Project description:A standard Affymetrix SNP6.0 assay was performed on the tumour samples of patients where we have exonic sequence data from both the tumour and normal DNA of the same patients. The resulting cellularity, copy number and ploidy information generated helped to inform bespoke algorithms in analysing the sequence data.
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 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 analyzed the miRNA expression in 6 breast cancer cell lines from young (HCC1500, HCC1937) and old (MCF-7, MDA-MB-231, HCC1806 and MDA-MB-468) patients with breast cancer using the GeneChip® miRNA 2.0 Array (Affymetrix, Santa Clara, CA, USA).
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.
