S1 File -

S1 Table. Primer sets and quantitative real-time PCR conditions for the quantification of LINE-1 and Alu methylation levels. The methylation-dependent-specific PCR (MSP) primers (Me-) and the methylation-independent PCR (MIP) primers were designed based on the consensus sequences of LINE-1 and Alu [23]. All non-CpG cytosines have been replaced by “t” in the forward primers and by “a” in the reverse primers. S2 Table. Correlation between the clinicopathological characteristics of cancer patients and LINE-1 and Alu methylation status in tissues of breast cancer and lung cancer (A) and in cfDNA from lung cancer patients (B). S1 Fig. The effect of excessive DNA input for bisulfite conversion on PCR amplification efficiency and the methylation levels of LINE-1 and Alu. The amplification efficiency of the MIP primers and MSP primers to different amounts of fully methylated human DNA (50 ng, 5 ng, 1 ng, 0.2 ng, and 0.02 ng). The ΔCT values significantly differ at input amounts from 50 ng to 1 ng with the LINE-1 (A) and Alu (B) targets. An increase in DNA input for bisulfite conversion was shown to associate with an under-methylated level of LINE-1 (C) and Alu (D). The Unpaired t-test was used in statistical analysis. The number of observations for each assay was ≥ 4. (ns) P > 0.05; (**) P S2 Fig. Correlation between age and LINE-1 and Alu methylation levels. LINE-1 methylation levels in cfDNA correlated with the age of healthy individuals (A) but did not with the age of lung cancer patients (B). Alu methylation levels in cfDNA are uncorrelated with the age of healthy individuals (C) and lung cancer patients (D). Methylation assessments were performed on two microliters of bisulfite-converted cfDNA. Spearman’s rank correlation test (A – D) was used in statistical analysis. (ZIP)