Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity

Chromosomal aberrations were studied both in a lung cancer cell line and colorectal cancer tumor samples. Results were verified by SKY karyotypes and by DNA ploidy analysis. The sensitivity of detecting chromosomal aberrations in tumor samples was evaluated by analyzing data from simulated mixtures of the lung cancer cell line H1395 and the normal cell line 1395BL from the same patient. Copy number analysis is presented on 12 colorectal cancer tumor samples and on in silico dilutions of a lung cancer cell line and its patient-matched blood cell line.