Analysis of Tumor RNA Variants using PMSG

使用 PMSG 分析肿瘤 RNA 变异

• 批准号: 7225620
• 负责人: Chaofu Shi
• 金额: $ 58.17万
• 依托单位: SPECTRAGENETICS
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-04-21 至 2009-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7225620
• 关键词: Biological Markers; Cancer Etiology; Cause of Death; Chromosomal Rearrangement; Clinical; Code; Communities; Coupled; DNA Repair Gene; DNA Resequencing; Detection; Diagnostic; Early Diagnosis; Endopeptidases; Escherichia coli; Etiology; FGFR3 gene; Frameshift Mutation; Gene Activation; Gene Mutation; Gene Targeting; Genes; Genetic; Genetic Polymorphism; Genetic Transcription; Genotype; Goals; Heterogeneity; In Vitro; Institution; Length; Malignant Neoplasms; Marketing; Medicine; Messenger RNA; Methods; Minority; Molecular; Mutation; Neoplasm Metastasis; Nucleic Acids; Pain; Pattern; Peptide Hydrolases; Peptides; Predisposition; Prevention; Procedures; Process; Protocols documentation; Purpose; RNA; RNA Splicing; Reaction; Reading Frames; Recurrence; Relative (related person); Research; Resistance; Sampling; Small Business Funding Mechanisms; Small Business Innovation Research Grant; Solutions; Standards of Weights and Measures; TP53 gene; Technology; Tissues; Transcript; Translating; Translations; Tumor Suppressor Genes; Variant; cost; drug development; genotyping technology; improved; mutant; new technology; outcome forecast; polypeptide; programs; prototype; repaired; response; tumor; tumorigenesis

DESCRIPTION (provided by applicant): Cancer is the second leading cause of death in the U.S. Mutations in critical oncogenes, tumor suppressor genes and DNA repair genes contribute to tumorigenesis, prognosis and response to therapy. SpectraGenetics was founded to provide molecular diagnostics to impact cancer medicine. Peptide Mass Signature Genotyping (PMSG) will deliver sensitive, accurate, high throughput gene resequencing solutions to research and clinical markets that are demanding genetic biomarkers as integral parts of their early detection and drug development programs. This novel technology translates coding sequences into peptides for analysis allowing for high level multiplexing. Comprehensive analysis is achieved using a combination of translation in multiple reading frames and specific protease cleavages. The purpose of this SBIR project is to build a prototype automated RT-PMSG (Reverse Transcript-PMSG) process to provide analysis of target gene mRNA with a sensitivity that enables detection of variants that may be present as a minority component of the sample, as is often the case in a tumor nucleic acid sample. An added value of the multiplexing capability of RT-PMSG is that it allows for detection and analysis of splice variants present in an RNA sample and this capability will be exploited. Specifically, methods will be developed to produce peptide analytes in vitro using E. coli extracts for coupled transcription/translation reactions. A combination of proteases and multiple reading frames will be configured to analyze target mRNAs. The procedures for RT-PMSG will be developed using TP53 and FGFR3 mutant and alternatively spliced transcripts. Standard protocols will be automated, and validated, to achieve high- throughput, cost-effective genotyping. A high-throughput comprehensive resequencing platform that can sensitively analyze tumor-related genes in tumor nucleic acid samples will have wide application in research and clinical institutions. There is a great hope within the community that a greater understanding and characterization of tumor etiology, progression, and recurrence will enable prevention, early detection and improved treatments to reduce the pain and suffering caused by cancer.

描述（由申请人提供）：癌症是美国第二大死亡原因，关键癌基因、肿瘤抑制基因和DNA修复基因的突变影响肿瘤的发生、预后和对治疗的反应。光谱遗传学的成立是为了提供分子诊断来影响癌症医学。肽质量特征基因分型（PMSG）将为研究和临床市场提供敏感、准确、高通量的基因重测序解决方案，这些市场需要基因生物标志物作为其早期检测和药物开发项目的组成部分。这种新技术将编码序列转化为多肽进行分析，从而实现高水平的多路复用。综合分析是通过结合多个阅读框的翻译和特定的蛋白酶裂解来实现的。本SBIR项目的目的是建立一个原型自动化RT-PMSG（逆转录- pmsg）过程，以提供具有灵敏度的靶基因mRNA分析，从而能够检测可能作为样品中少数成分存在的变体，正如肿瘤核酸样品中经常出现的情况。RT-PMSG的多路复用能力的一个附加价值是，它允许检测和分析RNA样品中存在的剪接变异体，并且这种能力将被利用。具体来说，我们将开发利用大肠杆菌提取物在体外产生肽分析物的方法，用于偶联转录/翻译反应。蛋白酶和多个阅读框的组合将被配置来分析目标mrna。RT-PMSG的程序将使用TP53和FGFR3突变体和选择性剪接转录物来开发。标准方案将自动化，并验证，以实现高通量，成本效益的基因分型。一个能够灵敏分析肿瘤核酸样本中肿瘤相关基因的高通量综合重测序平台将在研究和临床机构中得到广泛应用。医学界非常希望对肿瘤的病因、进展和复发有更深入的了解和表征，这将有助于预防、早期发现和改进治疗，以减少癌症引起的痛苦和痛苦。