Project description:To investigate the minimal genomic alterations in ameloblastoma, we have employed high-resolution CGH as a discovery platform to identify somatic genomic gains and losses in ameloblastoma tumors.
Project description:A series of studies have been published that evaluate the chromosomal copy number changes of different tumor classes using array Comparative Genomic Hybridization (array CGH), however the chromosomal aberrations that distinguish the different tumor classes have not been fully characterized. Therefore, we performed a meta-analysis of different array CGH data sets in an attempt to classify samples tested across different platforms. As opposed to RNA expression a common reference is used in dual channel CGH arrays: normal human DNA, theoretically facilitating cross-platform analysis. To this aim, cell line and primary cancer data sets from three different dual channel array CGH platforms obtained by four different institutes were integrated. The cell line data were used to develop preprocessing methods which performed noise reduction and transformed samples into a common format. The transformed array CGH profiles allowed perfect clustering by cell line, but importantly not by platform or institute. The same preprocessing procedures used for the cell line data were applied to data from 373 primary tumors profiled by array CGH, including controls. Results indicated that there is no apparent feature related to the institute or platform and that array CGH allows for unambiguous cross-platform meta-analysis. Major clusters with common tissue origin were identified. Interestingly, tumors of hematopoietic and mesenchymal origins cluster separately from tumors of epithelial origin. Therefore it can be concluded that chromosomal aberrations of tumors from hematopoietic and mesenchymal origin versus tumors of epithelial origin are distinct, and these differences can be picked up by metaanalysis of array CGH data. This suggests the possibility of prospectively using combined analysis of diverse copy number datasets for cancer subtype classification. Keywords: comparative genomic hybridization, meta-analysis, cancer
Project description:Aim of this study is to test if a reference channel of a different array can be used to make array CGH more sensitive, cost effective and less labor intensive. The BT474 breast cancer cell line was compared to a mix of normal reference DNAs hybridized on different arrays and days and DNA copy number profiles were evaluated. Quality was assessed, using regular dual channel array CGH as a standard, using four quality measures; i.e. the MAD (median absolute deviation) value of chromosome 2, an amplitude of the ErbB2 gene amplification, a deletion on chromosome 9 and a deflection on chromosome 8. In addition, the use of a reference channel of a different array was tested for genomic DNA derived from formalin-fixed paraffin-embedded tumor tissue samples. This so called across array CGH (aaCGH) analysis yielded slightly higher quality chromosomal copy number profiles when using the same dye compared to analysis using two different dyes, both when exchanging fluorescent signals of hybridizations performed on different arrays and on different days. This approach avoids redundant hybridizations of the same reference material in every experiment and allows hybridization of two test samples on one array. AaCGH analysis substantially reduces cost of consumables and labor while yielding at least equivalent quality as the dual channel procedure. Keywords: array CGH data, across array CGH analysis
Project description:We conducted microarray-based comparative genomic hybridization (array-CGH) with a DNA chip carrying 2,464 BAC clones to examine genomic aberrations of 236 neuroblastomas (112 sporadic and 124 mass screening-detected). In paralell, gene-expression profiling was also performed by using in-house cDNA microarrays. Keywords: Comparative genomic hybridization
Project description:In this study, we investigated CNAs of 4 tumor samples from 2 patients, including conventioanl chromophobe renal cell carcinoma(ChRCC), ChRCC with neuroendocrine differentiation and no-tumor region by 44k oligonucleotide-based array comparative genomic hybridization (array CGH).
Project description:In this study, we investigated CNAs of 20 primary clear cell renal cell caricinomas (ccRCCs), 20 corresponding metastases and another subsets of 30 primary ccRCCs by 44k oligonucleotide-based array comparative genomic hybridization (array CGH).