TaqMan SNP Genotyping Assay Research Articles

Interactions between UCP2 SNPs and telomere length exist in the absence of diabetes or pre-diabetes.

Mitochondrial uncoupling protein 2 (UCP2) can affect oxidative stress levels. UCP2 polymorphisms are associated with leukocyte telomere length (LTL) in Type 2 Diabetes, which also induces considerable background oxidative stress. The effects of UCP2 polymorphisms on LTL in populations without diabetes have not been well described. Our aims are to evaluate the interaction between LTL and UCP2 polymorphisms in 950 subjects without diabetes. The monochrome multiplex quantitative PCR method was used to measure relative LTL. Taqman SNP genotyping assay was applied to genotypes for UCP2 rs659366 and rs660339. We found shorter LTL associated with increased age (P < 0.001) and triglyceride levels (P = 0.041). After adjustment for cardiovascular risk factors, rs659336 GG genotype carriers demonstrated a shorter LTL (1.257 ± 0.186), compared to GA carriers (1.288 ± 0.230, P = 0.022) and AA carriers (1.314 ± 0.253, P = 0.002). LTL was shorter in the CC rs660339 genotype (1.254 ± 0.187) compared to TT (1.297 ± 0.242, P = 0.007) and CT carriers (1.292 ± 0.229, P = 0.016). The T allele of rs660339 is associated with a longer LTL of approximately 0.04 compared to CC homozygotes. Thus, UCP2 rs659366 A allele and rs660339 T allele are both related to longer LTL in subjects without diabetes, independent of cardiovascular risk factors.

Genetic variants in RNA-induced silencing complex genes and prostate cancer.

The purpose of this study is to evaluate the potential association between genetic variants in genes encoding the components of RNA-induced silencing complex and prostate cancer (PCa) risk. Genetic variants chosen for this study are rs3742330 in DICER1, rs4961280 in AGO2, rs784567 in TARBP2, rs7813 in GEMIN4 and rs197414 in GEMIN3. The study involved 355 PCa patients, 360 patients with benign prostatic hyperplasia and 318 healthy controls. For individuals diagnosed with PCa, clinicopathological characteristics including serum prostate-specific antigen level at diagnosis, Gleason score (GS) and clinical stage were determined. Genotyping was performed using high-resolution melting analysis, PCR-RFLP, TaqMan SNP Genotyping Assay and real-time PCR-based genotyping assay using specific probes. Allelic and genotypic associations were evaluated by unconditional linear and logistic regression methods. The study provided no evidence of association between the analyzed genetic variants and PCa risk. Nevertheless, allele A of rs784567 was found to confer the reduced risk of higher serum PSA level at diagnosis (P=0.046; Difference=-66.64, 95% CI -131.93 to 1.35, for log-additive model). Furthermore, rs4961280, as well as rs3742330, were shown to be associated with GS. These variants, together with rs7813, were found to be associated with the lower clinical stage of PCa. Also, rs3742330 minor allele G was found to be associated with lower PCa aggressiveness (P=0.036; OR 0.14, 95% CI 0.023-1.22, for recessive model). According to our data, rs3742330, rs4961280 and rs7813 qualify for potentially protective genetic variants against PCa progression. These variants were not shown to be associated with PCa risk.

Abstract 460: Diagnostic and prognostic value of expression of CCND1 splice variant cyclin D1b in papillary thyroid carcinoma

Abstract Background: An active cyclin D1 isoform, cyclin D1b, arises as a result of a failure to splice the fourth intron of the CCND1 pre-mRNA transcript. The expression of cyclin D1b has been associated with tumorigenesis and tumor progression in many types of human cancer. However, no studies with cyclin D1b have yet been reported in the thyroid cancer. Methods: We investigated the CCND1 rs9344 (cDNA 870) polymorphism by TaqMan SNP genotyping assay and expression profiles of mRNA and protein of full-length cyclin D1 (cyclin D1a) and cyclin D1b by quantative real-time PCR and immunohistochemistry in 286 thyroid tumors including 16 nodular hyperplasias, 33 follicular adenomas (FA), 179 papillary thyroid carcinomas (PTC), 32 follicular thyroid carcinomas (FTC), 5 poorly differentiated carcinomas (PDC), 4 anaplastic thyroid carcinomas (ATC), and 17 medullary thyroid carcinomas (MTC). The relationships between cyclin D1 expression levels and clinicopathological features were analyzed. Results: The cyclinD1b mRNA expression level in all thyroid tumors was significantly higher in the AA and GA genotype groups compared with the GG genotype group (p&amp;lt;0.001 and p = 0.006, respectively). The mRNA expression levels of cyclin D1b was significantly higher in PTCs when compared to benign or other malignant tumors (p&amp;lt;0.001) while no significant difference in cyclin D1a mRNA expression was observed according to the genotypes or tumor types. PTCs showed similar expression levels of cyclin D1b mRNA regardless of histologic subtypes, even when compared with follicular variant. In immunohistochemistry analysis, cyclin D1b overexpression was observed in PTC, PDC, ATC, and MTC, but not in FA and FTC. Cytoplasmic overexpression of cyclin D1b was significantly associated with advanced tumor stage in all PTCs (p = 0.025). Nuclear overexpression of cyclin D1b was associated with an increased incidence of lymph node metastases (p = 0.014) in classic PTCs. Conclusion: The A allele of the rs9344 polymorphism predisposes for cyclin D1b production in thyroid cancer. Cyclin D1b overexpression has a diagnostic biomarker utility to differentiate PTC from benign follicular nodules and may be functionally involved in the progression of the disease. Citation Format: Chan Kwon Jung, Sora Jeon, Yourha Kim, Ahwon Lee, Gyeong Sin Park. Diagnostic and prognostic value of expression of CCND1 splice variant cyclin D1b in papillary thyroid carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 460.

A Biomarker Panel to Detect Synchronous Neoplasm in Non-neoplastic Surveillance Biopsies from Patients with Ulcerative Colitis.

Patients with ulcerative colitis (UC) are at risk for colorectal neoplasia. Challenges associated with surveillance colonoscopy with random biopsies for detection of dysplasia/cancer are well-documented. This study extended our findings in UC-associated colorectal cancer to include low-grade dysplasia (LGD) patients, testing whether our biomarker panel detects any UC-associated neoplasm. DNA from the LGD area and the corresponding nonadjacent, non-dysplastic section from 171 UC-LGD patients was extracted. TaqMan SNP Genotyping Assays for TNF-α, IL-1β, and IL23R were used to evaluate polymorphisms for each gene. Bisulfite-treated DNA was used for methylation testing of RUNX3, COX2, and MINT1. LGD data were combined with UC-cancer patient data for statistical testing. Logistic regression analyses determined associations between genetic/epigenetic/clinical variables and UC-associated neoplasia. Receiver operating characteristic analyses were performed to determine the final synchronous neoplasm detection panel. Comparison of nonadjacent, non-dysplastic DNA from UC-neoplasm patients versus UC-controls indicated that TNF-α, IL-1β, and methylation of RUNX3, MINT1, and COX2 were significantly different (P < 0.0001). In multivariable analysis, all remained significant with an area under the curve of 0.85, exceeding the clinical variable panel area under the curve. Combining clinical and experimental variables yielded a neoplasm biomarker panel with an area under the curve of 0.95 (sensitivity and specificity of 82% and 91%, respectively). Analysis of DNA from LGD with known progression compared with LGD without progression indicated a significant difference in RUNX3 methylation. A combined clinical, genetic, and epigenetic model for detecting synchronous neoplasm by testing of non-neoplastic colonic tissue had favorable operating characteristics and could complement current patient care.

Lack of association between genotype score and sprint/power performance in the Japanese population.

This study aimed to examine the association between a total genotype score (TGS) based on previously published genetic polymorphism candidates and differences in sprint/power performance. Case-control association study. We analysed 21 polymorphisms, which have previously been associated with sprint/power performance and related phenotypes, in 211 Japanese sprint/power track and field athletes (77 regional, 72 national, and 62 international athletes) and 649 Japanese controls using the TaqMan SNP genotyping assay. We calculated the TGS (maximum value of 100 for the theoretically optimal polygenic score) for the 21 polymorphisms. All groups exhibited similar TGSs (control: 55.9±7.2, regional: 55.1±7.1, national: 56.1±7.4, and international: 56.0±7.8, p=0.827 by one-way analysis of variance). Nine of the 21 polymorphisms had the same direction of effect (odds ratio >1.0) as in previous studies, while 12 had the opposite direction of effect (odds ratio <1.0). Three polymorphisms (rs699 in AGT, rs41274853 in CNTFR, and rs7832552 in TRHR), which had the same direction of effect as in previous studies, were associated with international sprint/power athlete status (p<0.05). However, after multiple testing corrections, the statistical significance of these polymorphisms was not retained. These results suggest that TGSs based on the 21 previously published sprint/power performance-associated polymorphisms did not influence the sprint/power athlete status of Japanese track and field athletes. However, our results maintain the possibility that three of these polymorphisms might be associated with sprint/power performance.

Impact of the IL-17F, IL-23 and IL-23R on susceptibility and phenotype of systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is a disease characterized by excessive proinflammatory cytokine production and damage to multiple organ systems. To investigate the potential association between cytokine gene polymorphisms and SLE, we performed a case-control study based on Polish population. SLE patients and controls, were examined for IL-23A rs11171806 G/A and IL-23R (rs1884444 G/T, rs10489629 G/A) by TaqMan SNP genotyping assay, for IL-17F rs763780 A/G and rs2397084A/G using the PCR– RFLP method. An increased frequency of AG genotype as well as G allele of the IL-17F rs763780 was found in patients with SLE, as compared with healthy subjects (OR = 3.947; p = 0.001 and OR = 3.538; p = 0.002, respectively). Frequencies of the rs1884444 TT genotype (OR = 138.1) and the rs1884444 T allele (OR = 2.176) were also higher in SLE patients (both p < 0.0001). Overall, weak LD was observed between the IL-17F rs763780 A/G and rs2397084 A/G polymorphisms (D'-0.003, r2 – 0.000). From four possible haplotypes, frequencies of AG showed differences between both examined groups (p < 0.0001). We also observed a weak LD between the IL-23R rs10489629G/A and rs1884444 G/T (D'-0.199, r2 –0.026). The genotype–phenotype analysis showed significant association between the IL-17F rs2397084 and mean value of the hemoglobin (p = 0.01), the IL-17F rs763780 and age (p = 0.008) and lupus anticoagulant (p = 0.09), the IL-23 rs11171806 and urea (p = 0.08) and C3 complement (p = 0.03), and the IL-23R rs1884444 G/T and activated partial thromboplastin time (p = 0.06). Present findings indicated that IL-17F rs763780 A/G and IL-23R rs1884444 G/T polymorphisms may be involved in susceptibility to SLE in the Polish population.

Genetic Variants in IL-12B and IL-27 in the Polish Patients with Systemic Lupus Erythematosus.

To investigate the potential association between IL-12B and IL-27 gene polymorphisms and systemic lupus erythematosus (SLE), we performed a case-control study based on the Polish population. Patients with SLE and healthy individuals were examined for -6415 CTCTAA/GC (rs17860508) and +1188A/C (rs3212227) in IL-12B and -924A/G (rs153109) and 4730T/C (rs181206) in IL-27 gene polymorphisms using the high-resolution melting method, PCR-RFLP method and TaqMan SNP genotyping assay, respectively. An increased frequency of GC/GC genotype as well as GC allele of the IL-12B rs17860508 was found in patients with SLE, as compared with healthy subjects (P<0.001). We did not find differences in genotype and allele frequencies of the IL-12B rs3212227 and IL-27 rs153109 and rs181206 variants between patients with SLE and controls. IL-27 haplotype rs181206C/rs153109G indicated higher risk for SLE (P=0.002), whereas haplotype rs181206T/rs153109G indicated reduced risk for SLE (P=0.005). The IL-12B rs3212227 A/C polymorphism was associated with the mean value of the platelets (PLT), urea and complement C3 level. Furthermore, IL-12B rs17860508 genetic variant showed correlation with PLT, prothrombin time, international normalized ratio and alkaline phosphatase. Our results revealed that IL-12B rs17860508 and IL-27 haplotype CG are genetic risk factors for SLE and that both IL-12B rs17860508 and rs3212227 predict disease phenotype.

Clinical and genetic predictors of dipeptidyl peptidase-4 inhibitor treatment response in Type 2 diabetes mellitus.

To determine the clinical and genetic predictors of the dipeptidyl peptidase-4 (DPP-4) inhibitor treatment response in Type 2 diabetes mellitus (T2DM) patients. DPP4, WFS1 and KCNJ11 gene polymorphisms were genotyped in a cohort study of 662 T2DM patients treated with DPP-4 inhibitors sitagliptin, vildagliptin or linagliptin. Genotyping was performed by Applied Biosystems TaqMan SNP genotyping assay. Patients with triglyceride levels less than 1.7 mmol/l (odds ratio [OR]: 2.2.; 95% CI: 1.031-4.723), diastolic blood pressure (DBP) less than 90 mmHg (OR: 1.7; 95% CI: 1.009-2.892) and KCNJ11 rs2285676 (genotype CC) (OR: 2.0; 95% CI: 1.025-3.767) were more likely to response to DPP-4 inhibitor treatment compared with other patients, as measured by HbA1c levels. Triglycerides, DBP and KCNJ11 rs2285676 are predictors of the DPP-4 inhibitor treatment response in T2DM patients.

Association of 3′ nearby gene BTLA polymorphisms with the risk of renal cell carcinoma in the Polish population

ObjectiveT cells play an important role in antitumor immunity, and molecules regulating T-cell activity could influence cancer susceptibility. The distinct role of coinhibitory receptors in immunosurveillance has been considered. B- and T-lymphocyte attenuator (BTLA) is one of these receptors, which negatively regulate immune responses. The aim of this study was to investigate the association between BTLA gene polymorphisms and susceptibility to renal cell carcinoma (RCC) in the Polish population. MethodsAltogether 282 patients with RCC and 480 healthy subjects were genotyped for the following polymorphisms: rs2705511, rs1982809, rs9288952, rs16859633, rs9288953, rs2705535, and rs1844089 using the TaqManSNP Genotyping Assays. ResultsHere, we found that the presence of rs1982809G allele (genotype GG+AG) is associated with increased risk of RCC (odds ratio = 1.38; 95% CI: 1.03–1.86; P = 0.03). In patients with clear-cell RCC (ccRCC) with high-grade (3 and 4) tumors, the frequency of rs1982809[GG] genotype was significantly higher as compared to those with low-grade (1 and 2) tumors and to the controls (0.14 vs. 0.06, P = 0.05 and 0.14 vs. 0.06, P = 0.04, respectively). Moreover, we have noticed the trend for overrepresentation of carriers of rs2705511C allele in patients with RCC as compared with the controls (0.51 vs. 0.44, P = 0.08)Haplotype rs2705511C/rs1982809G/rs9288952A/rs9288953T/rs2705535C/rs1844089G (CGATCG) increased the risk of RCC of 46% (odds ratio = 1.46; 95% CI: 1.08–1.96; Pcorrected = 0.05). ConclusionOur results indicate that polymorphisms rs1982809 situated in 3′ UTR nearby region of BTLA gene might be considered as low-penetrating risk factor for RCC, but results have to be confirmed in further studies.

Association of TLR and TREM-1 gene polymorphisms with atherosclerosis severity in a Russian population

Local vascular immune response is primarily initiated via Toll-like receptors (TLRs) and triggering receptor expressed on myeloid cells-1 (TREM-1). We previously showed that certain TLR and TREM-1 gene polymorphisms are associated with coronary artery disease (CAD). Therefore, we hypothesized that these gene polymorphisms are associated with atherosclerosis severity. This study included 292 consecutive patients with CAD who were admitted to the Research Institute for Complex Issues of Cardiovascular Diseases (Kemerovo, Russian Federation) during 2011–2012. Sample genotyping was performed in 96-well format using the TaqMan SNP genotyping assay. We found that C/C genotype of the rs3804099 polymorphism within TLR2 gene and T/T genotype of the rs4711668 polymorphism within TREM-1 gene were significantly associated with severe coronary atherosclerosis while C allele of the rs5743551 polymorphism within TLR1 gene, A/G genotype of the rs4986790 polymorphism and C/T genotype of the rs4986791 polymorphism within TLR4 gene, and C allele of the rs3775073 polymorphism within TLR6 gene were significantly associated with severe noncoronary atherosclerosis. However, A/A genotype of the rs5743810 polymorphism within TLR6 gene was significantly associated with mild noncoronary atherosclerosis. We conclude that certain TLR and TREM-1 gene polymorphisms are significantly associated with atherosclerosis severity in a Russian population.

Association of the Neuropeptide Y LEU7PRO rs16139 and NEUREXIN 3 rs760288 Polymorphisms with Alcohol Dependence

Association of the Neuropeptide Y LEU7PRO rs16139 and NEUREXIN 3 rs760288 polymorphisms with alcohol dependence Objective: Alcoholism is associated with genetic variants of genes related to alcohol metabolizing enzymes, dopaminergic, gamma-aminobutyric acidergic, glutamatergic, opioid, cholinergic, and serotonergic systems. Neurpeptide Y system and Neurexins were shown to be associated with alcohol dependence. Recent studies identified new genetic polymorphisms related to endogenous cannabinoid system, neuropetide Y and neurexin. In the present study, we aimed to investigate the association of Neurpeptide Y LEU7PRO rs16139 and neurexin 3 gene rs760288 polymorphisms with alcohol dependence in patients with alcohol dependence and healthy control subjects. Methods: 123 patients who were diagnosed with alcohol dependence according to the DSM-IV criteria and 159 healthy volunteers were included in the study. Blood samples were used to investigate polymorphisms. The genotyping of the neurexin 3 gene rs760288 and the neuropetide Y gene Leu7Pro rs16139 polymorphisms was performed using TaqMan SNP Genotyping Assays Real-Time PCR System. Results: Of the 2 genetic polymorphisms investigated in the present study, we detected association between and neurexin 3 gene rs760288 polymorphisms with alcohol dependence. Conclusions: Neurexin gene polymorphisms might be an important factor in development of alcohol addiction.

5'UTR +24T>C CR2 is not associated with nasopharyngeal carcinoma development in the North Region of Portugal.

We have analysed the association of the +24T>C polymorphism (rs3813946) in CR2, the cellular receptor for Epstein-Barr virus (EBV), in the susceptibility for the development of nasopharyngeal carcinoma (NPC). A retrospective case-control study was developed with peripheral blood samples from 111 individuals with NPC and 608 healthy individuals (controls) from the North region of Portugal. The genotyping analysis was performed by allelic discrimination real-time PCR using a TaqMan(®) SNP Genotyping Assay. The genotype distribution was 62.2% TT, 34.2% TC and 3.6% CC for NPC patients; and 65.0%, 30.6% and 4.4%, respectively, for controls. Our study showed no statistical association between the genotype distribution in controls and all types of NPC (P=0.717); nevertheless, the analysis showed statistically significant differences (P=0.038) regarding cases with well- or moderately differentiated types of NPC suggesting that +24CC/CT genotypes are associated with increased risk (OR=4.16; 95% CI 1.28-15.7; P=0.016). This is the first study in Western populations to characterize the association of the CR2 +24T>C polymorphism in NPC development, and our results suggest that more studies are required to clarify the impact on NPC susceptibility in different populations.

Allelic Variants of KLK2 Gene Predict Presence of Prostate Cancer at Biopsy

Objective: Several single nucleotide polymorphisms associated with prostate cancer risk have been reported in recent years. We evaluated polymorphisms in the human glandular kallikrein 2 (KLK2) genes because the protein product of this gene is known to be increased in prostate cancer. Materials and methods: Blood samples were collected from sixty patients who underwent prostate biopsy sectioning, and from their genomic DNA the SNPs in KLK2 gene were investigated by direct DNA sequencing. Another 138 archived prostate tissue sections were also evaluated using the TaqMan SNP genotyping assay. Results: Eighteen known SNPs were identified in the KLK2 gene. The SNPs were located in introns, coding exons and untranslated regions of the gene. Further analysis showed that two of the SNPs were associated with prostate disease. The T/T allele of rs198977 was significantly predictive of the presence of prostate cancer at biopsy and was also associated with high tumour grade. The A/A allele of rs2664155 was also significantly associated with the presence of benign hyperplasia at biopsy. Conclusion: Our results support previous reports of association of the rs198977 SNP with prostate cancer risk and also indicated a link with the disease phenotype. However, the second SNP (rs2664155) was more associated with benign hyperplasia than prostate cancer risk. The method of TaqMan SNP genotyping could be clinically useful in genetic screening and risk stratification of patients for prostate diseases.

Evaluation of polymorphisms in microRNA biosynthesis genes and risk of laryngeal cancer in the Polish population.

MicroRNAs are the largest group of short regulatory RNAs. They regulate genes participating in many physiological and pathological processes. The role of micro RNAs in cancer development is also considerable. Therefore, the aim of this study was to evaluate the relationship between DROSHA (rs6877842) and DGCR8 (rs417309, rs1640299) gene polymorphisms with risk of occurrence of laryngeal cancer. The study included 100 patients and 100 healthy subjects. Genomic DNA was extracted from formalin-fixed, paraffin-embedded tissues. Analysis of the gene polymorphisms was performed using TaqMan SNP Genotyping Assay. The rs417309 AA genotype was found to be correlated with increased risk of larynx cancer. The rs1640299 TG and rs6877842 CG heterozygotes were significantly inversely associated with the presence of larynx cancer. Additionally, rs417309 AA genotype increased the risk of larynx cancer in the T1 stage, and the rs1640299 TG heterozygote occurred more frequently in the control group than those in the T3 and T4 stage. The rs417309 and rs1640299 polymorphisms of the DGCR8 gene as well as rs6877842 of the DROSHA gene might be associated with a risk of laryngeal cancer occurrence in the Polish population.

Association of the C2-CFB locus with non-infectious uveitis, specifically predisposed to Vogt-Koyanagi-Harada disease.

Complement component 2 (C2) and factor B (CFB) are regulators of complement system and involved in the alternative pathway, which have been identified to be associated with multiple immune-related diseases. This study aimed to investigate the association of these genes with non-infectious intermediate and posterior uveitis. A total of 260 Chinese non-infectious uveitis patients were recruited, including 97 patients with Vogt-Koyanagi-Harada disease (VKH), 70 patients with intermediate uveitis (IU) and 93 patients with Behçet's disease (BD). Two hundred and ninety-three normal control subjects were also recruited. Five SNPs across the C2/CFB region were selected and genotyped using TaqMan SNP Genotyping Assays. Association analysis was adjusted for gender and stratified by different subtypes. The CFB SNP rs1048709 was significantly associated with non-infectious uveitis [P corr = 0.01, OR 1.49 (allele model) and P corr = 0.04, OR 1.58 (dominant model), respectively], and similar association was also detected between rs1048709 and female uveitis patients (P corr = 0.01, OR 1.70 and P corr = 0.049, OR 184, respectively). Moreover, subgroup analyses showed that CFB-rs1048709 was specifically associated with VKH, where significantly higher frequencies of A allele and AA homozygosity were observed in VKH patients compared with controls (P corr = 0.025 and P corr = 0.035, respectively), whereas none of these five SNPs was associated with IU or BD. In addition, a haplotype block across CFB (GTG) was significantly predisposed to uveitis with protective effect (OR 0.66, P corr = 0.048). Our results revealed a significant association of CFB with non-infectious uveitis, particularly predisposed to VKH disease. Genetic differences for uveitis could be gender-specific.

The association of cholesterol absorption gene Numb polymorphism with Coronary Artery Disease among Han Chinese and Uighur Chinese in Xinjiang, China.

BackgroundHypercholesterolemia is a major risk factor for coronary artery disease (CAD). As Numb is an important regulating factor for intestinal cholesterol absorption and plasma cholesterol level, the aim of the present study is to assess the association between human Numb gene polymorphism and CAD among Han and Uighur Chinese.MethodsWe have conducted two independent case–control studies in Han Chinese (384 CAD patients and 433 controls) and Uighur Chinese (506 CAD patients and 351 controls) subjects. All subjects were genotyped for four kinds of SNPs (rs12435797, rs2108552, rs1019075 and rs17781919) and SNP is used as a genetic marker for human Numb gene. Genotyping was undertaken using TaqMan SNP genotyping assay, and the subjects’ ethnicity and gender were considered in the analysis.ResultsWe found that rs2108552 was associated with CAD in the dominant model (CC vs CG + GG) for the total Han Chinese population (n = 200) and Han Chinese males (n = 115) (P = 0.004 and P = 0.001, respectively). The difference remained statistically significant after multivariate adjustment (total: OR = 1.687, P = 0.004; male: OR = 1.498, P = 0.006). Further, for the total (n = 817) and male (n = 490) Han Chinese, the frequency of the haplotype (T-C-T-C) was significantly higher in the CAD patients than in the controls (P = 0.004 and P = 0.002), and the frequency of the haplotype (G-G-T-C) was significantly lower in the CAD patients than in the control subjects (P = 0.013, P = 0.007). In addition, for the total (n = 857) and male (n = 582) Uighur Chinese, we observed that rs12435797 was associated with CAD in an additive and recessive model (P = 0.021 and P = 0.009; P = 0.048 and P = 0.034). However, the difference did not remain statistically significant after multivariate adjustment. The overall distribution of rs2108552, rs1019075 and rs17781919 genotypes, alleles and the frequency of the haplotype established by four SNPs showed no significant difference between CAD patients and control subjects in the total, male and female Uighur Chinese.ConclusionsThe results of this study indicate that CC genotype of rs2108552 and T-C-T-C haplotypes in Numb gene is a possible risk genetic marker and G allele and G-G-T-C haplotypes is a possible protective genetic marker for CAD in male Han Chinese.

Gender-Specific Effect of CYP2C8*3 on the Risk of Essential Hypertension in Bulgarian Patients.

We conducted a case-control study to determine the contribution of polymorphisms in CYP2C8 (CYP2C8*3) and CYP2J2 (CYP2J2*7) to increased risk of coronary artery disease and essential hypertension in Bulgarians. The current analysis included 192 unrelated hypertensive patients, 261 patients with angiographically documented CAD (153 with myocardial infarction and 108 without myocardial infarction), and 496 population controls. The CYP2C8*3 and CYP2J2*7 polymorphisms were genotyped by TaqMan SNP Genotyping Assay. PLINK version 1.07 was used for the statistical analysis. No overall association was observed for the studied polymorphisms with coronary artery disease and essential hypertension. The frequency of -50T mutant allele of CYP2J2*7 was significantly higher in male with coronary artery disease without history of myocardial infarction (OR 2.16 95% CI 1.04-4.48 p=0.035) compared to population control group, but this association did not survive after Bonferroni correction (p adj=0.07). A significant association of CYP2C8*3 allele with increased risk of essential hypertension has found in men (OR 2.12 95% CI 1.18-3.81 p=0.015) and this relationship remained significant after adjustment for multiple comparisons (p adj=0.03). This is the first study showing significant gene-sex interaction for CYP2C8*3 with twofold increase in the relative risk of essential hypertension and a similar tendency for CYP2J2*7 associated with coronary artery disease without myocardial infarction in Bulgarian males. The association is not seen in females and in the whole group of patients. This result could be partly explained by the effect of estrogens on the vascular tone of coronary arteries and CYP2C8 gene expression.

HLA‐A*02:06 and PTGER3 polymorphism exerts additive effects in cold medicine‐related Stevens‐Johnson syndrome with severe ocular complications in Japanese and Korean populations

PurposeWe reported that PTGER3 SNPs were associated with Stevens‐Johnson syndrome (SJS)/toxic epidermal necrolysis (TEN) with severe ocular complications (SOC). We also reported that about 80% of our SJS/TEN patients had taken cold medicines within several days before disease onset and designated them cold medicine related‐SJS/TEN (CM‐SJS/TEN) patients, and that HLA‐A*02:06 was significantly associated with CM‐SJS/TEN in Japanese and Korean populations. Moreover, we documented that HLA‐A*02:06 with TLR3 polymorphisms exerted more than additive effects in SJS/TEN with SOC. In the current study we focused on CM‐SJS/TEN with SOC and analyzed an interactive effect between PTGER3 SNPs and HLA‐A*02:06 in Japanese and Korean populations.MethodsSamples from 132 Japanese patients with CM‐SJS/TEN with SOC were collected and 221 healthy Japanese volunteers were also recruited as controls. Samples from 30 Korean patients with CM‐SJS/TEN with SOC were collected and 120 healthy Korean volunteers were also recruited as controls. Genotyping of PTGER3 gene SNPs was performed using the TaqMan SNP genotyping assay or the DigiTag2 assay. HLA‐A genotyping was performed using using commercial bead‐based typing kits, WAK Flow.ResultsIn Japanese population, we found an interaction with additive effects between HLA‐A*02:06 and the high‐risk genotypes PTGER3 rs1327464 GA or AA (OR = 10.8, p = 2.56 × 10−7). Moreover, we also found an additive effect between HLA‐A*02:06 and the high‐risk genotypes PTGER3 rs1327464 GA or AA (OR = 14.2, p = 5.58 × 10−6).ConclusionsThese finding might show that the combination of these two polymorphisms could give improvements for a genetic testing as compared to using only one susceptibility gene.

Polymorphisms in the interleukin 4, interleukin 4 receptor and interleukin 13 genes and allergic phenotype: A case control study

PurposeInterleukin 4 (IL4), interleukin 4 receptor (IL4R) and interleukin 13 (IL13) play a key role in the pathogenesis of allergy and asthma development. IL4 and IL13 strongly influence bronchial hyperreactivity in response to allergen, airway remodeling, airway inflammation and airway smooth muscle proliferation. Both IL4 and IL13 exert biologic effect via interleukin 4 receptor. The aim of this study was to evaluate the impact of the polymorphisms within interleukin 4 (rs2243250, rs2227284), interleukin 4 receptor α chain (rs1805010, rs1805011) and interleukin 13 (rs20541) genes on the incidence of allergic phenotype in Polish pediatric population. Material/methodsWe compared 177 asthmatic pediatric patients with 194 healthy children. Five polymorphisms within IL4, IL13 and IL4Rα genes were analyzed. Genotypes of four polymorphisms (rs2243250, rs2227284, rs1805011, rs20541) were assigned by TaqMan SNP Genotyping Assays (Applied Biosystems), whereas rs18050100 polymorphism was established using PCR-RFLP method. ResultsWe observed an association of rs1805011 polymorphism of IL4Rα gene with allergy (p=0.021), mild asthma (p=0.00005) and atopic dermatitis (p=0.0056). Significant correlation was found between rs20541 in IL-13 gene and the positive skin prick test results (p=0.029), along with rs2243250 polymorphism with clinical atopy (p=0.033) and rs2227284 with total IgE levels (p=0.00047). No associations were found for rs1805010. ConclusionsOur results indicate that rs1805011 polymorphism of IL4Rα gene seems to influence allergy risk, especially mild asthma and atopic dermatitis predisposition in Polish children. Subgroup analysis of three other SNPs revealed possible influence on allergy development.

Abstract 2084: Genetic variation at a cis-acting C/EBPG binding site is associated with allele-specific ERCC5 transcript expression

Abstract Background: CCAAT/enhancer-binding protein gamma (C/EBPG) transcription factor expression is correlated with that of ERCC5 and other key DNA repair genes in normal bronchial epithelial cells (NBEC) suggesting a regulatory role. In prior studies, ERCC5 transcript expression was increased in a human lung carcinoma cell line H23 following CEBPG overexpression and in NBEC from 81 subjects, A allele at putative ERCC5 cis-regulatory SNP (rSNP) rs751402 and T allele at rSNP rs2296147 were associated with higher expression of ERCC5 marker SNP rs1047768 T allele transcript. rs751402 is located in open chromatin region identified by FAIRE-seq in NBEC and variation at rs751402 is predicted to alter binding of C/EBP. These studies support the hypothesis that allelic differential affinity to C/EBPG at rs751402 contributes to hereditary inter-individual variation in regulation of ERCC5 either directly or through interaction with complexes bound at rs2296147. The purpose of this study was to further investigate the role of C/EBPG in ERCC5 cis-regulation in an independent cohort of subjects and lung cancer cell lines. Methods: We knocked-down C/EBPG transcript level by C/EBPG siRNA transfection in human non-small cell lung carcinoma cell line H1703. Total and allele-specific expression (ASE) at rs1047768 was measured through multiplex competitive PCR-based amplicon sequencing library preparation followed by Illumina HiSeq next generation sequencing (NGS). This NGS controls for inter-target variation in PCR amplification during library preparation by measuring each transcript native template relative to a known number of synthetic competitive template internal standard copies. The genotype at rs751402 and rs2296147 in NBEC from 78 subjects and 14 human lung carcinoma cell lines was determined by TaqMan SNP genotyping assays. Direct assessment of the syntenic relationship of alleles in gDNA from poly-heterozygous individuals was assessed by allele-specific PCR followed by sequencing. Results: CEBPG transcript expression was knocked-down by 93% in H1703 cells and this was associated with 4-fold reduction in the ERCC5 transcript level at rs1047768. ERCC5 displayed significant inter-individual variation in allele specific expression (ASE) in NBEC from 85 subjects. Thirty nine out of 92 subjects including 3 cell lines were heterozygous at rs751402 and rs2296147 rSNPs and rs1047768 marker SNP and will be assessed for haplotypes comprising those sites. Conclusions: Results are consistent with CEBPG regulation of ERCC5 in the cell line H1703. The results obtained will enable us to test the hypothesis that haplotypes comprising particular alleles syntenic between rs1047768 and rs751402 are associated with higher allele-specific ERCC5 transcript abundance. Cell lines heterozygous at three sites will be subjected to CEBPG up and/or down regulation to assess effect on allele-specific ERCC5 expression at rs1047768. Citation Format: Xiaolu Zhang, Jiyoun Yeo, Erin Crawford, James C. Willey. Genetic variation at a cis-acting C/EBPG binding site is associated with allele-specific ERCC5 transcript expression. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2084. doi:10.1158/1538-7445.AM2015-2084