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| | December 2009 Volume 41, Issue 12 |  | | |  |  Editorial
News and Views
Research Highlights
Brief Communications
Articles
Letters
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| | | | | Advertisement | | Nature Methods focus
Next-generation sequencing data analysis
In the focus leading experts compare algorithms for the most common applications of next-generation sequencing. With this information users will be able to make informed choices to more easily convert the raw sequence data generated by next-generation-sequencing instruments into new biological results.
For FREE access visit: www.nature.com/nmeth/journal/v6/n11s | | | | | Editorial |  Top | |  | | | Cool as a cucumber p1259
doi:10.1038/ng1209-1259
The genome of the seventh plant to be sequenced, Cucumis sativus L., was assembled using the conventional long-read Sanger sequencing and higher-throughput short-read technology. This genome is the entry point for exploring the diversity and function of the Cucurbitaceae family of agriculturally important plants. Its compact genome, without evidence of recent duplication, will be useful in comparative analysis of plant genome evolution.
Full Text | PDF
| | News and Views | Top | | | | | | |  | Genetics
JOBS of the week | | Postdoctoral Scientist
Medical Research Council
Cambridge, CB2 0QH, UK | | Postdoctoral Fellow
University of California, San Diego
La Jolla | | Postdoctoral Research Associate
Princeton University
Princeton, NJ | | Postdoctoral Position In Animal Biotechnology
IAS-CAAS
Summer Palace, Beijing 100193, China | | PhD positions in Molecular Biology, Protein Studies, Signal Transduction
Massey University
Albany Highway, Gate 4, Auckland, New Zealand | | | | | | | | | | | | Research Highlights | Top | | | | | Research highlights p1267
doi:10.1038/ng1209-1267
Full Text | PDF
| | Brief Communications | Top | | | | | A small recurrent deletion within 15q13.3 is associated with a range of neurodevelopmental phenotypes pp1269 - 1271
Marwan Shinawi, Christian P Schaaf, Samarth S Bhatt, Zhilian Xia, Ankita Patel, Sau Wai Cheung, Brendan Lanpher, Sandra Nagl, Heinrich Stephan Herding, Claudia Nevinny-Stickel, LaDonna L Immken, Gayle Simpson Patel, Jennifer Ruth German, Arthur L Beaudet and Pawel Stankiewicz
doi:10.1038/ng.481
Arthur Beaudet and colleagues report a recurrent 680-kb deletion within chromosome 15q13.3 associated with a range of neurodevelopmental phenotypes, including developmental delay, mental retardation and seizures. The deletion lies within the previously reported 1.5-Mb 15q13.3 deletion and spans only two genes, CHRNA7 and OTUD7A.
First paragraph | Full Text | PDF
| | | | | Mutations in CCBE1 cause generalized lymph vessel dysplasia in humans pp1272 - 1274
Marielle Alders, Benjamin M Hogan, Evisa Gjini, Faranak Salehi, Lihadh Al-Gazali, Eric A Hennekam, Eva E Holmberg, Marcel M A M Mannens, Margot F Mulder, G Johan A Offerhaus, Trine E Prescott, Eelco J Schroor, Joke B G M Verheij, Merlijn Witte, Petra J Zwijnenburg, Mikka Vikkula, Stefan Schulte-Merker and Raoul C Hennekam
doi:10.1038/ng.484
Raoul Hennekam and colleagues report the identification of mutations in CCBE1 that cause Hennekam syndrome in humans. Features of Hennekam syndrome include lymphedema, lymphangiectasias, mental retardation and unusual facial characteristics. CCBE1 encodes Collagen and Calcium-Binding EGF domain-1, a secreted protein that has been shown to be required for embryonic lymphangiogenesis in zebrafish.
First paragraph | Full Text | PDF
| | | Advertisement | | SureSelect Target Enrichment System and the New Human All Exon Kit.
What if you could finally harness the potential of next-gen sequencing? With Agilent's SureSelect Target Enrichment System, you can. The new SureSelect Human All-Exon Kit enables you to target all human exons, focusing your work on a significant area of the genome-with greater depth of coverage and fewer sequencing reactions. Learn more and save up to 50% on your first order. | | | | | | Articles | Top | | | | | The genome of the cucumber, Cucumis sativus L. pp1275 - 1281
Sanwen Huang, Ruiqiang Li, Zhonghua Zhang, Li Li, Xingfang Gu, Wei Fan, William J Lucas, Xiaowu Wang, Bingyan Xie, Peixiang Ni, Yuanyuan Ren, Hongmei Zhu, Jun Li, Kui Lin, Weiwei Jin, Zhangjun Fei, Guangcun Li, Jack Staub, Andrzej Kilian, Edwin A G van der Vossen, Yang Wu, Jie Guo, Jun He, Zhiqi Jia, Yi Ren, Geng Tian, Yao Lu, Jue Ruan, Wubin Qian, Mingwei Wang, Quanfei Huang, Bo Li, Zhaoling Xuan, Jianjun Cao, Asan, Zhigang Wu, Juanbin Zhang, Qingle Cai, Yinqi Bai, Bowen Zhao, Yonghua Han, Ying Li, Xuefeng Li, Shenhao Wang, Qiuxiang Shi, Shiqiang Liu, Won Kyong Cho, Jae-Yean Kim, Yong Xu, Katarzyna Heller-Uszynska, Han Miao, Zhouchao Cheng, Shengping Zhang, Jian Wu, Yuhong Yang, Houxiang Kang, Man Li, Huiqing Liang, Xiaoli Ren, Zhongbin Shi, Ming Wen, Min Jian, Hailong Yang, Guojie Zhang, Zhentao Yang, Rui Chen, Shifang Liu, Jianwen Li, Lijia Ma, Hui Liu, Yan Zhou, Jing Zhao, Xiaodong Fang, Guoqing Li, Lin Fang, Yingrui Li, Dongyuan Liu, Hongkun Zheng, Yong Zhang, Nan Qin, Zhuo Li, Guohua Yang, Shuang Yang, Lars Bolund, Karsten Kristiansen, Hancheng Zheng, Shaochuan Li, Xiuqing Zhang, Huanming Yang, Jian Wang, Rifei Sun, Baoxi Zhang, Shuzhi Jiang, Jun Wang, Yongchen Du and Songgang Li
doi:10.1038/ng.475
Jun Wang and colleagues report the genome sequence of the cucumber. The cucumber genome is the seventh plant genome sequence to be reported and was assembled with a combination of traditional Sanger and next-generation sequencing methods.
Abstract | Full Text | PDF
| | | | | Comparative genomic and phylogeographic analysis of Mycobacterium leprae pp1282 - 1289
Marc Monot, Nadine Honoré, Thierry Garnier, Nora Zidane, Diana Sherafi, Alberto Paniz-Mondolfi, Masanori Matsuoka, G Michael Taylor, Helen D Donoghue, Abi Bouwman, Simon Mays, Claire Watson, Diana Lockwood, Ali Khamispour, Yahya Dowlati, Shen Jianping, Thomas H Rea, Lucio Vera-Cabrera, Mariane M Stefani, Sayera Banu, Murdo Macdonald, Bishwa Raj Sapkota, John S Spencer, Jérôme Thomas, Keith Harshman, Pushpendra Singh, Philippe Busso, Alexandre Gattiker, Jacques Rougemont, Patrick J Brennan and Stewart T Cole
doi:10.1038/ng.477
Stewart Cole and colleagues report the genome sequence and comparative analyses of Brazilian, Indian, North American and Thai strains of Mycobacterium leprae, the etiologial agent of leprosy. They define 16 sub-types of M. leprae and examine their geographical distribution.
Abstract | Full Text | PDF
See also: News and Views by Maiden
| | | | | HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C pp1290 - 1294
Rasmi Thomas, Richard Apps, Ying Qi, Xiaojiang Gao, Victoria Male, Colm O'hUigin, Geraldine O'Connor, Dongliang Ge, Jacques Fellay, Jeffrey N Martin, Joseph Margolick, James J Goedert, Susan Buchbinder, Gregory D Kirk, Maureen P Martin, Amalio Telenti, Steven G Deeks, Bruce D Walker, David Goldstein, Daniel W McVicar, Ashley Moffett and Mary Carrington
doi:10.1038/ng.486
Mary Carrington and colleagues follow up on an earlier association of a variant upstream of HLA-C to HIV viral load setpoint, showing that this variant is associated with high HLA-C cell surface expression and demonstrating a protective effect of the variant in viral load and disease progression.
Abstract | Full Text | PDF
| | | | | Etv4 and Etv5 are required downstream of GDNF and Ret for kidney branching morphogenesis pp1295 - 1302
Benson C Lu, Cristina Cebrian, Xuan Chi, Satu Kuure, Richard Kuo, Carlton M Bates, Silvia Arber, John Hassell, Lesley MacNeil, Masato Hoshi, Sanjay Jain, Naoya Asai, Masahide Takahashi, Kai M Schmidt-Ott, Jonathan Barasch, Vivette D'Agati and Frank Costantini
doi:10.1038/ng.476
Frank Costantini and colleagues report the identification of the ETS transcription factors, Etv4 and Etv5, as key targets of Ret signaling during kidney branching morphogenesis. Loss of Etv4 and Etv5 function in mice leads to complete failure of kidney development.
Abstract | Full Text | PDF
| | Letters | Top | | | | | Genome-wide association study identifies common variants at four loci as genetic risk factors for Parkinson's disease pp1303 - 1307
Wataru Satake, Yuko Nakabayashi, Ikuko Mizuta, Yushi Hirota, Chiyomi Ito, Michiaki Kubo, Takahisa Kawaguchi, Tatsuhiko Tsunoda, Masahiko Watanabe, Atsushi Takeda, Hiroyuki Tomiyama, Kenji Nakashima, Kazuko Hasegawa, Fumiya Obata, Takeo Yoshikawa, Hideshi Kawakami, Saburo Sakoda, Mitsutoshi Yamamoto, Nobutaka Hattori, Miho Murata, Yusuke Nakamura and Tatsushi Toda
doi:10.1038/ng.485
Tatsushi Toda and colleagues report results of a genome-wide association study of Parkinson's disease in the Japanese population. They identify four loci harboring common variants associated with Parkinson's disease, including two newly discovered risk regions on 1q32 and 4p15.
First paragraph | Full Text | PDF
See also: News and Views by Shulman & De Jager | Letter by Simon-Sanchez et al.
| | | | | Genome-wide association study reveals genetic risk underlying Parkinson's disease pp1308 - 1312
Javier Simón-Sánchez, Claudia Schulte, Jose M Bras, Manu Sharma, J Raphael Gibbs, Daniela Berg, Coro Paisan-Ruiz, Peter Lichtner, Sonja W Scholz, Dena G Hernandez, Rejko Krüger, Monica Federoff, Christine Klein, Alison Goate, Joel Perlmutter, Michael Bonin, Michael A Nalls, Thomas Illig, Christian Gieger, Henry Houlden, Michael Steffens, Michael S Okun, Brad A Racette, Mark R Cookson, Kelly D Foote, Hubert H Fernandez, Bryan J Traynor, Stefan Schreiber, Sampath Arepalli, Ryan Zonozi, Katrina Gwinn, Marcel van der Brug, Grisel Lopez, Stephen J Chanock, Arthur Schatzkin, Yikyung Park, Albert Hollenbeck, Jianjun Gao, Xuemei Huang, Nick W Wood, Delia Lorenz, Günther Deuschl, Honglei Chen, Olaf Riess, John A Hardy, Andrew B Singleton and Thomas Gasser
doi:10.1038/ng.487
Andrew Singleton, Thomas Gasser and colleagues report results of a genome-wide association study of Parkinson's disease among individuals of European ancestry. They find genome-wide significant associations at two loci, SNCA and MAPT, and provide supporting evidence for a new risk locus on 1q32.
First paragraph | Full Text | PDF
See also: News and Views by Shulman & De Jager | Letter by Satake et al.
| | | | | Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk pp1313 - 1318
Soumya Raychaudhuri, Brian P Thomson, Elaine F Remmers, Stephen Eyre, Anne Hinks, Candace Guiducci, Joseph J Catanese, Gang Xie, Eli A Stahl, Robert Chen, Lars Alfredsson, Christopher I Amos, Kristin G Ardlie, BIRAC Consortium, Anne Barton, John Bowes, Noel P Burtt, Monica Chang, Jonathan Coblyn, Karen H Costenbader, Lindsey A Criswell, J Bart A Crusius, Jing Cui, Phillip L De Jager, Bo Ding, Paul Emery, Edward Flynn, Pille Harrison, Lynne J Hocking, Tom W J Huizinga, Daniel L Kastner, Xiayi Ke, Fina A S Kurreeman, Annette T Lee, Xiangdong Liu, Yonghong Li, Paul Martin, Ann W Morgan, Leonid Padyukov, David M Reid, Mark Seielstad, Michael F Seldin, Nancy A Shadick, Sophia Steer, Paul P Tak, Wendy Thomson, Annette H M van der Helm-van Mil, Irene E van der Horst-Bruinsma, Michael E Weinblatt, Anthony G Wilson, Gert Jan Wolbink, Paul Wordsworth, YEAR Consortium, David Altshuler, Elizabeth W Karlson, Rene E M Toes, Niek de Vries, Ann B Begovich, Katherine A Siminovitch, Jane Worthington, Lars Klareskog, Peter K Gregersen, Mark J Daly and Robert M Plenge
doi:10.1038/ng.479
Soumya Raychaudhuri and colleagues demonstrate the utility of GRAIL, a software program used to prioritize results from genome-wide association studies for further replication, applied here to rheumatoid arthritis. The authors seek replication of their predictions in additional independent cohorts and report three new genetic loci associated with RA susceptibility.
First paragraph | Full Text | PDF
| | | | | Specific interaction between genotype, smoking and autoimmunity to citrullinated α-enolase in the etiology of rheumatoid arthritis pp1319 - 1324
Hiba Mahdi, Benjamin A Fisher, Henrik Källberg, Darren Plant, Vivianne Malmström, Johan Rönnelid, Peter Charles, Bo Ding, Lars Alfredsson, Leonid Padyukov, Deborah P M Symmons, Patrick J Venables, Lars Klareskog and Karin Lundberg
doi:10.1038/ng.480
Karin Lundberg and colleagues explore gene-gene and gene-environment interactions in susceptibility to rheumatoid arthritis, reporting an association of HLA-DRB1, PTPN22 and smoking stratified by the autoantigen CEP-1.
First paragraph | Full Text | PDF
| | | | | A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in the Japanese population pp1325 - 1329
Kouichi Asano, Tomonaga Matsushita, Junji Umeno, Naoya Hosono, Atsushi Takahashi, Takahisa Kawaguchi, Takayuki Matsumoto, Toshiyuki Matsui, Yoichi Kakuta, Yoshitaka Kinouchi, Tooru Shimosegawa, Masayo Hosokawa, Yoshiaki Arimura, Yasuhisa Shinomura, Yutaka Kiyohara, Tatsuhiko Tsunoda, Naoyuki Kamatani, Mitsuo Iida, Yusuke Nakamura and Michiaki Kubo
doi:10.1038/ng.482
Michiaki Kubo and colleagues report results of a genome-wide association study of ulcerative colitis in the Japanese population. Their study identifies three new susceptibility loci for this common inflammatory bowel disease, including FCGR2A, which has previously been implicated in other autoimmune diseases.
First paragraph | Full Text | PDF
See also: Letter by Barrett et al. | Letter by Imielinski et al.
| | | | | Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region pp1330 - 1334
The UK IBD Genetics Consortium & the Wellcome Trust Case Control
Consortium 2
doi:10.1038/ng.483
The UK IBD Genetics Consortium and the Wellcome Trust Case Control Consortium 2 report results of a genome-wide association study of ulcerative colitis. They identify three new loci associated with the disease, including the HNF4A region on 20q13.
First paragraph | Full Text | PDF
See also: Letter by Asano et al. | Letter by Imielinski et al.
| | | | | Common variants at five new loci associated with early-onset inflammatory bowel disease pp1335 - 1340
Marcin Imielinski, Robert N Baldassano, Anne Griffiths, Richard K Russell, Vito Annese, Marla Dubinsky, Subra Kugathasan, Jonathan P Bradfield, Thomas D Walters, Patrick Sleiman, Cecilia E Kim, Aleixo Muise, Kai Wang, Joseph T Glessner, Shehzad Saeed, Haitao Zhang, Edward C Frackelton, Cuiping Hou, James H Flory, George Otieno, Rosetta M Chiavacci, Robert Grundmeier, Massimo Castro, Anna Latiano, Bruno Dallapiccola, Joanne Stempak, Debra J Abrams, Kent Taylor, Dermot McGovern, Western Regional Research Alliance for Pediatric IBD, International IBD Genetics Consortium, Melvin B Heyman, George D Ferry, Barbara Kirschner, Jessica Lee, Jonah Essers, Richard Grand, Michael Stephens, Arie Levine, David Piccoli, Johan Van Limbergen, Salvatore Cucchiara, Dimitri S Monos, Stephen L Guthery, Lee Denson, David C Wilson, Struan F A Grant, Mark Daly, Mark S Silverberg, Jack Satsangi and Hakon Hakonarson
doi:10.1038/ng.489
Hakon Hakonarson and colleagues report the discovery of five new regions associated with susceptibility to early-onset inflammatory bowel disease. They also identify multiple loci previously implicated in the etiology of adult-onset Crohn's disease and/or ulcerative colitis as risk factors for early-onset forms of these diseases.
Abstract | Full Text | PDF
See also: Letter by Asano et al. | Letter by Barrett et al.
| | | | | Donor-recipient mismatch for common gene deletion polymorphisms in graft-versus-host disease pp1341 - 1344
Steven A McCarroll, James E Bradner, Hannu Turpeinen, Liisa Volin, Paul J Martin, Shannon D Chilewski, Joseph H Antin, Stephanie J Lee, Tapani Ruutu, Barry Storer, Edus H Warren, Bo Zhang, Lue Ping Zhao, David Ginsburg, Robert J Soiffer, Jukka Partanen, John A Hansen, Jerome Ritz, Aarno Palotie and David Altshuler
doi:10.1038/ng.490
Steven McCarroll and colleagues examine common gene deletions in individuals that have undergone bone marrow transplantation. They find that risk of acute graft-versus-host disease is greater when the donor and recipient are mismatched for a homozygous deletion of UGT2B17.
First paragraph | Full Text | PDF
See also: News and Views by Armour
| | | | | Genetic variants in TPMT and COMT are associated with hearing loss in children receiving cisplatin chemotherapy pp1345 - 1349
Colin J D Ross, Hagit Katzov-Eckert, Marie-Pierre Dubé, Beth Brooks, S Rod Rassekh, Amina Barhdadi, Yassamin Feroz-Zada, Henk Visscher, Andrew M K Brown, Michael J Rieder, Paul C Rogers, Michael S Phillips, Bruce C Carleton, Michael R Hayden and the CPNDS Consortium
doi:10.1038/ng.478
Colin Ross and colleagues report the association of variants in TPMT and COMT to cisplatin-induced hearing loss in children.
First paragraph | Full Text | PDF
| | | | | Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts pp1350 - 1353
Akiko Doi, In-Hyun Park, Bo Wen, Peter Murakami, Martin J Aryee, Rafael Irizarry, Brian Herb, Christine Ladd-Acosta, Junsung Rho, Sabine Loewer, Justine Miller, Thorsten Schlaeger, George Q Daley and Andrew P Feinberg
doi:10.1038/ng.471
Andrew Feinberg and colleagues show that differential methylation of CpG island shores distinguish human induced pluripotent stem cells from the fibroblasts from which they were derived. These differentially methylated regions of the genome can also distinguish normal colon tissue from colorectal cancer.
Abstract | Full Text | PDF
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