Figure 1. Selection of appropriate probes for analysis of frozen and FFPE samples.

(A) Preparation of frozen and FFPE samples. Three colon tumors (#1–3) were cut into two pieces; one was fixed with formalin and embedded in paraffin (FFPE), and the other was frozen with liquid nitrogen and stored at –80° C (frozen). Both tissues underwent DNA extraction and Infinium assays. (B) Plot of β-values. Probes showing the differences in β-values between frozen and FFPE samples of less than 0.1, i.e., between y = x + 0.1 and y = x−0.1, were extracted (red). (C) In total, 161,828 overlapped probes among three analyses (tumors #1, #2, and #3) were extracted and used for subsequent DNA methylation analysis.