Project description:We performed a comparison analysis of the Affymetrix arrays SNP6.0 genome wide array (SNP6.0) and cytogenetic 2.7M whole-genome array (Cyto2.7M) using nine human samples. We compared the two array types with respect to four parameters including the size and breakpoints of the alterations detected, the actual CN assigned to the CNVs as well as long stretches of loss of heterozygosity. Overall, we found very good consistency between the two types of array on all parameters compared, even in regions with very complex changes. This GEO submission contains the Cyto2.7M data. GEO submission, GSE37977 contains the SNP6.0 data.
Project description:We performed a comparison analysis of the Affymetrix arrays SNP6.0 genome wide array (SNP6.0) and cytogenetic 2.7M whole-genome array (Cyto2.7M) using nine human samples. We compared the two array types with respect to four parameters including the size and breakpoints of the alterations detected, the actual CN assigned to the CNVs as well as long stretches of loss of heterozygosity. Overall, we found very good consistency between the two types of array on all parameters compared, even in regions with very complex changes. This GEO submission contains the SNP6.0 data. GEO submission, GSE37978 contains the Cyto2.7M data.
Project description:We performed a comparison analysis of the Affymetrix arrays SNP6.0 genome wide array (SNP6.0) and cytogenetic 2.7M whole-genome array (Cyto2.7M) using nine human samples. We compared the two array types with respect to four parameters including the size and breakpoints of the alterations detected, the actual CN assigned to the CNVs as well as long stretches of loss of heterozygosity. Overall, we found very good consistency between the two types of array on all parameters compared, even in regions with very complex changes. This SuperSeries is composed of the SubSeries listed below.
Project description:Copy number profile of cultured Breast Cancer cell line measured by Affymetrix SNPs microarrays Whole genome copy number profile of 2 breast cancer cell lines were analyzed using Affymetrix SNP6.0 arrays
Project description:We present evidence for cytogenetic changes in two transformed ovarian surface epithelium cell lines, TOSE1 and TOSE4. hTERT-immortalised ovarian surface epithelial cell line spontaneously transformed as measured by growth in soft agar. These cells were grown on plastic, and genomic DNA was extracted and analyzed for cytogenetic changes. The genotyping Affymetrix SNP6.0 arrays were used to define copy number changes in the TOSE1 and TOSE4 cell lines.
Project description:We obtained gene expression data and HD-SNP6.0 copy number data from PTL, PCNSL and PMLBCL samples and performed an integrative analysis on them. RNA was whole genome amplified using Nugen.
