Gene expression profiles from formalin fixed paraffin embedded breast cancer tissue are largely comparable to fresh frozen matched tissue.
Gene expression profiles from formalin fixed paraffin embedded breast cancer tissue are largely comparable to fresh frozen matched tissue.
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DOI：
10.1371/journal.pone.0017163
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发表时间：
2011-02-11
期刊：
影响因子：
3.7
通讯作者：
Van't Veer LJ
中科院分区：
文献类型：
--
作者：
Mittempergher L;de Ronde JJ;Nieuwland M;Kerkhoven RM;Simon I;Rutgers EJ;Wessels LF;Van't Veer LJ
福尔马林固定石蜡包埋（FFPE）样品是癌症研究的宝贵资源。然而，新的癌症生物标志物的发现和开发通常需要新鲜冷冻（FF）样品。最近，专门开发了全基因组（WG）DASL（cDNA介导的退火、选择、延伸和连接）测定法来分析FFPE组织。然而，缺乏对使用该平台从FFPE RNA和新鲜冷冻（FF）RNA生成的数据的彻底比较。为此，我们对20个FFPE组织和20个匹配的FF组织进行了一式两份的分析，并评价了FFPE和匹配的FF材料的DASL结果的一致性。我们表明，在适当的归一化后，所有FFPE和FF对都表现出高水平的相似性（Pearson相关性>0.7），显著大于非配对样本之间的相似性。有趣的是，显示最高相关性的探针具有较高的G/C含量百分比，并且富集细胞周期基因。在冷冻材料上开发的基因表达特征的预测（内在亚型，基因组等级指数，70个基因特征）显示FFPE和FF匹配对之间的高度一致性。有趣的是，基于60个基因的DASL列表（与70个基因标签最佳匹配）的预测显示出与MammaPrint®结果非常高的一致性。我们证明，如果处理得当，使用DASL检测试剂盒从FFPE材料中生成的数据与从FF对应物中提取的数据相当。具体而言，特定疾病的一组已知预后基因的基因表达谱在两种情况之间具有高度可比性。这开辟了在基因表达分析中使用FFPE和FF材料的可能性，从而大大增加了癌症研究的潜在资源。
Formalin Fixed Paraffin Embedded (FFPE) samples represent a valuable resource for cancer research. However, the discovery and development of new cancer biomarkers often requires fresh frozen (FF) samples. Recently, the Whole Genome (WG) DASL (cDNA-mediated Annealing, Selection, extension and Ligation) assay was specifically developed to profile FFPE tissue. However, a thorough comparison of data generated from FFPE RNA and Fresh Frozen (FF) RNA using this platform is lacking. To this end we profiled, in duplicate, 20 FFPE tissues and 20 matched FF tissues and evaluated the concordance of the DASL results from FFPE and matched FF material. We show that after proper normalization, all FFPE and FF pairs exhibit a high level of similarity (Pearson correlation >0.7), significantly larger than the similarity between non-paired samples. Interestingly, the probes showing the highest correlation had a higher percentage G/C content and were enriched for cell cycle genes. Predictions of gene expression signatures developed on frozen material (Intrinsic subtype, Genomic Grade Index, 70 gene signature) showed a high level of concordance between FFPE and FF matched pairs. Interestingly, predictions based on a 60 gene DASL list (best match with the 70 gene signature) showed very high concordance with the MammaPrint® results. We demonstrate that data generated from FFPE material with the DASL assay, if properly processed, are comparable to data extracted from the FF counterpart. Specifically, gene expression profiles for a known set of prognostic genes for a specific disease are highly comparable between two conditions. This opens up the possibility of using both FFPE and FF material in gene expressions analyses, leading to a vast increase in the potential resources available for cancer research.
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David Gene功能分类工具：一种以生物模块为中心的新型算法，可在功能上分析大基因列表。
影响因子：
12.3
作者：
Huang, Da Wei;Sherman, Brad T;Tan, Qina;Collins, Jack R;Alvord, W Gregory;Roayaei, Jean;Stephens, Robert;Baseler, Michael W;Lane, H Clifford;Lempicki, Richard A
通讯作者：
Lempicki, Richard A
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9.8
作者：
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通讯作者：
Brown PO
影响因子：
6
作者：
Bibikova, M;Talantov, D;Fan, JB
通讯作者：
Fan, JB
影响因子：
4.4
作者：
Hu, Zhiyuan;Fan, Cheng;Perou, Charles M.
通讯作者：
Perou, Charles M.
影响因子：
158.5
作者：
Liu, Rui;Wang, Xinhao;Clarke, Michael F.
通讯作者：
Clarke, Michael F.