Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA134315 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The incidence of esophageal and junctional adenocarcinoma has increased 6-fold in the west in the last 30 years and 5 year survival remains <14%. We aimed to characterize genome-wide aberrations in esophageal adenocarcinoma to further understand disease pathogenesis and ultimately identify groups with differential survivals with implications for clinical management. Oligo-array-based high-resolution analysis of copy number changes in 89 fresh frozen esophageal adenocarcinoma resection sections with long-term clinical follow-up data was performed. Good quality array comparative genomic hybridization profiles were obtained from 56/89 of the samples (63%). Our analyses confirmed known genomic aberrations in esophageal adenocarcinoma and identified 3 novel genomic regions with copy number changes. A modified T test with adjusted Bonferroni correction identified 17 genes with significantly different log2 ratios (p<4x10-7), including 6 novel genes, that characterize a group with a poorer survival.
2011-05-09 | GSE25201 | GEO
Project description:The incidence of esophageal and junctional adenocarcinoma has increased 6-fold in the west in the last 30 years and 5 year survival remains <14%. We aimed to characterize genome-wide aberrations in esophageal adenocarcinoma to further understand disease pathogenesis and ultimately identify groups with differential survivals with implications for clinical management. Oligo-array-based high-resolution analysis of copy number changes in 89 fresh frozen esophageal adenocarcinoma resection sections with long-term clinical follow-up data was performed. Good quality array comparative genomic hybridization profiles were obtained from 56/89 of the samples (63%). Our analyses confirmed known genomic aberrations in esophageal adenocarcinoma and identified 3 novel genomic regions with copy number changes. A modified T test with adjusted Bonferroni correction identified 17 genes with significantly different log2 ratios (p<4x10-7), including 6 novel genes, that characterize a group with a poorer survival.
2011-02-01 | GSE20154 | GEO
Project description:The incidence of esophageal and junctional adenocarcinoma has increased 6-fold in the west in the last 30 years and 5 year survival remains <14%. We aimed to characterize genome-wide aberrations in esophageal adenocarcinoma to further understand disease pathogenesis and ultimately identify groups with differential survivals with implications for clinical management. Oligo-array-based high-resolution analysis of copy number changes in 89 fresh frozen esophageal adenocarcinoma resection sections with long-term clinical follow-up data was performed. Good quality array comparative genomic hybridization profiles were obtained from 56/89 of the samples (63%). Our analyses confirmed known genomic aberrations in esophageal adenocarcinoma and identified 3 novel genomic regions with copy number changes. A modified T test with adjusted Bonferroni correction identified 17 genes with significantly different log2 ratios (p<4x10-7), including 6 novel genes, that characterize a group with a poorer survival. Total DNA isolated from human tissue sections was used to make fluorescently labeled DNA that was hybridized to Illumina HumanCytoSNP-12 Beadarray. All protocols were carried out following Illumina's standard protocols. After hybridization, raw data were recorded and normalized using Illumina's BeadStudio software v2.0. Matched expression data: GSE25201 GSE19417 D2 MRC/OEA0022CJ5 (GSM482819) D3 MRC/OEA0032CJ5 (GSM482817) D27 MRC/OEA0272CJ1 (GSM482814) D36 MRC/OEA0362CJ3 (GSM482806) D37 MRC/OEA0372AJ0 (GSM482800) D96 MRC/OEA0962BJ0 (GSM482847) D118 MRC/OEA1172CJ1 (GSM482848) D138 MRC/OEA1382CJ0 (GSM482844) D156 MRC/OEA1562CJ2 (GSM482853)
2011-05-09 | E-GEOD-25201 | biostudies-arrayexpress
Project description:Esophageal adenocarcinoma is characterized by complex chromosomal alterations. Tumors were evaluated to identify regions of recurrent copy gains and losses and to determine the prognositic significance of the degree of segmental aneuploidy as measured by SNP array. 41 superficial esophageal adenocarcinomas were analyzed for copy number abnormalities. Matched normal lymph node tissue was used as a copy number reference.
2013-12-01 | E-GEOD-49396 | biostudies-arrayexpress
Project description:Integrated Analysis of Genome-Wide DNA Copy Number and Gene Expression with Patient Outcomes in Esophageal Adenocarcinoma [Copy Number]
| PRJNA294613 | ENA
Project description:Esophageal adenocarcinoma (EAC) is now the most common esophageal malignancy in the United States with >15,000 new cases per year. Prognosis for patients with EAC is poor due to both late diagnosis and early metastasis to lymph nodes. The goal of this study was to perform an integrated analysis of genome-wide DNA copy number changes, gene expression and patient clinical data in order to identify events and genes associated with clinical endpoints or that may play a key role in EAC development and therefore provide potential therapeutic targets. Specifically, we report on a series of 116 EAC specimens studied using Affymetrix SNP 6.0 and U133 Plus 2 GeneChip arrays plus additional cohorts of 73 and 114 EAC patients whose tumors were analyzed using Affymetrix StyI 250K arrays and fluorescence in-situ hybridization (FISH) respectively. Integration of this genomic data with clinical information and outcomes enabled identification of copy number changes and coordinate gene expression events that are associated with patient prognosis, that validate known or suspected oncogenes and tumor suppressor genes and that also facilitate identification of novel, putative driver genes in large regions of copy number gain and loss. These findings add to our understanding of the basic biology of EAC and provide a guide for development of novel prognostic tools and therapies.
2016-11-01 | GSE72660 | GEO
Project description:The incidence of esophageal and junctional adenocarcinoma has increased 6-fold in the west in the last 30 years and 5 year survival remains <14%. We aimed to characterize genome-wide aberrations in esophageal adenocarcinoma to further understand disease pathogenesis and ultimately identify groups with differential survivals with implications for clinical management. Oligo-array-based high-resolution analysis of copy number changes in 89 fresh frozen esophageal adenocarcinoma resection sections with long-term clinical follow-up data was performed. Good quality array comparative genomic hybridization profiles were obtained from 56/89 of the samples (63%). Our analyses confirmed known genomic aberrations in esophageal adenocarcinoma and identified 3 novel genomic regions with copy number changes. A modified T test with adjusted Bonferroni correction identified 17 genes with significantly different log2 ratios (p<4x10-7), including 6 novel genes, that characterize a group with a poorer survival. Total RNA isolated from human tissue sections was used to make fluorescently labeled cRNA that was hybridized to DNA oligonucleotide. Briefly, 4 µg of total RNA was used to synthesize dsDNA through reverse transcription. cRNA was produced by in vitro transcription and labeled postsynthetically with Cy3 or Cy5. Two populations of labeled cRNA, a reference population and an experimental population, were compared with each other by competitive hybridization to microarrays. Two hybridizations were done with each cRNA sample pair using a fluorescent dye reversal strategy. Human microarrays contained oligonucleotide probes corresponding to approximately 21,000 genes. All oligonucleotide probes on the microarrays were synthesized in situ with inkjet technology (Agilent Technologies, Palo Alto, CA). After hybridization, arrays were scanned and fluorescence intensities for each probe were recorded. Ratios of transcript abundance (experimental to control) were obtained following normalization and correction of the array intensity data. Gene expression data analysis was done with the Rosetta Resolver gene expression analysis software (version 7.0, Rosetta Biosoftware, Seattle, WA).
2011-02-01 | E-GEOD-20154 | biostudies-arrayexpress
Project description:Our aim is to identify frequent genomic aberrations both in ESCC and esophageal dysplasia, and to discover important copy number-driving genes and microRNAs in ESCC. We carried out array-based comparative genomic hybridization (array CGH) on 59 ESCC resection samples and 16 dysplasia biopsy samples. Expression of genes at 11q13.3 was analyzed by real-time PCR and immunohistochemistry (IHC). Integrated analysis was performed to identify genes or microRNAs with copy number-expression correlations. Two group experiment, esophageal dysplasia vs. esophageal squamous cell carcinoma. Biological replicates: 16 dysplasias vs. 59 carcinomas
2013-04-29 | E-GEOD-46452 | biostudies-arrayexpress
Project description:Our aim is to identify frequent genomic aberrations both in ESCC and esophageal dysplasia, and to discover important copy number-driving genes and microRNAs in ESCC. We carried out array-based comparative genomic hybridization (array CGH) on 59 ESCC resection samples and 16 dysplasia biopsy samples. Expression of genes at 11q13.3 was analyzed by real-time PCR and immunohistochemistry (IHC). Integrated analysis was performed to identify genes or microRNAs with copy number-expression correlations.
2013-04-29 | GSE46452 | GEO
Project description:Efforts to address the poor prognosis associated with esophageal adenocarcinoma (EAC) have been hampered by a lack of biomarkers to identify early disease and therapeutic targets. Despite extensive efforts to understand the somatic mutations associated with EAC over the past decade, a gap remains in understanding how the atlas of genomic aberrations in this cancer impacts the proteome and which somatic variants are of importance for the disease phenotype. We performed a quantitative proteomic analysis of 23 EACs and matched adjacent normal esophageal and gastric tissues. We explored the correlation of transcript and protein abundance using tissue-matched RNAseq and proteomic data from 7 patients and further integrated these data with a cohort of EAC RNA-seq data (n=264 patients), EAC whole-genome sequencing (n=454 patients) and external published datasets.
2024-08-10 | PXD042792 | Pride