3'-end sequencing for expression quantification (3SEQ) from archival tumor samples.
3'-end sequencing for expression quantification (3SEQ) from archival tumor samples.
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DOI：
10.1371/journal.pone.0008768
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发表时间：
2010-01-19
期刊：
影响因子：
3.7
通讯作者：
West RB
中科院分区：
文献类型：
--
作者：
Beck AH;Weng Z;Witten DM;Zhu S;Foley JW;Lacroute P;Smith CL;Tibshirani R;van de Rijn M;Sidow A;West RB
基因表达微阵列是最广泛使用的全基因组表达谱技术。然而，微阵列在福尔马林固定石蜡包埋组织 (FFPET) 上表现不佳。因此，微阵列不能有效地用于对绝大多数档案肿瘤样本进行基因表达谱分析。为了解决基因表达微阵列的这一局限性，我们设计了一种新的程序（表达定量的 3' 端测序 (3SEQ)），使用下一代测序对 FFPET 进行基因表达谱分析。我们通过 3SEQ 和微阵列对来自两个软组织肿瘤（硬纤维瘤型纤维瘤病 (DTF) 和孤立性纤维瘤 (SFT)）的冷冻组织和 FFPET 进行基因表达谱分析（总共 n = 23 个样本，每个样本均通过四种平台组织制备组合中的至少一种进行分析）。 3SEQ 数据分析揭示了许多基因在冷冻组织（~9.6K 基因）和 FFPET（~8.1K 基因）上的肿瘤类型（FDR<0.01）之间差异表达。对冷冻组织的微阵列数据分析显示较少的差异表达基因（~4.64K），对 FFPET 的微阵列数据分析显示很少（69）个差异表达基因。对来自冷冻组织和 FFPET 的 3SEQ 数据进行功能基因集分析，确定了已知在 DTF 和 SFT 发病机制中重要的生物途径，并提出了这些肿瘤中的几种其他候选致癌途径。这些发现表明，3SEQ 是一种从档案肿瘤样本中进行基因表达谱分析的有效技术，并可能促进转化癌症研究的重大进展。
Gene expression microarrays are the most widely used technique for genome-wide expression profiling. However, microarrays do not perform well on formalin fixed paraffin embedded tissue (FFPET). Consequently, microarrays cannot be effectively utilized to perform gene expression profiling on the vast majority of archival tumor samples. To address this limitation of gene expression microarrays, we designed a novel procedure (3′-end sequencing for expression quantification (3SEQ)) for gene expression profiling from FFPET using next-generation sequencing. We performed gene expression profiling by 3SEQ and microarray on both frozen tissue and FFPET from two soft tissue tumors (desmoid type fibromatosis (DTF) and solitary fibrous tumor (SFT)) (total n = 23 samples, which were each profiled by at least one of the four platform-tissue preparation combinations). Analysis of 3SEQ data revealed many genes differentially expressed between the tumor types (FDR<0.01) on both the frozen tissue (∼9.6K genes) and FFPET (∼8.1K genes). Analysis of microarray data from frozen tissue revealed fewer differentially expressed genes (∼4.64K), and analysis of microarray data on FFPET revealed very few (69) differentially expressed genes. Functional gene set analysis of 3SEQ data from both frozen tissue and FFPET identified biological pathways known to be important in DTF and SFT pathogenesis and suggested several additional candidate oncogenic pathways in these tumors. These findings demonstrate that 3SEQ is an effective technique for gene expression profiling from archival tumor samples and may facilitate significant advances in translational cancer research.
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影响因子：
56.9
作者：
Golub, TR;Slonim, DK;Lander, ES
通讯作者：
Lander, ES
影响因子：
3.5
作者：
Frank, Matthias;Doering, Claudia;Hansmann, Martin-Leo
通讯作者：
Hansmann, Martin-Leo
影响因子：
5
作者：
Beck, Andrew H.;Espinosa, Inigo;West, Robert B.
通讯作者：
West, Robert B.
DOI：
10.1056/nejmoa0804525
发表时间：
2008-11-06
期刊：
The New England journal of medicine
影响因子：
--
作者：
Hoshida Y;Villanueva A;Kobayashi M;Peix J;Chiang DY;Camargo A;Gupta S;Moore J;Wrobel MJ;Lerner J;Reich M;Chan JA;Glickman JN;Ikeda K;Hashimoto M;Watanabe G;Daidone MG;Roayaie S;Schwartz M;Thung S;Salvesen HB;Gabriel S;Mazzaferro V;Bruix J;Friedman SL;Kumada H;Llovet JM;Golub TR
通讯作者：
Golub TR
影响因子：
64.8
作者：
Alizadeh, AA;Eisen, MB;Staudt, LM
通讯作者：
Staudt, LM