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Exome sequencing greatly expedites the progressive research of Mendelian diseases
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《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
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
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
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
关键词: Clouston syndrome whole exome sequencing GJB6 gene novel variant unique phenotype
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《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
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.
《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
Liru Qiu, Fengjie Yang, Yonghua He, Huiqing Yuan, Jianhua Zhou
《医学前沿(英文)》 2018年 第12卷 第5期 页码 550-558 doi: 10.1007/s11684-017-0567-y
Cystic fibrosis (CF) is a fatal autosomal-recessive disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. CF is characterized by recurrent pulmonary infection with obstructive pulmonary disease. CF is common in the Caucasian population but is rare in the Chinese population. The symptoms of early-stage CF are often untypical and may sometimes manifest as Bartter syndrome (BS)-like hypokalemic alkalosis. Therefore, the ability of doctors to differentiate CF from BS-like hypokalemic alkalosis in Chinese infants is a great challenge in the timely and accurate diagnosis of CF. In China, sporadic CF has not been diagnosed in children younger than three years of age to date. Three infants, who were initially admitted to our hospital over the period of June 2013 to September 2014 with BS-like hypokalemic alkalosis, were diagnosed with CF through exome sequencing and sweat chloride measurement. The compound heterozygous mutations of the CFTR gene were detected in two infants, and a homozygous missense mutation was found in one infant. Among the six identified mutations, two are novel point mutations (c.1526G>C and c.3062C>T) that are possibly pathogenic. The three infants are the youngest Chinese patients to have been diagnosed with sporadic CF at a very early stage. Follow-up examination showed that all of the cases remained symptom-free after early intervention, indicating the potential benefit of very early diagnosis and timely intervention in children with CF. Our results demonstrate the necessity of distinguishing CF from BS in Chinese infants with hypokalemic alkalosis and the significant diagnostic value of powerful exome sequencing for rare genetic diseases. Furthermore, our findings expand the CFTR mutation spectrum associated with CF.
关键词: cystic fibrosis pseudo-Bartter syndrome hypokalemic alkalosis CFTR gene mutations infants diagnosis
《医学前沿(英文)》 2021年 第15卷 第3期 页码 438-447 doi: 10.1007/s11684-020-0826-1
关键词: sporadic thoracic aortic dissection exome sequencing gene COL3A1 case–control study extracellular matrix
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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
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
● Wastewater MPs exhibited resistomes and therefore health threats.
关键词: Microplastics Whole-genome metagenomic sequencing Plastisphere Plastic degradation MHETase
多囊卵巢综合征无排卵的胰岛素信号和雄激素合成的新遗传风险和代谢特征 Article
吴效科, 黄志超, 曹义娟, 李建, 李志强, 马红丽, 高敬书, 常惠, 张多加, 丛晶, 王宇, 吴奇, Xiaoxiao Han, Pui Wah Jacqueline Chung, Yiran Li, Xu Zheng, Lingxi Chen, Lin Zeng, Astrid Borchert, Hartmut Kuhn, Zi-Jiang Chen, Ernest Hung Yu Ng, Elisabet Stener-Victorin, 张和平, Richard S. Legro, Ben Willem J. Mol, 师咏勇
《工程(英文)》 2023年 第23卷 第4期 页码 103-111 doi: 10.1016/j.eng.2022.08.013
促排卵是多囊卵巢综合征(PCOS)不孕症的一线治疗方案。卵巢对促排卵治疗的排卵应答差被认为与胰岛素抵抗和高雄激素血症相关。在一个包含1000名PCOS不孕妇女(PCOSAct)的前瞻性队列中,我们开展了一项全外显子联合靶向单核苷酸多态性(SNP)测序以及代谢组学研究。在全基因组水平找出与无排卵显著相关的常见变异和罕见突变,并通过机器学习算法构建排卵预测模型。研究发现,ZNF438基因中标记为rs2994652 (p=2.47×10–8)的常见变异和REC114基因中的一个罕见功能突变(rs182542888,p=5.79×10–6)与促排卵治疗失败显著相关。携带rs2994652 A等位基因和REC114 p.Val101Leu (rs182542888)的PCOS不孕妇女进行促排卵治疗的总排卵率更低(分别为:比值比 (OR)=1.96,95% 置信区间(CI)[1.55~2.49];OR=11.52,95% CI [3.08~43.05]),出现排卵的间隔时间更长(平均56.7天vs.49.0天,p<0.001;78.1天vs.68.6天,p=0.014)。对于rs2994652突变者,L-苯丙氨酸水平升高并与胰岛素抵抗稳态模型(HOMA-IR)指数(r=0.22, p=0.05)和空腹血糖(r=0.33, p=0.003)呈正相关;对于rs182542888突变者,花生四烯酸代谢产物水平下降并与升高的抗苗勒管激素(r=-0.51, p=0.01)和总睾酮(r=-0.71, p=0.02)呈负相关。整合基因变异位点、代谢产物及临床特征的联合预测模型可提高对排卵的预测能力[曲线下面积(AUC)=76.7%]。ZNF438基因的一个常见变异和REC114基因的一个罕见功能突变,以及与二者相关的苯丙氨酸和花生四烯酸代谢物改变,与PCOS女性不孕症的促排卵治疗失败相关。
《工程管理前沿(英文)》 页码 439-454 doi: 10.1007/s42524-022-0211-7
关键词: megaproject organizational evolution whole lifecycle management project management team
Cell surface protein engineering for high-performance whole-cell catalysts
Hajime Nakatani,Katsutoshi Hori
《化学科学与工程前沿(英文)》 2017年 第11卷 第1期 页码 46-57 doi: 10.1007/s11705-017-1609-3
关键词: cell surface engineering surface display whole-cell catalysts bioprocess
Efficient acetoin production from pyruvate by engineered whole-cell biocatalysis
《化学科学与工程前沿(英文)》 2023年 第17卷 第4期 页码 425-436 doi: 10.1007/s11705-022-2229-0
关键词: acetoin pyruvate α-acetolactate synthetase α-acetolactate decarboxylase Halomonas bluephagenesis whole-cell biocatalysis
Whole-life Thinking and Engineering the Future
Roger Flanagan
《工程管理前沿(英文)》 2014年 第1卷 第3期 页码 290-296 doi: 10.15302/J-FEM-2014040
关键词: whole-life thinking systems thinking complexity chaos risk management through life
《医学前沿(英文)》 2022年 第16卷 第2期 页码 240-250 doi: 10.1007/s11684-021-0909-7
标题 作者 时间 类型 操作
A novel variant in the gene in a large Chinese family with a unique phenotype of Clouston syndrome
期刊论文
TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways
null
期刊论文
Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing
期刊论文
Clinical characterization and diagnosis of cystic fibrosis through exome sequencing in Chinese infants
Liru Qiu, Fengjie Yang, Yonghua He, Huiqing Yuan, Jianhua Zhou
期刊论文
Identification of variants associated with sporadic thoracic aortic dissection: a case--control study
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
多囊卵巢综合征无排卵的胰岛素信号和雄激素合成的新遗传风险和代谢特征
吴效科, 黄志超, 曹义娟, 李建, 李志强, 马红丽, 高敬书, 常惠, 张多加, 丛晶, 王宇, 吴奇, Xiaoxiao Han, Pui Wah Jacqueline Chung, Yiran Li, Xu Zheng, Lingxi Chen, Lin Zeng, Astrid Borchert, Hartmut Kuhn, Zi-Jiang Chen, Ernest Hung Yu Ng, Elisabet Stener-Victorin, 张和平, Richard S. Legro, Ben Willem J. Mol, 师咏勇
期刊论文
Organizational evolution of project management teams over the whole lifecycle of megaprojects: Case study
期刊论文
Cell surface protein engineering for high-performance whole-cell catalysts
Hajime Nakatani,Katsutoshi Hori
期刊论文