TABLE OF CONTENTS
| September 2012 Volume 44, Issue 9 |  | | |  |  Editorial
News and Views
Research Highlights
Brief Communications
Articles
Letters
Technical Report
Errata
Corrigendum
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| | | | Editorial |  Top | |  | | Genomes against parasites p961
doi:10.1038/ng.2407
Whereas once it was only possible to generate reference genome sequences one at a time, it is now feasible to design genomic experiments to maximize functional comparisons and contrasts among many genomes. Investigating the diversity of a number of related parasite genomes and their transcriptomes in multiple contexts increasingly shows us ways to intervene in the ecological and evolutionary strategies of pathogens.
| | News and Views | Top | | | | | | Research Highlights | Top | | | | African genomics | Chromatin and stress | Antiepileptic drugs in Alzheimer's | Disease-specific iPS cells | ISG15 and mycobacterial disease
| Brief Communications | Top | | | | Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci pp968 - 971
Kerstin U Ludwig, Elisabeth Mangold, Stefan Herms, Stefanie Nowak, Heiko Reutter, Anna Paul, Jessica Becker, Ruth Herberz, Taofik AlChawa, Entessar Nasser, Anne C Böhmer, Manuel Mattheisen, Margrieta A Alblas, Sandra Barth, Nadine Kluck, Carola Lauster, Bert Braumann, Rudolf H Reich, Alexander Hemprich, Simone Pötzsch, Bettina Blaumeiser, Nikolaos Daratsianos, Thomas Kreusch, Jeffrey C Murray, Mary L Marazita, Ingo Ruczinski, Alan F Scott, Terri H Beaty, Franz-Josef Kramer, Thomas F Wienker, Regine P Steegers-Theunissen, Michele Rubini, Peter A Mossey, Per Hoffmann, Christoph Lange, Sven Cichon, Peter Propping, Michael Knapp & Markus M Nöthen
doi:10.1038/ng.2360
Elisabeth Mangold and colleagues report a genome-wide meta-analyses of non-syndromic cleft lip with or without cleft palate (NSCL/P). They report six new genetic loci associated with risk for NSCL/P.
| | | | Exome sequencing identifies NMNAT1 mutations as a cause of Leber congenital amaurosis pp972 - 974
Pei-Wen Chiang, Juan Wang, Yang Chen, Quan Fu, Jing Zhong, Yanhua Chen, Xin Yi, Renhua Wu, Haixue Gan, Yong Shi, Yanling Chen, Christopher Barnett, Dianna Wheaton, Megan Day, Joanne Sutherland, Elise Heon, Richard G Weleber, Luis Alexandre Rassi Gabriel, Peikuan Cong, KuangHsiang Chuang, Sheng Ye, Juliana Maria Ferraz Sallum & Ming Qi
doi:10.1038/ng.2370
Ming Qi and colleagues report that compound heterozygous mutations in NMNAT1 cause Leber congenital amaurosis, a childhood form of retinal dystrophy. NMNAT1 encodes an enzyme previously implicated in protection against axonal degeneration.
| | | | Mutations in NMNAT1 cause Leber congenital amaurosis with early-onset severe macular and optic atrophy pp975 - 977
Isabelle Perrault, Sylvain Hanein, Xavier Zanlonghi, Valérie Serre, Michael Nicouleau, Sabine Defoort-Delhemmes, Nathalie Delphin, Lucas Fares-Taie, Sylvie Gerber, Olivia Xerri, Catherine Edelson, Alice Goldenberg, Alice Duncombe, Gylène Le Meur, Christian Hamel, Eduardo Silva, Patrick Nitschke, Patrick Calvas, Arnold Munnich, Olivier Roche, Hélène Dollfus, Josseline Kaplan & Jean-Michel Rozet
doi:10.1038/ng.2357
Josseline Kaplan, Jean-Michel Rozet and colleagues show that biallelic mutations in NMNAT1 cause an autosomal recessive form of Leber congenital amaurosis characterized by early-onset severe macular atrophy and optic atrophy.
| | | | Mouse ooplasm confers context-specific reprogramming capacity pp978 - 980
Michelle M Chan, Zachary D Smith, Dieter Egli, Aviv Regev and Alexander Meissner
doi:10.1038/ng.2382
Alex Meissner and colleagues report base pair-resolution methylation maps from donor fibroblasts and nuclear transfer-reconstructed mouse embryos. They compare methylation profiles to that present during normal fertilization and find that specific promoters and repeat elements exhibit differential dynamics.
See also: News and Views by Peat & Reik
| | | Advertisement | | Knome provides researchers and clinics with human whole genome interpretation software and services. Visit www.knome.com to learn how we can help you identify the variants, genes, and gene sets that underlie disease and drug response. |  |
| | | | Articles | Top | | | | Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes pp981 - 990
Andrew P Morris, Benjamin F Voight, Tanya M Teslovich, Teresa Ferreira, Ayellet V Segrè, Valgerdur Steinthorsdottir, Rona J Strawbridge, Hassan Khan, Harald Grallert, Anubha Mahajan, Inga Prokopenko, Hyun Min Kang, Christian Dina, Tonu Esko, Ross M Fraser, Stavroula Kanoni, Ashish Kumar, Vasiliki Lagou, Claudia Langenberg, Jian'an Luan, Cecilia M Lindgren, Martina Müller-Nurasyid, Sonali Pechlivanis, N William Rayner, Laura J Scott, Steven Wiltshire, Loic Yengo, Leena Kinnunen, Elizabeth J Rossin, Soumya Raychaudhuri, Andrew D Johnson, Antigone S Dimas, Ruth J F Loos, Sailaja Vedantam, Han Chen, Jose C Florez, Caroline Fox, Ching-Ti Liu, Denis Rybin, David J Couper, Wen Hong L Kao, Man Li, Marilyn C Cornelis, Peter Kraft, Qi Sun, Rob M van Dam, Heather M Stringham, Peter S Chines, Krista Fischer, Pierre Fontanillas, Oddgeir L Holmen, Sarah E Hunt, Anne U Jackson, Augustine Kong, Robert Lawrence, Julia Meyer, John R B Perry, Carl G P Platou, Simon Potter, Emil Rehnberg, Neil Robertson, Suthesh Sivapalaratnam, Alena Stančáková, Kathleen Stirrups, Gudmar Thorleifsson, Emmi Tikkanen, Andrew R Wood, Peter Almgren, Mustafa Atalay, Rafn Benediktsson, Lori L Bonnycastle, Noël Burtt, Jason Carey, Guillaume Charpentier, Andrew T Crenshaw, Alex S F Doney, Mozhgan Dorkhan, Sarah Edkins, Valur Emilsson, Elodie Eury, Tom Forsen, Karl Gertow, Bruna Gigante, George B Grant, Christopher J Groves, Candace Guiducci, Christian Herder, Astradur B Hreidarsson, Jennie Hui, Alan James, Anna Jonsson, Wolfgang Rathmann, Norman Klopp, Jasmina Kravic, Kaarel Krjutškov, Cordelia Langford, Karin Leander, Eero Lindholm, Stéphane Lobbens, Satu Männistö, Ghazala Mirza, Thomas W Mühleisen, Bill Musk, Melissa Parkin, Loukianos Rallidis, Jouko Saramies, Bengt Sennblad, Sonia Shah, Gunnar Sigurðsson, Angela Silveira, Gerald Steinbach, Barbara Thorand, Joseph Trakalo, Fabrizio Veglia, Roman Wennauer, Wendy Winckler, Delilah Zabaneh, Harry Campbell, Cornelia van Duijn, Andre G Uitterlinden, Albert Hofman, Eric Sijbrands, Goncalo R Abecasis, Katharine R Owen, Eleftheria Zeggini, Mieke D Trip, Nita G Forouhi, Ann-Christine Syvänen, Johan G Eriksson, Leena Peltonen, Markus M Nöthen, Beverley Balkau, Colin N A Palmer, Valeriya Lyssenko, Tiinamaija Tuomi, Bo Isomaa, David J Hunter, Lu Qi, Wellcome Trust Case Control Consortium, Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC) Investigators, Genetic Investigation of ANthropometric Traits (GIANT) Consortium, Asian Genetic Epidemiology Network–Type 2 Diabetes (AGEN-T2D) Consortium, South Asian Type 2 Diabetes (SAT2D) Consortium, Alan R Shuldiner, Michael Roden, Ines Barroso, Tom Wilsgaard, John Beilby, Kees Hovingh, Jackie F Price, James F Wilson, Rainer Rauramaa, Timo A Lakka, Lars Lind, George Dedoussis, Inger Njølstad, Nancy L Pedersen, Kay-Tee Khaw, Nicholas J Wareham, Sirkka M Keinanen-Kiukaanniemi, Timo E Saaristo, Eeva Korpi-Hyövälti, Juha Saltevo, Markku Laakso, Johanna Kuusisto, Andres Metspalu, Francis S Collins, Karen L Mohlke, Richard N Bergman, Jaakko Tuomilehto, Bernhard O Boehm, Christian Gieger, Kristian Hveem, Stephane Cauchi, Philippe Froguel, Damiano Baldassarre, Elena Tremoli, Steve E Humphries, Danish Saleheen, John Danesh, Erik Ingelsson, Samuli Ripatti, Veikko Salomaa, Raimund Erbel, Karl-Heinz Jöckel, Susanne Moebus, Annette Peters, Thomas Illig, Ulf de Faire, Anders Hamsten, Andrew D Morris, Peter J Donnelly, Timothy M Frayling, Andrew T Hattersley, Eric Boerwinkle, Olle Melander, Sekar Kathiresan, Peter M Nilsson, Panos Deloukas, Unnur Thorsteinsdottir, Leif C Groop, Kari Stefansson, Frank Hu, James S Pankow, Josée Dupuis, James B Meigs, David Altshuler, Michael Boehnke & Mark I McCarthy for the DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium
doi:10.1038/ng.2383
Mark McCarthy, Michael Boehnke, Andrew Morris and colleagues perform large-scale association analyses using the Metabochip to gain insights into the genetic architecture of type 2 diabetes. They report several new susceptibility loci, including two that show sex-differentiated effects on disease risk.
| | | | Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways pp991 - 1005
Robert A Scott, Vasiliki Lagou, Ryan P Welch, Eleanor Wheeler, May E Montasser, Jian'an Luan, Reedik Mägi, Rona J Strawbridge, Emil Rehnberg, Stefan Gustafsson, Stavroula Kanoni, Laura J Rasmussen-Torvik, Loïc Yengo, Cecile Lecoeur, Dmitry Shungin, Serena Sanna, Carlo Sidore, Paul C D Johnson, J Wouter Jukema, Toby Johnson, Anubha Mahajan, Niek Verweij, Gudmar Thorleifsson, Jouke-Jan Hottenga, Sonia Shah, Albert V Smith, Bengt Sennblad, Christian Gieger, Perttu Salo, Markus Perola, Nicholas J Timpson, David M Evans, Beate St Pourcain, Ying Wu, Jeanette S Andrews, Jennie Hui, Lawrence F Bielak, Wei Zhao, Momoko Horikoshi, Pau Navarro, Aaron Isaacs, Jeffrey R O'Connell, Kathleen Stirrups, Veronique Vitart, Caroline Hayward, Tõnu Esko, Evelin Mihailov, Ross M Fraser, Tove Fall, Benjamin F Voight, Soumya Raychaudhuri, Han Chen, Cecilia M Lindgren, Andrew P Morris, Nigel W Rayner, Neil Robertson, Denis Rybin, Ching-Ti Liu, Jacques S Beckmann, Sara M Willems, Peter S Chines, Anne U Jackson, Hyun Min Kang, Heather M Stringham, Kijoung Song, Toshiko Tanaka, John F Peden, Anuj Goel, Andrew A Hicks, Ping An, Martina Müller-Nurasyid, Anders Franco-Cereceda, Lasse Folkersen, Letizia Marullo, Hanneke Jansen, Albertine J Oldehinkel, Marcel Bruinenberg, James S Pankow, Kari E North, Nita G Forouhi, Ruth J F Loos, Sarah Edkins, Tibor V Varga, Göran Hallmans, Heikki Oksa, Mulas Antonella, Ramaiah Nagaraja, Stella Trompet, Ian Ford, Stephan J L Bakker, Augustine Kong, Meena Kumari, Bruna Gigante, Christian Herder, Patricia B Munroe, Mark Caulfield, Jula Antti, Massimo Mangino, Kerrin Small, Iva Miljkovic, Yongmei Liu, Mustafa Atalay, Wieland Kiess, Alan L James, Fernando Rivadeneira, Andre G Uitterlinden, Colin N A Palmer, Alex S F Doney, Gonneke Willemsen, Johannes H Smit, Susan Campbell, Ozren Polasek, Lori L Bonnycastle, Serge Hercberg, Maria Dimitriou, Jennifer L Bolton, Gerard R Fowkes, Peter Kovacs, Jaana Lindström, Tatijana Zemunik, Stefania Bandinelli, Sarah H Wild, Hanneke V Basart, Wolfgang Rathmann, Harald Grallert, DIAbetes Genetics Replication and Meta-analysis (DIAGRAM) Consortium, Winfried Maerz, Marcus E Kleber, Bernhard O Boehm, Annette Peters, Peter P Pramstaller, Michael A Province, Ingrid B Borecki, Nicholas D Hastie, Igor Rudan, Harry Campbell, Hugh Watkins, Martin Farrall, Michael Stumvoll, Luigi Ferrucci, Dawn M Waterworth, Richard N Bergman, Francis S Collins, Jaakko Tuomilehto, Richard M Watanabe, Eco J C de Geus, Brenda W Penninx, Albert Hofman, Ben A Oostra, Bruce M Psaty, Peter Vollenweider, James F Wilson, Alan F Wright, G Kees Hovingh, Andres Metspalu, Matti Uusitupa, Patrik K E Magnusson, Kirsten O Kyvik, Jaakko Kaprio, Jackie F Price, George V Dedoussis, Panos Deloukas, Pierre Meneton, Lars Lind, Michael Boehnke, Alan R Shuldiner, Cornelia M van Duijn, Andrew D Morris, Anke Toenjes, Patricia A Peyser, John P Beilby, Antje Körner, Johanna Kuusisto, Markku Laakso, Stefan R Bornstein, Peter E H Schwarz, Timo A Lakka, Rainer Rauramaa, Linda S Adair, George Davey Smith, Tim D Spector, Thomas Illig, Ulf de Faire, Anders Hamsten, Vilmundur Gudnason, Mika Kivimaki, Aroon Hingorani, Sirkka M Keinanen-Kiukaanniemi, Timo E Saaristo, Dorret I Boomsma, Kari Stefansson, Pim van der Harst, Josée Dupuis, Nancy L Pedersen, Naveed Sattar, Tamara B Harris, Francesco Cucca, Samuli Ripatti, Veikko Salomaa, Karen L Mohlke, Beverley Balkau, Philippe Froguel, Anneli Pouta, Marjo-Riitta Jarvelin, Nicholas J Wareham, Nabila Bouatia-Naji, Mark I McCarthy, Paul W Franks, James B Meigs, Tanya M Teslovich, Jose C Florez, Claudia Langenberg, Erik Ingelsson, Inga Prokopenko & Inês Barroso
doi:10.1038/ng.2385
Jose Florez, Claudia Langenberg, Erik Ingelsson, Inga Prokopenko, Inês Barroso and colleagues perform large-scale association analyses using the Metabochip to gain further insights into the genetic architecture of glucose regulation. They identify 38 new loci influencing 1 or more glycemic traits and show that many of these loci also modify risk of type 2 diabetes.
| | | | Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma pp1006 - 1014
Michael Krauthammer, Yong Kong, Byung Hak Ha, Perry Evans, Antonella Bacchiocchi, James P McCusker, Elaine Cheng, Matthew J Davis, Gerald Goh, Murim Choi, Stephan Ariyan, Deepak Narayan, Ken Dutton-Regester, Ana Capatana, Edna C Holman, Marcus Bosenberg, Mario Sznol, Harriet M Kluger, Douglas E Brash, David F Stern, Miguel A Materin, Roger S Lo, Shrikant Mane, Shuangge Ma, Kenneth K Kidd, Nicholas K Hayward, Richard P Lifton, Joseph Schlessinger, Titus J Boggon & Ruth Halaban
doi:10.1038/ng.2359
Ruth Halaban and colleagues report exome sequences of 147 melanoma tumors. They identified a recurrent somatic activating alteration in the Rho GTPase RAC1 in sun-exposed melanomas.
| | Letters | Top | | | | Evidence of widespread selection on standing variation in Europe at height-associated SNPs pp1015 - 1019
Michael C Turchin, Charleston WK Chiang, Cameron D Palmer, Sriram Sankararaman, David Reich, Genetic Investigation of ANthropometric Traits (GIANT) Consortium & Joel N Hirschhorn
doi:10.1038/ng.2368
Joel Hirschhorn and colleagues examine height-associated SNPs in northern- and southern-European populations. They report evidence of widespread weak selection on standing variation for height in humans.
| | | | Genome-wide association study identifies eight new risk loci for polycystic ovary syndrome pp1020 - 1025
Yongyong Shi, Han Zhao, Yuhua Shi, Yunxia Cao, Dongzi Yang, Zhiqiang Li, Bo Zhang, Xiaoyan Liang, Tao Li, Jianhua Chen, Jiawei Shen, Junzhao Zhao, Li You, Xuan Gao, Dongyi Zhu, Xiaoming Zhao, Ying Yan, Yingying Qin, Wenjin Li, Junhao Yan, Qingzhong Wang, Junli Zhao, Ling Geng, Jinlong Ma, Yueran Zhao, Guang He, Aiping Zhang, Shuhua Zou, Aijun Yang, Jiayin Liu, Weidong Li, Baojie Li, Chunling Wan, Ying Qin, Juanzi Shi, Jing Yang, Hong Jiang, Jin-e Xu, Xiujuan Qi, Yun Sun, Yajie Zhang, Cuifang Hao, Xiuqing Ju, Dongni Zhao, Chun-e Ren, Xiuqing Li, Wei Zhang, Yiwen Zhang, Jiangtao Zhang, Di Wu, Changming Zhang, Lin He & Zi-Jiang Chen
doi:10.1038/ng.2384
Zi-Jiang Chen and colleagues report a genome-wide association analysis for polycystic ovary syndrome (PCOS) in Han Chinese. They identify eight new susceptibility loci for PCOS in this population.
| | | | Genome-wide association study identifies a susceptibility locus for thyrotoxic periodic paralysis at 17q24.3 pp1026 - 1029
Ching-Lung Cheung, Kam-Shing Lau, Andrew Y Y Ho, Ka-Kui Lee, Sau-Cheung Tiu, Emmy Y F Lau, Jenny Leung, Man-Wo Tsang, Kin-Wah Chan, Chun-Yip Yeung, Yu-Cho Woo, Elaine Y N Cheung, Victor H F Hung, Ho-Kwong Pang, Chi-Sang Hung, Pak-Chung Sham & Annie W C Kung
doi:10.1038/ng.2367
Ching-Lung Cheung and colleagues report a genome-wide association study for thyrotoxic periodic paralysis (TPP), a life-threatening complication of thyrotoxicosis, in a Chinese population. They identify associated variants at 17q24.3 near KCNJ2.
| | | | De novo mutations in ATP1A3 cause alternating hemiplegia of childhood pp1030 - 1034
Erin L Heinzen, Kathryn J Swoboda, Yuki Hitomi, Fiorella Gurrieri, Sophie Nicole, Boukje de Vries, F Danilo Tiziano, Bertrand Fontaine, Nicole M Walley, Sinéad Heavin, Eleni Panagiotakaki, European Alternating Hemiplegia of Childhood (AHC) Genetics Consortium, Biobanca e Registro Clinico per l'Emiplegia Alternante (I.B.AHC) Consortium, European Network for Research on Alternating Hemiplegia (ENRAH) for Small and Medium-sized Enterpriese (SMEs) Consortium, Stefania Fiori, Emanuela Abiusi, Lorena Di Pietro, Matthew T Sweney, Tara M Newcomb, Louis Viollet, Chad Huff, Lynn B Jorde, Sandra P Reyna, Kelley J Murphy, Kevin V Shianna, Curtis E Gumbs, Latasha Little, Kenneth Silver, Louis J Ptáček, Joost Haan, Michel D Ferrari, Ann M Bye, Geoffrey K Herkes, Charlotte M Whitelaw, David Webb, Bryan J Lynch, Peter Uldall, Mary D King, Ingrid E Scheffer, Giovanni Neri, Alexis Arzimanoglou, Arn M J M van den Maagdenberg, Sanjay M Sisodiya, Mohamad A Mikati & David B Goldstein
doi:10.1038/ng.2358
David Goldstein, Mohamad Mikati and colleagues report identification of de novo mutations in ATP1A3 in alternating hemiplegia of childhood, which is a rare neurodevelopmental syndrome characterized by recurrent hemiplegic episodes and distinct neurologic manifestations.
| | | | Mutations in NMNAT1 cause Leber congenital amaurosis and identify a new disease pathway for retinal degeneration pp1035 - 1039
Robert K Koenekoop, Hui Wang, Jacek Majewski, Xia Wang, Irma Lopez, Huanan Ren, Yiyun Chen, Yumei Li, Gerald A Fishman, Mohammed Genead, Jeremy Schwartzentruber, Naimesh Solanki, Elias I Traboulsi, Jingliang Cheng, Clare V Logan, Martin McKibbin, Bruce E Hayward, David A Parry, Colin A Johnson, Mohammed Nageeb, Finding of Rare Disease Genes (FORGE) Canada Consortium, James A Poulter, Moin D Mohamed, Hussain Jafri, Yasmin Rashid, Graham R Taylor, Vafa Keser, Graeme Mardon, Huidan Xu, Chris F Inglehearn, Qing Fu, Carmel Toomes & Rui Chen
doi:10.1038/ng.2356
Rui Chen and colleagues identify mutations in NMNAT1 as a new cause of Leber congenital amaurosis. They further show that all examined individuals with NMNAT1 mutations have macular colobomas, a condition marked by severe degeneration of the central retina.
| | | | NMNAT1 mutations cause Leber congenital amaurosis pp1040 - 1045
Marni J Falk, Qi Zhang, Eiko Nakamaru-Ogiso, Chitra Kannabiran, Zoe Fonseca-Kelly, Christina Chakarova, Isabelle Audo, Donna S Mackay, Christina Zeitz, Arundhati Dev Borman, Magdalena Staniszewska, Rachna Shukla, Lakshmi Palavalli, Saddek Mohand-Said, Naushin H Waseem, Subhadra Jalali, Juan C Perin, Emily Place, Julian Ostrovsky, Rui Xiao, Shomi S Bhattacharya, Mark Consugar, Andrew R Webster, José-Alain Sahel, Anthony T Moore, Eliot L Berson, Qin Liu, Xiaowu Gai & Eric A Pierce
doi:10.1038/ng.2361
Eric Pierce, Xiaowu Gai and colleagues identify mutations in NMNAT1 as a new cause of Leber congenital amaurosis, an early-onset form of retinal degeneration. NMNAT1 encodes an isoform of nicotinamide mononucleotide adenylyltransferase, which is required for nicotinamide adenine dinucleotide (NAD+) biosynthesis.
| | | | The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum pp1046 - 1050
Daniel E Neafsey, Kevin Galinsky, Rays H Y Jiang, Lauren Young, Sean M Sykes, Sakina Saif, Sharvari Gujja, Jonathan M Goldberg, Sarah Young, Qiandong Zeng, Sinéad B Chapman, Aditya P Dash, Anupkumar R Anvikar, Patrick L Sutton, Bruce W Birren, Ananias A Escalante, John W Barnwell & Jane M Carlton
doi:10.1038/ng.2373
Jane Carlton and colleagues report the genome sequencing, de novo assembly and annotation of four Plasmodium vivax reference strains from diverse geographic locations. Their cross-species comparisons show that P. vivax has greater genetic diversity than Plasmodium falciparum.
See also: News and Views by Hall
| | | | Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade pp1051 - 1055
Shin-Ichiro Tachibana, Steven A Sullivan, Satoru Kawai, Shota Nakamura, Hyunjae R Kim, Naohisa Goto, Nobuko Arisue, Nirianne M Q Palacpac, Hajime Honma, Masanori Yagi, Takahiro Tougan, Yuko Katakai, Osamu Kaneko, Toshihiro Mita, Kiyoshi Kita, Yasuhiro Yasutomi, Patrick L Sutton, Rimma Shakhbatyan, Toshihiro Horii, Teruo Yasunaga, John W Barnwell, Ananias A Escalante, Jane M Carlton & Kazuyuki Tanabe
doi:10.1038/ng.2375
Jane Carlton, Kazuyuki Tanabe and colleagues report the draft genome sequences of three Plasmodium cynomolgi strains isolated from infected monkeys. Their comparative genomic analysis with P. vivax and P. knowlesi offers insights into these simian malaria parasites.
| | | | Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe pp1056 - 1059
Kathryn E Holt, Stephen Baker, François-Xavier Weill, Edward C Holmes, Andrew Kitchen, Jun Yu, Vartul Sangal, Derek J Brown, John E Coia, Dong Wook Kim, Seon Young Choi, Su Hee Kim, Wanderley D da Silveira, Derek J Pickard, Jeremy J Farrar, Julian Parkhill, Gordon Dougan & Nicholas R Thomson
doi:10.1038/ng.2369
Nicholas Thomson and colleagues report whole-genome sequencing of 132 globally distributed isolates of Shigella sonnei, a cause of human dysentery. Their phylogeographic analyses suggest that the current S. sonnei population is under 500 years old, and the authors are able to trace several distinct lineages that have spread out of Europe to other continents over the last few decades.
See also: News and Views by Feil
| | | | Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses pp1060 - 1065
Richard J O'Connell, Michael R Thon, Stéphane Hacquard, Stefan G Amyotte, Jochen Kleemann, Maria F Torres, Ulrike Damm, Ester A Buiate, Lynn Epstein, Noam Alkan, Janine Altmüller, Lucia Alvarado-Balderrama, Christopher A Bauser, Christian Becker, Bruce W Birren, Zehua Chen, Jaeyoung Choi, Jo Anne Crouch, Jonathan P Duvick, Mark A Farman, Pamela Gan, David Heiman, Bernard Henrissat, Richard J Howard, Mehdi Kabbage, Christian Koch, Barbara Kracher, Yasuyuki Kubo, Audrey D Law, Marc-Henri Lebrun, Yong-Hwan Lee, Itay Miyara, Neil Moore, Ulla Neumann, Karl Nordström, Daniel G Panaccione, Ralph Panstruga, Michael Place, Robert H Proctor, Dov Prusky, Gabriel Rech, Richard Reinhardt, Jeffrey A Rollins, Steve Rounsley, Christopher L Schardl, David C Schwartz, Narmada Shenoy, Ken Shirasu, Usha R Sikhakolli, Kurt Stüber, Serenella A Sukno, James A Sweigard, Yoshitaka Takano, Hiroyuki Takahara, Frances Trail, H Charlotte van der Does, Lars M Voll, Isa Will, Sarah Young, Qiandong Zeng, Jingze Zhang, Shiguo Zhou, Martin B Dickman, Paul Schulze-Lefert, Emiel Ver Loren van Themaat, Li-Jun Ma & Lisa J Vaillancourt
doi:10.1038/ng.2372
Richard O'Connell and colleagues report the genomes and transcriptomes of two Colletotrichum plant fungal pathogens. C. higginsianum infects Arabidopsis thaliana, and C. graminicola infects maize (Zea mays); comparative genomics in both species lead to molecular insights into the transition from biotrophic to necrotrophic life stages.
| | Technical Report | Top | | | | A mixed-model approach for genome-wide association studies of correlated traits in structured populations pp1066 - 1071
Arthur Korte, Bjarni J Vilhjalmsson, Vincent Segura, Alexander Platt, Quan Long and Magnus Nordborg
doi:10.1038/ng.2376
Magnus Nordborg and colleagues report a parameterized multi-trait mixed model (MTMM) method applied to genome-wide association studies of correlated phenotypes. They test this approach, using both human and Arabidopsis thaliana data sets, and demonstrate how it can be used to identify pleiotropic loci and gene by environment interactions.
| | Errata | Top | | | | Erratum: The Pediatric Cancer Genome Project p1072
James R Downing, Richard K Wilson, Jinghui Zhang, Elaine R Mardis, Ching-Hon Pui, Li Ding, Timothy J Ley and William E Evans
doi:10.1038/ng0912-1072c
| | | | Erratum: BAP1 loss defines a new class of renal cell carcinoma p1072
Samuel Peña-Llopis, Silvia Vega-Rubín-de-Celis, Arnold Liao, Nan Leng, Andrea Pavía-Jiménez, Shanshan Wang, Toshinari Yamasaki, Leah Zhrebker, Sharanya Sivanand, Patrick Spence, Lisa Kinch, Tina Hambuch, Suneer Jain, Yair Lotan, Vitaly Margulis, Arthur I Sagalowsky, Pia Banerji Summerour, Wareef Kabbani, S W Wendy Wong, Nick Grishin, Marc Laurent, Xian-Jin Xie, Christian D Haudenschild, Mark T Ross, David R Bentley, Payal Kapur & James Brugarolas
doi:10.1038/ng0912-1072b
| | Corrigendum | Top | | | | Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4 p1072
Psychiatric GWAS Consortium Bipolar Disorder Working Group
doi:10.1038/ng0912-1072a
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