Homozygous Minor Allele Research Articles

The FTO genotype as a useful predictor of body weight maintenance: Initial data from a 5-year follow-up study

ObjectiveWe examined associations between the fat-mass and obesity-associated (FTO) gene (rs9939609) and any weight change over a 5-year period following a 14-week lifestyle intervention among middle-aged Japanese women. Materials/MethodsOne hundred twenty-eight Japanese women (BMI >25kg/m2) participated in a 14-week weight loss intervention between 2004 and 2006. Of the participants, 62 consented to the 5-year follow-up measurement session. Of these women, 47 women who achieved a weight loss of at least 10% from their baseline values during the 14-week intervention were included in the analysis. Body weight, body fat, abdominal fat assessed by CT scans, and metabolic risk factors (i.e., blood pressure, lipids, and glucose) were measured at baseline, post-intervention, and at the 5-year follow-up. ResultsDuring the 5-year non-intervention period, increases in body weight, fat mass, total abdominal fat, and subcutaneous abdominal fat were significantly greater in subjects with the homozygous minor allele (AA genotype, n=4; 8.5%) than in those with the homozygous major allele (TT genotype, n=31; 66.0%) or heterozygous allele (TA genotype, n=12; 25.5%). In multiple regression analyses, the variation in rs9939609 was a significant and independent predictor (P<0.001) for regaining weight during the 5-year follow-up. ConclusionsOur data suggest that Japanese women with the risk allele (AA) of rs9939609 may have more difficulty preventing fat gain from reoccurring after weight loss intervention than women with the other genotypes.

Cholesteryl Ester Transfer Protein rs1532624 Gene Polymorphism is Associated with Reduced Response to Statin Therapy

The aim of the study was to determine the allele and genotype frequencies of rs1532624 SNP of the cholesteryl ester transfer protein gene (CETP) among 116 Jordanian patients taking statins, and to study the impact of the genotypes on response to statin therapy. The study was approved by the Institutional review Board (IRB) of The Jordan University Hospital. An informed consent was signed by every participant. A single fragment encoding a 307 bp sequence of the CETP gene, including the SNP of interest at position 14645 in intron 7, was amplified using a polymerase chain reaction (PCR) technique directly from whole blood. The PCR product was then subjected to DNA sequencing. The frequencies of the genotypes of the homozygous minor allele (AA), the homozygous major allele (CC), and the heterozygous allele (CA) were 0.121, 0.405, and 0.474, respectively. The minor allele (A) frequency was 0.358. The frequencies did not deviate from Hardy-Weinberg equilibrium. The lipid profile before the start of statin therapy was similar for all genotypes regarding total cholesterol (TC), low density lipoprotein cholesterol (LDL-C), and triglycerides, while high density lipoprotein cholesterol (HDL-C) was significantly higher in the AA genotype. The AA genotype was also associated with significantly lower CETP activity than the other genotypes. The response to statin therapy was less in the AA genotype than the other genotypes for TC and LDL-C. In conclusion, the homozygous minor allele subjects have higher base line HDL-C, and lower CETP activity than the other genotypes (CA and CC). They also have less reduction in TC and LDL-C after statin therapy.

The CETP polymorphism rs5882 is associated with triglyceride lowering in response to plant sterol consumption (1038.3)

Plant sterol (PS) consumption may lower triglyceride (TG) concentrations. However, human clinical trial evidence is inconsistent, with only some trials showing TG reductions. This heterogeneity in responsiveness of TG concentrations to PS consumption could have a genetic basis. Our objective was to investigate whether SNPs in genes related to TG metabolism could be associated with changes in TG concentrations following PS consumption. 63 mildly hypercholesterolemic adults, pre‐assessed for cholesterol synthesis using lathosterol to cholesterol ratio (L/C) (High, n=24, L/C = 2.03 ± 0.39 umol/mmol; Low, n=39, L/C =0.99±0.28 umol/mmol) consumed either 2g/d (free sterol) of PS ester or placebo in margarine for 28 d in a dual‐center, single‐blind, randomized, crossover design. Serum TG concentrations were measured at the end of each phase. Candidate SNPs and ApoE variant were accessed by TaqMan assay. PS consumption did not lower TG overall (p=0.0506), but had an interaction with rs5882 in CETP (p=0.0080). Homozygous minor allele (G/G=‐0.47mmol/L, p=0.0002, n=10) carriers of rs5882 had reductions in TG concentrations with PS consumption, while A/A (+0.01mmol/L, p =0.6634, n=25) and A/G (‐0.04mmol/L, p= 0.3399, n=28) carriers did not. rs5882 in CETP associated with TG lowering due to PS consumption, and could serve as a genetic marker to identify individuals who derive TG lowering benefits from PS consumption.Grant Funding Source: CIHR

Association of rheumatoid arthritis susceptibility gene with lipid profiles in patients with rheumatoid arthritis

RA patients have an increased risk of cardiovascular (CV) disease, although the mechanisms are unclear. As RA and CV disease may be associated through lipid profiles, we examined whether single nucleotide polymorphisms (SNPs) associated with RA susceptibility were associated with low-density lipoprotein (LDL), high-density lipoprotein (HDL) and triglyceride (TG) levels in RA subjects. Patients (n = 763) enrolled in the Veterans Affairs RA registry who were not on hydroxymethylglutaryl-CoA reductase inhibitor were genotyped for human leukocyte antigen shared epitope (HLA-DRB1-SE) and SNPs in the following genes: CTLA-4 (cytotoxic T-lymphocyte antigen 4), IL-10, PTPN22 (protein tyrosine phosphatase, non-receptor type 22), REL (c-Rel), STAT4 (signal transducer and activator of transcription protein), TNF- and TRAF1 (TNF receptor-associated factor 1). Other covariates included patient characteristics (age, gender, race, smoking status, education, BMI, modified CharlsonDeyo comorbidity index), CV characteristics (hypertension, diabetes, alcohol abuse), pharmacologic exposures (MTX, anti-TNF, glucocorticoids) and RA severity/activity markers (RA disease duration, mean DAS, CRP, RF positivity, anti-CCP positivity). Multivariate linear regression was performed to determine the factors associated with LDL, HDL and TG levels. The REL SNP rs9309331 homozygous minor allele was associated with higher LDL levels. Caucasian race and increasing BMI were associated with lower HDL. Factors associated with higher TG were diabetes, Caucasian race and higher BMI. The REL SNP rs9309331 was associated with LDL levels in our study. This association is a possible explanation of the increased risk of RA patients for CV disease and requires further inquiry.

Risk of gastric cancer is associated with PRKAA1 gene polymorphisms in Koreans.

To evaluate the association between genetic polymorphisms of the gene encoding AMP-activated protein kinase (PRKAA1) and the risk of gastric cancer. The study subjects consisted of 477 age- and sex-matched case-control pairs. Genotyping was performed for 5 tag single nucleotide polymorphisms (SNPs): rs13361707, rs154268, rs3805486, rs6882903, and rs10074991. Associations between gastric cancer and putative risk factors (including the SNPs) were analyzed with multivariate conditional logistic regression models, after adjusting for potential confounding factors. Multiple testing corrections were implemented following methodology for controlling the false discovery rate. Gene-based association tests were performed by using the versatile gene-based association study (VEGAS) method. In the dominant model, SNPs rs13361707 [odds ratio (OR) = 1.51, 95%CI: 1.07-2.11)], rs154268 (OR = 1.65, 95%CI: 1.22-2.22), rs6882903 (OR = 1.48, 95%CI: 1.09-2.00), and rs10074991 (OR = 1.53, 95%CI: 1.09-2.16) were significantly associated with an increased risk of gastric cancer. In the recessive model, SNPs rs154268 (OR = 1.66, 95%CI: 1.22-2.26), rs3805486 (OR = 0.63, 95%CI: 0.46-0.85), and rs10074991 (OR = 1.47, 95%CI: 1.15-1.88) were significant risk or protective factors for gastric cancer. In the codominant model, the ORs of each of the 5 SNPs were statistically significant. All SNPs in the model showed a dose-response relationship between the minor allele frequency and the risk of gastric cancer. Most notably, subjects with a homozygous minor allele in SNP rs10074991 showed 2.15 times the risk of gastric cancer as subjects without a minor allele. The PRKAA1 gene showed a significant gene-based association with gastric cancer in the VEGAS test. All 5 tested tag SNPs of the PRKAA1 gene (rs13361707, rs154268, rs3805486, rs6882903, and rs10074991) were significantly associated with gastric cancer.

Refinement of the prediction of N-acetyltransferase 2 (NAT2) phenotypes with respect to enzyme activity and urinary bladder cancer risk

Polymorphisms of N-acetyltransferase 2 (NAT2) are well known to modify urinary bladder cancer risk as well as efficacy and toxicity of pharmaceuticals via reduction in the enzyme's acetylation capacity. Nevertheless, the discussion about optimal NAT2 phenotype prediction, particularly differentiation between different degrees of slow acetylation, is still controversial. Therefore, we investigated the impact of single nucleotide polymorphisms and their haplotypes on slow acetylation in vivo and on bladder cancer risk. For this purpose, we used a study cohort of 1,712 bladder cancer cases and 2,020 controls genotyped for NAT2 by RFLP-PCR and for the tagSNP rs1495741 by TaqMan(®) assay. A subgroup of 344 individuals was phenotyped by the caffeine test in vivo. We identified an 'ultra-slow' acetylator phenotype based on combined *6A/*6A, *6A/*7B and *7B/*7B genotypes containing the homozygous minor alleles of C282T (rs1041983, *6A, *7B) and G590A (rs1799930, *6A). 'Ultra-slow' acetylators have significantly about 32 and 46% lower activities of caffeine metabolism compared with other slow acetylators and with the *5B/*5B genotypes, respectively (P<0.01, both). The 'ultra-slow' genotype showed an association with bladder cancer risk in the univariate analysis (OR=1.31, P=0.012) and a trend adjusted for age, gender and smoking habits (OR=1.22, P=0.082). In contrast, slow acetylators in general were not associated with bladder cancer risk, neither in the univariate (OR=1.02, P=0.78) nor in the adjusted (OR=0.98, P=0.77) analysis. In conclusion, this study suggests that NAT2 phenotype prediction should be refined by consideration of an 'ultra-slow' acetylation genotype.

Saturated fatty acids activate ERK signaling to downregulate hepatic sortilin 1 in obese and diabetic mice

Hepatic VLDL overproduction is a characteristic feature of diabetes and an important contributor to diabetic dyslipidemia. Hepatic sortilin 1 (Sort1), a cellular trafficking receptor, is a novel regulator of plasma lipid metabolism and reduces plasma cholesterol and triglycerides by inhibiting hepatic apolipoprotein B production. Elevated circulating free fatty acids play key roles in hepatic VLDL overproduction and the development of dyslipidemia. This study investigated the regulation of hepatic Sort1 in obesity and diabetes and the potential implications in diabetic dyslipidemia. Results showed that hepatic Sort1 protein was markedly decreased in mouse models of type I and type II diabetes and in human individuals with obesity and liver steatosis, whereas increasing hepatic Sort1 expression reduced plasma cholesterol and triglycerides in mice. Mechanistic studies showed that the saturated fatty acid palmitate activated extracellular signal-regulated kinase (ERK) and inhibited Sort1 protein by mechanisms involving Sort1 protein ubiquitination and degradation. Consistently, hepatic ERK signaling was activated in diabetic mice, whereas blocking ERK signaling by an ERK inhibitor increased hepatic Sort1 protein in mice. These results suggest that increased saturated fatty acids downregulate liver Sort1 protein, which may contribute to the development of dyslipidemia in obesity and diabetes.

Association Between Two Functional Fibrinogen-Related Polymorphisms and Ischemic Stroke: A Case–Control Study

Currently, there is a debate regarding the roles of two functional fibrinogen-related variants (rs6050 and rs1800790) and ischemic stroke (IS). A total of 1402 subjects (834 cases and 568 controls) were genotyped for single-nucleotide polymorphisms rs6050 and rs1800790 with the ligation detection reaction method. We found that the homozygous minor allele genotype (GG) of rs6050 significantly increased IS risk by 66%, whereas that of rs1800790 reduced risk by 59% (rs6050: odds ratio [OR]=1.660, 95% confidence intervals [CI]: 1.141-2.415, p=0.008; rs1800790: OR=0.413, 95% CI: 0.228-0.747, p=0.003). After stratifying IS by three common subtypes, consistent results were found in IS cases with large-artery atherosclerosis (rs6050: OR=2.116, 95% CI: 1.327-3.376, p=0.002; rs1800790: OR=0.191, 95% CI: 0.085-0.430, p=0.000), and we also observed that the homozygous minor allele genotype of rs6050 increased risk by 86% in IS cases with cardioembolism (OR=1.859, 95% CI: 1.243-2.782, p=0.003). However, a paradox of association was shown between these two sites and fibrinogen levels. In haplotype analysis, we found that those with haplotype AA (major allele of rs6050 and minor allele of rs1800790) could reduce susceptibility to IS by 35% (OR=0.650, 95% CI: 0.493-0.858, p=0.002). Our study suggested that minor allele G of rs6050 is a significant risk factor, which can increase IS risk in the Chinese Han population, while minor allele A of rs1800790 and the haplotype AA lower such risk.

Genome-Wide Association Study of Cognitive Decline in Schizophrenia

Genome-Wide Association Study of Cognitive Decline in Schizophrenia

Single Nucleotide Polymorphisms in the Wilms’ Tumour Gene 1 in Clear Cell Renal Cell Carcinoma

The Wilms’ tumour gene 1 (WT1) single nucleotide polymorphism (SNP) rs16754 has recently been described as an independent prognostic factor in acute myeloid leukaemia (AML) patients. It is of great interest to test whether WT1 SNPs can be used as a molecular marker in other cancer types in order to improve risk and treatment stratification. We performed sequencing analysis on all 10 exons of the WT1 gene in a total of 182 patients with clear cell renal cell carcinoma (ccRCC). Six different SNPs were identified, in descending order for minor allele frequency: rs2234582, rs16754, rs1799925, rs5030315, rs2234583, and rs2234581. At least one minor allele for WT1 SNP was identified in 61% of ccRCC patients. In the entire study population, only 6% carried two copies of the minor allele. The genotypes of WT1 SNPs in 78 tumour-free kidney tissue specimens were found to be in 95% concordance with corresponding tumour samples. No correlation was observed between WT1 SNP genotypes and RNA expression level. WT1 SNP genotypes did not associate with clinical and pathological characteristics. We found favourable outcomes associated with the homozygous minor allele for WT1 SNP. However, SNP genotypes did not show to be of prognostic significance when comparing wild-type versus homozygous or heterozygous for the minor allele in the entire cohort. None of the previously reported WT1 mutations in AML was found in the present study. A novel WT1 missense mutation was identified in only one patient. Our data suggest that common WT1 mutations are not involved in ccRCC. Due to too few cases harbouring the homozygous minor allele, the prognostic impact needs to be verified in larger study populations.

Association of a Common Variant at 10q26 and Benign Prostatic Hyperplasia Aggressiveness in Han Chinese Descent

Recent studies reported that rs2252004 at 10q26 was significantly associated with prostate cancer (PCa) risk in a Japanese population and was subsequently confirmed in a Chinese population. We aimed to assess the relationship between this locus and risk/aggressiveness of benign prostatic hyperplasia (BPH). The current study included 426 BPH cases and 1,008 controls from Xinhua Hospital in Shanghai, China. All BPH patients were treated with α-adrenergic blockers and 5α-reductase inhibitors for at least 9 months. Associations between rs2252004 and BPH risk/aggressiveness were tested using logistic regression. Associations between rs2252004 and clinical parameters including International Prostate Symptom Score (IPSS), total prostate volume (TPV), total PSA (tPSA), and free PSA (fPSA) were evaluated by linear regression. Allele “A” in rs2252004 was significantly associated with increased risk for aggressiveness of BPH in a Chinese population (OR = 1.42, 95% CI: 1.04–1.96, P = 0.03). Patients with the genotype “A/A” (homozygous minor allele) had an increase of IPSS and TPV after treatment (P = 0.045 and 0.024, resp.). No association was observed between rs2252004, BPH risk, and baseline clinicopathological traits (All P > 0.05). Our study is the first to show that rs2252004 at 10q26 was associated with BPH aggressiveness and efficacy of BPH treatment.

FADS1 FADS2 Gene Cluster, PUFA Intake and Blood Lipids in Children: Results from the GINIplus and LISAplus Studies

BackgroundElevated cholesterol levels in children can be a risk factor for cardiovascular diseases in later life. In adults, it has been shown that blood lipid levels are strongly influenced by polymorphisms in the fatty acid desaturase (FADS) gene cluster in addition to nutritional and other exogenous and endogenous determinants. Our aim was to investigate whether lipid levels are determined by the FADS genotype already in children and whether this association interacts with dietary intake of n-3 fatty acids.MethodsThe analysis was based on data of 2006 children from two German prospective birth cohort studies. Total cholesterol, HDL, LDL and triglycerides were measured at 10 years of age. Six single nucleotide polymorphisms (SNPs) of the FADS gene cluster were genotyped. Dietary n-3 fatty acid intake was assessed by food frequency questionnaire. Linear regression modeling was used to assess the association between lipid levels, n-3 fatty acid intake and FADS genotype.ResultsIndividuals carrying the homozygous minor allele had lower levels of total cholesterol [means ratio (MR) ranging from 0.96 (p = 0.0093) to 0.98 (p = 0.2949), depending on SNPs] and LDL [MR between 0.94 (p = 0.0179) and 0.97 (p = 0.2963)] compared to homozygous major allele carriers. Carriers of the heterozygous allele showed lower HDL levels [β between −0.04 (p = 0.0074) to −0.01 (p = 0.3318)] and higher triglyceride levels [MR ranging from 1.06 (p = 0.0065) to 1.07 (p = 0.0028)] compared to homozygous major allele carriers. A higher n-3 PUFA intake was associated with higher concentrations of total cholesterol, LDL, HDL and lower triglyceride levels, but these associations did not interact with the FADS1 FADS2 genotype.ConclusionTotal cholesterol, HDL, LDL and triglyceride concentrations may be influenced by the FADS1 FADS2 genotype already in 10 year old children. Genetically determined blood lipid levels during childhood might differentially predispose individuals to the development of cardiovascular diseases later in life.

Abstract 2633: Single nucleotide polymorphisms in one carbon metabolism genes are associated with methylation patterns and plasma metabolites in high risk smokers based on gender

Abstract Lung cancer is the leading cause of cancer related deaths and most lung cancers are detected at a late stage. Gene promoter hypermethylation is now regarded as a promising biomarker to identify early risk and progression of lung cancer. The one carbon metabolism pathway is postulated to affect DNA methylation because it is necessary for the generation of S-adenosyl methionine or (SAM), the methyl donor for cellular DNA methylation reactions, through complex interactions with metabolites including folate, homocysteine, and methionine. This study investigated the association of single nucleotide polymorphisms (SNPs) in one carbon metabolism related genes with DNA promoter hypermethylation in sputum cell DNA from current and former smokers in the Lovelace Smokers Cohort (n=907). The association of SNPs with methylation was analyzed by logistic regression using gender specific high and low methylation cutoffs from a 12 gene methylation panel as the outcome. SNPs in the cystathionine beta-synthase (CBS) and 5-methyltetrahydrofolate-homocysteine methyltransferase reductase (MTRR) genes were found to be statistically associated with methylation in a gender specific fashion (CBS SNP, OR=4.9; CI: 1.98, 12.2, p=.0006 in males) and (MTRR SNP, OR= 0.57, CI: 0.42, 0.77, p=0.0003 in females). Plasma homocysteine levels and the ratio of homocysteine to cystathionine increased in male samples with heterozygous or homozygous minor alleles of the CBS SNP compared to male samples with homozygous common alleles (n=86). This study suggests that SNPs in the CBS and MTRR genes are associated with methylation patterns in smokers by gender. The CBS SNP may be important in regulating plasma homocysteine and cystathionine levels that could theoretically mediate the aberrant DNA methylation in smokers at high risk to develop lung cancer. Grant Support: This work is supported by K01CA128823 NCI (Flores) and R01CA097356 NCI (Belinsky). Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2633. doi:1538-7445.AM2012-2633

Serum selenium and single-nucleotide polymorphisms in genes for selenoproteins: relationship to markers of oxidative stress in men from Auckland, New Zealand

There is controversy as to the recommended daily intake of selenium (Se), and whether current New Zealand diets are adequate in this nutrient. Various functional single-nucleotide polymorphisms (SNPs) polymorphisms may affect the efficacy of Se utilisation. These include the glutathione peroxidases GPx1 rs1050450, GPx4 rs713041, as well as selenoproteins SEPP1 rs3877899, SEL15 rs5845, SELS rs28665122 and SELS rs4965373. This cross-sectional study measured serum Se levels of 503 healthy Caucasian men in Auckland, New Zealand, between ages 20-81. The Se distribution was compared with activities of the antioxidant enzymes glutathione peroxidase and thioredoxin reductase, and DNA damage as measured by the single cell gel electrophoresis assay, both without and with a peroxide-induced oxidative challenge. Serum Se was measured using inductively coupled plasma-dynamic reaction cell-mass spectrometry, while selenoprotein SNPs were estimated using TaqMan(®) SNP genotyping assays. While antioxidant enzyme activities and DNA damage recorded after a peroxide challenge increased with increasing serum selenium, the inherent DNA damage levels in leukocytes showed no statistically significant relationship with serum selenium. However, these relationships and dietary Se requirements at the individual level were modified by several different SNPs in genes for selenoproteins. The GPx1 rs1050450 C allele was significantly associated with GPx activity. Significant correlations between serum Se level and GPX activity were seen with all genotypes except for homozygous minor allele carriers, while the GPx1 rs1050450 CT genotype showed the highest correlation. Several genotypes showed significant correlations between serum Se and TR activity with SEPP1 rs3877899 GG genotype showing the highest correlation. A significant decreasing trend in DNA damage with increasing serum Se was seen among GPx1 rs1050450 CC and GPx4 rs713041 TT genotype carriers up to a serum Se level of 116 and 149ng/ml, respectively. In the absence of this genetic information, we would recommend a serum Se concentration in the region of 100-150ng/ml as providing a useful compromise.

Analysis of the IDH1G105 (SNPrs11554137) Polymorphism in 961 AML Patients and in a Large Cohort of 475 Healthy Controls

Abstract 2518 Introduction:Mutations in IDH1 and IHD2 at arginines 132 and 140 or 172, respectively, have recently been shown to play an important role in AML. Also the IDH1105GGT minor allele of the IDH1G105 (SNPrs11554137) polymorphism that is localized in the same exon as the IDH1R132 mutation has recently been reported to be an adverse prognostic factor in AML (JCO: 14, 2356–2364, 2010). Aim: We aimed at further delineating the frequency and impact of the IDH1105GGT minor allele in AML and also analyzed a healthy control cohort. Methods:IDH1G105 (SNPrs11554137) was analyzed in 961 AML patients by a LightCycler-based melting curve assay. Female/male ratio was 433/528 and age ranged from 13.1–100.4 years (median, 66.7 years). The results were compared to a healthy control cohort from the KORA (Cooperative Health Research in the Region of Augsburg) survey S4, which consists of 475 cases who where matched to the leukemia samples with respect to sex (193f/282m) and age (median: 67, range 32–81 years). Informed consent for participation in anonymized genetic studies was obtained from all individuals. IDH1G105 in the healthy cohort was analyzed by Sanger sequencing. Further mutation analyses were available in subsets of the AML patients, respectively, as follows: (IDH1R132 n=625, IDH2R140 n=587, IDH2R172 n=590, FLT3-ITD n=629, FLT3-TKD n=503, NPM1 n=628, CEBPA n=587, RUNX1 n=231, MLL-PTD n=629, NRAS n=273, KRAS n=133, ASXL1 n=470) and were analyzed as described previously. A subcohort of 634 AML with intermediate risk karyotype was analyzed for survival. Female/male ratio of this subcohort was 280/354 and age ranged from 15.7–86.6 years (median, 66.9 years). The adverse impact of IDH1R132, IDH2R140 and IDH2R172 on the NPM1+/FLT3-ITD- group has been shown previously for this group (Blood 2010 116: Abstract 102). Results: The IDH1105GGT minor allele was detected in 11.2% (108/961) in AML and in 8.8% (42/475) of the KORA control. This slight difference does not reach statistical significance (p=0.17) and thus there is no indication that this variance is a predisposing factor for leukemia. Also the frequency of a homozygous IDH1105GGT minor allele was not different between the AML cohort (3/108, 2.8%) and the KORA cohort (2/42, 4.8%, n.s.). In the AML cohort there was no association of the IDH1105GGT minor allele with age, WBC, platelet count or any of the above mentioned molecular mutations. In contrast, some differences in survival were observed: patients with the IDH1105GGT minor allele had a longer event free survival (EFS) than those with the IDH1105GGC major allele (median: 30.1 vs. 21.6 months, p=0.052) in the intermediate risk cohort. This prognostically favourable effect of the IDH1105GGT minor allele was most prominent in the NPM1+/FLT3- group with a median EFS of 45.1 vs 23.5 months as compared to those with the IDH1105GGC major allele (p=0.015). Conclusions: 1) The polymorphic IDH1105GGT minor allele was not found to be a marker predisposing for AML. 2) No association of the IDH1105GGT minor allele to any mutation or other biological parameters was detected. 3) We were not able to reproduce the previously published adverse impact of the IDH1105GGT minor allele on survival in AML. In contrast, in our cohort of 475 patients with intermediate risk AML the EFS was even better in patients carrying the IDH1105GGT minor allele, especially in the subcohort with NPM1+/FLT3−ITD−. Thus, we would suppose that the IDH1105GGT minor allele is a favorable molecular marker in intermediate risk AML. However, as these findings are in contrast to previously published data, further confirmation in additional studies is necessary to draw firm conclusions on the utility of the IDH1105 polymorphism as a marker for diagnostics and prognosis in AML. Disclosures:Schnittger:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Eder:MLL Munich Leukemia Laboratory: Employment. Alpermann:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.

Different interaction concepts to detect gene-environment interactions in the context of upper aero-digestive tract cancer

Introduction: Tobacco smoking and consumption of alcoholic beverages are established causes of cancers of the upper aero-digestive tract (UADT) and reduced intake of vegetables and fruits are likely causes. Little is known, however, about the role of gene-environment interactions (GEIs) respecting nutritional factors. Material and Methods: The study is embedded in the Alcohol-Related Cancers and Genetic Susceptibility in Europe (ARCAGE) study, a multi-centre case-control study conducted 2002–2005 in 10 European countries (Lagiou, 2009). Dietary habits were assessed using a semi-quantitative food frequency questionnaire. The analysis dataset included 1,395 controls and 1,379 cases. We used approximately 50% of the data for an exploratory screening procedure to generate a list of several potential gene-nutrition interactions. The remaining 50% build an independent dataset, which is used to estimate interaction effects between genes and nutrition variables. Logistic regression models are applied to estimate various interaction effects that are based on odds ratios (OR) like RERI (relative excess risk due to interaction), AP (attributable proportion due to interaction), the synergy index (S) and the multiplicative synergy index (SM). Interaction measures of combined gene-nutrition information will be compared with interaction effects of stratified data. Results: We observe inverse interaction effects between fruit consumption and MTHFR (folate metabolism). Homozygous minor allele carriers (AA genotype) show a significantly increased OR with less than daily fruit consumption (OR=3.8, CI=2.2–3.8) compared to non-carriers with more than daily fruit consumption. RERI=1.99 (CI=-0.1–4.0) indicates that the excess risk due to the exposure combination of the AA-genotype and „daily fruit consumption“ is 1.99 times higher compared to participants being exposed to neither of these two factors. The synergy index shows a significant synergistic departure from additivity (S=3.3, CI=1.2–8.9). Discussion: We demonstrate that different interaction measures lead to different interpretations of „interaction“. This will be discussed in the context of GEIs that could modify the risk of UADT cancers.

Polymorphisms in WNT6 and WNT10A and Colorectal Adenoma Risk

The WNT/β-catenin signaling pathway upregulates transcription of genes involved in cell proliferation and cancer progression; it has been implicated in colorectal adenoma formation. To date, no studies have examined polymorphisms in WNT genes or WNT gene–environment interactions in relation to adenoma risk. Within a colonoscopy-based case-control study of 628 adenoma cases and 516 polyp-free controls, we analyzed two tagSNPs in WNT6 (rs6747776 G > C, rs6754599 G > C) and WNT10A (rs7349332 G > A, rs10177996 A > G). The WNT6 rs6747776 homozygous minor allele (CC) was associated with increased risk of colorectal adenoma (OR = 2.75, 95% CI: 1.03–7.31). We observed a statistically significant interaction between WNT6 rs6747776 and the proportion of calories from total fat (P-int = 0.02), where the highest risk was observed among those with minor alleles and lowest fat intake. We also detected a marginally significant (0.05 < P ≤ 0.10) interaction with fish intake (P-int = 0.09). Additionally, a marginally significant interaction was observed between proportion of calories from saturated fat and the WNT10A rs7349332 polymorphism. Our results suggest that genetic variability in the WNT pathway may play a role in colorectal adenoma formation or may partly mediate the increased risk of colorectal cancer associated with fat intake.

The association of the angiotensinogen gene with insulin sensitivity in humans: a tagging single nucleotide polymorphism and haplotype approach

The purpose of this study was to clarify the association of the angiotensinogen gene (AGT) with insulin sensitivity using single nucleotide polymorphism (SNP) and haplotype analyses in a white cohort. A candidate gene association study was conducted in white persons with and without hypertension (N = 449). Seventeen SNPs of the AGT gene and their haplotypes were analyzed for an association with homeostasis model assessment of insulin resistance (HOMA-IR). Multivariate regression model accounting for age, sex, body mass index, hypertension status, study site, and sibling relatedness was used to test the hypothesis. Nine of the 17 SNPs were significantly associated with lower HOMA-IR levels. Homozygous minor allele carriers of the most significant SNP, rs2493134 (GG), a surrogate for the gain-of-function mutation rs699 (AGT p.M268T), had significantly lower HOMA-IR levels (P = .0001) than heterozygous or homozygous major allele carriers (AG, AA). Direct genotyping of rs699 in a subset of the population showed similar results, with minor allele carriers exhibiting significantly decreased HOMA-IR levels (P = .003). Haplotype analysis demonstrated that haplotypes rs2493137A|rs5050A|rs3789678G|rs2493134A and rs2004776G|rs11122576A|rs699T|rs6687360G were also significantly associated with HOMA-IR (P = .0009, P = .02), and these results were driven by rs2493134 and rs699. This study confirms an association between the AGT gene and insulin sensitivity in white humans. Haplotype analysis extends this finding and implicates SNPs rs2493134 and rs699 as the most influential. Thus, AGT gene variants, previously shown to be associated with AGT levels, are also associated with insulin sensitivity; suggesting a relationship between the AGT gene, AGT levels, and insulin sensitivity in humans.

Polymorphism of SERPINE2 gene is associated with pulmonary emphysema in consecutive autopsy cases

BackgroundThe SERPINA1, SERPINA3, and SERPINE2 genes, which encode antiproteases, have been proposed to be susceptible genes for of chronic obstructive pulmonary disease (COPD) and related phenotypes. Whether they are associated with emphysema is not known.MethodsTwelve previously reported single nucleotide polymorphisms (SNPs) in SERPINA1 (rs8004738, rs17751769, rs709932, rs11832, rs1303, rs28929474, and rs17580), SERPINA3 (rs4934, rs17473, and rs1800463), and SERPINE2 (rs840088 and rs975278) were genotyped in samples obtained from 1,335 consecutive autopsies of elderly Japanese people. The association between these SNPs and the severity of emphysema, as assessed using macroscopic scores, was determined.ResultsEmphysema of more than moderate degree was detected in 189 subjects (14.1%) and showed a significant gender difference (males, 20.5% and females, 7.0%; p < 0.0001). Among the 12 examined SNPs, only rs975278 in the SERPINE2 gene was positively associated with emphysema. Unlike the major alleles, homozygous minor alleles of rs975278 were associated with emphysema (odds ratio (OR) = 1.54; 95% confidence interval (CI) = 1.02-2.30; p = 0.037) and the association was very prominent in smokers (OR = 2.02; 95% CI = 1.29-3.15; p = 0.002).ConclusionsSERPINE2 may be a risk factor for the development of emphysema and its association with emphysema may be stronger in smokers.

Variation in the Cox-2 Gene May Modify the Effect of Alendronate on Vertebral Fracture Prevention

Bisphosphonates such as alendronate, which are potent specific inhibitors of osteoclast-mediated bone resorption, are widely used for treatment of postmenopausal osteoporosis as well as other diseases related to bone remodeling. We evaluated whether the reportedly functional PTGS2 (prostaglandin-endoperoxide synthase 2/cyclooxygenase [COX] 2) genotypes influence the efficacy of alendronate on vertebral fracture prevention. Sixty postmenopausal osteoporotic women participated in this interventional study. The extent of vertebral fracture was evaluated in all participants before and after intervention using X-ray imaging. Alendronate (10mg/day), calcium (1gr/day) and vitamin D (400mg/day) were given to participants for 2 years. Laboratory measurements included circulating crosslaps, osteocalcin, PTH, osteoporotegrin, RANKL, vitamin D, TNF-α, IL-6, IL-1 levels. Hip and spine BMD (bone mass density) were measured using DEXA. Genotyping for cox-2 gene SNP (−765G/C) was performed using PCR- RFLP method. Genotype frequency of homozygous major allele (GG), heterozygous (GC) and homozygous minor allele (CC) were 61.7%, 33.3% and 5% respectively. Evaluation of vertebral fracture before alendronate therapy in participants demonstrated no significant difference between carriers of G and C alleles, although the difference appeared near to significant after alendronate therapy at the end of 2 years. Serum PTH level and L2-L4 BMD were significantly different between subjects with different alleles. Moreover, IL-1 had prominently higher concentration in C allele carries. Furthermore, there was a significant difference in terms of the extent of vertebral fracture between two allelic groups after two years of treatment. Since bone remodeling process has been proved to be affected by inflammatory factors; it appears that variation in COX-2 genotypes may influence alendronate efficacy in fracture prevention among postmenopausal osteoporotic women.