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Transcription profiling by array of breast cancer samples to define breast cancer subsets

ABSTRACT: A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | 537 samples on Affymetrix HG-U133 Plus 2,0 GeneChips arrays for 537 patients. 555 samples on CGH CIT v7 for 531 patients. Breast cancer molecular subtypes have been debated, pointing at their instability and dependence on the original set of samples or genes. Classification of breast cancer currently used in the clinic, albeit being simple, lacks precision. We aimed at defining more homogeneous breast cancer subsets at both the biological and clinical levels. | Submitter : Renaud Schiappa schiappar@ligue-cancer.net | Project leader : Charles Theillet charles.theillet@inserm.fr

ORGANISM(S): Homo sapiens

SUBMITTER: Guedj M

PROVIDER: S-ECPF-MTAB-365 | biostudies-other | 2012 Mar

REPOSITORIES: biostudies-other

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Transcription profiling by array of breast cancer samples to define breast cancer subsets

Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | 537 samples on Affymetrix HG-U133 Plus 2,0 GeneChips arrays for 537 patients. 555 samples on CGH CIT v7 for 531 patients. Breast cancer molecular subtypes have been debated, pointing at their instability and dependence on the original set of samples or genes. Classification of breast cancer currently used in the clinic, albeit being simple, lacks precision. We aimed at defining more homogeneous breast cancer subsets at both the biological and clinical levels. | Submitter : Renaud Schiappa schiappar@ligue-cancer.net | Project leader : Charles Theillet charles.theillet@inserm.fr

2011-09-15 | E-MTAB-365 | biostudies-arrayexpress

Transcription profiling by array of 17 human breast cancer samples

Project description:Cancer evolves dynamically, as clonal expansions supersede or overlap one another, driven by shifting selective pressures, mutational processes and disrupted cancer genes. These processes mark the genome, such that a cancer's life history is encrypted in the timing, ploidy, clonality and patterns of somatic mutation. We developed bioinformatic algorithms to decipher this narrative, and applied them to 21 breast cancer genomes. We find that mutational processes evolve across the lifespan of a breast tumor, with cancer-specific signatures of point mutations and chromosomal instability often emerging late but contributing extensive genetic variation. Subclonal diversification is prominent, providing insight into the dynamics of clonal expansion in breast cancer. Most point mutations are found in just a fraction of tumor cells, together with frequent variegation in chromosomal copy number. Every tumor studied here has a dominant subclonal lineage, representing more than 50% of tumor cells. Minimal expansion of these subclones occurs until many hundreds to thousands of mutations have accumulated, implying the existence of long-lived, quiescent lineages of cells that are capable of substantial proliferation upon acquisition of enabling genomic changes. Expansion of the dominant subclone to an appreciable mass may therefore represent the final rate-limiting step in a breast cancer's development, triggering diagnosis.

| S-ECPF-MTAB-1088 | biostudies-other

Transcription profiling by array of breast cancer samples treated and non-treated with celecoxib

Project description:Biopsies and surgical specimens were obtained from breast tumours treated and non-treated with celecoxib 400mg twice daily for 2 weeks

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Transcription profiling by array of human lung cancer samples

Project description:We identified a tumor signature of 5 genes that aggregates the 156 tumor and normal samples into the expected groups. We also identified a histology signature of 75 genes, which classifies the samples in the major histological subtypes of NSCLC. A prognostic signature of 17 genes showed the best association with post-surgery survival time. The performance of the signatures was validated using a patient cohort of similar size A genome-wide gene expression analysis was performed on a cohort of 91 patients. We used 91 tumor- and 65 adjacent normal lung tissue samples. We defined sets of predictor genes (probe sets) with the expression profiles. The power of predictor genes was evaluated using an independent cohort of 96 non-small cell lung cancer- and 6 normal lung samples

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Transcription profiling of human breast cancer samples

Project description:We measured baseline gene expression profiles for a set of breast tumors. Note: this experiment was modified in June 2008 when the CEL files associated with some hybridizations were changed.

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Transcription profiling by array of tumour samples from patients with a family history of breast cancer

Project description:Tumour samples from patients with a family history of breast cancer.

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Transcription profiling by array of human muscle-invasive bladder cancer samples

Project description:A Cartes d’Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net/). Seven transcriptome datasets corresponding to a new series of 85 MIBC (Muscle-invasive bladder cancer) and six publicly-available series (298 MIBC) were analyzed. Tumors were classified by consensus clustering. Overall survival was determined from Kaplan-Meier curves. The role of the EGFR pathway was investigated by pathway bioinformatics analysis, determination of the expression levels of its components (by microarray, RT-qPCR and western blot) and of EGFR copy number by CGH arrays. A 40-gene transcriptomic classifier was used to identify basal-like cell lines and a basal-like mouse model. Please note 'MIBC molecular subtype': tumors classification using consensus clustering.

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Transcription profiling of human pre-malignant breast cancer samples

Project description:Enlargement of normal terminal duct lobular units (TDLUs) by hyperplastic columnar epithelial cells is one of the most common abnormalities of growth in the adult female human breast. These hyperplastic enlarged lobular units (HELUs) are important clinically as the earliest histologically identifiable potential precursor of breast cancer. The causes of the hyperplasia are unknown but may include estrogen-simulated growth mediated by estrogen receptor alpha, which is highly elevated in HELUs and may be fundamental to their development. This study used DNA microarray technology and RNA from microdissected pure epithelial cells to learn more about changes in gene expression and molecular pathways associated with the development of HELUs from TDLUs Experiment Overall Design: Samples for the microarray studies were derived from 8 formalin-fixed paraffin-embedded tissue (FFPET) biopsies containing paired normal TDLUs and well-developed HELUs from non-cancerous adult female human breasts obtained within the past 3 years. Populations of nearly pure (>95%) epithelial cells were isolated from the TDLUs and HELUs in each biopsy (approximately 25,000 cells/sample) by laser capture microdissection (LCM)

| S-ECPF-GEOD-7377 | biostudies-other

Transcription profiling by array of human breast cancer metastases

Project description:Comparisons among breast cancer metastases at different organs revealed distinct microenvironments as characterized by cytokine content. Such microenvironment distinction might be important to dictate how the cancer cells adapt to survival before they successfully colonize. Experiment Overall Design: 58 breast cancer metastases from different organs were profiled and compared by the expression level of over 400 cytokines. 29 samples were incuded in this series. 29 others as well as 7 in the present series were profiled on U133A platforms and included in series GSE14018.

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Transcription profiling of human breast cancer samples - relapse free survival

Project description:This series represents 180 lymph-node negative relapse free patients and 106 lymph-node negate patients that developed a distant metastasis. Please see attached patient clinical parameters sheet for more information (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?view=data&acc=GSE2034&id=40089&db=GeoDb_blob26). Keywords: other

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