Simultaneous detection of the exon 10 polymorphism and a novel intronic single base insertion polymorphism in the XPD gene using single strand conformation polymorphism

We developed a new method based on the single strand conformation polymorphism (SSCP) technique for the detection of a G23591A (Asp312Asn) polymorphism in exon 10 of the XPD gene. In the process we also identified a novel polymorphism 23623C-ins (IVS10+17C-ins) in intron 10 of the same gene. With this newly developed SSCP-based method of genotyping we could detect both polymorphisms in the same assay and thus consequently determine the haplotype. In order to determine the population frequency of the novel polymorphism and the haplotype frequency, 302 healthy individuals were genotyped. The allelic frequency of the 23623C-ins intronic polymorphism was 0.16, whereas the frequency of the variant allele for the G23591A polymorphism was 0.39. Forty-three individuals (14%) were heterozygous for both polymorphisms but none carried polymorphic variants for both G23591A and 23623C-ins on the same allele. The effect of the novel intronic insertion polymorphism, which is located 16 nt downstream of the 3'-end of exon 10 of the XPD gene and involves a mononucleotide C repeat sequence, on expression remains to be determined.     

中国人群Auberger抗原基因多态性研究

目的 对中国人群Latheran血型系统中Auberger抗原的摹因多态性分布进行研究,建立起稳定、准确的Auberger抗原分子生物学的检测方法.方法 随机采集162名非血缘关系无偿志愿捐血者外周血样,直接进行Auberger血型抗原基因的第12外显子测序分析.对新位点突变应用聚合酶链反应-限制性片段长度多态性法电泳分析.结果 在162人份标本中Aua+b-(nt 1615A)119人,Aua+b(nt 1615A/G)40人,Aua-b+(nt 1615c)3人,Aua和Aub的基因频率分别为0.8580和0.1420.在1例基因为Aua纯合型个体中,出现nt1595G＞T突变,PCR产物经Hha Ⅰ限制性内切酶内切后,突变型和野生型的个体分别被分为不同片段,可证实该突变存在.结论 建立起Auberger抗原分子生物学的检测方法,得到中国人群Auberger抗原基因的多态性分布,发现一个新的Lutheran等位基因(GenBank注册号:EU2N1043).     

Identification of a novel Tru9 I polymorphism in the human vitamin D receptor gene

We found a novel Tru9 I restriction polymorphism in intron 8 of the vitamin D receptor (VDR) gene in healthy French Caucasians. It corresponds to a substitution of A for G at nucleotide +443 bp from the end of exon 8. The allelic frequency of G and A in 151 unrelated subjects was 0.894 and 0.106, respectively. This polymorphism is located in the reverse primer binding site of primers that have been frequently used in the literature to genotype a BsmI restriction polymorphism. The presence of the Tru9I A allele may result in allele drop-out when the BsmI restriction fragment length polymorphism (RFLP) is genotyped with the original set of primers. This novel Tru9I polymorphism may be useful for analysis of the VDR gene. Received: August 2, 1999 / Accepted: September 21, 1999     

Association of the estrogen receptor alpha gene polymorphisms with osteoporosis in the Mexican population

The estrogen receptor gene (ER alpha) has been implicated in the development of osteoporosis. In this study, the association of two ER alpha gene polymorphic markers (a TA dinucleotide repeat and a single nucleotide polymorphism, G2014A) with osteoporosis was tested in 70 osteoporotic women, 70 non-osteoporotic women and 500 subjects from the Mexican population. According to the genetic analysis of the Mexican population using eight unlinked polymorphic markers, we found that our population is structured into three subpopulations; therefore, the allele-phenotype relationship was analyzed with a statistical method that considered population stratification. We found that the G2014A polymorphism is associated with the presence of osteoporosis while the TA dinucleotide repeat is not. The G allele and the GG genotype frequencies of the G2014A marker were significantly higher in osteoporotic than in non-osteoporotic women. Likewise, subjects bearing the G allele in heterozygous or homozygous displayed lower values for lumbar bone mineral density and T score than those who did not present any G allele. The effect of confounders for osteoporosis on the association of G allele-osteoporosis was ruled out. In summary, we conclude that the G2014 polymorphism may become a useful marker for genetic studies of osteoporosis in the Mexican population.     

An association study of polymorphisms in the alpha-antichymotrypsin gene for Alzheimer disease in Han-Chinese

Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and DNA sequencing were employed to screen the coding region of the alpha-antichymotrypsin (AACT) gene in Han-Chinese population for polymorphism possibly associated with Alzheimer's disease (AD). Consequently, seven polymorphic sites including 25A>G, 39G>A, 370C>T, 662T>G, 892C>T, 923T>C and 1332A>G were detected. Of them, the 25A>G was reported previously and the others are all novel. We subsequently focused on the 25A>G and the 39G>A polymorphism that were of interest to us and conducted an association study of them by another scanning of 246 controls that matched the AD patients. Statistic test showed that both genotype (p=0.0378, Fisher's exact, two tailed) and allele frequency (p=0.0382, Fisher's exact, two tailed) of 39G>A are different between AD patients and the controls. As for 25A>G, lain only the heterozygous genotype A/G associates with AD (p=0.0220, chi(2)), but not the A allele frequency (p=0.1141, chi(2)).     

TNF-α-238G/A基因多态性与原发性肝癌的关系

目的 探讨肿瘤坏死因子-α（TNF-α）基因启动子-238G/A多态性与原发性肝癌（PHC）的相关关系.方法 应用聚合酶链反应-限制性片段长度多态性法（PCR-RFLP）检测100例PHC患者和150例健康对照者TNF-α基因启动子-238G/A多态性.结果 TNF-α-238基因型GG、GA频率在PHC组和对照组分别为95.3%和4.7%,88%和12%;等位基因G、A频率在PHC组和对照组分别为97.7%和4.7%,94%和6%.两组差异均有显著性（P＜0.05）,携带GA基因型个体患PHC的风险约是GG基因型的2.786倍（OR=2.786,95%CI=1.057～7.343）.结论 TNF-α-238G/A基因多态性与PHC的发病有相关性,A等位基因可能是PHC的遗传易感基因.     

Association of the R485K polymorphism of the factor V gene with poor response to activated protein C and increased risk of coronary artery disease in the Chinese population

Inherited predisposition to thrombosis contributes to the initiation and progression of coronary artery disease (CAD). The present study was designed to explore the relationship between genetic variation of coagulation factor V and occurrence of CAD. A total of 141 unrelated patients with CAD and 175 healthy controls were analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) for variation detection in all 25 exons of the factor V gene. Among the study subjects, 55 CAD patients and 73 controls were evaluated at random for response to activated protein C (APC) by Coatest APC resistance test. Polymorphisms in exon 4, 10, 13 and 16 of factor V gene were documented [642G-->T(S156), 1628--> A(R485K), 4070A-->G(H1299R) and 5380G A(V1736M), respectively]. The study also identified a novel polymorphism 327A G in exon 2 which did not alter the amino acid residue. Leiden mutation (R506Q) was not detected in any of our 316 subjects. Among the five polymorphisms, the allele frequency of 1628G--> A was significantly different between the CAD patients and the controls (0.36 vs. 0.21, p < 0.05). Subjects homozygous or heterozygous for the A allele of 1628G-->A polymorphism had lower normalized APC ratios than those with the GG genotype in the CAD group (1.16+/-0.13 and 1.18+/-0.23 vs. 1.36+/-0.33, p <0.05) and in the controls, indicating that A(1628) allele was associated with a poor response to APC. We conclude that the 1628G-->A (R485K) polymorphism of factor V is associated with a poor response to APC and increased risk for CAD.     

HLA‐A locus allelic dropout in Sanger sequence‐based typing due to the single nucleotide polymorphism of exon 1

The DNA‐based method is used widely for HLA genotyping in routine work, but some allele may be dropout in the genotyping procedure. Here, we reported a case with HLA‐A allele dropout in the Sanger PCR‐SBT test. The initial PCR‐SBT method with a commercial agent kit was not characterized, and the result of Luminex technology indicated the dropout as a HLA‐A*02 allele. Subsequently, the sequences of exons 2–4 were fully matched with the A*02:07 and A*11:01:01 by allele group‐specific primer amplification PCR‐SBT. On further analysis, a novel allele A*02:07:07 was identified, which has one nucleotide difference from A*02:07:01 at position 6 C>G of exon 1. According to the sequencing for 5′‐UTR to 3′‐UTR, the novel single nucleotide polymorphism of exon 1 was contributed to HLA‐A locus allele dropout in the sample. Our results indicated multiplatform analysis is necessary when a conclusive HLA type cannot be determined by a single methodology.     

TIM-4基因多态性与湖北地区汉族人群支气管哮喘易感性的研究

目的 探讨T细胞免疫球蛋白域及黏蛋白域蛋白-4(T cells immunoglobulindomain andmucindomain protein-4,TIM-4)基因外显子2区Lys65Lys(G/A)、外显子9区Val1365Met(G/A)的单核昔酸多态性(SNP)与湖北地区汉族人群支气管哮喘易感性的关系.方法 采用聚合酶链反应-限制性片段长度多态性(PCR-RFLP)的方法对湖北地区185例哮喘患者和162例健康者TIM-4基因外显子2区Lys65Lys(G/A)、外显子9区Vai365Met(G/A)的多态性进行分析,计算基因型和等位基因频率.结果 (1)湖北地区汉族人群健康者TIM-4基因外显子2区Lys65Lys(G/A)位G/G、G/A、A/A基因型频率分别为0.840、0.160、0,而哮喘人群其频率分别为0.859、0.141、0,其基因型和等位基因型频率与对照组相比差异均无统计学意义(P=0.603,P=0.618);(2)本试验未检测到TIM-4外显子9区Va1365Met(G/A)的多态性.结论 湖北地区汉族人群TIM-4基因外显子2区Lys65Lys(G/A)存在单核苷酸多态性变异,但该位点的变异与湖北地区汉族人群支气管哮喘易感性无关;TIM-4基因外显子9区Va1365Met(G/A)在湖北地区汉族人群中未发现单核苷酸多态性.     

No evidence for association between the −112G/A polymorphism of UGRP1 and childhood atopic asthma

BACKGROUND: Susceptibility to asthma is known to involve genetic factors. Genome-wide screens have indicated that the chromosome 5q31-q34 region is linked to and/or associated with asthma. A new gene, named UGRP1 and reported by Niimi et al., encodes uteroglobin-related protein and is expressed in the lung and trachea. Niimi et al. showed the -112G/A polymorphism of the UGRP1 gene to be associated with asthma in a case-control study. OBJECTIVE: The objective of the present study was to replicate this association and confirm the possible role of the UGRP1-112G/A polymorphism in the aetiology of childhood asthma in a Japanese population. METHODS AND RESULTS: We conducted a transmission disequilibrium test (TDT) in 131 families identified through paediatric patients being treated for asthma. A case-control study was also carried out by comparing the probands and 137 unrelated non-atopic non-asthmatic Japanese children and 211 unrelated healthy Japanese adults. The -112G/A polymorphism was genotyped by the PCR-RFLP method. The TDT revealed that the -112A allele was not preferentially transmitted to asthma-affected children (P=0.85). Neither the presence of at least one A allele in an individual's genotype (sum of the G/A and A/A genotypes) nor the -112A allele was more prevalent among the asthma subjects than among the control subjects. CONCLUSION: Our findings indicate that the UGRP1-112G/A polymorphism does not play a substantial role in genetic predisposition to childhood asthma in this Japanese population.     

Identification of two novel HLA class II alleles, DQB1*030503 and DRB1*0447

Two novel human leukocyte antigen (HLA) class II alleles have been identified in routine typing of bone marrow donors for the Australian Bone Marrow Donor Registry in Sydney, Australia. Sequence analysis of exon 2 of both the DQB1 and DRB1 genes revealed the novel polymorphism. A silent substitution of G to A at nucleotide position 210 has been identified for the DQB1*030503 allele when compared to the closest matched allele, DQB1*030501. There is no associated amino acid difference between the translated products of the two alleles. The second new allele is a variant of the DRB1 gene. The DRB1*0447 allele was identified with three nucleotide substitutions compared to the closest matched allele DRB1*0436. There is a silent mutation at nucleotide position 303, G to C and two substitutions at adjacent nucleotide positions 344 and 345, T to G and G to T, respectively. The latter two substitutions result in an amino acid change from valine to glycine at position 86, implicating a different specificity and affinity of antigen binding.     

A novel multiplex PCR-RFLP method for simultaneous detection of the MTHFR 677 C > T, eNOS +894 G > T and - eNOS -786 T > C variants among Malaysian Malays

ABSTRACT: BACKGROUND: Hyperhomocysteinemia as a consequence of the MTHFR 677 C > T variant is associated with cardiovascular disease and stroke. Another factor than can potentially contribute to these disorders is a depleted nitric oxide level, which can be due to the presence of eNOS +894 G > T and eNOS 786 T > C variants that make an individual more susceptible to endothelial dysfunction. A number of genotyping methods have been developed to investigate these variants. However, simultaneous detection methods using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis are still lacking. In this study, a novel multiplex PCR-RFLP method for the simultaneous detection of MTHFR 677 C > T and eNOS +894 G > T and eNOS 786 T > C variants was developed. A total of 114 healthy Malay subjects were recruited. The MTHFR 677 C > T and eNOS +894 G > T and eNOS 786 T > C variants were genotyped using the novel multiplex PCR-RFLP and confirmed by DNA sequencing as well as snpBLAST. Allele frequencies of MTHFR 677 C > T and eNOS +894 G > T and eNOS 786 T > C were calculated using the Hardy Weinberg equation. METHODS: The 114 healthy volunteers were recruited for this study, and their DNA was extracted. Primer pair was designed using Primer 3 Software version 0.4.0 and validated against the BLAST database. The primer specificity, functionality and annealing temperature were tested using uniplex PCR methods that were later combined into a single multiplex PCR. Restriction Fragment Length Polymorphism (RFLP) was performed in three separate tubes followed by agarose gel electrophoresis. PCR product residual was purified and sent for DNA sequencing. RESULTS: The allele frequencies for MTHFR 677 C > T were 0.89 (C allele) and 0.11 (T allele); for eNOS +894 G > T, the allele frequencies were 0.58 (G allele) and 0.43 (T allele); and for eNOS 786 T > C, the allele frequencies were 0.87 (T allele) and 0.13 (C allele). CONCLUSIONS: Our PCR-RFLP method is a simple, cost-effective and time-saving method. It can be used to successfully genotype subjects for the MTHFR 677 C > T and eNOS +894 G > T and eNOS 786 T > C variants simultaneously with 100 % concordance from DNA sequencing data. This method can be routinely used for rapid investigation of the MTHFR 677 C > T and eNOS +894 G > T and eNOS 786 T > C variants.     

CTLA-4 +49 A/G gene polymorphism in Croatian and Slovenian multiple sclerosis patients

Polymorphisms in the CTLA-4 gene are known to be important in several autoimmune diseases, including multiple sclerosis (MS). Previous studies on the impact of CTLA-4 +49 A/G gene polymorphism have given contradictory results. We investigated the possible influence of this polymorphism on MS susceptibility and disease behaviour in Croatian and Slovenian populations. Genotyping was performed in 367 patients with MS and 480 control subjects using PCR-RFLP method. The G allele was present in 216 (58.9%) patients with MS vs. 282 (58.7%) healthy controls (P = 0.975, OR = 1.01, 95% CI = 0.76-1.32). No significant differences were observed in CTLA-4 +49 A or G allele distribution between patients and controls, indicating that this polymorphism does not influence susceptibility to MS in the surveyed populations. No correlation was observed between G allele carrier status and age at disease onset, disease course or severity.     

蛋氨酸合酶基因A275 6G位点多态性与非综合征型唇腭裂的关联性研究

目的 研究蛋氨酸合酶基因(methionine synthase,MS)A2756G位点多态性与非综合征型唇腭裂(nonsyndromic cleft lip with or without cleft palate,NSCL/P)的关联性.方法 采用PCR-限制性片段长度多态性技术检测97个NSCL/P病例组核心家庭和104个对照家庭的MS基因A2756G位点的多态性;用人群关联研究分析、病例组核心家庭的传递不平衡检测(transmission disequilibrium test,TDT)、单体型的相对危险度分析(haplotype-based haplotype relative risk,HHRR)、家庭为基础的关联研究(family-based association tests,FBAT)等统计分析.结果 子代、父亲、母亲病例组和对照组之间基因型和等位基因的分布差异均无统计学意义(P>0.05);本研究中在子代和母亲组中未检出GG基因型,AG基因型相对于AA基因型的比值比OR和95%CI分别为子代1.78(0.74～4.34)、父亲0.80(0.36～1.79)、母亲1.26(0.54～2.93),G相对于A基因的OR和95%CI分别为子代1.70(0.78～3.73)、父亲0.88(0.49～1.75)、母亲1.23(0.59～2.60),携带有突变基因G并不能增加患NSCL/P的危险.病例组核心家庭分析,TDT分析χ2=0.034,P>0.05;HHRR分析χ2=0.03,P>0.05;FBAT分析Z=0.186,P>0.05.结论 结果未显示出MS基因A2756G位点多态性和NSCL/P发生的相关性,还待进一步研究.     

UCH-L1基因多态性与帕金森病的关联研究

目的 探讨泛素蛋白羧基水解酶L1(ubiquitin carboxy-terminal hydrolase-L1,UCH-L1)基因第3外显子54C/A及第4外显子277C/G多态与中国北方汉族人群散发性帕金森病(Parkinson'S disease,PD)的关联.方法 应用聚合酶链反应-限制性片段长度多态性方法,对75例散发性PD和100名健康对照者UCH-L1 C/A和C/G两个位点的基因型和等位基因分布频率进行检测.结果 (1)UCH-L1 C/A位点等位基因和基因型分布,在PD与对照组间差异有统计学意义(P<0.05),PD组的A等位基因和AA基因型明显低于对照组(P<0.05).(2)在对散发性PD与对照组UCH-L1基因分析中,未发现C/G的多态性.结论 (1)UCH-L1 C/A基因多态性与中国北方汉族人群散发性PD患者遗传易患性有关.(2)UCH-L1 C/G基因多态性与中国北方汉族人群散发性PD患者遗传易患性不关联.     

海洛因依赖与儿茶酚胺氧位甲基转移酶基因-287A/G多态性的关联研究

目的 探讨海洛因依赖和儿茶酚胺氧位甲基转移酶（catechol-O-methyltransferase,COMT)ADLD－287A/G多态性的关系。方法 采用PCR技术，检测了268例海洛因依赖者和177名正常对照的COMT基因－287A／G多态性。结果 海洛因依赖者COMT基因－287A／G多态的基因型AA的频率显著高于对照组9x^2=7.41,=0.025)，等位基因A的频率也显著高于对照组（X^2=5.69,P=0.017)。结论提示COMT基因－287A／G多态性与海洛因依赖的易感性有关。     

盐皮质激素受体基因多态性与妊高征相关性研究

目的探讨中国人群中盐皮质激素受体基因(MR)外显子3上A760G多态性与妊高征的相关性.方法以人外周血DNA为模板,通过聚合酶链式反应-等位特异性寡核苷酸杂交(PCR-ASO)方法测定95例随机妇女、101例正常孕妇、60例妊高征妇女的MR外显子3上A760G多态性频率.结果MR外显子3上A760G多态性位点中A等位基因和C等位基因在正常孕妇组中分别为83.17%与16.83%,在妊高征组中分别为84.17%与15.83%,在随机人群组中分别为86.84%与13.16%.结论中国人群中MR基因外显子3上存在A760G多态性,该多态性与妊高征不存在相关性.     

VEGF基因多态性与子宫内膜异位症和子宫腺肌病遗传易感性研究

目的 探讨血管内皮生长因子(vascular endothelial growth factor,VEGF)基因启动子区-460C/T和-1154G/A单核苷酸多态性与子宫内膜异位症和子宫腺肌病发病风险的关系.方法 采用聚合酶链反应-限制性片段长度多态方法检测344例子宫内膜异位症患者(内异症组)和360名对照妇女(对照组)、174例子宫腺肌病患者(腺肌病组)和199名对照妇女(对照组)的VEGF基因2个多态性位点的基因型频率分布情况.结果 VEGF-460C/T多态的基因型和等位基因频率分布在两病例组与其对照组间差异均无统计学意义(P>0.05).在内异症组和对照组中,VEGF-1154G/A多态的AA、GA、GG 3种基因型频率分别是1.7%、28.8%、69.5%和5.8%、32.8%、61.4%,两组比较差异有统计学意义(P=0.006);G、A等位基因频率分别是83.9%、16.1%和77.8%、22.2%,两组比较差异有统计学意义(P=0.004);与GA+AA基因型相比,携带GG基因型明显增加内异症的发病风险(OR=1.43,95%CI:1.05～1.96).在腺肌病组和对照组中,VEGF-1154G/A多态的AA、GA、GG 3种基因型频率分别是2.9%、23.6%、73.6%和7.0%、34.2%、58.8%.两组比较差异有统计学意义(P=0.007);G、A等位基因频率分别是85.3%、14.7%和75.9%、24.1%,两组比较差异有统计学意义(P=0.001);与GA+AA基因型相比,携带GG基因型明显增加腺肌病的发病风险(OR=1.95,95%CI:1.26～3.03).结论 VEGF基因启动子区-1154G/A多态与子宫内膜异位症和子宫腺肌病的发病风险明显相关,携带GG基因型显著增加子宫内膜异位症和子宫腺肌病的发病风险.     

PTPN22 G788A和A10281188G与广东地区人群RA易感性的关系研究

目的探讨蛋白酪氨酸磷酸酶非受体型22（PTPN22）基因多态性（rs33996649/G788A/R263Q和rs1310182/A10281188G）与广东地区汉族人群类风湿性关节炎（RA）易感性间的关系。方法选取广东地区人群中218例RA患者以及229例健康对照者进行病例对照研究,采用PCR-RFLP技术检测PTPN22G788A和A10281188G两个多态性位点的基因型,计算比较两组基因型和等位基因频率。结果 RA患者和健康对照者PTPN22在788位点均为G等位基因,未检测到A等位基因,没有发现单核苷酸多态性的存在;10281188位点G等位基因在病例组和对照组中的频率分别为12.4%和13.3%（P〉0.05）。结论广东地区人群PTPN22788位点不存在多态性,G788A和A10281188G基因位点与广东汉族人群RA的发病无相关性。     

Regulatory region polymorphisms of vitamin D receptor gene in pulmonary tuberculosis patients and normal healthy subjects of south India

Vitamin D receptor (VDR) gene variants are associated with differential susceptibility or resistance to tuberculosis in different ethnic groups. We investigated the polymorphisms in the 5' regulatory region of VDR gene in 206 normal healthy subjects and 166 patients with pulmonary tuberculosis from south India. Cdx-2 polymorphism was studied by polymerase chain reaction (PCR) with allele-specific primers, while genotyping of A1012G was done by PCR-based restriction fragment length polymorphism. A significantly decreased frequency of Cdx-2 G allele (P = 0.016) and G/G genotype (P = 0.010) and an increased frequency of A-A haplotype (A allele of Cdx-2 and A allele of A1012G) (P = 0.015) were observed in patients compared to controls. The study suggests that Cdx-2 G/G genotype may be associated with protection and A-A haplotype with susceptibility to tuberculosis.