Ghazani A A, Arneson N C R, Warren K, Done S J
Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
J Clin Pathol. 2006 Mar;59(3):311-5. doi: 10.1136/jcp.2005.029777.
Array comparative genomic hybridisation (CGH) is a powerful method for the genetic analysis of lesional and normal tissues to identify genomic imbalances associated with malignancies. However, the use of this technique with DNA extracted from archival formalin fixed, paraffin embedded (FFPE) tissue specimens, the most widely available resource for retrospective studies, is subject to quantitative and qualitative limitations. In this report, the suitability and integrity of the DNA extracted from FFPE MCF7 breast cancer cells fixed for different periods of time for array CGH applications were examined.
Using our established cDNA microarray protocol in conjunction with whole genome amplification methods, the genetic profiles of freshly harvested MCF7 cells and their matched FFPE counterparts were analysed. Congruent profiles between FFPE MCF7 cells and their fresh counterpart and between amplified and non-amplified FFPE MCF7 cells were observed. Our results demonstrate that formalin fixation of <20 hours has no significant adverse effect on the integrity of DNA for array CGH studies.
Our findings attest to the fidelity of our array CGH methods to effectively examine material recovered from FFPE tissue specimens for microarray applications. This in turn has great potential to identify novel diagnostic and prognostic markers for human disease.
阵列比较基因组杂交（CGH）是一种用于病变组织和正常组织基因分析的强大方法，可识别与恶性肿瘤相关的基因组失衡。然而，将该技术应用于从存档福尔马林固定石蜡包埋（FFPE）组织标本中提取的DNA时，这种最广泛用于回顾性研究的资源在定量和定性方面存在局限性。在本报告中，我们检测了从不同固定时间的FFPE MCF7乳腺癌细胞中提取的DNA用于阵列CGH分析的适用性和完整性。
使用我们建立的cDNA微阵列方案结合全基因组扩增方法，分析了新鲜收获的MCF7细胞及其匹配的FFPE细胞的基因图谱。观察到FFPE MCF7细胞与其新鲜对应物之间以及扩增和未扩增的FFPE MCF7细胞之间的图谱一致。我们的结果表明，福尔马林固定时间<20小时对阵列CGH研究中DNA的完整性没有显著不利影响。
我们的研究结果证明了我们的阵列CGH方法能够有效检测从FFPE组织标本中回收的材料用于微阵列分析的准确性。这反过来对于识别人类疾病的新型诊断和预后标志物具有巨大潜力。
