Dumenil Troy D, Wockner Leesa F, Bettington Mark, McKeone Diane M, Klein Kerenaftali, Bowdler Lisa M, Montgomery Grant W, Leggett Barbara A, Whitehall Vicki L J
Conjoint Gastroenterology Laboratory, Royal Brisbane and Women's Hospital, Clinical Research Centre and QIMR Berghofer Medical Research Institute, Brisbane, Australia.
Genes Chromosomes Cancer. 2014 Jul;53(7):537-48. doi: 10.1002/gcc.22164. Epub 2014 Mar 28.
Formalin fixation and embedding of clinical tissue samples in paraffin is a common method for archiving biological material. These samples are often well annotated and provide an invaluable resource for research. However, this process of fixation and storage of tissue leads to DNA damage and fragmentation. The use of DNA from formalin fixed, paraffin-embedded (FFPE) tissue to interrogate methylation levels on a genome-wide scale can pose challenges. We compared fresh and matched FFPE tissue DNA samples using the Illumina Infinium HD Human Methylation 450K BeadChip platform with a companion application for repair and "restoration" of DNA from FFPE tissue. Our results showed good correlation between fresh and FFPE sample data. FFPE DNA captured 99% of the CpG sites on the array on average. Significant cancer subgroups based on the CpG island methylator phenotype (CIMP) were clearly distinguished for both fresh and FFPE sample sets with cluster and scaling analysis. The DNA methylation status for the five standard CIMP panel genes which was evaluated for all samples by the MethyLight assay was correctly assigned in both fresh and FFPE samples by the array data. We conclude that the "restoration" method followed by assay on the Infinium HD Human Methylation 450K microarray can produce good quality data for DNA from FFPE samples.
将临床组织样本用福尔马林固定并包埋在石蜡中是保存生物材料的常用方法。这些样本通常注释详尽，为研究提供了宝贵资源。然而，组织的这种固定和储存过程会导致DNA损伤和片段化。使用来自福尔马林固定石蜡包埋（FFPE）组织的DNA在全基因组范围内检测甲基化水平可能会带来挑战。我们使用Illumina Infinium HD人类甲基化450K芯片平台以及一个用于修复和“恢复”FFPE组织DNA的配套应用程序，比较了新鲜组织和匹配的FFPE组织DNA样本。我们的结果显示新鲜样本和FFPE样本数据之间具有良好的相关性。FFPE DNA平均捕获了芯片上99%的CpG位点。通过聚类和尺度分析，对于新鲜样本和FFPE样本集，基于CpG岛甲基化表型（CIMP）的显著癌症亚组都能被清晰区分。通过MethyLight分析对所有样本评估的五个标准CIMP面板基因的DNA甲基化状态，在新鲜样本和FFPE样本中都能通过芯片数据正确确定。我们得出结论，在Infinium HD人类甲基化450K微阵列上进行检测之前采用的“恢复”方法，可以为FFPE样本的DNA产生高质量数据。
