Breast, colon, glioblastoma, lung, melanoma, ovarian, pancreas, prostate tumors and cell lines.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE31586 | GEO | 2011/08/24
SECONDARY ACCESSION(S): PRJNA145601
REPOSITORIES: GEO
Similar Datasets
Project description:DNA copy number profiling for all primary tumor samples and cell lines was performed by ROMA, a form of comparative genomic hybridization. The aim was to identify commonly amplifiied and deleted regions. 538 primary tumor samples and 253 human cell lines were analyzed.
2011-08-23 | E-GEOD-31586 | biostudies-arrayexpress
Project description:DNA copy number profiling for all primary tumor samples and HCC cell lines was performed by ROMA, a form of comparative genomic hybridization. The aim was to identify commonly amplifiied and deleted regions across human HCC.
2011-01-10 | GSE22916 | GEO
Project description:DNA copy number profiling for all primary tumor samples and HCC cell lines was performed by ROMA, a form of comparative genomic hybridization. The aim was to identify commonly amplifiied and deleted regions across human HCC. 88 primary HCC samples and 12 human HCC cell lines were analyzed.
2011-01-10 | E-GEOD-22916 | biostudies-arrayexpress
Project description:The identification of genetic and epigenetic alterations from primary tumor cells has become a common method to identify genes critical to the development and progression of cancer. We provide a bioinformatic analysis of copy number variation and DNA methylation covering the genetic landscape of ovarian cancer tumor cells. We individually examined the copy number variation and DNA methylation for 44 primary ovarian cancer samples and 7 ovarian normal samples using our MOMA-ROMA technology and Affymetrix expression data as well as 379 tumor samples analyzed by The Cancer Genome Atlas. We have identified 346 genes with significant deletions or amplifications among the tumor samples. Utilizing associated gene expression data we predict 156 genes with significantly altered copy number and correlated changes in expression. We identify changes in DNA methylation and expression for all amplified and deleted genes. We predicted 615 potential oncogenes and tumor suppressors candidates by integrating these multiple genomic and epigenetic data types. Expression data accompaniment to CSHL ROMA and MOMA3 human ovarian analysis.
2011-10-17 | GSE27943 | GEO
Project description:The identification of genetic and epigenetic alterations from primary tumor cells has become a common method to identify genes critical to the development and progression of cancer. We provide a bioinformatic analysis of copy number variation and DNA methylation covering the genetic landscape of ovarian cancer tumor cells. We individually examined the copy number variation and DNA methylation for 44 primary ovarian cancer samples and 7 ovarian normal samples using our MOMA-ROMA technology and Affymetrix expression data as well as 379 tumor samples analyzed by The Cancer Genome Atlas. We have identified 346 genes with significant deletions or amplifications among the tumor samples. Utilizing associated gene expression data we predict 156 genes with significantly altered copy number and correlated changes in expression. We identify changes in DNA methylation and expression for all amplified and deleted genes. We predicted 615 potential oncogenes and tumor suppressors candidates by integrating these multiple genomic and epigenetic data types. Expression data accompaniment to CSHL ROMA and MOMA3 human ovarian analysis. Correlation of expression to Methylation and Copy Number Variation in ovarian cancer.
2011-10-16 | E-GEOD-27943 | biostudies-arrayexpress
Project description:BackgroundUnderstanding socio-demographic inequalities in stage at diagnosis can inform priorities for cancer control.Patients and methodsWe analysed data on the stage at diagnosis of East of England patients diagnosed with any of 10 common cancers, 2006-2010. Stage information was available on 88 657 of 98 942 tumours (89.6%).ResultsSubstantial socio-demographic inequalities in advanced stage at diagnosis (i.e. stage III/IV) existed for seven cancers, but their magnitude and direction varied greatly by cancer: advanced stage at diagnosis was more likely for older patients with melanoma but less likely for older patients with lung cancer [odds ratios for 75-79 versus 65-69 1.60 (1.38-1.86) and 0.83 (0.77-0.89), respectively]. Deprived patients were more likely to be diagnosed in advanced stage for melanoma, prostate, endometrial and (female) breast cancer: odds ratios (most versus least deprived quintile) from 2.24 (1.66-3.03) for melanoma to 1.31 (1.15-1.49) for breast cancer. In England, elimination of socio-demographic inequalities in stage at diagnosis could decrease the number of patients with cancer diagnosed in advanced stage by ?5600 annually.ConclusionsThere are substantial socio-demographic inequalities in stage at diagnosis for most cancers. Earlier detection interventions and policies can be targeted on patients at higher risk of advanced stage diagnosis.
| S-EPMC3574550 | biostudies-literature
Project description:BackgroundStage at diagnosis strongly predicts cancer survival and understanding related inequalities could guide interventions.MethodsWe analysed incident cases diagnosed with 10 solid tumours included in the UK government target of 75% of patients diagnosed in TNM stage I/II by 2028. We examined socio-demographic differences in diagnosis at stage III/IV vs. I/II. Multiple imputation was used for missing stage at diagnosis (9% of tumours).ResultsOf the 202,001 cases, 57% were diagnosed in stage I/II (an absolute 18% 'gap' from the 75% target). The likelihood of diagnosis at stage III/IV increased in older age, though variably by cancer site, being strongest for prostate and endometrial cancer. Increasing level of deprivation was associated with advanced stage at diagnosis for all sites except lung and renal cancer. There were, inconsistent in direction, sex inequalities for four cancers. Eliminating socio-demographic inequalities would translate to 61% of patients with the 10 studied cancers being diagnosed at stage I/II, reducing the gap from target to 14%.ConclusionsPotential elimination of socio-demographic inequalities in stage at diagnosis would make a substantial, though partial, contribution to achieving stage shift targets. Earlier diagnosis strategies should additionally focus on the whole population and not only the high-risk socio-demographic groups.
| S-EPMC8007585 | biostudies-literature
Project description:ObjectiveWe investigated the association between cancer incidence and body mass index (BMI) variability calculated from the recall of weight at decades of age by participants in the USA Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial.MethodsA total of 89,822 individuals' BMI were recorded as recalled the participant's aged 30, 40, 50, 60, 70 years, and baseline. BMI variability was assessed using four indices: SD, coefficient of variation (CV), variability independent of the mean (VIM), and average real variability (ARV). The multivariate Cox regression analysis was performed to calculate hazard ratios (HRs) of these measures for incident cancers and corresponding 95% CIs.ResultsDuring the median follow-up of 11.8 years, there were newly diagnosed 5,012 cases of prostate cancer, 792 cases of lung cancer, 994 cases of colon cancer, and 132 cases of ovarian cancer. Compared with the lowest quartile (Q1) group, the highest quartile (Q4) group of BMI variability indices was associated with increased lung cancer risk, including BMI_SD (HR, 1.58; 95% CI, 1.17-2.12), BMI_CV (HR, 1.46; 95% CI, 1.10-1.94), BMI_VIM (HR, 1.73; 95% CI, 1.33-2.25), and BMI_ARV (HR, 2.17; 95% CI, 1.62-2.91). Associations between BMI variability and prostate, colon, and ovarian cancer incidences were of limited significance.ConclusionThe findings imply that maintaining a stable weight across adulthood is associated with a decreased incidence of lung cancer.
| S-EPMC9452651 | biostudies-literature
Project description:Mucinous ovarian tumors (MOTs) morphologically and epidemiologically resemble mucinous cystic neoplasms (MCNs) of the pancreas, sharing a similar stroma and both occurring disproportionately among young females. Additionally, MOTs and MCNs share similar clinical characteristics and immunohistochemical phenotypes. Exome sequencing has revealed frequent recurrent mutations in KRAS and RNF43 in both MOTs and MCNs. The cell of origin for these tumors remains unclear, but MOTs sometimes arise in the context of mature cystic teratomas and other primordial germ cell (PGC) tumors. We undertook the present study to investigate whether non-teratoma-associated MOTs and MCNs share a common cell of origin. Comparisons of the gene expression profiles of MOTs [including both the mucinous borderline ovarian tumors (MBOTs) and invasive mucinous ovarian carcinomas (MOCs)], high-grade serous ovarian carcinomas, ovarian surface epithelium, Fallopian tube epithelium, normal pancreatic tissue, pancreatic duct adenocarcinomas, MCNs, and single-cell RNA-sequencing of PGCs revealed that both MOTs and MCNs are more closely related to PGCs than to either eutopic epithelial tumors or normal epithelia. We hypothesize that MCNs may arise from PGCs that stopped in the dorsal pancreas during their descent to the gonads during early human embryogenesis, while MOTs arise from PGCs in the ovary. Together, these data suggest a common pathway for the development of MCNs and MOTs, and suggest that these tumors may be more properly classified as germ cell tumor variants. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
| S-EPMC6240919 | biostudies-literature
Project description:This SuperSeries is composed of the following subset Series: GSE35082: INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (expression) GSE35329: INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (SNP data) GSE35367: INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (CGH) Refer to individual Series
2012-07-31 | E-GEOD-35383 | biostudies-arrayexpress