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  • 1
    Keywords: DISEASE ; DISEASES ; GENE ; GENES ; PROTEIN ; PROTEINS ; RNA ; DNA ; recombination ; tumour ; BIOLOGY ; SEQUENCE ; chromosome ; NUMBER ; MUTATION ; inactivation ; REGION ; MUTATIONS ; EVOLUTION ; DEGRADATION ; CHROMOSOMES ; GENE FAMILY ; AID ; HUMAN GENOME SEQUENCE ; INACTIVATION CENTER ; LINKED MENTAL-RETARDATION ; MAMMALIAN Y-CHROMOSOME ; REPEAT HYPOTHESIS
    Abstract: The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence
    Type of Publication: Journal article published
    PubMed ID: 15772651
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  • 2
    Keywords: CANCER ; tumor ; carcinoma ; PROSTATE ; COMMON ; DIAGNOSIS ; COHORT ; MORTALITY ; RISK ; GENE ; GENES ; SAMPLE ; SAMPLES ; TUMORS ; validation ; MARKER ; ASSOCIATION ; polymorphism ; POLYMORPHISMS ; single nucleotide polymorphism ; BREAST ; breast cancer ; BREAST-CANCER ; NO ; STAGE ; COMPARATIVE GENOMIC HYBRIDIZATION ; HEALTH ; DIFFERENCE ; AGE ; WOMEN ; MEN ; prostate cancer ; PROSTATE-CANCER ; cancer risk ; REGION ; POPULATIONS ; CARRIERS ; case-control studies ; PREDICTORS ; LIFE-STYLE ; NESTED CASE-CONTROL ; SINGLE ; ONCOLOGY ; case control study ; case-control study ; RE ; VARIANT ; ALLELE ; GROWTH-FACTOR-I ; case control studies ; INTERVAL ; CARRIER ; GENOTYPE ; single-nucleotide ; USA ; NO ASSOCIATION ; cancer research ; CANCER-RISK ; MULTIETHNIC COHORT ; BASE-LINE CHARACTERISTICS ; nested case-control study ; case control ; case-control ; AFRICAN-AMERICAN
    Abstract: Two recent studies independently identified polymorphisms in the 8q24 region, including a single nucleotide polymorphism (rsl447295), strongly associated with prostate cancer risk. Here, we replicate the overall association in a large nested case-control study from the National Cancer Institute Breast and Prostate Cancer Cohort Consortium using 6,637 prostate cancer cases and 7,361 matched controls. We also examine whether this polymorphism is associated with breast cancer among 2,604 Caucasian breast cancer cases and 3,118 matched controls. The rs1447295 marker was strongly associated with prostate cancer among Caucasians (P = 1.23 x 10(-13)). When we exclude the Multiethnic Cohort samples, previously reported by Freedman et al., the association remains highly significant (P = 8.64 X 10(-13)). Compared with wild-type homozygotes, carriers with one copy of the minor allele had an ORAC = 1.34 (99% confidence intervals, 1.19-1.50) and carriers with two copies of the minor allele had an ORAA = 1.86 (99% confidence intervals, 1.30-2.67). Among African Americans, the genotype association was statistically significant in men diagnosed with prostate cancer at an early age (P = 0.011) and nonsignificant for those diagnosed at a later age (P = 0.924). This difference in risk by age at diagnosis was not present among Caucasians. We found no statistically significant difference in risk when tumors were classified by Gleason score, stage, or mortality. We found no association between rs1447295 and breast cancer risk (P = 0.590). Although the gene responsible has yet to be identified, the validation of this marker in this large sample of prostate cancer cases leaves little room for the possibility of a false-positive result
    Type of Publication: Journal article published
    PubMed ID: 17409400
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  • 3
    Keywords: CANCER ; PROSTATE ; COMMON ; CT ; SUPPORT ; COHORT ; POPULATION ; RISK ; GENE ; ASSOCIATION ; LINKAGE ; polymorphism ; POLYMORPHISMS ; single nucleotide polymorphism ; SUSCEPTIBILITY ; ALPHA ; BREAST ; breast cancer ; BREAST-CANCER ; hormone ; ENCODES ; HEALTH ; WOMEN ; SNP ; MEN ; prostate cancer ; PROSTATE-CANCER ; LINE ; REGION ; LINKAGE DISEQUILIBRIUM ; POPULATIONS ; POSTMENOPAUSAL WOMEN ; SINGLE ; DEFICIENCY ; ONCOLOGY ; ASSOCIATIONS ; SNPs ; CANCER SUSCEPTIBILITY ; METAANALYSIS ; biomarker ; INTERVAL ; HAPLOTYPE ; HAPLOTYPES ; single-nucleotide ; USA ; HORMONES ; STEROID-HORMONES ; odds ratio ; cancer research ; MULTIETHNIC COHORT ; PREDICT ; steroids ; postmenopausal ; block ; HORMONE-LEVELS ; EXONS ; GENETIC-VARIATION ; ANDROGEN RECEPTOR GENE ; BRAZILIAN PATIENTS ; SERUM ANDROGENS
    Abstract: CYP17 encodes cytochrome p450c17 alpha, which mediates activities essential for the production of sex steroids. Common germ line variation in the CYP17 gene has been related to inconsistent results in breast and prostate cancer, with most studies focusing on the nonsynonymous single nucleotide polymorphism (SNP) T27C (rs743572). We comprehensively characterized variation in CYP17 by direct sequencing of exons followed by dense genotyping across the 58 kb region around CYP17 in five racial/ethnic populations. Two blocks of strong linkage disequilibrium were identified and nine haplotype-tagging SNPs, including T27C, were chosen to predict common haplotypes (R-h(2) 〉= 0.85). These haplotype-tagging SNPs were genotyped in 8,138 prostate cancer cases and 9,033 controls, and 5,333 breast cancer cases and 7,069 controls from the Breast and Prostate Cancer Cohort Consortium. We observed borderline significant associations with prostate cancer for rs2486758 [TC versus TT, odds ratios (OR), 1.07; 95% confidence intervals (95% Cl), 1.00-1.14; CC versus TT, OR, 1.09; 95% CI, 0.95-1.26; P trend = 0.04] and rs6892 (AG versus AA, OR, 1.08; 95% CI, 1.00-1.15; GG versus AA, OR, 1.11; 95% CI, 0.95-1.30; P trend = 0.03). We also observed marginally significant associations with breast cancer for rs4919687 (GA versus GG, OR, 1.04; 95% CI, 0.97-1.12, AA versus GG, OR, 1.17; 95% CI, 1.03-1.34; P trend = 0.03) and rs4919682 (CT versus CC, OR, 1.04; 95% CI, 0.97-1.12; TT versus CC, OR, 1.16; 95% CI, 1.01-1.33; P trend = 0.04). Common variation at CYP17 was not associated with circulating sex steroid hormones in men or postmenopausal women. Our findings do not support the hypothesis that common germ line variation in CYP17 makes a substantial contribution to postmenopausal breast or prostate cancer susceptibility
    Type of Publication: Journal article published
    PubMed ID: 18006912
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  • 4
    Keywords: CANCER ; PATHWAY ; PROSTATE ; COHORT ; RISK ; GENE ; GENES ; BIOLOGY ; MOLECULAR-BIOLOGY ; ASSOCIATION ; CANDIDATE GENE ; POLYMORPHISMS ; hormone ; genetics ; SNP ; MEN ; prostate cancer ; PROSTATE-CANCER ; CARRIERS ; molecular biology ; VARIANT ; SNPs ; CANDIDATE GENES ; LEVEL ; USA ; HORMONES ; TESTOSTERONE ; CIRCULATING LEVELS ; LOCI ; HORMONE-BINDING GLOBULIN ; SERUM ANDROGENS ; CONSORTIUM ; ESTROGEN-RECEPTOR-ALPHA ; sex hormone-binding globulin ; 3 ; Genetic ; genetic variation ; SEX-STEROID-HORMONES
    Abstract: Twin studies suggest a heritable component to circulating sex steroid hormones and sex hormone-binding globulin (SHBG). In the NCI-Breast and Prostate Cancer Cohort Consortium, 874 SNPs in 37 candidate genes in the sex steroid hormone pathway were examined in relation to circulating levels of SHBG (N = 4720), testosterone (N = 4678), 3 alpha-androstanediol-glucuronide (N = 4767) and 17 beta-estradiol (N = 2014) in Caucasian men. rs1799941 in SHBG is highly significantly associated with circulating levels of SHBG (P = 4.52 x 10(-21)), consistent with previous studies, and testosterone (P = 7.54 x 10(-15)), with mean difference of 26.9 and 14.3%, respectively, comparing wild-type to homozygous variant carriers. Further noteworthy novel findings were observed between SNPs in ESR1 with testosterone levels (rs722208, mean difference = 8.8%, P = 7.37 x 10(-6)) and SRD5A2 with 3 alpha-androstanediol-glucuronide (rs2208532, mean difference = 11.8%, P = 1.82 x 10(-6)). Genetic variation in genes in the sex steroid hormone pathway is associated with differences in circulating SHBG and sex steroid hormones
    Type of Publication: Journal article published
    PubMed ID: 19574343
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  • 5
    Keywords: RECEPTOR ; APOPTOSIS ; CANCER ; EXPRESSION ; proliferation ; CELL ; CELL-PROLIFERATION ; MODEL ; MODELS ; PROSTATE ; COMMON ; COHORT ; HISTORY ; RISK ; GENE ; GENES ; FAMILY ; INDEX ; SEQUENCE ; ASSOCIATION ; polymorphism ; POLYMORPHISMS ; single nucleotide polymorphism ; VARIANTS ; BREAST ; NO ; STAGE ; HEALTH ; AGE ; family history ; SNP ; MEN ; prostate cancer ; PROSTATE-CANCER ; cancer risk ; HUMAN GENOME ; BETA ; POPULATIONS ; case-control studies ; BODY ; ESTROGEN-RECEPTOR ; REGRESSION-MODELS ; MASS INDEX ; MASSES ; BODIES ; SINGLE ; ONCOLOGY ; case control study ; case-control study ; REGRESSION ; FAMILIES ; VARIANT ; SINGLE NUCLEOTIDE POLYMORPHISMS ; SNPs ; GRADE ; regulation ; cell proliferation ; GROWTH-FACTOR-I ; ESTROGEN ; biomarker ; case control studies ; INTERVAL ; analysis ; methods ; HAPLOTYPE ; HAPLOTYPES ; LOCUS ; single-nucleotide ; estrogen receptor ; FAMILY-HISTORY ; USA ; INCREASED RISK ; cancer research ; CANCER-RISK ; MULTIETHNIC COHORT ; SET ; nested case-control study ; case control ; LOGISTIC-REGRESSION ; BODY-MASS ; BODY-MASS-INDEX ; ER-BETA ; EXONS ; GENETIC-VARIATION ; TAG SNPS
    Abstract: Background: Estrogen receptor beta (ESR2) may play a role in modulating prostate carcirtogenesis through the regulation of genes related to cell proliferation and apoptosis. Methods: We conducted nested case-control studies in the Breast and Prostate Cancer Cohort Consortium (BPC3) that pooled 8,323 prostate cancer cases and 9,412 controls from seven cohorts. Whites were the predominant ethnic group. We characterized genetic variation in ESR2 by resequencing exons in 190 breast and prostate cancer cases and genotyping a dense set of single nucleotide polymorphisms (SNP) spanning the locus in a multiethnic panel of 349 cancer-free subjects. We selected four haplotype-tagging SNPs (htSNP) to capture common ESR2 variation in Whites; these htSNPs were then genotyped in all cohorts. Conditional logistic regression models were used to assess the association between sequence variants of ESR2 and the risk of prostate cancer. We also investigated the effect modification by age, body mass index, and family history, as well as the association between sequence variants of ESR2 and advanced-stage (〉= T3b, N-1, or M-1) and high-grade (Gleason sum 〉= 8) prostate cancer, respectively. Results: The four tag SNPs in ESR2 were not significantly associated with prostate cancer risk, individually. The global test for the influence of any haplotype on the risk of prostate cancer was not significant (P = 0.31). However, we observed that men carrying two copies of one of the variant haplotypes (TACC) had a 1.46-fold increased risk of prostate cancer (99% confidence interval, 1.06-2.01) compared with men carrying zero copies of this variant haplotype. No SNPs or haplotypes were associated with advanced stage or high grade of prostate cancer. Conclusion: In our analysis focused on genetic variation common in Whites, we observed little evidence for any substantial association of inherited variation in ESR2 with risk of prostate cancer. A nominally significant (P 〈 0.01) association between the TACC haplotype and prostate cancer risk under the recessive model could be a chance finding and, in any event, would seem to contribute only slightly to the overall burden of prostate cancer
    Type of Publication: Journal article published
    PubMed ID: 17932344
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  • 6
    Keywords: CANCER ; GROWTH ; PROSTATE ; COMMON ; COHORT ; RISK ; GENE ; CARCINOGENESIS ; BIOMARKERS ; LINKAGE ; polymorphism ; POLYMORPHISMS ; VARIANTS ; BREAST ; hormone ; HEALTH ; AGE ; MEN ; prostate cancer ; PROSTATE-CANCER ; cancer risk ; LINKAGE DISEQUILIBRIUM ; GERMLINE ; POSTMENOPAUSAL WOMEN ; SINGLE ; VARIANT ; DETERMINANTS ; prospective studies ; GROWTH-FACTOR-I ; LEVEL ; biomarker ; EPIDEMIOLOGIC EVIDENCE ; HAPLOTYPE ; HAPLOTYPES ; LOCUS ; USA ; HORMONES ; HORMONE LEVELS ; TESTOSTERONE ; prospective ; prospective study ; STEROID-HORMONES ; JAPANESE ; UNIT ; cancer research ; CANCER-RISK ; ESTROGEN-LEVELS ; MULTIETHNIC COHORT ; ANDROGEN ; COMMON VARIANT ; SEX-HORMONES ; JAPANESE POPULATION ; androgens ; NONCARRIERS ; FREE TESTOSTERONE ; SERUM ANDROGENS ; CONSORTIUM ; 3 ; Genetic ; genetic variation ; COMMON VARIANTS ; GENE VARIANT ; ALLELIC VARIANTS ; ANDROGEN BIOSYNTHESIS ; UNRELATED INDIVIDUALS
    Abstract: Sex hormones, particularly the androgens, are important for the growth of the prostate gland and have been implicated in prostate cancer carcinogenesis, yet the determinants of endogenous steroid hormone levels remain poorly understood. Twin studies suggest a heritable component for circulating concentrations of sex hormones, although epidemiologic evidence linking steroid hormone gene variants to prostate cancer is limited. Here we report on findings from a comprehensive study of genetic variation at the CYP19A1 locus in relation to prostate cancer risk and to circulating steroid hormone concentrations in men by the Breast and Prostate Cancer Cohort Consortium (BPC3), a large collaborative prospective study. The BPC3 systematically characterized variation in CYP19A1 by targeted resequencing and dense genotyping; selected haplotype-tagging single nuclecitide polymorphisms (htSNP) that efficiently predict common variants in U.S. and Europe-an whites, Latinos, Japanese Americans, and Native Hawaiians; and genotyped these htSNPs; in 8,166 prostate cancer cases and 9,079 study-, age-, and ethnicity-matched controls. CYP19A1 htSNPs, two common missense variants and common haplotypes were not significantly associated with risk of prostate cancer. However, several htSNPs in linkage disequilibrium blocks 3 and 4 were significantly associated with a 5% to 10% difference in estradiol concentrations in men [association per copy of the two-SNP haplotype rs749292-rs727479 (A-A) versus noncarriers; P = 1 x 10(-5)], and with inverse, although less marked changes, in free testosterone concentrations. These results suggest that although germline variation in CYP19A1 characterized by the htSNPs produces measurable differences in sex hormone concentrations in men, they do not substantially influence risk of prostate cancer. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2734-44)
    Type of Publication: Journal article published
    PubMed ID: 19789370
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  • 7
    Keywords: CANCER ; COHORT ; RISK ; GENE ; RISK-FACTORS ; ASSOCIATION ; POLYMORPHISMS ; SUSCEPTIBILITY ; VARIANTS ; HEALTH ; COLON-CANCER ; ALCOHOL ; CONSUMPTION ; FRUIT ; LIFE-STYLE ; MASS INDEX ; CANCER SUSCEPTIBILITY ; METAANALYSIS ; VEGETABLE CONSUMPTION ; LOCI ; GENOME-WIDE ASSOCIATION ; sex ; SCAN ; RISK LOCI ; CHROMOSOME 8Q24
    Abstract: Genome-wide association studies (GWAS) have identified more than a dozen loci associated with colorectal cancer (CRC) risk. Here, we examined potential effect-modification between single-nucleotide polymorphisms (SNP) at 10 of these loci and probable or established environmental risk factors for CRC in 7,016 CRC cases and 9,723 controls from nine cohort and case-control studies. We used meta-analysis of an efficient empirical-Bayes estimator to detect potential multiplicative interactions between each of the SNPs [rs16892766 at8q23.3 (EIF3H/UTP23), rs6983267 at 8q24 (MYC), rs10795668 at 10p14 (FLJ3802842), rs3802842 at 11q23 (LOC120376), rs4444235 at 14q22.2 (BMP4), rs4779584 at 15q13 (GREM1), rs9929218 at 16q22.1 (CDH1), rs4939827 at 18q21 (SMAD7), rs10411210 at 19q13.1 (RHPN2), and rs961253 at 20p12.3 (BMP2)] and select major CRC risk factors (sex, body mass index, height, smoking status, aspirin/nonsteroidal anti-inflammatory drug use, alcohol use, and dietary intake of calcium, folate, red meat, processed meat, vegetables, fruit, and fiber). The strongest statistical evidence for a gene-environment interaction across studies was for vegetable consumption and rs16892766, located on chromosome 8q23.3, near the EIF3H and UTP23 genes (nominal P-interaction = 1.3 x 10(-4); adjusted P = 0.02). The magnitude of the main effect of the SNP increased with increasing levels of vegetable consumption. No other interactions were statistically significant after adjusting for multiple comparisons. Overall, the association of most CRC susceptibility loci identified in initial GWAS seems to be invariant to the other risk factors considered; however, our results suggest potential modification of the rs16892766 effect by vegetable consumption.
    Type of Publication: Journal article published
    PubMed ID: 22367214
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  • 8
    Keywords: CANCER ; GROWTH ; proliferation ; PATHWAY ; PROSTATE ; COHORT ; DISEASE ; HISTORY ; RISK ; GENE ; GENES ; FAMILY ; CARCINOGENESIS ; ASSOCIATION ; polymorphism ; POLYMORPHISMS ; single nucleotide polymorphism ; VARIANTS ; BREAST ; STAGE ; AGE ; OVARIAN-CANCER ; SNP ; MEN ; PROSTATE-CANCER ; FACTOR-I ; CELL-MIGRATION ; PHOSPHOINOSITIDE 3-KINASE ; signaling ; ONCOLOGY ; REGRESSION ; ASSOCIATIONS ; VARIANT ; SINGLE NUCLEOTIDE POLYMORPHISMS ; GROWTH-FACTOR-I ; BINDING PROTEIN-3 ; SINGLE-NUCLEOTIDE POLYMORPHISMS ; PHOSPHATIDYLINOSITOL 3-KINASE ; FACTOR (IGF)-I ; pooled analysis ; FAMILY-HISTORY ; INCREASED RISK ; CANCER-RISK ; genetic association ; single nucleotide ; REGULATORY SUBUNIT
    Abstract: The phosphatidylinositol 3-kinase (PI3K) pathway regulates various cellular processes, including cellular proliferation and intracellular trafficking, and may affect prostate carcinogenesis. Thus, we explored the association between single-nucleotide polymorphisms (SNP) in PI3K genes and prostate cancer. Pooled data from the National Cancer Institute Breast and Prostate Cancer Cohort Consortium were examined for associations between 89 SNPs in PI3K genes (PIK3C2B, PIK3AP1, PIK3C2A, PIK3CD, and PIK3R3) and prostate cancer risk in 8,309 cases and 9,286 controls. Odds ratios (OR) and 95% confidence intervals (95% CI) were estimated using logistic regression. SNP rs7556371 in PIK3C2B was significantly associated with prostate cancer risk [ORper (allele), 1.08 (95% CI, 1.03-1.14); P-trend = 0.0017] after adjustment for multiple testing (P-adj = 0.024). Simultaneous adjustment of rs7556371 for nearby SNPs strengthened the association [ORper (allele), 1.21 (95% CI, 1.09-1.34); P-trend = 0.0003]. The adjusted association was stronger for men who were diagnosed before the age of 65 years [ORper (allele), 1.47 (95% CI, 1.20-1.79); P-trend = 0.0001] or had a family history [ORper (allele) = 1.57 (95% CI, 1.11-2.23); P-trend = 0.0114], and was strongest in those with both characteristics [ORper (allele) = 2.31 (95% CI, 1.07-5.07), P-interaction = 0.005]. Increased risks were observed among men in the top tertile of circulating insulin-like growth factor-I (IGF-I) levels [ORper (allele) = 1.46 (95% CI, 1.04-2.06); P-trend = 0.075]. No differences were observed with disease aggressiveness (Gleason grade = 8 or stage T-3/T-4 or fatal). In conclusion, we observed a significant association between PIK3C2B and prostate cancer risk, especially for familial, early-onset disease, which may be attributable to IGF-dependent PI3K signaling. Cancer Res; 70(6); 2389-96. (C)2010 AACR
    Type of Publication: Journal article published
    PubMed ID: 20197460
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  • 9
    Keywords: DISEASES ; GENE ; METAANALYSIS ; INFERENCE ; 8Q24 ; susceptibility loci ; SCAN ; COMMON VARIANTS ; 5P15.33 ; MULTILOCUS GENOTYPE DATA ; RARE VARIANTS
    Abstract: Colorectal cancer is the second leading cause of cancer death in developed countries. Genome-wide association studies (GWAS) have successfully identified novel susceptibility loci for colorectal cancer. To follow up on these findings, and try to identify novel colorectal cancer susceptibility loci, we present results for GWAS of colorectal cancer (2,906 cases, 3,416 controls) that have not previously published main associations. Specifically, we calculated odds ratios and 95% confidence intervals using log-additive models for each study. In order to improve our power to detect novel colorectal cancer susceptibility loci, we performed a meta-analysis combining the results across studies. We selected the most statistically significant single nucleotide polymorphisms (SNPs) for replication using ten independent studies (8,161 cases and 9,101 controls). We again used a meta-analysis to summarize results for the replication studies alone, and for a combined analysis of GWAS and replication studies. We measured ten SNPs previously identified in colorectal cancer susceptibility loci and found eight to be associated with colorectal cancer (p value range 0.02 to 1.8 x 10(-8)). When we excluded studies that have previously published on these SNPs, five SNPs remained significant at p 〈 0.05 in the combined analysis. No novel susceptibility loci were significant in the replication study after adjustment for multiple testing, and none reached genome-wide significance from a combined analysis of GWAS and replication. We observed marginally significant evidence for a second independent SNP in the BMP2 region at chromosomal location 20p12 (rs4813802; replication p value 0.03; combined p value 7.3 x 10(-5)). In a region on 5p33.15, which includes the coding regions of the TERT-CLPTM1L genes and has been identified in GWAS to be associated with susceptibility to at least seven other cancers, we observed a marginally significant association with rs2853668 (replication p value 0.03; combined p value 1.9 x 10(-4)). Our study suggests a complex nature of the contribution of common genetic variants to risk for colorectal cancer
    Type of Publication: Journal article published
    PubMed ID: 21761138
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