Expression analysis of 13 squamous cell carcinomas arising in the vulva
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ABSTRACT: The genome of 14 vulvar SCC was analyzed by aCGH and microarray to identify common imbalances present in the tumors as well as which genes were deregulated. Overall there was a good concordance between the imbalances scored by aCGH and the level of gene expression found by microarray, i.e., the genes located in gained regions were overexpressed while those located in lost regions were found down-regulated. The whole-gene expression profile of 14 SCC of the vulva was compared to 5 normal vulvar samples to identify genes that were deregulated in the tumors genome. Vulvar hyperplasia 03-48 not further analyzed and not included in the normalized data but included in the non-normalized data
Project description:The genome of 14 vulvar SCC was analyzed by aCGH and microarray to identify common imbalances present in the tumors as well as which genes were deregulated. Overall there was a good concordance between the imbalances scored by aCGH and the level of gene expression found by microarray, i.e., the genes located in gained regions were overexpressed while those located in lost regions were found down-regulated.
Project description:The whole-gene expression profile of 24 endometrial stroma sarcol was used to identify genes that were deregulated in the tumors genome. The analysis was performed comparing the high-grade to the low-grade tumors.
Project description:The imbalances scored by arrayCGH mapped to different chromosomes with losses being more common than gains. Frequent losses of large chromosomal segments were scored from 3p and 8p whereas same-sized gains were frequent from 3q and 8q. This is the first study of vulvar tumors using arrayCGH, and some frequent imbalances could be defined precisely.
Project description:The imbalances scored by arrayCGH mapped to different chromosomes with losses being more common than gains. Frequent losses of large chromosomal segments were scored from 3p and 8p whereas same-sized gains were frequent from 3q and 8q. This is the first study of vulvar tumors using arrayCGH, and some frequent imbalances could be defined precisely. 14 patients we analyzed without replicates against a commercial common reference.
Project description:Lung cancer is the worldwide leading cause of death from cancer. This GEO series correspond to one of the BAC aCGH data sets used as validation cohort for the study: Landscape of somatic allelic imbalances and copy number alterations in human lung cancer, Int J Cancer 2012. Genomic profiling of 78 lung carcinomas using 32K BAC aCGH microarrays.
Project description:Primary tumor recurrence occurs commonly after surgical resection of lung squamous cell carcinoma (SCC). The aim of this study was to identify genes involved in recurrence in lung squamous cell carcinoma patients. Array comparative genomic hybridization (aCGH) was performed on DNA extracted from tumour tissue from 62 patients with primary lung squamous cell carcinomas. aCGH data was analysed to identify genes affected by copy number alterations that may be involved in SCC recurrence. Candidate genes were then selected for technical validation based on differential copy number between recurrence and non-recurrence SCC tumour samples. Genes technically validated advanced to tests of biological replication by qPCR using an independent test set of 72 primary lung SCC tumour samples. 18q22.3 loss was identified by aCGH as significantly associated with recurrence (p=0.038). Although aCGH copy number loss associated with recurrence was found for seven genes within 18q22.3, only SOCS6 copy number loss was both technically replicated by qPCR and biologically validated in the test set.
Project description:Chromosomal instability is one of the hallmarks of tumors, which can result in the gain or loss of specific genomic regions or even entire chromosomes. These copy number aberrations (CNAs) play an important role in carcinogenesis and malignant progression through CNA-induced gene expression alterations and, subsequently, key cancer-specific processes. In the current study, we applied aCGH analysis to screen out CNAs with potential prognostic value in lung SCC patients. Depending on their survival time, 100 patients with primary SCC were separated into high- or low-risk groups of prognosis, and copy number aberration (CNA) were analyzed by array-comparative genomic hybridization (array-CGH).