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Updated: Jul 12, 2025

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

RNA-seq RNAaccess被确定为低质量的FFPE样本基因表达分析的首选方法

Kai Song¹, Emon Elboudwarej¹, Xi Zhao¹

¹Gilead Sciences, Inc., Foster City, California, United States of America.

|October 26, 2023

概括

RNAaccess RNA-seq协议是最佳的基因表达造型的甲固定嵌入式 (FFPE) 样本,即使那些具有次优质的质量. 这种方法提高了生物标志物发现的可复制性和广泛的转录组覆盖率.

科学领域:

分子生物学分子生物学
基因组学就是基因组学.
生物技术是生物技术.

背景情况:

在临床研究中,形式氨固化嵌入 (FFPE) 样本被广泛使用,但对RNA完整性提出了挑战.
在FFPE组织中的RNA降解使使用RNA测序 (RNA-seq) 的精确基因表达概况复杂化.

研究的目的:

确定一个最佳的RNA-seq协议用于FFPE样本的基因表达概况.
建立FFPE组织的RNA-seq分析的质量控制参数.

主要方法:

使用FFPE和新鲜冷的三阴性乳腺癌组织的RNA-seq库制备方法 (RNAaccess,RiboZero,PolyA) 的比较.
将最佳方法应用于FFPE胃癌组织,以确定最低RNA质量 (DV200) 和输入要求.
与NanoString平台数据相关联的RNAaccessRNA-seq结果.

主要成果:

RNAaccess方法在FFPE样本的基因表达概况中显示了最高的一致性.
对于来自FFPE样本的可复制基因表达数据,建立了10%和10ngRNA输入的最小RNA DV200.
RNAaccess RNA-seq和NanoString平台显示了共享基因的高一致性,RNA-seq提供了更广泛的转录组覆盖范围.

结论:

建议使用RNAaccessRNA-seq协议对FFPE样本进行基因表达特征分析.
既定的最低RNA质量和输入要求有助于将低质量的FPE样本纳入分析.
这种方法可以增加使用档案FFPE组织的基因表达研究的统计能力.

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相关概念视频

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...