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.

Kresse et al. BMC Research Notes 2010 3:223   doi:10.1186/1756-0500-3-223

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