Computational Method for Estimating DNA Copy Numbers in Normal Samples, Cancer Cell Lines, and Solid Tumors Using Array Comparative Genomic Hybridization

Table 5

Comparison of the degree of contamination of cancer cell lines with CEPH cell line NA12776 determined using the picogreen quantitation (averaged over three measurements) and the algorithm presented in this paper.

Cancer cell line	Tissue type	Mix ratio from DNA quantitation	Mix ratio from CN analysis	Percent of SNPs with concordant CN values for contaminated versus pure cancer cell lines
HTB19	Breast	10±1%	9.6%	97.1%
HTB76	Ovary	20±4%	18.2%	98.6%
HTB127	Breast	30±4%	33.6%	98.5%
CCL228*	Colon	40±3%	43.4%	95.9%
CCL253*	Colon	50±2%	60.7%	88.2%
HTB119	Lung	60±2%	54.1%	99.8%
HTB9	Urinary bladder	70±2%	74.3%	97.0%
HTB41	Salivary gland	80±1%	84.7%	56.9%

∗For these two samples one of the picogreen measurements failed.