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

null

《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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Plastic materials and water sources actively select and shape wastewater plastispheres over time

《环境科学与工程前沿（英文）》 2022年 第16卷 第11期 doi: 10.1007/s11783-022-1580-1

摘要：

● Wastewater MPs exhibited resistomes and therefore health threats.

关键词： Microplastics     Whole-genome metagenomic sequencing     Plastisphere     Plastic degradation     MHETase    

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TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways

null

《医学前沿（英文）》 2015年 第9卷 第3期   页码 322-330 doi: 10.1007/s11684-015-0408-9

摘要：

This study systematically evaluates the TCGA whole-transcriptome sequencing data of hepatocellular carcinoma (HCC) by comparing the global gene expression profiles between tumors and their corresponding non-tumorous liver tissue. Based on the differential gene expression analysis, we identified a number of novel dysregulated genes, in addition to those previously reported. Top-listing upregulated (CENPF and FOXM1) and downregulated (CLEC4G, CRHBP, and CLEC1B) genes were successfully validated using qPCR on our cohort of 65 pairs of human HCCs. Further examination for the mechanistic overview by subjecting significantly upregulated and downregulated genes to gene set enrichment analysis showed that different cellular pathways were involved. This study provides useful information on the transcriptomic landscape and molecular mechanism of hepatocarcinogenesis for development of new biomarkers and further in-depth characterization.

关键词： TCGA     whole-transcriptome sequencing     HCC     liver cancer    

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Exome sequencing greatly expedites the progressive research of Mendelian diseases

null

《医学前沿（英文）》 2014年 第8卷 第1期   页码 42-57 doi: 10.1007/s11684-014-0303-9

摘要：

The advent of whole-exome sequencing (WES) has facilitated the discovery of rare structure and functional genetic variants. Combining exome sequencing with linkage studies is one of the most efficient strategies in searching disease genes for Mendelian diseases. WES has achieved great success in the past three years for Mendelian disease genetics and has identified over 150 new Mendelian disease genes. We illustrate the workflow of exome capture and sequencing to highlight the advantages of WES. We also indicate the progress and limitations of WES that can potentially result in failure to identify disease-causing mutations in part of patients. With an affordable cost, WES is expected to become the most commonly used tool for Mendelian disease gene identification. The variants detected cumulatively from previous WES studies will be widely used in future clinical services.

关键词： genetics     whole-exome sequencing     Mendelian disease     disease gene    

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

null

《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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An introduction to the medicinal plant genome project

Shilin Chen, Li Xiang, Xu Guo, Qiushi Li

《医学前沿（英文）》 2011年 第5卷 第2期   页码 178-184 doi: 10.1007/s11684-011-0131-0

摘要： In recent years, genomics has developed rapidly with the application of next-generation sequencing technology. However, very few studies have been carried out on genomics for medicinal plants. This paper introduces the genome research of medicinal plants, including genome sequencing, assembly, annotation, and functional genomics, to set up the foundation for the development of natural medicines and the selection of cultivars with good agricultural traits. This study places the study on traditional Chinese medicine into the frontier field of life science.

关键词： genomics     medicinal plant     sequencing     application    

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A novel variant in the gene in a large Chinese family with a unique phenotype of Clouston syndrome

《医学前沿（英文）》 2023年 第17卷 第2期   页码 330-338 doi: 10.1007/s11684-022-0933-2

摘要： Clouston syndrome (OMIM #129500), also known as hidrotic ectodermal dysplasia type 2, is a rare autosomal dominant skin disorder. To date, four mutations in the GJB6 gene, G11R, V37E, A88V, and D50N, have been confirmed to cause this condition. In previous studies, the focus has been mainly on gene sequencing, and there has been a lack of research on clinical manifestations and pathogenesis. To confirm the diagnosis of this pedigree at the molecular level and summarize and analyse the clinical phenotype of patients and to provide a basis for further study of the pathogenesis of the disease, we performed whole-exome and Sanger sequencing on a large Chinese Clouston syndrome pedigree. Detailed clinical examination included histopathology, hair microscopy, and scanning electron microscopy. We found a novel heterozygous missense variant (c.134G>C:p.G45A) for Clouston syndrome. We identified a new clinical phenotype involving all nail needling pain in all patients and found a special honeycomb hole structure in the patients’ hair under scanning electron microscopy. Our data reveal that a novel variant (c.134G>C:p.G45A) plays a likely pathogenic role in this pedigree and highlight that genetic testing is necessary for the diagnosis of Clouston syndrome.

关键词： Clouston syndrome     whole exome sequencing     GJB6 gene     novel variant     unique phenotype    

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Genome-wide analysis reveals selection for Chinese Rongchang pigs

Lei CHEN, Shilin TIAN, Long JIN, Zongyi GUO, Dan ZHU, Lan JING, Tiandong CHE, Qianzi TANG, Siqing CHEN, Liang ZHANG, Tinghuan ZHANG, Zuohua LIU, Jinyong WANG, Mingzhou LI

《农业科学与工程前沿（英文）》 2017年 第4卷 第3期   页码 319-326 doi: 10.15302/J-FASE-2017161

摘要： Livestock have undergone domestication and consequently strong selective pressure on genes or genomic regions that control desirable traits. To identify selection signatures in the genome of Chinese Rongchang pigs, we generated a total of about 170 Gb of DNA sequence data with about 6.4-fold coverage for each of six female individuals. By combining these data with the publically available genome data of 10 Asian wild boars, we identified 449 protein-coding genes with selection signatures in Rongchang pigs, which are mainly involved in growth and hormone binding, nervous system development, and drug metabolism. The accelerated evolution of these genes may contribute to the dramatic phenotypic differences between Rongchang pigs and Chinese wild boars. This study illustrated how domestication and subsequent artificial selection have shaped patterns of genetic variation in Rongchang pigs and provides valuable genetic resources that can enhance the use of pigs in agricultural production and biomedical studies.

关键词： domestication     genome     pig     re-sequencing     selection    

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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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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

摘要：

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。

关键词： 数据科学     人工智能     下一代测序     脱氧核糖核酸     癌症基因组     单细胞转录组学    

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Organizational evolution of project management teams over the whole lifecycle of megaprojects: Case study

《工程管理前沿（英文）》   页码 439-454 doi: 10.1007/s42524-022-0211-7

摘要： Project management teams are critical in the implementation of megaprojects, but their evolution throughout the project lifecycle has not been clearly explained. This paper explores the organizational evolution of megaproject management teams through a longitudinal retrospective case study of the Hong Kong–Zhuhai–Macao Bridge (HZMB) project. The organizational evolution is examined in terms of management objectives, management content, and organizational structure. The organizational evolution of the HZMB project management team exhibits stage differentiation with the coexistence of turbulence and stability. Changes in the external environment are the driving force for organizational evolution, whereas a flexible organizational strategy is critical in promoting this evolution. Basing on the HZMB case study, this paper summarizes six critical measures that facilitate the organizational evolution of megaproject management teams. Our findings add value to megaproject management theory and provide a better understanding of the dynamics and complexity of megaproject organizational management.

关键词： megaproject     organizational evolution     whole lifecycle management     project management team    

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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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标题 作者 时间 类型 操作

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

期刊论文

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

null

期刊论文

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

null

期刊论文

Plastic materials and water sources actively select and shape wastewater plastispheres over time

期刊论文

TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways

null

期刊论文

Exome sequencing greatly expedites the progressive research of Mendelian diseases

null

期刊论文

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

null

期刊论文

An introduction to the medicinal plant genome project

Shilin Chen, Li Xiang, Xu Guo, Qiushi Li

期刊论文

A novel variant in the gene in a large Chinese family with a unique phenotype of Clouston syndrome

期刊论文

Genome-wide analysis reveals selection for Chinese Rongchang pigs

Lei CHEN, Shilin TIAN, Long JIN, Zongyi GUO, Dan ZHU, Lan JING, Tiandong CHE, Qianzi TANG, Siqing CHEN, Liang ZHANG, Tinghuan ZHANG, Zuohua LIU, Jinyong WANG, Mingzhou LI

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

信息科学应引领未来的生物医学研究

Kenta Nakai

期刊论文

Organizational evolution of project management teams over the whole lifecycle of megaprojects: Case study

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