ArticleNucleic acids research2002
SNP typing by apyrase-mediated allele-specific primer extension on DNA microarrays.
Article in Nucleic acids research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 56 citations in OpenAlex.
- Real-time allelic assays of SARS-CoV-2 variants to enhance sewage surveillance.Water research · 2022Article
- A Mutagenic Primer Assay for Genotyping of the CRHR1 Gene Rare Variant rs1876828 (A/G) in Asians: A Cost-Effective SNP Typing.Journal of clinical laboratory analysis · 2016Article
- MICB Allele Genotyping on Microarrays by Improving the Specificity of Extension Primers.PloS one · 2015Article
- Comparison of PrASE and Pyrosequencing for SNP Genotyping.BMC genomics · 2006Article
- Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA.Nucleic acids research · 2006Article
- AccuTyping: new algorithms for automated analysis of data from high-throughput genotyping with oligonucleotide microarrays.Nucleic acids research · 2006Article
- Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI).Nucleic acids research · 2005Article
- Competitive enzymatic reaction to control allele-specific extensions.Nucleic acids research · 2005Article
- Demonstration of loss of heterozygosity by single-nucleotide polymorphism microarray analysis and alterations in strain morphology in Candida albicans strains during infection.Eukaryotic cell · 2005Article
- Viral and microbial genotyping by a combination of multiplex competitive hybridization and specific extension followed by hybridization to generic tag arrays.Nucleic acids research · 2003Article
- Rapid detection of the known SNPs of CYP2C9 using oligonucleotide microarray.World journal of gastroenterology · 2003Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This study reports the development of a microarray-based allele-specific extension method for typing of single nucleotide polymorphisms (SNPs). The use of allele-specific primers has been employed previously to identify single base variations but it is acknowledged that certain mismatches are not refractory to extension. Here we have overcome this limitation by introducing apyrase, a nucleotide-degrading enzyme, to the extension reaction. We have shown previously that DNA polymerases exhibit slower reaction kinetics when extending a mismatched primer compared with a matched primer. This kinetic difference is exploited in the apyrase-mediated allele-specific extension (AMASE) assay, allowing incorporation of nucleotides when the reaction kinetics are fast but degrading the nucleotides before extension when the reaction kinetics are slow. Here we show that five homozygous variants (14% of the total number of variants) that were incorrectly scored in the absence of apyrase were correctly typed when apyrase was included in the extension reaction. AMASE was performed in situ on the oligonucleotide microarrays using fluorescent nucleotides to type 10 SNPs and two indels in 17 individuals generating approximately 200 genotypes. Cluster analysis of these data shows three distinct clusters with clear-cut boundaries. We conclude that SNP typing on oligonucleotide microarrays by AMASE is an efficient, rapid and accurate technique for large-scale genotyping.
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