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Construction of SNP genetic maps based on targeted next-generation sequencing and QTL mapping of vital agronomic traits in faba bean(Vicia faba L.)

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Journal of Integrative Agriculture 2023年第9期22卷 2648-2659页

作者： LI Meng-wei HE Yu-hua LIU Rong LI Guan WANG Dong JI Yi-shan YAN Xin HUANG Shu-xian WANG Chen-yu MA Yu LIU Bei YANG Tao ZONG Xu-xiao National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081P.R.China Institute of Grain Crops Yunnan Academy of Agricultural SciencesKunming 650205P.R.China Department of Horticulture Washington State UniversityPullmanWA 99164USA China Golden Marker(Beijing)Biotech Co. Ltd.Beijing 102200P.R.China

Owing to the limitation of a large genome size(~13 Gb),the genetic and gene mapping studies on faba bean(Vicia faba L.)are lagging far behind those for other *** this study,we selected three purified faba bean lines(Yundou 8137,H0003712,and H000572)as parents and constructed two F2 *** two F2 populations,namely 167 F2 plants in Pop1(Yundou 8137×H0003712)and 204 F2 plants in Pop2(H000572×Yundou 8137),were genotyped using a targeted next-generation sequencing(TNGS)genotyping platform,and two high-density single nucleotide polymorphisms(SNP)genetic linkage maps of faba bean were *** map constructed from Pop1 contained 5103 SNPs with a length of 1333.31 cM and an average marker density of 0.26 *** map constructed from Pop2 contained 1904 SNPs with a greater length of 1610.61 *** these two F2 populations,QTL mapping identified 98 QTLs for 14 agronomic traits related to the flowers,pods,plant types and *** two maps were then merged into an integrated genetic linkage map containing 6895 SNPs,with a length of 3324.48 *** results not only lay the foundation for fine mapping and map-based cloning of related genes,but can also accelerate the molecular marker-assisted breeding of faba bean.

关键词： faba bean targeted next-generation sequencing single nucleotide polymorphisms genetic linkage map QTL mapping

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Prevalence of gene mutations in a Chinese 46,XY disorders of sex development cohort detected by targeted next-generation sequencing

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Asian Journal of Andrology 2021年第1期23卷 69-73页

作者： Bing-Qing Yu Zhao-Xiang Liu Yin-Jie Gao Xi Wang Jiang-Feng Mao Min Nie Xue-Yan Wu NHC Key Laboratory of Endocrinology Department of EndocrinologyPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijing 100730China

46,XY disorders of sex development(DSD)is characterized by incomplete masculinization genitalia,with gonadal dysplasia and with/without the presence of Mullerian *** least 30 genes related to 46,XY DSD have been ***,the clinical phenotypes of patients with different gene mutations overlap,and accurate diagnosis relies on gene sequencing ***,this study aims to determine the prevalence of pathogenic mutations in a Chinese cohort with 46,XY DSD by the targeted nextgeneration sequencing(NGS)***-seven 46,XY DSD patients were enrolled from the Peking Union Medical College Hospital(Beijing,China).A total of fifty-four rare variants were identified in 60 patients with 46,XY *** incidence of these rare variants was approximately 69.0%(60/87).Twenty-five novel variants and 29 reported variants were *** on the American College of Medical Genetics and Genomics(ACMG)guidelines,thirty-three variants were classified as pathogenic or likely pathogenic variants and 21 variants were assessed as variants of uncertain *** overall diagnostic rate was about 42.5%based on the pathogenic and likely pathogenic *** receptor{AR),steroid 5-alpha-reductase 2(SRD5A2)and nuclear receptor subfamily 5 Group A member 1(NR5A1)gene variants were identified in 21,13 and 13 patients,*** incidence of these three gene variants was about 78.3%(47/60)in patients with rare *** is concluded that targeted NGS is an effective method to detect pathogenic mutations in 46,XY DSD patients and AR,SRD5A2,and NR5A1 genes were the most common pathogenic genes in our cohort.

关键词： 46,XY disorders of sex development mutations targeted next-generation sequencing

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Diagnostic Value of targeted next-generation sequencing in Pulmonary Mycobacterial Infections

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Current Medical Science 2024年第5期44卷 947-953页

作者： Yu TAO Zi-wei ZHOU Yi-fei DUAN Jian-miao WANG Department of Respiratory and Critical Care Medicine Tongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China

Objective This study aimed to explore the diagnostic value of novel technique-targeted next-generation sequencing(tNGS)of bronchoalveolar lavage fluid(BALF)in pulmonary mycobacterial *** This retrospective study was conducted on patients who underwent bronchoscopy and tNGS,smear microscopy,and mycobacterial culture of *** with positive Mycobacterium tuberculosis(MTB)culture or GeneXpert results were classified into the tuberculosis case *** diagnosed with nontuberculous mycobacteria(NTM)-pulmonary disease(NTM-PD)composed the case group of NTM-PD *** control group comprised patients without tuberculosis or ***,specificity,and receiver operating characteristic(ROC)curves were used to evaluate the diagnostic *** For tuberculosis patients with positive mycobacterial culture results,the areas under the ROC curves(AUCs)for tNGS,GeneXpert,and smear microscopy were 0.975(95%CI:0.935,1.000),0.925(95%CI:0.859,0.991),and 0.675(95%CI:0.563,0.787),*** tuberculosis patients with positive GeneXpert results,the AUCs of tNGS,culture,and smear microscopy were 0.970(95%CI:0.931,1.000),0.850(95%CI:0.770,0.930),and 0.680(95%CI:0.579,0.781),*** NTM-PD,the AUCs of tNGS,culture,and smear-positive but GeneXpert-negative results were 0.987(95%CI:0.967,1.000),0.750(95%CI:0.622,0.878),and 0.615(95%CI:0.479,0.752),*** sensitivity and specificity of tNGS in NTM-PD patients were 100%and 97.5%,*** tNGS demonstrated superior diagnostic efficacy in mycobacterial infection,indicating its potential for clinical application.

关键词： targeted next-generation sequencing Mycobacterium tuberculosis nontuberculous mycobacteria bronchoalveolar lavage fluid

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Comprehensive analysis of genetic variations in strictly-defined Leber congenital amaurosis with whole-exome sequencing in Chinese

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International Journal of Ophthalmology(English edition) 2016年第9期9卷 1260-1264页

作者： Shi-Yuan Wang Qi Zhang Xiang Zhang Pei-Quan Zhao Department of Ophthalmology Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

AIM：To make a comprehensive analysis of the potential pathogenic genes related with Leber congenital amaurosis（LCA） in ***：LCA subjects and their families were retrospectively collected from 2013 to ***,whole-exome sequencing was performed in patients who had underwent gene mutation screening with nothing found,and then homozygous sites was selected,candidate sites were annotated,and pathogenic analysis was conducted using softwares including Sorting Tolerant from Intolerant（SIFT）,Polyphen-2,Mutation assessor,Condel,and Functional Analysis through Hidden Markov Models（FATHMM）.Furthermore,Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses of pathogenic genes were performed followed by co-segregation analysis using Fisher exact *** sequencing was used to validate single-nucleotide variations（SNVs）.Expanded verification was performed in the rest ***：Totally 51 LCA families with 53 patients and24 family members were recruited.A total of 104 SNVs（66 LCA-related genes and 15 co-segregated genes）were submitted for expand *** frequencies of homozygous mutation of KRT12 and CYP1A1 were simultaneously observed in 3 *** analysis showed that the potential pathogenic genes were mainly enriched in functions related to cell adhesion,biological adhesion,retinoid metabolic process,and eye development biological ***,WFS7 and STAU2 had the highest homozygous ***：LCA is a highly heterogeneous *** in KRT12,CVP1A1,WFS1,and STAU2 may be involved in the development of LCA.

关键词： Leber congenital amaurosis whole-exome sequencing targeted next-generation sequencing

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Clinical features and genetic spectrum in Chinese patients with recessive hereditary spastic paraplegia

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Translational Neurodegeneration 2019年第1期8卷 230-242页

作者： Qiao Wei Hai-Lin Dong Li-Ying Pan Cong-Xin Chen Yang-Tian Yan Rou-Min Wang Hong-Fu Li Zhi-Jun Liu Qing-Qing Tao Zhi-Ying Wu Department of Neurology and Research Center of Neurology in Second Affiliated Hospital and Key Laboratory of Medical Neurobiology of Zhejiang ProvinceZhejiang University School of Medicine88 Jiefang RoadHangzhou 310009China Longyan First Hospital Fujian Medical UniversityLongyanChina Department of Neurology and Institute of Neurology Huashan HospitalShanghai Medical CollegeFudan UniversityShanghaiChina Joint Institute for Genetics and Genome Medicine between Zhejiang University and University of Toronto Zhejiang UniversityHangzhouChina

Background:Although many causative genes of hereditary spastic paraplegia(HSP)have been uncovered in recent years,there are still approximately 50% of HSP patients without genetically diagnosis,especially in autosomal recessive(AR)HSP *** studies have been performed to determine the genetic spectrum and clinical profiles of recessive HSP patients in the Chinese ***:In this study,we investigated 24 Chinese index AR/sporadic patients by targeted next-generation sequencing(NGS),Sanger sequencing and multiplex ligation-dependent probe amplification(MLPA).Further functional studies were performed to identify pathogenicity of those uncertain significance ***:We identified 11 mutations in HSP related genes including 7 novel mutations,including two(p.V1979_L1980delinsX,p.F2343 fs)in SPG11,two(p.T55 M,p.S308 T)in AP5Z1,one(p.S242N)in ALDH18A1,one(p.D597fs)in GBA2,and one(p.Q486X)in ATP13A2 in 8 index patients and their family *** in ALDH18A1,AP5Z1,CAPN1 and ATP13A2 genes were firstly reported in the Chinese ***,the clinical phenotypes of the patients carrying mutations were described in *** mutation(p.S242 N)in ALDH18A1 decreased enzyme activity of P5CS and mutations(p.T55 M,p.S308 T)in AP5Z1 induced lysosomal ***:Our results expanded the genetic spectrum and clinical profiles of AR-HSP patients and further demonstrated the efficiency and reliability of targeted NGS diagnosing suspected HSP patients.

关键词： Hereditary spastic paraplegia Autosomal recessive targeted next-generation sequencing Chinese Genetic spectrum Phenotype

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Identification of a Novel Homozygous Splice-Site Mutation in SCARB2 that Causes Progressive Myoclonus Epilepsy with or without Renal Failure

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Chinese Medical Journal 2018年第13期131卷 1575-1583页

作者： Jin He Han Lin Jin-Jing Li Hui-Zhen Su Dan-Ni Wang Yu Lin Ning Wang Wan-Jin Chen Department of Neurology and Institute of Neurology First Affiliated Hospital Fujian Medical University Fuzhou Fujian 350005 China Fujian Key Laboratory of Molecular Neurology Fujian Medical University Fuzhou Fujian 350005 Ohina

Background： Progressive myoclonus epilepsies （PMEs） conaprise a group of rare genetic disorders characterized by action rnyoclonus, epileptic seizures, and ataxia with progressive neurologic decline. Due to clinical and genetic heterogeneity of PMEs, it is difficult to decide which genes are affected. The aim of this study was to report an action myoclonus with or without renal failure syndrome （EPM4） fhmily and summarize the clinical and genetic characteristics of all reported EPM4 patients. Meihods： In the present study, targeted next-generation sequencing （NGS） was applied to screen causative genes in a Chinese PME family. The candidaie variant was further confirmed by cosegregation analysis and further functional analysis, including the reverse transcription polymerase chain reaction and Western blot of the proband＇s muscle. Moreovel, literature data on the clinical and mutational features of all reported EPM4 patients were reviewed. Results： The gene analysis revealed a novel homozygous splicing mutation （c.995-1G〉A） of the SCARB2 gene in two brothers. Further functional analysis revealed that this mutation led to loss function of the SCARB2 protein. The classification of the candidate variant, according to the American College of Medical Genetics and Genomics standards and guidelines and functional analysis, was pathogenic. Therefore, these two brothers were finally diagnostically confirmed as EPM4. Conclusions： These present results suggest the potential for targeted NGS to conduct a more rapid and precise diagnosis for PME patients. A literature review revealed that mutations in the different functional domains of SCARB2 appear to be associated with the phenotype of EPM4.

关键词： Progressive Myoclonus Epilepsies Progressive Myoclonus Epilepsy with or without Renal Failure SCARB2 Gene targeted next-generation sequencing

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