Project description:Recents studies in mammalian genomes have uncovered the extent of copy number variation (CNV) that contributes to phenotypic diversity, including health and disease status. Here we report the first glimpse of CNVs in the pig genome covering part of the chromosomes 4, 7, 14 and 17 already sequenced and assembled. We used a custom tiling oligonucleotide array with a median probe spacing of 409 bp to screen 12 unrelated Duroc boar founders of a vast-family material. After a strict CNV calling pipeline it was identified 40 copy number variable regions covering all the four chromosomes, with some overlapping segmental duplications and pig unigenes. This CNV snapshot analysis lays the groundwork for a better understanding of porcine phenotypes and genotypes for the identification of important economic traits. Keywords: comparative genome hybridization, CNV, Sus Scrofa, Nimblegen tiling array
Project description:This study examines genomic copy-number variation between two African cichlid species through array comparative genomic hybridization. Probe level hybridization ratios were compared to copy number variation identified in Illumina and Pacific Biosciences genome assemblies from both species. Array comparative genomic hybridization was performed with 3 samples (1 replicate array setup) of genomic DNA from Maylandia zebra vs. Orechromis niloticus XX clone genomic DNA from University of Stirling clonal lines.
Project description:A copy-number variation (CNV) analysis was run on 40 CEU and YRI samples across an array set tiling across the human genome. The array contained 42 million oligos spread across 20 arrays. The final design provided 1 probe per 50bp average density across the genome.<br><br>PLEASE ACCESS FILES DIRECTLY FROM THE FTP SERVER - ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-40
Project description:The identification of genetic and epigenetic alterations from primary tumor cells has become a common method to identify genes critical to the development and progression of cancer. We provide a bioinformatic analysis of copy number variation and DNA methylation covering the genetic landscape of ovarian cancer tumor cells. We individually examined the copy number variation and DNA methylation for 44 primary ovarian cancer samples and 7 ovarian normal samples using our MOMA-ROMA technology and Affymetrix expression data as well as 379 tumor samples analyzed by The Cancer Genome Atlas. We have identified 346 genes with significant deletions or amplifications among the tumor samples. Utilizing associated gene expression data we predict 156 genes with significantly altered copy number and correlated changes in expression. We identify changes in DNA methylation and expression for all amplified and deleted genes. We predicted 615 potential oncogenes and tumor suppressors candidates by integrating these multiple genomic and epigenetic data types. This ROMA experiment was performed on Ovarian Tumor samples using the same platform as previously reported by Navin, N. et. al. Genome Res. 2010 Jan;20(1):68-80 (PMID: 19903760). Analysis of the array data was performed as previously reported in Chen, S. et. al. Cancer Biol Ther. 2008 Nov;7(11):1793-802. (PMID: 18836286 ).