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A HLA-A null allele (A*24:132N) with a stop codon in exon 3 generated by a point mutation. 由点突变产生的一个HLA-A空等位基因(A*24:132N),外显子3上有一个停止密码子。
Pub Date : 2012-11-01 Epub Date: 2012-08-24 DOI: 10.1111/j.1399-0039.2012.01949.x
H-Y Zou, S-Z Jin, Z Li

Exons 1-8 of HLA-A*24:132N allele are identical to those of HLA-A*24:02:01:01, except for one nucleotide change at nt 746 in exon 3 from C to A.

HLA-A*24:132N的外显子1-8与HLA-A*24:02:01的外显子相同,除了在第3外显子nt 746从C到A有一个核苷酸变化。
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引用次数: 3
Bioinformatic databases and resources in the public domain to aid HLA research. 在公共领域的生物信息学数据库和资源,以帮助HLA研究。
Pub Date : 2012-10-01 DOI: 10.1111/tan.12000
W Helmberg

Research in HLA as in any other field depends on information. Different groups have generated generic and specific resources and tools to support this research. The present review describes a qualified subset of these resources, which should cover the most important starting points for research in the HLA field. It discusses access to HLA allele sequences, allele frequencies, continues with general support to access to literature, DNA and protein sequence information, structural models, teaching books, databases with phenotypic datasets, alignment tools, peptide binding, statistical tools, guidelines and ambiguity coding. Following functionalities and databases have been included: IMGT/HLA, Immuno Polymorphism Database (IPD), allele frequencies*.net, a detailed look into NCBI (National Center of Biotechnology Information) with a subset of databases and tools, focusing on literature research, sequences, user-specific support tools and applications (PubMed, GenBank, MyNCBI, blast, Gene, MapViewer, Structure, CN3D, WorkBench, and dbMHC). This is followed by a brief survey of EBI-EMBL/Ensemble, the sequence alignment tool Clustal, the peptide and ligand databases SYFPEITHI and Immune Epitope Database, and last but not least statistical packages and HLA allele coding resources PyPop, the Immuno-genomics Data Analysis Working Group and the NMDP informatics section. All databases and tools can be freely accessed. Data linked to individuals, however, might require authorization by a data access committee.

HLA的研究和其他任何领域一样依赖于信息。不同的团体已经产生了通用的和特定的资源和工具来支持这项研究。本综述描述了这些资源的一个合格子集,它应该涵盖HLA领域研究的最重要的起点。它讨论了HLA等位基因序列、等位基因频率的获取,并继续提供对文献、DNA和蛋白质序列信息、结构模型、教材、带有表型数据集的数据库、比对工具、肽结合、统计工具、指南和模糊编码的一般支持。包括以下功能和数据库:IMGT/HLA,免疫多态性数据库(IPD),等位基因频率*.net,详细查看NCBI(国家生物技术信息中心)数据库和工具的子集,重点是文献研究,序列,用户特定的支持工具和应用程序(PubMed, GenBank, MyNCBI, blast, Gene, MapViewer, Structure, CN3D, WorkBench和dbMHC)。接下来是对EBI-EMBL/Ensemble,序列比对工具Clustal,肽和配体数据库SYFPEITHI和免疫表位数据库的简要调查,最后但同样重要的是统计软件包和HLA等位基因编码资源PyPop,免疫基因组学数据分析工作组和mdp信息学部分。所有数据库和工具都可以自由访问。然而,链接到个人的数据可能需要数据访问委员会的授权。
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引用次数: 9
Molecular ABO phenotyping in cynomolgus macaques using real-time quantitative PCR. 食蟹猕猴ABO分子表型的实时定量PCR分析。
Pub Date : 2012-10-01 Epub Date: 2012-08-03 DOI: 10.1111/j.1399-0039.2012.01935.x
A Premasuthan, J Ng, S Kanthaswamy, J S Trask, P Houghton, T Farkas, K Sestak, D G Smith

Macaques are commonly used in biomedical research as animal models of human disease. The ABO phenotype of donors and recipients plays an important role in the success of transplantation and stem cell research of both human and macaque tissue. Traditional serological methods for ABO phenotyping can be time consuming, provide ambiguous results and/or require tissue that is unavailable or unsuitable. We developed a novel method to detect the A, B, and AB phenotypes of macaques using real-time quantitative polymerase chain reaction. This method enables the simple and rapid screening of these phenotypes in macaques without the need for fresh blood or saliva. This study reports the distribution of the A, B, and AB phenotypes of captive cynomolgus macaques that, while regionally variable, closely resembles that of rhesus macaques. Blood group B, as in rhesus macaques, predominates in cynomolgus macaques and its frequency distribution leads to a probability of major incompatibility of 41%. No silencing mutations have been identified in exon 6 or 7 in macaques that could be responsible for the O phenotype, that, although rare, have been reported. The excess homozygosity of rhesus and cynomolgus macaque genotypes in this study, that assumes the absence of the O allele, suggests the possibility of some mechanism preventing the expression of the A and B transferases.

猕猴常被用作生物医学研究中人类疾病的动物模型。供体和受体的ABO表型在人类和猕猴组织移植和干细胞研究的成功中起着重要作用。ABO表型的传统血清学方法可能耗时,提供模棱两可的结果和/或需要不可用或不合适的组织。我们开发了一种利用实时定量聚合酶链反应检测猕猴a、B和AB表型的新方法。这种方法能够在不需要新鲜血液或唾液的情况下,简单快速地筛选这些表型。本研究报告了圈养食蟹猴的A、B和AB型的分布,尽管存在区域差异,但与恒河猴非常相似。与恒河猴一样,B血型在食蟹猴中占主导地位,其频率分布导致严重不相容的概率为41%。在猕猴的6号或7号外显子中没有发现沉默突变,这些突变可能导致O型表型,尽管罕见,但已有报道。本研究中恒河猴和食蟹猴基因型的过度纯合性,假设O等位基因缺失,提示可能存在某种机制阻止A和B转移酶的表达。
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引用次数: 8
Identification of a novel HLA allele, HLA-DQB1*06:51, in a Japanese rheumatoid arthritis patient. 日本类风湿关节炎患者HLA- dqb1 *06:51等位基因的鉴定
Pub Date : 2012-10-01 Epub Date: 2012-07-05 DOI: 10.1111/j.1399-0039.2012.01921.x
S Oka, H Furukawa, K Kashiwase, N Tsuchiya, S Tohma

A novel HLA allele, HLA-DQB1*06:51, was identified in a Japanese rheumatoid arthritis patient.

HLA- dqb1 *06:51是一种新的HLA等位基因。
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引用次数: 5
Three novel allelic variants of the RAET1E/ULBP4 gene in humans. 人类RAET1E/ULBP4基因的三个新的等位变异。
Pub Date : 2012-10-01 Epub Date: 2012-07-31 DOI: 10.1111/j.1399-0039.2012.01933.x
S T Cox, J A Madrigal, A Saudemont

Discovery of three novel alleles of RAET1E/ULBP4 by sequence-based typing: RAET1E*008, RAET1E*009 and RAET1E*010.

通过序列分型发现RAET1E/ULBP4的三个新等位基因:RAET1E*008、RAET1E*009和RAET1E*010。
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引用次数: 7
Identification of a new HLA-DRB1 *16 variant, DRB1*16:19 by sequence-based typing in a Chinese Han. 中国汉族HLA-DRB1 *16新变异DRB1*16:19的序列分型鉴定
Pub Date : 2012-10-01 Epub Date: 2012-07-14 DOI: 10.1111/j.1399-0039.2012.01925.x
Z Li, S-Z Jin, H-Y Zou, L-H Cheng

The sequence of the novel allele is identical to HLA-DRB1*16:02:01 except for one nucleotide change at nt203 (G→A), resulting in a coding change, 39 R (CGC)→H (CAC).

该等位基因的序列与HLA-DRB1*16:02:01相同,除了nt203 (G→A)发生了1个核苷酸变化,导致编码发生了39 R (CGC)→H (CAC)。
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引用次数: 0
Serum and CSF soluble CD26 and CD30 concentrations in healthy pediatric surgical outpatients. 健康儿科外科门诊患者血清和脑脊液可溶性CD26和CD30浓度
Pub Date : 2012-10-01 Epub Date: 2012-08-03 DOI: 10.1111/j.1399-0039.2012.01938.x
W Delezuch, P Marttinen, H Kokki, M Heikkinen, K Vanamo, K Pulkki, I Matinlauri

Activated T-helper type 1 (Th1) lymphocytes induce a cellular type immune response, and Th2 lymphocytes, a humoral or antibody-mediated type immune response. Soluble CD26 (sCD26) and soluble CD30 (sCD30) are regarded as markers of Th1 and Th2 lymphocyte activation, respectively. Serum from 112 generally healthy pediatric surgical patients and cerebrospinal fluid (CSF) from 39, aged 1-17 years were measured for sCD26 and sCD30 using an enzyme-linked immunosorbent assay method. The detection limit for sCD26 was 6.8 ng/ml and for sCD30, 1.9 IU/ml. For serum sCD26 and sCD30, 2.5% and 97.5% percentiles constituted the reference limits, and the 95% credible intervals for the percentiles were calculated using regression models with a Bayesian approach. A significant between-gender difference was observed (P = 0.015) in serum sCD26 concentration, of which the lower limits ranged between 273 and 716 ng/ml for girls and 235 and 797 ng/ml for boys. The upper limits ranged between 1456 and 1898 ng/ml for girls and between 1419 and 1981 ng/ml for boys. Moreover, the concentrations of sCD26 increased in infants and children up to 10 years in girls and 12 years in boys. After this however, the values decreased. The serum sCD30 concentration was highest among the youngest infants aged 1 year (80-193 IU/ml), after which a consistent age-related decrease was found. The lowest values were found at the age of 17 years (10-89 IU/ml). A significant between-gender difference in sCD30 concentration was observed (P = 0.019). sCD26 and sCD30 concentrations were low in the CSF samples analyzed: 13.3 ng/ml (median); range 8.3-51.5 ng/ml and 7.6 IU/ml; 2.1-18.5 IU/ml, respectively. Reference limits for serum sCD26 in children aged 1-17 years were established as being 235-1800 ng/ml in toddlers and 400-1800 ng/ml in female adolescents and 700-2000 ng/ml in male adolescents. For sCD30; reference limits of 80-190 IU/ml were established in the youngest age group and 10-90 IU/ml in adolescents.

激活的t辅助型1 (Th1)淋巴细胞诱导细胞型免疫反应,Th2淋巴细胞诱导体液或抗体介导型免疫反应。可溶性CD26 (sCD26)和可溶性CD30 (sCD30)分别被认为是Th1和Th2淋巴细胞活化的标志物。采用酶联免疫吸附法测定112例一般健康儿童外科患者的血清和39例1-17岁儿童的脑脊液中sCD26和sCD30的含量。sCD26和sCD30的检出限分别为6.8 ng/ml和1.9 IU/ml。血清sCD26和sCD30分别以2.5%和97.5%的百分位数为参考限,采用贝叶斯回归模型计算百分位数的95%可信区间。血清sCD26浓度在性别间存在显著差异(P = 0.015),女孩的下限为273 ~ 716 ng/ml,男孩的下限为235 ~ 797 ng/ml。女孩的上限为1456至1898纳克/毫升,男孩的上限为1419至1981纳克/毫升。此外,sCD26浓度在10岁以下女孩和12岁以下男孩的婴儿和儿童中增加。然而,在此之后,数值下降。血清sCD30浓度在1岁的最小婴儿中最高(80-193 IU/ml),之后发现与年龄相关的持续下降。最低值出现在17岁(10-89 IU/ml)。sCD30浓度在性别间差异有统计学意义(P = 0.019)。分析的脑脊液样本中sCD26和sCD30浓度较低:13.3 ng/ml(中位数);8.3-51.5 ng/ml和7.6 IU/ml;分别为2.1-18.5 IU/ml。1-17岁儿童血清sCD26的参考限值确定为:幼儿235-1800 ng/ml,女性青少年400-1800 ng/ml,男性青少年700-2000 ng/ml。sCD30;最小年龄组的参考值为80-190 IU/ml,青少年为10-90 IU/ml。
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引用次数: 13
A novel HLA-A31 allele, A*31:22, was identified by sequence-based typing. 通过序列分型鉴定出一种新的HLA-A31等位基因A*31:22。
Pub Date : 2012-10-01 Epub Date: 2012-08-03 DOI: 10.1111/j.1399-0039.2012.01943.x
W-W Zhang, X-F Li, X Zhang, J-P Li, Z-Q Li

The human leukocyte antigen HLA-A*31:22 allele shows a single nucleotide change at position 245 (A > C) of exon 2 from the closest matching allele HLA-A*31:01:02.

人白细胞抗原HLA-A*31:22等位基因在2外显子245位(a > C)与最近匹配的等位基因HLA-A*31:01:02发生单核苷酸变化。
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引用次数: 5
HLA population genetics: a Lebanese population. HLA群体遗传学:黎巴嫩人群。
Pub Date : 2012-10-01 DOI: 10.1111/j.1399-0039.2012.01936.x
Pedro Cano, Manuela Testi, Marco Andreani, Evelyne Khoriaty, Jad Bou Monsef, Tiziana Galluccio, Maria Troiano, Marcelo Fernandez-Vina, Adlette Inati

Human leukocyte antigen (HLA) typing was done in 426 Lebanese subjects of 88 families, in which 347 haplotypes were identified. The A, B, C, DRB1, DRB3/4/5, DQB1 and DPB1 loci were typed at high resolution. This study shows that information theory, as originally developed by Claude Shannon in 1948, provides a promising theoretical foundation to study the population genetics of a genetic system like HLA. Although Lebanese carry HLA alleles found in other populations, the association of these alleles into haplotypes is quite unique. Comparisons are made with the main ethnic groups. Two haplotypes well represented in the Lebanese population are not identified in any global population: L1 = {A*26:01:01 - B*35:01:01:01- C*04:01:01:01- DRB1*16:01:01 - DRB5*02:02 - DQB1*05:02:01} and L2 = {A*02:02 - B*41:01- C*17:01:01:01 -DRB1*11:04:01 - DRB3*02:02:01:01- DQB1*03:01:01:01}. By studying linkage disequilibrium in two blocks at a time, with the division of the blocks at different levels in consecutive cycles, conserved haplotypes in full linkage disequilibrium come to light, such as {A*26:01:01- B*35:01:01:01 - C*04:01:01:01 - DRB1*16:01:01 - DRB5*02:02 - DQB1*05:02:01- DPB1*03:01:01} and {A*33:01:01 - B*14:02:01 - C*08:02:01 - DRB1*01:02:01- DQB1*05:01:01:01 - DPB1*04:01:01:01}.

对黎巴嫩88个家族的426名受试者进行了人类白细胞抗原(HLA)分型,鉴定出347个单倍型。A、B、C、DRB1、DRB3/4/5、DQB1和DPB1位点高分辨率分型。这项研究表明,最初由Claude Shannon于1948年提出的信息论为研究HLA等遗传系统的群体遗传学提供了一个有希望的理论基础。尽管黎巴嫩人携带在其他人群中发现的HLA等位基因,但这些等位基因与单倍型的关联是相当独特的。与主要民族进行了比较。两种单倍型在黎巴嫩人口中有很好的代表性,但在全球任何人口中都没有发现:L1 = {A*26:01:01 - B*35:01:01:01- C*04:01:01 -DRB1* 16:01:01 - DRB5*02:02 - DQB1*05:02:01}和L2 = {A*02:02 - B*41:01- C*17:01:01 -DRB1*11:04:01 - DRB3*02:02:01 - DQB1*03:01:01}。通过对两个基因块的连锁不平衡进行研究,在连续的周期中对基因块进行不同程度的划分,发现了完全连锁不平衡的保守单倍型,如{a *26:01:01- B*35:01:01:01 - C*04:01:01 - DRB1*16:01:01 - DRB5*02:02 - DQB1*05:02:01- DPB1*03:01:01}和{a *33:01:01 - B*14:02:01 - C*08:02:01 - DRB1*01:02:01- DQB1*05:01:01 - DPB1*04:01:01}。
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引用次数: 6
A new HLA-B*40:186 allele identified by sequence-based typing in a Korean individual. 韩国人HLA-B*40:186等位基因序列分型分析
Pub Date : 2012-10-01 Epub Date: 2012-07-14 DOI: 10.1111/j.1399-0039.2012.01923.x
S Y Kim, K-H Shin, C E Yoon, O J Kwon, H H Kim

The new allele B*40:186 shows a one nucleotide substitution compared with B*40:01:02 at codon 56 (GGG → AGG) resulting in coding change, Gly to Arg.

新等位基因B*40:186与B*40:01:02在密码子56 (GGG→AGG)上发生1个核苷酸的替换,导致编码发生变化,从Gly到Arg。
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引用次数: 3
期刊
Tissue antigens
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