There is a need for inexpensive high throughput platforms for analyzing large number of single nucleotide polymorphisms. In this proposal, we describe the development of a technique, which will enable more than 10,000 SNPs to be analyzed in a single tube and its transfer to a commercial entity (ParAllele Genomcis Inc.). The technology exploits the specificity of padlock probes, and employs the fidelity of polymerase and ligase to accurately identify the nucleotide polymorphism. A molecular tag is designed in the backbone of the probe to allow parallel detection of many polymorphisms. In this way, the information of the polymorphism can be reformatted into the tag sequence, which is then amplified using general PCR primer. The amplification product is then screened on a complementary tag chip. This technology is expected to have applications in population genetics and large-scale disease association studies and unlike other available technologies uses very low amount of DNA sample per SNP screened.
