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  • 1
    Keywords: DISEASE ; VARIANTS ; OVARIAN-CANCER ; BLADDER-CANCER ; LINKAGE DISEQUILIBRIUM ; METAANALYSIS ; GENETIC SUSCEPTIBILITY ; imputation ; RISK LOCI ; RECOMBINATION HOTSPOTS
    Abstract: We performed a multistage genome-wide association study including 7,683 individuals with pancreatic cancer and 14,397 controls of European descent. Four new loci reached genome-wide significance: rs6971499 at 7q32.3 (LINC-PINT, per-allele odds ratio (OR) = 0.79, 95% confidence interval (CI) 0.74-0.84, P = 3.0 x 10(-12)), rs7190458 at 16q23.1 (BCAR1/CTRB1/CTRB2, OR = 1.46, 95% CI 1.30-1.65, P = 1.1 x 10(-10)), rs9581943 at 13q12.2 (PDX1, OR = 1.15, 95% CI 1.10-1.20, P = 2.4 x 10(-9)) and rs16986825 at 22q12.1 (ZNRF3, OR = 1.18, 95% CI 1.12-1.25, P = 1.2 x 10(-8)). We identified an independent signal in exon 2 of TERT at the established region 5p15.33 (rs2736098, OR = 0.80, 95% CI 0.76-0.85, P = 9.8 x 10(-14)). We also identified a locus at 8q24.21 (rs1561927, P = 1.3 x 10(-7)) that approached genome-wide significance located 455 kb telomeric of PVT1. Our study identified multiple new susceptibility alleles for pancreatic cancer that are worthy of follow-up studies.
    Type of Publication: Journal article published
    PubMed ID: 25086665
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  • 2
    Keywords: RECEPTOR ; CANCER ; GROWTH ; GROWTH-FACTOR ; proliferation ; tumor ; CELL-PROLIFERATION ; PATHWAY ; RISK ; GENE ; GENES ; PROTEIN ; TUMORS ; RELEASE ; PATIENT ; BINDING ; ASSOCIATION ; polymorphism ; POLYMORPHISMS ; single nucleotide polymorphism ; VARIANTS ; BREAST ; breast cancer ; BREAST-CANCER ; hormone ; COLORECTAL-CANCER ; PROSTATE-CANCER ; cancer risk ; case-control studies ; SOMATOSTATIN ; CANCER PATIENTS ; nutrition ; FACTOR-I ; BINDING PROTEIN ; SERUM ; SINGLE ; IGF-I ; BINDING-PROTEIN ; case-control study ; ASSOCIATIONS ; RE ; VARIANT ; SINGLE NUCLEOTIDE POLYMORPHISMS ; cell proliferation ; development ; GROWTH-FACTOR-I ; BINDING PROTEIN-3 ; LEVEL ; case control studies ; GENOTYPE DATA ; FACTOR (IGF)-I ; PREMENOPAUSAL WOMEN ; IGFBP3 ; insulin-like growth factor ; PLASMA-LEVELS ; SERUM-LEVELS
    Abstract: Insulin-like growth factor-I (IGF-I) stimulates cell proliferation and can enhance the development of tumors in different organs. Epidemiologic studies have shown that an elevated level of circulating IGF-I is associated to increased risk of breast cancer as well as other cancers. Genetic variants affecting the release or biological action of growth hormone (GH), the main stimulator of IGF-I production, may predict circulating levels of IGF-I and have an effect on cancer risk. We tested this hypothesis with a large case-control study of 807 breast cancer patients and 1,588 matched control subjects nested within the European Prospective Investigation into Cancer and Nutrition. We genotyped 22 common single nucleotide polymorphisms in 10 genes involved in GH production and action (GHRH, GHRHR, SST, SSTR1-SSTR5, POU1F1, and GH1), and in parallel, we measured serum levels of IGF-I and IGFBP-3, its major binding protein, in samples of cases and controls. SST and SSTR2 polymorphisms showed weak but statistically significant associations with breast cancer risk. SSTR5 polymorphisms were associated with IGF-I levels, whereas one polymorphism in GHRHR and one in POU1F1 were associated with IGFBP-3 levels. Our conclusion is that common genetic variation in the GH synthesis pathway, as measured by single nucleotide polymorphisms selected in the present study, is not a major determinant of IGF-I and IGFBP-3 circulating levels, and it does not play a major role in altering breast cancer risk
    Type of Publication: Journal article published
    PubMed ID: 16214911
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  • 3
    Keywords: INFORMATION ; SYSTEM ; TOOL ; FLOW ; polymorphism ; single nucleotide polymorphism ; SNP ; MANAGEMENT ; SINGLE ; PROGRAM ; RE ; REQUIREMENT ; SINGLE-NUCLEOTIDE POLYMORPHISMS ; NEED ; TECHNOLOGY
    Abstract: Background: Single Nucleotide Polymorphism ( SNP) genotyping is a major activity in biomedical research. The Taqman technology is one of the most commonly used approaches. It produces large amounts of data that are difficult to process by hand. Laboratories not equipped with a Laboratory Information Management System ( LIMS) need tools to organize the data flow. Results: We propose a package of Visual Basic programs focused on sample management and on the parsing of input and output TaqMan files. The code is written in Visual Basic, embedded in the Microsoft Office package, and it allows anyone to have access to those tools, without any programming skills and with basic computer requirements. Conclusion: We have created useful tools focused on management of TaqMan genotyping data, a critical issue in genotyping laboratories whithout a more sophisticated and expensive system, such as a LIMS
    Type of Publication: Journal article published
    PubMed ID: 16221298
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  • 4
    Keywords: RECEPTOR ; CANCER ; RISK ; GENE ; ASSOCIATION ; polymorphism ; BREAST-CANCER ; PROMOTER ; ENDOMETRIAL CANCER ; insulin ; ENDOMETRIAL ; GROWTH-FACTOR-I ; HORMONES ; OVARIAN ; ENDOGENOUS HORMONES ; FUNCTIONAL POLYMORPHISM
    Type of Publication: Journal article published
    PubMed ID: 16835347
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  • 5
    Keywords: CANCER ; EXPRESSION ; carcinoma ; CELL ; CELL LUNG-CANCER ; Germany ; POPULATION ; RISK ; GENE ; GENES ; CARCINOGENESIS ; ASSOCIATION ; polymorphism ; POLYMORPHISMS ; HEALTH ; PROMOTER ; case-control studies ; squamous cell carcinoma ; GASTRIC-CANCER ; EUROPE ; inflammation ; molecular epidemiology ; CYTOKINE ; CELL CARCINOMA ; ONCOLOGY ; case-control study ; RE ; INTERLEUKIN-1 ; PROMOTER POLYMORPHISM ; CYCLOOXYGENASE-2 ; case control studies ; methods ; INTERLEUKIN-8 ; oral cancer ; CANCERS ; ESOPHAGEAL CANCER ; SQUAMOUS-CELL ; INTERLEUKIN-8 PROMOTER ; larynx cancer ; pharynx cancer ; upper aerodigestive tract cancers
    Abstract: Objectives The purpose of this study was to investigate the role of polymorphisms of genes involved in inflammation in the risk of cancers of the upper aerodigestive tract (UADT). Methods We have evaluated the role of polymorphisms in key genes related to inflammation, namely IL1B (rs1143627), COX2/PTGS2 (rs5275), and IL8 (rs4073) in a large case-control study comprising 811 UADT cancer cases and 1,083 controls. Results An association was observed for squamous cell carcinoma of the pharynx for a polymorphism in the promoter of the IL1B gene, with an OR of 2.39 (95% CI = 1.19-4.81) for the homozygotes for the minor allele A promoter polymorphism of IL8 was associated with decreased risk of laryngeal cancer, with an OR of 0.70 (95% CI = 0.50-0.98) for carriers of the minor allele. Conclusions To our knowledge, this is the first report on the role of these polymorphisms with respect to UADT carcinogenesis. Our results suggest that inflammation-related polymorphisms play a role, albeit minor, in the risk of developing cancers of the upper aerodigestive tract
    Type of Publication: Journal article published
    PubMed ID: 17356794
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  • 6
    Keywords: CANCER ; CELL ; human ; LUNG ; MODEL ; PATHWAY ; PATHWAYS ; lung cancer ; LUNG-CANCER ; SUPPORT ; SYSTEM ; SYSTEMS ; RISK ; RISKS ; SITE ; ENZYMES ; GENE ; GENES ; GENOME ; PATIENT ; DNA ; MARKER ; BIOLOGY ; cell cycle ; CELL-CYCLE ; CYCLE ; SEQUENCE ; ASSOCIATION ; POLYMORPHISMS ; SUSCEPTIBILITY ; VARIANTS ; HEALTH ; DNA-REPAIR ; REPAIR ; COMPONENT ; MARKERS ; DAMAGE ; HUMAN GENOME ; REGION ; REGIONS ; DNA-DAMAGE ; CANCER-PATIENTS ; CANCER PATIENTS ; CYCLE CONTROL ; MULTICENTER ; DNA repair ; O-6-ALKYLGUANINE-DNA ALKYLTRANSFERASE ; ONCOLOGY ; RE ; VARIANT ; CHECKPOINT ; biomarker ; INTERVAL ; ENZYME ; analysis ; DNA damage ; HAPLOTYPE ; USA ; odds ratio ; cancer research ; cell cycle checkpoints ; modeling ; cell cycle control ; block ; nonsmokers ; INTEGRITY
    Abstract: The DNA repair systems maintain the integrity of the human genome and cell cycle checkpoints are a critical component of the cellular response to DNA damage. We hypothesized that genetic variants in DNA repair and cell cycle control pathways will influence the predisposition to lung cancer, and studied 27 variants in 17 DNA repair enzymes and 10 variants in eight cell cycle control genes in 1,604 lung cancer patients and 2,053 controls. To improve the estimation of risks for specific variants, we applied a Bayesian approach in which we allowed the prior knowledge regarding the evolutionary biology and physicochemical properties of the variant to be incorporated into the hierarchical model. Based on the estimation from the hierarchical modeling, MGMT 143V or 178R, and CHEK2 157I had an odds ratio of lung cancer equal to 1.45 [95% confidence interval (95% CI), 1.05-2.00], 1.18 (95% CI, 1.01-1.40), and 1.58 (95% CI, 1.14-2.17). The association of CHEK2 1571 seems to be overestimated in the conventional analysis. Nevertheless, this association seems to be robust in the hierarchical modeling. None of the pathways seem to have a prominent effect. In general, our study supports the notion that sequence variation may explain at least some of the variation of inherited susceptibility. In particular, further investigation of OGG1, MGMT, and CHEK2 focusing on the genetic regions where the present markers are located or the haplotype blocks tightly linked with these markers might be warranted
    Type of Publication: Journal article published
    PubMed ID: 18086781
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  • 7
    Keywords: CANCER ; GROWTH ; GROWTH-FACTOR ; BLOOD ; DENSITY ; COHORT ; NEW-YORK ; RISK ; GENE ; SAMPLE ; SAMPLES ; TISSUE ; primary ; RISK-FACTORS ; polymorphism ; POLYMORPHISMS ; single nucleotide polymorphism ; BREAST ; breast cancer ; BREAST-CANCER ; CARE ; DESIGN ; WOMEN ; SNP ; risk factors ; PROSTATE-CANCER ; cancer risk ; RECRUITMENT ; BINDING-PROTEINS ; NETHERLANDS ; POSTMENOPAUSAL WOMEN ; menopause ; SERUM ; ONCOLOGY ; RE ; INCREASE ; SINGLE NUCLEOTIDE POLYMORPHISMS ; SNPs ; GROWTH-FACTOR-I ; ALLELES ; LEVEL ; methods ; HAPLOTYPE ; GENOTYPE DATA ; USA ; PREMENOPAUSAL ; prospective study ; mammographic density ; RISK-FACTOR ; CANCER-RISK ; CIRCULATING LEVELS ; MULTIETHNIC COHORT ; Insulin-Like Growth Factor I ; NOV ; postmenopausal ; quantitative ; block ; breast density ; IGF1 ; breast cancer risk ; NUCLEOTIDE ; APOLIPOPROTEIN-E ISOFORMS ; Prospect-EPIC
    Abstract: Introduction High breast density is one of the strongest known risk factors for developing breast cancer. Insulin-like growth factor I (IGF-I) is a strong mitogen and has been suggested to increase breast cancer risk by increasing the amount of dense tissue in the female breast. Objectives We wanted to investigate the effect of common variation in the IGF-1 gene on serum IGF-I levels and on breast density. Design and methods Mammograms and blood samples of 1,928 premenopausal participants of the Dutch Prospect-EPIC cohort were collected at baseline. Using a haplotype tagging approach, 16 single nucleotide polymorphisms (SNP) from three blocks covering the IGF-1 gene were genotyped in all study participants. Breast density was assessed using a quantitative computer-assisted method. For a subgroup of women, who went through menopause within 5 years after recruitment (n = 656), premenopausal IGF-I levels and additionally postmenopausal breast density were determined. False positive report probabilities (FPRP) for statistically significant relations were calculated using the Wacholder method. Results The minor alleles of five SNPs in block 3 were significantly associated with elevated levels of IGF-I (rs9989002, rs2033178, rs7136446, rs978458, rs6220; P-values: 0.01-0.04). The same SNPs were related with modestly higher percent breast density before menopause and-in the subgroup of women that became postmenopausal during follow-up-with a modestly higher percent breast density after menopause. The most significant result, i.e. the relation between rs6220 and IGF-I levels, had an FPRP 〈 0.5 assuming prior probabilities of 0.01 and higher. Conclusion Common genetic variation in the IGF-1 gene is related to circulating levels of IGF-I, but the relationship with breast density is indecisive
    Type of Publication: Journal article published
    PubMed ID: 18064566
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  • 8
    Keywords: CANCER ; EXPRESSION ; CELL ; LUNG ; lung cancer ; LUNG-CANCER ; TOOL ; CANCER MORTALITY ; EXPOSURE ; MORTALITY ; RISK ; GENE ; GENES ; METABOLISM ; ACTIVATION ; RISK-FACTORS ; CARCINOGENESIS ; ASSOCIATION ; polymorphism ; POLYMORPHISMS ; single nucleotide polymorphism ; SUSCEPTIBILITY ; risk factors ; smoking ; METABOLIC-ACTIVATION ; GENOTYPES ; PHENOTYPE ; CARCINOGENS ; ANTIOXIDANT ; SMOKERS ; non-small cell lung cancer ; glutathione-S-transferase ; molecular epidemiology ; OCCUPATIONAL EXPOSURE ; PHASE-II ; DNA-ADDUCTS ; ONCOLOGY ; SINGLE NUCLEOTIDE POLYMORPHISMS ; SNPs ; GSTM1 ; CYP1A1 ; METHYLENETETRAHYDROFOLATE REDUCTASE ; LEVEL ; analysis ; PHASE ; phase II metabolism ; RISK-FACTOR ; population-based ; TOOLS ; ENGLAND ; CYP1B1 ; NAT2 ; GENE POLYMORPHISMS ; GENE POLYMORPHISM ; NORWAY ; NUCLEOTIDE ; COMT
    Abstract: Lung cancer is a leading cause of cancer mortality worldwide with smoking and occupational exposure to carcinogenic compounds as the major risk factors. Susceptibility to lung cancer is affected by existence of polymorphic genes controlling the levels of metabolic activation and detoxification of carcinogens. We have investigated 105 single nucleotide polymorphisms (SNPs) in 31 genes from the phase I and phase II metabolism genes and antioxidant defense genes for association with the risk of non-small cell lung cancer (NSCLC) in a Norwegian population-based study. Our results indicate that several SNPs in the phase I genes, CYP1B1, CYP2D6, CYP2E1 and CYP3A4, are associated with the risk of NSCLC. Moreover, significant associations with multiple SNPs in the phase II genes ALDH2, COMT, EPHX1, SOD2, NAT1, NAT2, GSTM3, GSTP1, GSTT2 and MPO were also found. We prioritized our findings by use of two different recently developed Bayesian statistical tools, employing conservative prior probabilities of association. When we corrected for multiple testing using these statistical tools, three novel associations of NSCLC risk with SNPs in the CYP1B1 (Arg48Gly), COMT (Val158Met) and GSTT2 (Met139Ile) genes were found noteworthy. However, only four of the previously reported associations with polymorphisms in the GSTP1 (Ala14Val), SOD2 (Val16Ala), EPHX1 (His139Arg) genes and the NAT1 fast acetylator phenotype remained significantly associated with lung cancer
    Type of Publication: Journal article published
    PubMed ID: 18258609
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  • 9
    Keywords: RECEPTOR ; CANCER ; Germany ; PROSTATE ; COMMON ; COHORT ; RISK ; GENE ; GENES ; SAMPLE ; RELEASE ; RISK-FACTORS ; GENETIC POLYMORPHISMS ; ASSOCIATION ; polymorphism ; POLYMORPHISMS ; single nucleotide polymorphism ; VARIANTS ; BREAST ; breast cancer ; BREAST-CANCER ; hormone ; prevention ; HEALTH ; WOMEN ; SNP ; prostate cancer ; PROSTATE-CANCER ; cancer risk ; RISK FACTOR ; POPULATIONS ; genetic polymorphism ; EPIC ; nutrition ; CODE ; SINGLE ; VARIANT ; SINGLE NUCLEOTIDE POLYMORPHISMS ; SNPs ; LEVEL ; HAPLOTYPE ; HORMONES ; TESTOSTERONE ; prospective ; RISK-FACTOR ; CANCER-RISK ; CIRCULATING LEVELS ; MULTIETHNIC COHORT ; BASE-LINE CHARACTERISTICS ; COMMON VARIANT ; LUTEINIZING-HORMONE ; androgens ; ESTROGENS ; CONSORTIUM ; androstenedione ; Genetic ; COMMON VARIANTS
    Abstract: Background: Gonadotropin releasing hormone (GNRH1) triggers the release of follicle stimulating hormone and luteinizing hormone from the pituitary. Genetic variants in the gene encoding GNRH1 or its receptor may influence breast cancer risk by modulating production of ovarian steroid hormones. We studied the association between breast cancer risk and polymorphisms in genes that code for GNRH1 and its receptor (GNRHR) in the large National Cancer Institute Breast and Prostate Cancer Cohort Consortium (NCI-BPC3). Methods: We sequenced exons of GNRH1 and GNRHR in 95 invasive breast cancer cases. Resulting single nucleotide polymorphisms ( SNPs) were genotyped and used to identify haplotype-tagging SNPs (htSNPS) in a panel of 349 healthy women. The htSNPs were genotyped in 5,603 invasive breast cancer cases and 7,480 controls from the Cancer Prevention Study-II (CPS-II), European Prospective Investigation on Cancer and Nutrition ( EPIC), Multiethnic Cohort (MEC), Nurses' Health Study ( NHS), and Women's Health Study (WHS). Circulating levels of sex steroids ( androstenedione, estradiol, estrone and testosterone) were also measured in 4713 study subjects. Results: Breast cancer risk was not associated with any polymorphism or haplotype in the GNRH1 and GNRHR genes, nor were there any statistically significant interactions with known breast cancer risk factors. Polymorphisms in these two genes were not strongly associated with circulating hormone levels. Conclusion: Common variants of the GNRH1 and GNRHR genes are not associated with risk of invasive breast cancer in Caucasians
    Type of Publication: Journal article published
    PubMed ID: 19640273
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  • 10
    Keywords: Germany ; human ; PATHWAY ; DISEASE ; DISEASES ; POPULATION ; RISK ; GENE ; GENES ; microarray ; COMPLEX ; COMPLEXES ; MARKER ; IMPACT ; ASSOCIATION ; polymorphism ; POLYMORPHISMS ; VARIANTS ; FREQUENCIES ; HUMANS ; microarrays ; genetics ; SNP ; affymetrix ; LINKAGE DISEQUILIBRIUM ; POPULATIONS ; VARIANT ; SINGLE NUCLEOTIDE POLYMORPHISMS ; CANDIDATE GENES ; POWER ; USA ; EXTENT ; GENOME-WIDE ASSOCIATION ; biotechnology ; Genetic ; WELL ; Genome-wide association studies ; COVERAGE ; Whole genome ; Illumina
    Abstract: Most genetic variants associated with complex diseases in humans are believed to have a small impact of risk. With traditional candidate gene/pathway approaches several associations with disease risk could be identified. However, now that genome-wide association Studies are feasible, the question arises if there is still a need for these approaches. By using HapMap data, we evaluated to which extent commercially available microarrays cover, through linkage disequilibrium, all currently known genes and biological processes in different populations. Furthermore, we estimated the power to detect all association with any specific SNP. Our study shows that coverage of individual genes and pathways by current commercial genotyping platforms is satisfactory for the vast majority of RefSeq gene regions. However, depending oil the gene or the population, there may still be a need for candidate gene approaches, especially when looking at polymorphisms with low allele frequencies. (C) 2009 Elsevier Inc. All rights reserved
    Type of Publication: Journal article published
    PubMed ID: 19162167
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