Identification of novel single nucleotide polymorphisms within the NOTCH4 gene and determination of association with MHC alleles

Mapping of disease susceptibility loci within the MHC has been partly hampered by the high degree of polymorphism of the HLA genes and the high level of linkage disequilibrium (LD) between markers within the MHC region. It is therefore important to identify new markers and determine the level of LD between HLA alleles and non‐HLA genes. The NOTCH4 gene lies at the centromeric end of the MHC class III region, approximately 335 kb telomeric of the DRB1 locus. The encoded protein is an oncogene that is important in regulating vascular development and remodelling. A recent report has linked polymorphisms within NOTCH4 with risk of developing schizophrenia. We have investigated if coding polymorphisms exist within this gene and have identified three single nucleotide polymorphisms; a synonomous T to C transition at +1297 (HGBASE accession number SNP000064386 ), a synonomous A to G transition at +3061 ( SNP000064387 ) and an A to G transition at +3063 which results in a replacement of glycine with aspartic acid at amino acid 279 ( SNP000064388 ). The allele frequencies of +1297T, +3061A and +3063G were 0.65, 0.66 and 0.66, respectively. Linkage disequilibrium was detected both between these markers and with MHC alleles. These findings can be used in the fine mapping of disease susceptibility alleles within the MHC.     

Identification of 11 novel and common single nucleotide polymorphisms in the interleukin-7 receptor-alpha gene and their associations with multiple sclerosis

We have investigated the interleukin-7 receptor (IL-7R) alpha-chain gene as a positional and functional candidate gene for susceptibility to multiple sclerosis (MS), in view of its chromosomal location on 5p14-p12, a region that has shown suggestive linkage in MS genome screens, and its role in T- and B-cell proliferation and reactivity. Amplification and DNA sequencing of the IL-7Ralpha gene in pooled and individual samples identified 13 single nucleotide polymorphisms (SNPs), 11 of which are novel, including three in the promoter region, three in exons encoding amino-acid changes (ACC(Thr)66ATC(Ile), ATC(Ile)244ACC(Thr), ATC(Ile)336GTC(Val)), four in introns and one in the 3' untranslated region. Four IL-7R haplotypes were identified for nine SNPs, showing linkage disequilibrium across the gene, and allowing haplotype frequency determination from just three of the nine SNPs. Genotyping of the -504 polymorphism in 101 MS and 90 controls showed a suggestive (P=0.1) association of the T allele with MS; however, this was not supported by transmission disequilibrium testing in 186 MS trio families (P=0.8). There were trends towards an increase of the GTG+ haplotype (odds ratio=1.45), and under-representation of the TTA+ haplotype (OR=0.65) in DRB1*1501-positive MS cases, suggesting that larger sample sizes and comparison in more defined MS patient groups may support an association with the IL-7R gene. These polymorphisms would also be useful for studying genetic associations with other immunologic diseases.     

Sequenom质谱法分析细胞毒性T淋巴细胞相关分子4基因多态性与宫颈癌易感性的关系

目的 探索细胞毒性T淋巴细胞相关分子4(cytotoxic T-lymphocyte-associated protein 4,CTLA4)基因单核苷酸多态性(single nucleotide polymorphism,SNPs)与宫颈癌易感性的关系.方法 应用sequenom MassARRAY时间飞行质谱系统对100例宫颈癌及100名健康对照者 CTLA4基因20个多态位点(CTLA4_1～CTLA4_20)进行基因型分型,统计分析基因型频率和肿瘤易感性的关系.结果 与正常人群中最常见的 CTLA4基因单倍型-1576A、-318C和1402G相比,带有单倍型-1576G、-318T或1402A的个体均显著增加宫颈癌的风险(P<0.05),相对风险度的比值比及其95%可信区间分别为2.87(1.75～4.76),4.02(1.72～9.09)和4.51(1.46～13.88),而其余基因型与宫颈癌发病风险没有显著的相关性;其中rs5742909易感位点与先前的报道相一致.而双荧光素酶报告基因实验进一步证明,位于基因启动子区域的rs11571316多态位点能显著影响报告基因的表达活性.结论 CTLA4基因启动子区域的SNP可能通过影响 CTLA4基因的表达水平来影响个体对宫颈癌的易感性.

Abstract：

Objective To evaluate the association between single nucleotide polymorphisms (SNPs) of cytotoxic T-lymphocyte-associated protein 4 (CTLA4) gene and susceptibility to cervical cancer. Methods One hundred patients and 100 healthy controls from Hubei province were genotyped for 20 polymorphic loci using Sequenom. Results The frequency of rs11571316 G allele and rs5742909 T allele, which are localized in the promoter region, and rs11571319 A allele, which is downstream of the gene, were significantly higher in patients than in controls. Luciferase assay showed that, as the previously reported rs5742909 T allele, rs11571316 G allele could significantly increase the expression of the reporter gene. Conclusion SNPs in the promoter region of CTLA4 gene might increase the susceptibility to cervical cancer by increasing CTLA4 gene expression.     

IL基因单核苷酸多态性与放射性肺损伤的关系研究

目的研究IL基因上rs16944(IL1-511C/T),rs1800587(IL1-899C/T),rs1800796(IL6-634C/G)位点单核苷酸多态性与放射性肺损伤之间的关系。方法 2010年3月至2012年6月期间接受胸部三维适形放疗的肺癌患者170例,抽取患者静脉血,提取基因组DNA,应用实时荧光定量PCR方法进行基因单核苷酸多态性的基因分型(IL1、IL6)。所有患者放疗后放射性肺损伤评价按NCI CTC 3.0急性放射性肺炎标准评价,SPSS13.0软件包进行数据分析。结果实验分为放射性肺损伤组和未发生放射性肺损伤组,IL1-511C/T、IL1-899C/T和IL6-634C/G的基因型分布频率在两组之间差异无统计学意义(P>0.05),IL1基因上等位基因T和C发生放射性肺损伤的风险相比差异无统计学意义(P>0.05),IL6基因上等位基因C和G发生放射性肺损伤的风险相比差异无统计学意义(P>0.05)。结论本研究未发现北方汉族人群中IL基因单核苷酸多态性与放射性肺损伤的发生相关。     

Two bi-allelic single nucleotide polymorphisms within the promoter region of the horse tumour necrosis factor alpha gene.

Primers based on GenBank sequences within the 5' untranslated region (UTR) of the human and horse tumour necrosis factor alpha (TNF-alpha) genes were designed and used to amplify a 522-bp product. Sequencing of five clones derived from five independent PCRs obtained from three different animals of three different breeds (Old Kladruber, Akhal-Teke and Shetland Pony) revealed a high level of sequence identity to the TNF-alpha promoter regions of other species. The existing GenBank horse sequences were confirmed and extended upstream by 230 nucleotides. Based on the sequence obtained, a new horse-specific forward primer was designed to amplify a 213-bp PCR product, which was screened for polymorphism using single-strand conformation polymorphism (SSCP). Three allelic variants of the horse TNF-alpha gene were identified and sequenced (GenBank accession numbers ADF 349558-60). Two single nucleotide polymorphisms explained the existence of the three SSCP alleles detected: C/T and T/C single base pair substitutions at positions 137 and 147, respectively. Differences in allelic frequencies between Old Kladruber and Akhal-Teke breeds were observed.     

Test of association between 10 single nucleotide polymorphisms in the oxytocin receptor gene and conduct disorder

Animal and human studies have implicated oxytocin in affiliative and prosocial behaviors. We tested whether genetic variation in the oxytocin receptor (OXTR) gene is associated with conduct disorder (CD). Utilizing a family-based sample of adolescent probands recruited from an adolescent substance abuse treatment program, control probands and their families (total sample, n=1750), we conducted three tests of association with CD and 10 single nucleotide polymorphisms (SNPs) in the OXTR gene: (a) family-based comparison utilizing the entire sample; (b) within-Whites, case-control comparison of adolescent patients with CD and controls without CD; and (c) within-Whites case-control comparison of parents of patients and parents of controls. Family-based association tests failed to show significant results (no results P<0.05). While strictly correcting for the number of tests (α=0.002), adolescent patients with CD did not differ significantly from adolescent controls in genotype frequency for the OXTR SNPs tested; similarly, comparison of OXTR genotype frequencies for parents failed to differentiate patient and control family type, except a trend association for rs237889 (P=0.004). We concluded that in this sample, 10 SNPs in the OXTR gene were not significantly associated with CD.     

Association of six polymorphisms of the NOTCH4 gene with schizophrenia in the Japanese population.

The NOTCH4 gene is located at 6p21.3 and involved in the development and patterning of the central nervous systems. Recently, Wei and Hemmings [2000] observed that the gene was associated with schizophrenia. Subsequent to the report, several studies investigated the gene in schizophrenia, with controversial and inconclusive results. In the present study, we investigated six polymorphisms (SNPs 1-5 and a CTG repeat) of the gene in Japanese subjects with schizophrenia (n = 284) and the same number of controls. The polymorphisms include SNP5, which has been observed to be associated with schizophrenia in a Chinese population and two new SNPs 3-4 adjacent to SNP5, in addition to the SNPs 1-2 and the CTG repeat, which were suggested for the association with the disease in the previous study. As a result, no significant difference in genotypic distributions or allelic frequencies of the six polymorphisms of the gene was observed between the patients and the controls. Also, no significant difference was found in frequencies of haplotypes of the six polymorphisms between the patients and the controls. However, the distribution of SNP2 was significantly deviated from Hardy-Weinberg equilibrium in the patients (P = 0.000986), not in the controls, which could be a chance or due to an association of SNP2 with the disease. In conclusion, the present study provided no clear evidence for an association between the NOTCH4 gene and schizophrenia in the Japanese population.     

PATZ1基因单核苷酸多态性与无精症的关系

目的 研究PATZ1基因的4个单核苷酸多态性(single nucleotide polymorphism,SNP)rs2240424、rs2057951、rs2240427和rs714909的多态性与无精症的关系.方法 用PCR-限制性片段长度多态性分析方法,在180例无精症患者和190名正常男性中对上述4个SNP位点的基因频率和基因型频率分布进行调查.结果 rs2057951位点的等位基因C(35.0%vs.27.6%,P=0.031)和带有等位基因C个体(CT+CC)(57.8%vs.46.3%,P=0.027)的频率在无精症患者显著高于正常男性.4种SNP的单倍型在两组人群中的分布差异有统计学意义(P=0.01),单倍型ACAC(11.1%vs.6.6%,P=0.029)和ACGC(11.2%vs.5.2%,P=0.003)在无精症患者中显著高于正常男性.结论 PTAZ1的rs2057951位点的等位基因C和单倍型ACAC和ACGC增加无精症的易感性,提示PTAZ1基因可能与无精症发病相关.     

贵州地区汉族人群GDF5基因单核苷酸多态性与成人终身高的关系

目的 探讨生长分化因子5(GDF5)基因rs143383、rs143384、rs6060369和rs224331位点单核苷酸多态性(SNPs)与贵州地区汉族人群成人终身高的相关性.方法 对贵州地区1 069例汉族健康体检者进行体格检查及问卷调查,收集抗凝血标本并提取DNA.用基质辅助激光解吸电离飞行时间质谱(MALDI-TOF MS)方法检测GDF5基因的SNPs,并分析其与身高的相关性.结果 成年女性中,GDF5基因rs143383、rs143384、rs6060369和rs224331基因型分布可分别解释身高变异的1.4％、0.9％、1.1％和1.0％(P＜0.05);在GDF5基因rs143383和rs143384位点,携带GG基因型的个体平均身高均为最高,分别比AG和AA基因型个体高1.7 cm (P＜0.01)、2.3 cm (P＜0.05)和1.6 cm (P＜0.05)、2.1 cm(P＜0.01);在GDF5基因rs6060369位点,携带CC基因型的个体平均身高分别比CT和TT基因型个体高1.7 cm (P＜0.05)和2.2 cm (P＜0.01).但是在成年男性中未发现GDF5基因上述SNPs位点与身高的相关性.结论 GDF5基因单核苷酸多态性与贵州地区成年汉族女性身高有关,GDF5基因可能是影响中国汉族成人女性身高个体差异的基因.     

Identification and mapping of single nucleotide polymorphisms in the varicella-zoster virus genome

We have analysed the expression and cellular localisation of the matrix protein VP40 from Ebola virus. Full-length VP40 and an N-terminal truncated construct missing the first 31 residues [VP40(31-326)] both locate to the plasma membrane of 293T cells when expressed transiently, while a C-terminal truncation of residues 213 to 326 [VP40(31-212)] shows only expression in the cytoplasm, when analysed by indirect immunofluorescence and plasma membrane preparations. In addition, we find that full-length VP40 [VP40(1-326)] and VP40(31-326) are both released into the cell culture supernatant and float up in sucrose gradients. The efficiency of their release, however, is dependent on the presence of the N-terminal 31 residues. VP40 that is released into the supernatant is resistant to trypsin digestion, a finding that is consistent with the formation of viruslike particles detected by electron microscopy. Together, these results provide strong evidence that Ebola virus VP40 is sufficient for virus assembly and budding from the plasma membrane.     

Large-scale validation of single nucleotide polymorphisms in gene regions

Genome-wide association studies using large numbers of bi-allelic single nucleotide polymorphisms (SNPs) have been proposed as a potentially powerful method for identifying genes involved in common diseases. To assemble a SNP collection appropriate for large-scale association, we designed assays for 226,099 publicly available SNPs located primarily within known and predicted gene regions. Allele frequencies were estimated in a sample of 92 CEPH Caucasians using chip-based MALDI-TOF mass spectrometry with pooled DNA. Of the 204,200 designed assays that were functional, 125,799 SNPs were determined to be polymorphic (minor allele frequency > 0.02), of which 101,729 map uniquely to the human genome. Many of the commonly available RefSNP annotations were predictive of polymorphic status and could be used to improve the selection of SNPs from the public domain for genetic research. The set of uniquely mapping, polymorphic SNPs is located within 10 kb of 66% of known and predicted genes annotated in LocusLink, which could prove useful for large-scale disease association studies.     

Clinical relevance of tag single nucleotide polymorphisms within the CAT gene in patients with PTSD in the Chongqing Han population

Background: Free radical-induced oxidative damage of the brain has been implicated in a number of psychiatric disorders, including post-traumatic stress disorder (PTSD). Catalase (CAT) is a major antioxidant enzyme and a number of polymorphisms in CAT have been shown to be associated with several diseases, including hypertension, diabetes mellitus, Alzheimer’s disease, and vitiligo. The aim of this study was to evaluate the association of CAT gene polymorphisms with PTSD in a case-control study. Materials and methods: A total of 460 unrelated adult Chinese Han adults, including 287 healthy volunteers and 173 patients with PTSD. Six tag single-nucleotide polymorphisms (tSNPs) were selected from the entire CAT gene through construction of haplotype bins, and they were genotyped using an improved multiplex ligation detection reaction (iMLDR) technique. Allelic frequencies and clinical characteristics were compared in two independent Chinese Han populations. Results: Six tag SNPs were identified in the Chinese Han population and all were common SNPs. However, we could detect no evidence of genetic association between six tag SNPs in the CAT gene and PTSD in the Chinese Han population. Conclusions: This result suggests that six tag SNPs of the CAT gene may not be associated with PTSD, and that CAT gene might not influence the development of PTSD in patients following exposure to a traumatic event, also may be the sample sizes too small to allow a meaningful test.     

CDS1 and promoter single nucleotide polymorphisms of the CTLA-4 gene in human myasthenia gravis

The cytotoxic T lymphocyte associated protein 4 (CTLA-4) gene (Ctla-4) is a candidate gene for autoimmune disease. We here report results of two single nucleotide polymorphisms (SNPs) in the Ctla-4, a +49 A/G SNP in CDS1 and a C/T promoter SNP at position -318. There were no differences in these two SNPs between patients and healthy individuals. The frequency of allele G and genotype G/G at position +49 in CDS1 was increased in patients with thymoma when compared with patients with normal and hyperplastic thymic histopathology. Patients with the G/G genotype had signs of immune activation manifested as higher levels of serum IL-1beta and higher percentage of CD28(+) T lymphocytes. There was a strong linkage between the 86bp allele in the 3'-UTR and the A(+49) allele in CDS1. Our results suggest that the SNP at position +49 in CDS1 might be associated with the manifestations of MG.     

The association of single nucleotide polymorphism within vascular endothelial growth factor gene with systemic lupus erythematosus and lupus nephritis

There were no statistically significant difference in allele and genotype frequency of the polymorphisms within the vascular endothelial growth factor (VEGF) gene (?460 and +405) between 193 systemic lupus erythematosus patients and 234 healthy controls. However, the +405 GG was significantly associated with lupus nephritis (LN) patients with low VEGF mRNA expression and LN with end‐stage renal disease.