ArticleNucleic acids research2001
Quantitative detection of single nucleotide polymorphisms for a pooled sample by a bioluminometric assay coupled with modified primer extension reactions (BAMPER).
Article in Nucleic acids research, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- A simple and flexible approach for detecting small numbers of SNPs.Frontiers in plant science · 2025Article
- Bibliometric analysis of real-time PCR-based pathogen detection in plant protection research: a comprehensive study.Frontiers in plant science · 2023Article
- Colorimetry-Based Phosphate Measurement for Polymerase Elongation.BioMed research international · 2023Article
- Evaluation of the correctable decoding sequencing as a new powerful strategy for DNA sequencing.Life science alliance · 2022Article
- Ultra-specific genotyping of single nucleotide variants by ligase-based loop-mediated isothermal amplification coupled with a modified ligation probe.RSC advances · 2021Article
- Archaeal Inorganic Pyrophosphatase Displays Robust Activity under High-Salt Conditions and in Organic Solvents.Applied and environmental microbiology · 2016Article
- MICB Allele Genotyping on Microarrays by Improving the Specificity of Extension Primers.PloS one · 2015Article
- Rapid and direct microRNA quantification by an enzymatic luminescence assay.Analytical biochemistry · 2012Article
- Article
- Genetic suppression of the circadian Clock mutation by the melatonin biosynthesis pathway.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Protocol: a simple gel-free method for SNP genotyping using allele-specific primers in rice and other plant species.Plant methods · 2010Article
- Selectivity of Enzymatic Conversion of Oligonucleotide Probes during Nucleotide Polymorphism Analysis of DNA.Acta naturae · 2010Article
- High-throughput single-base mismatch detection for genotyping of UDP-glucuronosyltransferase (UGT1A1) with probe capture assay coupled with modified allele-specific primer extension reaction (MASPER).Journal of clinical laboratory analysis · 2010Article
- Microarray-based estimation of SNP allele-frequency in pooled DNA using the Langmuir kinetic model.BMC genomics · 2008Article
- Quantitative Single-letter Sequencing: a method for simultaneously monitoring numerous known allelic variants in single DNA samples.BMC genomics · 2008Article
- Reliable allele detection using SNP-based PCR primers containing Locked Nucleic Acid: application in genetic mapping.Plant methods · 2007Article
- Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI).Nucleic acids research · 2005Article
- Quantifying mixed populations of drug-resistant human immunodeficiency virus type 1.Antimicrobial agents and chemotherapy · 2005Article
- A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays.Nucleic acids research · 2005Article
- A multi-enzyme model for Pyrosequencing.Nucleic acids research · 2004Article
Corrections and comments
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6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
A new method for SNP analysis based on the detection of pyrophosphate (PPi) is demonstrated, which is capable of detecting small allele frequency differences between two DNA pools for genetic association studies other than SNP typing. The method is based on specific primer extension reactions coupled with PPi detection. As the specificity of the primer-directed extension is not enough for quantitative SNP analysis, artificial mismatched bases are introduced into the 3'-terminal regions of the specific primers as a way of improving the switching characteristics of the primer extension reactions. The best position in the primer for such artificial mismatched bases is the third position from the primer 3'-terminus. Contamination with endogenous PPi, which produces a large background signal level in SNP analysis, was removed using PPase to degrade the PPi during the sample preparation process. It is possible to accurately and quantitatively analyze SNPs using a set of primers that correspond to the wild-type and mutant DNA segments. The termini of these primers are at the mutation positions. Various types of SNPs were successfully analyzed. It was possible to very accurately determine SNPs with frequencies as low 0.02. It is very reproducible and the allele frequency difference can be determined. It is accurate enough to detect meaningful genetic differences among pooled DNA samples. The method is sensitive enough to detect 14 amol ssM13 DNA. The proposed method seems very promising in terms of realizing a cost-effective, large-scale human genetic testing system.
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