Complete Linkage Disequilibrium Research Articles

Genetic Polymorphisms of CYP2C8 in the Czech Republic

CYP2C8 represents 7% of the hepatic cytochrome system and metabolizes around 5% of drugs in phase I processes. It also plays a significant role in metabolism of endogenous compounds. More than 20 single-nucleotide polymorphisms (SNPs) have been noted, mainly in exons 3, 5, and 8. The most studied SNPs may lead to decreased enzyme activity and may have impact on drug metabolism. Variant alleles are called CYP2C8*2 (I269F), CYP2C8*3 (R139K, K399R), and CYP2C8*4(I264M). Our aim was to investigate the frequency of major functional SNPs among the Czech population. DNA was isolated from whole blood of 161 healthy, young, and unrelated subjects (94 men and 67 women, aged from 23 to 28 years). The genotypes of polymorphic positions CYP2C8*2, CYP2C8*3 (G416A, A1196G), and CYP2C8*4 were determined by polymerase chain reaction-restriction fragment length polymorphism. Observed allele frequencies were 10.9%, 5.9%, and 0.3% for the alleles CYP2C8*3, CYP2C8*4, and CYP2C8*2, respectively. Both CYP2C8*3 (G416A, A1196G) alleles have been found in complete linkage disequilibrium. The allele distribution complies well with Hardy-Weinberg equilibrium. Allele frequencies of functionally important CYP2C8 variants in the Czech population are similar to that of other Caucasian populations.

Effects of Interleukin-10 Polymorphisms, Helicobacter pylori Infection, and Smoking on the Risk of Noncardia Gastric Cancer

ObjectiveBoth variations in the interleukin-10 (IL10) gene and environmental factors are thought to influence inflammation and gastric carcinogenesis. Therefore, we investigated the associations between IL10 polymorphisms, Helicobacter pylori (H. pylori) infection, and smoking in noncardia gastric carcinogenesis in Koreans.MethodsWe genotyped three promoter polymorphisms (-1082A>G, -819T>C, and -592 A>C) of IL10 in a case-control study of 495 noncardia gastric cancer patients and 495 sex- and age-matched healthy controls. Multiple logistic regression models were used to detect the effects of IL10 polymorphisms, H. pylori infection, and smoking on the risk of gastric cancer, which was stratified by the histological type of gastric cancer.ResultsThe IL10-819C and -592C alleles were found to have complete linkage disequilibrium, and all three IL10 polymorphisms were associated with an increased risk of intestinal-type noncardia gastric cancer. These associations were observed only in H. pylori-positive subjects and current smokers. A statistically significant interaction between the IL10-592 genotype and H. pylori infection on the risk of intestinal-type gastric cancer was observed (P for interaction = 0.047). In addition, H. pylori-positive smokers who were carriers of either the IL10-1082G (OR [95% CI] = 17.76 [6.17−51.06]) or the -592C (OR [95% CI] = 8.37 [2.79−25.16]) allele had an increased risk of intestinal-type gastric cancer compared to H. pylori-negative nonsmokers homozygous for IL10-1082A and -592A, respectively. The interaction between the IL10-1082 polymorphism and the combined effects of H. pylori infection and smoking tended towards significance (P for interaction = 0.080).ConclusionsInflammation-related genetic variants may interact with H. pylori infection and smoking to increase the risk of noncardia gastric cancer, particularly the intestinal-type. These findings may be helpful in identifying individuals at an increased risk for developing noncardia gastric cancer.

Sample Size and Statistical Power Calculation in Genetic Association Studies

A sample size with sufficient statistical power is critical to the success of genetic association studies to detect causal genes of human complex diseases. Genome-wide association studies require much larger sample sizes to achieve an adequate statistical power. We estimated the statistical power with increasing numbers of markers analyzed and compared the sample sizes that were required in case-control studies and case-parent studies. We computed the effective sample size and statistical power using Genetic Power Calculator. An analysis using a larger number of markers requires a larger sample size. Testing a single-nucleotide polymorphism (SNP) marker requires 248 cases, while testing 500,000 SNPs and 1 million markers requires 1,206 cases and 1,255 cases, respectively, under the assumption of an odds ratio of 2, 5% disease prevalence, 5% minor allele frequency, complete linkage disequilibrium (LD), 1:1 case/control ratio, and a 5% error rate in an allelic test. Under a dominant model, a smaller sample size is required to achieve 80% power than other genetic models. We found that a much lower sample size was required with a strong effect size, common SNP, and increased LD. In addition, studying a common disease in a case-control study of a 1:4 case-control ratio is one way to achieve higher statistical power. We also found that case-parent studies require more samples than case-control studies. Although we have not covered all plausible cases in study design, the estimates of sample size and statistical power computed under various assumptions in this study may be useful to determine the sample size in designing a population-based genetic association study.

Intronic SNPs of TP53 gene in chronic myeloid leukemia: Impact on drug response

Background:TP53, located on chromosome 17p13, is one of the most mutated genes affecting many types of human cancers. Thus, we aimed at investigating the association of SNPs in TP53 gene with chronic myeloid leukemia (CML).Materials and Methods:A total of 236 CML and 157 control samples were analysed for mutations in TP53 gene using polymerase chain reaction followed by direct sequencing.Results:Sequencing analysis for mutations in exons 7–9 of the TP53 gene revealed four SNPs, three in intron 7 (C14181T, T14201G, and C14310T) and one SNP in intron 6 (A13463G) of TP53 gene. The mutation C14181T is located at position 72 base pairs downstream of the 3′-end of exon 7 of the P53 gene. This mutation is in complete linkage disequilibrium with a T14201G mutation, 20 base pairs further downstream occurring at position 14201. This mutation occurred only in the presence of C14181T mutation and these mutations showed association with advanced phase and cytogenetic poor response. Another two novel mutations, C14310T in intron 7 and A13463G in intron 6 were also found to be associated with cytogenetic poor response.Conclusion:Our study suggests that TP53 intronic SNPs might have a strong influence on disease progression and poor response in CML patients.

P-221 - Association between microrna-206 gene polymorphisms and bipolar disorder in the han chinese population

Bioinformatic investigations indicate that has-mir-206 (microRNA-206, miRNA-206) could regulate BDNF protein synthesis by interfering with BDNF mRNA translation, which is disrupted in bipolar disorder (BPD). This study is to investigate whether miRNA-206 gene variants were associated with BPD susceptibility in a Han Chinese population. 342 patients who met DSM-IV criteria for bipolar disorder type I (BPD-I) or type II (BPD-II) and 386 matched health controls were enrolled into this study. The miRNA-206 gene and +/-500bp were selected for gene sequencing. For the case-control genetic comparisons, differences in the genotype and allele distributions between patients and controls were examined using Pearson's χ 2 test. Gene sequencing showed that there are two polymorphisms rs16882131(C/T) and rs62408583 (A/C) located at the upstream of miRNA-206 gene, which are complete linkage disequilibrium. The association analysis showed that there was no significant difference for genotype frequencies (χ 2 = 2.075, df = 2, P = 0.354) or for allele frequencies (χ 2 = 0.041, df = 1, P = 0.839) between BPD patients and controls. Similarly, no significant difference was found between BPD-I patients and controls (genotype χ 2 = 1.411, df = 2, P = 0.494; allele χ 2 = 0.380, df = 1, P = 0.538). However, there was significant difference between BPD-II patients and controls (genotype χ 2 = 7.933, df = 2, P = 0.019; allele χ 2 = 5.403, df = 1, P = 0.020). Our findings do not support that BPD susceptibility was associated with miRNA-206 gene polymorphisms in the studied Han Chinese population. The association between miRNA-206 gene polymorphisms and bipolar disorder type II is needed to be carefully interpreted. Further studies are necessary to elucidate the involvement miRNA-206 in the pathophysiology of BPD.

Combined analysis of the MspI and XbaI polymorphisms in intron 22 of the factor VIII gene for detection of hemophilia A in a Korean population

To determine the usefulness of MspI/int22h-1 (intron 22 homologous region-1) polymorphism of the factor VIII gene for molecular genetic diagnosis of hemophilia A in the Korean population, MspI/intron 22 and XbaI/intron 22 polymorphisms were analyzed in 101 unrelated Korean families with severe hemophilia A. The expected heterozygosity rates of MspI/int22h-1 and XbaI/int22h-1 polymorphisms were 49.5 and 43.6%, respectively; these polymorphisms were not in complete linkage disequilibrium. Combined analysis using both polymorphisms provided an informative rate of 66.3%. These results suggest that PCR analysis of the MspI/int22h-1 polymorphism of the factor VIII gene would be useful for carrier detection and prenatal diagnosis of hemophilia A in the Korean population.

Recipient CTLA-4*CT60-AA genotype is a prognostic factor for acute graft-versus-host disease in hematopoietic stem cell transplantation for thalassemia

Polymorphisms of the cytotoxic T-lymphocyte antigen-4 gene (CTLA-4) have been associated with autoimmune diseases and it has recently been reported that donor genotypes correlate with the outcome of allogeneic hematopoietic stem cell transplantation in leukemia patients. With the aim of confirming this finding in thalassemia patients, we investigated the influence of genotype distribution of 3 CTLA-4 gene polymorphisms in 72 thalassemia patients and their unrelated donors. A significant association was observed for recipient CT60-AA genotype and onset of grade II–IV (63.2% vs 24.5%; p = 0.001) and grade III–IV (36.4% vs 7.6%; p = 0.005) acute graft-versus-host disease (aGVHD). The same association was observed for the 88-base-pair allele of the CTLA-4 (AT)n polymorphism, which was determined to be in complete linkage disequilibrium with the CT60 A allele. Multinomial Cox regression demonstrated that this association was independent of CT60 donor genotypes or other risk factors (p = 0.016; hazard ratio = 2.8). Our data confirm that the genetic variability in CTLA-4 is an important prognostic factor for aGVHD and suggest that some of the risk factors for this complication are generated by recipient cells that persist after the myeloablative conditioning regimen.

P2-06-02: FOXO3a Genotype Predicts Age of Breast Cancer Onset and Correlates with Lymph Node Involvement.

Abstract Background: Ageing mechanisms and genetic traits underlying the aging process are intimately linked with mechanisms that protect against cancer. FOXO3a genotype might be an important clue in this regard, as single nucleotide polymorphisms in this gene have been related to longevity, but also to differences in cancer susceptibility. FOXO3a is thought to work as a cellular ‘switch', by either promoting apoptosis or halting proliferation and protecting from oxidative stress. We have assessed FOXO3a genotype in a cohort of breast cancer patients to investigate possible associations with patient and/or breast tumor characteristics. Patients and methods: Eligible subjects were all early breast cancer patients with upfront surgery, diagnosed at our center between 2000 till 2010, from which germline DNA (peripheral blood) was available. 2 SNP's in the FOXO3a gene, known to correlate with ageing or age associated diseases were assessed by Sequenom (rs 9400239 and rs 6911407). Results: 2047 patients were included in the study. Age at diagnosis was found to be lower for patients homozygous for the minor allele at position rs6911407 (genotype A/A) (median age at diagnosis 52 years; P=0.001;95% C.I. 50.7−53.3). Patients homozygous for the wild type allele (genotype C/C) at this position had a median age at diagnosis 55.0 years; 95% C.I. 54.0−56.0. After correction for possible confounding variables BMI at diagnosis and parity, the association between age at diagnosis still remained significant (P=0.025, N=1348). We also assessed the relationship of the specific genotypes with tumor characteristics. We found that rs6911407 is positively correlated with lymph node status. This finding remains significant after correction for possible confounding variables ER, PR, Her-2, tumor size and tumor grade (OR=1.224 for homozygous mutants versus wild type; P=0.014;95% C.I. 1.042−1.437). Conclusion: In our cohort of primary breast cancers, we found that patients homozygous for the minor allele at position rs 6911407 in the FOXO3a gene, develop breast cancer at younger age, and have more lymph node involvement compared to patients homozygous for the wild type allele. SNP's in nearly complete linkage disequilibrium with rs6911407 have previously been correlated with healthy longevity. At first sight, this seems contradictory with our current findings. However, our results are in accordance with the trade-off that has been described to exist between longevity and risk of cancer. It is generally assumed that FOXO3a and p53 function are oppositely controlled by common regulation systems, such that changes in FOXO activation would always be counterbalanced by an inverse change in p53 activation. If FOXO3a is strongly activated in order to protect against DNA damage (i.e. longevity function), p53-mediated cancer protection will concomitantly be diminished. This mechanism reconciles the apparent paradox between the longevity phenotype that has previously been linked with rs 6911407 on the one hand, and, on the other hand, our current findings of earlier breast cancer onset and increased lymph node metastasis. Further research on the function of FOXO3a in both aging and cancer is required to shed more light on the molecular mechanisms underlying these observations. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P2-06-02.

Fetal hemoglobin in sickle cell anemia: Molecular characterization of the unusually high fetal hemoglobin phenotype in African Americans

Fetal hemoglobin (HbF) is a major modifier of disease severity in sickle cell anemia (SCA). Three major HbF quantitative trait loci (QTL) are known: the Xmn I site upstream of (G)γ- globin gene (HBG2) on chromosome 11p15, BCL11A on chromosome 2p16, and HBS1L-MYB intergenic polymorphism (HMIP) on chromosome 6q23. However, the roles of these QTLs in patients with SCA with uncharacteristically high HbF are not known. We studied 20 African American patients with SCA with markedly elevated HbF (mean 17.2%). They had significantly higher minor allele frequencies (MAF) in two HbF QTLs, BCL11A, and HMIP, compared with those with low HbF. A 3-bp (TAC) deletion in complete linkage disequilibrium (LD) with the minor allele of rs9399137 in HMIP was also present significantly more often in these patients. To further explore other genetic loci that might be responsible for this high HbF, we sequenced a 14.1 kb DNA fragment between the (A)γ-(HBG1) and δ-globin genes (HBD). Thirty-eight SNPs were found. Four SNPs had significantly higher major allele frequencies in the unusually high HbF group. In silico analyses of these four polymorphisms predicted alteration in transcription factor binding sites in 3.

Replication and Extension of Association Between Common Genetic Variants in SIM1 and Human Adiposity

Haplo-insufficiency of the bHLH (basic helix-loop-helix) transcription factor single-minded 1 (SIM1) causes severe obesity in mice and humans. We hypothesized that common genetic variations in/near SIM1 could exert more subtle effects on its function and associate with human adiposity. First, SIM1 coding regions were sequenced in severely obese subjects, and two common nonsynonymous single-nucleotide polymorphisms (nsSNPs) in complete linkage disequilibrium (LD) were identified: Pro352Thr (rs3734354) and Ala371Val (rs3734355). We next carried out a SNP association study of five adiposity traits (BMI, % body fat, abdominal visceral and subcutaneous fat, and leptin concentrations) in 1,699 whites and 1,173 blacks. TagSNPs covering SIM1 and nearby conserved regions, and the only common nsSNP in SIM1's binding partner aryl-hydrocarbon receptor nuclear translocator 2 (ARNT2) (Gly679Ser/rs4072568), were investigated. The effects of rs3734355/4 on SIM1 activity were tested using an in vitro reporter assay. We replicated previous observations that homozygosity for the 371Val allele was associated with higher BMI in white males (P = 0.003). Together with previous findings in white males (combined n = 3,479), BMI was increased by 1.10kg/m(2) in 371Val homozygotes (95% confidence interval (CI): 0.25-1.95kg/m(2), P = 0.01). In vitro, the 352Thr-371Val haplotype impaired SIM1 transcriptional activity by 22% (P < 0.0001). TagSNP analysis of SIM1 revealed two SNPs in the 3' region (rs9390322 and rs7746743) and another in intron 5 (rs3734353) to be significantly associated with various adiposity measures in ethnicity- and sex-specific manners after multiple testing correction. In white males, rs4072568 in ARNT2 was also associated with BMI (P = 9 × 10(-4)) and % body fat (P = 0.001). Our findings implicate heritable defects of the SIM1-ARNT2 axis in the predisposition to human obesity.

Genetic variation and linkage disequilibrium in Bacillus anthracis

We performed whole-genome amplification followed by hybridization of custom-designed resequencing arrays to resequence 303 kb of genomic sequence from a worldwide panel of 39 Bacillus anthracis strains. We used an efficient algorithm contained within a custom software program, UniqueMER, to identify and mask repetitive sequences on the resequencing array to reduce false-positive identification of genetic variation, which can arise from cross-hybridization. We discovered a total of 240 single nucleotide variants (SNVs) and showed that B. anthracis strains have an average of 2.25 differences per 10,000 bases in the region we resequenced. Common SNVs in this region are found to be in complete linkage disequilibrium. These patterns of variation suggest there has been little if any historical recombination among B. anthracis strains since the origin of the pathogen. This pattern of common genetic variation suggests a framework for recognizing new or genetically engineered strains.

Carbonyl Reductase 1 Expression and Polymorphisms Influence Daunorubicin Metabolism in AML

Abstract 2484Treatment failure in AML can be attributed to resistance to chemotherapeutic drugs. Induction chemotherapy of AML involves combination of Daunorubicin (Dnr) and Cytarabine. Up-regulation in the expression of efflux transporters such as ABCB1 and ABCG2 has been shown to be one of the causes of Dnr resistance in AML. Apart from efflux transporters, increased expression of the Dnr metabolising enzymes (Carbonyl reductase 1 (CBR1) and CBR3) also can influence the cytotoxic activity of Dnr against leukemic cells. Aim of the present study is to investigate: i) the role of mRNA expression of Dnr metabolising enzymes (CBR1 and CBR3) on the in vitro cytotoxicity of Dnr in primary AML cells and ii) effect of Single nucleotide polymorphisms (SNPs) in CBR1 and CBR3 on the plasma pharmacokinetics of Dnr and Daunorubicinol (DOL) in AML patients.Ninety patients with AML (excluding AML-M3) at diagnosis before the initiation of therapy were included. Bone marrow (BM) was collected at diagnosis and blast percentage in our cohort of patients ranged from 20–100%. Mononuclear cells (MNCs) were isolated by density gradient centrifugation. Total RNA was extracted from BMMNCs and cDNA was prepared. CBR1 and CBR3 mRNA expression was measured using Taqman based quantitative RT-PCR normalized to GAPDH. In-vitro cytotoxicity of Dnr was determined by MTT cell viability assay. Intracellular levels of Dnr and DOL was estimated by HPLC coupled with Fluorescence detector (FD). SNPs in CBR1 and CBR3 were screened by PCR followed by sequencing. In addition, plasma samples during Dnr infusion was collected at 0, 1, 2, 4, 6 and 24hrs from 24 of the 90 AML patients. Levels of Dnr and DOL in the plasma samples were estimated by HPLC coupled with FD and Area under Curve (AUC) for Dnr and DOL were calculated.CBR1 (range: 0.02–253.15) and CBR3 (range: 8.24– 29296.67) mRNA expression showed wide inter-individual variation. Intracellular levels of Dnr (range: 17.98–1718ng/3×106cells) and DOL (range: 2.76–62.07ng/3×106cells) showed 95 and 22 fold variation respectively. IC50 of Dnr in these samples ranged from 0.05 to 3.15 μM. Based on the IC50, samples were categorized as sensitive (IC50<0.5μM), intermediate (IC50: 0.5–1.0μM) and resistant (IC50>1.0μM) to Dnr. CBR1 expression was significantly higher in resistant samples (median-102.99: range: 7.18–253.15) compared to intermediate (median- 29.73: range: 0.02–224.23) and sensitive samples (median-18.67: range: 0.34–105.40 p=0.0154) [Figure 1]. In addition, significant correlation between CBR1 expression and intracellular DOL levels was observed (r= 0.52; p<0.0001), as samples with higher CBR1 expression had increased DOL levels. CBR3 expression did not show any significant association with invitro cytotoxicity or intracellular DOL levels. [Display omitted] Five SNPs in CBR1 and 3 in CBR3 were identified. CBR1 SNPs, rs20572, rs9024 and rs25678 were in complete linkage disequilibrium (LD). Variant of rs25678 and rs20572/rs9024 had an allelic frequency of 0.244 and 0.20 respectively. Among CBR3 SNPs, variants of two non-synonymous polymorphisms rs8133502 and rs1056892 showed allelic frequency of 0.31 and 0.51 respectively. AUC of Dnr and DOL in plasma samples ranged from 22–2474ng*h/ml and 37–2027 ng*h/ml respectively while clearance of Dnr ranged from 0.04 to 3.34 L/h. Plasma DOL AUC, unlike in vitro intracellular DOL, did not show any significant association with CBR1 and CBR3 expression. In patients with variant rs25678 genotype, Dnr AUC was higher and clearance was lower compared to the wild type genotype, reaching a trend to statistical significance (p=0.0537 and 0.1184 for Dnr AUC and clearance). Influence of Dnr and DOL plasma levels on clinical outcome, if any, remains to be evaluated.This is the first report showing the influence of CBR1 and CBR3 in in-vitro cytotoxicity of Dnr and role of SNPs in CBR1 and CBR3 in plasma pharmacokinetics of Dnr in AML patients. To conclude, higher expression of CBR1 confers resistance to Dnr in primary AML cells and polymorphisms of this gene may influence the pharmacokinetics of Dnr. Disclosures:No relevant conflicts of interest to declare.

Genome-wide significant association between alcohol dependence and a variant in the ADH gene cluster.

Alcohol dependence (AD) is an important contributory factor to the global burden of disease. The etiology of AD involves both environmental and genetic factors, and the disorder has a heritability of around 50%. The aim of the present study was to identify susceptibility genes for AD by performing a genome-wide association study (GWAS). The sample comprised 1333 male in-patients with severe AD according to the Diagnostic and Statistical Manual of Mental Disorders, 4th edition, and 2168 controls. These included 487 patients and 1358 controls from a previous GWAS study by our group. All individuals were of German descent. Single-marker tests and a polygenic score-based analysis to assess the combined contribution of multiple markers with small effects were performed. The single nucleotide polymorphism (SNP) rs1789891, which is located between the ADH1B and ADH1C genes, achieved genome-wide significance [P = 1.27E-8, odds ratio (OR) = 1.46]. Other markers from this region were also associated with AD, and conditional analyses indicated that these made a partially independent contribution. The SNP rs1789891 is in complete linkage disequilibrium with the functional Arg272Gln variant (P = 1.24E-7, OR = 1.31) of the ADH1C gene, which has been reported to modify the rate of ethanol oxidation to acetaldehyde in vitro. A polygenic score-based approach produced a significant result (P = 9.66E-9). This is the first GWAS of AD to provide genome-wide significant support for the role of the ADH gene cluster and to suggest a polygenic component to the etiology of AD. The latter result may indicate that many more AD susceptibility genes still await identification.

P73 G4C14-to-A4T14 gene polymorphism and interaction with p53 exon 4 Arg72Pro on cancer susceptibility: a meta-analysis of the literature

The p73 gene (1p36-33) is involved in cancer development through cell growth inhibition by inducing apoptosis in a p53-like manner. The p73 G4C14-to-A4T14 dinucleotide polymorphism, consisting of two single-nucleotide polymorphisms in the non-coding region of exon 2 that are in complete linkage disequilibrium, has been extensively studied in association with cancer risk. We performed a meta-analysis of published studies that examined the association between this p73 G4C14-to-A4T14 polymorphism and cancer by searching for relevant studies on Medline and Embase up to February 28, 2010. Pooling data from 19 case-control studies that included 6510 cancer cases and 5711 controls, we found that carriers of the p73 G4C14-to-A4T14 homozygous variant genotype (AT/AT) had an increased global risk of cancer [odds ratio (OR) = 1.30, 95% confidence interval (CI), 1.03-1.65]. There was no evidence of an effect modification of p73 AT/AT by age, gender, ethnicity or smoking status in subgroup analyses; however, a 1.35-fold statistically significant increased risk was found among individuals <55 years old. In case-only analysis, the homozygous p73 G4C14-to-A4T14 variant of p73 genotype was associated with the presence of the p53 exon 4 Arg72Pro allele (OR = 1.30, 95% CI, 1.02-1.64), which is suggestive of a biological interaction between the two genes in carcinogenesis. In conclusion, the p73 G4C14-to-A4T14 homozygous variant genotype might be a risk factor for cancer, especially in combination with the p53 exon 4 Arg72Pro polymorphism. Further studies looking at p73 G4C14-to-A4T14 and p53 exon 4 Arg72Pro interaction are required to support our findings.

Variants of the human NR1I2 (PXR) locus in chronic periodontitis

Recent studies on genetic variants of the pregnane X receptor (PXR) revealed associations with the mucosal immune response. This study aimed to investigate the potential association of functional polymorphisms of the NR1I2 (PXR)-encoding gene (rs12721602, rs3814055, rs1523128, rs1523127, rs45610735, rs6785049, rs2276707 and rs3814057) with chronic periodontitis. At total of 402 periodontitis patients and 793 healthy individuals were genotyped using PCR and melting-curve analysis. Frequency distribution of genotypes for the eight single nucleotide polymorphisms showed no significant difference between patients with periodontitis and controls. Among the eight tested polymorphisms, two blocks were defined showing complete or almost complete linkage disequilibrium (linkage disequilibrium block 1: rs3814055 and rs1523127; and linkage disequilibrium block 2: rs6785049, rs2276707 and rs3814057). For one haplotype (GTGAG) composed of rs12721602, rs3814055, rs1523128, rs12721607 and rs6785049, a significant association with periodontitis was found [p-value after permutation with 100,000 iterations (p(permut.)) = 0.011, odds ratio = 0.46, 95% confidence interval: 0.25-0.84) following adjustment for age, gender and smoking. A rare haplotype of the NR1I2 (PXR) locus was associated with the individual susceptibility for chronic periodontitis in a German cohort. As a result of the borderline significance and the small effect size the present results need further confirmation.

An association study between polymorphism of alcohol dehydrogenase (ADH1B), aldehyde dehydrogenase (ALDH2), cytochrome (CYP4502E1), Catechol-O- Methyltransferase (COMT) and 5-hydroxytryptamine transporter (5-HTT) genes in Yunnan Han population with alcohol dependence

Alcohol dependence (AD) is a complex disease resulting from the inheritance of several susceptible genes and multiple environmental determinants. The aim of thisstudy was to identify the genetic risk factors which include alcohol metabolizing genes and neurotransmitter related genes for alcoholism in Yunnan Han population. Eight allelic variants of five genes were genotyped from 332 Yunnan Han individuals (including 118 alcohol-dependent patients (DSM-IV criteria) and 214 controls) using PCR-RFLP method. Those polymorphic sites included alcohol dehydrogenase (ADH1B), aldehyde dehydrogenase (ALDH2), cytochrome P-4502E1 (CYP2E1) PstI, Catechol-O-Methyltransferase (COMT) rs2075507 (5’region), rs737865 (intron1), rs4680 (Val158Met), rs165599 (3’region) and serotonin transporter (5-HTTLPR). Both genotype and allele frequencies of ALDH2 and CYP4502E1 as well as the allele frequency of ADH1B gene differed significantly between AD group and control group. The proportion of ALDH2 *1/*2 genotype and *2 allele was significantly smaller in patients than that in controls (χ2 = 6.554, p = 0.038; χ2 = 4.906, p = 0.027), while the proportion of c2 allele of CYP4502E1 was significantly higher (χ2 = 4.410, p = 0.036). Compared with the controls, the frequencies of the 5-HTTLPR L/L genotype and COMT rs737865 C/C genotype were significantly lower in AD group. Twelve COMT haplotypes (rs2075507, rs737865, rs4680 and rs165599) defined as H1 to H12 were obtained in this major minority population. The prevalence of the haplotype H1 ‘‘A-C-A-A’’ was significantly greater in alcoholics than the prevalence in their respective control group. There were no significant differences in the genotype frequencies of the COMT rs2075507, rs4680 and rs165599 polymorphisms between alcoholics and controls. COMT rs2075507 and rs737865 polymorphisms were in complete linkage disequilibrium in Han population of Yunnan Province. This study indicates that polymorphisms of ADH1B, ALDH2, CYP4502E1, COMT and 5-HTT were significantly associated with AD in Han majority. The ADH1B *2, ALDH2 *2 alleles, 5-HTTLPR L/L genotype and C/C genotype of the COMT rs737865 polymorphism had an important role in reducing the risk of AD while the c2 allele of CYP4502E1 increased the risk of AD. Therefore, the A-C-A-A haplotype may be a dangerous factor leading to AD. Key words: Yunnan Han population, polymorphism, alcohol dependence, genetic risk factor.

Genomewide Association betweenGLCCI1and Response to Glucocorticoid Therapy in Asthma

The response to treatment for asthma is characterized by wide interindividual variability, with a significant number of patients who have no response. We hypothesized that a genomewide association study would reveal novel pharmacogenetic determinants of the response to inhaled glucocorticoids. We analyzed a small number of statistically powerful variants selected on the basis of a family-based screening algorithm from among 534,290 single-nucleotide polymorphisms (SNPs) to determine changes in lung function in response to inhaled glucocorticoids. A significant, replicated association was found, and we characterized its functional effects. We identified a significant pharmacogenetic association at SNP rs37972, replicated in four independent populations totaling 935 persons (P=0.0007), which maps to the glucocorticoid-induced transcript 1 gene (GLCCI1) and is in complete linkage disequilibrium (i.e., perfectly correlated) with rs37973. Both rs37972 and rs37973 are associated with decrements in GLCCI1 expression. In isolated cell systems, the rs37973 variant is associated with significantly decreased luciferase reporter activity. Pooled data from treatment trials indicate reduced lung function in response to inhaled glucocorticoids in subjects with the variant allele (P=0.0007 for pooled data). Overall, the mean (±SE) increase in forced expiratory volume in 1 second in the treated subjects who were homozygous for the mutant rs37973 allele was only about one third of that seen in similarly treated subjects who were homozygous for the wild-type allele (3.2±1.6% vs. 9.4±1.1%), and their risk of a poor response was significantly higher (odds ratio, 2.36; 95% confidence interval, 1.27 to 4.41), with genotype accounting for about 6.6% of overall inhaled glucocorticoid response variability. A functional GLCCI1 variant is associated with substantial decrements in the response to inhaled glucocorticoids in patients with asthma.

Thrombomodulin Gene Variants Are Associated With Increased Mortality After Coronary Artery Bypass Surgery in Replicated Analyses

We tested the hypothesis that genetic variation in thrombotic and inflammatory pathways is independently associated with long-term mortality after coronary artery bypass graft (CABG) surgery. Two separate cohorts of patients undergoing CABG surgery at a single institution were examined, and all-cause mortality between 30 days and 5 years after the index CABG was ascertained from the National Death Index. In a discovery cohort of 1018 patients, a panel of 90 single-nucleotide polymorphisms (SNPs) in 49 candidate genes was tested with Cox proportional hazard models to identify clinical and genomic multivariate predictors of incident death. After adjustment for multiple comparisons and clinical predictors of mortality, the homozygote minor allele of a common variant in the thrombomodulin (THBD) gene (rs1042579) was independently associated with significantly increased risk of all-cause mortality (hazard ratio, 2.26; 95% CI, 1.31 to 3.92; P=0.003). Six tag SNPs in the THBD gene, 1 of which (rs3176123) in complete linkage disequilibrium with rs1042579, were then assessed in an independent validation cohort of 930 patients. After multivariate adjustment for the clinical predictors identified in the discovery cohort and multiple testing, the homozygote minor allele of rs3176123 independently predicted all-cause mortality (hazard ratio, 3.6; 95% CI, 1.67 to 7.78; P=0.001). In 2 independent cardiac surgery cohorts, linked common allelic variants in the THBD gene are independently associated with increased long-term mortality risk after CABG and significantly improve the classification ability of traditional postoperative mortality prediction models.

A SOCS-1 Promoter Variant Is Associated with Total Serum IgE Levels

SOCS-1 is a critical regulator of multiple signaling pathways, including those activated by cytokines that regulate Ig H chain class switching to IgE. Analysis of mice with mutations in the SOCS-1 gene demonstrated that IgE levels increase with loss of SOCS-1 alleles. This suggested that overall SOCS-1 acts as an inhibitor of IgE expression in vivo. A genetic association study was performed in 474 children enrolled in the Tucson Children's Respiratory Study to determine if genetic variation in the SOCS-1 locus correlates with altered levels of IgE. Carriers of the C-allele for a novel, 3' genomic single nucleotide polymorphism (SNP) in the SOCS-1 gene (SOCS1+1125G > C; rs33932899) were found to have significantly lower levels of serum IgE compared with those of homozygotes for the G-allele. Analysis demonstrated that the SOCS1+1125G > C SNP was in complete linkage disequilibrium with an SNP at position SOCS1-820G > T (rs33977706) of the SOCS-1 promoter. Carriers of the T-allele at the SOCS1-820G > T were also found to be associated with the decreased IgE. The promoter SNP increased transcriptional activity of the SOCS-1 promoter in reporter assays and human B cells. Consistent with this observation, the presence of this polymorphism within the promoter abolished binding of yin yang-1, which is identified as a negative regulator of SOCS-1 transcriptional activity. These data suggest that genetic variation in the SOCS-1 promoter may affect IgE production.

Associations between gene polymorphisms in fatty acid metabolism pathway and preterm delivery in a US urban black population

There is increasing evidence suggesting that higher intakes of fish or n-3 polyunsaturated fatty acids supplements may decrease the risk of preterm delivery (PTD). We hypothesized that genetic variants of the enzymes critical to fatty acids biosynthesis and metabolism may be associated with PTD. We genotyped 231 potentially functional single nucleotide polymorphisms (SNPs) and tagSNPs in 9 genes (FADS1, FADS2, PTGS1, PTGS2, ALOX5, ALOX5AP, PTGES, PTGES2, and PTGES3) among 1,110 black mothers, including 542 mothers who delivered preterm (<37 weeks gestation) and 568 mothers who delivered full-term babies (≥37 weeks gestation) at Boston Medical Center. After excluding SNPs that are in complete linkage disequilibrium or have lower minor allele frequency (<1%) or call rate (<90%), we examined the association of 206 SNPs with PTD using multiple logistic regression models. We also imputed 190 HapMap SNPs via program MACH and examined their associations with PTD. Finally, we explored gene-level and pathway-level associations with PTD using the adaptive rank truncated product (ARTP) methods. A total of 21 SNPs were associated with PTD (p value ranging from 0.003 to 0.05), including 3 imputed SNPs. Gene-level ARTP statistics indicated that the gene PTGES2 was significantly associated with PTD with a gene-based p value equal to 0.01. No pathway-based association was found. In this large and comprehensive candidate gene study, we found a modest association of genes in fatty acid metabolism pathway with PTD. Further investigation of these gene polymorphisms jointly with fatty acid measures and other genetic factors would help better understand the pathogenesis of PTD.