检索结果-南通市图书馆

Measurement of copy number variation in single cancer cells using rapid-emulsification digital droplet MDA

在线全文

学校读者我要写书评

暂无评论

Microsystems & Nanoengineering 2017年第1期3卷 260-266页

作者： Samuel C.Kim Gayatri Premasekharan Iain C.Clark Hawi B.Gemeda Pamela L.Paris Adam R.Abate Department of Bioengineering and Therapeutic Sciences University of CaliforniaSan Francisco(UCSF)California Institute for Quantitative Biosciences(QB3)San FranciscoSan FranciscoCA 94158USA Department of Urology Division of Hematology&OncologyUniversity of CaliforniaSan Francisco(UCSF)San FranciscoCA 94158USA

Uniform amplification of low-input DNA is important for applications across biology,including single-cell genomics,forensic science,and microbial and viral ***,the requisite biochemical amplification methods are prone to bias,skewing sequence proportions and obscuring signals relating to copy *** droplet multiple displacement amplification enables uniform amplification but requires expert knowledge of microfluidics to generate monodisperse *** addition,existing microfluidic methods are tedious and labor intensive for preparing many ***,we introduce rapid-emulsification multiple displacement amplification,a method to generate monodisperse droplets with a hand-held syringe and hierarchical droplet *** conventional microfluidic devices require >10 min to emulsify a sample,our system requires tens of seconds and yields data of equivalent *** demonstrate the approach by using it to accurately measure copy number variation(CNV)in single cancer cells.

关键词： amplification bias copy number variation ddMDA droplet microfluidics multiple displacement amplification

Scan of the endogenous retrovirus sequences across the swine genome and survey of their copy number variation and sequence diversity among various Chinese and Western pig breeds

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Zoological Research 2022年第3期43卷 423-441页

作者： Jia-Qi Chen Ming-Peng Zhang Xin-Kai Tong Jing-Quan Li Zhou Zhang Fei Huang Hui-Peng Du Meng Zhou Hua-Shui Ai Lu-Sheng Huang State Key Laboratory for Swine Genetic Improvement and Production Technology Jiangxi Agricultural UniversityNanchangJiangxi 330045China

In pig-to-human xenotransplantation,the transmission risk of porcine endogenous retroviruses(PERVs)is of great ***,the distribution of PERVs in pig genomes,their genetic variation among Eurasian pigs,and their evolutionary history remain *** scanned PERVs in the current pig reference genome(assembly Build 11.1),and identified 36 long complete or near-complete PERVs(lc PERVs)and 23 short incomplete PERVs(si PERVs).Besides three known PERVs(PERV-A,-B,and-C),four novel types(PERV-JX1,-JX2,-JX3,and-JX4)were detected in this *** to evolutionary analyses,the newly discovered PERVs were more ancient,and PERV-Bs probably experienced a bottleneck~0.5 million years ago(Ma).By analyzing63 high-quality porcine whole-genome resequencing data,we found that the PERV copy numbers in Chinese pigs were lower(32.0±4.0)than in Western pigs(49.1±6.5).Additionally,the PERV sequence diversity was lower in Chinese pigs than in Western *** the lc PERV copy numbers,PERV-A and-JX2 in Western pigs were higher than in Chinese ***,Bama Xiang(BMX)pigs had the lowest PERV copy number(27.8±5.1),and a BMX individual had no PERV-C and the lowest PERV copy number(23),suggesting that BMX pigs were more suitable for screening and/or modification as xenograft ***,we identified 451 PERV transposon insertion polymorphisms(TIPs),of which 86 were shared by all 10 Chinese and Western pig *** findings provide systematic insights into the genomic distribution,variation,evolution,and possible biological function of PERVs.

关键词： PERVs Chinese and Western pigs copy number variation Evolutionary history Biological function prediction

Clinical significance of germline copy number variation in susceptibility of human diseases

在线全文

学校读者我要写书评

暂无评论

Journal of Genetics and Genomics 2018年第1期45卷 3-12页

作者： Liwen Hu Xinyue Yao Hairong Huang Zhong Guo Xi Cheng Yang Xu Yi Shen Biao Xu Demin Li Department of Cardiothoracic Surgery Jinling Hospital School of Clinical Medicine Nanjing University Institute of Laboratory Medicine Jinling Hospital School of Clinical Medicine Nanjing University

Germline copy number variation （CNV） is considered to be an important form of human genetic poly- morphisms. Previous studies have identified amounts of CNVs in human genome by advanced technologies, such as comparative genomic hybridization, single nucleotide genotyping, and high-throughput sequencing. CNV is speculated to be derived from multiple mechanisms, such as nonallelic homologous recombination （NAHR） and nonhomologous end-joining （NHEJ）. CNVs cover a much larger genome scale than single nucleotide polymorphisms （SNPs）, and may alter gene expression levels by means of gene dosage, gene fusion, gene disruption, and long-range regulation effects, thus affecting individual phenotypes and playing crucial roles in human pathogenesis. The number of studies linking CNVs with common complex diseases has increased dramatically in recent years. Here, we provide a comprehensive review of the current understanding ofgermline CNVs, and summarize the association of germline CNVs with the susceptibility to a wide variety of human diseases that were identified in recent years. We also propose potential issues that should be addressed in future studies.

关键词： copy number variation Susceptibility Risk Cancer Neuropsychological disorders

Next‑Generation Sequencing‑Based copy number variation Analysis in Chinese Patients with Primary Ciliary Dyskinesia Revealed Novel DNAH5 copy number variations

在线全文

学校读者我要写书评

暂无评论

Phenomics 2024年第1期4卷 24-33页

作者： Weicheng Chen Zhuoyao Guo Mengru Li Wei Sheng Guoying Huang Cardiovascular Center Children’s Hospital of Fudan University399 Wanyuan RoadShanghai 201102China Respirology Department Children’s Hospital of Fudan UniversityShanghai 201102China

Primary ciliary dyskinesia(PCD)is a rare disorder characterized by extensive genetic ***,in the genetic pathogenesis of PCD,copy number variation(CNV)has not received sufcient attention and has rarely been reported,especially in ***-generation sequencing(NGS)followed by targeted CNV analysis was used in patients highly suspected to have PCD with negative results in routine whole-exome sequencing(WES)*** real-time polymerase chain reaction(qPCR)and Sanger sequencing were used to confrm these *** further characterize the ciliary phenotypes,high-speed video microscopy analysis(HSVA),transmission electron microscopy(TEM),and immunofuorescence(IF)analysis were *** 1(F1:II-1),a 0.6-year-old girl,came from a nonconsanguineous *** presented with situs inversus totalis,neonatal respiratory distress,and *** nasal nitric oxide level was markedly *** respiratory cilia beat with reduced *** revealed shortened outer dynein arms(ODA)of ***5:13717907-13722661del spanning exons 71–72 was identifed by NGS-based CNV *** 2(F2:IV-4),a 37-year-old man,and his eldest brother Patient 3(F2:IV-2)came from a consanguineous *** had sinusitis,bronchiectasis and situs inversus *** respiratory cilia of Patient 2 and Patient 3 were found to be uniformly immotile,with ODA *** novel homozygous deletions chr5:13720087_13733030delinsGTTTTC and chr5:13649539_13707643del,spanning exons 69–71 and exons 77–79 were identifed by NGS-based CNV *** in DNA copy number were confrmed by qPCR *** showed that the respiratory cilia of Patient 1 and Patient 2 were defcient in dynein axonemal heavy chain 5(DNAH5)protein *** report identifed three novel DNAH5 disease-associated variants by WES-based CNV *** study expands the genetic spectrum of PCD with DNAH5 in the Chinese population.

关键词： Primary ciliary dyskinesia DNAH5 gene copy number variation Phenotypic heterogeneity

Genetic copy number variations in Colon Mucosa Indicating Risk for Colorectal Cancer

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Journal of Cancer Therapy 2014年第14期5卷 1354-1361页

作者： Annika Gustafsson Asting Kristina K.Lagerstedt Erik Kristiansson Christina Lonnroth Marianne Andersson Elham Rekabdar Elisabeth Hansson Ulf Kressner Fredrik Enlund Kent Lundholm Department of Surgery Surgical Metabolic Research LaboratorySahlgrenska University HospitalUniversity of GothenburgGothenburgSweden Department of Mathematical Sciences Mathematical StatisticsChalmers University of TechnologyGothenburgSweden Genomics Core Facility Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden Department of Surgery Uddevalla HospitalUddevallaSweden Department of Surgery Danderyds HospitalStockholmSweden Department of Surgery South HospitalStockholmSweden Department of Clinical Chemistry Sahlgrenska University HospitalUniversity of GothenburgGothenburgSweden

Background: Sporadic colorectal tumors probably carry genetic alterations that may be related to familiar clusters according to risk loci visualized by SNP arrays on normal tissues. The aim of the present study was therefore to search for DNA regions (copy number variations, CNVs) as biomarkers associated to genetic susceptibility for early risk predictions of colorectal cancer. Such sequence alterations could provide additional information on phenotypic grouping of patients. Material and Methods: High resolution 105K oligonucleotide microarrays were used in search for CNV loci in DNA from tumor-free colon mucosa at primary operations for colon cancer in 60 unselected patients in comparison to DNA in buffy coat cells from 44 confirmed tumor-free and healthy blood donors. Array-detected CNVs were confirmed by Multiplex ligation-dependent probe amplification (MLPA). Results: A total number of 205 potential CNVs were present in DNA from colon mucosa. 184 (90%) of the 205 potential CNVs had been identified earlier in mucosa DNA from healthy individuals as reported to the Database of Genomic Variants. Remaining 21 (10%) CNVs were potentially novel sites. Two CNVs (3q23 and 10q21.1) were significantly related to colon cancer, but not confirmed in buffy coat DNA from the cancer patients. Conclusion: Our study reveals two CNVs that indicate increased risk for colon cancer;These DNA alterations may have? been acquired by colon stem cells with subsequent appearance among epithelial mucosa cells. Impact: Certain mucosa CNV alterations may indicate individual susceptibility for malignant transformation in relationship to intestinal toxins and bacterial growth.

关键词： copy number variation DNA Array CGH Colorectal Cancer

De novel heterozygous copy number deletion on 7q31.31-7q31.32 involving TSPAN12 gene with familial exudative vitreoretinopathy in a Chinese family

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

International Journal of Ophthalmology(English edition) 2023年第12期16卷 1952-1961页

作者： Shuang Zhang Hai-Ming Yong Gang Zou Mei-Jiao Ma Xue Rui Shang-Ying Yang Xun-Lun Sheng People’s Hospital of Ningxia Hui Autonomous Region Ningxia Medical UniversityNingxia Eye HospitalNingxia Clinical Research Center on Diseases of Blindness in EyeYinchuan 750001Ningxia Hui Autonomous RegionChina

AIM:To investigate the genetic and clinical characteristics of patients with a large heterozygous copy number deletion on ***:A family with familial exudative vitreoretinopathy(FEVR)phenotype was included in the ***-exome sequencing(WES)was initially used to locate copy number variations(CNVs)on 7q31.31-31.32,but failed to detect the precise *** long-read sequencing,Oxford Nanopore sequencing Technology(ONT)was used to get the accurate breakpoint which is verified by quantitative real-time polymerase chain reaction(QPCR)and Sanger ***:The proband,along with her father and younger brother,were found to have a heterozygous 4.5 Mb CNV deletion located on 7q31.31-31.32,which included the FEVRrelated gene *** specific deletion was confirmed as del(7)(q31.31q31.32)chr7:g.119451239_*** proband exhibited a phase 2A FEVR phenotype,characterized by a falciform retinal fold,macular dragging,and peripheral neovascularization with leaking of *** symptoms led to a significant decrease in visual acuity in both *** the other hand,the affected father and younger brother showed a milder ***:The heterozygous CNV deletion located on 7q31.31-7q31.32 is associated with the FEVR *** use of long-read sequencing techniques is essential for accurate molecular diagnosis of genetic disorders.

关键词： familial exudative vitreoretinopathy copy number variation copy number deletion TSPAN12 longread sequencing

Integrated Analysis of the Gene Expression Profiling and copy number Aberration of the Ovarian Cancer

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Journal of Cancer Therapy 2021年第6期12卷 387-398页

作者： Xi Liu Zhongqiang Liu Wanxin Yu Ning Zhan Liangxi Xie Wenjia Xie Zongda Zhu Zhenxiang Deng School of Medical Information and Engineering Guangdong Pharmaceutical University Guangzhou China Guangdong Province Precise Medicine and Big Data Engineering Technology Research Center for Traditional Chinese Medicine Guangzhou China Department of Radiation Oncology Nanfang Hospital Southern Medical University Guangzhou China Quanzhou First Hospital Affiliated to Fujian Medical University Quanzhou China Department of Radiation Oncology Xiang’an Hospital of Xiamen University School of Medicine Xiamen University Xiamen China

Objective: DNA copy number alterations and difference expression are frequently observed in ovarian cancer. The purpose of this way was to pinpoint gene expression change that was associated with alterations in DNA copy number and could therefore enlighten some potential oncogenes and stability genes with functional roles in cancers, and investigated the bioinformatics significance for those correlated genes. Method: We obtained the DNA copy number and mRNA expression data from the Cancer Genomic Atlas and identified the most statistically significant copy number alteration regions using the GISTIC. Then identified the significance genes between the tumor samples within the copy number alteration regions and analyzed the correlation using a binary matrix. The selected genes were subjected to bioinformatics analysis using GSEA tool. Results: GISTIC analysis results showed there were 45 significance copy number amplification regions in the ovarian cancer, SAM and Fisher’s exact test fou

关键词： Ovarian Cancer copy number variation Gene Differential Expression SAM Method GISTIC Method

Overexpression of anillin is related to poor prognosis in patients with hepatocellular carcinoma

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Hepatobiliary & Pancreatic Diseases International 2021年第4期20卷 337-344页

作者： Long-Hui Zhang Dong Wang Zhao Li Gang Wang Ding-Bao Chen Qian Cheng Shi-Hua Hu Ji-Ye Zhu Department of Hepatobiliary Surgery Peking University People’s HospitalBeijing 100044China Peking University Institute for Organ Transplantation Beijing 100044China Beijing Key Laboratory of Liver Cirrhosis and Liver Cancer Beijing 100044China Department of Pathology Peking University People’s HospitalBeijing 100044China

Background: Anillin(ANLN) is required for tumor growth. It has been proven that knockdown of ANLN effectively reduces the occurrence of hepatocellular carcinoma(HCC) in transgenic mice. However, the functional role of ANLN in HCC patients remains to be elucidated. Methods: Both microarray and TCGA project were used for the analyses of ANLN expression and regulation in HCC. The effect of ANLN on proliferation and cell cycle was detected by CCK-8, colony formation assay and flow cytometry. ANLN expression was measured by immunohistochemistry. Correlation between ANLN expression and clinicopathological features was assessed by Pearson Chi-square test and 5-year overall survival after liver resection was evaluated by Kaplan–Meier method. Results: Increased copy number, decreased methylation levels in the Cp G island and upregulated histone hypermethylation of ANLN were found in HCC. Knockdown of ANLN inhibited proliferation and induced G2/M phase arrest in SMMC-7721 cells. ANLN was mainly expressed in the nucleus and showed significantly higher expression levels in cancerous tissues than those in paired adjacent tissues. Moreover, nuclear ANLN expression levels in HCC metastases were significantly higher than those in primary HCC. The results of Cox proportional hazards regression model suggested that ANLN nuclear expression in HCC was an independent risk factor for poor 5-year overall survival of patients after liver resection. Conclusions: ANLN is a potential therapeutic target for HCC. Patients with nuclear ANLN overexpression in HCC tissue may need adjuvant therapy after liver resection.

关键词： Anillin DNA methylation copy number variation Hepatocellular carcinoma Prognosis

Comparative genomic analysis of esophageal squamous cell carcinoma and adenocarcinoma:New opportunities towards molecularly targeted therapy

在线全文

学校读者我要写书评

暂无评论

Acta Pharmaceutica Sinica B 2022年第3期12卷 1054-1067页

作者： Xu Zhang Yuxiang Wang Linghua Meng Division of Anti-tumor Pharmacology Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China University of Chinese Academy of Sciences Beijing 100049China

Esophageal cancer is one of the most lethal cancers worldwide because of its rapid progression and poor *** squamous cell carcinoma(ESCC)and esophageal adenocarcinoma(EAC)are two major subtypes of esophageal *** predominantly affects African and Asian populations,which is closely related to chronic smoking and alcohol *** typically arises in Barrett’s esophagus with a predilection for Western *** surgical operation and chemoradiotherapy have been applied to combat this deadly cancer,molecularly targeted therapy is still at the early *** the development of large-scale next-generation sequencing,various genomic alterations in ESCC and EAC have been revealed and their potential roles in the initiation and progression of esophageal cancer have been *** therapeutic targets have been identified and novel approaches have been developed to combat esophageal *** this review,we comprehensively analyze the genomic alterations in EAC and ESCC and summarize the potential role of the genetic alterations in the development of esophageal *** in the therapeutics based on the different tissue types and molecular signatures have also been reviewed and discussed.

关键词： Esophageal cancer Esophageal squamous cell carcinoma Esophageal adenocarcinoma Next-generation sequencing Genomic alteration Somatic mutation copy number variation Molecularly targeted therapy