Shan Q, Zheng Y, Chen G, Zheng G, Lu J, Lv X. Tag-extension-based method for sensitive and specific genotyping of single nucleotide polymorphism on microarray.
Clin Chim Acta 2009;
409:11-7. [PMID:
19654005 DOI:
10.1016/j.cca.2009.07.018]
[Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 07/08/2009] [Accepted: 07/27/2009] [Indexed: 11/17/2022]
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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