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| |  | TABLE OF CONTENTS
| June 2012 Volume 44, Issue 6 |  | | |  |  Editorial
News and Views
Research Highlights
Perspectives
Analysis
Brief Communications
Articles
Letters
Technical Report
Errata
Corrigendum
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| | | | Editorial |  Top | |  | | The '3Is' of animal experimentation p611
doi:10.1038/ng.2322
Animal experimentation in scientific research is a good thing: important, increasing and often irreplaceable. Careful experimental design and reporting are at least as important as attention to welfare in ensuring that the knowledge we gain justifies using live animals as experimental tools.
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| | News and Views | Top | | | | | | Research Highlights | Top | | | | Genetics of blond hair | How do you feel? | piRNA, epigenetics and memory formation | Epigenetic activation by long RNA | ITGA3 and epithelial integrity
| Perspectives | Top | | | | The Pediatric Cancer Genome Project pp619 - 622
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/ng.2287
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| | | | Exome sequencing and the genetic basis of complex traits pp623 - 630
Adam Kiezun, Kiran Garimella, Ron Do, Nathan O Stitziel, Benjamin M Neale, Paul J McLaren, Namrata Gupta, Pamela Sklar, Patrick F Sullivan, Jennifer L Moran, Christina M Hultman, Paul Lichtenstein, Patrik Magnusson, Thomas Lehner, Yin Yao Shugart, Alkes L Price, Paul I W de Bakker, Shaun M Purcell and Shamil R Sunyaev
doi:10.1038/ng.2303
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| | Analysis | Top | | | | Extremely low-coverage sequencing and imputation increases power for genome-wide association studies pp631 - 635
Bogdan Pasaniuc, Nadin Rohland, Paul J McLaren, Kiran Garimella, Noah Zaitlen, Heng Li, Namrata Gupta, Benjamin M Neale, Mark J Daly, Pamela Sklar, Patrick F Sullivan, Sarah Bergen, Jennifer L Moran, Christina M Hultman, Paul Lichtenstein, Patrik Magnusson, Shaun M Purcell, David W Haas, Liming Liang, Shamil Sunyaev, Nick Patterson, Paul I W de Bakker, David Reich and Alkes L Price
doi:10.1038/ng.2283
Bogdan Pasaniuc, David Reich, Alkes Price and colleagues report analyses considering the potential of genome-wide association studies (GWAS) based on extremely low-coverage sequence data sets combined with imputation using data sets from the 1000 Genomes Project. They show with simulations and real exome-sequencing data that low-coverage sequencing can increase power for GWAS relative to genotyping arrays.
Abstract | Full Text | PDF
| | Brief Communications | Top | | | | Mutations in KANSL1 cause the 17q21.31 microdeletion syndrome phenotype pp636 - 638
Marcella Zollino, Daniela Orteschi, Marina Murdolo, Serena Lattante, Domenica Battaglia, Chiara Stefanini, Eugenio Mercuri, Pietro Chiurazzi, Giovanni Neri and Giuseppe Marangi
doi:10.1038/ng.2257
Marcella Zollino and colleagues report mutations in the chromatin regulator KANSL1 in persons with 17q21.31 syndrome. This disorder is marked by distinctive facial features, moderate-to-severe intellectual disability, hypotonia and friendly behavior.
First paragraph | Full Text | PDF
| | | | Mutations in the chromatin modifier gene KANSL1 cause the 17q21.31 microdeletion syndrome pp639 - 641
David A Koolen, Jamie M Kramer, Kornelia Neveling, Willy M Nillesen, Heather L Moore-Barton, Frances V Elmslie, Annick Toutain, Jeanne Amiel, Valérie Malan, Anne Chun-Hui Tsai, Sau Wai Cheung, Christian Gilissen, Eugene T P Verwiel, Sarah Martens, Ton Feuth, Ernie M H F Bongers, Petra de Vries, Hans Scheffer, Lisenka E L M Vissers, Arjan P M de Brouwer, Han G Brunner, Joris A Veltman, Annette Schenck, Helger G Yntema & Bert B A de Vries
doi:10.1038/ng.2262
Bert DeVries and colleagues identify mutations in the chromatin regulator KANSL1 in 17q21.31 microdeletion syndrome. This syndrome is characterized by intellectual disability, hypotonia and distinctive facial features.
First paragraph | Full Text | PDF
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| | | | Articles | Top | | | | Detectable clonal mosaicism from birth to old age and its relationship to cancer pp642 - 650
Cathy C Laurie, Cecelia A Laurie, Kenneth Rice, Kimberly F Doheny, Leila R Zelnick, Caitlin P McHugh, Hua Ling, Kurt N Hetrick, Elizabeth W Pugh, Chris Amos, Qingyi Wei, Li-e Wang, Jeffrey E Lee, Kathleen C Barnes, Nadia N Hansel, Rasika Mathias, Denise Daley, Terri H Beaty, Alan F Scott, Ingo Ruczinski, Rob B Scharpf, Laura J Bierut, Sarah M Hartz, Maria Teresa Landi, Neal D Freedman, Lynn R Goldin, David Ginsburg, Jun Li, Karl C Desch, Sara S Strom, William J Blot, Lisa B Signorello, Sue A Ingles, Stephen J Chanock, Sonja I Berndt, Loic Le Marchand, Brian E Henderson, Kristine R Monroe, John A Heit, Mariza de Andrade, Sebastian M Armasu, Cynthia Regnier, William L Lowe, M Geoffrey Hayes, Mary L Marazita, Eleanor Feingold, Jeffrey C Murray, Mads Melbye, Bjarke Feenstra, Jae H Kang, Janey L Wiggs, Gail P Jarvik, Andrew N McDavid, Venkatraman E Seshan, Daniel B Mirel, Andrew Crenshaw, Nataliya Sharopova, Anastasia Wise, Jess Shen, David R Crosslin, David M Levine, Xiuwen Zheng, Jenna I Udren, Siiri Bennett, Sarah C Nelson, Stephanie M Gogarten, Matthew P Conomos, Patrick Heagerty, Teri Manolio, Louis R Pasquale, Christopher A Haiman, Neil Caporaso & Bruce S Weir
doi:10.1038/ng.2271
Cathy Laurie and colleagues detect mosaicism for large chromosomal abnormalities in peripheral blood in a subset of healthy individuals. They show that the frequency of such events increases with age and is associated with elevated risk of developing a subsequent hematological cancer.
Abstract | Full Text | PDF
See also: News and Views by Macosko & McCarroll
| | | | Detectable clonal mosaicism and its relationship to aging and cancer pp651 - 658
Kevin B Jacobs, Meredith Yeager, Weiyin Zhou, Sholom Wacholder, Zhaoming Wang, Benjamin Rodriguez-Santiago, Amy Hutchinson, Xiang Deng, Chenwei Liu, Marie-Josephe Horner, Michael Cullen, Caroline G Epstein, Laurie Burdett, Michael C Dean, Nilanjan Chatterjee, Joshua Sampson, Charles C Chung, Joseph Kovaks, Susan M Gapstur, Victoria L Stevens, Lauren T Teras, Mia M Gaudet, Demetrius Albanes, Stephanie J Weinstein, Jarmo Virtamo, Philip R Taylor, Neal D Freedman, Christian C Abnet, Alisa M Goldstein, Nan Hu, Kai Yu, Jian-Min Yuan, Linda Liao, Ti Ding, You-Lin Qiao, Yu-Tang Gao, Woon-Puay Koh, Yong-Bing Xiang, Ze-Zhong Tang, Jin-Hu Fan, Melinda C Aldrich, Christopher Amos, William J Blot, Cathryn H Bock, Elizabeth M Gillanders, Curtis C Harris, Christopher A Haiman, Brian E Henderson, Laurence N Kolonel, Loic Le Marchand, Lorna H McNeill, Benjamin A Rybicki, Ann G Schwartz, Lisa B Signorello, Margaret R Spitz, John K Wiencke, Margaret Wrensch, Xifeng Wu, Krista A Zanetti, Regina G Ziegler, Jonine D Figueroa, Montserrat Garcia-Closas, Nuria Malats, Gaelle Marenne, Ludmila Prokunina-Olsson, Dalsu Baris, Molly Schwenn, Alison Johnson, Maria Teresa Landi, Lynn Goldin, Dario Consonni, Pier Alberto Bertazzi, Melissa Rotunno, Preetha Rajaraman, Ulrika Andersson, Laura E Beane Freeman, Christine D Berg, Julie E Buring, Mary A Butler, Tania Carreon, Maria Feychting, Anders Ahlbom, J Michael Gaziano, Graham G Giles, Goran Hallmans, Susan E Hankinson, Patricia Hartge, Roger Henriksson, Peter D Inskip, Christoffer Johansen, Annelie Landgren, Roberta McKean-Cowdin, Dominique S Michaud, Beatrice S Melin, Ulrike Peters, Avima M Ruder, Howard D Sesso, Gianluca Severi, Xiao-Ou Shu, Kala Visvanathan, Emily White, Alicja Wolk, Anne Zeleniuch-Jacquotte, Wei Zheng, Debra T Silverman, Manolis Kogevinas, Juan R Gonzalez, Olaya Villa, Donghui Li, Eric J Duell, Harvey A Risch, Sara H Olson, Charles Kooperberg, Brian M Wolpin, Li Jiao, Manal Hassan, William Wheeler, Alan A Arslan, H Bas Bueno-de-Mesquita, Charles S Fuchs, Steven Gallinger, Myron D Gross, Elizabeth A Holly, Alison P Klein, Andrea LaCroix, Margaret T Mandelson, Gloria Petersen, Marie-Christine Boutron-Ruault, Paige M Bracci, Federico Canzian, Kenneth Chang, Michelle Cotterchio, Edward L Giovannucci, Michael Goggins, Judith A Hoffman Bolton, Mazda Jenab, Kay-Tee Khaw, Vittorio Krogh, Robert C Kurtz, Robert R McWilliams, Julie B Mendelsohn, Kari G Rabe, Elio Riboli, Anne Tjønneland, Geoffrey S Tobias, Dimitrios Trichopoulos, Joanne W Elena, Herbert Yu, Laufey Amundadottir, Rachael Z Stolzenberg-Solomon, Peter Kraft, Fredrick Schumacher, Daniel Stram, Sharon A Savage, Lisa Mirabello, Irene L Andrulis, Jay S Wunder, Ana Patiño García, Luis Sierrasesúmaga, Donald A Barkauskas, Richard G Gorlick, Mark Purdue, Wong-Ho Chow, Lee E Moore, Kendra L Schwartz, Faith G Davis, Ann W Hsing, Sonja I Berndt, Amanda Black, Nicolas Wentzensen, Louise A Brinton, Jolanta Lissowska, Beata Peplonska, Katherine A McGlynn, Michael B Cook, Barry I Graubard, Christian P Kratz, Mark H Greene, Ralph L Erickson, David J Hunter, Gilles Thomas, Robert N Hoover, Francisco X Real, Joseph F Fraumeni Jr, Neil E Caporaso, Margaret Tucker, Nathaniel Rothman, Luis A Pérez-Jurado & Stephen J Chanock
doi:10.1038/ng.2270
Luis Pérez-Jurado, Stephen Chanock and colleagues detect clonal chromosomal abnormalities in peripheral blood or buccal samples from individuals in the general population. They show that the frequency of such events increases with age and is associated with elevated risk of developing subsequent hematological cancers.
Abstract | Full Text | PDF
See also: News and Views by Macosko & McCarroll
| | | | A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance pp659 - 669
Alisa K Manning, Marie-France Hivert, Robert A Scott, Jonna L Grimsby, Nabila Bouatia-Naji, Han Chen, Denis Rybin, Ching-Ti Liu, Lawrence F Bielak, Inga Prokopenko, Najaf Amin, Daniel Barnes, Gemma Cadby, Jouke-Jan Hottenga, Erik Ingelsson, Anne U Jackson, Toby Johnson, Stavroula Kanoni, Claes Ladenvall, Vasiliki Lagou, Jari Lahti, Cecile Lecoeur, Yongmei Liu, Maria Teresa Martinez-Larrad, May E Montasser, Pau Navarro, John R B Perry, Laura J Rasmussen-Torvik, Perttu Salo, Naveed Sattar, Dmitry Shungin, Rona J Strawbridge, Toshiko Tanaka, Cornelia M van Duijn, Ping An, Mariza de Andrade, Jeanette S Andrews, Thor Aspelund, Mustafa Atalay, Yurii Aulchenko, Beverley Balkau, Stefania Bandinelli, Jacques S Beckmann, John P Beilby, Claire Bellis, Richard N Bergman, John Blangero, Mladen Boban, Michael Boehnke, Eric Boerwinkle, Lori L Bonnycastle, Dorret I Boomsma, Ingrid B Borecki, Yvonne Böttcher, Claude Bouchard, Eric Brunner, Danijela Budimir, Harry Campbell, Olga Carlson, Peter S Chines, Robert Clarke, Francis S Collins, Arturo Corbatón-Anchuelo, David Couper, Ulf de Faire, George V Dedoussis, Panos Deloukas, Maria Dimitriou, Josephine M Egan, Gudny Eiriksdottir, Michael R Erdos, Johan G Eriksson, Elodie Eury, Luigi Ferrucci, Ian Ford, Nita G Forouhi, Caroline S Fox, Maria Grazia Franzosi, Paul W Franks, Timothy M Frayling, Philippe Froguel, Pilar Galan, Eco de Geus, Bruna Gigante, Nicole L Glazer, Anuj Goel, Leif Groop, Vilmundur Gudnason, Göran Hallmans, Anders Hamsten, Ola Hansson, Tamara B Harris, Caroline Hayward, Simon Heath, Serge Hercberg, Andrew A Hicks, Aroon Hingorani, Albert Hofman, Jennie Hui, Joseph Hung, Marjo-Riitta Jarvelin, Min A Jhun, Paul C D Johnson, J Wouter Jukema, Antti Jula, W H Kao, Jaakko Kaprio, Sharon L R Kardia, Sirkka Keinanen-Kiukaanniemi, Mika Kivimaki, Ivana Kolcic, Peter Kovacs, Meena Kumari, Johanna Kuusisto, Kirsten Ohm Kyvik, Markku Laakso, Timo Lakka, Lars Lannfelt, G Mark Lathrop, Lenore J Launer, Karin Leander, Guo Li, Lars Lind, Jaana Lindstrom, Stéphane Lobbens, Ruth J F Loos, Jian'an Luan, Valeriya Lyssenko, Reedik Mägi, Patrik K E Magnusson, Michael Marmot, Pierre Meneton, Karen L Mohlke, Vincent Mooser, Mario A Morken, Iva Miljkovic, Narisu Narisu, Jeff O'Connell, Ken K Ong, Ben A Oostra, Lyle J Palmer, Aarno Palotie, James S Pankow, John F Peden, Nancy L Pedersen, Marina Pehlic, Leena Peltonen, Brenda Penninx, Marijana Pericic, Markus Perola, Louis Perusse, Patricia A Peyser, Ozren Polasek, Peter P Pramstaller, Michael A Province, Katri Räikkönen, Rainer Rauramaa, Emil Rehnberg, Ken Rice, Jerome I Rotter, Igor Rudan, Aimo Ruokonen, Timo Saaristo, Maria Sabater-Lleal, Veikko Salomaa, David B Savage, Richa Saxena, Peter Schwarz, Udo Seedorf, Bengt Sennblad, Manuel Serrano-Rios, Alan R Shuldiner, Eric J G Sijbrands, David S Siscovick, Johannes H Smit, Kerrin S Small, Nicholas L Smith, Albert Vernon Smith, Alena Stančáková, Kathleen Stirrups, Michael Stumvoll, Yan V Sun, Amy J Swift, Anke Tönjes, Jaakko Tuomilehto, Stella Trompet, Andre G Uitterlinden, Matti Uusitupa, Max Vikström, Veronique Vitart, Marie-Claude Vohl, Benjamin F Voight, Peter Vollenweider, Gerard Waeber, Dawn M Waterworth, Hugh Watkins, Eleanor Wheeler, Elisabeth Widen, Sarah H Wild, Sara M Willems, Gonneke Willemsen, James F Wilson, Jacqueline C M Witteman, Alan F Wright, Hanieh Yaghootkar, Diana Zelenika, Tatijana Zemunik, Lina Zgaga, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium, The Multiple Tissue Human Expression Resource (MUTHER) Consortium, Nicholas J Wareham, Mark I McCarthy, Ines Barroso, Richard M Watanabe, Jose C Florez, Josée Dupuis, James B Meigs & Claudia Langenberg
doi:10.1038/ng.2274
Claudia Langenberg, James Meigs and colleagues apply a joint meta-analysis approach that accounts for differences in body mass index to identify variants associated with glycemic traits. They report six new loci associated with fasting insulin levels and provide insights into the genetic basis of insulin resistance.
Abstract | Full Text | PDF
| | | Advertisement | | | | | | Letters | Top | | | | Meta-analysis identifies six new susceptibility loci for atrial fibrillation pp670 - 675
Patrick T Ellinor, Kathryn L Lunetta, Christine M Albert, Nicole L Glazer, Marylyn D Ritchie, Albert V Smith, Dan E Arking, Martina Müller-Nurasyid, Bouwe P Krijthe, Steven A Lubitz, Joshua C Bis, Mina K Chung, Marcus Dörr, Kouichi Ozaki, Jason D Roberts, J Gustav Smith, Arne Pfeufer, Moritz F Sinner, Kurt Lohman, Jingzhong Ding, Nicholas L Smith, Jonathan D Smith, Michiel Rienstra, Kenneth M Rice, David R Van Wagoner, Jared W Magnani, Reza Wakili, Sebastian Clauss, Jerome I Rotter, Gerhard Steinbeck, Lenore J Launer, Robert W Davies, Matthew Borkovich, Tamara B Harris, Honghuang Lin, Uwe Völker, Henry Völzke, David J Milan, Albert Hofman, Eric Boerwinkle, Lin Y Chen, Elsayed Z Soliman, Benjamin F Voight, Guo Li, Aravinda Chakravarti, Michiaki Kubo, Usha B Tedrow, Lynda M Rose, Paul M Ridker, David Conen, Tatsuhiko Tsunoda, Tetsushi Furukawa, Nona Sotoodehnia, Siyan Xu, Naoyuki Kamatani, Daniel Levy, Yusuke Nakamura, Babar Parvez, Saagar Mahida, Karen L Furie, Jonathan Rosand, Raafia Muhammad, Bruce M Psaty, Thomas Meitinger, Siegfried Perz, H-Erich Wichmann, Jacqueline C M Witteman, W H Linda Kao, Sekar Kathiresan, Dan M Roden, Andre G Uitterlinden, Fernando Rivadeneira, Barbara McKnight, Marketa Sjögren, Anne B Newman, Yongmei Liu, Michael H Gollob, Olle Melander, Toshihiro Tanaka, Bruno H Ch Stricker, Stephan B Felix, Alvaro Alonso, Dawood Darbar, John Barnard, Daniel I Chasman, Susan R Heckbert, Emelia J Benjamin, Vilmundur Gudnason & Stefan Kääb
doi:10.1038/ng.2261
Patrick Ellinor and colleagues report a meta-analysis of genome-wide association studies for atrial fibrillation in European populations. They identify six newly associated loci, four of which were replicated in a Japanese study.
First paragraph | Full Text | PDF
| | | | Genome-wide association analyses identify 13 new susceptibility loci for generalized vitiligo pp676 - 680
Ying Jin, Stanca A Birlea, Pamela R Fain, Tracey M Ferrara, Songtao Ben, Sheri L Riccardi, Joanne B Cole, Katherine Gowan, Paulene J Holland, Dorothy C Bennett, Rosalie M Luiten, Albert Wolkerstorfer, J P Wietze van der Veen, Anke Hartmann, Saskia Eichner, Gerold Schuler, Nanja van Geel, Jo Lambert, E Helen Kemp, David J Gawkrodger, Anthony P Weetman, Alain Taïeb, Thomas Jouary, Khaled Ezzedine, Margaret R Wallace, Wayne T McCormack, Mauro Picardo, Giovanni Leone, Andreas Overbeck, Nanette B Silverberg & Richard A Spritz
doi:10.1038/ng.2272
Richard Spritz and colleagues report genome-wide association analyses identifying 13 new susceptibility loci for generalized vitiligo. Their functional pathway analysis shows that many vitiligo susceptibility loci encode immunoregulatory proteins or melanocyte components.
First paragraph | Full Text | PDF
| | | | A genome-wide association study identifies susceptibility loci for Wilms tumor pp681 - 684
Clare Turnbull, Elizabeth R Perdeaux, David Pernet, Arlene Naranjo, Anthony Renwick, Sheila Seal, Rosa Maria Munoz-Xicola, Sandra Hanks, Ingrid Slade, Anna Zachariou, Margaret Warren-Perry, Elise Ruark, Mary Gerrard, Juliet Hale, Martin Hewitt, Janice Kohler, Sheila Lane, Gill Levitt, Mabrook Madi, Bruce Morland, Veronica Neefjes, James Nicholdson, Susan Picton, Barry Pizer, Milind Ronghe, Michael Stevens, Heidi Traunecker, Charles A Stiller, Kathy Pritchard-Jones, Jeffrey Dome, Paul Grundy and Nazneen Rahman
doi:10.1038/ng.2251
Nazneen Rahman and colleagues report the results of a genome-wide association study of Wilms tumor. They show that common variants at 2p24 and 11q14 influence susceptibility to this rare pediatric kidney tumor.
First paragraph | Full Text | PDF
| | | | Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer pp685 - 689
Christopher E Barbieri, Sylvan C Baca, Michael S Lawrence, Francesca Demichelis, Mirjam Blattner, Jean-Philippe Theurillat, Thomas A White, Petar Stojanov, Eliezer Van Allen, Nicolas Stransky, Elizabeth Nickerson, Sung-Suk Chae, Gunther Boysen, Daniel Auclair, Robert C Onofrio, Kyung Park, Naoki Kitabayashi, Theresa Y MacDonald, Karen Sheikh, Terry Vuong, Candace Guiducci, Kristian Cibulskis, Andrey Sivachenko, Scott L Carter, Gordon Saksena, Douglas Voet, Wasay M Hussain, Alex H Ramos, Wendy Winckler, Michelle C Redman, Kristin Ardlie, Ashutosh K Tewari, Juan Miguel Mosquera, Niels Rupp, Peter J Wild, Holger Moch, Colm Morrissey, Peter S Nelson, Philip W Kantoff, Stacey B Gabriel, Todd R Golub, Matthew Meyerson, Eric S Lander, Gad Getz, Mark A Rubin and Levi A Garraway
doi:10.1038/ng.2279
Levi Garraway and colleagues report exome sequencing of 112 prostate adenocarcinomas and matched normal tissues. They identify novel recurrent mutations in several genes, including MED12, FOXA1 and SPOP. They find that tumors harboring SPOP mutations lack the TMPRSS2-ERG fusion or other ETS rearrangements, supporting the hypothesis that SPOP mutation is an early driver event in prostate tumorigenesis.
First paragraph | Full Text | PDF
See also: News and Views by Hieronymus & Sawyers
| | | | Exome sequencing of liver fluke-associated cholangiocarcinoma pp690 - 693
Choon Kiat Ong, Chutima Subimerb, Chawalit Pairojkul, Sopit Wongkham, Ioana Cutcutache, Willie Yu, John R McPherson, George E Allen, Cedric Chuan Young Ng, Bernice Huimin Wong, Swe Swe Myint, Vikneswari Rajasegaran, Hong Lee Heng, Anna Gan, Zhi Jiang Zang, Yingting Wu, Jeanie Wu, Ming Hui Lee, DaChuan Huang, Pauline Ong, Waraporn Chan-on, Yun Cao, Chao-Nan Qian, Kiat Hon Lim, Aikseng Ooi, Karl Dykema, Kyle Furge, Veerapol Kukongviriyapan, Banchob Sripa, Chaisiri Wongkham, Puangrat Yongvanit, P Andrew Futreal, Vajarabhongsa Bhudhisawasdi, Steve Rozen, Patrick Tan and Bin Tean Teh
doi:10.1038/ng.2273
Bin Tean Teh and colleagues report exome sequencing of Opisthorchis viverrini-related cholangiocarcinoma, a fatal bile duct cancer associated with liver fluke infection.
First paragraph | Full Text | PDF
| | | | Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma pp694 - 698
Cécile Guichard, Giuliana Amaddeo, Sandrine Imbeaud, Yannick Ladeiro, Laura Pelletier, Ichrafe Ben Maad, Julien Calderaro, Paulette Bioulac-Sage, Mélanie Letexier, Françoise Degos, Bruno Clément, Charles Balabaud, Eric Chevet, Alexis Laurent, Gabrielle Couchy, Eric Letouzé, Fabien Calvo & Jessica Zucman-Rossi
doi:10.1038/ng.2256
Jessica Zucman-Rossi and colleagues report exome sequencing of 24 hepatocellular carcinomas and non-tumor liver tissues and copy-number analysis of 125 tumors. They identify new recurrent mutations in ARID1A, RPS6KA3, NFE2L2 and IRF2 in HCC.
First paragraph | Full Text | PDF
| | | | Hereditary mixed polyposis syndrome is caused by a 40-kb upstream duplication that leads to increased and ectopic expression of the BMP antagonist GREM1 pp699 - 703
Emma Jaeger, Simon Leedham, Annabelle Lewis, Stefania Segditsas, Martin Becker, Pedro Rodenas Cuadrado, Hayley Davis, Kulvinder Kaur, Karl Heinimann, Kimberley Howarth, James East, Jenny Taylor, Huw Thomas and Ian Tomlinson
doi:10.1038/ng.2263
Ian Tomlinson and colleagues identify a 40-kb duplication upstream of the gene that encodes the BMP antagonist GREM1 in families with hereditary mixed polyposis syndrome. The mutation is associated with increased allele-specific and ectopic expression of GREM1.
First paragraph | Full Text | PDF
| | | | Mutations in the RNA exosome component gene EXOSC3 cause pontocerebellar hypoplasia and spinal motor neuron degeneration pp704 - 708
Jijun Wan, Michael Yourshaw, Hafsa Mamsa, Sabine Rudnik-Schöneborn, Manoj P Menezes, Ji Eun Hong, Derek W Leong, Jan Senderek, Michael S Salman, David Chitayat, Pavel Seeman, Arpad von Moers, Luitgard Graul-Neumann, Andrew J Kornberg, Manuel Castro-Gago, María-Jesús Sobrido, Masafumi Sanefuji, Perry B Shieh, Noriko Salamon, Ronald C Kim, Harry V Vinters, Zugen Chen, Klaus Zerres, Monique M Ryan, Stanley F Nelson & Joanna C Jen
doi:10.1038/ng.2254
Jaonna Jen and colleagues identify mutations in EXOSC3, encoding a core RNA exosome component, causing pontocerebellar hypoplasia type 1 (PCH1), a recessive disorder with heterogeneous defects in brain development. Nine out of 13 individuals diagnosed with PCH1 had missense, frameshift or exon-skipping mutations in EXOSC3, suggesting a critical role of RNA metabolism in normal brain development.
First paragraph | Full Text | PDF
| | | | Mutations in IRX5 impair craniofacial development and germ cell migration via SDF1 pp709 - 713
Carine Bonnard, Anna C Strobl, Mohammad Shboul, Hane Lee, Barry Merriman, Stanley F Nelson, Osama H Ababneh, Elif Uz, Tulay Guran, Hulya Kayserili, Hanan Hamamy and Bruno Reversade
doi:10.1038/ng.2259
Bruno Reversade and colleagues show that mutations in IRX5 cause a recessive congenital disorder affecting the development of multiple organs. In follow-up studies in Xenopus laevis, they show that Irx5 influences cell migration by repressing expression of Sdf1.
First paragraph | Full Text | PDF
| | | | CCDC103 mutations cause primary ciliary dyskinesia by disrupting assembly of ciliary dynein arms pp714 - 719
Jennifer R Panizzi, Anita Becker-Heck, Victoria H Castleman, Dalal A Al-Mutairi, Yan Liu, Niki T Loges, Narendra Pathak, Christina Austin-Tse, Eamonn Sheridan, Miriam Schmidts, Heike Olbrich, Claudius Werner, Karsten Häffner, Nathan Hellman, Rahul Chodhari, Amar Gupta, Albrecht Kramer-Zucker, Felix Olale, Rebecca D Burdine, Alexander F Schier, Christopher O'Callaghan, Eddie M K Chung, Richard Reinhardt, Hannah M Mitchison, Stephen M King, Heymut Omran & Iain A Drummond
doi:10.1038/ng.2277
Iain Drummond, Heymut Omran, Stephen King and colleagues show that CCDC103 mutations cause primary ciliary dyskinesia. Their studies suggest that CCDC103 is a core axonemal factor that helps anchor dynein motor complexes to ciliary microtubules.
First paragraph | Full Text | PDF
| | | | Parallel domestication of the Shattering1 genes in cereals pp720 - 724
Zhongwei Lin, Xianran Li, Laura M Shannon, Cheng-Ting Yeh, Ming L Wang, Guihua Bai, Zhao Peng, Jiarui Li, Harold N Trick, Thomas E Clemente, John Doebley, Patrick S Schnable, Mitchell R Tuinstra, Tesfaye T Tesso, Frank White and Jianming Yu
doi:10.1038/ng.2281
A key step in domestication of cereals was loss of seed shattering. Jianming Yu and colleagues show that seed shattering is controlled by alleles at Sh1 in sorghum. The authors also identify an insertion in the ortholog of Sh1 in a shattering-resistant mutant in rice and orthologs of Sh1 located in two narrow quantitative trait locus (QTL) intervals that regulate shattering in maize. The data suggest parallel selection on Sh1 in the domestication of cereals.
First paragraph | Full Text | PDF
See also: News and Views by Olsen
| | Technical Report | Top | | | | A model-based approach for analysis of spatial structure in genetic data pp725 - 731
Wen-Yun Yang, John Novembre, Eleazar Eskin and Eran Halperin
doi:10.1038/ng.2285
Eleazar Eskin and colleagues report a new method to model the spatial structure of genetic variation, using a spatial ancestry analysis (SPA) approach for modeling of genotypes in two- or three-dimensional space. They apply this approach to a sample of 3,000 European individuals and identify SNPs that show extreme allele frequency gradients.
Abstract | Full Text | PDF
| | Errata | Top | | | | Erratum: Common variants at 6q22 and 17q21 are associated with intracranial volume p732
M Arfan Ikram, Myriam Fornage, Albert V Smith, Sudha Seshadri, Reinhold Schmidt, Stéphanie Debette, Henri A Vrooman, Sigurdur Sigurdsson, Stefan Ropele, H Rob Taal, Dennis O Mook-Kanamori, Laura H Coker, W T Longstreth Jr, Wiro J Niessen, Anita L DeStefano, Alexa Beiser, Alex P Zijdenbos, Maksim Struchalin, Clifford R Jack Jr, Fernando Rivadeneira, Andre G Uitterlinden, David S Knopman, Anna-Liisa Hartikainen, Craig E Pennell, Elisabeth Thiering, Eric A P Steegers, Hakon Hakonarson, Joachim Heinrich, Lyle J Palmer, Marjo-Riitta Jarvelin, Mark I McCarthy, Struan F A Grant, Beate St Pourcain, Nicholas J Timpson, George Davey Smith, Ulla Sovio the Early Growth Genetics (EGG) Consortium, Mike A Nalls, Rhoda Au, Albert Hofman, Haukur Gudnason, Aad van der Lugt, Tamara B Harris, William M Meeks, Meike W Vernooij, Mark A van Buchem, Diane Catellier, Vincent W V Jaddoe, Vilmundur Gudnason, B Gwen Windham, Philip A Wolf, Cornelia M van Duijn, Thomas H Mosley Jr, Helena Schmidt, Lenore J Launer, Monique M B Breteler & Charles DeCarli for the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium
doi:10.1038/ng0612-732c
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| | | | Erratum: A transposon in tb1 drove maize domestication p732
Miltos Tsiantis
doi:10.1038/ng0612-732b
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| | Corrigendum | Top | | | | Corrigendum: Arabidopsis thaliana as a model for the genetics of local adaptation p732
Brandon Gaut
doi:10.1038/ng0612-732a
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