Comprehensive Solution for Transcriptome Profiling of Archived Tissues

描述(由申请人提供)：这项建议的总体目标是通过使用下一代测序技术(RNA-Seq)的整个转录组图谱来扩大福尔马林固定石蜡包埋(FFPE)样本的分子分析能力。将制定一项端到端战略，其中包括实验和分析方法，以应对FFPE样品特有的挑战。这将使RNA-Seq应用于FFPE材料能够准确地描述：1)转录表达，2)体细胞突变，3)染色体重排。全面工作流程的战略还包括解决FFPE RNA-Seq的分析挑战，包括开发新的生物信息学工具以增强SNV和染色体重排的识别。这一第一阶段应用的主要目的是：目的1.建立一种严格的FFPE RNA鉴定方法，可预测测序质量。目的：开发针对FFPE RNA-Seq的生物信息学分析流水线。在成功完成这些目标后，将建立一个全面的工作流程，其中包括优化的实验方法和生物信息学工具，以使RNA-Seq能够用于无偏见地发现生物标记物。在第二阶段，RNA-Seq的能力将扩大，以进一步开发和优化方法，并用肿瘤学标本验证全面的工作流程。该项目符合Asuragen的专业知识和持续的使命，即开发尖端的生物信息学工具，并为研究和临床应用提供高质量的NGS分析和NGS产品。

DESCRIPTION (provided by applicant): The overall goal of this proposal is to expand the capability for molecular analyses of formalin fixed paraffin-embedded (FFPE) specimens through the use of whole transcriptome profiling with next generation sequencing technology (RNA-Seq). An end-to-end strategy will be developed that includes both experimental and analytical methods to address challenges specific to FFPE samples. This will enable the confident application of RNA-Seq to FFPE material to accurately profile: 1) transcriptional expression, 2) somatic mutations, and 3) chromosomal rearrangements. The strategy for the comprehensive workflow also includes resolving analysis challenges for FFPE RNA- Seq, including developing new bioinformatics tools to enhance the identification of SNV and chromosomal rearrangements. The primary aims of this Phase I application are: Aim 1. Develop a rigorous qualification assay for FFPE RNA that is predictive of sequencing quality. Aim 2. Develop bioinformatics analysis pipeline tailored to FFPE RNA-Seq. Upon the successful completion of these aims, a comprehensive workflow will be established which includes optimized experimental methods and bioinformatics tools to enable use of RNA-Seq for the unbiased discovery of biomarkers. In Phase II, RNA-Seq capabilities will be expanded to further develop and optimize methods, and validate the comprehensive workflow with oncology specimens. This project aligns with Asuragen's expertise and ongoing mission to develop leading-edge bioinformatics tools and to provide high quality NGS assays and NGS products for research and clinical applications.