乙型肝炎患者及其子女HBV DNA U5样序列单核苷酸多态性分析

目的进一步探讨乙型肝炎在患者及其亲子代之间的垂直传播。方法应用单核苷酸多态性(SNP)、聚合酶链反应-单链构象多态性(PCR-SSCP)分析等分子遗传学技术和方法检测了乙型肝炎患者家系30个,68例受试者。结果U5样序列PCR检测结果表明,游离型和整合型HBV DNA在乙型肝炎患者(HBP)与其发病后出生子女(HBPa)实验组检出率之间一致性增高,其检出率分别与乙型肝炎患者发病前出生子女(HBPb)和正常对照组的比较,差异均显著,P<0.05。乙型肝炎患者父子之间的SNP分析发现,在U5样序列区和非U5样序列区多个碱基位点处出现碱基替换、插入或缺失,1 908A→T1、950 G→T1、967 T→C,还存在1 900T缺失和1 903C插入等。乙型肝炎患者父子之间的SNP在1 9081、9501、9671、900和1 903位点一致。结论乙型肝炎可以在HBsAg阳性的男性乙型肝炎患者(MHBP)及其子女之间遗传传递,为乙型肝炎的遗传传递进一步提供了分子遗传学证据。     

PRKCI基因单核苷酸多态性与神经管畸形的相关性研究

目的探讨PRKCI基因单核苷酸多态性（SNP）与中国山西省神经管畸形（NTDs）发生的相关性。方法采用病例对照研究,利用MassARRAY分子量阵列分析平台,检测133例NTDs标本和135例非病理性胎儿标本PRKCI基因中17个标签SNPs的基因分型,分析其与NTDs发生的相关性。结果 17个SNPs位点中,16个的微效等位基因频率（MAF）与HapMap或dbSNP数据库的结果基本一致。除rs9876082外,其余SNPs位点的基因型分布和等位基因频率在病例组和对照组均无明显差异。rs9876082位点为纯合的微效等位基因A时,NTDs的发病率增加（P=0.035,比值比=2.135,95%可信区间=1.846-2.471）,但是调整其它变量后进行logistic回归分析,这种相关性不再明显（P=0.057）。结论 PRKCI基因rs9876082位点与NTDs的发生有弱的相关性,这种相关性需进一步加大样本进行验证,PRKCI基因可能不是通过其SNPs影响NTDs的易感性。     

Candidate gene analysis of SPARCL1 gene in patients with multiple sclerosis

Recently, proteomic analysis in cerebrospinal fluid (CSF) from patients with MS identified four proteins which are present in MS but not in normal human CSF, including SPARCL1, an extracellular matrix-associated protein member of the SPARC family. One hundred eighty-six patients with MS and 185 age-matched controls were genotyped for A/G single nucleotide polymorphism (SNP) in exon 1 (rs1049539), C/G SNP in exon 4 (rs1049544), resulting in a substitution of an aspartate with an histidine, and A/G substitution in the exon 5 (rs1130643), leading to the substitution of alanine with threonine. No significant differences in either allelic or genotypic frequency of the three SNPs were found (P>0.05), even in stratifying MS patients according to the course of the disease. Stratifying according to gender, a trend towards a decreased frequency of the C/C genotype of the rs1049544 was observed in male patients as compared with male controls (30.2% versus 44.0%; P=0.217). Despite proteomic studies in CSF from MS patients suggested an important role for SPARCL1 in the development of the disease, SPARCL1 gene does not appear to act as susceptibility factor for MS in the population investigated here. However, the frequency of the C/C genotype of rs1049544 was decreased in male patients, possibly conferring a lower risk of developing MS in male population. Further studies are needed to clarify this issue.     

Graves病候选基因多态性研究进展

Graves病是一种器官特异性自身免疫性疾病，它的病因学十分复杂，是遗传和环境因素相互作用的结果。近几年，人类基因组序列和SNP的研究使这类多基因疾病易感基因的鉴定取得很大进展。目前，Graves病候选基因研究多选择与该病病理过程有关的基因以及甲状腺固有基因，如：HLA系统基因、CTLA-4基因、TSH-R基因、TG基因等，并取得一定进展。本文就这些基因多态性与Graves病关系研究现状进行综述。     

载脂蛋白A5 553G/T单核苷酸多态性对血浆脂质代谢的影响

目的探讨载脂蛋白A5基因（apoa5）553G／T变异在中国镇江地区的频率分布及其对血浆脂质代谢的影响。方法采用聚合酶链反应-限制性片段长度多态性分析（PCR-RFLP）结合琼脂糖凝胶电泳技术检测152例健康人ApoA5 553G／T基因型及等位基因频率分布，同时采用生化方法测定所有研究对象的血浆脂质水平。结果ApoA5 553T等位基因频率为0．049。GG、GT、TT3种基因型中，GT杂合子个体和刀纯合子个体甘油三酯（TG）和低密度脂蛋白胆固醇（LDL-c）水平明显高于GG纯合子个体。T等位基因携带者（GT＋TT）的TG水平较非T等位基因携带者（GG）增高了54．6％（2．47±2．01mmol／L：1．20±1．13mmol／L，P〈0．05），LDL-c水平增高28．3％（3．33±1．03mmol／L：2．78±0．82mmol／L，P〈0．05）。非T等位基因携带者年龄与TG、胆固醇（TC）水平呈正相关，T等位基因携带者年龄与血脂各项指标不相关。男性T等位基因携带者较非T等位基因携带者TG水平增高77．1％（P〈0．01），高密度脂蛋白胆固醇（HDL-c）水平和载脂蛋白Al（ApoAl）水平分别降低6．7％（P〈0．05）和5．2％（P〈0．05），而女性T等位基因携带者较非T等位基因携带者TG水平增高23．1%（P〈0．05），HDL-c水平和ApoAl水平略降低，但无统计学意义（P〉0．05）。结论ApoA5 553G／T单核苷酸多态性对健康人群血浆TG有影响，553T等位基因与血浆TG和LDL-c水平增高有关，与HDL-c和ApoAl水平降低有关，这种作用在男性人群较女性人群更为明显。     

A common Ile796Val polymorphism of the human SREBP cleavage-activating protein (SCAP) gene

We identified a new common amino acid polymorphism of isoleucine/valine at codon 796 in exon 16 of the gene for human sterol regulatory element binding protein (SREBP) cleavage-activating protein (SCAP), a central regulator of lipid synthesis and metabolism in animal cells. It can be detected as an MslI restriction fragment length polymorphism. The allelic frequencies were: isoleucine (A) allele, 0.57 and valine (G) allele, 0.43. This polymorphism may be useful for genetic studies of disorders affecting intracellular lipid metabolism and hyperlipidemia. Received: August 17, 1999 / Accepted: August 19, 1999     

Identification of 156 novel SNPs in 29 genes encoding G-protein coupled receptors

We have been performing extensive screening on single nucleotide polymorphisms (SNPs) in and around genes encoding drug metabolizing enzymes, transporters, and receptors and have constructed the high-density SNP maps of such gene regions. In addition to genetic information reported earlier, we identified a total of 390 genetic variations, 358 SNPs and 32 genetic variations of other types, detected in 29 genes encoding G-protein coupled receptors in Japanese populations. Following a comparison of our data with SNPs in the dbSNP database in the US National Center for Biotechnology Information, 156 SNPs from these gene loci are considered to be novel. The fine-scale SNP maps constructed in this study should serve an important resource for studies of linkage-disequilibrium mapping for complex genetic diseases and drug-response phenotypes.     

A promoter SNP (-1323T>C) in G-substrate gene (GSBS) correlates with hypercholesterolemia

Factors predisposing to the phenotypic features of higher total cholesterol (TC) have not been clearly defined. Here we report an association between a promoter SNP (–1323T>C) in G-substrate gene (GSBS) and TC levels in 368 adult individuals from an east-central area of Japan. Age and gender-adjusted levels of LDL-cholesterol, TG, TC, and HDL-cholesterol were analyzed. When we separate the subjects into two genotypic groups regarding T allele, those who bear the T allele had significantly higher plasma TC levels than the others who lack the T allele (mean; 239.6 mg/dl vs. 210.6 mg/dl; p=0.003; Mann–Whitney test). Of the 341 individuals with the T allele, approximately 80% individuals presented with hypercholesterolemia, whereas only 44% were hypercholesterolemic among the 27 individuals without the T allele (p=0.0001). These results indicate a significant elevating effect of plasma TC levels by a SNP in the putative regulatory region of the G-substrate gene in our studied population. These data suggest that genetic variation at the G-substrate gene may be one of the determinants for plasma lipoprotein levels.     

乙肝病毒基因组中U5序列在乙肝患者垂直传递中的分析研究

目的研究乙肝病毒在乙肝患者垂直传递中的情况，方法运用分子遗传学的技术方法：单核苷酸多态性（SNP）及多聚酶链反应-单链构相多态性（PCR-SSCP），对30个家庭（68个病例）的乙肝患者及其子女进行了研究。结果在乙肝患者及其受感染后出生子女中游离型及整合型乙肝病毒持续增高，与感染前所生子女间比较差异显著（P〈0．05），SNP分析结果显示在乙肝病毒基因组中，U5序列和非U5序列中许多基因位点发生了碱基替换，插入或缺失，男性乙肝患者及其受感染子女的SNP分析结果被确定。结论乙肝病毒可通过男性患者传递至子女；至此，又一个分子遗传学证据证实了了乙肝病毒的遗传性传递。     

No evidence of association of FLJ10986 and ITPR2 with ALS in a large German cohort

A recent genome-wide association study (GWAS) found significant association of six single nucleotide polymorphisms (SNPs) in the gene FLJ10986 with sporadic amyotrophic lateral sclerosis (SALS). Another independent GWAS reported significant association of one SNP in the gene inositol 1,4,5-triphosphate receptor 2 (ITPR2) with SALS. These studies provided conflicting results. We examined the six most significant SNPs in FLJ10986 and one SNP in ITPR2 in a large cohort consisting of 595 SALS cases and 681 controls ascertained from Germany. Our results did not provide evidence for the association of these SNPs with SALS, suggesting a possible population-specific effect for FLJ10986 and ITPR2 that do not modulate the risk for SALS in the German population.     

Alpha tryptase allele of Tryptase 1 (TPSAB1) gene associated with Dengue Hemorrhagic Fever (DHF) and Dengue Shock Syndrome (DSS) in Vietnam and Philippines

We previously reported, significantly higher levels of Chymase and Tryptase in early stage plasma of DSS patients prior to the occurrence of shock suggesting a possible role of mast cells in dengue pathogenesis. To further investigate, we analyzed CMA1 promoter SNP (rs1800875) and TPSAB1 gene alleles, which encode the Human Chymase and α- and β- tryptase 1 enzymes respectively, for susceptibility to Dengue Hemorrhagic Fever (DHF) and Dengue Shock Syndrome (DSS) in patients from hospitals in Vietnam (Ho Chi Minh City and Vinh Long) and the Philippines. While the CMA1 promoter SNP (rs1800875) was not associated with DHF/DSS, the homozygous form of α-tryptase allele was associated with DSS patients in Vinh Long and the Philippines (OR = 3.52, p < 0.0001; OR = 3.37, p < 0.0001, respectively) and with DHF in Ho Chi Minh City (OR = 2.54, p = 0.0084). Also, a statistically significant association was observed when DHF and DSS were combined in Vinh Long (OR = 1.5, p = 0.034) and the Philippines (OR = 2.36, p = 0.0004); in Ho Chi Minh City when DHF and DSS were combine an association was observed, but it was not statistically significant (OR = 1.5, p = 0.0505). Therefore, the α-tryptase might have a possible effect on the susceptibility to severe form of Dengue infection.     

Characterization of 458 single nucleotide polymorphisms of disease candidate genes in the Korean population

Single nucleotide polymorphisms (SNPs) are considered as very promising genetic markers for complex disease gene hunting. However, it has been demonstrated that there are significant ethnic differences in genetic variations. In order to investigate the genetic variations in the Korean population and their ethnic differences, a large number of SNPs of 161 disease candidate genes were collected from a publicly available SNP database and then tested for the distribution of allele frequency in the Korean population. Of all 458 SNPs tested, approximately 43.9% were polymorphic in the Korean population, whereas 44.5% were monomorphic. The remaining 11.6% were failed in the test. Significant differences have been observed when SNP allele frequency pattern of Koreans was compared with those of Caucasians and Africans, whereas this pattern was highly similar between Korean and Japanese populations. Our data indicate that although many of the SNPs available in publicly available database, especially coding-region SNPs (cSNPs), can be used as informative genetic markers for disease association studies, an extensive verification of public SNPs in a particular population studied should be undertaken prior to their association studies. Electronic Publication     

Analysis of high-order SNP barcodes in mitochondrial D-loop for chronic dialysis susceptibility

ObjectivesPositively identifying disease-associated single nucleotide polymorphism (SNP) markers in genome-wide studies entails the complex association analysis of a huge number of SNPs. Such large numbers of SNP barcode (SNP/genotype combinations) continue to pose serious computational challenges, especially for high-dimensional data.MethodsWe propose a novel exploiting SNP barcode method based on differential evolution, termed IDE (improved differential evolution). IDE uses a “top combination strategy” to improve the ability of differential evolution to explore high-order SNP barcodes in high-dimensional data.ResultsWe simulate disease data and use real chronic dialysis data to test four global optimization algorithms. In 48 simulated disease models, we show that IDE outperforms existing global optimization algorithms in terms of exploring ability and power to detect the specific SNP/genotype combinations with a maximum difference between cases and controls. In real data, we show that IDE can be used to evaluate the relative effects of each individual SNP on disease susceptibility.ConclusionIDE generated significant SNP barcode with less computational complexity than the other algorithms, making IDE ideally suited for analysis of high-order SNP barcodes.     

Genomic structure and multiple single-nucleotide polymorphisms (SNPs) of the thiopurine S-methyltransferase (TPMT) gene

Thiopurine S-methyltransferase (TPMT) catalyzes the S-methylation of drugs such as azathiopurine, 6-mercaptopurine, and 6-thioguanine, which are widely prescribed for immunosuppressive or cytotoxic applications. We report here the entire genomic structure of the TPMT gene and the presence of 30 single-nucleotide polymorphisms (SNPs) within that structure. The gene spans a genomic region about 27 kb long and consists of nine exons. By screening its entire genomic sequence for SNPs in 48 Japanese chromosomes by direct DNA sequencing, we detected 1 SNP in the 870-bp promoter region, 26 SNPs in introns, and 3 SNPs in the 3' untranslated region (3'UTR) for investigating correlations between TPMT genotypes and the side-effects caused by thiopurine drugs. Received: June 26, 2000 / Accepted: July 31, 2000     

Catalog of 320 single nucleotide polymorphisms (SNPs) in 20 quinone oxidoreductase and sulfotransferase genes

Single nucleotide polymorphisms (SNPs) in genes encoding drug-metabolizing enzymes, transporters, receptors, and other drug targets have been widely implicated as contributors to differences among individuals as regards the efficacy and toxicity of many medications, as well as the susceptibility to complex diseases. By combining the polymerase chain reaction (PCR) technique with direct sequencing, we screened genomic DNAs from 48 Japa-nese volunteers for SNPs in genes encoding three quinone oxidoreductases (NQO1, NQO2, and PIG3) and 17 sulfotransferases (SULT1A1, SULT1A2, SULT1A3, SULT1C1, SULT1C2, SULT2A1, SULT2B1, ST1B2, TPST1, TPST2, SULTX3, STE, CST, HNK-1 ST, CHST2, CHST4, and CHST5). In all, we identified 320 SNPs from these 20 loci: 22 within coding elements, 21 in 5′ flanking regions, 10 in 5′ untranslated regions, 223 in introns, 19 in 3′ untranslated regions, and 25 in 3′ flanking regions. The ratio of transitions to transversions was approximately 2.3 to 1. Of the 22 coding SNPs, 6 were nonsynonymous substitutions that resulted in amino-acid substitutions. The high-density SNP maps we constructed from this data for each of the quinone oxidoreductases and sulfotransferases examined here should provide useful information for investigations designed to detect association(s) between genetic variations and common diseases or responsiveness to drug therapy. Received: January 12, 2001 / Accepted: January 19, 2001     

中国人群脂联素基因+45T/G多态性与冠心病相关性的Meta分析

目的:对中国人apMl基因+45T/G多态性与冠心病相关性的研究进行Meta分析。方法:通过文献检索收集2009年12月以前完成或发表的中国人apMl基因+45T/G多态性与CHD相关性的病例对照研究,剔除不符合要求的文献。采用ReviewManager4.2软件进行Meta分析,根据各入选文献的同质性检验结果进行数据合并,计算总OR值。绘制漏斗图和Egger’s回归分析检验发表偏倚,并通过改变样本含量进行敏感性分析。结果:共纳入符合条件的8组研究,包括CHD患者1929例,对照1641例;Meta分析结果显示中国人apMl基因+45T/G多态性与CHD易感性无明显相关性(P0.05);发表偏倚和敏感性分析显示本次Meta分析结果稳定可靠。结论:尚无足够证据表明中国人apMl基因+45T/G多态性与CHD易感性相关。     

Identification of a novel single nucleotide polymorphism (SNP) in the human organic cation transporter-like 2-antisense (ORCTL2S) gene

We found a single nucleotide polymorphism (SNP) in exon 3 of the human organic cation transporter-like 2-antisense (ORCTL2S) gene: a base substitution A266G which was confirmed by direct sequencing. Heterozygosity of the polymorphic alleles was 0.45 in a Japanese population. This polymorphism will be useful in the allelic expression analysis of the ORCTL2S gene. Received: September 13, 1999 / Accepted: September 27, 1999