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Exploring the cancer genome in the era of next-generation sequencing
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《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
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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《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
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
《医学前沿（英文）》 doi: 10.1007/s11684-023-1008-8
Genome-wide association studies: inherent limitations and future challenges
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《医学前沿（英文）》 2012年 第6卷 第4期 页码 444-450 doi: 10.1007/s11684-012-0225-3
Genome-wide association studies (GWAS) have achieved great success in identifying genetic variants related to complex human diseases such as cancer and have provided valuable insights into their genetic architecture. Recently, GWAS is quite the fashion in China. However, there are issues related to its nature. Enormous work needs to be done in the post-GWAS era. Deep sequencing followed by functional studies will be needed to elucidate the underpinning biological mechanisms and further translate GWAS findings into medical practice. Along with pharmacogenomics, the success of GWAS in identifying genetic risk factors and genetic differences in drug response has been gradually enabling personalized medicine. In this article, we used hepatocellular carcinoma (HCC) as an example to demonstrate some of the inherent limitations and summarized future challenges of GWAS.
关键词： genome-wide association studies (GWAS) genetic variant cancer limitation challenge
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
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
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
关键词： liquid metal material genome energy material material discovery advanced material room-temperature liquid alloy thermodynamics phase diagram
《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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《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
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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《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
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
信息科学应引领未来的生物医学研究 Perspective
Kenta Nakai
《工程（英文）》 2019年 第5卷 第6期 页码 1155-1158 doi: 10.1016/j.eng.2019.07.023
笔者从长期回顾的角度阐述了对人工智能（AI）/数据科学与生物医学之间关系的看法。随着新技术的不断出现，现代生物医学的发展持续加速。由于所有生命系统基本上都受其自身DNA中信息的支配，因此信息科学对生物医学的研究具有特别重要的意义。与物理学不同，在生物学中没有发现（或很少有）主导定律。因此，在生物学中，“数据到知识”方法很重要。人工智能在历史上一直应用于生物医学，最近的新闻表明，基于人工智能的方法在国际蛋白质结构预测竞争中获得了最佳性能，这可能被视为该领域的另一个里程碑。类似的方法可能有助于解决基因组序列解释中的问题，如确定患者基因组中的癌症驱动突变。最近，新一代测序（NGS）的爆炸性发展已产生大量数据，并且这种趋势将加速。NGS不仅用于“读取”DNA序列，而且还用于在单细胞水平上获得各种类型的信息。这些数据可以视为气候模拟中的网格数据点。数据科学和人工智能对于这些数据的综合解释/模拟都将变得至关重要，并将在未来的精密医学中起主导作用。
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
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.
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
《医学前沿（英文）》 页码 889-906 doi: 10.1007/s11684-023-0994-x
关键词： primary central nervous system lymphoma whole-genome sequencing TMSB4X copy number variation gene mutation
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
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
《医学前沿（英文）》 2021年 第15卷 第6期 页码 942-942 doi: 10.1007/s11684-021-0876-z
标题 作者 时间 类型 操作
Identification of cancer gene fusions based on advanced analysis of the human genome or transcriptome
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期刊论文
Topological reorganization and functional alteration of distinct genomic components in gallbladder cancer
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
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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
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