TaqMan Single Nucleotide Polymorphisms Genotyping Research Articles

EQTL variants in COL22A1 are associated with muscle injury in athletes.

The myotendinous junction (MTJ) is at high risk of muscle injury, and collagen XXII is strictly expressed at tissue junctions, specifically at the MTJ. We investigated the hypothesis that single-nucleotide polymorphisms (SNPs) related to collagen type XXII α-1 chain gene (COL22A1) mRNA expression are associated with susceptibility to muscle injury in athletes. History of muscle injury was assessed in 3,320 Japanese athletes using a questionnaire, and two expression quantitative trait loci (eQTL) SNPs for COL22A1 (rs11784270 A/C and rs6577958 T/C) were analyzed using the TaqMan SNP Genotyping Assay. rs11784270 [odds ratio (OR) = 1.80, 95% confidence interval (CI) = 1.27-2.62, P = 0.0006] and rs6577958 (OR = 1.45, 95% CI = 1.10-1.94, P = 0.0083) were significantly associated with muscle injury under A and T allele additive genetic models, respectively. These results suggest that the expression level of COL22A1 at the MTJ influences muscle injury risk in athletes.

Investigations of a Possible Role of SNPs in KAI1 Gene on Its Down-Regulation in Breast Cancer.

Objective: KAI1 (CD82) is a metastasis suppressor gene known to be down-regulated in carcinomas of breast, prostate and many other organs. The mechanism of KAI1 down-regulation is complex and not well understood. Here, we investigate the role of 8 SNPs (not previously studied) in KAI1 gene that could influence its expression in tumor tissue samples of breast cancer patients from the Eastern province of Saudi Arabia. Methods:Single nucleotide polymorphisms (SNPs) in KAI1 gene were selected from the NCBI website (dbSNP) and were then filtered for those SNPs causing stop codon mutations (rs139889503 and rs150533529) or nonsynonymous mutation in the 5’-UTR (rs11541048, rs77359459, rs115500759, rs182579675, rs200238062, and rs372733853). SNPs genotyping was performed using TaqMan SNP Genotyping Assay and the results were correlated with KAI1 protein expression profile by immunohistochemistry (IHC) on formalin-fixed paraffin-embedded (FFPE) samples of breast cancer and control none-neoplastic tissues. Results: KAI1 expression by IHC was observed in all none-neoplastic breast tissue samples and only in 35% out of the 59 breast cancer tissue samples. None of the samples was homozygous for the stop codon allele A in the SNP rs139889503 or allele T in the SNP rs150533529. The SNPs in the 5-UTR, rs11541048, rs115500759, and rs182579675, were only present in the homozygous state for the G and C alleles respectively in both cancer and control samples. The other SNPs in the 5’-UTR (rs77359459, rs200238062, and rs372733853) had no significant difference in the allele distribution between KAI1 expressing or none-expressing tissue samples. Conclusion:Our findings showed no significant effect of the studied SNPs on down-regulation of KAI1 expression.

Association of Genetic Polymorphisms in DC-SIGN, Toll-Like Receptor 3, and Tumor Necrosis Factor α Genes and the Lewis-Negative Phenotype With Chikungunya Infection and Disease in Nicaragua.

Chikungunya infections range from subclinical infection to debilitating arthralgia and to chronic inflammatory rheumatism. Tumor necrosis factor (TNF) α, DC-SIGN (dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin), Toll-like receptor (TLR) 3, and blood groups have been directly or indirectly implicated in the susceptibility and pathogenesis of chikungunya. To test the hypothesis that polymorphisms in genes coding for these molecules determine clinical outcomes of chikungunya infection, a retrospective case-control study was performed in León, Nicaragua. The study included 132 case patients and 132 controls, matched for age, sex and neighborhood. Case patients had clinical symptoms of chikungunya, which was diagnosed by means of polymerase chain reaction. Controls were individuals not reporting abrupt presentation of clinical chikungunya-like symptoms. Polymorphisms were identified by TaqMan single-nucleotide polymorphism genotyping assays. After adjustment for sociodemographic risk factors, chikungunya disease was associated with polymorphism in DC-SIGN and TLR3 genes (odds ratios, 5.2 and 3.3, respectively), and TNF-α with reduced persistent joint pain (0.24). Persistent joint pain was also associated with age, female sex and other comorbid conditions. Most interestingly, the Lewis-negative phenotype was strongly associated with both symptomatic chikungunya and immunoglobulin G seropositivity (odds ratios, 2.7, and 3.3, respectively). This study identified polymorphisms in DC-SIGN, TLR3, and TNF-α genes as well as Lewis-negative phenotype as risk factors for chikungunya infection and disease progression.

HSD3B1 (1245A>C) germline variant and clinical outcomes in metastatic castration-resistant prostate cancer patients treated with abiraterone and enzalutamide: results from two prospective studies

A common polymorphism (1245A>C) in the HSD3B1 gene is associated with increased de novo synthesis of androgens and worse outcomes in men treated with androgen-deprivation therapy for metastatic castration-sensitive prostate cancer. The objective of the study was to determine whether this polymorphism is associated with outcomes for metastatic castration-resistant prostate cancer (mCRPC) treated with abiraterone or enzalutamide. A total of 547 patients treated with abiraterone or enzalutamide from two prospective cohorts were evaluated. The HSD3B1 genotype was determined by targeted sequencing and/or TaqMan single-nucleotide polymorphism genotyping. In cohort 1, patients were randomized to receive abiraterone+ prednisone or enzalutamide. In cohort 2, patients received either agent according to investigator's choice. Prostate-specific antigen (PSA) response rate, time to PSA progression (TTPP), time to progression (TTP) and overall survival were determined. Associations between HSD3B1 genotypes and outcomes were evaluated via univariate Cox regression. Multivariable Cox model was used to determine the independent association of each covariate. The HSD3B1 variant genotype (CC) was present in 15% of patients and was associated with worse TTP [hazard ratio (HR) 1.31, 95% confidence interval (CI) 1.02-1.67, P= 0.032] and PSA response rates (48% for CC versus 62% and 65% for AA and AC, respectively [P= 0.019]), with no significant difference in TTPP (HR 1.28, 95% CI 0.99-1.66, P= 0.064). The effect of genotype was similar for treatment with abiraterone or enzalutamide with a negative test for interaction for TTPP (P= 0.997) and TTP (P= 0.749). Multivariable analysis did not show a significant association between genotype and TTP or TTPP. The HSD3B1 (CC) genotype was associated with shorter TTP and lower PSA response rate in patients with mCRPC treated with abiraterone or enzalutamide. However, the CC genotype did not provide prognostic information beyond that conferred by standard clinical variables, suggesting that it may not be a suitable stand-alone biomarker in mCRPC.

Impact of IL-17F 7488T/C Functional Polymorphism on Progressive Rheumatoid Arthritis: Novel Insight from the Molecular Dynamic Simulations

ABSTRACT Resorption of bones and cartilage coupled with structural changes in the inflamed joints are the major hallmark of rheumatoid arthritis (RA). Genetic polymorphisms in pro-inflammatory interleukins (ILs) appear to play an important role in the susceptibility towards progressive RA. We therefore aimed to investigate the association of single nucleotide polymorphisms (SNP), present in the hotspot coding/promoter regions of IL-6, −17 and −18, with RA susceptibility or severity in a larger study cohort from Pakistan together with finding clues as to how a functional SNP impacts the predisposition towards RA. TaqMan SNP genotyping approach was first used to assess IL-6 (rs1800795), IL-17 F (rs763780), IL-17A (rs2275913), and IL-18 (rs1946518) polymorphisms in 310 subjects (150 RA and 160 control). Molecular dynamic simulations (MDS) of wild- and mutant-type IL-17A with corresponding receptor were thereafter performed using AMBER-16; Chimera 1.13 was used for analyses. Our results showed the association of two SNPs, namely IL-6 − 174 G/C [allelic (OR = 0.960, 95% CI = 0.929–0.992, p = .009)] and IL-17 F 7488 T/C [allelic (OR = 0.907, 95%CI = 0.861–0.954, p = .000)] with increased RA risk in Pakistani subjects. When mapped, IL-17 F 7488 T/C was found involved in His161→Arg161 change near the C-terminus of IL-17 F. Comparative MDS revealed enhanced stability of the mutant hence advocating a potential role of IL-17F functional SNP in RA susceptibility and/or severity. This study provides a novel structural insight for SNP-derived functional mutation and its overall impact on binding with heterotrimeric receptor complex of IL-17 receptor thereby opening new avenues for understanding the biochemical basis of the disease.

Macrophage migration inhibitory factor -173 G>C single nucleotide polymorphism and its association with active pulmonary tuberculosis.

PurposeThe establishment of candidate genes associated with susceptibility to TB is a challenge especially due to divergent frequencies among different populations. The objective of this study was to evaluate the association between macrophage migration inhibitory factor (MIF) -173 G>C single nucleotide polymorphism (SNP) and susceptibility to pulmonary TB in a population of southern Brazil.MethodsCase-control study. Patients > 18 years old, diagnosed with pulmonary TB were included. The control group consisted of blood donors and household contacts, not relatives, healthy and > 18 years old. MIF -173 G>C SNPs were genotyped using real-time PCR using a TaqMan SNP Genotyping assay.Results174 patients and 166 controls were included. There were no statistically significant differences between cases and controls regarding genotype prevalence (p>0.05). Comparing patients with normal genotype (GG) with those with at least one C allele, there was also no statistically significant difference (p = 0.135). Also, there was no statistically significant difference comparing the homozygous for the mutation (CC) with the other patients (GG and CG) (p = 0.864).ConclusionsWe did not find association between MIF -173 G>C polymorphism and susceptibility to pulmonary TB.

P1570INTERLEUKIN-6 (RS1800795) AND PENTRAXIN 3 (RS2305619) GENETIC POLYMORPHISMS AND THEIR RELATION WITH INFLAMMATION AND ALL-CAUSE MORTALITY IN ESRD PATIENTS ON DIALYSIS

Abstract Background and Aims Chronic inflammation plays an important role in progression and outcome of chronic kidney disease (CKD) patients. The interleukin-6 (IL-6) polymorphism, rs1800795, is a single nucleotide polymorphism (SNP) in the promoter region (-174G/C) that regulates gene transcription and affects the levels of this cytokine. Genetic variants in the promotor region have been associated with a poor outcome in several pathologies, namely in coronary artery disease. Pentraxin 3 (PTX3) is an inflammatory protein, produced locally by different cell types (e.g. mononuclear phagocytes, dendritic cells, fibroblasts and endothelial cells). PTX3 polymorphism, rs2305619, is a SNP (+281A>G) in the intron 1 of PTX3 gene. PTX3 polymorphisms have been described as risk factor for development of coronary artery disease and for an impairment of kidney function. Our aim was to determine the allelic frequencies of IL6 and PTX3 in end-stage renal disease (ESRD) patients and controls, as well as their relationship with the inflammatory response. Method We studied 289 ESRD patients on hemodialysis (high-flux hemodialysis or hemodiafiltration) and 22 healthy individuals, matched for gender, body mass index, and, as far as possible, for age. Real-Time PCR TaqMan SNP genotyping assays were used to assess allelic frequencies of IL6 (rs1800795) and PTX3 (rs2305619). We evaluated the circulating levels of PTX3, growth differentiation factor (GDF)-15, high-sensitivity C-reactive protein (hsCRP), IL-6, tumor necrosis factor-alpha (TNF-α), soluble TNF receptor 2 (sTNFR2), hepcidin and transferrin, using commercially available kits. Deaths occurring along 1-year follow-up period were recorded and mortality rates were evaluated for homozygous and heterozygous alleles. Results Compared to controls, all inflammatory biomarkers were significantly higher in ESRD patients. Allelic frequencies in ESRD patients and controls were similar for both SNPs, IL-6 -174G/C and PTX3 +281A>G, considering the homozygous and the heterozygous alleles. For the IL-6 -174G/C, the CC patients, compared to GG and heterozygous patients, showed significantly higher GDF-15 and CRP concentrations and significantly lower values of transferrin; moreover, we found that CC patients presented a trend towards higher mortality rate (21%, 10% and 7% for CC, GG and GC, respectively; P=0.072). For PTX3 +281A>G polymorphism, the AA patients, compared to GG and heterozygous patients, presented higher hsCRP; no significant differences were found in mortality rate between different allele carrier groups (P=0.703). Conclusion Although no differences were found in the allelic frequencies between controls and ERSD patients, the CC patients for IL6 polymorphism (rs1800795) and AA patients for PTX3 polymorphism (rs2305619), showed an enhanced inflammatory response; the association of the IL6 polymorphism with a higher mortality needs further studies.

Lack of Association between IFNL3 Polymorphism and Human Papillomavirus Infection and Their Progression in HIV-Infected Women Receiving Antiretroviral Treatment

Background: It has been reported that interferon-λ3 (IFNL3)might influence the pathogenesis and clearance of human papillomavirus (HPV) infection. The impact of IFNL3 single-nucleotide polymorphism (SNP) on HPV infection is currently unknown. The aim of this study was to investigate the association between variants in the IFNL3 region and HPV infection in women with human immunodeficiency virus (HIV) infection. Methods: A total of 236 HIV patients, including 65 HPV-negative and 171 HPV DNA-positive women, were enrolled into this study. The IFNL3 rs12979860 polymorphism was genotyped using a predesigned TaqMan SNP genotyping assay. Results: Data showed no significant differences in genotypes or allele frequencies between the HPV DNA-positive and the HPV-negative women (p > 0.05). After dividing the HPV-positive women according to cytology results into patients with abnormal and normal lesions, the genotype and allele distribution of the SNP did not significantly differ between the 2 groups (p > 0.05). Conclusions: Our results showed that the IFNL3 rs12979860 polymorphism is not a major determinant of the susceptibility to HPV infection and their progression to abnormal cervical lesions in women living with HIV.

Interleukin-6-174G/C polymorphism is associated with a decreased risk of type 2 diabetes in patients with chronic hepatitis C virus.

BACKGROUNDChronic hepatitis C (CHC) is associated with type 2 diabetes mellitus. Although the pathogenesis remains to be elucidated, a growing evidence has suggested a role of pro-inflammatory immune response. Increased serum concentrations of Interleukin 6 (IL-6) have been associated with insulin resistance, type 2 diabetes mellitus as well as advanced forms of liver disease in chronic hepatitis C infection.AIMTo investigate the frequency of IL-6-174G/C (rs1800795) single nucleotide polymorphism (SNP) in CHC patients and in healthy subjects of the same ethnicity. Associations between type 2 diabetes mellitus (dependent variable) and demographic, clinical, nutritional, virological and, IL-6 genotyping data were also investigated in CHC patients.METHODSTwo hundred and forty-five patients with CHC and 179 healthy control subjects (blood donors) were prospectively included. Type 2 diabetes mellitus was diagnosed according to the criteria of the American Diabetes Association. Clinical, biochemical, histological and radiological methods were used for the diagnosis of the liver disease. IL-6 polymorphism was evaluated by Taqman SNP genotyping assay. The data were analysed by logistic regression models.RESULTSType 2 diabetes mellitus, blood hypertension and liver cirrhosis were observed in 20.8% (51/245), 40.0% (98/245) and 38.4% (94/245) of the patients, respectively. The frequency of the studied IL-6 SNP did not differ between the CHC patients and controls (P = 0.81) and all alleles were in Hardy-Weinberg equilibrium (P = 0.38). In the multivariate analysis, type 2 diabetes mellitus was inversely associated with GC and CC genotypes of IL-6-174 (OR = 0.42; 95%CI = 0.22-0.78; P = 0.006) and positively associated with blood hypertension (OR = 5.56; 95%CI = 2.79-11.09; P < 0.001).CONCLUSIONThis study was the first to show that GC and CC genotypes of IL-6-174 SNP are associated with a decreased risk of type 2 diabetes mellitus in patients chronically infected with hepatitis C virus. The identification of potential inflammatory mediators involved in the crosstalk between hepatitis C virus and the axis pancreas-liver remains important issues that deserve further investigations.

Impact of Genetic Variation in TLR4 3'UTR on NSCLC Genetic Susceptibility.

Toll-like receptors (TLRs) are expressed not only in immune cells but also in a variety of tumor cells. Single-nucleotide polymorphisms (SNPs) located in the TLRs' promoter or the 3′ untranslated region may affect gene expression by affecting the activity of the promoter or regulating the binding of mRNA to miRNA. This study aimed to investigate the association of the SNPs in TLR genes with the susceptibility to NSCLC. This case-control study involved 700 lung cancer patients and 700 healthy controls. All individuals were genotyped for all selected SNPs in TLR genes using polymerase chain reaction (PCR) test-based restriction fragment length polymorphism (PCR-RFLP) and TaqMan SNP genotyping assay. The association of genetic variations in TLRs with the susceptibility to NSCLC was evaluated by unconditional logistic regression with OR (95% CI). After evaluating transcriptional factor or miRNA binding capability by bioinformatics methods, six TLRs were identified for further analysis. We did not find that TLR3 rs5743303, TLR4 rs1927914, TLR4 rs11536891, TLR5 rs1640816, and TLR7 rs3853839 were associated with NSCLC risk (P > 0.05). Our data showed that TLR4 rs7869402 C > T polymorphism reduced the risk of NSCLC with OR (95% CI) of 0.63 (0.45–0.89). When stratified by gender and age, the individuals carrying at least one rs7869402T allele significantly decreased the NSCLC risk among males (OR = 0.58, 95% CI = 0.38–0.87) and among youngsters (OR = 0.43, 95% CI = 0.27–0.69). Smoking stratification analysis showed that the rs7869402T allele-containing genotype reduced the risk of NSCLC with OR (95% CI) of 0.50 (0.29–0.87) among smokers but not among nonsmokers (P > 0.05). When the individuals were classed by the pathological type, we found that the rs7869402T-containing genotype was associated with the risk of adenocarcinoma (OR = 0.62, 95% CI = 0.41–0.92) but not with that of squamous cell carcinoma (OR = 0.71, 95% CI = 0.44–1.13) and other types (OR = 0.23, 95% CI = 0.03–1.70). Compared with the TLR4 Ars1927914-Crs7869402-Trs11536891 haplotype, the Grs1927914-Trs7869402-Trs11536891 haplotype was associated with a decreased risk for developing NSCLC with OR (95% CI) of 0.57 (0.41–0.80). These results indicated that the TLR4 rs7869402 variation affects the genetic susceptibility to NSCLC.

Association of angiogenesis and inflammation-related gene functional polymorphisms with early-stage breast cancer prognosis.

Genetic variations in inflammation- and angiogenesis-related genes may alter the coded protein level and impact the pathogenesis of breast cancer (BC). The present study investigated the association of functional single nucleotide polymorphisms (SNPs) in the VEGFA, IL-1β, IL-1α and IL-6 genes with the early-stage BC phenotype and survival. Genomic DNA and clinical data were collected for 202 adult Eastern European (Lithuanian) women with primary I–II stage BC. Genotyping of the SNPs was performed using TaqMan SNP genotyping assays. Nine VEGFA, IL-1β, IL-1α and IL-6 polymorphisms were analysed. The VEGFA and IL-6 haplotypes were inferred using Phase software. Patients were prospectively followed-up for recurrence, occurrence of metastasis and mortality until April 30, 2019. All studied genotypes were in Hardy-Weinberg equilibrium and had the same distribution as the 1,000 Genomes project Phase 3 dataset for European population. Significant associations of the studied SNPs with clinicopathologic variables were observed between IL-1α rs1800587 C allele and larger primary tumour size; IL-6 rs1800797 A allele, rs1800797 GA genotype, rs1800795 C allele, IL-6 (rs1800797-re1800795) AC diplotype and hormonal receptor-positive disease; IL-6 rs1800797 A allele and HER2 negative status. In univariate Cox survival analysis, IL-1α rs1800587 CC and IL-6 rs1800797 GG genotype carriers exhibited worse disease-free survival (DFS), metastasis-free survival (MFS) and overall survival (OS). The IL-6 rs1800795 GG genotype was associated with worse OS. IL-6 (rs1800797, rs1800795) GG/GG diplotype carriers had shorter MFS and OS. Multivariate Cox survival analysis revealed that the IL-1α rs1800587 CC genotype was an independent negative prognostic factor for DFS, MFS and OS, and the IL6 GG/GG diplotype was an independent negative prognostic factor for MFS and OS. According to the present study, functional SNPs in the IL-1α and IL-6 genes may contribute to the identification of patients at higher risk of BC recurrence, development of metastases and worse OS among early-stage patients with BC.

Association of a Variant of CNR1 Gene Encoding Cannabinoid Receptor 1 With Gilles de la Tourette Syndrome.

BackgroundGilles de la Tourette syndrome (GTS) is a neuropsychiatric disorder of unknown etiology, although a major role of genetic factors has been established. Cannabis-based medicines may alleviate GTS-associated tics and variants of CNR1 gene encoding central cannabinoid receptor (CB1) are believed to be a risk factor for the development of some neurodevelopmental diseases. Our aim was to test the association of selected CNR1 gene variants with GTS.Material and MethodsThe cohort of GTS cases comprised 262 unrelated patients aged 3–53 years (mean age: 18.3 ± 9.1 years; 204 males (77.9%), 126 (48.1%) adults defined as ≥18 years). As a control group we enrolled 279 unrelated, ethnically and gender matched individuals with no diagnosed mental, neurological or general disorder, aged 13–54 years (mean age: 22.5 ± 3.0 years; 200 males, (74.1%). Both study and control groups were selected from Polish population, which is ethnically homogenous subgroup of Caucasian population. Four single nucleotide polymorphisms (SNPs) in CNR1 were selected: rs2023239, rs2180619, rs806379, and rs1049353 based on minor allele frequency in general population >15%. These variants were genotyped using a real-time quantitative polymerase chain reaction system (TaqMan SNP genotyping assay).ResultsWe found significant association of GTS clinical phenotype with rs2023239 variant. Minor allele C and CT+CC genotypes were found significantly more often in GTS patients compared to controls (17.4 vs 11.1%, p=0.003 and 32.8 vs 20.4%, p=0.001, respectively), and the difference remained significant after correction for multiple testing. C allele of rs2023239 polymorphism of the CNR1 gene was associated with the occurrence of tics. There were no statistically significant associations for rs806379, rs1049353 or rs2180619 variants.ConclusionOur findings suggest that C allele of rs2023239 polymorphism of the CNR1 gene is a risk factor of GTS in Polish population. The variant can be potentially associated with abnormal endocannabinoid transmission, which is suspected to be one of the causes of GTS.

Autophagy Genes (ATG16L1/IRGM) and IBD: Involvement of the ATG16L1 Gene in Algerian Patients with Crohn's Disease

Background: Chronic Inflammatory Bowel Diseases (IBD) including Crohn’s disease (CD) and ulcerative colitis (UC) are gastrointestinal disorders under the influence of a complex genetic basis. One hundred sixty-three predisposition loci were identified by genome-wide association (GWAS) studies, refocusing the pathogenesis of IBD on immunity genes. Autophagy is a fundamental mechanism in the maintenance of intestinal homeostasis. Failures of this mechanism appear to be a major risk factor in the setting up of chronic intestinal inflammation. Two single nucleotide polymorphisms (SNPs) within two genes, were selected namely (rs2241880 AaG) for ATG16L1 and (rs10065172 CaT) for IRGM.These two genes are both involved in the autophagy mechanism. We investigated these two SNP in an Algerian cohort for the first time since no previous association studies between IBD and the two studied genes were available for the Algerian population. Methods: A case-control study was performed on a cohort including 95 Algerian patients with Crohn's disease and ulcerative colitis versus 116 Controls. Genotyping of the cohort involved allelic discrimination by TaqMan SNP Genotyping Assay. Results: A statistically significant association of the rs2241880 AaGmutation of the ATG16L1 gene was demonstrated in IBD (p = 0.04) and, more particularly in Crohn's disease (p = 0.03).The presence of this mutation would increase the risk of Crohn's disease by a factor of 2 in its GG homozygous mutated form (OR = 2.11 95% CI (1.07-4.16)). No significant associations were found for the rs10065172 CaT mutation of the IRGM gene. Conclusion: Our data highlight the involvement of the ATG16L1 gene in the genesis and/or evolution of IBD cases, notably Crohn's disease, indicating the impact that deregulation of the autophagy mechanism could have on the Algerian population. Nevertheless, it would be interesting to expand the sampling and carry out the functional studies to elucidate the impact of the deregulation of the ATG16L1 gene in IBD.

Variants in the Upstream Region of the Insulin Receptor Substrate-1 Gene Is Associated with Major Depressive Disorder in the Han Chinese Population.

IntroductionMajor depressive disorder (MDD) is one of the most prevalent and disabling mental disorders, although its underlying genetic mechanism remains unknown. Insulin receptor substrate-1 (IRS-1) is one of the critical downstream molecules in the insulin resistance signaling pathway, linking depression and diabetes. Therefore, we hypothesized that IRS-1 would be a susceptible gene for MDD, and we aimed to examine the genetic association between IRS-1 and MDD.MethodsThis case-control study included 583 patients with MDD and 564 controls, and the genotypic and allelic distributions of the IRS-1 gene’s four single nucleotide polymorphisms (SNPs) were detected by TaqMan SNP genotyping technology. Of the 583 patients, 191 underwent a further detailed interview about symptom severity and family history of mental illness. The chi-square or t test was used to analyze the data, and analyses were performed using SPSS19.0 software.ResultsA haplotype in the 5ʹ-upstream region of IRS-1 consisting of rs13411764 and rs3820926 was a risk factor of MDD. Patients with a family history of mental illness were more likely to have a GG genotype in rs13411764 and a G-T haplotype containing rs13411714-rs3820926.DiscussionThe findings imply that the haplotype consisting of rs13411764 and rs3820926 in the upstream of IRS-1 is a risk factor for MDD. This haplotype could affect IRS-1 expression levels, and it is mostly inherited from parents. Thus, the presence of variants in the upstream region of IRS-1 is a risk factor of MDD, and this study could serve as a convincing reference for further studies.

Decreased H19, GAS5, and linc0597 Expression and Association Analysis of Related Gene Polymorphisms in Rheumatoid Arthritis

Long noncoding RNAs (lncRNAs) widely participate in human diseases by regulating gene transcription, modulating protein function, or acting as ceRNAs. Yet, their roles in rheumatoid arthritis (RA) remain obscure. In this study, the expression of three lncRNAs (H19, GAS5, and linc0597) in peripheral blood mononuclear cells (PBMCs) were detected in 77 RA patients and 78 controls using quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). The association of lncRNAs related gene polymorphisms with RA were evaluated in 828 RA patients and 780 controls using TaqMan single nucleotide polymorphism (SNP) genotyping assays. We observed that the expression levels of H19, GAS5 and linc0597 were down-regulated in PBMCs of RA patients, of which GAS5 level decreased in patients with hypocomplementemia, and negatively correlated with C-reactive protein (CRP) level in RA patients. Moreover, we highlighted two related potential functional SNPs, GAS5 rs6790 and linc0597 rs2680700 for associations with RA susceptibility. The precise roles of these lncRNAs in mechanism of RA remain to be further explored.

Investigation of the association between obesity and insulin-induced gene 1 polymorphism at 7q36.3 region in Uygur population in Xinjiang, China.

Background: Obesity is a common heritable trait and a major risk factors of chronic and metabolic diseases. Insulin-induced gene 1 (INSIG1) is known to play important roles in cholesterol and triacylglycerol (TAG) metabolism. In the present study, our primary objective was to explore whether the single nucleotide polymorphisms (SNPs) in INSIG1 gene were associated with obesity in Uygur subjects, in Xinjiang, China.Methods: We designed a case–control study including 516 obese patients and 463 age- and sex-matched control subjects. Three SNPs (rs2721, rs9767875 and rs9719268) were genotyped using TaqMan SNP genotyping assays.Results: For rs2721, the distribution of genotypes, dominant model (GT + TT vs GG), recessive model (TT vs GT + GG) showed significant differences between obese patients and the controls (P = 0.008, P = 0.005 and P = 0.035, respectively). For rs9719268, the distribution of genotypes showed significant differences between obese patients and the controls (P = 0.004). The dominant model (GT + TT vs GG) of rs2721 and rs9719268 GT genotype remain significantly associated with obesity after adjustment for confounders (OR = 1.393, 95% CI = 1.047–1.853, P = 0.023; OR = 1.631, 95% CI = 1.059–2.512, P = 0.026). The TG levels were significantly higher in rs2721 GT/TT genotypes than that in GG genotypes (P<0.05).Conclusions: Rs2721 and rs9719268 of INSIG1 gene are associated with obesity in Uygur subjects. Subjects with GT/TT genotype or T allele of rs2721 and GT genotype of rs9719268 were associated with an increased risk of obesity.

Calcium-sensing receptor gene (CASR) polymorphisms and CASR transcript level concerning dyslipidemia in hemodialysis patients: a cross-sectional study

BackgroundThere is scarce data on CASR associations with dyslipidemia. We investigated in hemodialysis (HD) patients whether CASR single nucleotide polymorphisms (SNPs) rs7652589 and rs1801725 have associations with dyslipidemia and show epistatic interactions with SNPs of the energy homeostasis-associated gene (ENHO), retinoid X receptor α gene (RXRA), and liver X receptor α gene (LXRA).MethodsThe study included 1208 HD subjects. For diagnosis of dyslipidemia, both K/DOQI criteria and atherogenic index ≥3.8 were used. CASR rs1801725 was genotyped by TaqMan SNP Genotyping Assay, other SNPs – by high-resolution melting curve analysis or polymerase chain reaction-restriction fragment length polymorphism, as appropriate. Relative transcript levels of CASR, ENHO, RXRA, and LXRA were measured in peripheral blood mononuclear cells. The occurrence of dyslipidemic phenotypes concerning tested polymorphisms was compared using models of inheritance. Haplotypes were estimated using the Haploview 4.2 software. Epistatic interactions between tested SNPs were analyzed using the logistic regression and epistasis option in the PLINK software.ResultsRs7652589 indicated a greater probability of atherogenic dyslipidemia in the dominant inheritance model (OR 1.4, 95%CI 1.0–2.0, P = 0.026), principally because of increased triglyceride (TG) levels. The rs1801725 variant allele was associated with a decreased probability of dyslipidemia characterized by non-HDL-cholesterol ≥130 mg/dL and TG ≥200 mg/dL (OR 0.6, 0.4–0.9, P = 0.012). There were no epistatic interactions between CASR and RXRA, LXRA, and ENHO regarding dyslipidemia. Both rs7652589 and rs1801725 SNPs were not in linkage disequilibrium (D’ = 0.091, r2 = 0.003 for the entire HD group) and their haplotypes did not correlate with dyslipidemia. Relative CASR transcript was lower at a borderline significance level in patients harboring the rs1801725 variant allele compared with homozygotes of the major allele (0.20, 0.06–7.80 vs. 0.43, 0.04–5.06, P = 0.058). CASR transcript correlated positively with RXRA transcript (adjusted P = 0.001), LXRA transcript (adjusted P = 0.0009), ENHO transcript (borderline significance, adjusted P = 0.055), dry body weight (adjusted P = 0.035), and renal replacement therapy duration (adjusted P = 0.013).ConclusionsCASR polymorphisms (rs7652589, rs1801725) are associated with dyslipidemia in HD patients. CASR correlates with RXRA, LXRA, and ENHO at the transcript level. Further investigations may elucidate whether other CASR SNPs contribute to associations shown in this study.

Genotypes of the Gene Encoding the Membrane Transporter SLC22A4 Are Associated with Molecular Relapse-Free Survival after Discontinuation of Imatinib Therapy in Patients with Chronic Myeloid Leukemia

Introduction: The single nucleotide polymorphism (SNP) rs460089 (G/C) located in the promotor of SLC22A4 (transporter hOCTN1) was identified as a prognostic factor for the outcome of chronic myeloid leukaemia patients treated with imatinib first line (Jaruskova et al. JECCR 2017). Patients with GC genotype had significantly higher probability of achievement of sustained major molecular response (MMR, BCR-ABL≤0.1% IS) as compared with patients with GG. We investigated differences in the outcome after imatinib cessation in EURO-SKI patients according to the genotypes of the SNP rs460089. Methods: DNA analysis was performed by TaqMan SNP genotyping assay using StepOnePlus RQ-PCR System (Thermofisher Scientific). In addition to the inclusion criteria defined for prognostic analysis in Saussele et al. (Lancet Oncology 2018), all patients with interferon pre-treatment were excluded. Data on sex, duration of IM treatment, of deep molecular response and age at time of imatinib discontinuation as well as molecular status at 6 months thereafter were available for 178 patients. Logistic regression was used to investigate factors affecting MMR maintenance at 6 months. Level of significance was 0.05. Results: Of 178 patients, 106 (60%) maintained MMR 6 months after imatinib stop. GC genotype was identified in 64 patients, GG in 96 and CC in 18. Most beneficial for MMR maintenance was genotype GC (72%, 95% confidence interval (CI): 60-82%), followed by CC (61%, CI: 38-80%) and GG (51%, CI: 41-61%). Overall, the SNP rs460089 was associated with MMR maintenance (p=0.0335) with a significantly higher odds ratio (OR) for maintenance for GC genotype vs. GG (2.451, CI: 1.247-4.819, p=0.0093) but not for CC vs. GG (1.507, CI: 0.539-4.216, p=0.4343). Only duration of TKI treatment was significant (OR: 1.157, CI: 1.014-1.319, p=0.0303) when added to genotypes in multiple regression. The OR of GC vs. GG was slightly modified to 2.311 (1.164-4.588, p=0.0166). Conclusions: Based on observed data we suppose that the GC genotype of the SNP rs460089 is associated with sufficient intracellular concentration of imatinib allowing more efficient targeting of CML cells during the treatment. This resulted in a higher proportion of patients who sustained MMR after imatinib stop as compared with patients with GG. Longer duration of imatinib treatment increased the probability of MMR maintenance after imatinib cessation also in patients with GG. The frequency of CC was low and outcome in between GC and GG. The SNP rs460089 may provide an independent prognostic factor for molecular response maintenance after imatinib cessation. Supported by MZCR 00023736. Disclosures Machova: Novartis: Consultancy; BMS: Consultancy, Research Funding; Incyte: Consultancy. Fabarius:Novartis: Research Funding. Brümmendorf:Pfizer: Consultancy, Research Funding; University Hospital of the RWTH Aachen: Employment; Merck: Consultancy; Ariad: Consultancy; Novartis: Consultancy, Research Funding; Janssen: Consultancy. Burchert:Novartis: Research Funding. Mustjoki:BMS: Honoraria, Research Funding; Novartis: Research Funding; Pfizer: Research Funding. Mayer:AOP Orphan Pharmaceuticals AG: Research Funding. Žáčková:Bristol Myers Squibb: Consultancy; Angelini: Consultancy; Incyte: Consultancy; Novartis: Consultancy. Panayiotidis:Bayer: Other: Support of clinical trial. Richter:Novartis: Consultancy; Pfizer: Consultancy, Research Funding. Hjorth-Hansen:BMS: Research Funding; Pfizer: Consultancy, Research Funding; Austrian Orphan Pharma: Consultancy, Research Funding. Saussele:Novartis: Honoraria, Research Funding; BMS: Honoraria, Research Funding; Pfizer: Honoraria; Incyte: Honoraria, Research Funding.

Association of single nucleotide polymorphisms at 20q12 with nonsyndromic cleft lip with or without cleft palate in a Southern Chinese Han cohort.

BackgroundNonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common congenital malformation in the world. Both environment and genetics are involved with the etiology of the disease. Genome‐wide association studies have identified two single nucleotide polymorphisms (SNPs) at chromosome 20q12 to be associated with NSCL/P. The current study aimed to explore the association of the two SNPs at 20q12 with NSCL/P and different subtypes in a Southern Chinese Han cohort.MethodsA total of 430 NSCL/P patients and 451 controls were recruited in the current study. Two SNPs including rs17820943 and rs6072081 at 20q12 were genotyped in the study cohort using Taqman SNP genotyping analysis. Chi‐Square test was used to compare allele and genotype frequencies of NSCL/P patients and control group.ResultsCase–control analysis showed that the allele and genotype of rs17820943 and rs6072081 were significantly associated with NSCL/P (p < .01). Comparison between subtypes of NSCL/P and controls showed that frequencies of the G allele and GG genotype of rs6072081 (p = 4.52 × 10−4 and p = .001 respectively), and those of the T allele and TT genotype of rs17820943 (p = 6.7 × 10−5 and p = 1.71 × 10–4 respectively) were decreased in cleft lip and palate (CLP). No significant association of the two SNPs with cleft lip only (CLO) and cleft palate only (CPO) was found (p > .05).ConclusionThese results showed that rs17820943 and rs6072081 at 20q12 were associated with NSCL/P, especially with the CLP subtype in a Southern Chinese Han cohort.

Study of rs12532, rs8670 Polymorphism of Msh Homeobox 1 (MSX1), rs61754301, rs4904155 Polymorphism of Paired Box Gene 9 (PAX9), and rs2240308 Polymorphism of Axis Inhibitor Protein 2 (AXIN2) Genes in Nonsyndromic Hypodontia.

The etiology of hypodontia is complex, in which both genetic and environmental factors can be related. The main objective of our study was to contribute to elucidating the genetic background of nonsyndromic hypodontia (NSH). In this order, we selected 97 NSH subjects (70 females and 27 males) from patients referred to orthodontic treatment, and we matched to each NSH subject a control by age and sex. DNA was obtained from epithelial cells from the oral mucosa. Genotyping of the PAX9 (rs4904155 and rs61754301), MSX1 (rs8670 and rs12532), and AXIN2 (rs2240308) SNPs was performed by using TaqMan SNP Genotyping Assays on a real-time PCR system. Single-nucleotide polymorphisms (SNPs) were studied for the whole NSH group and for frontal and lateral agenesis NSH subjects separately. Our results showed that the variant genotype (p=0.0008, OR = 2.9, 95% CI = 1.58–5.3) and variant T allele (p=0.0002, OR = 2.65, 95% CI = 1.6–4.39) of the MSX1 rs8670 SNP increased the risk of hypodontia in the studied population when the whole NSH group was compared with controls. The variant genotype of the MSX1 rs8670 SNP was the most frequent in frontal agenesis; meanwhile in the lateral agenesis NSH group, the AXIN2 rs2240308 SNP showed a higher frequency of the variant genotype, with a trend towards statistical significance. In conclusion, the results of the present study showed that the variant genotype and variant T allele of the MSX1 rs8670 SNP increased the risk of hypodontia in the studied population. The presence of the variant A allele of AXIN2 rs2240308 is associated with frontal agenesis but not with lateral agenesis.