李瑞强    Wei Fan    Geng Tian    Hongmei Zhu    Lin He    Cai Jing    Huang Quanfei    Qingle Cai    Bo li    Bai Yinqi    Zhihe Zhang    张亚平    Wen Wang    Jun Li    魏辅文    Heng Li    Min Jian    Li Jianwen    张兆雷    Rasmus wedel Nielsen    李大伟    Wanjun Gu    Yang Zhentao    Xuan Zhaoling    Oliver Ryder    Leung Frederick Chi-Ching    Yan Zhou    Cao Jianjun    Sun Xiao    Fu Yonggui    Xiaodong Fang    Xiaosen Guo    bo Wang    Rong Hou    Fujun Shen    Mu Bo    Peixiang Ni    Lin Runmao    Qian Wubin    WANG Guo-dong    Chang Yu    Nie Wenhui    Wang Jinhuan    Wu Zhigang    Huiqing Liang    Jiumeng Min    Wu Qi    Shifeng Cheng    Jue Ruan    Wang Mingwei    Shi Zhongbin    Wen Ming    Binghang Liu    Xiaoli Ren    Huisong Zheng    董东    Cook Kathleen    Shan Gao    Hao Zhang    Carolin Kosiol    Xie Xueying    Lu Zuhong    Hancheng Zheng    李英睿    Cynthia Steiner    Tommy tsan yuk Lam    Lin Siyuan    Qinghui Zhang    Guoqing Li    Tian Jing    Gong Timing    Hongde Liu    Zhang Dejin    方林    Chen Ye    Zhang Juanbin    Hu Wenbo    徐安龙    Ren Yuanyuan    Guo jie Zhang    Michael william Bruford    Qibin Li    Lijia Ma    Guo Y.    An Na    Hu Yujie    Zheng Yang    师咏勇    Li Zhiqiang    Liu Qing    Chen Yanling    Zhao Jing    Qu Ning    Shancen Zhao    Tian Feng    Wang Xiaoling    Wang Haiyin    Xu Lizhi    Xiao Liu    Tomáš Vinař    Wang Yajun    Takwah Lam    Siu ming Yiu    Shiping Liu    Hemin Zhang    Li Desheng    Huang Yan    Waeng Xia    Yang Guohua    Jiang Zhi    Junyi Wang    Nan Qin    Li Li    Jingxiang Li    Lars Bolund    Karsten Kristiansen    Gane ka shu Wong    Maynard Olson    Xiuqing Zhang    Songgang Li    杨焕明     汪建    Weng Jun   

Nature

2010

The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies. © 2010 Macmillan Publishers Limited. All rights reserved.

Hudson Thomas J.    Warwick Anderson    Aretz Axel    Anna Barker    Bell Cindy    Bernabé Rosa R.    Maharaj Kishan Bhan    Calvo Fabien    Eerola Iiro    Gerhard Daniela S.    Alan Guttmacher    Mark Guyer    Hemsley Fiona M.    Jennings Jennifer L.    David james Kerr    Klatt Peter    Patrik Kolar    Kusuda Jun    Lane David P.    Laplace Frank    Youyong Lü    Nettekoven Gerd    Bradley Ozenberger    Jane Peterson    Rao    Remacle Jacques    Alan Schafer    Tatsuhiro Shibata    Michael Michael R. Stratton    Vockley Joseph G.    Watanabe Koichi    杨焕明     Yuen M.    Bartha maria Knoppers    Martin Bobrow    Anne Cambon-Thomsen    Dressler Lynn G.    Dyke Stephanie O.M.    Joly Yann    Kazuto Kato    Karen Kennedy    Nicolás Pilar    Michael Parker    Rial-Sebbag Emmanuelle    Romeo-Casabona Carlos M.    Shaw Kenna M.    Wallace Susan    Wiesner Georgia L.    Nikolajs Zeps    Peter Lichter    Andrew Biankin    Christian Chabannon    Lynda Chin    Bruno Clément    Alava Enrique De    Degos Françoise    Martin Ferguson    Geary Peter    David neil Hayes    Amber Johns    Arek Kasprzyk    Nakagawa Hidewaki    Robert Penny    Miguel Ángel Piris Pinilla    Sarin Rajiv    Aldo Scarpa    De Vijver Marc Van    Andrew andrew Futreal    Hiroyuki Aburatani    Mònica Bayés    David dl Bowtell    Campbel Peter J.    Xavier Estivill    Sean Grimmond    Ivo Gut    Martin Hirst    López-Otín    Partha Pratim Majumder    Marco Marra    John McPherson    Zemin Ning    Puente Xose S.    阮一骏    Hendrik Stunnenberg    Swerdlow Harold P.    Victor Velculescu    Richard Wilson    Xue Hong H.    Liu Yang.    Paul Spellman    Gary Bader    Boutros Paul C.    Paul Flicek    Gad Getz    Guigó R.    Guangwu Guo    David Haussler    Heath Simon    Tim Hubbard    Jiang Tao    Steven Jones    Qibin Li    Lopez-Bigas N.    Ruibang Luo    Lakshmi Muthuswamy    Ouellette B.F. Francis    John Pearson    Víctor Quesada    Benjamin Raphael    Chris Sander    Terence Speed    Lincoln Stein    Joshua michael Stuart    Jon Teague    Yasushi Totoki    Tatsuhiko Tsunoda    Alfonso Valencia    David Wheeler    Wu Honglong    Shancen Zhao    Guangyu Zhou    Mark Lathrop    Gilles Thomas    Teruhiko Yoshida    Axton Myles    Gunter Chris    Miller Linda J.    Junjun Zhang    Haider    Wang Jianxin    Christina Yung    Cross Anthony    Liang Yong    Gnaneshan Saravanamuttu    Guberman Jonathan    Hsu Jack    Chalmers Don R.C.    Hasel Karl W.    Kaan Terry S.H.    Lowrance William W.    Masui Tohru    Laura lyman Rodriguez    Catherine Vergely    Bowtel David D.L.    Nicole Cloonan    DeFazio Anna    James richard Eshleman    Etemadmoghadam Dariush    Gardiner Brooke A.    James Kench    Robert lyndsay Sutherland    Tempero Margaret    Nick Waddell    Peter Wilson    Steven Gallinger    Mingsound Tsao    Shaw Patricia    Gloria moy Petersen    Mukhopadhyay Debabrata    Ronald anthony DePinho    Thayer Sarah    Shazand Kamran    Beck Tim    Sam Michelle    Timms Lee    Ballin Vanessa    季加孚    Xiuqing Zhang    Chen Feng    Xueda Hu    Yang Qi    Geng Tian    Lianhai Zhang    Xiaofang Xing    Li Xianghong    朱正刚    Yingyan Yu    于君    Tost Jörg    Paul Brennan    Ivana Holcátová    David Zaridze    Alvis Brāzma    Lars Egevad    Prokhortchouk Egor    Banks    Mathias Uhlén    Viksna Juris    Fredrik Pontén    Konstantin Skryabin    Futrea P. Andrew    Ewan Birney    Åke Borg    Anne lise Børresen-Dale    Carlos Caldas    John Foekens    Sancha Martin    Jorge sérgio reis Reis-Filho    Andrea lynn Richardson    Christos Sotiriou    Laura van Veer    Daniel Birnbaum    Blanché Hélène    Boucher Pascal    Sandrine Boyault    Masson-Jacquemier Jocelyne D.    Pauporté Iris    Pivot Xavier    Anne Vincent-Salomon    Tabone Eric    Theillet Charles    Treilleux Isabelle    Paulette Bioulac-Sage    Decaens Thomas    OiseDegos Franc    Franco Dominique    Gut Marta    Didier Samuel    Jessica Zucman-Rossi    Roland Eils    Benedikt Brors    Korbe Jan O.    Andrey Korshunov    Pablo Landgraf    Hans Lehrach    Stefan michael Pfister    Bernhard Radlwimmer    Guido Reifenberger    Michael Taylor    Christof von Von Kalle    Majumder Partha P.    Rao    Paolo paolo Pederzoli    Rita Lawlor.    Delledonne Massimo    Bardelli Alberto    Gress Thomas M    David Klimstra    Giuseppe Zamboni    Yusuke Nakamura    Satoru Miyano    Fujimoto Akihiro    Elías Campo    Sanjose Silvia De    Emili Montserrat    González-Dý́az Marcos    Pedro Jarès    Himmelbaue Heinz    Silvia Bea    Samuel Aparicio    Douglas Easton    弗朗西斯·柯林斯    Compton    Eric Steven Lander    Wylie Burke    Anthony richard Green    Stanley Hamilton    Olli pekka Kallioniemi -    Timothy Ley    Edison tak bun Liu    Brandon Wainwright   

Nature

2010

Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exornes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which represent strong candidates for altitude adaptation, were identified. The strongest signal of natural selection came from endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia. One single-nucleotide polymorphism (SNP) at EPASl shows a 78% frequency difference between Tibetan and Han samples, representing the fastest allele frequency change observed at any human gene to date. This SNP's association with erythrocyte abundance supports the role of EPASl in adaptation to hypoxia. Thus, a population genomic survey has revealed a functionally important locus in genetic adaptation to high altitude. Copyright 2010 by the American Association for the Advancement of Science; all rights reserved.

Xin Yi    Liang Yu    Emilia Huerta-Sánchez    Xin Jin    Cuo Zha Xi Ping    Pool John E.    Xu    Hui Jiang    Nicolas Vinckenbosch    Thorfinn sand Korneliussen    Hancheng Zheng    Liu Tao    Weiming He    Kui Li    Ruibang Luo    Nie Xifang    Wu Honglong    Zhao Meiru    Hongzhi Cao    Zou Jing    Shan Ying    Li Shuzheng    Yang Qi    Asan    Peixiang Ni    Geng Tian    Xu Junming    Xiao Liu    Jiang Tao    Renhua Wu    Guangyu Zhou    Tang Meifang    Junjie Qin    Wang Tong    Feng Shuijian    Li Guohong    Huasang    Luosang Jiangbai    Wang Wei    Chen Fang    Wang Yading    Zheng Xiaoguang    Zhuo Li    Bianba Zhuoma    Yang Ge    Wang Xinping    Tang Shuhui    Gao Guoyi    Chen Yong    Luo Zhen    Gusang Lamu    Cao Zheng    Qinghui Zhang    Ouyang Weihan    Xiaoli Ren    Huiqing Liang    Huisong Zheng    Huang Yebo    Jingxiang Li    Lars Bolund    Karsten Kristiansen    李英睿    Zhang    Xiuqing Zhang    李瑞强    Songgang Li    杨焕明     Rasmus wedel Nielsen    Jun Wang    Wang   

Science

2010

Background: With the advent of second-generation sequencing, the expression of gene transcripts can be digitally measured with high accuracy. The purpose of this study was to systematically profile the expression of both mRNA and miRNA genes in clear cell renal cell carcinoma (ccRCC) using massively parallel sequencing technology. Methodology: The expression of mRNAs and miRNAs were analyzed in tumor tissues and matched normal adjacent tissues obtained from 10 ccRCC patients without distant metastases. In a prevalence screen, some of the most interesting results were validated in a large cohort of ccRCC patients. Principal Findings: A total of 404 miRNAs and 9,799 mRNAs were detected to be differentially expressed in the 10 ccRCC patients. We also identified 56 novel miRNA candidates in at least two samples. In addition to confirming that canonical cancer genes and miRNAs (including VEGFA, DUSP9 and ERBB4; miR-210, miR-184 and miR-206) play pivotal roles in ccRCC development, promising novel candidates (such as PNCK and miR-122) without previous annotation in ccRCC carcinogenesis were also discovered in this study. Pathways controlling cell fates (e.g., cell cycle and apoptosis pathways) and cell communication (e.g., focal adhesion and ECM-receptor interaction) were found to be significantly more likely to be disrupted in ccRCC. Additionally, the results of the prevalence screen revealed that the expression of a miRNA gene cluster located on Xq27.3 was consistently downregulated in at least 76.7% of ~50 ccRCC patients. Conclusions: Our study provided a two-dimensional map of the mRNA and miRNA expression profiles of ccRCC using deep sequencing technology. Our results indicate that the phenotypic status of ccRCC is characterized by a loss of normal renal function, downregulation of metabolic genes, and upregulation of many signal transduction genes in key pathways. Furthermore, it can be concluded that downregulation of miRNA genes clustered on Xq27.3 is associated with ccRCC. © 2010 Zhou et al.

Zhou Liang    Chen Jiahao    Li Zhizhong    Xianxin Li    Xueda Hu    Yi Huang    Xiaokun Zhao    Chaozhao Liang    Yonggang Wang    Sun Liang    Min Shi    Xiaohong Xü    Shen Feng    Maoshan Chen    Han Zujing    Zhiyu Peng    Zhai Qingna    Jing Chen    Zhang Zhongfu    Yang Ruilin    Jiongxian Ye    Guan Zhichen    杨焕明     桂耀庭    Jun Wang    Zhiming Cai    Xiuqing Zhang   

PLoS ONE

2010

The alternative synonymous codons in Corynebacterium glutamicum, a well-known bacterium used in industry for the production of amino acid, have been investigated by multivariate analysis. As C. glutamicum is a GC-rich organism, G and C are expected to predominate at the third position of codons. Indeed, overall codon usage analyses have indicated that C and/or G ending codons are predominant in this organism. Through multivariate statistical analysis, apart from mutational selection, we identified three other trends of codon usage variation among the genes. Firstly, the majority of highly expressed genes are scattered towards the positive end of the first axis, whereas the majority of lowly expressed genes are clustered towards the other end of the first axis. Furthermore, the distinct difference in the two sets of genes was that the C ending codons are predominate in putatively highly expressed genes, suggesting that the C ending codons are translationally optimal in this organism. Secondly, the majority of the putatively highly expressed genes have a tendency to locate on the leading strand, which indicates that replicational and transciptional selection might be invoked. Thirdly, highly expressed genes are more conserved than lowly expressed genes by synonymous and nonsynonymous substitutions among orthologous genes fromthe genomes of C. glutamicum and C. diphtheriae. We also analyzed other factors such as the length of genes and hydrophobicity that might influence codon usage and found their contributions to be weak. © 2010 Guiming Liu et al.

Qiyu Bao    Liu Guiming    Jinyu Wu    杨焕明    

Comparative and Functional Genomics

2010

The YH database is a server that allows the user to easily browse and download data from the first Asian diploid genome. The aim of this platform is to facilitate the study of this Asian genome and to enable improved organization and presentation large-scale personal genome data. Powered by GBrowse, we illustrate here the genome sequences, SNPs, and sequencing reads in the MapView. The relationships between phenotype and genotype can be searched by location, dbSNP ID, HGMD ID, gene symbol and disease name. A BLAST web service is also provided for the purpose of aligning query sequence against YH genome consensus. The YH database is currently one of the three personal genome database, organizing the original data and analysis results in a user-friendly interface, which is an endeavor to achieve fundamental goals for establishing personal medicine. The database is available at http://yh.genomics.org. © 2008 The Author(s).

Guoqing Li    Lijia Ma    Song Chao    Yang Zhentao    Wang Xiulan    Huang Hui    李英睿    李瑞强    Xiuqing Zhang    杨焕明     Wang    Jun Wang   

Nucleic Acids Research

2009

Background: DNA methylation is a widely studied epigenetic mechanism known to correlate with gene repression and genomic stability. Development of sensitive methods for global detection of DNA methylation events is of particular importance. Results: We here describe a technique, called modified methylation-specific digital karyotyping (MMSDK) based on methylation-specific digital karyotyping (MSDK) with a novel sequencing approach. Briefly, after a tandem digestion of genomic DNA with a methylation-sensitive mapping enzyme and a fragmenting enzyme, short sequence tags are obtained. These tags are amplified, followed by direct, massively parallel sequencing (Solexa 1G Genome Analyzer). This method allows high-throughput and low-cost genome-wide DNA methylation mapping. We applied this method to investigate global DNA methylation profiles for widely used breast cancer cell lines, MCF-7 and MDA-MB-231, which are representatives for luminal-like and mesenchymal-like cancer types, respectively. By comparison, a highly similar overall DNA methylation pattern was revealed for the two cell lines. However a cohort of individual genomic loci with significantly different DNA methylation status between two cell lines was identified. Furthermore, we revealed a genome-wide significant correlation between gene expression and the methylation status of gene promoters with CpG islands (CGIs) in the two cancer cell lines, and a correlation of gene expression and the methylation status of promoters without CGIs in MCF-7 cells. Conclusion: The MMSDK method will be a valuable tool to increase the current knowledge of genome wide DNA methylation profiles. © 2009 Li et al; licensee BioMed Central Ltd.

Jian Li    Gao Fei    Ning Li    Shengting Li    Guangliang Yin    Geng Tian    Jia Shan'gang    Wang Kai    Xiuqing Zhang    杨焕明     Nielsen Anders Lade    Lars Bolund   

BMC Genomics

2009

A single-base pair resolution silkworm genetic variation map was constructed from 40 domesticated and wild silkworms, each sequenced to approximately threefold coverage, representing 99.88% of the genome. We identified ∼16 million single-nucleotide polymorphisms, many indels, and structural variations. We find that the domesticated silkworms are clearly genetically differentiated from the wild ones, but they have maintained large levels of genetic variability, suggesting a short domestication event involving a large number of individuals. We also identified signals of selection at 354 candidate genes that may have been important during domestication, some of which have enriched expression in the silk gland, midgut, and testis. These data add to our understanding of the domestication processes and may have applications in devising pest control strategies and advancing the use of silkworms as efficient bioreactors.

Qingyou Xia    Guo Y.    Ze Zhang    Li    Xuan Zhaoling    Zhuo Li    Fangyin Dai    李英睿    Daojun Cheng    李瑞强    Tingcai Cheng    Jiang Tao    Becquet Celine    许迅    Chun Liu    Zha Xingfu    Wei Fan    林影    Yihong Shen    Jiang Lan    Jeffrey Jensen    Ines Hellmann    Tang Si    Ping Zhao    Hanfu Xu    Chang Yu    Guo jie Zhang    Li Jun    Cao Jianjun    Shiping Liu    Ningjia He    Yan Zhou    Liu Hui    Zhao Jing    Chen Ye    Du Zhouhe    Guoqing Pan    Zhao Aichun    Shao Haojing    Zeng Wei    Ping Wu    Chunfeng Li    Pan Minimi    Li Jingjing    Yin Xuyang    李大伟    Juan Wang    Huisong Zheng    Wen Wang    Xiuqing Zhang    Songgang Li    杨焕明     Cheng Lu    Rasmus wedel Nielsen    Zhou Zeyang    汪建    向仲怀    Jun Wang   

Science

2009

Cucumber is an economically important crop as well as a model system for sex determination studies and plant vascular biology. Here we report the draft genome sequence of Cucumis sativus var. sativus L., assembled using a novel combination of traditional Sanger and next-generation Illumina GA sequencing technologies to obtain 72.2-fold genome coverage. The absence of recent whole-genome duplication, along with the presence of few tandem duplications, explains the small number of genes in the cucumber. Our study establishes that five of the cucumber's seven chromosomes arose from fusions of ten ancestral chromosomes after divergence from Cucumis melo. The sequenced cucumber genome affords insight into traits such as its sex expression, disease resistance, biosynthesis of cucurbitacin and 'fresh green' odor. We also identify 686 gene clusters related to phloem function. The cucumber genome provides a valuable resource for developing elite cultivars and for studying the evolution and function of the plant vascular system. © 2009 Nature America, Inc. All rights reserved.

Sanwen Huang    李瑞强    Zhonghua Zhang    Li Li    Xingfang Gu    Wei Fan    Lucas William J.    Xiaowu Wang    Xie Bingyan    Peixiang Ni    Ren Yuanyuan    Hongmei Zhu    Jun Li    Kui Lin    Weiwei Jin    费章君    Li Guangcun    Staub Jack    Kilian Andrzej    Edwin andries gerard Van Der Vossen    Wu Yang    Jie Guo    He Jun    Jia Zhiqi    Yi Ren    Geng Tian    Yao Lu    Jue Ruan    Qian Wubin    Wang Mingwei    Huang Quanfei    Bo li    Xuan Zhaoling    Cao Jianjun    Asan    Wu Zhigang    Zhang Juanbin    Qingle Cai    Bai Yinqi    Zhao Bowen    Han Yonghua    Li Ying    Li Xuefeng    Wang Shenhao    Shi Qiuxiang    Liu Shiqiang    Cho Won Kyong    Kim Jae-Yean    徐勇    Heller-Uszynska Katarzyna    Miao Han    Cheng Zhouchao    Zhang Shengping    Jian Wu    Yang Yuhong    Kang Houxiang    Li Man    Huiqing Liang    Xiaoli Ren    Shi Zhongbin    Wen Ming    Min Jian    Yang Hailong    Guo jie Zhang    Yang Zhentao    Rui Chen    Liu Shifang    Li Jianwen    Lijia Ma    Liu Hui    Yan Zhou    Zhao Jing    Xiaodong Fang    Guoqing Li    方林    李英睿    Dongyuan Liu    Hongkun Zheng    Zhang    Nan Qin    Zhuo Li    Yang Guohua    Yang Shuang    Lars Bolund    Karsten Kristiansen    Hancheng Zheng    Li Shaochuan    Xiuqing Zhang    杨焕明     汪建    孙日飞    Zhang Baoxi    Jiang Shuzhi    Jun Wang    Yongchen Du    Songgang Li   

Nature Genetics

2009

Many studies have suggested that adenosine diphosphate ribosyl transferase (ADPRT), X-ray repair cross-complementing 1 (XRCC1), and xeroderma pigmentosum complementary group D (XPD) are three major DNA base excision repair (BER) genes and that they act interactively in stimulating and executing BER processes. Polymorphisms of these genes may influence the rate of gene transcription, the stability of the messenger RNA, or the quantity and activity of the resulting protein. Thus, the susceptibility or severity of several disorders is influenced by possession of specific alleles of polymorphic genes. So, it is plausible that variations and mutations in these genes affect DNA repair capacity in normal populations, and thus facilitate cancer development in normal or exposed individuals. To promote translation of scientific findings for potential clinical application of DNA repair function, we have searched publications relevant to molecular epidemiology studies of associations between single-nucleotide polymorphisms (SNPs) in the genes, and several frequent human cancer. We have focused on five particular polymorphisms as our starting point: the T→C polymorphism (Val762Ala) in exon 17 of ADPRT, the novel transition at the promoter region (-77T→C) of XRCC1, two common nonsynonymous polymorphisms (Arg194Trp and Arg399Gln), and the C→A silent polymorphism (Arg156Arg) in exon 6 of XPD. We review here the case-control studies examining whether these polymorphisms are correlated with reduced DNA repair efficiency, their influence on the development of different solid tumors, and their possible interactions with other genetic factors and environmental exposures. © 2009 Humana Press.

Jun Jiang    Xiuqing Zhang    杨焕明     Wang Wendy   

Methods in Molecular Biology

2009