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| 1 | Next-generation sequencing technology:A technology review and future perspective显示文摘As one of the most powerful tools in biomedical research,DNA sequencing not only has been improving its productivity at an exponential growth rate but has also been evolving into a new layout of technological territories toward engineering and physical disciplines over the past three decades.In this technical review,we look into technical characteristics of the next-generation sequencers and provide insights into their future development and applications.We envisage that some of the emerging platforms are capable of supporting the USD1000 genome and USD100 genome goals if given a few years for technical maturation.We also suggest that scientists from China should play an active role in this campaign that will have a profound impact on both scientific research and societal healthcare systems. | ZHOU XiaoGuang1,REN LuFeng1,LI YunTao2,ZHANG Meng1,YU YuDe2 & YU Jun1 1 Key Laboratory of Genome Sciences and Information,Beijing Institute of Genomics,Chinese Academy of Sciences,Beijing 100029,China 2 Institute of Semiconductors,Chinese Academy of Sciences,Beijing 100083,China | 2010 | Science China(Life Sciences)2010，53，1： | 27 |
| 2 | The Chrysanthemum nankingense Genome Provides Insights into the Evolution and Diversification of Chrysanthemum Flowers and Medicinal Traits显示文摘The Asteraceae (Compositae),a large plant family of approximately 24 000-35 000 species,accounts for^10% of all angiosperm species and contributes a lot to plant diversity.The most representative members of the Asteraceae are the economically important chrysanthemums (Chrysanthemum L.)that diversified through reticulate evolution.Biodiversity is typically created by multiple evolutionary mechanisms such as wholegenome duplication 0NGD)or polyploidization and locally repetitive genome expansion.However,the lack of genomic data from chrysanthemum species has prevented an in-depth analysis of the evolutionary mechanisms involved in their diversification.Here,we used Oxford Nanopore long-read technologyto sequence the diploid Chrysanthemum nankingense genome,which represents one of the progenitor genomes of domesticated chrysanthemums.Our analysis revealed that the evolution of the C.nankingense genome was driven by bursts of repetitive element expansion and WGD events including a recentWGD that distinguishes chrysanthemum from sunflower,which diverged from chrysanthemum approximately 38.8 million years ago.Variations of ornamental and medicinal traits in chrysanthemums are linked to the expansion of candidate gene families by duplication events including paralogous gene duplication.Collectively,our study of the assembled reference genome offers new knowledge and resources to dissect the history and pattern of evolution and diversification of chrysanthemum plants,and also to accelerate their breeding and improvement. | Chi Song Yifei Liu Aiping Song Gangqiang Dong Hongbo Zhao Wei Sun Shyam Ramakrishnan Ying Wang Shuaibin Wang Tingzhao Li Yan Niu Jiafu Jiang Bin Dong Ye Xia Sumei Chen Zhigang Hu Fadi Chen Shilin Chen | 2018 | Molecular Plant2018，11，12： | 24 |
| 3 | Genome sequencing of the perciform fish Larimichthys crocea provides insights into molecular and genetic mechanisms of stress adaptation显示文摘With the support by the National 863Project,National Natural Science Foundation of China,and National Basic Research Program of China,Prof.Chen Xinhua’s laboratory at the Key Laboratory of Marine Biogenetic Resources,Third Institute of Oceanography,State Oceanic Administration,reported the genome sequencing of the perciform fish Larimichthys crocea(L.crocea),which was published in PLOS Genetics(2015,11(4):e1005118). | | 2015 | Science Foundation in China2015，23，3： | 24 |
| 4 | Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement显示文摘Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A. hypogaea genome and compared it with the related diploid Arachis duranensis and Arachis ipaensis genomes. We annotated 39 888 A-subgenome genes and 41 526 B-subgenome genes in allotetraploid peanut. The A. hypogaea subgenomes have evolved asymmetrically, with the B subgenome resembling the ancestral state and the A subgenome undergoing more gene disruption, loss, conversion, and transposable element proliferation, and having reduced gene expression during seed development despite lacking genome-wide expression dominance. Genomic and transcriptomic analyses identified more than 2 500 oil metabolism-related genes and revealed that most of them show altered expression early in seed development while their expression ceases during desiccation, presenting a comprehensive map of peanut lipid biosynthesis. The availability of these genomic resources will facilitate a better understanding of the complex genome architecture, agronomically and economically important genes, and genetic improvement of peanut. | Xiaoping Chen Qing Lu Hao Liu Jianan Zhang Yanbin Hong Haofa Lan Haifen Li Jinpeng Wang Haiyan Liu Shaoxiong Li Manish K.Pandey Zhikang Zhang Guiyuan Zhou Jigao Yu Guoqiang Zhang Jiaqing Yuan Xingyu Li Shijie Wen Fanbo Meng Shanlin Yu Xiyin Wang Kadambot H.M.Siddique Zhong-Jian Liu Andrew H.Paterson Rajeev K.Varshney Xuanqiang Liang | 2019 | Molecular Plant2019，12，7： | 23 |
| 5 | APC and K-ras gene mutation in aberrant crypt foci of human colon显示文摘AIM To study the genetic alteration in ACF andto define the possibility that ACF may be a veryearly morphological lesion with molecularchanges, and to explore the relationshipbetween ACF and colorectal adenoma evencarcinoma.METHODS DNA from 35 CRC, 15 adenomas, 34ACF and 10 normal mucus was isolated by meansof microdissection. Direct gene sequencing of K-ras gene including codon 12, 13 and 61 as well asthe mutation cluster region (MCR) of APC genewas performed.RESULTS K-ras gene mutation frequency inACF, adenoma and carcinoma was 17.6% (6/34), 13.3% (2/ 15), and 14.3% (5/ 35)respectively, showing no difference ( P > 0.05)in K-fas gene mutation among three pathologicprocedures. The K-ras gene mutation inadenoma, carcinoma and 4 ACF restricted incodon 12 (GGT→GAT), but the other 2 mutationsfrom ACF located in codon 13 (GGC→GAC). K-res gene mutation was found more frequently inolder patients and patients with polypoidcancer. No mutation in codon 61 was found in thethree tissue types. Mutation rate of APO gene inadenoma and carcinoma was 22.9% (8/35) and26.7% (4/ 15), which was higher than ACF(2.9%) (P < 0.05). APC gene mutation incarcinoma was not correlated with age ofpatients, location, size and differentiation oftumor.CONCLUSION ACF might be a very earlymorphological lesion in the tumorogenesis ofcolorectal tumor. The morphological feature andgene mutation status was different in ACF andadenoma. ACF is possibly putative'microadenoma' that might be the precursor ofadenoma. In addition, the development of asubgroup of colorectal carcinomas mightundergo a way of 'normal epithelium→ ACF→carcinomas'. | Ping Yuan~1 Meng Hong Sun~2 Jin Sheng Zhang~1 Xiong Zeng Zhu~2 Da Ren Shi~2 ~1Department of Pathology,Medical College of Fudan University,~2Department of Pathology,Cancer Hospital/Cancer Institute,Fudan University,Shanghai 200032,ChinaDr.Ping Yuan Studying Province.studying in Medical College of Fudan University,worked in Department of Pathology,Wannan Medical College,having eighteen papers published. | 2001 | World Journal of Gastroenterology2001，7，3： | 20 |
| 6 | 温度对污水脱氮系统污染物去除效果及氧化亚氮释放的影响显示文摘污水生物脱氮过程是大气中的氧化亚氮(N2O)的一个重要来源.以anoxic-oxic sequencing batch reactors(A/O SBRs)工艺为研究对象,考察了5组不同温度(10、20、25、30、35℃)条件下系统的污染物去除效果和氧化亚氮释放情况.结果表明,温度对COD的去除无显著影响,但对氮素的去除有明显影响:在一定范围内,随温度的升高氮的去除率升高,但温度超过25℃后,随着温度的上升氮的去除效果下降;温度对氧化亚氮的释放量有重要影响,随温度的升高氧化亚氮的释放量逐渐降低[释放量(以MLSS计)依次为:530.1、260.8、218.3、104.7、57.7μg.g-1].对于A/O SBRs工艺,氧化亚氮的释放主要集中的好氧段,缺氧段几乎无氧化亚氮释放. | 张婷婷 张建 杨芳 谢慧君 胡振 李一冉 | 2012 | 环境科学2012，33，4： | 18 |
| 7 | Porous graphene:Properties,preparation,and potential applications显示文摘Graphene has recently emerged as an important and exciting material.Inspired by its outstanding properties,many researchers have extensively studied graphene-related materials both experimentally and theoretically.Porous graphene is a collection of graphene-related materials with nanopores in the plane.Porous graphene exhibits properties distinct from those of graphene,and it has widespread potential applications in various fields such as gas separation,hydrogen storage,DNA sequencing,and supercapacitors.In this review,we summarize recent progress in studies of the properties,preparation,and potential applications of porous graphene,and show that porous graphene is a promising material with great potential for future development. | XU PengTao YANG JiXiang WANG KeSai ZHOU Zhen SHEN PanWen | 2012 | Chinese Science Bulletin2012，57，23： | 18 |
| 8 | Values of circulating GPC-3 mRNA and alpha-fetoprotein in detecting patients with hepatocellular carcinoma显示文摘BACKGROUND: The prognosis of hepatocellular carcinoma (HCC) is poor and its early diagnosis is of the utmost importance. This study aimed to investigate the values of glypican-3 (GPC-3) expression in the liver and sera and its gene transcription for diagnosis and monitoring of metastasis of HCC. METHODS: Liver GPC-3 was analyzed in HCC tissues from 36 patients by immunohistochemistry and Western blotting. GPC-3 mRNA from circulating peripheral blood mononuclear cells from 123 HCC patients or 246 patients with other diseases or 36 HCC tissues was amplified by RT-PCR, quantitative realtime PCR, and confirmed by DNA sequencing. Circulating GPC-3 level was detected by ELISA. RESULTS: The increasing expression of GPC-3 was observed from non-cancerous to cancerous tissues, with brown granule-like staining localized in tumor parts of atypical hyperplasia and HCC formation. The positive rate of GPC-3 was 80.6% in HCC, 41.7% in their paracancerous tissues, and none in distal cancerous tissues (P<0.001), with no significant difference in differentiation grade and tumor number except for size (Z=2.941, P=0.003). Serum GPC-3 was detected only in HCC (52.8%) and significant difference was found between GPC-3 and tumor size (χ2 =6.318, P=0.012) or HBV infection (χ2 =23.362, P<0.001). Circulating GPC-3 mRNA was detected in 70.7% of HCC tissues, with relation to TNM stage, periportal cancerous embolus, and extra-hepatic metastasis (P<0.001). The combination ofcirculating GPC-3, GPC-3 mRNA and alpha-fetoprotein is of complementary value for HCC diagnosis (94.3%). CONCLUSION: Both GPC-3 overexpression and GPC-3 mRNA abnormality could be used as markers for the diagnosis of HCC and monitoring its metastasis. | Min Yao Deng-Fu Yao Yin-Zhu Bian Wei Wu Xiao-Di Yan Dan-Dan Yu Li-Wei Qiu Jun-Ling Yang Hai-Jian Zhang Wen-Li Sai Jie Chen | 2013 | Hepatobiliary & Pancreatic Diseases International2013，12，2： | 18 |
| 9 | Overexpression of insulin-like growth factor-Ⅰ receptor as a pertinent biomarker for hepatocytes malignant transformation显示文摘AIM:To investigate the dynamic features of insulinlike growth factor-Ⅰreceptor(IGF-ⅠR)expression in rat hepatocarcinogenesis,and the relationship between IGF-ⅠR and hepatocytes malignant transformation at mRNA or protein level.METHODS:Hepatoma models were made by inducing with 2-fluorenylacetamide(2-FAA)on male SpragueDawley rats.Morphological changes of hepatocytes were observed by pathological Hematoxylin and eosin staining,the dynamic expressions of liver and serum IGF-ⅠR were quantitatively analyzed by an enzymelinked immunosorbent assay.The distribution of hepatic IGF-ⅠR was located by immunohistochemistry.The fragments of IGF-ⅠR gene were amplified by reverse transcription-polymerase chain reaction,and confirmed by sequencing.RESULTS:Rat hepatocytes after induced by 2-FAA were changed dynamically from granule-like degeneration,precancerous to hepatoma formation with the progressing increasing of hepatic mRNA or IGF-ⅠR expression.The incidences of liver IGF-ⅠR,IGF-ⅠR mRNA,specific IGF-ⅠR concentration(ng/mg wet liver),and serum IGF-ⅠR level(ng/mL)were 0.0%,0.0%,0.63±0.17,and 1.33±0.47 in the control;50.0%,61.1%,0.65±0.2,and 1.51±0.46 in the degeneration;88.9%,100%,0.66±0.14,and 1.92±0.29 in the precancerosis;and 100%,100%,0.96±0.09,and2.43±0.57 in the cancerous group,respectively.IGF-ⅠR expression in the cancerous group was significantly higher(P<0.01)than that in any of other groups at mRNA or protein level.The closely positive IGF-ⅠR relationship was found between livers and sera(r=0.91,t=14.222,P<0.01),respectively.CONCLUSION:IGF-ⅠR expression may participate in rat hepatocarcinogenesis and its abnormality should be an early marker for hepatocytes malignant transformation. | Xiao-Di Yan Min Yao Li Wang Hai-Jian Zhang Mei-Juan Yan Xing Gu Yun Shi Jie Chen Zhi-Zhen Dong Deng-Fu Yao | 2013 | World Journal of Gastroenterology2013，19，36： | 16 |
| 10 | Chromosomal level assembly and population sequencing of the Chinese tree shrew genome显示文摘Chinese tree shrews (Tupaia belangeri chinensis) have become an increasingly important experimental animal in biomedical research due to their close relationship to primates. An accurately sequenced and assembled genome is essential for understanding the genetic features and biology of this animal. In this study, we used long-read single-molecule sequencing and high-throughput chromosome conformation capture (Hi-C) technology to obtain a high-qualitychromosome-scale scaffolding of the Chinese tree shrew genome. The new reference genome (KIZ version 2: TS_2.0) resolved problems in presently available tree shrew genomes and enabled accurate identification of large and complex repeat regions, gene structures, and species-specific genomic structural variants. In addition, by sequencing the genomes of six Chinese tree shrew individuals, we produced a comprehensive map of 12.8 M single nucleotide polymorphisms and confirmed that the major histocompatibility complex (MHC) loci and immunoglobulin gene family exhibited high nucleotide diversity in the tree shrew genome. We updated the tree shrew genome database (TreeshrewDB v2.0: http://gffzzb70c77447da74c53hvup9oxou5uv66un9.ffgz.tsg.suse.edu.cn) to include the genome annotation information and genetic variations. The new high-quality reference genome of the Chinese tree shrew and the updated TreeshrewDB will facilitate the use of this animal in many different fields of research. | Yu Fan Mao-Sen Ye Jin-Yan Zhang Ling Xu Dan-Dan Yu Tian-Le Gu Yu-Lin Yao Jia-Qi Chen Long-Bao Lv Ping Zheng Dong-Dong Wu Guo-Jie Zhang Yong-Gang Yao | 2019 | Zoological Research2019，40，6： | 15 |
| 11 | Perspectives of DNA microarray and next-generation DNA sequencing technologies显示文摘DNA microarray and next-generation DNA sequencing technologies are important tools for high-throughput genome research,in revealing both the structural and functional characteristics of genomes.In the past decade the DNA microarray technologies have been widely applied in the studies of functional genomics,systems biology and pharmacogenomics.The next-generation DNA sequencing method was first introduced by the 454 Company in 2003,immediately followed by the establishment of the Solexa and Solid techniques by other biotech companies.Though it has not been long since the first emergence of this technology,with the fast and impressive improvement,the application of this technology has extended to almost all fields of genomics research,as a rival challenging the existing DNA microarray technology.This paper briefly reviews the working principles of these two technologies as well as their application and perspectives in genome research. | TENG XiaoKun1 & XIAO HuaSheng1,2 1 National Engineering Center for Biochip at Shanghai,Shanghai 201203,China 2 Shanghai-MOST Key Laboratory of Health and Disease Genomics,Chinese National Human Genome Center,Shanghai 201203,China | 2009 | Science China(Life Sciences)2009，52，1： | 15 |
| 12 | Review of current diagnostic methods and advances in Helicobacter pylori diagnostics in the era of next generation sequencing显示文摘Helicobacter pylori(H.pylori)infection is highly prevalent in the human population and may lead to severe gastrointestinal pathology including gastric and duodenal ulcers,mucosa associated tissue lymphoma and gastric adenocarcinoma.In recent years,an alarming increase in antimicrobial resistance and subsequently failing empiric H.pylori eradication therapies have been noted worldwide,also in many European countries.Therefore,rapid and accurate determination of H.pylori’s antibiotic susceptibility prior to the administration of eradication regimens becomes ever more important.Traditionally,detection of H.pylori and its antimicrobial resistance is done by culture and phenotypic drug susceptibility testing that are cumbersome with a long turn-around-time.Recent advances in diagnostics provide new tools,like real-time polymerase chain reaction(PCR)and line probe assays,to diagnose H.pylori infection and antimicrobial resistance to certain antibiotics,directly from clinical specimens.Moreover,high-throughput whole genome sequencing technologies allow the rapid analysis of the pathogen’s genome,thereby allowing identification of resistance mutations and associated antibiotic resistance.In the first part of this review,we will give an overview on currently available diagnostic methods for detection of H.pylori and its drug resistance and their implementation in H.pylori management.The second part of the review focusses on the use of next generation sequencing technology in H.pylori research.To this end,we conducted a literature search for original research articles in English using the terms“Helicobacter”,“transcriptomic”,“transcriptome”,“next generation sequencing”and“whole genome sequencing”.This review is aimed to bridge the gap between current diagnostic practice(histology,rapid urease test,H.pylori culture,PCR and line probe assays)and new sequencing technologies and their potential implementation in diagnostic laboratory settings in order to complement the currently recommended H.pylori management guidelines and subsequently improve public health. | Daniel Pohl Peter M Keller Valentine Bordier Karoline Wagner | 2019 | World Journal of Gastroenterology2019，25，32： | 15 |
| 13 | Application of next-generation sequencing technology to precision medicine in cancer: joint consensus of the Tumor Biomarker Committee of the Chinese Society of Clinical Oncology显示文摘Next-generation sequencing(NGS) technology is capable of sequencing millions or billions of DNA molecules simultaneously.Therefore, it represents a promising tool for the analysis of molecular targets for the initial diagnosis of disease, monitoring of disease progression, and identifying the mechanism of drug resistance. On behalf of the Tumor Biomarker Committee of the Chinese Society of Clinical Oncology(CSCO) and the China Actionable Genome Consortium(CAGC), the present expert group hereby proposes advisory guidelines on clinical applications of NGS technology for the analysis of cancer driver genes for precision cancer therapy. This group comprises an assembly of laboratory cancer geneticists, clinical oncologists, bioinformaticians,pathologists, and other professionals. After multiple rounds of discussions and revisions, the expert group has reached a preliminary consensus on the need of NGS in clinical diagnosis, its regulation, and compliance standards in clinical sample collection. Moreover, it has prepared NGS criteria, the sequencing standard operation procedure(SOP), data analysis, report, and NGS platform certification and validation. | Xuchao Zhang Zhiyong Liang Shengyue Wang Shun Lu Yong Song Ying Cheng Jianming Ying Weiping Liu Yingyong Hou Yangqiu Li Yi Liu Jun Hou Xiufeng Liu Jianyong Shao Yanhong Tai Zheng Wang Li Fu Hui Li Xiaojun Zhou Hua Bai Mengzhao Wang You Lu Jinji Yang Wenzhao Zhong Qing Zhou Xuening Yang Jie Wang Cheng Huang Xiaoqing Liu Xiaoyan Zhou Shirong Zhang Hongxia Tian Yu Chen Ruibao Ren Ning Liao Chunyan Wu Zhongzheng Zhu Hongming Pan Yanhong Gu Liwei Wang Yunpeng Liu Suzhan Zhang Tianshu Liu Gong Chen Zhimin Shao Binghe Xu Qingyuan Zhang Ruihua Xu Lin Shen Yilong Wu | 2019 | Cancer Biology & Medicine2019，16，1： | 14 |
| 14 | Altered oral microbiota in chronic hepatitis B patients with different tongue coatings显示文摘AIM To elucidate tongue coating microbiota and metabolic differences in chronic hepatitis B(CHB) patients with yellow or white tongue coatings.METHODS Tongue coating samples were collected from 53 CHBpatients(28 CHB yellow tongue coating patients and 25 CHB white tongue coating patients) and 22 healthy controls.Microbial DNA was extracted from the tongue samples,and the bacterial 16 S ribosomal RNA gene V3 region was amplified from all samples and sequenced with the Ion Torrent PGM^(TM)sequencing platform according to the standard protocols.The metabolites in the tongue coatings were evaluated using a liquid chromatographymass spectrometry(LC-MS) platform.Statistical analyses were then performed.RESULTS The relative compositions of the tongue coating microbiotas and metabolites in the CHB patients were significantly different from those of the healthy controls,but the tongue coating microbiota abundances and diversity levels were not significantly different.Compared with the CHB white tongue coating patients,the CHB yellow tongue coating patients had higher hepatitis B viral DNA(HBV-DNA) titers(median 21210 vs 500,respectively,P = 0.03) and a significantly lower level of Bacteroidetes(20.14% vs 27.93%,respectively,P = 0.013) and higher level of Proteobacteria(25.99% vs 18.17%,respectively,P = 0.045) in the microbial compositions at the phylum level.The inferred metagenomic pathways enriched in the CHB yellow tongue coating patients were mainly those involved in amino acid metabolism,which was consistent with the metabolic disorder.The abundances of bacteria from Bacteroidales at the order level were higher in the CHB white tongue coating patients(19.2% vs 27.22%,respectively,P = 0.011),whereas Neisseriales were enriched in the yellow tongue coating patients(21.85% vs 13.83%,respectively,P = 0.029).At the family level,the abundance of Neisseriaceae in the yellow tongue patients was positively correlated with the HBV-DNA level but negatively correlated with the S-adenosyl-L-methionine level.CONCLUSION This research illustrates specific clinical features and bacterial structures in CHB patients with different tongue coatings,which facilitates understanding of the traditional tongue diagnosis. | Yu Zhao Yu-Feng Mao Yi-Shuang Tang Ming-Zhu Ni Qiao-Hong Liu Yan Wang Qin Feng Jing-Hua Peng Yi-Yang Hu | 2018 | World Journal of Gastroenterology2018，24，30： | 13 |
| 15 | QTG-Seq Accelerates QTL Fine Mapping through QTL Partitioning and Whole-Genome Sequencing of Bulked Segregant Samples显示文摘Deciphering the genetic mechanisms underlying agronomic traits is of great importance for crop improvement. Most of these traits are controlled by multiple quantitative trait loci (QTLs), and identifying the underlying genes by conventional QTL fine-mapping is time-consuming and labor-intensive. Here, we devised a new method, named quantitative trait gene sequencing (QTG-seq), to accelerate QTL fine-mapping. QTGseq combines QTL partitioning to convert a quantitative trait into a near-qualitative trait, sequencing of bulked segregant pools from a large segregating population, and the use of a robust new algorithm for identifying candidate genes. Using QTG-seq, we fine-mapped a plant-height QTL in maize (Zea mays L.), qPH7, to a 300-kb genomic interval and verified that a gene encoding an NF-YC transcription factor was the functional gene. Functional analysis suggested that qPH7-encoding protein might influence plant height by interacting with a CO-like protein and an AP2 domain-containing protein. Selection footprint ana卜 ysis indicated that qPH7 was subject to strong selection during maize improvement. In summary, QTG-seq provides an efficient method for QTL fine-mapping in the era of “big data'. | Hongwei Zhang Xi Wang Qingchun Pan Pei Li Yunjun Liu Xiaoduo Lu Wanshun Zhong Minqi Li Linqian Han Juan Li Pingxi Wang Dongdong Li Yan Liu Qing Li Fang Yang Yuan-Ming Zhang Guoying Wang Lin Li | 2019 | Molecular Plant2019，12，3： | 13 |
| 16 | Piglet gut microbial shifts early in life:causes and effects显示文摘The gut microbiome has long been known to play fundamentally important roles in the animal health and the well-being of its host. As such, the establishment and maintenance of a beneficial gut microbiota early in life is crucial in pigs, since early gut colonizers are pivotal in the establishment of permanent microbial community structures affecting the health and growth performance of pigs later in life. Emphasizing this importance of early gut colonizers, it is critical to understand the factors impacting the establishment of the piglet gut microbiome at weaning. Factors include, among others, diet, in-feed antibiotics, probiotics and prebiotic administration. The impact of these factors on establishment of the gut microbiome of piglets at weaning includes effects on piglet gut microbial diversity, structure, and succession. In this review, we thoroughly reviewed the most recent findings on the piglet gut microbiome shifts as influenced by weaning, and how these microbiome changes brought about by various factors that have been shown to affect the development of microbiota in piglets. This review will provide a general overview of recent studies that can help to facilitate the design of new strategies to modulate the gut microbiome in order to enhance gastrointestinal health, growth performance and well-being of piglets. | Robin B.Guevarra Jun Hyung Lee Sun Hee Lee Min-Jae Seok Doo Wan Kim Bit Na Kang Timothy J.Johnson Richard E.Isaacson Hyeun Bum Kim | 2019 | Journal of Animal Science and Biotechnology2019，10，3： | 13 |
| 17 | An updated review of gastric cancer in the next-generation sequencing era:Insights from bench to bedside and vice versa显示文摘Gastric cancer(GC)is one of the most common malignancies and remains the second leading cause of cancer-related death worldwide.There is an increasing understanding of the roles that genetic and epigenetic alterations play in GCs.Recent studies using nextgeneration sequencing(NGS)have revealed a number of potential cancer-driving genes in GC.Whole-exome sequencing of GC has identified recurrent somatic mutations in the chromatin remodeling gene ARID1A and alterations in the cell adhesion gene FAT4,a member of the cadherin gene family.Mutations in chromatin remodeling genes(ARID1A,MLL3 and MLL)have been found in 47%of GCs.Whole-genome sequencing and whole-transcriptome sequencing analyses have also discovered novel alterations in GC.Recent studies of cancer epigenetics have revealed widespread alterations in genes involved in the epigenetic machinery,such as DNA methylation,histone modifications,nucleosome positioning,noncoding RNAs and microRNAs.Recent advances in molecular research on GC have resulted in the introduction of new diagnostic and therapeutic strategies into clinical settings.The antihuman epidermal growth receptor 2(HER2)antibody trastuzumab has led to an era of personalized therapy in GC.In addition,ramucirumab,a monoclonal antibody targeting vascular endothelial growth factor receptor(VEGFR)-2,is the first biological treatment that showed survival benefits as a single-agent therapy in patients with advanced GC who progressed after firstline chemotherapy.Using NGS to systematically identify gene alterations in GC is a promising approach with remarkable potential for investigating the pathogenesis of GC and identifying novel therapeutic targets,as well as useful biomarkers.In this review,we will summarize the recent advances in the understanding of the molecular pathogenesis of GC,focusing on the potential use of these genetic and epigenetic alterations as diagnostic biomarkers and novel therapeutic targets. | Hiroyuki Yamamoto Yoshiyuki Watanabe Tadateru Maehata Ryo Morita Yoshihito Yoshida Ritsuko Oikawa Shinya Ishigooka Shun-ichiro Ozawa Yasumasa Matsuo Kosuke Hosoya Masaki Yamashita Hiroaki Taniguchi Katsuhiko Nosho Hiromu Suzuki Hiroshi Yasuda Yasuhisa Shinomura Fumio Itoh | 2014 | World Journal of Gastroenterology2014，20，14： | 12 |
| 18 | Targeted therapy or immunotherapy? Optimal treatment in hepatocellular carcinoma显示文摘Hepatocellular carcinoma(HCC) is the fifth leading cause of cancer mortality in the United States and the second leading cause of cancer mortality worldwide. Sorafenib is the only food and drug administration(FDA) approved as first line systemic treatment in HCC. Regorafenib and nivolumab are the only FDA approved second line treatment after progression on sorafenib. We will discuss all potential first and second line options in HCC. In addition, we also will explore sequencing treatment options in HCC, and examine biomarkers that can potentially predict benefits from treatments such as immune checkpoint inhibitor. This minireview summarizes potential treatments in HCC based on clinical trials that have been published in manuscript or abstract format from 1994-2018. | Merly Contratto Jennifer Wu | 2018 | World Journal of Gastrointestinal Oncology2018，10，5： | 12 |
| 19 | DNA storage:research landscape and future prospects显示文摘The global demand for data storage is currently outpacing the world’s storage capabilities.DNA,the carrier of natural genetic information,offers a stable,resource-and energy-efficient and sustainable data storage solution.In this review,we summarize the fundamental theory,research history,and technical challenges of DNA storage.From a quantitative perspective,we evaluate the prospect of DNA,and organic polymers in general,as a novel class of data storage medium. | Yiming Dong Fajia Sun Zhi Ping Qi Ouyang Long Qian | 2020 | National Science Review2020，7，6： | 12 |
| 20 | Use of blood-based biomarkers for early diagnosis and surveillance of colorectal cancer显示文摘Early screening for colorectal cancer(CRC) holds the key to combat and control the increasing global burden of CRC morbidity and mortality. However, the current available screening modalities are severely inadequate because of their high cost and cumbersome preparatory procedures that ultimately lead to a low participation rate. People simply do not like to have colonoscopies. It would be ideal, therefore, to develop an alternative modality based on blood biomarkers as the first line screening test. This will allow for the differentiation of the general population from high risk individuals. Colonoscopy would then become the secondary test, to further screen the high risk segment of the population. This will encourage participation and therefore help to reach the goal of early detection and thereby reduce the anticipated increasing global CRC incidence rate. A blood-based screening test is anappealing alternative as it is non-invasive and poses minimal risk to patients. It is easy to perform, can be repeated at shorter intervals, and therefore would likely lead to a much higher participation rate. This review surveys various blood-based test strategies currently under investigation, discusses the potency of what is available, and assesses how new technology may contribute to future test design. | Ganepola AP Ganepola Joel Nizin John R Rutledge David H Chang | 2014 | World Journal of Gastrointestinal Oncology2014，6，4： | 11 |
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