Project description:Structural changes of chromosomes play important roles in the carcinogenesis of colorectal carcinoma (CRC). Here, by using SNP-typing arrays, we have tried to screen for recurrent chromosome copy number changes and loss-of-heterozygosity in the genome of colorectal carcinoma. Genomic DNA was isolated from tumor and paired normal tissues of CRC (n=94), and was hybridized to Affymetrix Mapping 50K Xba 240 arrays. Chromosome copy number and LOH likelihood score was inferred at every SNP locus with CNAG2.0 software (http://www.genome.umin.jp). Keywords: Comparative genomic hybridization
Project description:Integration of transcript expression, copy number and LOH analysis of infiltrating ductal carcinoma of the breast: copy number analysis
Project description:Structural changes of chromosomes play important roles in the carcinogenesis of colorectal carcinoma (CRC). Here, by using SNP-typing arrays, we have tried to screen for recurrent chromosome copy number changes and loss-of-heterozygosity in the genome of colorectal carcinoma. Genomic DNA was isolated from tumor and paired normal tissues of CRC (n=94), and was hybridized to Affymetrix Mapping 50K Xba 240 arrays. Chromosome copy number and LOH likelihood score was inferred at every SNP locus with CNAG2.0 software (http://www.genome.umin.jp). Experiment Overall Design: Tumor samples and paired normal tissues (n=94 for each) were hybridized to the microarrays. Signal intensity data as well as genotype data were compared between a pair of tumor and normal samples with CNAG2.0. The resultant copy number and LOH likelihood score for each sample are thus calculated from two datasets (tumor and normal).
Project description:Integration of transcript expression, copy number and LOH analysis of infiltrating ductal carcinoma of the breast: expression analysis
Project description:Chromosome 1p LOH was seen in one-third of cases. LOH events on chromosomes 11q and 1p were generally accompanied by copy number loss. The one exception was on chromosome 11p, where LOH in all 4 cases was accompanied by normal copy number or diploidy, implying uniparental disomy. Amplification of MYCN was also noted, and also, amplification of a second gene, ALK, in a single case. Keywords: SNP array analysis
Project description:This SuperSeries is composed of the following subset Series: GSE22544: Integration of transcript expression, copy number and LOH analysis of infiltrating ductal carcinoma of the breast: expression analysis GSE22839: Integration of transcript expression, copy number and LOH analysis of infiltrating ductal carcinoma of the breast: copy number analysis Refer to individual Series
