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Comprehensive genetic diagnosis of patients with Duchenne/Becker muscular dystrophy(DMD/BMD) and pathogenicity analysis of splice site variants in the DMD gene

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2019年第9期20卷 753-771页

作者： Yan-mei YANG Kai YAN Bei LIU Min CHEN Li-ya WANG Ying-zhi HUANG Ye-qing QIAN Yi-xi SUN Hong-ge LI Min-yue DONG Department of Reproductive genetics Women's HospitalSchool of MedicineZhejiang UniversityHangzhou 310006China Key Laboratory of Reproductive genetics(Zhejiang University) Ministry of EducationHangzhou 310006China Key Laboratory of Women's Reproductive Health of Zhejiang Province Hangzhou 310006China

Duchenne muscular dystrophy(DMD)and Becker muscular dystrophy(BMD)are caused by mutations in the DMD *** aim of this study is to identify pathogenic DMD variants in probands and reduce the risk of recurrence of the disease in affected *** in 100 unrelated DMD/BMD patients were detected by multiplex ligation-dependent probe amplification(MLPA)and next-generation sequencing(NGS).Pathogenic variants in DMD were successfully identified in all cases,and 11 of them were *** most common mutations were intragenic deletions(69%),with two hotspots located in the 5'end(exons 2–19)and the central of the DMD gene(exons 45–55),while point mutations were observed in 22%***,c.1149+1G>A and c.1150?2A>G were confirmed by hybrid minigene splicing assay(HMSA).This two splice site mutations would lead to two aberrant DMD isoforms which give rise to severely truncated ***,the clinical use of MLPA,NGS,and HMSA is an effective strategy to identify ***,eight embryos were terminated pregnancies according to prenatal diagnosis and a healthy boy was successfully delivered by preimplantation genetic diagnosis(PGD).Early and accurate genetic diagnosis is essential for prenatal diagnosis/PGD to reduce the risk of recurrence of DMD in affected families.

关键词： Dystrophin gene Variation genetic diagnosis Splice site mutation Hybrid minigene splicing assay

genetic diagnosis and Prenatal diagnosis of Haemophilia B in China by DHPLC and Direct Sequencing

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Genetic Diagnosis and Prenatal Diagnosis of Haemophilia B in...

Study on genetic diagnosis of Spinal Muscular Atrophy

广东省遗传学会第九届代表大会暨学术研讨会

作者： X Xiao XY.Lin SQ.Chen HY.Li YB.Guo WY.Jiang Department of Medical genetics Medical SchoolSun Yat-Sen University

Introduction Denaturing High Performance Liquid Chromatography(DHPLC)is accurate,sensitive,economic and high-throughput for detecting *** aim to establish a feasible protocol to provide genetic diagnosis and prenatal diagnosis for Chinese hemophilia B patients and carriers by DHPLC and *** The genetic diagnosis was performed on 5 unrelated families,and 4 of them asked for prenatal *** The results of DHPLC and Sequence analysis indicated that the patients and carriers from five families have the pathogenic mutations,c.l022G>A(p.R341Q),c.484C>T(p.R162X),***35C>T(p.R379X),c.799C>T(p.H267Y)and c.l232G>T(p.S4III),*** c.484C>T(p.R162X),the other4 mutations were firstly reported firstly in Chinese *** prenatal diagnosis,one of the fetuses was found to be hemizygote with the c.484C>T(p.R162X) mutation and another two fetus were found to be carriers of c.484C>T/C(p.R162X/C) and c.799C>T/C(p.H267Y/H) *** remaining two fetuses were diagnosed as normal and it was verified after they were *** A combination of DNA direct-sequencing with DHPLC is rapid and accurate for the genetic diagnosis including prenatal diagnosis of hemophilia B ***,the level of F9 clotting activity in umbilical cord blood couldn’t be used as a reference resource in the prenatal diagnosis of HB.

关键词： Hemophilia B genetic diagnosis Prenatal diagnosis Denaturing High Performance Liquid Chromatography(DHPLC) Direct-sequencing

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The Journal of Biomedical Research 1998年第1期22卷 2-6页

作者：丁新生姚娟程虹王颖侯熙德

An improved method of mismatching polymerase chain reactionrestrictive fragment length polymorphisms(PCR-RFLP) was performed in our lab for genetic diagnosis of spinal muscular atrophy(SMA). PCR amplification and restriction endonuclease digestion of exons 7 and 8 permit distinction of the telomeric survival motor neuron (SMN) gene and its centromeric copy. Lack of a PCR product from either exon and from either gene is indicative of homozygous deletion of that sequence, and a high correlation with clinical SMA. Our data showed: 9 cases in 10 presumed SMA children were positive, i.e. deletion of telomeric SMN gene. One case was negative. 20 cases of normal familial members and 20 cases of normal health persons were all negative. Our results matched the criteria and reports of foreign countries. The method we used is highly specific, sensitive and reliable and is suitable for genetic diagnosis of SMA and its prenatal diagnosis.

关键词： SMA genetic diagnosis PCR-RFLP genetic deletion

Improving genetic diagnosis of Mendelian disease with RNA sequencing:a narrative review

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Journal of Bio-X Research 2022年第1期5卷 1-6页

作者： Zhou Zhou Qing Sang Lei Wang Institute of Pediatrics Children's Hospital of Fudan Universitythe Shanghai Key Laboratory of Medical Epigeneticsthe Intemational Co-laboratory of Medical Epigenetics and Metabolismthe Ministry of Science and Technologythe Institutes of Biomedical Sciencesand the State Key L aboratory of Genetic EngineeringFudan University Shanghai Center for Women and Children's Health ShanghaiChina

Targeted sequencing and whole exome sequencing are the most common approaches used to detect causative variants in Mendelian diseases;however, using DNA-based sequencing techniques, the current molecular diagnostic yield is at best 50%. In recent years, RNA sequencing has been shown to be able to provide a genetic diagnosis in patients whose conditions were previously unable to be identified by DNA analysis. RNA sequencing can reveal expression outliers, aberrant splicing events, allele-specific expression, and new pathogenic variants, and as such can complement and expand on the traditional genomic methods used to diagnose Mendelian diseases. Therefore, RNA sequencing is expected to become a routine method for genetic diagnosis in the future. This article reviews the applications and challenges of RNA sequencing in the genetic diagnosis of Mendelian diseases.

关键词： aberrant splicing genetic diagnosis Mendelian disease review RNA sequencing

Comprehensive genetic diagnosis of Patients with DMD/BMD and Pathogenicity Analysis of Novel Splice-Site Variants in the DMD Gene

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Comprehensive Genetic Diagnosis of Patients with DMD/BMD and...

Beyond monogenetic rare variants:tackling the low rate of genetic diagnoses in predominantly antibody deficiency

2018年浙江省医学遗传学学术年会

作者： Yanmei Yang Kai Yan Bei Liu Liya Wang Min Chen Yingzhi Huang cYeqing Qian Yixi Sun Yuqin Luo Min-Yue Dong Women's Hospital Zhejiang University School of Medicine Key Laboratory of Reproductive genetics (Zhejiang University) Ministry of Education Key Laboratory of Women's Reproductive Health of Zhejiang Province

Background and Purpose:Duchenne muscular dystrophy(DMD) and Becker muscular dystrophy(BMD) are caused by mutations in the dystrophin gene(DMD).The aim of this study is to identify pathogenic DMD variants in probands and reduce the risk of recurrence of the disease in affected ***:DMD variations in 100 unrelated DMD/BMD patients were detected by multiplex ligationdependent probe amplification(MLPA),next-generation sequencing(NGS),and Sanger *** minigene splicing assay(HMSA) was performed to investigate the effect of novel splice-site *** diagnosis or preimplantation genetic diagnosis(PGD) was performed on carriers once a mutation was identified in family ***:The most common mutations were intragenic deletions(69%),with two hotspots located in the 5’ end(exon 2-19) and central of the DMD gene(exon 45-55).Additionally,point mutations,not deletions/dulplictions,were observed in 22% ***,fifteen novel variants were identified,including two novel splice-site mutations c.1149+1 G>A and c.1150-2 A>*** HMSA validated that these two novel splice-site mutations would lead to two DMD isoforms which gave rise to severely truncated *** embryos were terminated pregnancy according to prenatal diagnosis and a healthy boy was successfully delivered by ***:s:Therefore,the clinical utility of MLPA,NGS,Sanger sequencing,and HMSA is an effective strategy to identify causative mutations in *** genetic diagnosis and confirmation of variants are essential for appropriate genetic counseling and prenatal diagnosis/PGD to reduce the risk of recurrence of DMD in affected families.

关键词： dystrophin gene variation genetic diagnosis splice-site mutation hybrid minigene splicing assay

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Cellular & Molecular Immunology 2021年第3期18卷 588-603页

作者： Emily S.J.Edwards Julian J.Bosco Samar Ojaimi Robyn E.O’Hehir Menno C.van Zelm Department of Immunology and Pathology Central Clinical SchoolMonash UniversityMelbourneVICAustralia The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies MelbourneVICAustralia Department of Allergy Immunology and Respiratory MedicineCentral Clinical SchoolMonash University and AllergyAsthma and Clinical Immunology ServiceAlfred HospitalMelbourneVICAustralia Department of Infectious Diseases Monash HealthClaytonVICAustralia Centre for Inflammatory Diseases Monash HealthClaytonVICAustralia Department of Allergy and Immunology Monash HealthClaytonVICAustralia

Predominantly antibody deficiency(PAD)is the most prevalent form of primary immunodeficiency,and is characterized by broad clinical,immunological and genetic *** the current gold standard of whole exome sequencing for diagnosis,pathogenic gene variants are only identified in less than 20% of *** elucidation of the causal genes underlying PAD has provided many insights into the cellular and molecular mechanisms underpinning disease pathogenesis,many other genes may remain as yet undefined to enable definitive diagnosis,prognostic monitoring and targeted therapy of *** that many patients display a relatively late onset of disease presentation in their 2^(nd) or 3^(rd) decade of life,it is questionable whether a single genetic lesion underlies disease in all ***,combined effects of other gene variants and/or non-genetic factors,including specific infections can drive disease *** this review,we define(1)the clinical and immunological variability of PAD,(2)consider how genetic defects identified in PAD have given insight into B-cell immunobiology,(3)address recent technological advances in genomics and the challenges associated with identifying causal variants,and(4)discuss how functional validation of variants of unknown significance could potentially be translated into increased diagnostic rates,improved prognostic monitoring and personalized medicine for PAD patients.A multidisciplinary approach will be the key to curtailing the early mortality and high morbidity rates in this immune disorder.

关键词： Predominantly antibody deficiency genetic diagnosis Genomics Functional validation

genetic analysis of Chinese families reveals a novel truncation allele of the retinitis pigmentosa GTPase regulator gene

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International Journal of Ophthalmology(English edition) 2014年第5期7卷 753-758页

作者： Fang Hu Xiang-Yun Zeng Lin-Lin Liu Yao-Ling Luo Yi-Ping Jiang Hui Wang Jing Xie Cheng-Quan Hu Lin Gan Liang Huang Department of Ophthalmology the First Affiliated HospitalGannan Medical University Flaum Eye Institute and Department of Ophthalmology School of Medicine and DentistryUniversity of Rochester

AIMTo make comprehensive molecular diagnosis for retinitis pigmentosa (RP) patients in a consanguineous Han Chinese family using next generation sequencing based Capture-NGS screen technology.

关键词： retinitis pigmentosa GTPase regulator retinitis pigmentosa next-generation sequencing genetic diagnosis

Variants of genes encoding collagens and matrix metalloproteinase system increased the risk of aortic dissection

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Science China(Life Sciences) 2017年第1期60卷 57-65页

作者： Zongzhe Li Chengming Zhou Lun Tan Peng Chen Yanyan Cao Chenze Li Xianqing Li Jiangtao Yan Hesong Zeng Dao-Wu Wang Dao-Wen Wang Division of Cardiology Departments of Internal Medicine and Genetic Diagnosis CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and Technology Department of Cardiology the First Affiliated HospitalNanjing Medical University

Aortic dissection （AD） is a devastating, heterogeneous condition of aorta. The homeostasis between collagens and matrix metalloproteases （MMPs）/tissue inhibitors of MMPs （TIMPs） system in the extracellular matrix plays an important role for structure and functions of aorta. However, our knowledge on association between variants of genes in this system and pathogenesis of AD is very limited. We analyzed all yet known coding human genes of collagens （45 genes）, MMPs/TIMPs （27 genes） in 702 sporadic AD patients and in 163 matched healthy controls, by using massively targeted next-generation and Sanger sequencing. To define the pathogenesis of potential disease-causing candidate genes, we performed transcriptome sequencing and pedigree co-segregation analysis in some genes and generated Col5a2 knockout rats. We identified 257 pathogenic or likely pathogenic variants which involved 88.89% （64/72） genes in collagens-MMPs/TIMPs system and accounted for 31.05% （218/702） sporadic AD patients. In them, 84.86% patients （185/218） carried one variant, 12.84% two variants and 2.30% more than two variants. Importantly, we identified 52 novel probablY pathogenic loss-of-function （LOF） variants （20 nonsense, 16 frameshift, 14 splice sites, one stop-loss, one initiation codon） in 11.06% （50/452） AD patients, which were absent in 163 controls （P=2.5-10-5）. Transcriptome sequencing revealed that identified variants induced dyshomeostasis in expression of collagens-TIMPs/MMPs systems. The Col5a2-/- rats manifested growth retardation and aortic dysplasia. Our study provides a first comprehensive map of genetic alterations in collagens-MMPs/TIMPs system in sporadic AD patients and suggests that variants of these genes contribute largely to AD pathogenesis.

关键词： aortic dissection collagen matrix metalloproteinase next-generation sequencing genetic diagnosis

The forty years of medical genetics in China

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Journal of genetics and Genomics 2018年第11期45卷 569-582页

作者： Lei Cai Lan Alice Zheng Lin He Bio-X Institutes Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Collaborative Innovation Center for Genetics and DevelopmentShanghai Jiao Tong UniversityShanghai 200240China Shanghai Center for Women and Children's Health Shanghai 200062China Stanley Center Broad InstituteCambridgeMA 02142USA

Medical genetics is the newest cutting-edge discipline that focuses on solving medical problems using genetics knowledge and methods. In China, medical genetics research activities initiated from a poor inner basis but a prosperous outer environment. During the 40 years of reform and opening-up policy,Chinese scientists contributed significantly in the field of medical genetics, garnering considerable attention worldwide. In this review, we highlight the significant findings and/or results discovered by Chinese scientists in monogenic diseases, complex diseases, cancer, genetic diagnosis, as well as gene manipulation and gene therapy. Due to these achievements, China is widely recognized to be at the forefront of medical genetics research and development. However, the significant progress and development that has been achieved could not have been accomplished without sufficient funding and a wellconstructed logistics network. The successful implementation of translational and precise medicine sourced from medical genetics will depend on an open ethics policy and intellectual property protection,along with strong support at the national industry level.

关键词： Medical genetics GWAS CRISPR Cancer Monogenic diseases Complex diseases genetic diagnosis Gene therapy