Novel single nucleotide polymorphisms of the human colony-stimulating factor 2 (CSF2) gene identified by sequencing the entire gene

We describe three single nucleotide polymorphisms (SNPs) of the human colony-stimulating factor 2 (CSF2) gene and their allelic frequencies, as determined by direct sequencing of 48 alleles of the entire CSF2 gene. Three polymorphisms were identified, at nucleotide positions 1816 (T/C), 2284 (C/T), and 3079 (G/A). These polymorphisms will be useful in genetic studies not only of hematologic disorders but also of disorders of bone metabolism. Received: October 13, 2000 / Accepted: October 23, 2000     

Five novel single-nucleotide polymorphisms of human interferon gamma identified by sequencing the entire gene

Interferon gamma (IFNG) plays important roles in the regulation of bone remodelling. We describe here six single-nucleotide polymorphisms (SNPs) in the IFNG gene, five of which are novel, and their allelic frequencies in the Japanese population, as determined by sequencing 48 alleles of the entire gene. Four of these polymorphisms were identified inside the third intron, at nucleotide (nt) positions 2459 (A/G), 2671 (T/C), 3177 (T/G), and 3273 (G/A). In exon 4, SNPs were identified at nt positions 5199 (A/T) and 5272 (A/G). These polymorphic sites will be useful for genetic studies of disorders that affect the inflammatory process or calcium metabolism. Received: September 18, 2000 / Accepted: October 2, 2000     

Thirteen single-nucleotide polymorphisms in the human osteopontin gene identified by sequencing of the entire gene in Japanese individuals

Osteopontin (OPN) is one of the major noncollagenous bone matrix proteins produced by osteoblasts and osteoclasts. We systematically surveyed the entire structure of the OPN gene for single-nucleotide polymorphisms (SNPs) by directly sequencing 48 alleles derived from 24 unrelated Japanese individuals. We identified 13 SNPs in the OPN gene. Ten polymorphisms were identified in introns 1, 3, and 5; 2 in the coding region of exons 6 and 7; and 1 in the 3′ untranslated region of exon 7. Allele frequencies for some of the polymorphisms were significantly different from those reported in the United States National Center for Biotechnology Information (NCBI) dbSNP database. These polymorphisms will be useful in genetic studies to evaluate the role of OPN proteins in bone metabolism. Received: March 26, 2001 / Accepted: May 10, 2001     

Linkage disequilibrium and haplotype analysis among ten single-nucleotide polymorphisms of interleukin 11 identified by sequencing of the gene

Interleukin 11 (IL11) is a member of the interleukin 6 (IL6)-related cytokine subfamily, which stimulates T cell-dependent development of immunoglobulin-producing B cells. IL11 is also an important paracrine regulator of bone metabolism that induces formation of osteoclasts. In the work reported here, we sequenced the entire IL11 structural gene of 48 alleles in a Japanese test population. These experiments identified ten single-nucleotide polymorphisms (SNPs) and determined their allelic frequencies. One polymorphism was identified upstream of exon 1, one in exon 3, four in intron 4 and four in the 3′ untranslated region (3′UTR) of exon 5. Based on the genotype data, we constructed six haplotypes in the tested population. Two-way comparisons of SNPs revealed two combinations in complete linkage disequilibrium, one with SNPs at nucleotide positions 2753, 3644, 5154, and 5568, and another with SNPs at positions 3686, 5141, and 5734. These results will be useful in disease-association studies where a contribution of the human IL11 gene has been suspected, especially in disorders affecting immune response and bone metabolism. Received: March 23, 2001 / Accepted: May 2, 2001     

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.     

广西百色地区壮族妇女脂联素基因单核苷酸多态性与骨密度的关系

目的 探讨脂联素(APN)基因5个单核苷酸多态性(SNPs)与广西百色地区壮族妇女骨矿物质密度(BMD)的关系.方法 选取壮族女性239例跟骨骨量减少患者(LBM)和83例正常骨量组(NBM)进行病例对照研究,采用多重单碱基延伸SNP分型技术对壮族女性脂联素基因的5个位点(rs1063539、rs12495941、rs266729 、rs3774261 及rs710445)进行了基因分型,采用法国生产的Osteospace干式超声骨密度仪测量右侧跟骨超声振幅衰减(BUA).结果 仅rs1063539、rs12495941、rs266729及rs710445多态性分布符合Hardy-Weinberg遗传平衡定律(P>0.05).除rs3774261在骨量正常组的分布不符合Hardy-Weinberg平衡(P<0.05)之外,其余位点在正常组和骨量减少组基因型分布均符合Hardy-Weinberg平衡(P>0.05).其中,只有rs1063539 基因型在NOR和LBM组差异存在显著性(P=0.003),CG基因型者在LBM组人数明显多于GG型(P<0.01).调整年龄、体重、身高及体质指数后,以5个多态性位点作为自变量的多元 Logistic回归显示,仅rs1063539多态性与跟骨BUA相关性有统计学意义(adjusted OR=3.210,95%CI:1.631～6.137,P=0.001),并独立于骨量减少的传统危险因素.结论 APN基因第3外显子rs1063539多态性与壮族女性 BMD有一定关联,其中GG型对BMD具有一定的保护作用,CG型是BMD降低的危险因素.rs12495941、rs266729、rs3774261及rs710445多态性与壮族女性BMD无相关性.     

碱性成纤维生长因子基因单核苷酸多态性与广西壮族男性骨质疏松的关系

目的 探讨碱性成纤维生长因子(bFGF)基因5个单核苷酸多态性（SNPs）与广西百色地区壮族男性骨密度（BMD）的关系。方法 选取壮族男性147例跟骨骨量减少患者和154例骨量正常对照进行病例对照研究,采用单碱基延伸的单核苷酸多态性分型技术对广西百色地区301例壮族男性的脂联素基因的5个位点（rs308379、rs12644427、rs3789138、rs308442和rs3747676）进行了基因分型,采用法国生产的Osteospace干式超声骨密度仪测量右侧跟骨超声振幅衰减（BUA）。结果 rs308379、rs12644427、rs3789138、rs308442和rs3747676多态性分布均符合Hardy-Weinberg遗传平衡定律（ P >0.05）。以5个多态性位点作为自变量的多元Logistic回归显示,仅rs308442多态性与跟骨骨量减少显著相关（OR =1.831,95% CI :1.075~3.116, P =0.026）。 结论 bFGF基因第1内含子rs308442多态性与壮族男性 BMD可能有一定关联,其中TT型可能对BMD具有一定的保护作用,TA型是BMD降低的危险因素。rs308379、rs12644427、rs3789138及rs3747676多态性与壮族男性BMD无相关性。     

Twenty single nucleotide polymorphisms (SNPs) and their allelic frequencies in four genes that are responsible for familial long QT syndrome in the Japanese population

We report here 20 single nucleotide polymorphisms (SNPs), including 10 novel ones, and their allelic frequencies detected in four genes that are known to be responsible for familial long QT syndrome in the Japanese population; 7 polymorphisms are in the KCNQ1 gene, 6 in the KCNH2 gene, 5 in the SCN5A gene, and 2 in the KCNE1 gene. These data will be of use for genetic association studies of acquired cardiac arrhythmias. Received: December 25, 1999 / Accepted: December 27, 1999     

Association of single nucleotide polymorphisms of CDH13 gene with metabolic syndrome among ethnic Han ChineseCSCD

Objective: To assessthe association of single nucleotide polymorphisms (SNPs) of the T-cadherin (CDH13) gene with metabolic syndrome (MS) among ethnic Han Chinese. Methods: Genotypes of 6 SNPs(rsll646213, rsl2596316, rs3865188, rsl2444338, rsl2051272, and rs7195409) of the CDH13 gene among 453 patients with MS and 526 controls were determined with a TaqMan method, and their association with MS was assessed. Results: For 5 SNPs (rsll646213, rs3865188, rsl2444338, rsl2051272, and rs7195409), no difference was found in allelic and genotypic frequencies of the CDH13 gene between the two groups. Comparing with rsl2596316 (AA+GG) genotype, rsl2596316 AG genotype has significantly increased the risk of MS(P = 0.01, OR=1.38, 95%CI: 1.07-1.78), though no association was found between particular alleles of the rsl2596316 with MS. There was no difference in the frequencies of rsll646213-rsl2596316-rs3865188-rsl2444338-rsl2051272 haplotype between the two groups(P>0.05). Conclusion: No association was found between the five SNPs (rsll646213, rs3865188, rsl2444338, rsl2051272 and rs7195409) of the CDH13 gene with the MS, while the rsl2596316AG genotype of the CDH13 gene is associated with the susceptibility to MS among ethnic Han Chinese. © 2018 West China University of Medical Sciences. All rights reserved.     

骨保护素基因单核苷酸多态性与类风湿关节炎发病的相关性研究

 目的：探讨骨保护素（OPG）基因163A/G及245T/G单核苷酸多态性（SNPs）与我国汉族人群类风湿关节炎（RA）发病的相关性。方法：采用聚合酶链反应-限制性片段长度多态性（PCR-RFLP）技术检测我国南方汉族正常人群及RA患者的OPG 163A/G 和245T/G 2个SNP位点;进行Hardy-Weinberg平衡检验;计算基因型和等位基因频率,及这2个位点的连锁关系,并分析这2个SNP位点与RA的关系。结果：所研究基因分布符合Hardy-Weinberg平衡,163A/G 位点基因型AA、AG、GG分布频率在2组比较有显著差异（P<0.05）;等位基因A、G分布比较在2组有显著差异（P<0.05）,携带163GG基因型者发生RA的危险性是非携带者的1.219倍（OR=1219, 95％CI：1066~2.339, P<0.05)。但245T/G位点各基因型及等位基因频率在2组中均未见差异（P>005）。结论：OPG 基因 163A/G SNP可能与我国汉族人群RA发病相关,携带G等位基因可能是发病的危险因素。     

Single nucleotide polymorphisms in VEGF gene are associated with an increased risk of osteosarcoma

We aimed to assess whether the five common SNPs can affect the risk of osteosarcoma, and its association with demographic characteristics of osteosarcoma. 165 osteosarcoma patients and 330 cancer-free controls were enrolled into our study. Five common SNPs in VEGF gene, -2578C/A (rs699947), -1156G/A (rs1570360), +1612G/A (rs10434), +936C/T (rs3025039) and -634G/C (rs2010963), were detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Conditional logistic regression analyses found that individuals with AA genotype and A allele of rs699947 were associated with an increased risk of osteosarcoma. Individuals with GG genotype and G allele of rs2010963 were associated with an increased risk of osteosarcoma. By stratified analysis, AA genotype of rs699947 was associated with an increased risk of osteosarcoma in those with shorter age, males and a family history of cancer, and GG genotype of rs2010963 was correlated with an increased risk of osteosarcoma in those with shorter age, females and a family history of cancer. Our study suggests that rs699947 and rs2010963 polymorphisms may play a role in the pathogenesis of osteosarcoma.     

Interleukin-1 gene complex single nucleotide polymorphisms in systemic sclerosis: a further step ahead

Gene–gene and gene–environment interactions are difficult to detect by traditional parametric computational approaches. Novel nonparametric and model-free strategies, such as the multifactor dimensionality reduction (MDR) algorithm, are thus emerging as practical and feasible methods of analysis to model high-order epistatic interactions, integrating and complementing traditional logistic approaches. With traditional methods of analysis we showed that the interleukin-1β (IL-1β) C+3962T single nucleotide polymorphism (SNP), along with the Sc70 antibody and the diffuse cutaneous subset of systemic sclerosis, are important risk factors for the development of a severe ventilatory restriction in patients with systemic sclerosis (SSc); however the interactions among these and other genetic and environmental attributes were difficult to model. On the contrary, the MDR analysis detected significant two- or three-way interactions in the presence of nonlinearity. The best model identified by the multifactor dimensionality reduction algorithm included the antibody subset, the IL-1β C-511T and the interferon-γ AUTR5644T SNPs, with a testing accuracy of 85% (p < 0.001) and a cross-validation consistency of 10/10. This model outperformed any one- to-three-way model constructed by considering the three factors with main independent effects identified by traditional computational approaches. Epistatic interactions among IL-1 gene complex SNPs and clinical or environmental factors are more important than the singe attributes in the development of severe ventilatory restriction in SSc patients.     

Identification of 20 novel SNPs in the guanine nucleotide binding protein alpha 12 gene locus

Heterotrimeric guanine nucleotide binding proteins (G proteins) regulate various signals from transmembrane receptors to intracellular effectors thereby mediating cell growth, differentiation, and apoptosis. We have been publishing a series of genetic variations detected in the genomic regions corresponding to the potential drug target genes. As an addition to genetic information reported earlier, we provide here 20 novel single nucleotide polymorphisms (SNPs) in the region corresponding to a gene encoding subunits of G₁₂ protein, GNA12, in the Japanese population: 16 in introns, two in the coding region, and two in the 3 flanking region. We also identified 12 genetic variations of other types from this locus. The collection of genetic variations reported here will serve as a useful resource for analyzing potential associations between genotypes and susceptibility to common diseases as well as efficacy and/or adverse reactions to drugs.     

MMP14基因单核苷酸多态性在广西百色地区壮族人群中的分布

目的研究膜型基质金属蛋白酶-1(membrane-type 1 matrix metalloproteinase,MT1-MMP或MMP14)基因单核苷酸多态性(single nucleotide polymorphisms,SNPs)各等位基因及基因型在广西百色地区壮族人群中的分布频率。方法采用Multiplex SNaPshot SNP分型技术对百色地区624例壮族个体的MMP14染色体基因组的3个SNP进行基因分型。结合HapMap4个人群(HapMap-CEU、HapMap-YRI、HapMap-JPT和HapMap-HCB)的SNPs分型数据,分析这5个人群的遗传结构。结果壮族人群MMP14的基因型分布频率为:rs2269213(CC 55.4%、CA 39.2%和AA 5.4%)、rs2236303(CC 25.2%、CT50.8%和TT 24.0%)和rs743257(CC 37.0%、CT 48.7%和TT 14.3%)。MMP14基因SNPs在壮族人群的分布频率与HapMap-CEU、HapMap-YRI和HapMap-JPT的差异有统计学意义(P<0.05)。结论广西百色地区壮族人群中存在MMP14基因多态性,且与HapMap-CEU、HapMap-YRI和HapMap-JPT有差异的遗传成分存在,这种差异对人类学研究可能起重要的作用。     

Association of single nucleotide polymorphisms in the promoter region of the pro-opiomelanocortin gene (POMC) with low bone mineral density in adult women

Among multiple factors influencing osteoporosis, genetic variations involved in bone-mineral metabolism can affect risks predisposing to the disease onset. Here, we studied single-nucleotide polymorphisms (SNPs) in the pro-opiomelanocortin (POMC) gene for possible association with bone mineral density (BMD) among 384 adult Japanese women and observed significant correlation between adjusted BMD and three SNPs in the promoter region (r>0.14, p<0.01). The most significant correlation was observed for –2353G/A (r=–0.16, p=0.002); homozygous carriers of the major (G) allele had the highest BMD (0.405±0.054 g/cm²) while heterozygous carriers were intermediate (0.390±0.053 g/cm²) and homozygous A-allele carriers had the lowest BMDs (0.369±0.048 g/cm²). Although no association was detected between these SNPs and body weight or body mass index (BMI), significant association was detected between the –2313A/C genotype and plasma total cholesterol level (r=–0.12, p=0.019). We propose that POMC is among the likely susceptibility genes for osteoporosis and may also be involved in dyslipidemia.     

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     

Two single nucleotide polymorphisms of the hSNF5/INI1 gene

We found two single nucleotide polymorphisms at the hSNF5/INI1 gene located on 22q11.2, encoding a member of the chromatin-remodelling SWI/SNF multiprotein complexes. A guanine/adenine polymorphism at codon 299 in exon 7, and another guanine/adenine polymorphism at 39 bp upstream of exon 9 were identified. As the gene was recently identified as a tumor suppressor gene for malignant rhabdoid tumor, this polymorphism may be useful for the genetic study of susceptibility for human malignancies of various tissue origins. Received: March 19, 1999 / Accepted: April 16, 1999     

幼年特发性关节炎患儿甘露糖结合凝集素基因启动子区SNP研究

目的探讨甘露糖结合凝集素(MBL)基因启动子区单核苷酸多态性(SNP)与幼年特发性关节炎(JIA)易感性的关系。方法对50例JIA患儿和48名正常健康儿童MBL基因启动子区SNP位点-550(G/C,称H/L等位基因)和-221(G/C,称X/Y等位基因)采用等位基因特异性PCR法(PCR-SSP)检测,并分析其单元型及基因型频率。结果共检出HY、LY和LX三种单元型,在JIA患儿中的频率依次为0.540、0.270和0.190,而在正常儿童中频率分别为0.594、0.292和0.114;两组间各单元型比较均无显著性差异。结论MBL基因启动子区单核苷酸多态性与JIA无相关性。     

HTRA1基因单核苷酸多态性与类风湿性关节炎的关联性研究

目的 探讨HTRA1基因单核苷酸多态性(single nucleotide polymorphisms,SNPs)和类风湿性关节炎(rheumatoid arthritis,RA)及其患者血清类风湿因子(rheumatoid factor,RF)、C反应蛋白((C-reactive protein, CRP)之间的相关性.方法 采用Snapshot法测定344例RA患者和288名正常健康人HTRA1基因5个SNPs(rs2014307、rs2248799、rs2300433、rs714816、rs2268356)位点基因型,终点散射比浊法测定RA患者血清RF和CRP水平.结果 RA组HTRA1基因SNPs(rs2014307、rs2248799、rs2300433、rs714816、rs2268356)基因型与正常对照组间差异均无统计学意义(P>0.05),单倍型分析也显示H豫A1基因RA组与正常对照组间差异无统计学意义(P>0.05),RA患者HTRA1基闪SNPs位点(rs2014307、rs2248799、rs714816、rs2268356)不同基因型之间血清RF水平比较差异无统计学意义(P>0.05),而rs2300433位点基因型(AA+AG)组的RF水平明显高于GG组((P<0.05).结论 已分析的与HTRA1基因相关的5个SNPs与中国汉族人种RA遗传易感性不相关,HTRA1基因rs2300433位点不同基因型RA患者体内RF水平有差别,HTRA1基因表达的丝氨酸蛋白酶可能参与了RA患者RF的表达.     

Association of single nucleotide polymorphisms of LEPR gene with essential hypertension among ethnic Mongolian and Han Chinese from Inner Mongolia regionCSCD

Objective: To assess the association of single nucleotide polymorphisms (SNPs) of leptin receptor (LEPR) gene with essential hypertension (EH) and body mass index (BMI) among ethnic Mongolian and Han Chinese from Inner Mongolia region. Methods: In total 411 Han Chinese patients with EH and 480 healthy controls, together with 658 Mongolian patients with EH and 403 healthy controls, were collected. The SNPs of the LEPR gene were determined with ligase detection reaction (LDR). Logistic regression was used to analyze the association of the polymorphisms of each locus with EH and BMI. MDR software was used to analyze the interaction between above loci and environmental factors. Results: Genotypic frequencies of LEPR gene rs7555955, rsll37100 and rsll37101 loci had differed significantly among ethnic Hans with EH and the control group (All P <0. 05). While those of rs7555955, rsl805094, rsll37100, rsll579567, rsl805134 and rs6669354 loci had differed significantly among ethnic Mongolians with EH and the control group (All P<0. 05). After adjustment for confounders, logistic regression analysis indicated that age(Oi=2. 97, 95%CJ: 1. 94-3. 99), BMI (Ofl = 3. 93, 95%CI:2. 91-5. 96), and rsll37101 (AA) (Oi=3. 96, 95%CI-.l. 32-11. 90) were independent risk factors for EH among ethnic Hans, while age (Oi=2. 99, 95%C7:2. 98-4. 57), BMI (Oi = 3. 03, 95%CI-. 1. 05-1. 27), rs7555955 (AG, AA) (OR = 12.12, 95%CI:2.80-52.43) OP = 6.35, 95%CI: 1. 44-27. 94), and rs7555955 (GG) were independent risk factors for EH among ethnic Mongolians (P <0. 05). Conclusion: Age and BMI are independent risk factors for EH in both ethnic Han and Mongolian Chinese. rsll37101 locus is associated with EH among ethnic Hans, while rs7555955 locus is associated with EH among ethnic Mongolians. © 2018 MeDitorial Ltd. All rights reserved.