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The role of gene variants in the pathogenesis of neurodegenerative disorders as revealed by next generation sequencing studies:a review

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Translational Neurodegeneration 2017年第1期6卷 245-255页

作者： Shirley Yin-Yu Pang Kay-Cheong Teo Jacob Shujui Hsu Richard Shek-Kwan Chang Miaoxin Li Pak-Chung Sham Shu-Leong Ho Division of Neurology Department of MedicineQueen Mary HospitalUniversity of Hong KongHong KongPeople’s Republic of China Centre for Genomic Sciences University of Hong KongHong KongPeople’s Republic of China Department of Medical Genetics Zhongshan School of MedicineSun Yat-sen UniversityGuangzhouPeople’s Republic of China Key Laboratory of Tropical Disease Control(SYSU) Ministry of EducationGuangzhouPeople’s Republic of China

The clinical diagnosis of neurodegenerative disorders based on phenotype is difficult in heterogeneous conditions with overlapping *** does not take into account the disease etiology or the highly variable clinical course even amongst patients diagnosed with the same *** advent of next generation sequencing(NGS)has allowed for a system-wide,unbiased approach to identify all gene variants in the genome *** the plethora of new genes being identified,genetic rather than phenotype-based classification of Mendelian diseases such as spinocerebellar ataxia(SCA),hereditary spastic paraplegia(HSP)and Charcot-Marie-Tooth disease(CMT)has become widely *** has also become clear that gene variants play a role in common and predominantly sporadic neurodegenerative diseases such as Parkinson’s disease(PD)and amyotrophic lateral sclerosis(ALS).The observation of pleiotropy has emerged,with mutations in the same gene giving rise to diverse phenotypes,which further increases the complexity of phenotype-genotype *** mechanisms of pleiotropy include different downstream effects of different mutations in the same gene,presence of modifier genes,and oligogenic *** directions include development of bioinformatics tools and establishment of more extensive public genotype/phenotype databases to better distinguish deleterious gene variants from benign polymorphisms,translation of genetic findings into pathogenic mechanisms through in-vitro and in-vivo studies,and ultimately finding disease-modifying therapies for neurodegenerative disorders.

关键词： next generation sequencing Neurodegenerative diseases Genetics Pleiotropy

Fecal gene detection based on next generation sequencing for colorectal cancer diagnosis

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World Journal of Gastroenterology 2022年第25期28卷 2920-2936页

作者： Si-Yu He Ying-Chun Li Yong Wang Hai-Lin Peng Cheng-Lin Zhou Chuan-Meng Zhang Sheng-Lan Chen Jian-Feng Yin Mei Lin Department of Clinical Laboratory Taizhou People's Hospital(Postgraduate Training Base of Dalian Medical University)Taizhou 225300Jiangsu ProvinceChina Department of Clinical Laboratory The First People's Hospital of Tianmen CityTianmen 431700Hubei ProvinceChina Department of General Surgery Taizhou People's Hospital(Postgraduate Training Base of Dalian Medical University)Taizhou 225300Jiangsu ProvinceChina Central Laboratory Taizhou People's Hospital(Postgraduate training base of Dalian Medical University)Taizhou 225300Jiangsu ProvinceChina Department of Laboratory Taizhou Genewill Medical Laboratory Company LimitedTaizhou 225300Jiangsu ProvinceChina Department of Laboratory Jiangsu CoWin Biotech Co.Ltd.Taizhou 225300Jiangsu ProvinceChina

BACKGROUND Colorectal cancer(CRC)is one of the most common malignancies *** its insidious onset,the condition often already progresses to advanced stage when symptoms ***,early diagnosis is of great significance for timely clinical intervention,efficacy enhancement,and prognostic *** high throughput,fastness,and rich information,next generation sequencing(NGS)can greatly shorten the detection time,which is a widely used detection technique at *** To screen specific genes or gene combinations in fecal DNA that are suitable for diagnosis and prognostic prediction of CRC,and to establish a technological platform for CRC screening,diagnosis,and efficacy monitoring through fecal DNA *** NGS was used to sequence the stool DNA of patients with CRC,which were then compared with the genetic testing results of the stool samples of normal controls and patients with benign intestinal disease,as well as the tumor tissues of CRC *** genes or gene combinations in fecal DNA suitable for diagnosis and prognostic prediction of CRC were screened,and their significances in diagnosing CRC and predicting patients'prognosis were comprehensively *** High mutation frequencies of TP53,APC,and KRAS were detected in the stools and tumor tissues of CRC patients prior to ***,no pathogenic mutations of the above three genes were noted in the postoperative stools,the normal controls,or the benign intestinal disease *** indicates that tumor-specific DNA was detectable in the preoperative stools of CRC *** preoperative fecal expression of tumor-associated genes can reflect the gene mutations in tumor tissues to some *** to the postoperative stools and the stools in the two control groups,the pathogenic mutation frequencies of TP53 and KRAS were significantly higher for the preoperative stools(χ^(2)=7.328,P<0.05;χ^(2)=4.219,P<0.05),suggesting that fecal TP53 and KRAS ge

关键词： Colorectal cancer Feces next generation sequencing Diagnosis Gene

Sequence assembly using next generation sequencing data —challenges and solutions

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Science China(Life Sciences) 2014年第11期57卷 1140-1148页

作者： CHIN Francis Y.L. LEUNG Henry C.M. YIU S.M. Department of Computer Science The University of Hong Kong

Sequence assembling is an important step for bioinformatics *** the help of next generation sequencing(NGS)technology,high throughput DNA fragment(reads)can be randomly sampled from DNA or RNA molecular ***,as the positions of reads being sampled are unknown,assembling process is required for combining overlapped reads to reconstruct the original DNA or RNA *** with traditional Sanger sequencing methods,although the throughput of NGS reads increases,the read length is shorter and the error rate is *** introduces several problems in ***,paired-end reads instead of single-end reads can be sampled which contain more *** existing assemblers cannot fully utilize this information and fails to assemble longer *** this article,we will revisit the major problems of assembling NGS reads on genomic,transcriptomic,metagenomic and metatranscriptomic *** will also describe our IDBA package for solving these *** package has adopted several novel ideas in assembling,including using multiple k,local assembling and progressive depth *** with existence assemblers,IDBA has better performance on many simulated and real sequencing datasets.

关键词： genomic assembling de Bruijn graph paired-end reads next generation sequencing

Comparison of the experimental methods in haplotype sequencing via next generation sequencing

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Frontiers of Electrical and Electronic Engineering in China 2016年第2期4卷 106-114页

作者： Jing Tu Na Lu Mengqin Duan An Ju Xiao Sun Zuhong Lu State Key Laboratory of Bioelectronics Southeast University Nanjing 210096 China

Although the diploid nature has been observed for over 50 years, phasing the diploid is still a laborious task. The speed and throughput of next generation sequencing have largely increased in the past decades. However, the short read-length remains one of the biggest challenges of haplotype analysis. For instance, reads as short as 150 bp span no more than one variant in most cases. Numerous experimental technologies have been developed to overcome this challenge. Distance, complexity and accuracy of the linkages obtained are the main factors to evaluate the efficiency of whole genome haplotyping methods. Here, we review these experimental technologies, evaluating their efficiency in linkages obtaining and system complexity. The technologies are organized into four categories based on its strategy：（i） chromosomes separation, （ii） dilution pools, （iii） crosslinking and proximity ligation, （ix） long-read technologies. Within each category, several subsections are listed to classify each technology. Innovative experimental strategies are expected to have high-quality performance, low cost and be labor-saving, which will be largely desired in the future.

关键词： next generation sequencing haplotyping haplotype sequencing

next generation sequencing in Oncological Diagnostics: Hype or Hope?

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Journal of Biosciences and Medicines 2024年第2期12卷 244-256页

作者： Rana Hallak Manfred Kuepper Amer Al Chikh Youssef Department of Biochemistry Faculty of Pharmacy Al Rasheed University Ghabareb Syria Rana Hallak Clinical Laboratory Damascus Kafar Sousseh Syria Department of Biochemistry Faculty of Pharmacy Arab International University Ghabareb Syria Doctors Cancer Care Center Damascus Damascus Syria

The understanding of how genetic and epigenetic factors influence tumorigenesis, progression and invasion, is vastly growing since new technologies allow the analysis of the functional genome namely the exome, the transcriptome and the epigenome, besides enabling genome-wide assessment of genetic variations. With the advent of new drugs that are indicated tissue agnostic, depending on certain mutations, there is a growing demand for fast and cost-effective genetic diagnosis. The method in focus that already became an indispensable tool in viral diagnosis is next-generation sequencing (NGS). This approach allows sequencing of literally every DNA molecule in the sample and can either be used to assess numerous genetic markers of one patient at a time, or to assess fewer markers of many patients in parallel, which reduces costs. We submitted 23 samples of different tumor entities to four diagnostic companies with different analysis profiles. The results as disclosed and discussed in this report indicate that so far, the main application of NGS is rather in cancer research than in diagnosis, as none of the reports had a real impact on the therapeutic scheme. We are perfectly aware that such a small cohort cannot be generalized, but considering the costs vs. benefits, NGS should be engaged upon a very stringent evaluation only. However, in cases where obtaining a tissue biopsy is impossible or unfavorable, analysis of liquid biopsy by NGS provides a vital alternative.

关键词： Oncology next generation sequencing Tumor Diagnosis Personalized Medicine

A novel PIK3CD C896T mutation detected in bilateral sudden sensorineural hearing loss using next generation sequencing:An indication of primary immunodeficiency

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Journal of Otology 2016年第2期11卷 78-83页

作者： Jing Zou Xiangqiang Duan Guiliang Zheng Zhen Zhao Shiyue Chen Pu Dai Hongliang Zheng Department of Otolaryngology-Head and Neck Surgery Center for Otolaryngology-Head & Neck Surgery of Chinese PLA Changhai Hospital Second Military Medical University Department of Radiology National Key Discipline Changhai Hospital Second Military Medical University Department of Otolaryngology-Head and Neck Surgery Chinese PLA General Hospital

Objective:To investigate immune-related genetic background in bilateral sudden sensorineural hearing loss (SSNHL). Case report and methods: The case is a 45-year-old man presenting with a 7-year history of bilateral profound SSNHL. Blood biochemical testing demonstrated increased levels of total cholesterol (5.88 mmol/L). Tests for hepatitis B showed a positive antibody against the hepatitis B core antigen. Complement C3 was below the normal value, and complement C4 and IgG were in the lower range of normal values. CT images showed a normal inner ear and vestibular aqueduct but round window membranous ossification on both sides. A total number of 232 immune-associated genes were sequenced using the next generation sequencing technique. Results: Mutations were detected in 5 genes, including the phosphoinositide 3-kinase catalytic subunit delta (PIK3CD), caspase recruitment domain-containing protein 9 (CARD9), complement factor H-related (CFHR2), immunoglobulin lambda-like polypeptide 1 Protein (IGLL1), and transmembrane channel-like gene family 8 (TMC8). In the PIK3CD gene, a C896T substitute in exon 7 was detected. This mutation causes primary immunodeficiency and is an autosomal dominant disease. Conclusion: The PIK3CD C896T mutation responsible for primary immunodeficiency may contribute to the onset of bilateral SSNHL with subsequent rapid progression.

关键词： Sudden sensorineural hearing loss Immunology Genetics next generation sequencing

Confidence intervals for Markov chain transition probabilities based on next generation sequencing reads data

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Quantitative Biology 2020年第2期8卷 143-154页

作者： Lin Wan Xin Kang Jie Ren Fengzhu Sun NCMIS LSCAcademy of Mathematics and Systems ScienceChinese Academy of SciencesBeijing 100190China School of Mathematical Sciences Fudan UniversityShanghai 200433China Quantitative and Computational Biology Program University of Southern CaliforniaLos AngelesCA 90089USA

Background:Markov chains(MC)have been widely used to model molecular *** estimations of MC transition matrix and confidence intervals of the transition probabilities from long sequence data have been intensively studied in the past *** next generation sequencing(NGS),a large amount of short reads are *** short reads can overlap and some regions of the genome may not be sequenced resulting in a new type of *** on NGS data,the transition probabilities of MC can be estimated by moment ***,the classical asymptotic distribution theory for MC transition probability estimators based on long sequences is no longer ***:In this study,we present the asymptotic distributions of several statistics related to MC based on NGS *** show that,after scaling by the effective coverage d defined in a previous study by the authors,these statistics based on NGS data approximate to the same distributions as the corresponding statistics for long ***:We apply the asymptotic properties of these statistics for finding the theoretical confidence regions for MC transition probabilities based on NGS short reads *** validate our theoretical confidence intervals using both simulated data and real data sets,and compare the results with those by the parametric bootstrap ***:We find that the asymptotic distributions of these statistics and the theoretical confidence intervals of transition probabilities based on NGS data given in this study are highly accurate,providing a powerful tool for NGS data analysis.

关键词： Markov chains next generation sequencing transition probabilities confidence intervals

next generation sequencing in oral disease diagnostics

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World Journal of Stomatology 2018年第2期6卷 6-10页

作者： Gokul Sapna Sridharan Gokul Department of periodontics Nair Hospital Dental College Oral Pathology and Microbiology YMT Dental College and Hospital

DNA sequencing is the method of identifying the precise order of DNA nucleotides within a molecule. The information of DNA sequencing is of prime requisite for basic biological research as well as in various clinical *** can be used to determine the individual genetic sequence, larger genetic regions, chromosomes as well as to sequence RNA and proteins. Since the first DNA sequencing in 1970s, there has been tremendous advancements in the technologies aimed to determine the entire human genome. The need for rapid and accurate sequencing of human genome has resulted in the introduction of next generation sequencing(NGS) technology. NGS refers to the secondgeneration DNA sequencing technologies where millions of DNA can be sequenced simultaneously. Some of the next gen sequencing methods employed are Roche/454 life science, Illumina/Solexa, SOLiD system and *** of NGS in decoding the genomic database of various oral diseases may possess therapeutic and prognostic value. This presentation provides an overview of the basics of NGS and their potential applications in oral disease diagnostics.

关键词： Molecular diagnostics next generation sequencing Illumina Oral diseases Oral cancer

next generation sequencing of DNA pools

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Next generation sequencing of DNA pools