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Editorial

What's so funny about peace, love and understanding? p861

doi:10.1038/ng0809-861

The Mediterranean Medical Genetics Meeting 2009 at Bilkent University, in Ankara, Turkey, reaffirmed the commitment of a pragmatic group of scientifically excellent researchers to local problem solving and to the vision of borderless global collaboration in human genomics.


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Correspondence

Duplications of noncoding elements 5' of SOX9 are associated with brachydactyly-anonychia pp862 - 863

Ingo Kurth, Eva Klopocki, Sigmar Stricker, Jolieke van Oosterwijk, Sebastian Vanek, Jens Altmann, Heliosa G Santos, Jeske J T van Harssel, Thomy de Ravel, Andrew O M Wilkie, Andreas Gal & Stefan Mundlos

doi:10.1038/ng0809-862


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Research Highlights

Research highlights p870

doi:10.1038/ng0809-870


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Brief Communications

Genetic variants at 6p21.33 are associated with susceptibility to follicular lymphoma pp873 - 875

Christine F Skibola, Paige M Bracci, Eran Halperin, Lucia Conde, David W Craig, Luz Agana, Kelly Iyadurai, Nikolaus Becker, Angela Brooks-Wilson, John D Curry, John J Spinelli, Elizabeth A Holly, Jacques Riby, Luoping Zhang, Alexandra Nieters, Martyn T Smith & Kevin M Brown

doi:10.1038/ng.419

Christine Skibola and colleagues report a genome-wide association study for three subtypes of non-Hodgkin lymphoma. They report an association of a variant in the PSORS1 region in the MHC to increased risk of follicular lymphoma.


A sequence variant in ZFHX3 on 16q22 associates with atrial fibrillation and ischemic stroke pp876 - 878

Daniel F Gudbjartsson, Hilma Holm, Solveig Gretarsdottir, Gudmar Thorleifsson, G Bragi Walters, Gudmundur Thorgeirsson, Jeffrey Gulcher, Ellisiv B Mathiesen, Inger Njølstad, Audhild Nyrnes, Tom Wilsgaard, Erin M Hald, Kristian Hveem, Camilla Stoltenberg, Gayle Kucera, Tanya Stubblefield, Shannon Carter, Dan Roden, Maggie C Y Ng, Larry Baum, Wing Yee So, Ka Sing Wong, Juliana C N Chan, Christian Gieger, H-Erich Wichmann, Andreas Gschwendtner, Martin Dichgans, Gregor Kuhlenbäumer, Klaus Berger, E Bernd Ringelstein, Steve Bevan, Hugh S Markus, Konstantinos Kostulas, Jan Hillert, Sigurlaug Sveinbjörnsdóttir, Einar M Valdimarsson, Maja-Lisa Løchen, Ronald C W Ma, Dawood Darbar, Augustine Kong, David O Arnar, Unnur Thorsteinsdottir & Kari Stefansson

doi:10.1038/ng.417

Daniel Gudbjartsson and colleagues report a genome-wide association study for atrial fibrillation, a condition associated with increased risk of stroke. They report a variant in ZFHX3 associated with atrial fibrillation as well as ischemic stroke.


Variants in ZFHX3 are associated with atrial fibrillation in individuals of European ancestry pp879 - 881

Emelia J Benjamin, Kenneth M Rice, Dan E Arking, Arne Pfeufer, Charlotte van Noord, Albert V Smith, Renate B Schnabel, Joshua C Bis, Eric Boerwinkle, Moritz F Sinner, Abbas Dehghan, Steven A Lubitz, Ralph B D'Agostino Sr, Thomas Lumley, Georg B Ehret, Jan Heeringa, Thor Aspelund, Christopher Newton-Cheh, Martin G Larson, Kristin D Marciante, Elsayed Z Soliman, Fernando Rivadeneira, Thomas J Wang, Gudny Eiríksdottir, Daniel Levy, Bruce M Psaty, Man Li, Alanna M Chamberlain, Albert Hofman, Ramachandran S Vasan, Tamara B Harris, Jerome I Rotter, W H Linda Kao, Sunil K Agarwal, Bruno H Ch Stricker, Ke Wang, Lenore J Launer, Nicholas L Smith, Aravinda Chakravarti, André G Uitterlinden, Philip A Wolf, Nona Sotoodehnia, Anna Köttgen, Cornelia M van Duijn, Thomas Meitinger, Martina Mueller, Siegfried Perz, Gerhard Steinbeck, H-Erich Wichmann, Kathryn L Lunetta, Susan R Heckbert, Vilmundur Gudnason, Alvaro Alonso, Stefan Kääb, Patrick T Ellinor & Jacqueline C M Witteman

doi:10.1038/ng.416

Emelia Benjamin and colleagues report a meta-analysis of genome-wide association study data for atrial fibrillation, a condition associated with stroke and heart failure, in five European community-based cohorts of the CHARGE consortium. They report an association in ZFHX3 to atrial fibrillation, with replication in an independent cohort from the German AF Network.


The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer pp882 - 884

Mark M Pomerantz, Nasim Ahmadiyeh, Li Jia, Paula Herman, Michael P Verzi, Harshavardhan Doddapaneni, Christine A Beckwith, Jennifer A Chan, Adam Hills, Matt Davis, Keluo Yao, Sarah M Kehoe, Heinz-Josef Lenz, Christopher A Haiman, Chunli Yan, Brian E Henderson, Baruch Frenkel, Jordi Barretina, Adam Bass, Josep Tabernero, José Baselga, Meredith M Regan, J Robert Manak, Ramesh Shivdasani, Gerhard A Coetzee & Matthew L Freedman

doi:10.1038/ng.403

Matthew Freedman and colleagues show that a region on 8q24 associated with colorectal cancer risk functions as an enhancer and undergoes long-range interactions with MYC. They further show that alleles at the risk-associated SNP bind differentially to TCF7L2, a transcription factor in the Wnt pathway.

See also: News and Views by Harismendy & Frazer | Article by Tuupanen et al.


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Articles

The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling pp885 - 890

Sari Tuupanen, Mikko Turunen, Rainer Lehtonen, Outi Hallikas, Sakari Vanharanta, Teemu Kivioja, Mikael Björklund, Gonghong Wei, Jian Yan, Iina Niittymäki, Jukka-Pekka Mecklin, Heikki Järvinen, Ari Ristimäki, Mariachiara Di-Bernardo, Phil East, Luis Carvajal-Carmona, Richard S Houlston, Ian Tomlinson, Kimmo Palin, Esko Ukkonen, Auli Karhu, Jussi Taipale & Lauri A Aaltonen

doi:10.1038/ng.406

Lauri Aaltonen and colleagues show that a region on 8q24 associated with colorectal cancer risk functions as an enhancer and that the risk allele at this locus binds with higher affinity to the Wnt-regulated transcription factor TCF4 (also called TCF7L2), conferring enhanced responsiveness to Wnt signaling.

See also: News and Views by Harismendy & Frazer | Brief Communication by Pomerantz et al.


A mouse model of ATR-Seckel shows embryonic replicative stress and accelerated aging pp891 - 898

Matilde Murga, Samuel Bunting, Maria F Montaña, Rebeca Soria, Francisca Mulero, Marta Cañamero, Youngsoo Lee, Peter J McKinnon, Andre Nussenzweig & Oscar Fernandez-Capetillo

doi:10.1038/ng.420

Oscar Fernandez-Capetillo and colleagues report a mouse model of the human Seckel syndrome characterized by a deficiency in ATR. The Seckel mice show high levels of replicative stress during embryogenesis, and the adults show premature aging.

See also: News and Views by O'Driscoll


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Letters

Genome-wide association study identifies five susceptibility loci for glioma pp899 - 904

Sanjay Shete, Fay J Hosking, Lindsay B Robertson, Sara E Dobbins, Marc Sanson, Beatrice Malmer, Matthias Simon, Yannick Marie, Blandine Boisselier, Jean-Yves Delattre, Khe Hoang-Xuan, Soufiane El Hallani, Ahmed Idbaih, Diana Zelenika, Ulrika Andersson, Roger Henriksson, A Tommy Bergenheim, Maria Feychting, Stefan Lönn, Anders Ahlbom, Johannes Schramm, Michael Linnebank, Kari Hemminki, Rajiv Kumar, Sarah J Hepworth, Amy Price, Georgina Armstrong, Yanhong Liu, Xiangjun Gu, Robert Yu, Ching Lau, Minouk Schoemaker, Kenneth Muir, Anthony Swerdlow, Mark Lathrop, Melissa Bondy & Richard S Houlston

doi:10.1038/ng.407

Richard Houlston, Melissa Bondy and colleagues identify variants at five loci associated with glioma susceptibility, providing insights into the etiology of this primary brain tumor. The risk loci include common variants near TERT, CDKN2A-CDKN2B and RTEL1.


Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility pp905 - 908

Margaret Wrensch, Robert B Jenkins, Jeffrey S Chang, Ru-Fang Yeh, Yuanyuan Xiao, Paul A Decker, Karla V Ballman, Mitchel Berger, Jan C Buckner, Susan Chang, Caterina Giannini, Chandralekha Halder, Thomas M Kollmeyer, Matthew L Kosel, Daniel H LaChance, Lucie McCoy, Brian P O'Neill, Joe Patoka, Alexander R Pico, Michael Prados, Charles Quesenberry, Terri Rice, Amanda L Rynearson, Ivan Smirnov, Tarik Tihan, Joe Wiemels, Ping Yang & John K Wiencke

doi:10.1038/ng.408

Margaret Wrensch and colleagues report a genome-wide association and replication study for high-grade glioma. They show that common variants in the CDKN2B and RTEL1 regions are associated with risk of this aggressive brain tumor.


New common variants affecting susceptibility to basal cell carcinoma pp909 - 914

Simon N Stacey, Patrick Sulem, Gisli Masson, Sigurjon A Gudjonsson, Gudmar Thorleifsson, Margret Jakobsdottir, Asgeir Sigurdsson, Daniel F Gudbjartsson, Bardur Sigurgeirsson, Kristrun R Benediktsdottir, Kristin Thorisdottir, Rafn Ragnarsson, Dominique Scherer, Kari Hemminki, Peter Rudnai, Eugene Gurzau, Kvetoslava Koppova, Rafael Botella-Estrada, Virtudes Soriano, Pablo Juberias, Berta Saez, Yolanda Gilaberte, Victoria Fuentelsaz, Cristina Corredera, Matilde Grasa, Veronica Höiom, Annika Lindblom, Johannes J Bonenkamp, Michelle M van Rossum, Katja K H Aben, Esther de Vries, Mario Santinami, Maria G Di Mauro, Andrea Maurichi, Judith Wendt, Pia Hochleitner, Hubert Pehamberger, Julius Gudmundsson, Droplaug N Magnusdottir, Solveig Gretarsdottir, Hilma Holm, Valgerdur Steinthorsdottir, Michael L Frigge, Thorarinn Blondal, Jona Saemundsdottir, Hjördis Bjarnason, Kristleifur Kristjansson, Gyda Bjornsdottir, Ichiro Okamoto, Licia Rivoltini, Monica Rodolfo, Lambertus A Kiemeney, Johan Hansson, Eduardo Nagore, José I Mayordomo, Rajiv Kumar, Margaret R Karagas, Heather H Nelson, Jeffrey R Gulcher, Thorunn Rafnar, Unnur Thorsteinsdottir, Jon H Olafsson, Augustine Kong & Kari Stefansson

doi:10.1038/ng.412

Simon Stacey and colleagues report several new susceptibility variants for basal cell carcinoma, including coding variants in KRT5, a variant at 9p21 near CDKN2A and CDKN2B and a variant at 7q32 near KLF14. The latter is an imprinted gene, and the effect at this locus is dependent on the parental origin of the risk allele.


Genome-wide association study identifies variants at 9p21 and 22q13 associated with development of cutaneous nevi pp915 - 919

Mario Falchi, Veronique Bataille, Nicholas K Hayward, David L Duffy, Julia A Newton Bishop, Tomi Pastinen, Alessandra Cervino, Zhen Z Zhao, Panos Deloukas, Nicole Soranzo, David E Elder, Jennifer H Barrett, Nicholas G Martin, D Timothy Bishop, Grant W Montgomery & Timothy D Spector

doi:10.1038/ng.410

Timothy Spector, Mario Falchi and colleagues report a genome-wide association study for development of cutaneous nevi, the strongest known risk factor for cutaneous melanoma. They report two loci associated with nevus count, and show these loci are also associated with susceptibility to melanoma.


Genome-wide association study identifies three loci associated with melanoma risk pp920 - 925

D Timothy Bishop, Florence Demenais, Mark M Iles, Mark Harland, John C Taylor, Eve Corda, Juliette Randerson-Moor, Joanne F Aitken, Marie-Francoise Avril, Esther Azizi, Bert Bakker, Giovanna Bianchi-Scarrà, Brigitte Bressac-de Paillerets, Donato Calista, Lisa A Cannon-Albright, Thomas Chin-A-Woeng, Tadeusz De ogonbniak, Gilli Galore-Haskel, Paola Ghiorzo, Ivo Gut, Johan Hansson, Marko Hoc caronevar, Veronica Höiom, John L Hopper, Christian Ingvar, Peter A Kanetsky, Richard F Kefford, Maria Teresa Landi, Julie Lang, Jan Lubin acuteski, Rona Mackie, Josep Malvehy, Graham J Mann, Nicholas G Martin, Grant W Montgomery, Frans A van Nieuwpoort, Srdjan Novakovic, Håkan Olsson, Susana Puig, Marjan Weiss, Wilbert van Workum, Diana Zelenika, Kevin M Brown, Alisa M Goldstein, Elizabeth M Gillanders, Anne Boland, Pilar Galan, David E Elder, Nelleke A Gruis, Nicholas K Hayward, G Mark Lathrop, Jennifer H Barrett & Julia A Newton Bishop

doi:10.1038/ng.411

Timothy Bishop and colleagues from GenoMEL present a genome-wide association study for melanoma. They report three loci associated with susceptibility to melanoma, of which two were previously associated with pigmentation.


Sequence variants in the CLDN14 gene associate with kidney stones and bone mineral density pp926 - 930

Gudmar Thorleifsson, Hilma Holm, Vidar Edvardsson, G Bragi Walters, Unnur Styrkarsdottir, Daniel F Gudbjartsson, Patrick Sulem, Bjarni V Halldorsson, Femmie de Vegt, Frank C H d'Ancona, Martin den Heijer, Leifur Franzson, Claus Christiansen, Peter Alexandersen, Thorunn Rafnar, Kristleifur Kristjansson, Gunnar Sigurdsson, Lambertus A Kiemeney, Magnus Bodvarsson, Olafur S Indridason, Runolfur Palsson, Augustine Kong, Unnur Thorsteinsdottir & Kari Stefansson

doi:10.1038/ng.404

Gudmar Thorleifsson and colleagues report a genome-wide association study for kidney stones. They report common variants in CLDN14 associated with increased risk of kidney stone disease.


De novo copy number variants identify new genes and loci in isolated sporadic tetralogy of Fallot pp931 - 935

Steven C Greenway, Alexandre C Pereira, Jennifer C Lin, Steven R DePalma, Samuel J Israel, Sonia M Mesquita, Emel Ergul, Jessie H Conta, Joshua M Korn, Steven A McCarroll, Joshua M Gorham, Stacey Gabriel, David M Altshuler, Maria de Lourdes Quintanilla-Dieck, Maria Alexandra Artunduaga, Roland D Eavey, Robert M Plenge, Nancy A Shadick, Michael E Weinblatt, Philip L De Jager, David A Hafler, Roger E Breitbart, Jonathan G Seidman & Christine E Seidman

doi:10.1038/ng.415

Christine Seidman and colleagues report that 1% of individuals with sporadic non-syndromic tetralogy of Fallot show copy number gains or losses at chromosome 1q21.1. They also report copy number changes at other loci that likely contribute to the etiology of this congenital heart malformation.


Mutations affecting the secretory COPII coat component SEC23B cause congenital dyserythropoietic anemia type II pp936 - 940

Klaus Schwarz, Achille Iolascon, Fatima Verissimo, Nikolaus S Trede, Wyatt Horsley, Wen Chen, Barry H Paw, Karl-Peter Hopfner, Karlheinz Holzmann, Roberta Russo, Maria Rosaria Esposito, Daniela Spano, Luigia De Falco, Katja Heinrich, Brigitte Joggerst, Markus T Rojewski, Silverio Perrotta, Jonas Denecke, Ulrich Pannicke, Jean Delaunay, Rainer Pepperkok & Hermann Heimpel

doi:10.1038/ng.405

Klaus Schwarz and colleagues show that mutations affecting the secretory COPII coat component SEC23B cause congenital dyserythropoetic anemia type II, a rare disease marked by defective cytokinesis in erythroblasts and membrane abnormalities in nucleated and peripheral red blood cells.


H3.3/H2A.Z double variant–containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions pp941 - 945

Chunyuan Jin, Chongzhi Zang, Gang Wei, Kairong Cui, Weiqun Peng, Keji Zhao & Gary Felsenfeld

doi:10.1038/ng.409

Gary Felsenfeld and colleagues examine the distribution of H3.3- and H2A.Z-containing nucleosomes genome-wide. They find that regions at transcription start sites of active genes, which were thought to be "nucleosome-free regions," are enriched for unstable H2A.Z and H3.3 double-variant nucleosomes. These results suggest that double-variant nucleosomes may be important in the regulation of transcription factor access to promoters.

See also: News and Views by Henikoff


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Technical Report

A transposon-based chromosomal engineering method to survey a large cis-regulatory landscape in mice pp946 - 952

Chikara Kokubu, Kyoji Horie, Koichiro Abe, Ryuji Ikeda, Sumi Mizuno, Yoshihiro Uno, Sanae Ogiwara, Masato Ohtsuka, Ayako Isotani, Masaru Okabe, Kenji Imai & Junji Takeda

doi:10.1038/ng.397

Kokubu and colleagues have developed a method for mapping cis-regulatory elements in the mouse using targeted integration of the Sleeping Beauty transposon. This method also gives researchers the ability to generate targeted deletions for testing loss-of-function effects.


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