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Title: Evaluation of Different Oligonucleotide Base Substitutions at CpG Binding sites in Multiplex Bisulfite-PCR sequencing.
Austin Authors: Lu, Jennifer;Ru, Kelin;Candiloro, Ida L M;Dobrovic, Alexander ;Korbie, Darren;Trau, Matt
Affiliation: Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
Centre for Personalised Nanomedicine, Australian Institute for Nanoengineering and Biotechnology, University of Queensland, Brisbane, Australia
Peter MacCallum Cancer Center, Parkville, Australia
Issue Date: 2017 2017-05-22
Publication information: Scientific Reports 2017; 7: 45096
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 position of CpG's contained within the PCR primers. In this study, deoxyinosine-, 5-nitroindole-, mixed-base primers and primers with an abasic site were evaluated across a series of methylated controls. Primers that contained mixed- or deoxyinosine- base modifications performed most robustly. Mixed-base primers were further selected to determine the conditions that induce bias towards methylated templates. This identified an optimized set of conditions where the methylated state of bisulfite DNA templates can be accurately assessed using mixed-base primers, and expands the scope of bisulfite resequencing assays when working with challenging templates.
DOI: 10.1038/srep45096
ORCID: 0000-0003-3414-112X
PubMed URL: 28327639
Type: Journal Article
Appears in Collections:Journal articles

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