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。
相似文献
1
A novel method of amplification of FFPET-derived RNA enables accurate disease classification with microarrays.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。
J Mol Diagn. 2010 Sep;12(5):680-6. doi: 10.2353/jmoldx.2010.090164. Epub 2010 Aug 5.
2
Development of a microarray platform for FFPET profiling: application to the classification of human tumors.用于FFPET分析的微阵列平台的开发：在人类肿瘤分类中的应用。
J Transl Med. 2009 Jul 28;7:65. doi: 10.1186/1479-5876-7-65.
3
Microarray gene expression analysis of fixed archival tissue permits molecular classification and identification of potential therapeutic targets in diffuse large B-cell lymphoma.固定存档组织的基因表达微阵列分析可实现弥漫性大 B 细胞淋巴瘤的分子分类和潜在治疗靶点的鉴定。
J Mol Diagn. 2012 May-Jun;14(3):223-32. doi: 10.1016/j.jmoldx.2012.01.008. Epub 2012 Mar 22.
4
Genomic microarray analysis on formalin-fixed paraffin-embedded material for uveal melanoma prognostication.用于葡萄膜黑色素瘤预后评估的福尔马林固定石蜡包埋材料的基因组微阵列分析
Cancer Genet. 2014 Jul-Aug;207(7-8):306-15. doi: 10.1016/j.cancergen.2014.08.005. Epub 2014 Aug 29.
5
Prognostic Significance of Diffuse Large B-Cell Lymphoma Cell of Origin Determined by Digital Gene Expression in Formalin-Fixed Paraffin-Embedded Tissue Biopsies.通过数字基因表达确定福尔马林固定石蜡包埋组织活检中弥漫性大B细胞淋巴瘤细胞起源的预后意义
J Clin Oncol. 2015 Sep 10;33(26):2848-56. doi: 10.1200/JCO.2014.60.2383. Epub 2015 Aug 3.
6
Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours.通过对存档福尔马林固定石蜡包埋肿瘤进行Affymetrix微阵列分析获取生物学相关基因表达数据。
Br J Cancer. 2008 Apr 22;98(8):1403-14. doi: 10.1038/sj.bjc.6604316. Epub 2008 Apr 1.
7
3'-end sequencing for expression quantification (3SEQ) from archival tumor samples.从存档的肿瘤样本中进行表达定量的 3' 末端测序（3SEQ）。
PLoS One. 2010 Jan 19;5(1):e8768. doi: 10.1371/journal.pone.0008768.
8
Use of formalin-fixed paraffin-embedded tumor tissue as a DNA source in molecular epidemiological studies of pediatric CNS tumors.在儿童中枢神经系统肿瘤分子流行病学研究中，使用福尔马林固定石蜡包埋的肿瘤组织作为DNA来源。
Diagn Mol Pathol. 2012 Jun;21(2):105-13. doi: 10.1097/PDM.0b013e3182340a78.
9
An optimized workflow for improved gene expression profiling for formalin-fixed, paraffin-embedded tumor samples.一种用于优化福尔马林固定石蜡包埋肿瘤样本基因表达谱分析的工作流程。
J Clin Bioinforma. 2013 May 3;3(1):10. doi: 10.1186/2043-9113-3-10.
10
Preparation of archival formalin-fixed paraffin-embedded mouse liver samples for use with the Agilent gene expression microarray platform.制备用于安捷伦基因表达微阵列平台的存档福尔马林固定石蜡包埋小鼠肝脏样本。
J Pharmacol Toxicol Methods. 2013 Sep-Oct;68(2):260-268. doi: 10.1016/j.vascn.2013.02.008. Epub 2013 Mar 1.
引用本文的文献
1
Exploring the influence of pre-analytical variables on gene expression measurements and relative expression orderings in cancer research.探索分析前变量对癌症研究中基因表达测量及相对表达排序的影响。
Sci Rep. 2025 Feb 6;15(1):4489. doi: 10.1038/s41598-025-88756-0.
2
Assessment of 2-Year Storage Conditions on Protein, RNA, and DNA in Unstained Human Tissue Sections, Including a Novel Multiplex Digital Gene Expression Profiling Method with Implications for Biobanking.评估未经染色的人体组织切片中蛋白质、RNA 和 DNA 在 2 年储存条件下的变化，包括一种新的用于生物样本库的多重数字基因表达分析方法。
Biopreserv Biobank. 2022 Dec;20(6):473-484. doi: 10.1089/bio.2021.0023. Epub 2021 Sep 29.
3
Integrative analysis of hub genes and key pathway in two subtypes of diffuse large B-cell lymphoma by bioinformatics and basic experiments.基于生物信息学和基础实验的两种弥漫性大 B 细胞淋巴瘤亚型的枢纽基因和关键途径的综合分析。
J Clin Lab Anal. 2021 Nov;35(11):e23978. doi: 10.1002/jcla.23978. Epub 2021 Sep 21.
4
A refined cell-of-origin classifier with targeted NGS and artificial intelligence shows robust predictive value in DLBCL.一种经过改良的基于细胞起源的分类器，结合靶向 NGS 和人工智能，在弥漫性大 B 细胞淋巴瘤中显示出强大的预测价值。
Blood Adv. 2020 Jul 28;4(14):3391-3404. doi: 10.1182/bloodadvances.2020001949.
5
Remaining challenges in predicting patient outcomes for diffuse large B-cell lymphoma.弥漫性大 B 细胞淋巴瘤患者预后预测的尚存挑战。
Expert Rev Hematol. 2019 Nov;12(11):959-973. doi: 10.1080/17474086.2019.1660159. Epub 2019 Sep 12.
6
Integrating precision medicine through evaluation of cell of origin in treatment planning for diffuse large B-cell lymphoma.通过评估弥漫性大 B 细胞淋巴瘤治疗计划中的细胞起源，实现精准医学的整合。
Blood Cancer J. 2019 May 16;9(6):48. doi: 10.1038/s41408-019-0208-6.
7
Regional Molecular Signature of the Symptomatic Atherosclerotic Carotid Plaque.症状性动脉粥样硬化颈动脉斑块的区域性分子特征。
Neurosurgery. 2019 Aug 1;85(2):E284-E293. doi: 10.1093/neuros/nyy470.
8
Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays.从 Affymetrix 芯片上分析的 FFPE 衍生 RNA 中开发可靠基因表达模块的可行性。
PLoS One. 2018 Aug 31;13(8):e0203346. doi: 10.1371/journal.pone.0203346. eCollection 2018.
9
Abnormal Small Intestinal Epithelial Microvilli in Patients With Crohn's Disease.克罗恩病患者的异常小肠上皮微绒毛。
Gastroenterology. 2018 Sep;155(3):815-828. doi: 10.1053/j.gastro.2018.05.028. Epub 2018 May 18.
10
KLHL6 Is Preferentially Expressed in Germinal Center-Derived B-Cell Lymphomas.KLHL6在生发中心来源的B细胞淋巴瘤中优先表达。
Am J Clin Pathol. 2017 Nov 20;148(6):465-476. doi: 10.1093/ajcp/aqx099.
本文引用的文献
1
Differential efficacy of bortezomib plus chemotherapy within molecular subtypes of diffuse large B-cell lymphoma.硼替佐米联合化疗在弥漫性大B细胞淋巴瘤分子亚型中的疗效差异
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.大B细胞淋巴瘤中的基质基因特征
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.弥漫性大B细胞淋巴瘤的分子亚型通过不同的遗传途径产生。
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.组织处理和加工过程中影响从福尔马林固定、石蜡包埋组织中获取RNA的因素。
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.由CD21表达所监督的弥漫性大B细胞淋巴瘤的基因表达谱分析
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.福尔马林固定石蜡包埋（FFPE）样本RNA质量的决定因素。
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.基因表达谱在淋巴瘤中的诊断和预后意义
APMIS. 2007 Oct;115(10):1135-46. doi: 10.1111/j.1600-0463.2007.apm_867.xml.x.
8
MicroRNA expression distinguishes between germinal center B cell-like and activated B cell-like subtypes of diffuse large B cell lymphoma.微小RNA表达可区分弥漫性大B细胞淋巴瘤的生发中心B细胞样和活化B细胞样亚型。
Int J Cancer. 2007 Sep 1;121(5):1156-61. doi: 10.1002/ijc.22800.
9
Transformation of follicular lymphoma to diffuse large B-cell lymphoma proceeds by distinct oncogenic mechanisms.滤泡性淋巴瘤向弥漫性大B细胞淋巴瘤的转化通过不同的致癌机制进行。
Br J Haematol. 2007 Jan;136(2):286-93. doi: 10.1111/j.1365-2141.2006.06439.x.
10
Replacing cRNA targets with cDNA reduces microarray cross-hybridization.用互补DNA（cDNA）替代互补RNA（cRNA）靶标可减少微阵列交叉杂交。
Nat Biotechnol. 2006 Sep;24(9):1071-3. doi: 10.1038/nbt0906-1071.
Zotero 插件