Ma Tao Wang Junyi Zhou Gongke Yue Zhen Hu Quanjun Chen Yan Liu Bingbing Qiang Qiu 王卓 Zhang Jian Wang Kun Jiang Dechun Gou Caiyun Yu Lili Zhan Dongliang Zhou Ran Luo Wenchun Hui Ma Yang Yongzhi Shengkai Pan Fang Dongming Yadan Luo Wang Xia Wang Gaini Wang Juan Wang Qian Lu Xu Chen Zhe Liu Jinchao Yao Lu Ye Yin 杨焕明 Richard Abbott Wu Yuxia Wan Dongshi Li Jia Tongming Yin Lascoux Martin DiFazio Stephen P. Gerald Tuskan Liu Jianquan
Nature Communications
2014
Oesophageal cancer is one of the most aggressive cancers and is the sixth leading cause of cancer death worldwide. Approximately 70% of global oesophageal cancer cases occur in China, with oesophageal squamous cell carcinoma (ESCC) being the histopathological form in the vast majority of cases (>90%). Currently, there are limited clinical approaches for the early diagnosis and treatment of ESCC, resulting in a 10% five-year survival rate for patients. However, the full repertoire of genomic events leading to the pathogenesis of ESCC remains unclear. Here we describe a comprehensive genomic analysis of 158 ESCC cases, as part of the International Cancer Genome Consortium research project. We conducted whole-genome sequencing in 17 ESCC cases and whole-exome sequencing in 71 cases, of which 53 cases, plus an additional 70 ESCC cases not used in the whole-genome and whole-exome sequencing, were subjected to array comparative genomic hybridization analysis. We identified eight significantly mutated genes, of which six are well known tumour-associated genes (TP53, RB1, CDKN2A, PIK3CA, NOTCH1, NFE2L2), and two have not previously been described in ESCC (ADAM29 and FAM135B). Notably, FAM135B is identified as a novel cancer-implicated gene as assayed for its ability to promote malignancy of ESCC cells. Additionally, MIR548K, a microRNA encoded in the amplified 11q13.3-13.4 region, is characterized as a novel oncogene, and functional assays demonstrate that MIR548K enhances malignant phenotypes of ESCC cells. Moreover, we have found that several important histone regulator genes (MLL2 (also called KMT2D), ASH1L, MLL3 (KMT2C), SETD1B, CREBBP and EP300) are frequently altered in ESCC. Pathway assessment reveals that somatic aberrations are mainly involved in the Wnt, cell cycle and Notch pathways. Genomic analyses suggest that ESCC and head and neck squamous cell carcinoma share some common pathogenic mechanisms, and ESCC development is associated with alcohol drinking. This study has explored novel biological markers and tumorigenic pathways that would greatly improve therapeutic strategies for ESCC. © 2014 Macmillan Publishers Limited.
Song Yongmei Li Lin Ou Yun-wei Zhibo Gao Enmin Li Xiangchun Li Zhang Weimin Wang Jiaqian Liyan Xu Zhou Yong Ma Xiaojuan Liu Lingyan Zhao Zitong Huang Xuanlin Fan Jing Lijia Dong Chen Gang Ma Liying Yang Jie Longyun Chen Minghui He Miao Li Zhuang Xuehan Huang Kai Qiu Kunlong Yin Guangliang Guangwu Guo Qiang Feng Chen Peishan Zhiyong Wu Wu Jianyi Ma Ling Zhao Jinyang Luo Longhai Fu Ming Bainan Xu Chen Bo 李英睿 Tong Tong Wang Mingrong Zhihua Liu 林东昕 Xiuqing Zhang 杨焕明 王俊 詹启敏
Nature
2014
A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved.
Delaneau Olivier Marchini Jonathan McVeanh Gil A. Peter Donnelly Gerton Lunter Jonathan Marchini Simon Myers Gupta-Hinch Anjali Zamin Iqbal Iain Mathieson Andy Rimmer Dionysia kiara Xifara Kerasidou Angeliki Claire Churchhouse David Altshuler Stacey bolk Gabriel Eric Lander Namrata Gupta Mark Daly Mark DePristo Eric Banks Gaurav Bhatia Mauricio Carneiro Del Angel Guillermo Giulio Genovese Robert Handsaker Christopher Hartl Steven McCarroll James Nemesh Ryan Poplin Stephen Schaffner Khalid Shakir Pardis Sabeti Sharon Grossman Shervin Tabrizi Ridhi Tariyal Li Heng David Reich Richard Durbin Matthew Hurles Senduran Balasubramaniam John Burton Petr Danecek Keane Anja Kolb-Kokocinski McCarthy Shane E. Jim Stalker Michael Quail Ayub Qasim Yuan Chen Coffey Alison J. Colonna Vincenza Ni Huang Luke Jostins Aylwyn Scally Klaudia ho Walter Xue Yali Yujun Zhang Benjamin Blackburne Sarah Lindsay Zemin Ning Adam Frankish Jennifer Harrow Chris Tyler -S. Gonçalo Abecasis Hyunmin Kang Anderson Paul Thomas Blackwell Busonero Fabio Fuchsberger Christian Goo Jun Andrea Maschio Porcu Eleonora Carlo Sidore Tan Adrian Trost Mary Kate David Bentley Russell james Grocock Sean Humphray Terena James Zoya Kingsbury Markus Bauer Keira Cheetham Tony Cox Michael Eberle Lisa Murray Richard Shaw Aravinda Chakravarti Andrew Clark Alon Keinan Rodriguez-Flores Juan L. De LaVega Francisco M. Jeremiah Degenhardt Evan Eichler Paul Flicek Laura Clarke Rasko Leinonen Richard Smith Xiangqun Zheng-Bradley Kathryn Beal Fiona Cunningham Javier Herrero William McLaren Graham rs Ritchie Jonathan Barker Kelman Gavin Eugene Kulesha Rajesh Radhakrishnan Roa Asier Dmitriy Smirnov Ian Streeter Iliana Toneva Richard Gibbs Huyen Dinh Christie Kovář C Sandra Lee Lora Lewis Donna marie Muzny Reid Jeff Wang Min Fuli Yu Matthew Bainbridge Daniel Challis Uday Evani Lu James T. Uma Nagaswamy Aniko Sabo Wang Yi Jin Yu Gerald Fowler Walker Hale Divya Kalra Eric Green Bartha maria Knoppers Jan Korbel Tobias Rausch Sttz Adrian M. Charles Lee Griffin Lauren Hsieh Chih-Heng Ryan Mills Marcin Von Grotthuss Zhang Chengsheng Xinghua Shi Lehrach Hans Ralf Sudbrak Vyacheslav Amstislavskiy Matthias Lienhard Florian Mertes Marc Sultan Timmermann Bernd Yaspo Marie-Laure Herwig Sudbrak Ralf Elaine Mardis Wilson Richard K. Lucinda Fulton Robert Fulton George Weinstock Asif Chinwalla Ding Li David Dooling Daniel Koboldt Michael McLellan John Wallis Michael Wendl Qunyuan Zhang Gábor Marth Erik Garrison Deniz Kural Wanping Lee Leong Wen Fung Alistair Ward Jiantao Wu Zhang Mengyao Deborah Nickerson Can Alkan Fereydoun Hormozdiari Arthur Ko Peter Sudmant Jeanette Schmidt Davies Christopher J. Jeremy Gollub Teresa Webster Wong Brant Yiping Zhan Stephen Sherry Xiao Chunlin Deanna Church Ananiev Victor Belaia Zinaida Beloslyudtsev Dimitriy Nathan Bouk Chen Chao Cohen Robert F. Cook Charles John Garner Hefferon Timothy Kimelman Mikhail Liu Chunlei John Lopez Meric Peter Ostapchuk Yuri Phan Lon Ponomarov Sergiy Valerie Schneider Shekhtman Eugene Karl Sirotkin Douglas Slotta Zhang Hua 王俊 Xiaodong Fang Xiaosen Guo Min Jian Jiang Hui Jin Xin Li Guoqing Jingxiang Li Yingrui Li Xiao Liu Yao Lu Ma Xuedi Shuaishuai Tai Tang Meifang Wang Bo Guangbiao Wang Wu Honglong Renhua Wu Ye Yin Wenwei Zhang Zhao Jiao Zhao Meiru Zheng Xiaole Lachlan Hans Fang Lin Qibin Li Zhenyu Li Lin Haoxiang Liu Binghang Ruibang Luo Shao Haojing Wang Bingqiang Yinlong Xie Ye Chen Chang Yu Hancheng Zheng Zhu Hongmei Cai Hongyu Hongzhi Cao Yeyang Su Tian Zhongming 杨焕明 Yang Ling Zhu Jiayong Cai Zhiming Jian Wang Marcus Albrecht Tatiana Borodina Adam Auton Yoon Seungtai C. Lihm Jayon Makarov Vladimir Jin Hanjun Kim Wook Kim Ki Cheol Srikanth Gottipati Jones Danielle David Cooper Edward Ball Peter Stenson Bret Barnes Scott Kahn Kai Ye Batzer Mark A. Miriam Konkel Jerilyn Walker Daniel MacArthur Monkol Lek Mark Shriver Carlos Bustamante Simon pierre Gravel Kenny Eimear E. Jeffrey Kidd Phil Lacroute Brian Maples Andrés Moreno-Estrada Fouad Zakharia Brenna Henn Karla Sandoval Jake Byrnes Eran Halperin Yael Baran David Craig Alexis Christoforides Tyler Izatt Ahmet Kurdoglu Shripad Sinari Nils Homer Kevin Squire Jonathan Sebat Vineet Bafna Kenny Ye Burchard Esteban G. Ryan Hernandez Gignoux Christopher David Haussler Sol Katzman William james Kent Bryan Howie Andrés Ruíz-Linares Emmanouil t Dermitzakis Tuuli Lappalainen Devine Scott E. Liu Xinyue Maroo Ankit Luke Tallon Jeffrey Rosenfeld Michelson Leslie P. Angius Andrea Francesco Cucca Serena Sanna Abigail Bigham Jones Chris G. Reinier Frederic Yun Li Robert Lyons Schlessinger David Philip Awadalla Alan Hodgkinson Taras Oleksyk Juan carlos Martínez-Cruzado 符云新 Xiaoming Liu Xiong Momiao Lynn Jorde Witherspoon David J. Jinchuan Xing Brian Browning Iman Hajirasouliha Ken Chen Cornelis Albers Mark Gerstein Alexej Abyzov Jieming Chen Yao Fu Lukas Habegger Arif ozgun Harmanci Xinmengjasmine Mu Cristina Sisu Suganthi Balasubramanian Mike Jin Ekta Khurana Declan Clarke Jacob Michaelson OSullivan Chris Kathleen carole Barnes Neda Gharani Lorraine Toji Gerry Norman P. Jane Kaye Alastair Kent Rasika ann Mathias Pilar Ossorio Michael Parker Charles Rotimi Charmaine Royal Sarah Tishkoff Via Marc Walter Bodmer Bedoya Gabriel Yang Gao You Chu Jia Garcia-Montero Andrés Alberto Orfao Dutil Julie Lisa Brooks Adam Felsenfeld Jean McEwen Clemm Nicholas C. Mark Guyer Jane Peterson Audrey Duncanson Dunn Michael Leena johanna Peltonen
Nature Communications
2014
Primary renal cell carcinomas (pRCCs) have a high degree of intratumoral heterogeneity and are composed of multiple distinct subclones. However, it remains largely unknown that whether metastatic renal cell carcinomas (mRCCs) also have startling intratumoral heterogeneity or whether development of mRCCs is due to early dissemination or late diagnosis. To decipher the evolution of mRCC, we analyzed the multilayered molecular profiles of pRCC, local invasion of the vena cava (IVC), and distant metastasis to the brain (MB) from the same patient using whole-genome sequencing, whole-exome sequencing, DNA methylome profiling, and transcriptome sequencing. We found that mRCC had a lower degree of heterogeneity than pRCC and was likely to result from recent clonal expansion of a rare, advantageous subclone. Consequently, some key pathways that are targeted by clinically available drugs showed distinct expression patterns between pRCC and mRCC. From the genetic distances between different tumor subclones, we estimated that the progeny subclone giving rise to distant metastasis took over half a decade to acquire the full potential of metastasis since the birth of the subclone that evolved into IVC. Our evidence supported that mRCC was monoclonal and distant metastasis occurred late during renal cancer progression. Thus, there was a broad window for early detection of circulating tumor cells and future targeted treatments for patients with mRCCs should rely on the molecular profiles of metastases. What's new? While much is known about the intratumoral heterogeneity of primary renal cell carcinomas, the clonal composition of metastatic tumors remains unclear. To explore whether metastatic renal cell carcinomas stem from early dissemination or late diagnosis, the authors characterized the genetic, epigenetic and transcriptional profiles of multiple metastatic tumors from the same patient. They show that the metastatic tumor itself has a low degree of intratumoral heterogeneity, but likely results from the recent clonal expansion of a rare, advantageous subclone arising late within the primary tumor. This study highlights the therapeutic potential of early detection and molecular profiling of metastatic kidney tumors. © 2013 UICC.
Yi Huang Gao Shengjie Song Wu Song Pengfei Xiaojuan Sun Xueda Hu Zhang Shiqiang Yu Yuan Zhu Jialou Li Cailing Qin Zi-Ke Xie Liangfu Yao Qiong Aifa Tang Zesong Li Guangwu Guo Wan Shengqing Pei Dong Sun Liang Li Weiping Daping Wang 桂耀庭 杨焕明 Zhou Fang-Jian Xiuqing Zhang Zhiming Cai
International Journal of Cancer
2014
Background The A561C polymorphism of the E-selectin gene (SELE) has been reported to be associated with essential hypertension (EH) in several studies; however, results among these studies were inconsistent. Here, we conducted a meta-analysis to explore the association of the A561C polymorphism with EH. Methods Publications were retrieved through searching PubMed, Web of Science, the China National Knowledge Infrastructure (CNKI), China Biological Medicine, and the Wanfang database. Odds ratios (OR) and 95 % confidence intervals (CI) were calculated to estimate the strength of association of A561C with EH. Subgroup analysis was also performed to assess ethnic discrepancies. A total of seven studies comprising 2,127 EH patients and 2,078 controls were analyzed. Results In the dominant model analysis, we found significant associations between the A561C polymorphism and EH in all subjects (CC+AC vs. AA, OR = 1.96, 95 %CI 1.57-2.44, P = 0.381), in a Han Chinese subgroup (CC+AC vs. AA, OR = 2.38, 95 %CI 1.73-3.29, P = 0.269), and in non-Han Chinese minorities (CC+AC vs. AA, OR = 1.62, 95 %CI 1.19-2.21, P = 0.84). Conclusion The findings suggest that C allele carriers of the SELE gene polymorphism (A561C) might be predisposed to EH in the Chinese population. Further investigations in other ethnic populations should be conducted to verify these findings. © 2014 Urban & Vogel.
Ouyang Wu Aihua Tan 杨焕明 Gao Li Hongfan Lu Hu Yanlin Tang Haiying Zhang
Herz
2014
A single Mendelian trait has been mapped to the human Y chromosome: Y-linked hearing impairment. The molecular basis of this disorder is unknown. Here, we report the detailed characterization of the DFNY1 Y chromosome and its comparison with a closely related Y chromosome from an unaffected branch of the family. The DFNY1 chromosome carries a complex rearrangement, including duplication of several noncontiguous segments of the Y chromosome and insertion of ∼160 kb of DNA from chromosome 1, in the pericentric region of Yp. This segment of chromosome 1 is derived entirely from within a known hearing impairment locus, DFNA49. We suggest that a third copy of one or more genes from the shared segment of chromosome 1 might be responsible for the hearing-loss phenotype. © 2013 The American Society of Human Genetics.
Wang Qiu-Ju Yali Xue Yujun Zhang 龙泉 Fengtang Yang Turner Daniel J. Tomas Fitzgerald Ng Yali Zhao Yuan Chen Liu Qing-Jie Yang Han Dongyi Michael Quail Swerdlow Harold P. John Burton Fahey Ciara Zemin Ning Matthew Hurles Nigel Carter 杨焕明 Chris Tyler-Smith
American Journal of Human Genetics
2013
The human gut microbiota is a reservoir of antibiotic resistance genes, but little is known about their diversity and richness within the gut. Here we analyse the antibiotic resistance genes of gut microbiota from 162 individuals. We identify a total of 1,093 antibiotic resistance genes and find that Chinese individuals harbour the highest number and abundance of antibiotic resistance genes, followed by Danish and Spanish individuals. Single-nucleotide polymorphism-based analysis indicates that antibiotic resistance genes from the two European populations are more closely related while the Chinese ones are clustered separately. We also confirm high abundance of tetracycline resistance genes with this large cohort study. Our study provides a broad view of antibiotic resistance genes in the human gut microbiota. © 2013 Macmillan Publishers Limited. All rights reserved.
Yongfei Hu Xi Yang Junjie Qin Na Lu Gong Cheng Wu Na Pan Yuanlong Jing Li Liying Zhu Xin Wang MENG Zhi-qi 赵方庆 刘翟 Ma Juncai Nan Qin Xiang Chunsheng Yonghong Xiao 李兰娟 杨焕明 Jian Wang Ruifu Yang 高福 Jun Wang Baoli Zhu
Nature Communications
2013
Human utilization of the mulberry-silkworm interaction started at least 5,000 years ago and greatly influenced world history through the Silk Road. Complementing the silkworm genome sequence, here we describe the genome of a mulberry species Morus notabilis. In the 330-Mb genome assembly, we identify 128 Mb of repetitive sequences and 29,338 genes, 60.8% of which are supported by transcriptome sequencing. Mulberry gene sequences appear to evolve ∼3 times faster than other Rosales, perhaps facilitating the species' spread worldwide. The mulberry tree is among a few eudicots but several Rosales that have not preserved genome duplications in more than 100 million years; however, a neopolyploid series found in the mulberry tree and several others suggest that new duplications may confer benefits. Five predicted mulberry miRNAs are found in the haemolymph and silk glands of the silkworm, suggesting interactions at molecular levels in the plant-herbivore relationship. The identification and analyses of mulberry genes involved in diversifying selection, resistance and protease inhibitor expressed in the laticifers will accelerate the improvement of mulberry plants.
Ningjia He Zhang Chi Qi Xiwu Shancen Zhao 陶勇 Yang Guojun Taeho Lee Xiyin Wang Qingle Cai Dong Li Mengzhu Lu 廖森泰 Luo Guoqing He Rongjun Tan Xu Xu Yunmin Tian Li Zhao Aichun Jia Ling Fu Qiang Zeng Qiwei Gao Chuan Ma Bi Liang Jiubo Wang Xiling Shang Jingzhe Song Penghua Wu Hai-Yang Fan Li Wang Qing Shuai Qin Zhu Juanjuan Wei Congjin 朱克岩 Jin Dianchuan Wang Jinpeng Liu Tao Yu Maode Tang Cuiming Wang Zhenjiang Dai Fanwei Chen Jiafei Liu Yan Zhao Shutang Tianbao Lin 张守攻 Junyi Wang Jian Wang 杨焕明 Yang Guangwei Andrew Paterson Qingyou Xia Dongfeng Ji 向仲怀
Nature Communications
2013
Despite the high economic and ecological importance of forests, our knowledge of the genomic evolution of trees under salt stress remains very limited. Here we report the genome sequence of the desert poplar, Populus euphratica, which exhibits high tolerance to salt stress. Its genome is very similar and collinear to that of the closely related mesophytic congener, P. trichocarpa. However, we find that several gene families likely to be involved in tolerance to salt stress contain significantly more gene copies within the P. euphratica lineage. Furthermore, genes showing evidence of positive selection are significantly enriched in functional categories related to salt stress. Some of these genes, and others within the same categories, are significantly upregulated under salt stress relative to their expression in another salt-sensitive poplar. Our results provide an important background for understanding tree adaptation to salt stress and facilitating the genetic improvement of cultivated poplars for saline soils. © 2013 Macmillan Publishers Limited. All rights reserved.
Wang Jun Ma Tao Junyi Wang Zhou Gongke Yue Zhen Hu Quanjun Chen Yan Liu Bingbing Qiang Qiu 王卓 Zhang Jian Wang Kun Jiang Dechun Gou Caiyun Yu Lili Zhan Dongliang Zhou Ran Luo Wenchun Hui Ma Yang Yongzhi Shengkai Pan Fang Dongming Yadan Luo Wang Xia Wang Gaini Wang Juan Wang Qian Lu Xu Chen Zhe Liu Jinchao Yao Lu Ye Yin 杨焕明 Richard Abbott Wu Yuxia Wan Dongshi Li Jia Tongming Yin Lascoux Martin DiFazio Stephen P. Gerald Tuskan Jianquan Liu
Nature Communications
2013
Bladder cancer is one of the most common cancers worldwide, with transitional cell carcinoma (TCC) being the predominant form. Here we report a genomic analysis of TCC by both whole-genome and whole-exome sequencing of 99 individuals with TCC. Beyond confirming recurrent mutations in genes previously identified as being mutated in TCC, we identified additional altered genes and pathways that were implicated in TCC. Notably, we discovered frequent alterations in STAG2 and ESPL1, two genes involved in the sister chromatid cohesion and segregation (SCCS) process. Furthermore, we also detected a recurrent fusion involving FGFR3 and TACC3, another component of SCCS, by transcriptome sequencing of 42 DNA-sequenced tumors. Overall, 32 of the 99 tumors (32%) harbored genetic alterations in the SCCS process. Our analysis provides evidence that genetic alterations affecting the SCCS process may be involved in bladder tumorigenesis and identifies a new therapeutic possibility for bladder cancer.
Guangwu Guo Xiaojuan Sun 陈超 Wu Song Huang Peide Zesong Li Michael Dean Yi Huang Jia Wenlong Zhou Quan Aifa Tang Yang Zuoquan Xianxin Li Song Pengfei Xiaokun Zhao Rui Ye Zhang Shiqiang Lin Zhao Qi Mingfu Wan Shengqing Xie Liangfu Fan Fan Nickerson Michael L. Zou Xiangjun Xueda Hu Xing Li Lv Zhaojie Mei Hongbin Gao Shengjie Chaozhao Liang Zhibo Gao Lu Jingxiao Yu Yuan Liu Chunxiao Lin Li Xiaodong Fang Zhimao Jiang Yang Jie Li Cailing 赵鑫 Chen Jing 张芳 Lai Yongqi Lin Zheguang Zhou Fang-Jian Chen Hao Chan Hsiao Chang Tsang Shirley Dan Theodorescu 李英睿 Xiuqing Zhang Jian Wang 杨焕明 桂耀庭 王俊 Zhiming Cai
Nature Genetics
2013