Project description:The study was carried out to identify copy number variations using array-CGH in family having three children affected with albinism (OCA1B) and the males were affected with ID. Agilent’s SureScan microarray scanner with SurePrint G3 Human CGH, 8x60K array platform was used for the study. The probes used for the experiment was approximately 60000 oligonucleotide, allowing detection of deletions above 200 Kb and duplication above 500 kb in entire human genome. CytoGenomics software used to carryout data analysis revealed CNVs in participants.
Project description:The dataset comprises array CGH data of 64 prostate cancer specimens performed on Stanford cDNA microarrays, to accompany the study of J Lapointe et al (2007). For each array, Channel 2 represents Cy5-labeled prostate genomic DNA, and Channel 1 Cy3-labeled normal male genomic DNA. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set, array CGH
Project description:We used array CGH data from Eµ-myc lymphomas to assess significant differences in DNA copy number variation between Cluster 1 and Cluster 2 lymphomas.
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:This series represents the data set described in the publication “Allelic loss in a minimal region on chromosome 16q24 is associated with vitreous seeding of retinoblastoma Keywords: array CGH
Project description:This entry is part of a study comparing various array CGH platforms. In addition to the submitted data the following BT474 profiles were analyzed in this study: GSM69198 , GSM73557 and data from http://research.dfci.harvard.edu/meyersonlab/snp/snp.htm Keywords: Comparitive Genomic Hybridization (CGH) Platform Comparison
Project description:In this study, we extend array CGH technology by making the accurate detection of segmental aneusomies possible from a single lymphoblast and fibroblast following Phi29 DNA polymerase amplification Keywords: array CGH, aCGH
Project description:This series represents the data set described in the publication “Genetic and Immunohistochemical Analysis of Localized Extranodal and Nodal Dendritic Cell Tumours – An Outlook for Individualized Therapies in Rare Tumours” by Ullmann et al. (submitted). Keywords: array CGH