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

Table 1

Median signal intensities calculated using parameters generated in this paper.

Cell line	Median signal	Comment
PC3	0.36	Homozygous deletion of PTEN
Data for 28 male cell lines provided by Affymetrix	1.14	Single copy of X chromosome outside of pseudoautosomal regions
NA04626	2.72	47,XXX
NA01416E	3.41	48,XXXX
NA06061	4.1	49,XXXXX
HTB27	5.31	CN estimated by qPCR for CCND1 is 6.5±1.1
CRL1620	5.79	CN estimated by qPCR for EGFR is 8.6±1.4
CCL251	6.41	CN estimated by qPCR for CCND1 is 10.6±4.4
HTB25	8.22	CN estimated by qPCR for CCND1 is 13.8±1.4
CRL2338	8.82	CN estimated by qPCR for CCND1 is 16.6±0.7
HTB27	9.42	CN estimated by qPCR for ERBB2 is 18.6±2.7
CRL1978	7.95	CN estimated by qPCR for CCND1 is 19.6±6.5
HTB23	11.26	CN estimated by qPCR for CCND1 is 20.6±2.6
HTB19	10.13	CN estimated by qPCR for EGFR is 20.8±2.8
HTB127	13.93	CN estimated by qPCR for CCND1 is 26.1±5.5
CRL2321	14.13	CN estimated by qPCR for CCND1 is 26.6±5.7
HTB41	13.25	CN estimated by qPCR for CCND1 is 46.9±7.1
HTB128	17.92	CN estimated by qPCR for CCND1 is 54.4±14.7
HTB127	21.34	CN estimated by qPCR for ERBB2 is 56.5±3.9