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  • Title: Tag-extension-based method for sensitive and specific genotyping of single nucleotide polymorphism on microarray.
    Author: Shan Q, Zheng Y, Chen G, Zheng G, Lu J, Lv X.
    Journal: Clin Chim Acta; 2009 Nov; 409(1-2):11-7. PubMed ID: 19654005.
    Abstract:
    BACKGROUND: The obtainment of a large amount of single nucleotide polymorphism (SNP) information has emphasized a need for a sensitive, accurate and high-throughput strategy for SNP genotyping. We developed a reliable and potential microarray-based method to meet this demand. METHODS: A tag extension strategy is described to identify SNPs. The strategy is based on a fluorescent nucleotide extension from an extending primer that is hybridized to a bi-functional linker, which acts as an allele-specific primer that hybridizes with a PCR-amplified target DNA immobilized on a 3-dimensional (3-D) polyacrylamide gel microarray, as well as an extending template with a specific tag itself hybridized with a universal extension primer. Multiple fluorescence-dNTPs are simultaneously incorporated into the tagged linker. RESULTS: The method not only significantly enhanced the sensitivity, but also efficiently improved the specificity of SNP genotyping. 89 samples for 8025575C/G polymorphisms in gamma-aminobutyric acid A receptor, beta 3 (GABAB3) gene were accurately discriminated using this method. Sanger sequencing was performed to validate these results. CONCLUSION: Our experiments successfully demonstrated that a tag-extension-based method on microarray could be used as a high-throughput and useful tool to obtain SNP information.
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