Allelic expression monitoring by array-based genotyping

通过基于阵列的基因分型监测等位基因表达

• 批准号: 6790133
• 负责人: KEVIN L GUNDERSON
• 金额: $ 19.5万
• 依托单位: ILLUMINA, INC.
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-05-01 至 2005-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6790133
• 关键词: DNA primers; alleles; biotechnology; cell line; functional /structural genomics; gene expression; genetic screening; genotype; high throughput technology; human genetic material tag; method development; microarray technology; nucleic acid amplification techniques; polymerase chain reaction; single nucleotide polymorphism

DESCRIPTION (provided by applicant): The goal of this project is to develop a quantitative eDNA genotyping platform for measuring allelic gene expression. This will provide a tool for better understanding transcriptional regulation of the genome. Dysfunction in this regulation leads to a number of disease states including cancer. In particular, cancer genes are often activated or inactivated by genetic and epigenetie mechanisms leading to uncontrolled cell growth. Epigenetie mechanisms leading to aberrant transcriptional control include methylation of CpG islands, loss of imprinting, and chromatin modification. The proposed approach to eDNA genotyping involves direct hybridization of cDNA to a DNA oligonucleotide array and subsequent genotyping by an array-based allele-specific primer extension reaction. In addition to allelic expression, the array's utility in standard gene expression quantitation will also be demonstrated. Whole genome amplification of cDNA will be explored as a means to improve genotyping accuracy for low copy number transcripts. In phase I, a model system employing several hundred eDNA SNPs across a few hundred genes will be used on our Sentrix TM Array of Array TM platform. In phase II, the eDNA array will be scaled to our Sentrix BeadChip platform encompassing whole genome analysis of thousands of genes. To enable easy allele frequency calibration, the direct genotyping of gDNA on the eDNA array will also be explored. The culmination of these efforts will result in the whole genome allelic expression study of matched normal/tumor tissues to identify gene loci involved in tumor development.

描述（由申请人提供）：该项目的目的是开发一个定量的EDNA基因分型平台来测量等位基因表达。这将提供一种工具，以更好地理解基因组的转录调节。该调节中的功能障碍导致许多疾病状态在内。特别是，癌症基因通常被导致不受控制的细胞生长的遗传和表观遗传学机制激活或灭活。导致异常转录控制的表观遗传机制包括CPG岛的甲基化，烙印丧失和染色质修饰。提出的EDNA基因分型方法涉及将cDNA直接杂交到DNA寡核苷酸阵列，并通过基于阵列的等位基因特异性引物扩展反应进行基因分型。除等位基因表达外，还将证明阵列在标准基因表达定量中的效用。将探讨cDNA的整个基因组扩增，以提高低拷贝数转录本的基因分型精度。在第一阶段，在我们的阵列TM平台的Sentrix TM阵列上，将使用几百个基因上使用数百个EDNA SNP的模型系统。在第二阶段，EDNA阵列将缩放到我们的Sentrix Beadchip平台，其中包括数千个基因的整个基因组分析。为了启用易于的等位基因频率校准，还将探索GDNA在EDNA阵列上的直接基因分型。这些努力的高潮将导致对匹配的正常/肿瘤组织的整个基因组等位基因表达研究，以鉴定与肿瘤发育有关的基因基因座。