Typing of multiple single nucleotide polymorphisms in cytokine and receptor genes using SNaPshot

Associations have been described between polymorphisms in cytokine genes and severity of autoimmune diseases, outcome of infectious disease, and outcome following transplantation. Many methods now exist for typing single nucleotide polymorphisms (SNPs) and these can be applied to typing cytokine gene and cytokine receptor gene variation. A system for typing multiple cytokine and receptor gene polymorphisms using a primer extension method, SNaPshot (Applied Biosystems, Foster City, CA, USA), has been assessed. The development of this methodology may enable other laboratories to type for cytokine SNPs in different populations and facilitate research into the effect of genetic polymorphism in the cytokine network in transplantation and disease.     

Proinflammatory cytokine gene single nucleotide polymorphisms in common variable immunodeficiency

Common variable immunodeficiency (CVID) is a heterogeneous group of primary immunodeficiency diseases. Cytokine production could be affected in CVID patients, whereas its alteration could be due to genetic polymorphisms within coding and promoter regions of the cytokine genes. This study was performed to analyse the proinflammatory cytokine single nucleotide polymorphisms in CVID. The allele and genotype frequencies of a number polymorphic genes coding tumour necrosis factor (TNF)‐α, interleukin (IL)‐1α, IL‐1β, IL‐1R, IL‐1RA and IL‐6 were investigated and compared between two groups of CVID patients and controls. The IL‐6 GA genotype at position nt565 was significantly over‐represented in the patient group (P < 0·001), while the IL‐6 GG genotype at position ?174 (P = 0·006) and the GG genotype at position nt565 (P < 0·001) were significantly lower than controls. The TNF‐α AG genotype at position ?308 in the patient group was increased significantly in comparison with controls (P = 0·027), but the GG genotype at the same position was significantly decreased (P = 0·011). IL‐6 CA and GA haplotypes were the most frequent haplotypes in the patients (P < 0·005), whereas TNF‐α GA (P = 0·002) and IL‐6 GG (P < 0·001) haplotypes were decreased significantly in the patients in comparison with controls. Cytokine single nucleotide polymorphisms could have a role in pathophysiology of CVID. High production of TNF‐α is expected in some CVID patients based on the frequency of genotypes/haplotypes of these cytokine gene polymorphisms.     

Single nucleotide polymorphisms of cytokine genes in the healthy Slovak population

Cytokines are molecules that control and modulate the activities of numerous target cells via binding to specific receptors. The observed differences in the cytokine production among individuals can be, at least partially, explained by gene polymorphisms. Several cytokine gene polymorphisms have been identified to play a role in susceptibility to various diseases, including autoimmune, infectious, allergic or cardiovascular diseases. The aim of the current study was to determine allele and genotype frequencies of 22 polymorphisms in 13 cytokine genes in the healthy Slovak population and to compare them with data available from six populations from Central and Southern Europe. A polymerase chain reaction with sequence-specific primers was used to genotype polymorphisms within genes encoding IL-1alpha, IL-1beta, IL-1R, IL-1RA, IL-4Ralpha, IL-12, IFN-gamma, TGF-beta, TNF-alpha, IL-2, IL-4, IL-6 and IL-10 in a sample of 140 unrelated Slovak subjects. The allelic distribution of all polymorphisms in the Slovak population was very close to that in the geographically and historically closest populations in Central Europe--the Czech and the Polish. However, several differences were found between the Slovak and four populations from Southern Europe. The obtained data represent a basis for further studies on association of cytokine gene polymorphisms with some diseases.     

Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes

Analysis of human genetic variation can shed light on the problem of the genetic basis of complex disorders. Nonsynonymous single nucleotide polymorphisms (SNPs), which affect the amino acid sequence of proteins, are believed to be the most frequent type of variation associated with the respective disease phenotype. Complete enumeration of nonsynonymous SNPs in the candidate genes will enable further association studies on panels of affected and unaffected individuals. Experimental detection of SNPs requires implementation of expensive technologies and is still far from being routine. Alternatively, SNPs can be identified by computational analysis of a publicly available expressed sequence tag (EST) database following experimental verification. We performed in silico analysis of amino acid variation for 471 of proteins with a documented history of experimental variation studies and with confirmed association with human diseases. This allowed us to evaluate the level of completeness of the current knowledge of nonsynonymous SNPs in well studied, medically relevant genes and to estimate the proportion of new variants which can be added with the help of computer-aided mining in EST databases. Our results suggest that approx. 50% of frequent nonsynonymous variants are already stored in public databases. Computational methods based on the scan of an EST database can add significantly to the current knowledge, but they are greatly limited by the size of EST databases and the nonuniform coverage of genes by ESTs. Nevertheless, a considerable number of new candidate nonsynonymous SNPs in genes of medical interest were found by EST screening procedure.     

Replication of associations between cytokine and cytokine receptor single nucleotide polymorphisms and measles-specific adaptive immunophenotypic extremes

Our objective was to replicate previously reported associations between cytokine and cytokine receptor SNPs and humoral and CMI (cell-mediated immune) responses to measles vaccine. All subjects (n=758) received two doses of MMR (measles/mumps/rubella) vaccine. From these subjects, candidate cytokine and cytokine receptor SNPs were genotyped and analyzed in 29-30 subjects falling into one of four "extreme" humoral (Ab(high/low)) and CMI (CMI(high/low)) response quadrants. Associations between seven SNPs (out of 11 in the discovery study) and measles-specific neutralizing antibody levels and IFN-γ ELISPOT responses were evaluated using chi-square tests. We found one replicated association for SNP rs372889 in the IL12RB1 gene (P=0.03 for Ab(high)CMI(high) vs. Ab(low)CMI(low)). Our findings demonstrate the importance of replicating genotypic-phenotypic associations, which can be achieved using immunophenotypic extremes and smaller sample sizes. We speculate that IL12RB1 polymorphisms may affect IL-12 and IL-23 binding and downstream effects, which are critical cytokines in the CMI response to measles vaccine.     

Pro-inflammatory maternal cytokine profile in preterm delivery

PROBLEM: The objective of this study was to determine the levels of cytokines produced by maternal peripheral blood mononuclear cells (PBMC) upon stimulation with a mitogen, with autologous placental cells and with a trophoblast antigen extract. METHOD OF STUDY: Peripheral blood mononuclear cells from 54 women with a history of successful pregnancy and 30 women undergoing preterm delivery (PTD) were stimulated with the mitogen and antigens, and the cytokine levels in mitogen-stimulated culture supernatants assessed. RESULTS: Significantly higher levels of the type 1 cytokines, interferon (IFN)-gamma and interleukin (IL)-2, were produced by the PTD group than by the normal pregnancy group, which on the contrary showed significantly greater production of the type 2 cytokines, IL-4, IL-5 and IL-10. A comparison of the ratios of type 2 to type 1 cytokines is indicative of a type 1 cytokine bias in PTD. CONCLUSIONS: These data are suggestive of a maternal type 1 cytokine bias in PTD.     

单核苷酸多态性的应用

单核苷酸多态性(single nucleotide polymorphisms,SNPs)是基因组中最常见的一种遗传变异.随着人类基因组计划的完成,人们越来越注重它的医学意义及应用,特别是在利用SNPs进行连锁分析和关联分析,定位和寻找疾病致病基因方面有了很大进展.本文即对此作一综述.     

Automation in genotyping of single nucleotide polymorphisms

Automation for genotyping of single nucleotide polymorphisms (SNPs) can be split into the automation of the sample preparation and the automation of the analysis technology. SNP genotyping methods are reviewed and solutions for their automation discussed. A panacea for SNP genotyping does not exist. Different scientific questions require adapted solutions. The choice of a technology for SNP genotyping depends on whether few different SNPs are to be genotyped in many individuals, or many different SNPs are to be genotyped in few individuals. The requirements of throughput and the ease of establishing an SNP genotyping operation are important, as well as the degree of integration. The potential and state-of-the-art of different solutions are outlined.     

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     

Association of single nucleotide polymorphisms in MPO and COX genes with oral lichen planus

Oral lichen planus (OLP) is an intractable, chronic inflammatory disorder, and its pathogenesis is still largely unknown. Some literatures supported that genes involved in both oxidative stress and prostaglandin metabolism play an important role in the process of inflammation. To explore their association with OLP, we investigated four single nucleotide polymorphisms (SNPs) from myeloperoxidase (MPO) and cyclooxygenase (COX) genes in 475 Chinese individuals (242 case and 233 controls) by MassArray . Although the genotype distributions had no significant differences between the patients and controls, we found that in different gender, rs2243828 from MPO displayed the statistically significant variance genotype frequencies between patients and controls (P = 0.018 in females, P = 0.035 in males). Moreover, for the major allele recessive model, this SNP also showed a significant difference between case and control groups in males (P = 0.015). In this study, we first observed significant association with MPO polymorphism and OLP risk in different gender groups in Chinese, suggesting MPO polymorphism is a gender‐specific risk factor of OLP probably by influencing sex hormone‐sensitive elements to regulate inflammatory gene expression networks, and we further revealed that oxidative stress was actually involved in the pathogenesis of this disease. Moreover, these findings inspire us some constructive solutions to the treatment of this disease.     

Cytokine single nucleotide polymorphisms in Iran.

Overall expression and secretion of cytokines are dependent on genetic nucleotide variations within or adjacent to regulatory regions of cytokine genes. This study allows the comparison of the prevalence of particular genetic markers. In 40 Iranian healthy subjects, cytokine single nucleotide polymorphisms (SNPs) were used to determine allelic and genotypic frequencies for the following cytokine genes: interleukin-1alpha (IL-1alpha) (T/C -889), IL-1beta (C/T -511, T/C +3962), IL-12 ( C/A-1188), interferon-gamma (IFN-gamma) (A/T UTR 5644), transforming growth factor-beta (TGF-beta) (C/T codon 10, G/C codon 25), tumor necrosis factor alpha (TNF-alpha) (G/A -308, G/A -238), IL-2 (T/G -330, G/T +166), IL-4 (T/G -1089, T/C -590, T/C -33), IL-6 (G/C -174, G/A nt565), IL-10 (G/A -1082, C/T -819, C/A -592), IL-1R (C/T pst11970), IL-1RA (T/C mspa 111100), IL-4RA (G/A +1902). All typing was performed using the PCR-SSP assay. Iranian and Italian, English, German, and Greek populations had similar cytokine profiles, but in some cases, the Iranian allele and genotype frequencies were significantly different from those of other Asian and African American populations for the majority of polymorphisms.     

Mapping HLA for single nucleotide polymorphisms

Knowledge of DNA sequence variation may help us understand how genetic variability gives rise to functional variability and, in so doing, revolutionize the development of strategies to combat and prevent disease. Single nucleotide polymorphisms (SNPs) are stable, inherited, biallelic, single base pair differences which are present in the human genome at a density of 1 to 10 per 1,000 nucleotides. It is anticipated that SNPs will account for much of the functional heterogeneity in gene expression and protein activity exhibited in the human population. Susceptibility to or protection from a number of diseases, particularly those of autoimmune etiology, has been associated with specific alleles of the human leukocyte antigen (HLA) complex. Interestingly, the precise molecular defects in the HLA genes are unknown and the notion that non-HLA genes, within the same chromosomal region, are involved remains a formal possibility. We have determined the nucleotide sequence of a contiguous 2.2 Mbp segment of chromosome six that includes all of the HLA class I region, and have identified over 10,000 SNPs therein. Because of the derivative knowledge of gene and SNP content and position, the scientific community is now uniquely poised to identify disease-contributory SNPs that lie within the MHC.     

Computational prediction of the effects of non-synonymous single nucleotide polymorphisms in human DNA repair genes

Non-synonymous single nucleotide polymorphisms (nsSNPs) represent common genetic variation that alters encoded amino acids in proteins. All nsSNPs may potentially affect the structure or function of expressed proteins and could therefore have an impact on complex diseases. In an effort to evaluate the phenotypic effect of all known nsSNPs in human DNA repair genes, we have characterized each polymorphism in terms of different functional properties. The properties are computed based on amino acid characteristics (e.g. residue volume change); position-specific phylogenetic information from multiple sequence alignments and from prediction programs such as SIFT (Sorting Intolerant From Tolerant) and PolyPhen (Polymorphism Phenotyping). We provide a comprehensive, updated list of all validated nsSNPs from dbSNP (public database of human single nucleotide polymorphisms at National Center for Biotechnology Information, USA) located in human DNA repair genes. The list includes repair enzymes, genes associated with response to DNA damage as well as genes implicated with genetic instability or sensitivity to DNA damaging agents. Out of a total of 152 genes involved in DNA repair, 95 had validated nsSNPs in them. The fraction of nsSNPs that had high probability of being functionally significant was predicted to be 29.6% and 30.9%, by SIFT and PolyPhen respectively. The resulting list of annotated nsSNPs is available online (http://dna.uio.no/repairSNP), and is an ongoing project that will continue assessing the function of coding SNPs in human DNA repair genes.     

PDCD1 single nucleotide genes polymorphisms confer susceptibility to juvenile-onset systemic lupus erythematosus

Abstract

Juvenile-onset systemic lupus erythematosus (JSLE) is a multisystem autoimmune disease in which both the genetic and environmental factors seem to be involved in the etiopathogenesis of the disease. The aim of this study was to evaluate the association of programmed cell death 1 (PDCD1, also called PD-1) gene polymorphisms with JSLE susceptibility in Iranian population. In this case-control association study, three PDCD1 SNPs, including PD-1.1 G/A, PD-1.3 G/A and PD-1.9 C/T were genotyped in 50 Iranian patients with JSLE and 202 healthy unrelated controls, using PCR-RFLP method. The PD-1.1 A allele was found to be more frequent in the case group compared with controls (6% vs. 1.5%, p?=?0.024). Moreover, the GG genotype was less frequent in cases than in controls (88% vs. 97%, p?=?0.021). The other PDCD1 SNPs did not show association. At the haplotypic level, no significant differences was recognized between the two groups of case and control neither for the GAC (PD-1.1 G, PD-1.3 A, PD-1.9 C) nor for the GGC haplotype (PD-1.1 G, PD-1.3 G, PD-1.9 C). Our findings support the influence of the PD1.1 A SNP on the development of JSLE in Iranian population.     

Novel single nucleotide polymorphisms in the 3'-UTR of the TGFbetaRI and TGFbetaRIII genes.

Transforming growth factor beta (TGFbeta) family members are multifunctional cytokines that play a key role in cellular growth, proliferation and differentiation. Transmembrane signalling by TGFbeta occurs via a complex of the serine/threonine kinases TGFbeta type 1 (TGFbetaRI), type 2 (TGFbetaRII), and type 3 (TGFbetaRIII) receptors. Previous studies have implicated TGFbeta receptors (TGFbetaR) in a variety of important hereditary clinical disorders. Mutations of the TGFbetaR genes have been observed in several human cancers. The aim of this study was to identify and confirm novel single nucleotide polymorphisms (SNPs) in TGFbetaRI and RIII and to determine the relative allele and genotype frequencies of these SNPs. SNPs were identified from the examination of sequence alignments held in databases and were confirmed by DNA sequencing. A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was devised for genotyping TGFbeta receptor polymorphisms. DNA samples from 91 controls were examined. The observed heterozygosities of TGFbetaRI and TGFbetaRIII gene polymorphisms in the control population were 43 and 33%, respectively, suggesting these SNPs could be useful markers in disease association studies.     

Race, genes and preterm delivery

High rates of preterm delivery (PTD) among African Americans are the leading cause of excess infant mortality among African Americans. Failure to fully explain racial disparity in PTD has led to speculation that genetic factors might contribute to this disparity. Current evidence suggests that genetic factors contribute to PTD, but this does not imply that genetic factors contribute to racial disparity in PTD. Environmental factors clearly contribute to PTD. Many of these factors acting over a women's life prior to pregnancy disproportionately affect African Americans and contribute significantly to racial disparity in PTD. Thus, inferring genetic contribution to racial disparity in PTD by attempting to control for environmental factors measured at a single point in time is flawed. There is emerging evidence of gene-environment interactions for PTD, some of which disproportionately affect African Americans. There is also evidence of racial differences in the prevalence of polymorphisms potentially related to PTD. However, to date there is no direct evidence that these differences contribute significantly to racial disparity in PTD. Given the complexity of polygenic conditions such as PTD, the possibility of any single gene contributing substantially to racial disparity in PTD seems remote.     

Microsatellite single nucleotide polymorphisms in the HLA-DQ region

Abstract: Sequencing studies were performed in three previously described microsatellite and minisatellite markers located within the HLA-DQ region, DQCAR, DQCARII and G51152. Multiple nucleotide substitutions that did not change size polymorphisms were observed in all three markers. In all loci, the number of core repeats did not correlate with neighboring DQ allele sequence motifs while single nucleotide changes within or flanking the microsatellite sequence did. This result indicates higher mutation rates for microsatellite expansions/contractions than for nucleotide substitutions in these loci. Further analysis indicated an almost complete phylogenetic correspondence between DQCAR single nucleotide polymorphisms (SNPs) and DQB1 sequences on one side (1.0–1.5 kb apart) and a complete relationship between DQCARII and DQA1 sequences on the other (4.5 kb apart). In contrast, G51152 sequences did not correspond perfectly with DQB1 allelic sequences, thus suggesting the existence of several ancestral crossovers between this marker and DQB1 (20–25 kb). Sequencing microsatellites might be useful in disease mapping studies by increasing marker informativeness and by helping in the interpretation of association study results. It is also proposed that SNPs within the flanking region of CA repeats could be used to develop biallelic markers from already available mapped microsatellite markers.     

三种基因SNP与BAVM易感及出血风险的相关性研究

目的探讨白细胞介素-17（IL-17A）、转化生长因子-β（TGF-β）及其受体（TGFRl32）的单核苷酸多态性（SNP）与脑动静脉畸形（BAVM）易感及出血风险的相关性。方法前瞻性收集BAVM患者外周血（n=53）,健康对照人群来自体检中心（n=120）。采用聚合酶链反应．限制性片段长度多态性（PCR—RFLP）法,检测IL-17A-197G／A,TGF-β1—509C／T及TGFR-β2—875A／G基因的SNP特征,并做关联分析探讨以上基因SNP与BAVM易感及出血风险的相关性。结果BAVM组与对照组比较,IL-17A-197G／A和TGF-β1．509C／T基因型及基因频率分布上的差异无统计学意义（P〉O．05）,TGFR-β2—875A／G基因型及基因频率分布差异有统计学意义（P〈0．05）;BAVM出血组IL-17A-197G／A的G／G基因型和TGFR-β2—875A／G的G基因频率明显高于未出血组（P〈O．05）。结论TGFR-β2．875A／G的G／G基因型可能是中国南方人群易感BAVM的危险因素．IL-17A-197G／A的G／G基因型可能与BAVM易破裂出血风险有关。     

IL-10、MD-1基因单核苷酸多态性与哮喘易感性的相关性研究

目的:分析IL-10基因 rs1800896、rs3024492位点和髓样分化蛋白1(Myeloid differentiation 1,MD-1)基因rs7740529、rs2233128位点单核苷酸多态性(Single nucleotide polymorphism,SNP)与哮喘遗传易感性的相关性以及过敏性鼻炎(Allergic rhinitis,AR)对哮喘遗传易感性的影响.方法:应用Sequenom MassARRAY○ R SNP分型技术对141例哮喘患者和145例正常对照的四个SNP位点(rs1800896、rs3024492、rs7740529、rs2233128)进行基因分型,再将哮喘患者中确定有过敏性鼻炎和无过敏性鼻炎者分别与正常对照组比较.χ2检验统计分析病例组和对照组的基因型频率;采用非条件Logistic回归校正年龄、性别影响,计算比数比(OR)和95%可信区间(CI),以此评价各位点多态性与哮喘遗传易感性的相关性以及过敏性鼻炎对哮喘易感性的影响.结果:(1)IL-10 rs1800896多态性位点GG、GA、AA三种基因型分布频率在哮喘组、哮喘和过敏性鼻炎共患组、哮喘而无鼻炎组的分布频率和对照组相比,差异均有统计学意义(P＜0.001),有无过敏性鼻炎对其影响不明显.相较GG或AA基因型,携带基因型GA的个体,哮喘的患病风险明显降低(OR=0.033,95%CI:0.017～0.065).(2)MD-1 rs7740529位点CC、CT、TT三种基因型分布频率在哮喘患者组、哮喘和过敏性鼻炎共患组、哮喘而无鼻炎组的分布频率和对照组相比,差异也均有统计学意义(P≤0.005),有无过敏性鼻炎对其影响不明显.相比较CC或TT基因型,携带基因型CT的个体,哮喘的患病风险明显降低(OR=0.369,95%CI:0.225～0.606).(3)IL-10 rs3024492位点TA、AA基因型和MD-1 rs2233128位点AG、GG基因型在哮喘人群中的分布频率与对照组相比无统计学意义(P＞0.05).结论:IL-10 rs1800896与MD-1 rs7740529位点多态性与哮喘的遗传易感性相关,其杂合型的患病风险均明显降低,且有无过敏性鼻炎对其影响不明显.