title: DNA ligase-based strategy for quantifying heterogeneous DNA methylation without sequencing.
abstract: BACKGROUND
  DNA methylation is a potential source of disease biomarkers. Typically, methylation levels are measured at individual cytosine/guanine (CpG) sites or over a short region of interest. However, regions of interest often show heterogeneous methylation comprising multiple patterns of methylation (epialleles) on individual DNA strands. Heterogeneous methylation is largely ignored because digital methods are required to deconvolute these usually complex patterns of epialleles. Currently, only single-molecule approaches, such as next generation sequencing (NGS), can provide detailed epiallele information. Because NGS is not yet feasible for routine practice, we developed a single-molecule-like approach, named for epiallele quantification (EpiQ).
  
  
  METHODS
  EpiQ uses DNA ligases and the enhanced thermal instability of short (≤19 bases) mismatched DNA probes for the relative quantification of epialleles. The assay was developed using fluorescent detection on a gel and then adapted for electrochemical detection on a microfabricated device. NGS was used to validate the analytical accuracy of EpiQ.
  
  
  RESULTS
  In this proof of principle study, EpiQ detected with 90%-95% specificity each of the 8 possible epialleles for a 3-CpG cluster at the promoter region of the CDKN2B (p15) tumor suppressor gene. EpiQ successfully profiled heterogeneous methylation patterns in clinically derived samples, and the results were cross-validated with NGS.
  
  
  CONCLUSIONS
  EpiQ is a potential alternative tool for characterizing heterogeneous methylation, thus facilitating its use as a biomarker. EpiQ was developed on a gel-based assay but can also easily be adapted for miniaturized chip-based platforms.
authors.affiliation: Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), and.
authors.forename: Eugene J H
authors.initials: EJ
authors.lastname: Wee
authors.affiliation: Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), and.
authors.forename: Sakandar
authors.initials: S
authors.lastname: Rauf
authors.affiliation: Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), and.
authors.forename: Muhammad J A
authors.initials: MJ
authors.lastname: Shiddiky
authors.affiliation: Translational Genomics & Epigenomics Laboratory, Ludwig Institute for Cancer Research, Olivia Newton-John Cancer & Wellness Centre, Heidelberg, Victoria, Australia; Department of Pathology, University of Melbourne, Parkville, Victoria, Australia.
authors.forename: Alexander
authors.initials: A
authors.lastname: Dobrovic
authors.affiliation: Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), and School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia; m.trau@uq.edu.au.
authors.forename: Matt
authors.initials: M
authors.lastname: Trau
mesh_terms: D000483:Alleles; D018899:CpG Islands / Q000235:genetics*; D011088:DNA Ligases / Q000737:chemistry*; D019175:DNA Methylation / Q000235:genetics*; D055664:Electrochemical Techniques; D004591:Electrophoresis, Polyacrylamide Gel; D044127:Epigenesis, Genetic; D018740:Genetic Heterogeneity; D006801:Humans; D022521:Ligase Chain Reaction; D025202:Molecular Diagnostic Techniques / Q000295:instrumentation / Q000379:methods*; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA
chemical_list: D011088:DNA Ligases