Beta-2 adrenergic receptor genotypes and haplotypes in different ethnic groups

The human beta-2 adrenergic receptor (beta2AR) is responsible for the binding of endogenous catecholamines and their exogenously administered agonists and antagonists. Three functional polymorphisms in codons 16, 27 and 164 have been described which have clinical importance for several diseases, including asthma, hypertension, heart failure, cystic fibrosis and obesity, as well as response to beta-agonist therapy. These were evaluated in 726 individuals from 8 distinct ethnic populations (Chinese, Filipino, Southwest Asian, Saudi, Ghanaian, Kenyan, Sudanese, and European from Scotland). The results show that most haplotypes are shared among all populations, yet there are marked differences in their frequency distributions geographically. The genetic distance tree is different from standard human population distance trees, implying a different mode of evolution for this locus than that for human population gene-flow history. The multilocus frequency differences between the observed clusters of populations correspond to historical haplotype groupings that have been found to be functionally different with respect to multiple medically related phenotypes. Further studies are needed to see if functional relationships are the same across populations.     

Frequencies of UDP-glucuronosyltransferase 1 (UGT1A1) gene promoter polymorphisms among distinct ethnic groups from Brazil

A polymorphism in the promoter region of the UDP-glucuronosyltransferase 1 (UGT1A) gene is associated with Gilbert syndrome (GS), a benign form of mild unconjugated hyperbilirubinemia. We genotyped 157 individuals from Brazil, comprising 71 Caucasians, 54 African-derived subjects, and 32 Parakan? Indians. Frequencies of the alelle (TA)(7) associated with GS found in this study were 0.324, 0.407, and 0.328, respectively. The genotype frequencies differed significantly between Caucasians and African-derived individuals. The high frequencies of (TA)(7) polymorphism among the three groups confirm previous data that this polymorphism is very ancient and appears to be distributed throughout the world.     

Identification of three genomic haplotypes 5' to the human CD1D gene and their distribution in four ethnic groups

CD1d presents lipid antigen to a conserved population of natural killer (NK) T cells, which participate in host immune defense, tumor cell rejection and suppression of autoimmunity. The levels of human CD1d expression vary significantly between individuals. To understand such variation, we sequenced the region up to 1.7 kb 5' upstream of the translation start site and partially through exon 2 in 44 white Americans. We also studied two tagged single nucleotide polymorphisms (SNP) in 112 white Americans, 60 African-Americans, 88 Europeans, and 84 Chinese people from the region. Six SNP present in the region (-836C-->T, -773C-->T, -764C-->G, -713A-->T, -365A-->G and +363A-->G) were found to be in a complete linkage disequilibrium and comprised three haplotypes. Haplotype 1 had -836C, -773C, -764C, -713A, -365A and +363A. Haplotype 2 had -836C, -773T, -764C, -713A, -365A and +363A. Haplotype 3 had -836T, -773C, -764G, -713T, -365G and +363G. -773C-->T and -764C-->G can serve as the tagged SNP to differentiate the three haplotypes. The frequency of haplotype 1 was significantly higher in African Americans than in the other three ethnic groups, whereas the frequency of haplotype 3 was significantly higher in the Chinese people than those in the other three groups. The finding of the three haplotypes provides a genetic marker for CD1d and facilitates the study of the functional role of the genetic variations in human CD1d expression and regulation.     

Microtubule-associated protein 2 and tubulin are differently distributed in the dendrites of developing neurons

We have followed the appearance of two microtubule proteins, tubulin and microtubule-associated protein 2, in rat hippocampal neurons differentiating in cell culture. Double-label immunofluorescence staining showed that from day 1 in vitro onward tubulin appeared as filaments but that microtubule-associated protein 2 remained distributed throughout the cytoplasm. This difference persisted throughout development and was also detectable in cells that had reached morphological maturity. When cells were treated with the microtubule-depolymerizing agent nocodazole, the depolymerized tubulin became spread throughout the cytoplasm so that its distribution was then identical to microtubule associated protein 2. At the same time, multiple side branches began to emerge along the dendrites. When cells which had been exposed to nocodazole were allowed to recover before staining, the tubulin was again present as filaments but the microtubule-associated protein 2 remained distributed throughout the dendritic cytoplasm. Under these conditions the previously extended proximal side branches were resorbed into the main process. These results suggest that cellular microtubule-associated protein 2 is not necessarily exclusively associated with microtubules. Neuronal dendrites in particular appear to contain this protein at levels in excess of the capacity of microtubular microtubule-associated protein 2 binding sites. In view of the known effectiveness of microtubule-associated protein 2 as a promoter of tubulin polymerization, its abundance in dendrites suggests that it acts to ensure total polymerization of dendritic microtubules. In this way it would contribute both to the support of the growing process and the suppression of adventitious sidebranching.     

Distribution of CD36 deficiency in different Chinese ethnic groups

BackgroundCD36 is a multifunctional receptor in cells that plays a role in important cellular processes including immune regulation. Evidence indicates that mutations in the CD36 gene are associated with malaria. Moreover, studies on the frequency of CD36 deficiency have been conducted in specific provinces of China. However, the frequency of CD36 deficiency may differ among various ethnic populations. In this study, we analyzed the frequency of CD36 deficiency among seven different provinces and minorities in China.Methods and materialsIn this study, 5313 samples were randomly collected from seven provinces in China. CD36 deficiency on platelets and monocytes was determined via flow cytometry using a monoclonal antibody (mAb) against CD36. DNA sequencing analysis was performed to identify mutations associated with CD36 deficiency.ResultsThe frequency of CD36 deficiency among individuals from different provinces (n = 7) was 1.60%, comprising 0.38% of type-I deficiency and 1.22% of type-II deficiency. The distribution among provinces ranged from 0.81% to 1.99%. The largest ethnic group, Han, showed a lower frequency of deficiency than ethnic minorities (1.30% versus 2.37%). The most common mutations found in our overall cohort were 329-330delAC and 1228-1239delATTGTGCCTATT. Significant high frequencies of CD36 deficiency were detected in two ethnic minorities, Zhuang (3.69%) and BuYi (3.05%), living in southern China.ConclusionsThrough an analysis of a large cohort, we determined the frequencies of CD36 deficiency among different Chinese ethnic groups. A high frequency of type-I deficiency was found in certain minorities living in southern China, which is known to be vulnerable to malaria epidemics. These findings may help us understand the phenotypic consequences of CD36-deficient alleles associated with malaria.     

A novel HLA-DPA1*0204 allele was identified in a Chinese individual

We report here the identification of a novel human leukocyte antigen-DPA1*0204 allele that was detected by polymerase chain reaction sequence-based typing.     

Frequencies of UDP‐glucuronosyltransferase 1 (UGT1A1) gene promoter polymorphisms among distinct ethnic groups from Brazil

A polymorphism in the promoter region of the UDP‐glucuronosyltransferase 1 (UGT1A) gene is associated with Gilbert syndrome (GS), a benign form of mild unconjugated hyperbilirubinemia. We genotyped 157 individuals from Brazil, comprising 71 Caucasians, 54 African‐derived subjects, and 32 Parakanã Indians. Frequencies of the alelle (TA)₇ associated with GS found in this study were 0.324, 0.407, and 0.328, respectively. The genotype frequencies differed significantly between Caucasians and African‐derived individuals. The high frequencies of (TA)₇ polymorphism among the three groups confirm previous data that this polymorphism is very ancient and appears to be distributed throughout the world. © 2002 Wiley‐Liss, Inc.     

Molecular and serological characterization of HLA-B71 in association with different class I haplotypes or in different ethnic groups

Abstract: The HLA-B70 antigen is among the most common antigens present in African Americans; however, monospecific serologic reagents defining B70 and its subtypes, B71 and B72, are rare. We have recently reported the molecular characterization of a B71 allele (B*1510) from an African American individual carrying the haplotype HLA-A30, Cw3, B71(w6). In order to better define the degree of polymorphism of molecules carrying the B71 serological specificity in the human population, we have used serology, cDNA sequencing, and PCR/SSOP typing to characterize B71 alleles from additional individuals from different ethnic populations and carrying different class I haplotypes. All carried either B*1510 or B*1518 alleles. Other HLA-B alleles isolated from these individuals (B*5001, B*4901, B*3501, B*3701) were identical to previously reported sequences except for a novel B41 allele (B*4102) identified in one Hispanic individual. This allele has concurrently been identified by Rufer and colleagues in Caucasian individuals. The B*4102 allele differs from B*4101 at codons 95 (Leu/Trp) and 97 (Ser/Arg). In addition, the B*4102 allele differs from B*4101 by two silent substitutions at codons 94 (ACC/ACT) and 99 (TAC/TAT). Since the polymorphic sequence present in B*4102 is also present in other HLA-B alleles (e.g., B*2707, B*4002, B*0702), it may represent a gene conversion cassette. The allelic diversity at the class I loci and the scarcity of monospecific alloantisera support the importance of the application of molecular based methods to identify HLA class I alleles in matching unrelated donor/recipient pairs for bone marrow transplantation.     

先兆子痫患者HLA-DQA1、-DQB、-DPA1基因多态性

目的：探讨人类白细胞抗原HLA-DQA1、-DQB1、-DPA1基因多态性与先兆子痫发病的关系。方法：采用序列特异性引物技术（PCR-SSP） 对46例先兆子痫患者和105例正常孕妇及其新生儿进行HLA-DQ-DPA1等位基因分型。结果：所有标本共检出11种HLA-DQA1基因表型、16种HLA-DQB1基因表型、6种HLA-DPA1基因表型。先兆子痫患者HLA-DQB1＊0301基因频率高于正常孕妇，差异有显著性（Pc=0．032，RR=2．43，AR=0．30），其余各基因表型频率两组比较差异均无显著性。结论：HLA-DQB1＊0301基因可能是一种先兆子痫发病的易感基因。     

先兆子痫患者HLA-DQA1、-DQB1、-DPA1基因多态性

目的:探讨人类白细胞抗原HLA-DQ-A1、DQB1、DPA1基因多态性与先兆子痫发病的关系。方法:采用序列特异性引物技术(PCRSSP)对46例先兆子痫患者和105例正常孕妇及其新生儿进行HLA-DQ-DPA1等位基因分型。结果:所有标本共检出11种HLADQA1基因表型、16种HLADQB1基因表型、6种HLADPA1基因表型。先兆子痫患者HLA-DQ-B10301基因频率高于正常孕妇,差异有显著性(Pc=0.032,RR=2.43,AR=0.30),其余各基因表型频率两组比较差异均无显著性。结论:HLADQB10301基因可能是一种先兆子痫发病的易感基因。     

Catalog of 162 single nucleotide polymorphisms (SNPs) in a 4.7-kb region of the HLA-DP loci in southern Chinese ethnic groups

HLA class-II proteins are cell-surface molecules that present antigens to T cells, and their expressional regulation is crucial to the immune reaction. Sequence variation at the regulatory region can directly affect the gene expression level. We cloned and sequenced a 4.7-kb region containing the regulatory region, exon1, and partial intron1 of both HLA-DPA1 and DPB1 genes in 25 variable sequences from southern Chinese ethnic groups and got a high-density map of 162 single nucleotide polymorphisms (SNPs): seven in 5-flanking regions, four in 5-untranslated regions, and four in the coding regions. By comparing these data with SNPs in dbSNP database in the NCBI, 145 SNPs (89.5%) were novel. In addition, eight genetic variations of insertion-deletion polymorphisms (INDELs) were discovered within the 4.7-kb region. These high-resolution maps can be used as resources of markers for association studies of complex diseases, assessment of individuals predisposition to diseases, and tailoring of therapies, as well as research markers for population genetics and evolution.     

Novel rare mutations and promoter haplotypes in ABCA1 contribute to low-HDL-C levels

The ATP-binding cassette A1 (ABCA1) protein regulates plasma high-density lipoprotein (HDL) levels. Mutations in ABCA1 can cause HDL deficiency and increase the risk of premature coronary artery disease. Single nucleotide polymorphisms (SNPs) in ABCA1 are associated with variation in plasma HDL levels. We investigated the prevalence of mutations and common SNPs in ABCA1 in 154 low-HDL individuals and 102 high-HDL individuals. Mutations were identified in five of the low-HDL subjects, three having novel variants (I659V, R2004K, and A2028V) and two with a previously identified variant (R1068H). Analysis of four SNPs in the ABCA1 gene promoter (C-564T, G-407C, G-278C, and C-14T) identified the C-14T SNP and the TCCT haplotype to be over-represented in low-HDL individuals. The R1587K SNP was over-represented in low-HDL individuals, and the V825I and I883M SNPs over-represented in high-HDL individuals. We conclude that sequence variation in ABCA1 contributes significantly to variation in HDL levels.     

Seroepidemiological studies on hepatitis B and D viruses infection among five ethnic groups in southern Taiwan

In order to compare the prevalence of hepatitis B virus (HBV) and hepatitis D virus (HDV) infection among five ethnic groups in Pingtung County of southern Taiwan, a total of 240 serum samples were collected from September to October, 1985, from the following five ethnic groups: Taiwanese, Hakka, Mainland Chinese, aboriginal Paiwanese, and aboriginal Rukaiese. Ages of subjects ranged from 5 to 69 years. All sera were tested for hepatitis B surface antigen (HBsAg), surface antibody (anti-HBs), and core antibody (anti-HBc) by radioimmunoassay (RIA). Hepatitis B e antigen (HBeAg) and antibody to hepatitis D antigen (anti-HDV) were also tested for those with HBsAg-positive sera. Results showed that 44.1% of all sera examined were negative for HBsAG but positive for both anti-HBs and anti-HBc; additionally, 24.6% were negative for both HBsAg and anti-HBs but positive for anti-HBc. Only 134 serum samples showed negative results for HBV markers, indicating an HBV infection rate of 88.8%. The anti-HDV positive rate was estimated to be 2.7% among HBsAg-positive subjects. The HBsAg-positive rates among Rukaiese, Paiwanese, Hakka, Taiwanese, and Mainland Chinese were 25.8, 22.5, 16.7, 12.9, and 10.0%, respectively; while the prevalence rates of HBV infection among the above five groups were 94.2, 94.6, 85.4, 87.5, and 82.5%, respectively. Differences in the HBsAg-positive rate and HBV infection rate among these ethnic groups were statistically significant. We conclude that people living in Pingtung County are more frequently infected with HBV when compared with inhabitants in northern Taiwan.     

应用SBT直接测序分型法研究中国南方汉族人群HLA五个基因座单倍型

目的 研究中国南方汉族人群HLA-A、B、Cw、DRBl、DQBl等位基因多态性及单倍型的分布特征.方法 应用聚合酶链反应-直接测序分型(polymerase chain reaction sequence-based typing,PCR-SBT)法对186名中国南方汉族健康人群HLA-A、B、Cw、DRBl、DQBl进行基因分型.结果 检出的HLA-A、B、Cw、DRBl、DQBl等位基因分别有28、49、24、29、20种.经统计分析A*0207-B*4601(10.81%),A*3303-B*5801(6.14%),B*4601-DRBl*0901(6.22%),B*4001*DRBl*0901(3.78%),DRBl*0901-DQBl*0303(12.16%)和DRBl*1202-DQBl*0301(8.38%)单倍型呈强连锁不平衡单倍型(RLF≥0.5,X<'2>>3.84,P<0.05);A*0207-B*4601-Cw*0102(10.75%),A*3303-B*5801-Cw*0302(5.14%),A*0207-B*4601-DR*0901(5.07%),A*3303-B*5801-DRBl*0301(2.96%),A*0207-B*4601-Cw*0102-DRBl*0901-DQBl*0303(4.87%)和A*1101-B*1301-Cw*0304-DRBl*1501-DQBl*0601(2.43%)单倍型分别是中国南方汉族人群常见单倍型.结论 中国南方汉族人群HLA 5个基因座单倍型分布具有高度的遗传多态性且有其自身分布特点.本研究获得的较完整的HLA 5个基因座单倍型分布数据,将为人类学、HLA疾病相关性和器官移植等研究提供遗传学参考数据.     

SORL1 haplotypes modulate risk of Alzheimer's disease in Chinese

Genetic variants of the neuronal sortilin-related receptor (SORL1) have been demonstrated to modulate the risk of Alzheimer's disease (AD) in different American and European populations [Rogaeva, E., Meng, Y., Lee, J.H., Gu, Y., Kawarai, T., Zou, F., Katayama, T., Baldwin, C.T., Cheng, R., Hasegawa, H., Chen, F., Shibata, N., Lunetta, K.L., Pardossi-Piquard, R., Bohm, C., Wakutani, Y., Cupples, L.A., Cuenco, K.T., Green, R.C., Pinessi, L., Rainero, I., Sorbi, S., Bruni, A., Duara, R., Friedland, R.P., Inzelberg, R., Hampe, W., Bujo, H., Song, Y.Q., Andersen, O.M., Willnow, T.E., Graff-Radford, N., Petersen, R.C., Dickson, D., Der, S.D., Fraser, P.E., Schmitt-Ulms, G., Younkin, S., Mayeux, R., Farrer, L.A., St George-Hyslop, P., 2007. The neuronal sortilin-related receptor SORL1 is genetically associated with Alzheimer disease. Nat. Genet. 39 (2), 168-177]. We conducted haloptype analysis involving two genetic clusters of SORL1 in AD and controls among Han Chinese. rs3824968 (SNP 23) was associated with an increased risk of AD, and there was a trend towards association for rs1699102 (SNP 22) and rs2282649 (SNP 24). More robust associations were found for three-loci haplotypes. In particular, the GCA haplotype at SNPs 19-22-23 was associated with an increased risk (odds ratio 1.4), and CTC haplotype at SNPs 19-22-23 and TCT at SNPs 22-23-24 a decreased risk (odds ratio 0.67) of AD. The complete absence of some at-risk North European haplotypes in our Chinese study subjects was likely due to different ancestral origins, with allelic heterogeneity among races. However, our study suggests that certain SORL1 haplotypes at SNPs 19-24 modulated risk of AD in our Chinese population.     

Sequencing-based typing reveals new insight in HLA-DPA1 polymorphism

Abstract: An HLA-DPA1 sequencing-based typing (SBT) system has been developed to identify DPA1 alleles. Up to now eight DPA1 alleles have been defined. Six can be discriminated based upon exon 2 polymorphism. The three subtypes of DPA1*01: DPA1*0101, DPA1*0102 and DPA1*0103, have identical exon 2 sequences but show differences in exon 4. Exon 4 sequences were known for only the three DPA1*01 subtypes and for DPA1*0201. We now present additional sequence information for exon 4 and the unknown segments at the 3' end of exon 2. Additionally with the use of this sequencing technique it is also possible to identify previously unidentified polymorphism. We have studied the exon 2 and exon 4 polymorphism of DPA1 in 40 samples which include all known DPA1 alleles. A new allele, DPA1*01 new, was identified which differs by one nucleotide in exon 2 from DPA1*0103, resulting in an aspartic acid at codon 28. The DPA1*01 subtypes DPA1*0101 and DPA1*0102 could not be confirmed in samples which previously were used to define these subtypes, and consequently they do not exist. The exon 4 sequence of DPA1*0201 is corrected based on sequence data of DAUDI, the cell line in which DPA1*0202 was originally defined. The exon 4 regions of the remaining four alleles were resolved: the exon 4 regions of the alleles DPA1*02021 and DPA1*02022 were found to be identical to the — corrected — DPA1*0201 whereas the exon 4 region of DPA1*0301 differs by one nucleotide compared to DPA1*0103. The DPA1*0401 exon 4 region differs by one nucleotide compared to the corrected DPA1*0201. As is found in other class II genes, all exons of DPA1 show some polymorphism, but the polymorphism in exon 2 is sufficient to identify the different alleles.