Evaluation of high-resolution microarray platforms for genomic profiling of bone tumours

BMC Research Notes

Table 2 Reproducibility of replicate hybridisations and signal response to copy number

Platform	Corr TC-32	Corr OSA	0n: CDKN2A TC-32		1n: 9p21.3-p21.2 TC-32 Log₂ratio (SD)	2n: Chr 2 TC-32 Log₂ratio (SD)	3n: Chr 8 TC-32 Log₂ratio (SD)	4n: 1q TC-32 Log₂ratio (SD)	>10n: MDM2 OSA
			Log₂ratio (SD)	Size [kb]					Log₂ratio (SD)	Size [kb]
Theoretical value	1.0	1.0	< -3	-	-1.0	0.0	0.58	1.0	> 3	-
Affymetrix Genome-Wide Human SNP Array 6.0	0.75	0.84	-1.79 (0.93)	166	-0.53 (0.43)	0.00 (0.41)	0.34 (0.44)	0.56 (0.44)	1.86 (0.49)	146
			-2.09 (0.92)	148	-0.62 (0.35)	0.00 (0.32)	0.37 (0.34)	0.59 (0.34)	1.99 (0.50)	146
Agilent Human Genome CGH 244A	0.91	0.91	-4.72 (1.57)	135	-0.96 (0.31)	0.00 (0.19)	0.52 (0.27)	0.92 (0.22)	4.69 (0.24)	147
			-4.83 (1.53)	135	-0.97 (0.30)	0.01 (0.21)	0.54 (0.29)	0.95 (0.25)	4.74 (0.21)	147
Illumina HumanExon510 s-duo	0.96	0.94	-4.72 (1.07)	171	-0.67 (0.54)	-0.05 (0.20)	0.22 (0.29)	0.36 (0.26)	1.24 (0.59)	122
			-4.69 (0.91)	171	-0.67 (0.59)	-0.05 (0.20)	0.22 (0.29)	0.36 (0.26)	1.23 (0.58)	122
Nimblegen HG18 CGH 385 k WG Tiling v1.0	0.63	0.73	-0.85 (0.57)	169	-0.45 (0.30)	-0.06 (0.19)	0.24 (0.21)	0.48 (0.24)	2.58 (0.98)	156
			-0.88 (0.50)	169	-0.47 (0.29)	-0.06 (0.20)	0.26 (0.21)	0.53 (0.23)	2.46 (1.0)	156

Pearson's correlation of log₂ ratios for the replicate hybridisations based on all data points and the average log₂ ratio with standard deviation for six specific chromosomes or chromosomal regions, representing 0, 1, 2, 3 and 4 copies in TC-32, as well as high-level amplification in OSA, for each hybridisation. In addition, the measured size of the regions for homozygous deletion of the CDKN2A locus in TC-32 and high-level amplification of the MDM2 locus in OSA is given for each hybridisation.

ISSN: 1756-0500