title: High recovery of cell-free methylated DNA based on a rapid bisulfite-treatment protocol.
abstract: BACKGROUND
  Detection of cell-free methylated DNA in plasma is a promising tool for tumour diagnosis and monitoring. Due to the very low amounts of cell-free DNA in plasma, analytical sensitivity is of utmost importance. The vast majority of currently available methods for analysing DNA methylation are based on bisulfite-mediated deamination of cytosine. Cytosine is rapidly converted to uracil during bisulfite treatment, whereas 5-methylcytosine is only slowly converted. Hence, bisulfite treatment converts an epigenetic modification into a difference in sequence, amenable to analysis either by sequencing or PCR based methods. However, the recovery of bisulfite-converted DNA is very poor.
  
  
  RESULTS
  Here we introduce an alternative method for the crucial steps of bisulfite treatment with high recovery. The method is based on an accelerated deamination step and alkaline desulfonation in combination with magnetic silica purification of DNA, allowing preparation of deaminated DNA from patient samples in less than 2 hours.
  
  
  CONCLUSIONS
  The method presented here allows low levels of DNA to be easily and reliably analysed, a prerequisite for the clinical usefulness of cell-free methylated DNA detection in plasma.
authors.affiliation: Section of Molecular Diagnostics, Department of Clinical Biochemistry, Aalborg University Hospital, Denmark, DK. isp@rn.dk
authors.forename: Inge Søkilde
authors.initials: IS
authors.lastname: Pedersen
authors.forename: Henrik Bygum
authors.initials: HB
authors.lastname: Krarup
authors.forename: Ole
authors.initials: O
authors.lastname: Thorlacius-Ussing
authors.forename: Poul Henning
authors.initials: PH
authors.lastname: Madsen
mesh_terms: D002474:Cell-Free System; D004247:DNA / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D019175:DNA Methylation; D003641:Deamination; D005821:Genetic Techniques; D006801:Humans; D016133:Polymerase Chain Reaction; D013447:Sulfites / Q000737:chemistry / Q000378:metabolism*
chemical_list: D013447:Sulfites; D004247:DNA; C042345:hydrogen sulfite