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Open Access Correspondence

Comments on: Interpretation of genome-wide infinium methylation data from ligated DNA in formalin-fixed paraffin-embedded paired tumor and normal tissue

Christina Thirlwell*, Andrew Feber, Matthias Lechner, Andrew E Teschendorff* and Stephan Beck

Author Affiliations

Medical Genomics Laboratory, UCL Cancer Institute, 72, Huntley Street, London WC1E 6BT, UK

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BMC Research Notes 2012, 5:631  doi:10.1186/1756-0500-5-631

Published: 13 November 2012

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.