一种新型的 FFPET 衍生 RNA 扩增方法可通过微阵列实现准确的疾病分类。
A novel method of amplification of FFPET-derived RNA enables accurate disease classification with microarrays.
机构信息
Roche Molecular Diagnostics, Pleasanton, California, USA.
出版信息
J Mol Diagn. 2010 Sep;12(5):680-6. doi: 10.2353/jmoldx.2010.090164. Epub 2010 Aug 5.
Abstract
A new method for amplification and labeling of RNA is assessed that permits gene expression microarray analysis of formalin-fixed paraffin-embedded tissue (FFPET) samples. Valid biological data were obtained using gene expression microarrays of diffuse large B-cell lymphoma (DLBCL) FFPET samples. We examined 59 matched DLBCL patient samples, FFPET, and fresh/frozen. The samples contained both prognostic subgroups of DLBCL: germinal center B-cell (GCB) and activated B-cell (ABC). Fresh/frozen (FF) samples were amplified by both the traditional Eberwine oligo-dT method and a new method described herein. The matching FFPET samples were also amplified using the new method. Here we detail the comparison of results from all three datasets of matched samples. An established classification model built from previous data accurately classified these new samples. This new method provides a useful technology advance for microarray analysis of FFPET archival samples.
摘要
评估了一种新的 RNA 扩增和标记方法，该方法允许对福尔马林固定石蜡包埋组织（FFPET）样本进行基因表达微阵列分析。使用弥漫性大 B 细胞淋巴瘤（DLBCL）FFPET 样本的基因表达微阵列获得了有效的生物学数据。我们检查了 59 个匹配的 DLBCL 患者样本、FFPET 和新鲜/冷冻样本。这些样本包含了 DLBCL 的两个预后亚组：生发中心 B 细胞（GCB）和激活 B 细胞（ABC）。新鲜/冷冻（FF）样本均通过传统的 Eberwine 寡聚-dT 方法和本文所述的新方法进行扩增。新方法还扩增了匹配的 FFPET 样本。在这里，我们详细比较了所有三个匹配样本数据集的结果。从先前的数据中建立的分类模型准确地对这些新样本进行了分类。该新方法为 FFPET 存档样本的微阵列分析提供了有用的技术进步。
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Blood. 2009 Jun 11;113(24):6069-76. doi: 10.1182/blood-2009-01-199679. Epub 2009 Apr 20.
2
Stromal gene signatures in large-B-cell lymphomas.
N Engl J Med. 2008 Nov 27;359(22):2313-23. doi: 10.1056/NEJMoa0802885.
3
Molecular subtypes of diffuse large B-cell lymphoma arise by distinct genetic pathways.
Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13520-5. doi: 10.1073/pnas.0804295105. Epub 2008 Sep 2.
4
Factors in tissue handling and processing that impact RNA obtained from formalin-fixed, paraffin-embedded tissue.
J Histochem Cytochem. 2008 Nov;56(11):1033-42. doi: 10.1369/jhc.2008.951863. Epub 2008 Aug 18.
5
Gene expression profiling of diffuse large B-cell lymphoma supervised by CD21 expression.
Br J Haematol. 2008 Aug;142(4):562-70. doi: 10.1111/j.1365-2141.2008.07218.x. Epub 2008 Jun 5.
6
Determinants of RNA quality from FFPE samples.
PLoS One. 2007 Dec 5;2(12):e1261. doi: 10.1371/journal.pone.0001261.
7
Diagnostic and prognostic significance of gene expression profiling in lymphomas.
APMIS. 2007 Oct;115(10):1135-46. doi: 10.1111/j.1600-0463.2007.apm_867.xml.x.
8
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