Journal article

Evaluation of Different Oligonucleotide Base Substitutions at CpG Binding sites in Multiplex Bisulfite-PCR sequencing

Jennifer Lu, Kelin Ru, Ida Candiloro, Alexander Dobrovic, Darren Korbie, Matt Trau

Scientific Reports | NATURE PUBLISHING GROUP | Published : 2017

Abstract

Multiplex bisulfite-PCR sequencing is a convenient and scalable method for the quantitative determination of the methylation state of target DNA regions. A challenge of this application is the presence of CpGs in the same region where primers are being placed. A common solution to the presence of CpGs within a primer-binding region is to substitute a base degeneracy at the cytosine position. However, the efficacy of different substitutions and the extent to which bias towards methylated or unmethylated templates may occur has never been evaluated in bisulfite multiplex sequencing applications. In response, we examined the performance of four different primer substitutions at the cytosine pos..

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University of Melbourne Researchers

Grants

Awarded by National Breast Cancer Foundation, Australia


Funding Acknowledgements

This work was supported by the National Breast Cancer Foundation, Australia [Grant number CG-12-07].