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|  | | | | | | Editorial |  Top | |  | | EconOmics p715
doi:10.1038/ng.2688
Far from defending government spending on genomics as an economic stimulus, we celebrate this landmark contribution to our strategic intelligence on the evolving threats to our health, well-being and life on this planet. | | Obituary | Top | | | | David R. Cox 1946-2013 p716
Gregory S Barsh and Richard M Myers
doi:10.1038/ng.2679 | | News and Views | Top | | | | | | Research Highlights | Top | | | | Candidate drug for ALS | MKRN3 and pubertal timing | Heritability estimates | Congenital neutropenia and VPS45 | A secreted PTEN | Analysis | Top | | | | Genome-wide inference of natural selection on human transcription factor binding sites pp723 - 729
Leonardo Arbiza, Ilan Gronau, Bulent A Aksoy, Melissa J Hubisz, Brad Gulko, Alon Keinan & Adam Siepel
doi:10.1038/ng.2658
Adam Siepel and colleagues find that natural selection has exerted a significant influence on transcription factor binding sites in the human lineage using a new probabilistic method, INSIGHT. They analyzed whole-genome sequences from 54 individuals, as well as from several non-human primates, combined with chromatin immunoprecipitation and sequencing data sets to identify transcription factor binding sites and evidence of selection. | | Articles | Top | | | | Identification of multiple risk variants for ankylosing spondylitis through high-density genotyping of immune-related loci pp730 - 738
International Genetics of Ankylosing Spondylitis Consortium (IGAS)
doi:10.1038/ng.2667
Matthew Brown and colleagues identify multiple susceptibility variants for ankylosing spondylitis through an association study based on high-density genotyping of immune-related loci. Their findings implicate numerous biological pathways in the pathogenesis of this disease and highlight shared risk factors with other autoimmune diseases. | | | | Zbtb7a suppresses prostate cancer through repression of a Sox9-dependent pathway for cellular senescence bypass and tumor invasion pp739 - 746
Guocan Wang, Andrea Lunardi, Jiangwen Zhang, Zhenbang Chen, Ugo Ala, Kaitlyn A Webster, Yvonne Tay, Enrique Gonzalez-Billalabeitia, Ainara Egia, David R Shaffer, Brett Carver, Xue-Song Liu, Riccardo Taulli, Winston Patrick Kuo, Caterina Nardella, Sabina Signoretti, Carlos Cordon-Cardo, William L Gerald & Pier Paolo Pandolfi
doi:10.1038/ng.2654
The transcription factor Zbtb7a was previously described as an oncogene in non-Hodgkin lymphoma. Now, Pier Paolo Pandolfi and colleagues report that loss of Zbtb7a accelerates the progression of invasive prostate tumorigenesis in Pten-null mice and shows evidence of monoallelic loss in 18% of individuals with advanced prostate cancer.
See also: News and Views by Zhao & Nelson | | | | A co-clinical approach identifies mechanisms and potential therapies for androgen deprivation resistance in prostate cancer pp747 - 755
Andrea Lunardi, Ugo Ala, Mirjam T Epping, Leonardo Salmena, John G Clohessy, Kaitlyn A Webster, Guocan Wang, Roberta Mazzucchelli, Maristella Bianconi, Edward C Stack, Rosina Lis, Akash Patnaik, Lewis C Cantley, Glenn Bubley, Carlos Cordon-Cardo, William L Gerald, Rodolfo Montironi, Sabina Signoretti, Massimo Loda, Caterina Nardella & Pier Paolo Pandolfi
doi:10.1038/ng.2650
Pier Paolo Pandolfi and colleagues report that compound loss of Pten with Zbtb7a or Trp53 leads to de novo resistance to androgen deprivation therapy in prostate cancer. Integrative analysis of mouse and human data in a co-clinical approach identified XIAP and SRD5A1 inhibitors as potential therapies for castration-resistant prostate cancer.
See also: News and Views by Zhao & Nelson | | | | Forward genetic screen for malignant peripheral nerve sheath tumor formation identifies new genes and pathways driving tumorigenesis pp756 - 766
Eric P Rahrmann, Adrienne L Watson, Vincent W Keng, Kwangmin Choi, Branden S Moriarity, Dominic A Beckmann, Natalie K Wolf, Aaron Sarver, Margaret H Collins, Christopher L Moertel, Margaret R Wallace, Bernat Gel, Eduard Serra, Nancy Ratner & David A Largaespada
doi:10.1038/ng.2641
Eric Rahrmann and colleagues performed a transposon-based somatic mutagenesis screen for genes involved in malignant peripheral nerve sheath tumors (MPNSTs). They identified many recurrent transposon insertions and nominate Foxr2 as a new oncogene in MPNSTs. | | | | Combined sequence-based and genetic mapping analysis of complex traits in outbred rats pp767 - 775
Amelie Baud, Roel Hermsen, Victor Guryev, Pernilla Stridh, Delyth Graham, Martin W McBride, Tatiana Foroud, Sophie Calderari, Margarita Diez, Johan Ockinger, Amennai D Beyeen, Alan Gillett, Nada Abdelmagid, Andre Ortlieb Guerreiro-Cacais, Maja Jagodic, Jonatan Tuncel, Ulrika Norin, Elisabeth Beattie, Ngan Huynh, William H Miller, Daniel L Koller, Imranul Alam, Samreen Falak, Mary Osborne-Pellegrin, Esther Martinez-Membrives, Toni Canete, Gloria Blazquez, Elia Vicens-Costa, Carme Mont-Cardona, Sira Diaz-Moran, Adolf Tobena, Oliver Hummel, Diana Zelenika, Kathrin Saar, Giannino Patone, Anja Bauerfeind, Marie-Therese Bihoreau, Matthias Heinig, Young-Ae Lee, Carola Rintisch, Herbert Schulz, David A Wheeler, Kim C Worley, Donna M Muzny, Richard A Gibbs, Mark Lathrop, Nico Lansu, Pim Toonen, Frans Paul Ruzius, Ewart de Bruijn, Heidi Hauser, David J Adams, Thomas Keane, Santosh S Atanur, Tim J Aitman, Paul Flicek, Tomas Malinauskas, E Yvonne Jones, Diana Ekman, Regina Lopez-Aumatell, Anna F Dominiczak, Martina Johannesson, Rikard Holmdahl, Tomas Olsson, Dominique Gauguier, Norbert Hubner, Alberto Fernandez-Teruel, Edwin Cuppen, Richard Mott & Jonathan Flint for Rat Genome Sequencing and Mapping Consortium
doi:10.1038/ng.2644
The Rat Genome Sequencing and Mapping Consortium reports a combined sequence-based and genetic mapping analysis of 160 phenotypes in an outbred rat heterogeneous stock. They identify 31 genes involved in 27 different phenotypes. | | | | The duck genome and transcriptome provide insight into an avian influenza virus reservoir species OPEN pp776 - 783
Yinhua Huang, Yingrui Li, David W Burt, Hualan Chen, Yong Zhang, Wubin Qian, Heebal Kim, Shangquan Gan, Yiqiang Zhao, Jianwen Li, Kang Yi, Huapeng Feng, Pengyang Zhu, Bo Li, Qiuyue Liu, Suan Fairley, Katharine E Magor, Zhenlin Du, Xiaoxiang Hu, Laurie Goodman, Hakim Tafer, Alain Vignal, Taeheon Lee, Kyu-Won Kim, Zheya Sheng, Yang An, Steve Searle, Javier Herrero, Martien A M Groenen, Richard P M A Crooijmans, Thomas Faraut, Qingle Cai, Robert G Webster, Jerry R Aldridge, Wesley C Warren, Sebastian Bartschat, Stephanie Kehr, Manja Marz, Peter F Stadler, Jacqueline Smith, Robert H S Kraus, Yaofeng Zhao, Liming Ren, Jing Fei, Mireille Morisson, Pete Kaiser, Darren K Griffin, Man Rao, Frederique Pitel, Jun Wang & Ning Li
doi:10.1038/ng.2657
Ning Li and colleagues report the whole-genome sequence of the duck, Anas platyrhynchos, a natural host of avian influenza viruses. They examine host response to infection by comparing the lung transcriptomes of ducks that were infected with influenza A viruses. | | | | Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis pp784 - 790
Christopher B Ford, Rupal R Shah, Midori Kato Maeda, Sebastien Gagneux, Megan B Murray, Ted Cohen, James C Johnston, Jennifer Gardy, Marc Lipsitch & Sarah M Fortune
doi:10.1038/ng.2656
Sarah Fortune and colleagues report that Mycobacterium tuberculosis strains from lineage 2 acquire drug resistance in vitro more rapidly than strains from lineage 4 and show that this correlates with a higher in vivo mutation rate, as estimated from whole-genome sequencing of clinical isolates. They develop a stochastic mathematical model of the within-host evolution of drug resistance, using these mutation rate estimates to predict the rates of emergence of resistance in individuals with tuberculosis.
See also: News and Views by Gumbo | | Letters | Top | | | | The mutational landscape of adenoid cystic carcinoma pp791 - 798
Allen S Ho, Kasthuri Kannan, David M Roy, Luc G T Morris, Ian Ganly, Nora Katabi, Deepa Ramaswami, Logan A Walsh, Stephanie Eng, Jason T Huse, Jianan Zhang, Igor Dolgalev, Kety Huberman, Adriana Heguy, Agnes Viale, Marija Drobnjak, Margaret A Leversha, Christine E Rice, Bhuvanesh Singh, N Gopalakrishna Iyer, C Rene Leemans, Elisabeth Bloemena, Robert L Ferris, Raja R Seethala, Benjamin E Gross, Yupu Liang, Rileen Sinha, Luke Peng, Benjamin J Raphael, Sevin Turcan, Yongxing Gong, Nikolaus Schultz, Seungwon Kim, Simion Chiosea, Jatin P Shah, Chris Sander, William Lee & Timothy A Chan
doi:10.1038/ng.2643
Timothy Chan and colleagues report exome and genome sequencing of 60 adenoid cystic carcinoma (ACC) tumor-normal pairs. They identify multiple pathways recurrently disrupted in ACC and provide evidence that KDM6A and PIK3CA are functionally relevant candidate ACC driver genes. | | | | Genome-wide association study identifies two susceptibility loci for osteosarcoma pp799 - 803
Sharon A Savage, Lisa Mirabello, Zhaoming Wang, Julie M Gastier-Foster, Richard Gorlick, Chand Khanna, Adrienne M Flanagan, Roberto Tirabosco, Irene L Andrulis, Jay S Wunder, Nalan Gokgoz, Ana Patiño-Garcia, Luis Sierrasesúmaga, Fernando Lecanda, Nilgün Kurucu, Inci Ergurhan Ilhan, Neriman Sari, Massimo Serra, Claudia Hattinger, Piero Picci, Logan G Spector, Donald A Barkauskas, Neyssa Marina, Silvia Regina Caminada de Toledo, Antonio S Petrilli, Maria Fernanda Amary, Dina Halai, David M Thomas, Chester Douglass, Paul S Meltzer, Kevin Jacobs, Charles C Chung, Sonja I Berndt, Mark P Purdue, Neil E Caporaso, Margaret Tucker, Nathaniel Rothman, Maria Teresa Landi, Debra T Silverman, Peter Kraft, David J Hunter, Nuria Malats, Manolis Kogevinas, Sholom Wacholder, Rebecca Troisi, Lee Helman, Joseph F Fraumeni Jr, Meredith Yeager, Robert N Hoover & Stephen J Chanock
doi:10.1038/ng.2645
Sharon Savage and colleagues report the results of a genome-wide association study of osteosarcoma. They identify two susceptibility loci for this primary bone malignancy, including variants within the metabotropic glutamate receptor gene GRM4. | | | | Genome-wide association study of B cell non-Hodgkin lymphoma identifies 3q27 as a susceptibility locus in the Chinese population pp804 - 807
Dennis E K Tan, Jia Nee Foo, Jin-Xin Bei, Jiang Chang, Roujun Peng, Xiaohui Zheng, Lixuan Wei, Ying Huang, Wei Yen Lim, Juan Li, Qian Cui, Soo Hong Chew, Richard P Ebstein, Ponnudurai Kuperan, Soon Thye Lim, Miriam Tao, Suat Hoon Tan, Alvin Wong, Gee Chuan Wong, Soo Yong Tan, Siok Bian Ng, Yi-Xin Zeng, Chiea Chuen Khor, Dongxin Lin, Adeline L H Seow, Wei-Hua Jia & Jianjun Liu
doi:10.1038/ng.2666
Jianjun Liu, Wei-Hua Jia, Adeline Seow, Dongxin Lin and colleagues report a genome-wide association study of B cell non-Hodgkin lymphoma in individuals of Chinese ancestry. They identify a new susceptibility locus on chromosome 3q27 in the intergenic region between BCL6 (B cell lymphoma protein 6) and LPP (lipoma preferred partner). | | | | High-density genotyping study identifies four new susceptibility loci for atopic dermatitis pp808 - 812
David Ellinghaus, Hansjörg Baurecht, Jorge Esparza-Gordillo, Elke Rodríguez, Anja Matanovic, Ingo Marenholz, Norbert Hübner, Heidi Schaarschmidt, Natalija Novak, Sven Michel, Laura Maintz, Thomas Werfel, Ulf Meyer-Hoffert, Melanie Hotze, Holger Prokisch, Katharina Heim, Christian Herder, Tomomitsu Hirota, Mayumi Tamari, Michiaki Kubo, Atsushi Takahashi, Yusuke Nakamura, Lam C Tsoi, Philip Stuart, James T Elder, Liangdan Sun, Xianbo Zuo, Sen Yang, Xuejun Zhang, Per Hoffmann, Markus M Nöthen, Regina Fölster-Holst, Juliane Winkelmann, Thomas Illig, Bernhard O Boehm, Richard H Duerr, Carsten Büning, Stephan Brand, Jürgen Glas, Maeve A McAleer, Caoimhe M Fahy, Michael Kabesch, Sara Brown, W H Irwin McLean, Alan D Irvine, Stefan Schreiber, Young-Ae Lee, Andre Franke & Stephan Weidinger
doi:10.1038/ng.2642
Andre Franke and colleagues perform an association study of atopic dermatitis based on high-density genotyping using the Immunochip array. They identify four new susceptibility loci for this common inflammatory skin disease. | | | | A functional variant in the CFI gene confers a high risk of age-related macular degeneration pp813 - 817
Johannes P H van de Ven, Sara C Nilsson, Perciliz L Tan, Gabriëlle H S Buitendijk, Tina Ristau, Frida C Mohlin, Sander B Nabuurs, Frederieke E Schoenmaker-Koller, Dzenita Smailhodzic, Peter A Campochiaro, Donald J Zack, Maheswara R Duvvari, Bjorn Bakker, Codrut C Paun, Camiel J F Boon, Andre G Uitterlinden, Sandra Liakopoulos, B Jeroen Klevering, Sascha Fauser, Mohamed R Daha, Nicholas Katsanis, Caroline C W Klaver, Anna M Blom, Carel B Hoyng & Anneke I den Hollander
doi:10.1038/ng.2640
Johannes van de Ven and colleagues report a rare missense mutation in CFI encoding a p.Gly119Arg substitution that confers a high risk of AMD. Sera from AMD cases carrying the p.Gly119Arg variant mediate the degradation of C3b at a significantly lower level than sera from AMD cases without the CFI variant. | | | | A genome-wide association study identifies two risk loci for congenital heart malformations in Han Chinese populations pp818 - 821
Zhibin Hu, Yongyong Shi, Xuming Mo, Jing Xu, Bijun Zhao, Yuan Lin, Shiwei Yang, Zhengfeng Xu, Juncheng Dai, Shandong Pan, Min Da, Xiaowei Wang, Bo Qian, Yang Wen, Juan Wen, Jinliang Xing, Xuejiang Guo, Yankai Xia, Hongxia Ma, Guangfu Jin, Shiqiang Yu, Jiayin Liu, Zuomin Zhou, Xinru Wang, Yijiang Chen, Jiahao Sha & Hongbing Shen
doi:10.1038/ng.2636
Hongbing Shen, Zuomin Zhou, Yijiang Chen, Zhibin Hu and colleagues report genome-wide association analyses of sporadic non-syndromic congenital heart malformations in Han Chinese populations and identify two risk loci at 1p12 and 4q31. | | | | Genome-wide association study of multiple congenital heart disease phenotypes identifies a susceptibility locus for atrial septal defect at chromosome 4p16 pp822 - 824
Heather J Cordell, Jamie Bentham, Ana Topf, Diana Zelenika, Simon Heath, Chrysovalanto Mamasoula, Catherine Cosgrove, Gillian Blue, Javier Granados-Riveron, Kerry Setchfield, Chris Thornborough, Jeroen Breckpot, Rachel Soemedi, Ruairidh Martin, Thahira J Rahman, Darroch Hall, Klaartje van Engelen, Antoon F M Moorman, Aelko H Zwinderman, Phil Barnett, Tamara T Koopmann, Michiel E Adriaens, Andras Varro, Alfred L George Jr, Christobal dos Remedios, Nanette H Bishopric, Connie R Bezzina, John O'Sullivan, Marc Gewillig, Frances A Bu'Lock, David Winlaw, Shoumo Bhattacharya, Koen Devriendt, J David Brook, Barbara J M Mulder, Seema Mital, Alex V Postma, G Mark Lathrop, Martin Farrall, Judith A Goodship & Bernard D Keavney
doi:10.1038/ng.2637
Bernard Keavney, Judith Goodship and colleagues report a genome-wide association study of congenital heart disease and identify a region on chromosome 4p16 associated with risk of atrial septal defect. | | | | Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1 pp825 - 830
Gemma L Carvill, Sinéad B Heavin, Simone C Yendle, Jacinta M McMahon, Brian J O'Roak, Joseph Cook, Adiba Khan, Michael O Dorschner, Molly Weaver, Sophie Calvert, Stephen Malone, Geoffrey Wallace, Thorsten Stanley, Ann M E Bye, Andrew Bleasel, Katherine B Howell, Sara Kivity, Mark T Mackay, Victoria Rodriguez-Casero, Richard Webster, Amos Korczyn, Zaid Afawi, Nathanel Zelnick, Tally Lerman-Sagie, Dorit Lev, Rikke S Møller, Deepak Gill, Danielle M Andrade, Jeremy L Freeman, Lynette G Sadleir, Jay Shendure, Samuel F Berkovic, Ingrid E Scheffer & Heather C Mefford
doi:10.1038/ng.2646
Heather Mefford, Ingrid Scheffer and colleagues report targeted resequencing of 47 genes in 500 individuals with epileptic encephalopathies. They identify pathogenic mutations in 11% of their cohort and show that de novo mutations in CHD2 and SYNGAP1 cause epileptic encephalopathy. | | | | The Capsella rubella genome and the genomic consequences of rapid mating system evolution OPEN pp831 - 835
Tanja Slotte, Khaled M Hazzouri, J Arvid Ågren, Daniel Koenig, Florian Maumus, Ya-Long Guo, Kim Steige, Adrian E Platts, Juan S Escobar, L Killian Newman, Wei Wang, Terezie Mandáková, Emilio Vello, Lisa M Smith, Stefan R Henz, Joshua Steffen, Shohei Takuno, Yaniv Brandvain, Graham Coop, Peter Andolfatto, Tina T Hu, Mathieu Blanchette, Richard M Clark, Hadi Quesneville, Magnus Nordborg, Brandon S Gaut, Martin A Lysak, Jerry Jenkins, Jane Grimwood, Jarrod Chapman, Simon Prochnik, Shengqiang Shu, Daniel Rokhsar, Jeremy Schmutz, Detlef Weigel & Stephen I Wright
doi:10.1038/ng.2669
Stephen Wright, Detlef Weigel and colleagues report the whole-genome sequence of Capsella rubella, a highly selfing crucifer found throughout much of southern and western Europe. They compare mixed-stage flower bud transcriptomes from C. rubella and C. grandiflora, finding a shift in expression of genes associated with flowering phenotypes and providing insights into the transition to selfing. | | | | DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape pp836 - 841
Mingchao Xie, Chibo Hong, Bo Zhang, Rebecca F Lowdon, Xiaoyun Xing, Daofeng Li, Xin Zhou, Hyung Joo Lee, Cecile L Maire, Keith L Ligon, Philippe Gascard, Mahvash Sigaroudinia, Thea D Tlsty, Theresa Kadlecek, Arthur Weiss, Henriette O'Geen, Peggy J Farnham, Pamela A F Madden, Andrew J Mungall, Angela Tam, Baljit Kamoh, Stephanie Cho, Richard Moore, Martin Hirst, Marco A Marra, Joseph F Costello & Ting Wang
doi:10.1038/ng.2649
Ting Wang, Joseph Costello and colleagues report DNA methylation profiles of 11 human tissue types and show that DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer activity.
See also: News and Views by Mukamel & Tanay | | | Top | |  | | Advertisement | | Frontiers Research Topics
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