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single nucleotide polymorphisms and haplotypes analysis of DFNB1 locus in Chinese sporadic hearing impairment population

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Chinese Medical Journal 2009年第13期122卷 1549-1553页

作者： CHENG Hong-bo CHEN Zhi-bin WEI Qing-jun LU Ya-jie XING Guang-qian CAO Xin Department of Biotechnology Nanjing Medical University Nanjing Jiangsu 210029 China Department of Otorhinolaryngology First Affiliated Hospital of Nanjing Medical University Nanjing Jiangsu 210029 China

Background The DFNB1 locus, which contains the gap junction beta-2 （GJB2） and gap junction beta-6 （GJB6） genes, plays a key role in the nonsyndromic and sporadic hearing impairment. Mutations of DFNB1 result in autosomaJ recessive nonsyndromic hearing impairment （ARNSHI）. Previous researches have identified mutations in GJB2 and GJB6, but single nucleotide polymorphisms （SNPs） of DFNB1 locus have not been studied. So we chose five SNPs to evaluate whether there is difference between deafness people and normal-hearing people in Han Chinese. Methods Five SNPs in the DFNB1 region were examined using a case-control association study between cases with sporadic hearing impairment and controls with normal hearing. The HWEsoft and SHEsis softwares were used to analyze the results. Results single-locus association analysis showed a positive association for three SNPs： rs9315400, rs2274084 and 235delC. When we compared the distributions of the haplotypes, we also found significant differences between cases and controls in the haplotype combination of rs2274084 and rs2274083 （Х^2=12.978, df=3, global P=0.004719）. Conclusions The haplotypes composed of rs2274084 and rs2274083 suggested that C-C may be a risk haplotype for the sporadic hearing impairment while T-T may be protective against hearing impairment. From that point of view, we can conclude that the SNPs of DFNB1 locus also plays an important role in sporadic hearing impairment cases.

关键词： DFNB1 locus single nucleotide polymorphisms haplotype hearing impairment

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Association between single nucleotide polymorphisms of nLvALF1 and PEN2-1 genes and resistance to Vibrio parahaemolyticus in the Pacific white shrimp Litopenaeus vannamei

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Aquaculture and Fisheries 2022年第4期7卷 373-381页

作者： Pawapol Kongchum Suphavadee Chimtong Naparat Prapaiwong Faculty of Animal Sciences and Agricultural Technology Silpakorn UniversityPhetchaburi CampusCha-amPhetchaburi76120Thailand Samut Sakhon Coastal Aquaculture Research and Development Center MueangSamut Sakhon74000Thailand

Vibrio parahaemolyticus carrying a plasmid encoding the PirAvp and PirBvp toxins is the causative agent of acute hepatopancreatic necrosis disease(AHPND)in penaeid *** the Pacific white shrimp farming industry,one possible strategy to reduce economic loss due to AHPND is the development of a shrimp line resistant to the *** this study,we identified single nucleotide polymorphisms(SNPs)in the Litopenaeus vannamei anti-lipopolysaccharide factor 1(nLvALF1)and penaeidin 2-1(PEN2-1)genes,and we analyzed the associations between these SNPs and resistance/susceptibility to *** infection in the Pacific white ***(PL20)shrimp from a local hatchery in Prachuap Khiri Khan Province were challenged with an isolate of VPAHPND and mortality was observed for 14 *** was extracted from susceptible(died within 6 days)and resistant(survived the challenge)shrimp(45 individuals/group)and used for PCR amplifications of nLvALF1(397 bp)and PEN2-1(637 bp)gene *** products were sequenced by direct sequencing and SNPs were identified from sequencing *** and seven SNPs were identified in nLvALF1 and PEN2-1 gene fragments,*** of allele frequencies in susceptible and resistant samples using Chi-square tests revealed that four and six SNPs in nLvALF1 and PEN2-1,respectively,were associated with resistance/susceptibility to *** infection(P<0.05).The SNPs in the candidate genes identified here are potential DNA markers for breeding ***-resistant Pacific white shrimp in the study population;however,further validation will be required if these SNPs are to be used across populations.

关键词： single nucleotide polymorphisms Anti-lipopolysaccharide factor Penaeidin Early mortality syndrome Acute hepatopancreatic necrosis disease

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Association of single nucleotide polymorphisms of brain-derived neurotrophic factor gene and multidrug resistance 1 gene to refractory epilepsy in Chinese Han children

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Neural Regeneration Research 2009年第11期4卷 901-906页

作者： Guangxin Wang Zuocheng Yang Ruifeng Jin Ruopeng Sun Department of Paediatrics Qilu Hospital of Shandong University Jinan 250012 Shandong Province China Department of Paediatrics Third Xiangya Hospital of Central South University Changsha 410013 Hunan Province China Institute of Paediatrics Qilu Children's Hospital of Shandong University Jinan 250022 Shandong Province China

BACKGROUND： There are two hypotheses for the underlying cause of refractory epilepsy：＂target＂ and ＂transport＂. Studies have shown that brain-derived neurotrophic factor （BDNF） is over-expressed in refractory epilepsy. Multidrug resistance 1 （MDR1） gene encodes for P-glycoprotein, the primary ATP-binding cassette transporter in the human body. Some single nucleotide polymorphisms of the MDR1 gene have been associated with refractory epilepsy. OBJECTIVE： To investigate the association between BDNF gene C270T polymorphism and MDR1 T-129C polymorphism with refractory epilepsy in Chinese Han children through the use of polymerase chain reaction （PCR）-restriction fragment length polymorphism analysis. DESIGN, TIME AND SETTING： A case-control, genetic association study was performed at the Central Laboratory, Third Xiangya Hospital of Central South University from June 2005 to November 2007. PARTICIPANTS： A total of 84 cases of unrelated children with epilepsy, including 41 cases of refractory epilepsy and 43 cases of drug-responsive epilepsy, were enrolled. An additional 30 healthy, Chinese Han children, whose ages and gender matched the refractory epilepsy patients, were selected as normal controls. METHODS： Venous blood was collected and genomic DNA was extracted from the blood specimens. C270T polymorphism in BDNF gene and T-129C polymorphism in MDR1 gene were genotyped using PCR-restriction fragment length polymorphism analysis. Association analysis using the Ftest and Chi-square test was statistically performed between C270T polymorphism in BDNF gene and T-129C polymorphism in MDR1 gene and refractory epilepsy. MAIN OUTCOME MEASURES： The distribution of genotypes and allele frequencies of C270T polymorphism in BDNF gene and T-129C polymorphism in MDR1 gene. RESULTS： The distribution of CC, CT, and TT genotypes, as well as C and T allele frequencies, in the BDNF gene was not significantly different between the refractory epilepsy group, drug-responsive epilepsy group

关键词： brain-derived neurotrophic factor gene multidrug resistance 1 gene single nucleotide polymorphisms children refractory epilepsy

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Isolation,expression and single nucleotide polymorphisms(SNPs) analysis of LACCASE gene(LkLAC8) from Japanese larch(Larix kaempferi)

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Journal of Forestry Research 2017年第5期28卷 891-902页

作者： Changyong Liu Yunhui Xie Min Yi Shougong Zhang Xiaomei Sun State Key Laboratory of Tree Genetics and Breeding Research Institute of ForestryChinese Academy of Forestry Research Institute of Forestry Chinese Academy of Forestry State Academy of Forestry Administration School of Gardening and Landscape Design Jiangxi Agricultural University

nucleotide diversity (pi) and linkage disequilibrium (LD) analysis based on SNP marker could provide a sound basis for choosing an association analysis method. Japanese larch (Larix kaempferi) is an important timber coniferous tree species for pulping and papermaking, but its high lignin content has significantly restricted it application potential. In this study, the LACCASE gene, that plays an important regulatory role for lignin biosynthesis, was selected as research target. The full-length cDNA and genomic sequences of the encoding LkLAC8 gene were isolated from the LACCASE expressed sequence tags of the Japanese larch transcriptome database using the rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR). The cDNA was determined to be 1940 bp, with an open reading frame (ORF, 1734 bp) that encoded a protein of 577 AA. This protein contains four highly specific Cu2+ binding sites and 11 glycosylation sites, thus belonging to the LACCASE family. The deduced protein sequence shared an 89% identity with the PtaLAC from Pinus taeda. A real-time PCR analysis showed that the LkLAC8 transcript was expressed predominantly in mature xylem, with moderate levels in the immature xylem, cambium and mature leaves, the lowest in the roots. Lastly, the genomic sequences of LkLAC8 in 40 individuals from six naturally distributed populations of Japanese larch were amplified, and a total of 201 SNPs (103 and 98 mutation types of transition and transversion, respectively) were detected; the frequency of the SNPs was 1/19 bp. nucleotide diversity among the six populations ranged from 0.0034 to 0.0053, which suggested that there were no significant differences among the populations. The LD analysis showed that the LD level decayed rapidly within the increasing length of the LkLAC8 gene. These results implied that LD mapping and association analysis based on candidate gene may be feasible for the marker-assisted breeding of new germplasms with low lignin in Japanese lar

关键词： Gene cloning LACCASE Larix kaempferi Linkage disequilibrium Real-time PCR single nucleotide polymorphisms

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Association of eleven single nucleotide polymorphisms with refractive disorders from Eskisehir,Turkey

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International Journal of Ophthalmology(English edition) 2021年第6期14卷 812-817页

作者： Nadir Unlu Ebru Erzurumluoglu Gokalp Serap Arslan Oguz Cilingir Muzaffer Bilgin Engin Yildirim Huseyin Gursoy Department of Ophthalmology Eskisehir Osmangazi University Medical FacultyEskisehir 26040Turkey Department of Medical Genetics Eskisehir Osmangazi University Medical FacultyEskisehir 26040Turkey Department of Biostatistics Eskisehir Osmangazi University Medical FacultyEskisehir 26040Turkey Department of Pharmacology Eskisehir Osmangazi University Medical FacultyEskisehir 26040Turkey

AIM:To investigate relationship between refractive errors and eleven single nucleotide polymorphisms(SNPs)in HGF,GC,MFN1,GNB4,and VDR genes in Turkish ***:A group of 212 participants with myopia(n=91),hyperopia(n=45),and emmetropia(n=76)were investigated in this *** in HGF,GC,MFN1,GNB4 and VDR genes were studied by Snap Shot ***:The patients in this study consists of 47 female/44 male(age:23.47±4.30)patients with myopia,20 female/25 male(age:31.20±8.02)with hyperopia and 33 female/43 male(age:25.22±6.60)with *** genotype distribution of the rs7618348 polymorphism,which was the only statistically significant one between myopia and emmetropia *** genotype distribution of the rs3819545,rs3735520,rs7041,and rs2239182 polymorphisms,which were statistically significant between hyperopia and emmetropia ***:The importance of genetic predisposition to refractive errors with respect to etiology of the disease is *** is known that polymorphism studies may differ because of genetic diversity among populations so larger cohort studies are required in different populations to enlighten the etiology of the refractive errors.

关键词： refractive disorders myopia hyperopia genetics single nucleotide polymorphisms Turkey

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Relationship between single nucleotide polymorphisms in -174G/C and -634C/G Promoter Region of Interleukin-6 and Prostate Cancer

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Journal of Huazhong University of Science and Technology(Medical Sciences) 2008年第6期28卷 693-696页

作者：包世新杨为民周四维叶章群 Department of Urology Tongji HospitalTongji Medical CollegeHuazhong University of Science and Technology

The association between the single nucleotide polymorphisms （SNPs） in -174G/C and -634C/G of interleukin-6 （IL-6） promoter region and prostate cancer was examined in the population of Han people in Hubei region. TaqMan PCR was employed for the gene-typing of -174G/C and -634C/G in promoter region of IL-6 gene to compare the prostate cancer patients and normal controls in terms of genotype frequency, allele frequency and risk of prostate cancer. Enzyme-linked immu- nosorbent assay （ELISA） was used for the detection of IL-6 concentration in peripheral blood of the patients with prostate cancer and the relationship between the IL-6 level and the genotype was studied. Our results showed that in all the subjects, the genotype of genetic locus -174G/C was found to be GG and no CG and CC were observed. There was a significant difference in gene frequency of GG, CG and CC of -634C/G and allele frequency of G and C between prostate cancer patients and normal controls （P〈0.05） and the gene frequency of GG＋CG increased with the clinical stages and pathological grades of prostate cancer. The IL-6 level in GG＋CG group was significantly higher than that in CC group. It was concluded that no SNP in -174G/C IL-6 promoter region was found in the population of Han people in Hubei region. The SNP in -634C/G was, to some extent, associated with the development and progression of prostate cancer. The population with GG＋CG genetype has higher risk for prostate cancer.

关键词： interleukin-6 prostate cancer single nucleotide polymorphisms allele genetype

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single nucleotide polymorphisms in the TNFSF4 and TNFAIP3 gene are associated with systemic sclerosis in a Chinese Han population

Single nucleotide polymorphisms in the TNFSF4 and TNFAIP3 ge...

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第十三届全国免疫学学术大会

作者： Jing Li Yongzhe Li Peking Union Medical College Hospital

Objective: TNFSF4 and TNFAIP3 polymorphisms have been related to susceptibility for different autoimmune diseases including SSc in Caucasian *** the polymorphisms in the TNFSF4 and TNFAIP3 contribute to the development of SSc in Asians has not been *** we sought to explore genetic variants associated with TNFSF4 and TNFAIP3 in SSc and ***: The TNFSF4 SNPs(rs1234314, rs2205960, rs12039904 and rs844648) and TNFAIP3 SNPs(rs5029939 and rs6932056) were genotyped in a cohort of 1030 SSc patients and 1215 healthy controls, using the Sequenom MassArray system ***: The rs844648 in TNFSF4 region was significantly associated with SSc in the allelic and genotypic frequencies(p =1.7×10-3 and p=5.0×10-3).The allelic frequencies of the rs6932056 in the TNFAIP3 was significant difference between SSc patients and the controls(p=5.0×10-3).Other three TNFSF4 SNPs(rs1234314, rs2205960 and rs12039904) and the TNFAIP3 SNP(rs5029939) demonstrated weak association with SSc for the allelic frequency(ppolymorphisms were associated with SSc/ILD patients in a Chinese Han population, indicating that TNFSF4 and TNFAIP3 might be susceptibility genes for SSc/ILD in Chinese Han population.

关键词： single nucleotide polymorphisms TNFSF4 gene TNFAIP3 gene Systemic sclerosis Chinese Han populati

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Assessment of single nucleotide polymorphisms associated with steroid-induced ocular hypertension

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International Journal of Ophthalmology(English edition) 2020年第8期13卷 1294-1305页

作者： Lakshmi Badrinarayanan Srujana Chitipothu Sharada Ramasubramanyan Sarangapani Sripriya Pukhraj Rishi Ekta Rishi Ronnie George Baddireddi Subhadra Lakshmi Sailaja VElchuri Department of Nano-biotechnology KNBIRVO blockVision Research FoundationChennaiTamilNadu 600006India Department of Biotechnology Anna UniversityChennaiTamilNadu 600025India Central Research Instrumentation Facility KNBIRVO blockVision Research FoundationTamilNadu 600006India RS.Mehta Jain Department of Biochemistry and Cell BiologyKNBIRVO blockVision Research FoundationChennaiTamilNadu 600006India SNONGC Department of Genetics and Molecular Biology KNBIRVO blockVision Research FoundationChennaiTamilNadu 600006India Shri Bhagwan Mahavir Vitreo-Retinal Service Medical Research FoundationChennaiTamilNadu 600006India Smt.Jadhavbai Nathamal Singhree Glaucoma Service Medical Research FoundationChennaiTamilNadu 600006India

AIM:To access the association of forty-eight single nucleotide polymorphisms(SNPs)identified from Caucasian population with steroid-induced ocular hypertension(OHT)in India ***:Fifty-four triamcinolone-acetonide(TA)and for ty-seven dexamethasone(Dex)administered subjects were enrolled in the study after a written *** pressure(IOP)values were recorded for a period of 6-month post steroid injections and patients were grouped as steroid-responders(SR:IOP≥21 mm Hg)and non-responders(NR:IOP≤20 mm Hg).Genomic DNA was isolated from peripheral venous ***-eight SNPs identified in TA treated Caucasian patients by genome wide association study(GWAS)were genotyped using iPLEXTM MassA RRAY among TA as well as Dex administered Indian *** data of 48 general subjects from a previous study were considered as reference controls for statistical *** frequencies were calculated and P-value,Chi-square and odds ratio at 95%confidenceinterval of group A(steroid treated vs controls),group B(SR vs NR),group C(phenotype correlation:influence of time,severity and gender on IOP rise),were calculated.P30 mm Hg)and immediate(<1 wk)among TA-SR patients while it was noticed to be mild(<30 mm Hg)and between 1-2 mo among Dex-SR *** regression for risk factor correlation with OHT remained non-significant,hence these factors were not considered as confounding parameters for further ***133,rs34016742,rs274554,rs10936746,rs274547,rs804854,rs7751500,rs359498,and rs7547448 SNPs significantly varied even after Bonferroni corrections(P<0.0025;group A).rs1879370(TA)and rs6559662(Dex)were significantly(P<0.05)associated with OHT(group B).rs133(severe IOP rise),rs11047639 and rs1879370(male gender),and rs11171569(immediate IOP rise)significantly(P<0.05)infl

关键词： triamcinolone-acetonide dexamethasone ocular hypertension single nucleotide polymorphisms diabetes neurodegeneration myopia

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Genetic association analysis of CLEC5A and CLEC7A gene single-nucleotide polymorphisms and Crohn’s disease

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World Journal of Gastroenterology 2020年第18期26卷 2194-2202页

作者： Nagi Elleisy Sarah Rohde Astrid Huth Nicole Gittel Anne Glass Steffen Moller Georg Lamprecht Holger Schaffler Robert Jaster Department of Medicine Ⅱ Division of GastroenterologyRostock University Medical CenterRostock 18057Germany Institute for Biostatistics and Informatics in Medicine and Ageing Research Rostock 18057Germany

BACKGROUND Crohn’s disease(CD)is characterized by a multifactorial etiology and a significant impact of genetic *** NOD2 mutations represent well established risk factors of CD,the role of other genes is incompletely *** To challenge the hypothesis that single nucleotide polymorphisms(SNPs)in the genes CLEC5 A and CLEC7 A,two members of the C-type lectin domain family of pattern recognition receptors,may be associated with *** SNPs in CLEC5 A,CLEC7 A and the known CD risk gene NOD2 were studied using real time PCR-based SNP ***,DNA samples from 175 patients and 157 healthy donors were *** data were correlated with clinical characteristics of the patients and the results of gene expression data *** In accordance with previous studies,rs2066844 and rs2066847 in NOD2 were found to be significantly associated with CD(allelic P values=0.0368 and 0.0474,respectively).Intriguingly,for genotype AA of rs1285933 in CLEC5 A,a potential association with CD(recessive P=0.0523;odds ratio=1.90)was *** were no associations between CD and SNPs rs2078178 and rs16910631 in CLEC7 *** of rs1285933 had no impact on CLEC5 A gene *** contrast,genotype-dependent differences of CXCL5 expression in peripheral blood mononuclear cells were *** is no statistical interactionbetween the tested SNPs of NOD2 and CLEC5 A,suggesting of a novel pathway contributing to the *** Our data encourage enlarged follow-up studies to further address an association of SNP rs1285933 in CLEC5 A with *** C-type lectin domain family member also deserves attention regarding a potential role in the pathophysiology of CD.

关键词： Crohn’s disease single nucleotide polymorphisms NOD2 CLEC5A Gene expression CXCL5

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single-nucleotide polymorphisms based genetic risk score in the prediction of pancreatic cancer risk

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World Journal of Gastroenterology 2020年第22期26卷 3076-3086页

作者： Xiao-Yi Wang Hai-Tao Chen Rong Na De-Ke Jiang Xiao-Ling Lin Feng Yang Chen Jin De-Liang Fu Jian-Feng Xu Department of Pancreatic Surgery Pancreatic Disease InstituteHuashan HospitalFudan UniversityShanghai 200040China State Key Laboratory of Organ Failure Research Guangdong Key Laboratory of Viral Hepatitis ResearchDepartment of Infectious Diseases and Hepatology UnitNanfang HospitalSouthern Medical UniversityGuangzhou 510515Guangdong ProvinceChina Shanghai Medical College Fudan UniversityShanghai 200043China Department of Urology Ruijin HospitalShanghai Jiaotong University School of MedicineShanghai 200025China State Key Laboratory of Genetic Engineering School of Life ScienceFudan UniversityShanghai 200433China Program for Personalized Cancer Care and Department of Surgery North Shore University Health SystemEvanstonIL 60201United States

BACKGROUND Disease-related single nucleotide polymorphisms(SNPs)based genetic risk score(GRS)has been proven to provide independent inherited risk other than family history in multiple cancer *** To evaluate the potential of GRS in the prediction of pancreatic cancer *** In this case-control study(254 cases and 1200 controls),we aimed to evaluate the association between GRS and pancreatic ductal adenocarcinoma(PDAC)risk in the Chinese *** GRS was calculated based on the genotype information of 18 PDAC-related SNPs for each study subject(personal genotyping information of the SNPs)and was weighted by external odd ratios(ORs).RESULTS GRS was significantly different in cases and controls(1.96±3.84 in PDACs vs 1.09±0.94 in controls,P<0.0001).Logistic regression revealed GRS to be associated with PDAC risk[OR=1.23,95%confidence interval(CI):1.13-1.34,P<0.0001].GRS remained significantly associated with PDAC(OR=1.36,95%CI:1.06-1.74,P=0.015)after adjusting for age and *** analysis revealed an association of increased risk for PDAC with higher *** with low GRS(<1.0),subjects with high GRS(2.0)were 99%more likely to have PDAC(OR:1.99,95%CI:1.30-3.04,P=0.002).Participants with intermediate GRS(1.0-1.9)were 39%more likely to have PDAC(OR:1.39,95%CI:1.03-1.84,P=0.031).A positive trend was observed(P trend=0.0006).CONCLUSION GRS based on PDAC-associated SNPs could provide independent information on PDAC risk and may be used to predict a high risk PDAC population.

关键词： Pancreatic cancer single nucleotide polymorphisms Genetic risk score Chinese population Genome-wide association study

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