Savage Stephanie J, Hostetter Galen
Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA.
Methods Mol Biol. 2011;700:185-98. doi: 10.1007/978-1-61737-954-3_13.
Formalin fixation has been used to preserve tissues for more than a hundred years, and there are currently more than 300 million archival samples in the United States alone. The application of genomic protocols such as high-density oligonucleotide array Comparative Genomic Hybridization (aCGH) to formalin-fixed, paraffin-embedded (FFPE) tissues, therefore, opens an untapped resource of available tissues for research and facilitates utilization of existing clinical data in a research sample set. However, formalin fixation results in cross-linking of proteins and DNA, typically leading to such a significant degradation of DNA template that little is available for use in molecular applications. Here, we describe a protocol to circumvent formalin fixation artifact by utilizing enzymatic reactions to obtain quality DNA from a wide range of FFPE tissues for successful genome-wide discovery of gene dosage alterations in archival clinical samples.
福尔马林固定用于保存组织已有一百多年历史，仅在美国目前就有超过3亿份存档样本。因此，将诸如高密度寡核苷酸阵列比较基因组杂交（aCGH）等基因组学方法应用于福尔马林固定石蜡包埋（FFPE）组织，为研究开辟了尚未开发的可用组织资源，并有助于在研究样本集中利用现有的临床数据。然而，福尔马林固定会导致蛋白质和DNA交联，通常会使DNA模板严重降解，以至于几乎无法用于分子应用。在此，我们描述了一种方案，通过利用酶促反应从广泛的FFPE组织中获取高质量DNA，以规避福尔马林固定造成的假象，从而在存档临床样本中成功进行全基因组范围的基因剂量改变发现。
