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| |  | TABLE OF CONTENTS
| April 2012 Volume 44, Issue 4 |  | | |  |  Editorial
Correspondence
News and Views
Research Highlights
Analysis
Brief Communications
Articles
Letters
Technical Report
Corrigendum
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| | | | Editorial |  Top | |  | | Your data are not a product p357
doi:10.1038/ng.2244
The Portable Legal Consent for Common Genomics Research (PLC-CGR) is an experimental bioethics protocol that provides maximum utility to researchers who agree to its terms and protection for the de-identified personal and genomic data volunteered by informed research subjects. Data and resulting publications from this protocol are equally available to all academic, nonprofit and commercial competitors, so that intellectual property claims should arise only on new discoveries based on the data.
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| | Correspondence | Top | | | | The role of ATM in response to metformin treatment and activation of AMPK pp359 - 360
Sook Wah Yee, Ligong Chen and Kathleen M Giacomini
doi:10.1038/ng.2236
Full Text | PDF
| | | | To the Editor pp360 - 361
Angela Woods, James M Leiper and David Carling
doi:10.1038/ng.2235
Full Text | PDF
| | | | Zhou et al. reply pp361 - 362
Kaixin Zhou, Celine Bellenguez, Calum Sutherland, Grahame Hardie, Colin Palmer, Peter Donnelly and Ewan Pearson
doi:10.1038/ng.2234
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| | News and Views | Top | | | | | | Research Highlights | Top | | | | Single-cell cancer exomes | Tumor phylogenetics | Hematopoietic stem cell checkpoint | Loss-of-function variants | TTN mutations in cardiomyopathy
| Analysis | Top | | | | Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits pp369 - 375
Jian Yang, Teresa Ferreira, Andrew P Morris, Sarah E Medland, Genetic Investigation of ANthropometric Traits (GIANT) Consortium, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium, Pamela A F Madden, Andrew C Heath, Nicholas G Martin, Grant W Montgomery, Michael N Weedon, Ruth J Loos, Timothy M Frayling, Mark I McCarthy, Joel N Hirschhorn, Michael E Goddard & Peter M Visscher
doi:10.1038/ng.2213
Peter Visscher and colleagues report a new method for approximate conditional and joint association analysis that makes use of summary statistics from meta-analysis of GWAS. They apply this to meta-analysis summary data for height, body mass index and type 2 diabetes.
Abstract | Full Text | PDF
| | Brief Communications | Top | | | | Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome pp376 - 378
Yoshinori Tsurusaki, Nobuhiko Okamoto, Hirofumi Ohashi, Tomoki Kosho, Yoko Imai, Yumiko Hibi-Ko, Tadashi Kaname, Kenji Naritomi, Hiroshi Kawame, Keiko Wakui, Yoshimitsu Fukushima, Tomomi Homma, Mitsuhiro Kato, Yoko Hiraki, Takanori Yamagata, Shoji Yano, Seiji Mizuno, Satoru Sakazume, Takuma Ishii, Toshiro Nagai, Masaaki Shiina, Kazuhiro Ogata, Tohru Ohta, Norio Niikawa, Satoko Miyatake, Ippei Okada, Takeshi Mizuguchi, Hiroshi Doi, Hirotomo Saitsu, Noriko Miyake & Naomichi Matsumoto
doi:10.1038/ng.2219
Naomichi Matsumoto and colleagues report mutations in the SWI/SNF chromatin remodeling complex in Coffin-Siris syndrome. Twenty affected individuals (87%) harbored mutations in one of six SWI/SNF subunit genes: SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A or ARID1B.
First paragraph | Full Text | PDF
| | | | Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome pp379 - 380
Gijs W E Santen, Emmelien Aten, Yu Sun, Rowida Almomani, Christian Gilissen, Maartje Nielsen, Sarina G Kant, Irina N Snoeck, Els A J Peeters, Yvonne Hilhorst-Hofstee, Marja W Wessels, Nicolette S den Hollander, Claudia A L Ruivenkamp, Gert-Jan B van Ommen, Martijn H Breuning, Johan T den Dunnen, Arie van Haeringen & Marjolein Kriek
doi:10.1038/ng.2217
Gijs Santen and colleagues report mutations in the SWI/SNF subunit gene ARID1B in Coffin-Siris syndrome.
First paragraph | Full Text | PDF
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| | | | Articles | Top | | | | Mutations in axonemal dynein assembly factor DNAAF3 cause primary ciliary dyskinesia pp381 - 389
Hannah M Mitchison, Miriam Schmidts, Niki T Loges, Judy Freshour, Athina Dritsoula, Rob A Hirst, Christopher O'Callaghan, Hannah Blau, Maha Al Dabbagh, Heike Olbrich, Philip L Beales, Toshiki Yagi, Huda Mussaffi, Eddie M K Chung, Heymut Omran and David R Mitchell
doi:10.1038/ng.1106
David Mitchell, Hannah Mitchison and colleagues identify a new Chlamydomonas protein required for the preassembly of axonemal dyneins before their transport into cilia. They further show that mutations in the homologous gene in humans result in primary ciliary dyskinesia accompanied by defects in the assembly of inner and outer dynein arms.
Abstract | Full Text | PDF
| | | | Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration pp390 - 397
Colby Chiang, Jessie C Jacobsen, Carl Ernst, Carrie Hanscom, Adrian Heilbut, Ian Blumenthal, Ryan E Mills, Andrew Kirby, Amelia M Lindgren, Skye R Rudiger, Clive J McLaughlan, C Simon Bawden, Suzanne J Reid, Richard L M Faull, Russell G Snell, Ira M Hall, Yiping Shen, Toshiro K Ohsumi, Mark L Borowsky, Mark J Daly, Charles Lee, Cynthia C Morton, Marcy E MacDonald, James F Gusella & Michael E Talkowski
doi:10.1038/ng.2202
Michael Talkowski and colleagues examine karyotypically balanced genomic rearrangement landscapes in the germline at single-nucleotide resolution. They find predominant roles for complex reorganization and non-homologous repair in such 'chromothripsis' processes, suggesting a mechanism of template switching and blunt-end ligation.
Abstract | Full Text | PDF
| | | | Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells pp398 - 405
Matthias Stadtfeld, Effie Apostolou, Francesco Ferrari, Jiho Choi, Ryan M Walsh, Taiping Chen, Steen S K Ooi, Sang Yong Kim, Timothy H Bestor, Toshi Shioda, Peter J Park and Konrad Hochedlinger
doi:10.1038/ng.1110
Konrad Hochedlinger and colleagues show that ascorbic acid enhances cellular reprogramming by preventing hypermethylation of the imprinted Dlk1-Dio3 locus. They use this approach to generate adult mice derived entirely from induced pluripotent stem cells obtained through reprogramming of terminally differentiated B cells.
Abstract | Full Text | PDF
See also: News and Views by Esteban & Pei
| | | | Generation of functional insulin-producing cells in the gut by Foxo1 ablation pp406 - 412
Chutima Talchai, Shouhong Xuan, Tadahiro Kitamura, Ronald A DePinho and Domenico Accili
doi:10.1038/ng.2215
Domenico Accili and colleagues report that somatic ablation of Foxo1 in enteroendocrine progenitor cells leads to gut insulin-positive cells that have hallmarks of mature pancreatic β cells. Inactivating Foxo1 in the gut epithelium might provide a therapeutic mechanism for restoring insulin production in type 1 diabetes.
Abstract | Full Text | PDF
See also: News and Views by Kim
| | | | Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing pp413 - 419
Simon R Harris, Ian N Clarke, Helena M B Seth-Smith, Anthony W Solomon, Lesley T Cutcliffe, Peter Marsh, Rachel J Skilton, Martin J Holland, David Mabey, Rosanna W Peeling, David A Lewis, Brian G Spratt, Magnus Unemo, Kenneth Persson, Carina Bjartling, Robert Brunham, Henry J C de Vries, Servaas A Morré, Arjen Speksnijder, Cécile M Bébéar, Maïté Clerc, Bertille de Barbeyrac, Julian Parkhill & Nicholas R Thomson
doi:10.1038/ng.2214
Simon Harris and colleagues report whole-genome sequencing of 36 Chlamydia trachomatis representative strains from temporally and geographically diverse sources and use this to construct a genome-wide phylogeny of the species. They find that epidemic spread can be driven by clonal expansion from a single source and also report evidence for recombination in recent clinical strains both within and between biovars.
Abstract | Full Text | PDF
See also: News and Views by Joseph & Read
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| | | | Letters | Top | | | | Common genetic variants at the 11q13.3 renal cancer susceptibility locus influence binding of HIF to an enhancer of cyclin D1 expression pp420 - 425
Johannes Schödel, Chiara Bardella, Lina K Sciesielski, Jill M Brown, Chris W Pugh, Veronica Buckle, Ian P Tomlinson, Peter J Ratcliffe & David R Mole
doi:10.1038/ng.2204
Johannes Schödel and colleagues report the identification of a distant transcriptional enhancer of CCND1 at the recently identified renal cell carcinoma susceptibility locus at 11q13.3. The protective haplotype shows reduced binding of HIF-2α, reduced interaction with the transcriptional machinery and allelic imbalance in CCND1 expression. The study suggests that the hypoxia pathway is misregulated in renal cell carcinoma development.
First paragraph | Full Text | PDF
| | | | Common variants at 11q12, 10q26 and 3p11.2 are associated with prostate cancer susceptibility in Japanese pp426 - 429
Shusuke Akamatsu, Ryo Takata, Christopher A Haiman, Atsushi Takahashi, Takahiro Inoue, Michiaki Kubo, Mutsuo Furihata, Naoyuki Kamatani, Johji Inazawa, Gary K Chen, Loïc Le Marchand, Laurence N Kolonel, Takahiko Katoh, Yuko Yamano, Minoru Yamakado, Hiroyuki Takahashi, Hiroki Yamada, Shin Egawa, Tomoaki Fujioka, Brian E Henderson, Tomonori Habuchi, Osamu Ogawa, Yusuke Nakamura & Hidewaki Nakagawa
doi:10.1038/ng.1104
Hidewaki Nakagawa and colleagues identify three new genetic loci associated with prostate cancer in Japanese.
First paragraph | Full Text | PDF
| | | | A genome-wide association study identifies two susceptibility loci for duodenal ulcer in the Japanese population pp430 - 434
Chizu Tanikawa, Yuji Urabe, Keitaro Matsuo, Michiaki Kubo, Atsushi Takahashi, Hidemi Ito, Kazuo Tajima, Naoyuki Kamatani, Yusuke Nakamura and Koichi Matsuda
doi:10.1038/ng.1109
Koichi Matsuda and colleagues show that common variants at the PSCA and ABO loci are associated with susceptibility to duodenal ulcer. The variant at PSCA associated with increased risk of duodenal ulcer is also associated with reduced risk of gastric cancer.
First paragraph | Full Text | PDF
| | | | Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome pp435 - 439
Cornelis A Albers, Dirk S Paul, Harald Schulze, Kathleen Freson, Jonathan C Stephens, Peter A Smethurst, Jennifer D Jolley, Ana Cvejic, Myrto Kostadima, Paul Bertone, Martijn H Breuning, Najet Debili, Panos Deloukas, Rémi Favier, Janine Fiedler, Catherine M Hobbs, Ni Huang, Matthew E Hurles, Graham Kiddle, Ingrid Krapels, Paquita Nurden, Claudia A L Ruivenkamp, Jennifer G Sambrook, Kenneth Smith, Derek L Stemple, Gabriele Strauss, Chantal Thys, Chris van Geet, Ruth Newbury-Ecob, Willem H Ouwehand & Cedric Ghevaert
doi:10.1038/ng.1083
Cornelis Albers, Cedric Ghevaert and colleagues report that a majority of thrombocytopenia with absent radii (TAR) syndrome cases are caused by compound heterzygosity of a null allele and a low-frequency SNP in the regulatory regions of the RBM8A gene, which encodes the Y14 subunit of the exon-junction complex (EJC). TAR syndrome is the first reported human disorder caused by a defect in an EJC component.
First paragraph | Full Text | PDF
| | | | De novo mutations in the actin genes ACTB and ACTG1 cause Baraitser-Winter syndrome pp440 - 444
Jean-Baptiste Rivière, Bregje W M van Bon, Alexander Hoischen, Stanislav S Kholmanskikh, Brian J O'Roak, Christian Gilissen, Sabine Gijsen, Christopher T Sullivan, Susan L Christian, Omar A Abdul-Rahman, Joan F Atkin, Nicolas Chassaing, Valerie Drouin-Garraud, Andrew E Fry, Jean-Pierre Fryns, Karen W Gripp, Marlies Kempers, Tjitske Kleefstra, Grazia M S Mancini, Małgorzata J M Nowaczyk, Conny M A van Ravenswaaij-Arts, Tony Roscioli, Michael Marble, Jill A Rosenfeld, Victoria M Siu, Bert B A de Vries, Jay Shendure, Alain Verloes, Joris A Veltman, Han G Brunner, M Elizabeth Ross, Daniela T Pilz & William B Dobyns
doi:10.1038/ng.1091
William Dobyns, Daniela Pilz and colleagues show that de novo mutations in the actin genes ACTB and ACTG1 cause Baraitser-Winter syndrome, a developmental disorder characterized by distinct craniofacial features, ocular colobomata and defects in neuronal migration.
First paragraph | Full Text | PDF
| | | | Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome pp445 - 449
Jeroen K J Van Houdt, Beata Anna Nowakowska, Sérgio B Sousa, Barbera D C van Schaik, Eve Seuntjens, Nelson Avonce, Alejandro Sifrim, Omar A Abdul-Rahman, Marie-José H van den Boogaard, Armand Bottani, Marco Castori, Valérie Cormier-Daire, Matthew A Deardorff, Isabel Filges, Alan Fryer, Jean-Pierre Fryns, Simone Gana, Livia Garavelli, Gabriele Gillessen-Kaesbach, Bryan D Hall, Denise Horn, Danny Huylebroeck, Jakub Klapecki, Malgorzata Krajewska-Walasek, Alma Kuechler, Matthew A Lines, Saskia Maas, Kay D MacDermot, Shane McKee, Alex Magee, Stella A de Man, Yves Moreau, Fanny Morice-Picard, Ewa Obersztyn, Jacek Pilch, Elizabeth Rosser, Nora Shannon, Irene Stolte-Dijkstra, Patrick Van Dijck, Catheline Vilain, Annick Vogels, Emma Wakeling, Dagmar Wieczorek, Louise Wilson, Orsetta Zuffardi, Antoine H C van Kampen, Koenraad Devriendt, Raoul Hennekam & Joris Robert Vermeesch
doi:10.1038/ng.1105
Joris Vermeesch, Raoul Hennekam and colleagues show that missense mutations in the SWI/SNF family member gene SMARCA2 cause Nicolaides-Baraitser syndrome, a disorder characterized by sparse hair, distinctive facial morphology, distal limb anomalies and intellectual disability. The mutations cluster to sequences encoding ultra-conserved motifs in the catalytic ATPase region of the protein and likely act in a dominant-negative or gain-of-function fashion.
First paragraph | Full Text | PDF
| | | | Mutations affecting the cytoplasmic functions of the co-chaperone DNAJB6 cause limb-girdle muscular dystrophy pp450 - 455
Jaakko Sarparanta, Per Harald Jonson, Christelle Golzio, Satu Sandell, Helena Luque, Mark Screen, Kristin McDonald, Jeffrey M Stajich, Ibrahim Mahjneh, Anna Vihola, Olayinka Raheem, Sini Penttilä, Sara Lehtinen, Sanna Huovinen, Johanna Palmio, Giorgio Tasca, Enzo Ricci, Peter Hackman, Michael Hauser, Nicholas Katsanis & Bjarne Udd
doi:10.1038/ng.1103
Bjarne Udd and colleagues show that mutations affecting the cytoplasmic functions of the co-chaperone DNAJB6 result in limb-girdle muscular dystrophy. Their studies suggest that the mutations reduce the protective anti-aggregation effects of DNAJB6, leading to protein accumulation and autophagic pathology.
First paragraph | Full Text | PDF
| | | | KLHL3 mutations cause familial hyperkalemic hypertension by impairing ion transport in the distal nephron pp456 - 460
Hélène Louis-Dit-Picard, Julien Barc, Daniel Trujillano, Stéphanie Miserey-Lenkei, Nabila Bouatia-Naji, Olena Pylypenko, Geneviève Beaurain, Amélie Bonnefond, Olivier Sand, Christophe Simian, Emmanuelle Vidal-Petiot, Christelle Soukaseum, Chantal Mandet, Françoise Broux, Olivier Chabre, Michel Delahousse, Vincent Esnault, Béatrice Fiquet, Pascal Houillier, Corinne Isnard Bagnis, Jens Koenig, Martin Konrad, Paul Landais, Chebel Mourani, Patrick Niaudet, Vincent Probst, Christel Thauvin, Robert J Unwin, Steven D Soroka, Georg Ehret, Stephan Ossowski, Mark Caulfield, International Consortium for Blood Pressure (ICBP), Patrick Bruneval, Xavier Estivill, Philippe Froguel, Juliette Hadchouel, Jean-Jacques Schott & Xavier Jeunemaitre
doi:10.1038/ng.2218
Xavier Jeunemaitre, Jean-Jacques Schott and colleagues report mutations of KLHL3 in familial hyperkalemic hypertension. KLHL3 encodes a BTB-BACK-kelch family actin-binding protein and regulates cell surface localization of the NaNa+-Cl- cotransporter, a key regulator of ion resorption, at the distal nephron.
First paragraph | Full Text | PDF
| | | | A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion pp461 - 466
Gaëlle Pierron, Franck Tirode, Carlo Lucchesi, Stéphanie Reynaud, Stelly Ballet, Sarah Cohen-Gogo, Virginie Perrin, Jean-Michel Coindre & Olivier Delattre
doi:10.1038/ng.1107
Olivier Delattre and colleagues report the discovery of a new subset of sarcoma defined by fusion of the BCOR and CCNB3 genes. By gene expression profiling, they show that BCOR-CCNB3-positive cases are biologically distinct from other sarcomas, particularly Ewing sarcoma.
First paragraph | Full Text | PDF
| | Technical Report | Top | | | | Reverse breeding in Arabidopsis thaliana generates homozygous parental lines from a heterozygous plant pp467 - 470
Erik Wijnker, Kees van Dun, C Bastiaan de Snoo, Cilia L C Lelivelt, Joost J B Keurentjes, Nazatul Shima Naharudin, Maruthachalam Ravi, Simon W L Chan, Hans de Jong and Rob Dirks
doi:10.1038/ng.2203
To take advantage of hybrid vigor, most crop plants are grown with hybrid seeds, which are produced afresh by crossing elite inbred lines. Here, Erik Wijnker and colleagues demonstrate the feasibility of reverse breeding, a method that enables the generation of homozygous parental lines from a hybrid individual in the plant model organism Arabidopsis thaliana. Homozygous parents can be maintained indefinitely, better facilitating future improvements.
Abstract | Full Text | PDF
| | Corrigendum | Top | | | | Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations p471
Brian J O'Roak, Pelagia Deriziotis, Choli Lee, Laura Vives, Jerrod J Schwartz, Santhosh Girirajan, Emre Karakoc, Alexandra P MacKenzie, Sarah B Ng, Carl Baker, Mark J Rieder, Deborah A Nickerson, Raphael Bernier, Simon E Fisher, Jay Shendure and Evan E Eichler
doi:10.1038/ng0412-471
Full Text | PDF
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This conference will provide unique insights gained in the current genomic study of diseases ranging from the discovery of disease-associated variants to the resulting insights into disease biology and the potential for clinical application of genomic findings.
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