A microarray based STR genotyping system utilizing RecA-mediated ligation and nan

基于微阵列的 STR 基因分型系统，利用 RecA 介导的连接和 nan

• 批准号: 7478895
• 负责人: ROBERT E WAGNER
• 金额: $ 22.59万
• 依托单位: GENE CHECK, INC.
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-05-01 至 2009-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7478895
• 关键词: Base Pairing; Biological Assay; Body part; Class; Code; Condition; DNA; DNA biosynthesis; Data; Detection; Disease; Electronics; Exhibits; Fluorescence; Forensic Medicine; Generations; Genes; Genetic; Genetic Markers; Genetic Polymorphism; Genetic Predisposition to Disease; Genomics; Genotype; Goals; Hereditary Disease; Histocompatibility Testing; Hour; Human; Human Genome; Human Identifications; Hybridization Array; In Situ; Individual; Iodide Peroxidase; Label; Lead; Length; Ligation; Mediating; Medical; Medical Technology; Microsatellite Repeats; Military Personnel; Modification; Monitor; Nanosphere; Nucleotides; Numbers; Oligonucleotide Probes; Oligonucleotides; Phase; Polymerase Chain Reaction; Polymorphism Analysis; Predisposition; Reaction; Relative (related person); Sampling; Sensitivity and Specificity; Signal Transduction; Single Nucleotide Polymorphism; Site; Slide; Specificity; Speed; Standards of Weights and Measures; System; Systems Analysis; Tandem Repeat Sequences; Technology; Time; Transplantation; base; cost; day; design; improved; nanoparticle; size

DESCRIPTION (provided by applicant): Tandem repeat sequences (STR) are distributed widely in the human genome. These sites exhibit high levels of length polymorphism, as a result of their relative instability during DNA replication, i.e., the tendency for slippage to occur between the template and newly synthesized strands causing deletion or addition of repeat units. Changes in STR repeat number can lead to heritable genetic predispositions and disease. However, their variability makes them good markers for genetic studies. One class, the microsatellites containing 4 base pair repeat units, has been selected by the FBI as the basis for a genetic identification system, termed CODIS. Current analysis systems require a 1-2 day assay and employ electrophoretic separation of DNA fragments that contain the STR locus for accurate sizing and identification of the repeat number. The long-term goal of this project is to develop a simple, cost-effective and automatable assay system for STR analysis that allows human identification in less than 2 hours from sample to result by avoiding the need for electrophoretic separation and potentially avoiding the need for PCR amplification. In Phase I of this proposal we will use a single locus (TPOX) to demonstrate that accurate microarray based STR analysis is technically feasible and sufficiently rapid. In Phase II we will expand this assay to include several other CODIS loci, and attempt to increase assay speed further by eliminating the PCR step. Our approach to achieving these goals combines the technologies of two companies. Gene Check, Inc. has developed RML technology in which RecA catalyzes specific base pairing of oligonucleotide probes at the STR locus with subsequent ligation into specific products that reflect the length of the STR locus. Each product is coded with a unique recognition sequence, which allows their separation by hybridization to a microarray. Nanosphere has developed an automated microarray-based assay platform with sufficient specificity and sensitivity to allow SNP detection from total genomic DNA without PCR amplification by employing nanoparticle detection technology. Our preliminary data suggest that the Phase I tasks can be accomplished within a 6-12 month period. This will lay the groundwork for the proposed Phase II extension of this technology to several additional FBI CODIS STR loci, and assay and system designs to avoid PCR. Moreover, the results should allow us to assess the potential of this technology for medical applications, such as tissue typing, transplantation monitoring, and analysis of genetic conditions or predispositions mediated by relatively short nucleotide repeat polymorphisms.

描述（由申请人提供）：串联重复序列（STR）在人类基因组中广泛分布。这些位点表现出高度的长度多态性，因为它们在DNA复制过程中相对不稳定，即在模板和新合成的链之间发生滑移的趋势，导致重复单元的删除或添加。STR重复数的改变可导致遗传易感性和疾病。然而，它们的可变性使它们成为基因研究的良好标记。一类是含有4个碱基对重复单元的微型卫星，它已被联邦调查局（FBI）选为基因识别系统（CODIS）的基础。目前的分析系统需要1-2天的测定，并采用电泳分离包含STR位点的DNA片段，以准确确定重复数的大小和鉴定。