Whole transcriptome RNA-Seq analysis of breast cancer recurrence risk using formalin-fixed paraffin-embedded tumor tissue.
Whole transcriptome RNA-Seq analysis of breast cancer recurrence risk using formalin-fixed paraffin-embedded tumor tissue.
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DOI：
10.1371/journal.pone.0040092
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Baker J
中科院分区：
文献类型：
--
作者：
Sinicropi D;Qu K;Collin F;Crager M;Liu ML;Pelham RJ;Pho M;Dei Rossi A;Jeong J;Scott A;Ambannavar R;Zheng C;Mena R;Esteban J;Stephans J;Morlan J;Baker J
基于RT-PCR的福尔马林固定石蜡包埋(FFPE)组织的基因表达谱发现的RNA生物标记物构成了广泛使用的临床诊断测试的基础；然而，RT-PCR实际上限制了可以询问的转录本的数量。我们已经开发和优化了RNA-Seq文库化学以及生物信息学和生物统计学方法，用于从FFPE组织中提取整个转录组。这种化学适应了低RNA输入和样本多路传输。这两种方法都能够重新发现以前通过对136名患者进行RT-PCR分析而确定的疾病复发风险的RNA生物标记物，也能够识别以前在单独的患者队列中使用DNA微阵列发现的高比例的复发风险标记物，这证明这种RNA-Seq技术对于生物标记物的发现具有足够的精确度和灵敏度。在136名患者队列中，超过2000个RNA与乳腺癌复发风险密切相关(FDR<；10%)。其中许多是内含子RNA，其相应的外显子与疾病复发无关。许多与复发风险相关的RNA属于新的RNA网络。在其他乳腺癌队列的整个转录组RNA-Seq筛查中测试这些新关联的有效性将是重要的。
RNA biomarkers discovered by RT-PCR-based gene expression profiling of archival formalin-fixed paraffin-embedded (FFPE) tissue form the basis for widely used clinical diagnostic tests; however, RT-PCR is practically constrained in the number of transcripts that can be interrogated. We have developed and optimized RNA-Seq library chemistry as well as bioinformatics and biostatistical methods for whole transcriptome profiling from FFPE tissue. The chemistry accommodates low RNA inputs and sample multiplexing. These methods both enable rediscovery of RNA biomarkers for disease recurrence risk that were previously identified by RT-PCR analysis of a cohort of 136 patients, and also identify a high percentage of recurrence risk markers that were previously discovered using DNA microarrays in a separate cohort of patients, evidence that this RNA-Seq technology has sufficient precision and sensitivity for biomarker discovery. More than two thousand RNAs are strongly associated with breast cancer recurrence risk in the 136 patient cohort (FDR <10%). Many of these are intronic RNAs for which corresponding exons are not also associated with disease recurrence. A number of the RNAs associated with recurrence risk belong to novel RNA networks. It will be important to test the validity of these novel associations in whole transcriptome RNA-Seq screens of other breast cancer cohorts.
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158.5
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通讯作者：
KETNER, M