Identification of rare levels of methylated tumor DNA fragments using an optimized bias based pre-amplification-digital droplet PCR (OBBPA-ddPCR).

ABSTRACT:

Background

The analysis of aberrant DNA methylations is used for the diagnosis of cancer as significant changes in the gene methylation pattern are often detected during early carcinogenesis. In this study, we evaluated the performance of a two-step method that combines pre-amplification with ddPCR technique.

Results

By using ddPCR, the dependence of amplification efficiency for methylated and unmethylated DNA fragments on the relevant MgCl₂ concentration and the annealing temperature was established in addition to the primer design. We found that the efficiency can be adjusted toward methylated sequences by using primers covering one to four CpG sites under appropriately selected MgCl₂ concentration and annealing temperature. Applying a PCR bias betwee

SUBMITTER: Menschikowski M 

PROVIDER: S-EPMC6281424 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature