Nature Genetics Contents: December 2013 pp 1411 - 1516

Advertisement Finally! Antibodies you can TRUST.   Partnering with epigenetics experts including the BLUEPRINT Epigenome consortium, Diagenode has developed the absolute best epigenetics antibodies with the highest specificity and sensitivity available. Achieve unparalleled MeDIP, ChIP, and ChIP-seq results with validated antibodies you can trust. Learn more.   TABLE OF CONTENTS December 2013 Volume 45, Issue 12 Editorial News and Views Research Highlights Analysis Brief Communication Articles Letters Corrigendum Advertisement RNA-Sequencing from FFPE Samples NOW you can achieve comparable RNA-Sequencing data from FFPE samples. In this technote, EA/Quintiles unveils new methods to address the challenges of molecular analysis from FFPE samples. Read about this protocol and our comparison of results from FFPE vs. matched fresh-frozen tissue. 919-405-2248 * 866-293-6094  Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Eppendorf - System solutions for your workflows Do you know that Eppendorf offers products to prepare your samples with reproducible conditions? You can also find a lot of products around your PCR workflow and various new possibilities will show up using our brand new 5 mL system    Editorial Top A bubble popper   p1411 doi:10.1038/ng.2845 The assertions in a scientific article that invite testing can be specifically tagged for peer reviewers to evaluate relative to the experimental evidence offered. Isolated observations as well as theories that are not yet publishable can be tagged and immediately released like free-floating bubbles. These can then be considered as useful negative results when popped by experiment or as publishable advances when corroborated by further evidence gathered during attempts at refutation. News and Views Top Epigenetics, vitamin supplements and cellular reprogramming   pp1412 - 1413 Martin F Pera doi:10.1038/ng.2834 The simple addition of vitamin C to cell culture medium can induce extensive remodeling of the cellular epigenome and facilitates reprogramming of somatic cells to pluripotency. A new study shows that the activity of the enzyme TET1 can inhibit or enhance reprogramming efficiency, dependent on the presence or absence of vitamin C. See also: Letter by Chen et al. Recurrent H3.3 alterations in childhood tumors   pp1413 - 1414 Anders M Lindroth & Christoph Plass doi:10.1038/ng.2832 Comprehensive sequencing of benign and malignant tumors has recently uncovered new driver mutations in childhood tumors. A new report now describes frequent histone H3.3 alterations in chondroblastoma and giant cell tumor of bone, emphasizing the importance of this histone variant in pediatric cancers. See also: Letter by Behjati et al. The search for ESR1 mutations in breast cancer   pp1415 - 1416 Steffi Oesterreich & Nancy E Davidson doi:10.1038/ng.2831 Two new studies report the identification of activating ESR1 gene mutations in aromatase inhibitor-resistant metastatic breast cancers. This insight into therapeutic resistance suggests new approaches that may be useful in the management of endocrine-resistant breast cancer. See also: Article by Toy et al. | Letter by Robinson et al. Genetics JOBS of the week Postdoc in Genetics and Mechanisms of Parkinson's Disease Harbin Institute of Technology Postdoctoral Fellowship - Genetics of Cognition and Schizophrenia Istituto Italiano di Tecnologia (IIT) Postdoctoral Position in Yeast Genetics and Biochemistry Max Planck Institute of Immunobiology and Epigenetics Molecular Biology and Genetics Bilkent University Endowed Professor, Genetics Boston University More Science jobs from Genetics EVENT Malaria Experimental Genetics 09.02.14 Cambridge, UK More science events from Research Highlights Top Polygenic architecture | Capturing ancient DNA | Super stretchy enhancers | Tumor suppressors, oncogenes and aneuploidy | PIK3CD mutations cause immunodeficiency Analysis Top Evaluating empirical bounds on complex disease genetic architecture   pp1418 - 1427 Vineeta Agarwala, Jason Flannick, Shamil Sunyaev, GoT2D Consortium & David Altshuler doi:10.1038/ng.2804 David Altshuler and colleagues explore the genetic architecture of type 2 diabetes (T2D) using an integrated population genetics-based simulation framework calibrated with empirical data. Whereas they are able to exclude more extreme models, for example, those in which either common or rare variants explain all of the disease heritability, they find that a broad range of architecture remains consistent with current empirical data and suggest that continued large-scale sequencing and genotyping studies will be needed to more precisely characterize the genetic architecture of complex traits such as T2D. Brief Communication Top Frequent truncating mutations of STAG2 in bladder cancer   pp1428 - 1430 David A Solomon, Jung-Sik Kim, Jolanta Bondaruk, Shahrokh F Shariat, Zeng-Feng Wang, Abdel G Elkahloun, Tomoko Ozawa, Julia Gerard, DaZhong Zhuang, Shizhen Zhang, Neema Navai, Arlene Siefker-Radtke, Joanna J Phillips, Brian D Robinson, Mark A Rubin, Björn Volkmer, Richard Hautmann, Rainer Küfer, Pancras C W Hogendoorn, George Netto, Dan Theodorescu, C David James, Bogdan Czerniak, Markku Miettinen & Todd Waldman doi:10.1038/ng.2800 Todd Waldman and colleagues screened 2,214 tumors for loss of STAG2 expression using immunohistochemistry. They followed up by sequencing STAG2 in 111 urothelial carcinomas and found mutations in 23 of the cases, identifying STAG2 as one of the most commonly mutated genes in bladder cancer. Articles Top Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars   pp1431 - 1438 Mingzhou Li, Shilin Tian, Long Jin, Guangyu Zhou, Ying Li, Yuan Zhang, Tao Wang, Carol K L Yeung, Lei Chen, Jideng Ma, Jinbo Zhang, Anan Jiang, Ji Li, Chaowei Zhou, Jie Zhang, Yingkai Liu, Xiaoqing Sun, Hongwei Zhao, Zexiong Niu, Pinger Lou, Lingjin Xian, Xiaoyong Shen, Shaoqing Liu, Shunhua Zhang, Mingwang Zhang, Li Zhu, Surong Shuai, Lin Bai, Guoqing Tang, Haifeng Liu, Yanzhi Jiang, Miaomiao Mai, Jian Xiao, Xun Wang, Qi Zhou, Zhiquan Wang, Paul Stothard, Ming Xue, Xiaolian Gao, Zonggang Luo, Yiren Gu, Hongmei Zhu, Xiaoxiang Hu, Yaofeng Zhao, Graham S Plastow, Jinyong Wang, Zhi Jiang, Kui Li, Ning Li, Xuewei Li & Ruiqiang Li doi:10.1038/ng.2811 Ruiqiang Li and colleagues report the whole-genome sequencing of a Tibetan female wild boar, as well as resequencing of 48 domestic pigs and wild boar from Tibet and China. Their analysis provides insights into the genetic diversity, population structure and evolution of the wild boar. ESR1 ligand-binding domain mutations in hormone-resistant breast cancer   pp1439 - 1445 Weiyi Toy, Yang Shen, Helen Won, Bradley Green, Rita A Sakr, Marie Will, Zhiqiang Li, Kinisha Gala, Sean Fanning, Tari A King, Clifford Hudis, David Chen, Tetiana Taran, Gabriel Hortobagyi, Geoffrey Greene, Michael Berger, José Baselga & Sarat Chandarlapaty doi:10.1038/ng.2822 Sarat Chandarlapaty and colleagues report the identification of mutations in the ESR1 gene affecting the ligand-binding domain of the encoded estrogen receptor in 20% of metastatic hormone-resistant breast cancers. They determine that the mutant receptor has a hormone-independent active state that likely promotes resistance to estrogen-depriving therapies. See also: News and Views by Oesterreich & Davidson Letters Top Activating ESR1 mutations in hormone-resistant metastatic breast cancer   pp1446 - 1451 Dan R Robinson, Yi-Mi Wu, Pankaj Vats, Fengyun Su, Robert J Lonigro, Xuhong Cao, Shanker Kalyana-Sundaram, Rui Wang, Yu Ning, Lynda Hodges, Amy Gursky, Javed Siddiqui, Scott A Tomlins, Sameek Roychowdhury, Kenneth J Pienta, Scott Y Kim, J Scott Roberts, James M Rae, Catherine H Van Poznak, Daniel F Hayes, Rashmi Chugh, Lakshmi P Kunju, Moshe Talpaz, Anne F Schott & Arul M Chinnaiyan doi:10.1038/ng.2823 Arul Chinnaiyan and colleagues report the results of prospective clinical sequencing of 11 estrogen receptor-positive metastatic breast cancers. They identify ESR1 mutations affecting the ligand-binding domain in six hormone-resistant metastatic breast cancers and show that the mutant estrogen receptors are constitutively active and continue to be responsive to anti-estrogen therapies in vitro. See also: News and Views by Oesterreich & Davidson Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease   pp1452 - 1458 Jean-Charles Lambert, Carla A Ibrahim-Verbaas, Denise Harold, Adam C Naj, Rebecca Sims, Céline Bellenguez, Gyungah Jun, Anita L DeStefano, Joshua C Bis, Gary W Beecham, Benjamin Grenier-Boley, Giancarlo Russo, Tricia A Thornton-Wells, Nicola Jones, Albert V Smith, Vincent Chouraki, Charlene Thomas, M Arfan Ikram, Diana Zelenika, Badri N Vardarajan, Yoichiro Kamatani, Chiao-Feng Lin, Amy Gerrish, Helena Schmidt, Brian Kunkle, Melanie L Dunstan, Agustin Ruiz, Marie-Thérèse Bihoreau, Seung-Hoan Choi, Christiane Reitz, Florence Pasquier, Paul Hollingworth, Alfredo Ramirez, Olivier Hanon, Annette L Fitzpatrick, Joseph D Buxbaum, Dominique Campion, Paul K Crane, Clinton Baldwin, Tim Becker, Vilmundur Gudnason, Carlos Cruchaga, David Craig, Najaf Amin, Claudine Berr, Oscar L Lopez, Philip L De Jager, Vincent Deramecourt, Janet A Johnston, Denis Evans, Simon Lovestone, Luc Letenneur, Francisco J Morón, David C Rubinsztein, Gudny Eiriksdottir, Kristel Sleegers, Alison M Goate, Nathalie Fiévet, Matthew J Huentelman, Michael Gill, Kristelle Brown, M Ilyas Kamboh, Lina Keller, Pascale Barberger-Gateau, Bernadette McGuinness, Eric B Larson, Robert Green, Amanda J Myers, Carole Dufouil, Stephen Todd, David Wallon, Seth Love, Ekaterina Rogaeva, John Gallacher, Peter St George-Hyslop, Jordi Clarimon, Alberto Lleo, Anthony Bayer, Debby W Tsuang, Lei Yu, Magda Tsolaki, Paola Bossù, Gianfranco Spalletta, Petroula Proitsi, John Collinge, Sandro Sorbi, Florentino Sanchez-Garcia, Nick C Fox, John Hardy, Maria Candida Deniz Naranjo, Paolo Bosco, Robert Clarke, Carol Brayne, Daniela Galimberti, Michelangelo Mancuso, Fiona Matthews, European Alzheimer's Disease Initiative (EADI), Genetic and Environmental Risk in Alzheimer's Disease (GERAD), Alzheimer's Disease Genetic Consortium (ADGC), Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE), Susanne Moebus, Patrizia Mecocci, Maria Del Zompo, Wolfgang Maier, Harald Hampel, Alberto Pilotto, Maria Bullido, Francesco Panza, Paolo Caffarra, Benedetta Nacmias, John R Gilbert, Manuel Mayhaus, Lars Lannfelt, Hakon Hakonarson, Sabrina Pichler, Minerva M Carrasquillo, Martin Ingelsson, Duane Beekly, Victoria Alvarez, Fanggeng Zou, Otto Valladares, Steven G Younkin, Eliecer Coto, Kara L Hamilton-Nelson, Wei Gu, Cristina Razquin, Pau Pastor, Ignacio Mateo, Michael J Owen, Kelley M Faber, Palmi V Jonsson, Onofre Combarros, Michael C O'Donovan, Laura B Cantwell, Hilkka Soininen, Deborah Blacker, Simon Mead, Thomas H Mosley Jr, David A Bennett, Tamara B Harris, Laura Fratiglioni, Clive Holmes, Renee F A G de Bruijn, Peter Passmore, Thomas J Montine, Karolien Bettens, Jerome I Rotter, Alexis Brice, Kevin Morgan, Tatiana M Foroud, Walter A Kukull, Didier Hannequin, John F Powell, Michael A Nalls, Karen Ritchie, Kathryn L Lunetta, John S K Kauwe, Eric Boerwinkle, Matthias Riemenschneider, Mercè Boada, Mikko Hiltunen, Eden R Martin, Reinhold Schmidt, Dan Rujescu, Li-San Wang, Jean-François Dartigues, Richard Mayeux, Christophe Tzourio, Albert Hofman, Markus M Nöthen, Caroline Graff, Bruce M Psaty, Lesley Jones, Jonathan L Haines, Peter A Holmans, Mark Lathrop, Margaret A Pericak-Vance, Lenore J Launer, Lindsay A Farrer, Cornelia M van Duijn, Christine Van Broeckhoven, Valentina Moskvina, Sudha Seshadri, Julie Williams, Gerard D Schellenberg & Philippe Amouyel doi:10.1038/ng.2802 Philippe Amouyel, Julie Williams, Gerard Schellenberg, Sudha Seshadri and colleagues report a meta-analysis of genome-wide association studies for late-onset Alzheimer's disease in 17,008 cases and 37,154 controls with replication in an additional 8,572 cases and 11,312 controls. They identify 11 loci newly associated with Alzheimer's disease. Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation   pp1459 - 1463 Guangwu Guo, Xiaojuan Sun, Chao Chen, Song Wu, Peide Huang, Zesong Li, Michael Dean, Yi Huang, Wenlong Jia, Quan Zhou, Aifa Tang, Zuoquan Yang, Xianxin Li, Pengfei Song, Xiaokun Zhao, Rui Ye, Shiqiang Zhang, Zhao Lin, Mingfu Qi, Shengqing Wan, Liangfu Xie, Fan Fan, Michael L Nickerson, Xiangjun Zou, Xueda Hu, Li Xing, Zhaojie Lv, Hongbin Mei, Shengjie Gao, Chaozhao Liang, Zhibo Gao, Jingxiao Lu, Yuan Yu, Chunxiao Liu, Lin Li, Xiaodong Fang, Zhimao Jiang, Jie Yang, Cailing Li, Xin Zhao, Jing Chen, Fang Zhang, Yongqi Lai, Zheguang Lin, Fangjian Zhou, Hao Chen, Hsiao Chang Chan, Shirley Tsang, Dan Theodorescu, Yingrui Li, Xiuqing Zhang, Jian Wang, Huanming Yang, Yaoting Gui, Jun Wang & Zhiming Cai doi:10.1038/ng.2798 Zhiming Cai and colleagues report whole-genome and whole-exome sequencing of 99 paired tumor-normal samples of transitional cell carcinoma of the bladder. They find that 32% of tumors harbor alterations in genes involved in sister chromatid cohesion, including STAG2, ESPL1, NIPBL, SMC1A and SMC3. Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy   pp1464 - 1469 Cristina Balbás-Martínez, Ana Sagrera, Enrique Carrillo-de-Santa-Pau, Julie Earl, Mirari Márquez, Miguel Vazquez, Eleonora Lapi, Francesc Castro-Giner, Sergi Beltran, Mònica Bayés, Alfredo Carrato, Juan C Cigudosa, Orlando Domínguez, Marta Gut, Jesús Herranz, Núria Juanpere, Manolis Kogevinas, Xavier Langa, Elena López-Knowles, José A Lorente, Josep Lloreta, David G Pisano, Laia Richart, Daniel Rico, Rocío N Salgado, Adonina Tardón, Stephen Chanock, Simon Heath, Alfonso Valencia, Ana Losada, Ivo Gut, Núria Malats & Francisco X Real doi:10.1038/ng.2799 Francisco Real and colleagues report exome sequencing in urothelial bladder tumors. They show that STAG2, a subunit of the cohesin complex, is recurrently mutated and provide evidence that STAG2 loss does not lead to increases in aneuploidy. Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas   pp1470 - 1473 Yuchen Jiao, Timothy M Pawlik, Robert A Anders, Florin M Selaru, Mirte M Streppel, Donald J Lucas, Noushin Niknafs, Violeta Beleva Guthrie, Anirban Maitra, Pedram Argani, G Johan A Offerhaus, Juan Carlos Roa, Lewis R Roberts, Gregory J Gores, Irinel Popescu, Sorin T Alexandrescu, Simona Dima, Matteo Fassan, Michele Simbolo, Andrea Mafficini, Paola Capelli, Rita T Lawlor, Andrea Ruzzenente, Alfredo Guglielmi, Giampaolo Tortora, Filippo de Braud, Aldo Scarpa, William Jarnagin, David Klimstra, Rachel Karchin, Victor E Velculescu, Ralph H Hruban, Bert Vogelstein, Kenneth W Kinzler, Nickolas Papadopoulos & Laura D Wood doi:10.1038/ng.2813 Laura Wood, Kenneth Kinzler, Nickolas Papadopoulos, Aldo Scarpa and colleagues report exome sequencing of intrahepatic cholangiocarcinomas. They identify recurrent somatic mutations in BAP1, ARID1A and PBRM1. Exome sequencing identifies distinct mutational patterns in liver fluke-related and non-infection-related bile duct cancers   pp1474 - 1478 Waraporn Chan-on, Maarja-Liisa Nairismägi, Choon Kiat Ong, Weng Khong Lim, Simona Dima, Chawalit Pairojkul, Kiat Hon Lim, John R McPherson, Ioana Cutcutache, Hong Lee Heng, London Ooi, Alexander Chung, Pierce Chow, Peng Chung Cheow, Ser Yee Lee, Su Pin Choo, Iain Bee Huat Tan, Dan Duda, Anca Nastase, Swe Swe Myint, Bernice Huimin Wong, Anna Gan, Vikneswari Rajasegaran, Cedric Chuan Young Ng, Sanjanaa Nagarajan, Apinya Jusakul, Shenli Zhang, Priya Vohra, Willie Yu, DaChuan Huang, Paiboon Sithithaworn, Puangrat Yongvanit, Sopit Wongkham, Narong Khuntikeo, Vajaraphongsa Bhudhisawasdi, Irinel Popescu, Steven G Rozen, Patrick Tan & Bin Tean Teh doi:10.1038/ng.2806 Bin Tean Teh, Patrick Tan, Steven Rozen, Irinel Popescu and colleagues report exome sequencing of cholangiocarcinomas, including cases caused by liver fluke (Opisthorchis viverrini) infection and cases caused by non-O. viverrini etiologies. They identify recurrent somatic mutations in BAP1 and ARID1A and demonstrate different mutation patterns in liver fluke infection-related and non-infection-related cancers. Distinct H3F3A and H3F3B driver mutations define chondroblastoma and giant cell tumor of bone   pp1479 - 1482 Sam Behjati, Patrick S Tarpey, Nadège Presneau, Susanne Scheipl, Nischalan Pillay, Peter Van Loo, David C Wedge, Susanna L Cooke, Gunes Gundem, Helen Davies, Serena Nik-Zainal, Sancha Martin, Stuart McLaren, Victoria Goodie, Ben Robinson, Adam Butler, Jon W Teague, Dina Halai, Bhavisha Khatri, Ola Myklebost, Daniel Baumhoer, Gernot Jundt, Rifat Hamoudi, Roberto Tirabosco, M Fernanda Amary, P Andrew Futreal, Michael R Stratton, Peter J Campbell & Adrienne M Flanagan/font> doi:10.1038/ng.2814 Adrienne Flanagan and colleagues identify distinct driver mutations in H3F3A and H3F3B in chondroblastoma and giant cell tumor of bone. The mutations occur in over 90% of tumors and exhibit a high degree of tumor type specificity. See also: News and Views by Lindroth & Plass Somatic mutation of CDKN1B in small intestine neuroendocrine tumors   pp1483 - 1486 Joshua M Francis, Adam Kiezun, Alex H Ramos, Stefano Serra, Chandra Sekhar Pedamallu, Zhi Rong Qian, Michaela S Banck, Rahul Kanwar, Amit A Kulkarni, Anna Karpathakis, Veronica Manzo, Tanupriya Contractor, Juliet Philips, Elizabeth Nickerson, Nam Pho, Susanne M Hooshmand, Lauren K Brais, Michael S Lawrence, Trevor Pugh, Aaron McKenna, Andrey Sivachenko, Kristian Cibulskis, Scott L Carter, Akinyemi I Ojesina, Samuel Freeman, Robert T Jones, Douglas Voet, Gordon Saksena, Daniel Auclair, Robert Onofrio, Erica Shefler, Carrie Sougnez, Jonna Grimsby, Lisa Green, Niall Lennon, Tim Meyer, Martyn Caplin, Daniel C Chung, Andreas S Beutler, Shuji Ogino, Christina Thirlwell, Ramesh Shivdasani, Sylvia L Asa, Chris R Harris, Gad Getz, Matthew Kulke & Matthew Meyerson doi:10.1038/ng.2821 Matthew Meyerson and colleagues report whole-exome and whole-genome sequencing of 55 small intestine neuroendocrine tumors. They identify recurrent somatic mutations in CDKN1B, implicating cell cycle dysregulation in the pathogenesis of these tumors. A genome-wide association study identifies new susceptibility loci for esophageal adenocarcinoma and Barrett's esophagus   pp1487 - 1493 David M Levine, Weronica E Ek, Rui Zhang, Xinxue Liu, Lynn Onstad, Cassandra Sather, Pierre Lao-Sirieix, Marilie D Gammon, Douglas A Corley, Nicholas J Shaheen, Nigel C Bird, Laura J Hardie, Liam J Murray, Brian J Reid, Wong-Ho Chow, Harvey A Risch, Olof Nyrén, Weimin Ye, Geoffrey Liu, Yvonne Romero, Leslie Bernstein, Anna H Wu, Alan G Casson, Stephen J Chanock, Patricia Harrington, Isabel Caldas, Irene Debiram-Beecham, Carlos Caldas, Nicholas K Hayward, Paul D Pharoah, Rebecca C Fitzgerald, Stuart MacGregor, David C Whiteman & Thomas L Vaughan doi:10.1038/ng.2796 Thomas Vaughan and colleagues report a genome-wide association study of esophageal adenocarcinoma together with its precancerous lesion, Barrett's esophagus. They identified three loci associated with susceptibility to this cancer. Inherited GATA3 variants are associated with Ph-like childhood acute lymphoblastic leukemia and risk of relapse   pp1494 - 1498 Virginia Perez-Andreu, Kathryn G Roberts, Richard C Harvey, Wenjian Yang, Cheng Cheng, Deqing Pei, Heng Xu, Julie Gastier-Foster, Shuyu E, Joshua Yew-Suang Lim, I-Ming Chen, Yiping Fan, Meenakshi Devidas, Michael J Borowitz, Colton Smith, Geoffrey Neale, Esteban G Burchard, Dara G Torgerson, Federico Antillon Klussmann, Cesar Rolando Najera Villagran, Naomi J Winick, Bruce M Camitta, Elizabeth Raetz, Brent Wood, Feng Yue, William L Carroll, Eric Larsen, W Paul Bowman, Mignon L Loh, Michael Dean, Deepa Bhojwani, Ching-Hon Pui, William E Evans, Mary V Relling, Stephen P Hunger, Cheryl L Willman, Charles G Mullighan & Jun J Yang doi:10.1038/ng.2803 Jun Yang and colleagues show that common variants in GATA3 are associated with risk of Ph-like acute lymphoblastic leukemia (ALL). They further show that these variants are associated with variation in GATA3 expression levels and with risk of ALL relapse. New loci associated with chronic hepatitis B virus infection in Han Chinese   pp1499 - 1503 Zhibin Hu, Yao Liu, Xiangjun Zhai, Juncheng Dai, Guangfu Jin, Li Wang, Liguo Zhu, Yuan Yang, Jibin Liu, Minjie Chu, Juan Wen, Kaipeng Xie, Guoming Du, Qungang Wang, Yuchun Zhou, Minquan Cao, Li Liu, Yisha He, Ying Wang, Gangqiao Zhou, Weihua Jia, Jiachun Lu, Shengping Li, Jianjun Liu, Haitao Yang, Yongyong Shi, Weiping Zhou & Hongbing Shen doi:10.1038/ng.2809 Hongbing Shen and colleagues report a genome-wide association study for chronic hepatitis B virus (HBV) infection in Han Chinese populations. They identify two loci newly associated with HBV infection near HLA-C and UBLE2L3 and replicate previous associations at HLA-DP and HLA-DQ. Vitamin C modulates TET1 function during somatic cell reprogramming   pp1504 - 1509 Jiekai Chen, Lin Guo, Lei Zhang, Haoyu Wu, Jiaqi Yang, He Liu, Xiaoshan Wang, Xiao Hu, Tianpeng Gu, Zhiwei Zhou, Jing Liu, Jiadong Liu, Hongling Wu, Shi-Qing Mao, Kunlun Mo, Yingying Li, Keyu Lai, Jing Qi, Hongjie Yao, Guangjin Pan, Guo-Liang Xu & Duanqing Pei doi:10.1038/ng.2807 Guo-Liang Xu, Duanqing Pei and colleagues show that during induced pluripotent cell reprogramming Tet1 regulates 5-hydroxymethylcytosine levels at loci critical for mesenchymal-to-epithelial transition in a vitamin C-dependent fashion. They also show that Tet1 either enhances or inhibits somatic cell reprogramming, depending on the absence or presence of vitamin C, respectively. See also: News and Views by Pera A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity   pp1510 - 1515 Jianjian Qi, Xin Liu, Di Shen, Han Miao, Bingyan Xie, Xixiang Li, Peng Zeng, Shenhao Wang, Yi Shang, Xingfang Gu, Yongchen Du, Ying Li, Tao Lin, Jinhong Yuan, Xueyong Yang, Jinfeng Chen, Huiming Chen, Xingyao Xiong, Ke Huang, Zhangjun Fei, Linyong Mao, Li Tian, Thomas Städler, Susanne S Renner, Sophien Kamoun, William J Lucas, Zhonghua Zhang & Sanwen Huang doi:10.1038/ng.2801 Sanwen Huang and colleagues report a genomic variation map of cucumber. They report the resequencing of 115 cucumber accessions and de novo assembly of the wild cucumber genome. Corrigendum Top Corrigendum: The landscape of somatic mutations in Down syndrome-related myeloid disorders   p1516 Kenichi Yoshida, Tsutomu Toki, Yusuke Okuno, Rika Kanezaki, Yuichi Shiraishi, Aiko Sato-Otsubo, Masashi Sanada, Myoung-ja Park, Kiminori Terui, Hiromichi Suzuki, Ayana Kon, Yasunobu Nagata, Yusuke Sato, RuNan Wang, Norio Shiba, Kenichi Chiba, Hiroko Tanaka, Asahito Hama, Hideki Muramatsu, Daisuke Hasegawa, Kazuhiro Nakamura, Hirokazu Kanegane, Keiko Tsukamoto, Souichi Adachi, Kiyoshi Kawakami, Koji Kato, Ryosei Nishimura, Shai Izraeli, Yasuhide Hayashi, Satoru Miyano, Seiji Kojima, Etsuro Ito & Seishi Ogawa doi:10.1038/ng1213-1516 Top Advertisement (Epi)genetics of pregnancy-associated diseases (open access) In this mini review, Marie van Dijk and Cees Oudejans describe the current knowledge regarding genetics and epigenetics of pregnancy-associated diseases with placental origin. We discuss the effect on genetic linkage analyses when the fetal genotype determines the maternal phenotype.  Read many more high-quality articles from Frontiers in Genetics    Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com More Nature Events

You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at: www.nature.com/myaccount (You will need to log in to be recognised as a nature.com registrant) For further technical assistance, please contact our registration department For print subscription enquiries, please contact our subscription department For other enquiries, please contact our customer feedback department Nature Publishing Group | 75 Varick Street, 9th Floor | New York | NY 10013-1917 | USA Nature Publishing Group's worldwide offices: London - Paris - Munich - New Delhi - Tokyo - Melbourne San Diego - San Francisco - Washington - New York - Boston Macmillan Publishers Limited is a company incorporated in England and Wales under company number 785998 and whose registered office is located at Brunel Road, Houndmills, Basingstoke, Hampshire RG21 6XS. © 2013 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.