In this study the authors compared the sequence types （STs） designed by sequence based typing （SBT） of 4 clinical and 12 environmental strains of Legionella pneumophila serogroup 1 （LP1） which were isolated from...In this study the authors compared the sequence types （STs） designed by sequence based typing （SBT） of 4 clinical and 12 environmental strains of Legionella pneumophila serogroup 1 （LP1） which were isolated from hospital facilities for the mentally disabled. The strains were selected after a retrospective surveillance of 565 clinical records （2002-2009） and investigations of water circuit. It was possible to correlate two clinical strains with the corresponding environment, which were collected from showers that had exposed the patients （ST685, ST16） and two clinical strains present in the same structure （STI）. The other environmental strains were isolated from water in the department with confirmed or suspected clinical cases. All the strains （seven） from the first structure had ST188; two from the second structure had ST34; and the last from the third structure, gave an ST694. The results were compared with the European Working Group for Legionella Infections （EWGLI） database： the ST 1, 16, 34 and 188 were already known in literature, among clinical and nosocomial cases, especially for ST 1, the most distributed worldwide. Two STs were new to the database. ST685 was isolated both from a patient and from the water; ST694, which was found exclusively in the environmental compartment of a control structure （no cases of legionellosis and low number of nosocomial pneumonia）, was unknown in the literature and the authors could only speculate on its possible minor virulence and/or distribution. The implementation of SBT and international comparisons may be useful to gain genotypic knowledge of circulating environmental strains, also verifying their presence in the clinical setting.展开更多
Human leukocyte antigen (HLA) system is the most polymorphic region known in the human genome. In the present study, we analyzed for the first time the HLA-A gene polymorphisms defined by the high-resolution typing me...Human leukocyte antigen (HLA) system is the most polymorphic region known in the human genome. In the present study, we analyzed for the first time the HLA-A gene polymorphisms defined by the high-resolution typing methods-sequence-based typing (SBT) in 161 Northern Chinese Han people. A total of 74 different HLA-A gene types and 36 alleles were detected. The most frequent alleles were A*110101 (GP=0.2360), A*24020101 (GF=0.1646), and A*020101 (GF=0.1553); followed by A*3303 (GF=0.1180), A*3001 (GF=0.0590), and A*310102 (GF=0.0404). The frequencies of following alleles, A*0203, A*0205, A*0206, A*0207, A*030101, A*2423, A*2601, A*3201, and A*3301, are all higher than 0.0093. The homozygous alleles include A*020101, A*110101, A*24020101 and A*310102. Heterozygosity (H), polymorphism information content (PIC), discrimination power (DP) and probability of paternity exclusion (PPE) of HLA-A in the samples were calculated and their values were 0.8705, 0.8491, 0.6014, and 0.9475, respectively. These results by SBT analysis of HLA-A polymorphism in Northern Chinese Han population, especially the allele subtypes character, will be of great interest for clinical transplantation, disease-associated study and forensic identification. Implementation of high-resolution typing methods allows a significantly wider spectrum of HLA variation including rare alleles. This spectrum will further be extensively utilized in many fields.展开更多
目的研究PCR-SBT法HLA基因分型结果判读中出现的模棱两可问题并提出解决策略。方法对306名随机抽取的组织配型患者的DNA采用PCR-序列特异性引物(Sequence Specific Primer,SSP)低分辨方法检测,同时采用PCR-SBT法进行HLA-A,B,DRB1高分辨...目的研究PCR-SBT法HLA基因分型结果判读中出现的模棱两可问题并提出解决策略。方法对306名随机抽取的组织配型患者的DNA采用PCR-序列特异性引物(Sequence Specific Primer,SSP)低分辨方法检测,同时采用PCR-SBT法进行HLA-A,B,DRB1高分辨基因分型。PCR-SBT法模棱两可结果用PCR-SSP高分辨方法复核确认。结果所有306例检测标本的高低分辨血清学抗原一致,经PCR-SBT基因测序方法检测有111份模棱两可结果,占36.3%(111/306)。其中HLA-A座位有30对等位基因存在模棱两可结果,占所有检测标本等位基因总数的3.3%;HLA-B座位有66对,占7.2%;HLA-DRB1座位有36对,占3.9%。所有模棱两可标本经PCR-SSP HLA基因高分辨分型试剂PCR-SSP等方法复核确认。结论针对PCR-SBT法进行HLA-A,B,DRB1高分辨基因分型模棱两可结果所建立的解决策略,对于提高HLA数据分型的速度和分型准确性有重要意义。展开更多
目的:直接测序法及外显子3 DNA片段克隆测序定确认MICA新的等位基因MICA*002:04。方法:用组特异性引物分别扩增MICA基因,采用Sequence Base Typing(SBT)法分型技术及PCR片段克隆测序法对MICA多态性基因的外显子2、3、4、5进行双向测序...目的:直接测序法及外显子3 DNA片段克隆测序定确认MICA新的等位基因MICA*002:04。方法:用组特异性引物分别扩增MICA基因,采用Sequence Base Typing(SBT)法分型技术及PCR片段克隆测序法对MICA多态性基因的外显子2、3、4、5进行双向测序。结果:发现1个与MICA*002:01序列相近的新等位基因,在外显子3上有1个碱基位置与国际通用MICA数据库不相符。该基因与MICA*002:01相比在外显子3的碱基位置486出现突变(C→A),密码子位置20由GCC→GCA,相应编码氨基酸是同义突变。结论:DNA测序结果表明该基因序列为新的MICA等位基因,已提交GenBank,于2010年9月被世界卫生组织HLA因子命名委员会正式命名为MICA*002:04。展开更多
文摘In this study the authors compared the sequence types （STs） designed by sequence based typing （SBT） of 4 clinical and 12 environmental strains of Legionella pneumophila serogroup 1 （LP1） which were isolated from hospital facilities for the mentally disabled. The strains were selected after a retrospective surveillance of 565 clinical records （2002-2009） and investigations of water circuit. It was possible to correlate two clinical strains with the corresponding environment, which were collected from showers that had exposed the patients （ST685, ST16） and two clinical strains present in the same structure （STI）. The other environmental strains were isolated from water in the department with confirmed or suspected clinical cases. All the strains （seven） from the first structure had ST188; two from the second structure had ST34; and the last from the third structure, gave an ST694. The results were compared with the European Working Group for Legionella Infections （EWGLI） database： the ST 1, 16, 34 and 188 were already known in literature, among clinical and nosocomial cases, especially for ST 1, the most distributed worldwide. Two STs were new to the database. ST685 was isolated both from a patient and from the water; ST694, which was found exclusively in the environmental compartment of a control structure （no cases of legionellosis and low number of nosocomial pneumonia）, was unknown in the literature and the authors could only speculate on its possible minor virulence and/or distribution. The implementation of SBT and international comparisons may be useful to gain genotypic knowledge of circulating environmental strains, also verifying their presence in the clinical setting.
文摘Human leukocyte antigen (HLA) system is the most polymorphic region known in the human genome. In the present study, we analyzed for the first time the HLA-A gene polymorphisms defined by the high-resolution typing methods-sequence-based typing (SBT) in 161 Northern Chinese Han people. A total of 74 different HLA-A gene types and 36 alleles were detected. The most frequent alleles were A*110101 (GP=0.2360), A*24020101 (GF=0.1646), and A*020101 (GF=0.1553); followed by A*3303 (GF=0.1180), A*3001 (GF=0.0590), and A*310102 (GF=0.0404). The frequencies of following alleles, A*0203, A*0205, A*0206, A*0207, A*030101, A*2423, A*2601, A*3201, and A*3301, are all higher than 0.0093. The homozygous alleles include A*020101, A*110101, A*24020101 and A*310102. Heterozygosity (H), polymorphism information content (PIC), discrimination power (DP) and probability of paternity exclusion (PPE) of HLA-A in the samples were calculated and their values were 0.8705, 0.8491, 0.6014, and 0.9475, respectively. These results by SBT analysis of HLA-A polymorphism in Northern Chinese Han population, especially the allele subtypes character, will be of great interest for clinical transplantation, disease-associated study and forensic identification. Implementation of high-resolution typing methods allows a significantly wider spectrum of HLA variation including rare alleles. This spectrum will further be extensively utilized in many fields.
文摘目的研究PCR-SBT法HLA基因分型结果判读中出现的模棱两可问题并提出解决策略。方法对306名随机抽取的组织配型患者的DNA采用PCR-序列特异性引物(Sequence Specific Primer,SSP)低分辨方法检测,同时采用PCR-SBT法进行HLA-A,B,DRB1高分辨基因分型。PCR-SBT法模棱两可结果用PCR-SSP高分辨方法复核确认。结果所有306例检测标本的高低分辨血清学抗原一致,经PCR-SBT基因测序方法检测有111份模棱两可结果,占36.3%(111/306)。其中HLA-A座位有30对等位基因存在模棱两可结果,占所有检测标本等位基因总数的3.3%;HLA-B座位有66对,占7.2%;HLA-DRB1座位有36对,占3.9%。所有模棱两可标本经PCR-SSP HLA基因高分辨分型试剂PCR-SSP等方法复核确认。结论针对PCR-SBT法进行HLA-A,B,DRB1高分辨基因分型模棱两可结果所建立的解决策略,对于提高HLA数据分型的速度和分型准确性有重要意义。
文摘目的:直接测序法及外显子3 DNA片段克隆测序定确认MICA新的等位基因MICA*002:04。方法:用组特异性引物分别扩增MICA基因,采用Sequence Base Typing(SBT)法分型技术及PCR片段克隆测序法对MICA多态性基因的外显子2、3、4、5进行双向测序。结果:发现1个与MICA*002:01序列相近的新等位基因,在外显子3上有1个碱基位置与国际通用MICA数据库不相符。该基因与MICA*002:01相比在外显子3的碱基位置486出现突变(C→A),密码子位置20由GCC→GCA,相应编码氨基酸是同义突变。结论:DNA测序结果表明该基因序列为新的MICA等位基因,已提交GenBank,于2010年9月被世界卫生组织HLA因子命名委员会正式命名为MICA*002:04。
