Advance online publication
The latest research papers, published online ahead of print. These online versions are definitive and may be cited using the digital object identifier (DOI).
About advance online publicationBrief Communications
Mutations in CCBE1 cause generalized lymph vessel dysplasia in humans
Marielle Alders, Benjamin M Hogan, Evisa Gjini, Faranak Salehi, Lihadh Al-Gazali, Eric A Hennekam, Eva E Holmberg, Marcel M A M Mannens, Margot F Mulder, G Johan A Offerhaus, Trine E Prescott, Eelco J Schroor, Joke B G M Verheij, Merlijn Witte, Petra J Zwijnenburg, Mikka Vikkula, Stefan Schulte-Merker & Raoul C Hennekam
Published online: 22 November 2009 | doi:10.1038/ng.484
Raoul Hennekam and colleagues report the identification of mutations in CCBE1 that cause Hennekam syndrome in humans. Features of Hennekam syndrome include lymphedema, lymphangiectasias, mental retardation and unusual facial characteristics. CCBE1 encodes Collagen and Calcium-Binding EGF domain-1, a secreted protein that has been shown to be required for embryonic lymphangiogenesis in zebrafish.
Abstract - Mutations in : CCBE1: cause generalized lymph vessel dysplasia in humans | Full Text - Mutations in CCBE1 cause generalized lymph vessel dysplasia in humans | PDF (545 KB) - Mutations in CCBE1 cause generalized lymph vessel dysplasia in humans | Supplementary information
A small recurrent deletion within 15q13.3 is associated with a range of neurodevelopmental phenotypes
Marwan Shinawi, Christian P Schaaf, Samarth S Bhatt, Zhilian Xia, Ankita Patel, Sau Wai Cheung, Brendan Lanpher, Sandra Nagl, Heinrich Stephan Herding, Claudia Nevinny-Stickel, LaDonna L Immken, Gayle Simpson Patel, Jennifer Ruth German, Arthur L Beaudet & Pawel Stankiewicz
Published online: 08 November 2009 | doi:10.1038/ng.481
Arthur Beaudet and colleagues report a recurrent 680-kb deletion within chromosome 15q13.3 associated with a range of neurodevelopmental phenotypes, including developmental delay, mental retardation and seizures. The deletion lies within the previously reported 1.5-Mb 15q13.3 deletion and spans only two genes, CHRNA7 and OTUD7A.
Abstract - A small recurrent deletion within 15q13.3 is associated with a range of neurodevelopmental phenotypes | Full Text - A small recurrent deletion within 15q13.3 is associated with a range of neurodevelopmental phenotypes | PDF (424 KB) - A small recurrent deletion within 15q13.3 is associated with a range of neurodevelopmental phenotypes | Supplementary information
Articles
HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C
Rasmi Thomas, Richard Apps, Ying Qi, Xiaojiang Gao, Victoria Male, Colm O'hUigin, Geraldine O'Connor, Dongliang Ge, Jacques Fellay, Jeffrey N Martin, Joseph Margolick, James J Goedert, Susan Buchbinder, Gregory D Kirk, Maureen P Martin, Amalio Telenti, Steven G Deeks, Bruce D Walker, David Goldstein, Daniel W McVicar, Ashley Moffett & Mary Carrington
Published online: 22 November 2009 | doi:10.1038/ng.486
Mary Carrington and colleagues follow up on an earlier association of a variant upstream of HLA-C to HIV viral load setpoint, showing that this variant is associated with high HLA-C cell surface expression and demonstrating a protective effect of the variant in viral load and disease progression.
Abstract - HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of : HLA-C | Full Text - HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C | PDF (544 KB) - HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C | Supplementary information
Exome sequencing identifies the cause of a mendelian disorder
Sarah B Ng, Kati J Buckingham, Choli Lee, Abigail W Bigham, Holly K Tabor, Karin M Dent, Chad D Huff, Paul T Shannon, Ethylin Wang Jabs, Deborah A Nickerson, Jay Shendure & Michael J Bamshad
Published online: 13 November 2009 | doi:10.1038/ng.499
Michael Bamshad, Jay Shendure and colleagues report the first application of exome resequencing to identify the cause of a mendelian disorder. They sequenced the exomes of four individuals with Miller syndrome in three independent families and identify mutations in DHODH, a key enzyme in the pyrimidine de novo biosynthesis pathway, as causal for the disorder.
Abstract - Exome sequencing identifies the cause of a mendelian disorder | Full Text - Exome sequencing identifies the cause of a mendelian disorder | PDF (523 KB) - Exome sequencing identifies the cause of a mendelian disorder | Supplementary information
Etv4 and Etv5 are required downstream of GDNF and Ret for kidney branching morphogenesis
Benson C Lu, Cristina Cebrian, Xuan Chi, Satu Kuure, Richard Kuo, Carlton M Bates, Silvia Arber, John Hassell, Lesley MacNeil, Masato Hoshi, Sanjay Jain, Naoya Asai, Masahide Takahashi, Kai M Schmidt-Ott, Jonathan Barasch, Vivette D'Agati & Frank Costantini
Published online: 08 November 2009 | doi:10.1038/ng.476
Frank Costantini and colleagues report the identification of the ETS transcription factors, Etv4 and Etv5, as key targets of Ret signaling during kidney branching morphogenesis. Loss of Etv4 and Etv5 function in mice leads to complete failure of kidney development.
Abstract - Etv4 and Etv5 are required downstream of GDNF and Ret for kidney branching morphogenesis | Full Text - Etv4 and Etv5 are required downstream of GDNF and Ret for kidney branching morphogenesis | PDF (1,443 KB) - Etv4 and Etv5 are required downstream of GDNF and Ret for kidney branching morphogenesis | Supplementary information
The genome of the cucumber, Cucumis sativus L.
Sanwen Huang, Ruiqiang Li, Zhonghua Zhang, Li Li, Xingfang Gu, Wei Fan, William J Lucas, Xiaowu Wang, Bingyan Xie, Peixiang Ni, Yuanyuan Ren, Hongmei Zhu, Jun Li, Kui Lin, Weiwei Jin, Zhangjun Fei, Guangcun Li, Jack Staub, Andrzej Kilian, Edwin A G van der Vossen, Yang Wu, Jie Guo, Jun He, Zhiqi Jia, Yi Ren, Geng Tian, Yao Lu, Jue Ruan, Wubin Qian, Mingwei Wang, Quanfei Huang, Bo Li, Zhaoling Xuan, Jianjun Cao, Asan, Zhigang Wu, Juanbin Zhang, Qingle Cai, Yinqi Bai, Bowen Zhao, Yonghua Han, Ying Li, Xuefeng Li, Shenhao Wang, Qiuxiang Shi, Shiqiang Liu, Won Kyong Cho, Jae-Yean Kim, Yong Xu, Katarzyna Heller-Uszynska, Han Miao, Zhouchao Cheng, Shengping Zhang, Jian Wu, Yuhong Yang, Houxiang Kang, Man Li, Huiqing Liang, Xiaoli Ren, Zhongbin Shi, Ming Wen, Min Jian, Hailong Yang, Guojie Zhang, Zhentao Yang, Rui Chen, Shifang Liu, Jianwen Li, Lijia Ma, Hui Liu, Yan Zhou, Jing Zhao, Xiaodong Fang, Guoqing Li, Lin Fang, Yingrui Li, Dongyuan Liu, Hongkun Zheng, Yong Zhang, Nan Qin, Zhuo Li, Guohua Yang, Shuang Yang, Lars Bolund, Karsten Kristiansen, Hancheng Zheng, Shaochuan Li, Xiuqing Zhang, Huanming Yang, Jian Wang, Rifei Sun, Baoxi Zhang, Shuzhi Jiang, Jun Wang, Yongchen Du & Songgang Li
Published online: 01 November 2009 | doi:10.1038/ng.475
Jun Wang and colleagues report the genome sequence of the cucumber. The cucumber genome is the seventh plant genome sequence to be reported and was assembled with a combination of traditional Sanger and next-generation sequencing methods.
Abstract - The genome of the cucumber, : Cucumis sativus: L. | Full Text - The genome of the cucumber, Cucumis sativus L. | PDF (1,380 KB) - The genome of the cucumber, Cucumis sativus L. | Supplementary information
Comparative genomic and phylogeographic analysis of Mycobacterium leprae
Marc Monot, Nadine Honoré, Thierry Garnier, Nora Zidane, Diana Sherafi, Alberto Paniz-Mondolfi, Masanori Matsuoka, G Michael Taylor, Helen D Donoghue, Abi Bouwman, Simon Mays, Claire Watson, Diana Lockwood, Ali Khamispour, Yahya Dowlati, Shen Jianping, Thomas H Rea, Lucio Vera-Cabrera, Mariane M Stefani, Sayera Banu, Murdo Macdonald, Bishwa Raj Sapkota, John S Spencer, Jérôme Thomas, Keith Harshman, Pushpendra Singh, Philippe Busso, Alexandre Gattiker, Jacques Rougemont, Patrick J Brennan & Stewart T Cole
Published online: 01 November 2009 | doi:10.1038/ng.477
Stewart Cole and colleagues report the genome sequence and comparative analyses of Brazilian, Indian, North American and Thai strains of Mycobacterium leprae, the etiologial agent of leprosy. They define 16 sub-types of M. leprae and examine their geographical distribution.
Abstract - Comparative genomic and phylogeographic analysis of : Mycobacterium leprae | Full Text - Comparative genomic and phylogeographic analysis of Mycobacterium leprae | PDF (986 KB) - Comparative genomic and phylogeographic analysis of Mycobacterium leprae | Supplementary information
Letters
Donor-recipient mismatch for common gene deletion polymorphisms in graft-versus-host disease
Steven A McCarroll, James E Bradner, Hannu Turpeinen, Liisa Volin, Paul J Martin, Shannon D Chilewski, Joseph H Antin, Stephanie J Lee, Tapani Ruutu, Barry Storer, Edus H Warren, Bo Zhang, Lue Ping Zhao, David Ginsburg, Robert J Soiffer, Jukka Partanen, John A Hansen, Jerome Ritz, Aarno Palotie & David Altshuler
Published online: 22 November 2009 | doi:10.1038/ng.490
Steven McCarroll and colleagues examine common gene deletions in individuals that have undergone bone marrow transplantation. They find that risk of acute graft-versus-host disease is greater when the donor and recipient are mismatched for a homozygous deletion of UGT2B17.
First Paragraph - Donor-recipient mismatch for common gene deletion polymorphisms in graft-versus-host disease | Full Text - Donor-recipient mismatch for common gene deletion polymorphisms in graft-versus-host disease | PDF (336 KB) - Donor-recipient mismatch for common gene deletion polymorphisms in graft-versus-host disease | Supplementary information
A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in the Japanese population
Kouichi Asano, Tomonaga Matsushita, Junji Umeno, Naoya Hosono, Atsushi Takahashi, Takahisa Kawaguchi, Takayuki Matsumoto, Toshiyuki Matsui, Yoichi Kakuta, Yoshitaka Kinouchi, Tooru Shimosegawa, Masayo Hosokawa, Yoshiaki Arimura, Yasuhisa Shinomura, Yutaka Kiyohara, Tatsuhiko Tsunoda, Naoyuki Kamatani, Mitsuo Iida, Yusuke Nakamura & Michiaki Kubo
Published online: 15 November 2009 | doi:10.1038/ng.482
Michiaki Kubo and colleagues report results of a genome-wide association study of ulcerative colitis in the Japanese population. Their study identifies three new susceptibility loci for this common inflammatory bowel disease, including FCGR2A, which has previously been implicated in other autoimmune diseases.
First Paragraph - A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in the Japanese population | Full Text - A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in the Japanese population | PDF (979 KB) - A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in the Japanese population | Supplementary information
Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region
The UK IBD Genetics Consortium & the Wellcome Trust Case Control Consortium 2
Published online: 15 November 2009 | doi:10.1038/ng.483
The UK IBD Genetics Consortium and the Wellcome Trust Case Control Consortium 2 report results of a genome-wide association study of ulcerative colitis. They identify three new loci associated with the disease, including the HNF4A region on 20q13.
First Paragraph - Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the : HNF4A: region | Full Text - Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region | PDF (624 KB) - Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region | Supplementary information
Common variants at five new loci associated with early-onset inflammatory bowel disease
Marcin Imielinski, Robert N Baldassano, Anne Griffiths, Richard K Russell, Vito Annese, Marla Dubinsky, Subra Kugathasan, Jonathan P Bradfield, Thomas D Walters, Patrick Sleiman, Cecilia E Kim, Aleixo Muise, Kai Wang, Joseph T Glessner, Shehzad Saeed, Haitao Zhang, Edward C Frackelton, Cuiping Hou, James H Flory, George Otieno, Rosetta M Chiavacci, Robert Grundmeier, Massimo Castro, Anna Latiano, Bruno Dallapiccola, Joanne Stempak, Debra J Abrams, Kent Taylor, Dermot McGovern, Western Regional Research Alliance for Pediatric IBD, International IBD Genetics Consortium, Melvin B Heyman, George D Ferry, Barbara Kirschner, Jessica Lee, Jonah Essers, Richard Grand, Michael Stephens, Arie Levine, David Piccoli, Johan Van Limbergen, Salvatore Cucchiara, Dimitri S Monos, Stephen L Guthery, Lee Denson, David C Wilson, Struan F A Grant, Mark Daly, Mark S Silverberg, Jack Satsangi & Hakon Hakonarson
Published online: 15 November 2009 | doi:10.1038/ng.489
Hakon Hakonarson and colleagues report the discovery of five new regions associated with susceptibility to early-onset inflammatory bowel disease. They also identify multiple loci previously implicated in the etiology of adult-onset Crohn's disease and/or ulcerative colitis as risk factors for early-onset forms of these diseases.
Abstract - Common variants at five new loci associated with early-onset inflammatory bowel disease | Full Text - Common variants at five new loci associated with early-onset inflammatory bowel disease | PDF (708 KB) - Common variants at five new loci associated with early-onset inflammatory bowel disease | Supplementary information
Genome-wide association study identifies common variants at four loci as genetic risk factors for Parkinson's disease
Wataru Satake, Yuko Nakabayashi, Ikuko Mizuta, Yushi Hirota, Chiyomi Ito, Michiaki Kubo, Takahisa Kawaguchi, Tatsuhiko Tsunoda, Masahiko Watanabe, Atsushi Takeda, Hiroyuki Tomiyama, Kenji Nakashima, Kazuko Hasegawa, Fumiya Obata, Takeo Yoshikawa, Hideshi Kawakami, Saburo Sakoda, Mitsutoshi Yamamoto, Nobutaka Hattori, Miho Murata, Yusuke Nakamura & Tatsushi Toda
Published online: 15 November 2009 | doi:10.1038/ng.485
Tatsushi Toda and colleagues report results of a genome-wide association study of Parkinson's disease in the Japanese population. They identify four loci harboring common variants associated with Parkinson's disease, including two newly discovered risk regions on 1q32 and 4p15.
First Paragraph - Genome-wide association study identifies common variants at four loci as genetic risk factors for Parkinson's disease | Full Text - Genome-wide association study identifies common variants at four loci as genetic risk factors for Parkinson's disease | PDF (1,981 KB) - Genome-wide association study identifies common variants at four loci as genetic risk factors for Parkinson's disease | Supplementary information
Genome-wide association study reveals genetic risk underlying Parkinson's disease
Javier Simón-Sánchez, Claudia Schulte, Jose M Bras, Manu Sharma, J Raphael Gibbs, Daniela Berg, Coro Paisan-Ruiz, Peter Lichtner, Sonja W Scholz, Dena G Hernandez, Rejko Krüger, Monica Federoff, Christine Klein, Alison Goate, Joel Perlmutter, Michael Bonin, Michael A Nalls, Thomas Illig, Christian Gieger, Henry Houlden, Michael Steffens, Michael S Okun, Brad A Racette, Mark R Cookson, Kelly D Foote, Hubert H Fernandez, Bryan J Traynor, Stefan Schreiber, Sampath Arepalli, Ryan Zonozi, Katrina Gwinn, Marcel van der Brug, Grisel Lopez, Stephen J Chanock, Arthur Schatzkin, Yikyung Park, Albert Hollenbeck, Jianjun Gao, Xuemei Huang, Nick W Wood, Delia Lorenz, Günther Deuschl, Honglei Chen, Olaf Riess, John A Hardy, Andrew B Singleton & Thomas Gasser
Published online: 15 November 2009 | doi:10.1038/ng.487
Andrew Singleton, Thomas Gasser and colleagues report results of a genome-wide association study of Parkinson's disease among individuals of European ancestry. They find genome-wide significant associations at two loci, SNCA and MAPT, and provide supporting evidence for a new risk locus on 1q32.
First Paragraph - Genome-wide association study reveals genetic risk underlying Parkinson's disease | Full Text - Genome-wide association study reveals genetic risk underlying Parkinson's disease | PDF (673 KB) - Genome-wide association study reveals genetic risk underlying Parkinson's disease | Supplementary information
Specific interaction between genotype, smoking and autoimmunity to citrullinated 
-enolase in the etiology of rheumatoid arthritis
Hiba Mahdi, Benjamin A Fisher, Henrik Källberg, Darren Plant, Vivianne Malmström, Johan Rönnelid, Peter Charles, Bo Ding, Lars Alfredsson, Leonid Padyukov, Deborah P M Symmons, Patrick J Venables, Lars Klareskog & Karin Lundberg
Published online: 08 November 2009 | doi:10.1038/ng.480
Karin Lundberg and colleagues explore gene-gene and gene-environment interactions in susceptibility to rheumatoid arthritis, reporting an association of HLA-DRB1, PTPN22 and smoking stratified by the autoantigen CEP-1.
First Paragraph - Specific interaction between genotype, smoking and autoimmunity to citrullinated [alpha]-enolase in the etiology of rheumatoid arthritis | Full Text - Specific interaction between genotype, smoking and autoimmunity to citrullinated 
-enolase in the etiology of rheumatoid arthritis | PDF (728 KB) - Specific interaction between genotype, smoking and autoimmunity to citrullinated -enolase in the etiology of rheumatoid arthritis |
Supplementary information
Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk
Soumya Raychaudhuri, Brian P Thomson, Elaine F Remmers, Stephen Eyre, Anne Hinks, Candace Guiducci, Joseph J Catanese, Gang Xie, Eli A Stahl, Robert Chen, Lars Alfredsson, Christopher I Amos, Kristin G Ardlie, BIRAC Consortium, Anne Barton, John Bowes, Noel P Burtt, Monica Chang, Jonathan Coblyn, Karen H Costenbader, Lindsey A Criswell, J Bart A Crusius, Jing Cui, Phillip L De Jager, Bo Ding, Paul Emery, Edward Flynn, Pille Harrison, Lynne J Hocking, Tom W J Huizinga, Daniel L Kastner, Xiayi Ke, Fina A S Kurreeman, Annette T Lee, Xiangdong Liu, Yonghong Li, Paul Martin, Ann W Morgan, Leonid Padyukov, David M Reid, Mark Seielstad, Michael F Seldin, Nancy A Shadick, Sophia Steer, Paul P Tak, Wendy Thomson, Annette H M van der Helm-van Mil, Irene E van der Horst-Bruinsma, Michael E Weinblatt, Anthony G Wilson, Gert Jan Wolbink, Paul Wordsworth, YEAR Consortium, David Altshuler, Elizabeth W Karlson, Rene E M Toes, Niek de Vries, Ann B Begovich, Katherine A Siminovitch, Jane Worthington, Lars Klareskog, Peter K Gregersen, Mark J Daly & Robert M Plenge
Published online: 08 November 2009 | doi:10.1038/ng.479
Soumya Raychaudhuri and colleagues demonstrate the utility of GRAIL, a software program used to prioritize results from genome-wide association studies for further replication, applied here to rheumatoid arthritis. The authors seek replication of their predictions in additional independent cohorts and report three new genetic loci associated with RA susceptibility.
First Paragraph - Genetic variants at : CD28: , : PRDM1: and : CD2/CD58: are associated with rheumatoid arthritis risk | Full Text - Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk | PDF (745 KB) - Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk | Supplementary information
Genetic variants in TPMT and COMT are associated with hearing loss in children receiving cisplatin chemotherapy
Colin J D Ross, Hagit Katzov-Eckert, Marie-Pierre Dubé, Beth Brooks, S Rod Rassekh, Amina Barhdadi, Yassamin Feroz-Zada, Henk Visscher, Andrew M K Brown, Michael J Rieder, Paul C Rogers, Michael S Phillips, Bruce C Carleton, Michael R Hayden & the CPNDS Consortium
Published online: 08 November 2009 | doi:10.1038/ng.478
Colin Ross and colleagues report the association of variants in TPMT and COMT to cisplatin-induced hearing loss in children.
First Paragraph - Genetic variants in : TPMT: and : COMT: are associated with hearing loss in children receiving cisplatin chemotherapy | Full Text - Genetic variants in TPMT and COMT are associated with hearing loss in children receiving cisplatin chemotherapy | PDF (580 KB) - Genetic variants in TPMT and COMT are associated with hearing loss in children receiving cisplatin chemotherapy | Supplementary information
Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts
Akiko Doi, In-Hyun Park, Bo Wen, Peter Murakami, Martin J Aryee, Rafael Irizarry, Brian Herb, Christine Ladd-Acosta, Junsung Rho, Sabine Loewer, Justine Miller, Thorsten Schlaeger, George Q Daley & Andrew P Feinberg
Published online: 01 November 2009 | doi:10.1038/ng.471
Andrew Feinberg and colleagues show that differential methylation of CpG island shores distinguish human induced pluripotent stem cells from the fibroblasts from which they were derived. These differentially methylated regions of the genome can also distinguish normal colon tissue from colorectal cancer.
Abstract - Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts | Full Text - Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts | PDF (717 KB) - Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts | Supplementary information
Until print versions of AOP papers are published, they should be cited in the style "Author(s) Nature Genetics advance online publication, day month year (doi:10.1038/ngXXXXX)". Once the print version (identical to the AOP) is published, it should be cited as follows: "Author(s) Nature Genetics volume, page (year); advance online publication, (doi:10.1038/ngXXXXX)".
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