title: Comments on: Interpretation of genome-wide infinium methylation data from ligated DNA in formalin-fixed paraffin-embedded paired tumor and normal tissue.
abstract: BMC Research Notes recently published a research article regarding the use of ligated DNA extracted from formalin-fixed paraffin embedded (FFPE) tissue on the Illumina Infinium methylation platform - "Interpretation of genome-wide infinium methylation data from ligated DNA in formalin-fixed, paraffin-embedded paired tumor and normal tissue" Jasmine et al. BMC Research Notes 2012, 5:117. This article repeatedly refers to our previous work and concludes that methylation data obtained from ligated FFPE extracted DNA should be used with great caution. In this Discussion we review the data analysis performed in Jasmine et al's paper and suggest limitations which subsequently lead the authors to draw what we believe are incorrect conclusions. Moreover, we continue to analyse genome-wide methylation data from DNA extracted from FFPE tissue successfully on both the HumMeth27 and 450 K arrays.
authors.affiliation: Medical Genomics Laboratory, UCL Cancer Institute, 72, Huntley Street,London WC1E 6BT, UK.
authors.forename: Christina
authors.initials: C
authors.lastname: Thirlwell
authors.forename: Andrew
authors.initials: A
authors.lastname: Feber
authors.forename: Matthias
authors.initials: M
authors.lastname: Lechner
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Teschendorff
authors.forename: Stephan
authors.initials: S
authors.lastname: Beck
mesh_terms: D003106:Colon / Q000378:metabolism*; D015179:Colorectal Neoplasms / Q000378:metabolism*; D004247:DNA / Q000378:metabolism*; D006801:Humans; D008297:Male; D020641:Polymorphism, Single Nucleotide
chemical_list: D004247:DNA