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Exploring the cancer genome in the era of next-generation sequencing

null

《医学前沿（英文）》 2012年 第6卷 第1期   页码 48-55 doi: 10.1007/s11684-012-0182-x

摘要：

The emergence of next-generation sequencing technologies has led to dramatic advances in cancer genome studies. The increased efficiency and resolution of next-generation sequencing greatly facilitate the detection of genetic, genomic, and epigenomic alterations, such as single nucleotide mutations, small insertions and deletions, chromosomal rearrangements, copy number variations, and DNA methylation. Comprehensive analysis of cancer genomes through approaches of whole genome, exome, and transcriptome sequencing has significantly improved the understanding of cancer biology, diagnosis, and therapy. The present study briefly reviews the recent pioneering studies on cancer genome sequencing and provides an unprecedented insight into the landscape of genomic alterations in human sporadic cancers.

关键词： next-generation sequencing     cancer genome     whole genome sequencing     exome     transcriptome    

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The development and application of genome editing technology in ruminants: a review

Mengke YUAN, Yuanpeng GAO, Jing HAN, Teng WU, Jingcheng ZHANG, Yongke WEI, Yong ZHANG

《农业科学与工程前沿（英文）》 2020年 第7卷 第2期   页码 171-180 doi: 10.15302/J-FASE-2019302

摘要：

Transgenic ruminants are a valuable resource for both animal breeding and biomedical research. The development of transgenic breeding is proceeding slowly, because it suffers from low efficiency of gene transfer and possible safety problems from uncontrolled random integration. However, new breeding methods combined with genome editing and somatic cell nuclear transfer or microinjection can offer an economic and efficient way to produce gene-edited ruminants, which can serve as bioreactors or have improved disease resistance, animal welfare and product quality. Recent advances in precise genome editing technologies, especially clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 nucleases, are enabling the systematic development of gene-edited ruminant production. This review covers the development of gene-edited ruminants, the particulars of site-specific engineered nucleases and the state of the art and new insights into practical applications and social acceptance of genome editing technology in ruminants. It is concluded that the production of gene-edited ruminants is feasible and through improvements in genome editing technology it is possible to help feed the world.

关键词： bioreactors     breeding     engineered endonucleases     genome editing     ruminants    

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Liquid metal material genome: Initiation of a new research track towards discovery of advanced energy

Lei WANG, Jing LIU

《能源前沿（英文）》 2013年 第7卷 第3期   页码 317-332 doi: 10.1007/s11708-013-0271-9

摘要： As the basis of modern industry, the roles materials play are becoming increasingly vital in this day and age. With many superior physical properties over conventional fluids, the low melting point liquid metal material, especially room-temperature liquid metal, is recently found to be uniquely useful in a wide variety of emerging areas from energy, electronics to medical sciences. However, with the coming enormous utilization of such materials, serious issues also arise which urgently need to be addressed. A biggest concern to impede the large scale application of room-temperature liquid metal technologies is that there is currently a strong shortage of the materials and species available to meet the tough requirements such as cost, melting point, electrical and thermal conductivity, etc. Inspired by the Material Genome Initiative as issued in 2011 by the United States of America, a more specific and focused project initiative was proposed in this paper—the liquid metal material genome aimed to discover advanced new functional alloys with low melting point so as to fulfill various increasing needs. The basic schemes and road map for this new research program, which is expected to have a worldwide significance, were outlined. The theoretical strategies and experimental methods in the research and development of liquid metal material genome were introduced. Particularly, the calculation of phase diagram (CALPHAD) approach as a highly effective way for material design was discussed. Further, the first-principles (FP) calculation was suggested to combine with the statistical thermodynamics to calculate the thermodynamic functions so as to enrich the CALPHAD database of liquid metals. When the experimental data are too scarce to perform a regular treatment, the combination of FP calculation, cluster variation method (CVM) or molecular dynamics (MD), and CALPHAD, referred to as the mixed FP-CVM-CALPHAD method can be a promising way to solve the problem. Except for the theoretical strategies, several parallel processing experimental methods were also analyzed, which can help improve the efficiency of finding new liquid metal materials and reducing the cost. The liquid metal material genome proposal as initiated in this paper will accelerate the process of finding and utilization of new functional materials.

关键词： liquid metal material genome     energy material     material discovery     advanced material     room-temperature liquid alloy     thermodynamics     phase diagram    

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GENOME EDITING: A GROUND BREAKING RESEARCH HAS BEEN RANKED TOP 10 ENGINEERING FRONTS FROM 2017 TO 2021

《农业科学与工程前沿（英文）》 2022年 第9卷 第2期   页码 309-311 doi: 10.15302/J-FASE-2022440

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Transforming bacterial disease surveillance and investigation using whole-genome sequence to probe the

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《医学前沿（英文）》 2018年 第12卷 第1期   页码 23-33 doi: 10.1007/s11684-017-0607-7

摘要：

Two decades have passed since the first bacterial whole-genome sequencing, which provides new opportunity for microbial genome. Consequently, considerable genetic diversity encoded by bacterial genomes and among the strains in the same species has been revealed. In recent years, genome sequencing techniques and bioinformatics have developed rapidly, which has resulted in transformation and expedited the application of strategy and methodology for bacterial genome comparison used in dissection of infectious disease epidemics. Bacterial whole-genome sequencing and bioinformatic computing allow genotyping to satisfy the requirements of epidemiological study in disease control. In this review, we outline the significance and summarize the roles of bacterial genome sequencing in the context of bacterial disease control and prevention. We discuss the applications of bacterial genome sequencing in outbreak detection, source tracing, transmission mode discovery, and new epidemic clone identification. Wide applications of genome sequencing and data sharing in infectious disease surveillance networks will considerably promote outbreak detection and early warning to prevent the dissemination of bacterial diseases.

关键词： genome sequencing     genomic epidemiology     bacteria     surveillance     infectious diseases    

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Advancement in genetic variants conferring obesity susceptibility from genome-wide association studies

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《医学前沿（英文）》 2015年 第9卷 第2期   页码 146-161 doi: 10.1007/s11684-014-0373-8

摘要：

Obesity prevalence has increased in recent years. Lifestyle change fuels obesity, but genetic factors cause more than 50% of average variations in obesity. The advent of genome-wide association studies (GWAS) has hastened the progress of polygenic obesity research. As of this writing, more than 73 obesity susceptibility loci have been identified in ethnic groups through GWAS. The identified loci explain only 2% to 4% of obesity heritability, thereby indicating that a large proportion of loci remain undiscovered. Thus, the next step is to identify and confirm novel loci, which may exhibit smaller effects and lower allele frequencies than established loci. However, achieving these tasks has been difficult for researchers. GWAS help researchers discover the causal loci. Moreover, numerous biological studies have been performed on the polygenic effects on obesity, such as studies on fat mass- and obesity-associated gene (FTO), but the role of these polygenic effects in the mechanism of obesity remains unclear. Thus, obesity-causing variations should be identified, and insights into the biology of polygenic effects on obesity are needed.

关键词： obesity     genetics     genome-wide association studies     body mass index     fat mass- and obesity-associated gene    

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A brief review of genome editing technology for generating animal models

Haoyi WANG, Sen WU, Mario R. CAPECCHI, Rudolf JAENISCH

《农业科学与工程前沿（英文）》 2020年 第7卷 第2期   页码 123-128 doi: 10.15302/J-FASE-2019309

摘要：

The recent development of genome editing technologies has given researchers unprecedented power to alter DNA sequences at chosen genomic loci, thereby generating various genetically edited animal models. This mini-review briefly summarizes the development of major genome editing tools, focusing on the application of these tools to generate animal models in multiple species.

关键词： animal model     CRISPR     genome editing     TALEN     ZFN    

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Highlights of special issue “Genome Editing in Agriculture: Technology, Applications and Regulations”

Yaofeng ZHAO, Caixia GAO, Sen WU

《农业科学与工程前沿（英文）》 2020年 第7卷 第2期   页码 121-122 doi: 10.15302/J-FASE-2019317

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Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing

《医学前沿（英文）》   页码 889-906 doi: 10.1007/s11684-023-0994-x

摘要： Primary central nervous system lymphoma (PCNSL) is an uncommon non-Hodgkin’s lymphoma with poor prognosis. This study aimed to depict the genetic landscape of Chinese PCNSLs. Whole-genome sequencing was performed on 68 newly diagnosed Chinese PCNSL samples, whose genomic characteristics and clinicopathologic features were also analyzed. Structural variations were identified in all patients with a mean of 349, which did not significantly influence prognosis. Copy loss occurred in all samples, while gains were detected in 77.9% of the samples. The high level of copy number variations was significantly associated with poor progression-free survival (PFS) and overall survival (OS). A total of 263 genes mutated in coding regions were identified, including 6 newly discovered genes (ROBO2, KMT2C, CXCR4, MYOM2, BCLAF1, and NRXN3) detected in ≥ 10% of the cases. CD79B mutation was significantly associated with lower PFS, TMSB4X mutation and high expression of TMSB4X protein was associated with lower OS. A prognostic risk scoring system was also established for PCNSL, which included Karnofsky performance status and six mutated genes (BRD4, EBF1, BTG1, CCND3, STAG2, and TMSB4X). Collectively, this study comprehensively reveals the genomic landscape of newly diagnosed Chinese PCNSLs, thereby enriching the present understanding of the genetic mechanisms of PCNSL.

关键词： primary central nervous system lymphoma     whole-genome sequencing     TMSB4X     copy number variation     gene mutation    

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Embryo-mediated genome editing for accelerated genetic improvement of livestock

Zachariah MCLEAN, Björn OBACK, Götz LAIBLE

《农业科学与工程前沿（英文）》 2020年 第7卷 第2期   页码 148-160 doi: 10.15302/J-FASE-2019305

摘要：

Selecting beneficial DNA variants is the main goal of animal breeding. However, this process is inherently inefficient because each animal only carries a fraction of all desirable variants. Genome editing technology with its ability to directly introduce beneficial sequence variants offers new opportunities to modernize animal breeding by overcoming this biological limitation and accelerating genetic gains. To realize rapid genetic gain, precise edits need to be introduced into genomically-selected embryos, which minimizes the genetic lag. However, embryo-mediated precision editing by homology-directed repair (HDR) mechanisms is currently an inefficient process that often produces mosaic embryos and greatly limits the numbers of available edited embryos. This review provides a summary of genome editing in bovine embryos and proposes an embryo-mediated accelerated breeding scheme that overcomes the present efficiency limitations of HDR editing in bovine embryos. It integrates embryo-based genomic selection with precise multi-editing and uses embryonic cloning with elite edited blastomeres or embryonic pluripotent stem cells to resolve mosaicism, enable multiplex editing and multiply rare elite genotypes. Such a breeding strategy would enable a more targeted, accelerated approach for livestock improvement that allows stacking of beneficial variants, even including novel traits from outside the breeding population, in the most recent elite genetic background, essentially within a single generation.

关键词： animal breeding     cattle     cloning     CRISPR/Cas9     cytoplasmic injection     embryo     genome editing     germline chimaeras     HDR     livestock improvement     TALENs    

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Identification of cancer gene fusions based on advanced analysis of the human genome or transcriptome

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《医学前沿（英文）》 2013年 第7卷 第3期   页码 280-289 doi: 10.1007/s11684-013-0265-3

摘要：

Many gene fusions have been recognized as important diagnostic and/or prognostic markers in human malignancies. In recent years, novel gene fusions have been identified in cases without prior knowledge of the genetic background. Accompanied by a powerful computational data analysis method, new genome-wide screening approaches were used to detect cryptic genomic aberrations. This review focused on advanced genome-wide screening approaches in fusion gene identification, such as microarray-based approaches, next-generation sequencing, and NanoString nCounter gene expression system. The fundamental rationale and strategy for fusion gene identification using each biotech platform are also discussed.

关键词： gene fusion     cancer     microarray     next-generation sequencing     NanoString nCounter system    

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Genome-edited crops: how to move them from laboratory to market

Kunling CHEN, Caixia GAO

《农业科学与工程前沿（英文）》 2020年 第7卷 第2期   页码 181-187 doi: 10.15302/J-FASE-2020332

摘要：

Recent breakthroughs in CRISPR technology allow specific genome manipulation of almost all crops and have initiated a revolution in precision crop breeding. Rationally-based regulation and widespread public acceptance are needed to propel genome-edited crops from laboratory to market and to translate this innovative technology into agricultural productivity.

关键词： CRISPR/Cas     genome editing     base editing     precision breeding     regulation    

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Transcriptome resources and genome-wide marker development for Japanese larch (

Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG

《农业科学与工程前沿（英文）》 2014年 第1卷 第1期   页码 77-84 doi: 10.15302/J-FASE-2014010

摘要： While the differential responses of trees to changes in climatic and environmental conditions have been demonstrated as they age, the underlying mechanisms and age control of tree growth and development are complex and poorly understood particularly at a molecular level. In this paper, we present a transcriptome analysis of , a deciduous conifer that is widely-grown in the northern hemisphere and of significant ecological and economic value. Using high-throughput RNA sequencing, we obtained about 26 million reads from the stems of 1-, 2-, 5-, 10-, 25- and 50-year-old trees. Combining these with the published Roche 454 sequencing reads and the expressed sequence tags (both mainly from embryogenic cell cultures), we assembled 26670549 reads into 146786 transcripts, of which we annotated 79182 to support investigations of the molecular basis of tree aging and adaption, somatic embryogenesis and wood formation. Using these sequences we also identified many single-nucleotide polymorphisms, simple sequence repeats, and insertion and deletion markers to assist breeding and genetic diversity studies of .

关键词： Larix     transcriptome     age     wood formation     somatic embryogenesis     molecular marker    

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Genome reprogramming for synthetic biology

Kylie Standage-Beier,Xiao Wang

《化学科学与工程前沿（英文）》 2017年 第11卷 第1期   页码 37-45 doi: 10.1007/s11705-017-1618-2

摘要： The ability to go from a digitized DNA sequence to a predictable biological function is central to synthetic biology. Genome engineering tools facilitate rewriting and implementation of engineered DNA sequences. Recent development of new programmable tools to reengineer genomes has spurred myriad advances in synthetic biology. Tools such as clustered regularly interspace short palindromic repeats enable RNA-guided rational redesign of organisms and implementation of synthetic gene systems. New directed evolution methods generate organisms with radically restructured genomes. These restructured organisms have useful new phenotypes for biotechnology, such as bacteriophage resistance and increased genetic stability. Advanced DNA synthesis and assembly methods have also enabled the construction of fully synthetic organisms, such as J. Craig Venter Institute (JCVI)-syn 3.0. Here we summarize the recent advances in programmable genome engineering tools.

关键词： CRISPR     genome engineering     synthetic biology     rational design    

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Systems understanding of plant–pathogen interactions through genome-wide protein–protein interaction

Hong LI,Ziding ZHANG

《农业科学与工程前沿（英文）》 2016年 第3卷 第2期   页码 102-112 doi: 10.15302/J-FASE-2016100

摘要： Plants are frequently affected by pathogen infections. To effectively defend against such infections, two major modes of innate immunity have evolved in plants; pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity. Although the molecular components as well as the corresponding pathways involved in these two processes have been identified, many aspects of the molecular mechanisms of the plant immune system remain elusive. Recently, the rapid development of omics techniques (e.g., genomics, proteomics and transcriptomics) has provided a great opportunity to explore plant–pathogen interactions from a systems perspective and studies on protein–protein interactions (PPIs) between plants and pathogens have been carried out and characterized at the network level. In this review, we introduce experimental and computational identification methods of PPIs, popular PPI network analysis approaches, and existing bioinformatics resources/tools related to PPIs. Then, we focus on reviewing the progress in genome-wide PPI networks related to plant–pathogen interactions, including pathogen-centric PPI networks, plant-centric PPI networks and interspecies PPI networks between plants and pathogens. We anticipate genome-wide PPI network analysis will provide a clearer understanding of plant–pathogen interactions and will offer some new opportunities for crop protection and improvement.

关键词： plant–pathogen interactions     systems biology     omics     plant immunity     protein–protein interaction     network    

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标题 作者 时间 类型 操作

Exploring the cancer genome in the era of next-generation sequencing

null

期刊论文

The development and application of genome editing technology in ruminants: a review

Mengke YUAN, Yuanpeng GAO, Jing HAN, Teng WU, Jingcheng ZHANG, Yongke WEI, Yong ZHANG

期刊论文

Liquid metal material genome: Initiation of a new research track towards discovery of advanced energy

Lei WANG, Jing LIU

期刊论文

GENOME EDITING: A GROUND BREAKING RESEARCH HAS BEEN RANKED TOP 10 ENGINEERING FRONTS FROM 2017 TO 2021

期刊论文

Transforming bacterial disease surveillance and investigation using whole-genome sequence to probe the

null

期刊论文

Advancement in genetic variants conferring obesity susceptibility from genome-wide association studies

null

期刊论文

A brief review of genome editing technology for generating animal models

Haoyi WANG, Sen WU, Mario R. CAPECCHI, Rudolf JAENISCH

期刊论文

Highlights of special issue “Genome Editing in Agriculture: Technology, Applications and Regulations”

Yaofeng ZHAO, Caixia GAO, Sen WU

期刊论文

Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing

期刊论文

Embryo-mediated genome editing for accelerated genetic improvement of livestock

Zachariah MCLEAN, Björn OBACK, Götz LAIBLE

期刊论文

Identification of cancer gene fusions based on advanced analysis of the human genome or transcriptome

null

期刊论文

Genome-edited crops: how to move them from laboratory to market

Kunling CHEN, Caixia GAO

期刊论文

Transcriptome resources and genome-wide marker development for Japanese larch (

Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG

期刊论文

Genome reprogramming for synthetic biology

Kylie Standage-Beier,Xiao Wang

期刊论文

Systems understanding of plant–pathogen interactions through genome-wide protein–protein interaction

Hong LI,Ziding ZHANG

期刊论文