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=== Quantitatively estimation to the level of cancer DNA fractions in the plasma === By computationally mixing the sequencing reads from cancer tissues and whole blood samples (WBC), we created synthetic admixtures at various levels of tumor fraction. We found that MHL is 2-5 folder higher than the methylation level of individual CpG sites across the full range of tumor fractions. Remarkably, MHL provides additional gain of signal-to-noise ratio (mean divided by standard deviation) compared with AMF as the fraction of tumor DNA decreases below 10%, which is typical for clinical samples. We then took the individual plasma data sets, and predicted the tumor fraction based on the MHL distribution established by computational mixing. Except for a small number (N<5) of outliers, we observed significantly higher average MHL in cancer plasma than in normal plasma. Note that all Group II MHBs were selected without using any information from the plasma samples, and hence they should be generally applicable to other plasma samples. Interestingly, we also found that the estimated tumor DNA fraction were positive correlated with normalized cfDNA yield from the cancer patients (P<0.000023).
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