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  • GENOME-WIDE ASSOCIATION  (3)
  • carcinoma  (3)
Keywords
  • 1
    Keywords: RECEPTOR ; CANCER ; POPULATION ; RISK ; SITE ; DISTINCT ; GENE ; GENES ; GENOME ; RESOLUTION ; BINDING ; SEQUENCE ; ASSOCIATION ; SUSCEPTIBILITY ; SUSCEPTIBILITY LOCUS ; ALPHA ; BREAST ; breast cancer ; BREAST-CANCER ; genetics ; SNP ; POPULATIONS ; PROJECT ; ESTROGEN-RECEPTOR ; HETEROGENEITY ; ORIGIN ; TAMOXIFEN ; ASSOCIATIONS ; SNPs ; SCIENCE ; ESTROGEN ; HAPLOTYPE ; LOCUS ; TRAITS ; estrogen receptor ; BINDING-SITE ; CHINESE POPULATION ; GENOME-WIDE ASSOCIATION ; AFRICAN-AMERICAN ; ESTROGEN-RECEPTOR-ALPHA ; CONFER SUSCEPTIBILITY ; BINDING SITE ; Genetic ; COMMON VARIANTS ; ANCESTRY ; PANEL ; CAUSAL VARIANTS
    Abstract: We used an approach that we term ancestry-shift refinement mapping to investigate an association, originally discovered in a GWAS of a Chinese population, between rs2046210[T] and breast cancer susceptibility. The locus is on 6q25.1 in proximity to the C6orf97 and estrogen receptor alpha (ESR1) genes. We identified a panel of SNPs that are correlated with rs2046210 in Chinese, but not necessarily so in other ancestral populations, and genotyped them in breast cancer case: control samples of Asian, European, and African origin, a total of 10,176 cases and 13,286 controls. We found that rs2046210[T] does not confer substantial risk of breast cancer in Europeans and Africans (OR = 1.04, P = 0.099, and OR = 0.98, P = 0.77, respectively). Rather, in those ancestries, an association signal arises from a group of less common SNPs typified by rs9397435. The rs9397435[G] allele was found to confer risk of breast cancer in European (OR = 1.15, P = 1.2x10(-3)), African (OR = 1.35, P = 0.014), and Asian (OR = 1.23, P = 2.9x10(-4)) population samples. Combined over all ancestries, the OR was 1.19 (P = 3.9x10(-7)), was without significant heterogeneity between ancestries (P-het = 0.36) and the SNP fully accounted for the association signal in each ancestry. Haplotypes bearing rs9397435[G] are well tagged by rs2046210[ T] only in Asians. The rs9397435[G] allele showed associations with both estrogen receptor positive and estrogen receptor negative breast cancer. Using early-draft data from the 1,000 Genomes project, we found that the risk allele of a novel SNP (rs77275268), which is closely correlated with rs9397435, disrupts a partially methylated CpG sequence within a known CTCF binding site. These studies demonstrate that shifting the analysis among ancestral populations can provide valuable resolution in association mapping
    Type of Publication: Journal article published
    PubMed ID: 20661439
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  • 2
    Keywords: EXPRESSION ; BREAST-CANCER ; REDUCED RISK ; SKIN-CANCER ; CASP8 GENE ; GENOME-WIDE ASSOCIATION ; COMMON VARIANTS ; SEQUENCE VARIANTS ; INACTIVATING MUTATIONS ; GENETIC-VARIANTS
    Abstract: In an ongoing screen for DNA sequence variants that confer risk of cutaneous basal cell carcinoma (BCC), we conduct a genome-wide association study (GWAS) of 24,988,228 SNPs and small indels detected through whole-genome sequencing of 2,636 Icelanders and imputed into 4,572 BCC patients and 266,358 controls. Here we show the discovery of four new BCC susceptibility loci: 2p24 MYCN (rs57244888[C], OR=0.76, P=4.7 x 10(-12)), 2q33 CASP8-ALS2CR12 (rs13014235[C], OR=1.15, P=1.5 x 10(-9)), 8q21 ZFHX4 (rs28727938[G], OR=0.70, P=3.5 x 10(-12)) and 10p14 GATA3 (rs73635312[A], OR=0.74, P=2.4 x 10(-16)). Fine mapping reveals that two variants correlated with rs73635312[A] occur in conserved binding sites for the GATA3 transcription factor. In addition, expression microarrays and RNA-seq show that rs13014235[C] and a related SNP rs700635[C] are associated with expression of CASP8 splice variants in which sequences from intron 8 are retained.
    Type of Publication: Journal article published
    PubMed ID: 25855136
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  • 3
    Keywords: carcinoma ; CELL ; DISEASE ; EPIDEMIOLOGY ; NEW-YORK ; RISK ; GENE ; GENES ; SAMPLE ; TIME ; RISK-FACTORS ; SEQUENCE ; ASSOCIATION ; SIGNAL ; VARIANTS ; NO ; HEALTH ; genetics ; SNP ; risk factors ; MELANOMA ; HUMAN HOMOLOG ; INDIVIDUALS ; EUROPE ; heredity ; SKIN-CANCER ; basal cell carcinoma ; CELL CARCINOMA ; VARIANT ; SNPs ; CANDIDATE GENES ; EUROPEANS ; USA ; PIGMENTATION ; CANDIDATE ; RISK-FACTOR ; SIGNALS ; COMMON VARIANT ; SET ; NOV ; association study ; BASAL-CELL ; GENOME-WIDE ; CITRULLINATION ; GENETIC-DETERMINANTS ; PEPTIDYLARGININE DEIMINASE
    Abstract: To search for new sequence variants that confer risk of cutaneous basal cell carcinoma (BCC), we conducted a genome-wide SNP association study of 930 Icelanders with BCC and 33,117 controls. After analyzing 304,083 SNPs, we observed signals from loci at 1p36 and 1q42, and replicated these associations in additional sample sets from Iceland and Eastern Europe. Overall, the most significant signals were from rs7538876 on 1p36 (OR = 1.28, P = 4.4 x 10(-12)) and rs801114 on 1q42 (OR = 1.28, P = 5.9 x. 10(-12)). The 1p36 locus contains the candidate genes PADI4, PADI6, RCC2 and ARHGEF10L, and the gene nearest to the 1q42 locus is the ras-homolog RHOU. Neither locus was associated with fair pigmentation traits that are known risk factors for BCC, and no risk was observed for melanoma. Approximately 1.6% of individuals of European ancestry are homozygous for both variants, and their estimated risk of BCC is 2.68 times that of noncarriers
    Type of Publication: Journal article published
    PubMed ID: 18849993
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  • 4
    Keywords: SPECTRA ; carcinoma ; CELL ; NEW-YORK ; POPULATION ; RISK ; RISK-FACTORS ; SKIN ; ASSOCIATION ; polymorphism ; SUSCEPTIBILITY ; VARIANTS ; ACID ; genetics ; MELANOMA ; POPULATIONS ; INDIVIDUALS ; heredity ; MELANOCORTIN-1 RECEPTOR MC1R ; basal cell carcinoma ; CELL CARCINOMA ; VARIANT ; INCREASE ; hair ; HAPLOTYPE ; NONMELANOMA SKIN-CANCER ; USA ; PIGMENTATION ; INCREASES ; GENOME-WIDE ASSOCIATION ; association study ; BASAL-CELL ; CONFERS RISK ; AGOUTI ; EYE-COLOR ; GENE VARIANTS ; MC1R
    Abstract: Fair color increases risk of cutaneous melanoma (CM) and basal cell carcinoma (BCC). Recent genome-wide association studies have identified variants affecting hair, eye and skin pigmentation in Europeans. Here, we assess the effect of these variants on risk of CM and BCC in European populations comprising 2,121 individuals with CM, 2,163 individuals with BCC and over 40,000 controls. A haplotype near ASIP, known to affect a similar spectrum of pigmentation traits as MC1R variants, conferred significant risk of CM (odds ratio (OR) 1.45, P = 1.2 x 10(-9)) and BCC (OR = 1.33, P = 1.2 x 10(-6)). The variant in TYR encoding the R402Q amino acid substitution, previously shown to affect eye color and tanning response, conferred risk of CM (OR = 1.21, P = 2.8 x 10(-7)) and BCC (OR = 1.14, P = 6.1 x 10(-4)). An eye color variant in TYRP1 was associated with risk of CM (OR = 1.15, P = 4.6 x 10(-4)). The association of all three variants is robust with respect to adjustment for the effect of pigmentation
    Type of Publication: Journal article published
    PubMed ID: 18488027
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  • 5
    Keywords: carcinoma ; SURGERY ; validation ; BREAST-CANCER ; statistics ; chemotherapy ; MASS-SPECTROMETRY ; PROFILE ; PROTEIN PROFILES ; prognostic ; proteomic ; CLINICAL PROTEOMICS ; gastric cancer biomarker
    Abstract: Gastric cancer is a commonly diagnosed solid tumor which is associated with a dismal prognosis making early diagnosis essential Thus, this study aimed to identify novel biomarkers in gastric cancer Serum of patients with advanced gastric cancer was collected according to a predefined schedule prior to first-line chemotherapy with epirubicin (50 mg/m(2), day 1), cisplatin (60 mg/m(2), day 1) and capecitabine (1,000 mg/m(2), twice daily on days 1-14) The serum was collected serially before the treatment cycles and then analyzed by SELDI-TOF MS Normal control subjects were matched according to age, gender and serum collection Serum proteomic mass spectrometry data of all subjects were processed using the tbimass R-package and compared We analyzed i) whether proteomic profile changes were associated with a response to chemotherapy and survival, and ii) whether changes in proteomic profiles occurring during the time period of chemotherapy were associated with tumor response In total, 82 patients with adenocarcinoma of the stomach (mean age 57 years, males 69 5%) were treated with a mean number of five chemotherapy cycles The overall tumor response rate, complete and partial remission combined, was 37%, median time to progression was 7 months (95% CI, 6-8) and median overall survival 11 months (95% CI, 95-12) By comparing 77 serum samples of patients with normal matched controls, we identified 32 proteins which discriminated the two groups By selecting the most differentiating proteins, we built a classification model that correctly categorized 81% of the gastric cancer patients and 90% of the normal controls
    Type of Publication: Journal article published
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