Figure 5.

Benefits of read-pattern analysis. Single CpG loci values can confound the methylation call. Consider a scenario of detection of cancer using methylation. (a) Sequence reads in a given region are nearly identical to the reference pattern but are dissimilar due to an error of the methyltransferase. The overall methylation percentage is calculated as 25%. The methylation level of this region is different from that of the reference and, hence, a false positive methylation call can occur. (b) Although the CpG methylation level is the same in the former scenario, there is a molecule that is perfectly methylated. In this case, we consider that this region has a methylated molecule because the multiple CpG site error of methyltransferase in a single DNA molecule occurs with very low probability. Therefore, we call this true positive methylation. (c) In early cancer, there is a small cancer DNA burden in the blood that is nearly undetectable using single CpG methylation (here 2% of methylation). Unless utilizing the methylation pattern of molecules, a false negative result occurs.