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  • 1
    Keywords: EXPRESSION ; Germany ; human ; MODEL ; PATHWAY ; PATHWAYS ; SYSTEM ; DISEASE ; DISEASES ; CDNA ; GENE ; GENES ; GENOME ; EPITHELIA ; TISSUE ; COMPLEX ; COMPLEXES ; MESSENGER-RNA ; BIOLOGY ; chromosome ; MOUSE ; IDENTIFICATION ; HEALTH ; DATABASE ; HUMAN GENOME ; HEREDITARY ; INTERFACE ; ORGANIZATION ; GENE-EXPRESSION PROFILE ; TRANSCRIPTS ; ADULT ; RESOURCE ; CANDIDATE GENES ; NEIBANK PROJECT ; SEQUENCE TAG ANALYSIS ; SUPPRESSION SUBTRACTIVE HYBRIDIZATION
    Abstract: Background: The mammalian retina is a valuable model system to study neuronal biology in health and disease. To obtain insight into intrinsic processes of the retina, great efforts are directed towards the identification and characterization of transcripts with functional relevance to this tissue. Results: With the goal to assemble a first genome-wide reference transcriptome of the adult mammalian retina, referred to as the retinome, we have extracted 13,037 non-redundant annotated genes from nearly 500,000 published datasets on redundant retina/retinal pigment epithelium (RPE) transcripts. The data were generated from 27 independent studies employing a wide range of molecular and biocomputational approaches. Comparison to known retina-/RPE-specific pathways and established retinal gene networks suggest that the reference retinome may represent up to 90% of the retinal transcripts. We show that the distribution of retinal genes along the chromosomes is not random but exhibits a higher order organization closely following the previously observed clustering of genes with increased expression. Conclusion: The genome wide retinome map offers a rational basis for selecting suggestive candidate genes for hereditary as well as complex retinal diseases facilitating elaborate studies into normal and pathological pathways. To make this unique resource freely available we have built a database providing a query interface to the reference retinome [ 1]
    Type of Publication: Journal article published
    PubMed ID: 15283859
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  • 2
    Keywords: RECEPTOR ; CANCER ; EXPRESSION ; AGENTS ; Germany ; THERAPY ; RISK ; GENE ; GENE-EXPRESSION ; GENES ; transcription ; TIME ; PATIENT ; TRANSCRIPTION FACTOR ; IMPACT ; RISK-FACTORS ; ASSOCIATION ; polymorphism ; POLYMORPHISMS ; SUSCEPTIBILITY ; VARIANTS ; ALPHA ; BREAST ; breast cancer ; BREAST-CANCER ; ACID ; hormone ; gene expression ; risk factors ; cancer risk ; HIGH-RISK ; DNA-DAMAGE ; EXCHANGE ; CANCER-PATIENTS ; DIABETES-MELLITUS ; CANCER PATIENTS ; ESTROGEN-RECEPTOR ; TAMOXIFEN ; signaling ; CBP ; REGRESSION ; ASSOCIATIONS ; RE ; VARIANT ; ESTROGEN ; CANCER DEVELOPMENT ; NUCLEAR RECEPTORS ; estrogen receptor ; p300 ; RISK-FACTOR ; CANCER-RISK ; FAMILIAL BREAST ; familial breast cancer ; OVARIAN ; MUTATION ANALYSIS ; genotype combination ; GAMMA COACTIVATOR ; PREINVASIVE MAMMARY-TUMORS ; STEROID-HORMONE RECEPTORS
    Abstract: The mitogen effect of the ovarian steroid estrogen is a strong risk factor for breast cancer development. This effect is mainly mediated by the estrogen receptor alpha, a hormone inducible transcription factor, which activates gene expression through recruiting multiple coactivators, such as PPARGC1A, PPARGC1B and EP300. We tested the hypothesis that non-conservative, putative functional amino acid exchanges in PPARGC1A, PPARGC1B and EP300 act as low-penetrance familial breast cancer risk factors. The analysis of 816 BRCA1/2 mutation-negative familial breast cancer patients and 1012 controls revealed an association of the PPARGC1A Thr612Met polymorphism with familial breast cancer (OR = 1.35, 95% CI 1.00-1.81, P = 0.049), high-risk familial breast cancer (OR = 1.51, 95% CI 1.08-2.12, P = 0.017) and bilateral familial breast cancer (OR = 2.30, 95% CI 1.24-4.28, P = 0.009). Logistic regression analyses of the PPARGC1B Ala203Pro variant showed an increased familial breast cancer risk of heterozygous and homozygous variant allele carriers (OR = 1.48, 95% CI 1.15-1.91, P = 0.002). The genotype-combination analysis of the associated PPARGC1A Thr612Met variant and the associated PPARGC1B Ala203Pro variant suggests an allele dose-dependent breast cancer risk (P-trend = 0.0004). Our results indicate for the first time the importance of inherited variants in the estrogen receptor coactivator genes PPARGC1A and PPARGC1B for familial breast cancer susceptibility. Owing to their impact on estrogen signaling, these polymorphisms might also influence adjuvant anti-estrogen therapy, using agents such as tamoxifen and raloxifen, and outcome of breast cancer patients
    Type of Publication: Journal article published
    PubMed ID: 16704985
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  • 3
    Keywords: ACTIVATION, ACTIVATOR, AGE, ALLELE, ALLELES, APOPTOSIS, ASSOCIATION, BREAST, breast cancer, BREAST-C
    Abstract: The Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway mediates the signals of a wide range of cytokines, growth factors and hormones. Thus, aberrant activation of the JAK/STAT pathway may predispose to malignancy due to deregulation of proliferation, differentiation or apoptosis. In this study, we investigated whether genetic variation in the JAK2 gene and the STAT gene region (STAT3, STAT5A and STAT5B) is associated with breast cancer (BC) risk. We carried out a case-control study using a German sample set with 441 familial, unrelated BC cases and 552 controls matched by age, ethnicity and geographical region. A second similar set (381 cases, 460 controls) was applied to validate the findings. Haplotypes in the JAK2gene were not associated with the risk of BC. In the STAT gene region, the rare haplotype CAGCC containing the variant alleles of each single nucleotide polymorphism (SNP) was associated with an increased risk odds ratio (OR=5.83,95% confidence interval (CI) 1.51-26.28). According to Akaike's information criterion, the best model to describe the relationship between the haplotypes and BC was based on the SNIPS rs6503691 (STAT5B) and rs7211777 (STAT3). Carriers of the AC haplotype, which represents the variant alleles of both SNIPS, were at an increased risk (OR= 1.41, 95% Cl 1.09-1.82). A decreased risk was observed for carriers of the AT haplotype (OR= 0.60, 95% Cl 0.38-0.94). Furthermore, individuals with the AC/GC diplotype were at a significantly increased risk (OR=1.88, 95% Cl 1.13-3.14). The observed genetic variation may also influence the inter-individual variation in response to STAT-signalling targeted therapy
    Type of Publication: Journal article published
    PubMed ID: 17639043
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  • 4
    Keywords: RECEPTOR ; CANCER ; CELLS ; Germany ; human ; KINASE ; RISK ; SITE ; SITES ; PROTEIN ; PROTEINS ; DIFFERENTIATION ; TIME ; PATIENT ; IMPACT ; DOMAIN ; BINDING ; PHOSPHORYLATION ; PROTEIN-KINASE ; ASSOCIATION ; polymorphism ; SUSCEPTIBILITY ; VARIANTS ; ALPHA ; BREAST ; breast cancer ; BREAST-CANCER ; ACID ; TARGET ; resistance ; cancer risk ; GROWTH-INHIBITION ; LOCALIZATION ; PKA ; EXCHANGE ; CANCER-PATIENTS ; specificity ; CANCER PATIENTS ; OVEREXPRESSION ; CYCLIC-AMP ; ESTROGEN-RECEPTOR ; TAMOXIFEN ; SUBCELLULAR-LOCALIZATION ; RE ; VARIANT ; HUMAN CANCER ; ESTROGEN ; INTERVAL ; analysis ; estrogen receptor ; HUMAN CANCERS ; RISK-FACTOR ; CANCERS ; CANCER-RISK ; FAMILIAL BREAST ; familial breast cancer ; PROTEIN-KINASE-A ; breast cancer susceptibility ; ALPHA SUBUNIT ; ANTISENSE OLIGODEOXYNUCLEOTIDE ; D-AKAP2 ; RII-BETA SUBUNIT
    Abstract: Overexpression of cAMP-dependent protein kinase A (PKA) is a hallmark of the great majority of human cancers including breast cancer. A-kinase anchoring proteins (AKAPs) coordinate the specificity of PKA signalling by localizing the kinase to its subcellular sites. We tested the hypothesis whether the functional amino acid exchange Ile646Val, located in the kinase-binding domain of AKAP10, is a low-penetrance familial breast cancer risk factor. Ile646Val alters the binding of AKAP10 to PKA and is associated with morbidity. The analysis of 787 BRCA1/2 mutation-negative familial breast cancer patients and 993 controls revealed an association of the AKAP10 Ile646Val polymorphism with increased familial breast cancer risk [odds ratio (OR) = 1.25, 95% confidence interval (CI) 1.03-1.51, P = 0.024]. Our previous study has shown that AKAP13 Lys526Gln is associated with familial breast cancer (OR = 1.58). Here, we discovered that carriers of both variants, AKAP10 Ile646Val and AKAP13 Lys526Gln, are at a further enhanced breast cancer risk (OR = 2.41, 95% CI 1.30-4.46, P = 0.005). PKA is a major target of therapeutic anticancer strategies. Phosphorylation of the estrogen receptor (ER) alpha by PKA induces resistance against the anti-estrogen tamoxifen. Our results indicate for the first time the importance of AKAP10 Ile646Val for familial breast cancer susceptibility. Due to the impact of Ile646Val on the subcellular localization of PKA, it will be interesting to investigate whether this polymorphism influences the effectiveness of PKA and tamoxifen based therapeutic anticancer concepts
    Type of Publication: Journal article published
    PubMed ID: 16956908
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  • 5
    Keywords: RECEPTOR ; CANCER ; EXPRESSION ; Germany ; THERAPY ; POPULATION ; RISK ; SITES ; GENE ; GENES ; HYBRIDIZATION ; PROTEIN ; MESSENGER-RNA ; CARCINOGENESIS ; BINDING ; DOWN-REGULATION ; TYROSINE KINASE INHIBITOR ; ASSOCIATION ; polymorphism ; BREAST ; breast cancer ; BREAST-CANCER ; WOMEN ; TUMOR PROGRESSION ; SNP ; TARGETS ; REPRESSION ; RETINOIC ACID ; VARIANT ; THERAPIES ; SINGLE NUCLEOTIDE POLYMORPHISMS ; BINDING-SITES ; CONFER SUSCEPTIBILITY ; therapeutic ; COMMON VARIANTS ; CHROMOSOME 6Q ; II RECEPTOR
    Abstract: MicroRNAs (miRNAs) negatively regulate expression of target transcripts by hybridization to complementary sites of their messenger RNA targets. Chen et al. have described several putative functional single nucleotide polymorphisms (SNPs) in miRNA target sites. Here, we selected 11 miRNA target site SNPs located in 3' untranslated regions of genes involved in cancer and breast cancer to analyze their impact on breast cancer risk using a large familial study population. Whereas no association was observed for 10 SNPs, a significant association was revealed for the variant affecting a miRNA target site in the estrogen receptor (ESR) 1. Age stratification showed that the association was stronger in premenopausal women [C versus T: odds ratio (OR) = 0.60, confidence interval (CI) = 0.41-0.89, P = 0.010]. Furthermore, the effect was stronger in high-risk familial cases (C versus T: OR = 0.42, CI = 0.25-0.71, P = 0.0009). Clinical studies have shown that elimination of ESR1 significantly reduces breast cancer risk. Thus, therapies that inhibit ESR1 are used for breast cancer treatment. According to in silico analysis, ESR1_rs2747648 affects the binding capacity of miR-453, which is stronger when the C allele is present. In contrast, the T allele attenuates the binding of miR-453, which might lead to a reduced miRNA-mediated ESR1 repression, in consequence higher ESR1 protein levels and an increased breast cancer risk. Thus, the breast cancer protective effect observed for the C allele in premenopausal women is biologically reasonable. The analysis of large study populations in multicentre collaboration will be needed to verify the association and answer questions regarding the possible impact of this variant on therapeutic and clinical outcome
    Type of Publication: Journal article published
    PubMed ID: 19028706
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  • 6
    Keywords: CANCER ; Germany ; DISEASE ; POPULATION ; RISK ; MESSENGER-RNA ; IMPACT ; ASSOCIATION ; polymorphism ; POLYMORPHISMS ; SUSCEPTIBILITY ; VARIANTS ; BREAST ; breast cancer ; BREAST-CANCER ; BRCA1 ; OVARIAN-CANCER ; MUTATION ; SNP ; cancer risk ; MUTATIONS ; US ; case-control studies ; BRCA1/2 ; case control study ; case-control study ; GENETIC EPIDEMIOLOGY ; BRCA2 ; VARIANT ; SNPs ; MUTATION CARRIERS ; USA ; CANCER-RISK ; NOV ; breast cancer risk ; BRCA1 and BRCA2 ; Codon-usage ; SILENT ; SYNONYMOUS SNP
    Abstract: Mutations in BRCA1 and BRCA2 are associated with increased breast cancer risk. While numerous non-synonymous SNPs in BRCA1/2 have been investigated for breast cancer risk, the impact of synonymous SNPs has not been studied so far. Recently, it has been reported that synonymous SNPs leading to an aberration from the preferred codon-usage can have functional effects and consequently be associated with disease. This motivated us to search for SNPs with the tendency to differential codon-usage in BRCA1/BRCA2. Based on defined criteria, two codon-usage-changing variants, Ser455Ser (1365A 〉 G) and Ser2414Ser (7242A 〉 G), were detected in BRCA2, whereas no such variant could be identified in BRCA1. We investigated the impact of these variants on breast cancer risk in a large case-control study. However, both SNPs, BRCA2 Ser2414Ser (7242A 〉 G) and Ser455Ser (1365A 〉 G), showed no association with breast cancer risk. This indicates that these codon-usage-changing SNPs have no major impact on familial breast cancer risk
    Type of Publication: Journal article published
    PubMed ID: 19229607
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  • 7
    Keywords: POPULATION ; RISK ; TUMORS ; ASSOCIATION ; VARIANTS ; breast cancer ; SELECTION ; SUBTYPES ; breast cancer risk ; CONSORTIUM ; INVESTIGATORS ; MODIFIERS ; COMMON VARIANTS ; GENETIC-VARIANTS ; SUSCEPTIBILITY ALLELES ; ZNF365
    Abstract: BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7 x 10(-8), HR = 1.14, 95% CI: 1.09-1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4 x 10(-8), HR = 1.27, 95% CI: 1.17-1.38) and 4q32.3 (rs4691139, P = 3.4 x 10(-8), HR = 1.20, 95% CI: 1.17-1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific association. The 17q21.31 locus was also associated with ovarian cancer risk in 8,211 BRCA2 carriers (P = 2 x 10(-4)). These loci may lead to an improved understanding of the etiology of breast and ovarian tumors in BRCA1 carriers. Based on the joint distribution of the known BRCA1 breast cancer risk-modifying loci, we estimated that the breast cancer lifetime risks for the 5% of BRCA1 carriers at lowest risk are 28%-50% compared to 81%-100% for the 5% at highest risk. Similarly, based on the known ovarian cancer risk-modifying loci, the 5% of BRCA1 carriers at lowest risk have an estimated lifetime risk of developing ovarian cancer of 28% or lower, whereas the 5% at highest risk will have a risk of 63% or higher. Such differences in risk may have important implications for risk prediction and clinical management for BRCA1 carriers
    Type of Publication: Journal article published
    PubMed ID: 23544013
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  • 8
    Keywords: CANCER ; EXPRESSION ; Germany ; human ; DISEASE ; RISK ; GENE ; GENES ; GENOME ; IMPACT ; CARCINOGENESIS ; RAT ; SEQUENCE ; ASSOCIATION ; polymorphism ; POLYMORPHISMS ; BREAST ; breast cancer ; BREAST-CANCER ; MOUSE ; Drosophila ; NUMBER ; AGE ; SIGNAL-TRANSDUCTION ; cancer risk ; HUMAN GENOME ; REGION ; REGIONS ; SELECTION ; MOLECULAR-CLONING ; ONCOLOGY ; SNPs ; SINGLE-NUCLEOTIDE POLYMORPHISMS ; CANCER-RISK ; familial breast cancer ; ENGLAND ; GENOMES ; CONSERVED NONCODING SEQUENCES ; GENE LOSS ; PROTEIN EVOLUTION ; RAB GTPASES
    Abstract: Ultraconserved elements (UCEs) are segments of 〉200 bp length showing absolute sequence identity between orthologous regions of human, rat and mouse genomes. The selection factors acting on these UCEs are still unknown. Recent studies have shown that UCEs function as long-range enhancers of flanking genes or are involved in splicing when overlapping with exons. The depletion of UCEs among copy number variation as well as the significant under-representation of single-nucleotide polymorphisms (SNPs) within UCEs have also revealed their evolutional and functional importance indicating their potential impact on disease, such as cancer. In the present study, we investigated the influence of six SNPs within UCEs on familial breast cancer risk. Two out of six SNPs showed an association with familial breast cancer risk. Whereas rs9572903 showed only a borderline significant association, the frequency of the rare [G] allele of rs2056116 was higher in cases than in controls indicating an increased familial breast cancer risk ([G] versus [A]: odds ratio (OR) = 1.18, 95% confidence interval (CI) 1.06-1.30, P = 0.0020; [GG] versus [AA]: OR = 1.41, 95% CI 1.15-1.74, P = 0.0011). Interestingly, comparing with the older age group, the ORs were increased in woman younger than 50 years of age ([G] versus [A]: OR = 1.27, 95% CI 1.11-1.45, P = 0.0005; [GG] versus [AA]: OR = 1.60, 95% CI 1.22-2.10, P = 0.0007) pointing to an age- or hormone-related effect. This is the first study indicating that SNPs in UCEs might be associated with cancer risk
    Type of Publication: Journal article published
    PubMed ID: 18174240
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  • 9
    Keywords: APOPTOSIS ; CANCER ; CELLS ; EXPRESSION ; proliferation ; CELL ; Germany ; PATHWAY ; PATHWAYS ; COHORT ; RISK ; SITE ; SITES ; GENE ; GENES ; DIFFERENTIATION ; ASSOCIATION ; polymorphism ; POLYMORPHISMS ; single nucleotide polymorphism ; BREAST ; breast cancer ; BREAST-CANCER ; MATURATION ; TARGET ; AGE ; OVARIAN-CANCER ; MUTATION ; SNP ; REGION ; REGIONS ; MUTATIONS ; ONCOGENE ; FREQUENT ; REPRESSION ; ESTROGEN-RECEPTOR ; CELL-DIFFERENTIATION ; ONCOLOGY ; case-control study ; TUMOR INVASION ; VARIANT ; TRANSLATION ; development ; cell differentiation ; CANCER-RISK ; familial breast cancer ; miRNA ; MICRORNA ; breast cancer risk ; Genetic ; single nucleotide ; LOOP ; RNA-INTERFERENCE ; TARGET SITE ; MICRORNA PRECURSORS ; REGULATED MICRORNA ; SP PROTEINS
    Abstract: MicroRNAs (miRNAs) regulate pathways involved in cell differentiation, proliferation, development, and apoptosis by degradation of target mRNAs and/or repression of their translation. Although the single nucleotide polymorphisms (SNPs) in miRNAs target sites have been studied, the effects of SNPs in miRNAs are largely unknown. In our study, we first systematically sequenced miRNA genes reported to be involved in breast cancer to identify/verify SNPs. We analyzed four SNPs, one located in the pre-miRNA and the other three located in miRNA flanking regions, for a putative association with breast cancer risk. The SNP rs895819, located in the terminal loop of pre-miRNA-27a, showed a protective effect. In a large familial breast cancer study cohort, the rare [G] allele of rs895819 was found to be less frequent in the cases than in the controls, indicating a reduced familial breast cancer risk ([G] vs. [A]: OR = 0.88, 95% CI 0.78-0.99, P = 0.0287). Furthermore, age stratification revealed that the protective effect was mainly observed in the age group 〈 50 years of age ([G] vs. [A]: OR = 0.83, 95% CI 0.70-0.98, P = 0.0314), whereas no significant effect was observed in the age group a parts per thousand yen 50 years of age, indicating a possible hormone-related effect. It has been shown that artificial mutations in the terminal loop of miR-27a can block the maturation process of the miRNA. We hypothesize that the G-variant of rs895819 might impair the maturation of the oncogenic miR-27a and thus, is associated with familial breast cancer risk
    Type of Publication: Journal article published
    PubMed ID: 19921425
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  • 10
    Keywords: CANCER ; EXPRESSION ; Germany ; human ; RISK ; SITE ; GENE ; GENES ; PATIENT ; IMPACT ; RISK-FACTORS ; BINDING ; ASSOCIATION ; polymorphism ; POLYMORPHISMS ; SUSCEPTIBILITY ; VARIANTS ; BREAST ; breast cancer ; BREAST-CANCER ; ACID ; OVARIAN-CANCER ; MUTATION ; risk factors ; p53 ; cancer risk ; MUTATIONS ; HIGH-RISK ; EXCHANGE ; CANCER-PATIENTS ; CANCER PATIENTS ; DISORDERS ; RE ; VARIANT ; BINDING-SITE ; INCREASED RISK ; RISK-FACTOR ; CANCER-RISK ; FAMILIAL BREAST ; familial breast cancer ; RARE ; MspI ; DNA HELICASE ; FUNCTIONAL INTERACTION ; HOLLIDAY JUNCTIONS ; JAPANESE POPULATION ; POLYMORPHIC VARIANT ; RECQ HELICASES ; ROTHMUND-THOMSON-SYNDROME ; SYNDROME PROTEIN
    Abstract: Mutations of the human RecQ helicase genes WRN and BLM lead to rare autosomal recessive disorders, Werner and Bloom syndromes, which are associated with premature ageing and cancer predisposition. We tested the hypothesis whether three polymorphic, non-conservative amino acid exchanges in WRN and BLM act as low-penetrance familial breast cancer risk factors. Moreover, we examined the putative impact of p53 MspI 1798G 〉 A, which is completely linked to p53PIN3, a 16 bp insertion/duplication that has been associated with reduced p53 expression, on familial breast cancer risk. Genotyping analyses, performed on 816 BRCA1/2 mutation-negative German familial breast cancer patients and 1012 German controls, revealed a significant association of the WRN Cys1367Arg polymorphism with familial breast cancer (OR = 1.28, 95% CI 1.06-1.54) and high-risk familial breast cancer (OR = 1.32, 95 % CI 1.06-1.65). The analysis of p53 MspI 1798G 〉 A, which is completely linked to p53PIN3, showed a significantly increased familial breast cancer risk for carriers of the 16 bp insertion/duplication, following a recessive mode (OR = 2.15, 95% CI = 1.124.11). WRN Cys1367Arg, located in the C-terminus, the binding site of p53, is predicted to be damaging. The joint effect of WRN Cys1367Arg and p53 MspI resulted in an increased breast cancer risk compared to the single polymorphisms (OR = 3.39, 95% CI 1.19-9.71). In conclusion, our study indicates the importance of inherited variants in the WRN and p53 genes for familial breast cancer susceptibility
    Type of Publication: Journal article published
    PubMed ID: 16501249
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