Affymetrix SNP array analysis of the breast cell lines MCF10A, MCF10AT, MCF10CA1h and MCF10CA1a

To characterize genomic instability in breast cancer progression, we examined copy number loss and copy number gain in the MCF10A series of cell lines. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from breast cell lines. The resulting CEL files were normalized individually to a set of CEL files from 127 female CEPH lymphoblastoid cell lines (see linked supplementary file GSE19920_ceph_controls.txt.gz). Copy number variations were determined by an unpaired analysis.