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In the analysis above, the percentage methylation was averaged between methylated tissue samples when methylation data were available for more than one clinical sample per case.
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Pseudogenes not associated with genes had less methylation in tissue samples that were highly methylated in the parental gene.
In addition, all pseudogenes examined were methylated in all tissue samples.
A majority of the 27 CpG sites inspected within this pseudogene were methylated in all tissue samples.
NRG1 was also methylated in tumour tissue samples while it was not in uncultured normal breast epithelium.
ESR1 was methylated in all tissue samples, whereas APC was unmethylated in one case and RASSF1A in three cases.
We selected methylated genes for classification by ranking genes with P values for testing differential methylation between tumor and normal tissue samples.
Therefore, failure to detect the methylated alleles with the tissue samples should genuinely reflect the lack of methylated targets.
Probes identified as imprinted by partial methylation status in tissue samples were consistently partially methylated in the cell line samples as well.
While these two genes were frequently methylated in 149 CRC tissue samples in the previous study, it was confirmed that they were also frequently methylated in this additional set of CRC tissue samples.
We found these five genes were significantly differentially methylated between the tumor and normal tissue samples.
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