Comprehensive Solution for Transcriptome Profiling of Archived Tissues

存档组织转录组分析的综合解决方案

• 批准号: 8758248
• 负责人: Brian Clifton Haynes
• 金额: $ 22.5万
• 依托单位: ASURAGEN, INC.
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-07-18 至 2016-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8758248
• 关键词: Accounting; Address; Archives; Bioinformatics; Biological; Biological Assay; Biological Markers; Chromosomal Rearrangement; Clinical; Complex Mixtures; DNA; DNA Damage; Data; Data Quality; Deamination; Detection; Environmental Health; Event; Formaldehyde; Formalin; Freezing; Functional RNA; Gene Expression Profile; Gene Fusion; Genes; Genetic; Genetic Transcription; Genomics; Goals; Housekeeping Gene; Libraries; Light; Methods; Metric; Mission; Modeling; Molecular; Morphologic artifacts; Nucleotides; Paraffin Embedding; Performance; Phase; Positioning Attribute; Precursor RNA; Preparation; Process; Qualifying; Quality Control; RNA; RNA Editing; Relative (related person); Research; Sampling; Sequence Analysis; Solutions; Somatic Mutation; Specimen; Technology; Tissue Sample; Tissues; Toxicology; Transcript; Variant; adduct; analytical method; base; clinical application; design; expectation; improved; insight; mRNA Precursor; next generation sequencing; novel; oncology; public health relevance; sample fixation; tissue fixing; tool; transcriptome sequencing; tumor

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.

描述（由申请方提供）：本提案的总体目标是通过使用下一代测序技术（RNA-Seq）进行全转录组分析，扩展福尔马林固定石蜡包埋（FFPE）标本的分子分析能力。将制定端到端战略，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能够可靠地应用于FFPE材料，以准确地分析：1）转录表达，2）体细胞突变，和3）染色体重排。 全面工作流程的策略还包括解决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和染色体重排的鉴定。第一阶段申请的主要目标是：目标1。开发一种可预测测序质量的FFPE RNA的严格鉴定试验。 目标2.开发适合FFPE RNA-Seq的生物信息学分析管道。 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，以便使用RNA-Seq来无偏见地发现生物标志物。在第二阶段，RNA-Seq能力将得到扩展，以进一步开发和优化方法，并验证肿瘤标本的综合工作流程。该项目符合Asuragen的专业知识和正在进行的使命，即开发领先的生物信息学工具，并为研究和临床应用提供高质量的NGS检测和NGS产品。