The association of the JAK2 46/1 haplotype with non-splanchnic venous thrombosis

Background

The inherited JAK2 46/1 haplotype is strongly associated with the development of myeloproliferative neoplasms (MPNs), and its increased frequency has also been reported in splanchnic venous thrombosis (SVT). In the present study, the role of the JAK2 46/1 haplotype in non-splanchnic venous thrombosis (non-SVT) was investigated.

Methods and Results

We genotyped 438 patients with non-SVT, 226 patients with MPNs and 459 healthy controls for three single nucleotide polymorphisms (SNPs) which tag the JAK2 46/1 haplotype (rs12342421 G > C, rs12343867 T > C and rs10974944 C > G). We found statistically significant association of the rs12342421 GC + CC genotypes (OR = 1.40; p = 0.023) and the rs12343867 TC + CC genotypes (OR = 1.83; p = 7.02x10^- 5) with non-SVT. We also found that the CC haplotype of these two SNPs was associated with an increased risk of the disease (OR = 1.68; p = 0.009). Stratification analysis indicated that the observed association of the JAK2 46/1 haplotype with non-SVT was probably largely free of confounding effect of thrombophilic risk factors. In addition, we established a strong association of SNPs rs12342421 and rs10974944 and their CG haplotype with MPNs and with JAK2 V617F-positive MPNs.

Conclusions

This study provides statistical evidence that SNPs rs12342421 and rs12343867 are associated with an increased risk of non-SVT. Consistently, haplotypes of the SNPs were also associated with non-SVT risk, suggesting that inherited genetic variation in the JAK2 gene may play a role in the pathogenesis of non-SVT. Furthermore, the reported associations of the JAK2 46/1 haplotype with MPNs as well as with the occurrence of the JAK2 V617F mutation in MPNs were confirmed.     

Replication of the MTHFD1L gene association with late-onset Alzheimer's disease in a Northern Han Chinese population

We conducted a replication study of the 2 genetic variants, rs11754661 and rs2073067, in MTHFD1L that have been recently reported to be associated with late-onset Alzheimer's disease (LOAD) in a genome-wide study in Caucasians. The associations were evaluated in a case-control sample comprising 1,189 Northern Han-Chinese individuals. The rs11754661 polymorphism is associated with LOAD (OR = 1.727; p = 0.016). For rs2073067, LOAD association was found only in APOEε4 carriers (OR = 0.400; p < 0.001). Haplotype analysis revealed the "AC" haplotype increased the risk of developing LOAD (OR = 1.730; p = 0.015). Our findings support a role of MTHFD1L gene in LOAD.     

Effect of rs11614913 Polymorphism on Mature miR196a2 Expression and its Target Gene HOXC8 Expression in Human Glioma

miRNA polymorphisms are recently identified as a risk factor for various cancers, and it is associated with change in the expression of target genes in vitro. rs11614913 polymorphism in miR196a2 was associated with risk of glioma in Chinese population. In this study, we have evaluated the role of rs11614913 polymorphism and glioma risk in Indian population in 180 cases and controls. Seventy-two glioma tissue-blood pairs were also assessed for mutation in this SNP. Further, the effect of this polymorphism on mature miR196a2 expression and HOXC8 gene expression was analysed in 33 glioma tissue samples with different genotypes. Allelic discrimination assay was performed for genotyping and quantitative real time PCR for the expression of miR196a2 and HOXC8 gene. We could not find any association between rs11614913 polymorphism and glioma risk in Indian population. The rs11614913 genotyping of glioma tissue and blood pair revealed presence of mutations showing changes from C to T allele in majority of samples. The expression of the mature miR196a2 was significantly high in glioma samples, but there was no difference in expression with genotype. HOXC8 gene expression was not significantly different in glioma tissue when compared to non-glioma and interestingly there was a significant difference in expression with different genotypes, especially TT genotype was showing over expression when compared to other genotypes. Our study suggests that the rs11614913 polymorphism does not affect the mature miRNA expression, but shows its effect through target gene HOXC8 expression in glioma.     

The role of the RTEL1 rs2297440 polymorphism in the risk of glioma development: a meta-analysis

The regulator of the telomere elongation helicase1 (RTEL1) gene plays a crucial role in the DNA double-stand break-repair pathway by maintaining genomic stability. Recent epidemiological studies showed that the rs2297440 polymorphism in the RTEL1 gene was a potential risk locus for glioma development, but the results were inconclusive. To clarify the association between this polymorphism and the risk of glioma, we performed a comprehensive meta-analysis. The PubMed, EMBASE, Web of Science, and China National Knowledge Infrastructure databases were systematically searched to identify all relevant published studies up to 30 August 2015. Four eligible studies were finally included. The pooled results indicated that the RTEL1 rs2297440 polymorphism moderately increased the risk of glioma in all genetic models. A comparison of the dominant model CT + CC versus TT (OR 1.40; 95 % CI 1.24–1.60; p < 0.001) indicated that having the C allele conferred a 40 % increased risk of developing glioma. In a subgroup analysis based on geographic location (Europe, Asia, and America), there was an association between the rs2297440 polymorphism and the risk of glioma in all three areas. The results of the subgroup analysis based on source of control indicated an elevated risk of glioma in population-based control studies. This meta-analysis demonstrates that the RTEL1 rs2297440 polymorphism plays a moderate, but significant role in the risk of glioma. Further studies with larger sample sizes are necessary to confirm this finding.     

Association between chromogranin A gene polymorphism and schizophrenia in the Japanese population

It has been reported that expression of the chromogranin A (CHGA) gene is reduced in the prefrontal cortex and cerebrospinal fluid of patients with schizophrenia. Single-marker and haplotype analyses of SNPs within the CHGA gene were performed in 633 subjects with schizophrenia and 589 healthy controls. A significant association with schizophrenia was observed to one SNP marker, rs9658635 (p=0.0269), and with a 2 marker haplotype (p=0.0016). Significant association of rs9658635 was then replicated in a second independent cohort (377 schizophrenia and 338 control samples) (p=0.007). These results suggest that the CHGA gene is associated with the risk of developing schizophrenia in the Japanese population.     

Somatostatin genetic variants modify the risk for Alzheimer's disease among Finnish patients

The levels of somatostatin are consistently decreased in the brain and cerebrospinal fluid of Alzheimer's disease (AD) patients. The somatostatin gene is located on chromosome 3q27.3 close to an association region identified in late-onset AD patients originating from Finland. Since somatostatin is a good candidate on both positional and functional grounds, we studied whether single nucleotide polymorphisms (SNPs) in the somatostatin gene were associated with AD in the Finnish population. We genotyped three SNPs within this gene in Finnish AD patients (n = 424) and non-demented controls (n = 466). AD patients were compared with non-demented control subjects using single-locus and haplotype approaches. In the whole study group, the age, sex and APOE adjusted OR for the risk of AD in C-allele carriers of the SNP rs4988 514 was 1.42 (p <0.05). Interestingly, in APOE epsilon4-allele carriers, the age and sex adjusted OR for the risk of AD in C-allele carriers of the rs4988 514 increased to 2.05 (p <0.01). Additionally, SNP rs4988514 may interact with the APOE epsilon4-allele to increase the risk of AD. Assessment of individual haplotype distributions revealed a 2-fold overrepresentation of the TCG haplotype of SNPs rs3864101, rs4988 514 and rs7624 906 in the AD APOE epsilon4-allele group (p <0.01). Conversely, a major haplotype TTG was significantly underrepresented among all the AD patients as well as APOE epsilon4-allele carrying AD patients. Thus the major haplotype TTG of somatostatin may have a protective effect against AD. This first genetic association study between somatostatin and AD indicates that genetic variations in the somatostatin gene may modify the risk for AD among Finnish AD subjects.     

Associations of <Emphasis Type="Italic">TF</Emphasis> Gene Polymorphisms with the Risk of Ischemic Stroke

Ischemic stroke (IS) is the main cause of mortality and disability in China; thus, this study aimed to examine the association between six variants and their haplotypes within the transferrin (TF) gene and the risk of IS in the Southern Chinese Han population. Genotyping was performed using the Sequenom MassARRAY platform for 249 IS patients and 249 age- and sex-matched controls. The association between polymorphisms and IS risk was tested by Chi squared test and haplotype and stratification analysis. Odds ratios (ORs) and confidence intervals (CIs) were estimated by unconditional logistic regression analysis. The results of genetic model analyses indicated that the two SNPs (rs1880669 and rs2692695) were associated with decreased IS risk under the co-dominant, dominant, and additive models. Additionally, rs4525863 was also associated with decreased IS risk both under the dominant and additive models in males. Moreover, the CG haplotype of TF (rs1880669 and rs2692695) was significantly associated with a decreased risk of IS in the total population and males. Our findings suggested that polymorphisms (rs4525863, rs1880669, and rs2692695) of the TF gene might be a protective factor for IS in Southern Chinese Han population. Further large prospective studies are required to confirm these findings.     

Melatonin pathway genes are associated with progressive subtypes and disability status in multiple sclerosis among Finnish patients

In this study we investigated the relationship between melatonin pathway and multiple sclerosis (MS) in a high-risk Finnish population by studying the single nucleotide polymorphisms (SNPs) in the genes coding for critical enzymes and receptors involved in the melatonin pathway. A total of 590 subjects (193 MS patients and 397 healthy controls) were genotyped for seven SNPs in four genes including tryptophan hydroxylases (TPH)1 and 2, arylalkylamine N-acetyltransferase (AANAT) and melatonin receptor 1B (MTNR1B). An overrepresentation of T allele carriers of a functional polymorphism (G-703T, rs4570625) in the promoter region of TPH2 gene was observed in the progressive MS subtypes. The haplotype rs4570625-rs10506645TT of TPH2 gene was associated with the risk of severe disability in primary progressive MS (PPMS), while haplotype rs4570625-rs10506645TC appeared to be protective against disability in secondary progressive MS (SPMS). In the MTNR1B gene, the haplotype rs10830963-rs4753426GC was associated with the risk of SPMS, whereas another haplotype rs10830963-rs4753426GT showed an association with the risk of PPMS. These data showing the association of polymorphisms in the TPH2 and MTNR1B genes with the progressive subtypes of MS and disability suggest dysregulation in melatonin pathway. Melatonin pathway seems to be involved in disease progression, and therefore its potential effects in overcoming MS-related neurodegeneration may be worth evaluating in future clinical trials.     

Association of the MAPT locus with Parkinson’s disease

Background and purpose: Whilst an association between the tau gene (MAPT)‐containing H1 haplotype and supranuclear gaze palsy (PSP) has long been recognized, the effect of H1 on risk for Parkinson’s disease (PD) has remained more contentious. Methods: Herein, we examined the association of H1 and PD in three Caucasian PD patient–control series from Ireland, Norway, and the US (combined: n = 2619), by genotyping two H1/H2 single nucleotide polymorphisms (SNPs) in MAPT (rs1052553) and in the Saitohin gene (rs62063857) and one H1‐specific SNP (rs242557). Results: We identified a significant association between H1/H2 and risk of PD (rs1052553 OR: 1.43, CI: 1.23–1.64; rs62063857 OR: 1.45, CI: 1.27–1.67), but no effect of the H1‐specific SNP rs242557 (OR: 0.92, CI: 0.82–1.03). Conclusions: Our findings show that the H1 haplotype is a significant risk factor for PD. However, one H1‐specific SNP (rs242557) previously implicated in PSP did not alter the risk of PD, indicating that distinct H1 sub‐haplotypes probably drive the associations with PD and PSP.     

Two Novel SNPs in the PLCL2 Gene Associated with Large Artery Atherosclerotic Stroke Identified by Fine-Mapping

A genome-wide association study (GWAS) reported that the single nucleotide polymorphism (SNP) rs4618210 in the PLCL2 gene is related to myocardial infarction (MI) in the Japanese population, but no study has examined the correlation of PLCL2 with ischemic stroke (IS). The present study was designed to investigate whether the genetic variation in PLCL2 is associated with large artery atherosclerotic (LAA) stroke in a Han Chinese population. Tagging SNPs (tSNPs) of the PLCL2 gene were determined by a fine-mapping strategy and were genotyped by improved multiplex ligation detection reaction (iMLDR) technology in 669 LAA stroke patients and 668 healthy controls. A logistic regression model was used to analyze the associations between genetic variation at PLCL2 and the risk of LAA stroke. Two SNPs were significantly associated with the risk of LAA stroke after adjusting for potential confounders: for rs4685423, the AA genotype and CA genotype decreased the risk of LAA stroke compared with the CC genotype (multivariate-adjusted, P = 0.001); for rs4618210, the AA genotype and GA genotype decreased the risk of LAA stroke compared with the GG genotype (multivariate-adjusted, P = 0.007). In addition, haplotype analysis indicated that compared with haplotype TTT, haplotype TAT decreased the risk of LAA stroke in block 2 (adjusted OR, 0.706; 95% CI, 0.550–0.907; P = 0.006). The analysis of SNP–SNP interactions showed that rs4685423 was the most influential contributor to LAA stroke risk. SNPs rs4685423 and rs4618210 in the PLCL2 gene may be related to the risk of LAA stroke in Han Chinese.     

Association of GABRB3 polymorphisms with autism spectrum disorders in Korean trios

BACKGROUND/AIMS: Autism spectrum disorders (ASD) are complex neuropsychiatric disorders having a genetic risk factor. The association and linkage study for the gamma-aminobutyric acid type A receptor beta3 subunit gene (GABRB3), located within the chromosome 15q11-q13 autism candidate region, and ASD have been evaluated. The aim of this study was to investigate the association between GABRB3 and ASD in the Korean population. METHODS: The present study was conducted with the detection of four single-nucleotide polymorphisms (rs1426217, rs2081648, rs890317, rs981778) in GABRB3 and association analysis in 104 Korean ASD trios using the transmission disequilibrium test. RESULTS: The transmission disequilibrium test demonstrated that an allele at rs2081648 showed preferential transmission (p = 0.027). One haplotype, including all examined markers in GABRB3, demonstrated significant association (p = 0.043), but the global chi2 test for haplotype transmission did not reveal an association between GABRB3 and ASD (chi2 = 15.516, d.f. = 15). CONCLUSION: Our finding suggested that single-nucleotide polymorphisms in GABRB3 may play a significant role in the genetic predisposition to ASD in the Korean population.     

Association of specific haplotypes of neurotrophic tyrosine kinase receptor 2 gene (NTRK2) with vulnerability to nicotine dependence in African-Americans and European-Americans.

BACKGROUND: The gene encoding neurotrophic tyrosine kinase receptor 2 (NTRK2) has been localized to a region on chromosome 9q22-q23 that showed a "suggestive" linkage to nicotine dependence (ND) in our previous linkage analyses. However, no association of NTRK2 with ND has been identified. METHODS: Family-based association analyses of 2037 participants (1366 African Americans [AA], 671 European Americans [EA]) representing 602 nuclear families were performed to evaluate association of nine single nucleotide polymorphisms (SNPs) within NTRK2 with ND. RESULTS: Individual SNP-based association analysis indicated that in the EA sample, SNPs rs1659400 and rs1187272 were significantly associated with at least one adjusted ND measure. Haplotype analysis revealed that even after Bonferroni correction, the haplotype T-T-A of rs1659400-rs1187272-rs1122530 had a highly significant positive association, with adjusted ND measures in the EA sample (max Z = 3.78; p = .0001, frequency 59.9%). We further identified a major haplotype, T-G-C-A-A (26%), formed by rs993315-rs736744-rs920776-rs4075274-rs729560, which showed a significant positive association (max Z = 2.97, p = .003) with adjusted ND measures in the AA sample. CONCLUSIONS: These results strongly suggest that NTRK2 is a susceptibility gene for ND. These findings imply that NTRK2 plays a role in the etiology of ND and represents an important biological candidate for further investigation.     

中国人群VEGFR2 rs2071559与胶质瘤风险的潜在关联性研究

目的探讨中国人群血管内皮细胞生长因子受体2（VEGFR2）多态性与胶质瘤发生风险之间的潜在关联性。方法采用病例-对照研究方法,对504例胶质瘤患者和527例对照者进行血液样本和病历资料收集,以及流行病学问卷调查。Qiagen Blood试剂盒行DNA提取和浓度标化、分装,Mass ARRAY系统等位基因特异性基质辅助激光解析离子化-时间飞跃质谱法完成VEGFR2 rs2071559基因分型,Haplo View 4.1统计软件检验Hardy-Weinberg遗传平衡状态,SPSS 17.0统计软件分析单核苷酸多态性差异。结果 （1）单核苷酸多态性基因分型,VEGFR2 rs2071559分型成功率达99.70%,Hardy-Weinberg遗传平衡检验表明对照组VEGFR2 rs2071559基因型频率处于平衡状态（P=0.451）,具有群体代表性。（2）等位基因频率分析,VEGFR2 rs2071559之C等位基因是胶质瘤危险等位基因,与胶质瘤风险增加有关（OR=1.424,95%CI：1.186~1.710;P=0.000）。（3）基因型分析,VEGFR2 rs2071559之CT和CC基因型与胶质瘤风险增加有关（校正OR=1.407,95%CI：1.071~1.847,P=0.014;校正OR=1.947,95%CI：1.294~2.928,P=0.001）。结论中国人群VEGFR2 rs2071559之CT和CC基因型或C等位基因与胶质瘤风险增加有关,但VEGFR2 rs2071559多态性在胶质瘤易感性中的作用尚待进一步研究。     

Association of SNPs and haplotypes in APOL1, 2 and 4 with schizophrenia

Prior work found the APOL1, 2 and 4 genes, located on chromosome 22q12.3-q13.1, to be upregulated in brains of schizophrenic patients. We performed a family-based association study using 130 SNPs tagging the APOL gene family (APOL1-6). The subjects were 112 African-American (AA), 114 European-American (EA), 109 Chinese (Ch) and 42 Japanese (Jp) families with schizophrenia (377 families, 1161 genotyped members and 647 genotyped affected in total). Seven SNPs had p-values<0.05 in the APOL1, 2 and 4 regions for the AA, EA and combined (AA and EA) samples. In the AA sample, two SNPs, rs9610449 and rs6000200 showed low p-values; and a haplotype which comprised these two SNPs yielded a p-value of 0.00029 using the global test (GT) and the allele specific test (AST). The two SNPs and the haplotype were associated with risk for schizophrenia in African-Americans. In the combined (AA and EA) sample, two SNPs, rs2003813 and rs2157249 showed low p-values; and a three SNP haplotype including these two SNPs was significant using the GT (p=0.0013) and the AST (p=0.000090). The association of this haplotype with schizophrenia was significant for the entire (AA, EA, Ch and Jp) sample using the GT (p=0.00054) and the AST (p=0.00011). Although our study is not definitive, it suggests that the APOL genes should be more extensively studied in schizophrenia.     

色氨酸羟化酶2基因和家庭环境因素与反社会人格障碍的关联分析

目的 探讨色氨酸羟化酶2(TPH2)基因、家庭环境因素及其交互作用与反社会人格障碍(ASPD)的关系.方法 选取TPH2基因rs4290270和rs7305115 2个多态性位点,采用聚合酶链反应-限制性片段长度多态性基因分型技术,测定117例反社会人格障碍患者(ASPD组)和142名健康人(对照组)的TPH2基因多态性分布,并运用家庭环境量表-中文版(Family Environment ScaleChinese Version,FES-CV)评估家庭环境.结果 ASPD组TPH2基因rs4290270、rs7305115 2个多态性位点的基因型和等位基因频率分布与对照组比较,差异均无统计学意义(P>0.05).ASPD组TA单体型频率显著高于对照组,差异有统计学意义(x2=6.177,P<0.05),相对危险度的估计值(OR)为1.865,95%可信区间(CI)为1.135～3.065;其他单体型在2组间的差异无统计学意义.家庭环境中的情感表达和道德宗教观2个因子与TA单体型存在交互作用(P<0.05),OR值分别为1.122和1.080,95%CI分别为1.043～1.206和1.010～1.155.结论 TPH2单体型TA可能与ASPD的发生有关,负性的家庭环境可能进一步加重携带危险单体型对个体的不利影响,个体发生反社会人格障碍的易感性更高.

Abstract：

objective To study the association of tryptophan hydroxylase 2(TPH2)gene polymorphism and family environment with antisocial personality disorder(ASPD)in Chinese Han population.Methods The single nucleotide polymorphism(SNPs)of TPH2,rs4290270 and rs7305115 were analyzed by PCR-RFLP genotyping assay in 117 ASPD patients and 142 healthy controls.The family Environment Scale-Chinese Version(FES-CV)was used to evaluate the family environment of all subjects.Results There were no significant differences between ASPD and controls in genotype and allele frequencies of rs4290270 and rs7305115.The distributions of TA haplotype was significantly more frequent in patients than in controls[odds ratio(OR)1.865,95%confidence interval(CI)1.135-3.065,P<0.05].Interactions between genetic and environmental(G×E)revealed that expressiveness and moralreligious emphasis increased the risk of ASPD in the presence of TA haplotype[OR=1.122,95%CI 1.043-1.206;OR=1.080,95%CI 1.010-1.155,P<0.05].Conclusion The results suggest that TA haplotype might be with higher susceptibility for ASPD and adversity family environments might increase the risk of ASPD in ones with risk haplotype.     

Polymorphisms at the LDLR locus may be associated with ischemic cerebrovascular disease independent of lipid profile

The low-density lipoprotein receptor (LDLR) gene has been reported to be associated with cerebral infarction. This study aimed to explore 2 genetic LDLR variants, rs688 and rs5925, for their potential roles in cerebral infarction. This genetic association study was conducted within an isolated Taiwanese population; 815 ischemic stroke patients (431 with atherothrombotic stroke and 384 with lacunar infarction) and 430 normal controls were enrolled. There was no significant difference in the genetic frequency of rs688 and rs5925 between the control group and overall ischemic stroke, atherothrombotic stroke, or lacunar infarct groups. However, when analyzing the association between the haplotypes related to rs688 and rs5925 and cerebral ischemic stroke, the most common haplotype allele CT was used as the reference allele, and the haplotype TC associated with a 65% increased risk of overall ischemic stroke, 72% increased risk of atherothrombotic stroke, and 70% increased risk of lacunar infarction; this indicated a synergistic effect between these 2 single-nucleotide polymorphisms. The LDLR analysis based on the haplotypes rs688 and rs5925 was conducted in a Taiwanese population and provided preliminary evidence suggesting that genetic polymorphisms of LDLR are associated with cerebral infarction.     

Confirmation of association between autism and the mitochondrial aspartate/glutamate carrier SLC25A12 gene on chromosome 2q31

OBJECTIVE: Autism is a neurodevelopmental disorder with childhood onset and a known major genetic component. A recent study identified a highly significant association between autism and a two-single-nucleotide-polymorphism haplotype in the SLC25A12 gene, with a homozygote genotype relative risk between 2.4 and 4.8. The authors' goal was to investigate this association with autism in Irish affected child-parent trios because replication in an independent sample is essential in the validation of such potentially important findings. METHOD: Markers rs2056202 and rs2292813 were genotyped in a total of 158 trios (442 individuals). The Transmission Disequilibrium Test was used to examine these markers for association with autism. RESULTS: In agreement with the recent study, the authors found significant association between autism and the C alleles of both rs2056202 and rs2292813 as well as the two-marker haplotype. CONCLUSIONS: These findings provide replication of the association between autism and SLC25A12.     

白细胞介素-1B多态性与神经胶质瘤的关联

目的 探讨白细胞介素-1B(IL-1B)多态性与神经胶质瘤的相关性.方法 采用聚合酶链反应-限制性片段长度多态性检测152例神经胶质瘤患者和201例正常对照组IL-1B-511C/T和-31T/C多态性.结果 IL-1 B-511 C/T位点:与CC基因型相比,TT基因型显著增加了神经胶质瘤的发病风险(x2 =5.61,P=0.021).与C等位基因相比,T等位基因显著增加了神经胶质瘤的发病风险(x2 =5.71,P=0.019).未发现IL-1B-31T/C多态性频率分布在对照组和神经胶质瘤组之间存在明显差异.IL-1B-511C/T和-31T/C两位点单倍型分析显示,-511C/-31T单倍型显著降低了神经胶质瘤的发病风险(x2=4.89,P=0.03),-511T/-31C单倍型显著增加了神经胶质瘤的发病风险(x2=18.55,P＜0.001).结论 IL-1B可能是中国人群神经胶质瘤发病的易感基因.