, Hywel J., Williamson, Kathleen A., Wilson, Crispian, Wilson, Scott G., Wong, Kim, Xu, Changjiang, Yang, Jian, Zhang, Feng, Zhang, Pingbo, Zheng, Hou Feng, Hendricks, Audrey E., Bochukova, Elena G., Marenne, Gaã«lle, Keogh, Julia M., Atanassova, Neli, Bounds, Rebecca, Wheeler, Eleanor, Mistry, Vanisha, Henning, Elana, Kã¶rner, Antje, Muddyman, Dawn, Mccarthy, Shane, Hinney, Anke, Hebebrand, Johanne, Scott, Robert A., Langenberg, Claudia, Wareham, Nick J., Surendran, Praveen, Howson, Joanna M., Butterworth, Adam S., Danesh, John, Nordestgaard, Bã¸rge G, Nielsen, Sune F, Afzal, Shoaib, Papadia, Sofia, Ashford, Sofie, Garg, Sumedha, Millhauser, Glenn L., Palomino, Rafael I., Kwasniewska, Alexandra, Tachmazidou, Ioanna, O'Rahilly, Stephen, Zeggini, Eleftheria, Barroso, Inãª, Farooqi, I. Sadaf, Benzeval, Michaela, Burton, Jonathan, Buck, Nichola, Jã¤ckle, Annette, Kumari, Meena, Laurie, Heather, Lynn, Peter, Pudney, Stephen, Rabe, Birgitta, Wolke, Dieter, Overvad, Kim, Tjã¸nneland, Anne, Clavel chapelon, Francoise, Kaaks, Rudolf, Boeing, Heiner, Trichopoulou, Antonia, Ferrari, Pietro, Palli, Domenico, Krogha, Vittorio, Panico, Salvatore, Tuminoa, Rosario, Matullo, Giuseppe, Boer, Jolanda, Van Der Schouw, Yvonne, Weiderpass, Elisabete, Quiros, J. Ramon, Sã¡nchez, Marã­a josã©, Navarro, Carmen, Moreno iribas, Conchi, Arriola, Larraitz, Melander, Olle, Wennberg, Patrik, Key, Timothy J., Riboli, Elio, Turki, Saeed Al, Anderson, Carl A., Anney, Richard, Antony, Dinu, Soler Artigas, Marã­a, Ayub, Muhammad, Bala, Senduran, Barrett, Jeffrey C., Beales, Phil, Bentham, Jamie, Bhattacharyaa, Shoumo, Birney, Ewan, Blackwooda, Dougla, Bobrow, Martin, Bolton, Patrick F., Boustred, Chri, Breen, Gerome, Calissanoa, Mattia, Carss, Keren, Charlton, Ruth, Chatterjee, Krishna, Chen, Lu, Ciampia, Antonio, Cirak, Sebahattin, Clapham, Peter, Clement, Gail, Coates, Guy, Coccaa, Massimiliano, Collier, David A., Cosgrove, Catherine, Coxa, Tony, Craddock, Nick, Crooks, Lucy, Curran, Sarah, Curtis, David, Daly, Allan, Danecek, Petr, Day, Ian N. M., Day williams, Aaron, Dominiczak, Anna, Down, Thoma, Du, Yuanping, Dunham, Ian, Durbin, Richard, Edkins, Sarah, Ekong, Rosemary, Ellis, Peter, Evansa, David M., Fitzpatrick, David R., Flicek, Paul, Floyd, Jame, Foley, A. Reghan, Franklin, Christopher S., Futema, Marta, Gallagher, Louise, Gaunt, Tom R., Geihs, Matthia, Geschwind, Daniel, Greenwood, Celia M. T., Griffin, Heather, Grozeva, Detelina, Guo, Xiaosen, Guo, Xueqin, Gurling, Hugh, Hart, Deborah, Holmans, Peter, Howie, Bryan, Huang, Jie, Huang, Liren, Hubbard, Tim, Humphries, Steve E., Hurles, Matthew E., Hysi, Pirro, Iotchkova, Valentina, Jackson, David K., Jamshidi, Yalda, Joyce, Chri, Karczewski, Konrad J., Kaye, Jane, Keane, Thoma, Kemp, John P., Kennedy, Karen, Kent, Alastair, Khawaja, Farrah, Van Kogelenberg, Margriet, Kolb kokocinski, Anja, Lachance, Genevieve, Langford, Cordelia, Lawson, Daniel, Lee, Irene, Lek, Monkol, Li, Rui, Li, Yingrui, Liang, Jieqin, Lin, Hong, Liu, Ryan, Lã¶nnqvist, Jouko, Lopes, Luis R., Lopes, Margarida, Macarthur, Daniel G., Mangino, Massimo, Marchini, Jonathan, Maslen, John, Mathieson, Iain, Mcguffin, Peter, Mcintosh, Andrew M., Mckechanie, Andrew G., Mcquillin, Andrew, Memari, Yasin, Metrustry, Sarah, Migone, Nicola, Min, Josine L., Mitchison, Hannah M., Moayyeri, Alireza, Morris, Andrew, Morris, Jame, Muntoni, Francesco, Northstone, Kate, O'Donovan, Michael C., Onoufriadis, Alexandro, Oualkacha, Karim, Owen, Michael J., Palotie, Aarno, Panoutsopoulou, Kalliope, Parker, Victoria, Parr, Jeremy R., Paternoster, Lavinia, Paunio, Tiina, Payne, Felicity, Payne, Stewart J., Perry, John R. B., Pietilainen, Olli, Plagnol, Vincent, Pollitt, Rebecca C., Porteous, David J., Povey, Sue, Quail, Michael A., Quaye, Lydia, Raymond, F. Lucy, Rehnstrã¶m, Karola, Richards, J. Brent, Ridout, Cheryl K., Ring, Susan, Ritchie, Graham R. S., Roberts, Nicola, Robinson, Rachel L., Savage, David B., Scambler, Peter, Schiffels, Stephan, Schmidts, Miriam, Schoenmakers, Nadia, Scott, Richard H., Semple, Robert K., Serra, Eva, Sharp, Sally I., Shaw, Adam, Shihab, Hashem A., Shin, So youn, Skuse, David, Small, Kerrin S., Smee, Carol, Smith, Blair H., Davey Smith, George, Soranzo, Nicole, Southam, Lorraine, Spasic boskovic, Olivera, Spector, Timothy D., St Clair, David, St Pourcain, Beate, Stalker, Jim, Stevens, Elizabeth, Sun, Jianping, Surdulescu, Gabriela, Suvisaari, Jaana, Syrris, Petro, Taylor, Rohan, Tian, Jing, Timpson, Nicholas J., Tobin, Martin D., Valdes, Ana M., Vandersteen, Anthony M., Vijayarangakannan, Parthiban, Visscher, Peter M., Wain, Louise V., Walter, Klaudia, Walters, James T. R., Wang, Guangbiao, Wang, Jun, Wang, Yu, Ward, Kirsten, Whyte, Tamieka, Williams, Hywel J., Williamson, Kathleen A., Wilson, Crispian, Wilson, Scott G., Wong, Kim, Xu, Changjiang, Yang, Jian, Zhang, Feng, Zhang, Pingbo, and Zheng, Hou feng

Subjects
Multidisciplinary, Journal Article, General
Abstract

Obesity is a genetically heterogeneous disorder. Using targeted and whole-exome sequencing, we studied 32 human and 87 rodent obesity genes in 2,548 severely obese children and 1,117 controls. We identified 52 variants contributing to obesity in 2% of cases including multiple novel variants in GNAS, which were sometimes found with accelerated growth rather than short stature as describedw previously. Nominally significant associations were found for rare functional variants in BBS1, BBS9, GNAS, MKKS, CLOCK and ANGPTL6. The p.S284X variant in ANGPTL6 drives the association signal (rs201622589, MAF∼0.1%, odds ratio = 10.13, p-value = 0.042) and results in complete loss of secretion in cells. Further analysis including additional case-control studies and population controls (N = 260,642) did not support association of this variant with obesity (odds ratio = 2.34, p-value = 2.59 × 10-3), highlighting the challenges of testing rare variant associations and the need for very large sample sizes. Further validation in cohorts with severe obesity and engineering the variants in model organisms will be needed to explore whether human variants in ANGPTL6 and other genes that lead to obesity when deleted in mice, do contribute to obesity. Such studies may yield druggable targets for weight loss therapies.

Published
2017

28. The sequence and analysis of a Chinese pig genome

Author

Fang Xiaodong, Mu Yulian, Huang Zhiyong, Li Yong, Han Lijuan, Zhang Yanfeng, Feng Yue, Chen Yuanxin, Jiang Xuanting, Zhao Wei, Sun Xiaoqing, Xiong Zhiqiang, Yang Lan, Liu Huan, Fan Dingding, Mao Likai, Ren Lijie, Liu Chuxin, Wang Juan, Li Kui, Wang Guangbiao, Yang Shulin, Lai Liangxue, Zhang Guojie, Li Yingrui, Wang Jun, Bolund Lars, Yang Huanming, Wang Jian, Feng Shutang, Li Songgang, and Du Yutao

Subjects
Wuzhishan pig, Genome, Homozygosis, Transposable element, Endogenous retrovirus, Animal model, Computer applications to medicine. Medical informatics, R858-859.7
Abstract

Abstract Background The pig is an economically important food source, amounting to approximately 40% of all meat consumed worldwide. Pigs also serve as an important model organism because of their similarity to humans at the anatomical, physiological and genetic level, making them very useful for studying a variety of human diseases. A pig strain of particular interest is the miniature pig, specifically the Wuzhishan pig (WZSP), as it has been extensively inbred. Its high level of homozygosity offers increased ease for selective breeding for specific traits and a more straightforward understanding of the genetic changes that underlie its biological characteristics. WZSP also serves as a promising means for applications in surgery, tissue engineering, and xenotransplantation. Here, we report the sequencing and analysis of an inbreeding WZSP genome. Results Our results reveal some unique genomic features, including a relatively high level of homozygosity in the diploid genome, an unusual distribution of heterozygosity, an over-representation of tRNA-derived transposable elements, a small amount of porcine endogenous retrovirus, and a lack of type C retroviruses. In addition, we carried out systematic research on gene evolution, together with a detailed investigation of the counterparts of human drug target genes. Conclusion Our results provide the opportunity to more clearly define the genomic character of pig, which could enhance our ability to create more useful pig models.

Published
2012
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29. Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia

Author

Gorman, Kathleen M., primary, Meyer, Esther, additional, Grozeva, Detelina, additional, Spinelli, Egidio, additional, McTague, Amy, additional, Sanchis-Juan, Alba, additional, Carss, Keren J., additional, Bryant, Emily, additional, Reich, Adi, additional, Schneider, Amy L., additional, Pressler, Ronit M., additional, Simpson, Michael A., additional, Debelle, Geoff D., additional, Wassmer, Evangeline, additional, Morton, Jenny, additional, Sieciechowicz, Diana, additional, Jan-Kamsteeg, Eric, additional, Paciorkowski, Alex R., additional, King, Mary D., additional, Cross, J. Helen, additional, Poduri, Annapurna, additional, Mefford, Heather C., additional, Scheffer, Ingrid E., additional, Haack, Tobias B., additional, McCullagh, Gary, additional, Millichap, John J., additional, Carvill, Gemma L., additional, Clayton-Smith, Jill, additional, Maher, Eamonn R., additional, Raymond, F. Lucy, additional, Kurian, Manju A., additional, McRae, Jeremy F., additional, Clayton, Stephen, additional, Fitzgerald, Tomas W., additional, Kaplanis, Joanna, additional, Prigmore, Elena, additional, Rajan, Diana, additional, Sifrim, Alejandro, additional, Aitken, Stuart, additional, Akawi, Nadia, additional, Alvi, Mohsan, additional, Ambridge, Kirsty, additional, Barrett, Daniel M., additional, Bayzetinova, Tanya, additional, Jones, Philip, additional, Jones, Wendy D., additional, King, Daniel, additional, Krishnappa, Netravathi, additional, Mason, Laura E., additional, Singh, Tarjinder, additional, Tivey, Adrian R., additional, Ahmed, Munaza, additional, Anjum, Uruj, additional, Archer, Hayley, additional, Armstrong, Ruth, additional, Awada, Jana, additional, Balasubramanian, Meena, additional, Banka, Siddharth, additional, Baralle, Diana, additional, Barnicoat, Angela, additional, Batstone, Paul, additional, Baty, David, additional, Bennett, Chris, additional, Berg, Jonathan, additional, Bernhard, Birgitta, additional, Bevan, A. Paul, additional, Bitner-Glindzicz, Maria, additional, Blair, Edward, additional, Blyth, Moira, additional, Bohanna, David, additional, Bourdon, Louise, additional, Bourn, David, additional, Bradley, Lisa, additional, Brady, Angela, additional, Brent, Simon, additional, Brewer, Carole, additional, Brunstrom, Kate, additional, Bunyan, David J., additional, Burn, John, additional, Canham, Natalie, additional, Castle, Bruce, additional, Chandler, Kate, additional, Chatzimichali, Elena, additional, Cilliers, Deirdre, additional, Clarke, Angus, additional, Clasper, Susan, additional, Clowes, Virginia, additional, Coates, Andrea, additional, Cole, Trevor, additional, Colgiu, Irina, additional, Collins, Amanda, additional, Collinson, Morag N., additional, Connell, Fiona, additional, Cooper, Nicola, additional, Cox, Helen, additional, Cresswell, Lara, additional, Cross, Gareth, additional, Crow, Yanick, additional, D’Alessandro, Mariella, additional, Dabir, Tabib, additional, Davidson, Rosemarie, additional, Davies, Sally, additional, de Vries, Dylan, additional, Dean, John, additional, Deshpande, Charu, additional, Devlin, Gemma, additional, Dixit, Abhijit, additional, Dobbie, Angus, additional, Donaldson, Alan, additional, Donnai, Dian, additional, Donnelly, Deirdre, additional, Donnelly, Carina, additional, Douglas, Angela, additional, Douzgou, Sofia, additional, Duncan, Alexis, additional, Eason, Jacqueline, additional, Ellard, Sian, additional, Ellis, Ian, additional, Elmslie, Frances, additional, Evans, Karenza, additional, Everest, Sarah, additional, Fendick, Tina, additional, Fisher, Richard, additional, Flinter, Frances, additional, Foulds, Nicola, additional, Fry, Andrew, additional, Fryer, Alan, additional, Gardiner, Carol, additional, Gaunt, Lorraine, additional, Ghali, Neeti, additional, Gibbons, Richard, additional, Gill, Harinder, additional, Goodship, Judith, additional, Goudie, David, additional, Gray, Emma, additional, Green, Andrew, additional, Greene, Philip, additional, Greenhalgh, Lynn, additional, Gribble, Susan, additional, Harrison, Rachel, additional, Harrison, Lucy, additional, Harrison, Victoria, additional, Hawkins, Rose, additional, He, Liu, additional, Hellens, Stephen, additional, Henderson, Alex, additional, Hewitt, Sarah, additional, Hildyard, Lucy, additional, Hobson, Emma, additional, Holden, Simon, additional, Holder, Muriel, additional, Holder, Susan, additional, Hollingsworth, Georgina, additional, Homfray, Tessa, additional, Humphreys, Mervyn, additional, Hurst, Jane, additional, Hutton, Ben, additional, Ingram, Stuart, additional, Irving, Melita, additional, Islam, Lily, additional, Jackson, Andrew, additional, Jarvis, Joanna, additional, Jenkins, Lucy, additional, Johnson, Diana, additional, Jones, Elizabeth, additional, Josifova, Dragana, additional, Joss, Shelagh, additional, Kaemba, Beckie, additional, Kazembe, Sandra, additional, Kelsell, Rosemary, additional, Kerr, Bronwyn, additional, Kingston, Helen, additional, Kini, Usha, additional, Kinning, Esther, additional, Kirby, Gail, additional, Kirk, Claire, additional, Kivuva, Emma, additional, Kraus, Alison, additional, Kumar, Dhavendra, additional, Kumar, V. K. Ajith, additional, Lachlan, Katherine, additional, Lam, Wayne, additional, Lampe, Anne, additional, Langman, Caroline, additional, Lees, Melissa, additional, Lim, Derek, additional, Longman, Cheryl, additional, Lowther, Gordon, additional, Lynch, Sally A., additional, Magee, Alex, additional, Maher, Eddy, additional, Male, Alison, additional, Mansour, Sahar, additional, Marks, Karen, additional, Martin, Katherine, additional, Maye, Una, additional, McCann, Emma, additional, McConnell, Vivienne, additional, McEntagart, Meriel, additional, McGowan, Ruth, additional, McKay, Kirsten, additional, McKee, Shane, additional, McMullan, Dominic J., additional, McNerlan, Susan, additional, McWilliam, Catherine, additional, Mehta, Sarju, additional, Metcalfe, Kay, additional, Middleton, Anna, additional, Miedzybrodzka, Zosia, additional, Miles, Emma, additional, Mohammed, Shehla, additional, Montgomery, Tara, additional, Moore, David, additional, Morgan, Sian, additional, Mugalaasi, Hood, additional, Murday, Victoria, additional, Murphy, Helen, additional, Naik, Swati, additional, Nemeth, Andrea, additional, Nevitt, Louise, additional, Newbury-Ecob, Ruth, additional, Norman, Andrew, additional, O’Shea, Rosie, additional, Ogilvie, Caroline, additional, Ong, Kai-Ren, additional, Park, Soo-Mi, additional, Parker, Michael J., additional, Patel, Chirag, additional, Paterson, Joan, additional, Payne, Stewart, additional, Perrett, Daniel, additional, Phipps, Julie, additional, Pilz, Daniela T., additional, Pollard, Martin, additional, Pottinger, Caroline, additional, Poulton, Joanna, additional, Pratt, Norman, additional, Prescott, Katrina, additional, Price, Sue, additional, Pridham, Abigail, additional, Procter, Annie, additional, Purnell, Hellen, additional, Quarrell, Oliver, additional, Ragge, Nicola, additional, Rahbari, Raheleh, additional, Randall, Josh, additional, Rankin, Julia, additional, Raymond, Lucy, additional, Rice, Debbie, additional, Robert, Leema, additional, Roberts, Eileen, additional, Roberts, Jonathan, additional, Roberts, Paul, additional, Roberts, Gillian, additional, Ross, Alison, additional, Rosser, Elisabeth, additional, Saggar, Anand, additional, Samant, Shalaka, additional, Sampson, Julian, additional, Sandford, Richard, additional, Sarkar, Ajoy, additional, Schweiger, Susann, additional, Scott, Richard, additional, Scurr, Ingrid, additional, Selby, Ann, additional, Seller, Anneke, additional, Sequeira, Cheryl, additional, Shannon, Nora, additional, Sharif, Saba, additional, Shaw-Smith, Charles, additional, Shearing, Emma, additional, Shears, Debbie, additional, Sheridan, Eamonn, additional, Simonic, Ingrid, additional, Singzon, Roldan, additional, Skitt, Zara, additional, Smith, Audrey, additional, Smith, Kath, additional, Smithson, Sarah, additional, Sneddon, Linda, additional, Splitt, Miranda, additional, Squires, Miranda, additional, Stewart, Fiona, additional, Stewart, Helen, additional, Straub, Volker, additional, Suri, Mohnish, additional, Sutton, Vivienne, additional, Swaminathan, Ganesh Jawahar, additional, Sweeney, Elizabeth, additional, Tatton-Brown, Kate, additional, Taylor, Cat, additional, Taylor, Rohan, additional, Tein, Mark, additional, Temple, I. Karen, additional, Thomson, Jenny, additional, Tischkowitz, Marc, additional, Tomkins, Susan, additional, Torokwa, Audrey, additional, Treacy, Becky, additional, Turner, Claire, additional, Turnpenny, Peter, additional, Tysoe, Carolyn, additional, Vandersteen, Anthony, additional, Varghese, Vinod, additional, Vasudevan, Pradeep, additional, Vijayarangakannan, Parthiban, additional, Vogt, Julie, additional, Wakeling, Emma, additional, Wallwark, Sarah, additional, Waters, Jonathon, additional, Weber, Astrid, additional, Wellesley, Diana, additional, Whiteford, Margo, additional, Widaa, Sara, additional, Wilcox, Sarah, additional, Wilkinson, Emily, additional, Williams, Denise, additional, Williams, Nicola, additional, Wilson, Louise, additional, Woods, Geoff, additional, Wragg, Christopher, additional, Wright, Michael, additional, Yates, Laura, additional, Yau, Michael, additional, Nellåker, Chris, additional, Parker, Michael, additional, Firth, Helen V., additional, Wright, Caroline F., additional, FitzPatrick, David R., additional, Barrett, Jeffrey C., additional, Hurles, Matthew E., additional, Al Turki, Saeed, additional, Anderson, Carl, additional, Anney, Richard, additional, Antony, Dinu, additional, Artigas, Maria Soler, additional, Ayub, Muhammad, additional, Balasubramaniam, Senduran, additional, Barroso, Inês, additional, Beales, Phil, additional, Bentham, Jamie, additional, Bhattacharya, Shoumo, additional, Birney, Ewan, additional, Blackwood, Douglas, additional, Bobrow, Martin, additional, Bochukova, Elena, additional, Bolton, Patrick, additional, Bounds, Rebecca, additional, Boustred, Chris, additional, Breen, Gerome, additional, Calissano, Mattia, additional, Carss, Keren, additional, Chatterjee, Krishna, additional, Chen, Lu, additional, Ciampi, Antonio, additional, Cirak, Sebhattin, additional, Clapham, Peter, additional, Clement, Gail, additional, Coates, Guy, additional, Collier, David, additional, Cosgrove, Catherine, additional, Cox, Tony, additional, Craddock, Nick, additional, Crooks, Lucy, additional, Curran, Sarah, additional, Curtis, David, additional, Daly, Allan, additional, Day-Williams, Aaron, additional, Day, Ian N.M., additional, Down, Thomas, additional, Du, Yuanping, additional, Dunham, Ian, additional, Edkins, Sarah, additional, Ellis, Peter, additional, Evans, David, additional, Faroogi, Sadaf, additional, Fatemifar, Ghazaleh, additional, Fitzpatrick, David R., additional, Flicek, Paul, additional, Flyod, James, additional, Foley, A. Reghan, additional, Franklin, Christopher S., additional, Futema, Marta, additional, Gallagher, Louise, additional, Geihs, Matthias, additional, Geschwind, Daniel, additional, Griffin, Heather, additional, Guo, Xueqin, additional, Guo, Xiaosen, additional, Gurling, Hugh, additional, Hart, Deborah, additional, Hendricks, Audrey, additional, Holmans, Peter, additional, Howie, Bryan, additional, Huang, Liren, additional, Hubbard, Tim, additional, Humphries, Steve E., additional, Hysi, Pirro, additional, Jackson, David K., additional, Jamshidi, Yalda, additional, Jing, Tian, additional, Joyce, Chris, additional, Kaye, Jane, additional, Keane, Thomas, additional, Keogh, Julia, additional, Kemp, John, additional, Kennedy, Karen, additional, Kolb-Kokocinski, Anja, additional, Lachance, Genevieve, additional, Langford, Cordelia, additional, Lawson, Daniel, additional, Lee, Irene, additional, Lek, Monkol, additional, Liang, Jieqin, additional, Lin, Hong, additional, Li, Rui, additional, Li, Yingrui, additional, Liu, Ryan, additional, Lönnqvist, Jouko, additional, Lopes, Margarida, additional, Iotchkova, Valentina, additional, MacArthur, Daniel, additional, Marchini, Jonathan, additional, Maslen, John, additional, Massimo, Mangino, additional, Mathieson, Iain, additional, Marenne, Gaëlle, additional, McGuffin, Peter, additional, McIntosh, Andrew, additional, McKechanie, Andrew G., additional, McQuillin, Andrew, additional, Metrustry, Sarah, additional, Mitchison, Hannah, additional, Moayyeri, Alireza, additional, Morris, James, additional, Muntoni, Francesco, additional, Northstone, Kate, additional, O'Donnovan, Michael, additional, Onoufriadis, Alexandros, additional, O'Rahilly, Stephen, additional, Oualkacha, Karim, additional, Owen, Michael J., additional, Palotie, Aarno, additional, Panoutsopoulou, Kalliope, additional, Parker, Victoria, additional, Parr, Jeremy R., additional, Paternoster, Lavinia, additional, Paunio, Tiina, additional, Payne, Felicity, additional, Pietilainen, Olli, additional, Plagnol, Vincent, additional, Quaye, Lydia, additional, Quail, Michael A., additional, Rehnström, Karola, additional, Ring, Susan, additional, Ritchie, Graham R.S., additional, Roberts, Nicola, additional, Savage, David B., additional, Scambler, Peter, additional, Schiffels, Stephen, additional, Schmidts, Miriam, additional, Schoenmakers, Nadia, additional, Semple, Robert K., additional, Serra, Eva, additional, Sharp, Sally I., additional, Shin, So-Youn, additional, Skuse, David, additional, Small, Kerrin, additional, Southam, Lorraine, additional, Spasic-Boskovic, Olivera, additional, St Clair, David, additional, Stalker, Jim, additional, Stevens, Elizabeth, additional, St Pourcian, Beate, additional, Sun, Jianping, additional, Suvisaari, Jaana, additional, Tachmazidou, Ionna, additional, Tobin, Martin D., additional, Valdes, Ana, additional, Van Kogelenberg, Margriet, additional, Visscher, Peter M., additional, Wain, Louise V., additional, Walters, James T.R., additional, Wang, Guangbiao, additional, Wang, Jun, additional, Wang, Yu, additional, Ward, Kirsten, additional, Wheeler, Elanor, additional, Whyte, Tamieka, additional, Williams, Hywel, additional, Williamson, Kathleen A., additional, Wilson, Crispian, additional, Wong, Kim, additional, Xu, ChangJiang, additional, Yang, Jian, additional, Zhang, Fend, additional, Zhang, Pingbo, additional, Aitman, Timothy, additional, Alachkar, Hana, additional, Ali, Sonia, additional, Allen, Louise, additional, Allsup, David, additional, Ambegaonkar, Gautum, additional, Anderson, Julie, additional, Antrobus, Richard, additional, Arno, Gavin, additional, Arumugakani, Gururaj, additional, Ashford, Sofie, additional, Astle, William, additional, Attwood, Antony, additional, Austin, Steve, additional, Bacchelli, Chiara, additional, Bakchoul, Tamam, additional, Bariana, Tadbir K., additional, Baxendale, Helen, additional, Bennett, David, additional, Bethune, Claire, additional, Bibi, Shahnaz, additional, Bleda, Marta, additional, Boggard, Harm, additional, Bolton-Maggs, Paula, additional, Booth, Claire, additional, Bradley, John R., additional, Brady, Angie, additional, Brown, Matthew, additional, Browning, Michael, additional, Bryson, Christine, additional, Burns, Siobhan, additional, Calleja, Paul, additional, Carmichael, Jenny, additional, Caulfield, Mark, additional, Chalmers, Elizabeth, additional, Chandra, Anita, additional, Chinnery, Patrick, additional, Chitre, Manali, additional, Church, Colin, additional, Clement, Emma, additional, Clements-Brod, Naomi, additional, Coghlan, Gerry, additional, Collins, Peter, additional, Cooper, Nichola, additional, Creaser-Myers, Amanda, additional, DaCosta, Rosa, additional, Daugherty, Louise, additional, Davies, Sophie, additional, Davis, John, additional, De Vries, Minka, additional, Deegan, Patrick, additional, Deevi, Sri V.V., additional, Devlin, Lisa, additional, Dewhurst, Eleanor, additional, Doffinger, Rainer, additional, Dormand, Natalie, additional, Drewe, Elizabeth, additional, Edgar, David, additional, Egner, William, additional, Erber, Wendy N., additional, Erwood, Marie, additional, Everington, Tamara, additional, Favier, Remi, additional, Firth, Helen, additional, Fletcher, Debra, additional, Fox, James C., additional, Frary, Amy, additional, Freson, Kathleen, additional, Furie, Bruce, additional, Furnell, Abigail, additional, Gale, Daniel, additional, Gardham, Alice, additional, Gattens, Michael, additional, Ghataorhe, Pavandeep K., additional, Ghurye, Rohit, additional, Gibbs, Simon, additional, Gilmour, Kimberley, additional, Gissen, Paul, additional, Goddard, Sarah, additional, Gomez, Keith, additional, Gordins, Pavel, additional, Gräf, Stefan, additional, Greene, Daniel, additional, Greenhalgh, Alan, additional, Greinacher, Andreas, additional, Grigoriadou, Sofia, additional, Hackett, Scott, additional, Hadinnapola, Charaka, additional, Hague, Rosie, additional, Haimel, Matthias, additional, Halmagyi, Csaba, additional, Hammerton, Tracey, additional, Hart, Daniel, additional, Hayman, Grant, additional, Heemskerk, Johan W.M., additional, Henderson, Robert, additional, Hensiek, Anke, additional, Henskens, Yvonne, additional, Herwadkar, Archana, additional, Hu, Fengyuan, additional, Huissoon, Aarnoud, additional, Humbert, Marc, additional, James, Roger, additional, Jolles, Stephen, additional, Kazmi, Rashid, additional, Keeling, David, additional, Kelleher, Peter, additional, Kelly, Anne M., additional, Kennedy, Fiona, additional, Kiely, David, additional, Kingston, Nathalie, additional, Koziell, Ania, additional, Krishnakumar, Deepa, additional, Kuijpers, Taco W., additional, Kumararatne, Dinakantha, additional, Kurian, Manju, additional, Laffan, Michael A., additional, Lambert, Michele P., additional, Allen, Hana Lango, additional, Lawrie, Allan, additional, Lear, Sara, additional, Lentaigne, Claire, additional, Liesner, Ri, additional, Linger, Rachel, additional, Longhurst, Hilary, additional, Lorenzo, Lorena, additional, Machado, Rajiv, additional, Mackenzie, Rob, additional, MacLaren, Robert, additional, Maher, Eamonn, additional, Maimaris, Jesmeen, additional, Mangles, Sarah, additional, Manson, Ania, additional, Mapeta, Rutendo, additional, Markus, Hugh S., additional, Martin, Jennifer, additional, Masati, Larahmie, additional, Mathias, Mary, additional, Matser, Vera, additional, Maw, Anna, additional, McDermott, Elizabeth, additional, McJannet, Coleen, additional, Meacham, Stuart, additional, Meehan, Sharon, additional, Megy, Karyn, additional, Michaelides, Michel, additional, Millar, Carolyn M., additional, Moledina, Shahin, additional, Moore, Anthony, additional, Morrell, Nicholas, additional, Mumford, Andrew, additional, Murng, Sai, additional, Murphy, Elaine, additional, Nejentsev, Sergey, additional, Noorani, Sadia, additional, Nurden, Paquita, additional, Oksenhendler, Eric, additional, Ouwehand, Willem H., additional, Papadia, Sofia, additional, Parker, Alasdair, additional, Pasi, John, additional, Patch, Chris, additional, Payne, Jeanette, additional, Peacock, Andrew, additional, Peerlinck, Kathelijne, additional, Penkett, Christopher J., additional, Pepke-Zaba, Joanna, additional, Perry, David J., additional, Pollock, Val, additional, Polwarth, Gary, additional, Ponsford, Mark, additional, Qasim, Waseem, additional, Quinti, Isabella, additional, Rankin, Stuart, additional, Rehnstrom, Karola, additional, Reid, Evan, additional, Rhodes, Christopher J., additional, Richards, Michael, additional, Richardson, Sylvia, additional, Richter, Alex, additional, Roberts, Irene, additional, Rondina, Matthew, additional, Roughley, Catherine, additional, Rue-Albrecht, Kevin, additional, Samarghitean, Crina, additional, Santra, Saikat, additional, Sargur, Ravishankar, additional, Savic, Sinisa, additional, Schulman, Sol, additional, Schulze, Harald, additional, Scully, Marie, additional, Seneviratne, Suranjith, additional, Sewell, Carrock, additional, Shamardina, Olga, additional, Shipley, Debbie, additional, Simeoni, Ilenia, additional, Sivapalaratnam, Suthesh, additional, Smith, Kenneth, additional, Sohal, Aman, additional, Southgate, Laura, additional, Staines, Simon, additional, Staples, Emily, additional, Stauss, Hans, additional, Stein, Penelope, additional, Stephens, Jonathan, additional, Stirrups, Kathleen, additional, Stock, Sophie, additional, Suntharalingam, Jay, additional, Tait, R. Campbell, additional, Talks, Kate, additional, Tan, Yvonne, additional, Thachil, Jecko, additional, Thaventhiran, James, additional, Thomas, Ellen, additional, Thomas, Moira, additional, Thompson, Dorothy, additional, Thrasher, Adrian, additional, Titterton, Catherine, additional, Toh, Cheng-Hock, additional, Toshner, Mark, additional, Treacy, Carmen, additional, Trembath, Richard, additional, Tuna, Salih, additional, Turek, Wojciech, additional, Turro, Ernest, additional, Van Geet, Chris, additional, Veltman, Marijke, additional, von Ziegenweldt, Julie, additional, Vonk Noordegraaf, Anton, additional, Wanjiku, Ivy, additional, Warner, Timothy Q., additional, Watkins, Hugh, additional, Webster, Andrew, additional, Welch, Steve, additional, Westbury, Sarah, additional, Wharton, John, additional, Whitehorn, Deborah, additional, Wilkins, Martin, additional, Willcocks, Lisa, additional, Williamson, Catherine, additional, Woods, Geoffrey, additional, Wort, John, additional, Yeatman, Nigel, additional, Yong, Patrick, additional, Young, Tim, additional, and Yu, Ping, additional

Published
2019
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30. Extended Risley scanning system with 30?×?360 coverage

Author

Lyu, Jiangbo, Chen, Zhiyu, Wang, Guangbiao, Tan, Meng, Lu, Rongguo, Cao, Zizheng, and Liu, Yong

Abstract

We propose a beam scanning system based on an extended Risley prism structure. This system uses a rotating mirror structure and expands the original construction of the balanced and stable Risley prism. There is much research on extended Risley prism structures, but the scanned angle of their extended systems is less than 180°. The proposed system in this paper can expand scanned angle to 360°, showing practical significance and application value in the field of beam scanning. This is achieved by using reflectors and multiple transmitter and receiver structures with optimized positions and transmission directions. Simulation results show that the scanning range is 360° and ±14^∘ in the horizontal and vertical directions, respectively, at 110 m while the angular resolution is 0.2^∘×2^∘.

Published
2021

31. Design a common optical path system for near- and far-field detection of optical phased array chips.

Author

Shen, Yanhua, Fan, Xingxin, Chen, Zhiyu, Huang, Jiawei, Lu, Rongguo, Wang, Guangbiao, Cao, Zizheng, and Liu, Yong

Subjects
PHASED array antennas, FOCAL length, SPATIAL resolution, ZOOM lenses, DESIGN
Abstract

With the development of optical phased array (OPA) chips, it is urgent to design an optical system for detecting OPA chips. We propose a near- and far-field common optical path detection system adapted to commercial cameras. By changing the focal length of the rear set of lenses, the optical system can be used to realize the near-field detection, far-field field of view (FOV) detection, and far-field resolution detection of OPA chips. The object spatial resolution of the near-field system is 1.11 μm , and the far-field system can achieve ±45 deg FOV detection and 0.0185 deg angular resolution. Simulation results show that it can be used to characterize the far-field spot with 0.1 deg resolution. The optical system is designed with spherical lenses, and its imaging performance approaches the diffraction limit. [ABSTRACT FROM AUTHOR]

Published
2024
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32. Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity

Author

UMC Utrecht, Cardiovasculaire Epidemiologie, Circulatory Health, JC onderzoeksprogramma Cardiovasculaire Epidemiologie, Hendricks, Audrey E., Bochukova, Elena G., Marenne, Gaëlle, Keogh, Julia M., Atanassova, Neli, Bounds, Rebecca, Wheeler, Eleanor, Mistry, Vanisha, Henning, Elana, Körner, Antje, Muddyman, Dawn, McCarthy, Shane, Hinney, Anke, Hebebrand, Johannes, Scott, Robert A., Langenberg, Claudia, Wareham, Nick J., Surendran, Praveen, Howson, Joanna M M, Butterworth, Adam S., Danesh, John, Nordestgaard, Børge G., Nielsen, Sune F., Afzal, Shoaib, Papadia, Sofia, Ashford, Sofie, Garg, Sumedha, Millhauser, Glenn L., Palomino, Rafael I., Kwasniewska, Alexandra, Tachmazidou, Ioanna, O'Rahilly, Stephen, Zeggini, Eleftheria, Barroso, Inês, Farooqi, I. Sadaf, Benzeval, Michaela, Burton, Jonathan, Buck, Nicholas, Jäckle, Annette, Kumari, Meena, Laurie, Heather, Lynn, Peter, Pudney, Stephen, Rabe, Birgitta, Wolke, Dieter, Overvad, Kim, Tjønneland, Anne, Clavel-Chapelon, Francoise, Kaaks, Rudolf, Boeing, Heiner, Trichopoulou, Antonia, Ferrari, Pietro, Palli, Domenico, Krogha, Vittorio, Panico, Salvatore, Tuminoa, Rosario, Matullo, Giuseppe, Boer, Jolanda Ma, Van Der Schouw, Yvonne, Weiderpass, Elisabete, Quiros, J. Ramon, Sánchez, María José, Navarro, Carmen, Moreno-Iribas, Conchi, Arriola, Larraitz, Melander, Olle, Wennberg, Patrik, Key, Timothy J., Riboli, Elio, Al-Turki, Saeed, Anderson, Carl A, Anney, Richard, Antony, Dinu, Soler Artigas, María, Ayub, Muhammad, Bala, Senduran, Barrett, Jeffrey C, Beales, Phil, Bentham, Jamie, Bhattacharyaa, Shoumo, Birney, Ewan, Blackwooda, Douglas, Bobrow, Martin, Bolton, Patrick F., Boustred, Chris, Breen, Gerome, Calissanoa, Mattia, Carss, Keren, Charlton, Ruth, Chatterjee, Krishna, Chen, Lu, Ciampia, Antonio, Cirak, Sebahattin, Clapham, Peter, Clement, Gail, Coates, Guy, Coccaa, Massimiliano, Collier, David A, Cosgrove, Catherine, Coxa, Tony, Craddock, Nick, Crooks, Lucy, Curran, Sarah, Curtis, David, Daly, Allan, Danecek, Petr, Day, Ian N M, Day-Williams, Aaron G, Dominiczak, Anna, Down, Thomas, Du, Yuanping, Dunham, Ian, Durbin, Richard, Edkins, Sarah, Ekong, Rosemary, Ellis, Peter, Evansa, David M., FitzPatrick, David R., Flicek, Paul, Floyd, James S., Foley, A. Reghan, Franklin, Christopher S., Futema, Marta, Gallagher, Louise, Gaunt, Tom R., Geihs, Matthias, Geschwind, Daniel H., Greenwood, Celia M.T., Griffin, Heather, Grozeva, Detelina, Guo, Xiaosen, Guo, Xueqin, Gurling, Hugh, Hart, Deborah J., Holmans, Peter A, Howie, Bryan, Huang, Jie, Huang, Liren, Hubbard, Tim, Humphries, Steve E., Hurles, Matthew E., Hysi, Pirro G., Iotchkova, Valentina, Jackson, David K., Jamshidi, Yalda, Joyce, Chris, Karczewski, Konrad J., Kaye, Jane, Keane, Thomas, Kemp, John P., Kennedy, Karen, Kent, Alastair, Khawaja, Farrah, Van Kogelenberg, Margriet, Kolb-Kokocinski, Anja, Lachance, Genevieve, Langford, Cordelia, Lawson, Daniel, Lee, Irene, Lek, Monkol, Li, Rui, Li, Yingrui, Liang, Jieqin, Lin, Hong, Liu, Ryan, Lönnqvist, Jouko, Lopes, Luis R., Lopes, Margarida, MacArthur, Daniel G., Mangino, Massimo, Marchini, Jonathan, Maslen, John, Mathieson, Iain, McGuffin, Peter, McIntosh, Andrew M., McKechanie, Andrew G., McQuillin, Andrew, Memari, Yasin, Metrustry, Sarah, Migone, Nicola, Min, Josine L., Mitchison, Hannah M, Moayyeri, Alireza, Morris, Andrew D., Morris, James, Muntoni, Francesco, Northstone, Kate, O'Donovan, Michael C., Onoufriadis, Alexandros, Oualkacha, Karim, Owen, Michael J, Palotie, Aarno, Panoutsopoulou, Kalliope, Parker, Victoria, Parr, Jeremy R., Paternoster, Lavinia, Paunio, Tiina, Payne, Felicity, Payne, Stewart J., Perry, John R. B., Pietilainen, Olli, Plagnol, Vincent, Pollitt, Rebecca C., Porteous, David J., Povey, Sue, Quail, Michael A., Quaye, Lydia, Raymond, F. Lucy, Rehnström, Karola, Richards, J Brent, Ridout, Cheryl K., Ring, Susan M., Ritchie, Graham R.S., Roberts, Nicola, Robinson, Rachel L., Savage, David B., Scambler, Peter, Schiffels, Stephan, Schmidts, Miriam, Schoenmakers, Nadia, Scott, Richard H., Semple, Robert K., Serra, Eva, Sharp, Sally I., Shaw, Adam, Shihab, Hashem A., Shin, So Youn, Skuse, David, Small, Kerrin S, Smee, Carol, Smith, Blair H., Davey Smith, George, Soranzo, Nicole, Southam, Lorraine, Spasic-Boskovic, Olivera, Spector, Timothy D, St Clair, David, St Pourcain, Beate, Stalker, Jim, Stevens, Elizabeth, Sun, Jianping, Surdulescu, Gabriela L, Suvisaari, Jaana, Syrris, Petros, Taylor, Rohan, Tian, Jing, Timpson, Nicholas J., Tobin, Martin D, Valdes, Ana M., Vandersteen, Anthony M., Vijayarangakannan, Parthiban, Visscher, Peter M., Wain, Louise V., Walter, Klaudia, Walters, James T.R., Wang, Guangbiao, Wang, Jun, Wang, Nai-Yu, Ward, Kirsten, Whyte, Tamieka, Williams, Hywel J., Williamson, Kathleen A., Wilson, Crispian, Wilson, Scott G., Wong, Kim, Xu, Changjiang, Yang, Jian, Zhang, Feng, Zhang, Pingbo, Zheng, Hou Feng, UMC Utrecht, Cardiovasculaire Epidemiologie, Circulatory Health, JC onderzoeksprogramma Cardiovasculaire Epidemiologie, Hendricks, Audrey E., Bochukova, Elena G., Marenne, Gaëlle, Keogh, Julia M., Atanassova, Neli, Bounds, Rebecca, Wheeler, Eleanor, Mistry, Vanisha, Henning, Elana, Körner, Antje, Muddyman, Dawn, McCarthy, Shane, Hinney, Anke, Hebebrand, Johannes, Scott, Robert A., Langenberg, Claudia, Wareham, Nick J., Surendran, Praveen, Howson, Joanna M M, Butterworth, Adam S., Danesh, John, Nordestgaard, Børge G., Nielsen, Sune F., Afzal, Shoaib, Papadia, Sofia, Ashford, Sofie, Garg, Sumedha, Millhauser, Glenn L., Palomino, Rafael I., Kwasniewska, Alexandra, Tachmazidou, Ioanna, O'Rahilly, Stephen, Zeggini, Eleftheria, Barroso, Inês, Farooqi, I. Sadaf, Benzeval, Michaela, Burton, Jonathan, Buck, Nicholas, Jäckle, Annette, Kumari, Meena, Laurie, Heather, Lynn, Peter, Pudney, Stephen, Rabe, Birgitta, Wolke, Dieter, Overvad, Kim, Tjønneland, Anne, Clavel-Chapelon, Francoise, Kaaks, Rudolf, Boeing, Heiner, Trichopoulou, Antonia, Ferrari, Pietro, Palli, Domenico, Krogha, Vittorio, Panico, Salvatore, Tuminoa, Rosario, Matullo, Giuseppe, Boer, Jolanda Ma, Van Der Schouw, Yvonne, Weiderpass, Elisabete, Quiros, J. Ramon, Sánchez, María José, Navarro, Carmen, Moreno-Iribas, Conchi, Arriola, Larraitz, Melander, Olle, Wennberg, Patrik, Key, Timothy J., Riboli, Elio, Al-Turki, Saeed, Anderson, Carl A, Anney, Richard, Antony, Dinu, Soler Artigas, María, Ayub, Muhammad, Bala, Senduran, Barrett, Jeffrey C, Beales, Phil, Bentham, Jamie, Bhattacharyaa, Shoumo, Birney, Ewan, Blackwooda, Douglas, Bobrow, Martin, Bolton, Patrick F., Boustred, Chris, Breen, Gerome, Calissanoa, Mattia, Carss, Keren, Charlton, Ruth, Chatterjee, Krishna, Chen, Lu, Ciampia, Antonio, Cirak, Sebahattin, Clapham, Peter, Clement, Gail, Coates, Guy, Coccaa, Massimiliano, Collier, David A, Cosgrove, Catherine, Coxa, Tony, Craddock, Nick, Crooks, Lucy, Curran, Sarah, Curtis, David, Daly, Allan, Danecek, Petr, Day, Ian N M, Day-Williams, Aaron G, Dominiczak, Anna, Down, Thomas, Du, Yuanping, Dunham, Ian, Durbin, Richard, Edkins, Sarah, Ekong, Rosemary, Ellis, Peter, Evansa, David M., FitzPatrick, David R., Flicek, Paul, Floyd, James S., Foley, A. Reghan, Franklin, Christopher S., Futema, Marta, Gallagher, Louise, Gaunt, Tom R., Geihs, Matthias, Geschwind, Daniel H., Greenwood, Celia M.T., Griffin, Heather, Grozeva, Detelina, Guo, Xiaosen, Guo, Xueqin, Gurling, Hugh, Hart, Deborah J., Holmans, Peter A, Howie, Bryan, Huang, Jie, Huang, Liren, Hubbard, Tim, Humphries, Steve E., Hurles, Matthew E., Hysi, Pirro G., Iotchkova, Valentina, Jackson, David K., Jamshidi, Yalda, Joyce, Chris, Karczewski, Konrad J., Kaye, Jane, Keane, Thomas, Kemp, John P., Kennedy, Karen, Kent, Alastair, Khawaja, Farrah, Van Kogelenberg, Margriet, Kolb-Kokocinski, Anja, Lachance, Genevieve, Langford, Cordelia, Lawson, Daniel, Lee, Irene, Lek, Monkol, Li, Rui, Li, Yingrui, Liang, Jieqin, Lin, Hong, Liu, Ryan, Lönnqvist, Jouko, Lopes, Luis R., Lopes, Margarida, MacArthur, Daniel G., Mangino, Massimo, Marchini, Jonathan, Maslen, John, Mathieson, Iain, McGuffin, Peter, McIntosh, Andrew M., McKechanie, Andrew G., McQuillin, Andrew, Memari, Yasin, Metrustry, Sarah, Migone, Nicola, Min, Josine L., Mitchison, Hannah M, Moayyeri, Alireza, Morris, Andrew D., Morris, James, Muntoni, Francesco, Northstone, Kate, O'Donovan, Michael C., Onoufriadis, Alexandros, Oualkacha, Karim, Owen, Michael J, Palotie, Aarno, Panoutsopoulou, Kalliope, Parker, Victoria, Parr, Jeremy R., Paternoster, Lavinia, Paunio, Tiina, Payne, Felicity, Payne, Stewart J., Perry, John R. B., Pietilainen, Olli, Plagnol, Vincent, Pollitt, Rebecca C., Porteous, David J., Povey, Sue, Quail, Michael A., Quaye, Lydia, Raymond, F. Lucy, Rehnström, Karola, Richards, J Brent, Ridout, Cheryl K., Ring, Susan M., Ritchie, Graham R.S., Roberts, Nicola, Robinson, Rachel L., Savage, David B., Scambler, Peter, Schiffels, Stephan, Schmidts, Miriam, Schoenmakers, Nadia, Scott, Richard H., Semple, Robert K., Serra, Eva, Sharp, Sally I., Shaw, Adam, Shihab, Hashem A., Shin, So Youn, Skuse, David, Small, Kerrin S, Smee, Carol, Smith, Blair H., Davey Smith, George, Soranzo, Nicole, Southam, Lorraine, Spasic-Boskovic, Olivera, Spector, Timothy D, St Clair, David, St Pourcain, Beate, Stalker, Jim, Stevens, Elizabeth, Sun, Jianping, Surdulescu, Gabriela L, Suvisaari, Jaana, Syrris, Petros, Taylor, Rohan, Tian, Jing, Timpson, Nicholas J., Tobin, Martin D, Valdes, Ana M., Vandersteen, Anthony M., Vijayarangakannan, Parthiban, Visscher, Peter M., Wain, Louise V., Walter, Klaudia, Walters, James T.R., Wang, Guangbiao, Wang, Jun, Wang, Nai-Yu, Ward, Kirsten, Whyte, Tamieka, Williams, Hywel J., Williamson, Kathleen A., Wilson, Crispian, Wilson, Scott G., Wong, Kim, Xu, Changjiang, Yang, Jian, Zhang, Feng, Zhang, Pingbo, and Zheng, Hou Feng

Published
2017

33. A global reference for human genetic variation

Author

Guo, Xiaosen, Tang, Meifang, Lan, Tianming, Li, Jingxiang, Fang, Xiaodong, Lee, Sandra, Li, Guoqing, Chang, Yuqi, Lu, Yao, Korchina, Viktoriya, Feng, Qiang, Ma, Xuedi, Wang, Guangbiao, Gibbs, Richard A., Doddapaneni, Harsha, Jiang, Hui, Liu, Xiao, Kovar, Christie, Zhu, Yiming, Jian, Min, Li, Yingrui, Boerwinkle, Eric, Muzny, Donna, Wang, Bo, Reid, Jeffrey G., Xu, Xun, Wang, Jun, Jin, Xin, Wu, Honglong, Han, Yi, Wu, Renhua, and Liu, Shengmao

Abstract

The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.

Published
2015
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34. The stepwise evolution of the exome during acquisition of docetaxel resistance in breast cancer cells

Author

Hansen, Stine Ninel, Ehlers, Natasja Spring, Zhu, Shida, Thomsen, Mathilde Borg Houlberg, Nielsen, Rikke Linnemann, Liu, Dongbing, Wang, Guangbiao, Hou, Yong, Zhang, Xiuqing, Xu, Xun, Bolund, Lars, Yang, Huanming, Wang, Jun, Moreira, José, Ditzel, Henrik Jørn, Brünner, Nils, Rasmussen, Anne-Sofie Schrohl, Stenvang, Jan, Gupta, Ramneek, Hansen, Stine Ninel, Ehlers, Natasja Spring, Zhu, Shida, Thomsen, Mathilde Borg Houlberg, Nielsen, Rikke Linnemann, Liu, Dongbing, Wang, Guangbiao, Hou, Yong, Zhang, Xiuqing, Xu, Xun, Bolund, Lars, Yang, Huanming, Wang, Jun, Moreira, José, Ditzel, Henrik Jørn, Brünner, Nils, Rasmussen, Anne-Sofie Schrohl, Stenvang, Jan, and Gupta, Ramneek

Abstract

Background: Resistance to taxane-based therapy in breast cancer patients is a major clinical problem that may be addressed through insight of the genomic alterations leading to taxane resistance in breast cancer cells. In the current study we used whole exome sequencing to discover somatic genomic alterations, evolving across evolutionary stages during the acquisition of docetaxel resistance in breast cancer cell lines. Results: Two human breast cancer in vitro models (MCF-7 and MDA-MB-231) of the step-wise acquisition of docetaxel resistance were developed by exposing cells to 18 gradually increasing concentrations of docetaxel. Whole exome sequencing performed at five successive stages during this process was used to identify single point mutational events, insertions/deletions and copy number alterations associated with the acquisition of docetaxel resistance. Acquired coding variation undergoing positive selection and harboring characteristics likely to be functional were further prioritized using network-based approaches. A number of genomic changes were found to be undergoing evolutionary selection, some of which were likely to be functional. Of the five stages of progression toward resistance, most resistance relevant genomic variation appeared to arise midway towards fully resistant cells corresponding to passage 31 (5 nM docetaxel) for MDA-MB-231 and passage 16 (1.2 nM docetaxel) for MCF-7, and where the cells also exhibited a period of reduced growth rate or arrest, respectively. MCF-7 cell acquired several copy number gains on chromosome 7, including ABC transporter genes, including ABCB1 and ABCB4, as well as DMTF1, CLDN12, CROT, and SRI. For MDA-MB-231 numerous copy number losses on chromosome X involving more than 30 genes was observed. Of these genes, CASK, POLA1, PRDX4, MED14 and PIGA were highly prioritized by the applied network-based gene ranking approach. At higher docetaxel concentration MCF-7 subclones exhibited a copy number loss in E, Background: Resistance to taxane-based therapy in breast cancer patients is a major clinical problem that may be addressed through insight of the genomic alterations leading to taxane resistance in breast cancer cells. In the current study we used whole exome sequencing to discover somatic genomic alterations, evolving across evolutionary stages during the acquisition of docetaxel resistance in breast cancer cell lines. Results: Two human breast cancer in vitro models (MCF-7 and MDA-MB-231) of the step-wise acquisition of docetaxel resistance were developed by exposing cells to 18 gradually increasing concentrations of docetaxel. Whole exome sequencing performed at five successive stages during this process was used to identify single point mutational events, insertions/deletions and copy number alterations associated with the acquisition of docetaxel resistance. Acquired coding variation undergoing positive selection and harboring characteristics likely to be functional were further prioritized using network-based approaches. A number of genomic changes were found to be undergoing evolutionary selection, some of which were likely to be functional. Of the five stages of progression toward resistance, most resistance relevant genomic variation appeared to arise midway towards fully resistant cells corresponding to passage 31 (5 nM docetaxel) for MDA-MB-231 and passage 16 (1.2 nM docetaxel) for MCF-7, and where the cells also exhibited a period of reduced growth rate or arrest, respectively. MCF-7 cell acquired several copy number gains on chromosome 7, including ABC transporter genes, including ABCB1 and ABCB4, as well as DMTF1, CLDN12, CROT, and SRI. For MDA-MB-231 numerous copy number losses on chromosome X involving more than 30 genes was observed. Of these genes, CASK, POLA1, PRDX4, MED14 and PIGA were highly prioritized by the applied network-based gene ranking approach. At higher docetaxel concentration MCF-7 subclones exhibited a copy number loss in E

Published
2016

35. CONVERGE dataset: 12,000 whole-genome sequences representative of the Han Chinese population

Author

Cai, Na, primary, Bigdeli, Tim, additional, Kretzschmar, Warren, additional, Li, Yihan, additional, Liang, Jieqin, additional, Song, Li, additional, Hu, Jingchu, additional, Li, Qibin, additional, Jin, Wei, additional, Hu, Zhenfei, additional, Wang, Guangbiao, additional, Wang, Linmao, additional, Qian, Puyi, additional, Liu, Yuan, additional, Jiang, Tao, additional, Lu, Yao, additional, Zhang, Xiuqing, additional, Yin, Ye, additional, Li, Yingrui, additional, Xu, Xun, additional, Gan, Xiangchao, additional, Reimers, Mark, additional, Webb, Todd, additional, Riley, Brien, additional, Bacanu, Silviu, additional, Peterson, Roseann E, additional, Chen, Yiping, additional, Zhong, Hui, additional, Liu, Zhengrong, additional, Wang, Gang, additional, Sun, Jing, additional, Sang, Hong, additional, Jiang, Guoqing, additional, Zhou, Xiaoyan, additional, Li, Yi, additional, Zhang, Wei, additional, Wang, Xueyi, additional, Fang, Xiang, additional, Pan, Runde, additional, Miao, Guodong, additional, Zhang, Qiwen, additional, Hu, Jian, additional, Yu, Fengyu, additional, Du, Bo, additional, Sang, Wenhua, additional, Li, Keqing, additional, Chen, Guibing, additional, Cai, Min, additional, Yang, Lijun, additional, Yang, Donglin, additional, Ha, Baowei, additional, Hong, Xiaohong, additional, Deng, Hong, additional, Li, Gongying, additional, Li, Kan, additional, Song, Yan, additional, Gao, Shugui, additional, Zhang, Jinbei, additional, Gan, Zhaoyu, additional, Meng, Huaqing, additional, Pan, Jiyang, additional, Gao, Chengge, additional, Zhang, Kerang, additional, Sun, Ning, additional, Li, Youhui, additional, Niu, Qihui, additional, Zhang, Yutang, additional, Liu, Tieqiao, additional, Hu, Chunmei, additional, Zhang, Zhen, additional, Lv, Luxian, additional, Dong, Jicheng, additional, Wang, Xiaoping, additional, Tao, Ming, additional, Wang, Xumei, additional, Xia, Jing, additional, Rong, Han, additional, He, Qiang, additional, Liu, Tiebang, additional, Huang, Guoping, additional, Mei, Qiyi, additional, Shen, Zhenming, additional, Liu, Ying, additional, Shen, Jianhua, additional, Tian, Tian, additional, Liu, Xiaojuan, additional, Wu, Wenyuan, additional, Gu, Danhua, additional, Fu, Guangyi, additional, Shi, Jianguo, additional, Chen, Yunchun, additional, Gao, Jingfang, additional, Liu, Lanfen, additional, Wang, Lina, additional, Yang, Fuzhong, additional, Cong, Enzhao, additional, Marchini, Jonathan, additional, Yang, Huanming, additional, Wang, Jian, additional, Shi, Shenxun, additional, Mott, Richard, additional, Wang, Jun, additional, Kendler, Kenneth S, additional, and Flint, Jonathan, additional

Published
2016
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36. The stepwise evolution of the exome during acquisition of docetaxel resistance in breast cancer cells

Author

Hansen, Stine Ninel, primary, Ehlers, Natasja Spring, additional, Zhu, Shida, additional, Thomsen, Mathilde Borg Houlberg, additional, Nielsen, Rikke Linnemann, additional, Liu, Dongbing, additional, Wang, Guangbiao, additional, Hou, Yong, additional, Zhang, Xiuqing, additional, Xu, Xun, additional, Bolund, Lars, additional, Yang, Huanming, additional, Wang, Jun, additional, Moreira, Jose, additional, Ditzel, Henrik J, additional, Brünner, Nils, additional, Schrohl, Anne-Sofie, additional, Stenvang, Jan, additional, and Gupta, Ramneek, additional

Published
2016
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37. Whole-genome sequence-based analysis of thyroid function

Author

Taylor, Peter N., Porcu, Eleonora, Chew, Shelby, Campbell, Purdey J., Traglia, Michela, Brown, Suzanne J., Mullin, Benjamin H., Shihab, Hashem A., Min, Josine, Walter, Klaudia, Memari, Yasin, Huang, Jie, Barnes, Michael R., Beilby, John P., Charoen, Pimphen, Danecek, Petr, Dudbridge, Frank, Forgetta, Vincenzo, Greenwood, Celia, Grundberg, Elin, Johnson, Andrew D., Hui, Jennie, Lim, Ee M., McCarthy, Shane, Muddyman, Dawn, Panicker, Vijay, Perry, John R.B., Bell, Jordana T., Yuan, Wei, Relton, Caroline, Gaunt, Tom, Schlessinger, David, Abecasis, Goncalo, Cucca, Francesco, Surdulescu, Gabriela L., Woltersdorf, Wolfram, Zeggini, Eleftheria, Zheng, Hou-Feng, Toniolo, Daniela, Dayan, Colin M., Naitza, Silvia, Walsh, John P., Spector, Tim, Davey Smith, George, Durbin, Richard, Brent Richards, J., Sanna, Serena, Soranzo, Nicole, Timpson, Nicholas J., Wilson, Scott G., Turki, Saeed Al, Anderson, Carl, Anney, Richard, Antony, Dinu, Artigas, Maria Soler, Ayub, Muhammad, Balasubramaniam, Senduran, Barrett, Jeffrey C., Barroso, Inês, Beales, Phil, Bentham, Jamie, Bhattacharya, Shoumo, Birney, Ewan, Blackwood, Douglas, Bobrow, Martin, Bochukova, Elena, Bolton, Patrick, Bounds, Rebecca, Boustred, Chris, Breen, Gerome, Calissano, Mattia, Carss, Keren, Chatterjee, Krishna, Chen, Lu, Ciampi, Antonio, Cirak, Sebhattin, Clapham, Peter, Clement, Gail, Coates, Guy, Collier, David, Cosgrove, Catherine, Cox, Tony, Craddock, Nick, Crooks, Lucy, Curran, Sarah, Curtis, David, Daly, Allan, Day-Williams, Aaron, Day, Ian N.M., Down, Thomas, Du, Yuanping, Dunham, Ian, Edkins, Sarah, Ellis, Peter, Evans, David, Faroogi, Sadaf, Fatemifar, Ghazaleh, Fitzpatrick, David R., Flicek, Paul, Flyod, James, Foley, A. Reghan, Franklin, Christopher S., Futema, Marta, Gallagher, Louise, Geihs, Matthias, Geschwind, Daniel, Griffin, Heather, Grozeva, Detelina, Guo, Xueqin, Guo, Xiaosen, Gurling, Hugh, Hart, Deborah, Hendricks, Audrey, Holmans, Peter, Howie, Bryan, Huang, Liren, Hubbard, Tim, Humphries, Steve E., Hurles, Matthew E., Hysi, Pirro, Jackson, David K., Jamshidi, Yalda, Jing, Tian, Joyce, Chris, Kaye, Jane, Keane, Thomas, Keogh, Julia, Kemp, John, Kennedy, Karen, Kolb-Kokocinski, Anja, Lachance, Genevieve, Langford, Cordelia, Lawson, Daniel, Lee, Irene, Lek, Monkol, Liang, Jieqin, Lin, Hong, Li, Rui, Li, Yingrui, Liu, Ryan, Lönnqvist, Jouko, Lopes, Margarida, Lotchkova, Valentina, MacArthur, Daniel, Marchini, Jonathan, Maslen, John, Massimo, Mangino, Mathieson, Iain, Marenne, Gaëlle, McGuffin, Peter, McIntosh, Andrew, McKechanie, Andrew G., McQuillin, Andrew, Metrustry, Sarah, Mitchison, Hannah, Moayyeri, Alireza, Morris, James, Muntoni, Francesco, Northstone, Kate, O'Donnovan, Michael, Onoufriadis, Alexandros, O'Rahilly, Stephen, Oualkacha, Karim, Owen, Michael J., Palotie, Aarno, Panoutsopoulou, Kalliope, Parker, Victoria, Parr, Jeremy R., Paternoster, Lavinia, Paunio, Tiina, Payne, Felicity, Pietilainen, Olli, Plagnol, Vincent, Quaye, Lydia, Quai, Michael A., Raymond, Lucy, Rehnström, Karola, Richards, Brent, Ring, Susan, Ritchie, Graham R.S., Roberts, Nicola, Savage, David B., Scambler, Peter, Schiffels, Stephen, Schmidts, Miriam, Schoenmakers, Nadia, Semple, Robert K., Serra, Eva, Sharp, Sally I., Shin, So-Youn, Skuse, David, Small, Kerrin, Southam, Lorraine, Spasic-Boskovic, Olivera, Clair, David St, Stalker, Jim, Stevens, Elizabeth, Pourcian, Beate St, Sun, Jianping, Suvisaari, Jaana, Tachmazidou, Ionna, Tobin, Martin D., Valdes, Ana, Kogelenberg, Margriet Van, Vijayarangakannan, Parthiban, Visscher, Peter M., Wain, Louise V., Walters, James T.R., Wang, Guangbiao, Wang, Jun, Wang, Yu, Ward, Kirsten, Wheeler, Elanor, Whyte, Tamieka, Williams, Hywel, Williamson, Kathleen A., Wilson, Crispian, Wong, Kim, Xu, ChangJiang, Yang, Jian, Zhang, Fend, Zhang, Pingbo, Taylor, Peter N., Porcu, Eleonora, Chew, Shelby, Campbell, Purdey J., Traglia, Michela, Brown, Suzanne J., Mullin, Benjamin H., Shihab, Hashem A., Min, Josine, Walter, Klaudia, Memari, Yasin, Huang, Jie, Barnes, Michael R., Beilby, John P., Charoen, Pimphen, Danecek, Petr, Dudbridge, Frank, Forgetta, Vincenzo, Greenwood, Celia, Grundberg, Elin, Johnson, Andrew D., Hui, Jennie, Lim, Ee M., McCarthy, Shane, Muddyman, Dawn, Panicker, Vijay, Perry, John R.B., Bell, Jordana T., Yuan, Wei, Relton, Caroline, Gaunt, Tom, Schlessinger, David, Abecasis, Goncalo, Cucca, Francesco, Surdulescu, Gabriela L., Woltersdorf, Wolfram, Zeggini, Eleftheria, Zheng, Hou-Feng, Toniolo, Daniela, Dayan, Colin M., Naitza, Silvia, Walsh, John P., Spector, Tim, Davey Smith, George, Durbin, Richard, Brent Richards, J., Sanna, Serena, Soranzo, Nicole, Timpson, Nicholas J., Wilson, Scott G., Turki, Saeed Al, Anderson, Carl, Anney, Richard, Antony, Dinu, Artigas, Maria Soler, Ayub, Muhammad, Balasubramaniam, Senduran, Barrett, Jeffrey C., Barroso, Inês, Beales, Phil, Bentham, Jamie, Bhattacharya, Shoumo, Birney, Ewan, Blackwood, Douglas, Bobrow, Martin, Bochukova, Elena, Bolton, Patrick, Bounds, Rebecca, Boustred, Chris, Breen, Gerome, Calissano, Mattia, Carss, Keren, Chatterjee, Krishna, Chen, Lu, Ciampi, Antonio, Cirak, Sebhattin, Clapham, Peter, Clement, Gail, Coates, Guy, Collier, David, Cosgrove, Catherine, Cox, Tony, Craddock, Nick, Crooks, Lucy, Curran, Sarah, Curtis, David, Daly, Allan, Day-Williams, Aaron, Day, Ian N.M., Down, Thomas, Du, Yuanping, Dunham, Ian, Edkins, Sarah, Ellis, Peter, Evans, David, Faroogi, Sadaf, Fatemifar, Ghazaleh, Fitzpatrick, David R., Flicek, Paul, Flyod, James, Foley, A. Reghan, Franklin, Christopher S., Futema, Marta, Gallagher, Louise, Geihs, Matthias, Geschwind, Daniel, Griffin, Heather, Grozeva, Detelina, Guo, Xueqin, Guo, Xiaosen, Gurling, Hugh, Hart, Deborah, Hendricks, Audrey, Holmans, Peter, Howie, Bryan, Huang, Liren, Hubbard, Tim, Humphries, Steve E., Hurles, Matthew E., Hysi, Pirro, Jackson, David K., Jamshidi, Yalda, Jing, Tian, Joyce, Chris, Kaye, Jane, Keane, Thomas, Keogh, Julia, Kemp, John, Kennedy, Karen, Kolb-Kokocinski, Anja, Lachance, Genevieve, Langford, Cordelia, Lawson, Daniel, Lee, Irene, Lek, Monkol, Liang, Jieqin, Lin, Hong, Li, Rui, Li, Yingrui, Liu, Ryan, Lönnqvist, Jouko, Lopes, Margarida, Lotchkova, Valentina, MacArthur, Daniel, Marchini, Jonathan, Maslen, John, Massimo, Mangino, Mathieson, Iain, Marenne, Gaëlle, McGuffin, Peter, McIntosh, Andrew, McKechanie, Andrew G., McQuillin, Andrew, Metrustry, Sarah, Mitchison, Hannah, Moayyeri, Alireza, Morris, James, Muntoni, Francesco, Northstone, Kate, O'Donnovan, Michael, Onoufriadis, Alexandros, O'Rahilly, Stephen, Oualkacha, Karim, Owen, Michael J., Palotie, Aarno, Panoutsopoulou, Kalliope, Parker, Victoria, Parr, Jeremy R., Paternoster, Lavinia, Paunio, Tiina, Payne, Felicity, Pietilainen, Olli, Plagnol, Vincent, Quaye, Lydia, Quai, Michael A., Raymond, Lucy, Rehnström, Karola, Richards, Brent, Ring, Susan, Ritchie, Graham R.S., Roberts, Nicola, Savage, David B., Scambler, Peter, Schiffels, Stephen, Schmidts, Miriam, Schoenmakers, Nadia, Semple, Robert K., Serra, Eva, Sharp, Sally I., Shin, So-Youn, Skuse, David, Small, Kerrin, Southam, Lorraine, Spasic-Boskovic, Olivera, Clair, David St, Stalker, Jim, Stevens, Elizabeth, Pourcian, Beate St, Sun, Jianping, Suvisaari, Jaana, Tachmazidou, Ionna, Tobin, Martin D., Valdes, Ana, Kogelenberg, Margriet Van, Vijayarangakannan, Parthiban, Visscher, Peter M., Wain, Louise V., Walters, James T.R., Wang, Guangbiao, Wang, Jun, Wang, Yu, Ward, Kirsten, Wheeler, Elanor, Whyte, Tamieka, Williams, Hywel, Williamson, Kathleen A., Wilson, Crispian, Wong, Kim, Xu, ChangJiang, Yang, Jian, Zhang, Fend, and Zhang, Pingbo

Abstract

Normal thyroid function is essential for health, but its genetic architecture remains poorly understood. Here, for the heritable thyroid traits thyrotropin (TSH) and free ​thyroxine (FT4), we analyse whole-genome sequence data from the UK10K project (N=2,287). Using additional whole-genome sequence and deeply imputed data sets, we report meta-analysis results for common variants (MAF≥1%) associated with TSH and FT4 (N=16,335). For TSH, we identify a novel variant in ​SYN2 (MAF=23.5%, P=6.15 × 10−9) and a new independent variant in ​PDE8B (MAF=10.4%, P=5.94 × 10−14). For FT4, we report a low-frequency variant near ​B4GALT6/​SLC25A52 (MAF=3.2%, P=1.27 × 10−9) tagging a rare ​TTR variant (MAF=0.4%, P=2.14 × 10−11). All common variants explain ≥20% of the variance in TSH and FT4. Analysis of rare variants (MAF<1%) using sequence kernel association testing reveals a novel association with FT4 in ​NRG1. Our results demonstrate that increased coverage in whole-genome sequence association studies identifies novel variants associated with thyroid function.

Published
2015

38. Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

Author

Huang, Jie, Howie, Bryan, Mccarthy, Shane, Memari, Yasin, Walter, Klaudia, Min, Josine L., Danecek, Petr, Malerba, Giovanni, Trabetti, Elisabetta, Zheng, Hou-feng, Al Turki, Saeed, Amuzu, Antoinette, Anderson, Carl A., Anney, Richard, Antony, Dinu, Artigas, María Soler, Ayub, Muhammad, Bala, Senduran, Barrett, Jeffrey C., Barroso, Inês, Beales, Phil, Benn, Marianne, Bentham, Jamie, Bhattacharya, Shoumo, Birney, Ewan, Blackwood, Douglas, Bobrow, Martin, Bochukova, Elena, Bolton, Patrick F., Bounds, Rebecca, Boustred, Chris, Breen, Gerome, Calissano, Mattia, Carss, Keren, Pablo Casas, Juan, Chambers, John C., Charlton, Ruth, Chatterjee, Krishna, Chen, Lu, Ciampi, Antonio, Cirak, Sebahattin, Clapham, Peter, Clement, Gail, Coates, Guy, Cocca, Massimiliano, Collier, David A., Cosgrove, Catherine, Cox, Tony, Craddock, Nick, Crooks, Lucy, Curran, Sarah, Curtis, David, Daly, Allan, Day, Ian N. M., Day-williams, Aaron, Dedoussis, George, Down, Thomas, Du, Yuanping, Van Duijn, Cornelia M., Dunham, Ian, Edkins, Sarah, Ekong, Rosemary, Ellis, Peter, Evans, David M., Farooqi, I. Sadaf, Fitzpatrick, David R., Flicek, Paul, Floyd, James, Foley, A. Reghan, Franklin, Christopher S., Futema, Marta, Gallagher, Louise, Gasparini, Paolo, Gaunt, Tom R., Geihs, Matthias, Geschwind, Daniel, Greenwood, Celia, Griffin, Heather, Grozeva, Detelina, Guo, Xiaosen, Guo, Xueqin, Gurling, Hugh, Hart, Deborah, Hendricks, Audrey E., Holmans, Peter, Huang, Liren, Hubbard, Tim, Humphries, Steve E., Hurles, Matthew E., Hysi, Pirro, Iotchkova, Valentina, Isaacs, Aaron, Jackson, David K., Jamshidi, Yalda, Johnson, Jon, Joyce, Chris, Karczewski, Konrad J., Kaye, Jane, Keane, Thomas, Kemp, John P., Kennedy, Karen, Kent, Alastair, Keogh, Julia, Khawaja, Farrah, Kleber, Marcus E., Van Kogelenberg, Margriet, Kolb-kokocinski, Anja, Kooner, Jaspal S., Lachance, Genevieve, Langenberg, Claudia, Langford, Cordelia, Lawson, Daniel, Lee, Irene, Van Leeuwen, Elisabeth M., Lek, Monkol, Li, Rui, Li, Yingrui, Liang, Jieqin, Lin, Hong, Liu, Ryan, Lönnqvist, Jouko, Lopes, Luis R., Lopes, Margarida, Luan, Jian'an, Macarthur, Daniel G., Mangino, Massimo, Marenne, Gaëlle, März, Winfried, Maslen, John, Matchan, Angela, Mathieson, Iain, Mcguffin, Peter, Mcintosh, Andrew M., Mckechanie, Andrew G., Mcquillin, Andrew, Metrustry, Sarah, Migone, Nicola, Mitchison, Hannah M., Moayyeri, Alireza, Morris, James, Morris, Richard, Muddyman, Dawn, Muntoni, Francesco, Nordestgaard, Børge, Northstone, Kate, O'donovan, Michael C., O'rahilly, Stephen, Onoufriadis, Alexandros, Oualkacha, Karim, Owen, Michael J., Palotie, Aarno, Panoutsopoulou, Kalliope, Parker, Victoria, Parr, Jeremy R., Paternoster, Lavinia, Paunio, Tiina, Payne, Felicity, Payne, Stewart J., Perry, John R. B., Pietilainen, Olli, Plagnol, Vincent, Pollitt, Rebecca C., Povey, Sue, Quail, Michael A., Quaye, Lydia, Raymond, Lucy, Rehnström, Karola, Ridout, Cheryl K., Ring, Susan, Ritchie, Graham R. S., Roberts, Nicola, Robinson, Rachel L., Savage, David B., Scambler, Peter, Schiffels, Stephan, Schmidts, Miriam, Schoenmakers, Nadia, Scott, Richard H., Scott, Robert A., Semple, Robert K., Serra, Eva, Sharp, Sally I., Shaw, Adam, Shihab, Hashem A., Shin, So-youn, Skuse, David, Small, Kerrin S., Smee, Carol, Smith, George Davey, Southam, Lorraine, Spasic-boskovic, Olivera, Spector, Timothy D., St Clair, David, St Pourcain, Beate, Stalker, Jim, Stevens, Elizabeth, Sun, Jianping, Surdulescu, Gabriela, Suvisaari, Jaana, Syrris, Petros, Tachmazidou, Ioanna, Taylor, Rohan, Tian, Jing, Tobin, Martin D., Toniolo, Daniela, Traglia, Michela, Tybjærg-Hansen, Anne, Valdes, Ana M., Vandersteen, Anthony M., Varbo, Anette, Vijayarangakannan, Parthiban, Visscher, Peter M., Wain, Louise V., Walters, James T. R., Wang, Guangbiao, Wang, Jun, Wang, Yu, Ward, Kirsten, Wheeler, Eleanor, Whincup, Peter, Whyte, Tamieka, Williams, Hywel J., Williamson, Kathleen A., Wilson, Crispian, Wilson, Scott G., Wong, Kim, Xu, Changjiang, Yang, Jian, Zaza, Gianluigi, Zeggini, Eleftheria, Zhang, Feng, Zhang, Pingbo, Zhang, Weihua, Gambaro, Giovanni, Richards, J. Brent, Durbin, Richard, Timpson, Nicholas J., Marchini, Jonathan, Soranzo, Nicole, Huang, Jie, Howie, Bryan, Mccarthy, Shane, Memari, Yasin, Walter, Klaudia, Min, Josine L., Danecek, Petr, Malerba, Giovanni, Trabetti, Elisabetta, Zheng, Hou-feng, Al Turki, Saeed, Amuzu, Antoinette, Anderson, Carl A., Anney, Richard, Antony, Dinu, Artigas, María Soler, Ayub, Muhammad, Bala, Senduran, Barrett, Jeffrey C., Barroso, Inês, Beales, Phil, Benn, Marianne, Bentham, Jamie, Bhattacharya, Shoumo, Birney, Ewan, Blackwood, Douglas, Bobrow, Martin, Bochukova, Elena, Bolton, Patrick F., Bounds, Rebecca, Boustred, Chris, Breen, Gerome, Calissano, Mattia, Carss, Keren, Pablo Casas, Juan, Chambers, John C., Charlton, Ruth, Chatterjee, Krishna, Chen, Lu, Ciampi, Antonio, Cirak, Sebahattin, Clapham, Peter, Clement, Gail, Coates, Guy, Cocca, Massimiliano, Collier, David A., Cosgrove, Catherine, Cox, Tony, Craddock, Nick, Crooks, Lucy, Curran, Sarah, Curtis, David, Daly, Allan, Day, Ian N. M., Day-williams, Aaron, Dedoussis, George, Down, Thomas, Du, Yuanping, Van Duijn, Cornelia M., Dunham, Ian, Edkins, Sarah, Ekong, Rosemary, Ellis, Peter, Evans, David M., Farooqi, I. Sadaf, Fitzpatrick, David R., Flicek, Paul, Floyd, James, Foley, A. Reghan, Franklin, Christopher S., Futema, Marta, Gallagher, Louise, Gasparini, Paolo, Gaunt, Tom R., Geihs, Matthias, Geschwind, Daniel, Greenwood, Celia, Griffin, Heather, Grozeva, Detelina, Guo, Xiaosen, Guo, Xueqin, Gurling, Hugh, Hart, Deborah, Hendricks, Audrey E., Holmans, Peter, Huang, Liren, Hubbard, Tim, Humphries, Steve E., Hurles, Matthew E., Hysi, Pirro, Iotchkova, Valentina, Isaacs, Aaron, Jackson, David K., Jamshidi, Yalda, Johnson, Jon, Joyce, Chris, Karczewski, Konrad J., Kaye, Jane, Keane, Thomas, Kemp, John P., Kennedy, Karen, Kent, Alastair, Keogh, Julia, Khawaja, Farrah, Kleber, Marcus E., Van Kogelenberg, Margriet, Kolb-kokocinski, Anja, Kooner, Jaspal S., Lachance, Genevieve, Langenberg, Claudia, Langford, Cordelia, Lawson, Daniel, Lee, Irene, Van Leeuwen, Elisabeth M., Lek, Monkol, Li, Rui, Li, Yingrui, Liang, Jieqin, Lin, Hong, Liu, Ryan, Lönnqvist, Jouko, Lopes, Luis R., Lopes, Margarida, Luan, Jian'an, Macarthur, Daniel G., Mangino, Massimo, Marenne, Gaëlle, März, Winfried, Maslen, John, Matchan, Angela, Mathieson, Iain, Mcguffin, Peter, Mcintosh, Andrew M., Mckechanie, Andrew G., Mcquillin, Andrew, Metrustry, Sarah, Migone, Nicola, Mitchison, Hannah M., Moayyeri, Alireza, Morris, James, Morris, Richard, Muddyman, Dawn, Muntoni, Francesco, Nordestgaard, Børge, Northstone, Kate, O'donovan, Michael C., O'rahilly, Stephen, Onoufriadis, Alexandros, Oualkacha, Karim, Owen, Michael J., Palotie, Aarno, Panoutsopoulou, Kalliope, Parker, Victoria, Parr, Jeremy R., Paternoster, Lavinia, Paunio, Tiina, Payne, Felicity, Payne, Stewart J., Perry, John R. B., Pietilainen, Olli, Plagnol, Vincent, Pollitt, Rebecca C., Povey, Sue, Quail, Michael A., Quaye, Lydia, Raymond, Lucy, Rehnström, Karola, Ridout, Cheryl K., Ring, Susan, Ritchie, Graham R. S., Roberts, Nicola, Robinson, Rachel L., Savage, David B., Scambler, Peter, Schiffels, Stephan, Schmidts, Miriam, Schoenmakers, Nadia, Scott, Richard H., Scott, Robert A., Semple, Robert K., Serra, Eva, Sharp, Sally I., Shaw, Adam, Shihab, Hashem A., Shin, So-youn, Skuse, David, Small, Kerrin S., Smee, Carol, Smith, George Davey, Southam, Lorraine, Spasic-boskovic, Olivera, Spector, Timothy D., St Clair, David, St Pourcain, Beate, Stalker, Jim, Stevens, Elizabeth, Sun, Jianping, Surdulescu, Gabriela, Suvisaari, Jaana, Syrris, Petros, Tachmazidou, Ioanna, Taylor, Rohan, Tian, Jing, Tobin, Martin D., Toniolo, Daniela, Traglia, Michela, Tybjærg-Hansen, Anne, Valdes, Ana M., Vandersteen, Anthony M., Varbo, Anette, Vijayarangakannan, Parthiban, Visscher, Peter M., Wain, Louise V., Walters, James T. R., Wang, Guangbiao, Wang, Jun, Wang, Yu, Ward, Kirsten, Wheeler, Eleanor, Whincup, Peter, Whyte, Tamieka, Williams, Hywel J., Williamson, Kathleen A., Wilson, Crispian, Wilson, Scott G., Wong, Kim, Xu, Changjiang, Yang, Jian, Zaza, Gianluigi, Zeggini, Eleftheria, Zhang, Feng, Zhang, Pingbo, Zhang, Weihua, Gambaro, Giovanni, Richards, J. Brent, Durbin, Richard, Timpson, Nicholas J., Marchini, Jonathan, and Soranzo, Nicole

Published
2015

39. Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder by Whole-Genome Sequencing

Author

Anagnostou, Evdokia, Cao, Dandan, Drmic, Irene E., Jiang, Yong-hui, Marshall, Christian R., Luo, Jun, Chrysler, Christina, Wang, Mingbang, Yuen, Ryan K.C., Lau, Lynette, Howe, Jennifer L., Carter, Melissa T., Lajonchere, Clara, Walker, Susan, Ring, Robert H., Wang, Guangbiao, He, Mingze, Nalpathamkalam, Thomas, Shi, Yujian, Ju, Jia, Mei, Junpu, Uddin, Mohammed, Thiruvahindrapuram, Bhooma, Chen, Nong, Wang, Jian, Thompson, Ann, Liang, Jieqin, Jin, Xin, Wu, Xueli, Zwaigenbaum, Lonnie, Merico, Daniele, and Wang, Zhe

Subjects
mental disorders
Abstract

Autism Spectrum Disorder (ASD) demonstrates high heritability and familial clustering, yet the genetic causes remain only partially understood as a result of extensive clinical and genomic heterogeneity. Whole-genome sequencing (WGS) shows promise as a tool for identifying ASD risk genes as well as unreported mutations in known loci, but an assessment of its full utility in an ASD group has not been performed. We used WGS to examine 32 families with ASD to detect de novo or rare inherited genetic variants predicted to be deleterious (loss-of-function and damaging missense mutations). Among ASD probands, we identified deleterious de novo mutations in six of 32 (19%) families and X-linked or autosomal inherited alterations in ten of 32 (31%) families (some had combinations of mutations). The proportion of families identified with such putative mutations was larger than has been previously reported; this yield was in part due to the comprehensive and uniform coverage afforded by WGS. Deleterious variants were found in four unrecognized, nine known, and eight candidate ASD risk genes. Examples include CAPRIN1 and AFF2 (both linked to FMR1, which is involved in fragile X syndrome), VIP (involved in social-cognitive deficits), and other genes such as SCN2A and KCNQ2 (linked to epilepsy), NRXN1, and CHD7, which causes ASD-associated CHARGE syndrome. Taken together, these results suggest that WGS and thorough bioinformatic analyses for de novo and rare inherited mutations will improve the detection of genetic variants likely to be associated with ASD or its accompanying clinical symptoms.

Published
2013
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42. The genome of the pear (Pyrus bretschneideri Rehd.)

Author

Wu, Jun, Wang, Zhiwen, Shi, Zebin, Zhang, Shu, Ming, Ray, Zhu, Shilin, Khan, M. Awail, Tao, Shutian, Korban, Schuyler S., Wang, Hao, Chen, Nancy J., Nishio, Takeshi, Xu, Xun, Cong, Lin, Qi, Kaijie, Huang, Xiaosan, Wang, Yingtao, Zhao, Xiang, Wu, Juyou, Deng, Cao, Gou, Caiyun, Zhou, Weili, Yin, Hao, Qin, Gaihua, Sha, Yuhui, Tao, Ye, Chen, Hui, Yang, Yanan, Song, Yue, Zhan, Dongliang, Wang, Juan, Li, Leiting, Dai, Meisong, Gu, Chao, Wang, Yuezhi, Shi, Daihu, Wang, Xiaowei, Zhang, Huping, Zeng, Liang, Zheng, Danman, Wang, Chunlei, Chen, Maoshan, Wang, Guangbiao, Xie, Lin, Sovero, Valpuri, Sha, Shoufeng, Huang, Wenjiang, Zhang, Shujun, Zhang, Mingyue, Sun, Jiangmei, Xu, Linlin, Li, Yuan, Liu, Xing, Li, Qingsong, Shen, Jiahui, Wang, Junyi, Paull, Robert, Bennetzen, Jeffrey, Wang, Jun, Zhang, Shaoling, Wu, Jun, Wang, Zhiwen, Shi, Zebin, Zhang, Shu, Ming, Ray, Zhu, Shilin, Khan, M. Awail, Tao, Shutian, Korban, Schuyler S., Wang, Hao, Chen, Nancy J., Nishio, Takeshi, Xu, Xun, Cong, Lin, Qi, Kaijie, Huang, Xiaosan, Wang, Yingtao, Zhao, Xiang, Wu, Juyou, Deng, Cao, Gou, Caiyun, Zhou, Weili, Yin, Hao, Qin, Gaihua, Sha, Yuhui, Tao, Ye, Chen, Hui, Yang, Yanan, Song, Yue, Zhan, Dongliang, Wang, Juan, Li, Leiting, Dai, Meisong, Gu, Chao, Wang, Yuezhi, Shi, Daihu, Wang, Xiaowei, Zhang, Huping, Zeng, Liang, Zheng, Danman, Wang, Chunlei, Chen, Maoshan, Wang, Guangbiao, Xie, Lin, Sovero, Valpuri, Sha, Shoufeng, Huang, Wenjiang, Zhang, Shujun, Zhang, Mingyue, Sun, Jiangmei, Xu, Linlin, Li, Yuan, Liu, Xing, Li, Qingsong, Shen, Jiahui, Wang, Junyi, Paull, Robert, Bennetzen, Jeffrey, Wang, Jun, and Zhang, Shaoling

Abstract

The draft genome of the pear (Pyrus bretschneideri) using a combination of BAC-by-BAC and next-generation sequencing is reported. A 512.0-Mb sequence corresponding to 97.1% of the estimated genome size of this highly heterozygous species is assembled with 194× coverage. High-density genetic maps comprising 2005 SNP markers anchored 75.5% of the sequence to all 17 chromosomes. The pear genome encodes 42,812 protein-coding genes, and of these, ~28.5% encode multiple isoforms. Repetitive sequences of 271.9 Mb in length, accounting for 53.1% of the pear genome, are identified. Simulation of eudicots to the ancestor of Rosaceae has reconstructed nine ancestral chromosomes. Pear and apple diverged from each other ~5.4-21.5 million years ago, and a recent whole-genome duplication (WGD) event must have occurred 30-45 MYA prior to their divergence, but following divergence from strawberry. When compared with the apple genome sequence, size differences between the apple and pear genomes are confirmed mainly due to the presence of repetitive sequences predominantly contributed by transposable elements (TEs), while genic regions are similar in both species. Genes critical for self-incompatibility, lignified stone cells (a unique feature of pear fruit), sorbitol metabolism, and volatile compounds of fruit have also been identified. Multiple candidate SFB genes appear as tandem repeats in the S-locus region of pear; while lignin synthesis-related gene family expansion and highly expressed gene families of HCT, C3'H, and CCOMT contribute to high accumulation of both G-lignin and S-lignin. Moreover, alpha-linolenic acid metabolism is a key pathway for aroma in pear fruit.

Published
2013

43. Detection of clinically relevant genetic variants in autism spectrum disorder by whole-genome sequencing

Author

Jiang, Yong-hui, Yuen, Ryan K.C., Wang, Mingbang, Jin, Xin, Chen, Nong, Wu, Xueli, Ju, Jia, Mei, Junpu, Shi, Yujian, He, Mingze, Wang, Guangbiao, Liang, Jieqin, Wang, Zhe, Cao, Dandan, Carter, Melissa T., Chrysler, Christina, Drmic, Irene E., Howe, Jennifer L., Lau, Lynette, Marshall, Christian R., Merico, Daniele, Nalpathamkalam, Thomas, Thiruvahindrapuram, Bhooma, Thompson, Ann, Uddin, Mohammed, Walker, Susan, Luo, Jun, Anagnostou, Evdokia, Zwaigenbaum, Lonnie, Ring, Robert H., Wang, Jian, Lajonchere, Clara, Wang, Jun, Shih, Andy, Szatmari, Peter, Yang, Huanming, Dawson, Geraldine, Li, Yingrui, Scherer, Stephen W., Jiang, Yong-hui, Yuen, Ryan K.C., Wang, Mingbang, Jin, Xin, Chen, Nong, Wu, Xueli, Ju, Jia, Mei, Junpu, Shi, Yujian, He, Mingze, Wang, Guangbiao, Liang, Jieqin, Wang, Zhe, Cao, Dandan, Carter, Melissa T., Chrysler, Christina, Drmic, Irene E., Howe, Jennifer L., Lau, Lynette, Marshall, Christian R., Merico, Daniele, Nalpathamkalam, Thomas, Thiruvahindrapuram, Bhooma, Thompson, Ann, Uddin, Mohammed, Walker, Susan, Luo, Jun, Anagnostou, Evdokia, Zwaigenbaum, Lonnie, Ring, Robert H., Wang, Jian, Lajonchere, Clara, Wang, Jun, Shih, Andy, Szatmari, Peter, Yang, Huanming, Dawson, Geraldine, Li, Yingrui, and Scherer, Stephen W.

Published
2013

44. The sequence and analysis of a Chinese pig genome

Author

Fang, Xiaodong, Mu, Yulian, Huang, Zhiyong, Li, Yong, Han, Lijuan, Zhang, Yanfeng, Feng, Yue, Chen, Yuanxin, Jiang, Xuanting, Zhao, Wei, Sun, Xiaoqing, Xiong, Zhiqiang, Yang, Lan, Liu, Huan, Fan, Dingding, Mao, Likai, Ren, Lijie, Liu, Chuxin, Wang, Juan, Li, Kui, Wang, Guangbiao, Yang, Shulin, Lai, Liangxue, Zhang, Guojie, Li, Yingrui, Wang, Jun, Bolund, Lars, Yang, Huanming, Wang, Jian, Feng, Shutang, Li, Songgang, Du, Yutao, Fang, Xiaodong, Mu, Yulian, Huang, Zhiyong, Li, Yong, Han, Lijuan, Zhang, Yanfeng, Feng, Yue, Chen, Yuanxin, Jiang, Xuanting, Zhao, Wei, Sun, Xiaoqing, Xiong, Zhiqiang, Yang, Lan, Liu, Huan, Fan, Dingding, Mao, Likai, Ren, Lijie, Liu, Chuxin, Wang, Juan, Li, Kui, Wang, Guangbiao, Yang, Shulin, Lai, Liangxue, Zhang, Guojie, Li, Yingrui, Wang, Jun, Bolund, Lars, Yang, Huanming, Wang, Jian, Feng, Shutang, Li, Songgang, and Du, Yutao

Published
2012

45. Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder by Whole-Genome Sequencing

Author

Jiang, Yong-hui, primary, Yuen, Ryan K.C., additional, Jin, Xin, additional, Wang, Mingbang, additional, Chen, Nong, additional, Wu, Xueli, additional, Ju, Jia, additional, Mei, Junpu, additional, Shi, Yujian, additional, He, Mingze, additional, Wang, Guangbiao, additional, Liang, Jieqin, additional, Wang, Zhe, additional, Cao, Dandan, additional, Carter, Melissa T., additional, Chrysler, Christina, additional, Drmic, Irene E., additional, Howe, Jennifer L., additional, Lau, Lynette, additional, Marshall, Christian R., additional, Merico, Daniele, additional, Nalpathamkalam, Thomas, additional, Thiruvahindrapuram, Bhooma, additional, Thompson, Ann, additional, Uddin, Mohammed, additional, Walker, Susan, additional, Luo, Jun, additional, Anagnostou, Evdokia, additional, Zwaigenbaum, Lonnie, additional, Ring, Robert H., additional, Wang, Jian, additional, Lajonchere, Clara, additional, Wang, Jun, additional, Shih, Andy, additional, Szatmari, Peter, additional, Yang, Huanming, additional, Dawson, Geraldine, additional, Li, Yingrui, additional, and Scherer, Stephen W., additional

Published
2013
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46. The genome of the pear (Pyrus bretschneideri Rehd.)

Author

Wu, Jun, primary, Wang, Zhiwen, additional, Shi, Zebin, additional, Zhang, Shu, additional, Ming, Ray, additional, Zhu, Shilin, additional, Khan, M. Awais, additional, Tao, Shutian, additional, Korban, Schuyler S., additional, Wang, Hao, additional, Chen, Nancy J., additional, Nishio, Takeshi, additional, Xu, Xun, additional, Cong, Lin, additional, Qi, Kaijie, additional, Huang, Xiaosan, additional, Wang, Yingtao, additional, Zhao, Xiang, additional, Wu, Juyou, additional, Deng, Cao, additional, Gou, Caiyun, additional, Zhou, Weili, additional, Yin, Hao, additional, Qin, Gaihua, additional, Sha, Yuhui, additional, Tao, Ye, additional, Chen, Hui, additional, Yang, Yanan, additional, Song, Yue, additional, Zhan, Dongliang, additional, Wang, Juan, additional, Li, Leiting, additional, Dai, Meisong, additional, Gu, Chao, additional, Wang, Yuezhi, additional, Shi, Daihu, additional, Wang, Xiaowei, additional, Zhang, Huping, additional, Zeng, Liang, additional, Zheng, Danman, additional, Wang, Chunlei, additional, Chen, Maoshan, additional, Wang, Guangbiao, additional, Xie, Lin, additional, Sovero, Valpuri, additional, Sha, Shoufeng, additional, Huang, Wenjiang, additional, Zhang, Shujun, additional, Zhang, Mingyue, additional, Sun, Jiangmei, additional, Xu, Linlin, additional, Li, Yuan, additional, Liu, Xing, additional, Li, Qingsong, additional, Shen, Jiahui, additional, Wang, Junyi, additional, Paull, Robert E., additional, Bennetzen, Jeffrey L., additional, Wang, Jun, additional, and Zhang, Shaoling, additional

Published
2012
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48. A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans

Author

Timpson, Nicholas J., Walter, Klaudia, Min, Josine L., Tachmazidou, Ioanna, Malerba, Giovanni, Shin, So-Youn, Chen, Lu, Futema, Marta, Southam, Lorraine, Iotchkova, Valentina, Cocca, Massimiliano, Huang, Jie, Memari, Yasin, McCarthy, Shane, Danecek, Petr, Muddyman, Dawn, Mangino, Massimo, Menni, Cristina, Perry, John R. B., Ring, Susan M., Gaye, Amadou, Dedoussis, George, Farmaki, Aliki-Eleni, Burton, Paul, Talmud, Philippa J., Gambaro, Giovanni, Spector, Tim D., Smith, George Davey, Durbin, Richard, Richards, J Brent, Humphries, Steve E., Zeggini, Eleftheria, Soranzo, Nicole, Al Turki, Saeed, Anderson, Carl, Anney, Richard, Antony, Dinu, Soler Artigas, Maria, Ayub, Muhammad, Balasubramaniam, Senduran, Barrett, Jeffrey C., Barroso, Inês, Beales, Phil, Bentham, Jamie, Bhattacharya, Shoumo, Birney, Ewan, Blackwood, Douglas, Bobrow, Martin, Bochukova, Elena, Bolton, Patrick, Bounds, Rebecca, Boustred, Chris, Breen, Gerome, Calissano, Mattia, Carss, Keren, Chatterjee, Krishna, Ciampi, Antonio, Cirak, Sebhattin, Clapham, Peter, Clement, Gail, Coates, Guy, Collier, David, Cosgrove, Catherine, Cox, Tony, Craddock, Nick, Crooks, Lucy, Curran, Sarah, Curtis, David, Daly, Allan, Davey Smith, George, Day-Williams, Aaron, Day, Ian N. M., Down, Thomas, Du, Yuanping, Dunham, Ian, Edkins, Sarah, Ellis, Peter, Evans, David, Faroogi, Sadaf, Fatemifar, Ghazaleh, Fitzpatrick, David R., Flicek, Paul, Flyod, James, Foley, A Reghan, Franklin, Christopher S, Gallagher, Louise, Gaunt, Tom, Geihs, Matthias, Geschwind, Daniel, Greenwood, Celia, Griffin, Heather, Grozeva, Detelina, Guo, Xueqin, Guo, Xiaosen, Gurling, Hugh, Hart, Deborah, Hendricks, Audrey, Holmans, Peter, Howie, Bryan, Huang, Liren, Hubbard, Tim, Hurles, Matthew E., Hysi, Pirro, Jackson, David K., Jamshidi, Yalda, Jing, Tian, Joyce, Chris, Kaye, Jane, Keane, Thomas, Keogh, Julia, Kemp, John, Kennedy, Karen, Kolb-Kokocinski, Anja, Lachance, Genevieve, Langford, Cordelia, Lawson, Daniel, Lee, Irene, Lek, Monkol, Liang, Jieqin, Lin, Hong, Li, Rui, Li, Yingrui, Liu, Ryan, Lönnqvist, Jouko, Lopes, Margarida, Lotchkova, Valentina, MacArthur, Daniel, Marchini, Jonathan, Maslen, John, Massimo, Mangino, Mathieson, Iain, Marenne, Gaëlle, McGuffin, Peter, McIntosh, Andrew, McKechanie, Andrew G., McQuillin, Andrew, Metrustry, Sarah, Min, Josine, Mitchison, Hannah, Moayyeri, Alireza, Morris, James, Muntoni, Francesco, Northstone, Kate, O'Donnovan, Michael, Onoufriadis, Alexandros, O'Rahilly, Stephen, Oualkacha, Karim, Owen, Michael J., Palotie, Aarno, Panoutsopoulou, Kalliope, Parker, Victoria, Parr, Jeremy R., Paternoster, Lavinia, Paunio, Tiina, Payne, Felicity, Perry, John, Pietilainen, Olli, Plagnol, Vincent, Quaye, Lydia, Quail, Michael A., Raymond, Lucy, Rehnström, Karola, Richards, Brent, Ring, Susan, Ritchie, Graham R. S., Roberts, Nicola, Savage, David B., Scambler, Peter, Schiffels, Stephen, Schmidts, Miriam, Schoenmakers, Nadia, Semple, Robert K., Serra, Eva, Sharp, Sally I., Shihab, Hasheem, Skuse, David, Small, Kerrin, Spasic-Boskovic, Olivera, Spector, Tim, St Clair, David, Stalker, Jim, Stevens, Elizabeth, St Pourcian, Beate, Sun, Jianping, Surdulescu, Gabriela, Suvisaari, Jaana, Tachmazidou, Ionna, Timpson, Nicholas, Tobin, Martin D., Valdes, Ana, Van Kogelenberg, Margriet, Vijayarangakannan, Parthiban, Visscher, Peter M., Wain, Louise V., Walters, James T. R., Wang, Guangbiao, Wang, Jun, Wang, Yu, Ward, Kirsten, Wheeler, Elanor, Whyte, Tamieka, Williams, Hywel, Williamson, Kathleen A., Wilson, Crispian, Wilson, Scott G., Wong, Kim, Xu, ChangJiang, Yang, Jian, Zhang, Fend, Zhang, Pingbo, and Zheng, Hou-Feng

Abstract

The analysis of rich catalogues of genetic variation from population-based sequencing provides an opportunity to screen for functional effects. Here we report a rare variant in APOC3 (rs138326449-A, minor allele frequency ~0.25% (UK)) associated with plasma triglyceride (TG) levels (−1.43 s.d. (s.e.=0.27 per minor allele (P-value=8.0 × 10−8)) discovered in 3,202 individuals with low read-depth, whole-genome sequence. We replicate this in 12,831 participants from five additional samples of Northern and Southern European origin (−1.0 s.d. (s.e.=0.173), P-value=7.32 × 10−9). This is consistent with an effect between 0.5 and 1.5 mmol l−1 dependent on population. We show that a single predicted splice donor variant is responsible for association signals and is independent of known common variants. Analyses suggest an independent relationship between rs138326449 and high-density lipoprotein (HDL) levels. This represents one of the first examples of a rare, large effect variant identified from whole-genome sequencing at a population scale.

Published
2014
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49. Numerical and Orthogonal Study on Optimization Analysis of Structure Parameters of Bubble Breaker for Electrical Submersible Pump System

Author

Xie, Chuan, Liu, Yonghui, Li, Xiaoping, Wang, Guangbiao, Wang, Qinghua, and Zeng, Fanhua

Abstract

Under slug flow conditions, electrical submersible pumps (ESPs) show a low efficiency due to Taylor bubbles, which cause pressure surging and gas pockets and the further deterioration of pressure boosting ability. In this study, a novel downhole bubble breaker is designed for mitigating the impact in ESP under slug flow conditions. The computational fluid dynamics-population balance model (CFD-PBM) coupled approach was used to calculate the bubble breaker's average bubble diameter to evaluate its efficiency. Meanwhile, experimental studies were conducted and compared with numerical results. Also, matlab and DIP-image technology was used to calculate the bubble diameter. Compared with experimental results, the simulation results agree well. Furthermore, the novel bubble breaker's performance was studied by orthogonal approach. The best result of range analysis is A2B3C4D1E4 (α = 30 deg, L = 300 mm, R = 2:1, vsg = 0.2 m/s, and vsl = 0.08 m/s), and sensitively analysis results present that the range of impact intensity are A (inlet angle) > E (superficial gas velocity) > B (total length) > D (superficial liquid velocity) > C (ratio of the gas–liquid channel). The optimal structure's bubble diameters are all less than that of the original structure, with a superficial gas velocity range of 0.2–0.6 m/s. The downstream bubble diameter of the optimal bubble is about 31.6% lower than the original structure at the maximum value point.

Published
2022
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50. A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans

Author

Timpson, Nicholas J., Walter, Klaudia, Min, Josine L., Tachmazidou, Ioanna, Malerba, Giovanni, Shin, So-Youn, Chen, Lu, Futema, Marta, Southam, Lorraine, Iotchkova, Valentina, Cocca, Massimiliano, Huang, Jie, Memari, Yasin, McCarthy, Shane, Danecek, Petr, Muddyman, Dawn, Mangino, Massimo, Menni, Cristina, Perry, John R. B., Ring, Susan M., Gaye, Amadou, Dedoussis, George, Farmaki, Aliki-Eleni, Burton, Paul, Talmud, Philippa J., Gambaro, Giovanni, Spector, Tim D., Smith, George Davey, Durbin, Richard, Richards, J Brent, Humphries, Steve E., Zeggini, Eleftheria, Soranzo, Nicole, Al Turki, Saeed, Anderson, Carl, Anney, Richard, Antony, Dinu, Soler Artigas, Maria, Ayub, Muhammad, Balasubramaniam, Senduran, Barrett, Jeffrey C., Barroso, Inês, Beales, Phil, Bentham, Jamie, Bhattacharya, Shoumo, Birney, Ewan, Blackwood, Douglas, Bobrow, Martin, Bochukova, Elena, Bolton, Patrick, Bounds, Rebecca, Boustred, Chris, Breen, Gerome, Calissano, Mattia, Carss, Keren, Chatterjee, Krishna, Ciampi, Antonio, Cirak, Sebhattin, Clapham, Peter, Clement, Gail, Coates, Guy, Collier, David, Cosgrove, Catherine, Cox, Tony, Craddock, Nick, Crooks, Lucy, Curran, Sarah, Curtis, David, Daly, Allan, Davey Smith, George, Day-Williams, Aaron, Day, Ian N. M., Down, Thomas, Du, Yuanping, Dunham, Ian, Edkins, Sarah, Ellis, Peter, Evans, David, Faroogi, Sadaf, Fatemifar, Ghazaleh, Fitzpatrick, David R., Flicek, Paul, Flyod, James, Foley, A Reghan, Franklin, Christopher S, Gallagher, Louise, Gaunt, Tom, Geihs, Matthias, Geschwind, Daniel, Greenwood, Celia, Griffin, Heather, Grozeva, Detelina, Guo, Xueqin, Guo, Xiaosen, Gurling, Hugh, Hart, Deborah, Hendricks, Audrey, Holmans, Peter, Howie, Bryan, Huang, Liren, Hubbard, Tim, Hurles, Matthew E., Hysi, Pirro, Jackson, David K., Jamshidi, Yalda, Jing, Tian, Joyce, Chris, Kaye, Jane, Keane, Thomas, Keogh, Julia, Kemp, John, Kennedy, Karen, Kolb-Kokocinski, Anja, Lachance, Genevieve, Langford, Cordelia, Lawson, Daniel, Lee, Irene, Lek, Monkol, Liang, Jieqin, Lin, Hong, Li, Rui, Li, Yingrui, Liu, Ryan, Lönnqvist, Jouko, Lopes, Margarida, Lotchkova, Valentina, MacArthur, Daniel, Marchini, Jonathan, Maslen, John, Massimo, Mangino, Mathieson, Iain, Marenne, Gaëlle, McGuffin, Peter, McIntosh, Andrew, McKechanie, Andrew G., McQuillin, Andrew, Metrustry, Sarah, Min, Josine, Mitchison, Hannah, Moayyeri, Alireza, Morris, James, Muntoni, Francesco, Northstone, Kate, O'Donnovan, Michael, Onoufriadis, Alexandros, O'Rahilly, Stephen, Oualkacha, Karim, Owen, Michael J., Palotie, Aarno, Panoutsopoulou, Kalliope, Parker, Victoria, Parr, Jeremy R., Paternoster, Lavinia, Paunio, Tiina, Payne, Felicity, Perry, John, Pietilainen, Olli, Plagnol, Vincent, Quaye, Lydia, Quail, Michael A., Raymond, Lucy, Rehnström, Karola, Richards, Brent, Ring, Susan, Ritchie, Graham R. S., Roberts, Nicola, Savage, David B., Scambler, Peter, Schiffels, Stephen, Schmidts, Miriam, Schoenmakers, Nadia, Semple, Robert K., Serra, Eva, Sharp, Sally I., Shihab, Hasheem, Skuse, David, Small, Kerrin, Spasic-Boskovic, Olivera, Spector, Tim, St Clair, David, Stalker, Jim, Stevens, Elizabeth, St Pourcian, Beate, Sun, Jianping, Surdulescu, Gabriela, Suvisaari, Jaana, Tachmazidou, Ionna, Timpson, Nicholas, Tobin, Martin D., Valdes, Ana, Van Kogelenberg, Margriet, Vijayarangakannan, Parthiban, Visscher, Peter M., Wain, Louise V., Walters, James T. R., Wang, Guangbiao, Wang, Jun, Wang, Yu, Ward, Kirsten, Wheeler, Elanor, Whyte, Tamieka, Williams, Hywel, Williamson, Kathleen A., Wilson, Crispian, Wilson, Scott G., Wong, Kim, Xu, ChangJiang, Yang, Jian, Zhang, Fend, Zhang, Pingbo, Zheng, Hou-Feng, Timpson, Nicholas J., Walter, Klaudia, Min, Josine L., Tachmazidou, Ioanna, Malerba, Giovanni, Shin, So-Youn, Chen, Lu, Futema, Marta, Southam, Lorraine, Iotchkova, Valentina, Cocca, Massimiliano, Huang, Jie, Memari, Yasin, McCarthy, Shane, Danecek, Petr, Muddyman, Dawn, Mangino, Massimo, Menni, Cristina, Perry, John R. B., Ring, Susan M., Gaye, Amadou, Dedoussis, George, Farmaki, Aliki-Eleni, Burton, Paul, Talmud, Philippa J., Gambaro, Giovanni, Spector, Tim D., Smith, George Davey, Durbin, Richard, Richards, J Brent, Humphries, Steve E., Zeggini, Eleftheria, Soranzo, Nicole, Al Turki, Saeed, Anderson, Carl, Anney, Richard, Antony, Dinu, Soler Artigas, Maria, Ayub, Muhammad, Balasubramaniam, Senduran, Barrett, Jeffrey C., Barroso, Inês, Beales, Phil, Bentham, Jamie, Bhattacharya, Shoumo, Birney, Ewan, Blackwood, Douglas, Bobrow, Martin, Bochukova, Elena, Bolton, Patrick, Bounds, Rebecca, Boustred, Chris, Breen, Gerome, Calissano, Mattia, Carss, Keren, Chatterjee, Krishna, Ciampi, Antonio, Cirak, Sebhattin, Clapham, Peter, Clement, Gail, Coates, Guy, Collier, David, Cosgrove, Catherine, Cox, Tony, Craddock, Nick, Crooks, Lucy, Curran, Sarah, Curtis, David, Daly, Allan, Davey Smith, George, Day-Williams, Aaron, Day, Ian N. M., Down, Thomas, Du, Yuanping, Dunham, Ian, Edkins, Sarah, Ellis, Peter, Evans, David, Faroogi, Sadaf, Fatemifar, Ghazaleh, Fitzpatrick, David R., Flicek, Paul, Flyod, James, Foley, A Reghan, Franklin, Christopher S, Gallagher, Louise, Gaunt, Tom, Geihs, Matthias, Geschwind, Daniel, Greenwood, Celia, Griffin, Heather, Grozeva, Detelina, Guo, Xueqin, Guo, Xiaosen, Gurling, Hugh, Hart, Deborah, Hendricks, Audrey, Holmans, Peter, Howie, Bryan, Huang, Liren, Hubbard, Tim, Hurles, Matthew E., Hysi, Pirro, Jackson, David K., Jamshidi, Yalda, Jing, Tian, Joyce, Chris, Kaye, Jane, Keane, Thomas, Keogh, Julia, Kemp, John, Kennedy, Karen, Kolb-Kokocinski, Anja, Lachance, Genevieve, Langford, Cordelia, Lawson, Daniel, Lee, Irene, Lek, Monkol, Liang, Jieqin, Lin, Hong, Li, Rui, Li, Yingrui, Liu, Ryan, Lönnqvist, Jouko, Lopes, Margarida, Lotchkova, Valentina, MacArthur, Daniel, Marchini, Jonathan, Maslen, John, Massimo, Mangino, Mathieson, Iain, Marenne, Gaëlle, McGuffin, Peter, McIntosh, Andrew, McKechanie, Andrew G., McQuillin, Andrew, Metrustry, Sarah, Min, Josine, Mitchison, Hannah, Moayyeri, Alireza, Morris, James, Muntoni, Francesco, Northstone, Kate, O'Donnovan, Michael, Onoufriadis, Alexandros, O'Rahilly, Stephen, Oualkacha, Karim, Owen, Michael J., Palotie, Aarno, Panoutsopoulou, Kalliope, Parker, Victoria, Parr, Jeremy R., Paternoster, Lavinia, Paunio, Tiina, Payne, Felicity, Perry, John, Pietilainen, Olli, Plagnol, Vincent, Quaye, Lydia, Quail, Michael A., Raymond, Lucy, Rehnström, Karola, Richards, Brent, Ring, Susan, Ritchie, Graham R. S., Roberts, Nicola, Savage, David B., Scambler, Peter, Schiffels, Stephen, Schmidts, Miriam, Schoenmakers, Nadia, Semple, Robert K., Serra, Eva, Sharp, Sally I., Shihab, Hasheem, Skuse, David, Small, Kerrin, Spasic-Boskovic, Olivera, Spector, Tim, St Clair, David, Stalker, Jim, Stevens, Elizabeth, St Pourcian, Beate, Sun, Jianping, Surdulescu, Gabriela, Suvisaari, Jaana, Tachmazidou, Ionna, Timpson, Nicholas, Tobin, Martin D., Valdes, Ana, Van Kogelenberg, Margriet, Vijayarangakannan, Parthiban, Visscher, Peter M., Wain, Louise V., Walters, James T. R., Wang, Guangbiao, Wang, Jun, Wang, Yu, Ward, Kirsten, Wheeler, Elanor, Whyte, Tamieka, Williams, Hywel, Williamson, Kathleen A., Wilson, Crispian, Wilson, Scott G., Wong, Kim, Xu, ChangJiang, Yang, Jian, Zhang, Fend, Zhang, Pingbo, and Zheng, Hou-Feng

Abstract

The analysis of rich catalogues of genetic variation from population-based sequencing provides an opportunity to screen for functional effects. Here we report a rare variant in ​APOC3 (rs138326449-A, minor allele frequency ~0.25% (UK)) associated with plasma triglyceride (TG) levels (−1.43 s.d. (s.e.=0.27 per minor allele (P-value=8.0 × 10−8)) discovered in 3,202 individuals with low read-depth, whole-genome sequence. We replicate this in 12,831 participants from five additional samples of Northern and Southern European origin (−1.0 s.d. (s.e.=0.173), P-value=7.32 × 10−9). This is consistent with an effect between 0.5 and 1.5 mmol l−1 dependent on population. We show that a single predicted splice donor variant is responsible for association signals and is independent of known common variants. Analyses suggest an independent relationship between rs138326449 and high-density lipoprotein (HDL) levels. This represents one of the first examples of a rare, large effect variant identified from whole-genome sequencing at a population scale.

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