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《医学前沿(英文)》 doi: 10.1007/s11684-023-1050-6
关键词: pancreatic cancer cancer screening single cell molecular alterations precancerous lesion therapy resistance
《医学前沿(英文)》 2023年 第17卷 第4期 页码 758-767 doi: 10.1007/s11684-022-0981-7
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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
Statistical considerations for genomic selection
Huimin KANG, Lei ZHOU, Jianfeng LIU
《农业科学与工程前沿(英文)》 2017年 第4卷 第3期 页码 268-278 doi: 10.15302/J-FASE-2017164
关键词: genomic estimated breeding value genomic selection linkage disequilibrium statistical methods
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《医学前沿(英文)》 2018年 第12卷 第1期 页码 76-83 doi: 10.1007/s11684-017-0609-5
Tuberculosis (TB) has remained an ongoing concern in China. The national scale-up of the Directly Observed Treatment, Short Course (DOTS) program has accelerated the fight against TB in China. Nevertheless, many challenges still remain, including the spread of drug-resistant strains, high disease burden in rural areas, and enormous rural-to-urban migrations. Whether incident active TB represents recent transmission or endogenous reactivation has helped to prioritize the strategies for TB control. Evidence from molecular epidemiology studies has delineated the recent transmission of ( ) strains in many settings. However, the transmission patterns of TB in most areas of China are still not clear. Studies carried out to date could not capture the real burden of recent transmission of the disease in China because of the retrospective study design, incomplete sampling, and use of low-resolution genotyping methods. We reviewed the implementations of molecular epidemiology of TB in China, the estimated disease burden due to recent transmission of strains, the primary transmission of drug-resistant TB, and the evaluation of a feasible genotyping method of strains in circulation.
关键词: tuberculosis recent transmission molecular epidemiology China
Chronic hepatitis B virus infection: epidemiology, prevention, and treatment in China
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《医学前沿(英文)》 2014年 第8卷 第2期 页码 135-144 doi: 10.1007/s11684-014-0331-5
Chronic hepatitis B is a major health problem in China. The universal vaccination program since 1992 has changed the epidemiology of hepatitis B virus infection in China from highly to moderately endemic. The most prevalent hepatitis B virus strains in China are genotypes B and C, whereas those in western provinces are genotypes D and C/D hybrid. Chronic hepatitis B poses a heavy burden to the society in China. Different treatment strategies have been explored to improve patient outcomes in a cost-effective manner. However, antiviral drugs with a low genetic barrier to resistance are still extensively used because of the generally low income and limited resources in China. Individualized antiviral therapy is closely associated with translational medicine, which utilizes information from studies on genomics, immune biomarkers, and fibrosis. The results of these studies are crucial in further improving treatment outcomes.
The epidemiology of norovirus gastroenteritis in China: disease burden and distribution of genotypes
Honglu Zhou, Songmei Wang, Lorenz von Seidlein, Xuanyi Wang
《医学前沿(英文)》 2020年 第14卷 第1期 页码 1-7 doi: 10.1007/s11684-019-0733-5
关键词: molecular epidemiology norovirus disease burden genotype China
GLOBAL GENOMIC PREDICTION IN HORTICULTURAL CROPS: PROMISES, PROGRESS, CHALLENGES AND OUTLOOK
《农业科学与工程前沿(英文)》 2021年 第8卷 第2期
Horticultural crops are a major source of high value nutritious food, and new improved cultivars developed through breeding are required for sustainable production in the face of abiotic and biotic stresses, and to deliver novel, premium products to consumers. However, grower confidence in the performance of new germplasm, particularly across environmental variability, is important for commercial adoption and germplasm-environment matching to optimize production.
GLOBAL GENOMIC PREDICTION IN HORTICULTURAL CROPS: PROMISES, PROGRESS, CHALLENGES AND OUTLOOK
Craig HARDNER, Satish KUMAR, Dorrie MAIN, Cameron PEACE
《农业科学与工程前沿(英文)》 页码 353-355 doi: 10.15302/J-FASE-2021387
《医学前沿(英文)》 doi: 10.1007/s11684-023-1008-8
Detection of genomic signatures for pig hairlessness using high-density SNP data
Ying SU,Yi LONG,Xinjun LIAO,Huashui AI,Zhiyan ZHANG,Bin YANG,Shijun XIAO,Jianhong TANG,Wenshui XIN,Lusheng HUANG,Jun REN,Nengshui DING
《农业科学与工程前沿(英文)》 2014年 第1卷 第4期 页码 307-313 doi: 10.15302/J-FASE-2014039
2008—2017年河南省腹泻患者来源单相鼠伤寒沙门菌ST34的基因组流行病学特征研究 Article
穆玉娇, 李瑞超, 杜鹏程, 张沛, 李岩, 崔生辉, Séamus Fanning, 白莉
《工程(英文)》 2022年 第15卷 第8期 页码 34-44 doi: 10.1016/j.eng.2022.05.006
单相鼠伤寒沙门菌(Salmonella enterica serovar 4,[5],12:i:-, S. 4,[5],12:i:-)作为鼠伤寒沙门菌的变种,已成为全球公共卫生领域备受关注的新兴血清型,其在中国的基因组流行病学特征尚不明确。本研究对2008-2017年分离自腹泻患者的100株序列型34型(ST34)S. 4,[5],12:i:-开展的流行情况、耐药表型和群体基因组学的分析发现:多数菌株对氨苄西林、链霉素、磺胺类和四环素耐药(耐药表型ASSuT);基于贝叶斯系统发育分析,中国分离株起源于欧洲谱系,进化为携带不同耐药基因和质粒的两个分支。进化支1中gyrA基因点突变和质粒介导喹诺酮耐药基因携带率较高,而进化支2中多数菌株fljBA操纵子插入了耐药编码区域[编码ASSuT耐药表型,包括blaTEM-1B(氨苄西林耐药)、strAB(链霉素耐药)、sul2(磺胺类耐药)和tet(B)(四环素耐药)],导致了血清型单相变异。IncHI2质粒是该血清型中导致细菌严重耐药的主要可移动遗传元件,普遍存在于进化支1的分离株中。综上,多重耐药S. 4,[5],12:i:-菌株在中国的流行情况日益严重,且进化为携带不同耐药基因的多个谱系,需采取有效措施控制此人畜共患病原体的传播,并基于“同一健康”策略开展监测及制定干预策略。
《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
Genomic variations in the counterpart normal controls of lung squamous cell carcinomas
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《医学前沿(英文)》 2018年 第12卷 第3期 页码 280-288 doi: 10.1007/s11684-017-0580-1
Lung squamous cell carcinoma (LUSC) causes approximately 400 000 deaths each year worldwide. The occurrence of LUSC is attributed to exposure to cigarette smoke, which induces the development of numerous genomic abnormalities. However, few studies have investigated the genomic variations that occur only in normal tissues that have been similarly exposed to tobacco smoke as tumor tissues. In this study, we sequenced the whole genomes of three normal lung tissue samples and their paired adjacent squamous cell carcinomas. We then called genomic variations specific to the normal lung tissues through filtering the genomic sequence of the normal lung tissues against that of the paired tumors, the reference human genome, the dbSNP138 common germline variants, and the variations derived from sequencing artifacts. To expand these observations, the whole exome sequences of 478 counterpart normal controls (CNCs) and paired LUSCs of The Cancer Genome Atlas (TCGA) dataset were analyzed. Sixteen genomic variations were called in the three normal lung tissues. These variations were confirmed by Sanger capillary sequencing. A mean of 0.5661 exonic variations/Mb and 7.7887 altered genes per sample were identified in the CNC genome sequences of TCGA. In these CNCs, C:G→T:A transitions, which are the genomic signatures of tobacco carcinogen N-methyl-N-nitro-N-nitrosoguanidine, were the predominant nucleotide changes. Twenty five genes in CNCs had a variation rate that exceeded 2%, including ARSD (18.62%), MUC4 (8.79%), and RBMX (7.11%). CNC variations in CTAGE5 and USP17L7 were associated with the poor prognosis of patients with LUSC. Our results uncovered previously unreported genomic variations in CNCs, rather than LUSCs, that may be involved in the development of LUSC.
关键词: lung cancer counterpart normal control genomic variations
Tumor growth and metastasis can be inhibited by maintaining genomic stability in cancer cells
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《医学前沿(英文)》 2015年 第9卷 第1期 页码 57-62 doi: 10.1007/s11684-015-0389-8
The existence of cancer stem cells, stem-like cancer cells (SLCCs), or tumor-initiating cells is considered as the cause of tumor formation and recurrence, indicating the importance of studying novel therapy that targets SLCCs. The origin of SLCCs is controversial because of two competing hypotheses: SLCCs are either transformed from tissue adult stem cells or dedifferentiated from transformed progenitor cells. Our previous research demonstrates that SLCCs are inducible by increasing genomic instability in cancer cells. In this study, to block the emergence of SLCCs, aminoethyl isothiourea (AET), a compound that clears free radicals and is used to protect patients from radioactive exposure, was used as an agent that maintains genomic stability in combination with mitomycin C (MMC), a commonly used chemotherapeutic drug that damages DNA. Using a rabbit tumor model with VX2 hepatic carcinoma, we found that MMC alone increased lung metastases and disadvantaged survival outcome, but the combination of MMC and AET reversed this effect and even prolonged overall survival. Moreover, in a VX2 xenograft model by immunocompromised mice, MMC alone enriched tumor-initiating cells, but the administration of MMC in combination with AET eliminated tumor cells effectively. Furthermore, MMC alone enhanced genomic instability, but MMC combined with AET attenuated the extent of genomic instability in primary VX2 tumor tissue. Taken together, our data suggest that the genomic protector AET can inhibit the induction of SLCCs, and this combination treatment by AET and cytotoxic agents should be considered as a promising strategy for future clinical evaluation.
关键词: rabbit VX2 liver tumor mitomycin C AET stem-like cancer cells genomic instability
标题 作者 时间 类型 操作
Improving the prognosis of pancreatic cancer: insights from epidemiology, genomic alterations, and therapeutic
期刊论文
Primary assessment of the diversity of Omicron sublineages and the epidemiologic features of autumn/winter 2022 COVID-19 wave in Chinese mainland
期刊论文
Transforming bacterial disease surveillance and investigation using whole-genome sequence to probe the trace
null
期刊论文
Recent transmission of Mycobacterium tuberculosis in China: the implication of molecular epidemiology
null
期刊论文
The epidemiology of norovirus gastroenteritis in China: disease burden and distribution of genotypes
Honglu Zhou, Songmei Wang, Lorenz von Seidlein, Xuanyi Wang
期刊论文
GLOBAL GENOMIC PREDICTION IN HORTICULTURAL CROPS: PROMISES, PROGRESS, CHALLENGES AND OUTLOOK
Craig HARDNER, Satish KUMAR, Dorrie MAIN, Cameron PEACE
期刊论文
Topological reorganization and functional alteration of distinct genomic components in gallbladder cancer
期刊论文
Detection of genomic signatures for pig hairlessness using high-density SNP data
Ying SU,Yi LONG,Xinjun LIAO,Huashui AI,Zhiyan ZHANG,Bin YANG,Shijun XIAO,Jianhong TANG,Wenshui XIN,Lusheng HUANG,Jun REN,Nengshui DING
期刊论文
Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing
期刊论文