An Innovative, High-Throughput Method of SNP Haplotyping

本提案的目的是开发一种创新的、高通量的、可靠的和准确的SNP单体型分型方法。迄今为止，还没有高通量、可靠的SNP单体型分型方法可用。该建议的具体目的是开发一种新的，等位基因特异性的寡核苷酸杂交方法，用于使用微阵列或384孔微量滴定板格式进行单倍型测定。这些格式将允许高通量测定个体的两条染色体的含有2个SNP（微量滴定板格式）或多个SNP（微阵列格式）的单倍型。加/减，杂交模式的自动评分将确定两条染色体的单倍型。以高通量方式精确单倍型SNP基因座的能力具有重要的应用：1）饱和基因分型研究，其使用单倍型来缩小由先前用单个SNP或其它标记进行的连锁研究限定的候选基因组区域，2）位于候选基因组区域中的基因或由其它方法鉴定的候选基因的连锁不平衡和关联研究，3）分析大量样品中先前确定与特定疾病易感性相关的单倍型，4）与疾病易感性、药物遗传学和免疫学谱相关的单倍型的诊断测试和试剂盒。拟定商业应用：高通量、准确可靠的SNP单体型分析技术将为连锁不平衡和关联研究提供支持。这样的研究将允许对糖尿病、冠状动脉疾病和哮喘等复杂性状进行遗传解剖。这对于许多常见疾病的理解和诊断、诊断/预后测试试剂盒的开发和新的治疗方法的发现具有重要的商业应用。

The objective of this proposal is to develop an innovative, high- throughput, reliable and accurate method of SNP-haplotyping. To date, there are no high-throughput, reliable SNP-haplotyping methods available. The specific aims of this proposal are designed to develop a novel, allele-specific oligonucleotide hybridization approach for haplotype determination using either a microarray or a 384 well microtiter-plate format. These formats will allow the high-throughput determination of haplotypes containing 2 SNPs (microtiter-plate format) or multiple SNPs (microarray format) for both chromosomes of an individual. Plus/minus, automatable scoring of hybridization patterns will determine the haplotypes for both chromosomes. The ability to accurately haplotype SNP loci in a high-throughput fashion has important applications for; 1) saturation genotyping studies using haplotypes to narrow candidate genomic regions defined by previous linkage studies carried out with individual SNPs or other markers, 2) linkage disequilibriurn and association studies of genes located in candidate genomic regions or candidate genes identified by other methods, 3) analyzing large numbers of samples for haplotypes previously determined to be associated with the susceptibility of a particular disease, 4) diagnostic tests and kits for haplotypes associated with disease susceptibility, pharmacogenetic and immunologic profiling. PROPOSED COMMERCIAL APPLICATION: A high-throughput, accurate and reliable SNP-haplotyping technology will support population analyses for linkage disequilibrium and association studies. Such studies will allow the genetic dissection of complex traits such as diabetes, coronary artery disease and asthma. This has significant commercial application for the understanding and diagnosis of many common diseases, the development of diagnostic/prognostic test kits and the discovery of novel therapeutic treatments.