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We finally checked the potential for age prediction using the methylation levels of the age-associated signature, regardless of tissue type.
Similarly as in our discovery cohort, hierarchical clustering using the methylation levels of these CpGs identified two main clusters, one that consisted primarily of fusion-positive tumors (89 %) and the other that consisted mostly of fusion-negative tumors (95%%; Fig. 4c).
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In addition to the analysis using the methylation level of a single gene, we performed an exploratory analysis by combining methylation of three marker genes.
We used the methylation levels (TaqMeth V) for NEFH to construct Receiver Operating Characteristic (ROC) curves for the detection of ESCC.
Importantly, we were able to use the methylation levels of the cluster to stratify the patients for overall survival, pointing to the potential prognostic and therapeutic significance for this epigenetic modification.
Similar results were obtained in this study when we used the methylation level of anti-sense (data not shown).
The BeadChips were scanned using a BeadStation, and the methylation level (beta value) calculated for each queried CpG locus using the Methylation Module of BeadStudio software.
Male methylation levels were used as the methylation level of the Xa.
RRBS assays were used to determine the methylation levels of more than 1.3 million CpG sites (approximately 6% of all CpG sites in the entire genome).
Sequenom MassARRAY platform (MassARRAY) was used to examine the methylation levels of ALDH2 promoter upstream sequence.
Illumina Human Methylation27 DNA analysis bead chips were used to determine the methylation levels of 27,578 CpG sites.
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