ArticleGenome research2000
A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays.
Article in Genome research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
- Design and Validation of Specific Oligonucleotide Probes on Planar Magnetic Biosensors.Analytical chemistry · 2024Article
- From early methods for DNA diagnostics to genomes and epigenomes at high resolution during four decades - a personal perspective.Upsala journal of medical sciences · 2024Review
- Rapid Genetic Diagnosis for Okinawan Patients with Enlarged Vestibular Aqueduct Using Single-Stranded Tag Hybridization Chromatographic Printed-Array Strip.Journal of clinical medicine · 2022Article
- Effect of Protein Genotypes on Physicochemical Properties and Protein Functionality of Bovine Milk: A Review.Foods (Basel, Switzerland) · 2021Review
- Rapid repair of human disease-specific single-nucleotide variants by One-SHOT genome editing.Scientific reports · 2020Article
- Genetic Association and Altered Gene Expression ofBiomedicines · 2018Article
- High-Efficiency Reverse (5'→3') Synthesis of Complex DNA Microarrays.Scientific reports · 2018Article
- Single Nucleotide Polymorphism Genotyping in Single-Molecule Electronic Circuits.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2017Article
- The importance of gene-environment interactions in human obesity.Clinical science (London, England : 1979) · 2016Review
- Fast genotyping of known SNPs through approximate k-mer matching.Bioinformatics (Oxford, England) · 2016Article
- MICB Allele Genotyping on Microarrays by Improving the Specificity of Extension Primers.PloS one · 2015Article
- Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics.International journal of molecular sciences · 2014Review
- Article
- Segmental duplication as one of the driving forces underlying the diversity of the human immunoglobulin heavy chain variable gene region.BMC genomics · 2011Article
- Detection of single-nucleotide polymorphism on uidA gene of Escherichia coli by a multiplexed electrochemical DNA biosensor with oligonucleotide-incorporated nonfouling surface.Sensors (Basel, Switzerland) · 2011Article
- Extensive analysis of D7S486 in primary gastric cancer supports TESTIN as a candidate tumor suppressor gene.Molecular cancer · 2010Article
- Fluorescent analogs of biomolecular building blocks: design, properties, and applications.Chemical reviews · 2010Review
- Photoinitiator nucleotide for quantifying nucleic Acid hybridization.Biomacromolecules · 2010Article
- Genetic association and interaction analysis of USF1 and APOA5 on lipid levels and atherosclerosis.Arteriosclerosis, thrombosis, and vascular biology · 2010Article
- Modic changes and interleukin 1 gene locus polymorphisms in occupational cohort of middle-aged men.European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society · 2009Article
23 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This study describes a practical system that allows high-throughput genotyping of single nucleotide polymorphisms (SNPs) and detection of mutations by allele-specific extension on primer arrays. The method relies on the sequence-specific extension of two immobilized allele-specific primers that differ at their 3'-nucleotide defining the alleles, by a reverse transcriptase (RT) enzyme at optimized reaction conditions. We show the potential of this simple one-step procedure performed on spotted primer arrays of low redundancy by generating over 8000 genotypes for 40 mutations or SNPs. The genotypes formed three easily identifiable clusters and all known genotypes were assigned correctly. Higher degrees of multiplexing will be possible with this system as the power of discrimination between genotypes remained unaltered in the presence of over 100 amplicons in a single reaction. The enzyme-assisted reaction provides highly specific allele distinction, evidenced by its ability to detect minority sequence variants present in 5% of a sample at multiple sites. The assay format based on miniaturized reaction chambers at standard 384-well spacing on microscope slides carrying arrays with two primers per SNP for 80 samples results in low consumption of reagents and makes parallel analysis of a large number of samples convenient. In the assay one or two fluorescent nucleotide analogs are used as labels, and thus the genotyping results can be interpreted with presently available array scanners and software. The general accessibility, simple set-up, and the robust procedure of the array-based genotyping system described here will offer an easy way to increase the throughput of SNP typing in any molecular biology laboratory.
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Registered trials
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