Table of contents


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Editorial

Data divorce p1157

doi:10.1038/ng1109-1157


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Obituary

Richard S. Spielman 1946–2009 p1159

Jurg Ott

doi:10.1038/ng1109-1159


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News and Views


Not so lost in the genetic crowd pp1163 - 1164

Nicholas J Schork & Vikas Bansal

doi:10.1038/ng1109-1163

See also: Letter by Jacobs et al.


DNA methylation is a guardian of stem cell self-renewal and multipotency pp1164 - 1166

Laurraine-Marcelle Gereige & Hanna K A Mikkola

doi:10.1038/ng1109-1164

See also: Article by Bröske et al.


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Research Highlights

Research highlights p1167

doi:10.1038/ng1109-1167


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Brief Communications

Genome-wide association study identifies variants in TMPRSS6 associated with hemoglobin levels pp1170 - 1172

John C Chambers, Weihua Zhang, Yun Li, Joban Sehmi, Mark N Wass, Delilah Zabaneh, Clive Hoggart, Henry Bayele, Mark I McCarthy, Leena Peltonen, Nelson B Freimer, Surjit K Srai, Patrick H Maxwell, Michael J E Sternberg, Aimo Ruokonen, Gonçalo Abecasis, Marjo-Riitta Jarvelin, James Scott, Paul Elliott & Jaspal S Kooner

doi:10.1038/ng.462

John Chambers and colleagues report the association of SNPs in TMPRSS6, which encodes a regulator of hepicidin synthesis, to hemoglobin levels.

See also: News and Views by Andrews | Brief Communication by Benyamin et al. | Article by Soranzo et al. | Article by Ganesh et al.


Common variants in TMPRSS6 are associated with iron status and erythrocyte volume pp1173 - 1175

Beben Benyamin, Manuel A R Ferreira, Gonneke Willemsen, Scott Gordon, Rita P S Middelberg, Brian P McEvoy, Jouke-Jan Hottenga, Anjali K Henders, Megan J Campbell, Leanne Wallace, Ian H Frazer, Andrew C Heath, Eco J C de Geus, Dale R Nyholt, Peter M Visscher, Brenda W Penninx, Dorret I Boomsma, Nicholas G Martin, Grant W Montgomery & John B Whitfield

doi:10.1038/ng.456

Beben Benyamin and colleagues report a genome-wide association study to iron status, identifying variants in TMPRSS6 associated with serum iron, transferrin saturation and erythrocyte volume.

See also: News and Views by Andrews | Brief Communication by Chambers et al. | Article by Soranzo et al. | Article by Ganesh et al.


T (brachyury) gene duplication confers major susceptibility to familial chordoma pp1176 - 1178

Xiaohong R Yang, David Ng, David A Alcorta, Norbert J Liebsch, Eamonn Sheridan, Sufeng Li, Alisa M Goldstein, Dilys M Parry & Michael J Kelley

doi:10.1038/ng.454

Dilys Parry and colleagues show that duplications of the T gene confer susceptibility to familial chordoma, a cancer of presumed notochordal origin. The T gene product, known as brachyury, is a transcription factor that plays an important role in notochord development.


Mutations in FAM134B, encoding a newly identified Golgi protein, cause severe sensory and autonomic neuropathy pp1179 - 1181

Ingo Kurth, Torsten Pamminger, J Christopher Hennings, Désirée Soehendra, Antje K Huebner, Annelies Rotthier, Jonathan Baets, Jan Senderek, Haluk Topaloglu, Sandra A Farrell, Gudrun Nürnberg, Peter Nürnberg, Peter De Jonghe, Andreas Gal, Christoph Kaether, Vincent Timmerman & Christian A Hübner

doi:10.1038/ng.464

Ingo Kurth and Christian Hübner report the identification of loss-of-function mutations in FAM134B, which encodes a novel cis-Golgi protein, in hereditary sensory and autonomic neuropathy type II.


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Articles

A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium pp1182 - 1190

Nicole Soranzo, Tim D Spector, Massimo Mangino, Brigitte Kühnel, Augusto Rendon, Alexander Teumer, Christina Willenborg, Benjamin Wright, Li Chen, Mingyao Li, Perttu Salo, Benjamin F Voight, Philippa Burns, Roman A Laskowski, Yali Xue, Stephan Menzel, David Altshuler, John R Bradley, Suzannah Bumpstead, Mary-Susan Burnett, Joseph Devaney, Angela Döring, Roberto Elosua, Stephen E Epstein, Wendy Erber, Mario Falchi, Stephen F Garner, Mohammed J R Ghori, Alison H Goodall, Rhian Gwilliam, Hakon H Hakonarson, Alistair S Hall, Naomi Hammond, Christian Hengstenberg, Thomas Illig, Inke R König, Christopher W Knouff, Ruth McPherson, Olle Melander, Vincent Mooser, Matthias Nauck, Markku S Nieminen, Christopher J O'Donnell, Leena Peltonen, Simon C Potter, Holger Prokisch, Daniel J Rader, Catherine M Rice, Robert Roberts, Veikko Salomaa, Jennifer Sambrook, Stefan Schreiber, Heribert Schunkert, Stephen M Schwartz, Jovana Serbanovic-Canic, Juha Sinisalo, David S Siscovick, Klaus Stark, Ida Surakka, Jonathan Stephens, John R Thompson, Uwe Völker, Henry Völzke, Nicholas A Watkins, George A Wells, H-Erich Wichmann, David A Van Heel, Chris Tyler-Smith, Swee Lay Thein, Sekar Kathiresan, Markus Perola, Muredach P Reilly, Alexandre F R Stewart, Jeanette Erdmann, Nilesh J Samani, Christa Meisinger, Andreas Greinacher, Panos Deloukas, Willem H Ouwehand & Christian Gieger

doi:10.1038/ng.467

Nicole Soranzo and colleagues report a meta-analysis of genome-wide association datasets identifying 22 associations to 8 clinically relevant hematological traits. They also identify a long-range haplotype at 12q24 that includes variants associated with platelet counts as well as coronary artery disease and shows evidence of a selective sweep in Europeans.

See also: News and Views by Andrews | Brief Communication by Chambers et al. | Brief Communication by Benyamin et al. | Article by Ganesh et al.


Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium pp1191 - 1198

Santhi K Ganesh, Neil A Zakai, Frank J A van Rooij, Nicole Soranzo, Albert V Smith, Michael A Nalls, Ming-Huei Chen, Anna Kottgen, Nicole L Glazer, Abbas Dehghan, Brigitte Kuhnel, Thor Aspelund, Qiong Yang, Toshiko Tanaka, Andrew Jaffe, Joshua C M Bis, Germaine C Verwoert, Alexander Teumer, Caroline S Fox, Jack M Guralnik, Georg B Ehret, Kenneth Rice, Janine F Felix, Augusto Rendon, Gudny Eiriksdottir, Daniel Levy, Kushang V Patel, Eric Boerwinkle, Jerome I Rotter, Albert Hofman, Jennifer G Sambrook, Dena G Hernandez, Gang Zheng, Stefania Bandinelli, Andrew B Singleton, Josef Coresh, Thomas Lumley, André G Uitterlinden, Janine M vanGils, Lenore J Launer, L Adrienne Cupples, Ben A Oostra, Jaap-Jan Zwaginga, Willem H Ouwehand, Swee-Lay Thein, Christa Meisinger, Panos Deloukas, Matthias Nauck, Tim D Spector, Christian Gieger, Vilmundur Gudnason, Cornelia M van Duijn, Bruce M Psaty, Luigi Ferrucci, Aravinda Chakravarti, Andreas Greinacher, Christopher J O'Donnell, Jacqueline C M Witteman, Susan Furth, Mary Cushman, Tamara B Harris & Jing-Ping Lin

doi:10.1038/ng.466

Santhi Ganesh and colleagues report meta-analyses of genome-wide association studies of six erythrocyte traits within the CHARGE consortium, with replication in cohorts of the HaemGen consortium. They report 23 loci associated with a range of clinically relevant red blood cell traits.

See also: News and Views by Andrews | Brief Communication by Chambers et al. | Brief Communication by Benyamin et al. | Article by Soranzo et al.


Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies pp1199 - 1206

Fernando Rivadeneira, Unnur Styrkársdottir, Karol Estrada, Bjarni V Halldórsson, Yi-Hsiang Hsu, J Brent Richards, M Carola Zillikens, Fotini K Kavvoura, Najaf Amin, Yurii S Aulchenko, L Adrienne Cupples, Panagiotis Deloukas, Serkalem Demissie, Elin Grundberg, Albert Hofman, Augustine Kong, David Karasik, Joyce B van Meurs, Ben Oostra, Tomi Pastinen, Huibert A P Pols, Gunnar Sigurdsson, Nicole Soranzo, Gudmar Thorleifsson, Unnur Thorsteinsdottir, Frances M K Williams, Scott G Wilson, Yanhua Zhou, Stuart H Ralston, Cornelia M van Duijn, Timothy Spector, Douglas P Kiel, Kari Stefansson, John P A Ioannidis & André G Uitterlinden for the Genetic Factors for Osteoporosis (GEFOS) Consortium

doi:10.1038/ng.446

Fernando Rivadeneira and colleagues report findings from a large-scale meta-analysis of genome-wide association studies for bone mineral density. The loci identified in this study map to genes in signaling pathways relevant to bone metabolism and highlight the complex genetic architecture underlying osteoporosis.


DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction pp1207 - 1215

Ann-Marie Bröske, Lena Vockentanz, Shabnam Kharazi, Matthew R Huska, Elena Mancini, Marina Scheller, Christiane Kuhl, Andreas Enns, Marco Prinz, Rudolf Jaenisch, Claus Nerlov, Achim Leutz, Miguel A Andrade-Navarro, Sten Eirik W Jacobsen & Frank Rosenbauer

doi:10.1038/ng.463

Frank Rosenbauer and colleagues show that alternative functional programs of hematopoietic stem cells are governed by gradual differences in the cellular DNA methylation level.

See also: News and Views by Gereige & Mikkola


Global patterns of cis variation in human cells revealed by high-density allelic expression analysis pp1216 - 1222

Bing Ge, Dmitry K Pokholok, Tony Kwan, Elin Grundberg, Lisanne Morcos, Dominique J Verlaan, Jennie Le, Vonda Koka, Kevin C L Lam, Vincent Gagné, Joana Dias, Rose Hoberman, Alexandre Montpetit, Marie-Michele Joly, Edward J Harvey, Daniel Sinnett, Patrick Beaulieu, Robert Hamon, Alexandru Graziani, Ken Dewar, Eef Harmsen, Jacek Majewski, Harald H H Göring, Anna K Naumova, Mathieu Blanchette, Kevin L Gunderson & Tomi Pastinen

doi:10.1038/ng.473

Tomi Pastinen and colleagues report a genome-wide analysis of allelic expression variation in lymphoblastoid cell lines from HapMap individuals.


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Letters

Microduplications of 16p11.2 are associated with schizophrenia pp1223 - 1227

Shane E McCarthy, Vladimir Makarov, George Kirov, Anjene M Addington, Jon McClellan, Seungtai Yoon, Diana O Perkins, Diane E Dickel, Mary Kusenda, Olga Krastoshevsky, Verena Krause, Ravinesh A Kumar, Detelina Grozeva, Dheeraj Malhotra, Tom Walsh, Elaine H Zackai, Paige Kaplan, Jaya Ganesh, Ian D Krantz, Nancy B Spinner, Patricia Roccanova, Abhishek Bhandari, Kevin Pavon, B Lakshmi, Anthony Leotta, Jude Kendall, Yoon-ha Lee, Vladimir Vacic, Sydney Gary, Lilia M Iakoucheva, Timothy J Crow, Susan L Christian, Jeffrey A Lieberman, T Scott Stroup, Terho Lehtimäki, Kaija Puura, Chad Haldeman-Englert, Justin Pearl, Meredith Goodell, Virginia L Willour, Pamela DeRosse, Jo Steele, Layla Kassem, Jessica Wolff, Nisha Chitkara, Francis J McMahon, Anil K Malhotra, James B Potash, Thomas G Schulze, Markus M Nöthen, Sven Cichon, Marcella Rietschel, Ellen Leibenluft, Vlad Kustanovich, Clara M Lajonchere, James S Sutcliffe, David Skuse, Michael Gill, Louise Gallagher, Nancy R Mendell, Wellcome Trust Case Control Consortium, Nick Craddock, Michael J Owen, Michael C O'Donovan, Tamim H Shaikh, Ezra Susser, Lynn E DeLisi, Patrick F Sullivan, Curtis K Deutsch, Judith Rapoport, Deborah L Levy, Mary-Claire King & Jonathan Sebat

doi:10.1038/ng.474

Jonathan Sebat and colleagues report the association of microduplication on chromosome 16p11.2 with schizophrenia, while the reciprocal microdeletion was associated with autism and developmental disorders.


A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus pp1228 - 1233

Vesela Gateva, Johanna K Sandling, Geoff Hom, Kimberly E Taylor, Sharon A Chung, Xin Sun, Ward Ortmann, Roman Kosoy, Ricardo C Ferreira, Gunnel Nordmark, Iva Gunnarsson, Elisabet Svenungsson, Leonid Padyukov, Gunnar Sturfelt, Andreas Jönsen, Anders A Bengtsson, Solbritt Rantapää-Dahlqvist, Emily C Baechler, Elizabeth E Brown, Graciela S Alarcón, Jeffrey C Edberg, Rosalind Ramsey-Goldman, Gerald McGwin Jr, John D Reveille, Luis M Vilá, Robert P Kimberly, Susan Manzi, Michelle A Petri, Annette Lee, Peter K Gregersen, Michael F Seldin, Lars Rönnblom, Lindsey A Criswell, Ann-Christine Syvänen, Timothy W Behrens & Robert R Graham

doi:10.1038/ng.468

Robert Graham and colleagues report results of a large-scale replication study for systemic lupus erythematosus (SLE) in individuals of European ancestry. Their findings expand the number of confirmed SLE susceptibility loci and implicate several key immunologic pathways in SLE pathogenesis.


Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus pp1234 - 1237

Jian-Wen Han, Hou-Feng Zheng, Yong Cui, Liang-Dan Sun, Dong-Qing Ye, Zhi Hu, Jin-Hua Xu, Zhi-Ming Cai, Wei Huang, Guo-Ping Zhao, Hong-Fu Xie, Hong Fang, Qian-Jin Lu, Jian-Hua Xu, Xiang-Pei Li, Yun-Feng Pan, Dan-Qi Deng, Fan-Qin Zeng, Zhi-Zhong Ye, Xiao-Yan Zhang, Qing-Wen Wang, Fei Hao, Li Ma, Xian-Bo Zuo, Fu-Sheng Zhou, Wen-Hui Du, Yi-Lin Cheng, Jian-Qiang Yang, Song-Ke Shen, Jian Li, Yu-Jun Sheng, Xiao-Xia Zuo, Wei-Fang Zhu, Fei Gao, Pei-Lian Zhang, Qing Guo, Bo Li, Min Gao, Feng-Li Xiao, Cheng Quan, Chi Zhang, Zheng Zhang, Kun-Ju Zhu, Yang Li, Da-Yan Hu, Wen-Sheng Lu, Jian-Lin Huang, Sheng-Xiu Liu, Hui Li, Yun-Qing Ren, Zai-Xing Wang, Chun-Jun Yang, Pei-Guang Wang, Wen-Ming Zhou, Yong-Mei Lv, An-Ping Zhang, Sheng-Quan Zhang, Da Lin, Yi Li, Hui Qi Low, Min Shen, Zhi-Fang Zhai, Ying Wang, Feng-Yu Zhang, Sen Yang, Jian-Jun Liu & Xue-Jun Zhang

doi:10.1038/ng.472

Xuejun Zhang and colleagues report results of a genome-wide association study of systemic lupus erythematosus (SLE) in a Chinese Han population. Their work identifies nine new SLE susceptibility loci and reveals overlap in the spectrum of risk alleles shared between Chinese Han and European populations.


SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas pp1238 - 1242

Adam J Bass, Hideo Watanabe, Craig H Mermel, Soyoung Yu, Sven Perner, Roel G Verhaak, So Young Kim, Leslie Wardwell, Pablo Tamayo, Irit Gat-Viks, Alex H Ramos, Michele S Woo, Barbara A Weir, Gad Getz, Rameen Beroukhim, Michael O'Kelly, Amit Dutt, Orit Rozenblatt-Rosen, Piotr Dziunycz, Justin Komisarof, Lucian R Chirieac, Christopher J LaFargue, Veit Scheble, Theresia Wilbertz, Changqing Ma, Shilpa Rao, Hiroshi Nakagawa, Douglas B Stairs, Lin Lin, Thomas J Giordano, Patrick Wagner, John D Minna, Adi F Gazdar, Chang Qi Zhu, Marcia S Brose, Ivan Cecconello, Ulysses Ribeiro Jr, Suely K Marie, Olav Dahl, Ramesh A Shivdasani, Ming-Sound Tsao, Mark A Rubin, Kwok K Wong, Aviv Regev, William C Hahn, David G Beer, Anil K Rustgi & Matthew Meyerson

doi:10.1038/ng.465

Matthew Meyerson and colleagues report that SOX2, which encodes a transcription factor necessary for normal esophageal development, is an amplified lineage survival oncogene in lung and esophageal squamous cell carcinomas.


Rearrangement of CRLF2 in B-progenitor– and Down syndrome–associated acute lymphoblastic leukemia pp1243 - 1246

Charles G Mullighan, J Racquel Collins-Underwood, Letha A A Phillips, Michael G Loudin, Wei Liu, Jinghui Zhang, Jing Ma, Elaine Coustan-Smith, Richard C Harvey, Cheryl L Willman, Fady M Mikhail, Julia Meyer, Andrew J Carroll, Richard T Williams, Jinjun Cheng, Nyla A Heerema, Giuseppe Basso, Andrea Pession, Ching-Hon Pui, Susana C Raimondi, Stephen P Hunger, James R Downing, William L Carroll & Karen R Rabin

doi:10.1038/ng.469

Charles Mullighan and colleagues report a recurrent rearrangement of CRLF2 in B-progenitor and Down syndrome-associated acute lymphoblastic leukemia. Their genetic and functional evidence indicates that CRLF2 cooperates with activated JAK2 to promote leukemogenesis.


Activating mutations in FGFR3 and HRAS reveal a shared genetic origin for congenital disorders and testicular tumors pp1247 - 1252

Anne Goriely, Ruth M S Hansen, Indira B Taylor, Inge A Olesen, Grete Krag Jacobsen, Simon J McGowan, Susanne P Pfeifer, Gilean A T McVean, Ewa Rajpert-De Meyts & Andrew O M Wilkie

doi:10.1038/ng.470

Andrew Wilkie and colleagues report that activating paternal-effect mutations in FGFR3 and HRAS promote clonal expansion in the testis, leading to spermatocytic seminomas. The same mutation in FGFR3 leads to the lethal disorder thanatophoric dysplasia, revealing a shared genetic mechanism for congenital disorders and testicular tumors.


A new statistic and its power to infer membership in a genome-wide association study using genotype frequencies pp1253 - 1257

Kevin B Jacobs, Meredith Yeager, Sholom Wacholder, David Craig, Peter Kraft, David J Hunter, Justin Paschal, Teri A Manolio, Margaret Tucker, Robert N Hoover, Gilles D Thomas, Stephen J Chanock & Nilanjan Chatterjee

doi:10.1038/ng.455

Kevin Jacobs and colleagues report a new test statistic for detection of membership of an individual within a genome-wide association study, based on reporting of study genotype frequencies.

See also: News and Views by Schork & Bansal


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