BioMed Research International / 2010 / Article / Tab 5

Research Article

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 lineTissue typeMix ratio from DNA quantitationMix ratio from CN analysisPercent of SNPs with concordant CN values for contaminated versus pure cancer cell lines

HTB19Breast 1 0 ± 1 % 9.6%97.1%
HTB76Ovary 2 0 ± 4 % 18.2%98.6%
HTB127Breast 3 0 ± 4 % 33.6%98.5%
CCL228*Colon 4 0 ± 3 % 43.4%95.9%
CCL253*Colon 5 0 ± 2 % 60.7%88.2%
HTB119Lung 6 0 ± 2 % 54.1%99.8%
HTB9Urinary bladder 7 0 ± 2 % 74.3%97.0%
HTB41Salivary gland 8 0 ± 1 % 84.7%56.9%

For these two samples one of the picogreen measurements failed.

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