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Expression data from colorectal cancer patients

ABSTRACT: The study consist of patients who presented at Memorial Sloan-Kettering Cancer Center with a colonic neoplasm between 1992 and 2004. Biological specimens used in this study include primary colon adenocarcinomas, adenomas, metastasis and corresponding normal mucosae. 390 expression arrays

ORGANISM(S): Homo sapiens

SUBMITTER: Michal Sheffer

PROVIDER: E-GEOD-41258 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Association of survival and disease progression with chromosomal instability: a genomic exploration of colorectal cancer.

Sheffer Michal M Bacolod Manny D MD Zuk Or O Giardina Sarah F SF Pincas Hanna H Barany Francis F Paty Philip B PB Gerald William L WL Notterman Daniel A DA Domany Eytan E

Proceedings of the National Academy of Sciences of the United States of America 20090409 17

During disease progression the cells that comprise solid malignancies undergo significant changes in gene copy number and chromosome structure. Colorectal cancer provides an excellent model to study this process. To indentify and characterize chromosomal abnormalities in colorectal cancer, we performed a statistical analysis of 299 expression and 130 SNP arrays profiled at different stages of the disease, including normal tissue, adenoma, stages 1-4 adenocarcinoma, and metastasis. We identified ...[more]

PMID: 19359472

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Expression data from colorectal cancer patients

Project description:The study consist of patients who presented at Memorial Sloan-Kettering Cancer Center with a colonic neoplasm between 1992 and 2004. Biological specimens used in this study include primary colon adenocarcinomas, adenomas, metastasis and corresponding normal mucosae.

2012-10-02 | GSE41258 | GEO

Subpopulations of MDA-MB-231 and Primary Breast Cancers

Project description:Subpopulations of MDA-MB-231 that exhibit different metastatic tropisms when injected into immuno-deficient mice. Also, a cohort of primary breast cancers surgically resected at the Memorial Sloan-Kettering Cancer Center (MSKCC). Keywords = Breast cancer Keywords = lung metastasis Keywords: parallel sample

2005-07-28 | GSE2603 | GEO

Identification of candidate microRNAs in colorectal adenomas and adenocarcinomas

Project description:We showed that some microRNAs could be characteristic of the progression from adenoma to adenocarcinoma in colorectal cancer. 48 colorectal biopsy samples (28 adenomas, 15 adenocarcinomas and 5 normal mucosae) were analyzed. We generated three comparisons: adenomas versus. normal mucosae, adenocarcinomas versus. normal mucosae, and adenocarcinomas versus. adenomas.

2013-08-30 | E-GEOD-50194 | biostudies-arrayexpress

Transcription profiling of human primary breast tumors and MDA-MB-231 subpopulations

2008-06-12 | E-GEOD-2603 | biostudies-arrayexpress

RNA sequencing quantitative analysis of exosome miRNAs in plasma in Metastatic renal cell carcinoma (mRCC)

Project description:Purpose: Since clinical characteristics are often inaccurate and subjective, we evaluated the prognostic value of plasma exosomal miRNAs to predict survival in metastatic renal cell cancer (mRCC). Methods: RNA sequencing was performed to identify candidate exosomal miRNAs associated with overall survival in a screening cohort of 41 mRCC patients.Candidate miRNAs were further evaluated for prognosis by TaqMan quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) in a follow-up cohort of 65 mRCC patients. Results: RNA sequencing in screening cohort generated 3.75 million mappable reads per patient, of those with normalized read counts>8 RPM (reads per million), 93.8% were mapped to miRNAs for a total of 322 unique miRNAs. Cox regression analysis identified 20 miRNAs that were associated with overall survival (OS, FDR< 0.05). Among these 20 significant miRNAs, three were validated in a separate independent cohort of 65 patients with mRCC.Patients with lower expression of miR-26a1-3p, miR-let-7i-5p and miR-615-3p had a significantly poorer OS than those with higher expression. Multivariate model by combining miR-let-7i-5p and the Memorial Sloan-Kettering Cancer Center (MSKCC) score significantly improved survival prediction. Conclusions: Our study identifies multiple plasma exosomal miRNAs showing association with survival in mRCC stage patients. Multivariate model by combining miR-let-7i-5p and the Memorial Sloan-Kettering Cancer Center (MSKCC) score significantly improved survival prediction.

2017-10-31 | GSE93175 | GEO

A unique pair of microarray datasets for microRNA profiling: data with careful design (Dataset A)

Project description:We set out to demonstrate the logistic feasibility of careful study design in microarray studies and the level of scientific benefits it can provide, in comparison with post-hoc data adjustment such as normalization, for preventing confounding handling effects and improving the accuracy and reproducibility of disease-relevant biomarker detection. Towards this end, we conducted a study of microRNA expression using endometroid endometrial cancer tumors (n=96) and serous ovarian cancer tumors (n=96) that were all primary, untreated, and collected in 2000-2012 at Memorial Sloan Kettering Cancer Center. The same set of tumor tissue samples were profiled twice using the Agilent microRNA microarrays with different study designs.

2018-01-08 | GSE108838 | GEO

Gene expression data from patients with pancreatic ductal adenocarcinoma

Project description:Pancreatic ductal adenocarcinoma (PDAC) is one of the most treatment-resistant malignancies in human. To perform transcriptomic profiling on PDAC, we collected primary PDAC tissues from surgically resected PDAC patients at the Memorial-Sloan Kettering Cancer Center (NY, USA). Morphogenesis of epithelial tissues relies on the precise developmental control of cell polarity and architecture. In the early Drosophila embryo, the primary epithelium forms during cellularisation, following a tightly controlled genetic programme where specific sets of genes are up-regulated. Some of them, for instance, control membrane invagination between the nuclei anchored at the apical surface of the syncytium. We used microarrays to detail transcritomic profiling of PDACs.

2021-09-23 | GSE184585 | GEO

Long Term Bowel Function Following Rectal Cancer Surgery

Project description:* In this longitudinal study, 171 patients were evaluated and compared based on the radiation therapy they received. * Bowel function was assessed longitudinally with Memorial Sloan Kettering Cancer Center and Wexner scores every 6 months after restoration of bowel continuity. Patients with at least two follow-up visits were included.

| 2719648 | ecrin-mdr-crc

The effectiveness of self-management intervention program for the management of bowel symptoms after shincter preserving surgery in rectal cancer patients

Project description:intervention group:self management intervention program for bowel symptoms after SPS;Control group:routine care Primary outcome(s): Low anterior resection syndrone;Memorial Sloan-Kettering Cancer Center Bowel Function Questionnaire;bowel symptom self-management behavior;Quality of life;self efficacy in bowel symptom management Study Design: Randomized parallel controlled trial

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Transcription profiling of human cisplatin based chemotherarpy adult male germ cell tumor patients - validation set for prediction of outcome

Project description:This series represents expression profiles of 34 non-seminoma germ cell tumors (NSGCTs) from patients who received cisplatin based chemotherarpy for treatment of their disease for whom full clinical follow-up information was available. These specimens were used as a validation set to test outcome prediction models using a subset of previously profiled GCT specimens (see GEO accession #GSE3218). Experiment Overall Design: Tumor tissues were collected under IRB-approved protocols at the Memorial Sloan-Kettering Cancer Center, New York, between 1987 and 2003. The tumor samples consist of 34 NSGCT specimens. RNA was isolated, labeled, and hybridized to Affymetrix U133A and U133B microarrays using standard protocols. Data were processed by the RMA method.

2008-10-26 | E-GEOD-10783 | biostudies-arrayexpress

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