Thirlwell Christina, Feber Andrew, Lechner Matthias, Teschendorff Andrew E, Beck Stephan
Medical Genomics Laboratory, UCL Cancer Institute, 72, Huntley Street,London WC1E 6BT, UK.
BMC Res Notes. 2012 Nov 13;5:631. doi: 10.1186/1756-0500-5-631.
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.
《BMC研究笔记》最近发表了一篇关于在Illumina Infinium甲基化平台上使用从福尔马林固定石蜡包埋（FFPE）组织中提取的连接DNA的研究文章——“福尔马林固定、石蜡包埋的配对肿瘤和正常组织中连接DNA的全基因组Infinium甲基化数据解读”，作者为贾斯敏等人。《BMC研究笔记》2012年，第5卷：第117页。本文多次提及我们之前的工作，并得出结论：从FFPE提取的连接DNA获得的甲基化数据应极其谨慎地使用。在本讨论中，我们回顾了贾斯敏等人论文中进行的数据分析，并指出了一些局限性，这些局限性随后导致作者得出了我们认为不正确的结论。此外，我们继续成功地在HumMeth27和450K阵列上分析了从FFPE组织中提取的DNA的全基因组甲基化数据。
